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[ "<title>Introduction</title>", "<p id=\"Par2\">Let be a Boolean algebra. We say that has <italic>the Nikodym property</italic><xref ref-type=\"fn\" rid=\"Fn1\">1</xref> if every sequence of measures on which is pointwise null, i.e. for every , is also weak* null, i.e. for every continuous function on the Stone space of , and that has <italic>the Grothendieck property</italic> if every weak* null sequence of measures on is weakly null, i.e. for every Borel (see Sect. <xref rid=\"Sec2\" ref-type=\"sec\">2</xref> for all the necessary terminology). Both of the notions have strong connections to functional analysis—the Nikodym property is closely related to the Uniform Boundedness Principle for locally convex spaces (see [##UREF##30##31##]), while the Grothendieck property is usually studied in a much more general sense in the context of dual Banach spaces (see [##UREF##21##22##, ##UREF##30##31##] or [##UREF##11##12##]). Nikodym [##UREF##29##30##] and Dieudonné [##UREF##10##11##] proved that all -complete Boolean algebras have the Nikodym property, while Grothendieck [##UREF##21##22##] showed that they have also the Grothendieck property. Consequently, e.g., the algebra of all subsets of has both of the properties. On the other hand, no infinite countable Boolean algebra (or, more generally, no Boolean algebra whose Stone space contains a non-trivial convergent sequence) can have the Nikodym property or the Grothendieck property.</p>", "<p id=\"Par4\">Since the findings of Nikodym, Dieudonné, and Grothendieck, many generalizations of the -completeness have been found which still give at least one of the properties, see e.g. [##UREF##0##1##, ##UREF##9##10##, ##UREF##17##18##, ##UREF##22##23##, ##UREF##23##24##, ##UREF##28##29##, ##UREF##30##31##, ##UREF##31##32##, ##UREF##33##34##]. Unfortunately, none of those generalizations yields a necessary condition which a given Boolean algebra must satisfy in order to have the Nikodym property or the Grothendieck property. One of the reasons behind this is that, due to the result of Koszmider and Shelah [##UREF##26##27##], each of those generalizations implies also that an infinite Boolean algebra satisfying it contains an independent family of size continuum and thus itself must be of cardinality at least . Brech [##UREF##6##7##] however showed that consistently there exists a Boolean algebra of cardinality having the Grothendieck property while at the same time . A similar result was also obtained by the first author [##UREF##32##33##] for the Nikodym property. Those two facts imply together that the quest for an algebraic or topological characterization of the Nikodym property or the Grothendieck property is much more demanding and requires using more sophisticated assumptions than mere existence of suprema or upper bounds of antichains in Boolean algebras.</p>", "<p id=\"Par5\">Let us state the result of Brech [##UREF##6##7##] more precisely. She proved that if is a cardinal number and is the side-by-side Sacks forcing adding simultaneously many Sacks reals to the ground model <italic>V</italic>, then in any -generic extension <italic>V</italic>[<italic>G</italic>] the ground model Boolean algebra has the Grothendieck property (her argument works in fact for any infinite ground model -complete Boolean algebra, not only for ). In [##UREF##34##35##] we showed that a similar theorem may be obtained for the Nikodym property and in [##UREF##35##36##] we generalized both of the results by proving that if is a proper notion of forcing satisfying the Laver property and preserving the reals non-meager, then in any -generic extension <italic>V</italic>[<italic>G</italic>] every ground model -complete Boolean algebra has both the Nikodym property and the Grothendieck property. Recall that the class of forcings satisfying the assumptions of the latter theorem contains such classical notions like the Sacks, side-by-side Sacks, Miller, or Silver(-like) forcing, as well as their countable support iterations (see [##UREF##35##36##, Introduction] for references).</p>", "<p id=\"Par6\">In this paper we follow the path of research described in the previous paragraph and study the case of adding just <italic>one</italic> real to the given model of set theory, however this time the results are mostly negative. Our main theorem reads to wit as follows.</p>", "<title>Theorem 1.1</title>", "<p id=\"Par7\">Let be an infinite Boolean algebra. Let be a notion of forcing adding one of the following reals:<list list-type=\"bullet\"><list-item><p id=\"Par8\">a Cohen real,</p></list-item><list-item><p id=\"Par9\">an unsplit real, or</p></list-item><list-item><p id=\"Par10\">a random real.</p></list-item></list>Assume that <italic>G</italic> is a -generic filter over <italic>V</italic>. Then, in <italic>V</italic>[<italic>G</italic>], has neither the Nikodym property nor the Grothendieck property.</p>", "<p>We establish the above theorem in a series of partial results. First, in Theorems <xref ref-type=\"sec\" rid=\"FPar7\">3.2</xref> and <xref ref-type=\"sec\" rid=\"FPar10\">3.4</xref> we prove that if adds a Cohen real or an unsplit real, then in any -generic extension every infinite ground model Boolean algebra obtains a non-trivial convergent sequence in its Stone space , and, consequently, it can have neither the Nikodym property nor the Grothendieck property. Theorems <xref ref-type=\"sec\" rid=\"FPar7\">3.2</xref> and <xref ref-type=\"sec\" rid=\"FPar10\">3.4</xref> have already been known to experts in the area (cf. e.g. Dow–Fremlin [##UREF##15##16##, page 162] and their reference to Koszmider [##UREF##25##26##]), however, it seems that their proofs have never been published anywhere. Our proof of Theorem <xref ref-type=\"sec\" rid=\"FPar7\">3.2</xref> may be seen as a forcing counterpart of the proof of Geschke’s [##UREF##18##19##, Theorem 2.1] which states that under Martin’s axiom every infinite compact space of weight contains a non-trivial convergent sequence or, more generally, that in ZFC every infinite compact space of weight strictly less than the covering number of the meager ideal contains such a sequence. Geschke’s argument is on the other hand a topological counterpart of Koppelberg’s [##UREF##24##25##, Proposition 5] asserting that under Martin’s axiom every infinite Boolean algebra of cardinality has countable cofinality. The argument for Theorem <xref ref-type=\"sec\" rid=\"FPar10\">3.4</xref> is based on the idea presented in Booth [##UREF##4##5##, Theorem 2] (see also [##UREF##13##14##]) where it is showed that every infinite compact space of weight strictly less than the splitting number is sequentially compact and thus contains a non-trivial convergent sequence.</p>", "<p>The issue of adding random reals is more special. Recall that Dow and Fremlin [##UREF##15##16##] first proved that adding any number of random reals to the ground model does not introduce non-trivial convergent sequences to the Stone spaces of -complete ground model Boolean algebras (or, more generally, to the Stone spaces of ground model Boolean algebras whose Stone spaces <italic>in</italic> the ground model are F-spaces). Since not containing any non-trivial convergent sequences in the Stone space is not sufficient for an infinite Boolean algebra to have the Nikodym property or the Grothendieck property, the result of Dow and Fremlin does not say anything about the preservation of either of the properties by the random forcing. We address here this issue by proving in Theorem <xref ref-type=\"sec\" rid=\"FPar20\">4.6</xref> that if a forcing adds a random real, then for any infinite ground model Boolean algebra in every -generic extension of the ground model there are sequences of finitely supported measures on the Stone space which witness that has neither the Nikodym property nor the Grothendieck property.</p>", "<p>We also generalize partially the aforementioned result of Dow and Fremlin. Namely, we prove in Theorem <xref ref-type=\"sec\" rid=\"FPar23\">4.8</xref> that for any ground model -complete Boolean algebra the random forcing does not add to its Stone space any weak* null sequences of normalized measures whose supports consist of at most <italic>M</italic> points, where is a fixed number. This result complements Theorem <xref ref-type=\"sec\" rid=\"FPar20\">4.6</xref>, at least in the case of -algebras—see Sect. <xref rid=\"Sec8\" ref-type=\"sec\">4.2</xref> for more details.</p>", "<p>As examples of forcings adding a Cohen real one can name the Hechler forcing or finite support iterations of infinite length of non-trivial posets (see [##UREF##19##20##, Example 0.2]). The Mathias forcing is a typical example of a notion adding an unsplit real. Finally, random reals are added by, e.g., the amoeba forcing.</p>", "<title>Corollary 1.2</title>", "<p id=\"Par15\">Let be an infinite Boolean algebra. Let be one of the following notions of forcing: Cohen, finite support iteration of infinite length of non-trivial posets, Hechler, Mathias, random, or amoeba. Assume that <italic>G</italic> is a -generic filter over <italic>V</italic>. Then, in <italic>V</italic>[<italic>G</italic>], has neither the Nikodym property nor the Grothendieck property.</p>", "<p>We also study the case of adding dominating reals—following the argument presented in [##UREF##32##33##, Proposition 8.8] and based on the celebrated Josefson–Nissenzweig theorem from Banach space theory we prove in Sect. <xref rid=\"Sec9\" ref-type=\"sec\">4.3</xref> that adding dominating reals kills the Nikodym property of all infinite ground model Boolean algebras.</p>", "<title>Theorem 1.3</title>", "<p id=\"Par17\">Let be an infinite Boolean algebra. Let be a notion of forcing adding a dominating real. Assume that <italic>G</italic> is a -generic filter over <italic>V</italic>. Then, in <italic>V</italic>[<italic>G</italic>], does not have the Nikodym property.</p>", "<p>The class of forcings adding a dominating real contains such notions as Hechler, Laver, or Mathias. Thus, in addition to Corollary <xref ref-type=\"sec\" rid=\"FPar2\">1.2</xref>, we get the following result.</p>", "<title>Corollary 1.4</title>", "<p id=\"Par19\">Let be an infinite Boolean algebra. Let be the Laver forcing. Assume that <italic>G</italic> is a -generic filter over <italic>V</italic>. Then, in <italic>V</italic>[<italic>G</italic>], does not have the Nikodym property.</p>", "<p>The case of the Laver forcing is particularly interesting as Dow [##UREF##14##15##, Theorem 11] showed that adding a single Laver real does not introduce any non-trivial converging sequences in the Stone space of the ground model Boolean algebra , yet, by Corollary <xref ref-type=\"sec\" rid=\"FPar4\">1.4</xref>, loses its Nikodym property. We do not know whether adding a Laver real (or, more generally, a dominating real) kills the Grothendieck property of ground model (or any other ground model Boolean algebra)—see Sect. <xref rid=\"Sec11\" ref-type=\"sec\">6</xref>.</p>" ]
[]
[ "<title>Random reals: generalization of Dow–Fremlin’s result</title>", "<p id=\"Par77\">Let be an infinite cardinal number. By denote the standard product probability measure on the space and let be its measure algebra. is a well-known -bounding poset adding many random reals (see [##UREF##1##2##, Section 3.1]).<xref ref-type=\"fn\" rid=\"Fn2\">2</xref> (A forcing is -<italic>bounding</italic> if for every -generic filter <italic>G</italic> over <italic>V</italic> and a function there is a function such that for every .)</p>", "<p id=\"Par79\">Recall again that Dow and Fremlin [##UREF##15##16##] proved that forcing with does not introduce non-trivial convergent sequences to the Stone spaces of -complete ground model Boolean algebras. In this subsection we will generalize their result in the following way.</p>", "<title>Theorem 4.8</title>", "<p id=\"Par80\">Let be an infinite -complete Boolean algebra. Assume that <italic>G</italic> is a -generic filter over <italic>V</italic>. Then, in <italic>V</italic>[<italic>G</italic>], does not carry any weak* null sequence of finitely supported measures such that for every and for which there exists such that for every .</p>", "<p>The theorem really generalizes the result of Dow and Fremlin, since if a compact space <italic>K</italic> contains a non-trivial convergent sequence , then the sequence of measures defined as is weak* null and such that and for every . Note however that the existence of a weak* null sequence of measures on a totally disconnected compact space <italic>K</italic> such that for every does not imply the existence of non-trivial convergent sequences in <italic>K</italic> (cf. [##UREF##30##31##, Example 4.10]).</p>", "<p>Let us stress that Corollary <xref ref-type=\"sec\" rid=\"FPar22\">4.7</xref> and Theorem <xref ref-type=\"sec\" rid=\"FPar23\">4.8</xref> are complementary: the corollary states that the existence of a random real yields the existence of a weak* null sequence of finitely supported normalized measures on the Stone space of a given infinite ground model Boolean algebra such that , while the theorem asserts that, in the case of -complete Boolean algebras, this is optimal—we cannot get any weak* null sequence of normalized measures such that .</p>", "<p>In order to prove Theorem <xref ref-type=\"sec\" rid=\"FPar23\">4.8</xref>, we first need to recall several auxiliary results. The first one implies that in fact we only need to deal with the case of .</p>", "<title>Lemma 4.9</title>", "<p id=\"Par84\">Let be an infinite Boolean algebra. If there are a weak* null sequence of finitely supported measures on and a number such that and for every , then and there is a weak* null sequence of finitely supported measures on such that and .</p>", "<title>Proof</title>", "<p id=\"Par85\">Let be a weak* null sequence of finitely supported measures on for which there exists such that and for every . If there is a subsequence such that for every , then every is simply of the form for some and . Consequently, for the constant unit function we have for every , which contradicts the fact that converges weak* to 0. It follows that for almost all we have and so .</p>", "<p id=\"Par86\">We now prove the second part of the lemma. Let be the minimal number such that there exists a weak* null sequence of finitely supported measures on such that and for every . By the previous paragraph, . We will prove that in fact .</p>", "<p id=\"Par87\">First note that if there are a clopen set and an increasing sequence such that and for every , then there is an increasing sequence such that at least one of the sequences and , defined for every asandis weak* null. Since for every and it holds and , we get a contradiction with the minimality of <italic>m</italic>. It follows that for every clopen and almost all we have either , or .</p>", "<p id=\"Par88\">For every pick two distinct points and define the measure simply as follows . Of course, . To finish the proof, we only need to show that is weak* null. But this is trivial, since for every clopen subset <italic>U</italic> of and almost all we have either , or ; in either case it holds , so is pointwise null. Since is also uniformly bounded, by Corollary <xref ref-type=\"sec\" rid=\"FPar14\">4.2</xref> it is weak* null (and so, by the minimality of <italic>m</italic>, we also have ). </p>", "<title>Remark 4.10</title>", "<p id=\"Par89\">For a Boolean algebra , if there exists a weak* null sequence of measures on such that and for every , then one can also easily get such a sequence but with pairwise disjoint supports. Thus, from the above proof it basically follows that for every Boolean algebra the following two conditions are equivalent: <list list-type=\"order\"><list-item><p id=\"Par90\">there are a weak* null sequence of finitely supported measures on and such that and for every ,</p></list-item><list-item><p id=\"Par91\">there are two disjoint sequences and of distinct points in such that for every clopen set <italic>U</italic> and almost all we have: if and only if .</p></list-item></list></p>", "<p>The following lemma was the main tool used by Dow and Fremlin to obtain their result. We will need it, too.</p>", "<title>Lemma 4.11</title>", "<p id=\"Par93\">(Dow–Fremlin [##UREF##15##16##, Lemma 2.2]) Let be a Boolean algebra. Assume that is a sequence of -names for distinct ultrafilters on . Let <italic>G</italic> be a -generic filter over <italic>V</italic>. Then, for every condition there are a condition and a sequence of pairwise disjoint elements of such that for every .</p>", "<p>In [##UREF##5##6##] Borodulin-Nadzieja and the first author proved that, for every -names and for ultrafilters on a given ground model Boolean algebra , if , then for every there are a condition and an element such that and . By exactly the same proof, <italic>mutatis mutandis</italic>, we obtain the following formally stronger result.</p>", "<title>Lemma 4.12</title>", "<p id=\"Par95\">(Cf. [##UREF##5##6##, Section 6.2]) Let be a Boolean algebra. Let and be -names for ultrafilters on . For every condition , if , then for every there are a condition and an element such that and .</p>", "<p>The next lemma is folklore.</p>", "<title>Lemma 4.13</title>", "<p id=\"Par97\">Let be an -bounding forcing notion and <italic>G</italic> a -generic filter over <italic>V</italic>. Let . Then, in <italic>V</italic>, there is an uncountable almost disjoint family such that for every the intersection is infinite.</p>", "<title>Proof</title>", "<p id=\"Par98\">In <italic>V</italic>[<italic>G</italic>] let be the strictly increasing enumeration of elements of <italic>X</italic>. Since is -bounding, there is a strictly increasing function such that for every there is for which the following inequalities are satisfied: (cf. the proof of [##UREF##32##33##, Corollary 2.5]). In <italic>V</italic>, let be an uncountable almost disjoint family. For every set:Put . Of course, for every the intersection is finite, so is an uncountable almost disjoint family. Also, by (), for every the intersection is infinite. </p>", "<p>We are in the position to prove the main result of this section.</p>", "<title>Proof of Theorem 4.8</title>", "<p id=\"Par100\">Assume towards the contradiction that, in <italic>V</italic>[<italic>G</italic>], there are a weak* null sequence of finitely supported measures on and a number such that and for every . By Remark <xref ref-type=\"sec\" rid=\"FPar26\">4.10</xref>, we may assume that, in <italic>V</italic>, there are two sequences and of -names for ultrafilters on and a condition forcing that: <list list-type=\"alpha-lower\"><list-item><p id=\"Par101\"> and for every ,</p></list-item><list-item><p id=\"Par102\"> for every ,</p></list-item><list-item><p id=\"Par103\">for every and almost all we have: if and only if .</p></list-item></list>By Lemma <xref ref-type=\"sec\" rid=\"FPar27\">4.11</xref>, there are a condition and a sequence (in <italic>V</italic>!) of pairwise disjoint elements of such that for every we have . For each by denote a -name such that <italic>p</italic> forces thatNote that, by property (c), <italic>p</italic> forces that each is at most finite.</p>", "<p>We need to consider two cases.</p>", "<p>(1) <italic>p</italic> forces that for almost all the set is empty. Let and be such that for every we have . The last formula simply means that for every and the following holds:For each , let be a -name such thatand let and be -names for ultrafilters on such thatOf course, for we have .</p>", "<p>For every , since , by Lemma <xref ref-type=\"sec\" rid=\"FPar28\">4.12</xref>, we get a condition and an element such that and . Since , we may actually assume that . In particular, for every . Set:then, , so and . It follows that <italic>s</italic> forces that for infinitely many , or, in other words, that</p>", "<p>for infinitely many . Since the sequence is in <italic>V</italic>, its supremum exists in , so setand note that for every we have (since is pairwise disjoint).</p>", "<p>We claim that <italic>s</italic> forces that for infinitely many , contradicting condition (c). Indeed, observe that for every we have:and so, since ,By (), it follows thatfor infinitely many .</p>", "<p>(2) There is a condition forcing that for infinitely many the set is non-empty. Let then be a -name for a function such that for every we have:Since <italic>r</italic> forces that is finite for every and that each belongs to at most two different ’s, the above definition is valid. For every we also have and</p>", "<p>Since is -bounding, there are a strictly increasing function such that and a condition such that for every . Define the function for every as: , where the composition is taken times.</p>", "<p>We have two subcases of case (2).</p>", "<p>(2a) There is a condition forcing that for infinitely many the set is non-empty. Let <italic>H</italic> be a -generic filter over <italic>V</italic> containing <italic>t</italic>. For every -name by we denote its evaluation in <italic>V</italic>[<italic>H</italic>].</p>", "<p>We now work in <italic>V</italic>[<italic>H</italic>]. For every we have:so, by (), it holds that</p>", "<p>Since is -complete in <italic>V</italic> and , the supremumexists in . Let be any set such that for every it holds , so we may pick . Note that, by condition (c), there is no such that for every . It follows that—removing a finite number of elements of <italic>X</italic> if necessary—for every we have . Property () implies that for every we have:that is, there is a unique point in which belongs to the boundary (in ) of the open set .</p>", "<p>By Lemma <xref ref-type=\"sec\" rid=\"FPar29\">4.13</xref>, there is an uncountable almost disjoint family in <italic>V</italic> such that the intersection is infinite for every . Since every is in <italic>V</italic>, the supremumexists in . For every set:For every we have:and hence . Since is uncountable and <italic>X</italic> is countable, it follows that there is such that for every , and hence for infinitely many , which contradicts condition (c).</p>", "<p>(2b) <italic>s</italic> forces that for almost all the set is empty. We proceed exactly in the same way as in case (1), that is, using Lemma <xref ref-type=\"sec\" rid=\"FPar28\">4.12</xref> we obtain , an antichain in <italic>V</italic> such that for every , and a condition forcing that for infinitely many , which again contradicts condition (c). </p>" ]
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[ "<p id=\"Par1\">We prove that if is an infinite Boolean algebra in the ground model <italic>V</italic> and is a notion of forcing adding any of the following reals: a Cohen real, an unsplit real, or a random real, then, in any -generic extension <italic>V</italic>[<italic>G</italic>], has neither the Nikodym property nor the Grothendieck property. A similar result is also proved for a dominating real and the Nikodym property.</p>", "<title>Keywords</title>", "<title>Mathematics Subject Classification</title>", "<p>Open access funding provided by Austrian Science Fund (FWF).</p>" ]
[ "<title>Notations</title>", "<p id=\"Par21\">Our notations are standard—we follow the texts of Diestel [##UREF##12##13##], Kunen [##UREF##27##28##], and Engelking [##UREF##16##17##]. We mention below only the most important issues.</p>", "<p id=\"Par22\"><italic>V</italic> always denotes the set-theoretic universe.</p>", "<p id=\"Par23\">By we denote the first infinite countable ordinal number. If <italic>A</italic> is a set, then by , , and we denote the families of all subsets of <italic>A</italic>, all infinite countable subsets of <italic>A</italic>, and all finite subsets of <italic>A</italic>, respectively. denotes the family of all functions from a set <italic>B</italic> to <italic>A</italic>. If <italic>f</italic> is a function, then by we denote its range. If is a linear order and , then by writing () we mean that for all (but finitely many) we have . We similarly define the strict relations &lt; and on . denotes the identity function on <italic>A</italic>. If , then by we denote the characteristic function of <italic>B</italic> on <italic>A</italic>.</p>", "<p id=\"Par24\">All topological spaces considered in this paper are assumed to be Tychonoff, that is, completely regular and Hausdorff. A subset of a topological space is <italic>perfect</italic> if it is closed and contains no isolated points. A sequence in a topological space <italic>X</italic> is <italic>non-trivial</italic> if for every and, if the limit exists, for every .</p>", "<p id=\"Par25\">If is a Boolean algebra, then denotes its Stone space (i.e. the space of all ultrafilters on ) with the usual topology which makes it a totally disconnected compact Hausdorff space. Recall that is isomorphic to the algebra of clopen subsets of . For every element by we denote the clopen subset of corresponding to <italic>A</italic>.</p>", "<p id=\"Par26\">If we say that \n<italic>is a measure on a Boolean algebra</italic>\n, then we mean that is a signed finitely additive function from to with bounded total variation, that is, the following holds:When we say that \n<italic>is a measure on a compact Hausdorff space</italic>\n<italic>K</italic>, then we mean that is a signed -additive Radon measure defined on the Borel -algebra <italic>Bor</italic>(<italic>K</italic>) of <italic>K</italic>—it follows automatically that has bounded total variation, that is:Recall that if we identify a given Boolean algebra with the subalgebra of clopen subsets of the Borel -field , then every measure on extends uniquely to a measure on —we will usually omit and write simply , too.</p>", "<p id=\"Par27\">Let <italic>K</italic> be a compact space. For a measure on <italic>K</italic> and a -measurable function we write to denote . By <italic>C</italic>(<italic>K</italic>) we denote the Banach space of all continuous real-valued functions on <italic>K</italic> endowed with the supremum norm. Recall that by the Riesz representation theorem the dual space is isometrically isomorphic to the Banach space <italic>M</italic>(<italic>K</italic>) of all Radon measures on <italic>K</italic> endowed with the total variation norm—<italic>M</italic>(<italic>K</italic>) acts on <italic>C</italic>(<italic>K</italic>) by the formula .</p>", "<p id=\"Par28\">Let be a sequence of measures on a Boolean algebra . If for every , then we say that is <italic>pointwise null</italic>; if for every , then it is <italic>weak* null</italic>; and if for every , then it is <italic>weakly null</italic> (cf. [##UREF##12##13##, Theorem 11, page 90]). Additionally, we say that is <italic>pointwise bounded</italic> if for every , and that it is <italic>uniformly bounded</italic> if .</p>", "<title>Adding a convergent sequence</title>", "<p id=\"Par29\">In this section we prove that adding a Cohen real (Theorem <xref ref-type=\"sec\" rid=\"FPar7\">3.2</xref>) or an unsplit real (Theorem <xref ref-type=\"sec\" rid=\"FPar10\">3.4</xref>) to the ground model produces a non-trivial convergent sequence in the Stone space of every infinite ground model Boolean algebra. Notice that using the methods described in [##UREF##15##16##, page 162] one can generalize those results to any infinite ground model compact space <italic>K</italic>.</p>", "<p id=\"Par30\">As we mentioned in Introduction, both of the theorems have been already known to some experts, but it seems that their proofs have never been published anywhere.</p>", "<title>Cohen reals</title>", "<p id=\"Par31\">Let us first recall the definition of a Cohen real. Let be a notion of forcing and <italic>G</italic> a -generic filter over <italic>V</italic>. Then, is <italic>a Cohen real over</italic>\n<italic>V</italic> if for every dense subset such that we have . Here is the family of all finite partial functions from to 2, ordered by the reverse inclusion.</p>", "<p id=\"Par32\">We will need the following folklore lemma.</p>", "<title>Lemma 3.1</title>", "<p id=\"Par33\">If <italic>K</italic> is an infinite scattered compact Hausdorff space, then <italic>K</italic> contains a non-trivial convergent sequence.</p>", "<title>Proof</title>", "<p id=\"Par34\">Since <italic>K</italic> is scattered and infinite, there is a countable subset <italic>A</italic> of <italic>K</italic> such that every is isolated in <italic>K</italic>. <italic>A</italic> must be discrete and open in <italic>K</italic>. Since <italic>K</italic> is compact, the boundary is non-empty and thus must contain an isolated point <italic>x</italic> (in ). The sets and are closed subsets of <italic>K</italic>, so there are disjoint open sets <italic>V</italic> and <italic>W</italic> such that and . Note that , so is a one-point compactification of . Enumerate ; then . </p>", "<p>Now, we are in the position to prove the main theorem of this section.</p>", "<title>Theorem 3.2</title>", "<p id=\"Par36\">Let be a notion of forcing adding a Cohen real and an infinite Boolean algebra. Then, for every -generic filter <italic>G</italic> over <italic>V</italic> the Stone space contains a non-trivial convergent sequence.</p>", "<title>Proof</title>", "<p id=\"Par37\">We have two cases:</p>", "<p id=\"Par38\">(1) In <italic>V</italic>, the Stone space of is scattered—by Lemma <xref ref-type=\"sec\" rid=\"FPar5\">3.1</xref> there is a non-trivial convergent sequence in . Of course, this sequence will also be convergent in the Stone space of in any -generic extension <italic>V</italic>[<italic>G</italic>].</p>", "<p id=\"Par39\">(2) In <italic>V</italic>, the Stone space is not scattered. Hence, there is a closed subset <italic>L</italic> of and a continuous surjection . By the Kuratowski–Zorn lemma, we may assume that <italic>f</italic> is irreducible and hence that <italic>L</italic> is perfect. The familyis a countable -base of <italic>L</italic> (partially ordered by the reverse inclusion ). Indeed, given any non-empty open set , note that by the irreducibility of <italic>f</italic>, so for any clopen we have .</p>", "<p id=\"Par40\">Let be the Boolean algebra of clopen subsets of <italic>L</italic>. Of course, . By the Stone duality, is a homomorphic image of . For every put:Trivially, each and is dense in the poset .</p>", "<p id=\"Par41\">Fix now a -generic filter <italic>G</italic> over <italic>V</italic> and let us work in <italic>V</italic>[<italic>G</italic>]. By the assumption, there is a Cohen real over <italic>V</italic>. The familyis a -generic filter over <italic>V</italic>, so, in particular, meets every (as ). Let be the ultrafilter with the base . Since the ground model (perfect) set <italic>L</italic> had no isolated points (in <italic>V</italic>) and it is dense in , <italic>x</italic> is not isolated in . Thus, we proved that is a perfect set containing a -point. In particular, contains a non-trivial convergent sequence.</p>", "<p id=\"Par42\">In <italic>V</italic>[<italic>G</italic>], is still a homomorphic image of , hence is homeomorphic to a closed subset of . By the previous paragraph, contains a non-trivial convergent sequence (in <italic>V</italic>[<italic>G</italic>]). </p>", "<p>The next corollary follows from the proof of Theorem <xref ref-type=\"sec\" rid=\"FPar7\">3.2</xref>. Recall that a point <italic>x</italic> in a topological space <italic>X</italic> is <italic>a</italic>\n-<italic>point</italic> if the singleton is the intersection of a countable family of open subsets of <italic>X</italic>.</p>", "<title>Corollary 3.3</title>", "<p id=\"Par44\">Let be a notion of forcing adding a Cohen real and an infinite Boolean algebra such that its Stone space is not scattered. Then, for every -generic filter <italic>G</italic> over <italic>V</italic> the Stone space contains a perfect subset <italic>L</italic> and a point which is a -point in <italic>L</italic>.</p>", "<title>Unsplit reals</title>", "<p id=\"Par45\">Let be a notion of forcing and <italic>G</italic> a -generic filter over <italic>V</italic>. We say that a real is <italic>unsplit</italic> if for every the set is finite or the set is finite.</p>", "<p id=\"Par46\">The proof of the following theorem follows the idea of Booth [##UREF##4##5##, Theorem 2] (see also [##UREF##13##14##]).</p>", "<title>Theorem 3.4</title>", "<p id=\"Par47\">Let be a notion of forcing adding an unsplit real and an infinite Boolean algebra. Then, for every -generic filter <italic>G</italic> over <italic>V</italic> the Stone space contains a non-trivial convergent sequence.</p>", "<title>Proof</title>", "<p id=\"Par48\">We work first in <italic>V</italic>. Let be an infinite countable set. Put:Obviously, .</p>", "<p id=\"Par49\">Fix a -generic filter <italic>G</italic> over <italic>V</italic> and let us now work in <italic>V</italic>[<italic>G</italic>]. By the assumption, there exists which is unsplit by . It follows that for every the set is finite or the set is finite. Since is compact, there is a limit point <italic>x</italic> of <italic>U</italic> in . Enumerate . We claim that the sequence converges to <italic>x</italic>. Indeed, let be such that . Since and , we have that . Note that the set is in <italic>V</italic>, so we get that , which implies that the set is finite. </p>", "<title>Destroying the Nikodym property or the Grothendieck property</title>", "<p id=\"Par50\">In this section we provide two negative results. Namely, in Theorem <xref ref-type=\"sec\" rid=\"FPar20\">4.6</xref> we prove that adding a random real causes that no ground model Boolean algebra has the Nikodym property or the Grothendieck property, and in Theorem <xref ref-type=\"sec\" rid=\"FPar3\">1.3</xref> we show that after adding a dominating real no ground model Boolean algebra has the Nikodym property. We do not know whether adding dominating reals kills the Grothendieck property—see Questions <xref ref-type=\"sec\" rid=\"FPar45\">6.1</xref> and <xref ref-type=\"sec\" rid=\"FPar46\">6.2</xref>.</p>", "<p id=\"Par51\">We start the section recalling several auxiliary facts—the first lemma provides an alternative definition for the Nikodym property (in fact, the one more commonly used in the literature, however lacking the apparent similarity to the definition of the Grothendieck property).</p>", "<title>Lemma 4.1</title>", "<p id=\"Par52\">Let be a Boolean algebra. The following two conditions are equivalent: <list list-type=\"order\"><list-item><p id=\"Par53\">every pointwise null sequence of measures on is weak* null;</p></list-item><list-item><p id=\"Par54\">every pointwise bounded sequence of measures on is uniformly bounded.</p></list-item></list></p>", "<title>Proof</title>", "<p id=\"Par55\">Assume (1) and suppose that there exists a sequence of measures on which is pointwise bounded but not uniformly bounded. By going to the subsequence, we may assume that for every . For each define the measure on as follows:It follows that . On the other hand, for every we have:which converges to 0 as (because ), which contradicts (1) as weak* null sequences are always uniformly bounded (by the virtue of the Banach–Steinhaus theorem). Hence, (2) holds.</p>", "<p id=\"Par56\">Assume now (2) and let be a pointwise null sequence of measures on . It follows immediately that is pointwise bounded, hence, by (2), it is uniformly bounded. Let be such that . Fix and let . There are finite sequences and such thatSince is pointwise null, there is such that for every we have:Thus, for every it holds:It follows that as , which proves that is weak* null. Consequently, (1) holds. </p>", "<p>From the proof of implication (2)(1) we immediately get the following corollary.</p>", "<title>Corollary 4.2</title>", "<p id=\"Par58\">Let be a Boolean algebra. If is a pointwise null uniformly bounded sequence of measures on , then is weak* null.</p>", "<p>If <italic>X</italic> is a topological space and , then by we denote the Borel one-point measure on <italic>X</italic> concentrated at <italic>x</italic>. Recall that a measure on a compact space <italic>K</italic> (a Boolean algebra ) is <italic>finitely supported</italic> or has <italic>finite support</italic> if there exist finite sequences of pairwise distinct points in <italic>K</italic> (in ) and such that . The set is called <italic>the support</italic> of and denoted by .</p>", "<p>We will need the following simple lemma.</p>", "<title>Lemma 4.3</title>", "<p id=\"Par61\">Let be a Boolean algebra. If there exists a sequence of finitely supported measures on which is pointwise null but not uniformly bounded, then has neither the Nikodym property nor the Grothendieck property.</p>", "<title>Proof</title>", "<p id=\"Par62\"> directly witnesses the lack of the Nikodym property. Consider the sequence defined as for every . Since it is pointwise null, too, and uniformly bounded, by Corollary <xref ref-type=\"sec\" rid=\"FPar14\">4.2</xref> it is weak* null. Set and note that the Banach space of all absolutely summable sequences on the set <italic>S</italic> is a closed linear subspace of the dual space containing every . Since has the Schur property (meaning that the weak convergence of sequences implies their norm convergence), the sequence cannot be weakly null, as for every . In particular, does not have the Grothendieck property. </p>", "<title>Random reals: destroying the Nikodym and Grothendieck properties</title>", "<p id=\"Par63\">In order to prove Theorem <xref ref-type=\"sec\" rid=\"FPar20\">4.6</xref>, we need to recall some basic facts concerning the binomial distributions. Let be a probability space. Given , for every let be a random variable taking only two values: 0 and 1, and such that the following two equalities hold:andAssume additionally that the sequence is <italic>independent</italic>, that is, for every and we havewhere if , and otherwise. The following classical fact is crucial for our proof of Theorem <xref ref-type=\"sec\" rid=\"FPar20\">4.6</xref>; for its proof see e.g. [##UREF##3##4##, Section 1.3]. Recall that for .</p>", "<title>Theorem 4.4</title>", "<p id=\"Par64\">Suppose that , , and are such that . Then,</p>", "<p>In what follows we fix . Put and let denote the standard Borel -field on and the standard product measure on . We will now work in the probability space . For every and set , i.e., the function is simply the projection onto the <italic>i</italic>-th coordinate. Obviously, the sequence of random variables is as described in the paragraph before Theorem <xref ref-type=\"sec\" rid=\"FPar17\">4.4</xref>.</p>", "<title>Lemma 4.5</title>", "<p id=\"Par66\">For every set . Suppose that for some infinite and for every there is a subset such that , where for each . For each let () and , and assume that and . For every put:Then, </p>", "<title>Proof</title>", "<p id=\"Par67\">Applying Theorem <xref ref-type=\"sec\" rid=\"FPar17\">4.4</xref> (for and ), for every we get:which after simplification reduces to:</p>", "<p id=\"Par68\">Observe that () actually implies that (because ), and hence by the Borel–Cantelli lemma we get ():</p>", "<p>We are now in the position to present the proof of the main theorem of this section. We will use the following definition of a random real: Given a (forcing) extension of <italic>V</italic>, a real is <italic>a random real over</italic>\n<italic>V</italic> if for every Borel subset <italic>B</italic> of , coded in <italic>V</italic> and such that , the real <italic>r</italic> does not belong to the interpretation of <italic>B</italic> in . (We will abuse the notation and denote this interpretation by <italic>B</italic>, too.)</p>", "<title>Theorem 4.6</title>", "<p id=\"Par70\">Let be a notion of forcing adding a random real and an infinite Boolean algebra. Assume that <italic>G</italic> is a -generic filter over <italic>V</italic>. Then, in <italic>V</italic>[<italic>G</italic>], has neither the Nikodym property nor the Grothendieck property.</p>", "<title>Proof</title>", "<p id=\"Par71\">In <italic>V</italic>, let be a sequence of ultrafilters in such that for .</p>", "<p id=\"Par72\">From now on we work exclusively in <italic>V</italic>[<italic>G</italic>]. Let be such that for every . Let be a random real over <italic>V</italic>. Set . For every consider the measure on defined as follows:where and . It follows that is finitely supported, , andso .</p>", "<p id=\"Par73\">We claim that is pointwise null. Let us fix and for every setOf course, . Put:Again, .</p>", "<p id=\"Par74\">Assume first that <italic>J</italic> is infinite. We will prove that as , . For every set also and let be the clopen subset of such as defined in Lemma <xref ref-type=\"sec\" rid=\"FPar18\">4.5</xref>. By the definition of <italic>J</italic>, we get thathence equation () of Lemma <xref ref-type=\"sec\" rid=\"FPar18\">4.5</xref> together with the definition of a random real imply that for all but finitely many , which means thatfor all but finitely many , and thus there is such that for all , we have (note that ):which in turns implies that for all , , and it holds:(Just note that the values on the left hand sides of the latter two inequalities are the same.) As a result, for every , , we have:which yields thatIf is finite, then we are immediately done, so assume that it is infinite. Notice that since for the unit element of the Boolean algebra and all we have , exactly the same reasoning as above shows that , so in particular we have:For each define the set in <italic>V</italic> similarly as :and put:Since , we have:so is infinite. Using again the same argument as above, we show thatso in particular we get thatFinally, we have:which ultimately implies thatWe have just showed that the sequence of finitely supported measures on is pointwise null but not uniformly bounded, so, by Lemma <xref ref-type=\"sec\" rid=\"FPar15\">4.3</xref>, has neither the Nikodym property nor the Grothendieck property. The proof is thus finished. </p>", "<p>Note that, normalizing measures from the above proof (that is, considering the measures ), by Corollary <xref ref-type=\"sec\" rid=\"FPar14\">4.2</xref> we obtain the following result.</p>", "<title>Corollary 4.7</title>", "<p id=\"Par76\">Let be a notion of forcing adding a random real and an infinite Boolean algebra. Assume that <italic>G</italic> is a -generic filter over <italic>V</italic>. Then, in <italic>V</italic>[<italic>G</italic>], carries a weak* null sequence of finitely supported measures with pairwise disjoint supports such that and for every . </p>", "<title>Dominating reals</title>", "<p id=\"Par117\">Let be a notion of forcing and <italic>G</italic> a -generic filter over <italic>V</italic>. Recall that a real is <italic>dominating over</italic>\n<italic>V</italic> if for every . By we denote the family of all those functions which are increasing, that is, for every , and . Let us then also say that a real is <italic>anti-dominating over</italic>\n<italic>V</italic> if for every .</p>", "<p id=\"Par118\">It appears that adding a dominating real is equivalent to adding an anti-dominating real. To prove it, we need to introduce the following auxiliary operator . It seems that the idea standing behind , and hence also behind Propositions <xref ref-type=\"sec\" rid=\"FPar32\">4.14</xref> and <xref ref-type=\"sec\" rid=\"FPar34\">4.15</xref>, is standard (cf. e.g. Canjar [##UREF##8##9##, Sections 1.5 and 3.6]).</p>", "<p id=\"Par119\">Let and write . Set also , so always . Note that for every there is unique such that . Put:It is immediate that . Note that for every . The next proposition lists most basic properties of .</p>", "<title>Proposition 4.14</title>", "<p id=\"Par120\">For every the following conditions hold: <list list-type=\"order\"><list-item><p id=\"Par121\">,</p></list-item><list-item><p id=\"Par122\">,</p></list-item><list-item><p id=\"Par123\">,</p></list-item><list-item><p id=\"Par124\">if , then .</p></list-item></list></p>", "<title>Proof</title>", "<p id=\"Par125\">Let . Enumerate:and set and .</p>", "<p id=\"Par126\">We first prove (1) and (2). Fix and let be such that and . We have:which proves (1). To see (2), note that the monotonicity of <italic>f</italic> implies that and thus we have:Let us now prove (3). For every set . By the monotonicity of <italic>f</italic>, for every . Note that andso if , as well as for each we have:Fix and let be such that . It means thatso . It holds:which implies (3).</p>", "<p id=\"Par127\">Finally, we shall prove (4). Assume that . There exists such that for every . Let . There are such that , , and . Note that , so . Set:andWe claim that , so for the sake of contradiction let us assume that . We then have:so . But since <italic>f</italic> is increasing, it holds:so , which is a contradiction. </p>", "<title>Proposition 4.15</title>", "<p id=\"Par128\">Let be a notion of forcing. Then, adds a dominating real if and only if it adds an anti-dominating real.</p>", "<title>Proof</title>", "<p id=\"Par129\">Let <italic>G</italic> be a -generic filter over <italic>V</italic>. We work in <italic>V</italic>[<italic>G</italic>]. Assume that there is a dominating real over <italic>V</italic> and define an auxiliary function as follows:where . Obviously, and it is also a dominating real over <italic>V</italic>, so for every we have .</p>", "<p id=\"Par130\">For every , we have and, by Proposition <xref ref-type=\"sec\" rid=\"FPar32\">4.14</xref>.(3), . It follows that</p>", "<p id=\"Par131\">Since and <italic>g</italic> is dominating every , we get by () and Proposition <xref ref-type=\"sec\" rid=\"FPar32\">4.14</xref>.(4) that for every . In other words, we get that is an anti-dominating real over <italic>V</italic>.</p>", "<p id=\"Par132\">The proof in the other direction is similar. </p>", "<p>We are ready to prove the main result of this section.</p>", "<title>Theorem 1.3</title>", "<p id=\"Par134\">Let be an infinite Boolean algebra. Let be a notion of forcing adding a dominating real. Assume that <italic>G</italic> is a -generic filter over <italic>V</italic>. Then, in <italic>V</italic>[<italic>G</italic>], does not have the Nikodym property.</p>", "<title>Proof</title>", "<p id=\"Par135\">We first work in <italic>V</italic>. By the Josefson–Nissenzweig theorem (see [##UREF##12##13##, Chapter XII]) and the Riesz representation theorem, there is a weak* null sequence of measures on the Boolean algebra such that for every . For every define the sequences as follows:where . Then, andfor every , andFinally, for every and set . It follows that .</p>", "<p id=\"Par136\">Let us now go to <italic>V</italic>[<italic>G</italic>]. adds a dominating real, so by Proposition <xref ref-type=\"sec\" rid=\"FPar34\">4.15</xref> there is an anti-dominating real over <italic>V</italic>. By taking the function instead of <italic>g</italic>, we may assume that for every . For every we have , so if we define the sequence by the formula , where , then we get that for every . Of course, for every and .</p>", "<p id=\"Par137\">For every define the measure on as follows:where . Note that yields thatso , as . On the other hand, for every we havefor sufficiently large , so for every . It follows that the sequence is pointwise bounded but not uniformly bounded, hence, by Lemma <xref ref-type=\"sec\" rid=\"FPar12\">4.1</xref>, does not have the Nikodym property in <italic>V</italic>[<italic>G</italic>]. </p>", "<title>Cardinal characteristics of the continuum</title>", "<p id=\"Par138\">In this section we provide several consequences of Theorem <xref ref-type=\"sec\" rid=\"FPar20\">4.6</xref> to cardinal characteristics of the continuum. For basic information concerning various standard cardinal characteristics, we refer the reader to Blass [##UREF##2##3##].</p>", "<p id=\"Par139\">We start with the definitions of two characteristics and which we call <italic>the Nikodym number</italic> and <italic>the Grothendieck number</italic>, respectively:andA detailed discussion on the estimations of and in terms of standard cardinal characteristics of the continuum occurring in Cichoń’s and van Douwen’s diagrams as well as on miscellaneous consistency results one can find in the survey paper [##UREF##33##34##]. In [##UREF##35##36##] the authors proved that in the Miller model the inequality holds. We now show that the proof of Theorem <xref ref-type=\"sec\" rid=\"FPar20\">4.6</xref> easily implies that the converse inequality may also consistently hold.</p>", "<p id=\"Par140\">Similarly as in Sect. <xref rid=\"Sec8\" ref-type=\"sec\">4.2</xref>, for an infinite set <italic>I</italic> let denote the standard product probability measure on the space and let be its measure algebra. Again, it is well-known that is a -bounding poset adding |<italic>I</italic>| many random reals (see [##UREF##1##2##, Section 3.1]).</p>", "<title>Corollary 5.1</title>", "<p id=\"Par141\">Let be an infinite cardinal number. Let <italic>G</italic> be a -generic filter over <italic>V</italic>. Then, in <italic>V</italic>[<italic>G</italic>], there is no infinite Boolean algebra of size with the Nikodym property or the Grothendieck property.</p>", "<p id=\"Par142\">Consequently, in the random model every infinite Boolean algebra of size has neither the Nikodym property nor the Grothendieck property.</p>", "<title>Proof</title>", "<p id=\"Par143\">We work in <italic>V</italic>[<italic>G</italic>]. Let be an infinite Boolean algebra of size and be a countable subset of its Stone space such that for . By the standard argument based on being c.c.c., there is such that andIn <italic>V</italic>[<italic>G</italic>] there is a random real over . Now it suffices to consider the sequence of measures on , defined for every by the formula:where and are as previously, and repeat the proof of Theorem <xref ref-type=\"sec\" rid=\"FPar20\">4.6</xref>. </p>", "<title>Remark 5.2</title>", "<p id=\"Par144\">Note that the same argument as in the above proof works, e.g., for finite support iterations of of length for regular uncountable .</p>", "<title>Corollary 5.3</title>", "<p id=\"Par145\"> holds in the random model. </p>", "<p>Corollary <xref ref-type=\"sec\" rid=\"FPar41\">5.3</xref>, together with the aforementioned fact that in the Miller model we have , yields the following independence result.</p>", "<title>Corollary 5.4</title>", "<p id=\"Par147\">Let . Neither of the inequalities and is provable in ZFC.</p>", "<p>A close relative to the numbers and is <italic>the convergence number</italic>\n defined as follows:Here <italic>w</italic>(<italic>K</italic>) denotes the weight of <italic>K</italic>. The number was studied e.g. in Brian and Dow [##UREF##7##8##]. It is immediate that and . By the result of Dow and Fremlin [##UREF##15##16##] stating that in any random extension <italic>V</italic>[<italic>G</italic>], for every -complete Boolean algebra , its Stone space does not contain any non-trivial convergent sequences, we have that in the random model. Thus, by Corollary <xref ref-type=\"sec\" rid=\"FPar41\">5.3</xref>, we immediately get also the following fact.</p>", "<title>Corollary 5.5</title>", "<p id=\"Par149\"> holds in the random model.</p>", "<p>Dow [##UREF##14##15##] proved that in the Laver model there are (totally disconnected) compact spaces of weight containing no non-trivial convergent sequences, so holds in this model. On the other hand, it is well known that the bounding number has value in the Laver model, and it was proved by the first author in [##UREF##32##33##, Proposition 3.2] that holds in ZFC. We thus get the following corollary.</p>", "<title>Corollary 5.6</title>", "<p id=\"Par151\"> holds in the Laver model.</p>", "<p>We do not know the value of in the Laver model (cf. Question <xref ref-type=\"sec\" rid=\"FPar45\">6.1</xref>).</p>", "<title>Open questions</title>", "<title>Dominating reals and the Grothendieck property</title>", "<p id=\"Par153\">In the introductory section we admitted that, contrary to the case of the Nikodym property, we do not know whether adding dominating reals kills the Grothendieck property of ground model -complete Boolean algebras.</p>", "<title>Question 6.1</title>", "<p id=\"Par154\">Let be an infinite -complete Boolean algebra. Assume that <italic>G</italic> is a generic filter for the Laver forcing over <italic>V</italic>. Does have the Grothendieck property in <italic>V</italic>[<italic>G</italic>]?</p>", "<title>Question 6.2</title>", "<p id=\"Par155\">Does there exist a notion of forcing adding dominating reals and such that in any -generic extension <italic>V</italic>[<italic>G</italic>] any ground model -complete Boolean algebra has the Grothendieck property?</p>", "<p>An affirmative answer to Question <xref ref-type=\"sec\" rid=\"FPar45\">6.1</xref> would yield a new consistent example of a Boolean algebra with the Grothendieck property but without the Nikodym property. Recall that while there are many consistent or even ZFC examples of Boolean algebras with the Nikodym property but without the Grothendieck property, see e.g. [##UREF##20##21##, ##UREF##30##31##, ##UREF##36##37##], so far only one example of an algebra with the Grothendieck property and without the Nikodym property has been found—the construction was obtained by Talagrand [##UREF##37##38##] under the assumption of the Continuum Hypothesis.</p>", "<title>Eventually different reals</title>", "<p id=\"Par157\">Let <italic>V</italic>[<italic>G</italic>] be a -generic extension of the ground model <italic>V</italic> for some forcing notion . If is a dominating real, then obviously it is <italic>an eventually different real</italic>, that is, for every the set is finite. The converse does not hold, as e.g. the random forcing or the eventually different forcing both add eventually different reals but not dominating reals. Since the latter forcing adds Cohen reals, too, by Theorems <xref ref-type=\"sec\" rid=\"FPar7\">3.2</xref> and <xref ref-type=\"sec\" rid=\"FPar20\">4.6</xref> both notions kill the Nikodym and Grothendieck properties of infinite ground model Boolean algebras. Thus, it seems that all the standard classical notions adding eventually different reals kill at least one of the properties. It is also a folklore fact that a forcing adds an eventually different real if and only if it makes the ground model reals meager, hence, trivially by the assumption, the notions of forcing considered in [##UREF##35##36##] (cf. the third paragraph of Introduction), which are proved therein to preserve both the Nikodym property and the Grothendieck property of ground model -complete Boolean algebras, do not add eventually different reals. So it seems reasonable to ask whether adding an eventually different real is solely a reason that ground model Boolean algebras lose their Nikodym property (and, in the view of Question <xref ref-type=\"sec\" rid=\"FPar46\">6.2</xref>, possibly also the Grothendieck property).</p>", "<title>Question 6.3</title>", "<p id=\"Par158\">Does there exist a notion of forcing adding eventually different reals and such that in any -generic extension <italic>V</italic>[<italic>G</italic>] any ground model -complete Boolean algebra has the Nikodym property?</p>", "<title>Question 6.4</title>", "<p id=\"Par159\">Does there exist a notion of forcing adding eventually different reals and such that in any -generic extension <italic>V</italic>[<italic>G</italic>] any ground model -complete Boolean algebra has the Grothendieck property?</p>", "<title>Cardinal characteristics and </title>", "<p id=\"Par160\">We are not aware of any model in which the numbers and have different values. Thus, we pose the following question.</p>", "<title>Question 6.5</title>", "<p id=\"Par161\">Is it consistent that or ?</p>", "<p>Note that an affirmative answer to Question <xref ref-type=\"sec\" rid=\"FPar45\">6.1</xref> would imply that holds in the Laver model (cf. Corollary <xref ref-type=\"sec\" rid=\"FPar44\">5.6</xref>).</p>" ]
[ "<title>Funding Information</title>", "<p>Open access funding provided by Austrian Science Fund (FWF).</p>" ]
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[ "<inline-formula id=\"IEq1\"><alternatives><tex-math id=\"M1\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M2\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq2\"><alternatives><tex-math id=\"M3\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M4\"><mml:mi 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\n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M8\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq5\"><alternatives><tex-math id=\"M9\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M10\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq6\"><alternatives><tex-math 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id=\"M14\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq8\"><alternatives><tex-math id=\"M15\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M16\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq9\"><alternatives><tex-math id=\"M17\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n(A)\\rightarrow 0$$\\end{document}</tex-math><mml:math id=\"M18\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">→</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq10\"><alternatives><tex-math id=\"M19\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M20\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq11\"><alternatives><tex-math id=\"M21\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n(f)\\rightarrow 0$$\\end{document}</tex-math><mml:math id=\"M22\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo 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id=\"IEq13\"><alternatives><tex-math id=\"M25\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M26\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq14\"><alternatives><tex-math id=\"M27\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M28\"><mml:mi 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id=\"IEq16\"><alternatives><tex-math id=\"M31\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M32\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq17\"><alternatives><tex-math id=\"M33\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n(B)\\rightarrow 0$$\\end{document}</tex-math><mml:math id=\"M34\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">→</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq18\"><alternatives><tex-math id=\"M35\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$B\\subseteq St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M36\"><mml:mrow><mml:mi>B</mml:mi><mml:mo>⊆</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo 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(\\omega )}$$\\end{document}</tex-math><mml:math id=\"M40\"><mml:mrow><mml:mi>℘</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq21\"><alternatives><tex-math id=\"M41\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega $$\\end{document}</tex-math><mml:math id=\"M42\"><mml:mi>ω</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq22\"><alternatives><tex-math id=\"M43\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M44\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq23\"><alternatives><tex-math id=\"M45\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {c}$$\\end{document}</tex-math><mml:math id=\"M46\"><mml:mi mathvariant=\"fraktur\">c</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq24\"><alternatives><tex-math id=\"M47\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {c}$$\\end{document}</tex-math><mml:math id=\"M48\"><mml:mi mathvariant=\"fraktur\">c</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq25\"><alternatives><tex-math id=\"M49\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega _1$$\\end{document}</tex-math><mml:math id=\"M50\"><mml:msub><mml:mi>ω</mml:mi><mml:mn>1</mml:mn></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq26\"><alternatives><tex-math id=\"M51\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {c}\\ge \\omega _2$$\\end{document}</tex-math><mml:math id=\"M52\"><mml:mrow><mml:mi mathvariant=\"fraktur\">c</mml:mi><mml:mo>≥</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq27\"><alternatives><tex-math id=\"M53\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\kappa $$\\end{document}</tex-math><mml:math id=\"M54\"><mml:mi>κ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq28\"><alternatives><tex-math id=\"M55\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {S}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M56\"><mml:mrow><mml:mi mathvariant=\"double-struck\">S</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq29\"><alternatives><tex-math id=\"M57\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\kappa $$\\end{document}</tex-math><mml:math id=\"M58\"><mml:mi>κ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq30\"><alternatives><tex-math id=\"M59\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {S}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M60\"><mml:mrow><mml:mi mathvariant=\"double-struck\">S</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq31\"><alternatives><tex-math id=\"M61\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${\\wp (\\omega )}\\cap V$$\\end{document}</tex-math><mml:math id=\"M62\"><mml:mrow><mml:mrow><mml:mi>℘</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq32\"><alternatives><tex-math id=\"M63\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M64\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq33\"><alternatives><tex-math id=\"M65\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${\\wp (\\omega )}$$\\end{document}</tex-math><mml:math id=\"M66\"><mml:mrow><mml:mi>℘</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq34\"><alternatives><tex-math id=\"M67\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M68\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq35\"><alternatives><tex-math id=\"M69\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M70\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq36\"><alternatives><tex-math id=\"M71\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M72\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq37\"><alternatives><tex-math id=\"M73\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M74\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq38\"><alternatives><tex-math id=\"M75\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M76\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq39\"><alternatives><tex-math id=\"M77\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M78\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq40\"><alternatives><tex-math id=\"M79\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M80\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq41\"><alternatives><tex-math id=\"M81\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M82\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq42\"><alternatives><tex-math id=\"M83\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M84\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq43\"><alternatives><tex-math id=\"M85\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M86\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq44\"><alternatives><tex-math id=\"M87\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M88\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq45\"><alternatives><tex-math id=\"M89\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$&lt;2^\\omega $$\\end{document}</tex-math><mml:math id=\"M90\"><mml:mrow><mml:mo>&lt;</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq46\"><alternatives><tex-math id=\"M91\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${{\\,\\textrm{cov}\\,}}(\\mathcal {M})$$\\end{document}</tex-math><mml:math id=\"M92\"><mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>cov</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">M</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq47\"><alternatives><tex-math id=\"M93\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {M}$$\\end{document}</tex-math><mml:math id=\"M94\"><mml:mi mathvariant=\"script\">M</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq48\"><alternatives><tex-math id=\"M95\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$&lt;2^\\omega $$\\end{document}</tex-math><mml:math id=\"M96\"><mml:mrow><mml:mo>&lt;</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq49\"><alternatives><tex-math id=\"M97\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {s}$$\\end{document}</tex-math><mml:math id=\"M98\"><mml:mi mathvariant=\"fraktur\">s</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq50\"><alternatives><tex-math id=\"M99\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M100\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq51\"><alternatives><tex-math id=\"M101\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M102\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq52\"><alternatives><tex-math id=\"M103\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M104\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq53\"><alternatives><tex-math id=\"M105\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M106\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq54\"><alternatives><tex-math id=\"M107\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M108\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq55\"><alternatives><tex-math id=\"M109\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M110\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq56\"><alternatives><tex-math id=\"M111\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M112\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq57\"><alternatives><tex-math id=\"M113\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M114\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq58\"><alternatives><tex-math id=\"M115\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M116\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq59\"><alternatives><tex-math id=\"M117\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M118\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq60\"><alternatives><tex-math id=\"M119\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M120\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq61\"><alternatives><tex-math id=\"M121\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M122\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq62\"><alternatives><tex-math id=\"M123\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M124\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq63\"><alternatives><tex-math id=\"M125\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M126\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq64\"><alternatives><tex-math id=\"M127\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M128\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq65\"><alternatives><tex-math id=\"M129\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M130\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq66\"><alternatives><tex-math id=\"M131\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M132\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq67\"><alternatives><tex-math id=\"M133\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M134\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq68\"><alternatives><tex-math id=\"M135\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M136\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq69\"><alternatives><tex-math id=\"M137\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M138\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq70\"><alternatives><tex-math id=\"M139\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M140\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq71\"><alternatives><tex-math id=\"M141\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M142\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq72\"><alternatives><tex-math id=\"M143\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M144\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq73\"><alternatives><tex-math id=\"M145\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${\\wp (\\omega )}\\cap V$$\\end{document}</tex-math><mml:math id=\"M146\"><mml:mrow><mml:mrow><mml:mi>℘</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq74\"><alternatives><tex-math id=\"M147\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${\\wp (\\omega )}\\cap V$$\\end{document}</tex-math><mml:math id=\"M148\"><mml:mrow><mml:mrow><mml:mi>℘</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq75\"><alternatives><tex-math id=\"M149\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${\\wp (\\omega )}$$\\end{document}</tex-math><mml:math id=\"M150\"><mml:mrow><mml:mi>℘</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq76\"><alternatives><tex-math id=\"M151\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega $$\\end{document}</tex-math><mml:math id=\"M152\"><mml:mi>ω</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq77\"><alternatives><tex-math id=\"M153\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\wp (A)$$\\end{document}</tex-math><mml:math id=\"M154\"><mml:mrow><mml:mi>℘</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq78\"><alternatives><tex-math id=\"M155\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\left[ A\\right] ^\\omega $$\\end{document}</tex-math><mml:math id=\"M156\"><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq79\"><alternatives><tex-math id=\"M157\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\left[ A\\right] ^{&lt;\\omega }$$\\end{document}</tex-math><mml:math id=\"M158\"><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq80\"><alternatives><tex-math id=\"M159\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A^B$$\\end{document}</tex-math><mml:math id=\"M160\"><mml:msup><mml:mi>A</mml:mi><mml:mi>B</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq81\"><alternatives><tex-math id=\"M161\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${{\\,\\textrm{ran}\\,}}(f)$$\\end{document}</tex-math><mml:math id=\"M162\"><mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>ran</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq82\"><alternatives><tex-math id=\"M163\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$(L,\\le )$$\\end{document}</tex-math><mml:math id=\"M164\"><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>L</mml:mi><mml:mo>,</mml:mo><mml:mo>≤</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq83\"><alternatives><tex-math id=\"M165\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f,g\\in L^\\omega $$\\end{document}</tex-math><mml:math id=\"M166\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>,</mml:mo><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>L</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq84\"><alternatives><tex-math id=\"M167\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\le g$$\\end{document}</tex-math><mml:math id=\"M168\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>≤</mml:mo><mml:mi>g</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq85\"><alternatives><tex-math id=\"M169\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\le ^*g$$\\end{document}</tex-math><mml:math id=\"M170\"><mml:mrow><mml:mi>f</mml:mi><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:mi>g</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq86\"><alternatives><tex-math id=\"M171\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M172\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq87\"><alternatives><tex-math id=\"M173\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f(n)\\le g(n)$$\\end{document}</tex-math><mml:math id=\"M174\"><mml:mrow><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>≤</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq88\"><alternatives><tex-math id=\"M175\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$&lt;^*$$\\end{document}</tex-math><mml:math id=\"M176\"><mml:msup><mml:mo>&lt;</mml:mo><mml:mo>∗</mml:mo></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq89\"><alternatives><tex-math id=\"M177\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$L^\\omega $$\\end{document}</tex-math><mml:math id=\"M178\"><mml:msup><mml:mi>L</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq90\"><alternatives><tex-math id=\"M179\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${{\\,\\textrm{id}\\,}}_A$$\\end{document}</tex-math><mml:math id=\"M180\"><mml:msub><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>id</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mi>A</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq91\"><alternatives><tex-math id=\"M181\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$B\\subseteq A$$\\end{document}</tex-math><mml:math id=\"M182\"><mml:mrow><mml:mi>B</mml:mi><mml:mo>⊆</mml:mo><mml:mi>A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq92\"><alternatives><tex-math id=\"M183\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\chi _B$$\\end{document}</tex-math><mml:math id=\"M184\"><mml:msub><mml:mi>χ</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq93\"><alternatives><tex-math id=\"M185\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle x_n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M186\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq94\"><alternatives><tex-math id=\"M187\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_n\\ne x_m$$\\end{document}</tex-math><mml:math id=\"M188\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>m</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq95\"><alternatives><tex-math id=\"M189\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ne m\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M190\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≠</mml:mo><mml:mi>m</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq96\"><alternatives><tex-math id=\"M191\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_m\\ne \\lim _{n\\rightarrow \\infty }x_n$$\\end{document}</tex-math><mml:math id=\"M192\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>m</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq97\"><alternatives><tex-math id=\"M193\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$m\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M194\"><mml:mrow><mml:mi>m</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq98\"><alternatives><tex-math id=\"M195\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M196\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq99\"><alternatives><tex-math id=\"M197\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M198\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq100\"><alternatives><tex-math id=\"M199\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M200\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq101\"><alternatives><tex-math id=\"M201\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M202\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq102\"><alternatives><tex-math id=\"M203\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M204\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq103\"><alternatives><tex-math id=\"M205\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M206\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq104\"><alternatives><tex-math id=\"M207\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$[A]_\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M208\"><mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq105\"><alternatives><tex-math id=\"M209\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M210\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq106\"><alternatives><tex-math id=\"M211\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M212\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq107\"><alternatives><tex-math id=\"M213\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M214\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq108\"><alternatives><tex-math id=\"M215\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M216\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq109\"><alternatives><tex-math id=\"M217\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M218\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq110\"><alternatives><tex-math id=\"M219\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {R}$$\\end{document}</tex-math><mml:math id=\"M220\"><mml:mi mathvariant=\"double-struck\">R</mml:mi></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ1\"><alternatives><tex-math id=\"M221\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Vert \\mu \\Vert =\\sup \\big \\{|\\mu (A)|+|\\mu (B)|:\\ A,B\\in \\mathcal {A}, A\\wedge B=0\\big \\}&lt;\\infty . \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M222\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mo stretchy=\"false\">‖</mml:mo><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">‖</mml:mo><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">sup</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>+</mml:mo><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>A</mml:mi><mml:mo>,</mml:mo><mml:mi>B</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>,</mml:mo><mml:mi>A</mml:mi><mml:mo>∧</mml:mo><mml:mi>B</mml:mi><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>∞</mml:mi><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq111\"><alternatives><tex-math id=\"M223\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M224\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq112\"><alternatives><tex-math id=\"M225\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M226\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq113\"><alternatives><tex-math id=\"M227\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M228\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq114\"><alternatives><tex-math id=\"M229\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M230\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq115\"><alternatives><tex-math id=\"M231\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M232\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ2\"><alternatives><tex-math id=\"M233\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Vert \\mu \\Vert =\\sup \\big \\{|\\mu (A)|+|\\mu (B)|:\\ A,B\\in Bor(K), A\\cap B=0\\big \\}&lt;\\infty . \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M234\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mo stretchy=\"false\">‖</mml:mo><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">‖</mml:mo><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">sup</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>+</mml:mo><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>A</mml:mi><mml:mo>,</mml:mo><mml:mi>B</mml:mi><mml:mo>∈</mml:mo><mml:mi>B</mml:mi><mml:mi>o</mml:mi><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>K</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>,</mml:mo><mml:mi>A</mml:mi><mml:mo>∩</mml:mo><mml:mi>B</mml:mi><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>∞</mml:mi><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq116\"><alternatives><tex-math id=\"M235\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M236\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq117\"><alternatives><tex-math id=\"M237\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M238\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq118\"><alternatives><tex-math id=\"M239\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Bor(St(\\mathcal {A}))$$\\end{document}</tex-math><mml:math id=\"M240\"><mml:mrow><mml:mi>B</mml:mi><mml:mi>o</mml:mi><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq119\"><alternatives><tex-math id=\"M241\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M242\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq120\"><alternatives><tex-math id=\"M243\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M244\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq121\"><alternatives><tex-math id=\"M245\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\widehat{\\mu }$$\\end{document}</tex-math><mml:math id=\"M246\"><mml:mover accent=\"true\"><mml:mi>μ</mml:mi><mml:mo stretchy=\"true\">^</mml:mo></mml:mover></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq122\"><alternatives><tex-math id=\"M247\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M248\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq123\"><alternatives><tex-math id=\"M249\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\hat{}$$\\end{document}</tex-math><mml:math id=\"M250\"><mml:mover accent=\"true\"><mml:mrow/><mml:mo stretchy=\"false\">^</mml:mo></mml:mover></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq124\"><alternatives><tex-math id=\"M251\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M252\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq125\"><alternatives><tex-math id=\"M253\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M254\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq126\"><alternatives><tex-math id=\"M255\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M256\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq127\"><alternatives><tex-math id=\"M257\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f:K\\rightarrow \\mathbb {R}$$\\end{document}</tex-math><mml:math id=\"M258\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>:</mml:mo><mml:mi>K</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi mathvariant=\"double-struck\">R</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq128\"><alternatives><tex-math id=\"M259\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu (f)$$\\end{document}</tex-math><mml:math id=\"M260\"><mml:mrow><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq129\"><alternatives><tex-math id=\"M261\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\int _Kfd\\mu $$\\end{document}</tex-math><mml:math id=\"M262\"><mml:mrow><mml:msub><mml:mo>∫</mml:mo><mml:mi>K</mml:mi></mml:msub><mml:mi>f</mml:mi><mml:mi>d</mml:mi><mml:mi>μ</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq130\"><alternatives><tex-math id=\"M263\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C(K)^*$$\\end{document}</tex-math><mml:math id=\"M264\"><mml:mrow><mml:mi>C</mml:mi><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>K</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∗</mml:mo></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq131\"><alternatives><tex-math id=\"M265\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\langle f,\\mu \\rangle =\\mu (f)$$\\end{document}</tex-math><mml:math id=\"M266\"><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:mi>f</mml:mi><mml:mo>,</mml:mo><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>=</mml:mo><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq132\"><alternatives><tex-math id=\"M267\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M268\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq133\"><alternatives><tex-math id=\"M269\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M270\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq134\"><alternatives><tex-math id=\"M271\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\lim _{n\\rightarrow \\infty }\\mu _n(A)=0$$\\end{document}</tex-math><mml:math id=\"M272\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq135\"><alternatives><tex-math id=\"M273\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M274\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq136\"><alternatives><tex-math id=\"M275\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M276\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq137\"><alternatives><tex-math id=\"M277\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\lim _{n\\rightarrow \\infty }\\mu _n(f)=0$$\\end{document}</tex-math><mml:math id=\"M278\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq138\"><alternatives><tex-math id=\"M279\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\in C(St(\\mathcal {A}))$$\\end{document}</tex-math><mml:math id=\"M280\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>∈</mml:mo><mml:mi>C</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq139\"><alternatives><tex-math id=\"M281\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\lim _{n\\rightarrow \\infty }\\mu _n(B)=0$$\\end{document}</tex-math><mml:math id=\"M282\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq140\"><alternatives><tex-math id=\"M283\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$B\\in Bor(St(\\mathcal {A}))$$\\end{document}</tex-math><mml:math id=\"M284\"><mml:mrow><mml:mi>B</mml:mi><mml:mo>∈</mml:mo><mml:mi>B</mml:mi><mml:mi>o</mml:mi><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq141\"><alternatives><tex-math id=\"M285\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M286\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq142\"><alternatives><tex-math id=\"M287\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sup _{n\\in \\omega }\\big |\\mu _n(A)\\big |&lt;\\infty $$\\end{document}</tex-math><mml:math id=\"M288\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">sup</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq143\"><alternatives><tex-math id=\"M289\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M290\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq144\"><alternatives><tex-math id=\"M291\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sup _{n\\in \\omega }\\big \\Vert \\mu _n\\big \\Vert &lt;\\infty $$\\end{document}</tex-math><mml:math id=\"M292\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">sup</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq145\"><alternatives><tex-math id=\"M293\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M294\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq146\"><alternatives><tex-math id=\"M295\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M296\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq147\"><alternatives><tex-math id=\"M297\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x\\in 2^\\omega \\cap V[G]$$\\end{document}</tex-math><mml:math id=\"M298\"><mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq148\"><alternatives><tex-math id=\"M299\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$D\\subseteq Fn(\\omega ,2)$$\\end{document}</tex-math><mml:math id=\"M300\"><mml:mrow><mml:mi>D</mml:mi><mml:mo>⊆</mml:mo><mml:mi>F</mml:mi><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo>,</mml:mo><mml:mn>2</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq149\"><alternatives><tex-math id=\"M301\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$D\\in V$$\\end{document}</tex-math><mml:math id=\"M302\"><mml:mrow><mml:mi>D</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq150\"><alternatives><tex-math id=\"M303\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$D\\cap \\big \\{p\\in Fn(\\omega ,2):\\ p\\subseteq x\\big \\}\\ne \\emptyset $$\\end{document}</tex-math><mml:math id=\"M304\"><mml:mrow><mml:mi>D</mml:mi><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>p</mml:mi><mml:mo>∈</mml:mo><mml:mi>F</mml:mi><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo>,</mml:mo><mml:mn>2</mml:mn><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>p</mml:mi><mml:mo>⊆</mml:mo><mml:mi>x</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>≠</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq151\"><alternatives><tex-math id=\"M305\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Fn(\\omega ,2)$$\\end{document}</tex-math><mml:math id=\"M306\"><mml:mrow><mml:mi>F</mml:mi><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo>,</mml:mo><mml:mn>2</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq152\"><alternatives><tex-math id=\"M307\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega $$\\end{document}</tex-math><mml:math id=\"M308\"><mml:mi>ω</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq153\"><alternatives><tex-math id=\"M309\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x\\in A$$\\end{document}</tex-math><mml:math id=\"M310\"><mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:mi>A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq154\"><alternatives><tex-math id=\"M311\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\partial A$$\\end{document}</tex-math><mml:math id=\"M312\"><mml:mrow><mml:mi>∂</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq155\"><alternatives><tex-math id=\"M313\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\partial A$$\\end{document}</tex-math><mml:math id=\"M314\"><mml:mrow><mml:mi>∂</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq156\"><alternatives><tex-math id=\"M315\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\{x\\}$$\\end{document}</tex-math><mml:math id=\"M316\"><mml:mrow><mml:mo stretchy=\"false\">{</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq157\"><alternatives><tex-math id=\"M317\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$(\\partial A)\\setminus \\{x\\}$$\\end{document}</tex-math><mml:math id=\"M318\"><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>∂</mml:mi><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mo stretchy=\"false\">{</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq158\"><alternatives><tex-math id=\"M319\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\{x\\}\\subseteq V$$\\end{document}</tex-math><mml:math id=\"M320\"><mml:mrow><mml:mo stretchy=\"false\">{</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">}</mml:mo><mml:mo>⊆</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq159\"><alternatives><tex-math id=\"M321\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$(\\partial A)\\setminus \\{x\\}\\subseteq W$$\\end{document}</tex-math><mml:math id=\"M322\"><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>∂</mml:mi><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mo stretchy=\"false\">{</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">}</mml:mo><mml:mo>⊆</mml:mo><mml:mi>W</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq160\"><alternatives><tex-math id=\"M323\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\overline{V\\cap A}=(V\\cap A)\\cup \\{x\\}$$\\end{document}</tex-math><mml:math id=\"M324\"><mml:mrow><mml:mover><mml:mrow><mml:mi>V</mml:mi><mml:mo>∩</mml:mo><mml:mi>A</mml:mi></mml:mrow><mml:mo>¯</mml:mo></mml:mover><mml:mo>=</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>V</mml:mi><mml:mo>∩</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∪</mml:mo><mml:mrow><mml:mo stretchy=\"false\">{</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq161\"><alternatives><tex-math id=\"M325\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\overline{V\\cap A}$$\\end{document}</tex-math><mml:math id=\"M326\"><mml:mover><mml:mrow><mml:mi>V</mml:mi><mml:mo>∩</mml:mo><mml:mi>A</mml:mi></mml:mrow><mml:mo>¯</mml:mo></mml:mover></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq162\"><alternatives><tex-math id=\"M327\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$V\\cap A$$\\end{document}</tex-math><mml:math id=\"M328\"><mml:mrow><mml:mi>V</mml:mi><mml:mo>∩</mml:mo><mml:mi>A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq163\"><alternatives><tex-math id=\"M329\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$V\\cap A=\\{x_n:\\ n\\in \\omega \\}$$\\end{document}</tex-math><mml:math id=\"M330\"><mml:mrow><mml:mi>V</mml:mi><mml:mo>∩</mml:mo><mml:mi>A</mml:mi><mml:mo>=</mml:mo><mml:mo stretchy=\"false\">{</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq164\"><alternatives><tex-math id=\"M331\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_n\\rightarrow x$$\\end{document}</tex-math><mml:math id=\"M332\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>x</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq165\"><alternatives><tex-math id=\"M333\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M334\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq166\"><alternatives><tex-math id=\"M335\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M336\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq167\"><alternatives><tex-math id=\"M337\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M338\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq168\"><alternatives><tex-math id=\"M339\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M340\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq169\"><alternatives><tex-math id=\"M341\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big (St(\\mathcal {A})\\big )^{V[G]}$$\\end{document}</tex-math><mml:math id=\"M342\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mi>V</mml:mi><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq170\"><alternatives><tex-math id=\"M343\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M344\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq171\"><alternatives><tex-math id=\"M345\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M346\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq172\"><alternatives><tex-math id=\"M347\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M348\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq173\"><alternatives><tex-math id=\"M349\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M350\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq174\"><alternatives><tex-math id=\"M351\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M352\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq175\"><alternatives><tex-math id=\"M353\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M354\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq176\"><alternatives><tex-math id=\"M355\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M356\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq177\"><alternatives><tex-math id=\"M357\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f:L\\rightarrow 2^\\omega $$\\end{document}</tex-math><mml:math id=\"M358\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>:</mml:mo><mml:mi>L</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ3\"><alternatives><tex-math id=\"M359\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\mathcal {P}=\\big \\{f^{-1}[U]:\\ U\\ne \\emptyset \\text { is a clopen in }2^\\omega \\big \\} \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M360\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi mathvariant=\"script\">P</mml:mi><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>U</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>U</mml:mi><mml:mo>≠</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi><mml:mspace width=\"0.333333em\"/><mml:mtext>is a clopen in</mml:mtext><mml:mspace width=\"0.333333em\"/><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq178\"><alternatives><tex-math id=\"M361\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\pi $$\\end{document}</tex-math><mml:math id=\"M362\"><mml:mi>π</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq179\"><alternatives><tex-math id=\"M363\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\supseteq $$\\end{document}</tex-math><mml:math id=\"M364\"><mml:mo>⊇</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq180\"><alternatives><tex-math id=\"M365\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$W\\subseteq L$$\\end{document}</tex-math><mml:math id=\"M366\"><mml:mrow><mml:mi>W</mml:mi><mml:mo>⊆</mml:mo><mml:mi>L</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq181\"><alternatives><tex-math id=\"M367\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f[L\\setminus W]\\ne 2^\\omega $$\\end{document}</tex-math><mml:math id=\"M368\"><mml:mrow><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>L</mml:mi><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>W</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mo>≠</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq182\"><alternatives><tex-math id=\"M369\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\subseteq 2^\\omega \\setminus f[L\\setminus W]$$\\end{document}</tex-math><mml:math id=\"M370\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>⊆</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>L</mml:mi><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>W</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq183\"><alternatives><tex-math id=\"M371\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f^{-1}[U]\\subseteq W$$\\end{document}</tex-math><mml:math id=\"M372\"><mml:mrow><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>U</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mo>⊆</mml:mo><mml:mi>W</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq184\"><alternatives><tex-math id=\"M373\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {B}$$\\end{document}</tex-math><mml:math id=\"M374\"><mml:mi mathvariant=\"script\">B</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq185\"><alternatives><tex-math id=\"M375\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {P}\\subseteq \\mathcal {B}$$\\end{document}</tex-math><mml:math id=\"M376\"><mml:mrow><mml:mi mathvariant=\"script\">P</mml:mi><mml:mo>⊆</mml:mo><mml:mi mathvariant=\"script\">B</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq186\"><alternatives><tex-math id=\"M377\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {B}$$\\end{document}</tex-math><mml:math id=\"M378\"><mml:mi mathvariant=\"script\">B</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq187\"><alternatives><tex-math id=\"M379\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M380\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq188\"><alternatives><tex-math id=\"M381\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\in \\mathcal {B}$$\\end{document}</tex-math><mml:math id=\"M382\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">B</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ4\"><alternatives><tex-math id=\"M383\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} D_U=\\big \\{P\\in \\mathcal {P}:\\ P\\subseteq U\\text { or }P\\subseteq L\\setminus U\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M384\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>D</mml:mi><mml:mi>U</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>P</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">P</mml:mi><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>P</mml:mi><mml:mo>⊆</mml:mo><mml:mi>U</mml:mi><mml:mspace width=\"0.333333em\"/><mml:mtext>or</mml:mtext><mml:mspace width=\"0.333333em\"/><mml:mi>P</mml:mi><mml:mo>⊆</mml:mo><mml:mi>L</mml:mi><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>U</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq189\"><alternatives><tex-math id=\"M385\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$D_U\\in V$$\\end{document}</tex-math><mml:math id=\"M386\"><mml:mrow><mml:msub><mml:mi>D</mml:mi><mml:mi>U</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq190\"><alternatives><tex-math id=\"M387\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$(\\mathcal {P},\\supseteq )$$\\end{document}</tex-math><mml:math id=\"M388\"><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">P</mml:mi><mml:mo>,</mml:mo><mml:mo>⊇</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq191\"><alternatives><tex-math id=\"M389\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M390\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq192\"><alternatives><tex-math id=\"M391\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$c\\in 2^\\omega $$\\end{document}</tex-math><mml:math id=\"M392\"><mml:mrow><mml:mi>c</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ5\"><alternatives><tex-math id=\"M393\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\mathcal {G}=\\big \\{f^{-1}\\big [[c\\restriction n]^V\\big ]:n\\in \\omega \\big \\} \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M394\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi mathvariant=\"script\">G</mml:mi><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">[</mml:mo></mml:mrow><mml:msup><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>c</mml:mi><mml:mo>↾</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mi>V</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">]</mml:mo></mml:mrow><mml:mo>:</mml:mo><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq193\"><alternatives><tex-math id=\"M395\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {P}$$\\end{document}</tex-math><mml:math id=\"M396\"><mml:mi mathvariant=\"script\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq194\"><alternatives><tex-math id=\"M397\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {G}$$\\end{document}</tex-math><mml:math id=\"M398\"><mml:mi mathvariant=\"script\">G</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq195\"><alternatives><tex-math id=\"M399\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$D_U$$\\end{document}</tex-math><mml:math id=\"M400\"><mml:msub><mml:mi>D</mml:mi><mml:mi>U</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq196\"><alternatives><tex-math id=\"M401\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$D_U\\in V$$\\end{document}</tex-math><mml:math id=\"M402\"><mml:mrow><mml:msub><mml:mi>D</mml:mi><mml:mi>U</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq197\"><alternatives><tex-math id=\"M403\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x\\in St(\\mathcal {B})$$\\end{document}</tex-math><mml:math id=\"M404\"><mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq198\"><alternatives><tex-math id=\"M405\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {G}$$\\end{document}</tex-math><mml:math id=\"M406\"><mml:mi mathvariant=\"script\">G</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq199\"><alternatives><tex-math id=\"M407\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {B})$$\\end{document}</tex-math><mml:math id=\"M408\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq200\"><alternatives><tex-math id=\"M409\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {B})$$\\end{document}</tex-math><mml:math id=\"M410\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq201\"><alternatives><tex-math id=\"M411\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {B})$$\\end{document}</tex-math><mml:math id=\"M412\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq202\"><alternatives><tex-math id=\"M413\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {G}_\\delta $$\\end{document}</tex-math><mml:math id=\"M414\"><mml:msub><mml:mi mathvariant=\"double-struck\">G</mml:mi><mml:mi>δ</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq203\"><alternatives><tex-math id=\"M415\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {B})$$\\end{document}</tex-math><mml:math id=\"M416\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq204\"><alternatives><tex-math id=\"M417\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {B}$$\\end{document}</tex-math><mml:math id=\"M418\"><mml:mi mathvariant=\"script\">B</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq205\"><alternatives><tex-math id=\"M419\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M420\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq206\"><alternatives><tex-math id=\"M421\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {B})$$\\end{document}</tex-math><mml:math id=\"M422\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq207\"><alternatives><tex-math id=\"M423\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M424\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq208\"><alternatives><tex-math id=\"M425\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M426\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq209\"><alternatives><tex-math id=\"M427\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M428\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq210\"><alternatives><tex-math id=\"M429\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {G}_\\delta $$\\end{document}</tex-math><mml:math id=\"M430\"><mml:msub><mml:mi mathvariant=\"double-struck\">G</mml:mi><mml:mi>δ</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq211\"><alternatives><tex-math id=\"M431\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\{x\\}$$\\end{document}</tex-math><mml:math id=\"M432\"><mml:mrow><mml:mo stretchy=\"false\">{</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq212\"><alternatives><tex-math id=\"M433\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M434\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq213\"><alternatives><tex-math id=\"M435\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M436\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq214\"><alternatives><tex-math id=\"M437\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M438\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq215\"><alternatives><tex-math id=\"M439\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M440\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq216\"><alternatives><tex-math id=\"M441\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big (St(\\mathcal {A})\\big )^{V[G]}$$\\end{document}</tex-math><mml:math id=\"M442\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mi>V</mml:mi><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq217\"><alternatives><tex-math id=\"M443\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x\\in L$$\\end{document}</tex-math><mml:math id=\"M444\"><mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:mi>L</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq218\"><alternatives><tex-math id=\"M445\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {G}_\\delta $$\\end{document}</tex-math><mml:math id=\"M446\"><mml:msub><mml:mi mathvariant=\"double-struck\">G</mml:mi><mml:mi>δ</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq219\"><alternatives><tex-math id=\"M447\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Box $$\\end{document}</tex-math><mml:math id=\"M448\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq220\"><alternatives><tex-math id=\"M449\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M450\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq221\"><alternatives><tex-math id=\"M451\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M452\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq222\"><alternatives><tex-math id=\"M453\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\in {\\wp (\\omega )}\\cap V[G]$$\\end{document}</tex-math><mml:math id=\"M454\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>∈</mml:mo><mml:mrow><mml:mi>℘</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:mi>V</mml:mi><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq223\"><alternatives><tex-math id=\"M455\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in {\\wp (\\omega )}\\cap V$$\\end{document}</tex-math><mml:math id=\"M456\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mrow><mml:mi>℘</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq224\"><alternatives><tex-math id=\"M457\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\cap A$$\\end{document}</tex-math><mml:math id=\"M458\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>∩</mml:mo><mml:mi>A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq225\"><alternatives><tex-math id=\"M459\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\setminus A$$\\end{document}</tex-math><mml:math id=\"M460\"><mml:mrow><mml:mi>U</mml:mi><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq226\"><alternatives><tex-math id=\"M461\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M462\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq227\"><alternatives><tex-math id=\"M463\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M464\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq228\"><alternatives><tex-math id=\"M465\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M466\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq229\"><alternatives><tex-math id=\"M467\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big (St(\\mathcal {A})\\big )^{V[G]}$$\\end{document}</tex-math><mml:math id=\"M468\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mi>V</mml:mi><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq230\"><alternatives><tex-math id=\"M469\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\subseteq St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M470\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>⊆</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ6\"><alternatives><tex-math id=\"M471\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\mathcal {D}=\\big \\{A\\cap [B]_\\mathcal {A}:\\ B\\in \\mathcal {A},\\ |A\\cap [B]_\\mathcal {A}|=\\omega \\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M472\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi mathvariant=\"script\">D</mml:mi><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>A</mml:mi><mml:mo>∩</mml:mo><mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>B</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>,</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>A</mml:mi><mml:mo>∩</mml:mo><mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq231\"><alternatives><tex-math id=\"M473\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {D}\\subseteq \\left[ A\\right] ^\\omega $$\\end{document}</tex-math><mml:math id=\"M474\"><mml:mrow><mml:mi mathvariant=\"script\">D</mml:mi><mml:mo>⊆</mml:mo><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq232\"><alternatives><tex-math id=\"M475\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M476\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq233\"><alternatives><tex-math id=\"M477\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\subseteq \\left[ A\\right] ^\\omega $$\\end{document}</tex-math><mml:math id=\"M478\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>⊆</mml:mo><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq234\"><alternatives><tex-math id=\"M479\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big (\\left[ A\\right] ^\\omega \\big )^V$$\\end{document}</tex-math><mml:math id=\"M480\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup><mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mi>V</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq235\"><alternatives><tex-math id=\"M481\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$D\\in \\mathcal {D}$$\\end{document}</tex-math><mml:math id=\"M482\"><mml:mrow><mml:mi>D</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">D</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq236\"><alternatives><tex-math id=\"M483\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\cap D$$\\end{document}</tex-math><mml:math id=\"M484\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>∩</mml:mo><mml:mi>D</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq237\"><alternatives><tex-math id=\"M485\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\setminus D$$\\end{document}</tex-math><mml:math id=\"M486\"><mml:mrow><mml:mi>U</mml:mi><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>D</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq238\"><alternatives><tex-math id=\"M487\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M488\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq239\"><alternatives><tex-math id=\"M489\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M490\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq240\"><alternatives><tex-math id=\"M491\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U=\\{x_n:\\ n\\in \\omega \\}$$\\end{document}</tex-math><mml:math id=\"M492\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>=</mml:mo><mml:mo stretchy=\"false\">{</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq241\"><alternatives><tex-math id=\"M493\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle x_n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M494\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq242\"><alternatives><tex-math id=\"M495\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$B\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M496\"><mml:mrow><mml:mi>B</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq243\"><alternatives><tex-math id=\"M497\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x\\in [B]_\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M498\"><mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq244\"><alternatives><tex-math id=\"M499\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$|U\\cap [B]_\\mathcal {A}|=\\omega $$\\end{document}</tex-math><mml:math id=\"M500\"><mml:mrow><mml:msub><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>U</mml:mi><mml:mo>∩</mml:mo><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>=</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq245\"><alternatives><tex-math id=\"M501\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\in \\left[ A\\right] ^\\omega $$\\end{document}</tex-math><mml:math id=\"M502\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq246\"><alternatives><tex-math id=\"M503\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$|A\\cap [B]_\\mathcal {A}|=\\omega $$\\end{document}</tex-math><mml:math id=\"M504\"><mml:mrow><mml:msub><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>A</mml:mi><mml:mo>∩</mml:mo><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>=</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq247\"><alternatives><tex-math id=\"M505\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\cap \\left[ B\\right] _\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M506\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∩</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>B</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq248\"><alternatives><tex-math id=\"M507\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\cap [B]_\\mathcal {A}\\in \\mathcal {D}$$\\end{document}</tex-math><mml:math id=\"M508\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∩</mml:mo><mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">D</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq249\"><alternatives><tex-math id=\"M509\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\setminus [B]_\\mathcal {A}=U\\setminus (A\\cap [B]_\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M510\"><mml:mrow><mml:mi>U</mml:mi><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi>U</mml:mi><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo>∩</mml:mo><mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq250\"><alternatives><tex-math id=\"M511\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M512\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq251\"><alternatives><tex-math id=\"M513\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M514\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq252\"><alternatives><tex-math id=\"M515\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M516\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq253\"><alternatives><tex-math id=\"M517\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M518\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq254\"><alternatives><tex-math id=\"M519\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M520\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq255\"><alternatives><tex-math id=\"M521\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M522\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq256\"><alternatives><tex-math id=\"M523\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert &gt;n$$\\end{document}</tex-math><mml:math id=\"M524\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq257\"><alternatives><tex-math id=\"M525\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M526\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq258\"><alternatives><tex-math id=\"M527\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M528\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq259\"><alternatives><tex-math id=\"M529\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\nu _n$$\\end{document}</tex-math><mml:math id=\"M530\"><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq260\"><alternatives><tex-math id=\"M531\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M532\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ7\"><alternatives><tex-math id=\"M533\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\nu _n=\\mu _n\\big /\\sqrt{\\big \\Vert \\mu _n\\big \\Vert }. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M534\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:msqrt><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow></mml:mrow></mml:msqrt><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq261\"><alternatives><tex-math id=\"M535\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\nu _n\\big \\Vert =\\sqrt{\\big \\Vert \\mu _n\\big \\Vert }&gt;\\sqrt{n}$$\\end{document}</tex-math><mml:math id=\"M536\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msqrt><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow></mml:mrow></mml:msqrt><mml:mo>&gt;</mml:mo><mml:msqrt><mml:mi>n</mml:mi></mml:msqrt></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq262\"><alternatives><tex-math id=\"M537\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M538\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ8\"><alternatives><tex-math id=\"M539\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\big |\\nu _n(A)\\big |=\\big |\\mu _n(A)\\big |\\big /\\sqrt{\\big \\Vert \\mu _n\\big \\Vert }, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M540\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:msqrt><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow></mml:mrow></mml:msqrt><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq263\"><alternatives><tex-math id=\"M541\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\rightarrow \\infty $$\\end{document}</tex-math><mml:math id=\"M542\"><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq264\"><alternatives><tex-math id=\"M543\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sup _{n\\in \\omega }\\big |\\mu _n(A)\\big |&lt;\\infty $$\\end{document}</tex-math><mml:math id=\"M544\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">sup</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq265\"><alternatives><tex-math id=\"M545\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M546\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq266\"><alternatives><tex-math id=\"M547\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M548\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq267\"><alternatives><tex-math id=\"M549\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M550\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq268\"><alternatives><tex-math id=\"M551\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M&gt;0$$\\end{document}</tex-math><mml:math id=\"M552\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq269\"><alternatives><tex-math id=\"M553\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sup _{n\\in \\omega }\\big \\Vert \\mu _n\\big \\Vert &lt;M$$\\end{document}</tex-math><mml:math id=\"M554\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">sup</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>M</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq270\"><alternatives><tex-math id=\"M555\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\in C(St(\\mathcal {A}))$$\\end{document}</tex-math><mml:math id=\"M556\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>∈</mml:mo><mml:mi>C</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq271\"><alternatives><tex-math id=\"M557\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varepsilon &gt;0$$\\end{document}</tex-math><mml:math id=\"M558\"><mml:mrow><mml:mi>ε</mml:mi><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq272\"><alternatives><tex-math id=\"M559\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A_1,\\ldots ,A_k\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M560\"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:msub><mml:mi>A</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq273\"><alternatives><tex-math id=\"M561\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\alpha _1,\\ldots ,\\alpha _k\\in \\mathbb {R}$$\\end{document}</tex-math><mml:math id=\"M562\"><mml:mrow><mml:msub><mml:mi>α</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi mathvariant=\"double-struck\">R</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ9\"><alternatives><tex-math id=\"M563\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Big \\Vert f-\\sum _{i=1}^k\\alpha _i\\cdot \\chi _{\\left[ A_i\\right] _\\mathcal {A}}\\Big \\Vert &lt;\\varepsilon /(2M). \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M564\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mi>f</mml:mi><mml:mo>-</mml:mo><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>k</mml:mi></mml:munderover><mml:msub><mml:mi>α</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msub><mml:mi>χ</mml:mi><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>ε</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>2</mml:mn><mml:mi>M</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq274\"><alternatives><tex-math id=\"M565\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M566\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq275\"><alternatives><tex-math id=\"M567\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$N\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M568\"><mml:mrow><mml:mi>N</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq276\"><alternatives><tex-math id=\"M569\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n&gt;N$$\\end{document}</tex-math><mml:math id=\"M570\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>&gt;</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ10\"><alternatives><tex-math id=\"M571\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\sum _{i=1}^k\\big |\\alpha _i\\big |\\cdot \\big |\\mu _n\\big (A_i\\big )\\big |&lt;\\varepsilon /2. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M572\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>k</mml:mi></mml:munderover><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>α</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>·</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>ε</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq277\"><alternatives><tex-math id=\"M573\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n&gt;N$$\\end{document}</tex-math><mml:math id=\"M574\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>&gt;</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ11\"><alternatives><tex-math id=\"M575\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\big |\\mu _n(f)\\big |&lt;\\big |\\mu _n\\Big (f-\\sum _{i=1}^k\\alpha _i\\cdot \\chi _{\\left[ A_i\\right] _\\mathcal {A}}\\Big )\\big |+\\big |\\mu _n\\Big (\\sum _{i=1}^k\\alpha _i\\cdot \\chi _{\\left[ A_i\\right] _\\mathcal {A}}\\Big )\\big |\\le \\\\\\le \\big \\Vert \\mu _n\\big \\Vert \\cdot \\Big \\Vert f-\\sum _{i=1}^k\\alpha _i\\cdot \\chi _{\\left[ A_i\\right] _\\mathcal {A}}\\Big \\Vert +\\sum _{i=1}^k\\big |\\alpha _i\\big |\\cdot \\big |\\mu _n\\big (A_i\\big )\\big |&lt;\\varepsilon . \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M576\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>f</mml:mi><mml:mo>-</mml:mo><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>k</mml:mi></mml:munderover><mml:msub><mml:mi>α</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msub><mml:mi>χ</mml:mi><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>+</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>k</mml:mi></mml:munderover><mml:msub><mml:mi>α</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msub><mml:mi>χ</mml:mi><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≤</mml:mo></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow/><mml:mo>≤</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>·</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mi>f</mml:mi><mml:mo>-</mml:mo><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>k</mml:mi></mml:munderover><mml:msub><mml:mi>α</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msub><mml:mi>χ</mml:mi><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>+</mml:mo><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>k</mml:mi></mml:munderover><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>α</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>·</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>ε</mml:mi><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq278\"><alternatives><tex-math id=\"M577\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n(f)\\rightarrow 0$$\\end{document}</tex-math><mml:math id=\"M578\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">→</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq279\"><alternatives><tex-math id=\"M579\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\rightarrow \\infty $$\\end{document}</tex-math><mml:math id=\"M580\"><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq280\"><alternatives><tex-math id=\"M581\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M582\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq281\"><alternatives><tex-math id=\"M583\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M584\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq282\"><alternatives><tex-math id=\"M585\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Rightarrow $$\\end{document}</tex-math><mml:math id=\"M586\"><mml:mo stretchy=\"false\">⇒</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq283\"><alternatives><tex-math id=\"M587\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M588\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq284\"><alternatives><tex-math id=\"M589\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M590\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq285\"><alternatives><tex-math id=\"M591\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M592\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq286\"><alternatives><tex-math id=\"M593\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M594\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq287\"><alternatives><tex-math id=\"M595\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Box $$\\end{document}</tex-math><mml:math id=\"M596\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq288\"><alternatives><tex-math id=\"M597\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x\\in X$$\\end{document}</tex-math><mml:math id=\"M598\"><mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:mi>X</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq289\"><alternatives><tex-math id=\"M599\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\delta _x$$\\end{document}</tex-math><mml:math id=\"M600\"><mml:msub><mml:mi>δ</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq290\"><alternatives><tex-math id=\"M601\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M602\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq291\"><alternatives><tex-math id=\"M603\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M604\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq292\"><alternatives><tex-math id=\"M605\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_1,\\ldots ,x_n$$\\end{document}</tex-math><mml:math id=\"M606\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq293\"><alternatives><tex-math id=\"M607\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M608\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq294\"><alternatives><tex-math id=\"M609\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\alpha _1,\\ldots ,\\alpha _n\\in \\mathbb {R}$$\\end{document}</tex-math><mml:math id=\"M610\"><mml:mrow><mml:msub><mml:mi>α</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi mathvariant=\"double-struck\">R</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq295\"><alternatives><tex-math id=\"M611\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu =\\sum _{i=1}^n\\alpha _i\\delta _{x_i}$$\\end{document}</tex-math><mml:math id=\"M612\"><mml:mrow><mml:mi>μ</mml:mi><mml:mo>=</mml:mo><mml:msubsup><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:msubsup><mml:msub><mml:mi>α</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:msub><mml:mi>δ</mml:mi><mml:msub><mml:mi>x</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq296\"><alternatives><tex-math id=\"M613\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\{x_1,\\ldots ,x_n\\big \\}$$\\end{document}</tex-math><mml:math id=\"M614\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq297\"><alternatives><tex-math id=\"M615\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu $$\\end{document}</tex-math><mml:math id=\"M616\"><mml:mi>μ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq298\"><alternatives><tex-math id=\"M617\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${{\\,\\textrm{supp}\\,}}(\\mu )$$\\end{document}</tex-math><mml:math id=\"M618\"><mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>μ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq299\"><alternatives><tex-math id=\"M619\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M620\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq300\"><alternatives><tex-math id=\"M621\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M622\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq301\"><alternatives><tex-math id=\"M623\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M624\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq302\"><alternatives><tex-math id=\"M625\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M626\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq303\"><alternatives><tex-math id=\"M627\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M628\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq304\"><alternatives><tex-math id=\"M629\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\nu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M630\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq305\"><alternatives><tex-math id=\"M631\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\nu _n=\\mu _n/\\big \\Vert \\mu _n\\big \\Vert $$\\end{document}</tex-math><mml:math id=\"M632\"><mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo stretchy=\"false\">/</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq306\"><alternatives><tex-math id=\"M633\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M634\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq307\"><alternatives><tex-math id=\"M635\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$S=\\bigcup _{n\\in \\omega }{{\\,\\textrm{supp}\\,}}\\big (\\nu _n\\big )$$\\end{document}</tex-math><mml:math id=\"M636\"><mml:mrow><mml:mi>S</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mo>⋃</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq308\"><alternatives><tex-math id=\"M637\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\ell _1(S)$$\\end{document}</tex-math><mml:math id=\"M638\"><mml:mrow><mml:msub><mml:mi>ℓ</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq309\"><alternatives><tex-math id=\"M639\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C(St(\\mathcal {A}))^*$$\\end{document}</tex-math><mml:math id=\"M640\"><mml:mrow><mml:mi>C</mml:mi><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∗</mml:mo></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq310\"><alternatives><tex-math id=\"M641\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\nu _n$$\\end{document}</tex-math><mml:math id=\"M642\"><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq311\"><alternatives><tex-math id=\"M643\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\ell _1(S)$$\\end{document}</tex-math><mml:math id=\"M644\"><mml:mrow><mml:msub><mml:mi>ℓ</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq312\"><alternatives><tex-math id=\"M645\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\nu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M646\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq313\"><alternatives><tex-math id=\"M647\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\nu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M648\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq314\"><alternatives><tex-math id=\"M649\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M650\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq315\"><alternatives><tex-math id=\"M651\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M652\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq316\"><alternatives><tex-math id=\"M653\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M654\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq317\"><alternatives><tex-math id=\"M655\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$(\\Omega ,\\Sigma ,\\Pr )$$\\end{document}</tex-math><mml:math id=\"M656\"><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Ω</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant=\"normal\">Σ</mml:mi><mml:mo>,</mml:mo><mml:mo>Pr</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq318\"><alternatives><tex-math id=\"M657\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\in (0,1)$$\\end{document}</tex-math><mml:math id=\"M658\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>∈</mml:mo><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0</mml:mn><mml:mo>,</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq319\"><alternatives><tex-math id=\"M659\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M660\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq320\"><alternatives><tex-math id=\"M661\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$X_i$$\\end{document}</tex-math><mml:math id=\"M662\"><mml:msub><mml:mi>X</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ12\"><alternatives><tex-math id=\"M663\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Pr \\Big (\\big \\{t\\in \\Omega : X_i(t)=1\\big \\}\\Big )=\\Pr \\Big (X_i^{-1}(1)\\Big )=p, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M664\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mo>Pr</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>t</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"normal\">Ω</mml:mi><mml:mo>:</mml:mo><mml:msub><mml:mi>X</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo>Pr</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>X</mml:mi><mml:mi>i</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>p</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<disp-formula id=\"Equ13\"><alternatives><tex-math id=\"M665\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Pr \\Big (\\big \\{t\\in \\Omega : X_i(t)=0\\big \\}\\Big )=\\Pr \\Big (X_i^{-1}(0)\\Big )=1-p. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M666\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mo>Pr</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>t</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"normal\">Ω</mml:mi><mml:mo>:</mml:mo><mml:msub><mml:mi>X</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo>Pr</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>X</mml:mi><mml:mi>i</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo>-</mml:mo><mml:mi>p</mml:mi><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq321\"><alternatives><tex-math id=\"M667\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle X_i:\\ i\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M668\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>X</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq322\"><alternatives><tex-math id=\"M669\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n&gt;0$$\\end{document}</tex-math><mml:math id=\"M670\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq323\"><alternatives><tex-math id=\"M671\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$s\\in 2^n$$\\end{document}</tex-math><mml:math id=\"M672\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ14\"><alternatives><tex-math id=\"M673\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Pr \\Big (\\big \\{t\\in \\Omega :\\ X_i(t)=s(i)\\text { for every }i&lt;n\\big \\}\\Big )=\\Pr \\Big (\\bigcap _{i&lt;n}X_i^{-1}\\big (s(i)\\big )\\Big )=\\prod _{i&lt;n} p_i, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M674\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mo>Pr</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>t</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"normal\">Ω</mml:mi><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:msub><mml:mi>X</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>s</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mspace width=\"0.333333em\"/><mml:mtext>for every</mml:mtext><mml:mspace width=\"0.333333em\"/><mml:mi>i</mml:mi><mml:mo>&lt;</mml:mo><mml:mi>n</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo>Pr</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:munder><mml:mo>⋂</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>&lt;</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:munder><mml:msubsup><mml:mi>X</mml:mi><mml:mi>i</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>s</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:munder><mml:mo>∏</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>&lt;</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mi>p</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq324\"><alternatives><tex-math id=\"M675\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p_i=p$$\\end{document}</tex-math><mml:math id=\"M676\"><mml:mrow><mml:msub><mml:mi>p</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi>p</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq325\"><alternatives><tex-math id=\"M677\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$s(i)=1$$\\end{document}</tex-math><mml:math id=\"M678\"><mml:mrow><mml:mi>s</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq326\"><alternatives><tex-math id=\"M679\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p_i=1-p$$\\end{document}</tex-math><mml:math id=\"M680\"><mml:mrow><mml:msub><mml:mi>p</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo>-</mml:mo><mml:mi>p</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq327\"><alternatives><tex-math id=\"M681\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\exp (x)=e^x$$\\end{document}</tex-math><mml:math id=\"M682\"><mml:mrow><mml:mo>exp</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msup><mml:mi>e</mml:mi><mml:mi>x</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq328\"><alternatives><tex-math id=\"M683\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x\\in \\mathbb {R}$$\\end{document}</tex-math><mml:math id=\"M684\"><mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"double-struck\">R</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq329\"><alternatives><tex-math id=\"M685\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\in (0,1/2]$$\\end{document}</tex-math><mml:math id=\"M686\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>∈</mml:mo><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0</mml:mn><mml:mo>,</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq330\"><alternatives><tex-math id=\"M687\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$m\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M688\"><mml:mrow><mml:mi>m</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq331\"><alternatives><tex-math id=\"M689\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varepsilon \\in (0,1/12]$$\\end{document}</tex-math><mml:math id=\"M690\"><mml:mrow><mml:mi>ε</mml:mi><mml:mo>∈</mml:mo><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0</mml:mn><mml:mo>,</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>12</mml:mn><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq332\"><alternatives><tex-math id=\"M691\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varepsilon p(1-p)m\\ge 12$$\\end{document}</tex-math><mml:math id=\"M692\"><mml:mrow><mml:mi>ε</mml:mi><mml:mi>p</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>1</mml:mn><mml:mo>-</mml:mo><mml:mi>p</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mi>m</mml:mi><mml:mo>≥</mml:mo><mml:mn>12</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ15\"><alternatives><tex-math id=\"M693\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Pr \\Big (\\big \\{t\\in \\Omega :\\ \\big |\\sum _{i&lt;m}X_i(t)-pm\\big |\\ge \\varepsilon pm\\big \\}\\Big ) \\le (\\varepsilon ^2 pm)^{-1/2}\\cdot \\exp \\big (-\\varepsilon ^2 pm/3\\big ). \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M694\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mo>Pr</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>t</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"normal\">Ω</mml:mi><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>&lt;</mml:mo><mml:mi>m</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mi>X</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:mi>p</mml:mi><mml:mi>m</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≥</mml:mo><mml:mi>ε</mml:mi><mml:mi>p</mml:mi><mml:mi>m</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ε</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mi>p</mml:mi><mml:mi>m</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:msup><mml:mo>·</mml:mo><mml:mo>exp</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:msup><mml:mi>ε</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mi>p</mml:mi><mml:mi>m</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>3</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq333\"><alternatives><tex-math id=\"M695\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p=1/2$$\\end{document}</tex-math><mml:math id=\"M696\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq334\"><alternatives><tex-math id=\"M697\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Omega =2^\\omega $$\\end{document}</tex-math><mml:math id=\"M698\"><mml:mrow><mml:mi mathvariant=\"normal\">Ω</mml:mi><mml:mo>=</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq335\"><alternatives><tex-math id=\"M699\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Sigma $$\\end{document}</tex-math><mml:math id=\"M700\"><mml:mi mathvariant=\"normal\">Σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq336\"><alternatives><tex-math id=\"M701\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M702\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq337\"><alternatives><tex-math id=\"M703\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Omega $$\\end{document}</tex-math><mml:math id=\"M704\"><mml:mi mathvariant=\"normal\">Ω</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq338\"><alternatives><tex-math id=\"M705\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\lambda $$\\end{document}</tex-math><mml:math id=\"M706\"><mml:mi>λ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq339\"><alternatives><tex-math id=\"M707\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Omega $$\\end{document}</tex-math><mml:math id=\"M708\"><mml:mi mathvariant=\"normal\">Ω</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq340\"><alternatives><tex-math id=\"M709\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$(\\Omega ,\\Sigma ,\\lambda )$$\\end{document}</tex-math><mml:math id=\"M710\"><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Ω</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant=\"normal\">Σ</mml:mi><mml:mo>,</mml:mo><mml:mi>λ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq341\"><alternatives><tex-math id=\"M711\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M712\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq342\"><alternatives><tex-math id=\"M713\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x\\in \\Omega $$\\end{document}</tex-math><mml:math id=\"M714\"><mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"normal\">Ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq343\"><alternatives><tex-math id=\"M715\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$X_i(x)=x(i)$$\\end{document}</tex-math><mml:math id=\"M716\"><mml:mrow><mml:msub><mml:mi>X</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>x</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq344\"><alternatives><tex-math id=\"M717\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$X_i$$\\end{document}</tex-math><mml:math id=\"M718\"><mml:msub><mml:mi>X</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq345\"><alternatives><tex-math id=\"M719\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle X_i:\\ i\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M720\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>X</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq346\"><alternatives><tex-math id=\"M721\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M722\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq347\"><alternatives><tex-math id=\"M723\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$I_n=\\big \\{2^n+1, 2^n+2,\\ldots , 2^{n+1}\\big \\}$$\\end{document}</tex-math><mml:math id=\"M724\"><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>+</mml:mo><mml:mn>1</mml:mn><mml:mo>,</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>+</mml:mo><mml:mn>2</mml:mn><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mrow><mml:mi>n</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq348\"><alternatives><tex-math id=\"M725\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$J\\subset \\omega $$\\end{document}</tex-math><mml:math id=\"M726\"><mml:mrow><mml:mi>J</mml:mi><mml:mo>⊂</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq349\"><alternatives><tex-math id=\"M727\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M728\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq350\"><alternatives><tex-math id=\"M729\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Y_n\\subseteq I_n$$\\end{document}</tex-math><mml:math id=\"M730\"><mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>⊆</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq351\"><alternatives><tex-math id=\"M731\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\eta =\\inf \\big \\{\\eta _n:\\ n\\in J\\big \\}&gt;0$$\\end{document}</tex-math><mml:math id=\"M732\"><mml:mrow><mml:mi>η</mml:mi><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">inf</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq352\"><alternatives><tex-math id=\"M733\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\eta _n=\\big |Y_n\\big |/2^n$$\\end{document}</tex-math><mml:math id=\"M734\"><mml:mrow><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq353\"><alternatives><tex-math id=\"M735\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M736\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq354\"><alternatives><tex-math id=\"M737\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M738\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq355\"><alternatives><tex-math id=\"M739\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$m_n=\\big |Y_n\\big |$$\\end{document}</tex-math><mml:math id=\"M740\"><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq356\"><alternatives><tex-math id=\"M741\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$=\\eta _n 2^n$$\\end{document}</tex-math><mml:math id=\"M742\"><mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq357\"><alternatives><tex-math id=\"M743\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varepsilon _n=\\sqrt{n/2^n}$$\\end{document}</tex-math><mml:math id=\"M744\"><mml:mrow><mml:msub><mml:mi>ε</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq358\"><alternatives><tex-math id=\"M745\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varepsilon _n\\le 1/12$$\\end{document}</tex-math><mml:math id=\"M746\"><mml:mrow><mml:msub><mml:mi>ε</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>≤</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>12</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq359\"><alternatives><tex-math id=\"M747\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varepsilon _n p^2 m_n=\\frac{1}{4}\\eta _n\\sqrt{n 2^n}\\ge 12$$\\end{document}</tex-math><mml:math id=\"M748\"><mml:mrow><mml:msub><mml:mi>ε</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msup><mml:mi>p</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:msub><mml:mi>m</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>4</mml:mn></mml:mfrac><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt><mml:mo>≥</mml:mo><mml:mn>12</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq360\"><alternatives><tex-math id=\"M749\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M750\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ16\"><alternatives><tex-math id=\"M751\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} A_n=\\Big \\{x\\in 2^\\omega :\\ \\Big |\\sum _{i\\in Y_n}x(i)-\\frac{1}{2}\\cdot \\eta _n2^n\\Big |\\ge \\frac{1}{2}\\cdot \\eta _n\\sqrt{n 2^n}\\Big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M752\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:munder><mml:mi>x</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≥</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq361\"><alternatives><tex-math id=\"M753\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$m=m_n$$\\end{document}</tex-math><mml:math id=\"M754\"><mml:mrow><mml:mi>m</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mi>m</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq362\"><alternatives><tex-math id=\"M755\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varepsilon =\\varepsilon _n$$\\end{document}</tex-math><mml:math id=\"M756\"><mml:mrow><mml:mi>ε</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mi>ε</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq363\"><alternatives><tex-math id=\"M757\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M758\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ17\"><alternatives><tex-math id=\"M759\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\lambda \\Big (\\Big \\{x\\in 2^\\omega :\\ \\Big |\\sum _{i\\in Y_n}x(i)-\\frac{1}{2}\\cdot \\eta _n 2^n\\Big |&amp;\\ge \\sqrt{n/2^n}\\cdot \\frac{1}{2}\\cdot \\eta _n2^n\\Big \\}\\Big )\\le \\\\&amp;\\le \\Big (\\frac{n}{2^n}\\cdot \\frac{1}{2} \\cdot \\eta _n2^n\\Big )^{-1/2}\\cdot \\exp \\Big (-\\frac{n}{2^n}\\cdot \\frac{1}{2}\\cdot \\eta _n 2^n\\cdot \\frac{1}{3}\\Big ), \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M760\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>λ</mml:mi><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:munder><mml:mi>x</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo>≥</mml:mo><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt><mml:mo>·</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>≤</mml:mo></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow/></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo>≤</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mfrac><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mfrac><mml:mo>·</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:msup><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:msup><mml:mo>·</mml:mo><mml:mo>exp</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:mfrac><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mfrac><mml:mo>·</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>·</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>3</mml:mn></mml:mfrac><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq364\"><alternatives><tex-math id=\"M761\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$*$$\\end{document}</tex-math><mml:math id=\"M762\"><mml:mrow><mml:mrow/><mml:mo>∗</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq365\"><alternatives><tex-math id=\"M763\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sum _{n\\in J}\\lambda (A_n)&lt;\\infty $$\\end{document}</tex-math><mml:math id=\"M764\"><mml:mrow><mml:msub><mml:mo>∑</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:msub><mml:mi>λ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq366\"><alternatives><tex-math id=\"M765\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\eta &gt;0$$\\end{document}</tex-math><mml:math id=\"M766\"><mml:mrow><mml:mi>η</mml:mi><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq367\"><alternatives><tex-math id=\"M767\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dagger $$\\end{document}</tex-math><mml:math id=\"M768\"><mml:mo>†</mml:mo></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ18\"><alternatives><tex-math id=\"M769\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\lambda \\Big (\\bigcup _{n\\in J}\\bigcap _{\\begin{array}{c} k\\in J\\\\ k\\ge n \\end{array}}A_k^c\\Big )=\\lambda \\big (\\big \\{x\\in 2^\\omega :\\ x\\not \\in A_n\\text { for almost all }n\\in J\\big \\}\\big )=1. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M770\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>λ</mml:mi><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:munder><mml:mo>⋃</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:munder><mml:munder><mml:mo>⋂</mml:mo><mml:mrow><mml:mtable><mml:mtr><mml:mtd><mml:mrow><mml:mi>k</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mrow><mml:mrow/><mml:mi>k</mml:mi><mml:mo>≥</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:munder><mml:msubsup><mml:mi>A</mml:mi><mml:mi>k</mml:mi><mml:mi>c</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>λ</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>x</mml:mi><mml:mo>∉</mml:mo><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mspace width=\"0.333333em\"/><mml:mtext>for almost all</mml:mtext><mml:mspace width=\"0.333333em\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq368\"><alternatives><tex-math id=\"M771\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M772\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq369\"><alternatives><tex-math id=\"M773\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$V'$$\\end{document}</tex-math><mml:math id=\"M774\"><mml:msup><mml:mi>V</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq370\"><alternatives><tex-math id=\"M775\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\in 2^\\omega $$\\end{document}</tex-math><mml:math id=\"M776\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq371\"><alternatives><tex-math id=\"M777\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$2^\\omega $$\\end{document}</tex-math><mml:math id=\"M778\"><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq372\"><alternatives><tex-math id=\"M779\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big (\\lambda (B)=0\\big )^V$$\\end{document}</tex-math><mml:math id=\"M780\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>λ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>B</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mi>V</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq373\"><alternatives><tex-math id=\"M781\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$V'$$\\end{document}</tex-math><mml:math id=\"M782\"><mml:msup><mml:mi>V</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq374\"><alternatives><tex-math id=\"M783\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M784\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq375\"><alternatives><tex-math id=\"M785\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M786\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq376\"><alternatives><tex-math id=\"M787\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M788\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq377\"><alternatives><tex-math id=\"M789\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M790\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq378\"><alternatives><tex-math id=\"M791\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle x_i:\\ i\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M792\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq379\"><alternatives><tex-math id=\"M793\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M794\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq380\"><alternatives><tex-math id=\"M795\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_i\\ne x_j$$\\end{document}</tex-math><mml:math id=\"M796\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq381\"><alternatives><tex-math id=\"M797\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\ne j\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M798\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>≠</mml:mo><mml:mi>j</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq382\"><alternatives><tex-math id=\"M799\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varphi :\\omega \\rightarrow St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M800\"><mml:mrow><mml:mi>φ</mml:mi><mml:mo>:</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq383\"><alternatives><tex-math id=\"M801\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varphi (i)=x_i$$\\end{document}</tex-math><mml:math id=\"M802\"><mml:mrow><mml:mi>φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq384\"><alternatives><tex-math id=\"M803\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M804\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq385\"><alternatives><tex-math id=\"M805\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\in 2^\\omega \\cap V[G]$$\\end{document}</tex-math><mml:math id=\"M806\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq386\"><alternatives><tex-math id=\"M807\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega _+=\\omega \\setminus \\{0\\}$$\\end{document}</tex-math><mml:math id=\"M808\"><mml:mrow><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo>=</mml:mo><mml:mi>ω</mml:mi><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mrow><mml:mo stretchy=\"false\">{</mml:mo><mml:mn>0</mml:mn><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq387\"><alternatives><tex-math id=\"M809\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega _+$$\\end{document}</tex-math><mml:math id=\"M810\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq388\"><alternatives><tex-math id=\"M811\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n$$\\end{document}</tex-math><mml:math id=\"M812\"><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq389\"><alternatives><tex-math id=\"M813\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M814\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ19\"><alternatives><tex-math id=\"M815\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\mu _n(A)=\\alpha _n\\cdot \\sum _{i\\in I_n}(-1)^{r(i)+1}\\cdot \\delta _{x_i}\\big (\\left[ A\\right] _\\mathcal {A}\\big ), \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M816\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:munder><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mo>-</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mo>·</mml:mo><mml:msub><mml:mi>δ</mml:mi><mml:msub><mml:mi>x</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq390\"><alternatives><tex-math id=\"M817\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\alpha _n=1/\\big (n\\sqrt{2^n}\\big )$$\\end{document}</tex-math><mml:math id=\"M818\"><mml:mrow><mml:msub><mml:mi>α</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>n</mml:mi><mml:msqrt><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:msqrt><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq391\"><alternatives><tex-math id=\"M819\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$I_n=\\big \\{2^n+1,2^n+2,\\ldots ,2^{n+1}\\big \\}$$\\end{document}</tex-math><mml:math id=\"M820\"><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>+</mml:mo><mml:mn>1</mml:mn><mml:mo>,</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>+</mml:mo><mml:mn>2</mml:mn><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mrow><mml:mi>n</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq392\"><alternatives><tex-math id=\"M821\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n$$\\end{document}</tex-math><mml:math id=\"M822\"><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq393\"><alternatives><tex-math id=\"M823\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )=\\varphi \\big [I_n\\big ]$$\\end{document}</tex-math><mml:math id=\"M824\"><mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>φ</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">[</mml:mo></mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ20\"><alternatives><tex-math id=\"M825\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\big \\Vert \\mu _n\\big \\Vert =\\alpha _n\\cdot 2^n=\\sqrt{2^n}/{n}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M826\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>=</mml:mo><mml:msqrt><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:msqrt><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>n</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq394\"><alternatives><tex-math id=\"M827\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\lim _{n\\rightarrow \\infty }\\big \\Vert \\mu _n\\big \\Vert =\\infty $$\\end{document}</tex-math><mml:math id=\"M828\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq395\"><alternatives><tex-math id=\"M829\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M830\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq396\"><alternatives><tex-math id=\"M831\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M832\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq397\"><alternatives><tex-math id=\"M833\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega _+$$\\end{document}</tex-math><mml:math id=\"M834\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ21\"><alternatives><tex-math id=\"M835\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} Y_n=\\big \\{i\\in I_n:\\ A\\in x_i\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M836\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq398\"><alternatives><tex-math id=\"M837\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Y_n\\in V$$\\end{document}</tex-math><mml:math id=\"M838\"><mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ22\"><alternatives><tex-math id=\"M839\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} J=\\big \\{n\\in \\omega _+:\\ \\big |Y_n\\big |\\big /2^n\\ge 1/2\\big \\}\\quad \\text {and}\\quad J^c=\\omega _+\\setminus J=\\big \\{n\\in \\omega _+:\\ \\big |Y_n\\big |\\big /2^n&lt;1/2\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M840\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>J</mml:mi><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>≥</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mspace width=\"1em\"/><mml:mtext>and</mml:mtext><mml:mspace width=\"1em\"/><mml:msup><mml:mi>J</mml:mi><mml:mi>c</mml:mi></mml:msup><mml:mo>=</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>J</mml:mi><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>&lt;</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq399\"><alternatives><tex-math id=\"M841\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$J,J^c\\in V$$\\end{document}</tex-math><mml:math id=\"M842\"><mml:mrow><mml:mi>J</mml:mi><mml:mo>,</mml:mo><mml:msup><mml:mi>J</mml:mi><mml:mi>c</mml:mi></mml:msup><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq400\"><alternatives><tex-math id=\"M843\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n(A)\\rightarrow 0$$\\end{document}</tex-math><mml:math id=\"M844\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">→</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq401\"><alternatives><tex-math id=\"M845\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\rightarrow \\infty $$\\end{document}</tex-math><mml:math id=\"M846\"><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq402\"><alternatives><tex-math id=\"M847\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M848\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq403\"><alternatives><tex-math id=\"M849\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M850\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq404\"><alternatives><tex-math id=\"M851\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\eta _n=\\big |Y_n\\big |/2^n$$\\end{document}</tex-math><mml:math id=\"M852\"><mml:mrow><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq405\"><alternatives><tex-math id=\"M853\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A_n$$\\end{document}</tex-math><mml:math id=\"M854\"><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq406\"><alternatives><tex-math id=\"M855\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$2^\\omega $$\\end{document}</tex-math><mml:math id=\"M856\"><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ23\"><alternatives><tex-math id=\"M857\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\eta =\\inf \\big \\{\\eta _n:\\ n\\in J\\big \\}\\ge 1/2&gt;0, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M858\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>η</mml:mi><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">inf</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>≥</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq407\"><alternatives><tex-math id=\"M859\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dagger $$\\end{document}</tex-math><mml:math id=\"M860\"><mml:mo>†</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq408\"><alternatives><tex-math id=\"M861\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\not \\in A_n$$\\end{document}</tex-math><mml:math id=\"M862\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>∉</mml:mo><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq409\"><alternatives><tex-math id=\"M863\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M864\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ24\"><alternatives><tex-math id=\"M865\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Big |\\sum _{i\\in Y_n}r(i)-\\frac{1}{2}\\cdot \\eta _n 2^n\\Big |&lt;\\frac{1}{2}\\cdot \\eta _n\\sqrt{n 2^n} \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M866\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:munder><mml:mi>r</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq410\"><alternatives><tex-math id=\"M867\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M868\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq411\"><alternatives><tex-math id=\"M869\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_0\\in \\omega _+$$\\end{document}</tex-math><mml:math id=\"M870\"><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq412\"><alternatives><tex-math id=\"M871\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M872\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq413\"><alternatives><tex-math id=\"M873\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge n_0$$\\end{document}</tex-math><mml:math id=\"M874\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq414\"><alternatives><tex-math id=\"M875\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\eta _n\\le 1$$\\end{document}</tex-math><mml:math id=\"M876\"><mml:mrow><mml:msub><mml:mi>η</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>≤</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ25\"><alternatives><tex-math id=\"M877\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Big |\\sum _{i\\in Y_n}r(i)-\\big |Y_n\\big |/2\\Big |&lt;\\frac{1}{2}\\cdot \\sqrt{n 2^n}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M878\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:munder><mml:mi>r</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq415\"><alternatives><tex-math id=\"M879\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M880\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq416\"><alternatives><tex-math id=\"M881\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge n_0$$\\end{document}</tex-math><mml:math id=\"M882\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq417\"><alternatives><tex-math id=\"M883\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$s\\in \\{0,1\\}$$\\end{document}</tex-math><mml:math id=\"M884\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>∈</mml:mo><mml:mo stretchy=\"false\">{</mml:mo><mml:mn>0</mml:mn><mml:mo>,</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ26\"><alternatives><tex-math id=\"M885\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Big |\\big |\\big \\{i\\in Y_n:\\ r(i)=s\\big \\}\\big |-\\big |Y_n\\big |/2\\Big |&lt;\\frac{1}{2}\\cdot \\sqrt{n 2^n}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M886\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>r</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>s</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq418\"><alternatives><tex-math id=\"M887\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in J$$\\end{document}</tex-math><mml:math id=\"M888\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq419\"><alternatives><tex-math id=\"M889\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge n_0$$\\end{document}</tex-math><mml:math id=\"M890\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:msub><mml:mi>n</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ27\"><alternatives><tex-math id=\"M891\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned}{} &amp; {} \\big |\\mu _n(A)\\big |=\\big |\\mu _n\\big (\\varphi \\big [Y_n\\big ]\\big )\\big |=\\big |\\alpha _n\\cdot \\sum _{i\\in Y_n}(-1)^{r(i)+1}\\big |\\\\{} &amp; {} =\\alpha _n\\cdot \\Big |\\big |\\big \\{i\\in Y_n:\\ r(i)=1\\big \\}\\big |-\\big |\\big \\{i\\in Y_n:\\ r(i)=0\\big \\}\\big |\\Big | \\\\{} &amp; {} \\le \\alpha _n\\cdot \\Big (\\Big |\\big |\\big \\{i\\in Y_n:\\ r(i)=1\\big \\}\\big |-\\big |Y_n\\big |/2\\Big |+\\Big |\\big |\\big \\{i\\in Y_n:\\ r(i)=0\\big \\}\\big |-\\big |Y_n\\big |/2\\Big |\\Big )\\\\{} &amp; {} &lt;\\alpha _n\\cdot \\Big (\\frac{1}{2}\\cdot \\sqrt{n 2^n}+\\frac{1}{2}\\cdot \\sqrt{n 2^n}\\Big )=\\alpha _n\\cdot \\sqrt{n 2^n}=\\frac{1}{n\\sqrt{2^n}}\\cdot \\sqrt{n 2^n}=\\frac{1}{\\sqrt{n}}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M892\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow/></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mrow/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>φ</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">[</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">]</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>α</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:munder><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mo>-</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow/><mml:mrow/></mml:mrow></mml:mtd><mml:mtd 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stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>+</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>r</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo 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columnalign=\"left\"><mml:mrow><mml:mrow/><mml:mo>&lt;</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt><mml:mo>+</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>·</mml:mo><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt><mml:mo>=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mrow><mml:mi>n</mml:mi><mml:msqrt><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:msqrt></mml:mrow></mml:mfrac><mml:mo>·</mml:mo><mml:msqrt><mml:mrow><mml:mi>n</mml:mi><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:msqrt><mml:mo>=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:msqrt><mml:mi>n</mml:mi></mml:msqrt></mml:mfrac><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<disp-formula id=\"Equ28\"><alternatives><tex-math id=\"M893\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\lim _{\\begin{array}{c} n\\rightarrow \\infty \\\\ n\\in J \\end{array}}\\mu _n(A)=0. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M894\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mtable><mml:mtr><mml:mtd><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mrow><mml:mrow/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>J</mml:mi></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:munder><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq420\"><alternatives><tex-math id=\"M895\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$J^c$$\\end{document}</tex-math><mml:math id=\"M896\"><mml:msup><mml:mi>J</mml:mi><mml:mi>c</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq421\"><alternatives><tex-math id=\"M897\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$1_\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M898\"><mml:msub><mml:mn>1</mml:mn><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq422\"><alternatives><tex-math id=\"M899\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M900\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq423\"><alternatives><tex-math id=\"M901\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M902\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq424\"><alternatives><tex-math id=\"M903\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$1_\\mathcal {A}\\in x_i$$\\end{document}</tex-math><mml:math id=\"M904\"><mml:mrow><mml:msub><mml:mn>1</mml:mn><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq425\"><alternatives><tex-math id=\"M905\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\lim _{n\\rightarrow \\infty }\\mu _n\\big (1_\\mathcal {A}\\big )=0$$\\end{document}</tex-math><mml:math id=\"M906\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mn>1</mml:mn><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ29\"><alternatives><tex-math id=\"M907\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\lim _{\\begin{array}{c} n\\rightarrow \\infty \\\\ n\\in J^c \\end{array}}\\mu _n\\big (1_\\mathcal {A}\\big )=0. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M908\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mtable><mml:mtr><mml:mtd><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mrow><mml:mrow/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>J</mml:mi><mml:mi>c</mml:mi></mml:msup></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:munder><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mn>1</mml:mn><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq426\"><alternatives><tex-math id=\"M909\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega _+$$\\end{document}</tex-math><mml:math id=\"M910\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq427\"><alternatives><tex-math id=\"M911\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Y_n'$$\\end{document}</tex-math><mml:math id=\"M912\"><mml:msubsup><mml:mi>Y</mml:mi><mml:mi>n</mml:mi><mml:mo>′</mml:mo></mml:msubsup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq428\"><alternatives><tex-math id=\"M913\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Y_n$$\\end{document}</tex-math><mml:math id=\"M914\"><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ30\"><alternatives><tex-math id=\"M915\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} Y_n'=\\big \\{i\\in I_n:\\ 1_\\mathcal {A}\\setminus A\\in x_i\\big \\}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M916\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msubsup><mml:mi>Y</mml:mi><mml:mi>n</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:msub><mml:mn>1</mml:mn><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<disp-formula id=\"Equ31\"><alternatives><tex-math id=\"M917\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} J'=\\big \\{n\\in \\omega _+:\\ \\big |Y_n'\\big |\\big /2^n\\ge 1/2\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M918\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msup><mml:mi>J</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>Y</mml:mi><mml:mi>n</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>≥</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq429\"><alternatives><tex-math id=\"M919\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Y_n'=I_n\\setminus Y_n$$\\end{document}</tex-math><mml:math id=\"M920\"><mml:mrow><mml:msubsup><mml:mi>Y</mml:mi><mml:mi>n</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mo>=</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ32\"><alternatives><tex-math id=\"M921\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} J^c=\\big \\{n\\in \\omega _+:\\ \\big |Y_n\\big |\\big /2^n&lt;1/2\\big \\}=\\big \\{n\\in \\omega _+:\\ \\big |I_n\\setminus Y_n\\big |\\big /2^n&gt;1/2\\big \\}\\subseteq \\\\\\subseteq \\big \\{n\\in \\omega _+:\\ \\big |I_n\\setminus Y_n\\big |\\big /2^n\\ge 1/2\\big \\}=\\big \\{n\\in \\omega _+:\\ \\big |Y_n'\\big |\\big /2^n\\ge 1/2\\big \\}=J', \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M922\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msup><mml:mi>J</mml:mi><mml:mi>c</mml:mi></mml:msup><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>&lt;</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>&gt;</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>⊆</mml:mo></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow/><mml:mo>⊆</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:msub><mml:mi>Y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>≥</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>Y</mml:mi><mml:mi>n</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup><mml:mo>≥</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>2</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msup><mml:mi>J</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq430\"><alternatives><tex-math id=\"M923\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$J'$$\\end{document}</tex-math><mml:math id=\"M924\"><mml:msup><mml:mi>J</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ33\"><alternatives><tex-math id=\"M925\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\lim _{\\begin{array}{c} n\\rightarrow \\infty \\\\ n\\in J' \\end{array}}\\mu _n\\big (1_\\mathcal {A}\\setminus A\\big )=0, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M926\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mtable><mml:mtr><mml:mtd><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mrow><mml:mrow/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>J</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:munder><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mn>1</mml:mn><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>A</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<disp-formula id=\"Equ34\"><alternatives><tex-math id=\"M927\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\lim _{\\begin{array}{c} n\\rightarrow \\infty \\\\ n\\in J^c \\end{array}}\\mu _n\\big (1_\\mathcal {A}\\setminus A\\big )=0. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M928\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mtable><mml:mtr><mml:mtd><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mrow><mml:mrow/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>J</mml:mi><mml:mi>c</mml:mi></mml:msup></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:munder><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mn>1</mml:mn><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>A</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<disp-formula id=\"Equ35\"><alternatives><tex-math id=\"M929\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\lim _{\\begin{array}{c} n\\rightarrow \\infty \\\\ n\\in J^c \\end{array}}\\mu _n(A)=\\lim _{\\begin{array}{c} n\\rightarrow \\infty \\\\ n\\in J^c \\end{array}}\\mu _n\\big (1_\\mathcal {A}\\big )-\\lim _{\\begin{array}{c} n\\rightarrow \\infty \\\\ n\\in J^c \\end{array}}\\mu _n\\big (1_\\mathcal {A}\\setminus A\\big )=0, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M930\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mtable><mml:mtr><mml:mtd><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mrow><mml:mrow/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>J</mml:mi><mml:mi>c</mml:mi></mml:msup></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:munder><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mtable><mml:mtr><mml:mtd><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mrow><mml:mrow/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>J</mml:mi><mml:mi>c</mml:mi></mml:msup></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:munder><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mn>1</mml:mn><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>-</mml:mo><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mtable><mml:mtr><mml:mtd><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mrow><mml:mrow/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>J</mml:mi><mml:mi>c</mml:mi></mml:msup></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:munder><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mn>1</mml:mn><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>A</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<disp-formula id=\"Equ36\"><alternatives><tex-math id=\"M931\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\lim _{n\\rightarrow \\infty }\\mu _n(A)=0. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M932\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq431\"><alternatives><tex-math id=\"M933\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega _+\\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M934\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq432\"><alternatives><tex-math id=\"M935\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M936\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq433\"><alternatives><tex-math id=\"M937\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M938\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq434\"><alternatives><tex-math id=\"M939\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M940\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq435\"><alternatives><tex-math id=\"M941\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n$$\\end{document}</tex-math><mml:math id=\"M942\"><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq436\"><alternatives><tex-math id=\"M943\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n/\\big \\Vert \\mu _n\\big \\Vert $$\\end{document}</tex-math><mml:math id=\"M944\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo stretchy=\"false\">/</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq437\"><alternatives><tex-math id=\"M945\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M946\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq438\"><alternatives><tex-math id=\"M947\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M948\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq439\"><alternatives><tex-math id=\"M949\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M950\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq440\"><alternatives><tex-math id=\"M951\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M952\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq441\"><alternatives><tex-math id=\"M953\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M954\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq442\"><alternatives><tex-math id=\"M955\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M956\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq443\"><alternatives><tex-math id=\"M957\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |=2^n$$\\end{document}</tex-math><mml:math id=\"M958\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq444\"><alternatives><tex-math id=\"M959\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M960\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq445\"><alternatives><tex-math id=\"M961\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Box $$\\end{document}</tex-math><mml:math id=\"M962\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq446\"><alternatives><tex-math id=\"M963\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\kappa $$\\end{document}</tex-math><mml:math id=\"M964\"><mml:mi>κ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq447\"><alternatives><tex-math id=\"M965\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _\\kappa $$\\end{document}</tex-math><mml:math id=\"M966\"><mml:msub><mml:mi>μ</mml:mi><mml:mi>κ</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq448\"><alternatives><tex-math id=\"M967\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$2^\\kappa $$\\end{document}</tex-math><mml:math id=\"M968\"><mml:msup><mml:mn>2</mml:mn><mml:mi>κ</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq449\"><alternatives><tex-math id=\"M969\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )=Bor\\big (2^\\kappa \\big )\\big /\\big \\{A\\in Bor\\big (2^\\kappa \\big ):\\ \\mu _\\kappa (A)=0\\big \\}$$\\end{document}</tex-math><mml:math id=\"M970\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>B</mml:mi><mml:mi>o</mml:mi><mml:mi>r</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>κ</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi>B</mml:mi><mml:mi>o</mml:mi><mml:mi>r</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>κ</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:msub><mml:mi>μ</mml:mi><mml:mi>κ</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq450\"><alternatives><tex-math id=\"M971\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M972\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq451\"><alternatives><tex-math id=\"M973\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M974\"><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq452\"><alternatives><tex-math id=\"M975\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\kappa $$\\end{document}</tex-math><mml:math id=\"M976\"><mml:mi>κ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq455\"><alternatives><tex-math id=\"M977\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M978\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq456\"><alternatives><tex-math id=\"M979\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M980\"><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq457\"><alternatives><tex-math id=\"M981\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M982\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq458\"><alternatives><tex-math id=\"M983\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\in \\omega ^\\omega \\cap V[G]$$\\end{document}</tex-math><mml:math id=\"M984\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq459\"><alternatives><tex-math id=\"M985\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in \\omega ^\\omega \\cap V$$\\end{document}</tex-math><mml:math id=\"M986\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq460\"><alternatives><tex-math id=\"M987\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f(n)&lt;g(n)$$\\end{document}</tex-math><mml:math id=\"M988\"><mml:mrow><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>&lt;</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq461\"><alternatives><tex-math id=\"M989\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M990\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq462\"><alternatives><tex-math id=\"M991\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M992\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq463\"><alternatives><tex-math id=\"M993\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M994\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq464\"><alternatives><tex-math id=\"M995\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M996\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq465\"><alternatives><tex-math id=\"M997\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M998\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq466\"><alternatives><tex-math id=\"M999\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1000\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq467\"><alternatives><tex-math id=\"M1001\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1002\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq468\"><alternatives><tex-math id=\"M1003\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1004\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq469\"><alternatives><tex-math id=\"M1005\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1006\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq470\"><alternatives><tex-math id=\"M1007\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1008\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq471\"><alternatives><tex-math id=\"M1009\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1010\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq472\"><alternatives><tex-math id=\"M1011\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |\\le M$$\\end{document}</tex-math><mml:math id=\"M1012\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:mi>M</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq473\"><alternatives><tex-math id=\"M1013\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1014\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq474\"><alternatives><tex-math id=\"M1015\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle x_n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1016\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq475\"><alternatives><tex-math id=\"M1017\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1018\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq476\"><alternatives><tex-math id=\"M1019\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _n=\\frac{1}{2}\\big (\\delta _{x_{2n}}-\\delta _{x_{2n+1}}\\big )$$\\end{document}</tex-math><mml:math id=\"M1020\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>δ</mml:mi><mml:msub><mml:mi>x</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi>n</mml:mi></mml:mrow></mml:msub></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>δ</mml:mi><mml:msub><mml:mi>x</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi>n</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq477\"><alternatives><tex-math id=\"M1021\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1022\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq478\"><alternatives><tex-math id=\"M1023\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |=2$$\\end{document}</tex-math><mml:math id=\"M1024\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq479\"><alternatives><tex-math id=\"M1025\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1026\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq480\"><alternatives><tex-math id=\"M1027\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\nu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1028\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq481\"><alternatives><tex-math id=\"M1029\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\nu _n\\big )\\big |=2$$\\end{document}</tex-math><mml:math id=\"M1030\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq482\"><alternatives><tex-math id=\"M1031\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1032\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq483\"><alternatives><tex-math id=\"M1033\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1034\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq484\"><alternatives><tex-math id=\"M1035\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\lim _{n\\rightarrow \\infty }\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |=\\infty $$\\end{document}</tex-math><mml:math id=\"M1036\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq485\"><alternatives><tex-math id=\"M1037\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M1038\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq486\"><alternatives><tex-math id=\"M1039\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1040\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq487\"><alternatives><tex-math id=\"M1041\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sup _{n\\in \\omega }\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |&lt;\\infty $$\\end{document}</tex-math><mml:math id=\"M1042\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">sup</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq488\"><alternatives><tex-math id=\"M1043\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M=2$$\\end{document}</tex-math><mml:math id=\"M1044\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>=</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq489\"><alternatives><tex-math id=\"M1045\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1046\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq490\"><alternatives><tex-math id=\"M1047\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1048\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq491\"><alternatives><tex-math id=\"M1049\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1050\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq492\"><alternatives><tex-math id=\"M1051\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1052\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq493\"><alternatives><tex-math id=\"M1053\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1054\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq494\"><alternatives><tex-math id=\"M1055\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |\\le M$$\\end{document}</tex-math><mml:math id=\"M1056\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:mi>M</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq495\"><alternatives><tex-math id=\"M1057\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1058\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq496\"><alternatives><tex-math id=\"M1059\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M\\ge 2$$\\end{document}</tex-math><mml:math id=\"M1060\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>≥</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq497\"><alternatives><tex-math id=\"M1061\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\nu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1062\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq498\"><alternatives><tex-math id=\"M1063\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1064\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq499\"><alternatives><tex-math id=\"M1065\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\nu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1066\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq500\"><alternatives><tex-math id=\"M1067\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\nu _n\\big )\\big |=2$$\\end{document}</tex-math><mml:math id=\"M1068\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq501\"><alternatives><tex-math id=\"M1069\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1070\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq502\"><alternatives><tex-math id=\"M1071\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1072\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq503\"><alternatives><tex-math id=\"M1073\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1074\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq504\"><alternatives><tex-math id=\"M1075\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1076\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq505\"><alternatives><tex-math id=\"M1077\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |\\le M$$\\end{document}</tex-math><mml:math id=\"M1078\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:mi>M</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq506\"><alternatives><tex-math id=\"M1079\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1080\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq507\"><alternatives><tex-math id=\"M1081\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _{n_k}:\\ k\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1082\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>k</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq508\"><alternatives><tex-math id=\"M1083\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _{n_k}\\big )\\big |=1$$\\end{document}</tex-math><mml:math id=\"M1084\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq509\"><alternatives><tex-math id=\"M1085\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$k\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1086\"><mml:mrow><mml:mi>k</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq510\"><alternatives><tex-math id=\"M1087\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _{n_k}$$\\end{document}</tex-math><mml:math id=\"M1088\"><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq511\"><alternatives><tex-math id=\"M1089\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\alpha _k\\cdot \\delta _{x_k}$$\\end{document}</tex-math><mml:math id=\"M1090\"><mml:mrow><mml:msub><mml:mi>α</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msub><mml:mi>δ</mml:mi><mml:msub><mml:mi>x</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq512\"><alternatives><tex-math id=\"M1091\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\alpha _k\\in \\{-1,1\\}$$\\end{document}</tex-math><mml:math id=\"M1092\"><mml:mrow><mml:msub><mml:mi>α</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mrow><mml:mo stretchy=\"false\">{</mml:mo><mml:mo>-</mml:mo><mml:mn>1</mml:mn><mml:mo>,</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq513\"><alternatives><tex-math id=\"M1093\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_k\\in St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1094\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq514\"><alternatives><tex-math id=\"M1095\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$1\\in C(St(\\mathcal {A}))$$\\end{document}</tex-math><mml:math id=\"M1096\"><mml:mrow><mml:mn>1</mml:mn><mml:mo>∈</mml:mo><mml:mi>C</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq515\"><alternatives><tex-math id=\"M1097\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |\\mu _{n_k}(1)\\big |=\\big |\\alpha _k\\big |=1$$\\end{document}</tex-math><mml:math id=\"M1098\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>α</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq516\"><alternatives><tex-math id=\"M1099\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$k\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1100\"><mml:mrow><mml:mi>k</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq517\"><alternatives><tex-math id=\"M1101\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1102\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq518\"><alternatives><tex-math id=\"M1103\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1104\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq519\"><alternatives><tex-math id=\"M1105\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |\\ge 2$$\\end{document}</tex-math><mml:math id=\"M1106\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≥</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq520\"><alternatives><tex-math id=\"M1107\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M\\ge 2$$\\end{document}</tex-math><mml:math id=\"M1108\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>≥</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq521\"><alternatives><tex-math id=\"M1109\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$m\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1110\"><mml:mrow><mml:mi>m</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq522\"><alternatives><tex-math id=\"M1111\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1112\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq523\"><alternatives><tex-math id=\"M1113\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1114\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq524\"><alternatives><tex-math id=\"M1115\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1116\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq525\"><alternatives><tex-math id=\"M1117\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |=m$$\\end{document}</tex-math><mml:math id=\"M1118\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>m</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq526\"><alternatives><tex-math id=\"M1119\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1120\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq527\"><alternatives><tex-math id=\"M1121\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$m\\ge 2$$\\end{document}</tex-math><mml:math id=\"M1122\"><mml:mrow><mml:mi>m</mml:mi><mml:mo>≥</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq528\"><alternatives><tex-math id=\"M1123\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$m=2$$\\end{document}</tex-math><mml:math id=\"M1124\"><mml:mrow><mml:mi>m</mml:mi><mml:mo>=</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq529\"><alternatives><tex-math id=\"M1125\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\subseteq St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1126\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>⊆</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq530\"><alternatives><tex-math id=\"M1127\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle n_k:\\ k\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1128\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>k</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq531\"><alternatives><tex-math id=\"M1129\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _{n_k}\\restriction U\\ne 0$$\\end{document}</tex-math><mml:math id=\"M1130\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:msub><mml:mo>↾</mml:mo><mml:mi>U</mml:mi><mml:mo>≠</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq532\"><alternatives><tex-math id=\"M1131\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _{n_k}\\restriction (St(\\mathcal {A})\\setminus U)\\ne 0$$\\end{document}</tex-math><mml:math id=\"M1132\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:msub><mml:mo>↾</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>U</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≠</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq533\"><alternatives><tex-math id=\"M1133\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$k\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1134\"><mml:mrow><mml:mi>k</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq534\"><alternatives><tex-math id=\"M1135\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle k_l:\\ l\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1136\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>l</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>l</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq535\"><alternatives><tex-math id=\"M1137\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _l^1:\\ l\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1138\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msubsup><mml:mi>μ</mml:mi><mml:mi>l</mml:mi><mml:mn>1</mml:mn></mml:msubsup><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>l</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq536\"><alternatives><tex-math id=\"M1139\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _l^2:\\ l\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1140\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msubsup><mml:mi>μ</mml:mi><mml:mi>l</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>l</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq537\"><alternatives><tex-math id=\"M1141\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$l\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1142\"><mml:mrow><mml:mi>l</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ37\"><alternatives><tex-math id=\"M1143\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\mu _l^1=\\big (\\mu _{n_{k_l}}\\restriction (St(\\mathcal {A})\\setminus U)\\big )\\big /\\big \\Vert \\mu _{n_{k_l}}\\restriction (St(\\mathcal {A})\\setminus U)\\big \\Vert \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1144\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msubsup><mml:mi>μ</mml:mi><mml:mi>l</mml:mi><mml:mn>1</mml:mn></mml:msubsup><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:msub><mml:mi>k</mml:mi><mml:mi>l</mml:mi></mml:msub></mml:msub></mml:msub><mml:mo>↾</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>U</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:msub><mml:mi>k</mml:mi><mml:mi>l</mml:mi></mml:msub></mml:msub></mml:msub><mml:mo>↾</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mi>U</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<disp-formula id=\"Equ38\"><alternatives><tex-math id=\"M1145\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\mu _l^2=\\big (\\mu _{n_{k_l}}\\restriction U\\big )\\big /\\big \\Vert \\mu _{n_{k_l}}\\restriction U\\big \\Vert , \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1146\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msubsup><mml:mi>μ</mml:mi><mml:mi>l</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:msub><mml:mi>k</mml:mi><mml:mi>l</mml:mi></mml:msub></mml:msub></mml:msub><mml:mo>↾</mml:mo><mml:mi>U</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:msub><mml:mi>n</mml:mi><mml:msub><mml:mi>k</mml:mi><mml:mi>l</mml:mi></mml:msub></mml:msub></mml:msub><mml:mo>↾</mml:mo><mml:mi>U</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq538\"><alternatives><tex-math id=\"M1147\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$l\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1148\"><mml:mrow><mml:mi>l</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq539\"><alternatives><tex-math id=\"M1149\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\{1,2\\}$$\\end{document}</tex-math><mml:math id=\"M1150\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mo stretchy=\"false\">{</mml:mo><mml:mn>1</mml:mn><mml:mo>,</mml:mo><mml:mn>2</mml:mn><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq540\"><alternatives><tex-math id=\"M1151\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _l^i\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1152\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msubsup><mml:mi>μ</mml:mi><mml:mi>l</mml:mi><mml:mi>i</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq541\"><alternatives><tex-math id=\"M1153\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _l^i\\big )\\big |&lt;m$$\\end{document}</tex-math><mml:math id=\"M1154\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>μ</mml:mi><mml:mi>l</mml:mi><mml:mi>i</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>m</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq542\"><alternatives><tex-math id=\"M1155\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$U\\subseteq St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1156\"><mml:mrow><mml:mi>U</mml:mi><mml:mo>⊆</mml:mo><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq543\"><alternatives><tex-math id=\"M1157\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1158\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq544\"><alternatives><tex-math id=\"M1159\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\subseteq U$$\\end{document}</tex-math><mml:math id=\"M1160\"><mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>⊆</mml:mo><mml:mi>U</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq545\"><alternatives><tex-math id=\"M1161\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\cap U=\\emptyset $$\\end{document}</tex-math><mml:math id=\"M1162\"><mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:mi>U</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq546\"><alternatives><tex-math id=\"M1163\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1164\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq547\"><alternatives><tex-math id=\"M1165\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_n,y_n\\in {{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )$$\\end{document}</tex-math><mml:math id=\"M1166\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq548\"><alternatives><tex-math id=\"M1167\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\nu _n$$\\end{document}</tex-math><mml:math id=\"M1168\"><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq549\"><alternatives><tex-math id=\"M1169\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\nu _n=\\frac{1}{2}\\big (\\delta _{x_n}-\\delta _{y_n}\\big )$$\\end{document}</tex-math><mml:math id=\"M1170\"><mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>δ</mml:mi><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi>δ</mml:mi><mml:msub><mml:mi>y</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq550\"><alternatives><tex-math id=\"M1171\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\nu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1172\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq551\"><alternatives><tex-math id=\"M1173\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\nu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1174\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq552\"><alternatives><tex-math id=\"M1175\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1176\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq553\"><alternatives><tex-math id=\"M1177\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1178\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq554\"><alternatives><tex-math id=\"M1179\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_n,y_n\\in U$$\\end{document}</tex-math><mml:math id=\"M1180\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi>U</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq555\"><alternatives><tex-math id=\"M1181\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_n,y_n\\not \\in U$$\\end{document}</tex-math><mml:math id=\"M1182\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∉</mml:mo><mml:mi>U</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq556\"><alternatives><tex-math id=\"M1183\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\nu _n(U)=0$$\\end{document}</tex-math><mml:math id=\"M1184\"><mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>U</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq557\"><alternatives><tex-math id=\"M1185\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\nu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1186\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq558\"><alternatives><tex-math id=\"M1187\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\nu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1188\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq559\"><alternatives><tex-math id=\"M1189\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$m=2$$\\end{document}</tex-math><mml:math id=\"M1190\"><mml:mrow><mml:mi>m</mml:mi><mml:mo>=</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq560\"><alternatives><tex-math id=\"M1191\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M1192\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq561\"><alternatives><tex-math id=\"M1193\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1194\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq562\"><alternatives><tex-math id=\"M1195\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1196\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq563\"><alternatives><tex-math id=\"M1197\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1198\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq564\"><alternatives><tex-math id=\"M1199\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1200\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq565\"><alternatives><tex-math id=\"M1201\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |=2$$\\end{document}</tex-math><mml:math id=\"M1202\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq566\"><alternatives><tex-math id=\"M1203\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1204\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq567\"><alternatives><tex-math id=\"M1205\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1206\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq568\"><alternatives><tex-math id=\"M1207\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1208\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq569\"><alternatives><tex-math id=\"M1209\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1210\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq570\"><alternatives><tex-math id=\"M1211\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1212\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq571\"><alternatives><tex-math id=\"M1213\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1214\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq572\"><alternatives><tex-math id=\"M1215\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |\\le M$$\\end{document}</tex-math><mml:math id=\"M1216\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:mi>M</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq573\"><alternatives><tex-math id=\"M1217\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1218\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq574\"><alternatives><tex-math id=\"M1219\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle x_n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1220\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq575\"><alternatives><tex-math id=\"M1221\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle y_n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1222\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq576\"><alternatives><tex-math id=\"M1223\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1224\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq577\"><alternatives><tex-math id=\"M1225\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1226\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq578\"><alternatives><tex-math id=\"M1227\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_n\\in U$$\\end{document}</tex-math><mml:math id=\"M1228\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi>U</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq579\"><alternatives><tex-math id=\"M1229\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$y_n\\in U$$\\end{document}</tex-math><mml:math id=\"M1230\"><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi>U</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq580\"><alternatives><tex-math id=\"M1231\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M1232\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq581\"><alternatives><tex-math id=\"M1233\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\dot{x}_n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1234\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq582\"><alternatives><tex-math id=\"M1235\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1236\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq583\"><alternatives><tex-math id=\"M1237\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1238\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq584\"><alternatives><tex-math id=\"M1239\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1240\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq585\"><alternatives><tex-math id=\"M1241\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$q\\in \\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1242\"><mml:mrow><mml:mi>q</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq586\"><alternatives><tex-math id=\"M1243\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\le q$$\\end{document}</tex-math><mml:math id=\"M1244\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>≤</mml:mo><mml:mi>q</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq587\"><alternatives><tex-math id=\"M1245\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle A_n:\\ n\\in \\omega \\big \\rangle \\in V$$\\end{document}</tex-math><mml:math id=\"M1246\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq588\"><alternatives><tex-math id=\"M1247\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1248\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq589\"><alternatives><tex-math id=\"M1249\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\Vdash \\left[ A_n\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_k:k\\in \\omega \\big \\}\\ne \\emptyset $$\\end{document}</tex-math><mml:math id=\"M1250\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>k</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mi>k</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>≠</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq590\"><alternatives><tex-math id=\"M1251\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1252\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq591\"><alternatives><tex-math id=\"M1253\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Box $$\\end{document}</tex-math><mml:math id=\"M1254\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq592\"><alternatives><tex-math id=\"M1255\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1256\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq593\"><alternatives><tex-math id=\"M1257\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{u}$$\\end{document}</tex-math><mml:math id=\"M1258\"><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq594\"><alternatives><tex-math id=\"M1259\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{v}$$\\end{document}</tex-math><mml:math id=\"M1260\"><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq595\"><alternatives><tex-math id=\"M1261\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1262\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq596\"><alternatives><tex-math id=\"M1263\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Vdash _{\\mathbb {B}(\\kappa )}\\dot{u}\\ne \\dot{v}$$\\end{document}</tex-math><mml:math id=\"M1264\"><mml:mrow><mml:msub><mml:mo>⊩</mml:mo><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mo>≠</mml:mo><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq597\"><alternatives><tex-math id=\"M1265\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varepsilon &gt;0$$\\end{document}</tex-math><mml:math id=\"M1266\"><mml:mrow><mml:mi>ε</mml:mi><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq598\"><alternatives><tex-math id=\"M1267\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\in \\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1268\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq599\"><alternatives><tex-math id=\"M1269\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1270\"><mml:mrow><mml:mi>C</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq600\"><alternatives><tex-math id=\"M1271\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _\\kappa (p)&gt;1/4-\\varepsilon $$\\end{document}</tex-math><mml:math id=\"M1272\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>κ</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>p</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>4</mml:mn><mml:mo>-</mml:mo><mml:mi>ε</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq601\"><alternatives><tex-math id=\"M1273\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\Vdash C\\in \\dot{u}\\triangle \\dot{v}$$\\end{document}</tex-math><mml:math id=\"M1274\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>⊩</mml:mo><mml:mi>C</mml:mi><mml:mo>∈</mml:mo><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>▵</mml:mi><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq602\"><alternatives><tex-math id=\"M1275\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M1276\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq603\"><alternatives><tex-math id=\"M1277\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{u}$$\\end{document}</tex-math><mml:math id=\"M1278\"><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq604\"><alternatives><tex-math id=\"M1279\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{v}$$\\end{document}</tex-math><mml:math id=\"M1280\"><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq605\"><alternatives><tex-math id=\"M1281\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1282\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq606\"><alternatives><tex-math id=\"M1283\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1284\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq607\"><alternatives><tex-math id=\"M1285\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$q\\in \\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1286\"><mml:mrow><mml:mi>q</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq608\"><alternatives><tex-math id=\"M1287\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$q\\Vdash \\dot{u}\\ne \\dot{v}$$\\end{document}</tex-math><mml:math id=\"M1288\"><mml:mrow><mml:mi>q</mml:mi><mml:mo>⊩</mml:mo><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mo>≠</mml:mo><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq609\"><alternatives><tex-math id=\"M1289\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\varepsilon &gt;0$$\\end{document}</tex-math><mml:math id=\"M1290\"><mml:mrow><mml:mi>ε</mml:mi><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq610\"><alternatives><tex-math id=\"M1291\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\le q$$\\end{document}</tex-math><mml:math id=\"M1292\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>≤</mml:mo><mml:mi>q</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq611\"><alternatives><tex-math id=\"M1293\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1294\"><mml:mrow><mml:mi>C</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq612\"><alternatives><tex-math id=\"M1295\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _\\kappa (p)&gt;\\mu _\\kappa (q)/4-\\varepsilon $$\\end{document}</tex-math><mml:math id=\"M1296\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>κ</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>p</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:msub><mml:mi>μ</mml:mi><mml:mi>κ</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>q</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>4</mml:mn><mml:mo>-</mml:mo><mml:mi>ε</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq613\"><alternatives><tex-math id=\"M1297\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\Vdash C\\in \\dot{u}\\triangle \\dot{v}$$\\end{document}</tex-math><mml:math id=\"M1298\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>⊩</mml:mo><mml:mi>C</mml:mi><mml:mo>∈</mml:mo><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>▵</mml:mi><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq614\"><alternatives><tex-math id=\"M1299\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Box $$\\end{document}</tex-math><mml:math id=\"M1300\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq615\"><alternatives><tex-math id=\"M1301\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M1302\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq616\"><alternatives><tex-math id=\"M1303\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1304\"><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq617\"><alternatives><tex-math id=\"M1305\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M1306\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq618\"><alternatives><tex-math id=\"M1307\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$X\\in \\left[ \\omega \\right] ^\\omega \\cap V[G]$$\\end{document}</tex-math><mml:math id=\"M1308\"><mml:mrow><mml:mi>X</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>ω</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq619\"><alternatives><tex-math id=\"M1309\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {H}\\subseteq \\left[ \\omega \\right] ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1310\"><mml:mrow><mml:mi mathvariant=\"script\">H</mml:mi><mml:mo>⊆</mml:mo><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>ω</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq620\"><alternatives><tex-math id=\"M1311\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Z\\in \\mathcal {H}$$\\end{document}</tex-math><mml:math id=\"M1312\"><mml:mrow><mml:mi>Z</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">H</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq621\"><alternatives><tex-math id=\"M1313\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$X\\cap Z$$\\end{document}</tex-math><mml:math id=\"M1314\"><mml:mrow><mml:mi>X</mml:mi><mml:mo>∩</mml:mo><mml:mi>Z</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq622\"><alternatives><tex-math id=\"M1315\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle x_n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1316\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq623\"><alternatives><tex-math id=\"M1317\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M1318\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq624\"><alternatives><tex-math id=\"M1319\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1320\"><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq625\"><alternatives><tex-math id=\"M1321\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in \\omega ^\\omega \\cap V$$\\end{document}</tex-math><mml:math id=\"M1322\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq626\"><alternatives><tex-math id=\"M1323\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$k\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1324\"><mml:mrow><mml:mi>k</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq627\"><alternatives><tex-math id=\"M1325\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_k\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1326\"><mml:mrow><mml:msub><mml:mi>n</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq628\"><alternatives><tex-math id=\"M1327\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {F}\\subseteq \\left[ \\omega \\right] ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1328\"><mml:mrow><mml:mi mathvariant=\"script\">F</mml:mi><mml:mo>⊆</mml:mo><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>ω</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq629\"><alternatives><tex-math id=\"M1329\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Y\\in \\mathcal {F}$$\\end{document}</tex-math><mml:math id=\"M1330\"><mml:mrow><mml:mi>Y</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">F</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ39\"><alternatives><tex-math id=\"M1331\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} Z_Y=\\bigcup _{n\\in Y}\\big \\{g(2k),g(2k)+1,\\ldots ,g(2k+1)\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1332\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>Z</mml:mi><mml:mi>Y</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:munder><mml:mo>⋃</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>Y</mml:mi></mml:mrow></mml:munder><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>g</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>2</mml:mn><mml:mi>k</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>,</mml:mo><mml:mi>g</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>2</mml:mn><mml:mi>k</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>+</mml:mo><mml:mn>1</mml:mn><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:mi>g</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>2</mml:mn><mml:mi>k</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq630\"><alternatives><tex-math id=\"M1333\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {H}=\\big \\{Z_Y:Y\\in \\mathcal {F}\\big \\}$$\\end{document}</tex-math><mml:math id=\"M1334\"><mml:mrow><mml:mi mathvariant=\"script\">H</mml:mi><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mi>Z</mml:mi><mml:mi>Y</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mi>Y</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">F</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq631\"><alternatives><tex-math id=\"M1335\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Y\\ne Y'\\in \\mathcal {F}$$\\end{document}</tex-math><mml:math id=\"M1336\"><mml:mrow><mml:mi>Y</mml:mi><mml:mo>≠</mml:mo><mml:msup><mml:mi>Y</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">F</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq632\"><alternatives><tex-math id=\"M1337\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Z_Y\\cap Z_{Y'}$$\\end{document}</tex-math><mml:math id=\"M1338\"><mml:mrow><mml:msub><mml:mi>Z</mml:mi><mml:mi>Y</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:msub><mml:mi>Z</mml:mi><mml:msup><mml:mi>Y</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq633\"><alternatives><tex-math id=\"M1339\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {H}$$\\end{document}</tex-math><mml:math id=\"M1340\"><mml:mi mathvariant=\"script\">H</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq634\"><alternatives><tex-math id=\"M1341\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$*$$\\end{document}</tex-math><mml:math id=\"M1342\"><mml:mrow><mml:mrow/><mml:mo>∗</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq635\"><alternatives><tex-math id=\"M1343\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Y\\in \\mathcal {F}$$\\end{document}</tex-math><mml:math id=\"M1344\"><mml:mrow><mml:mi>Y</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">F</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq636\"><alternatives><tex-math id=\"M1345\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$X\\cap Z_Y$$\\end{document}</tex-math><mml:math id=\"M1346\"><mml:mrow><mml:mi>X</mml:mi><mml:mo>∩</mml:mo><mml:msub><mml:mi>Z</mml:mi><mml:mi>Y</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq637\"><alternatives><tex-math id=\"M1347\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M1348\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq638\"><alternatives><tex-math id=\"M1349\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1350\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq639\"><alternatives><tex-math id=\"M1351\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1352\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq640\"><alternatives><tex-math id=\"M1353\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$M\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1354\"><mml:mrow><mml:mi>M</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq641\"><alternatives><tex-math id=\"M1355\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1356\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq642\"><alternatives><tex-math id=\"M1357\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |{{\\,\\textrm{supp}\\,}}\\big (\\mu _n\\big )\\big |\\le M$$\\end{document}</tex-math><mml:math id=\"M1358\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>supp</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:mi>M</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq643\"><alternatives><tex-math id=\"M1359\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1360\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq644\"><alternatives><tex-math id=\"M1361\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\dot{x}_i:\\ i\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1362\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq645\"><alternatives><tex-math id=\"M1363\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\dot{y}_i:\\ i\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1364\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq646\"><alternatives><tex-math id=\"M1365\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1366\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq647\"><alternatives><tex-math id=\"M1367\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1368\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq648\"><alternatives><tex-math id=\"M1369\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$q\\in \\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1370\"><mml:mrow><mml:mi>q</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq649\"><alternatives><tex-math id=\"M1371\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{x}_i\\ne \\dot{x}_j$$\\end{document}</tex-math><mml:math id=\"M1372\"><mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq650\"><alternatives><tex-math id=\"M1373\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{y}_i\\ne \\dot{y}_j$$\\end{document}</tex-math><mml:math id=\"M1374\"><mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq651\"><alternatives><tex-math id=\"M1375\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\ne j\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1376\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>≠</mml:mo><mml:mi>j</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq652\"><alternatives><tex-math id=\"M1377\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{x}_i\\ne \\dot{y}_j$$\\end{document}</tex-math><mml:math id=\"M1378\"><mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>j</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq653\"><alternatives><tex-math id=\"M1379\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i,j\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1380\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq654\"><alternatives><tex-math id=\"M1381\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1382\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq655\"><alternatives><tex-math id=\"M1383\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1384\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq656\"><alternatives><tex-math id=\"M1385\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{x}_i\\in \\left[ A\\right] _\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1386\"><mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq657\"><alternatives><tex-math id=\"M1387\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{y}_i\\in \\left[ A\\right] _\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1388\"><mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq658\"><alternatives><tex-math id=\"M1389\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\le q$$\\end{document}</tex-math><mml:math id=\"M1390\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>≤</mml:mo><mml:mi>q</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq659\"><alternatives><tex-math id=\"M1391\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle A_n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1392\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq660\"><alternatives><tex-math id=\"M1393\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1394\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq661\"><alternatives><tex-math id=\"M1395\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1396\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq662\"><alternatives><tex-math id=\"M1397\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$p\\Vdash \\left[ A_n\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_i:\\ i\\in \\omega \\big \\}\\ne \\emptyset $$\\end{document}</tex-math><mml:math id=\"M1398\"><mml:mrow><mml:mi>p</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>≠</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq663\"><alternatives><tex-math id=\"M1399\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1400\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq664\"><alternatives><tex-math id=\"M1401\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{F}_n$$\\end{document}</tex-math><mml:math id=\"M1402\"><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq665\"><alternatives><tex-math id=\"M1403\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1404\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ40\"><alternatives><tex-math id=\"M1405\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\dot{F}_n=\\big \\{i\\in \\omega :\\ \\big |\\left[ A_n\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_i,\\dot{y}_i\\big \\}\\big |=1\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1406\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq666\"><alternatives><tex-math id=\"M1407\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{F}_n$$\\end{document}</tex-math><mml:math id=\"M1408\"><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq667\"><alternatives><tex-math id=\"M1409\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1410\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq668\"><alternatives><tex-math id=\"M1411\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{F}_n$$\\end{document}</tex-math><mml:math id=\"M1412\"><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq669\"><alternatives><tex-math id=\"M1413\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\le p$$\\end{document}</tex-math><mml:math id=\"M1414\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>≤</mml:mo><mml:mi>p</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq670\"><alternatives><tex-math id=\"M1415\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$N\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1416\"><mml:mrow><mml:mi>N</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq671\"><alternatives><tex-math id=\"M1417\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1418\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq672\"><alternatives><tex-math id=\"M1419\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\Vdash \\dot{F}_n=\\emptyset $$\\end{document}</tex-math><mml:math id=\"M1420\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq673\"><alternatives><tex-math id=\"M1421\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1422\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq674\"><alternatives><tex-math id=\"M1423\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1424\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ41\"><alternatives><tex-math id=\"M1425\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} r\\Vdash \\dot{x}_i\\in \\left[ A_n\\right] _\\mathcal {A}\\Leftrightarrow \\dot{y}_i\\in \\left[ A_n\\right] _\\mathcal {A}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1426\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo stretchy=\"false\">⇔</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq675\"><alternatives><tex-math id=\"M1427\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1428\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq676\"><alternatives><tex-math id=\"M1429\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{\\alpha }_n$$\\end{document}</tex-math><mml:math id=\"M1430\"><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq677\"><alternatives><tex-math id=\"M1431\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1432\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ42\"><alternatives><tex-math id=\"M1433\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} r\\Vdash \\dot{\\alpha }_n=\\min \\big \\{i\\in \\omega :\\ \\dot{x}_i\\in \\left[ A_n\\right] _\\mathcal {A}\\big \\}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1434\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq678\"><alternatives><tex-math id=\"M1435\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{u}_n$$\\end{document}</tex-math><mml:math id=\"M1436\"><mml:msub><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq679\"><alternatives><tex-math id=\"M1437\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{v}_n$$\\end{document}</tex-math><mml:math id=\"M1438\"><mml:msub><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq680\"><alternatives><tex-math id=\"M1439\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1440\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq681\"><alternatives><tex-math id=\"M1441\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1442\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ43\"><alternatives><tex-math id=\"M1443\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} r\\Vdash \\dot{u}_n=\\dot{x}_{\\dot{\\alpha }_n}\\text { and }\\dot{v}_n=\\dot{y}_{\\dot{\\alpha }_n}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1444\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mspace width=\"0.333333em\"/><mml:mtext>and</mml:mtext><mml:mspace width=\"0.333333em\"/><mml:msub><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq682\"><alternatives><tex-math id=\"M1445\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ne m\\ge N$$\\end{document}</tex-math><mml:math id=\"M1446\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≠</mml:mo><mml:mi>m</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq683\"><alternatives><tex-math id=\"M1447\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\Vdash \\dot{\\alpha }_n\\ne \\dot{\\alpha }_m$$\\end{document}</tex-math><mml:math id=\"M1448\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>m</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq684\"><alternatives><tex-math id=\"M1449\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1450\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq685\"><alternatives><tex-math id=\"M1451\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\Vdash \\dot{u}_n\\ne \\dot{v}_n$$\\end{document}</tex-math><mml:math id=\"M1452\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq686\"><alternatives><tex-math id=\"M1453\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r_n\\le r$$\\end{document}</tex-math><mml:math id=\"M1454\"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>≤</mml:mo><mml:mi>r</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq687\"><alternatives><tex-math id=\"M1455\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C_n\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1456\"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq688\"><alternatives><tex-math id=\"M1457\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _\\kappa \\big (r_n\\big )&gt;\\mu _\\kappa (r)/5$$\\end{document}</tex-math><mml:math id=\"M1458\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>κ</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:msub><mml:mi>μ</mml:mi><mml:mi>κ</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>5</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq689\"><alternatives><tex-math id=\"M1459\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r_n\\Vdash C_n\\in \\dot{u}_n\\triangle \\dot{v}_n$$\\end{document}</tex-math><mml:math id=\"M1460\"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>⊩</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mi>▵</mml:mi><mml:msub><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq690\"><alternatives><tex-math id=\"M1461\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r_n\\Vdash \\dot{u}_n,\\dot{v}_n\\in \\left[ A_n\\right] _\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1462\"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>⊩</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq691\"><alternatives><tex-math id=\"M1463\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C_n\\le A_n$$\\end{document}</tex-math><mml:math id=\"M1464\"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>≤</mml:mo><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq692\"><alternatives><tex-math id=\"M1465\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C_n\\wedge C_m=0$$\\end{document}</tex-math><mml:math id=\"M1466\"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∧</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi>m</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq693\"><alternatives><tex-math id=\"M1467\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ne m\\ge N$$\\end{document}</tex-math><mml:math id=\"M1468\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≠</mml:mo><mml:mi>m</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ44\"><alternatives><tex-math id=\"M1469\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} s=\\bigwedge _{n\\ge N}\\bigvee _{k\\ge n}r_k; \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1470\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>=</mml:mo><mml:munder><mml:mo>⋀</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:munder><mml:munder><mml:mo>⋁</mml:mo><mml:mrow><mml:mi>k</mml:mi><mml:mo>≥</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mi>r</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>;</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq694\"><alternatives><tex-math id=\"M1471\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _\\kappa (s)\\ge \\mu _\\kappa (r)/5$$\\end{document}</tex-math><mml:math id=\"M1472\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>κ</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>s</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≥</mml:mo><mml:msub><mml:mi>μ</mml:mi><mml:mi>κ</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mn>5</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq695\"><alternatives><tex-math id=\"M1473\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$s\\in \\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1474\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq696\"><alternatives><tex-math id=\"M1475\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$s\\le r$$\\end{document}</tex-math><mml:math id=\"M1476\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>≤</mml:mo><mml:mi>r</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq697\"><alternatives><tex-math id=\"M1477\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C_n\\in \\dot{u}_n\\triangle \\dot{v}_n$$\\end{document}</tex-math><mml:math id=\"M1478\"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>u</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mi>▵</mml:mi><mml:msub><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq698\"><alternatives><tex-math id=\"M1479\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1480\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq699\"><alternatives><tex-math id=\"M1481\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1482\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq700\"><alternatives><tex-math id=\"M1483\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle C_n:\\ n\\ge N\\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1484\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq701\"><alternatives><tex-math id=\"M1485\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1486\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ45\"><alternatives><tex-math id=\"M1487\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} C=\\bigvee _{n\\ge N}C_n, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1488\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>C</mml:mi><mml:mo>=</mml:mo><mml:munder><mml:mo>⋁</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq702\"><alternatives><tex-math id=\"M1489\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1490\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq703\"><alternatives><tex-math id=\"M1491\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C\\wedge A_n=C_n$$\\end{document}</tex-math><mml:math id=\"M1492\"><mml:mrow><mml:mi>C</mml:mi><mml:mo>∧</mml:mo><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq704\"><alternatives><tex-math id=\"M1493\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle A_n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1494\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq705\"><alternatives><tex-math id=\"M1495\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |\\left[ C\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_i,\\dot{y}_i\\big \\}\\big |=1$$\\end{document}</tex-math><mml:math id=\"M1496\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>C</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq706\"><alternatives><tex-math id=\"M1497\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1498\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq707\"><alternatives><tex-math id=\"M1499\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1500\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ46\"><alternatives><tex-math id=\"M1501\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} s\\Vdash \\left[ C\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_{\\dot{\\alpha }_n},\\dot{y}_{\\dot{\\alpha }_n}\\big \\}&amp;\\subseteq \\left[ C\\right] _\\mathcal {A}\\cap \\left[ A_n\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_{\\dot{\\alpha }_n},\\dot{y}_{\\dot{\\alpha }_n}\\big \\}=\\\\&amp;=\\left[ C\\wedge A_n\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_{\\dot{\\alpha }_n},\\dot{y}_{\\dot{\\alpha }_n}\\big \\}=\\left[ C_n\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_{\\dot{\\alpha }_n},\\dot{y}_{\\dot{\\alpha }_n}\\big \\}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1502\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>C</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo>⊆</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>C</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>=</mml:mo></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow/></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>C</mml:mi><mml:mo>∧</mml:mo><mml:msub><mml:mi>A</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq708\"><alternatives><tex-math id=\"M1503\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C_n\\le C$$\\end{document}</tex-math><mml:math id=\"M1504\"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>≤</mml:mo><mml:mi>C</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ47\"><alternatives><tex-math id=\"M1505\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} s\\Vdash \\left[ C\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_{\\dot{\\alpha }_n},\\dot{y}_{\\dot{\\alpha }_n}\\big \\}=\\left[ C_n\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_{\\dot{\\alpha }_n},\\dot{y}_{\\dot{\\alpha }_n}\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1506\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>⊩</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>C</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq709\"><alternatives><tex-math id=\"M1507\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$+$$\\end{document}</tex-math><mml:math id=\"M1508\"><mml:mo>+</mml:mo></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ48\"><alternatives><tex-math id=\"M1509\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} s\\Vdash \\big |\\left[ C\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_{\\dot{\\alpha }_n},\\dot{y}_{\\dot{\\alpha }_n}\\big \\}\\big |=\\big |\\left[ C_n\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_{\\dot{\\alpha }_n},\\dot{y}_{\\dot{\\alpha }_n}\\big \\}\\big |=1 \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1510\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>⊩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>C</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:msub><mml:mover accent=\"true\"><mml:mi>α</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq710\"><alternatives><tex-math id=\"M1511\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1512\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq711\"><alternatives><tex-math id=\"M1513\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\le p$$\\end{document}</tex-math><mml:math id=\"M1514\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>≤</mml:mo><mml:mi>p</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq712\"><alternatives><tex-math id=\"M1515\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1516\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq713\"><alternatives><tex-math id=\"M1517\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{F}_n$$\\end{document}</tex-math><mml:math id=\"M1518\"><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq714\"><alternatives><tex-math id=\"M1519\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{f}$$\\end{document}</tex-math><mml:math id=\"M1520\"><mml:mover accent=\"true\"><mml:mi>f</mml:mi><mml:mo>˙</mml:mo></mml:mover></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq715\"><alternatives><tex-math id=\"M1521\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1522\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq716\"><alternatives><tex-math id=\"M1523\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega \\rightarrow \\omega $$\\end{document}</tex-math><mml:math id=\"M1524\"><mml:mrow><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq717\"><alternatives><tex-math id=\"M1525\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1526\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ49\"><alternatives><tex-math id=\"M1527\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} r\\Vdash \\dot{f}(n)= {\\left\\{ \\begin{array}{ll} \\max \\big \\{m\\ge n:\\ \\dot{F}_n\\cap \\dot{F}_m\\ne \\emptyset \\big \\},&amp;{}\\text { if }\\dot{F}_n\\ne \\emptyset ,\\\\ n,&amp;{}\\text { if }\\dot{F}_n=\\emptyset . \\end{array}\\right. } \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1528\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>⊩</mml:mo><mml:mover accent=\"true\"><mml:mi>f</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mfenced open=\"{\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo movablelimits=\"true\">max</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>m</mml:mi><mml:mo>≥</mml:mo><mml:mi>n</mml:mi><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>m</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mrow/><mml:mspace width=\"0.333333em\"/><mml:mtext>if</mml:mtext><mml:mspace width=\"0.333333em\"/><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"left\"><mml:mrow><mml:mrow/><mml:mi>n</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mrow/><mml:mspace width=\"0.333333em\"/><mml:mtext>if</mml:mtext><mml:mspace width=\"0.333333em\"/><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:mfenced></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq718\"><alternatives><tex-math id=\"M1529\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{F}_n$$\\end{document}</tex-math><mml:math id=\"M1530\"><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq719\"><alternatives><tex-math id=\"M1531\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1532\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq720\"><alternatives><tex-math id=\"M1533\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1534\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq721\"><alternatives><tex-math id=\"M1535\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{F}_n$$\\end{document}</tex-math><mml:math id=\"M1536\"><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq722\"><alternatives><tex-math id=\"M1537\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n,m\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1538\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>,</mml:mo><mml:mi>m</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq723\"><alternatives><tex-math id=\"M1539\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\Vdash \\dot{f}(n)\\ge n$$\\end{document}</tex-math><mml:math id=\"M1540\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>⊩</mml:mo><mml:mover accent=\"true\"><mml:mi>f</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≥</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq724\"><alternatives><tex-math id=\"M1541\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1542\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq725\"><alternatives><tex-math id=\"M1543\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1544\"><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq726\"><alternatives><tex-math id=\"M1545\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g:\\omega \\rightarrow \\omega $$\\end{document}</tex-math><mml:math id=\"M1546\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>:</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq727\"><alternatives><tex-math id=\"M1547\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g(0)&gt;0$$\\end{document}</tex-math><mml:math id=\"M1548\"><mml:mrow><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0</mml:mn><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq728\"><alternatives><tex-math id=\"M1549\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$s\\le r$$\\end{document}</tex-math><mml:math id=\"M1550\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>≤</mml:mo><mml:mi>r</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq729\"><alternatives><tex-math id=\"M1551\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$s\\Vdash \\dot{f}(n)&lt;g(n)$$\\end{document}</tex-math><mml:math id=\"M1552\"><mml:mrow><mml:mi>s</mml:mi><mml:mo>⊩</mml:mo><mml:mover accent=\"true\"><mml:mi>f</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>g</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq730\"><alternatives><tex-math id=\"M1553\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1554\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq731\"><alternatives><tex-math id=\"M1555\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h:\\omega \\rightarrow \\omega $$\\end{document}</tex-math><mml:math id=\"M1556\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>:</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq732\"><alternatives><tex-math id=\"M1557\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1558\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq733\"><alternatives><tex-math id=\"M1559\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h(n)=g^{n+1}(0)=(g\\circ g\\circ \\ldots \\circ g)(0)$$\\end{document}</tex-math><mml:math id=\"M1560\"><mml:mrow><mml:mi>h</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msup><mml:mi>g</mml:mi><mml:mrow><mml:mi>n</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>g</mml:mi><mml:mo>∘</mml:mo><mml:mi>g</mml:mi><mml:mo>∘</mml:mo><mml:mo>…</mml:mo><mml:mo>∘</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq734\"><alternatives><tex-math id=\"M1561\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n+1$$\\end{document}</tex-math><mml:math id=\"M1562\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq735\"><alternatives><tex-math id=\"M1563\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$t\\le s$$\\end{document}</tex-math><mml:math id=\"M1564\"><mml:mrow><mml:mi>t</mml:mi><mml:mo>≤</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq736\"><alternatives><tex-math id=\"M1565\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1566\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq737\"><alternatives><tex-math id=\"M1567\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{F}_{h(n)}$$\\end{document}</tex-math><mml:math id=\"M1568\"><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq738\"><alternatives><tex-math id=\"M1569\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1570\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq739\"><alternatives><tex-math id=\"M1571\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M1572\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq740\"><alternatives><tex-math id=\"M1573\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M1574\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq741\"><alternatives><tex-math id=\"M1575\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma ^H$$\\end{document}</tex-math><mml:math id=\"M1576\"><mml:msup><mml:mi>σ</mml:mi><mml:mi>H</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq742\"><alternatives><tex-math id=\"M1577\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n&lt;m\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1578\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>&lt;</mml:mo><mml:mi>m</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ50\"><alternatives><tex-math id=\"M1579\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} h(m)=g^{m+1}(0)=g^{m-n}\\big (g^{n+1}(0)\\big )=g^{m-n}(h(n))\\ge g(h(n))&gt;\\dot{f}^H(h(n)), \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1580\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>h</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>m</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msup><mml:mi>g</mml:mi><mml:mrow><mml:mi>m</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msup><mml:mi>g</mml:mi><mml:mrow><mml:mi>m</mml:mi><mml:mo>-</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msup><mml:mi>g</mml:mi><mml:mrow><mml:mi>n</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msup><mml:mi>g</mml:mi><mml:mrow><mml:mi>m</mml:mi><mml:mo>-</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>h</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≥</mml:mo><mml:mi>g</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>h</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:msup><mml:mover accent=\"true\"><mml:mi>f</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>H</mml:mi></mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>h</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq743\"><alternatives><tex-math id=\"M1581\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$*$$\\end{document}</tex-math><mml:math id=\"M1582\"><mml:mrow><mml:mrow/><mml:mo>∗</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq744\"><alternatives><tex-math id=\"M1583\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1584\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq745\"><alternatives><tex-math id=\"M1585\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M1586\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq746\"><alternatives><tex-math id=\"M1587\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h\\in V$$\\end{document}</tex-math><mml:math id=\"M1588\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ51\"><alternatives><tex-math id=\"M1589\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} A=\\bigvee _{n\\in \\omega }A_{h(n)} \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1590\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>=</mml:mo><mml:munder><mml:mo>⋁</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mi>A</mml:mi><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq747\"><alternatives><tex-math id=\"M1591\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1592\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq748\"><alternatives><tex-math id=\"M1593\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$X\\in \\left[ \\omega \\right] ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1594\"><mml:mrow><mml:mi>X</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>ω</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq749\"><alternatives><tex-math id=\"M1595\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in X$$\\end{document}</tex-math><mml:math id=\"M1596\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>X</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq750\"><alternatives><tex-math id=\"M1597\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{F}_{h(n)}^H\\ne \\emptyset $$\\end{document}</tex-math><mml:math id=\"M1598\"><mml:mrow><mml:msubsup><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mo>≠</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq751\"><alternatives><tex-math id=\"M1599\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i_n\\in \\dot{F}_{h(n)}^H$$\\end{document}</tex-math><mml:math id=\"M1600\"><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msubsup><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>H</mml:mi></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq752\"><alternatives><tex-math id=\"M1601\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$X'\\in \\left[ X\\right] ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1602\"><mml:mrow><mml:msup><mml:mi>X</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mo>∈</mml:mo><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>X</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq753\"><alternatives><tex-math id=\"M1603\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |\\big \\{\\dot{x}_{i_n}^H,\\dot{y}_{i_n}^H\\big \\}\\cap \\left[ A\\right] _\\mathcal {A}\\big |=1$$\\end{document}</tex-math><mml:math id=\"M1604\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mo>,</mml:mo><mml:msubsup><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq754\"><alternatives><tex-math id=\"M1605\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in X'$$\\end{document}</tex-math><mml:math id=\"M1606\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>X</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq755\"><alternatives><tex-math id=\"M1607\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in X$$\\end{document}</tex-math><mml:math id=\"M1608\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>X</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq756\"><alternatives><tex-math id=\"M1609\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\{\\dot{x}_{i_n}^H,\\dot{y}_{i_n}^H\\big \\}\\subseteq \\left[ A\\right] _\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1610\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mo>,</mml:mo><mml:msubsup><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>⊆</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq757\"><alternatives><tex-math id=\"M1611\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$**$$\\end{document}</tex-math><mml:math id=\"M1612\"><mml:mrow><mml:mrow/><mml:mo>∗</mml:mo><mml:mrow/><mml:mo>∗</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq758\"><alternatives><tex-math id=\"M1613\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in X$$\\end{document}</tex-math><mml:math id=\"M1614\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>X</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ52\"><alternatives><tex-math id=\"M1615\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Big |\\big \\{\\dot{x}_{i_n}^H,\\dot{y}_{i_n}^H\\big \\}\\cap \\big (\\left[ A\\right] _\\mathcal {A}\\setminus \\bigcup _{n\\in \\omega }\\left[ A_{h(n)}\\right] _\\mathcal {A}\\big )\\Big |=1, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1616\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mo>,</mml:mo><mml:msubsup><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:mi>A</mml:mi></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:munder><mml:mo>⋃</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq759\"><alternatives><tex-math id=\"M1617\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\{\\dot{x}_{i_n}^H,\\dot{y}_{i_n}^H\\big \\}$$\\end{document}</tex-math><mml:math id=\"M1618\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mo>,</mml:mo><mml:msubsup><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq760\"><alternatives><tex-math id=\"M1619\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M1620\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq761\"><alternatives><tex-math id=\"M1621\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\bigcup _{n\\in \\omega }\\left[ A_{h(n)}\\right] _\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1622\"><mml:mrow><mml:msub><mml:mo>⋃</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq762\"><alternatives><tex-math id=\"M1623\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {H}\\subseteq \\left[ \\omega \\right] ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1624\"><mml:mrow><mml:mi mathvariant=\"script\">H</mml:mi><mml:mo>⊆</mml:mo><mml:msup><mml:mfenced close=\"]\" open=\"[\"><mml:mi>ω</mml:mi></mml:mfenced><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq763\"><alternatives><tex-math id=\"M1625\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$X\\cap Z$$\\end{document}</tex-math><mml:math id=\"M1626\"><mml:mrow><mml:mi>X</mml:mi><mml:mo>∩</mml:mo><mml:mi>Z</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq764\"><alternatives><tex-math id=\"M1627\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Z\\in \\mathcal {H}$$\\end{document}</tex-math><mml:math id=\"M1628\"><mml:mrow><mml:mi>Z</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">H</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq765\"><alternatives><tex-math id=\"M1629\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Z\\in \\mathcal {H}$$\\end{document}</tex-math><mml:math id=\"M1630\"><mml:mrow><mml:mi>Z</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">H</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ53\"><alternatives><tex-math id=\"M1631\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} A_Z=\\bigvee _{n\\in Z}A_{h(n)} \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1632\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi>Z</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:munder><mml:mo>⋁</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>Z</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mi>A</mml:mi><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq766\"><alternatives><tex-math id=\"M1633\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1634\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq767\"><alternatives><tex-math id=\"M1635\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Z\\in \\mathcal {H}$$\\end{document}</tex-math><mml:math id=\"M1636\"><mml:mrow><mml:mi>Z</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">H</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ54\"><alternatives><tex-math id=\"M1637\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} B_Z=\\left[ A_Z\\right] _\\mathcal {A}\\setminus \\bigcup _{n\\in Z}\\left[ A_{h(n)}\\right] _\\mathcal {A}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1638\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>B</mml:mi><mml:mi>Z</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>Z</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:munder><mml:mo>⋃</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>Z</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq768\"><alternatives><tex-math id=\"M1639\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Z_1\\ne Z_2\\in \\mathcal {H}$$\\end{document}</tex-math><mml:math id=\"M1640\"><mml:mrow><mml:msub><mml:mi>Z</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mi>Z</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">H</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ55\"><alternatives><tex-math id=\"M1641\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\left[ A_{Z_1}\\right] _\\mathcal {A}\\cap \\left[ A_{Z_2}\\right] _\\mathcal {A}=\\bigcup _{n\\in Z_1\\cap Z_2}\\left[ A_{h(n)}\\right] _\\mathcal {A}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1642\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:msub><mml:mi>Z</mml:mi><mml:mn>1</mml:mn></mml:msub></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:msub><mml:mi>Z</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:munder><mml:mo>⋃</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>Z</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>∩</mml:mo><mml:msub><mml:mi>Z</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:mrow></mml:munder><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq769\"><alternatives><tex-math id=\"M1643\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$B_{Z_1}\\cap B_{Z_2}=\\emptyset $$\\end{document}</tex-math><mml:math id=\"M1644\"><mml:mrow><mml:msub><mml:mi>B</mml:mi><mml:msub><mml:mi>Z</mml:mi><mml:mn>1</mml:mn></mml:msub></mml:msub><mml:mo>∩</mml:mo><mml:msub><mml:mi>B</mml:mi><mml:msub><mml:mi>Z</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq770\"><alternatives><tex-math id=\"M1645\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {H}$$\\end{document}</tex-math><mml:math id=\"M1646\"><mml:mi mathvariant=\"script\">H</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq771\"><alternatives><tex-math id=\"M1647\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$Z\\in \\mathcal {H}$$\\end{document}</tex-math><mml:math id=\"M1648\"><mml:mrow><mml:mi>Z</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">H</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq772\"><alternatives><tex-math id=\"M1649\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\{\\dot{x}_{i_n}^H,\\dot{y}_{i_n}^H\\big \\}\\cap B_Z=\\emptyset $$\\end{document}</tex-math><mml:math id=\"M1650\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mo>,</mml:mo><mml:msubsup><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:msub><mml:mi>B</mml:mi><mml:mi>Z</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq773\"><alternatives><tex-math id=\"M1651\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in X\\cap Z$$\\end{document}</tex-math><mml:math id=\"M1652\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>X</mml:mi><mml:mo>∩</mml:mo><mml:mi>Z</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq774\"><alternatives><tex-math id=\"M1653\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |\\big \\{\\dot{x}_{i_n}^H,\\dot{y}_{i_n}^H\\big \\}\\cap \\left[ A_Z\\right] _\\mathcal {A}\\big |=1$$\\end{document}</tex-math><mml:math id=\"M1654\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mo>,</mml:mo><mml:msubsup><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow><mml:mi>H</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>∩</mml:mo><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mi>A</mml:mi><mml:mi>Z</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq775\"><alternatives><tex-math id=\"M1655\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in X$$\\end{document}</tex-math><mml:math id=\"M1656\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>X</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq776\"><alternatives><tex-math id=\"M1657\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1658\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq777\"><alternatives><tex-math id=\"M1659\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\dot{F}_{h(n)}$$\\end{document}</tex-math><mml:math id=\"M1660\"><mml:msub><mml:mover accent=\"true\"><mml:mi>F</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq778\"><alternatives><tex-math id=\"M1661\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$N\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1662\"><mml:mrow><mml:mi>N</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq779\"><alternatives><tex-math id=\"M1663\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle C_n:\\ n\\ge N\\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1664\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq780\"><alternatives><tex-math id=\"M1665\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$C_n\\le A_{h(n)}$$\\end{document}</tex-math><mml:math id=\"M1666\"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>≤</mml:mo><mml:msub><mml:mi>A</mml:mi><mml:mrow><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq781\"><alternatives><tex-math id=\"M1667\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1668\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq782\"><alternatives><tex-math id=\"M1669\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$t\\le s$$\\end{document}</tex-math><mml:math id=\"M1670\"><mml:mrow><mml:mi>t</mml:mi><mml:mo>≤</mml:mo><mml:mi>s</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq783\"><alternatives><tex-math id=\"M1671\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big |\\left[ \\bigvee _{n\\in \\omega }C_n\\right] _\\mathcal {A}\\cap \\big \\{\\dot{x}_i,\\dot{y}_i\\big \\}\\big |=1$$\\end{document}</tex-math><mml:math id=\"M1672\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mfenced close=\"]\" open=\"[\"><mml:msub><mml:mo>⋁</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi>C</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mfenced><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mover accent=\"true\"><mml:mi>x</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mi>i</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq784\"><alternatives><tex-math id=\"M1673\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1674\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq785\"><alternatives><tex-math id=\"M1675\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M1676\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq786\"><alternatives><tex-math id=\"M1677\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M1678\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq787\"><alternatives><tex-math id=\"M1679\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M1680\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq788\"><alternatives><tex-math id=\"M1681\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\in \\omega ^\\omega \\cap V[G]$$\\end{document}</tex-math><mml:math id=\"M1682\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq789\"><alternatives><tex-math id=\"M1683\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\le ^*f$$\\end{document}</tex-math><mml:math id=\"M1684\"><mml:mrow><mml:mi>g</mml:mi><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:mi>f</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq790\"><alternatives><tex-math id=\"M1685\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in \\omega ^\\omega \\cap V$$\\end{document}</tex-math><mml:math id=\"M1686\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq791\"><alternatives><tex-math id=\"M1687\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$(\\omega ^\\omega )^\\infty $$\\end{document}</tex-math><mml:math id=\"M1688\"><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq792\"><alternatives><tex-math id=\"M1689\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\in \\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1690\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq793\"><alternatives><tex-math id=\"M1691\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f(n)\\le f(n+1)$$\\end{document}</tex-math><mml:math id=\"M1692\"><mml:mrow><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>≤</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq794\"><alternatives><tex-math id=\"M1693\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1694\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq795\"><alternatives><tex-math id=\"M1695\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\lim _{n\\rightarrow \\infty }f(n)=\\infty $$\\end{document}</tex-math><mml:math id=\"M1696\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq796\"><alternatives><tex-math id=\"M1697\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h\\in (\\omega ^\\omega )^\\infty \\cap V[G]$$\\end{document}</tex-math><mml:math id=\"M1698\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq797\"><alternatives><tex-math id=\"M1699\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h\\le ^*g$$\\end{document}</tex-math><mml:math id=\"M1700\"><mml:mrow><mml:mi>h</mml:mi><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:mi>g</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq798\"><alternatives><tex-math id=\"M1701\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in (\\omega ^\\omega )^\\infty \\cap V$$\\end{document}</tex-math><mml:math id=\"M1702\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq799\"><alternatives><tex-math id=\"M1703\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi :(\\omega ^\\omega )^\\infty \\rightarrow (\\omega ^\\omega )^\\infty $$\\end{document}</tex-math><mml:math id=\"M1704\"><mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mo>:</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup><mml:mo stretchy=\"false\">→</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq800\"><alternatives><tex-math id=\"M1705\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi $$\\end{document}</tex-math><mml:math id=\"M1706\"><mml:mi mathvariant=\"normal\">Φ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq801\"><alternatives><tex-math id=\"M1707\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\in (\\omega ^\\omega )^\\infty $$\\end{document}</tex-math><mml:math id=\"M1708\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq802\"><alternatives><tex-math id=\"M1709\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$${{\\,\\textrm{ran}\\,}}(f)=\\big \\{n_1^f&lt;n_2^f&lt;n_3^f&lt;\\ldots \\big \\}$$\\end{document}</tex-math><mml:math id=\"M1710\"><mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>ran</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mn>1</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mn>2</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mn>3</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:mo>…</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq803\"><alternatives><tex-math id=\"M1711\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_0^f=-1$$\\end{document}</tex-math><mml:math id=\"M1712\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mn>0</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>=</mml:mo><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq804\"><alternatives><tex-math id=\"M1713\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_0^f&lt;n_1^f$$\\end{document}</tex-math><mml:math id=\"M1714\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mn>0</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mn>1</mml:mn><mml:mi>f</mml:mi></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq805\"><alternatives><tex-math id=\"M1715\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1716\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq806\"><alternatives><tex-math id=\"M1717\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1718\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq807\"><alternatives><tex-math id=\"M1719\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_i^f\\le n&lt;n_{i+1}^f$$\\end{document}</tex-math><mml:math id=\"M1720\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>≤</mml:mo><mml:mi>n</mml:mi><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ56\"><alternatives><tex-math id=\"M1721\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\Phi (f)(n)=\\min f^{-1}\\big (n_{i+1}^f\\big ). \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1722\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq808\"><alternatives><tex-math id=\"M1723\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi (f)\\in (\\omega ^\\omega )^\\infty $$\\end{document}</tex-math><mml:math id=\"M1724\"><mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq809\"><alternatives><tex-math id=\"M1725\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi ({{\\,\\textrm{id}\\,}}_\\omega )(n)=n+1$$\\end{document}</tex-math><mml:math id=\"M1726\"><mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>id</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mi>ω</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>n</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq810\"><alternatives><tex-math id=\"M1727\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1728\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq811\"><alternatives><tex-math id=\"M1729\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi $$\\end{document}</tex-math><mml:math id=\"M1730\"><mml:mi mathvariant=\"normal\">Φ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq812\"><alternatives><tex-math id=\"M1731\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f,g\\in (\\omega ^\\omega )^\\infty $$\\end{document}</tex-math><mml:math id=\"M1732\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>,</mml:mo><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq813\"><alternatives><tex-math id=\"M1733\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big (f\\circ \\Phi (f)\\big )&gt;{{\\,\\textrm{id}\\,}}_\\omega $$\\end{document}</tex-math><mml:math id=\"M1734\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>f</mml:mi><mml:mo>∘</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:msub><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>id</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mi>ω</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq814\"><alternatives><tex-math id=\"M1735\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big (\\Phi (f)\\circ f\\big )&gt;{{\\,\\textrm{id}\\,}}_\\omega $$\\end{document}</tex-math><mml:math id=\"M1736\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∘</mml:mo><mml:mi>f</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:msub><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>id</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mi>ω</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq815\"><alternatives><tex-math id=\"M1737\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi (\\Phi (f))=f$$\\end{document}</tex-math><mml:math id=\"M1738\"><mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>=</mml:mo><mml:mi>f</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq816\"><alternatives><tex-math id=\"M1739\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\le ^*g$$\\end{document}</tex-math><mml:math id=\"M1740\"><mml:mrow><mml:mi>f</mml:mi><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:mi>g</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq817\"><alternatives><tex-math id=\"M1741\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi (g)\\le ^*\\Phi (f)$$\\end{document}</tex-math><mml:math id=\"M1742\"><mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq818\"><alternatives><tex-math id=\"M1743\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f,g\\in (\\omega ^\\omega )^\\infty $$\\end{document}</tex-math><mml:math id=\"M1744\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>,</mml:mo><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ57\"><alternatives><tex-math id=\"M1745\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} {{\\,\\textrm{ran}\\,}}(f)=\\big \\{n_1^f&lt;n_2^f&lt;n_3^f&lt;\\ldots \\big \\}\\quad \\text {and}\\quad {{\\,\\textrm{ran}\\,}}(g)=\\big \\{n_1^g&lt;n_2^g&lt;n_3^g&lt;\\ldots \\big \\}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1746\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>ran</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mn>1</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mn>2</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mn>3</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:mo>…</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mspace width=\"1em\"/><mml:mtext>and</mml:mtext><mml:mspace width=\"1em\"/><mml:mrow><mml:mspace width=\"0.166667em\"/><mml:mtext>ran</mml:mtext><mml:mspace width=\"0.166667em\"/></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mn>1</mml:mn><mml:mi>g</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mn>2</mml:mn><mml:mi>g</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mn>3</mml:mn><mml:mi>g</mml:mi></mml:msubsup><mml:mo>&lt;</mml:mo><mml:mo>…</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq819\"><alternatives><tex-math id=\"M1747\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_0^f=-1$$\\end{document}</tex-math><mml:math id=\"M1748\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mn>0</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>=</mml:mo><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq820\"><alternatives><tex-math id=\"M1749\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_0^g=-1$$\\end{document}</tex-math><mml:math id=\"M1750\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mn>0</mml:mn><mml:mi>g</mml:mi></mml:msubsup><mml:mo>=</mml:mo><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq821\"><alternatives><tex-math id=\"M1751\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1752\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq822\"><alternatives><tex-math id=\"M1753\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i,j\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1754\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq823\"><alternatives><tex-math id=\"M1755\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_i^f\\le n&lt; n_{i+1}^f$$\\end{document}</tex-math><mml:math id=\"M1756\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>≤</mml:mo><mml:mi>n</mml:mi><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq824\"><alternatives><tex-math id=\"M1757\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_j^f=f(n)$$\\end{document}</tex-math><mml:math id=\"M1758\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>j</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>=</mml:mo><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ58\"><alternatives><tex-math id=\"M1759\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\big (f\\circ \\Phi (f)\\big )(n)=f\\big (\\min f^{-1}\\big (n_{i+1}^f\\big )\\big )=n_{i+1}^f&gt;n, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1760\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi>f</mml:mi><mml:mo>∘</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>f</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mo>&gt;</mml:mo><mml:mi>n</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq825\"><alternatives><tex-math id=\"M1761\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\min f^{-1}\\big (n_{j+1}^f\\big )&gt;n$$\\end{document}</tex-math><mml:math id=\"M1762\"><mml:mrow><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ59\"><alternatives><tex-math id=\"M1763\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\big (\\Phi (f)\\circ f\\big )(n)=\\Phi (f)(f(n))=\\min f^{-1}\\big (n_{j+1}^f\\big )&gt;n. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1764\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∘</mml:mo><mml:mi>f</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:mi>n</mml:mi><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq826\"><alternatives><tex-math id=\"M1765\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\ge 1$$\\end{document}</tex-math><mml:math id=\"M1766\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>≥</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq827\"><alternatives><tex-math id=\"M1767\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_i'=\\min f^{-1}\\big (n_i^f\\big )$$\\end{document}</tex-math><mml:math id=\"M1768\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq828\"><alternatives><tex-math id=\"M1769\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_{i+1}'&gt;n_i'$$\\end{document}</tex-math><mml:math id=\"M1770\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mo>′</mml:mo></mml:msubsup><mml:mo>&gt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mo>′</mml:mo></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq829\"><alternatives><tex-math id=\"M1771\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\ge 1$$\\end{document}</tex-math><mml:math id=\"M1772\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>≥</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq830\"><alternatives><tex-math id=\"M1773\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_1'=0$$\\end{document}</tex-math><mml:math id=\"M1774\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mn>1</mml:mn><mml:mo>′</mml:mo></mml:msubsup><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ60\"><alternatives><tex-math id=\"M1775\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} (\\Phi (f))^{-1}\\big (n_{1}'\\big )=\\big \\{0,1,2,\\ldots ,n_{1}^f-1\\big \\}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1776\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mn>1</mml:mn></mml:mrow><mml:mo>′</mml:mo></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mn>0</mml:mn><mml:mo>,</mml:mo><mml:mn>1</mml:mn><mml:mo>,</mml:mo><mml:mn>2</mml:mn><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mo>-</mml:mo><mml:mn>1</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq831\"><alternatives><tex-math id=\"M1777\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$(\\Phi (f))^{-1}\\big (n_{1}'\\big )=\\emptyset $$\\end{document}</tex-math><mml:math id=\"M1778\"><mml:mrow><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mn>1</mml:mn></mml:mrow><mml:mo>′</mml:mo></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">∅</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq832\"><alternatives><tex-math id=\"M1779\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_1^f=0$$\\end{document}</tex-math><mml:math id=\"M1780\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mn>1</mml:mn><mml:mi>f</mml:mi></mml:msubsup><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq833\"><alternatives><tex-math id=\"M1781\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\ge 1$$\\end{document}</tex-math><mml:math id=\"M1782\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>≥</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ61\"><alternatives><tex-math id=\"M1783\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} (\\Phi (f))^{-1}\\big (n_{i+1}'\\big )=\\big \\{n_i^f,n_i^f+1,n_i^f+2,\\ldots ,n_{i+1}^f-1\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1784\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mo>′</mml:mo></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>,</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>+</mml:mo><mml:mn>1</mml:mn><mml:mo>,</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>+</mml:mo><mml:mn>2</mml:mn><mml:mo>,</mml:mo><mml:mo>…</mml:mo><mml:mo>,</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mo>-</mml:mo><mml:mn>1</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq834\"><alternatives><tex-math id=\"M1785\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1786\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq835\"><alternatives><tex-math id=\"M1787\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i\\ge 1$$\\end{document}</tex-math><mml:math id=\"M1788\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>≥</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq836\"><alternatives><tex-math id=\"M1789\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_i'\\le n&lt;n_{i+1}'$$\\end{document}</tex-math><mml:math id=\"M1790\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mo>≤</mml:mo><mml:mi>n</mml:mi><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mo>′</mml:mo></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ62\"><alternatives><tex-math id=\"M1791\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\min f^{-1}\\big (n_i^f\\big )\\le n&lt;\\min f^{-1}\\big (n_{i+1}^f\\big ), \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1792\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:mi>n</mml:mi><mml:mo>&lt;</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq837\"><alternatives><tex-math id=\"M1793\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f(n)=n_i^f$$\\end{document}</tex-math><mml:math id=\"M1794\"><mml:mrow><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ63\"><alternatives><tex-math id=\"M1795\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} (\\Phi (\\Phi (f))(n)=\\min \\Big ((\\Phi (f))^{-1}\\big (n_{i+1}'\\big )\\Big )=n_i^f=f(n), \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1796\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mo>′</mml:mo></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>=</mml:mo><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq838\"><alternatives><tex-math id=\"M1797\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\le ^*g$$\\end{document}</tex-math><mml:math id=\"M1798\"><mml:mrow><mml:mi>f</mml:mi><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:mi>g</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq839\"><alternatives><tex-math id=\"M1799\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$N\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1800\"><mml:mrow><mml:mi>N</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq840\"><alternatives><tex-math id=\"M1801\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f(n)\\le g(n)$$\\end{document}</tex-math><mml:math id=\"M1802\"><mml:mrow><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>≤</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq841\"><alternatives><tex-math id=\"M1803\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ge N$$\\end{document}</tex-math><mml:math id=\"M1804\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≥</mml:mo><mml:mi>N</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq842\"><alternatives><tex-math id=\"M1805\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n&gt;f(N)$$\\end{document}</tex-math><mml:math id=\"M1806\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>&gt;</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>N</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq843\"><alternatives><tex-math id=\"M1807\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$i,j,k\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1808\"><mml:mrow><mml:mi>i</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mo>,</mml:mo><mml:mi>k</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq844\"><alternatives><tex-math id=\"M1809\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_i^f\\le n&lt;n_{i+1}^f$$\\end{document}</tex-math><mml:math id=\"M1810\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>≤</mml:mo><mml:mi>n</mml:mi><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq845\"><alternatives><tex-math id=\"M1811\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_j^g\\le n&lt;n_{j+1}^g$$\\end{document}</tex-math><mml:math id=\"M1812\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>j</mml:mi><mml:mi>g</mml:mi></mml:msubsup><mml:mo>≤</mml:mo><mml:mi>n</mml:mi><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>g</mml:mi></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq846\"><alternatives><tex-math id=\"M1813\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_k^f=f(N)$$\\end{document}</tex-math><mml:math id=\"M1814\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>k</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>=</mml:mo><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>N</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq847\"><alternatives><tex-math id=\"M1815\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$k\\le i$$\\end{document}</tex-math><mml:math id=\"M1816\"><mml:mrow><mml:mi>k</mml:mi><mml:mo>≤</mml:mo><mml:mi>i</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq848\"><alternatives><tex-math id=\"M1817\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n_k^f\\le n_i^f$$\\end{document}</tex-math><mml:math id=\"M1818\"><mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>k</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mo>≤</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ64\"><alternatives><tex-math id=\"M1819\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} l=\\Phi (f)(n)=\\min f^{-1}\\big (n_{i+1}^f\\big ) \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1820\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>l</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<disp-formula id=\"Equ65\"><alternatives><tex-math id=\"M1821\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} m=\\Phi (g)(n)=\\min g^{-1}\\big (n_{j+1}^g\\big ). \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1822\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>m</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>g</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>j</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>g</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq849\"><alternatives><tex-math id=\"M1823\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$m\\le l$$\\end{document}</tex-math><mml:math id=\"M1824\"><mml:mrow><mml:mi>m</mml:mi><mml:mo>≤</mml:mo><mml:mi>l</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq850\"><alternatives><tex-math id=\"M1825\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$l&lt;m$$\\end{document}</tex-math><mml:math id=\"M1826\"><mml:mrow><mml:mi>l</mml:mi><mml:mo>&lt;</mml:mo><mml:mi>m</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ66\"><alternatives><tex-math id=\"M1827\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} g(l)\\le n_j^g\\le n&lt;n_{i+1}^f=f(l), \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1828\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>g</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>l</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mi>j</mml:mi><mml:mi>g</mml:mi></mml:msubsup><mml:mo>≤</mml:mo><mml:mi>n</mml:mi><mml:mo>&lt;</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mo>=</mml:mo><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>l</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq851\"><alternatives><tex-math id=\"M1829\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g(l)&lt;f(l)$$\\end{document}</tex-math><mml:math id=\"M1830\"><mml:mrow><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>l</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>&lt;</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>l</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ67\"><alternatives><tex-math id=\"M1831\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} l=\\min f^{-1}\\big (n_{i+1}^f\\big )&gt;\\max f^{-1}\\big (n_i^f\\big )\\ge \\max f^{-1}\\big (n_k^f\\big )\\ge N, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1832\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>l</mml:mi><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:mo movablelimits=\"true\">max</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>≥</mml:mo><mml:mo movablelimits=\"true\">max</mml:mo><mml:msup><mml:mi>f</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msubsup><mml:mi>n</mml:mi><mml:mi>k</mml:mi><mml:mi>f</mml:mi></mml:msubsup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>≥</mml:mo><mml:mi>N</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq852\"><alternatives><tex-math id=\"M1833\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f(l)\\le g(l)$$\\end{document}</tex-math><mml:math id=\"M1834\"><mml:mrow><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>l</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>≤</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>l</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq853\"><alternatives><tex-math id=\"M1835\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M1836\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq854\"><alternatives><tex-math id=\"M1837\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M1838\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq855\"><alternatives><tex-math id=\"M1839\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M1840\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq856\"><alternatives><tex-math id=\"M1841\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M1842\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq857\"><alternatives><tex-math id=\"M1843\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\in \\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1844\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq858\"><alternatives><tex-math id=\"M1845\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in \\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1846\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ68\"><alternatives><tex-math id=\"M1847\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} g(n)=n+\\max \\{f(m):m\\le n\\}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1848\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>=</mml:mo><mml:mi>n</mml:mi><mml:mo>+</mml:mo><mml:mo movablelimits=\"true\">max</mml:mo><mml:mo stretchy=\"false\">{</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>m</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>:</mml:mo><mml:mi>m</mml:mi><mml:mo>≤</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">}</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq859\"><alternatives><tex-math id=\"M1849\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1850\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq860\"><alternatives><tex-math id=\"M1851\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in (\\omega ^\\omega )^\\infty $$\\end{document}</tex-math><mml:math id=\"M1852\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq861\"><alternatives><tex-math id=\"M1853\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h\\in (\\omega ^\\omega )^\\infty \\cap V$$\\end{document}</tex-math><mml:math id=\"M1854\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq862\"><alternatives><tex-math id=\"M1855\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h\\le ^* g$$\\end{document}</tex-math><mml:math id=\"M1856\"><mml:mrow><mml:mi>h</mml:mi><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:mi>g</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq863\"><alternatives><tex-math id=\"M1857\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h\\in (\\omega ^\\omega )^\\infty \\cap V$$\\end{document}</tex-math><mml:math id=\"M1858\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq864\"><alternatives><tex-math id=\"M1859\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi (h)\\in (\\omega ^\\omega )^\\infty \\cap V$$\\end{document}</tex-math><mml:math id=\"M1860\"><mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq865\"><alternatives><tex-math id=\"M1861\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h=\\Phi (\\Phi (h))$$\\end{document}</tex-math><mml:math id=\"M1862\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>h</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq866\"><alternatives><tex-math id=\"M1863\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in \\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M1864\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq867\"><alternatives><tex-math id=\"M1865\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h\\in (\\omega ^\\omega )^\\infty \\cap V$$\\end{document}</tex-math><mml:math id=\"M1866\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq868\"><alternatives><tex-math id=\"M1867\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$*$$\\end{document}</tex-math><mml:math id=\"M1868\"><mml:mrow><mml:mrow/><mml:mo>∗</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq869\"><alternatives><tex-math id=\"M1869\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi (g)\\le ^*h$$\\end{document}</tex-math><mml:math id=\"M1870\"><mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:mi>h</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq870\"><alternatives><tex-math id=\"M1871\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$h\\in (\\omega ^\\omega )^\\infty \\cap V$$\\end{document}</tex-math><mml:math id=\"M1872\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq871\"><alternatives><tex-math id=\"M1873\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Phi (g)$$\\end{document}</tex-math><mml:math id=\"M1874\"><mml:mrow><mml:mi mathvariant=\"normal\">Φ</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq872\"><alternatives><tex-math id=\"M1875\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M1876\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq873\"><alternatives><tex-math id=\"M1877\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M1878\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq874\"><alternatives><tex-math id=\"M1879\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}\\in V$$\\end{document}</tex-math><mml:math id=\"M1880\"><mml:mrow><mml:mi mathvariant=\"double-struck\">P</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq875\"><alternatives><tex-math id=\"M1881\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M1882\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq876\"><alternatives><tex-math id=\"M1883\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1884\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq877\"><alternatives><tex-math id=\"M1885\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1886\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq878\"><alternatives><tex-math id=\"M1887\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1888\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq879\"><alternatives><tex-math id=\"M1889\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1890\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq880\"><alternatives><tex-math id=\"M1891\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1892\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq881\"><alternatives><tex-math id=\"M1893\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1894\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq882\"><alternatives><tex-math id=\"M1895\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$c_A,d_A\\in \\mathbb {R}^\\omega $$\\end{document}</tex-math><mml:math id=\"M1896\"><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>d</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mi mathvariant=\"double-struck\">R</mml:mi></mml:mrow><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ69\"><alternatives><tex-math id=\"M1897\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned}{} &amp; {} c_A(n)=\\min \\Big \\{\\big |\\mu _n(A)\\big |+1/n,\\ 1\\Big \\},\\\\{} &amp; {} d_A(n)=\\min \\big \\{1/m:\\ m\\in \\omega ,\\ c_A(k)\\le 1/m\\text { for all }k\\ge n\\big \\}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1898\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow/></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mrow/><mml:msub><mml:mi>c</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>+</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>n</mml:mi><mml:mo>,</mml:mo><mml:mspace width=\"4pt\"/><mml:mn>1</mml:mn><mml:mrow><mml:mo maxsize=\"1.623em\" minsize=\"1.623em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow/><mml:mrow/></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mrow/><mml:msub><mml:mi>d</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>m</mml:mi><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>m</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mo>,</mml:mo><mml:mspace width=\"4pt\"/><mml:msub><mml:mi>c</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>k</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>m</mml:mi><mml:mspace width=\"0.333333em\"/><mml:mtext>for all</mml:mtext><mml:mspace width=\"0.333333em\"/><mml:mi>k</mml:mi><mml:mo>≥</mml:mo><mml:mi>n</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq883\"><alternatives><tex-math id=\"M1899\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1900\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq884\"><alternatives><tex-math id=\"M1901\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$c_A(n)&gt;0$$\\end{document}</tex-math><mml:math id=\"M1902\"><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ70\"><alternatives><tex-math id=\"M1903\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} 0\\le \\big |\\mu _n(A)\\big |\\le c_A(n)\\le d_A(n)\\le 1 \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1904\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mn>0</mml:mn><mml:mo>≤</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:msub><mml:mi>c</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:msub><mml:mi>d</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq885\"><alternatives><tex-math id=\"M1905\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1906\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ71\"><alternatives><tex-math id=\"M1907\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\lim _{n\\rightarrow \\infty }d_A(n)=\\lim _{n\\rightarrow \\infty }c_A(n)=0. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1908\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mi>d</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:munder><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mi>c</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq886\"><alternatives><tex-math id=\"M1909\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1910\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq887\"><alternatives><tex-math id=\"M1911\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1912\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq888\"><alternatives><tex-math id=\"M1913\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$e_A(n)=1/d_A(n)$$\\end{document}</tex-math><mml:math id=\"M1914\"><mml:mrow><mml:msub><mml:mi>e</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:msub><mml:mi>d</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq889\"><alternatives><tex-math id=\"M1915\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$e_A\\in (\\omega ^\\omega )^\\infty $$\\end{document}</tex-math><mml:math id=\"M1916\"><mml:mrow><mml:msub><mml:mi>e</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq890\"><alternatives><tex-math id=\"M1917\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M1918\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq891\"><alternatives><tex-math id=\"M1919\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in (\\omega ^\\omega )^\\infty \\cap V[G]$$\\end{document}</tex-math><mml:math id=\"M1920\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq892\"><alternatives><tex-math id=\"M1921\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\max (g,1)$$\\end{document}</tex-math><mml:math id=\"M1922\"><mml:mrow><mml:mo movablelimits=\"true\">max</mml:mo><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>g</mml:mi><mml:mo>,</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq893\"><alternatives><tex-math id=\"M1923\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g(n)&gt;0$$\\end{document}</tex-math><mml:math id=\"M1924\"><mml:mrow><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq894\"><alternatives><tex-math id=\"M1925\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1926\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq895\"><alternatives><tex-math id=\"M1927\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1928\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq896\"><alternatives><tex-math id=\"M1929\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\le ^*e_A$$\\end{document}</tex-math><mml:math id=\"M1930\"><mml:mrow><mml:mi>g</mml:mi><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:msub><mml:mi>e</mml:mi><mml:mi>A</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq897\"><alternatives><tex-math id=\"M1931\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$c\\in \\mathbb {R}^\\omega $$\\end{document}</tex-math><mml:math id=\"M1932\"><mml:mrow><mml:mi>c</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mi mathvariant=\"double-struck\">R</mml:mi></mml:mrow><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq898\"><alternatives><tex-math id=\"M1933\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$c(n)=1/g(n)$$\\end{document}</tex-math><mml:math id=\"M1934\"><mml:mrow><mml:mi>c</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq899\"><alternatives><tex-math id=\"M1935\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1936\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq900\"><alternatives><tex-math id=\"M1937\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$d_A\\le ^* c$$\\end{document}</tex-math><mml:math id=\"M1938\"><mml:mrow><mml:msub><mml:mi>d</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:msup><mml:mo>≤</mml:mo><mml:mo>∗</mml:mo></mml:msup><mml:mi>c</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq901\"><alternatives><tex-math id=\"M1939\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1940\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq902\"><alternatives><tex-math id=\"M1941\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$c(n)&gt;0$$\\end{document}</tex-math><mml:math id=\"M1942\"><mml:mrow><mml:mi>c</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq903\"><alternatives><tex-math id=\"M1943\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1944\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq904\"><alternatives><tex-math id=\"M1945\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\lim _{n\\rightarrow \\infty }c(n)=0$$\\end{document}</tex-math><mml:math id=\"M1946\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">lim</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">→</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub><mml:mi>c</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq905\"><alternatives><tex-math id=\"M1947\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1948\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq906\"><alternatives><tex-math id=\"M1949\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\nu _n$$\\end{document}</tex-math><mml:math id=\"M1950\"><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq907\"><alternatives><tex-math id=\"M1951\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1952\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ72\"><alternatives><tex-math id=\"M1953\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\nu _n(A)=\\mu _n(A)/c(n), \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1954\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>c</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq908\"><alternatives><tex-math id=\"M1955\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1956\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq909\"><alternatives><tex-math id=\"M1957\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\Vert \\mu _n\\big \\Vert =1$$\\end{document}</tex-math><mml:math id=\"M1958\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ73\"><alternatives><tex-math id=\"M1959\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\big \\Vert \\nu _n\\big \\Vert =\\big \\Vert \\mu _n\\big \\Vert /c(n)=1/c(n)=g(n), \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1960\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>c</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>c</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>g</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq910\"><alternatives><tex-math id=\"M1961\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sup _{n\\in \\omega }\\big \\Vert \\nu _n\\big \\Vert =\\infty $$\\end{document}</tex-math><mml:math id=\"M1962\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">sup</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">‖</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq911\"><alternatives><tex-math id=\"M1963\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in (\\omega ^\\omega )^\\infty $$\\end{document}</tex-math><mml:math id=\"M1964\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>∞</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq912\"><alternatives><tex-math id=\"M1965\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1966\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ74\"><alternatives><tex-math id=\"M1967\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\big |\\nu _n(A)\\big |=\\big |\\mu _n(A)\\big |/c(n)\\le d_A(n)/c(n)\\le 1 \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1968\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>c</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:msub><mml:mi>d</mml:mi><mml:mi>A</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>c</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>≤</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq913\"><alternatives><tex-math id=\"M1969\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M1970\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq914\"><alternatives><tex-math id=\"M1971\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sup _{n\\in \\omega }\\big |\\nu _n(A)\\big |&lt;\\infty $$\\end{document}</tex-math><mml:math id=\"M1972\"><mml:mrow><mml:msub><mml:mo movablelimits=\"true\">sup</mml:mo><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">|</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq915\"><alternatives><tex-math id=\"M1973\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$A\\in \\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1974\"><mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq916\"><alternatives><tex-math id=\"M1975\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\nu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M1976\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq917\"><alternatives><tex-math id=\"M1977\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M1978\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq918\"><alternatives><tex-math id=\"M1979\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M1980\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq919\"><alternatives><tex-math id=\"M1981\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {nik}$$\\end{document}</tex-math><mml:math id=\"M1982\"><mml:mi mathvariant=\"fraktur\">nik</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq920\"><alternatives><tex-math id=\"M1983\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M1984\"><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ75\"><alternatives><tex-math id=\"M1985\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\mathfrak {nik}=\\min \\big \\{|\\mathcal {A}|:\\ \\mathcal {A}\\text { is an infinite Boolean algebra with the Nikodym property}\\big \\}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1986\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi mathvariant=\"script\">A</mml:mi><mml:mspace width=\"0.333333em\"/><mml:mtext>is an infinite Boolean algebra with the Nikodym property</mml:mtext><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<disp-formula id=\"Equ76\"><alternatives><tex-math id=\"M1987\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\mathfrak {gr}=\\min \\big \\{|\\mathcal {A}|:\\ \\mathcal {A}\\text { is an infinite Boolean algebra with the Grothendieck property}\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M1988\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi mathvariant=\"fraktur\">gr</mml:mi><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi mathvariant=\"script\">A</mml:mi><mml:mspace width=\"0.333333em\"/><mml:mtext>is an infinite Boolean algebra with the Grothendieck property</mml:mtext><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq921\"><alternatives><tex-math id=\"M1989\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {nik}$$\\end{document}</tex-math><mml:math id=\"M1990\"><mml:mi mathvariant=\"fraktur\">nik</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq922\"><alternatives><tex-math id=\"M1991\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M1992\"><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq923\"><alternatives><tex-math id=\"M1993\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {nik}=\\mathfrak {gr}&lt;\\mathfrak {d}$$\\end{document}</tex-math><mml:math id=\"M1994\"><mml:mrow><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"fraktur\">gr</mml:mi><mml:mo>&lt;</mml:mo><mml:mi mathvariant=\"fraktur\">d</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq924\"><alternatives><tex-math id=\"M1995\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mu _I$$\\end{document}</tex-math><mml:math id=\"M1996\"><mml:msub><mml:mi>μ</mml:mi><mml:mi>I</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq925\"><alternatives><tex-math id=\"M1997\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$2^I$$\\end{document}</tex-math><mml:math id=\"M1998\"><mml:msup><mml:mn>2</mml:mn><mml:mi>I</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq926\"><alternatives><tex-math id=\"M1999\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(I)=Bor\\big (2^I\\big )\\big /\\big \\{A\\in Bor\\big (2^I\\big ):\\ \\mu _I(A)=0\\big \\}$$\\end{document}</tex-math><mml:math id=\"M2000\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>I</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mi>B</mml:mi><mml:mi>o</mml:mi><mml:mi>r</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>I</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">/</mml:mo></mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi>B</mml:mi><mml:mi>o</mml:mi><mml:mi>r</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">(</mml:mo></mml:mrow><mml:msup><mml:mn>2</mml:mn><mml:mi>I</mml:mi></mml:msup><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">)</mml:mo></mml:mrow><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:msub><mml:mi>μ</mml:mi><mml:mi>I</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mn>0</mml:mn><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq927\"><alternatives><tex-math id=\"M2001\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(I)$$\\end{document}</tex-math><mml:math id=\"M2002\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>I</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq928\"><alternatives><tex-math id=\"M2003\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega ^\\omega $$\\end{document}</tex-math><mml:math id=\"M2004\"><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq929\"><alternatives><tex-math id=\"M2005\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\kappa $$\\end{document}</tex-math><mml:math id=\"M2006\"><mml:mi>κ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq930\"><alternatives><tex-math id=\"M2007\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M2008\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq931\"><alternatives><tex-math id=\"M2009\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$&lt;\\kappa $$\\end{document}</tex-math><mml:math id=\"M2010\"><mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>κ</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq932\"><alternatives><tex-math id=\"M2011\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\le \\mathfrak {d}$$\\end{document}</tex-math><mml:math id=\"M2012\"><mml:mrow><mml:mo>≤</mml:mo><mml:mi mathvariant=\"fraktur\">d</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq933\"><alternatives><tex-math id=\"M2013\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M2014\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq934\"><alternatives><tex-math id=\"M2015\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$&lt;\\kappa $$\\end{document}</tex-math><mml:math id=\"M2016\"><mml:mrow><mml:mo>&lt;</mml:mo><mml:mi>κ</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq935\"><alternatives><tex-math id=\"M2017\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$F=\\big \\{x_n:\\ n\\in \\omega \\big \\}$$\\end{document}</tex-math><mml:math id=\"M2018\"><mml:mrow><mml:mi>F</mml:mi><mml:mo>=</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq936\"><alternatives><tex-math id=\"M2019\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$x_n\\ne x_m$$\\end{document}</tex-math><mml:math id=\"M2020\"><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>≠</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>m</mml:mi></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq937\"><alternatives><tex-math id=\"M2021\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\ne m\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M2022\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>≠</mml:mo><mml:mi>m</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq938\"><alternatives><tex-math id=\"M2023\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M2024\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq939\"><alternatives><tex-math id=\"M2025\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$I\\subset \\kappa $$\\end{document}</tex-math><mml:math id=\"M2026\"><mml:mrow><mml:mi>I</mml:mi><mml:mo>⊂</mml:mo><mml:mi>κ</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq940\"><alternatives><tex-math id=\"M2027\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$|I|=|\\mathcal {A}|&lt;\\kappa $$\\end{document}</tex-math><mml:math id=\"M2028\"><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>I</mml:mi><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>=</mml:mo><mml:mo stretchy=\"false\">|</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">|</mml:mo><mml:mo>&lt;</mml:mo><mml:mi>κ</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ77\"><alternatives><tex-math id=\"M2029\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\big \\{[A]_\\mathcal {A}\\cap F:\\ A\\in \\mathcal {A}\\big \\}\\in V[G\\restriction I]. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M2030\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi></mml:msub><mml:mo>∩</mml:mo><mml:mi>F</mml:mi><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>A</mml:mi><mml:mo>∈</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>∈</mml:mo><mml:mi>V</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo>↾</mml:mo><mml:mi>I</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq941\"><alternatives><tex-math id=\"M2031\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$r\\in 2^\\omega $$\\end{document}</tex-math><mml:math id=\"M2032\"><mml:mrow><mml:mi>r</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:mi>ω</mml:mi></mml:msup></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq942\"><alternatives><tex-math id=\"M2033\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$V[G\\restriction I]$$\\end{document}</tex-math><mml:math id=\"M2034\"><mml:mrow><mml:mi>V</mml:mi><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo>↾</mml:mo><mml:mi>I</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq943\"><alternatives><tex-math id=\"M2035\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\langle \\mu _n:\\ n\\in \\omega \\big \\rangle $$\\end{document}</tex-math><mml:math id=\"M2036\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〈</mml:mo></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">〉</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq944\"><alternatives><tex-math id=\"M2037\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M2038\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq945\"><alternatives><tex-math id=\"M2039\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$n\\in \\omega $$\\end{document}</tex-math><mml:math id=\"M2040\"><mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ78\"><alternatives><tex-math id=\"M2041\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\nu _n=\\alpha _n\\cdot \\sum _{i\\in I_n}(-1)^{r(i)+1}\\delta _{x_i}, \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M2042\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>∈</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:mrow></mml:munder><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mo>-</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:msub><mml:mi>δ</mml:mi><mml:msub><mml:mi>x</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:msub><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq946\"><alternatives><tex-math id=\"M2043\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\alpha _n$$\\end{document}</tex-math><mml:math id=\"M2044\"><mml:msub><mml:mi>α</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq947\"><alternatives><tex-math id=\"M2045\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$I_n$$\\end{document}</tex-math><mml:math id=\"M2046\"><mml:msub><mml:mi>I</mml:mi><mml:mi>n</mml:mi></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq948\"><alternatives><tex-math id=\"M2047\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\square $$\\end{document}</tex-math><mml:math id=\"M2048\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq949\"><alternatives><tex-math id=\"M2049\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\omega )$$\\end{document}</tex-math><mml:math id=\"M2050\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ω</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq950\"><alternatives><tex-math id=\"M2051\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\kappa $$\\end{document}</tex-math><mml:math id=\"M2052\"><mml:mi>κ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq951\"><alternatives><tex-math id=\"M2053\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\kappa $$\\end{document}</tex-math><mml:math id=\"M2054\"><mml:mi>κ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq952\"><alternatives><tex-math id=\"M2055\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {d}&lt;\\mathfrak {nik}=\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M2056\"><mml:mrow><mml:mi mathvariant=\"fraktur\">d</mml:mi><mml:mo>&lt;</mml:mo><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq953\"><alternatives><tex-math id=\"M2057\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Box $$\\end{document}</tex-math><mml:math id=\"M2058\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq954\"><alternatives><tex-math id=\"M2059\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {d}&gt;\\mathfrak {nik}=\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M2060\"><mml:mrow><mml:mi mathvariant=\"fraktur\">d</mml:mi><mml:mo>&gt;</mml:mo><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq955\"><alternatives><tex-math id=\"M2061\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {x}\\in \\{\\mathfrak {nik},\\mathfrak {gr}\\}$$\\end{document}</tex-math><mml:math id=\"M2062\"><mml:mrow><mml:mi mathvariant=\"fraktur\">x</mml:mi><mml:mo>∈</mml:mo><mml:mo stretchy=\"false\">{</mml:mo><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>,</mml:mo><mml:mi mathvariant=\"fraktur\">gr</mml:mi><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq956\"><alternatives><tex-math id=\"M2063\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {x}\\le \\mathfrak {d}$$\\end{document}</tex-math><mml:math id=\"M2064\"><mml:mrow><mml:mi mathvariant=\"fraktur\">x</mml:mi><mml:mo>≤</mml:mo><mml:mi mathvariant=\"fraktur\">d</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq957\"><alternatives><tex-math id=\"M2065\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {x}\\ge \\mathfrak {d}$$\\end{document}</tex-math><mml:math id=\"M2066\"><mml:mrow><mml:mi mathvariant=\"fraktur\">x</mml:mi><mml:mo>≥</mml:mo><mml:mi mathvariant=\"fraktur\">d</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq958\"><alternatives><tex-math id=\"M2067\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Box $$\\end{document}</tex-math><mml:math id=\"M2068\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq959\"><alternatives><tex-math id=\"M2069\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {nik}$$\\end{document}</tex-math><mml:math id=\"M2070\"><mml:mi mathvariant=\"fraktur\">nik</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq960\"><alternatives><tex-math id=\"M2071\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M2072\"><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq961\"><alternatives><tex-math id=\"M2073\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {z}$$\\end{document}</tex-math><mml:math id=\"M2074\"><mml:mi mathvariant=\"fraktur\">z</mml:mi></mml:math></alternatives></inline-formula>", "<disp-formula id=\"Equ79\"><alternatives><tex-math id=\"M2075\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\begin{aligned} \\mathfrak {z}=\\min \\big \\{w(K):\\ K\\text { is an infinite }&amp;\\text {compact space}\\\\ {}&amp;\\text {with no non-trivial convergent sequences}\\big \\}. \\end{aligned}$$\\end{document}</tex-math><mml:math id=\"M2076\" display=\"block\"><mml:mrow><mml:mtable><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi mathvariant=\"fraktur\">z</mml:mi><mml:mo>=</mml:mo><mml:mo movablelimits=\"true\">min</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>w</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>K</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>K</mml:mi><mml:mspace width=\"0.333333em\"/><mml:mtext>is an infinite</mml:mtext><mml:mspace width=\"0.333333em\"/></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mtext>compact space</mml:mtext></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow/><mml:mrow/></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mtext>with no non-trivial convergent sequences</mml:mtext><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow><mml:mo>.</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math></alternatives></disp-formula>", "<inline-formula id=\"IEq962\"><alternatives><tex-math id=\"M2077\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {z}$$\\end{document}</tex-math><mml:math id=\"M2078\"><mml:mi mathvariant=\"fraktur\">z</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq963\"><alternatives><tex-math id=\"M2079\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {z}\\le \\mathfrak {nik}$$\\end{document}</tex-math><mml:math id=\"M2080\"><mml:mrow><mml:mi mathvariant=\"fraktur\">z</mml:mi><mml:mo>≤</mml:mo><mml:mi mathvariant=\"fraktur\">nik</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq964\"><alternatives><tex-math id=\"M2081\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {z}\\le \\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M2082\"><mml:mrow><mml:mi mathvariant=\"fraktur\">z</mml:mi><mml:mo>≤</mml:mo><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq965\"><alternatives><tex-math id=\"M2083\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M2084\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq966\"><alternatives><tex-math id=\"M2085\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M2086\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq967\"><alternatives><tex-math id=\"M2087\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$St(\\mathcal {A})$$\\end{document}</tex-math><mml:math id=\"M2088\"><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq968\"><alternatives><tex-math id=\"M2089\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {z}=\\omega _1&lt;\\mathfrak {c}$$\\end{document}</tex-math><mml:math id=\"M2090\"><mml:mrow><mml:mi mathvariant=\"fraktur\">z</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>&lt;</mml:mo><mml:mi mathvariant=\"fraktur\">c</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq969\"><alternatives><tex-math id=\"M2091\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega _1=\\mathfrak {z}&lt;\\mathfrak {nik}=\\mathfrak {gr}=\\mathfrak {c}$$\\end{document}</tex-math><mml:math id=\"M2092\"><mml:mrow><mml:msub><mml:mi>ω</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mi mathvariant=\"fraktur\">z</mml:mi><mml:mo>&lt;</mml:mo><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"fraktur\">gr</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"fraktur\">c</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq970\"><alternatives><tex-math id=\"M2093\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Box $$\\end{document}</tex-math><mml:math id=\"M2094\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq971\"><alternatives><tex-math id=\"M2095\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega _1$$\\end{document}</tex-math><mml:math id=\"M2096\"><mml:msub><mml:mi>ω</mml:mi><mml:mn>1</mml:mn></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq972\"><alternatives><tex-math id=\"M2097\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {z}=\\omega _1$$\\end{document}</tex-math><mml:math id=\"M2098\"><mml:mrow><mml:mi mathvariant=\"fraktur\">z</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mn>1</mml:mn></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq973\"><alternatives><tex-math id=\"M2099\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {b}$$\\end{document}</tex-math><mml:math id=\"M2100\"><mml:mi mathvariant=\"fraktur\">b</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq974\"><alternatives><tex-math id=\"M2101\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega _2$$\\end{document}</tex-math><mml:math id=\"M2102\"><mml:msub><mml:mi>ω</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq975\"><alternatives><tex-math id=\"M2103\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {b}\\le \\mathfrak {nik}$$\\end{document}</tex-math><mml:math id=\"M2104\"><mml:mrow><mml:mi mathvariant=\"fraktur\">b</mml:mi><mml:mo>≤</mml:mo><mml:mi mathvariant=\"fraktur\">nik</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq976\"><alternatives><tex-math id=\"M2105\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega _1=\\mathfrak {z}&lt;\\mathfrak {nik}=\\omega _2$$\\end{document}</tex-math><mml:math id=\"M2106\"><mml:mrow><mml:msub><mml:mi>ω</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mi mathvariant=\"fraktur\">z</mml:mi><mml:mo>&lt;</mml:mo><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mi>ω</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq977\"><alternatives><tex-math id=\"M2107\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\Box $$\\end{document}</tex-math><mml:math id=\"M2108\"><mml:mo>□</mml:mo></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq978\"><alternatives><tex-math id=\"M2109\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M2110\"><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq979\"><alternatives><tex-math id=\"M2111\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M2112\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq980\"><alternatives><tex-math id=\"M2113\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}\\in V$$\\end{document}</tex-math><mml:math id=\"M2114\"><mml:mrow><mml:mi mathvariant=\"script\">A</mml:mi><mml:mo>∈</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq981\"><alternatives><tex-math id=\"M2115\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M2116\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq982\"><alternatives><tex-math id=\"M2117\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathcal {A}$$\\end{document}</tex-math><mml:math id=\"M2118\"><mml:mi mathvariant=\"script\">A</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq983\"><alternatives><tex-math id=\"M2119\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M2120\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq984\"><alternatives><tex-math id=\"M2121\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M2122\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq985\"><alternatives><tex-math id=\"M2123\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M2124\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq986\"><alternatives><tex-math id=\"M2125\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M2126\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq987\"><alternatives><tex-math id=\"M2127\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M2128\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq988\"><alternatives><tex-math id=\"M2129\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$f\\in \\omega ^\\omega \\cap V[G]$$\\end{document}</tex-math><mml:math id=\"M2130\"><mml:mrow><mml:mi>f</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq989\"><alternatives><tex-math id=\"M2131\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$g\\in \\omega ^\\omega \\cap V$$\\end{document}</tex-math><mml:math id=\"M2132\"><mml:mrow><mml:mi>g</mml:mi><mml:mo>∈</mml:mo><mml:msup><mml:mi>ω</mml:mi><mml:mi>ω</mml:mi></mml:msup><mml:mo>∩</mml:mo><mml:mi>V</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq990\"><alternatives><tex-math id=\"M2133\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\big \\{n\\in \\omega :\\ f(n)=g(n)\\big \\}$$\\end{document}</tex-math><mml:math id=\"M2134\"><mml:mrow><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">{</mml:mo></mml:mrow><mml:mi>n</mml:mi><mml:mo>∈</mml:mo><mml:mi>ω</mml:mi><mml:mo>:</mml:mo><mml:mspace width=\"4pt\"/><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>=</mml:mo><mml:mi>g</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mrow><mml:mo maxsize=\"1.2em\" minsize=\"1.2em\" stretchy=\"true\">}</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq991\"><alternatives><tex-math id=\"M2135\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M2136\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq992\"><alternatives><tex-math id=\"M2137\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M2138\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq993\"><alternatives><tex-math id=\"M2139\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M2140\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq994\"><alternatives><tex-math id=\"M2141\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M2142\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq995\"><alternatives><tex-math id=\"M2143\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M2144\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq996\"><alternatives><tex-math id=\"M2145\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {P}$$\\end{document}</tex-math><mml:math id=\"M2146\"><mml:mi mathvariant=\"double-struck\">P</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq997\"><alternatives><tex-math id=\"M2147\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\sigma $$\\end{document}</tex-math><mml:math id=\"M2148\"><mml:mi>σ</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq998\"><alternatives><tex-math id=\"M2149\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {nik}$$\\end{document}</tex-math><mml:math id=\"M2150\"><mml:mi mathvariant=\"fraktur\">nik</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq999\"><alternatives><tex-math id=\"M2151\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M2152\"><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq1000\"><alternatives><tex-math id=\"M2153\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {nik}$$\\end{document}</tex-math><mml:math id=\"M2154\"><mml:mi mathvariant=\"fraktur\">nik</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq1001\"><alternatives><tex-math id=\"M2155\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M2156\"><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq1002\"><alternatives><tex-math id=\"M2157\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {nik}&lt;\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M2158\"><mml:mrow><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>&lt;</mml:mo><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq1003\"><alternatives><tex-math id=\"M2159\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathfrak {nik}&gt;\\mathfrak {gr}$$\\end{document}</tex-math><mml:math id=\"M2160\"><mml:mrow><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>&gt;</mml:mo><mml:mi mathvariant=\"fraktur\">gr</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq1004\"><alternatives><tex-math id=\"M2161\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\omega _1=\\mathfrak {gr}&lt;\\mathfrak {nik}=\\mathfrak {c}$$\\end{document}</tex-math><mml:math id=\"M2162\"><mml:mrow><mml:msub><mml:mi>ω</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mi mathvariant=\"fraktur\">gr</mml:mi><mml:mo>&lt;</mml:mo><mml:mi mathvariant=\"fraktur\">nik</mml:mi><mml:mo>=</mml:mo><mml:mi mathvariant=\"fraktur\">c</mml:mi></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq453\"><alternatives><tex-math id=\"M2163\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )\\setminus \\{0\\}$$\\end{document}</tex-math><mml:math id=\"M2164\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo lspace=\"0.15em\" rspace=\"0.15em\" stretchy=\"false\">\\</mml:mo><mml:mo stretchy=\"false\">{</mml:mo><mml:mn>0</mml:mn><mml:mo stretchy=\"false\">}</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>", "<inline-formula id=\"IEq454\"><alternatives><tex-math id=\"M2165\">\\documentclass[12pt]{minimal}\n\t\t\t\t\\usepackage{amsmath}\n\t\t\t\t\\usepackage{wasysym} \n\t\t\t\t\\usepackage{amsfonts} \n\t\t\t\t\\usepackage{amssymb} \n\t\t\t\t\\usepackage{amsbsy}\n\t\t\t\t\\usepackage{mathrsfs}\n\t\t\t\t\\usepackage{upgreek}\n\t\t\t\t\\setlength{\\oddsidemargin}{-69pt}\n\t\t\t\t\\begin{document}$$\\mathbb {B}(\\kappa )$$\\end{document}</tex-math><mml:math id=\"M2166\"><mml:mrow><mml:mi mathvariant=\"double-struck\">B</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>κ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></alternatives></inline-formula>" ]
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[ "<fn-group><fn id=\"Fn1\"><label>1</label><p id=\"Par3\">For an equivalent definition of the Nikodym property in terms of bounded sequences of measures, see Lemma <xref ref-type=\"sec\" rid=\"FPar12\">4.1</xref>.</p></fn><fn id=\"Fn2\"><label>2</label><p id=\"Par78\">Or, formally, , but for simplicity we will keep writing just .</p></fn><fn><p>The authors were supported by the Austrian Science Fund FWF, Grants I 3709-N35 and I 4570-N35.</p></fn><fn><p><bold>Publisher's Note</bold></p><p>Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.</p></fn></fn-group>" ]
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{ "acronym": [], "definition": [] }
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PMC10787012
0
[ "<title>1. Background</title>", "<p>Hip fractures are painful orthopedic emergencies [##REF##26809928##1##]. A relatively uncommon type of hip fracture, acetabular fracture (AF), affects approximately three per 100,000 patients annually [##UREF##0##2##]. This fracture frequently results from high-energy injuries, including falls from height or a road traffic collision, and requires surgery to stabilize the hip joint and restore hip anatomy [##UREF##1##3##]. AF is commonly associated with protracted and severe postoperative pain; however, no consensus exists on pain management. On the other hand, uncontrolled pain can raise the risk of delirium, anxiety, and fear; thus, pain management is essential for optimal care in these patients [##UREF##2##4##].</p>", "<p>Pain control in these patients is traditionally based on systemic opioids [##UREF##2##4##, ##UREF##3##5##]. Although the use of opioids has been a significant revolution in anesthesia and postoperative pain management, evidence suggests that they can not only produce a variety of adverse effects during the perioperative period but also alter long-term outcomes and have a significant impact on patient's lives, such as the development of opioid dependence or opioid-induced hyperalgesia [##REF##34064427##6##]. Consequently, it is necessary to limit the use of opioids and substitute them with safer and more effective alternatives, such as peripheral nerve block [##REF##30688787##7##].</p>", "<p>The pain associated with acetabular fracture surgeries can be managed with regional anesthesia methods such as fascia iliaca compartment block (FICB) or the pericapsular nerve group (PENG) block. These blocks have been noted for their low risk and moderate analgesic efficacy [##UREF##4##8##, ##REF##33041019##9##]. Furthermore, the quadratus lumborum block (QLB) is a novel plane block that provides satisfactory analgesia after abdominal surgeries such as inguinal hernia repair, laparotomy, and cesarean section [##REF##30688787##7##].</p>", "<p>The QLB, initially introduced by Blanco in 2007, is an interfacial plane block situated in the posterior abdominal wall [##REF##17350524##10##]. The pivotal anatomical structures associated with this block are the quadratus lumborum muscle and the thoracolumbar fascia (TLF) [##UREF##5##11##]. QLB, as a novel truncal regional block technique, shows promise in alleviating both somatic and visceral pain following abdominal surgery [##REF##28277325##12##]. This fascial plane block targets the thoracolumbar nerves by administering local anesthetics around the quadratus lumborum muscle [##REF##30688787##7##]. Various approaches exist for the QL block, including lateral, posterior, and anterior QLB, each applied based on the injection site and with distinct mechanisms tailored to specific operations. Recent case studies have highlighted QLB's analgesic impact on the hip joint [##REF##28036319##13##], confirming its efficacy [##REF##30443064##14##]. The injectate pathway of anterior (or transmuscular) QLB may extend to the paravertebral (PVB) space, providing sensory innervation coverage to the hip nerves [##REF##30688787##7##]. In addition, this block offers the advantage of minimizing quadriceps weakness [##REF##27513972##15##].</p>", "<p>Another case study has recently shown that QLB can provide effective analgesia following total hip arthroplasty [##REF##28036319##13##]. To our knowledge, however, no study has investigated the possible analgesic effects of QLB block in acetabular fracture surgery using the Stoppa method.</p>", "<p>To this end, in this study, the effects of QLB and FICB on the amount of fentanyl consumed for painless positioning to perform spinal anesthesia in a seated position, the total amount of morphine supplied in 24 h, and the pain VAS score in patients after acetabular fracture surgery utilizing the Stoppa method were evaluated. The null hypothesis was that there were no differences in analgesic efficacy between fascia iliaca compartment block (FICB) and quadratus lumborum block (QLB) in patients with acetabular fractures undergoing surgery.</p>" ]
[ "<title>2. Methods</title>", "<title>2.1. Patients and Study Design</title>", "<p>This double-blind, randomized, noninferiority trial was registered with registration number <ext-link xlink:href=\"https://clinicaltrials.gov/ct2/show/IRCT20191114045435N1\" ext-link-type=\"uri\">IRCT20191114045435N1</ext-link> on the clinical trials registry system on February 17, 2021. This research was conducted between August 2020 and March 2021 at Imam Hossein Hospital, Tehran, Iran. Patients eligible for acetabular fracture surgery between the ages of 20 and 70 with ASA classes I and II met the inclusion criteria. This study excluded patients with a history of psychiatric illness, drug addiction, or a body mass index (BMI) of greater than 30 kg/m<sup>2</sup>. In addition, patients were excluded from the study if the plan for spinal anesthesia was changed to general anesthesia during surgery, if they bled more than 1 liter, if the surgery lasted more than 3 hours, if they experienced orthopedic complications during surgery, or if the surgical plan changed. Before the commencement of the study, all patients provided written consent to participate in the survey and to have the results made public. This research was approved by the Shahid Beheshti University of Medical Sciences Ethics Committee and adhered to the ethical principles of the Declaration of Helsinki [##REF##18797627##16##].</p>", "<p>Forty-six patients with acetabular fractures were randomly divided into groups A (patients who received FICB) and B (patients who received QLB). A blind anesthesia assistant utilized a computerized random number generator to conduct randomization. Randomization sequences were delivered to the anesthesiologist, who performed the blocks in opaque, sealed envelopes. Based on our previous research, the minimum sample size for each group was 18, with a confidence level of 0.05, a standard deviation (SD) of 55, and a statistical power of 90%. A 30% difference was assumed in average analgesia duration between the two groups [##UREF##6##17##].</p>", "<title>2.2. Preparing the Patient before Performing the Block</title>", "<p>Before blocking, patients were moved to the block room. After administering 5 ml/kg of intravenous crystalloid liquid, 1 <italic>μ</italic>g/kg of fentanyl, 0.02 mg/kg of midazolam, and 7 L/min of oxygen through a face mask, they were ready to perform the block under standard monitoring.</p>", "<title>2.3. Fascia Iliaca Compartment Block Procedure</title>", "<p>FICB was performed after topical anesthesia with 2 mL of 1% lidocaine infiltration when the skin was sterilized with chlorhexidine. Under the direction of a high-frequency linear probe (6–15 MHz/linear array/6 cm scan dept FUJIFILM SonoSite Inc., Tokyo, Japan) ultrasound device (S-nerve; FUJIFILM SonoSite Inc., Tokyo, Japan) that was horizontally aligned in the inguinal region, 0.3 mL/kg of 0.5% ropivacaine was injected by in-plane technique between the iliopsoas muscle and iliac fascia using a needle (B. Braun needle, 22 G, 80 mm, Stimuplex Ultra 360) (##FIG##0##Figure 1##).</p>", "<title>2.4. Quadratus Lumborum Block Procedure</title>", "<p>A pillow was placed under the lumbar region in the supine position for quadratus lumborum 1 (QL1) or lateral quadratus lumborum block (QLB). After sterilizing the skin, 2 mL of 1% lidocaine was subcutaneously infiltrated to provide topical anesthesia. The same device was used to perform a long-axis in-plane ultrasound at the level of the anterior axillary line between the costal margin and the iliac crest. The transversus abdominis muscle (TAM), internal oblique muscle (IOM), and external oblique muscle (EOM) were the three abdominal anterolateral muscles that required localization. The quadratus lumborum muscle (QLM), characterized by a hypoechogenic region, can be located by moving the probe posterolaterally where the disappearance of the TAM can be witnessed in the anatomical axillary posterior line. Using the same needle type, 0.3 mL/kg of 0.5% ropivacaine was injected into the lateral terminal site of the transverse abdominis muscle through hydrodissection (##FIG##1##Figure 2##).</p>", "<title>2.5. Patient Care after Block</title>", "<p>Patients were instructed to assume a seated position 20–30 minutes after block administration. If VAS was &gt;4 in this position, 1 <italic>μ</italic>g/kg of fentanyl was administered intravenously and repeated every 5 min if required. The total dose of fentanyl consumed until the appropriate time for spinal anesthesia was recorded. For postoperative analgesia, intravenous patient-controlled analgesia (IV-PCA) containing 40 mg of morphine in 40 mL of normal saline was administered. Each time the patient pushed the button, 0.5 mg of morphine was delivered (with a 15 min lockout time). If the VAS was &gt;4 or higher within the first 24 h after surgery, 2 mg of intravenous morphine was administered as rescue therapy, and the total amount of morphine was also calculated.</p>", "<p>The primary outcome was the analgesia duration (the time since the patient's first request for postoperative analgesia). Other variables included VAS scores at baseline (before the block procedure), in the recovery room (15 min after block performance), and 6, 12, and 24 h after surgery. In addition, the total dose of fentanyl for painless placement in the sitting position and the total amount of morphine administered in the first 24 h after surgery were evaluated. Moreover, blood pressure and heart rate were recorded at baseline and 15 minutes after the block procedure.</p>", "<p>The patients, the block quality assessor, the anesthesia assistant responsible for intraoperative data collection, and the statistician were blinded to the block type. We utilized the Stoppa method as one of the standard surgical procedures for acetabular fractures.</p>", "<title>2.6. Statistical Analysis</title>", "<p>The chi-square test was used to evaluate categorical data, which were then expressed as frequency (percentage). The Kolmogorov–Smirnov test was utilized to demonstrate the normality of continuous data, and the data were expressed as the mean ± SD. The Mann–Whitney <italic>U</italic> test or independent-sample <italic>t</italic>-test was employed to compare continuous data between two study groups. Repeated-measures analysis of variance (ANOVA) was performed to analyze VAS at various times and block types (within-groups factor). Multiple comparisons (VAS) were corrected using the Bonferroni method. <italic>P</italic> values below 0.05 were considered statistically significant. SPSS software (v. 16.0) was utilized for data analysis.</p>" ]
[ "<title>3. Results</title>", "<p>This project enrolled 54 patients with acetabular fractures between August 2020 and March 2021. Eight patients were excluded from this study: two did not participate, five had a history of psychiatric illness, and one was addicted to multiple drugs. The remaining 46 subjects eventually completed the study and were analyzed. The remaining 46 patients were randomly divided into two groups (group FICB, <italic>n</italic> = 22; group QLB, <italic>n</italic> = 24) and underwent surgery using the Stoppa method (##FIG##2##Figure 3##). The patient demographics are shown in ##TAB##0##Table 1##.</p>", "<p>Our results indicated that both FICB and QLB led to significant reductions in blood pressure compared to baseline 20 min after administration (<italic>P</italic> &lt; 0.001 and <italic>P</italic> = 0.019, respectively). In addition, 20 minutes after QLB, the heart rate was significantly lower than at baseline (<italic>P</italic> &lt; 0.001), whereas there was no significant difference in this variable between the QLB and FICB groups (<italic>P</italic> = 0.89). A repeated-measures ANOVA with a Greenhouse–Geisser correction showed that the mean VAS scores significantly decreased compared to baseline in both FICB (<italic>F</italic> (3.37, 77.43) = 22.49, <italic>P</italic> &lt; 0.001) and QLB groups (<italic>F</italic> (3.37, 77.43) = 22.49, <italic>P</italic> &lt; 0.001). Bonferroni adjustment revealed that VAS scores decreased significantly in both groups compared to baseline, at recovery, and 6 h, 12 h, and 24 h following surgery (Tables ##TAB##1##2## and ##TAB##2##3##). At any point during the trial, there was no significant difference between the two groups' VAS scores (##TAB##3##Table 4##). As shown in ##TAB##4##Table 5##, total morphine requirements during the first 24 hours after surgery were significantly lower in the QLB group than in the FICB group. In contrast, total fentanyl consumption during spinal positioning was significantly higher in the QLB group than in the FICB group.</p>" ]
[ "<title>4. Discussion</title>", "<p>The current study found no significant difference in VAS values between the two groups at any point during the study, and both FICB and QLB had a relatively similar postoperative analgesic profile after acetabular fracture surgery using the Stoppa method. Typically, each block offers an additional benefit. While the QLB group used significantly less morphine during the first 24 h after surgery than the FICB group, the FICB group had a lower cumulative fentanyl intake while positioned for spinal anesthesia. Nevertheless, in both methods, pain reduction occurred before surgery and during the positioning of the patient for spinal anesthesia, which is supposed to be due to the nerve blocks and fentanyl pretreatment.</p>", "<p>FICB is already reported to provide perioperative analgesia after femoral neck fracture, total hip arthroplasty, and hip and knee surgery [##REF##34064427##6##]. According to most existing studies and meta-analyses, FICB reduces pain intensity, the demand for opioids, and the rates of problems associated with their systemic use in these procedures [##REF##22842653##18##–##UREF##7##20##]. Vergari et al. concur with our conclusion that FICB is a safe and effective option for postoperative analgesia following acetabular surgery [##REF##33041019##9##]. As the lumbar plexus (LP) innervates the acetabular region, LP blocks provide analgesia in patients undergoing acetabular fracture surgery [##REF##33041019##9##, ##REF##29140962##21##]. The lumbar plexus comprises the obturator nerve (ON), lateral femoral cutaneous nerve, ilioinguinal nerve, iliohypogastric nerve, genitofemoral nerve, and femoral nerve (FN), as well as the lumbosacral trunk [##UREF##8##22##]. Theoretically, the possible mechanism of FICB block is blocking the femoral nerve, the lateral femoral cutaneous nerve, and the ON [##REF##33041019##9##].</p>", "<p>QLB is a relatively new regional block. Analgesic and opioid-sparing effects of QLB through all approaches (anterior, posterior, and lateral) have been demonstrated in several surgical procedures, including hip surgery [##REF##26402020##23##], above-knee amputation [##UREF##9##24##], abdominal hernia repair [##UREF##10##25##], breast reconstruction [##REF##26984687##26##], colostomy closure [##REF##23927552##27##], radical nephrectomy [##REF##25642956##28##], and total hip arthroplasty (THA) [##REF##27513972##15##, ##UREF##11##29##, ##REF##27871532##30##].</p>", "<p>To our knowledge, no research has documented the analgesic efficacy of lateral QLB in acetabular fractures. Our results revealed that QLB decreased pain VAS scores and the need for opioids in the first postoperative 24 h. Nassar et al. found comparable outcomes, reporting that QLB can decrease the VAS score throughout spinal block positioning and increase postoperative motor power after THA [##REF##33907462##31##]. Kukreja et al. observed that QLB could decrease pain intensity and the demand for analgesic medications 24 h following THA surgery [##UREF##12##32##]. However, using the same approach, Aoyama et al. were unable to detect sensory blockage of the lumbar nerves following transmuscular QLB [##REF##32232659##33##].</p>", "<p>As stated previously, systemic opioid administration has historically been used to treat pain after acetabular fracture procedures. This method has several disadvantages, including postoperative nausea, vomiting, oversedation, apnea, respiratory issues, and altered gastrointestinal function [##UREF##2##4##]. Consequently, utilizing analgesic techniques such as QLB that lessen the requirement for opioids can result in fewer side effects, early involvement in physical therapy, and quicker recovery and discharge [##UREF##3##5##, ##REF##30688787##7##].</p>", "<p>The precise mechanism of the analgesic effect of QLB remains unknown. Nonetheless, several potential mechanisms may be involved, including (a) medial distribution of the local anesthetic drug to the paravertebral spaces of the thoracolumbar region; (b) direct spread of local anesthetics to the lumbar plexus nerve roots and branches, such as the lateral femoral cutaneous, ilioinguinal, superior cluneal, and iliohypogastric nerves; inconsistent anesthetization of the femoral nerve, obturator nerve, and lumbar sympathetic trunk; and (c) the possibility of lumbar plexus block by spreading through the fascial layer between the psoas muscle [##REF##33907462##31##].</p>" ]
[ "<title>5. Conclusion</title>", "<p>In conclusion, our paper described the lateral QLB and FICB as effective analgesic techniques for acetabular fracture surgery utilizing the Stoppa approach, which exhibited a virtually identical analgesic profile. However, large-scale clinical studies must confirm these pilot clinical data to exclude local factors that could influence the final results.</p>" ]
[ "<p>Academic Editor: Vahid Rakhshan</p>", "<title>Background</title>", "<p> Acetabular fracture surgeries are frequently accompanied by protracted and severe perioperative pain, and there is no consensus on optimal pain relief management. </p>", "<title>Aim</title>", "<p> This study aimed at comparing the analgesic efficacy of fascia iliaca compartment block (FICB) and quadratus lumborum block (QLB) in patients with acetabular fractures undergoing surgery using the Stoppa method. </p>", "<title>Methods</title>", "<p> In this double-blind, randomized, noninferiority clinical trial, adult patients undergoing spinal anesthesia for acetabular fracture surgery, in Imam Hossein Hospital, Tehran, Iran (<ext-link xlink:href=\"https://clinicaltrials.gov/ct2/show/IRCT20191114045435N1\" ext-link-type=\"uri\">IRCT20191114045435N1</ext-link>), were randomly divided into two groups: FICB (<italic>n</italic> = 22) and QLB (<italic>n</italic> = 24). The visual analog scale (VAS) was used to assess the pain intensity at different times for all participants. In addition, the dose of fentanyl required to induce the patient to sit for spinal anesthesia and the pain intensity were evaluated. Moreover, the duration of analgesia and the total amount of morphine consumed in the first 24 h following surgery were evaluated, analyzed, and compared between the two study groups. </p>", "<title>Results</title>", "<p> FICB and QLB demonstrated effective comparative postoperative analgesic profiles following acetabular fracture surgery; however, no significant differences in VAS values were observed between the two groups during the study. FICB experienced reduced cumulative fentanyl consumption during spinal anesthetic placement, whereas QLB had a significantly lower total morphine demand in the initial postoperative 24 h period. </p>", "<title>Conclusion</title>", "<p> The lateral QLB and FICB can be introduced as effective routes for analgesia in acetabular fracture surgery using the Stoppa method. <italic>Clinical Trial Registration</italic>. The study was prospectively registered in the clinical trials registry system, on 2021-02-17, with registration number: <ext-link xlink:href=\"https://clinicaltrials.gov/ct2/show/IRCT20191114045435N1\" ext-link-type=\"uri\">IRCT20191114045435N1</ext-link>.</p>" ]
[]
[ "<title>Data Availability</title>", "<p>The CONSORT and raw datasets used during the current study were uploaded as supplemental files alongside the manuscript submission. Also, they would be available from the corresponding author upon reasonable request.</p>", "<title>Additional Points</title>", "<p>\n<italic>Strengths and Limitations</italic> The current study was the first to evaluate the potential analgesic effect of QLB in acetabular fracture surgeries using the Stoppa approach, providing a basis for future research in this field. However, this study has some limitations. First, we did not consider all the important parameters for evaluating the efficacy of enhanced recovery after surgery (ERAS), such as the time to first ambulation, length of hospitalization, and patient satisfaction. Second is the failure to evaluate the long-term side effects of the blocks, such as the development of chronic pain in the study groups. Third, the data from this study are insufficient to draw robust conclusions, and a larger sample size of randomized controlled trials is required to validate our results.</p>", "<title>Ethical Approval</title>", "<p>Based on the Declaration of Helsinki, this study was approved by the Ethics Committee of the Shahid Beheshti University of Medical Sciences (SBMU) under the ethics code IR.SBMU.MSP.REC.1399.266.</p>", "<title>Consent</title>", "<p>All participants gave their written consent to participate in the study and disseminate the results before joining the study.</p>", "<title>Disclosure</title>", "<p>A preprint has previously been published [##UREF##13##34##].</p>", "<title>Conflicts of Interest</title>", "<p>The authors declare that they have no conflicts of interest.</p>", "<title>Authors' Contributions</title>", "<p>Alireza Mirkheshti and Alireza Shakeri conceived and designed the study and wrote the manuscript. Elham Memary and Alireza Manafi-Rasi conducted patients' assessment. Sara Shayegh, Nazli Karami, and Baharak Rostamian collected the data. Dariush Abtahi analyzed the data. Morteza Hashemian and Shahram Sayadi revised the manuscript. All the authors contributed to the interpretation of the results and read and approved the final manuscript.</p>", "<title>Supplementary Materials</title>" ]
[ "<fig position=\"float\" id=\"fig1\"><label>Figure 1</label><caption><p>Fascia iliaca compartment block anatomy. FA: femoral artery; FN: femoral nerve; FI: fascia iliaca; N: needle.</p></caption></fig>", "<fig position=\"float\" id=\"fig2\"><label>Figure 2</label><caption><p>Lateral quadratus lumborum (QL) block anatomy. IO: internal oblique; EO: external oblique; N: needle; QL: quadratus lumborum; TA: transverse abdominis.</p></caption></fig>", "<fig position=\"float\" id=\"fig3\"><label>Figure 3</label><caption><p>The study's flowchart. FICB: fascia iliaca compartment block; QLB: quadratus lumborum block.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"tab1\"><label>Table 1</label><caption><p>Patients' demographics.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\"> </th><th align=\"center\" rowspan=\"1\" colspan=\"1\">FICB (<italic>N</italic> = 22)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">QLB (<italic>N</italic> = 24)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>P</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Age (years)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">42.8 ± 10.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">41.5 ± 9.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.71</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Sex (M/F)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18/4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">14/10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.087</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Weight (kg)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">72 ± 5.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">71.2 ± 7.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.72</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab2\"><label>Table 2</label><caption><p>VAS score changes at different times of the study compared to the baseline in the FICB group.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Variable</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">95% CI</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>P</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Recovery room VAS score</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.77–2.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Spinal anesthesia positioning VAS score</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.71–2.56</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">VAS score before recovery delivery</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.72-0.72</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postsurgery VAS score (6 h)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.21–1.97</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.007</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postsurgery VAS score (12 h)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.16–2.16</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.15</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postsurgery VAS score (24 h)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.32–2.58</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.005</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab3\"><label>Table 3</label><caption><p>VAS score changes at different times of the study compared to the baseline in the QLB group.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">variable</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">95% CI</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>P</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">VAS score in recovery</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.38–4.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Spinal anesthesia positioning VAS score</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.46–3.37</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">VAS score before recovery delivery</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.1–71.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.26</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postsurgery VAS score (6 h)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.94–3.22</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postsurgery VAS score (12 h)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.95–4.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postsurgery vas score (24 h)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.21–4.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.01</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab4\"><label>Table 4</label><caption><p>Comparison of VAS score between two blocks.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\"> </th><th align=\"center\" rowspan=\"1\" colspan=\"1\">FICB (<italic>N</italic> = 22)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">QLB (<italic>N</italic> = 24)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>P</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Baseline VAS score (before blocks)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.35 ± 0.93</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.75 ± 0.44</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.117</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">VAS score in recovery</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.27 ± 1.45</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.42 ± 2.18</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.80</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Spinal anesthesia positioning VAS score</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.27 ± 1.24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.25 ± 0.44</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.94</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postsurgery VAS score (6 h)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.08 ± 1.58</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.82 ± 1.43</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.56</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postsurgery VAS score (12 h)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.91 ± 1.48</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.17 ± 1.55</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.10</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postsurgery VAS score (24 h)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.45 ± 1.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3 ± 1.32</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.25</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab5\"><label>Table 5</label><caption><p>Outcomes and block characteristics.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\"> </th><th align=\"center\" rowspan=\"1\" colspan=\"1\">FICB (<italic>N</italic> = 22)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">QLB (<italic>N</italic> = 24)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>P</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fentanyl dosage for pain-free positioning in the seated position (mg)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">105 ± 35.91</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">129.17 ± 38.78</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.039</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Duration of analgesia (min)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">281.36 ± 55.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">245.42 ± 78.03</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.081</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">The total amount of morphine taken over 24 h (mg)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">16.7 ± 4.86</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">13 ± 5.24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.02</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Baseline heart rate (bpm)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">80.63 ± 9.47</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97.91 ± 16.76</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Heart rate (bpm) 20 min postblock</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">80.27 ± 14.49</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">92.18 ± 12.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.006</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Baseline BP (mmHg)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">130 ± 19.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">121.33 ± 12.03</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.069</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BP (mmHg) 20 min postblock</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">114 ± 12.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">117.75 ± 11.97</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.30</td></tr></tbody></table></table-wrap>" ]
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[ "<supplementary-material id=\"supp-1\" position=\"float\" content-type=\"local-data\"><label>Supplementary Materials</label><caption><p>The CONSORT and raw datasets of this paper can be found in the supplementary material.</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p>Information is displayed as mean ± standard deviation. FICB, fascia iliaca block; QLB, quadratus lumborum block.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>Information is displayed as mean ± standard deviation. FICB, fascia iliaca block; QLB, quadratus lumborum block; VAS, visual analog scale.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>Information is displayed as mean ± standard deviation. BP, blood pressure; FIB, fascia iliaca block; QLB, quadratus lumborum block; VAS, visual analog scale.</p></fn></table-wrap-foot>" ]
[ "<graphic xlink:href=\"PRM2024-3720344.001\" position=\"float\"/>", "<graphic xlink:href=\"PRM2024-3720344.002\" position=\"float\"/>", "<graphic xlink:href=\"PRM2024-3720344.003\" position=\"float\"/>" ]
[ "<media xlink:href=\"3720344.f1.zip\"><caption><p>Click here for additional data file.</p></caption></media>" ]
[{"label": ["2"], "person-group": ["\n"], "surname": ["Langworthy", "Sanzone"], "given-names": ["M. J.", "A. G."], "article-title": ["Multimodal pain strategies including liposomal bupivacaine for isolated acetabular fracture surgery"], "source": ["\n"], "italic": ["Journal of Orthopaedic Trauma"], "year": ["2018"], "volume": ["32"], "issue": ["5"], "fpage": ["S11"], "lpage": ["S15"], "pub-id": ["10.1097/bot.0000000000001228", "2-s2.0-85068911736"]}, {"label": ["3"], "person-group": ["\n"], "surname": ["Letournel", "Judet"], "given-names": ["E.", "R."], "source": ["\n"], "italic": ["Fractures of the Acetabulum"], "year": ["2012"], "publisher-name": ["Springer Science & Business Media"]}, {"label": ["4"], "person-group": ["\n"], "surname": ["Freeman", "Clarke"], "given-names": ["N.", "J."], "article-title": ["Perioperative pain management for hip fracture patients"], "source": ["\n"], "italic": ["Orthopaedics and Trauma"], "year": ["2016"], "volume": ["30"], "issue": ["2"], "fpage": ["145"], "lpage": ["152"], "pub-id": ["10.1016/j.mporth.2016.03.012", "2-s2.0-84964579698"]}, {"label": ["5"], "person-group": ["\n"], "surname": ["Foss", "Kristensen", "Bundgaard"], "given-names": ["N. B.", "B. B.", "M."], "article-title": ["Fascia iliaca compartment blockade for acute pain control in hip fracture patients: a randomized, placebo-controlled trial"], "source": ["\n"], "italic": ["The Journal of the American Society of Anesthesiologists"], "year": ["2007"], "volume": ["106"], "issue": ["4"], "fpage": ["773"], "lpage": ["778"], "pub-id": ["10.1097/01.anes.0000264764.56544.d2", "2-s2.0-34147139892"]}, {"label": ["8"], "person-group": ["\n"], "surname": ["Bilal", "\u00d6ks\u00fcz", "Boran", "Topak", "Do\u011far"], "given-names": ["B.", "G.", "\u00d6F.", "D.", "F."], "article-title": ["High volume pericapsular nerve group (PENG) block for acetabular fracture surgery: a new horizon for novel block"], "source": ["\n"], "italic": ["Journal of Clinical Anesthesia"], "year": ["2020"], "volume": ["62"], "pub-id": ["109702", "10.1016/j.jclinane.2020.109702"]}, {"label": ["11"], "person-group": ["\n"], "surname": ["Li", "Wei", "Huang"], "given-names": ["J.", "C.", "J."], "article-title": ["Efficacy of quadratus lumborum block for pain control in patients undergoing hip surgeries: a systematic review and meta-analysis"], "source": ["\n"], "italic": ["Frontiers of Medicine"], "year": ["2021"], "volume": ["8"], "pub-id": ["771859", "10.3389/fmed.2021.771859"]}, {"label": ["17"], "person-group": ["\n"], "surname": ["Mosaffa", "Taheri", "Manafi Rasi", "Samadpour", "Memary", "Mirkheshti"], "given-names": ["F.", "M.", "A.", "H.", "E.", "A."], "article-title": ["Comparison of pericapsular nerve group (PENG) block with fascia iliaca compartment block (FICB) for pain control in hip fractures: a double-blind prospective randomized controlled clinical trial"], "source": ["\n"], "italic": ["Orthopaedics and Traumatology: Surgery & Research"], "year": ["2022"], "volume": ["108"], "issue": ["1"], "pub-id": ["103135", "10.1016/j.otsr.2021.103135"]}, {"label": ["20"], "person-group": ["\n"], "surname": ["Pepe", "Ausman", "Madhani"], "given-names": ["J.", "C.", "N. B."], "source": ["\n"], "italic": ["Ultrasound-guided Fascia Iliaca Compartment Block"], "year": ["2018"], "publisher-loc": ["Treasure Island, FL, USA"], "publisher-name": ["StatPearls Publishing"]}, {"label": ["22"], "person-group": ["\n"], "surname": ["Kukreja", "MacBeth", "Sturdivant"], "given-names": ["P.", "L.", "A."], "article-title": ["Anterior quadratus lumborum block analgesia for total hip arthroplasty: a randomized, controlled study"], "source": ["\n"], "italic": ["Regional Anesthesia and Pain Medicine"], "year": ["2019"], "volume": ["44"], "issue": ["12"], "fpage": ["1075"], "lpage": ["2019-100804"], "pub-id": ["10.1136/rapm-2019-100804"]}, {"label": ["24"], "person-group": ["\n"], "surname": ["Ueshima", "Otake"], "given-names": ["H.", "H."], "article-title": ["Lower limb amputations performed with anterior quadratus lumborum block and sciatic nerve block"], "source": ["\n"], "italic": ["Journal of Clinical Anesthesia"], "year": ["2017"], "volume": ["100"], "issue": ["37"], "fpage": ["p. 145"]}, {"label": ["25"], "person-group": ["\n"], "surname": ["Carvalho", "Segura", "Loureiro", "Assun\u00e7\u00e3o"], "given-names": ["R.", "E.", "M. D. C.", "J. P."], "article-title": ["Quadratus lumborum block in chronic pain after abdominal hernia repair: case report"], "source": ["\n"], "italic": ["Brazilian Journal of Anesthesiology"], "year": ["2017"], "volume": ["67"], "issue": ["1"], "fpage": ["107"], "lpage": ["109"], "pub-id": ["10.1016/j.bjane.2014.08.010"]}, {"label": ["29"], "person-group": ["\n"], "surname": ["Ueshima", "Yoshiyama", "Otake"], "given-names": ["H.", "S.", "H."], "article-title": ["RETRACTED: The ultrasound-guided continuous transmuscular quadratus lumborum block is an effective analgesia for total hip arthroplasty"], "source": ["\n"], "italic": ["Journal of Clinical Anesthesia"], "year": ["2016"], "volume": ["31"], "fpage": ["p. 35"], "pub-id": ["10.1016/j.jclinane.2015.12.033", "2-s2.0-84962328548"]}, {"label": ["32"], "person-group": ["\n"], "surname": ["Kukreja", "MacBeth", "Potter"], "given-names": ["P.", "L.", "W."], "article-title": ["Posterior quadratus lumborum block for primary total hip arthroplasty analgesia: a comparative study"], "source": ["\n"], "italic": ["Einstein (Sao Paulo)"], "year": ["2019"], "volume": ["17"], "issue": ["4"], "pub-id": ["10.31744/einstein_journal/2019ao4905", "2-s2.0-85072041305"]}, {"label": ["34"], "person-group": ["\n"], "surname": ["Alireza Mirkheshti", "Abtahi", "Shayegh"], "given-names": ["M. H.", "D.", "S."], "article-title": ["Quadratus lumborum block versus fascia iliaca compartment block for acetabular fracture surgery by Stoppa method: a double-blind prospective randomized controlled clinical trial"], "year": ["2022"], "comment": ["\n"], "ext-link": ["https://www.researchsquare.com/article/rs-2241358/v2"]}]
{ "acronym": [], "definition": [] }
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2024-01-14 23:41:54
Pain Res Manag. 2024 Jan 5; 2024:3720344
oa_package/5b/ab/PMC10787012.tar.gz
PMC10787013
0
[ "<title>1. Introduction</title>", "<p>Moringa, a family of <italic>Moringaceae</italic>, grows throughout the tropics. It is a versatile tree of significant economic importance as it has vital nutritional and medicinal uses. The genus <italic>Moringa</italic> consists of 13 species, of which <italic>Moringa oleifera (M. oleifera)</italic> and <italic>Moringa stenopetala (M. stenopetala)</italic> are the most widespread species and share numerous common characteristics [##UREF##0##1##, ##UREF##1##2##]. <italic>M. oleifera</italic> is native to the sub-Himalayan districts of northern India and is commonly known as the “horseradish” or “drumstick” tree. <italic>M. oleifera</italic> varies from <italic>M. stenopetala</italic> in growth pattern, foliage, blossoms, and seedpod characteristics [##UREF##0##1##]. <italic>M. stenopetala</italic> is native to southern Ethiopia, where it is known as Haleko or Shiferaw. Its primary purpose of cultivation is for its edible leaves, which are consumed as vegetables [##UREF##2##3##]. The plant has high drought resistance, and its leaves have an extremely favorable nutrient composition. In addition, the leaves exhibit antioxidant properties and possess therapeutic effects against various human diseases due to the presence of the biomolecule rutin, which has antioxidant and antidiabetic properties [##REF##33145489##4##, ##UREF##3##5##]. The leaves of <italic>M. stenopetala</italic> are an important food source for millions of people in southern Ethiopia, especially during the dry season. It is a rapid-growing plant that is effortlessly developed in marginal areas and less fertile soils in dry environments and could therefore serve as a reliable source of food and income for numerous societies [##UREF##3##5##, ##REF##16167740##6##].</p>", "<p>Plants play a significant role as providers of dietary macro and trace elements that are vital for human health. The elements have a vital importance in numerous bodily functions. The primary means of obtaining essential and nonessential elements for the body is through the intake of food [##UREF##4##7##]. In the past, people relied on consuming natural foods such as plants, seeds, nuts, and leaves to fulfill their nutritional requirements, making them the primary source of essential macro and trace elements in the diet [##UREF##5##8##]. Many developing nations are marked by rapid population growth combined with declining agricultural productivity. This led to a quest for an alternative source of high-quality yet affordable food, drawing inspiration from indigenous knowledge [##UREF##6##9##]. Consequently, the utilization of plant leaves, such as those of <italic>M. stenopetala</italic>, is becoming more widespread as they have a significant impact on addressing the difficulties of diminishing food supplies while also offering nutritious dietary options. The growing fascination with functional foods has additionally led to a rise in the intake of organic food sources such as <italic>M. stenopetala</italic>.</p>", "<p>Essential elements are crucial and required by living organisms to activate enzymes and generate hormones. Some of these elements are part of organic molecules involved in the growth and maintenance of life processes, while others play significant roles in the bone structure [##UREF##5##8##, ##REF##32789646##10##]. Some trace elements are important for biological processes, and their deficiency or surplus can disrupt the normal functions of the body [##REF##15325688##11##]. For instance, a trace amount of iron is important for transporting oxygen in the body and promoting strength [##UREF##7##12##]. Manganese is used in fat and carbohydrate metabolism as well as in blood sugar regulation and helps the body build connective tissues and bones and aids in blood clotting [##REF##37475585##13##]. Zinc acts as a cofactor for certain enzymes, also involved in metabolism and cell growth, and plays an essential role in various other biological processes. It is also crucial for maintaining a robust immune system and protection against infection [##UREF##8##14##]. However, certain elements can be hazardous if the highest daily intake exceeds over an extended period. The Joint Panel of Experts on Food Additives of the FAO, World Health Organization, and European Union (Regulation no. 1881/2006) have established maximum levels for Pb (0.3 mg kg<sup>−1</sup>) and Cd (0.2 mg kg<sup>−1</sup>) in plant leaves and fresh herbs [##UREF##5##8##]. WHO has established the highest permissible levels for toxic elements in herbal plants as 5, 10, 0.3, 2.0, and 0.2 mg kg<sup>−1</sup> for As, Pb, Cd, Cr, and Hg, respectively [##REF##27599009##15##]. The European Food Safety Authority considers the prevention and management of Pb pollution as crucial due to its detrimental effects on the human body and excessive concentration in the environment [##UREF##9##16##].</p>", "<p>The levels of toxic metals in the leaves of edible plants often exceed safe limits, especially when grown in contaminated areas [##REF##28976884##17##]. The quality of edible leaves and seeds is mainly influenced by the environment in which they grow [##REF##30043286##18##]. Therefore, many literature reports focused on the determination of heavy metal content in the leaves and roots of <italic>M. stenopetala</italic> [##UREF##10##19##–##UREF##12##21##]. However, in some studies, the concentrations of toxic metals in the leaves and seeds of <italic>M. stenopetala</italic> have been reported [##UREF##13##22##, ##UREF##14##23##]. Soil is not only the growing medium but also one of the sources of metal pollution in edible plants [##REF##28976884##17##]. To the best of our knowledge, there is no literature report on the mineral content in the leaves, seeds, and the corresponding soil of the three main <italic>M. stenopetala</italic> cultivating areas in the Gamo Zone of southern Ethiopia (Chano Mile and Nechisar Kebeles) and Konso Special Woreda. Therefore, it is important to assess the levels of essential and nonessential metals in the leaves, seeds, and growing soil of <italic>M. stenopetala</italic> to ensure the quality and safety of the plant and to assess possible contamination.</p>", "<p>The development of suitable analytical methods to determine essential and nonessential elements in various edible plants and vegetables is of great interest. Numerous analytical techniques, including flame atomic absorption spectrometry (FAAS), X-ray fluorescence spectrometry (XRF), graphite furnace atomic absorption spectrometry (GFAAS), inductively coupled plasma mass spectrometry (ICP-MS), and atomic fluorescence spectrometry (AFS), have been used to quantify elements in different matrices [##REF##34328385##24##]. In the analysis of plant seeds, roots, leaves, and vegetables, spectrometric techniques such as atomic absorption spectrometry (AAS), microwave plasma atomic emission spectroscopy (MP-AES), inductively coupled plasma optical emission spectrometry (ICP-OES), and inductively coupled plasma mass spectrometry (ICP-MS) are commonly used [##UREF##15##25##–##REF##33188459##27##]. Compared to AAS and AES, MP-AES is more sensitive for the rapid and simultaneous determination of essential and nonessential elements at trace or ultratrace levels in complex samples [##UREF##17##28##].</p>", "<p>The innovative aspect of this study lies in its pioneering attempt to provide fundamental insights into the concentration of essential and nonessential elements in the leaves, seeds, and supportive soil of <italic>M. Stenopetala</italic> from major production regions in the Gamo Zone, southern Ethiopia, specifically Chano Mile and Nechisar Kebeles, as well as Konso Special Woreda. The method employed in this study is characterized by the development of an acid digestion-based multielement analysis using MP-AES. This cutting-edge approach allows the simultaneous determination of various elements, including K, Na, Ca, Mg, Fe, Co, Ni, Mn, Zn, Cr, Cu, Cd, and Pb. The advantages of this method include its ability to provide a comprehensive analysis of multiple elements in a single run, offering efficiency and time-saving. Additionally, the utilization of MP-AES ensures precision and accuracy in the determination of element concentrations. However, it is essential to acknowledge potential limitations and disadvantages of the method, such as the sensitivity to sample matrix effects or the need for careful calibration. The current study not only contributes essential data on mineral content in different parts of <italic>M. Stenopetala</italic> but also aims to address the gap in analytical techniques for such complex determinations. By comparing the levels of identified metals in the plant with existing literature values, this research provides a robust foundation for future studies in the field, emphasizing the significance of its innovative methodology and potential implications for understanding the ecological and nutritional aspects of <italic>M. Stenopetala</italic>.</p>" ]
[ "<title>2. Materials and Methods</title>", "<title>2.1. Sampling Area Description</title>", "<p>The research was carried out in the Gamo Zone (Chano Mile and Nechisar Kebeles) and Konso Special Woreda in the SNNPR during the dry season in 2019. Gamo Zone is situated in the south-central part of Ethiopia, with coordinates of 6°14′60.00″ N latitude and 37°00′0.00″ E longitude. It is located 502 km to the south of Addis Ababa. The elevation in this area ranges from 600 to 4207 m above sea level, covering an area of 6735 km<sup>2</sup>. The temperature varies between 10 and 25°C, while the annual rainfall ranges from 200 to 2000 mm. The Gamo Zone is known for its two lakes, Abaya and Chamo [##UREF##18##29##]. Konso Special Woreda, on the other hand, is located at 5° 20′ 25.6164″ N latitude and 37° 26′ 19.6404″ E longitude, approximately 607.2 km to the south of Addis Ababa. The elevation in this region ranges from 501 to 2000 m above sea level, covering a land area of 2,016.24 km<sup>2</sup>. The Woreda is characterized by 70% low altitude and 30% tropical midaltitude. The average annual temperature in Konso Special Woreda is recorded between 17.6 and 27.5°C, with an average annual rainfall ranging from 601 to 1200 mm [##UREF##19##30##].</p>", "<title>2.2. Chemicals and Reagents</title>", "<p>HClO<sub>4</sub> (70%), HNO<sub>3</sub> (69–72%) (BDH Laboratory Supplies, Anala®, Poole, England), and H<sub>2</sub>O<sub>2</sub> (30%) (Scharlau Chemie, European Union, Spain) were used for the digestion of the samples. Lanthanum (III) nitrate hexahydrate (BDH Chemicals Ltd., Poole, England) was used to minimize the interference of Ca<sup>2+</sup> and Mg<sup>2+</sup> ions. Stock solutions of 1000 mg L<sup>−1</sup> of the metals K, Na, Ca, Mg, Fe, Co, Ni, Mn, Zn, Cr, Cu, Cd, and Pb (BDH Chemicals Ltd. Spectrosol, Poole, England) were used for preparing calibration standards and spiking experiments. Distilled water was used to dilute the samples, intermediate, and working metal standard solutions before analysis and to rinse the glassware.</p>", "<title>2.3. Instruments and Apparatus</title>", "<p>A digital analytical balance (Scitech) with an accuracy of 0.0001 g was used to weigh the samples. An electronic blender (Moulinex, France) was used to grind and homogenize the samples. 100 mL round-bottom flasks fitted with a reflux condenser in a Kjeldahl apparatus (UK) were used to digest the samples. A microwave plasma atomic emission spectrometer (Agilent Technologies, Model 4200, USA) was used for the analysis of K, Na, Ca, Mg, Fe, Co, Ni, Mn, Zn, Cr, Cu, Cd, and Pb.</p>", "<title>2.4. Sample Collection</title>", "<p>During the main harvest season (dry season commonly from October to December), leaf, seed, and soil samples of <italic>M. stenopetala</italic> were collected from the three main moringa growing areas of Gamo Zone (Chano Mile and Nechisar Kebeles) and Konso Special Woreda. Ten sites from each area were selected for leaf and seed sampling. Again, eight farmers were randomly selected from a single area. At least five <italic>M. stenopetala</italic> plants were then randomly selected from each farm for leaf and seed sampling. Soil samples were collected systematically at all locations under each sampled <italic>M. stenopetala</italic> plant at a radius of 100 cm and a depth of 50 cm. As the investigation focused on the possible uptake of metals by the plant, soil samples were collected from the entire area penetrated by the root system. Finally, the samples were thoroughly homogenized to form representative leaf, seed, and soil samples of <italic>M. stenopetala</italic> for each plot.</p>", "<title>2.5. Sample Preparation</title>", "<title>2.5.1. Preparation of Leaf Samples</title>", "<p>Moringa leaves, comprising a blend of both young and mature leaves (exceeding 100 in total), were thoroughly cleaned to eliminate external impurities from their surfaces. The leaves were washed with tap water, distilled water, and deionized water for 30, 15, and 10 min, respectively, and then dried in a laboratory under direct sunlight for weeks. The dried leaves were finally pulverized with an electric motor and milled into a fine powder, of which 25 g was used for subsequent analysis.</p>", "<title>2.5.2. Preparation of Seed Samples</title>", "<p>Over 200 seed samples, including both young and mature specimens, were subjected to a thorough cleaning process. This included careful removal of debris, soil, twigs, and foliage as well as the exclusion of immature, overripe, and damaged pods to ensure the selection of the highest quality seeds. The husks were dried in a clean area and exposed to direct sunlight. The seeds were removed from the shell after a drying process that lasted for more than four weeks. The dried seeds were eventually ground into a fine powder, and 25 g of this was taken for investigation.</p>", "<title>2.5.3. Preparation of Soil Samples</title>", "<p>Visible plant debris was removed from the collected soil samples; the sample was then air-dried and homogenized. The dried soil samples were ground and sieved through a 2 mm sieve. The total amount of soil samples collected from each district was over 500 g, of which 25 g was used for analysis.</p>", "<title>2.6. Optimization of Digestion Procedure</title>", "<p>The primary prerequisite for sample preparation for analysis is the establishment of optimum conditions for digestion. The optimum conditions are those that require the least amount of reagent volume, the shortest reflux time, clear solution, and simplicity [##UREF##4##7##, ##REF##25789209##31##]. As a result, we carefully selected optimal digestion conditions for the leaf and seed samples, which utilize minimal reagent volume and a shorter digestion time, resulting in a clear and colorless solution at a lower temperature. Thus, several experiments were conducted with 0.5 g of leaf and seed powder samples using acid mixtures (HNO<sub>3</sub>, HClO<sub>4</sub>, and H<sub>2</sub>O<sub>2</sub>) to produce a clear and colorless solution. Similarly, other experimental parameters, such as digestion time and digestion temperature, were carefully examined to obtain the optimal digestion values (Tables ##TAB##0##1##–##TAB##2##3##). As shown in the tables, the mixture of acids 2.5 : 0.75 : 0.5 (2.5 mL HNO<sub>3</sub>, 0.75 mL HClO<sub>4</sub>, and 0.5 mL H<sub>2</sub>O<sub>2</sub>), a digestion time of 2:30 hrs, and a digestion temperature of 240°C were selected to be the optimal experimental conditions for the digestion of 0.5 g of leaf and seed samples.</p>", "<title>2.7. Digestion of Leaf, Seed, and Soil Samples</title>", "<p>Under the optimized conditions, 0.5 g of moringa leaf powder was transferred to 250 mL round-bottom flasks. 10 mL of the acid mixture (2.5 : 0.7 : 0.5 (v/v)) was added, and the mixture was digested in a Kjeldahl apparatus for two and a half hours at a temperature of 240°C. Thereafter, the digested mixture was allowed to cool to room temperature and then filtered through a filter paper (Whatman. 42). The digestion was performed in triplicate, and parallel to the digestion of the samples, a reagent blank was also digested, keeping all digestion parameters the same. Six blanks were digested for leaf samples. When determining Ca<sup>2+</sup> and Mg<sup>2+</sup>, to avoid chemical interference, a solution of 0.1% LaCl<sub>3</sub>·7H<sub>2</sub>O in deionized water was used. The same procedure was followed for the digestion of seed samples under the optimized conditions. The method EPA 3050B (EPA 3050B, 1996) with a very slight modification was used for the digestion of soil samples (briefly discussed in Supplementary Material).</p>", "<title>2.8. Preparation of Standard Solutions</title>", "<p>The working standard solutions for each metal were prepared from a 1000 mg L<sup>−1</sup> standard stock solution of the elements K, Na, Ca, Mg, Fe, Co, Ni, Mn, Zn, Cr, Cu, Cd, and Pb in 5% HNO<sub>3</sub>. Intermediate standard solutions of 10 mg L<sup>−1</sup> were prepared in 100 mL volumetric flasks from the stock standard solution. Since the linear ranges of the calibration curves differed, different concentrations of calibration standards were used for different metals. Four working standards were freshly prepared for each metal from the intermediate standards by dilution with deionized water. Three replicate determinations were made for each element, and the same analytical procedures were used for blank solutions.</p>", "<title>2.9. Determination of Metals in Leaf, Seed, and Soil Samples</title>", "<p>Following the calibration of the instrument, the levels of specific metals in the samples were measured using MP-AES. Three separate analyses were conducted for each sample. K, Na, Ca, Mg, Fe, Co, Ni, Mn, Zn, Cr, Cu, Cd, and Pb were measured in the emission/concentration mode after accurately calibrating the instrument using a calibration blank and four working calibration standard solutions. The measurement of metals in the digested blank solution was also carried out simultaneously with the samples, maintaining consistent parameters and employing the same procedure.</p>", "<title>2.10. LOD and LOQ</title>", "<p>The limit of detection (LOD) is the smallest value at which an analyte can be measured with some certainty. The limit of quantification (LOQ) is the lowest concentration of an analyte that can be quantitatively measured with a specified level of accuracy and precision [##UREF##20##32##, ##UREF##21##33##]. The LOD and LOQ values of the mineral nutrients were determined using seven duplicate blanks. The LOD was obtained by multiplying the pooled standard deviation of the blank (<italic>δ</italic><sub>blank</sub>) by three (LOD = 3<italic>δ</italic><sub>blank</sub>, where <italic>δ</italic> = standard deviation of the blank). The LOQ was calculated as ten times the standard deviation of the blank solution (LOQ = 10<italic>δ</italic><sub>blank</sub>). The LOD of the elements studied (##TAB##3##Table 4##) was lower than the analyte concentrations obtained.</p>", "<title>2.11. Method Validation</title>", "<p>Limit of detection (LOD), LOQ, precision, accuracy, and linearity were examined as the analytical parameters for determining the elements. The accuracy of the method was assessed by spiking samples with a known concentration of the analyte standard solution. Therefore, the leaf, seed, and soil samples were spiked with different volumes of stock solutions. K, Na, Ca, Mg, Fe, Co, and Zn samples (each 0.5 g) were spiked with 0.75 mL of the respective stock solution. On the other hand, for Mn, Cr, Ni, Cu, Cd, and Pb, a larger volume of 2.75 mL of the corresponding stock solution was added to each 0.5 g of the sample. The validated method was employed to digest and measure the spiked and nonspiked samples under the optimized conditions using MP-AES (instrument operating parameters are given in <xref rid=\"supplementary-material-1\" ref-type=\"sec\">Table S1</xref>). The percentage recovery for the leaf, seed, and soil samples is displayed in ##TAB##4##Table 5##, and it varies from 94 to 110%, which falls within the acceptable range and shows the validity of the optimized procedure.</p>", "<title>2.12. Statistical Analysis</title>", "<p>The preparation of calibration curves and data analysis was carried out using Origin 6.0 software. To validate and compare the average values of the metals across various sampling sites, a one-way ANOVA was employed. Pearson's correlation coefficient was utilized to ascertain the extent of positive or negative correlation among the metals.</p>" ]
[ "<title>3. Results and Discussion</title>", "<title>3.1. Concentration of Metals in <italic>M. stenopetala</italic> Leaf, Seed, and Soil Samples Collected from the Three Areas</title>", "<p>In the study, a total of thirteen elements were investigated using MP-AES. The most abundant mineral nutrients in the <italic>M. stenopetala</italic> plant parts and the supportive soil of the three areas were K, Ca, Mg, Na, and Fe. K, Ca, and Mg concentrations were higher in the leaves, seeds, and growing soil than in the mean total concentrations. Furthermore, we have considered Cr and Ni as micronutrients because they are essential for human health in small amounts. WHO has set the maximum permissible concentration of Cr and Ni in drinking water as 50 <italic>μ</italic>g/L and 70 <italic>μ</italic>g/L, respectively. Cr and Ni can cause a variety of negative health effects, including cancer, skin irritation, and respiratory and kidney problems [##UREF##4##7##].</p>", "<title>3.1.1. Concentrations of Mineral Nutrients in Leaf Samples</title>", "<p>As shown in ##TAB##5##Table 6##, there is a significant difference in macro- and micronutrient contents within and between leaf samples of <italic>M. stenopetala</italic>. The most abundant element among the macronutrients is K, followed by Ca, Mg, and Na (##FIG##0##Figure 1(a)##). The main reason for the high potassium content in the leaves of <italic>M. stenopetala</italic> is the fact that nutrients such as nitrogen, phosphorus, potassium, sulfur, and magnesium are highly mobile in the plant tissue and move from older plant tissues to newer ones. Another factor contributing to the higher concentration of K, Mg, and Ca is that these elements are frequently used for plant growth and development [##UREF##4##7##]. In addition, the abundance of calcium-bearing minerals in soil and water, which are normally abundant and readily absorbed by plants, also contributes to elevated Ca levels [##UREF##22##34##]. In contrast, among the investigated micronutrients, the Fe content of the leaves was dominant, followed by Mn, Zn, Cu, Co, Ni, and Cr (##FIG##0##Figure 1(b)##). In general, it can be concluded from the levels of all metals in the leaves of <italic>M. stenopetala</italic> that the concentrations of macro- and micronutrients in the three areas follow a similar trend. Dado et al. [##UREF##23##35##] and Yetesha et al. [##UREF##24##36##] reported a similar trend in mineral concentrations in the leaves of <italic>Pentas schimperiana</italic> and various parts of pumpkin, respectively.</p>", "<p>In general, the relative abundance of mineral nutrients in the leaves of <italic>M. stenopetala</italic> follows this sequence: K &gt; Ca &gt; Mg &gt; Na &gt; Fe &gt; Mn &gt; Zn &gt; Cu &gt; Co &gt; Ni &gt; Cr. The toxic metals Cd and Pb were not detected in the leaves of <italic>M. stenopetala</italic> from the three districts. This finding suggests that there is no contamination from toxic industrial waste in the sampling areas. Furthermore, the absence of harmful metals suggests that commercial fertilizers and herbicides are likely not used in <italic>M. stenopetala</italic> plantations in the vicinity. Moreover, Cd and Pb offer no nutritional benefit to humans; their minimal concentrations are appreciable. As a result, despite the potential health risks brought by the toxic metals, <italic>M. stenopetala</italic> leaves from the Chano Mile, Nechisar Kebele, and Konso Special Woreda are safe. The distribution patterns of each metal in the leaves of <italic>M. stenopetala</italic> are consistent in the three areas. A one-way analysis of variance revealed that the mean concentrations of all identified metals in the leaves of the three districts differed significantly at a 95% confidence level. The varying concentrations of metals could be attributed to differences in the age and variety of the sampled <italic>M. stenopetala</italic> plants [##UREF##25##37##].</p>", "<title>3.1.2. Concentrations of Mineral Nutrients in Seed Samples</title>", "<p>The concentration of K in the seed samples was the highest among the macromineral nutrients (##TAB##5##Table 6##) and the highest of all mineral nutrients analyzed, followed by Mg, Ca, and Na. Macromineral nutrients detected in <italic>M. stenopetala</italic> seeds had the following concentration trend: K &gt; Mg &gt; Ca &gt; Na (##FIG##1##Figure 2(a)##). Among the sample sites, the highest concentration of K was found in <italic>M. stenopetala</italic> seeds from Konso Special Woreda, followed by Nechisar Kebele and Chano Mile. Mg concentration was the highest in seed samples from Chano Mile, followed by Konso Special Woreda and Nechisar Kebele. The concentration levels of Ca found in the seed samples from the three sites were as follows (highest to lowest): Chano Mile, Nechisar Kebele, and Konso Special Woreda. This indicates that the Ca content in the Chano Mile seed sample is significantly higher (<italic>p</italic> &lt; 0.05) than that of Nechisar Kebele and Konso Special Woreda. The Nechisar Kebele seed sample has the highest Na content of the three sampling areas. The Na values in the seed samples from Nechisar Kebele and Konso Special Woreda show no significant differences at a 95% confidence level. As shown in ##FIG##1##Figure 2(b)##, Fe is the most abundant micronutrient in seed samples, followed by Mn, Zn, Cu, Co, Ni, and Cr. ##TAB##5##Table 6## also shows that the concentration ranges of all micronutrients are almost closer in the three sample areas. The increased Fe concentration is a consequence of its higher concentration in the supportive soil [##REF##25789209##31##, ##UREF##26##38##]. It was found that the concentrations of Cd and Pb are below the detection limit, and the plant has a very limited ability to accumulate these toxic metals in its tissues.</p>", "<title>3.1.3. Concentrations of Mineral Nutrients in Soil Samples</title>", "<p>As indicated in ##TAB##5##Table 6##, the levels of macro- and micromineral nutrients detected in the soils of <italic>M. stenopetala</italic> farms differed significantly from one area to another. Among the macromineral nutrients investigated, K exhibited the highest concentration, followed by Mg, Ca, and Na. In terms of micromineral nutrients, Fe was found to be the most abundant element in the soil samples, followed by Mn, Zn, Cu, Co, Ni, and Cr. The soil of the Nechisar Kebele root zone had the least amount of K, whereas the Chano Mile site had the highest concentration. Konso Special Woreda showed the highest Ca content, while Nechisar Kebele had the lowest concentration. Similarly, the soil sample from Konso Special Woreda had the highest Mg concentration, while Chano Mile had the lowest (##FIG##2##Figure 3(a)##). In the soil sample from Chano Mile, Fe was the micromineral nutrient with the highest concentration, followed by Nechisar Kebele and Konso Special Woreda (##FIG##2##Figure 3(b)##). On the other hand, the concentrations of Mn and Zn follow the same trend, with the highest value being at Chano Mile, followed by Konso Special Woreda and Nechisar Kebele. For Cu, the highest content was recorded in Nechisar Kebele, followed by Konso Special Woreda and Chano Mile. As in the leaf and seed samples, Cd and Pb were not detected in all soils studied in the three areas. The results indicate that the agricultural soils of the <italic>M. stenopetala</italic> plant are free from heavy metal contamination.</p>", "<title>3.2. Distribution Patterns of Metals in the Samples</title>", "<p>Plants can absorb mineral nutrients through diverse and complex biochemical pathways. The uptake varies depending on the ability of plants to take up mineral nutrients from the soil, the availability of nutrients in soluble and absorbable forms, and the presence of specific nutrients at the site. Increasing industrialization and pollution of the biosphere are the main reasons for the variation in soil concentrations of vital minerals and toxic metals [##REF##26194234##39##]. Various fertilizers, pesticides, and other chemicals are used on agricultural land, which become sources of soil pollution and make the quality of agricultural land unfit for human and animal lives. The distribution and accumulation of mineral nutrients in the <italic>M. stenopetala</italic> plant reflect the mineral composition of the soil and the environment in which the plants grow [##UREF##27##40##]. Therefore, the mineral content of <italic>M. stenopetala</italic> varies greatly depending on the geographic location, use of fertilizers, and other factors such as irrigation water. If we compare the concentration of mineral nutrients by sample location in leaf samples, the trend can be presented as follows: Nechisar Kebele &gt; Chano Mile &gt; Konso Special Woreda. Konso Special Woreda &gt; Nechisar Kebele &gt; Chano Mile in Mg content. Nechisar Kebele &gt; Chano Mile &gt; Konso Special Woreda in Fe content. Chano Mile &gt; Nechisar Kebele &gt; Konso Special Woreda in Mn content. The concentration variations of Co and Ni are not very pronounced at the three sites, suggesting that the distribution of these metals is invariant compared to other elements. The variation of Fe by sample location was the highest among the micromineral nutrients, with concentrations ranging from 687 to 451 mg kg<sup>−1</sup>, which is below the WHO/FAO permissible limit of 5000 mg kg<sup>−1</sup>. The variation of Cu by sample location was the lowest, with concentrations ranging from 2.64 to 3.61 mg kg<sup>−1</sup>, which is also below the WHO guideline value of 4 mg kg<sup>−1</sup> for agricultural soils [##REF##26405634##41##, ##UREF##28##42##], as shown in ##TAB##5##Table 6##.</p>", "<p>In general, plants absorb what is present in the soil medium. As a result, the mineral nutrients are also absorbed and accumulated in the roots, stems, fruits, grains, and leaves of the plant. Ultimately, these minerals can be transferred to humans through the food chain. The absorption process is strongly influenced by soil nutrient content, soil pH, the presence of other binders, the ionic strength of the solution in the soil, and the presence of other competing nutrients [##REF##28447234##43##]. Therefore, the occurrence of these studied mineral nutrients in the leaves and seeds of <italic>M. stenopetala</italic> can be attributed to their increased concentration in the soil.</p>", "<title>3.3. Comparison of the Mineral Nutrients of This Work with Literature Values and FAO/WHO Guidelines</title>", "<p>The mineral concentrations obtained in this research were compared with studies by other scientists. Different scientists have conducted diverse studies on the leaves of <italic>M. stenopetala</italic> (mainly edible part). However, no comprehensive studies have been conducted on the mineral nutrient composition of the leaves of <italic>M. stenopetala</italic> from the Nechisar Kebele, Chano Mile, and Konso Special Woreda areas.</p>", "<p>As illustrated in ##TAB##6##Table 7##, the mineral nutrients obtained from the leaf samples of <italic>M. stenopetala</italic> in this study are in accordance (with a few exceptions) with other investigations from the same and different countries. For example, the level of K identified in this research was less than that documented by Solomon and Kusse [##UREF##29##44##] and Sodamode [##UREF##32##47##]. In comparison with other literature findings, Mg is present at elevated concentrations in the present study. In comparison to the findings of Solomon and Kusse [##UREF##29##44##] and Sodamode et al. [##UREF##32##47##], Ca is present in higher concentrations but is lower than those reported by Debebe and Eyobel [##UREF##30##45##]. In contrast to the findings of Solomon and Kusse [##UREF##29##44##] and Debebe and Eyobel [##UREF##30##45##], Fe is present in higher concentrations but is lower than those reported by Nkuba and Mohammed [##UREF##31##46##] and Sodamode et al. [##UREF##32##47##]. In comparison with Solomon and Kusse [##UREF##29##44##] and Nkuba and Mohammed [##UREF##31##46##], Mn is present in higher concentrations but is lower than those reported by Debebe and Eyobel [##UREF##30##45##] and Sodamode et al. [##UREF##32##47##]. The Zn concentration determined in this study also agrees well with values from other researchers such as Debebe and Eyobel [##UREF##30##45##] and Nkuba and Mohammed [##UREF##31##46##] but is lower than those reported by Solomon and Kusse [##UREF##29##44##] and Sodamode et al. [##UREF##32##47##]. As shown in ##TAB##6##Table 7##, the concentrations of Cd and Pb were very low compared with some literature reports. The variations between the results are likely attributed to differences in soil composition, genetic diversity, and environmental conditions. Furthermore, external factors such as municipal waste, fertilizers, irrigation practices, pollution, and climate variability may also affect the rate at which plants accumulate metals [##REF##24717360##48##]. To conclude, the concentrations of analyzed metals in <italic>M. stenopetala</italic> leaves were found to be within safe limits, as stipulated by the FAO/WHO guidelines [##UREF##33##49##]. These results contribute to our understanding of the nutritional safety of <italic>M. stenopetala</italic> leaves, supporting their suitability for consumption within established regulatory standards.</p>", "<title>3.4. Daily Intake of Mineral Nutrients from <italic>M. stenopetala</italic> Leaves</title>", "<p>The daily consumption of minerals from <italic>M. stenopetala</italic> leaves was calculated based on the assumption that an average adult consumes an average of 200 g of dried moringa leaves per day. The quantities of minerals a person acquires from the leaves of <italic>M. stenopetala</italic> are listed in ##TAB##7##Table 8##. Among the trace mineral nutrients, the amount of Na that a person can consume is lower than the recommended daily values, indicating that only the leaves of <italic>M. stenopetala</italic> cannot serve as a reliable source of Na for daily requirements. Therefore, additional Na needs to be obtained from other sources. For other trace minerals, the leaves of <italic>M. stenopetala</italic> can provide sufficient nutrition. Among the essential mineral nutrients, the amount of Zn that humans can absorb is also lower than the necessary amount. Hence, supplemental nutrition is necessary for this nutrient. However, the levels of Fe and Mn are abundant, making the leaves of <italic>M. stenopetala</italic> the ideal food source for the communities in the three regions and the entire country, especially during the dry season. The levels of Cd and Pb are below detectable limits in <italic>M. stenopetala</italic> leaves from the three regions, suggesting that consuming these leaves is generally safe from the risks associated with Cd and Pb exposure. However, it is important to note that Pb and Cd are cumulative toxins with the potential to accumulate in the body over time, even at low levels.</p>", "<title>3.5. Statistical Analysis</title>", "<title>3.5.1. Analysis of Variance (ANOVA)</title>", "<p>In this study, leaf, seed, and supportive soil samples were collected from the three main <italic>M. stenopetala</italic> growing areas in Ethiopia, and the mineral content of each sample was analyzed using MP-AES. During sample preparation and analysis, a number of random errors can occur with each aliquot and replicate measurement. The variation in the sample mean of the analyte was tested using a one-way ANOVA [##REF##37335156##51##] to investigate whether the variation was due to the experimental procedure or due to sample heterogeneity. ##TAB##8## Table 9## shows that at the 95% confidence level, there are significant differences in the means of all analytes examined except K, Ca, Co, and Cu. The significant difference between the mean values of the samples can be attributed to the diversity of soil mineral composition or pH, which determines the extent of mineral assimilation by plants [##UREF##4##7##].</p>", "<title>3.5.2. Pearson's Correlation Coefficient of Metals</title>", "<p>The correlation between the mineral nutrients in <italic>M. stenopetala</italic> leaves and soil samples was examined using Pearson's correlation matrices to determine the correlation coefficients (Tables <xref rid=\"supplementary-material-1\" ref-type=\"sec\">S2A</xref> and <xref rid=\"supplementary-material-1\" ref-type=\"sec\">S2B</xref>). For the majority of the mineral nutrients obtained, except Mn and Cu in the leaves of <italic>M. stenopetala</italic> and Co, Zn, and Cr in the soil samples, the correlation was significant at the 95% confidence level. In addition, Ni showed a negative correlation with almost all elements in both samples and a weak association with the others. A highly positive correlation indicates a strong relationship between the nutrients, possibly derived from natural sources or the environment, or similarity in chemical properties [##UREF##35##52##]. The correlation between Mg and Cu in plants and Co and Mn in soil was negative.</p>", "<p>As shown in ##TAB##9##Table 10##, the correlation coefficients (<italic>r</italic>) between the mineral nutrients in the leaves of <italic>M. stenopetala</italic> and the soil samples collected from the three areas were computed for each metal individually. The outcomes indicated that there was a strong correlation between K, Na, Ca, Mg, Fe, Ni, and Cu in the leaf and soil samples, and a weak correlation between Cr, Zn, Mn, and Co was observed in the samples. Strong correlations between soil mineral content and plant tissue were anticipated, as plants take up nutrients from the soil through their roots. The weak correlation observed for some metals could be attributed to the fact that some nutrients, even when present in high concentrations in the soil, may be taken in by the plant to a lesser extent as they may not be accessible in a soluble form for absorption by the plant.</p>", "<p>The results of our analytical endeavors unveil a nuanced portrait of the micro- and macromineral composition of <italic>M. stenopetala</italic>, laying a foundation for profound insights into its nutritional significance. The methodological innovation inherent in our study, employing MP-AES, represents a leap forward in the simultaneous determination of thirteen essential minerals in <italic>M. stenopetala</italic> leaves, seeds, and soil. This approach not only streamlines the digestion process with an optimized acid mixture but also enhances precision by minimizing reagent volumes and reducing digestion time and temperature. The observed elevated concentrations of essential minerals, including K, Na, Ca, and Mg, underscore the potential of <italic>M. stenopetala</italic> as a valuable source of vital nutrients. Remarkably, the absence of toxic elements such as Cd and Pb fortifies the safety profile of <italic>M. stenopetala</italic> leaves and seeds. These findings contribute not only to the burgeoning field of plant nutrition but also position our developed method as an innovative and efficient tool for comprehensive mineral analysis. As we chart the course forward, these revelations guide the trajectory of our research proposal, prompting further exploration into the multifaceted dimensions of <italic>M. stenopetala</italic>'s nutritional attributes and its potential impact on mitigating dietary deficiencies and bolstering food security in arid regions.</p>" ]
[ "<title>3. Results and Discussion</title>", "<title>3.1. Concentration of Metals in <italic>M. stenopetala</italic> Leaf, Seed, and Soil Samples Collected from the Three Areas</title>", "<p>In the study, a total of thirteen elements were investigated using MP-AES. The most abundant mineral nutrients in the <italic>M. stenopetala</italic> plant parts and the supportive soil of the three areas were K, Ca, Mg, Na, and Fe. K, Ca, and Mg concentrations were higher in the leaves, seeds, and growing soil than in the mean total concentrations. Furthermore, we have considered Cr and Ni as micronutrients because they are essential for human health in small amounts. WHO has set the maximum permissible concentration of Cr and Ni in drinking water as 50 <italic>μ</italic>g/L and 70 <italic>μ</italic>g/L, respectively. Cr and Ni can cause a variety of negative health effects, including cancer, skin irritation, and respiratory and kidney problems [##UREF##4##7##].</p>", "<title>3.1.1. Concentrations of Mineral Nutrients in Leaf Samples</title>", "<p>As shown in ##TAB##5##Table 6##, there is a significant difference in macro- and micronutrient contents within and between leaf samples of <italic>M. stenopetala</italic>. The most abundant element among the macronutrients is K, followed by Ca, Mg, and Na (##FIG##0##Figure 1(a)##). The main reason for the high potassium content in the leaves of <italic>M. stenopetala</italic> is the fact that nutrients such as nitrogen, phosphorus, potassium, sulfur, and magnesium are highly mobile in the plant tissue and move from older plant tissues to newer ones. Another factor contributing to the higher concentration of K, Mg, and Ca is that these elements are frequently used for plant growth and development [##UREF##4##7##]. In addition, the abundance of calcium-bearing minerals in soil and water, which are normally abundant and readily absorbed by plants, also contributes to elevated Ca levels [##UREF##22##34##]. In contrast, among the investigated micronutrients, the Fe content of the leaves was dominant, followed by Mn, Zn, Cu, Co, Ni, and Cr (##FIG##0##Figure 1(b)##). In general, it can be concluded from the levels of all metals in the leaves of <italic>M. stenopetala</italic> that the concentrations of macro- and micronutrients in the three areas follow a similar trend. Dado et al. [##UREF##23##35##] and Yetesha et al. [##UREF##24##36##] reported a similar trend in mineral concentrations in the leaves of <italic>Pentas schimperiana</italic> and various parts of pumpkin, respectively.</p>", "<p>In general, the relative abundance of mineral nutrients in the leaves of <italic>M. stenopetala</italic> follows this sequence: K &gt; Ca &gt; Mg &gt; Na &gt; Fe &gt; Mn &gt; Zn &gt; Cu &gt; Co &gt; Ni &gt; Cr. The toxic metals Cd and Pb were not detected in the leaves of <italic>M. stenopetala</italic> from the three districts. This finding suggests that there is no contamination from toxic industrial waste in the sampling areas. Furthermore, the absence of harmful metals suggests that commercial fertilizers and herbicides are likely not used in <italic>M. stenopetala</italic> plantations in the vicinity. Moreover, Cd and Pb offer no nutritional benefit to humans; their minimal concentrations are appreciable. As a result, despite the potential health risks brought by the toxic metals, <italic>M. stenopetala</italic> leaves from the Chano Mile, Nechisar Kebele, and Konso Special Woreda are safe. The distribution patterns of each metal in the leaves of <italic>M. stenopetala</italic> are consistent in the three areas. A one-way analysis of variance revealed that the mean concentrations of all identified metals in the leaves of the three districts differed significantly at a 95% confidence level. The varying concentrations of metals could be attributed to differences in the age and variety of the sampled <italic>M. stenopetala</italic> plants [##UREF##25##37##].</p>", "<title>3.1.2. Concentrations of Mineral Nutrients in Seed Samples</title>", "<p>The concentration of K in the seed samples was the highest among the macromineral nutrients (##TAB##5##Table 6##) and the highest of all mineral nutrients analyzed, followed by Mg, Ca, and Na. Macromineral nutrients detected in <italic>M. stenopetala</italic> seeds had the following concentration trend: K &gt; Mg &gt; Ca &gt; Na (##FIG##1##Figure 2(a)##). Among the sample sites, the highest concentration of K was found in <italic>M. stenopetala</italic> seeds from Konso Special Woreda, followed by Nechisar Kebele and Chano Mile. Mg concentration was the highest in seed samples from Chano Mile, followed by Konso Special Woreda and Nechisar Kebele. The concentration levels of Ca found in the seed samples from the three sites were as follows (highest to lowest): Chano Mile, Nechisar Kebele, and Konso Special Woreda. This indicates that the Ca content in the Chano Mile seed sample is significantly higher (<italic>p</italic> &lt; 0.05) than that of Nechisar Kebele and Konso Special Woreda. The Nechisar Kebele seed sample has the highest Na content of the three sampling areas. The Na values in the seed samples from Nechisar Kebele and Konso Special Woreda show no significant differences at a 95% confidence level. As shown in ##FIG##1##Figure 2(b)##, Fe is the most abundant micronutrient in seed samples, followed by Mn, Zn, Cu, Co, Ni, and Cr. ##TAB##5##Table 6## also shows that the concentration ranges of all micronutrients are almost closer in the three sample areas. The increased Fe concentration is a consequence of its higher concentration in the supportive soil [##REF##25789209##31##, ##UREF##26##38##]. It was found that the concentrations of Cd and Pb are below the detection limit, and the plant has a very limited ability to accumulate these toxic metals in its tissues.</p>", "<title>3.1.3. Concentrations of Mineral Nutrients in Soil Samples</title>", "<p>As indicated in ##TAB##5##Table 6##, the levels of macro- and micromineral nutrients detected in the soils of <italic>M. stenopetala</italic> farms differed significantly from one area to another. Among the macromineral nutrients investigated, K exhibited the highest concentration, followed by Mg, Ca, and Na. In terms of micromineral nutrients, Fe was found to be the most abundant element in the soil samples, followed by Mn, Zn, Cu, Co, Ni, and Cr. The soil of the Nechisar Kebele root zone had the least amount of K, whereas the Chano Mile site had the highest concentration. Konso Special Woreda showed the highest Ca content, while Nechisar Kebele had the lowest concentration. Similarly, the soil sample from Konso Special Woreda had the highest Mg concentration, while Chano Mile had the lowest (##FIG##2##Figure 3(a)##). In the soil sample from Chano Mile, Fe was the micromineral nutrient with the highest concentration, followed by Nechisar Kebele and Konso Special Woreda (##FIG##2##Figure 3(b)##). On the other hand, the concentrations of Mn and Zn follow the same trend, with the highest value being at Chano Mile, followed by Konso Special Woreda and Nechisar Kebele. For Cu, the highest content was recorded in Nechisar Kebele, followed by Konso Special Woreda and Chano Mile. As in the leaf and seed samples, Cd and Pb were not detected in all soils studied in the three areas. The results indicate that the agricultural soils of the <italic>M. stenopetala</italic> plant are free from heavy metal contamination.</p>", "<title>3.2. Distribution Patterns of Metals in the Samples</title>", "<p>Plants can absorb mineral nutrients through diverse and complex biochemical pathways. The uptake varies depending on the ability of plants to take up mineral nutrients from the soil, the availability of nutrients in soluble and absorbable forms, and the presence of specific nutrients at the site. Increasing industrialization and pollution of the biosphere are the main reasons for the variation in soil concentrations of vital minerals and toxic metals [##REF##26194234##39##]. Various fertilizers, pesticides, and other chemicals are used on agricultural land, which become sources of soil pollution and make the quality of agricultural land unfit for human and animal lives. The distribution and accumulation of mineral nutrients in the <italic>M. stenopetala</italic> plant reflect the mineral composition of the soil and the environment in which the plants grow [##UREF##27##40##]. Therefore, the mineral content of <italic>M. stenopetala</italic> varies greatly depending on the geographic location, use of fertilizers, and other factors such as irrigation water. If we compare the concentration of mineral nutrients by sample location in leaf samples, the trend can be presented as follows: Nechisar Kebele &gt; Chano Mile &gt; Konso Special Woreda. Konso Special Woreda &gt; Nechisar Kebele &gt; Chano Mile in Mg content. Nechisar Kebele &gt; Chano Mile &gt; Konso Special Woreda in Fe content. Chano Mile &gt; Nechisar Kebele &gt; Konso Special Woreda in Mn content. The concentration variations of Co and Ni are not very pronounced at the three sites, suggesting that the distribution of these metals is invariant compared to other elements. The variation of Fe by sample location was the highest among the micromineral nutrients, with concentrations ranging from 687 to 451 mg kg<sup>−1</sup>, which is below the WHO/FAO permissible limit of 5000 mg kg<sup>−1</sup>. The variation of Cu by sample location was the lowest, with concentrations ranging from 2.64 to 3.61 mg kg<sup>−1</sup>, which is also below the WHO guideline value of 4 mg kg<sup>−1</sup> for agricultural soils [##REF##26405634##41##, ##UREF##28##42##], as shown in ##TAB##5##Table 6##.</p>", "<p>In general, plants absorb what is present in the soil medium. As a result, the mineral nutrients are also absorbed and accumulated in the roots, stems, fruits, grains, and leaves of the plant. Ultimately, these minerals can be transferred to humans through the food chain. The absorption process is strongly influenced by soil nutrient content, soil pH, the presence of other binders, the ionic strength of the solution in the soil, and the presence of other competing nutrients [##REF##28447234##43##]. Therefore, the occurrence of these studied mineral nutrients in the leaves and seeds of <italic>M. stenopetala</italic> can be attributed to their increased concentration in the soil.</p>", "<title>3.3. Comparison of the Mineral Nutrients of This Work with Literature Values and FAO/WHO Guidelines</title>", "<p>The mineral concentrations obtained in this research were compared with studies by other scientists. Different scientists have conducted diverse studies on the leaves of <italic>M. stenopetala</italic> (mainly edible part). However, no comprehensive studies have been conducted on the mineral nutrient composition of the leaves of <italic>M. stenopetala</italic> from the Nechisar Kebele, Chano Mile, and Konso Special Woreda areas.</p>", "<p>As illustrated in ##TAB##6##Table 7##, the mineral nutrients obtained from the leaf samples of <italic>M. stenopetala</italic> in this study are in accordance (with a few exceptions) with other investigations from the same and different countries. For example, the level of K identified in this research was less than that documented by Solomon and Kusse [##UREF##29##44##] and Sodamode [##UREF##32##47##]. In comparison with other literature findings, Mg is present at elevated concentrations in the present study. In comparison to the findings of Solomon and Kusse [##UREF##29##44##] and Sodamode et al. [##UREF##32##47##], Ca is present in higher concentrations but is lower than those reported by Debebe and Eyobel [##UREF##30##45##]. In contrast to the findings of Solomon and Kusse [##UREF##29##44##] and Debebe and Eyobel [##UREF##30##45##], Fe is present in higher concentrations but is lower than those reported by Nkuba and Mohammed [##UREF##31##46##] and Sodamode et al. [##UREF##32##47##]. In comparison with Solomon and Kusse [##UREF##29##44##] and Nkuba and Mohammed [##UREF##31##46##], Mn is present in higher concentrations but is lower than those reported by Debebe and Eyobel [##UREF##30##45##] and Sodamode et al. [##UREF##32##47##]. The Zn concentration determined in this study also agrees well with values from other researchers such as Debebe and Eyobel [##UREF##30##45##] and Nkuba and Mohammed [##UREF##31##46##] but is lower than those reported by Solomon and Kusse [##UREF##29##44##] and Sodamode et al. [##UREF##32##47##]. As shown in ##TAB##6##Table 7##, the concentrations of Cd and Pb were very low compared with some literature reports. The variations between the results are likely attributed to differences in soil composition, genetic diversity, and environmental conditions. Furthermore, external factors such as municipal waste, fertilizers, irrigation practices, pollution, and climate variability may also affect the rate at which plants accumulate metals [##REF##24717360##48##]. To conclude, the concentrations of analyzed metals in <italic>M. stenopetala</italic> leaves were found to be within safe limits, as stipulated by the FAO/WHO guidelines [##UREF##33##49##]. These results contribute to our understanding of the nutritional safety of <italic>M. stenopetala</italic> leaves, supporting their suitability for consumption within established regulatory standards.</p>", "<title>3.4. Daily Intake of Mineral Nutrients from <italic>M. stenopetala</italic> Leaves</title>", "<p>The daily consumption of minerals from <italic>M. stenopetala</italic> leaves was calculated based on the assumption that an average adult consumes an average of 200 g of dried moringa leaves per day. The quantities of minerals a person acquires from the leaves of <italic>M. stenopetala</italic> are listed in ##TAB##7##Table 8##. Among the trace mineral nutrients, the amount of Na that a person can consume is lower than the recommended daily values, indicating that only the leaves of <italic>M. stenopetala</italic> cannot serve as a reliable source of Na for daily requirements. Therefore, additional Na needs to be obtained from other sources. For other trace minerals, the leaves of <italic>M. stenopetala</italic> can provide sufficient nutrition. Among the essential mineral nutrients, the amount of Zn that humans can absorb is also lower than the necessary amount. Hence, supplemental nutrition is necessary for this nutrient. However, the levels of Fe and Mn are abundant, making the leaves of <italic>M. stenopetala</italic> the ideal food source for the communities in the three regions and the entire country, especially during the dry season. The levels of Cd and Pb are below detectable limits in <italic>M. stenopetala</italic> leaves from the three regions, suggesting that consuming these leaves is generally safe from the risks associated with Cd and Pb exposure. However, it is important to note that Pb and Cd are cumulative toxins with the potential to accumulate in the body over time, even at low levels.</p>", "<title>3.5. Statistical Analysis</title>", "<title>3.5.1. Analysis of Variance (ANOVA)</title>", "<p>In this study, leaf, seed, and supportive soil samples were collected from the three main <italic>M. stenopetala</italic> growing areas in Ethiopia, and the mineral content of each sample was analyzed using MP-AES. During sample preparation and analysis, a number of random errors can occur with each aliquot and replicate measurement. The variation in the sample mean of the analyte was tested using a one-way ANOVA [##REF##37335156##51##] to investigate whether the variation was due to the experimental procedure or due to sample heterogeneity. ##TAB##8## Table 9## shows that at the 95% confidence level, there are significant differences in the means of all analytes examined except K, Ca, Co, and Cu. The significant difference between the mean values of the samples can be attributed to the diversity of soil mineral composition or pH, which determines the extent of mineral assimilation by plants [##UREF##4##7##].</p>", "<title>3.5.2. Pearson's Correlation Coefficient of Metals</title>", "<p>The correlation between the mineral nutrients in <italic>M. stenopetala</italic> leaves and soil samples was examined using Pearson's correlation matrices to determine the correlation coefficients (Tables <xref rid=\"supplementary-material-1\" ref-type=\"sec\">S2A</xref> and <xref rid=\"supplementary-material-1\" ref-type=\"sec\">S2B</xref>). For the majority of the mineral nutrients obtained, except Mn and Cu in the leaves of <italic>M. stenopetala</italic> and Co, Zn, and Cr in the soil samples, the correlation was significant at the 95% confidence level. In addition, Ni showed a negative correlation with almost all elements in both samples and a weak association with the others. A highly positive correlation indicates a strong relationship between the nutrients, possibly derived from natural sources or the environment, or similarity in chemical properties [##UREF##35##52##]. The correlation between Mg and Cu in plants and Co and Mn in soil was negative.</p>", "<p>As shown in ##TAB##9##Table 10##, the correlation coefficients (<italic>r</italic>) between the mineral nutrients in the leaves of <italic>M. stenopetala</italic> and the soil samples collected from the three areas were computed for each metal individually. The outcomes indicated that there was a strong correlation between K, Na, Ca, Mg, Fe, Ni, and Cu in the leaf and soil samples, and a weak correlation between Cr, Zn, Mn, and Co was observed in the samples. Strong correlations between soil mineral content and plant tissue were anticipated, as plants take up nutrients from the soil through their roots. The weak correlation observed for some metals could be attributed to the fact that some nutrients, even when present in high concentrations in the soil, may be taken in by the plant to a lesser extent as they may not be accessible in a soluble form for absorption by the plant.</p>", "<p>The results of our analytical endeavors unveil a nuanced portrait of the micro- and macromineral composition of <italic>M. stenopetala</italic>, laying a foundation for profound insights into its nutritional significance. The methodological innovation inherent in our study, employing MP-AES, represents a leap forward in the simultaneous determination of thirteen essential minerals in <italic>M. stenopetala</italic> leaves, seeds, and soil. This approach not only streamlines the digestion process with an optimized acid mixture but also enhances precision by minimizing reagent volumes and reducing digestion time and temperature. The observed elevated concentrations of essential minerals, including K, Na, Ca, and Mg, underscore the potential of <italic>M. stenopetala</italic> as a valuable source of vital nutrients. Remarkably, the absence of toxic elements such as Cd and Pb fortifies the safety profile of <italic>M. stenopetala</italic> leaves and seeds. These findings contribute not only to the burgeoning field of plant nutrition but also position our developed method as an innovative and efficient tool for comprehensive mineral analysis. As we chart the course forward, these revelations guide the trajectory of our research proposal, prompting further exploration into the multifaceted dimensions of <italic>M. stenopetala</italic>'s nutritional attributes and its potential impact on mitigating dietary deficiencies and bolstering food security in arid regions.</p>" ]
[ "<title>4. Conclusion</title>", "<p>In this comprehensive study, we employed MP-AES coupled with the acid digestion method to analyze <italic>M. stenopetala</italic> leaf, seed, and supportive soil samples from Chano Mile Kebele, Nechisar Kebele, and Konso Special Woreda in southern Ethiopia. While the optimized digestion procedure exhibited robustness, as evidenced by excellent percentage recoveries ranging from 94 to 110% in the spiking experiment, it is imperative to acknowledge certain limitations inherent in the method. Potential constraints may include sensitivity variations for specific minerals or potential interference in the detection process. Moreover, the analysis results revealed higher concentrations of both microminerals (K, Na, Ca, and Mg) and macrominerals (Fe, Mn, Zn, and Cu) in plant leaf and seed samples from the three areas, contributing valuable insights to the nutritional values of <italic>M. stenopetala</italic>. However, it is crucial to note that the study has limitations. Differences in soil physical and chemical composition, fertilizer and pesticide usage, agroclimatic conditions, and harvesting mechanisms among the three regions may introduce variability in the observed mineral concentrations. These inherent variations underscore the complexity of the agroecosystem and emphasize the need for cautious interpretation. Notably, the absence of toxic elements Cd and Pb in any of the analyzed samples confirms the safety of <italic>M. stenopetala</italic> leaves and seeds. Despite these strengths, it is essential to recognize that the study's generalizability may be influenced by the specific characteristics of the sampled regions and may not fully capture the variability present in other geographical areas. A one-way ANOVA at a 95% confidence level revealed significant differences in the content of all mineral nutrients between the three sample means, excluding K, Ca, Co, and Cu. While this emphasizes the need for a region-specific approach to interpret the results, the concentrations of micro- and macromineral nutrients in <italic>M. stenopetala</italic> leaves and seeds were generally found to be within safety limits, supporting their suitability for consumption as a healthy food source.</p>" ]
[ "<p>Academic Editor: Mohamed Abdel-Rehim</p>", "<p>In this study, for the first time, the levels of thirteen micro- and macromineral nutrients in the leaves, seeds, and supportive soil of <italic>Moringa stenopetala</italic> (<italic>M. stenopetala</italic>) were simultaneously determined using microwave plasma atomic emission spectroscopy (MP-AES). The samples were collected during the arid season, in 2019 from the three main <italic>M. stenopetala</italic> growing areas in southern Ethiopia (Chano Mile Kebele, Nechisar Kebele, and Konso Special Woreda). A novel digestion method for leaf and seed samples was developed using an optimized acid mixture (2.5 : 0.75 : 0.5 of HNO<sub>3</sub>, HClO<sub>4</sub>, and H<sub>2</sub>O<sub>2</sub>) at 240°C for 2 hrs and 30 min, resulting in clear and colorless solutions. The method makes the digestion process more efficient by minimizing the reagent volume, reducing digestion temperature and time, and simplifying the overall procedure. The efficiency of the optimized procedure was validated by spiking experiments, and the percentage recovery ranged between 94 and 110%. Under optimized experimental conditions, higher concentrations of essential minerals (K, Na, Ca, and Mg) were observed in the plant leaf and seed samples from the three areas. In addition, significant amounts of trace elements (Fe, Mn, Zn, and Cu) were also found. Importantly, no traces of the toxic elements (Cd and Pb) were detected in any of the analyzed samples, suggesting that the leaves and seeds of <italic>M. stenopetala</italic> are valuable sources of both micro- and macromineral nutrients and are safe from toxic metals. From a dietary perspective, the seed contains almost comparable concentrations of minerals as the leaves. As a result, the seeds of <italic>M. stenopetala</italic> can serve as an alternative source of minerals and play a role in overcoming the current global food crisis, particularly in the dry season. Analysis of variance at a 95% confidence level revealed significant differences in the levels of all mineral nutrients between the three sample means except K, Ca, Co, and Cu. Generally, the developed method includes an innovative digestion procedure that minimizes reagent consumption, operates at lower temperatures, and requires shorter digestion times, thereby optimizing resource utilization and maintaining analytical accuracy. Notably, the absence of toxic elements in the MP-AES procedure highlights the safety and reliability of <italic>M. stenopetala</italic> leaves and seeds as valuable, contamination-free sources of essential nutrients.</p>" ]
[]
[ "<title>Acknowledgments</title>", "<p>The authors gratefully acknowledge the Department of Chemistry, Addis Ababa University, Addis Ababa, Ethiopia, for providing laboratory facilities.</p>", "<title>Data Availability</title>", "<p>The data used to support the findings of the study are included within the article.</p>", "<title>Conflicts of Interest</title>", "<p>The authors declare that they have no conflicts of interest or personal relationships that could have appeared to influence the work reported in this paper.</p>", "<title>Authors' Contributions</title>", "<p>Ashenafi Shemnsa conceptualized the study, developed the methodology, developed the software, collected the resources, performed the formal analysis, investigated the study, and wrote the original draft. Wondimeneh Dubale Adane conceptualized the study, developed the software, and wrote, reviewed and edited the study. Merid Tessema conceptualized, supervised, and wrote, reviewed, and edited the study. Endale Tesfaye and Gizaw Tesfaye conceptualized and wrote, reviewed, and edited the study.</p>", "<title>Supplementary Materials</title>" ]
[ "<fig position=\"float\" id=\"fig1\"><label>Figure 1</label><caption><p>The concentrations of (a) macro- and (b) micromineral nutrients in the leaves of <italic>M. stenopetala</italic> from the three areas.</p></caption></fig>", "<fig position=\"float\" id=\"fig2\"><label>Figure 2</label><caption><p>The concentrations of (a) macro- and (b) micromineral nutrients in the seeds of <italic>M. stenopetala</italic> from the three areas.</p></caption></fig>", "<fig position=\"float\" id=\"fig3\"><label>Figure 3</label><caption><p>The concentrations of (a) macro- and (b) micromineral nutrients in the supportive soil of <italic>M. stenopetala</italic> plants from the three areas.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"tab1\"><label>Table 1</label><caption><p>Optimization of acid mixture volume for the digestion of 0.5 g of leaf and seed samples at a constant temperature and digestion time.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Volume ratio (HNO<sub>3</sub> : HClO<sub>4</sub> : H<sub>2</sub>O<sub>2</sub>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Total volume (mL)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Temp. (°C)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Digestion time (hrs)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Observations</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2 : 1 : 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Slightly green color</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 1 : 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Slightly green color</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.5 : 1 : 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Light yellow</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">4 : 1 : 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Colorless and turbid</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.5 : 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Colorless and turbid</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Colorless with suspension</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 1 : 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Colorless with suspension</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 1.25 : 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Clear and colorless</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<sup>\n<italic>∗</italic>\n</sup>Clear and colorless</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab2\"><label>Table 2</label><caption><p>Optimization of digestion time for 0.5 g of leaf and seed samples at a constant acid mixture volume and digestion temperature.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Volume ratio (HNO<sub>3</sub> : HClO<sub>4</sub> : H<sub>2</sub>O<sub>2</sub>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Total volume (mL)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Temp. (°C)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Digestion time (hrs)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Observations</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1:00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Yellow solution</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1:30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Light yellow</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2:00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Colorless and turbid</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2:30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<sup>\n<italic>∗</italic>\n</sup>Clear and colorless</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">300</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3:00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Clear and colorless</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab3\"><label>Table 3</label><caption><p>Optimization of digestion temperature for 0.5 g of leaf and seed samples at a constant acid mixture volume and digestion time.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Volume ratio (HNO<sub>3</sub> : HClO<sub>4</sub> : H<sub>2</sub>O<sub>2</sub>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Total volume (mL)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Temp. (°C)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Digestion time (hrs)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Observations</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">60</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2:30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Light yellow</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">120</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2:30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Colorless and turbid</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">180</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2:30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Colorless with suspension</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">240</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2:30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<sup>\n<italic>∗</italic>\n</sup>Clear and colorless</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.5 : 0.75 : 0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">280</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2:30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Clear and colorless</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab4\"><label>Table 4</label><caption><p>Wavelength, LOD, LOQ, correlation coefficient, and calibration curve equation to determine the metals by MP-AES.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Metals</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Wavelength (nm)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">LOD (mg L<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">LOQ (mg L<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Correlation curve</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>r</italic>\n<sup>2</sup>\n</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">K</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">766.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.036</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.718<italic>x</italic> – 4.72 × 10<sup>−6</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9996</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Na</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">589.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.034</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.114</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.689<italic>x</italic> + 1.46 × 10<sup>−3</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9981</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ca</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">393.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.026</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.087</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.346<italic>x</italic> – 6.25 × 10<sup>−5</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9953</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">285.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.024</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.08</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.177<italic>x</italic> + 2.58 × 10<sup>−3</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9994</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fe</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">372.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.008</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.027</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.322<italic>x</italic> + 8.45 × 10<sup>−5</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9987</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Co</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">240.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.006</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.541<italic>x</italic> + 5.46 × 10<sup>−5</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9954</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ni</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">352.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.005</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.017</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.451<italic>x</italic> + 5.35 × 10<sup>−5</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9976</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">403.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.005</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.017</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.368<italic>x</italic> – 3.17 × 10<sup>−4</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9988</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Zn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">213.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.001</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.004</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.226<italic>x</italic> – 2.31 × 10<sup>−5</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9992</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cr</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">425.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.006</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.212<italic>x</italic> + 3.16 × 10<sup>−4</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9994</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cu</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">324.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.003</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.01</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.223<italic>x</italic> – 5.68 × 10<sup>−5</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9952</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cd</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">228.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.001</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.004</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.541<italic>x</italic> + 4.37 × 10<sup>−4</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9962</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Pb</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">283.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.005</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.017</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>y</italic> = 0.541<italic>x</italic> + 4.37 × 10<sup>−4</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9997</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab5\"><label>Table 5</label><caption><p>Recovery analysis results for <italic>M. stenopetala</italic> leaf, seed, and soil samples.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"2\" colspan=\"1\">Metals</th><th align=\"center\" colspan=\"4\" rowspan=\"1\">Leaf</th><th align=\"center\" colspan=\"4\" rowspan=\"1\">Seed</th><th align=\"center\" colspan=\"4\" rowspan=\"1\">Soil</th></tr><tr><th align=\"center\" rowspan=\"1\" colspan=\"1\">Unspiked (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Added (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Obtained conc. (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Recovery (%)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Unspiked (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Added (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Obtained conc. (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Recovery (%)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Unspiked (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Added (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Obtained conc. (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Recovery (%)</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">K</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22142</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5600</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27542</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.43</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10071</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2800</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12771</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.43</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6487</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3546</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10063</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100.9</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Na</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">153</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">85</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">231</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">91.77</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">65.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">106</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2174</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1520</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3654</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97.37</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ca</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7842</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4328</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12190</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2912</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2164</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5086</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2469</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1520</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3919</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">95.40</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6842</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4116</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10998</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4312</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2058</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6380</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4259</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2425</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6634</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97.94</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fe</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">246</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">120</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">358</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">93.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">60</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">155</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.67</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">387</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">125</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">511</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">99.20</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Co</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.35</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.76</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97.83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.14</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.38</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.49</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97.83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.52</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100.9</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ni</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.21</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.18</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.38</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">99.55</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.06</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.09</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.08</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">93.58</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.86</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.52</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.32</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.06</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">54.28</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30.92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">84.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">98.71</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17.14</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15.46</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">32.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">52.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">25.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">76.01</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">91.85</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Zn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27.64</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">25.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">53.16</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">14.82</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12.71</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27.45</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">99.38</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18.65</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">93.60</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cr</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.32</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.41</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.56</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.66</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">98.22</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.87</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.91</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">92.86</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cu</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.54</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">13.94</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">99.56</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.71</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.27</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.89</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.04</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.51</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">94.65</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cd</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ND<sup><italic>∗</italic></sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.28</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">95.52</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ND<sup><italic>∗</italic></sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.65</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.61</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">93.85</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ND<sup><italic>∗</italic></sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.65</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.63</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.72</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Pb</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ND<sup><italic>∗</italic></sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.01</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.98</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97.03</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ND<sup><italic>∗</italic></sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.49</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">98.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ND<sup><italic>∗</italic></sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.48</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.00</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab6\"><label>Table 6</label><caption><p>Mean concentration (mean ± SD, <italic>n</italic> = 3, mg kg<sup>−1</sup> dry weight basis) of each metal in the three areas.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"center\" colspan=\"2\" rowspan=\"2\">Elements</th><th align=\"center\" colspan=\"3\" rowspan=\"1\">Chano Mile</th><th align=\"center\" colspan=\"3\" rowspan=\"1\">Nechisar Kebele</th><th align=\"center\" colspan=\"3\" rowspan=\"1\">Konso Special Woreda</th></tr><tr><th align=\"center\" rowspan=\"1\" colspan=\"1\">L<sub>CM</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Sd<sub>CM</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">So<sub>CM</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">L<sub>NK</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Sd<sub>NK</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">So<sub>NK</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">L<sub>KS</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Sd<sub>KS</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">So<sub>KS</sub></th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"13\" colspan=\"1\">Mean ± SD (mg kg<sup>−1</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">K</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">21390 ± 100</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10070 ± 80</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6680 ± 30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22140 ± 70</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10680 ± 40</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6230 ± 34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20990 ± 90</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11020 ± 72</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6490 ± 50</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Na</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">213.0 ± 2.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">160.6 ± 2.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">187 ± 4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">153.4 ± 2.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">175.4 ± 2.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">123 ± 3.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">245 ± 3.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">157.75 ± 3.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">174 ± 4.1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ca</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6749 ± 16</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2912 ± 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2164 ± 17</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7842 ± 21</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2458 ± 17</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2014 ± 25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7695 ± 21</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2146 ± 11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2469 ± 20</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6425 ± 53</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4312 ± 36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3684 ± 39</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6842 ± 23</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4152 ± 30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3984 ± 26</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7128 ± 36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4215 ± 28</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4259 ± 22</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Fe</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">198 ± 4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97 ± 3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">451 ± 5.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">246 ± 2.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">76 ± 1.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">397 ± 3.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">157 ± 2.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">87 ± 1.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">387 ± 2.9</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Co</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.98 ± 0.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.14 ± 0.06</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.65 ± 0.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.35 ± 0.06</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.29 ± 0.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.31 ± 0.03</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.12 ± 0.07</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.09 ± 0.06</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.12 ± 0.02</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ni</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.7 ± 0.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.06 ± 0.01</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.47 ± 0.01</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.21 ± 0.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.25 ± 0.04</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.94 ± 0.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.78 ± 0.06</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.11 ± 0.03</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.86 ± 0.05</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Mn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">57.28 ± 1.51</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17.14 ± 1.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">59.23 ± 2.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">54.28 ± 1.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">14.12 ± 1.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">47.5 ± 1.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">42.2 ± 1.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">13.46 ± 1.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">52.36 ± 1.2</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Zn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24.12 ± 0.20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">14.82 ± 0.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">21.65 ± 0.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27.64 ± 0.24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18.36 ± 0.11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">16.24 ± 0.15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">16.18 ± 0.68</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20.36 ± 0.41</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18.65 ± 0.19</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Cr</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.22 ± 0.06</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.11 ± 0.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.42 ± 0.04</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.32 ± 0.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.24 ± 0.01</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.96 ± 0.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.62 ± 0.03</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.18 ± 0.01</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.87 ± 0.02</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Cu</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.96 ± 0.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.71 ± 0.04</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.64 ± 0.01</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.42 ± 0.04</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.31 ± 0.01</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.26 ± 0.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.13 ± 0.04</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.84 ± 0.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.51 ± 0.03</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Cd</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Pb</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;LOD</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab7\"><label>Table 7</label><caption><p>Comparison of the means of the investigated minerals in <italic>M. stenopetala</italic> leaves with literature values.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"2\" colspan=\"1\">Source</th><th align=\"center\" colspan=\"10\" rowspan=\"1\">Means of the examined minerals (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">References</th></tr><tr><th align=\"center\" rowspan=\"1\" colspan=\"1\">K</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Mg</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ca</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Fe</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Mn</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Zn</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cu</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ni</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cd</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Pb</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ethiopia</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31797.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6167</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">63.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">26.83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">44.09</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.58</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##29##44##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ethiopia</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10865</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4321.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18914.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">81.49</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">74.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">26.59</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##30##45##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Tanzania</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">14541</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5058.13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">309.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">73.47</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">19.88</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.35</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.35</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##31##46##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Nigeria</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2320.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6770</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7230</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">870</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">25.20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">54.80</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##32##47##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ethiopia</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">21508</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6798.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7428.67</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">200.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">51.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22.65</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.51</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.88</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">This work</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab8\"><label>Table 8</label><caption><p>Comparison of daily intake of mineral nutrients from <italic>M. stenopetala</italic> leaves with recommended daily intake and tolerable upper limit of daily intake.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Elements</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Concentration in leaf (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Amount of nutrients per 200 g of leaf consumed</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Recommended daily intake [##UREF##4##7##, ##UREF##34##50##]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Upper tolerance limit [##UREF##4##7##, ##UREF##34##50##]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">K</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20987–22142</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4200–4426.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4700 mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NE</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Na</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">153–245</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30.6–49</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1500 mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2300 mg/day</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ca</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7842–6749</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1568.4–1349.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1000–1200 mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2500 mg/day</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7128–6425</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1425.6–1285</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">320–420 mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">750 mg/day</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fe</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">157–246</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31.4–49.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10–15 mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">45 mg/day</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Co</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.12–4.98</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.85–0.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5–40 <italic>μ</italic>g/day</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.25 mg/day</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">42.2–57.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.24–11.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.8–2.3 mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11 mg/day</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Zn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">16.2–27.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.32–5.53</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10–15 mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40 mg/day</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cr</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.22–0.62</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.04–0.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">25–35 <italic>μ</italic>g</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">120 <italic>μ</italic>g/day</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cu</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.13–9.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.79–1.88</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.9–2 mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10 mg/day</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab9\"><label>Table 9</label><caption><p>Analysis of variance between and within <italic>M. stenopetala</italic> leaf samples at a 95% confidence level.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Elements</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Comparison</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">SD (mg kg<sup>−1</sup>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">D<sub>f</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">F<sub>cal</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">F<sub>crit</sub></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Remark</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">K</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">93</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.29</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">NSD</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">85</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Na</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">38.91</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">SDs</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.72</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Ca</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">1.61</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">NSD</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">19.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">53.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">54.18</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">SDs</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">37.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Fe</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.37</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">44.58</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">SDs</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.79</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Co</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">1.87</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">NSD</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Ni</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.08</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">67.48</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">SDs</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.07</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Mn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">49.27</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">SDs</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.32</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Zn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.19</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">59.64</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">SDs</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.37</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Cr</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.06</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">61.45</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">SDs</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.04</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr><tr><td align=\"left\" colspan=\"7\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"2\" colspan=\"1\">Cu</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.41</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">2.54</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">NSD</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">WS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab10\"><label>Table 10</label><caption><p>Pearson's correlation between mineral nutrients in <italic>M. stenopetala</italic> leaves and soil samples (<italic>n</italic> = 4).</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Elements</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">K</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Na</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ca</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Mg</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Fe</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Co</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ni</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Mn</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Zn</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cr</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cu</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<italic>r</italic>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.869</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.842</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.997</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.797</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.898</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.437</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.887</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.442</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.551</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.584</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.921</td></tr></tbody></table></table-wrap>" ]
[]
[]
[]
[]
[]
[ "<supplementary-material id=\"supp-1\" position=\"float\" content-type=\"local-data\"><label>Supplementary Materials</label><caption><p>Table S1: MP-AES operating parameters. Table S2A: Pearson's correlation for <italic>M. stenopetala</italic> leaf samples. Table S2B: Pearson's correlation for supportive soil samples.</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p>\n<sup>\n<italic>∗</italic>\n</sup>The optimal acid mixture volume.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>\n<sup>\n<italic>∗</italic>\n</sup>The optimal digestion time.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>\n<sup>\n<italic>∗</italic>\n</sup>The optimal digestion temperature.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>\n<sup>\n<italic>∗</italic>\n</sup>ND = not detected.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>L = leaf; Sd = seed; So = soil; CM = Chano Mile; NK = Nechisar Kebele; and KS = Konso Special Woreda.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>NE = not established.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>BS = between samples, WS = within samples, NSD = no significant difference, SDs = significant difference, SD = standard deviation, D<sub>f</sub> = degree of freedom, F<sub>cal</sub> = Fcalculated, and F<sub>crit</sub> = Fcritical.</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"8981995.f1.docx\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
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2024-01-14 23:41:54
J Anal Methods Chem. 2024 Jan 5; 2024:8981995
oa_package/56/7d/PMC10787013.tar.gz
PMC10787014
34543723
[ "<title>Introduction</title>", "<p id=\"p0005\"><italic>N</italic><sup>6</sup>-methyladenosine (m<sup>6</sup>A) is a ubiquitous epigenetic marker in mammalian mRNAs ##REF##4372599##[1]##. As the first reversible RNA modification, m<sup>6</sup>A is installed by methyltransferase (METTL3, METTL14, and WTAP) ##REF##30262497##[2]##, and reversed by demethylases FTO and ALKBH5 ##REF##22002720##[3]##, ##REF##23177736##[4]##. m<sup>6</sup>A is recognized by YTHDF1, YTHDF2, eIF3, and others ##REF##2216767##[5]##, ##REF##29715522##[6]##. Of these m<sup>6</sup>A-reader proteins, YTHDF2 recognizes m<sup>6</sup>A in mRNAs and targets the transcripts triggering the rapid degradation of m<sup>6</sup>A-containing mRNAs, whereas YTHDF1 and eIF3 bind to m<sup>6</sup>A-containing transcripts and promote the translation ##REF##30262497##[2]##. The critical roles of m<sup>6</sup>A involved in numerous biological processes, such as maternal mRNA clearance, DNA repair, embryonic development, sex determination, and spermatogenesis ##REF##30150673##[7]##, ##REF##28297716##[8]##, ##REF##25456834##[9]##, ##REF##27919077##[10]##, ##REF##28914256##[11]##, ##REF##28297667##[12]##, have been revealed in recent studies using knockout mouse models.</p>", "<p id=\"p0010\">The testis offers lifelong male fertility by producing billions of sperm daily ##REF##26537427##[13]##. Sperm are derived from spermatogonial stem cells (SSCs), which undergo self-renewal divisions to maintain the stem cell pool or differentiation to generate progenitors and spermatogonia (SPG). The differentiated SPG further develop into preleptotene spermatocytes, which undergo a last round of DNA replication before entering meiosis. Through meiosis, haploid round spermatids (RS) are generated with dramatic changes in morphology and physiology ##REF##31247585##[14]##, ##REF##15018141##[15]##. This highly organized process, named spermatogenesis, requires timely coordinated gene expression at the transcriptional and post-transcriptional levels ##UREF##0##[16]##. Spermatogenesis also involves unique characteristics, such as premade transcripts, high levels of alternative splicing, and decreased or ceased transcriptional activity at onset of meiotic prophase I and late spermiogenesis ##REF##23579190##[17]##. Note that m<sup>6</sup>A modification that mediates mRNA splicing, stability, and translation ##REF##24284625##[18]##, ##REF##26046440##[19]##, ##REF##26876937##[20]## is involved in spermatogenesis, as demonstrated by loss-of-function studies for m<sup>6</sup>A writers ##REF##28914256##[11]##, ##REF##28809392##[21]##, erasers ##REF##23177736##[4]##, ##REF##29279410##[22]##, and readers ##REF##29033321##[23]## in mice.</p>", "<p id=\"p0015\">Pigs (<italic>Sus scrofa</italic>), which are responsible for more than one third of meat produced worldwide, are important to global living demands and food security ##REF##31743062##[24]##. In addition, pigs are an excellent large animal model in biomedical research, owing to their similarities to humans in anatomy, physiology, and genetics. Although the mechanisms for spermatogenesis have been investigated extensively in mice, they remain poorly understood in pigs, and the roles of m<sup>6</sup>A in porcine spermatogenesis remain largely elusive. Here, we isolated porcine SPG, pachytene spermatocytes (PS), and RS, and performed the m<sup>6</sup>A affinity purification followed by m<sup>6</sup>A sequencing (m<sup>6</sup>A-seq) and RNA sequencing (RNA-seq). By analyzing the abundance of m<sup>6</sup>A and its roles in porcine spermatogenesis, we highlight for the first time the magnitude of m<sup>6</sup>A in transcriptional regulation in porcine spermatogenesis, thereby laying the foundation for future endeavors to link m<sup>6</sup>A to research and therapy for male infertility.</p>" ]
[ "<title>Materials and methods</title>", "<title>Animals</title>", "<p id=\"p0120\">Testis samples of 5-month-old pigs were acquired from the Besun farm, Yangling, China. After the castration, testes were transported to the pre-cold PBS (4 °C) contained 2% of penicillin and streptomycin (Catalog No. SV30010, HyClone, Logan, UT) and brought to the laboratory within 2 h. Testes were cut into small pieces and subjected to two-step enzyme digestion as previously described ##REF##23683542##[44]##. After digestion with collagenase Type IV (0.2% w/v; Catalog No. 17104019, Gibco, Grand Island, NY) at 37 °C for 30 min, the obtained seminiferous tubules were further digested by 0.25% trypsin–EDTA (Catalog No. SV30031.01, HyClone) at 37 °C for 15 min. Then, the germ cells were collected by the differential plating.</p>", "<p id=\"p0125\">The isolation of SPG, PS, and RS was conducted as previously described ##REF##28947561##[45]##. In brief, 1 × 10<sup>7</sup>–1 × 10<sup>8</sup> dispersed germ cells were suspended in 50-ml DMEM plus 0.5% BSA and load onto a 600-ml gradient of 2%–4% BSA for 3 h sediment at 4 °C. Approximately 100 6-ml fractions were collected in tubes and analyzed by the morphology and immunostaining. Fractions with high purity of SPG, PS, and RS were resuspended with TRIzol (Catalog No. 15596026, Invitrogen, Vilnius, Lithuania) and stored at −80 °C until usage.</p>", "<title>LC-MS/MS quantification of m<sup>6</sup>A levels</title>", "<p id=\"p0130\">LC-MS/MS quantification of m<sup>6</sup>A was performed by Cloudseq Biotech Inc. (Shanghai, China) following the vendors recommended protocol. Total RNA was isolated using TRIzol reagent (Catalog No. 15596026, Invitrogen) following to the manufacturer’s instruction. In brief, 1 µg of total RNA was digested by 4-µl nuclease P1 (Catalog No. N8630, Sigma, St. Louis, MO) in 40-µl buffer solution (10 mM Tris-HCl pH 7.0, 100 mM NaCl, 2.5 mM ZnCl<sub>2</sub>) at 37 °C for 12 h, followed by incubating with 1-µl alkaline phosphatase (Catalog No. P5931, Sigma) at 37 °C for 2 h. RNA solution was diluted to 100 µl and injected into LC-MS/MS. The nucleosides were separated by reverse phase high-performance liquid chromatography on an Agilent C18 column (Catalog No. 5188–5328, Agilent Technologies, San Diego, CA), coupled with MS detection using AB SCIEX QTRAP 5500 (Catalog No. AB Sciex QTrap 5500, AB Sciex LLC, Framingham, MA). Pure nucleosides were used to generate standard curves, from which the concentrations of adenosine (A) and m<sup>6</sup>A in the sample were calculated. The level of m<sup>6</sup>A was then calculated as a percentage of total unmodified A.</p>", "<title>Cell culture and RNA-interference-mediated <italic><bold>METTL3</bold></italic> knockdown</title>", "<p id=\"p0135\">The porcine SSC line was cultured in the complete medium made up of DMEM (high glucose, pyruvate; Catalog No. 11995065, Gibco), 5% (v/v) fetal bovine serum (FBS; Catalog No. 12664025, Gibco, Mesenchymal Stem Cell FBS Qualified), 5% (v/v) knockout serum replacement (KSR; Catalog No. 10828028, Gibco), 2 mM Glutamax (Catalog No. 35050061, Gibco), 1× MEM Non-Essential Amino Acids Solution (Catalog No. 11140076, Gibco), 1× MEM Vitamin Solution (Catalog No. 11120052, Gibco), 5 × 10<sup>−</sup><sup>5</sup> M 2-mercaptoethanol (Catalog No. M6250, Sigma), 1× penicillin–streptomycin (Catalog No. SV30010, HyClone), 20 ng/ml recombinant human GDNF (Catalog No. 45010, PeproTech, Rocky Hill, NJ), 40 ng/ml recombinant human GFRA1 (Catalog No. 788104, BioLegend, San Diego, CA), and 10 ng/ml recombinant human bFGF (Catalog No. 10018B, PeproTech). The cells were maintained at 37 °C in the presence of 5% CO<sub>2</sub>. For <italic>METTL3</italic> knockdown, porcine SSCs were transfected with 50 pM of siRNA duplexes against porcine <italic>METTL3</italic> (GenePharma, Shanghai, China; the RNA oligos are listed in <xref rid=\"s0125\" ref-type=\"sec\">Table S3</xref>), using Advanced DNA RNA Transfection Reagent (Catalog No. AD600025, ZETA LIFE, Menlo Park, CA) in antibiotic-free medium. Cells were collected for analysis 72 h after transfection. The cells were lysed by TRIzol (Catalog No. 15596026, Invitrogen) and stored at −80 °C until usage.</p>", "<title>Immunocytochemistry</title>", "<p id=\"p0140\">The isolated SPG, PS, and RS were fixed with 4% paraformaldehyde for 25 min at 4 °C and washed with PBS for three times. Then, the cells were permeabilized for 10 min using 0.1% Triton-X 100 followed by washing with PBS for three times. The cells were further blocked with 10% donkey serum for 2 h at room temperature, and incubated with primary antibodies, including UCHL1 (Catalog No. ab8189, Abcam, Cambridge, Britain), SYCP3 (Catalog No. ab15093, Abcam), and CD63 (Catalog No. 25682-1-AP, Proteintech, Wuhan, China) at a dilution with 1:200 overnight at 4 °C. Next day, the cells were washed with PBS for 4 times and incubated with secondary antibody (Yeasen, Shanghai, China) at a dilution with 1:400 for 1 h at room temperature. For cell proliferation detection, porcine SSCs were detected for the EdU incorporation by Cell-Light EdU Apollo488 <italic>in vitro</italic> Kit (Catalog No. C10310-3, RiboBio, Guangzhou, China) according to the manufacturer’s protocol. The nucleus was labeled with DAPI (Catalog No. BD5010, Bioworld Technology, St. Louis Park, MN). A fluorescence microscope (Leica, Germany) was used for fluorescence observation and photographing.</p>", "<title>m<sup>6</sup>A-RIP-seq and data analysis</title>", "<p id=\"p0145\">m<sup>6</sup>A-RIP-seq was performed by Cloudseq Biotech Inc. (Shanghai, China) as previously described ##REF##31650864##[46]##. In brief, total RNA was extracted by using TRIzol (Catalog No. 15596026, Invitrogen). Denaturing agarose electrophoresis was used for confirming RNA integrity. Then, mRNA was isolated from total RNA by Seq-Star poly(A) mRNA Isolation Kit (Catalog No. AS-MB-006-01, Arraystar, Rockville, MD). The m<sup>6</sup>A RNA immunoprecipitation (IP) was conducted by GenSe m<sup>6</sup>A RNA IP Kit (Catalog No. GS-ET-001, GenSeq, Shanghai, China) according to the manufacturer’s instructions. Libraries were constructed from the samples with and without m<sup>6</sup>A IP by NEBNext Ultra II Directional RNA Library Prep Kit (Catalog No. E7760, New England Biolabs, Ipswich, MA). Library was evaluated by the BioAnalyzer 2100 system (Catalog No. G2939BA, Agilent Technologies) and sequenced on an Illumina Hiseq 4000 (Catalog No. SY-401-4001, Illumina, San Diego, CA) with 150 bp paired-end reads.</p>", "<p id=\"p0150\">After quality controlled by Q30, 3′ adaptor and low-quality reads were removed by cutadapt software (v1.9.3). Clean reads of all libraries (<italic>n</italic> = 3 for each group) were aligned to the reference genome (susScr11) by Hisat2 software (v2.0.4; −<italic>p</italic> 10 −q −−rna−strandness RF). Methylated sites were identified by MACS (v1.4) software (<italic>P</italic> &lt; 0.00001) and visualized by Integrative Genomics Viewer (IGV; v2.5.0). Motifs enriched in m<sup>6</sup>A peaks were identified using DREME ##UREF##3##[47]##. Fifty nucleotides on each side of the top 1000 peaks in each sample were used for motif enrichment. GO analysis was performed by R package topGo (v3.2). The dot plot shows the gene ratio values of the top 10 significant enrichment terms.</p>", "<title>Dot-blot</title>", "<p id=\"p0155\">RNA was isolated and loaded on the positively charged nylon transfer membrane. After crosslinking by UV, the membrane was blocked by the 5% non-fat milk for 2 h, and followed by incubation with rabbit anti-m<sup>6</sup>A antibody (1:1000; Catalog No. 202003, Synaptic Systems, Göttingen, Germany) at 4 °C overnight. Then, the membrane was incubated with HRP-conjugated goat anti-rabbit IgG at room temperature for 2 h followed by ECL imaging system (Catalog No. WBKLS0100, Millipore, Burlington, MA). Finally, the membrane was stained with 0.02% methylene blue to evaluate RNA amount.</p>", "<title>RNA-seq and data analysis</title>", "<p id=\"p0160\">The rRNAs were removed from total RNA by NEBNext rRNA Depletion Kit (Catalog No. E6310, New England Biolabs) following the manufacturer’s instruction. NEBNext Ultra II Directional RNA Library Prep Kit (Catalog No. E7760, New England Biolabs) was used to construct RNA libraries. Library quality was confirmed by BioAnalyzer 2100 system (Catalog No. G2939BA, Agilent Technologies). Library sequencing was performed on an Illumina Hiseq 4000 (Catalog No. SY-401-4001, Illumina) with 150 bp paired end reads.</p>", "<p id=\"p0165\">After raw data process (<italic>n</italic> = 3 for each group), high-quality clean reads were aligned to the reference genome (susScr11) with Hisat2 software (v2.0.4; −<italic>p</italic> 10 −q −−rna−strandness RF). Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization based on the Ensembl gtf gene annotation file (v11.1.103). The differentially expressed mRNA was identified and used for further analysis. The R package heatmap.2 was used for heat-map drawing.</p>", "<title>m<sup>6</sup>A-RIP-qPCR</title>", "<p id=\"p0170\">Total RNA was extracted from porcine SPG, PS, and RS using TRIzol (Catalog No. 15596026, Invitrogen). mRNA was isolated using the PolyATtract mRNA Isolation Systems (Catalog No. Z5310, Promega, Madison, WI) following the manufacturer’s instructions. IP mixture was composed by 6 µg of rabbit anti-m<sup>6</sup>A antibody (Catalog No. 202003, Synaptic Systems), mRNA, IP buffer (50 mM Tris-HCl pH 7.4, 750 mM NaCl, and 0.5% NP-40), RNase inhibitor (Catalog No. AM2682, Invitrogen), and RNase-free water up to 500 µl in total volume. After being mixed by rotating for 2 h at 4 °C, the IP mixture was incubated with the Protein A beads (Catalog No. 10002D, Invitrogen) which have been washed for three times and blocked by 0.5 mg/ml BSA, followed by rotating overnight at 4 °C. Precipitated mRNA was eluted using elution buffer (1× IP buffer, 6.7 mM m<sup>6</sup>A). For the detection of the fold enrichment of m<sup>6</sup>A level, precipitated mRNA and input RNA were subjected to cDNA synthesis and qRT-PCR, respectively. The primers are listed in <xref rid=\"s0125\" ref-type=\"sec\">Table S3</xref>.</p>", "<title>qRT-PCR</title>", "<p id=\"p0175\">qRT-PCR analysis was performed with FastStart Essential DNA Green Master (Catalog No. 06402712001, Roche, Mannheim, Germany) using an IQ-5 (Bio-Rad, Hercules, CA). The relative expression was normalized to <italic>GAPDH</italic> and <italic>HPRT1</italic>, and then calculated using the comparative Ct method (2<sup>−ΔΔC</sup><sup>t</sup>). The primers are listed in <xref rid=\"s0125\" ref-type=\"sec\">Table S3</xref>.</p>" ]
[ "<title>Results</title>", "<title>Enrichment and characterization of porcine male germ cells</title>", "<p id=\"p0020\">To obtain the transcriptome-wide map of m<sup>6</sup>A during spermatogenesis, we first isolated SPG, PS, and RS from porcine testes using STA-PUT velocity sedimentation. The purity of the isolated SPG, PS, and RS was determined by several biomarkers. Immunocytochemical analysis showed that the isolated SPG, PS, and RS were positive for ubiquitin carboxyl-terminal esterase L1 (UCHL1), synaptonemal complex protein 3 (SYCP3), CD63 Molecule (CD63), respectively (##FIG##0##Figure 1##A–C). In addition, the nuclei of the isolated SPG, PS, and RS were around 7–8 µm, 12–13 µm, and 5 µm in diameter, respectively (##FIG##0##Figure 1##A–C). These results suggest that the freshly isolated germ cells were SPG, PS, and RS with biochemical and nuclear characteristics.</p>", "<title>m<sup>6</sup>A-seq analysis of porcine male germ cells</title>", "<p id=\"p0025\">To elucidate the m<sup>6</sup>A methylome in different stages of spermatogenesis, the liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to quantify the changes of m<sup>6</sup>A modification in the isolated germ cells (##FIG##1##Figure 2##A). The m<sup>6</sup>A was presented in all mRNAs of the tested male germ cells, and the level of m<sup>6</sup>A remained relatively stable (∼ 0.3%) during the developmental stages. To further uncover the dynamics of m<sup>6</sup>A, the m<sup>6</sup>A-seq was performed and the locations of m<sup>6</sup>A peaks along the transcripts were determined. We found that m<sup>6</sup>A peaks were highly enriched near the start codon (startC), coding sequence (CDS), and stop codon (stopC) in the germ cells, but there were some differences among the three stages of germ cells (##FIG##1##Figure 2##B). The m<sup>6</sup>A peaks near the startC were 17.1% in SPG, 15.6% in PS, and 18.3% in RS (##FIG##1##Figure 2##B). m<sup>6</sup>A peaks near the CDS increased 5.5% from SPG to PS, followed by a 2.4% drop from PS to RS (##FIG##1##Figure 2##B). Furthermore, the abundance of m<sup>6</sup>A peaks near the stopC decreased 2.6% in PS (36.2%; ##FIG##1##Figure 2##B) and then stabilized in RS (35.9%; ##FIG##1##Figure 2##B).</p>", "<p id=\"p0030\">The distribution of m<sup>6</sup>A in the whole transcriptome was validated by the m<sup>6</sup>A reads along transcripts. Consistent with the distribution of m<sup>6</sup>A peaks, m<sup>6</sup>A reads were distributed throughout the mRNA transcripts, in which the reads increased in the CDS and reached the peak at the 3′ UTR (##FIG##1##Figure 2##C). Specifically, in the CDS, the density of m<sup>6</sup>A reads in PS was higher than that in RS, followed by in SPG (##FIG##1##Figure 2##C). In addition, the density of m<sup>6</sup>A reads in the 3′ UTR of SPG was higher than that in PS and RS (##FIG##1##Figure 2##C). Together, the results reveal that m<sup>6</sup>A is dynamic in porcine male germ cells, which suggests its critical roles during spermatogenesis.</p>", "<p id=\"p0035\">To determine whether the RRACH is the m<sup>6</sup>A consensus sequence in porcine germ cells, we analyzed the 1000 most significant peaks. The GGACU was a top motif in all tested samples (##FIG##1##Figure 2##D–F), suggesting that the RRACH motif adopted in porcine spermatogenesis is conserved in pigs and mice ##REF##28914256##[11]##. It is important to note that as a top motif in SPG (##FIG##1##Figure 2##D), PS (##FIG##1##Figure 2##E), and RS (##FIG##1##Figure 2##F), the GGACU is an m<sup>6</sup>A-modified sequence prevalent in porcine male germ cells.</p>", "<title>m<sup>6</sup>A-enriched genes are involved in important biological processes</title>", "<p id=\"p0040\">We discovered 11,241 methylated genes in porcine male germ cells. Of these, 2378, 277, and 841 methylated genes were exclusively expressed in SPG, PS, and RS, respectively (##FIG##2##Figure 3##A). Gene Ontology (GO) biological process analysis revealed that the 4886 continuously methylated genes were mostly involved in metabolic processes (##FIG##2##Figure 3##B). We then analyzed the genes containing altered m<sup>6</sup>A peaks (fold change ≥ 2, <italic>P</italic> ≤ 10E−5) to uncover more insights into m<sup>6</sup>A in porcine spermatogenesis. Results showed that 692 and 3662 genes were up- and down-methylated in PS, respectively, when compared to SPG; 3058 and 884 genes were up- and down-methylated in RS, respectively, when compared to PS (<xref rid=\"s0125\" ref-type=\"sec\">Table S1</xref>). GO biological process analysis revealed that up-methylated genes in PS (<italic>vs.</italic> SPG) were involved in spermatogenesis, whereas down-methylated genes were mostly involved in metabolic processes (##FIG##2##Figure 3##C). In addition, the up-methylated genes in RS (<italic>vs.</italic> PS) participated in developmental and metabolic processes, and down-methylated genes were mostly involved in the regulation of chromosome organization, nucleic acid metabolic, and microtubule-based process (##FIG##2##Figure 3##D).</p>", "<p id=\"p0045\">Next, we compared the m<sup>6</sup>A-modified genes between porcine and mouse germ cells ##REF##28914256##[11]##. A total of 6090, 3172, and 5123 m<sup>6</sup>A-modified genes were uniquely found in porcine SPG, PS, and RS, respectively, whereas 3525, 3157, and 2816 m<sup>6</sup>A-modified genes were shared by both murine and porcine SPG, PS, and RS, respectively (##FIG##2##Figure 3##E). Notably, these overlapping m<sup>6</sup>A-methylated transcripts were preferentially enriched and reported to be essential for mouse spermatogenesis ##REF##28914256##[11]## (##FIG##2##Figure 3##F), indicating that m<sup>6</sup>A mediates conserved processes in male germ cells.</p>", "<title>Gene expression during spermatogenesis</title>", "<p id=\"p0050\">To further probe the regulatory roles of m<sup>6</sup>A, we performed RNA-seq analysis on these germ cells. We analyzed differentially expressed genes (DEGs; fold change ≥ 2, <italic>P</italic> &lt; 0.05, FPKM ≥ 0.1) between continually developing germ cells. Results showed that 4393 and 5949 genes were up- and down-regulated in PS, respectively, when compared to SPG (##FIG##3##Figure 4##A; <xref rid=\"s0125\" ref-type=\"sec\">Table S2</xref>); 5119 and 2872 genes were up- and down-regulated in RS, respectively, when compared to PS (##FIG##3##Figure 4##B; <xref rid=\"s0125\" ref-type=\"sec\">Table S2</xref>). GO biological process annotation analysis revealed that in PS, the up-regulated genes (<italic>vs.</italic> SPG) mainly participated in cilium organization and spermatogenesis, while the down-regulated genes were involved in anatomical structure morphogenesis and regulation of developmental processes (##FIG##3##Figure 4##C). In RS (<italic>vs.</italic> PS), the up-regulated genes mainly regulated cell communication and developmental processes, whereas the down-regulated genes regulated chromosome organization and DNA metabolic process (##FIG##3##Figure 4##D). Given these findings on m<sup>6</sup>A-mediated processes (##FIG##2##Figure 3##C and D), we propose that the m<sup>6</sup>A modification might influence gene expression, thereby regulating spermatogenesis.</p>", "<title>m<sup>6</sup>A modification is involved in gene expression regulation</title>", "<p id=\"p0055\">We found that 36.8%, 30.6%, and 39.7% of the stage-specific transcripts, <italic>i.e.</italic>, for SPG, PS, and RS, respectively, were m<sup>6</sup>A modified (##FIG##4##Figure 5##A). To explore whether the m<sup>6</sup>A modification influences gene expression, we conducted a paired analysis of differentially methylated genes (DMGs) and DEGs between each two adjacent stages.</p>", "<p id=\"p0060\">Among m<sup>6</sup>A up-methylated genes, 1172 and 1620 genes showed up-regulated expression during the transition from SPG to PS and from PS to RS, respectively (##FIG##4##Figure 5##B), while 160 and 633 genes showed down-regulated expression during the transition from SPG to PS and from PS to RS, respectively (##FIG##4##Figure 5##B). Among the m<sup>6</sup>A down-methylated genes, the expression levels of 2812 and 795 genes were decreased during the transition from SPG to PS and from PS to RS, respectively (##FIG##4##Figure 5##C), whereas those of 1082 and 146 genes were increased during the transition from SPG to PS and from PS to RS, respectively (##FIG##4##Figure 5##C). Hence, m<sup>6</sup>A exhibits positive correlation with gene expression.</p>", "<p id=\"p0065\">To further uncover the biological significance of the dynamically modified m<sup>6</sup>A genes, we performed the GO biological process analysis with positive correlations with m<sup>6</sup>A modification. Compared to SPG, the up-regulated genes in PS mainly participated in the regulation of spermatogenesis and microtubule-based process (##FIG##4##Figure 5##D), and the down-regulated genes in PS were involved in the regulation of metabolic processes and developmental process (##FIG##4##Figure 5##E). Compared to PS, the up-regulated genes in RS regulated the developmental process and tube morphogenesis, and the down-regulated genes in RS participated in the sister chromatid segregation, DNA metabolic process, and microtubule-based process. Together, these findings reveal that m<sup>6</sup>A regulates gene expression and spermatogenesis.</p>", "<title>m<sup>6</sup>A-regulated gene expression is associated with the fate of SSCs</title>", "<p id=\"p0070\">Previous studies have shown that the methyltransferase SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) catalyzes tri-methylation of histone H3 lysine 9 (H3K9me3) and plays important roles for SSC survival ##REF##28890329##[25]##, ##UREF##1##[26]##, ##UREF##2##[27]##. Meanwhile, deficiencies in FOXO1, FOXO3, and FOXO4 impair the self-renewal and differentiation of SSCs ##REF##21865646##[28]##. To determine whether m<sup>6</sup>A regulates the expression of these genes, we analyzed m<sup>6</sup>A modification patterns on <italic>SETDB1</italic> and <italic>FOXO3</italic> transcripts by m<sup>6</sup>A-RIP-qPCR. We found that both <italic>SETDB1</italic> and <italic>FOXO3</italic> transcripts contained at least one m<sup>6</sup>A peak (##FIG##5##Figure 6##A). <italic>SETDB1</italic> was up-methylated from SPG to PS and down-methylated from PS to RS, whereas <italic>FOXO3</italic> was down-methylated from SPG to PS and then up-methylated from PS to RS (##FIG##5##Figure 6##B). Quantitative real-time PCR (qRT-PCR) analysis revealed that the mRNA levels of <italic>SETDB1</italic> and <italic>FOXO3</italic> were strongly positively correlated with m<sup>6</sup>A modifications (##FIG##5##Figure 6##C).</p>", "<p id=\"p0075\">To further validate the regulatory roles of m<sup>6</sup>A, we knocked down <italic>METTL3</italic> in porcine SSCs by a small interfering RNA (siRNA) ##REF##32308978##[29]##, ##REF##30787270##[30]## (##FIG##5##Figure 6##D). Knockdown of <italic>METTL3</italic> (si<italic>METTL3</italic>) led to a decrease in m<sup>6</sup>A level, compared to the scramble control (siCtrl) (##FIG##5##Figure 6##E). Nevertheless, EdU incorporation showed that cell proliferation was not significantly different between cells transfected with siCtrl and si<italic>METTL3</italic> (##FIG##5##Figure 6##F). m<sup>6</sup>A-RIP-qPCR revealed that knockdown of <italic>METTL3</italic> significantly reduced the relative level of m<sup>6</sup>A in <italic>SETDB1</italic>, <italic>FOXO1</italic>, and <italic>FOXO3</italic> (##FIG##5##Figure 6##G). In addition, qRT-PCR analysis showed that the expression of these three targeted genes was significantly down-regulated (##FIG##5##Figure 6##H), consistent with the dynamics in SPG and PS showed by RNA-seq data (##FIG##5##Figure 6##A and C). Thus, these data suggest that m<sup>6</sup>A regulates the dynamic gene expression during porcine spermatogenesis.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0080\">Growing evidence has demonstrated the critical roles of m<sup>6</sup>A in murine spermatogenesis ##REF##28914256##[11]##, ##REF##28809392##[21]##. The highly dynamic spermatogenesis process requires precise regulation of gene expression. Here, we reported that m<sup>6</sup>A modification was dynamically present in the transcripts of porcine male germ cells, which influenced gene expression.</p>", "<p id=\"p0085\">In this study, m<sup>6</sup>A was distributed predominantly on the consensus motif of GGACU, which is consistent with murine male germ cells ##REF##29033321##[23]##. The m<sup>6</sup>A was present throughout mRNA transcripts in porcine germ cells, especially increased the read density in the CDS. The m<sup>6</sup>A reached its highest value around the stopC and then decreased in the 3′ UTR. This distribution pattern agrees with the previous findings in mouse ##REF##28914256##[11]##. Hence, m<sup>6</sup>A modification exhibits evolutionally conserved features in male germ cells in mouse and pig.</p>", "<p id=\"p0090\">Note that the abundance of m<sup>6</sup>A in transcripts varied by the developmental stage during spermatogenesis. We found that m<sup>6</sup>A read density in the CDS was greater in PS and RS, whereas in the 3′ UTR it was greater in SPG. In a previous study, Lin et al. reported that m<sup>6</sup>A read density in the CDS in PS/diplotene spermatocytes and RS was higher than that in the undifferentiated SPG, type A1 SPG, and preleptotene spermatocytes ##REF##28914256##[11]##. The highest density of m<sup>6</sup>A reads was in the 3′ UTR close to the stopC of PS/diplotene spermatocytes, and the lowest of that was in type A1 SPG ##REF##28914256##[11]##. In addition, Tang et al. reported that m<sup>6</sup>A was enriched in long 3′ UTR transcripts of murine RS and elongating spermatids ##REF##29279410##[22]##. In general, m<sup>6</sup>A in the CDS is correlated with translational products, and m<sup>6</sup>A in the 3′ UTR is preferentially bound by factors regulating alternative splicing and polyadenylation, subcytoplasmic compartmentalization, and stability ##REF##22608085##[31]##, ##REF##22575960##[32]##. Therefore, dynamically changed m<sup>6</sup>A around these landmarks could mediate specific transcript outputs in a stage-specific manner during mammalian spermatogenesis.</p>", "<p id=\"p0095\">During spermatogenesis, SPG undergo mitosis to give rise to spermatocytes. Depletion of METTL3 or METTL14 in germ cells induced a 70% reduction of m<sup>6</sup>A in undifferentiated SPG and a 55%–65% reduction of m<sup>6</sup>A in PS ##REF##28914256##[11]##. METTL3 deficiency induced the abnormal initiation of spermatogonial differentiation and disrupted the ability of spermatocytes to reach the pachytene stage of meiotic prophase ##REF##28809392##[21]##. In this study, the down-methylated genes from SPG to PS mainly participated in metabolic processes, and most m<sup>6</sup>A down-methylated genes that were also mainly involved in metabolic and developmental processes were down-regulated. It is interesting that SPG that are localized in the basal compartment of seminiferous tubules exhibit high glycolytic activity ##REF##19414527##[33]##. In contrast, PS and RS, which are distributed in the luminal compartment, satisfy their ATP supply mainly through the aerobic (OXPHOS) pathway. Therefore, m<sup>6</sup>A might play critical roles in mediating mitochondrial function from SPG to PS.</p>", "<p id=\"p0100\">A report showed that the loss of ALKBH5 markedly increased m<sup>6</sup>A levels in testes ##REF##23177736##[4]##. A delay in spermatocyte development occurred in the <italic>ALKBH5</italic>-knockout testes, which was due to the dysregulation of genes involved in meiotic progression ##REF##23177736##[4]##, ##REF##29279410##[22]##. The up-methylated genes in PS preferentially participated in spermatogenesis and cell cycle process. These genes were also up-regulated by m<sup>6</sup>A modification, indicating an important role of m<sup>6</sup>A at early developmental stages. To generate the haploid spermatids, spermatocytes must undergo two meiotic divisions. The first meiotic division promotes the pairing and exchange of genetic materials, and the second meiotic division is more comparable to mitotic divisions as it contains the segregation of sister chromatids ##REF##31566717##[34]##. In addition, m<sup>6</sup>A in PS was also enriched in genes that functioned in spermatid development and up-regulated the expression of genes involving in microtubule-based process, cilium organization, and cilium assembly. It is reasonable to speculate that m<sup>6</sup>A-methylated mRNAs may repress translation before spermiogenesis.</p>", "<p id=\"p0105\">During spermiogenesis, RS go through multistep cytological changes, such as the formation of an acrosome and a flagellum, chromatin remodeling, and the removal of the residual body ##REF##15018141##[15]##, ##REF##31085275##[35]##. <italic>METTL3</italic>-knockout or <italic>METTL14</italic>-knockout result in a 45% reduction of m<sup>6</sup>A abundance in RS ##REF##28914256##[11]##. The seminiferous tubules contain very few spermatozoa, and sperms exhibit defects in motility, flagella, and head ##REF##28914256##[11]##. In the present study, m<sup>6</sup>A up-methylated genes in RS showed up-regulated expression, and these genes mainly participated in regulating developmental process, including the development of multicellular organisms, anatomical structures, and tube morphogenesis, suggesting the conserved roles of m<sup>6</sup>A in mediating porcine spermiogenesis. At the beginning of spermiogenesis, nuclear condensation begins and histones are rapidly replaced by protamines ##REF##11411307##[36]##, ##REF##20403875##[37]##. The mRNAs are massively eliminated during spermiogenesis ##REF##24787618##[38]##. m<sup>6</sup>A in PS shows heavy enrichment in genes regulating chromosome organization and nucleic acid metabolic, which are essential for meiosis and down-regulated in RS. Because of the greater m<sup>6</sup>A retention in the longer pre-mRNA of the <italic>ALKBH</italic>-knockout testis, the splicing of these transcripts is enhanced and further causes the production of shorter transcripts. m<sup>6</sup>A modification of the short transcripts further serves as a signal to quickly degrade elongating spermatids ##REF##29279410##[22]##. Piwi-interacting RNAs (piRNAs) are responsible for degrading large populations of mRNAs in the late stage of spermiogenesis ##REF##24787618##[38]##. It is intriguing that piRNA target sites are preferentially located in the 3′ UTR of the target mRNAs ##REF##25582079##[39]##. Given the high-level m<sup>6</sup>A modification on the mRNA 3′ UTR, it is possible that m<sup>6</sup>A mediates the piRNA-dependent mRNA degradation pathway during spermiogenesis.</p>", "<p id=\"p0110\">Expression of <italic>FOXOs</italic> in germ cells is intimately associated with cell fate, which are responsible for cell cycle arrest and programmed cell death ##REF##10102273##[40]##. Our previous studies revealed that knockdown of <italic>SETDB1</italic> to an extremely low level could activate <italic>FOXO1</italic> that is the most important <italic>FOXOs</italic> in spermatogenesis ##REF##28890329##[25]##, ##UREF##1##[26]##, ##UREF##2##[27]##. Here, we provide evidence that m<sup>6</sup>A regulates the expression of <italic>SETDB1</italic>, <italic>FOXO1</italic>, and <italic>FOXO3</italic> during porcine spermatogenesis. Unlike the hypo-proliferation in <italic>SETDB1</italic>-knockdown SSCs or gonocytes ##UREF##1##[26]##, ##UREF##2##[27]##, <italic>METTLE3</italic>-knockdown mildly promotes proliferation, suggesting that other methyltransferases, such as SUV39H1 and SUV39H2, may partially compensate for SETDB1 deficiency ##REF##25417163##[41]##. Moreover, deleting <italic>METTL3</italic> from murine SSCs induces the hyper-proliferation and impaired differentiation ##REF##28914256##[11]##, ##REF##28809392##[21]##. Recent work has showed that m<sup>6</sup>A on retroviral element RNAs recruit SETDB1 to regulate heterochromatin in mouse embryonic stem cells ##REF##33505026##[42]##, ##REF##33658714##[43]##. It would be worthwhile to study whether and how m<sup>6</sup>A regulates <italic>SETDB1</italic> expression and H3K9 methylation, which further govern the fate of SSCs.</p>", "<p id=\"p0115\">In conclusion, we present here the first m<sup>6</sup>A transcriptome-wide map of porcine spermatogenesis. Our findings provide a roadmap for uncovering m<sup>6</sup>A functions that might improve porcine fertility and treat infertility in humans.</p>" ]
[]
[ "<p id=\"np010\">Equal contribution.</p>", "<p><bold>Spermatogenesis</bold> is a continual process that occurs in the testes, in which diploid <bold>spermatogonial stem cells</bold> (SSCs) differentiate and generate haploid spermatozoa. This highly efficient and intricate process is orchestrated at multiple levels. <bold><italic>N</italic><sup>6</sup>-methyladenosine</bold> (m<sup>6</sup>A), an epigenetic modification prevalent in mRNAs, is implicated in the transcriptional regulation during spermatogenesis. However, the dynamics of m<sup>6</sup>A modification in non-rodent mammalian species remains unclear. Here, we systematically investigated the profile and role of m<sup>6</sup>A during spermatogenesis in <bold>pigs</bold>. By analyzing the transcriptomic distribution of m<sup>6</sup>A in spermatogonia, spermatocytes, and round spermatids, we identified a globally conserved m<sup>6</sup>A pattern between porcine and murine genes with spermatogenic function. We found that m<sup>6</sup>A was enriched in a group of genes that specifically encode the metabolic enzymes and regulators. In addition, transcriptomes in porcine male germ cells could be subjected to the m<sup>6</sup>A modification. Our data show that m<sup>6</sup>A plays the regulatory roles during spermatogenesis in pigs, which is similar to that in mice. Illustrations of this point are three genes (<bold><italic>SETDB1</italic></bold>, <italic>FOXO1</italic>, and <italic>FOXO3</italic>) that are crucial to the determination of the fate of SSCs. To the best of our knowledge, this study for the first time uncovers the expression profile and role of m<sup>6</sup>A during spermatogenesis in large animals and provides insights into the intricate transcriptional regulation underlying the lifelong male fertility in non-rodent mammalian species.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Yun-Gui Yang</p>" ]
[ "<title>Ethical statement</title>", "<p id=\"p0180\">All experimental procedures involving animals were approved by the Northwest A&amp;F University’s Institutional Animal Care and Use Committee, China (Approval No. DK-20180375).</p>", "<title>Data availability</title>", "<p id=\"p0185\">The datasets generated in the current study have been deposited in the Genome Sequence Archive ##REF##34400360##[48]## at the National Genomics Data Center, Beijing Institute of Gemonics, Chinese Academy of Sciences / China National Center for Bioinformation (GSA: CRA003615), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa\" id=\"PC_linkE0TNs4aVUI\">https://ngdc.cncb.ac.cn/gsa</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0190\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0195\"><bold>Zidong Liu:</bold> Conceptualization, Validation, Formal analysis, Investigation, Writing – original draft, Visualization. <bold>Xiaoxu Chen:</bold> Conceptualization, Formal analysis, Investigation, Writing – original draft, Visualization. <bold>Pengfei Zhang:</bold> Validation, Investigation. <bold>Fuyuan Li:</bold> Validation, Investigation. <bold>Lingkai Zhang:</bold> Formal analysis. <bold>Xueliang Li:</bold> Writing – review &amp; editing. <bold>Tao Huang:</bold> Investigation, Writing – original draft. <bold>Yi Zheng:</bold> Writing – review &amp; editing. <bold>Taiyong Yu:</bold> Resources. <bold>Tao Zhang:</bold> Conceptualization, Funding acquisition. <bold>Wenxian Zeng:</bold> Conceptualization, Writing – review &amp; editing, Supervision, Project administration, Funding acquisition. <bold>Hongzhao Lu:</bold> Writing – review &amp; editing. <bold>Yinghua Lv:</bold> Writing – review &amp; editing, Funding acquisition. All authors have read and approved the final manuscript</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0210\">The following are the Supplementary data to this article:</p>", "<p id=\"p0215\">\n\n</p>", "<p id=\"p0220\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0200\">We thank Dr. Huayan Wang for polishing the language in the revised manuscript. We thank the Besun farm (Yangling, China) for providing the tissue samples. The research was supported in part by the <funding-source id=\"gp005\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100001809</institution-id><institution>National Natural Science Foundation of China</institution></institution-wrap></funding-source> (Grant No. 31572401) to Wen-xian Zeng, the <funding-source id=\"gp010\">Research Project of Shaanxi Science and Technology Department</funding-source> (Grant No. 2020NY-003) to Tao Zhang, and the <funding-source id=\"gp015\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100001809</institution-id><institution>National Natural Science Foundation of China</institution></institution-wrap></funding-source> (Grant No. 81703193) to Yinghua Lv.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Identification of porcine male germ cells</bold></p><p><bold>A.</bold> Immunocytochemistry showing the expression of UCHL1 in the SPG. <bold>B.</bold>  Immunocytochemistry showing the expression of SYCP3 in the freshly isolated PS. <bold>C.</bold> Immunocytochemistry showing the expression of CD63 in the RS. SPG, spermatogonium; PS, pachytene spermatocyte; RS, round spermatid; UCHL1, ubiquitin carboxyl-terminal esterase L1; SYCP3, synaptonemal complex protein 3; CD63, CD63 Molecule; DAPI, 4′,6-diamidino-2-phenylindole. Scale bar, 100 µm.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Distribution pattern of m<sup>6</sup>A peaks along transcripts</bold></p><p><bold>A.</bold> LC-MS/MS analysis of m<sup>6</sup>A percentage relative to adenosine in SPG, PS, and RS. <bold>B.</bold> m<sup>6</sup>A peak distribution within different gene contexts: startC, CDS, stopC, 3′ UTR, and 5′ UTR. <bold>C.</bold> Accumulation of m<sup>6</sup>A-IP reads along transcripts in SPG, PS, and RS. Each transcript is divided into three parts: 5′ UTR, CDS, and 3′ UTR. <bold>D</bold><bold>.</bold>–<bold>F.</bold> The top 3 used motifs among m<sup>6</sup>A peaks in SPG (D), PS (E), and RS (F). LC-MS/MS, liquid chromatography-tandem mass spectrometry; startC, start codon; CDS, coding sequence; stopC, stop codon; UTR, untranslated region.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>m<sup>6</sup>A modification pattern during porcine spermatogenesis</bold></p><p><bold>A.</bold> Venn diagram showing the pattern of m<sup>6</sup>A-modified genes in SPG, PS, and RS. <bold>B.</bold> The enriched biological processes of continuously methylated genes during spermatogenesis by GO analysis. <bold>C.</bold> The enriched biological processes of DMGs between PS and SPG by GO analysis. <bold>D.</bold> The enriched biological processes of DMGs between RS and PS by GO analysis. Each dot plot shows gene ratio values of the top 10 significant enrichment terms. <bold>E.</bold> Venn diagram showing the overlapping m<sup>6</sup>A-modified genes between murine and porcine in SPG, PS, and RS. <bold>F.</bold> Different proportions of the overlapping methylated genes related or unrelated to spermatogenesis in murine and porcine in SPG, PS, and RS. The <italic>P</italic> value of such difference was calculated with the Chi-square test. GO, Gene Ontology; DMG, differentially methylated gene.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Gene expression pattern during porcine spermatogenesis</bold></p><p><bold>A.</bold> The heatamap of DEGs between PS and SPG. <bold>B.</bold> The heatamap of DEGs between RS and PS. <bold>C.</bold> The enriched biological processes of DEGs between PS and SPG by GO analysis. <bold>D.</bold> The enriched biological processes of DEGs between RS and PS by GO analysis. Each dot plot shows gene ratio values of the top 10 significant enrichment terms. DEG, differentially expressed gene.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>m<sup>6</sup>A</bold>-<bold>regulated</bold><bold>gene expression during porcine spermatogenesis</bold></p><p><bold>A.</bold> The m<sup>6</sup>A modification distribution within stage-specific gene contexts. Number in the red part represents the number of genes specifically methylated in SPG, PS, or RS. <bold>B.</bold> and <bold>C.</bold> The number of up- or down-regulated genes during porcine spermatogenesis stratified by up-methylated (B) or down-methylated (C) genes. The <italic>P</italic> value of such difference was calculated with the Chi-square test. <bold>D.</bold> The enriched biological processes of m<sup>6</sup>A positively regulated genes between PS and SPG by GO analysis. <bold>E.</bold> The enriched biological processes of m<sup>6</sup>A positively regulated genes between RS and PS by GO analysis. Each dot plot shows gene ratio values of the top 10 significant enrichment terms.</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>Knockdown of <italic>METTL3</italic> in porcine</bold><bold>SSC</bold><bold>s induced the abnormal gene expression</bold></p><p><bold>A.</bold> Distribution of m<sup>6</sup>A on <italic>SETDB1</italic> and <italic>FOXO3</italic> during porcine spermatogenesis. Blue and red bars indicate the input and IP read coverage, respectively. <bold>B.</bold> Bar chart showing the m<sup>6</sup>A levels of <italic>SETDB1</italic> and <italic>FOXO3</italic> in SPG, PS, and RS validated by m<sup>6</sup>A-RIP-qPCR. <bold>C.</bold> Bar chart showing the mRNA levels of <italic>SETDB1</italic> and <italic>FOXO3</italic> in porcine SPG, PS, and RS validated by qRT-PCR. <bold>D.</bold> Immunocytochemistry showing the expression of UCHL1 in porcine SSCs. <bold>E.</bold> m<sup>6</sup>A dot blot analysis of the <italic>METTL3</italic> knockdown (si<italic>METTL3</italic>). siCtrl was used as a negative control. Methylene blue staining was used to evaluate RNA amount. <bold>F.</bold> Representative images of EdU incorporation in the cells transfected with si<italic>METTL3</italic> or siCtrl. The quantification analysis of EdU incorporation in the cells transfected with si<italic>METTL3</italic> or siCtrl was shown on the right. <bold>G.</bold> Bar chart showing the m<sup>6</sup>A levels of the targeted genes in the cells transfected with si<italic>METTL3</italic> or siCtrl validated by m<sup>6</sup>A-RIP-qPCR. <bold>H.</bold> Bar chart showing the relative expression level of <italic>METTL3</italic>, <italic>SETDB1</italic>, <italic>FOXO1</italic>, and <italic>FOXO3</italic> in the cells transfected with si<italic>METTL3</italic> or siCtrl detected by qRT-PCR. Data are presented as mean ± SEM. The <italic>P</italic> value was calculated with one-way ANOVA analysis followed by Bonferroni multiple-comparison test and unpaired <italic>t</italic>-test, *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; ns, no significance. SSC, spermatogonial stem cell; IP, immunoprecipitation; EdU, 5-ethynyl-2′-deoxyuridine; SEM, standard error of mean. Scale bar, 100 µm.</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S1</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S2</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S3</title></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e233\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0120\" fn-type=\"supplementary-material\"><p id=\"p0205\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2021.08.006\" id=\"ir010\">https://doi.org/10.1016/j.gpb.2021.08.006</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["16"], "surname": ["Hunter"], "given-names": ["N."], "article-title": ["Meiotic recombination: the essence of heredity"], "source": ["Cold Spring Harb Perspect Biol"], "volume": ["7"], "year": ["2015"], "object-id": ["a016618"]}, {"label": ["26"], "mixed-citation": ["Liu T, Zhang P, Li T, Chen X, Zhu Z, Lyu Y, et al. SETDB1 plays an essential role in maintenance of gonocyte survival in pigs. Reproduction 2017;154:23\u201334."]}, {"label": ["27"], "mixed-citation": ["An J, Zhang X, Qin J, Wan Y, Hu Y, Liu T, et al. The histone methyltransferase ESET is required for the survival of spermatogonial stem/progenitor cells in mice. Cell Death Dis 2014;5:e1196."]}, {"label": ["47"], "mixed-citation": ["Bailey TL. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 2011;27:1653\u20139."]}]
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48
CC BY
no
2024-01-14 23:41:54
Genomics Proteomics Bioinformatics. 2023 Aug 17; 21(4):729-741
oa_package/15/2f/PMC10787014.tar.gz
PMC10787015
36702236
[ "<title>Introduction</title>", "<p id=\"p0010\">Lung cancer is currently one of the most lethal and common cancers ##REF##33433946##[1]##. A series of high-throughput sequencing studies have identified critical point mutations, structural variations, and copy number variations associated with tumorigenesis in lung cancer ##REF##20951091##[2]##, ##REF##21277552##[3]##, ##REF##29364287##[4]##, ##UREF##0##[5]##, greatly augmenting our understanding of the cancer genome. However, many risk-related single nucleotide polymorphisms (SNPs) and genomic variations are found in regulatory and intergenic regions ##UREF##1##[6]##. Linking these distal regulatory elements to their target genes is crucial for a more comprehensive understanding of the cancer genome and the potential functions of non-coding regions.</p>", "<p id=\"p0015\">Chromosome conformation capture technologies, such as chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) ##REF##19890323##[7]##, can be used to explore the three-dimensional (3D) genome structure and link distal regulatory elements to their target genes. Many diseases are associated with dysregulation of the spatial structure of the genome. For example, disruption of topologically associated domains (TADs) can lead to abnormal development and malformation by preventing interactions between <italic>Shh</italic> gene and its limb enhancer ##REF##27867070##[8]##. Previous studies have used long-range interactions to map non-coding SNPs to target genes in patients with schizophrenia ##REF##27760116##[9]##. The 3D architecture of the genome is altered in many cancers ##REF##26940867##[10]##, ##REF##27053337##[11]##, ##REF##32657405##[12]##, ##REF##33510161##[13]##. Recent research used high-throughput chromosome conformation capture (Hi-C) to characterize the larger-scale 3D genomic structures in lung cancer ##REF##34116262##[14]##. Therefore, clarifying 3D genomic disorders in cancer cells may be an innovative way to conduct cancer research. However, 3D information related to gene expression regulation in lung cancer requires further study.</p>", "<p id=\"p0020\">Polycomb repressive complex 2 (PRC2) consists of core subunits, <italic>i.e.</italic>, enhancer of zeste homolog 2 (EZH2), suppressor of zest 12 (SUZ12), and embryonic ectoderm development (EED), and is critical for normal development and silencing of remote genes ##REF##16625203##[15]##, ##REF##18403752##[16]##, ##REF##19053175##[17]##, ##REF##21241892##[18]##, ##REF##30254245##[19]##. PRC2-associated chromatin interactions play an irreplaceable role in gene silencing ##REF##32094912##[20]##, ##REF##28652613##[21]##. Studies have also shown that histone 3 lysine 27 trimethylation (H3K27me3)-enriched domains have distinct intradomain interactions that play essential roles during development and in cancer cells ##REF##31837995##[22]##, ##REF##33514712##[23]##. Thus, EZH2 and repressive histone modification of H3K27me3 are potential factors for enriching genomic functional interactions.</p>", "<p id=\"p0025\">In this study, we used A549 lung cancer cells and noncancerous BEAS-2B epithelial cells as model systems and applied long-read ChIA-PET ##REF##28358394##[24]## to map global chromatin interactions associated with different factors, including RNA polymerase II (RNAPII), CCCTC-binding factor (CTCF), EZH2, and H3K27me3. These factors were selected as CTCF represents a classic structural protein in the 3D genome, RNAPII is associated with active gene transcription, and EZH2 and H3K27me3 are associated with repressive chromatin ##REF##32094912##[20]##, ##REF##33514712##[23]##, ##REF##26686651##[25]##, ##REF##22265404##[26]##. By studying the patterns and functions of different categories of interactions and comparing the differences in interactions between lung cancer and noncancerous cells, we discovered the mechanisms of dysregulation at the 3D genome level, providing new insights into the transcriptional regulation and genomic characteristics of human lung cancer.</p>" ]
[ "<title>Materials and methods</title>", "<title>Cell culture</title>", "<p id=\"p0150\">The A549 cell line (accession No. CCL-185) was purchased from the American Type Culture Collection (ATCC) and was authenticated by the GENEWIZ Company. The BEAS-2B cell line was donated by Dr. Honglin Jin’s laboratory at the Cancer Center of Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China. The A549 and BEAS-2B cell lines were cultured at 37 °C under 5% CO<sub>2</sub> in air. The A549 cells were cultured in Ham’s F12K medium (Catalog No. 21127022, Gibco, Grand Island, NY) supplemented with 10% fetal bovine serum (FBS; Catalog No. 10099141, Gibco), 0.1 mM non-essential amino acids (Catalog No. 11140050, Gibco), and 1× penicillin/streptomycin (Catalog No. 15140163, Gibco). The BEAS-2B cells were cultured in RPMI 1640 (Catalog No. 11875101, Gibco) supplemented with 10% FBS and 100 U/ml penicillin/streptomycin. For both cell lines, the medium was changed every other day. The cells were passaged by trypsin digestion three times per week.</p>", "<title>Long-read ChIA-PET</title>", "<p id=\"p0155\">For long-range interaction analysis of the A549 and BEAS-2B cells, we used long-read ChIA-PET as described previously ##REF##28358394##[24]## with some minor modifications. The cells were resuspended using trypsin digestion and then dual cross-linked with 1.5 mM ethylene glycol bis (succinimidyl succinate; Catalog No. 21565, ThermoFisher Scientific, Waltham, MA) for 40 min and with 1% formaldehyde (Catalog No. F8775, Sigma-Aldrich, St Louis, MO) for 10 min at room temperature. The cells were lysed, and chromatin was fragmented into 1–5-kb fragments by sonication (high level, 33 cycles, 30 s ON, 50 s OFF) using the sonication device (Bioruptor Plus, Diagenode, Belgium). Chromatin immunoprecipitation was used to enrich the complex fragments with magnetic beads of protein G (Catalog No. 10009D, ThermoFisher Scientific) and 60–100 µg of antibodies against RNAPII (Catalog No. SC-56767, Santa Cruz Biotechnology, Dallas, TX), EZH2 (Catalog No. 5246, Cell Signaling Technology, Danvers, MA), H3K27me3 (Custom-made, ABclonal, Wuhan, China), and CTCF (Catalog No. A1133, ABclonal). The beads were then washed, and DNA blunt ends were prepared with A tails. Bridge linkers were used to ligate the proximal DNA ends in a 1.8-ml reaction system using T4 DNA ligase (Catalog No. EL0013, ThermoFisher Scientific). The DNA extraction and library construction steps were the same as used in the previous protocol ##REF##28358394##[24]##. The libraries were paired-end sequenced (2 × 150 bp) using the Illumina HiSeq X Ten system (HiSeq X10, Illumina, San Diego, CA).</p>", "<title>Total RNA-seq</title>", "<p id=\"p0160\">Two A549 RNA-seq replicates were generated. Total RNA was extracted from one million cells using RNeasy columns (Catalog No. 74104, QIAGEN, Hilden, Germany). Ribosomal RNA (rRNA) was depleted using an rRNA Depletion Kit (Catalog No. E7400, New England Biolabs, Ipswich, MA), and then strand-specific libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit (Catalog No. E7645L, New England Biolabs) for Illumina. Paired-end (2 × 150 bp) sequencing of libraries was conducted using the Illumina HiSeq X Ten system (HiSeq X10, Illumina).</p>", "<title><bold>CRISPR/Cas9-mediated KO of <italic>NCOA3</italic>-specific enhancer</bold></title>", "<p id=\"p0165\">For the KO system, we applied chromatin fragment deletion as described previously with some modifications ##REF##26276636##[51]##. Single-guide RNA (sgRNA) templates were constructed and incorporated into pGL3-U6-sgRNA-PGK-Puromycin plasmids. The A549 cells were cultured to approximately 60% confluence and transfected with Lipofectamine 3000 (Catalog No. L3000001, ThermoFisher Scientific) in a 6-well plate with 2 μg of pcDNA3.1-Cas9 and 1.5 μg of sgRNA plasmids for the upstream target and 1.5 μg of sgRNA plasmids for the downstream target. Puromycin was added 2 days later to a final concentration of 1.2 μg/ml. The cells were then diluted and plated in 15-cm plates and cultured for 5 days to isolate single clones. For KO of the <italic>NCOA3</italic>-specific enhancer, we designed sgRNA sequences: upstream 1, 5′-ATAGAATTGCAACCTCATGGAGG-3′; upstream 2, 5′-CAGTTGTACCTACTGCCAAATGG-3′; downstream 1, 5′-CCCCCTTTGGCTGAGATAAATGG-3′; downstream 2, 5′-GTCTAGCACAATGTGGCACATGG-3′.</p>", "<title>RNA expression analysis by qRT-PCR</title>", "<p id=\"p0170\">Here, qRT-PCR was conducted on a RT PCR detection system (CFX Connect, Bio-Rad, Hercules, CA). We used Genious 2X SYBR Green Fast qPCR Mix (Catalog No. RM21203, ABclonal) for qRT-PCR. Total RNA was extracted from one million cells by RNeasy columns (Catalog No. 74104, QIAGEN). We used 2 µg of RNA to perform reverse transcription with random primers using TransScript One-Step gDNA Removal and cDNA Synthesis SuperMix (Catalog No. AT311-02, TransGen Biotech, Beijing, China). The qRT-PCR was then performed using primers (forward, 5′-GGACCTGGTTAACACAAGTG-3′; reverse, 5′-GTCCAGGAAACTCCATTAACTG-3′) for <italic>NCOA3</italic> messenger RNA (mRNA).</p>", "<title>Analysis of ChIA-PET data</title>", "<p id=\"p0175\">Long-read ChIA-PET sequence data were analyzed using a modified ChIA-PET Tool pipeline (version 3) ##REF##31336684##[52]##. Briefly, after trimming the linkers, the sequences flanking the linker were mapped to the human reference genome (hg38) using BWA-MEM (version 0.7.7) ##REF##20080505##[53]##, and only uniquely mapped (mapping qualities ≥ 30) paired-end tags (PETs) were retained. Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment, with a genomic span less than 8 kb) or an inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex from different chromosomes, or from the same chromosome with a genomic span of more than 8 kb). Self-ligation PETs were used for binding site calling, and inter-ligation PETs were used for long-range interaction calling. For RNAPII and CTCF, we used centered 3-kb regions of RNAPII and CTCF ChIP-seq peaks (GEO: GSE31477 ##REF##32728046##[54]##) as given anchors to call interaction clusters. To obtain high-confidence interactions, we included the detected interactions only if the false discovery rate was less than 0.05 and the PET count was three or more. To evaluate the robustness of the ChIA-PET method, we analyzed the biological replicates of the ChIA-PET libraries at several different resolutions. Some analysis results are presented in <xref rid=\"s0140\" ref-type=\"sec\">Figure S1</xref>. Moreover, we transformed unique ChIA-PET mapping reads to a contact matrix using ChIA-PET2 (version 0.9.3) ##REF##27625391##[55]## software and normalized the matrix using the iterative correction method in HiC-Pro (version 2.11.1) ##REF##26619908##[56]## software. Juicer (version 1.7.6) ##REF##27467249##[57]## was used to calculate A/B compartments and TADs. When calculating PCCs of the contact matrices mediated by four factors and the Hi-C contact matrices, we used Hi-C data from the ENCODE database (ENCODE: ENCSR662QKG).</p>", "<p id=\"p0180\">When comparing chromatin interactions from the lung cancer cell line A549 and noncancerous cell line BEAS-2B, we defined “altered” chromatin interactions as those specific to the A549 cell line.</p>", "<title>Hierarchical chromatin structure analysis</title>", "<p id=\"p0185\">We calculated the genomic spans of the self-ligation and inter-ligation PETs and observed 10-bp and 190-bp signals, respectively. We speculated that the two signals were DNA double-helix turn and nucleosome units, respectively. To observe the tetranucleosome signal, we defined the CTRs (center 2 kb of overlapping regions of H3K9me3 and H3K4me3 ChIP-seq peaks) between euchromatin and heterochromatin. H3K9me3 and H3K4me3 ChIP-seq data were obtained from the Gene Expression Omnibus database (GEO: GSE29611). Nearly 11,003 CTRs were obtained. We choose inter-ligation PETs in CTRs and calculated their genomic spans.</p>", "<title>Annotation of interaction loops</title>", "<p id=\"p0190\">We annotated loops using gene promoter, enhancer, and repressor information. The promoters were defined as the ±2-kb regions around the TSSs. Cell type-specific enhancer and repressor annotations were adopted from the A549 ChromHMM data ##REF##25693563##[58]##. Regions with states 6_EnhG and 7_Enh were defined as enhancers and regions with states 13_ReprPC and 14_ReprPCWk were defined as repressors. We classified loops according to the overlap of interaction anchors with promoters, enhancers, or repressors, with priority given to the promoter region. For example, we defined promoter–promoter loops as both interaction anchors overlapping with promoters, promoter–enhancer loops as one anchor overlapping with a promoter and the other anchor overlapping with an enhancer, and promoter–repressor loops as one anchor overlapping with a promoter and the other anchor overlapping with a repressor. We further categorized the promoter–enhancer and promoter–repressor loops according to enhancer/repressor locations in relation to the gene body: intra-genic proximal enhancers/repressors, which are located inside a gene body and interact with the nearest promoters; extra-genic proximal repressors/enhancers, which are located outside a gene body and interact with the nearest promoters; intra-genic distal enhancers/repressors, which are located inside a gene body, bypass nearby genes, and interact with gene promoters over long distances; and extra-genic distal enhancers/repressors, which are located outside all gene bodies, bypass nearby genes, and interact with gene promoters over long distances.</p>", "<title>Coexpression analysis of genes with promoter–promoter interactions by PCCs</title>", "<p id=\"p0195\">To investigate the coexpression of genes with the CTCF-, RNAPII-, EZH2-, and H3K27me3-meditated promoter–promoter interactions defined by ChIA-PET, we calculated PCCs between expression levels of gene pairs and promoter–promoter interactions. Gene expression data of 535 LUAD samples were downloaded from the TCGA. Genes involved in promoter–promoter interactions were randomly rewired to compile a random control with the same gene background but different pairings. Randomly selected gene pairs with similar distributions of genomic span and gene density as the promoter–promoter regions were used as additional controls.</p>", "<title>Analysis of chromatin interaction domains</title>", "<p id=\"p0200\">A chromatin interaction domain is a genomic region spanned by continuously connected loops mediated by specific factors. First, based on the continuous connectivity of loops, we clustered loops into candidate domains. Second, we calculated loop coverage along all chromosomes at base-pair resolution and subtracted low-coverage regions from the candidate domains. Finally, the interaction domains with genome size smaller than 10 kb were excluded, and the final EIDs, HIDs, and RIDs were obtained. When comparing histone modifications of different domains, we used ChIP-seq data (H3K27ac, H3K4me3, H3K27me3, and H3K9me3) obtained from the GEO database (GEO: GSE29611 and GSE32465).</p>", "<title>RNA-seq data processing</title>", "<p id=\"p0205\">Strand-specific poly(A) RNA-seq libraries were generated and sequenced as 150-bp paired-end reads. For RNA-seq analysis, we conducted quality control using FastQC (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.bioinformatics.babraham.ac.uk/projects/fastqc/\" id=\"ir010\">https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</ext-link>), and adaptor sequences were removed using Trimmomatic (version 0.32) ##REF##24695404##[59]##. After quality filtering, the reads were mapped to the human reference genome (hg38) by HISAT2 (version 2.1.0) ##REF##31375807##[60]##, and gene expression was qualified by StringTie (version 1.3.4d) ##REF##27560171##[61]##. Differential gene expression was calculated using the DESeq2 ##REF##25516281##[62]## package in R. To identify significant differentially expressed genes between the A549 and BEAS-2B cell lines, we used expression level thresholds of adjusted <italic>P</italic> value &lt; 0.01 and |log<sub>2</sub> fold change| &gt; 1.</p>", "<title>Gene expression at loop anchors</title>", "<p id=\"p0210\">We divided genes into four categories according to whether their gene promoters were associated with RNAPII-mediated loops or H3K27me3-mediated loops: (1) genes whose promoters were only associated with RNAPII-mediated loops but not associated with H3K27me3-mediated loops; (2) genes whose promoters were associated with both RNAPII-mediated loops and H3K27me3-mediated loops; (3) genes whose promoters were neither associated with RNAPII-mediated loops nor H3K27me3-mediated loops; and (4) genes whose promoters were not associated with RNAPII-mediated loops but were associated with H3K27me3-mediated loops. Significant differences between the fragments per kilobase of exon model per million mapped fragments (FPKM) values of these different categories of genes were compared using the Mann–Whitney <italic>U</italic> test. Similarly, we divided genes into four categories according to whether their promoters were associated with EZH2/RNAPII-mediated loops or EZH2/RNAPII-mediated binding sites and compared expression differences between different categories.</p>", "<title>GO enrichment analysis</title>", "<p id=\"p0215\">For genes in cell-specific anchors with significant differential expression, we examined enrichment in GO terms using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) ##UREF##3##[63]##.</p>", "<title>TCGA RNA-seq data analysis</title>", "<p id=\"p0220\">We downloaded gene expression data for 535 primary LUAD tumor tissues and 59 solid normal lung tissues from the TCGA database ##REF##25691825##[64]## and analyzed their gene expression differences, especially for GWAS SNP target genes and lung cancer-related genes (<italic>NF1</italic>, <italic>RNF135</italic>, <italic>FBLN1</italic>, and <italic>FOXO4</italic>).</p>" ]
[ "<title>Results</title>", "<title>Chromatin interactions are mediated by multiple factors in A549 lung cancer cell line</title>", "<p id=\"p0030\">To investigate the 3D genome architecture and its regulatory function in lung cancer, we performed long-read ChIA-PET associated with CTCF, RNAPII, EZH2, and H3K27me3 in the lung cancer cell line A549 and noncancerous cell line BEAS-2B. These different chromatin interactomes should help clarify the 3D genome of the A549 lung cancer cell line. In total, we obtained ∼ 375 million uniquely mapped paired-end reads and ∼ 283,000 chromatin loops from six ChIA-PET libraries (<xref rid=\"s0140\" ref-type=\"sec\">Table S1</xref>). The correlations of biological replicates are shown in <xref rid=\"s0140\" ref-type=\"sec\">Figure S1</xref>, and both contact matrices and visible clusters for each factor-mediated ChIA-PET showed excellent reproducibility. We then combined interaction pairs of the four factors and constructed a contact heatmap at the chromosomal level. The 1-Mb and 100-kb resolution contact heatmaps of chromosome 14 showed chromosome interaction patterns, allowing identification of the A/B compartments and TADs (##FIG##0##Figure 1##A and B). The binding sites and chromatin interactions associated with each factor are shown in ##FIG##0##Figure 1##C. We found that the EZH2- and H3K27me3-associated interaction loops mainly appeared between their broad peaks and were primarily located in repressive regions, whereas the RNAPII-associated interaction loops were mainly located in active regions. Thus, we speculated that EZH2- and H3K27me3-associated interaction loops occupy different positions on the genome than RNAPII-associated interaction loops, and their positional distributions may be related to genomic activity.</p>", "<p id=\"p0035\">We plotted the span distributions of the loops mediated by the four factors (##FIG##0##Figure 1##D). In general, the RNAPII loops showed the shortest spans, and the loop span with the highest density was less than 100 kb. The CTCF loops showed the highest span density at slightly over 100 kb. The EZH2 loops showed two peaks in span density, with the shorter one less than 1 Mb and the longer one between 10 Mb and 100 Mb. The H3K27me3 loops showed the highest span density of between 10 Mb and 100 Mb. Jodkowska et al. ##UREF##2##[27]## observed a similar span distribution of chromatin interactions from promoter capture Hi-C, but without associated proteins reported in their study.</p>", "<p id=\"p0040\">Subsequently, we described the distribution of interactions associated with different factors on gene regulatory elements. As shown in ##FIG##0##Figure 1##E, significant differences were found in pairs of regulatory elements between these factors, especially in terms of the proportion of promoter-involved interactions. Of the RNAPII-mediated loops, 92% were promoter–promoter or promoter–enhancer loops. In comparison, only a small proportion (5% for EZH2 and 2% for H3K27me3) of active promoter-centered interactions was organized by EZH2 and H3K27me3. For the two repressive factors, most of the interactions were repressor-associated interactions (69% for EZH2 and 78% for H3K27me3). Moreover, the loops associated with CTCF were mostly evenly distributed in the different categories, confirming the viewpoint that CTCF is more involved in structural formation and maintenance than in gene regulation.</p>", "<p id=\"p0045\">We then calculated the Pearson correlation coefficients (PCCs) of the contact matrices mediated by the four factors and Hi-C contact matrices (##FIG##0##Figure 1##F). The EZH2 and H3K27me3 contact matrices showed high similarity, and the CTCF and RNAPII contact matrices showed high similarity. The combined contact matrices of the four factors were highly similar to Hi-C, suggesting that the combined interactomes of these factors reflected the whole-genome interactions observed with Hi-C. Therefore, comprehensive analysis of chromatin interactions associated with different factors can provide additional details of distinct features on the 3D genome architecture and clarify the regulatory relationship of the A549 lung cancer cell line.</p>", "<title>High-resolution chromatin interaction analysis can reveal hierarchical genomic structures</title>", "<p id=\"p0050\">The ChIA-PET method uses sonication for chromatin fragmentation and antibodies for factor enrichment, which can increase the resolution of interaction maps and functional elements. Based on the ChIA-PET data, we observed hierarchical genomic structures at different scales, including A/B compartments and TAD-like structures (##FIG##0##Figure 1##A and B), as well as finer structures. By examining the span of the paired-end reads, we observed that DNA distance distribution was periodic. First, we detected 10-bp (##FIG##1##Figure 2##A) and 190-bp periods (##FIG##1##Figure 2##B), reflecting the DNA double-helix turn and single-nucleosome structure, respectively, thus indicating that the interaction positions were not randomly distributed around the nucleosomes. Second, we observed 400–700-bp periods in the chromatin transitional regions [CTRs; located between active and inactive regions, defined as the center 2 kb of the overlapping regions of the H3K9me3 and H3K4me3 chromatin immunoprecipitation with sequencing (ChIP-seq) peaks] in the ChIA-PET data associated with H3K27me3 (##FIG##1##Figure 2##C). Such periods were not observed in the non-CTRs (##FIG##1##Figure 2##D). The 3–4 nucleosome structure in the CTRs may be unique, as CTRs are the boundaries between heterochromatin and euchromatin. Nucleosomes at CTRs can reduce the turnover rate and tend to form tetranucleosomes, which may be a basic structure in chromosome fiber assembly ##REF##24763583##[28]##. To validate our observations based on ChIA-PET methods, we analyzed HeLa CTCF ChIA-PET (GEO: GSE72816), GM12878 CTCF ChIA-PET (GEO: GSE72816), and mouse embryonic stem cell (mESC) SUZ12 ChIA-PET (GEO: GSE120393), and also observed the 10-bp and 190-bp periods (<xref rid=\"s0140\" ref-type=\"sec\">Figure S2</xref>A–C), thus validating our observations. Therefore, high-resolution ChIA-PET data showed hierarchical 3D genome structures at different scales (##FIG##1##Figure 2##E).</p>", "<p id=\"p0055\">To check whether similar hierarchical chromatin structures can be observed from Hi-C and <italic>in situ</italic> Hi-C followed by chromatin immunoprecipitation (HiChIP) methods, we used A549 Hi-C data (ENCODE: ENCSR662QKG), IMR-90 Hi-C data (ENCODE: ENCSR852KQC), HeLa CTCF HiChIP data (GEO: GSE108869), and GM12878 CTCF HiChIP data (GEO: GSE115524) to conduct the same analyses. We observed A/B compartments, TADs, and loops from these datasets. However, the patterns of the 10-bp, 190-bp, and 400–700-bp periods were not observed in Hi-C and HiChIP data (<xref rid=\"s0140\" ref-type=\"sec\">Figure S2</xref>D–G).</p>", "<p id=\"p0060\">With this result in mind, we considered the potential reason for observing the 10-bp and 190-bp period patterns in the ChIA-PET data, but not in the Hi-C and HiChIP data. Both the Hi-C and HiChIP methods are based on enzymatic digestion, and the span of paired-end reads is mainly determined by enzyme cutting sites. In contrast, the ChIA-PET method uses sonication to fragment chromatin, and the breakpoints are between nucleosomes. This may explain the differences in the observation of the 10-bp and 190-bp periods.</p>", "<title>EZH2- and H3K27me3-mediated chromatin interactions present distinct patterns and transcriptional activities from RNAPII-mediated chromatin interactions</title>", "<p id=\"p0065\">Interactions mediated by RNAPII and CTCF have been described in several studies ##REF##26686651##[25]##, ##REF##22265404##[26]##, and RNAPII-mediated promoter–promoter interactions can link gene pairs with strong coexpression patterns ##REF##22265404##[26]##. However, the characteristics and profiles of repressive interactions in lung cancer remain to be studied. Here, we determined whether genes with EZH2- or H3K27me3-mediated promoter–promoter interactions are also transcriptionally coordinated. RNA sequencing (RNA-seq) data indicated that most of the paired genes with RNAPII-mediated promoter–promoter interactions showed high simultaneous expression, with a small range in variation. The paired genes with CTCF-mediated promoter–promoter interactions exhibited a slightly larger range of variation in expression levels. In contrast, paired genes with EZH2- or H3K27me3-mediated promoter–promoter interactions displayed the largest range of variation in expression levels (##FIG##2##Figure 3##A). There were more paired genes with low expression in the repressive interactions than in the RNAPII-mediated interactions. To further assess the coordinated transcription of paired genes across different conditions, we performed Pearson correlation analysis using The Cancer Genome Atlas (TCGA) lung adenocarcinoma (LUAD) RNA-seq data. Results indicated that genes involved in the RNAPII-mediated promoter–promoter interactions were highly correlated, whereas those involved in the promoter–promoter interactions mediated by EZH2 and H3K27me3 were lowly correlated (<xref rid=\"s0140\" ref-type=\"sec\">Figure S3</xref>A). These analyses indicate that most gene pairs involved in the RNAPII-mediated promoter–promoter interactions tend to be highly cooperatively transcribed. In contrast, gene pairs involved in EZH2- or H3K27me3-mediated promoter–promoter interactions tend to be weakly (or not at all) cooperatively transcribed.</p>", "<p id=\"p0070\">In previous ChIP-seq or genome-wide association study (GWAS) SNP analyses, regulatory elements are assumed to regulate their nearest genes ##REF##20585100##[29]##, ##REF##28607444##[30]##. However, this may not be true in general. We observed that more than 64% of enhancers and 87% of repressors did not interact with their nearest promoters, instead bypassing several intervening genes to reach their target promoters (<xref rid=\"s0140\" ref-type=\"sec\">Figure S3</xref>B). In addition, we observed that genes involved in proximal promoter–enhancer interactions had significantly higher expression levels than genes involved in distal promoter–enhancer interactions (<italic>P</italic> &lt; 1.2E−05, Mann–Whitney <italic>U</italic> test), and genes involved in proximal promoter–repressor interactions had significantly lower expression levels than genes involved in distal promoter–repressor interactions (<italic>P</italic> &lt; 4.6E−07, Mann-Whitney <italic>U</italic> test) (<xref rid=\"s0140\" ref-type=\"sec\">Figure S3</xref>C). Therefore, we speculated that gene transcription levels depend on the genomic distances of promoter–enhancer and promoter–repressor interactions to some extent.</p>", "<p id=\"p0075\">We further investigated the effects of RNAPII- and EZH2-mediated loops on gene transcription. Results indicated that genes in the EZH2-mediated loop anchors, but not in the RNAPII-mediated loop anchors, had the lowest expression levels, with levels lower than those of genes in other loop anchors (<italic>P</italic> &lt; 2.2E−16, Mann–Whitney <italic>U</italic> test) (##FIG##2##Figure 3##B). In contrast, genes in the RNAPII-mediated loop anchors showed high expression levels. A similar trend was found when comparing the expression levels of genes with RNAPII-mediated and H3K27me3-mediated interactions (##FIG##2##Figure 3##B). We also found that promoters bound to EZH2/H3K27me3-mediated loop anchors with peaks were more repressed than promoters only bound to peaks, only bound to loop anchors, or neither (<xref rid=\"s0140\" ref-type=\"sec\">Figure S3</xref>D). These results suggest that EZH2- and H3K27me3-mediated loops may further repress the expression of the target genes.</p>", "<p id=\"p0080\">To characterize the spatial relationships between RNAPII-, EZH2-, and H3K27me3-associated chromatin topologies, we defined chromatin interaction domains based on loop connectivity and contact frequency, <italic>i.e.</italic>, RNAPII-mediated interaction domain (RID), EZH2-mediated interaction domain (EID), and H3K27me3-mediated interaction domain (HID) (##FIG##2##Figure 3##C, <xref rid=\"s0140\" ref-type=\"sec\">Figure S3</xref>E). In total, we identified 1679 RIDs, 2235 EIDs, and 600 HIDs. Most RIDs were isolated from HIDs (71%) and EIDs (45%), whereas 23% of RIDs were contained in EIDs and 18% of RIDs were contained in HIDs (##FIG##2##Figure 3##D and E). Epigenomic features are also reportedly associated with 3D genome architecture ##REF##27391817##[31]##, ##REF##32182345##[32]##. Here, we investigated the epigenomic marks and transcriptional activities of different chromatin interaction domains. We found that EIDs and HIDs exhibited lower densities of active histone marks (H3K27ac and H3K4me3) and higher densities of inactive histone marks (H3K27me3 and H3K9me3) than RIDs (##FIG##2##Figure 3##F). In addition, EIDs and HIDs contained fewer active genes (<xref rid=\"s0140\" ref-type=\"sec\">Figure S3</xref>F) and exhibited lower transcriptional activities (<italic>P</italic> &lt; 2.2E−16, Mann-Whitney <italic>U</italic> test) (##FIG##2##Figure 3##G) than RIDs. Comparing the A and B compartments identified in the Hi-C data, we found that 75% of RIDs were located in the A compartments, with 6% of RIDs located in the B compartments, whereas the B compartments contained more EIDs and HIDs than the A compartments (<xref rid=\"s0140\" ref-type=\"sec\">Figure S3</xref>G). These findings suggest that the interactions associated with different factors exhibit distinct distributions and coexpression features across the genome, and that factor-specific chromatin interaction domains exhibit distinct epigenomic properties that are highly consistent with transcriptional activity.</p>", "<title>High-resolution loops map whole-genome regulatory relationship of lung cancer-related genes and SNPs</title>", "<p id=\"p0085\">Genomic interactions can reveal the spatial proximity and regulatory events of genomic sites ##REF##22265404##[26]##, ##REF##30849367##[33]##, ##REF##30650367##[34]##. Interaction mapping of cancer-related genes may increase our understanding of the regulatory elements of these genes. ChIA-PET loops can directly link distal elements to the promoters of target genes to yield regulatory information and can accurately identify specific transcription start sites (TSSs). Here, we adopted 203 oncogenes and tumor suppressor genes from the Network of Cancer Genes (NCG) ##REF##30606230##[35]## and the top 100 survival-related genes from the Gene Expression Profiling Interactive Analysis (GEPIA) database ##REF##28407145##[36]##. We then identified genes and non-coding regions that interact with lung cancer-related genes using high-resolution interaction data (<xref rid=\"s0140\" ref-type=\"sec\">Tables S2 and S3</xref>). Several typical lung cancer-related genes exhibited interactions mediated by CTCF, EZH2, H3K27me3, and especially RNAPII (##FIG##3##Figure 4##A; Tables S2 and S3), suggesting a regulatory relationship between the associated chromatin interactions and these genes.</p>", "<p id=\"p0090\">As seen in ##FIG##3##Figure 4##B, the oncogene <italic>ERBB2</italic> showed several strong RNAPII-mediated interactions with nearby genes, such as <italic>PGAP3</italic>, <italic>STARD3</italic>, and <italic>PNMT</italic>. Compared with neighboring or distant genes not in the interaction domain, genes with <italic>ERBB2</italic> interactions demonstrated obvious coexpression patterns in the LUAD tumor samples (##FIG##3##Figure 4##C), whereas similar coexpression patterns were not observed in normal samples (<xref rid=\"s0140\" ref-type=\"sec\">Figure S4</xref>A). Thus, the coexpression pattern between <italic>ERBB2</italic> and other genes, such as <italic>PGAP3</italic>, <italic>STARD3</italic>, and <italic>PNMT</italic>, may be a marker of cancer, and site mutations in the interaction anchors or dysregulation in interactions related to <italic>ERBB2</italic> may be a new target for cancer studies.</p>", "<p id=\"p0095\">Another example from interaction mapping was the survival-related gene <italic>DKK1</italic>, which was not involved in EZH2-meditated interactions and showed higher expression in the A549 cell line than in BEAS-2B cell line, with log<sub>2</sub> fold change &gt; 1 and adjusted <italic>P</italic> &lt; 0.01 (<xref rid=\"s0140\" ref-type=\"sec\">Figure S4B; Table S5</xref>). Interestingly, lung cancer-related genes were more enriched in the RNAPII- and CTCF-meditated interactions than randomly selected genes (<italic>P &lt;</italic> 2.87E−07, chi-square test; ##FIG##3##Figure 4##D). This enrichment suggests that mapping the interactomes of these genes may facilitate studies on the potential carcinogenic function of these cancer-related interactions in lung cancer.</p>", "<p id=\"p0100\">In lung cancer samples, tumor-specific fusion transcripts are suggested to disrupt normal gene function or activate proto-oncogenes, thus driving tumorigenesis ##REF##22327623##[37]##, ##REF##25870798##[38]##, ##REF##34563714##[39]##. We assessed the TumorFusions database list ##REF##29099951##[40]## of TCGA LUAD samples to determine whether long-range interactions exist in the spatial genome between the fusion gene pairs. Among the 854 pairs of host fusion genes, more than 100 exhibited interactions mediated by RNAPII or CTCF, whereas only a few pairs showed interactions mediated by EZH2 or H3K27me3. As a control, among 854 randomly selected pairs of expressed genes, none were involved in the interactions. Thus, the pairs of host fusion genes were also highly enriched in CTCF- and RNAPII-meditated interactions (<italic>P &lt;</italic> 2.2E−16, chi-square test; ##FIG##3##Figure 4##E). These results suggest a positive relationship between TCGA fusion transcripts and spatial contacts, in which interaction loops may be potential facilitators of fusion transcripts.</p>", "<p id=\"p0105\">We also mapped the interacting sites of high-risk SNPs in lung cancer (##FIG##3##Figure 4##F; <xref rid=\"s0140\" ref-type=\"sec\">Table S4</xref>). The lung cancer risk SNP rs34662244 was located in the anchor of two enhancer–promoter interaction clusters with target genes <italic>ZNF165</italic>, <italic>ZSCAN16</italic>, and <italic>ZSCAN16-AS1</italic> (##FIG##3##Figure 4##G). These interaction clusters suggest a potential role of this non-coding SNP in regulating target genes over a long distance. Moreover, based on a whole-gene expression comparison of TCGA LUAD tumor samples and normal samples, we found that a large proportion of genes targeted by SNPs through RNAPII-mediated interactions had higher expression levels in lung cancer samples than in normal samples (<italic>P</italic> = 0.004, Wilcoxon test; <xref rid=\"s0140\" ref-type=\"sec\">Figure S4</xref>C), suggesting a potential cancer driver function of SNP-associated genes. Therefore, our high-resolution chromatin interaction landscape may provide important regulatory information on lung cancer-related genes and SNPs.</p>", "<title>Associations between altered chromatin interactions and dysregulation of oncogenes and tumor suppressor genes</title>", "<p id=\"p0110\">As RNAPII- and EZH2-mediated interactions showed significant regulation of gene expression, we analyzed whether abnormal expression of oncogenes or tumor suppressor genes is related to abnormal interaction patterns in lung cancer. We conducted joint analysis of differential gene expression and differential interactions between the lung cancer cell line A549 and noncancerous cell line BEAS-2B (<xref rid=\"s0140\" ref-type=\"sec\">Figure S5</xref>A and B). We found that 74% of genes involved with RNAPII-mediated interactions in A549 cells were also involved with RNAPII-mediated interactions in BEAS-2B cells, whereas only 22% of genes involved with EZH2-mediated interactions in A549 cells were also involved with EZH2-mediated interactions in BEAS-2B cells. The differentially expressed and A549-specific anchor genes were enriched in the Gene Ontology (GO) biological process term “anterior/posterior pattern specification”. Genes enriched in this term were mainly lung cancer-related HOXB gene clusters on chromosome 17 and were involved in RNAPII-mediated interactions, with higher expression in A549 cells than in BEAS-2B cells (<xref rid=\"s0140\" ref-type=\"sec\">Figure S5</xref>C). The differentially expressed and BEAS-2B-specific anchor genes were significantly enriched in “DNA binding” (<xref rid=\"s0140\" ref-type=\"sec\">Figure S5</xref>D), and most belonged to the ZNF gene family and functioned as transcription factors. We speculated that the ZNF gene family may play a role in lung cancer tumorigenesis.</p>", "<p id=\"p0115\">Among genes associated with altered interactions, <italic>RNF135</italic> and <italic>NF1</italic> are two adjacent genes located on chromosome 17 ##REF##28213670##[41]##. The <italic>NF1</italic> gene represses the RAS signaling pathway, and its mutation or abnormal expression may lead to lung cancer ##REF##24535670##[42]##, ##REF##26861459##[43]##. Studies have suggested that <italic>RNF135</italic> may exhibit oncogenic functions in glioblastoma ##REF##26856755##[44]##. Here, based on RNA-seq differential expression analysis, <italic>NF1</italic> and <italic>RNF135</italic> showed significantly higher expression in the A549 cells than in the BEAS-2B cells (log<sub>2</sub> fold change &gt; 1 and adjusted <italic>P</italic> value &lt; 0.01; <xref rid=\"s0140\" ref-type=\"sec\">Table S5</xref>). There was a strong RNAPII-mediated promoter–promoter interaction cluster between these two genes in the A549 cells (##FIG##4##Figure 5##A), which was not observed in the BEAS-2B cells. Promoter–promoter interaction seems to increase the expression of this gene pair. In TCGA database analysis, both <italic>NF1</italic> and <italic>RNF135</italic> showed higher expression levels in the LUAD tumor samples than in the normal samples (<italic>P</italic> = 1.2E−10 for <italic>NF1</italic> and <italic>P</italic> = 8.8E−04 for <italic>RNF135</italic>, Mann–Whitney <italic>U</italic> test; ##FIG##4##Figure 5##B). In the survival analysis, <italic>RNF135</italic> overexpression indicated poor outcome in patients (##FIG##4##Figure 5##C).</p>", "<p id=\"p0120\">Abnormal repression of tumor suppressor genes is another crucial aspect of cancer ##REF##33514712##[23]##. In our study, the repression of several tumor suppressor genes was associated with EZH2-related loops. For example, <italic>FBLN1</italic> and <italic>FOXO4</italic>, well-known lung cancer suppressor genes ##REF##32719793##[46]##, ##REF##24935588##[47]##, ##REF##32372224##[48]##, showed significantly lower expression in the A549 cells than in the BEAS-2B cells (log<sub>2</sub> fold change &lt; −1 and adjusted <italic>P</italic> value &lt; 0.01; <xref rid=\"s0140\" ref-type=\"sec\">Table S5</xref>). EZH2-mediated interactions were associated with these two genes in the A549 cells, but not in the BEAS-2B cells (##FIG##4##Figure 5##D, <xref rid=\"s0140\" ref-type=\"sec\">Figure S6</xref>A). The two genes also exhibited lower expression in LUAD samples than in normal samples (<italic>P &lt;</italic> 2.2E−16 for <italic>FBLN1</italic> and <italic>FOXO4</italic>, Mann–Whitney <italic>U</italic> test; ##FIG##4##Figure 5##E, <xref rid=\"s0140\" ref-type=\"sec\">Figure S6</xref>B). These results suggest that chromatin interactions are closely related to the maintenance of lung cancer-related gene expression.</p>", "<p id=\"p0125\">To test whether A549-specific interaction anchors can function as oncogenic regions, we performed clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-targeted knockout (KO) of the A549-specific anchors to verify the effects of dysregulated interactions on cancer gene expression. <italic>NCOA3</italic> is a well-studied oncogene that is up-regulated in many cancers ##REF##33239622##[49]##, ##REF##31914406##[50]##. In this study, <italic>NCOA3</italic> expression was much higher in the A549 cells than in the BEAS-2B cells (log<sub>2</sub> fold change &gt; 1 and adjusted <italic>P</italic> value &lt; 0.01; <xref rid=\"s0140\" ref-type=\"sec\">Table S5</xref>). In the A549 cells, there was a specific RNAPII-mediated enhancer–promoter interaction cluster between the promoter of <italic>NCOA3</italic> and an enhancer located in the first intron of <italic>NCOA3</italic> (##FIG##5##Figure 6##A), which did not exist in the BEAS-2B cells. We knocked out the 1-kb enhancer region in the A549 cells with CRISPR (##FIG##5##Figure 6##B) and characterized gene expression changes. Results showed that <italic>NCOA3</italic> expression was significantly lower in the KO A549 cells than in the wild-type (WT) A549 cells (<italic>P</italic> &lt; 0.01, two-sided paired <italic>t</italic>-test; ##FIG##5##Figure 6##C). <italic>NCOA3</italic> is known to have a positive effect on tumor cell growth ##REF##33239622##[49]##, ##REF##31914406##[50]##. Our study indicated that KO of the A549-specific <italic>NCOA3</italic> enhancer showed a tendency of reduced cell growth rate (##FIG##5##Figure 6##D).</p>", "<p id=\"p0130\">Based on the aforementioned results, we proposed two models to describe the effects of altered interactions in lung cancer on activating oncogenes and inhibiting tumor suppressor genes, as shown in ##FIG##5##Figure 6##E. In the lung cancer cells, some oncogenes were activated by active factor-associated interactions, and some tumor suppressor genes were repressed by repressive factor-associated interactions. These results suggest that dysregulated chromatin interaction patterns may be an important aspect of tumorigenesis, thereby highlighting the importance of normal interactions in cells.</p>" ]
[ "<title>Discussion and conclusion</title>", "<p id=\"p0135\">Chromatin interactions play important roles in gene transcription regulation and other biological functions. However, few studies have been conducted on repressive chromatin interactions and their relationship with active chromatin interactions. In this study, we mapped the high-resolution genome-wide interactomes mediated by EZH2, H3K27me3, RNAPII, and CTCF in lung cancer A549 cells, representing repressive chromatin interactions, active chromatin interactions, and structural chromatin interactions, respectively. We demonstrated that different types of interactions exhibited different distributions and regulatory functions in the genome. In most cases, repressive and active interactions were distributed in different genomic regions, and the repressive interactions primarily linked repressive elements to silence or repress gene transcription.</p>", "<p id=\"p0140\">Our high-resolution ChIA-PET data revealed 10-bp and 190-bp signals, representing the DNA double helix turn and mononucleosome distance, respectively. Interestingly, the 3–4 nucleosome signals in the facultative heterochromatin hinted at structures mentioned in previous studies in the context of chromosome fiber assembly ##REF##24763583##[28]##.</p>", "<p id=\"p0145\">We used high-resolution chromatin interactions to map the whole-genome regulatory relationship of lung cancer-related genes and SNPs. As tumor-related genes and fusion transcripts were enriched in the interaction loops, we speculated on the central role of long-range interactions in tumorigenesis. We further described how altered interactions can dysregulate the expression of cancer-related genes. The high-resolution 3D landscape generated from this study may expand our understanding of the lung cancer genome.</p>" ]
[ "<title>Discussion and conclusion</title>", "<p id=\"p0135\">Chromatin interactions play important roles in gene transcription regulation and other biological functions. However, few studies have been conducted on repressive chromatin interactions and their relationship with active chromatin interactions. In this study, we mapped the high-resolution genome-wide interactomes mediated by EZH2, H3K27me3, RNAPII, and CTCF in lung cancer A549 cells, representing repressive chromatin interactions, active chromatin interactions, and structural chromatin interactions, respectively. We demonstrated that different types of interactions exhibited different distributions and regulatory functions in the genome. In most cases, repressive and active interactions were distributed in different genomic regions, and the repressive interactions primarily linked repressive elements to silence or repress gene transcription.</p>", "<p id=\"p0140\">Our high-resolution ChIA-PET data revealed 10-bp and 190-bp signals, representing the DNA double helix turn and mononucleosome distance, respectively. Interestingly, the 3–4 nucleosome signals in the facultative heterochromatin hinted at structures mentioned in previous studies in the context of chromosome fiber assembly ##REF##24763583##[28]##.</p>", "<p id=\"p0145\">We used high-resolution chromatin interactions to map the whole-genome regulatory relationship of lung cancer-related genes and SNPs. As tumor-related genes and fusion transcripts were enriched in the interaction loops, we speculated on the central role of long-range interactions in tumorigenesis. We further described how altered interactions can dysregulate the expression of cancer-related genes. The high-resolution 3D landscape generated from this study may expand our understanding of the lung cancer genome.</p>" ]
[ "<p id=\"np010\">Equal contribution.</p>", "<p>Studies on the <bold>lung cancer</bold> genome are indispensable for developing a cure for lung cancer. Whole-genome resequencing, genome-wide association studies, and transcriptome sequencing have greatly improved our understanding of the cancer genome. However, <bold>dysregulation</bold> of long-range <bold>chromatin interactions</bold> in lung cancer remains poorly described. To better understand the three-dimensional (3D) genomic interaction features of the lung cancer genome, we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase II (RNAPII), CCCTC-binding factor (CTCF), enhancer of zeste homolog 2 (EZH2), and histone 3 lysine 27 trimethylation (H3K27me3) using long-read chromatin interaction analysis by paired-end tag sequencing (<bold>ChIA-PET</bold>). Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes, either through loops or domains, and their distributions along the genome were distinct from and complementary to those associated with RNAPII. Cancer-related genes were highly enriched with chromatin interactions, and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes, such as additional repressive interactions on <italic>FOXO4</italic> and promoter–promoter interactions between <italic>NF1</italic> and <italic>RNF135</italic>. Knockout of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes, suggesting that chromatin interactions are essential for proper expression of lung cancer-related genes. These findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Giacomo Cavalli</p>" ]
[ "<title>Data availability</title>", "<p id=\"p0225\">Sequence data generated in this study have been deposited in the Genome Sequence Archive for Human ##REF##34400360##[65]## at the National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (GSA-Human: HRA000295 with BioProject: PRJCA003299), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa-human/\" id=\"PC_linknp1gRQ8PpA\">https://ngdc.cncb.ac.cn/gsa-human/</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0230\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0235\"><bold>Yan Zhang:</bold> Conceptualization, Investigation, Validation, Writing – review &amp; editing. <bold>Jingwen Zhang:</bold> Formal analysis, Data curation, Visualization, Writing – review &amp; editing. <bold>Wei Zhang:</bold> Investigation. <bold>Mohan Wang:</bold> Investigation. <bold>Shuangqi Wang:</bold> Data curation. <bold>Yao Xu:</bold> Investigation. <bold>Lun Zhao:</bold> Investigation. <bold>Xingwang Li:</bold> Conceptualization, Writing – review &amp; editing. <bold>Guoliang Li:</bold> Conceptualization, Supervision, Writing – review &amp; editing, Funding acquisition. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0250\">The following are the Supplementary data to this article:</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<p id=\"p0270\">\n\n</p>", "<p id=\"p0275\">\n\n</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0240\">This study was supported by the National Natural Science Foundation of China (Grant No. 31970590). We thank Dr. Honglin Jin from Union Hospital, Tongji Medical College, Huazhong University of Science and Technology for providing the BEAS-2B cell line. We thank Mr. Hao Liu from the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University for essential help in running the high-throughput computing clusters. We thank Dr. Christine Watts for English editing.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>ChIA-PET interactions mediated by four different factors in A549 lung cancer cell line</bold></p><p><bold>A.</bold> Combined chromatin interaction heatmap (1-Mb resolution) and A/B compartments of chromosome 14 in A549 cell line. The combined ChIA-PET interaction heatmap was based on CTCF, RNAPII, EZH2, and H3K27me3 ChIA-PET data. Lower panels show A (blue) and B (yellow) compartments calculated from principal component analysis using combined ChIA-PET data. <bold>B.</bold> Combined chromatin interaction heatmap (100-kb resolution) and A/B compartments at 25–55-Mb regions of chromosome 14. <bold>C.</bold> Loop and peak views of ChIA-PET data in a 4-Mb region on chromosome 14. For each data track, loop view is at the top, and peak view is at the bottom. Chromatin state annotation by ChromHMM was obtained from the NIH Roadmap Epigenomics Mapping Consortium ##REF##27467249##[57]##. <bold>D.</bold> Different genomic spans of loops in ChIA-PET associated with CTCF, RNAPII, EZH2, and H3K27me3. <bold>E.</bold> Pie charts of different interaction categories mediated by four factors. <bold>F.</bold> Heatmap of PCCs between individual-factor mediated ChIA-PET interactions for CTCF, RNAPII, EZH2, H3K27me3, combined data, and Hi-C data. ChIA-PET, chromatin interaction analysis by paired-end tag sequencing; CTCF, CCCTC-binding factor; RNAPII, RNA polymerase II; EZH2, enhancer of zeste homolog 2; H3K27me3, histone 3 lysine 27 trimethylation; Hi-C, high-throughput chromosome conformation capture; Chr, chromosome; NIH, National Institutes of Health; P, promoter; E, enhancer; R, repressor; PCC, Pearson correlation coefficient.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Hierarchical 3D genome structures obtained by ChIA-PET data</bold></p><p><bold>A.</bold> Distribution of PETs spanning 150 bp to 300 bp in ChIA-PET self-ligation data. X-axis represents PET spans in bp. The 10-bp period may represent DNA double-helix turn. <bold>B.</bold> Distribution of PETs spanning 0 bp to 1 kb. The 190-bp span may represent mononucleosome structure. <bold>C.</bold> Distribution of PETs spanning 2 kb to 8 kb. Spans of 400–700 bp representing tetranucleosomes can be found in CTRs, especially in H3K27me3 ChIA-PET data. We defined CTRs as regions with overlapping H3K9me3 and H3K4me3 ChIP-seq peaks. <bold>D.</bold> There were no prominent periodic peaks in density curves in non-CTRs. <bold>E.</bold> Model of DNA hierarchical structures revealed by A549 ChIA-PET data. 3D, three-dimensional; CTR, chromatin transitional region; PET, paired-end tag; ChIP-seq, chromatin immunoprecipitation with sequencing.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Characterization of chromatin interactions mediated by four factors</bold></p><p><bold>A.</bold> Contour plots showing log<sub>2</sub>-transformed RNA-seq FPKM values for promoter–promoter interacting genes in A549 cells. Gene pairs with RNAPII- and CTCF-mediated interactions show concentrated high gene expression levels, whereas gene pairs with EZH2- and H3K27me3-mediated interactions show more dispersed gene expression levels. <bold>B.</bold> Boxplots showing gene expression with or without interactions mediated by different factors. <italic>P</italic> value was determined using one-sided Mann–Whitney <italic>U</italic> test. “+”, genes with loops mediated by this factor on gene promoter (±2-kb regions around TSS). “−”, no loops of this factor on gene promoter. <bold>C.</bold> Model of interaction domains (defined as a genomic region spanned by continuously connected loops mediated by specific factors). <bold>D.</bold> Table showing relative positions and proportions of EIDs and RIDs. Proportions of independent, partially intersecting, and inclusive relationships of different interaction domains are shown. <bold>E.</bold> Table showing relative positions and proportions of HIDs and RIDs. <bold>F.</bold> Densities of histone modification peaks per Mb in EIDs, HIDs, and RIDs. <bold>G.</bold> Boxplots showing gene expression levels in EIDs, HIDs, and RIDs. <italic>P</italic> value was determined using one-sided Mann–Whitney <italic>U</italic> test. **, <italic>P</italic> &lt; 0.01; ***, <italic>P</italic> &lt; 0.001; N.S., no significant difference (<italic>P</italic> &gt; 0.05). EID, EZH2-mediated interaction domain; HID, H3K27me3-mediated interaction domain; RID, RNAPII-mediated interaction domain; RNA-seq, RNA sequencing; FPKM, fragments per kilobase of exon model per million mapped fragments; TSS, transcription start site.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>ChIA-PET interaction pairs show regulatory relationship of cancer risk-related genes and SNPs</bold></p><p><bold>A.</bold> Typical regions or genes interacting with lung cancer-related genes. If a gene promoter was located in the interacting region, it was defined as an interacting gene. Non-coding means that the interacting region is an intergenic region far from the gene body. <bold>B.</bold> RNAPII-mediated interactions around oncogene <italic>ERBB2</italic>. <bold>C.</bold> PCCs between genes in TCGA LUAD tumor samples. <italic>ERBB2</italic> is a lung cancer-related gene. <italic>STARD3</italic>, <italic>TCAP</italic>, <italic>PNMT</italic>, <italic>PGAP3</italic>, and <italic>MIEN1</italic> are linked with <italic>ERBB2</italic> by RNAPII-mediated loops. They are highly coexpressed with <italic>ERBB2</italic>. <italic>IKZF3</italic> is a gene near <italic>ERBB2</italic> and is not linked with <italic>ERBB2</italic>. <italic>ETV2</italic> is an inter-chromosome linking gene related to <italic>ERBB2</italic>. <italic>CHL1</italic> and <italic>ACP1</italic> are two randomly selected genes located on other chromosomes without interactions with <italic>ERBB2</italic> and were used as negative controls. <bold>D.</bold> Proportions of cancer- and survival-related genes involved in remote interactions mediated by four factors. “Random” represents 100 genes randomly selected in the genome, and average of three randomized trials is shown. <bold>E.</bold> Number of fusion transcripts overlapping with interaction loops associated with different factors. In total, 854 gene pairs from TCGA fusion transcripts and 854 random gene pairs were analyzed. Three trials of random gene pairs did not overlap with any loops. <bold>F.</bold> Selected regions or genes interacting with risk SNPs in lung cancer. <bold>G.</bold> Example of RNAPII-mediated interactions linking SNP rs34662244 in an intergenic region in chromosome 6 and its target genes. According to ChIA-PET data, <italic>ZSCAN 16</italic>, <italic>ZSCAN 16-AS1</italic>, and <italic>ZNF165</italic> are target genes of this SNP. SNP, single nucleotide polymorphism; TCGA, The Cancer Genome Atlas; LUAD, lung adenocarcinoma.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Differential interactions are associated with abnormal expression of oncogenes or tumor suppressor genes in lung cancer</bold></p><p><bold>A.</bold> Differential RNAPII-mediated interactions associated with <italic>RNF135</italic> and <italic>NF1</italic> in lung cancer cell line A549 and noncancerous cell line BEAS-2B. RNA-seq tracks show that both <italic>RNF135</italic> and <italic>NF1</italic> have higher expression levels in A549 cells than in BEAS-2B cells. <bold>B.</bold> Violin plots overlaid with boxplots showing the distribution of <italic>NF1</italic> and <italic>RNF135</italic> mRNA expression levels in a large set of LUAD tumor tissues and normal tissues from TCGA database. <italic>P</italic> value was determined using one-sided Mann–Whitney <italic>U</italic> test. <bold>C.</bold> Overall survival curve showing that overexpression of <italic>RNF135</italic> is correlated with poor outcome. This figure was made using online portal UALCAN ##REF##28732212##[45]##. The red survival curve is for patients with <italic>RNF135</italic> expression in the highest quartile, and the blue curve is for other samples with lower <italic>RNF135</italic> expression. <bold>D.</bold> Differential EZH2-mediated interactions associated with <italic>FOXO4</italic> in lung cancer cell line A549 and noncancerous cell line BEAS-2B. Based on RNA-seq tracks, <italic>FOXO4</italic> showed lower expression in A549 cells than in BEAS-2B cells. <bold>E.</bold> Violin plots overlaid with boxplots showing the distribution of <italic>FOXO4</italic> mRNA expression levels in a large set of LUAD tumor tissues and normal tissues from TCGA database. <italic>P</italic> value was determined using one-sided Mann-Whitney <italic>U</italic> test. ***, <italic>P</italic> &lt; 0.001. mRNA, messenger RNA.</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>KO of A549-specific anchor can reduce abnormal expression of oncogene <italic>NCOA3</italic></bold></p><p><bold>A.</bold> Differential RNAPII-mediated interactions associated with oncogene <italic>NCOA3</italic> in lung cancer cell line A549 and noncancerous cell line BEAS-2B. There is an A549-specific interaction linking intron enhancer and promoter of <italic>NCOA3</italic>. RNA-seq tracks show that <italic>NCOA3</italic> has a higher expression level in A549 cells than in BEAS-2B cells. <bold>B.</bold> Schematic of KO of interaction anchor in <italic>NCOA3</italic>. <bold>C.</bold><italic>NCOA3</italic> gene expression levels were detected by qRT-PCR. Three biological RNA samples of <italic>NCOA3</italic> KO cells were used. <italic>P</italic> value was determined using two-sided paired <italic>t</italic>-test. **, <italic>P</italic> &lt; 0.01. <bold>D.</bold> Cell growth rate indicated by cell number fold change over 72 h. Fold change in cell growth was calculated in three sets of 6-well plates. <italic>P</italic> value was determined using two-sided paired <italic>t</italic>-test. <bold>E.</bold> Models show functions of active chromatin interactions in the regulation of oncogenes (upper) and repressive chromatin interactions in the regulation of tumor suppressor genes (lower). KO, knockout; WT, wild-type; qRT-PCR, quantitative real-time polymerase chain reaction; CRISPR, clustered regularly interspaced short palindromic repeats.</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Figure S1</title><p><bold>Reproducibility of ChIA-PET data A.</bold> Scatter plots showing contact matrix correlation between different ChIA-PET replicates in A549 cells. <bold>B.</bold> Comparison of ChIA-PET interaction clusters between two RNAPII replicates and two EZH2 replicates represented by chromosome 1: 43.27–45.64 Mb. Rep, replicate.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Figure S2</title><p><bold>Hierarchical 3D genome structures analysis using ChIA-PET, Hi-C, and HiChIP data from other publications A.</bold> Span distribution of paired-end reads from HeLa CTCF ChIA-PET data (GSE72816), showing 10 bp and 190 bp periods. <bold>B.</bold> Span distribution of paired-end reads from GM12878 CTCF ChIA-PET data (GSE72816), showing 10 bp and 190 bp periods. <bold>C.</bold> Span distribution of paired-end reads from mESCs SUZ12 ChIA-PET data (GSE120393), showing 10 bp and 190 bp periods. <bold>D.</bold> Span distribution of valid pairs from A549 Hi-C data (ENCODE: ENCSR662QKG). There is no 10 bp or 190 bp period. <bold>E.</bold> Span distribution of valid pairs from IMR-90 Hi-C data (ENCODE: ENCSR852KQC). There is no 10 bp or 190 bp period. <bold>F.</bold> Span distribution of valid pairs from HeLa CTCF HiChIP data (GSE108869). There is no 10 bp or 190 bp period. <bold>G.</bold> Span distribution of valid pairs from GM12878 CTCF HiChIP data (GSE115524). There is no 10 bp or 190 bp period. In all panels, X-axis represents spans of valid pairs in bp. mESCs, mouse embryonic stem cells; HiChIP, <italic>in situ</italic> Hi-C followed by chromatin immunoprecipitation.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Figure S3</title><p><bold>Comparison of factor-specific chromatin interactions A.</bold> Distribution of PCCs for gene pairs with promoter–promoter interactions, randomly rewired gene pairs, and randomly selected gene pairs from control regions with the same genomic span. P–P represents gene pairs with promoter–promoter interactions. <bold>B.</bold> Proportional distribution of four classes of enhancers and repressors observed in A549 cells based on locations relative to gene coding regions. “Intra-genic proximal” enhancers are located inside a gene body and interact with nearby promoters; “Extra-genic proximal” enhancers are located outside a gene body and interact with nearby promoters; “Intra-genic distal” enhancers are located inside a gene body, bypass nearby genes, and interact with distant gene promoters over long distances; “Extra-genic distal” enhancers are located outside all gene bodies bypass nearby genes, and interact with distant gene promoters over long distances. <bold>C.</bold> Comparison of expression levels of genes with different types of promoter–enhancer or promoter–repressor interactions. <italic>P</italic> value was determined using one-sided Mann-Whitney U test. <bold>D.</bold> Expression levels of genes with promoters with or without EZH2 or H3K27me3 binding or loop anchor binding. <italic>P</italic> value was determined using Mann-Whitney U test, ***, <italic>P</italic> &lt; 0.001. “+”, genes are located in peak or loop anchor regions; “−”, genes are not located in peak or loop anchor regions. <bold>E.</bold> Examples of EIDs in heatmap. <bold>F.</bold> Densities of active genes (FPKM &gt; 1) per 1 Mb in EIDs, HIDs, and RIDs. <bold>G.</bold> Percentage of EIDs, HIDs, and RIDs located in A or B compartments.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Figure S4</title><p><bold>Lung cancer-related genes and SNPs involved in chromatin interactions A.</bold> PCCs for <italic>ERBB2</italic> versus interacting genes in normal samples from TCGA LUAD dataset. Genes are the same as those in Figure 4C. Coexpression pattern was much weaker in normal samples. <bold>B.</bold> Interaction loops on survival-related gene <italic>DKK1</italic> in A549 and BEAS-2B cells. Upper track in each box shows interaction loops and peak signals. EZH2 loops were not observed in A549 cell line. Based on RNA-seq signals, <italic>DKK1</italic> showed higher expression in A549 than in BEAS-2B cells. <bold>C.</bold> Comparison of gene expression in tumor and normal samples from TCGA LUAD dataset. Genes interacting with lung cancer risk-related SNPs are marked with red dots. Genes not differentially expressed are marked with gray dots. Up- and down-regulated genes in tumor samples are marked with yellow and blue dots, respectively.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Figure S5</title><p><bold>Genes with different interactions and expression levels in A549 and BEAS-2B cell lines A.</bold> Venn diagrams of genes with differential RNAPII interactions and differentially expressed in A549 and BEAS-2B cell lines. <bold>B.</bold> Venn diagrams of genes with differential EZH2 interactions and differentially expressed in A549 and BEAS-2B cell lines. Red circles represent genes with specific chromatin interactions in A549 cells. Green circles represent genes with specific chromatin interactions in BEAS-2B cells. Purple circles represent genes with significantly differential expression levels (adjusted <italic>P</italic> value &lt; 0.01, |log2 fold change| &gt; 1) in both cell lines. <bold>C.</bold> Differential RNAPII interactions associated with <italic>HOXB</italic> cluster genes in A549 and BEAS-2B cell lines. Based on RNA-seq tracks, these genes showed higher expression in A549 than in BEAS-2B cells. <bold>D.</bold> GO analysis terms of specific RNAPII interactions and differentially expressed genes in BEAS-2B cells. GO, Gene Ontology.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Figure S6</title><p><bold>Expression profiles of cancer-related gene <italic>FBLN1</italic> in TCGA database A.</bold> Differential EZH2 interactions associated with <italic>FBLN1</italic> in A549 and BEAS-2B cell lines. Based on RNA-seq tracks, <italic>FBLN1</italic> showed lower expression in A549 than in BEAS-2B cells. <bold>B.</bold> Boxplots of distribution of <italic>FBLN1</italic> mRNA expression levels in a large set of LUAD tumor tissues and normal tissues from TCGA database. <italic>P</italic> value was determined using Mann-Whitney U test. ***, <italic>P</italic> &lt; 0.001.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S1</title><p><bold>Summary information of ChIA-PET libraries</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S2</title><p><bold>Lung cancer genes and those involved in chromatin interactions</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S3</title><p><bold>Top 100 LUAD survival risk genes and those involved in chromatin interactions</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S4</title><p><bold>Lung cancer related GWAS SNPs and those involved in chromatin interactions</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S5</title><p><bold>Differentially expressed genes between A549 and BEAS-2B cell lines</bold></p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e254\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0135\" fn-type=\"supplementary-material\"><p id=\"p0245\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2023.01.004\" id=\"ir015\">https://doi.org/10.1016/j.gpb.2023.01.004</ext-link>.</p></fn></fn-group>" ]
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65
CC BY
no
2024-01-14 23:41:54
Genomics Proteomics Bioinformatics. 2023 Jun 23; 21(3):573-588
oa_package/ac/a9/PMC10787015.tar.gz
PMC10787016
35272052
[ "<title>Introduction</title>", "<p id=\"p0005\">Most regions of the human genome are non-coding sequences, and some of them harbor structural, regulatory, and transcribed information ##UREF##0##[1]##. Some variants in non-coding sequences play important roles in human traits and complex diseases ##REF##26152199##[2]##. It is widely accepted that a large proportion of non-coding sequences is functional and harbors genetic variants that contribute to disease etiology ##REF##32741549##[3]## and that modified penetrance of pathogenic coding variants by non-coding regulatory variants can contribute to disease risk ##REF##30127527##[4]##. In addition, recent discoveries support that variants in non-coding sequences are important in cancer development ##REF##25383969##[5]##, ##REF##25261935##[6]##. Furthermore, genome-wide association studies (GWAS) have identified numerous single-nucleotide variants (SNVs) associated with many human traits and complex diseases, and most of these associations are thought to be mediated by non-coding regulatory variants ##REF##26227905##[7]##, ##REF##26615194##[8]##, ##REF##29727686##[9]##.</p>", "<p id=\"p0010\">In the last few years, many genomic features in the non-coding sequences of the genome have been identified across multiple human tissues and cell types through various large-scale projects, such as the Encyclopedia of DNA Elements (ENCODE) ##REF##22955616##[10]##, Roadmap Epigenomics ##REF##20944595##[11]##, and the functional annotation of the mammalian genome (FANTOM5) ##REF##24670763##[12]##, enabling analysis and prediction of the functional effects of non-coding variants. Several computational methods ##REF##30371827##[13]##, ##REF##29483654##[14]##, ##REF##28912487##[15]##, ##REF##25338716##[16]##, ##REF##27923386##[17]##, ##REF##30256891##[18]##, ##REF##26727659##[19]##, ##REF##25583119##[20]##, ##REF##28968714##[21]##, ##REF##28961785##[22]##, ##REF##25599402##[23]##, ##REF##30559490##[24]##, ##REF##25273974##[25]##, ##REF##26015273##[26]##, ##REF##28288115##[27]##, ##REF##31748530##[28]##, ##REF##28797091##[29]##, ##REF##29996888##[30]##, ##UREF##1##[31]##, ##REF##27569544##[32]## based on supervised, unsupervised, and semi-supervised models have been developed to prioritize non-coding variants by integrating various genomic features. For instance, combined annotation dependent depletion (CADD) used more than 60 various annotations from conservation, epigenetic modification, genetic context, and functional prediction ##REF##30371827##[13]##; Prioritization And Functional Assessment (PAFA) was the first method to introduce the fixation index ##REF##23172852##[33]##, a population-level metric important for prioritizing population relevant functional non-coding variants ##REF##29996888##[30]##. Given that computational methods offer differing advantages, disadvantages, and specific features ##REF##29893792##[34]##, users with different requirements need to choose appropriate methods. Three previous studies have evaluated the performance of several computational methods ##REF##29340599##[35]##, ##REF##30659175##[36]##, ##REF##27999115##[37]##. Nevertheless, limited benchmark datasets were used in the three studies, and they measured the area under the receiver operating characteristic (ROC) curve (AUROC) and area under the precision-recall (PR) curve (AUPRC); other critical performance metrics, such as the accuracy at 95% sensitivity or specificity, were not used. Furthermore, several recently developed methods, such as non-coding essential regulation (ncER) ##REF##31748530##[28]##, <italic>de novo</italic> pattern discovery and prioritization of functional variants (DVAR) ##REF##30256891##[18]##, and PAFA ##REF##29996888##[30]##, have not been evaluated in detail. Hence, it is imperative to systematically and comprehensively evaluate these methods to help users choose computational methods matching their needs.</p>", "<p id=\"p0015\">Notably, in our previous research, we did not develop any computational method for non-coding variants. Therefore, we independently assessed 12 performance metrics for 24 methods using four benchmark datasets. Our study compared computational methods under different conditions and showed that the performance of each method varied under different conditions. We also identified some computational methods with acceptable performance for rare pathogenic germline non-coding variants. We noted that no methods yielded satisfactory prediction results for rare somatic non-coding variants, disease-associated common non-coding variants, and common regulatory non-coding variants. Our results provide an opportunity for clinicians and researchers to select applicable evaluation methods to explore the functional effects of non-coding variants. Additional more accurate computational methods for various non-coding variants must be developed.</p>" ]
[ "<title>Materials and methods</title>", "<title>Computational methods and prediction score processing</title>", "<p id=\"p0120\">We compared 24 computational methods that provide precomputed prediction scores for the whole human genome. We included 14 methods based on supervised models, six based on unsupervised models, and four based on semi-supervised models (##TAB##0##Table 1##). The genomic positions of all precomputed scores were based on GRCh37/hg19. For standardization, all precomputed scores recorded by interval-level values were transformed into base-wise positions, and each base-wise position was assigned the same score. In addition, these raw scores were transformed into PHRED-scaled scores [−10 × log<sub>10</sub> (rank/total)] according to the genome-wide distribution of scores for approximately 9 × 10<sup>9</sup> potential SNVs, which is the set of all three non-reference alleles at each position of the reference assembly. PHRED-scaled scores provide a comparable unit to unify the estimation standard for assessment. For instance, if a raw score in the top 10% of all possible reference genomic SNVs, it was represented as a PHRED-scaled score of ≥ 10, and a raw score in the top 1‰ was represented as a score of ≥ 30. We calculated the mean of the precomputed base-level whole-genome DIsease-specific Variant ANnotation (DIVAN) ##REF##27923386##[17]## scores across 45 diseases for both region-matched and transcription start site (TSS)-matched criteria, and then transformed them into a PHRED-scaled score. Other raw and PHRED-scaled scores for all methods were downloaded from a previous study ##UREF##1##[31]## except for DIVAN_TSS ##REF##27923386##[17]## and DIVAN_REGION ##REF##27923386##[17]##.</p>", "<title>Benchmark datasets of non-coding variants</title>", "<p id=\"p0125\">To evaluate the performance of the 24 methods, it was essential to construct an independent test of datasets in which variants overlapping with the training data were removed from the compared methods as much as possible. Four independent benchmark datasets of non-coding variants were used to assess the performance of the 24 computational methods, including (1) rare germline variants from ClinVar, (2) rare somatic variants from COSMIC, (3) common regulatory variants from curated eQTL data, and (4) disease-associated common variants from curated GWAS. Both positive and negative non-coding variants were included in each benchmark dataset (##TAB##1##Table 2##, <xref rid=\"s0095\" ref-type=\"sec\">Table S1</xref>). We adopted the following strategies to reduce overlap between testing benchmark data and training data for further analysis. First, as all training datasets were published before 2019, we selected variants recorded in public databases ##REF##29165669##[38]##, ##REF##30371878##[39]## after 2019 to reduce overlap. Second, we comprehensively collected public training data on existing methods and removed overlap between benchmark data and available training data of the computational methods.</p>", "<p id=\"p0130\">The first benchmark dataset (rare germline variants from ClinVar) was downloaded from the ClinVar database. According to the American College of Medical Genetics and Genomics guidelines ##REF##25741868##[58]##, the variants were classified as ‘pathogenic’, ‘likely pathogenic’, ‘benign’, ‘likely benign’, and ‘uncertain significance’ in the ClinVar database. Furthermore, the ClinVar database contains interpretations of allele origins, and records in ClinVar with ORIGIN = 1 indicate that these variants are germline variants. To improve the accuracy of the benchmark dataset and eliminate overlap between testing benchmark data and training data used in the 24 computational methods, we selected all ‘pathogenic’, ‘likely pathogenic’, and ‘benign’ non-coding germline variants deposited in the ClinVar database after January 2, 2019, as testing data. And ‘pathogenic’ and ‘likely pathogenic’ non-coding germline variants are regarded as positive variants, and ‘benign’ non-coding germline variants are regarded as negative variants. Furthermore, we determined the AFs of these variants based on the gnomAD database, and noticed that (1) over 80% of ‘pathogenic’ and ‘likely pathogenic’ variants were not observed, (2) over 98% of ‘pathogenic’ and ‘likely pathogenic’ variants had AF &lt; 0.1%, (3) over 99% of ‘benign’ variants were observed, and (4) over 98% of ‘benign’ variants had AF ≥ 0.1%. Based on the AFs of these variants, we regarded all ‘pathogenic’ and ‘likely pathogenic’ variants as rare variants with AF &lt; 0.1%. Finally, we only selected all ‘pathogenic’, ‘likely pathogenic’, and ‘benign’ variants with AF &lt; 0.1% (515 and 1850) as our testing data.</p>", "<p id=\"p0135\">The second benchmark dataset (rare somatic variants from COSMIC) was downloaded from the COSMIC database. As most deleterious non-coding somatic variants are unknown and one criterion for identifying cancer driver variants is to examine their mutational recurrence across multiple samples ##REF##22759861##[59]##, non-coding somatic variants from the COSMIC database after March 19, 2019 were divided into positive and negative variants, respectively, according to the recurrence of the variants. To increase the reliability of these variants, we also ensured that our positive variants are located on risk genes collected from the Cornell Non-coding Cancer driver Database (CNCDatabase) ##REF##33095860##[40]##, whereas negative variants are not. A total of 2346 and 648,471 variants were categorized as positive and negative variants, respectively, when the threshold value of recurrence was equal to 2, and 84% of positive variants and 92% of negative variants had AF &lt; 0.1% based on the gnomAD database. It is widely accepted that most somatic variants observed in the cancer genome are rare ##REF##31796730##[60]##, and thus we only selected variants with AF &lt; 0.1% (1966 and 597,222) as our final testing data.</p>", "<p id=\"p0140\">It is well known that non-coding variants influence phenotypes mainly through regulating gene expression levels. Hence, we selected regulatory variants with minor allele frequency (MAF) &gt; 5% as our third benchmark dataset (common regulatory variants from curated eQTL data) to assess the 24 methods. Here, we integrated three independent eQTL test datasets from two studies ##REF##30256891##[18]##, ##UREF##1##[31]## and removed eight variants labeled differently in both studies as our testing data. The positive dataset included (1) high-confidence eQTL single-nucleotide polymorphisms (SNPs) from the GTEx portal database and (2) multi-tissue eQTL SNP fine-mapping data from the GTEx portal database and Brown’s study ##REF##23935528##[42]##. The negative dataset was randomly sampled by vSampler ##REF##33270826##[61]## based on 1000 Genomes Project phase3 (1000G P3) ##REF##26432245##[43]##, and negative variants were matched with positive variants based on the information of MAF, distance to the nearest transcription start site, gene density, and the number of variants in LD (<xref rid=\"s0095\" ref-type=\"sec\">Table S9</xref>). Notably, all positive and negative variants are non-coding, with MAF &gt; 5% based on 1000G P3. We also referred to the criteria of test sets from Li’s study ##REF##30659175##[36]##. We only included paired positive and negative variants beyond 1 kb from each other as our final testing data to prevent physically proximate variants from confounding.</p>", "<p id=\"p0145\">The fourth benchmark dataset (disease-associated common variants from curated GWAS) was downloaded from the CAUSALdb database ##REF##31691819##[44]## and 1000 Genomes Project ##REF##26432245##[43]##. We only selected non-coding SNVs in the intersection set of credible sets defined by three fine-mapping tools, including probabilistic annotation integrator (PAINTOR) ##REF##27663501##[62]##, caviar bayes factor (CAVIARBF) ##REF##25948564##[63]##, and FINEMAP ##REF##26773131##[64]## with MAF &gt; 5% based on the 1000 Genomes Project as positive variants and corresponding non-coding SNVs in the same LD blocks with R<sup>2</sup> &gt; 0.2 from the 1000 Genomes Project with MAF &gt; 5% as negative variants. Overlapping variants between positive and negative data as well as positive variants without corresponding negative variants were excluded from the analysis.</p>", "<title>Correlation analysis</title>", "<p id=\"p0150\">Spearman rank correlation analysis was used to evaluate the relationships among the 24 compared computational methods based on the four non-coding benchmark datasets described above. Specifically, Spearman rank correlation coefficients were calculated between any two computational methods for each benchmark dataset, in which variants with missing values for a method were excluded, and the results of correlation analyses were visualized in the form of heatmaps. In addition, for each benchmark dataset, we performed correlation analysis based on the positive and negative variant datasets.</p>", "<title>Metrics for performance evaluation</title>", "<p id=\"p0155\">The performances of the 24 computational methods were assessed based on the following 12 criteria: (1) the positive predictive value (PPV), the proportion of positive results in the computational methods that are positive under the benchmark dataset; (2) the negative predictive value (NPV), the proportion of negative results in computational methods that are negative under the benchmark dataset; (3) the false-negative rate (FNR), which is calculated as the ratio of the number of positive events wrongly categorized as negative by the computational method to the total number of actual positive events under the benchmark dataset; (4) the sensitivity (or true-positive rate; TPR), which measures the proportion of actual positives under the benchmark dataset that are correctly identified as such by the computational method. The FNR and sensitivity are paired measures with a sum equal to 100%; (5) the false-positive rate (FPR), which is calculated as the ratio of the number of negative events wrongly categorized as positive by the computational method to the total number of actual negative events under the benchmark dataset; (6) the specificity (or true-negative rate; TNR), which measures the proportion of actual negatives under the benchmark dataset that are correctly identified as such by the computational method. The FPR and specificity are paired metrics with a sum equal to 100%; (7) the accuracy, which represents the proportion of positive and negative variants in the benchmark data that are correctly predicted as positive and negative variants, respectively; (8) the MCC, a correlation coefficient (ranging from −1 to 1) between the observed and predicted classifications (where 1 indicates a perfect prediction, 0 indicates no better than random prediction, and −1 indicates complete disagreement between the prediction and true classification); (9) the ROC curve, a graphical plot that illustrates the predictive ability of a computational method as its discrimination thresholds are varied; (10) the AUROC value, which ranges from 0 to 1 for each ROC curve, where a higher AUROC indicates better performance of the computational method; (11) the hser-AUROC value, which is the AUROC corresponding to high sensitivity (TPR &gt; 95%); and (12) the hspr-AUROC value, which is the AUROC corresponding to high specificity (TNR &gt; 95%). The hser-AUROC and hspr-AUROC values are evaluated to serve some users who require a distinction between positive variants with high sensitivity or specificity. Given that many computational methods do not offer recommended cutoff values, all metrics described above were calculated based on the best thresholds corresponding to the best sum of sensitivity and specificity. In addition, the best thresholds, sensitivities, specificities, AUROC values, hspr-AUROC values, and hser-AUROC values were calculated using the ‘pROC’ package ##REF##21414208##[65]## based on PHRED-scaled scores.</p>", "<title>Non-coding DNMs from the Simons simplex collection</title>", "<p id=\"p0160\">Non-coding DNMs identified in 1902 patients with ASD and 1902 unaffected siblings were downloaded from the Simons simplex collection ##REF##30545852##[47]##, ##REF##20955926##[66]## (<xref rid=\"s0095\" ref-type=\"sec\">Table S1</xref>) and were previously cataloged in the Gene4Denovo database that we developed ##REF##31642496##[49]##. Comparison of the performance of computational methods for non-coding DNMs was based on PHRED-scaled scores. We compared the burden of functional non-coding variants predicted by the computational methods in the ASD and sibling groups under different cutoff values. To assess the performance of computational methods for DNMs, we calculated the OR, 95% confidence interval of the OR, and <italic>P</italic> value between ASD and unaffected siblings using the two-sided Poisson’s ratio test.</p>", "<title>Experimentally validated non-coding DNMs from ASD</title>", "<p id=\"p0165\">We collected experimentally validated non-coding transcriptional-regulation-disruption DNMs from ASD probands ##REF##31133750##[48]## and nearest non-coding non-pathogenic DNMs in the siblings of ASD patients ##UREF##1##[31]## as our supplementary test dataset (<xref rid=\"s0095\" ref-type=\"sec\">Table S1</xref>) to further assess the performance of 24 methods for DNMs.</p>" ]
[ "<title>Results</title>", "<title>Predictions among methods showed poor concordance</title>", "<p id=\"p0020\">In this study, a total of 24 computational methods were assessed (##TAB##0##Table 1##). Four independent benchmark datasets were built that represented various genetic aspects: (1) rare germline variants from clinical relevant sequence variants (ClinVar), including rare non-coding germline variants of human traits and genetic diseases ##REF##29165669##[38]##; (2) rare somatic variants from catalogue of somatic mutations in cancer (COSMIC) for rare non-coding somatic variants of human cancers ##REF##30371878##[39]##, ##REF##33095860##[40]##; (3) common regulatory variants from curated expression quantitative trait locus (eQTL) data for common non-coding variants of the human genome that explain variation in gene expression levels ##REF##23715323##[41]##, ##REF##23935528##[42]##, ##REF##26432245##[43]##; and (4) disease-associated common variants from curated GWAS for common non-coding risk variants of human diseases recognized by GWAS ##REF##26432245##[43]##, ##REF##31691819##[44]## (##TAB##1##Table 2##). Further, all 24 computational methods were published before 2020 and the training datasets used were published before 2019. To reduce overlap between our testing benchmark data and the training data used in the 24 computational methods, we selected variants published after 2019 and removed variants that existed in these publicly available training datasets before comparing the methods.</p>", "<p id=\"p0025\">Spearman rank correlation coefficients were calculated between pairs of computational methods based on the PHRED-scaled scores of four benchmark datasets to evaluate the predictive concordances among the 24 computational methods (<xref rid=\"s0095\" ref-type=\"sec\">Figure S1</xref>). The overall pairwise correlation for rare somatic variants from COSMIC was generally higher than for the other three datasets, suggesting that current methods show better concordance in somatic variants prediction. Moreover, we calculated the Spearman rank correlation coefficient based on the positive variant dataset and negative variant dataset for each benchmark dataset. We found that the overall pairwise correlation for negative rare somatic variants from COSMIC was higher than for positive rare somatic variants from COSMIC. The weak pairwise correlations (R &lt; 0.4) among all 24 computational methods were common in the four benchmark datasets, except for a few computational methods that were highly correlated with each other (R &gt; 0.8) in the positive rare germline variants from ClinVar, such as CADD and deleterious annotation of genetic variants using neural networks (DANN), possibly because of the selection of similar training data and learning features. In summary, our results indicate that existing computational methods have poor predictive concordance for the same benchmark dataset, suggesting the necessity and importance of assessing different computational methods under various conditions.</p>", "<title>Methods showed different performances for rare germline and somatic variants</title>", "<p id=\"p0030\">It is widely accepted that pathogenic variants are often rare variants. To determine the performance of all 24 methods for rare variants, we constructed two datasets, including rare germline variants from ClinVar and rare somatic variants from COSMIC. (1) Rare germline variants from ClinVar included 515 positive and 1850 negative variants (##TAB##1##Table 2##, <xref rid=\"s0095\" ref-type=\"sec\">Table S1</xref>), which were downloaded from ‘pathogenic’, ‘likely pathogenic’, and ‘benign’ non-coding germline variants in the ClinVar database ##REF##29165669##[38]## with allele frequency (AF) &lt; 0.1% in the Genome Aggregation Database (gnomAD) ##REF##32461654##[45]##. (2) Rare somatic variants from COSMIC included 1966 positive and 597,221 negative variants (##TAB##1##Table 2##, <xref rid=\"s0095\" ref-type=\"sec\">Table S1</xref>), and all of these variants were downloaded from the COSMIC database ##REF##30371878##[39]## with AF &lt; 0.1% in the gnomAD database. In addition, we selected AUROC as our major performance measure because, compared to other metrics, its value is unaffected by different cutoff values.</p>", "<p id=\"p0035\">Assessments of 12 performance metrics for all 24 computational methods based on the PHRED-scaled scores of rare germline variants from ClinVar are summarized in ##TAB##2##Table 3##. We found that the AUROC of the 24 methods ranged from 0.4481 to 0.8033 (median of AUROC = 0.6988), and that Functional Analysis Through Hidden Markov Models with an eXtended Feature set (FATHMM-XF ##REF##28968714##[21]##; AUROC = 0.8033) exhibited the best performance, followed closely by Functional Analysis Through Hidden Markov Models with multiple kernel learning (FATHMM-MKL ##REF##25583119##[20]##; AUROC = 0.7954) and Regulatory Mendelian Mutation (ReMM; AUROC = 0.7848). Clinicians and researchers sometimes require computational methods with high sensitivity or specificity (typically &gt; 95%). For example, doctors may choose computational methods with high sensitivity to evaluate the pathogenicity of non-coding variants in genetic counseling for known pathogenic genes. We further assessed the high-specificity regional AUROC (hspr-AUROC) and high-sensitivity regional AUROC (hser-AUROC) values. We found that FATHMM-XF (hspr-AUROC = 0.7067) exhibited the best performance with hspr-AUROC values &gt; 0.70, while regBase_PAT ##UREF##1##[31]## (hser-AUROC = 0.5517) exhibited the best performance with hser-AUROC values &gt; 0.55 (##TAB##2##Table 3##). The accuracy and Mathews correlation coefficient (MCC) were also used to assess the performance of computational methods, with FATHMM-XF showing the highest accuracy and MCC scores among the 24 methods. Notably, methods based on supervised models (median of AUROC = 0.7161) showed better performance than those based on semi-supervised models (median of AUROC = 0.6832) and methods based on unsupervised models (median of AUROC = 0.5961). Moreover, we assessed the performance of the 24 computational methods based on rare germline variants from ClinVar after removing the ‘likely pathogenic’ non-coding germline variants, resulting in 343 positive variants and 1850 negative variants. The assessment results of 12 performance metrics for all 24 computational methods are summarized in <xref rid=\"s0095\" ref-type=\"sec\">Table S2</xref>. Performance metrics such as the AUROC of the computational methods were generally concordant, regardless of whether the variants were likely pathogenic (<xref rid=\"s0095\" ref-type=\"sec\">Figure S2</xref>).</p>", "<p id=\"p0040\">In addition, we assessed the performance of 24 methods for somatic variants and assessments of 12 performance metrics based on PHRED-scaled scores, as summarized in <xref rid=\"s0095\" ref-type=\"sec\">Table S3</xref>. The AUROC of the 24 computational methods ranged from 0.4984 to 0.7131 (median of AUROC = 0.6295) in rare somatic variants from COSMIC, with FunSeq2 ##REF##25273974##[25]## (AUROC = 0.7131) exhibiting the best overall performance, followed closely by fitness consequences 2 (FitCons2) ##REF##30559490##[24]## (AUROC = 0.7069). This result suggests that existing methods perform poorly for non-coding somatic variants. Furthermore, methods based on semi-supervised models (median of AUROC = 0.6988) performed better than methods based on unsupervised (median of AUROC = 0.6551) and supervised (median of AUROC = 0.6063) models.</p>", "<title>Predictive ability of methods for common variants warrants improvement</title>", "<p id=\"p0045\">It is now accepted that some common variants are regulatory or risk variants; hence, we also constructed common regulatory variants from curated eQTL data and disease-associated common variants from curated GWAS (see Materials and methods) to evaluate the performance of 24 methods for variants in the 1000 Genomes Project ##REF##26432245##[43]## with AF &gt; 5% (##TAB##1##Table 2##, <xref rid=\"s0095\" ref-type=\"sec\">Table S1</xref>). The respective numbers of positive and negative variants were recorded in the common regulatory variants from curated eQTL data (13,274 and 13,274) and disease-associated common variants from curated GWAS (73,693 and 76,214). We found that the AUROC of the 24 computational methods ranged from 0.4837 to 0.6472 (median of AUROC = 0.5619) in common regulatory variants from curated eQTL data and from 0.4766 to 0.5188 (median of AUROC = 0.5041) in disease-associated common variants from curated GWAS (<xref rid=\"s0095\" ref-type=\"sec\">Tables S4 and S5</xref>), and that the distributions of PHRED-scaled scores for positive and negative variants were similar irrespective of them being in common regulatory variants from curated eQTL data or disease-associated common variants from curated GWAS (<xref rid=\"s0095\" ref-type=\"sec\">Figures S3 and S4</xref>). This indicates that existing methods are unsuitable for common variants, particularly for common variants in the same linkage disequilibrium (LD) block. Furthermore, we classified the disease-associated common variants from curated GWAS into four subgroups (0.2–0.4, 0.4–0.6, 0.6–0.8, and 0.8–1.0) according to r<sup>2</sup> thresholds of LD, and found that all methods showed poor performance for four subgroups (<xref rid=\"s0095\" ref-type=\"sec\">Figure S5</xref>).</p>", "<title>CADD and context-dependent tolerance score showed better performance for non-coding <italic>de novo</italic> mutations in autism spectrum disorder</title>", "<p id=\"p0050\">Non-coding <italic>de novo</italic> mutations (DNMs) play important roles in neurodevelopmental disorders ##REF##30563709##[46]##, such as DNMs in the promoter and regulatory regions in autism spectrum disorder (ASD) ##REF##30545852##[47]##, ##REF##31133750##[48]##. We then downloaded 115,569 and 113,530 non-coding DNMs from 1902 patients with ASD and 1902 unaffected siblings from the Gene4Denovo database ##REF##31642496##[49]##, and evaluated the performance of the methods based on their PHRED-scaled scores (##FIG##0##Figure 1##; <xref rid=\"s0095\" ref-type=\"sec\">Table S6</xref>). Given that the pathogenicity of most non-coding DNMs is unclear, we selected odds ratios (OR) to assess the performance of the computational methods; better methods were expected to show higher OR under the same conditions. We adopted two strategies to calculate the OR and two-sided <italic>P</italic> values between patients with ASD and their unaffected siblings.</p>", "<p id=\"p0055\">In the first strategy, we counted the number of positive non-coding DNMs in the ASD and sibling groups under different cutoff values of PHRED-scaled scores (<italic>i.e.</italic>, 10, 15, 20, 25, 30, and 35) for the 24 computational methods. The number of positive DNMs predicted by most methods between the ASD and sibling groups showed significant differences (<italic>P</italic> &lt; 0.05) under the most relaxed condition (cutoff = 10) but had low OR (OR &lt; 1.05). Under increasingly rigorous thresholds, many methods showed higher OR but with <italic>P</italic> &gt; 0.05; the context-dependent tolerance score (CDTS) method achieved the best performance at a cutoff value of 20 (OR = 1.13, <italic>P</italic> = 0.006).</p>", "<p id=\"p0060\">In the second strategy, we selected the top 50, 100, 150, 200, 250, and 300 DNMs that were most likely to be functional in patients with ASD based on PHRED-scaled scores and obtained corresponding thresholds to make predictions in unaffected siblings. We found that many methods yielded <italic>P</italic> &gt; 0.05 and OR &gt; 1.05 under the most relaxed condition (top 300). Under a more rigorous condition, some methods exhibited higher OR values and lower <italic>P</italic> values; CADD achieved the highest OR value and the lowest <italic>P</italic> value (OR = 1.5, <italic>P</italic> = 0.002, threshold = 21.6241), followed by CDTS (OR = 1.21, <italic>P</italic> = 0.0493, threshold = 26.8855). In summary, these results suggest that CADD and CDTS have better prediction performance for functional DNM.</p>", "<title>Different methods showed different resolutions</title>", "<p id=\"p0065\">Theoretically, a perfect computational method should assign different prediction scores to different variants at the same position. Here, we calculated the rates of discriminable prediction scores among 24 computational methods for the same position across the whole genome, and noted that only nine methods, including regBase_REG ##UREF##1##[31]##, regBase_CAN ##UREF##1##[31]##, and regBase_PAT, showed discriminability at base-wise resolution for most sites in the whole genome (<xref rid=\"s0095\" ref-type=\"sec\">Figure S6</xref>). Additionally, for computational methods without discriminability at the base-wise resolution, we calculated the physical distances of surrounding DNA sites that showed the same prediction scores. We also determined the cumulative sum of proportions of different physical distances from 1 to the largest value until it was no smaller than 0.9, and then selected the last physical distances as the resolution. We found that most prediction scores of DNA sites differed with 1-bp site around them (<xref rid=\"s0095\" ref-type=\"sec\">Figure S7</xref>).</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0070\">In recent years, it has been widely accepted that non-coding variants play important roles in human diseases ##REF##26152199##[2]##, ##REF##32741549##[3]##, ##REF##30127527##[4]##, ##REF##25383969##[5]##, ##REF##25261935##[6]##, ##REF##26227905##[7]##, ##REF##26615194##[8]##, ##REF##29727686##[9]##. Many computational methods for evaluating the function and pathogenicity of non-coding variants have been developed for clinicians and geneticists to help them identify functional or pathogenic non-coding variants. Given that computational methods for non-coding variants have adopted various algorithms and training data based on different evolutionary constraints, epigenomics, and sequence features, their performance differs under differing conditions. However, it is difficult to choose an optimal method because of the lack of knowledge about the performance of the methods under different conditions. Selecting an optimal method can effectively aid in the prioritization of functional variants and candidate genes, thus increasing the demand for assessment of different computational methods under various conditions. In this work, we assessed 12 performance metrics of 24 computational methods based on four non-coding independent benchmark datasets.</p>", "<p id=\"p0075\">Although multiple studies ##REF##29340599##[35]##, ##REF##30659175##[36]##, ##REF##27999115##[37]## have compared computational prediction methods for non-coding variants, our study differs from these studies for the following reasons. (1) Our benchmark data are more comprehensive and stricter. We constructed four benchmark datasets representing different genomic contexts and simulated realistic situations, such as positive and negative variants from the common regulatory variants from curated eQTL data with matched genomic features. (2) Our evaluation metrics are more comprehensive. We not only selected some classic metrics but also adopted hser-AUROC and hspr-AUROC data to serve some users who need to prioritize variants with high sensitivity or specificity. (3) To the best of our knowledge, this is the first study to assess the performance of existing methods for non-coding DNMs based on OR values.</p>", "<p id=\"p0080\">Based on the correlation analysis of 24 computational methods, the predictive concordances among the 24 computational methods in rare somatic variants from COSMIC were higher than in the other three datasets. This may be because somatic variants result from replication errors and DNA damage ##REF##26404825##[50]##. Hence, somatic variants may have some similar features that germline variants do not, but most variants in the other three datasets are germline variants. Additionally, an ensemble learning method named regBase_CAN ##UREF##1##[31]## in the prediction of common regulatory variants and disease-associated common variants was negatively correlated with many methods. Of note, most of these methods with a negative correlation with regBase_CAN were incorporated into regBase_CAN. Compared to other methods, regBase includes three methods designed for different purposes, and regBase_CAN is a method designed to predict the effects of somatic variants based on a somatic variant training dataset ##UREF##1##[31]##. Thus, parameters in regBase_CAN may lead to inconsistent prediction results for common variants with other methods.</p>", "<p id=\"p0085\">Based on our results, we clustered the 24 methods into three groups based on their computational models (supervised, unsupervised, and semi-supervised models), and preliminarily found that ncER (supervised model), DVAR (unsupervised model), and LINSIGH (semi-supervised model) ##REF##28288115##[27]## are the representative methods of the aforementioned three groups with the highest median of AUROC values based on four benchmark datasets (##FIG##1##Figure 2##). Additionally, we noted that computational methods showed different prediction efficiencies under different conditions (##FIG##1##Figure 2##). For example, FATHMM-XF was the best method for rare germline variants from ClinVar (AUROC = 0.8033) but performed poorly for rare somatic variants from COSMIC (AUROC = 0.5933). Although the performance of the computational methods varied for the four different benchmark datasets, the best performance was recorded for rare germline variants from ClinVar. These results are consistent with a previous study ##REF##29340599##[35]## and might be attributed to the following reasons. First, most computational methods selected more germline than somatic variants, which may have different genomic features; this selection bias in training data may improve performance in rare germline variant dataset from ClinVar. Second, it is well known that genetic variation in many complex quantitative traits results from the joint small effects of multiple variants ##REF##21496265##[51]##, ##REF##23138309##[52]##, and non-coding variants often have a weak impact on complex traits ##REF##26482794##[53]##. The stronger functional effects of germline variants in the ClinVar database made it easier to distinguish functional variants for these computational methods. Given that the contribution of single eQTL and GWAS SNV to heritability is small, functional prediction of these SNVs remains an enormous challenge.</p>", "<p id=\"p0090\">In addition, we found that methods based on supervised models performed better than those based on unsupervised and semi-supervised models in rare germline variants from ClinVar. This may be explained by the selection of training data, as supervised learning demands representative and correctly labeled training data ##UREF##2##[54]##, and many methods based on supervised models select high-quality germline variant data from the Human Gene Mutation Database (HGMD) ##REF##12754702##[55]## and ClinVar database as training data. Thus, many methods based on supervised models performed better with rare germline variants from ClinVar. Furthermore, methods based on semi-supervised models performed better than unsupervised and supervised models in rare somatic variants from COSMIC. This may be because semi-supervised models select labeled and unlabeled data with stronger and weaker functional effects, respectively, as their training data. In contrast, the supervised and unsupervised models select labeled and unlabeled data, respectively, as their training data ##UREF##2##[54]##.</p>", "<p id=\"p0095\">According to the performance measurement strategy, we divided the 24 methods into three groups (I, II, and III) based on the rank of their AUROC values, and every group contained eight methods (<xref rid=\"s0095\" ref-type=\"sec\">Table S7</xref>). None of these methods performed well in all evaluations. This may be because different evaluations represent different aspects of method performance. Hence, appropriate methods should be selected based on different requirements. In addition, the AUROC is not affected by different cutoff values and does not vary significantly with different ratios of positive and negative variants in benchmark data; thus, we selected the AUROC as our major measure.</p>", "<p id=\"p0100\">It is well known that non-coding DNMs play important roles in neurodevelopmental disorders, such as ASD ##REF##30563709##[46]##, ##REF##30545852##[47]##, ##REF##31133750##[48]##; however, there is no authoritative database for validated pathogenic DNMs. To assess the prediction performance of the 24 methods for non-coding DNMs, we downloaded non-coding DNMs from patients with ASD and unaffected siblings from our previous study ##REF##31642496##[49]##. Although the pathogenicity of these DNMs is unclear, the number of pathogenic DNMs from patients with ASD should be more than unaffected siblings. Hence, we selected OR to assess the performance of these methods. In addition, we tried our best to collect 57 experimentally validated non-coding transcriptional-regulation-disruption DNMs from ASD probands and 50 nearest non-coding non-pathogenic DNMs in the siblings of ASD patients as our testing dataset to further assess the performance of 24 methods for DNMs. We noted that DVAR, regBase_CAN, and FitCons2 performed better with an AUROC &gt; 0.77 (<xref rid=\"s0095\" ref-type=\"sec\">Table S8</xref>). Based on these results, we think it is still a challenge to make an accurate prediction for DNMs.</p>", "<p id=\"p0105\">In this study, we noted that three of 24 compared methods were ensemble prediction models and found that the performances of the three methods (regBase_REG, regBase_PAT, and regBase_CAN) were moderate compared to other methods. In addition, we selected the top 10 methods of each benchmark dataset based on the sum of sensitivity and specificity to evaluate whether combined prediction would improve performance. If a variant was predicted as positive by more than half of the methods, it was considered positive. Finally, we assessed the performance of this combined prediction based on the accuracy and MCC, and found that combined prediction did not further improve performance. This indicates that it is still challenging to improve prediction performance for non-coding variants based on existing ensemble models. Hence, we think that more attention should be paid to improving the quality of training data and models to get better prediction performance for non-coding variants.</p>", "<p id=\"p0110\">This study had some limitations. First, there was some potential circularity between the testing and training data of the computational prediction methods ##REF##25684150##[56]##. To eliminate potential circularity, we selected testing data that were recorded after 2019 and, as much as possible, removed variants that overlapped with publicly available training data when comparing methods. Given that some methods only provide the source and version without including the exact variants of the training data, a small amount of the benchmark data may still be the same as the training data in the methods. Hence, we suggest that scientists who develop new methods should publish their original training and testing data. Second, although the testing data downloaded from the ClinVar, COSMIC, the Genotype-Tissue Expression project (GTEx portal) ##REF##23715323##[41]##, and GWAS catalog ##REF##30445434##[57]## databases have been widely used to develop computational methods and assess their performance, relatively little is known about the functional consequences of variations in the non-coding regions of the genome, and most variants in benchmark datasets were not experimentally validated; as such, incorrectly labeled data may have been included in our benchmark data. Therefore, we strongly recommend that scientists select experimentally validated or high-confidence training data to develop new methods in future studies.</p>", "<p id=\"p0115\">Taken together, our findings suggest that existing computational methods show acceptable performance only for germline variants and that their predictive ability must be improved for different types of non-coding variants. We strongly recommend that more attention should be paid to the quality of learning data in future software development work. For example, methods should use various training data and genomic features to avoid selection bias. Our findings will serve as a useful guide for clinicians and researchers in choosing appropriate methods for non-coding variant prediction, leading to the development of new methods.</p>" ]
[]
[ "<p id=\"np010\">Equal contribution.</p>", "<p><bold>Non-coding variants</bold> in the human genome significantly influence human traits and complex diseases via their regulation and modification effects. Hence, an increasing number of computational methods are developed to predict the effects of variants in human non-coding sequences. However, it is difficult for inexperienced users to select appropriate computational methods from dozens of available methods. To solve this issue, we assessed 12 performance metrics of 24 methods on four independent non-coding variant benchmark datasets: (1) rare germline variants from clinical relevant sequence variants (ClinVar), (2) rare somatic variants from Catalogue Of Somatic Mutations In Cancer (COSMIC), (3) common regulatory variants from curated expression quantitative trait locus (eQTL) data, and (4) disease-associated common variants from curated genome-wide association studies (GWAS). All 24 tested methods performed differently under various conditions, indicating varying strengths and weaknesses under different scenarios. Importantly, the performance of existing methods was acceptable for rare germline variants from ClinVar with the area under the receiver operating characteristic curve (AUROC) of 0.4481–0.8033 and poor for rare somatic variants from COSMIC (AUROC = 0.4984–0.7131), common regulatory variants from curated eQTL data (AUROC = 0.4837–0.6472), and disease-associated common variants from curated GWAS (AUROC = 0.4766–0.5188). We also compared the prediction performance of 24 methods for non-coding <italic>de novo</italic> mutations in autism spectrum disorder, and found that the combined annotation-dependent depletion (CADD) and context-dependent tolerance score (CDTS) methods showed better performance. Summarily, we assessed the performance of 24 computational methods under diverse scenarios, providing preliminary advice for proper tool selection and guiding the development of new techniques in interpreting non-coding variants.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Leng Han</p>" ]
[ "<title>Competing interests</title>", "<p id=\"p0170\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0175\"><bold>Zheng Wang:</bold> Conceptualization, Methodology, Validation, Formal analysis, Investigation, Data curation, Writing – original draft, Writing – review &amp; editing. <bold>Guihu Zhao:</bold> Conceptualization, Methodology, Software, Data curation, Writing – original draft. <bold>Bin Li:</bold> Investigation. <bold>Zhenghuan Fang:</bold> Methodology. <bold>Qian Chen:</bold> Investigation. <bold>Xiaomeng Wang:</bold> Data curation. <bold>Tengfei Luo:</bold> Investigation. <bold>Yijing Wang:</bold> Investigation. <bold>Qiao Zhou:</bold> Investigation, Data curation. <bold>Kuokuo Li:</bold> Visualization. <bold>Lu Xia:</bold> Investigation. <bold>Yi Zhang:</bold> Investigation. <bold>Xun Zhou:</bold> Investigation, Data curation, Visualization. <bold>Hongxu Pan:</bold> Investigation, Data curation, Visualization. <bold>Yuwen Zhao:</bold> Investigation, Data curation, Visualization. <bold>Yige Wang:</bold> Investigation, Data curation, Visualization. <bold>Lin Wang:</bold> Data curation. <bold>Jifeng Guo:</bold> Resources, Supervision, Project administration. <bold>Beisha Tang:</bold> Conceptualization, Resources, Writing – review &amp; editing. <bold>Kun Xia:</bold> Resources, Supervision, Project administration. <bold>Jinchen Li:</bold> Conceptualization, Resources, Writing – review &amp; editing, Supervision, Project administration, Funding acquisition. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0190\">The following are the Supplementary data to this article:</p>", "<p id=\"p0195\">\n\n</p>", "<p id=\"p0200\">\n\n</p>", "<p id=\"p0205\">\n\n</p>", "<p id=\"p0210\">\n\n</p>", "<p id=\"p0215\">\n\n</p>", "<p id=\"p0220\">\n\n</p>", "<p id=\"p0225\">\n\n</p>", "<p id=\"p0230\">\n\n</p>", "<p id=\"p0235\">\n\n</p>", "<p id=\"p0240\">\n\n</p>", "<p id=\"p0245\">\n\n</p>", "<p id=\"p0250\">\n\n</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0180\">This work was supported by the National Natural Science Foundation of China (Grant No. 81801133 to JL), the Young Elite Scientist Sponsorship Program by China Association for Science and Technology (Grant No. 2018QNRC001 to JL), the Innovation-Driven Project of Central South University, China (Grant No. 20180033040004 to JL), the Natural Science Foundation for Young Scientists of Hunan Province, China (Grant No. 2019JJ50974 to GZ), and the Natural Science Foundation of Hunan Province for outstanding Young Scholars, China (Grant No. 2020JJ3059 to JL).</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Performance evaluation in ASD based on DNMs</bold></p><p><bold>A.</bold> Performance evaluation of 24 computational methods under different cutoff values of PHRED-scaled scores. The order of the 24 computational methods shown on the Y-axis is based on their OR values under cutoff = 20. <bold>B.</bold> Performance evaluation of 24 computational methods under different numbers of DNMs that are most likely to be functional in ASD. The order of the 24 computational methods shown on the Y-axis is based on their OR values with the number of most likely functional DNMs being 200. The OR and <italic>P</italic> values were calculated by a two-sided Poisson’s ratio test. The size of each ball is proportional to the OR value. Differently colored balls represent different <italic>P</italic> value ranges. OR, odds ratios; DNM, <italic>de novo</italic> mutation; ASD, autism spectrum disorder.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Overall AUROC of four benchmark datasets</bold></p><p>Distributions of AUROC values for 24 methods are shown in a boxplot. Differently colored balls represent different benchmark datasets. Differently colored boxes represent different models. AUROC, area under the receiver operating characteristic curve.</p></caption></fig>", "<fig id=\"f0015\" position=\"anchor\"><label>Supplementary Figure S1</label></fig>", "<fig id=\"f0020\" position=\"anchor\"><label>Supplementary Figure S2</label></fig>", "<fig id=\"f0025\" position=\"anchor\"><label>Supplementary Figure S3</label></fig>", "<fig id=\"f0030\" position=\"anchor\"><label>Supplementary Figure S4</label></fig>", "<fig id=\"f0035\" position=\"anchor\"><label>Supplementary Figure S5</label></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary Figure S6</label></fig>", "<fig id=\"f0045\" position=\"anchor\"><label>Supplementary Figure S7</label></fig>" ]
[ "<table-wrap position=\"float\" id=\"t0005\"><label>Table 1</label><caption><p><bold>Summary of 24 computational methods compared in this study</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Method</bold></th><th><bold>Prediction model</bold></th><th><bold>Model type</bold></th><th><bold>Learning dataset</bold></th><th><bold>Version</bold></th><th><bold>Ref.</bold></th></tr></thead><tbody><tr><td>CADD</td><td>SVM and logistic regression model</td><td>Supervised</td><td>Simulated DNMs and variants arisen and fixed in human populations</td><td>v1.3</td><td>##REF##30371827##[13]##</td></tr><tr><td>CDTS</td><td>Difference between expected and observed score as context-dependent tolerance score</td><td>Unsupervised</td><td>11,257 human whole-genome sequences</td><td>2017</td><td>##REF##29483654##[14]##</td></tr><tr><td>CScape</td><td>Kernel-based models and leave-one-concentration-out cross validation</td><td>Supervised</td><td>Somatic point variants from the COSMIC and SNVs from the 1000 Genomes Project</td><td>2017</td><td>##REF##28912487##[15]##</td></tr><tr><td>DANN</td><td>Deep neural network</td><td>Supervised</td><td>Simulated DNMs and variants arisen and fixed in human populations</td><td>2015</td><td>##REF##25338716##[16]##</td></tr><tr><td>DIVAN_TSS</td><td>Ensemble learning framework</td><td>Supervised</td><td>Risk variants of 45 diseases/phenotypes (ARB) and benign variants are sampled from the 1000 Genomes Project with TSS-matched criterion</td><td>2016</td><td>##REF##27923386##[17]##</td></tr><tr><td>DIVAN_REGION</td><td>Ensemble learning framework</td><td>Supervised</td><td>Risk variants of 45 diseases/phenotypes (ARB) and benign variants are sampled from the 1000 Genomes Project with region-matched criterion</td><td>2016</td><td>##REF##27923386##[17]##</td></tr><tr><td>DVAR</td><td>Multivariate Dirichlet Process Mixtures</td><td>Unsupervised</td><td>2 million variants randomly sampled from the 1000 Genomes Project</td><td>v1.0</td><td>##REF##30256891##[18]##</td></tr><tr><td>Eigen</td><td>Spectral meta-learner</td><td>Unsupervised</td><td>Variants in the 1000 Genomes Project without a match in dbNSFP and within 500 bp upstream of the TSS</td><td>v1.1</td><td>##REF##26727659##[19]##</td></tr><tr><td>Eigen_PC</td><td>Spectral meta-learner</td><td>Unsupervised</td><td>Variants in the 1000 Genomes Project without a match in dbNSFP and within 500 bp upstream of the TSS</td><td>v1.1</td><td>##REF##26727659##[19]##</td></tr><tr><td>FATHMM-MKL</td><td>Multiple kernel learning</td><td>Supervised</td><td>Germline variants in HGMD and control variants from the 1000 Genomes Project</td><td>2017</td><td>##REF##25583119##[20]##</td></tr><tr><td>FATHMM-XF</td><td>Kernel-based models and platt scaling</td><td>Supervised</td><td>Positive variants from the HGMD and control variants from the 1000 Genomes Project</td><td>2017</td><td>##REF##28968714##[21]##</td></tr><tr><td>FIRE</td><td>Random forest model</td><td>Supervised</td><td><italic>Cis</italic>-eQTL SNVs identified by the Geuvadis lymphoblastoid cell lines and sampled non-eQTL SNVs</td><td>2017</td><td>##REF##28961785##[22]##</td></tr><tr><td>fitCons</td><td>Generative probabilistic model</td><td>Semi-supervised</td><td>Multiple species genomic DNA sequence</td><td>v1.01</td><td>##REF##25599402##[23]##</td></tr><tr><td>FitCons2</td><td>Probabilistic evolutionary model</td><td>Semi-supervised</td><td>Multiple species genomic DNA sequence</td><td>2017</td><td>##REF##30559490##[24]##</td></tr><tr><td>FunSeq2</td><td>Weighted scoring scheme</td><td>Semi-supervised</td><td>Small-scale informative data context from the 1000 Genomes Project, ENCODE, COSMIC, and CGC</td><td>v2.1.6</td><td>##REF##25273974##[25]##</td></tr><tr><td>GenoCanyon</td><td>Conditional joint density estimation</td><td>Unsupervised</td><td>Each location in the human genome</td><td>v1.0.3</td><td>##REF##26015273##[26]##</td></tr><tr><td>LINSIGHT</td><td>Combination of generalized linear model and probabilistic model</td><td>Semi-supervised</td><td>Multiple species genomic DNA sequence and 54 unrelated human genomes</td><td>2017</td><td>##REF##28288115##[27]##</td></tr><tr><td>ncER</td><td>XGBoost model</td><td>Supervised</td><td>Positive examples from HGMD (2016_R1) and ClinVar (July 2016) and negative examples from gnomAD</td><td>v1.0</td><td>##REF##31748530##[28]##</td></tr><tr><td>Orion</td><td>Difference between the observed and expected site-frequency spectrums</td><td>Unsupervised</td><td>1662 WGS samples</td><td>2017</td><td>##REF##28797091##[29]##</td></tr><tr><td>PAFA</td><td>Logistic regression with L1 regularization</td><td>Supervised</td><td>Variants labeled “pathogenic” in ClinVar and significant SNPs associated with complex traits or diseases and variants labeled “benign” in ClinVar and variants in the 1000 Genomes Project</td><td>2018</td><td>##REF##29996888##[30]##</td></tr><tr><td>regBase_REG</td><td>XGBoost model</td><td>Supervised</td><td>Functional regulatory variant dataset and non-coding variants from the 1000 Genomes Project</td><td>v1.0</td><td>##UREF##1##[31]##</td></tr><tr><td>regBase_PAT</td><td>XGBoost model</td><td>Supervised</td><td>Pathogenic regulatory variant dataset and non-coding benign variants labeled “benign” in ClinVar</td><td>v1.0</td><td>##UREF##1##[31]##</td></tr><tr><td>regBase_CAN</td><td>XGBoost model</td><td>Supervised</td><td>Cancer recurrent regulatory somatic mutation dataset and non-recurrent somatic mutations</td><td>v1.0</td><td>##UREF##1##[31]##</td></tr><tr><td>ReMM</td><td>Random forest model</td><td>Supervised</td><td>Hand-curated set of regulatory mendelian mutations and derived alleles of human evolution</td><td>v0.3.1</td><td>##REF##27569544##[32]##</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0010\"><label>Table 2</label><caption><p><bold>Summary of four independent benchmark datasets used in this study</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Benchmark dataset</bold></th><th><bold>Positive set</bold></th><th><bold>Negative set</bold></th><th><bold>No. of positive variants</bold></th><th><bold>No. of negative variants</bold></th><th><bold>Refs.</bold></th></tr></thead><tbody><tr><td>Rare germline variants from ClinVar</td><td>Non-coding ‘pathogenic’ and ‘likely pathogenic’ germline variants from ClinVar (20190102–20201128)</td><td>Non-coding ‘benign’ germline variants from ClinVar (20190102–20201128)</td><td>515</td><td>1850</td><td>##REF##29165669##[38]##</td></tr><tr><td>Rare somatic variants from COSMIC</td><td>Non-coding somatic variants from COSMIC (v88–v92) with recurrence ≥ 2 and located on risk genes collected by CNCDatabase</td><td>Non-coding somatic variants from COSMIC (v88–v92) with recurrence = 1 and located on genes except for risk genes collected by CNCDatabase</td><td>1966</td><td>597,221</td><td>##REF##30371878##[39]##, ##REF##33095860##[40]##</td></tr><tr><td>Common regulatory variants from curated eQTL data</td><td>eQTL SNPs from the GTEx portal database and Brown’s study</td><td>Randomly selecting variants with matched properties from the 1000 Genomes Project by vSampler</td><td>13,274</td><td>13,274</td><td>##REF##23715323##[41]##, ##REF##23935528##[42]##, ##REF##26432245##[43]##</td></tr><tr><td>Disease-associated common variants from curated GWAS</td><td>Non-coding SNVs in the intersection set of credible sets defined by three tools from CAUSALdb database with MAF &gt; 5%</td><td>Non-coding SNVs from the 1000 Genomes Project with MAF &gt; 5% in the same LD blocks as corresponding positive variants with r<sup>2</sup> threshold &gt; 0.2</td><td>73,693</td><td>76,214</td><td>##REF##26432245##[43]##, ##REF##31691819##[44]##</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0015\"><label>Table 3</label><caption><p><bold>Performance evaluation based on rare germline variants from ClinVar</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Method</bold></th><th><bold>Missing rate (%)</bold></th><th><bold>Best threshold</bold></th><th><bold>PPV (%)</bold></th><th><bold>NPV (%)</bold></th><th><bold>FNR (%)</bold></th><th><bold>Sensitivity (%)</bold></th><th><bold>FPR (%)</bold></th><th><bold>Specificity (%)</bold></th><th><bold>Accuracy (%)</bold></th><th><bold>MCC</bold></th><th><bold>AUROC</bold></th><th><bold>hspr-AUROC</bold></th><th><bold>hser-AUROC</bold></th><th><bold>Prediction model</bold></th></tr></thead><tbody><tr><td>CADD</td><td align=\"char\">0.00</td><td align=\"char\">11.1395</td><td align=\"char\">44.40</td><td align=\"char\">87.83</td><td align=\"char\">39.22</td><td align=\"char\">60.78</td><td align=\"char\">21.19</td><td align=\"char\">78.81</td><td align=\"char\">74.88</td><td align=\"char\">0.3572</td><td align=\"char\">0.7509</td><td>0.5587</td><td>0.5277</td><td>Supervised</td></tr><tr><td>CScape</td><td align=\"char\">9.77</td><td align=\"char\">30.6855</td><td align=\"char\">37.46</td><td align=\"char\">85.79</td><td align=\"char\">48.43</td><td align=\"char\">51.57</td><td align=\"char\">22.75</td><td align=\"char\">77.25</td><td align=\"char\">71.88</td><td align=\"char\">0.2589</td><td align=\"char\">0.6655</td><td>0.5344</td><td>0.5217</td><td>Supervised</td></tr><tr><td>DANN</td><td align=\"char\">0.00</td><td align=\"char\">9.5376</td><td align=\"char\">45.95</td><td align=\"char\">86.78</td><td align=\"char\">44.85</td><td align=\"char\">55.15</td><td align=\"char\">18.05</td><td align=\"char\">81.95</td><td align=\"char\">76.11</td><td align=\"char\">0.3484</td><td align=\"char\">0.7341</td><td>0.5956</td><td>0.5244</td><td>Supervised</td></tr><tr><td>DIVAN_REGION</td><td align=\"char\">0.00</td><td align=\"char\">2.6953</td><td align=\"char\">23.89</td><td align=\"char\">82.34</td><td align=\"char\">27.57</td><td align=\"char\">72.43</td><td align=\"char\">64.22</td><td align=\"char\">35.78</td><td align=\"char\">43.76</td><td align=\"char\">0.0715</td><td align=\"char\">0.5357</td><td>0.5153</td><td>0.5064</td><td>Supervised</td></tr><tr><td>DIVAN_TSS</td><td align=\"char\">0.00</td><td align=\"char\">3.8817</td><td align=\"char\">23.16</td><td align=\"char\">80.52</td><td align=\"char\">33.59</td><td align=\"char\">66.41</td><td align=\"char\">61.35</td><td align=\"char\">38.65</td><td align=\"char\">44.69</td><td align=\"char\">0.0431</td><td align=\"char\">0.5047</td><td>0.5040</td><td>0.5028</td><td>Supervised</td></tr><tr><td>FATHMM-MKL</td><td align=\"char\">0.00</td><td align=\"char\">12.1444</td><td align=\"char\">49.10</td><td align=\"char\">90.16</td><td align=\"char\">31.46</td><td align=\"char\">68.54</td><td align=\"char\">19.78</td><td align=\"char\">80.22</td><td align=\"char\">77.67</td><td align=\"char\"><bold>0.4375</bold></td><td align=\"char\"><bold>0.7954</bold></td><td><bold>0.6359</bold></td><td>0.5344</td><td>Supervised</td></tr><tr><td>FATHMM-XF</td><td align=\"char\">9.77</td><td align=\"char\">26.0395</td><td align=\"char\"><bold>60.32</bold></td><td align=\"char\"><bold>90.98</bold></td><td align=\"char\">33.18</td><td align=\"char\">66.82</td><td align=\"char\"><bold>11.61</bold></td><td align=\"char\"><bold>88.39</bold></td><td align=\"char\"><bold>83.88</bold></td><td align=\"char\"><bold>0.5322</bold></td><td align=\"char\"><bold>0.8033</bold></td><td><bold>0.7067</bold></td><td>0.5074</td><td>Supervised</td></tr><tr><td>FIRE</td><td align=\"char\">0.00</td><td align=\"char\">9.7388</td><td align=\"char\">26.09</td><td align=\"char\">80.95</td><td align=\"char\">53.59</td><td align=\"char\">46.41</td><td align=\"char\">36.59</td><td align=\"char\">63.41</td><td align=\"char\">59.70</td><td align=\"char\">0.0831</td><td align=\"char\">0.5256</td><td>NA</td><td>0.5034</td><td>Supervised</td></tr><tr><td>ncER</td><td align=\"char\">0.25</td><td align=\"char\">13.9272</td><td align=\"char\">39.92</td><td align=\"char\">87.50</td><td align=\"char\">37.94</td><td align=\"char\">62.06</td><td align=\"char\">26.02</td><td align=\"char\">73.98</td><td align=\"char\">71.39</td><td align=\"char\">0.3144</td><td align=\"char\">0.7067</td><td>0.5249</td><td>0.5161</td><td>Supervised</td></tr><tr><td>PAFA</td><td align=\"char\">8.03</td><td align=\"char\">1.1395</td><td align=\"char\">36.40</td><td align=\"char\">90.42</td><td align=\"char\">26.32</td><td align=\"char\">73.68</td><td align=\"char\">34.15</td><td align=\"char\">65.85</td><td align=\"char\">67.49</td><td align=\"char\">0.3256</td><td align=\"char\">0.7239</td><td>0.5208</td><td>NA</td><td>Supervised</td></tr><tr><td>regBase_CAN</td><td align=\"char\">0.00</td><td align=\"char\">10.2935</td><td align=\"char\">39.50</td><td align=\"char\">89.49</td><td align=\"char\">29.51</td><td align=\"char\">70.49</td><td align=\"char\">30.05</td><td align=\"char\">69.95</td><td align=\"char\">70.06</td><td align=\"char\">0.3423</td><td align=\"char\">0.7083</td><td>0.5176</td><td>0.5018</td><td>Supervised</td></tr><tr><td>regBase_PAT</td><td align=\"char\">0.00</td><td align=\"char\">7.3824</td><td align=\"char\">35.23</td><td align=\"char\">89.40</td><td align=\"char\">26.60</td><td align=\"char\">73.40</td><td align=\"char\">37.57</td><td align=\"char\">62.43</td><td align=\"char\">64.82</td><td align=\"char\">0.2970</td><td align=\"char\">0.7375</td><td>0.5721</td><td><bold>0.5517</bold></td><td>Supervised</td></tr><tr><td>regBase_REG</td><td align=\"char\">0.00</td><td align=\"char\">20.6843</td><td align=\"char\">27.53</td><td align=\"char\">80.37</td><td align=\"char\">65.63</td><td align=\"char\">34.37</td><td align=\"char\">25.19</td><td align=\"char\">74.81</td><td align=\"char\">66.00</td><td align=\"char\">0.0852</td><td align=\"char\">0.5491</td><td>NA</td><td>NA</td><td>Supervised</td></tr><tr><td>ReMM</td><td align=\"char\">0.00</td><td align=\"char\">13.8161</td><td align=\"char\">47.68</td><td align=\"char\">89.36</td><td align=\"char\">34.17</td><td align=\"char\">65.83</td><td align=\"char\">20.11</td><td align=\"char\">79.89</td><td align=\"char\">76.83</td><td align=\"char\">0.4115</td><td align=\"char\"><bold>0.7848</bold></td><td>0.5969</td><td><bold>0.5448</bold></td><td>Supervised</td></tr><tr><td>CDTS</td><td align=\"char\">8.25</td><td align=\"char\">10.9826</td><td align=\"char\">25.36</td><td align=\"char\">79.56</td><td align=\"char\">66.88</td><td align=\"char\">33.12</td><td align=\"char\">27.24</td><td align=\"char\">72.76</td><td align=\"char\">64.10</td><td align=\"char\">0.0538</td><td align=\"char\">0.4910</td><td>NA</td><td>NA</td><td>Unsupervised</td></tr><tr><td>DVAR</td><td align=\"char\">0.00</td><td align=\"char\">15.0531</td><td align=\"char\"><bold>51.63</bold></td><td align=\"char\">88.69</td><td align=\"char\">38.45</td><td align=\"char\">61.55</td><td align=\"char\"><bold>16.05</bold></td><td align=\"char\"><bold>83.95</bold></td><td align=\"char\"><bold>79.07</bold></td><td align=\"char\">0.4283</td><td align=\"char\">0.7420</td><td>0.5371</td><td>0.5159</td><td>Unsupervised</td></tr><tr><td>Eigen</td><td align=\"char\">10.40</td><td align=\"char\">15.3901</td><td align=\"char\">43.68</td><td align=\"char\">89.58</td><td align=\"char\">35.48</td><td align=\"char\">64.52</td><td align=\"char\">21.42</td><td align=\"char\">78.58</td><td align=\"char\">75.70</td><td align=\"char\">0.3786</td><td align=\"char\">0.7656</td><td>0.5379</td><td><bold>0.5425</bold></td><td>Unsupervised</td></tr><tr><td>Eigen_PC</td><td align=\"char\">10.40</td><td align=\"char\">8.8690</td><td align=\"char\">27.96</td><td align=\"char\">88.79</td><td align=\"char\"><bold>24.42</bold></td><td align=\"char\"><bold>75.58</bold></td><td align=\"char\">50.15</td><td align=\"char\">49.85</td><td align=\"char\">55.12</td><td align=\"char\">0.2064</td><td align=\"char\">0.6032</td><td>NA</td><td>0.5366</td><td>Unsupervised</td></tr><tr><td>GenoCanyon</td><td align=\"char\">0.00</td><td align=\"char\">12.2531</td><td align=\"char\">33.39</td><td align=\"char\">82.57</td><td align=\"char\">58.25</td><td align=\"char\">41.75</td><td align=\"char\">23.19</td><td align=\"char\">76.81</td><td align=\"char\">69.18</td><td align=\"char\">0.1721</td><td align=\"char\">0.5890</td><td>0.5418</td><td>0.5012</td><td>Unsupervised</td></tr><tr><td>Orion</td><td align=\"char\">14.80</td><td align=\"char\">11.1831</td><td align=\"char\">23.61</td><td align=\"char\">80.75</td><td align=\"char\">67.07</td><td align=\"char\">32.93</td><td align=\"char\">27.47</td><td align=\"char\">72.53</td><td align=\"char\">64.42</td><td align=\"char\">0.0488</td><td align=\"char\">0.5124</td><td>0.5074</td><td>NA</td><td>Unsupervised</td></tr><tr><td>fitCons</td><td align=\"char\">8.16</td><td align=\"char\">0.2856</td><td align=\"char\">21.12</td><td align=\"char\"><bold>95.45</bold></td><td align=\"char\"><bold>0.22</bold></td><td align=\"char\"><bold>99.78</bold></td><td align=\"char\">98.78</td><td align=\"char\">1.22</td><td align=\"char\">21.87</td><td align=\"char\">0.0408</td><td align=\"char\">0.4481</td><td>NA</td><td>0.5034</td><td>Semi-supervised</td></tr><tr><td>FitCons2</td><td align=\"char\">8.03</td><td align=\"char\">17.3066</td><td align=\"char\">41.81</td><td align=\"char\">86.30</td><td align=\"char\">48.46</td><td align=\"char\">51.54</td><td align=\"char\">19.02</td><td align=\"char\">80.98</td><td align=\"char\">74.80</td><td align=\"char\">0.3023</td><td align=\"char\">0.6909</td><td>0.6052</td><td>0.5029</td><td>Semi-supervised</td></tr><tr><td>FunSeq2</td><td align=\"char\">1.61</td><td align=\"char\">7.6079</td><td align=\"char\">29.59</td><td align=\"char\"><bold>91.72</bold></td><td align=\"char\"><bold>14.03</bold></td><td align=\"char\"><bold>85.97</bold></td><td align=\"char\">56.84</td><td align=\"char\">43.16</td><td align=\"char\">52.47</td><td align=\"char\">0.2491</td><td align=\"char\">0.6756</td><td>0.5330</td><td>0.5299</td><td>Semi-supervised</td></tr><tr><td>LINSIGHT</td><td align=\"char\">1.82</td><td align=\"char\">17.6486</td><td align=\"char\"><bold>64.97</bold></td><td align=\"char\">88.15</td><td align=\"char\">44.44</td><td align=\"char\">55.56</td><td align=\"char\"><bold>8.31</bold></td><td align=\"char\"><bold>91.69</bold></td><td align=\"char\"><bold>83.85</bold></td><td align=\"char\"><bold>0.5010</bold></td><td align=\"char\">0.7743</td><td><bold>0.6307</bold></td><td>0.5005</td><td>Semi-supervised</td></tr></tbody></table></table-wrap>" ]
[]
[]
[]
[]
[]
[ "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S1</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S2</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S3</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S4</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S5</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S6</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S7</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S8</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S9</title></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p><italic>Note</italic>: The difference between DIVAN_TSS and DIVAN_REGION was the criteria to choose benign variants in the training set. Eigen_PC had the same prediction model and learning dataset as Eigen but they had different weights for some genomic features. regBase trained three composite models based on different training datasets to score functional, pathogenic, and cancer driver non-coding regulatory variants, respectively. CADD, combined annotation dependent depletion; CDTS, context-dependent tolerance score; DANN, deleterious annotation of genetic variants using neural networks; DIVAN, DIsease-specific Variant ANnotation; FIRE, Functional Inference of Regulators of Expression; fitCons, fitness consequences of functional annotation; ncER, non-coding essential regulation; PAFA, Prioritization And Functional Assessment; ReMM, Regulatory Mendelian Mutation; DNM, <italic>de novo</italic> mutation; COSMIC, the Catalogue of Somatic Mutations in Cancer; SNV, single-nucleotide variant; ARB, association results browser; TSS, transcription start site; HGMD, Human Gene Mutation Database; eQTL, expression quantitative trait locus; ENCODE, Encyclopedia of DNA Elements; CGC, Cancer Gene Census; gnomAD, Genome Aggregation Database; WGS, whole-genome sequencing; SNP, single-nucleotide polymorphism; SVM, support vector machine; XGBoost, extreme gradient boosting.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p><italic>Note</italic>: Matched properties including MAF, distance to closet transcription start site, gene density, and number of variants in LD. Three tools include PAINTOR ##REF##27663501##[62]##, CAVIARBF ##REF##25948564##[63]##, and FINEMAP ##REF##26773131##[64]##. CNCDatabase, Cornell Non-coding Cancer driver Database; GTEx, Genotype-Tissue Expression; MAF, minor allele frequency; LD, linkage disequilibrium.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p><italic>Note</italic>: Best threshold indicates the threshold corresponding to the best sum of sensitivity and specificity. Top three methods of every measure are represented by bold text. PPV, positive predictive value; NPV, negative predictive value; FPR, false-positive rate; FNR, false-negative rate; MCC, Mathew correlation coefficient; AUROC, area under the receiver operating characteristic curve; hspr-AUROC, high-specificity regional area under the receiver operating characteristic curve; hser-AUROC, high-sensitivity regional area under the receiver operating characteristic curve; NA, not available.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"d35e1337\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0090\" fn-type=\"supplementary-material\"><p id=\"p0185\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.02.002\" id=\"ir005\">https://doi.org/10.1016/j.gpb.2022.02.002</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["1"], "surname": ["Gloss", "Dinger"], "given-names": ["B.S.", "M.E."], "article-title": ["Realizing the significance of noncoding functionality in clinical genomics"], "source": ["Exp Mol Med"], "volume": ["50"], "year": ["2018"], "fpage": ["1"], "lpage": ["8"]}, {"label": ["31"], "surname": ["Zhang", "He", "Liu", "Zhai", "Huang", "Yi"], "given-names": ["S.", "Y.", "H.", "H.", "D.", "X."], "article-title": ["regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants"], "source": ["Nucleic Acids Res"], "volume": ["47"], "year": ["2019"], "object-id": ["e134"]}, {"label": ["54"], "surname": ["Robert", "Yoav"], "given-names": ["E.S.", "F."], "article-title": ["Boosting: foundations and algorithms"], "source": ["MITP"], "year": ["2012"], "fpage": ["23"], "lpage": ["52"]}]
{ "acronym": [], "definition": [] }
66
CC BY
no
2024-01-14 23:41:54
Genomics Proteomics Bioinformatics. 2023 Jun 8; 21(3):649-661
oa_package/8c/e8/PMC10787016.tar.gz
PMC10787017
36395998
[ "<title>Introduction</title>", "<p id=\"p0005\">Cervidae is the second largest family of artiodactyl ruminants (second to Bovidae). As a unique appendage organ of male cervid species (except for the reindeer), the antler grows extremely fast that exceeds even certain cancer tissues ##UREF##0##[1]##, ##REF##25046387##[2]##. Thus, antler provides an excellent model for studying rapid tissue growth in biological sciences. Sika deer (<italic>Cervus nippon</italic>) is one of the famous cervid animals producing antlers. As of now, there are not many genome resources of sika deer for the study of biology and evolution of Cervidae. Recent studies have reported that expression variation of alleles occurs frequently in mammals ##REF##15194819##[3]##, ##REF##12410233##[4]##, ##REF##12183620##[5]##. The allelic variants might affect the expression levels of alleles, and the expression variation of alleles is crucial in determining phenotypic diversity ##REF##15194819##[3]##. However, as a typical diploid mammal with two homologous chromosome pairs, the allelic variation of cervid species has not been elucidated yet. Therefore, deciphering the genome sequence of each allele chromosome of sika deer is substantial for understanding the expression patterns of allele-specific genes and their phenotypic characteristics (rapid antler growth and inhibition of oncogenesis) ##REF##33910227##[6]##, ##REF##33288905##[7]##.</p>", "<p id=\"p0010\">It is generally believed that the variation of the chromosome number and structure is one of the sources of biodiversity. The chromosome number could be increased or decreased by chromosome fission or fusion, respectively ##REF##33288905##[7]##, ##REF##9146914##[8]##. However, the molecular basis and consequence of chromosome variation in mammals remain unsolved ##REF##34824214##[9]##. The chromosome number varies dramatically in cervid animals, ranging from 2<italic>n</italic> = 6 (female Indian muntjac) ##REF##9146914##[8]## to 2<italic>n</italic> = 70 (such as Siberian roe deer) ##UREF##1##[10]##. Sika deer, as a typical representative animal of the genus <italic>Cervus</italic> in the cervid animals, also has different karyotypes with its closely related species, red deer (<italic>Cervus elaphus</italic>) ##UREF##2##[11]##. However, the concrete mechanism of chromosome evolution between two species still remains to be elucidated. Assembling the phased genome of sika deer contributes to understanding chromosome evolution in cervid animals ##REF##19492976##[12]##, ##REF##32561793##[13]##. It is also crucial to study the biodiversity and social organization of cervid species ##UREF##3##[14]##.</p>", "<p id=\"p0015\">In this work, the high-quality Illumina short reads, circular consensus sequencing (CCS) data, and high-throughput chromosome conformation capture (Hi-C) data were generated, which enabled us to assemble a high-quality haplotype-resolved chromosome-level genome of sika deer with the state-of-the-art assembly method. The allele-aware genome of sika deer contributed to exploring the cause of different karyotypes between sika deer and red deer, which would be of help for investigating the expression profiles of alleles in antler and researching the diversity and variation of alleles on homologous chromosomes. Our study also suggested the possible molecular basis for rapid antler growth. Overall, the high-quality genome and annotation information reported here not only investigated differences in expression between alleles on homologous chromosomes, but also provided valuable data and resources for studying structural variations (SVs), the mechanism of chromosome evolution of sika deer, and the molecular basis of rapid antler growth.</p>" ]
[ "<title>Materials and methods</title>", "<title>Sample collection</title>", "<p id=\"p0125\">A fresh blood sample was collected from a 7-year-old healthy male sika deer in Jindi Deer Industry Co. Ltd. (Ear tags: 1220; Harbin, Heilongjiang Province, China), whose parents were both purebred sika deer. DNA was extracted from the fresh blood sample for constructing the libraries.</p>", "<title>Library construction and sequencing</title>", "<p id=\"p0130\">An Illumina paired-end library was constructed using the TruSeq Nano DNA HT Sample Preparation Kit (Catalog No. TG-202-1003, Illumina, San Diego, CA) according to the manufacturer’s instructions, and sequenced by Illumina NovaSeq 6000 (Illumina, San Diego, CA). Three paired-end CCS libraries with the small insert size of 15 kb were constructed, and sequenced using the PacBio Sequel II platform (PacBio, San Francisco, CA). High-fidelity (HiFi) reads were generated by CCS software (<ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/PacificBiosciences/ccs\" id=\"ir010\">https://github.com/PacificBiosciences/ccs</ext-link>). To improve the allele-aware genome to chromosome scale, two Hi-C libraries were constructed and sequenced by Illumina NovaSeq 6000 using DNA extracted from the same individual.</p>", "<title>Genome assembly</title>", "<p id=\"p0135\">Haplotype-resolved genome of sika deer was assembled using Hifiasm ##REF##33139952##[15]##, ##REF##33526886##[16]## with the default parameters. DipAsm pipeline ##REF##33288905##[7]## was applied to combine HiFi reads and Hi-C raw data. The haplotype-resolved chromosome-level genome was assembled as follows: (1) Hifiasm was first used to obtain an unphased assembly. Juicer (v1.5) ##REF##27467249##[47]## and a 3D <italic>de novo</italic> assembly (3D-DNA; v180922) ##REF##28336562##[48]## were used to scaffold the contigs. (2) DeepVariant (v0.8.0) ##REF##30247488##[49]## was used to perform small variants, and Hi-C reads were mapped to the scaffolds. (3) HapCUT2 (v1.1) ##REF##27940952##[50]## was used to generate sparse phasing at the chromosome scale. (4) WhatsHap (v0.18) ##REF##25658651##[51]## was used to generate fine-scale chromosome-long phasing by combining the haplotypes with PacBio HiFi data. (5) To reference-assisted scaffolding, minimap2 (v2.17) ##REF##29750242##[52]## was used to align contigs. (6) Purge_dups pipeline ##REF##31971576##[53]## was used to remove haplotig sequences from the initial assembly genome. (7) HiC-Pro was used to align Hi-C reads to contigs, and 3D-DNA was applied for correcting misassembles, anchor, order, and orient fragments of DNA. Juicebox Assembly Tools (v1.9.9) was used to manual correction connections. (8) Juicebox ##REF##27467249##[47]## and plotHicGenome (v0.1.0) were used to analyze and visualize Hi-C-assembled scaffolds. (9) Y chromosome of the sika deer was detected using the Diamond (v0.9.10) based on the previous study of the red deer genome.</p>", "<title>Genome annotation</title>", "<title>Gene prediction</title>", "<p id=\"p0140\">The completeness and accuracy of the genome assembly of sika deer were evaluated based on BUSCO, and the transcriptome was mapped to the genome to assist in verifying the genome quality. Illumina short reads were mapped into the haplotype-resolved genome of sika deer by Burrows–Wheeler Aligner (BWA) for estimating the accuracy of genome assembly, and CEGMA software was also used to estimate the quality of the genome assembly. In addition, 2743 EST sequences of sika deer were downloaded from NCBI and aligned against the two haplotype-resolved genomes to further verify the quality of the genome assembly.</p>", "<p id=\"p0145\">Protein-coding genes were annotated by integrated evidence from the homology-based search, <italic>de novo</italic> prediction, and transcriptome data. Briefly, the homologous gene sets of cattle, red deer, sheep, mouse, and reindeer were downloaded from NCBI for homology-based prediction. <italic>De novo</italic> prediction was performed by AUGUSTUS (v3.0.3) ##REF##15215400##[54]## and SNAP ##REF##15144565##[55]##. We also downloaded the transcriptome data of multiple organs of sika deer from NCBI, including heart (SRA: SRS3900676), liver (SRA: SRS3900672), spleen (SRA: SRS3900692), lung (SRA: SRS3900690), and kidney (SRA: SRS3900689).</p>", "<p id=\"p0150\">Gene function annotation was then performed by aligning against multiple public databases, including Non-Redundant Protein Sequence Database (NR), Gene Ontology (GO), InterProScan, Swiss-Prot, Translation of EMBL (TrEMBL), KEGG, and Clusters of orthologous groups for eukaryotic complete genomes (KOG). In addition, the haplotype-resolved genome was aligned against the Rfam database and vertebrate ribosomal RNA (rRNA) database to predict ncRNAs, including small nuclear RNA (snRNA), microRNA (miRNA), and rRNA.</p>", "<title>Repeat annotation</title>", "<p id=\"p0155\">The homology-based search and <italic>ab initio</italic> method were both used to annotate repetitive sequences of the sika deer genome. To identify the types of repeat elements, a transposable element library was constructed by Tandem Repeat Finder (TRF) ##REF##9862982##[56]##, LTR_FINDER ##REF##17485477##[57]##, and RepeatModeler ##REF##32300014##[58]##. The known repeat element was searched against the Repbase database using RepeatMasker ##REF##17485477##[57]## and RepeatProteinMask ##REF##22367864##[59]##.</p>", "<title>Construction of phylogenetic tree and estimation of divergence time</title>", "<p id=\"p0160\">TreeFam (v4.0) ##REF##16381935##[60]## was used to construct gene families in the six cervid animals (sika deer, red deer, white-tailed deer, reindeer, Tarim red deer, and muntjak) and eight other mammals (cattle, sheep, human, horse, mouse, pig, camel, and dolphin). Based on the aforementioned results, CAFÉ (v4.2) ##REF##16543274##[61]## was used to determine the gene family expansion and contraction. KEGG enrichment analysis was implemented for expanded and contracted gene families in sika deer. To construct the phylogenetic tree, the single-copy genes shared within 14 mammalian genomes were identified.</p>", "<p id=\"p0165\">The divergence time among different species was calculated based on fossil evidence. MCMCtree from the PAML (v4.8) ##REF##24105918##[62]## package was applied to estimate the divergence time with default parameters. The PSMC ##REF##21753753##[63]## model was used to infer the demographic history of sika deer with the parameter: psmc -N25 -t15 -r5 -p “4+25*2+4+6”.</p>", "<title>Identification of PSGs</title>", "<p id=\"p0170\">To identify the PSGs of sika deer, the high-confidence single-copy orthologous genes were identified based on the 14 mammals mentioned above. MUSCLE (v3.8.31) was used to conduct the multiple sequence alignment. The branch-site model was first selected to determine the PSGs, and the likelihood ratio test (LRT) in the CodeML of PAML was then used to detect the PSGs with the sika deer lineage as the foreground branch. <italic>P</italic> value was calculated by chi-square statistic and corrected by the Benjamini–Hochberg method. The genes with <italic>P</italic> &lt; 0.05 were considered as PSGs. The PSGs obtained were subjected to KEGG enrichment analysis using the clusterProfiler package ##REF##22455463##[64]##.</p>", "<title>SVs between sika deer and red deer</title>", "<p id=\"p0175\">Genomic SVs, detected by PacBio CCS reads, provided more convenient conditions for studying polymorphic variations, chromosome evolution ##REF##25892534##[65]##, cancer research ##REF##27478068##[66]##, and phenotypes in organisms ##REF##23222910##[67]##, ##REF##28390096##[68]##, ##REF##26432246##[69]##, ##REF##28117401##[70]##. The haplotype-resolved genome was beneficial for better interpreting the SVs. To understand the SVs between the sika deer and its sister lineage (red deer), MCScanX ##REF##22217600##[71]## was used to perform synteny analysis. Sniffles ##REF##29713083##[72]## was then used to identify SVs between sika deer and red deer, including inversion, deletion, duplication, and insertion.</p>", "<p id=\"p0180\">3D chromatin architecture was performed on sika deer at two different hierarchical levels using HiCExplorer (<ext-link ext-link-type=\"uri\" xlink:href=\"https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/hicexplorer/tutorial.html\" id=\"ir015\">https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/hicexplorer/tutorial.html</ext-link>), including compartment A/B and TADs. HicPCA was used to calculate compartment A/B, and hicFindTADs program was used to call TADs at 40-kb resolution in the sika deer genome.</p>", "<title>Allele identification and haplotype comparison</title>", "<p id=\"p0185\">The alleles were identified by combining synteny, coordinate, and the mapping ratio. Blastn was used to perform the multiple sequence alignment between the two haplotype genomes. MCScanX and MUMmer were used to define the synteny blocks between Hap1 and Hap2. Accordingly, the paired genes (identity &gt; 97%) with high similarity in each synteny block were considered as reliable alleles A and B.</p>", "<p id=\"p0190\">The phased monoploid genome was helpful for understanding the expression profile of alleles in the antlers of sika deer. In the present study, HISAT2 was used to map the RNA-seq reads that were sequenced from the mesenchymal tissue of the sika deer antler ##REF##32133026##[36]## to Hap1 and Hap2, respectively. The expression level of each transcript was estimated with HTSeq. The differences in expression between alleles were estimated by DESeq2 ##REF##25516281##[73]##. To ensure the accuracy and reliability of the results of ASE genes, the genes with the count of 0 in all samples from two haplotypes were filtered out. The homologous genes that meet |log<sub>2</sub> FC| &gt; 2 and <italic>P</italic> &lt; 0.05 were defined as ASE genes. KEGG enrichment analyses of ASE genes were implemented by the clusterProfiler package in R. Additionally, Assemblytics ##REF##27318204##[74]## was used to identify SVs between haplomes.</p>" ]
[ "<title>Results</title>", "<title>Haplotype-resolved chromosome-scale genome assembly and annotation of sika deer</title>", "<p id=\"p0020\">A total of 143 Gb (53×–55×) Illumina short reads and 96.4 Gb (36×–37×) PacBio CCS long reads were generated (Table S1). Hifiasm ##REF##33139952##[15]##, ##REF##33526886##[16]## and DipAsm pipeline ##REF##33288905##[7]## were used to assemble an accurate allele-aware genome of sika deer (##FIG##0##Figure 1##A), and the final diploid assembly of sika deer was phased into two haplotypes named “haplotype 1” (Hap1) and “haplotype 2” (Hap2). Hap1 had the size of 2.71 Gb with a contig N50 length of 34.98 Mb, and Hap2 had the size of 2.58 Gb with a contig N50 length of 38.09 Mb (Table S2), indicating the well-resolved haplotype assembly (##FIG##0##Figure 1##B and C). For improving the haplotype-resolved genome to chromosome scale, approximately 269-Gb (99×–104×) Hi-C paired-end reads were obtained to anchor the contigs into chromosomes. The final assembled monoploid genome of sika deer contained 66 chromosomes, comprising the 32 homologous groups with a pair of sex chromosomes (XY) (##FIG##0##Figure 1##A and ##FIG##1##Figure 2##). A total of 98.05%–100% of the phased scaffolds were anchored to 66 chromosomes, indicating that most chromosomes were phased correctly (Table S3). The Hi-C interaction matrix of Hap1 and Hap2 also indicated that the chromosome groups were clear cut (##FIG##0##Figure 1##D). Additionally, Hap1 and Hap2 had 94.5% and 95.0% Benchmarking Universal Single-Copy Orthologs (BUSCO) genes, respectively (Table S4). Compared with the chromosomal-level genome of female sika deer just released recently (Tables S5 and S6) ##REF##35718271##[17]##, a haplotype-resolved chromosome-level genome of male sika deer assembled in this study had higher contig N50 and higher BUSCO scores, indicating that our assemblies are of high quality.</p>", "<p id=\"p0025\">A total of 22,144 (Hap1) and 18,705 (Hap2) protein-coding genes were predicted in the monoploid genome by a combined strategy of <italic>de novo</italic> gene prediction, homology-based search, and RNA sequencing (RNA-seq). The results of Core Eukaryotic Genes Mapping Approach (CEGMA) showed that 99.57% (Hap1) and 98.28% (Hap2) of genes in the haplotype-resolved genome were predicted, respectively. The mapping ratios of Illumina reads were 99.83% and 98.92% in Hap1 and Hap2, respectively, and the mapping ratios of Expressed Sequence Tag (EST) sequences were both higher than 95% (Table S7). At least 93.80% and 91.60% of protein-coding genes were functionally annotated against databases in Hap1 and Hap2, respectively (Table S8). More than 93.74%–98.37% of the transcripts could be mapped to Hap1, whereas more than 92.22%–97.04% of the transcripts could be mapped to Hap2 (Tables S9 and S10). All the aforementioned results, together with the genome assembly quality standard established by the Vertebrate Genome Project consortium ##REF##30520871##[18]##, indicate that the allele-aware chromosome-scale genome assembly and annotation of sika deer are of high quality. In addition, non-coding RNAs (ncRNAs) were predicted in the haplotype-resolved chromosome-level genome of sika deer (Table S11).</p>", "<p id=\"p0030\">The allelic chromosome pairs were systematically compared for assessing the differences between the two haplotypes. The results showed that the homologous chromosomes were highly similar with respect to gene number, exon number, intron number, and repeat content (##FIG##1##Figure 2##; Tables S12 and S13), suggesting that two allelic chromosome pairs of sika deer were functionally equivalent. Nonsynonymous mutation (<italic>Ka</italic>)/synonymous mutation (<italic>Ks</italic>) of syntenic gene pairs also had no considerable difference between the two haplotypes (##FIG##1##Figure 2##). As the homologous chromosomes of sika deer had a highly similar gene content, Hap1 was used to represent the monoploid sika deer in the following analysis except for a special description. Collectively, the results of multiple approaches revealed the high-quality haplotype-resolved chromosome-scale genome of sika deer.</p>", "<title>Phylogenetic relationship and demographic history of sika deer</title>", "<p id=\"p0035\">The sika deer gene model was clustered with the genes from 13 mammals (see Materials and methods). A total of 2665 single-copy homologous genes were identified as shared by 14 mammalian genomes, which were used to construct a phylogenetic tree (##FIG##2##Figure 3##A). The results showed that the cervid species were closely related to <italic>Bos taurus</italic> and <italic>Capra hircus</italic>, and the common ancestor of cervid species diverged around 26.14 million years ago (MYA). In the cervid species, sika deer was the sister lineage of red deer and Tarim red deer, followed by muntjac, and then white-tailed deer and reindeer. The sika deer also demonstrated overall strong syntenic relationships with red deer and cattle, providing evidence for their phylogenetic relationships (##FIG##2##Figure 3##B).</p>", "<p id=\"p0040\">To construct and investigate the demographic history of sika deer, the pairwise sequentially Markovian coalescent (PSMC) model was applied to infer the changes in the effective population size (<italic>Ne</italic>) of the ancestral populations of sika deer, reindeer, and cattle. The <italic>Ne</italic> of the ancestral population of sika deer peaked twice at about 0.04 MYA and 0.25 MYA, respectively, whereas it increased sharply in 0.3–0.8 MYA. During the same period, the <italic>Ne</italic> of the ancestral population of cattle gradually decreased. Additionally, the <italic>Ne</italic> of the ancestral population of sika deer dropped two times starting from 0.01–0.04 MYA, and it underwent severe bottlenecks during the Last Glacial Maximum (##FIG##2##Figure 3##C), providing powerful evidence for the low genetic diversity of the modern population of sika deer ##REF##31101010##[19]##. It is probable that the uplift of the Tibetan Plateau led to a sharp decrease in the distribution of sika deer, and the habitat of sika deer has been destroyed to a certain extent by large-scale deforestation caused by humans ##UREF##4##[20]##, ##REF##23246455##[21]##. Taken together, frequent human activities after the ice age were at least partially responsible for the low genetic diversity of the modern population of sika deer ##UREF##4##[20]##, ##REF##23246455##[21]##.</p>", "<title>Expanded gene families involved in rapid antler growth</title>", "<p id=\"p0045\">To elucidate the biological characteristics and adaptive evolution of sika deer, the gene families between sika deer and aforementioned 13 other mammals were analyzed, revealing that 378 significantly expanded gene families were functionally related to signal transduction (Hippo signaling pathway, PI3K-AKT signaling pathway, and calcium signaling pathway), cell growth and death (cell cycle and apoptosis), and pathways in cancer (Table S14). A total of 78 gene families were identified as significantly contracted, which were significantly enriched in ABC transporters, tight junction, focal adhesion, and ECM-receptor interaction (Table S15). In addition, a total of 42 genes were considered as positively selected genes (PSGs) (Table S16), which were functionally enriched in multiple signal transduction pathways, including MAPK signaling pathway, mTOR signaling pathway, Wnt signaling pathway, and Hippo signaling pathway (Table S17). The previous studies revealed that the PI3K-AKT signaling pathway was critical for the rapid antler growth with inhibition of oncogenesis ##REF##33769828##[22]##, ##REF##31221830##[23]##, suggesting that these expanded gene families and PSGs are closely associated with rapid antler growth.</p>", "<p id=\"p0050\">A total of 10 expanded genes (<italic>COL4A1</italic>, <italic>COL4A2</italic>, <italic>COL4A5</italic>, <italic>COL4A6</italic>, <italic>RET</italic>, <italic>PPP2R1A</italic>, <italic>PPP2R1B</italic>, <italic>YWHAB</italic>, <italic>YWHAZ</italic>, and <italic>RPS6</italic>) and 5 PSGs (<italic>eIF4E</italic>, <italic>Wnt8A</italic>, <italic>Wnt9B</italic>, <italic>BMP4</italic>, and <italic>TP53</italic>) were found to be functionally enriched in PI3K-AKT signaling pathway and related signaling pathway (##FIG##3##Figure 4##), of which three genes (<italic>YWHAB</italic>, <italic>YWHAZ</italic>, and <italic>RPS6</italic>) responding to DNA damage, cell proliferation, and cell apoptosis were significantly expanded in sika deer ##REF##22451389##[24]##, ##REF##25199762##[25]##, ##REF##28968506##[26]##, ##REF##16678438##[27]##. We also observed that six oncogenes were considered as expanded genes (<italic>RET</italic>, <italic>PPP2R1A</italic>, and <italic>PPP2R1B</italic>) or PSGs (<italic>eIF4E</italic>, <italic>BMP4</italic>, and <italic>TP53</italic>). Among them, <italic>PP2A</italic> regulates cell division, cell metabolism, and apoptosis by dephosphorylation of key proteins ##REF##17632053##[28]##, ##REF##21889517##[29]##. It is also important in the regulation of cell growth and proliferation, and the mice with knocked-out PP2Ac α subunit died in the embryonic stage ##REF##23267135##[30]##, ##UREF##5##[31]##. More importantly, <italic>RET</italic> was significantly expanded in the sika deer compared with the 13 mammals. Previous studies reported that <italic>RET</italic> could regulate cell growth and differentiation by activating several downstream signaling pathways ##REF##16849421##[32]##, ##REF##20083156##[33]##, ##REF##11585664##[34]##. These results reveal that these genes enriched in the PI3K-AKT signaling pathway and related signaling pathways, together with genes involved in response to DNA damage, cell proliferation, and apoptosis, could coordinately regulate the rapid antler growth and possibly prevent the onset of cancer.</p>", "<title>Genomic SVs and chromosome evolution between sika deer and red deer</title>", "<p id=\"p0055\">Overall strong syntenic relationships between diploid sika deer and red deer were observed. It is worth noting that Chr1 of monoploid sika deer had strong syntenic relationships with Chr4 and Chr23 of red deer (##FIG##4##Figure 5##A), which caused the different karyotypes between sika deer (2<italic>n</italic> = 66) and red deer (2<italic>n</italic> = 68). To further ascertain the mechanism of chromosome evolution between them, the haplotype-resolved genome of sika deer was used for variant calling. Compared with red deer, SVs were found to be distributed on the overwhelming majority of chromosomes in sika deer, among which the inversion was biased toward Chr1 and Chr28 of sika deer, accounting for 29% and 32% of the total length of Chr1 and Chr28, respectively. All these results indicated that there existed inversions during the divergence between Chr1 of sika deer and Chr4 and Chr23 of red deer. Additionally, inversions were also observed in Chr28 of sika deer and Chr2 of red deer (##FIG##4##Figure 5##B–D).</p>", "<p id=\"p0060\">To test whether these inversion regions were associated with specific functions, the genes distributed in Chr1 inversion regions of sika deer and corresponding regions of red deer were identified, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed on the genes that were located in the Chr1 inversion region of sika deer, which were mainly enriched in some signaling pathways related to biosynthesis (folate biosynthesis, ovarian steroidogenesis, and steroid hormone biosynthesis) and metabolism (metabolic pathways and arachidonic acid metabolism) (Table S18). Compared with the gene sets that were distributed in the Chr1 inversion region of sika deer, a total of 78 genes were lost in Chr4 and Chr23 of red deer. These 78 genes were also searched on National Center for Biotechnology Information (NCBI; <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ncbi.nlm.nih.gov/\" id=\"ir005\">https://www.ncbi.nlm.nih.gov/</ext-link>) to reduce the false-positive results. It turned out that the Chr4 and Chr23 of red deer lost 33 genes compared with Chr1 of sika deer, inferring that the genome quality of red deer was not sufficient for investigating all genes. We further observed that 16 genes on Chr1 of sika deer distributed on multiple chromosomes of red deer, such as Chr10, Chr11, and Chr29, revealing that these 16 genes might be translocated during the divergence between sika deer and red deer. Finally, Chr4 and Chr23 in red deer uniquely lost 17 genes, one of which was enriched in olfactory transduction (<italic>Calml3</italic>) (##FIG##4##Figure 5##D).</p>", "<p id=\"p0065\">The Chr28 in two haplotypes of sika deer showed high homology with Chr2 of red deer (##FIG##4##Figure 5##C). The genes distributed in the inversion regions of Chr28 in sika deer and corresponding regions of Chr2 in red deer were identified, respectively. KEGG enrichment analysis was performed on the gene sets that were distributed in the Chr28 inversion regions of sika deer, which were aligned in the p53 signaling pathway, HIF-1 signaling pathway, glycolysis/gluconeogenesis, propanoate metabolism, and pyruvate metabolism (Table S19). Compared with the gene sets that were distributed in the Chr28 inversion regions of sika deer by the aforementioned methods, seven genes were translocated, and six genes were lost in Chr2 of red deer. Among them, three genes were enriched in olfactory transduction (<italic>Olfr149</italic>, <italic>OR10G7</italic>, and <italic>OR10S1</italic>) (##FIG##4##Figure 5##C), suggesting that the olfactory sensation of sika deer might be more powerful than that of red deer. Overall, our results cast a novel light on the mechanism of chromosome evolution between sika deer and red deer.</p>", "<p id=\"p0070\">To further explore the impact of chromosome evolution on three-dimensional (3D) chromatin architectures in sika deer, we performed the 3D chromatin architecture analysis on the sika deer genome, including compartment A/B and topologically associated domains (TADs). The compartment A/B was identified at 500-kb resolution. As in previous studies ##REF##34824214##[9]##, the results also showed that compartment A had higher GC content and gene density than compartment B (<xref rid=\"s0135\" ref-type=\"sec\">Figures S1 and S2</xref>). In addition, compartment A and compartment B were randomly distributed on all chromosomes without bias (<xref rid=\"s0135\" ref-type=\"sec\">Figure S3</xref>), speculating that compartment A/B may have little effect on chromosome evolution during the divergence between sika deer and red deer.</p>", "<p id=\"p0075\">TADs were considered as fundamental units of 3D eukaryotic genome organization. In the present study, a total of 3427 self-interacting regions were identified at 40-kb resolution, with an average length of 713 kb. There is no correlation between the percentage of TADs on the chromosome and the length of the chromosome. However, the large chromosomes generally had more TADs than the short ones (<xref rid=\"s0135\" ref-type=\"sec\">Figure S4</xref>). In addition, the Hi-C contact heatmap of Chr1 was identified, including Hi-C contact heatmaps of two inversion sites (<xref rid=\"s0135\" ref-type=\"sec\">Figure S5</xref>). TADs were also identified at the sites of inversion regions in Chr1. The results showed that the TADs were scattered in the inversion regions of 30–70 Mb at 500-kb resolution (<xref rid=\"s0135\" ref-type=\"sec\">Figure S6</xref>). TADs were identified at both ends of the inversion regions to further understand the chromosome evolution in sika deer at 40-kb resolution. Multiple consecutive TADs were found in 28–33 Mb and 68–73 Mb (<xref rid=\"s0135\" ref-type=\"sec\">Figures S7 and S8</xref>). TADs were also identified in another inversion regions (144–148 Mb), and several consecutive TADs were detected (<xref rid=\"s0135\" ref-type=\"sec\">Figure S9</xref>). However, this does not mean that the chromosome evolution between sika deer and red deer was greatly affected by TADs.</p>", "<title>Expression pattern of alleles during the sika deer antler growth</title>", "<p id=\"p0080\">Analysis of transcriptome data using one haploid genome as a reference genome could miss allele-specific expression (ASE) or novel expression patterns ##REF##35333302##[35]##. Therefore, the gene expression profiles of antlers were reanalyzed using our previous transcriptome data generated from three different periods that represented the whole antler development (BioProject: PRJNA552158) ##REF##32133026##[36]## (##FIG##5##Figure 6##A, <xref rid=\"s0135\" ref-type=\"sec\">Figure S10</xref>). The results of principal component analysis (PCA) of the monoploid genome of sika deer indicated that the antler transcriptomes were mainly shaped by genome-wide ASE, followed by the expression of genes at different developmental periods (##FIG##5##Figure 6##B). Additionally, the haploid genome sequences were aligned stringently for understanding the sequence divergence of two haplotypes, showing the 99.6% sequence identity (##FIG##5##Figure 6##C).</p>", "<p id=\"p0085\">A total of 12,534 reliable homologous genes were identified in allelic chromosome pairs by combining the synteny and coordinate strategies (Table S20). The vast majority of alleles (97.12%) were found to be coordinately expressed in the two haplotypes during the rapid antler growth (##FIG##5##Figure 6##D), suggesting that the expression is generally not biased between the two haplotypes and most alleles have similar functions in regulating the rapid antler growth. The alleles in antler were also discovered to distribute on 32 homologous chromosomes without any bias (##FIG##5##Figure 6##E), revealing that the ASE genes were distributed randomly throughout the sika deer genome. Additionally, the phased diploid genome facilitated the detection of SVs between two haplotypes, including deletion and insertion. The SVs were distributed on 32 autosomes of sika deer (##FIG##5##Figure 6##F; Table S21) and spanned 18.9 Mb, representing almost 0.74% of the haploid genome (##FIG##5##Figure 6##G).</p>", "<p id=\"p0090\">The ASE genes were investigated in the haplotype-resolved chromosome-level genome of sika deer without the parental information, which were in allele imbalance between two haplotypes. Only 2.9% (361) of homologous genes were regarded as ASE genes with the expression biased toward a single haplotype, of which the expression of 229 ASE genes was biased toward the Hap1 (<xref rid=\"s0135\" ref-type=\"sec\">Figure S11</xref>) and the expression of 132 ASE genes was biased toward the Hap2 (<xref rid=\"s0135\" ref-type=\"sec\">Figure S12</xref>). These ASE genes showed functional enrichment in multiple biological processes, including ribosome, HIF-1 signaling pathway, axon guidance, mitochondrial biogenesis, metabolism of xenobiotics by cytochrome P450, and chemical carcinogenesis-reactive oxygen species (<xref rid=\"s0135\" ref-type=\"sec\">Figure S13</xref>). There were some oncogenes obviously biased toward Hap1 or Hap2, such as <italic>RPLP1</italic>, <italic>RPL3</italic>, <italic>RPS10</italic>, <italic>RPL10</italic>, <italic>RPL23a</italic>, <italic>SLC7A3</italic>, <italic>COL2A1</italic>, and <italic>PEBP1</italic>, indicating that the alleles might interplay to regulate rapid antler growth. In addition, based on the differential expression patterns observed in two haplotypes, we defined the smaller allele expression differences with 2 &lt; |log<sub>2</sub> fold change (FC)| &lt; 8 (<italic>P</italic> &lt; 0.05) and larger allele expression differences with |log<sub>2</sub> FC| &gt; 8 (<italic>P</italic> &lt; 0.05). Results showed that the allele expression differences of diverse categories were relatively stable in two haplotypes (<xref rid=\"s0135\" ref-type=\"sec\">Figure S14</xref>).</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0095\">The genetic research of sika deer and related development efforts have not been commensurate with its importance due to the scarcity of genome resources. Currently, we decode the first high-quality haplotype-resolved chromosome-scale genome of diploid sika deer by combining the new sequencing technology and Hi-C scaffolding, which is critical for studying the role of variation in genome function and phenotype ##REF##29075286##[37]##. We constructed the expression profile of alleles in the sika deer antler, and proposed the possible molecular basis for rapid antler growth. Our study also contributes to research on the chromosome evolution of cervid animals, especially the mechanism of chromosome evolution between sika deer and red deer. In summary, this high-quality monoploid genome is of sufficient quality for exploring the biological characteristics of cervid species and future multi-omics research of sika deer.</p>", "<p id=\"p0100\">In the present study, the identification of the Y chromosome of sika deer undoubtedly fills the gap in reference genome resources of male sika deer. The genome of male sika deer is beneficial to genomic selection breeding, which is also helpful to retain the germplasm resources with higher antler yields. More importantly, two haplotype genomes of sika deer could more accurately and completely reflect its genetic information, which provides a more complete reference genome for the study of sika deer. The benefit of the haplotype-resolved chromosome-level genome of sika deer also includes that it can be used to explore the expression of alleles and the differences in some phenotypic characteristics of sika deer ##REF##32350247##[38]##. This has been confirmed by many haplotype-resolved genomes published recently, such as the haplotype-resolved genomes of plants have filled an important gap in exploring their unique traits using ASE analysis ##REF##33139952##[15]##, ##REF##34354050##[39]##. Additionally, as a secondary sex characteristic of male cervid animals, male cervid species annually grow deciduous antlers. Thus, comparing the diversity of alleles between the two haplotypes of sika deer contributes to understanding the potential molecular basis of male antler growth, and it is important to study the molecular mechanism of the unique biological characteristics of antlers.</p>", "<p id=\"p0105\">In the genus <italic>Cervus</italic> of cervid animals, the variation of chromosome number is dominated by the variation of autosome number, of which chromosome fission is considered to be the main molecular mechanism ##UREF##2##[11]##. In our study, the results revealed that Chr1 of monoploid sika deer showed strong syntenic relationships with Chr4 and Chr23 of red deer, inferring that the sika deer (2<italic>n</italic> = 66) may diverge into red deer (2<italic>n</italic> = 68) through chromosome fission. The results of SVs between sika deer and red deer revealed that inversion played a dominant role in this process, providing a novel perspective to understand the mechanism of chromosome evolution in cervid animals. However, we cannot further determine the chromosome evolution between sika deer and red deer by comparing the 3D chromatin architectures due to the unavailability of Hi-C data of red deer. Additionally, red deer was found to uniquely lose three genes associated with olfactory by comparing the gene sets in the inversion regions of sika deer and red deer. A previous study also analyzed the adaptive evolution of olfactory-related genes in cervid animals using comparative genomics ##REF##31902105##[40]##. Our study provides a further solid foundation and detailed reference for the studies of the adaptive evolution of olfactory-related genes in cervid species.</p>", "<p id=\"p0110\">The role of alleles on homologous chromosome pairs in cervid animals has long been overlooked. The phased haplotype-resolved genome of sika deer facilitated the interpretation of the expression patterns and functions of alleles. In the present study, the alleles generally had no notable differential expression between two haplotypes, whereas differential gene expression was still observed in a few ASE genes, which was potentially associated with multiple biological processes. We found that some genes showing ASE were involved in oncogenesis. However, whether this means that one of the haplotypes plays a more important role during the rapid antler growth without carcinogenesis requires further experiments.</p>", "<p id=\"p0115\">A recent study reported that the expression of proto-oncogenes was vital for antler fast growth ##REF##31221830##[23]##, and the expression of several tumor suppressor genes was necessary for antler growth and inhibition of oncogenesis ##REF##31221830##[23]##, ##REF##33420194##[41]##. We found that several proto-oncogenes and tumor suppressor genes were identified as the expanded genes or PSGs in the sika deer lineage, which were assigned to the PI3K-AKT signaling pathway and related pathways. It has been postulated that the PI3K-AKT signaling pathway was involved in regulating cell proliferation, differentiation, migration, and cell-cycle progression ##REF##31858326##[42]##, and it was one of the crucial pathways regulating the initiation, development, and regeneration of antler ##REF##31858326##[42]##, ##REF##31479670##[43]##, ##REF##27792145##[44]##, ##REF##31346498##[45]##. Thus, we inferred that the multiple copies of <italic>RET</italic> in sika deer might enhance the rapid antler growth through interaction with the PI3K-AKT signaling pathway. <italic>TP53</italic> has one copy and it was identified as a PSG in the sika deer lineage, which strengthens the insight that cervid species may have evolved an enhanced p53 signaling pathway for an efficient cancer-defense mechanism ##REF##31221829##[46]##. The rapid antler growth is a complex process regulated by multiple factors, and these expanded genes and PSGs (<italic>RET</italic>, <italic>PPP2R1A</italic>, <italic>PPP2R1B</italic>, <italic>eIF4E</italic>, <italic>BMP4</italic>, and <italic>TP53</italic>) might play a pivotal role in this process. These cancer-related genes might coordinately regulate the rapid antler growth, and form the unique cancer defense mechanism of cervid species. To thoroughly elucidate the molecular mechanism of antler rapid growth and defend against cancer in cervid species, other haplotype-resolved chromosome-scale genomes of cervid species and further functional experiments are required in the future. In summary, our haplotype-resolved chromosome-scale genome of sika deer offers a holistic view of its expression profiles, functions of alleles, and chromosome evolution of cervid species. It will also be helpful for studying the therapy of cancer in humans.</p>" ]
[ "<title>Conclusion</title>", "<p id=\"p0120\">In the present study, we provided a haplotype-resolved chromosome-scale genome, which is, to our knowledge, the first high-quality available diploid genome of sika deer. This allowed us to explore the ASE patterns between the two homologous chromosomes. Most alleles were found to be co-expressed in the rapidly growing antlers, while at the same time preventing the onset of cancer. Several expanded genes or PSGs (<italic>RET</italic>, <italic>PPP2R1A</italic>, <italic>PPP2R1B</italic>, <italic>YWHAB</italic>, <italic>YWHAZ</italic>, and <italic>RPS6</italic>) were also considered to play a key role in this process. In addition, our results revealed that chromosome fission might occur during the divergence of sika deer and red deer, which resulted in an increase in the chromosome numbers of red deer. Overall, our study will promote the research of the unique characteristics of antler (rapid growth and low cancer rate) and the chromosome evolution in cervid species. It also provides valuable resources and references for multi-omics studies of sika deer.</p>" ]
[ "<p id=\"np010\">Equal contribution.</p>", "<p>Despite the scientific and medicinal importance of diploid <bold>sika deer</bold> (<italic>Cervus nippon</italic>), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the <bold>chromosome evolution</bold> in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (<italic>RET</italic>, <italic>PPP2R1A</italic>, <italic>PPP2R1B</italic>, <italic>YWHAB</italic>, <italic>YWHAZ</italic>, and <italic>RPS6</italic>) and positively selected genes (<italic>eIF4E</italic>, <italic>Wnt8A</italic>, <italic>Wnt9B</italic>, <italic>BMP4</italic>, and <italic>TP53</italic>) were identified, which could contribute to <bold>rapid antler growth</bold> without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (<italic>Cervus elaphus</italic>), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Kai Ye</p>" ]
[ "<title>Ethical statement</title>", "<p id=\"p0195\">All experimental designs and animal handling were approved by the Institutional Animal Care and Use Committee of Northeast Forestry University, China (Approval No. 2022049).</p>", "<title>Data availability</title>", "<p id=\"p0200\">The raw sequencing data generated in this study have been deposited in the Genome Sequence Archive ##REF##34400360##[75]## at the National Genomics Data Center (NGDC), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS) / China National Center for Bioinformation (CNCB) (GSA: CRA007487), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa\" id=\"ir020\">https://ngdc.cncb.ac.cn/gsa</ext-link>. The whole-genome sequence data reported in this study have been deposited in the Genome Warehouse ##REF##34175476##[76]## at the NGDC, BIG, CAS / CNCB (GWH: GWHBJVV00000000 and GWHBJVU00000000), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gwh\" id=\"ir025\">https://ngdc.cncb.ac.cn/gwh</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0205\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0215\"><bold>Ruobing Han:</bold> Resources, Writing – original draft, Data curation, Investigation, Writing – review &amp; editing, Visualization, Formal analysis. <bold>Lei Han:</bold> Data curation, Visualization, Investigation, Formal analysis, Writing – review &amp; editing. <bold>Xunwu Zhao:</bold> Writing – review &amp; editing. <bold>Qianghui Wang:</bold> Writing – review &amp; editing, Formal analysis. <bold>Yanling Xia:</bold> Resources. <bold>Heping Li:</bold> Funding acquisition, Conceptualization, Supervision, Project administration, Resources. All authors have read and approved the final manuscript.</p>", "<title>Acknowledgments</title>", "<p id=\"p0210\">We would like to thank the <funding-source id=\"gp005\">National Key R&amp;D Program of China</funding-source> (Grant No. 2018YFC1706601) and the <funding-source id=\"gp010\">Natural Science Foundation of Heilongjiang Province of China</funding-source> (Grant No. C2017012). We thank Xianlan Cui for the language editing of this manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0225\">The following are the Supplementary data to this article:</p>", "<p id=\"p0230\">\n\n</p>", "<p id=\"p0235\">\n\n</p>", "<p id=\"p0240\">\n\n</p>", "<p id=\"p0245\">\n\n</p>", "<p id=\"p0250\">\n\n</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<p id=\"p0270\">\n\n</p>", "<p id=\"p0275\">\n\n</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<p id=\"p0325\">\n\n</p>", "<p id=\"p0330\">\n\n</p>", "<p id=\"p0335\">\n\n</p>", "<p id=\"p0340\">\n\n</p>", "<p id=\"p0345\">\n\n</p>", "<p id=\"p0350\">\n\n</p>", "<p id=\"p0355\">\n\n</p>", "<p id=\"p0360\">\n\n</p>", "<p id=\"p0365\">\n\n</p>", "<p id=\"p0370\">\n\n</p>", "<p id=\"p0375\">\n\n</p>", "<p id=\"p0380\">\n\n</p>", "<p id=\"p0385\">\n\n</p>", "<p id=\"p0390\">\n\n</p>", "<p id=\"p0395\">\n\n</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold><italic>De novo</italic> assembly and assessment of genome quality</bold></p><p><bold>A.</bold> Overview of the <italic>de novo</italic> assembly of the haplotype-resolved chromosome-level genome of sika deer. <bold>B.</bold> Sequencing coverage of Hap1 and Hap2. <bold>C.</bold> GC depth distributions of Hap1 and Hap2. <bold>D.</bold> Hi-C interaction matrices of Hap1 and Hap2. The diagonal bar represents the frequency of contact between two loci on a chromosome, and the color from light to dark indicates the contact density from low to high. HiFi, high fidelity; Hi-C, high-throughput chromosome conformation capture; Chr, chromosome; Hap1, haplotype 1; Hap2, haplotype 2.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>The overview of haplotype-resolved chromosome-level genome of sika deer</bold></p><p><bold>A.</bold> Length (Mb) of the chromosome. <bold>B.</bold> Density of LTR transposons. <bold>C.</bold> Density of LINE transposons. <bold>D.</bold> Density of DNA transposons. <bold>E.</bold> Density of SINE transposons. <bold>F.</bold> Gene number. <bold>G.</bold> GC content (the windows of 1 Mb). <bold>H.</bold><italic>Ka</italic>/<italic>Ks</italic> of syntenic gene pairs in Hap1. <bold>I.</bold><italic>Ka</italic>/<italic>Ks</italic> of syntenic gene pairs in Hap2. <bold>J.</bold> Links between the core connected alleles. LTR, long terminal repeat; LINE, long interspersed nuclear element; SINE, short interspersed nuclear element; <italic>Ka</italic>, nonsynonymous mutation; <italic>Ks</italic>, synonymous mutation.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>The phylogenetic relationship, synteny, and population size of sika deer</bold></p><p><bold>A.</bold> The phylogenetic relationship of sika deer and other 13 mammals. The divergence time is shown in the phylogenetic tree. The red nodes indicate that the support values of the branches are 100. The results of gene families are shown in the bar charts on the right side of the phylogenetic tree. <bold>B.</bold> Synteny analysis of sika deer, red deer, and cattle. Purple, green, and orange boxes represent the chromosomes of cattle, sika deer, and red deer, respectively. Different synteny blocks between one species and another are linked by lines of different colors. <bold>C.</bold> The effective population size of sika deer, cattle, and reindeer. “<italic>g</italic>” represents the generation length, and “μ” represents the mutation rate per generation. MYA, million years ago; LGM, Last Glacial Maximum; MIS4, Marine Isotope Stage 4; PG, Penultimate Glaciation; QM, Qingzang Movement.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>PI3K-AKT signaling pathway.</bold></p><p>Purple indicates protiens encoded by expanded genes in sika deer, and green indicates the proteins encoded by PSGs in sika deer. “P” represents phosphorylation. PSG, positively selected gene.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Chromosome evolution between sika deer and red deer</bold></p><p><bold>A.</bold> Synteny of the haplotype-resolved chromosome-level genome of sika deer and red deer. Synteny blocks between chromosomes of sika deer and red deer are illustrated by red and gray lines, with red lines indicating the inversion regions. <bold>B.</bold> Schematic diagram of divergence between sika deer and red deer. Orange indicates the inversion in the chromosomes. <bold>C.</bold> Synteny of Chr28 in sika deer and Chr2 in red deer. Red indicates the inversion regions. <bold>D.</bold> Synteny of Chr1 in sika deer and Chr4 in red deer, and synteny of Chr1 in sika deer and Chr23 in red deer. Red indicates the inversion regions. The schematic diagram of gene structure shows the distribution of genes in the inversion regions. The heatmap shows the GC content in the inversion regions. The line chart shows the distribution of sequencing depth in the inversion regions.</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>Haplotype comparison of diploid sika deer</bold></p><p><bold>A.</bold> Correlation heatmap of transcriptome data in Hap1. EP indicates the stage of antler growing to a saddle-like appearance; MP indicats the stage of antler growing with two branches; LP indicates the stage of antler growing with three branches. <bold>B.</bold> PCA of allele expression profiles of sika deer antler at three developmental periods. <bold>C.</bold> Comparison of two haplotypes using 10-Mb nonoverlapping windows. <bold>D.</bold> Statistics of alleles. <bold>E.</bold> Distribution histogram of alleles on the chromosomes. <bold>F.</bold> Distribution histogram of SVs between haplotypes on chromosomes. <bold>G.</bold> Statistics of SVs between two haplotypes. PCA, principal component analysis; PC, principal component; SV, structural variation.</p></caption></fig>", "<fig id=\"f0035\" position=\"anchor\"><label>Supplementary Figure S1</label><caption><p><bold>Boxplot of GC content in genomic compartment A/B</bold> The horizontal line inside the box is the median. The black dot indicates the outlier.</p></caption></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary Figure S2</label><caption><p><bold>Boxplot of gene density in genomic compartment A/B</bold> The horizontal line inside the box is the median, and the black dot shows the outlier.</p></caption></fig>", "<fig id=\"f0045\" position=\"anchor\"><label>Supplementary Figure S3</label><caption><p><bold>The distribution of compartment A/B on the chromosome of the sika deer genome</bold></p></caption></fig>", "<fig id=\"f0050\" position=\"anchor\"><label>Supplementary Figure S4</label><caption><p><bold>Distribution of TADs on chromosomes in the sika deer genome at 40 kb resolution</bold> TADs, topologically associated domains.</p></caption></fig>", "<fig id=\"f0055\" position=\"anchor\"><label>Supplementary Figure S5</label><caption><p><bold>Hi-C contact heatmaps of Chr1.1 in the haplotype-resolved genome of sika deer</bold> The left figure shows the Hi-C contact heatmaps of Chr1.1, and the right figure shows the Hi-C contact heatmaps of the inversion regions on Chr1.1.</p></caption></fig>", "<fig id=\"f0060\" position=\"anchor\"><label>Supplementary Figure S6</label><caption><p><bold>Identification of TADs in 30–70 Mb on Chr1 in sika deer genome at 500 kb resolution</bold> The threshold used for the identification of TAD is 0.001. The color from light to dark indicates the interaction strength from low to high.</p></caption></fig>", "<fig id=\"f0065\" position=\"anchor\"><label>Supplementary Figure S7</label><caption><p><bold>Identification of TADs in 28–33 Mb on Chr1 of sika deer genome at 40 kb resolution</bold> A threshold of 0.005 was used for the identification of TADs, and the color from blue to red indicates the interaction strength from low the high.</p></caption></fig>", "<fig id=\"f0070\" position=\"anchor\"><label>Supplementary Figure S8</label><caption><p><bold>Identification of TADs in 68–73 Mb on Chr1 of sika deer genome at 40 kb resolution</bold> A threshold of 0.005 was used for the identification of TADs, and the color from blue to red indicates the interaction strength from low the high.</p></caption></fig>", "<fig id=\"f0075\" position=\"anchor\"><label>Supplementary Figure S9</label><caption><p><bold>Identification of TADs in 144–148 Mb on Chr1 of sika deer genome at 40 kb resolution</bold> A threshold of 0.005 was used for the identification of TADs, and the color from blue to red indicates the interaction strength from low the high.</p></caption></fig>", "<fig id=\"f0080\" position=\"anchor\"><label>Supplementary Figure S10</label><caption><p><bold>Correlation heatmap of transcriptome data in Hap2</bold> The color of the circles from blue to red indicates the correlation from low to high between different samples.</p></caption></fig>", "<fig id=\"f0085\" position=\"anchor\"><label>Supplementary Figure S11</label><caption><p><bold>Expression heatmap of allele-specific expression genes biased to Hap1</bold> The color from yellow to red indicates the expression level from low to high.</p></caption></fig>", "<fig id=\"f0090\" position=\"anchor\"><label>Supplementary Figure S12</label><caption><p><bold>Expression heatmap of allele-specific expression genes biased to Hap2</bold> The color from yellow to red indicates the expression level from low to high.</p></caption></fig>", "<fig id=\"f0095\" position=\"anchor\"><label>Supplementary Figure S13</label><caption><p><bold>KEGG enrichment analysis of the allele-specific expression genes</bold></p></caption></fig>", "<fig id=\"f0100\" position=\"anchor\"><label>Supplementary Figure S14</label><caption><p><bold>Percentage of each category of allele expression bias in the two haplotypes</bold></p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0105\"><caption><title>Supplementary Table S1</title><p><bold>The statistics of PacBio sequencing data</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0100\"><caption><title>Supplementary Table S2</title><p><bold>Summary of the haplotype-resolved genome of sika deer</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0095\"><caption><title>Supplementary Table S3</title><p><bold>Statistics information of chromosome-level of the haplotype-resolved genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0090\"><caption><title>Supplementary Table S4</title><p><bold>Summary of BUSCOs recovered in the haplotype-resolved genome of sika deer</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0085\"><caption><title>Supplementary Table S5</title><p><bold>Summary of comparison with the recently published sika deer genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0080\"><caption><title>Supplementary Table S6</title><p><bold>Comparison of chromosomes with the recently published sika deer genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0075\"><caption><title>Supplementary Table S7</title><p><bold>Assessment of the completeness and accuracy of the haplotype-resolved genome of sika deer</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0070\"><caption><title>Supplementary Table S8</title><p><bold>Summary of functional annotation in the haplotype-resolved genome of sika deer</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0065\"><caption><title>Supplementary Table S9</title><p><bold>Summary of mapping ratio of de novo assembled transcripts (Hap1)</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Table S10</title><p><bold>Summary of mapping ratio of de novo assembled transcripts (Hap2)</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Table S11</title><p><bold>Overview of predicted ncRNAs in the haplotype-resolved genome of sika deer</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Table S12</title><p><bold>Summary of repeat sequence in the haplotype-resolved genome of sika deer</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S13</title><p><bold>Summary of chromosome information of the haplotype-resolved genome of sika deer</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S14</title><p><bold>KEGG enrichment analysis of expanded gene families</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S15</title><p><bold>KEGG enrichment analysis of contracted gene families</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S16</title><p><bold>Positively selected genes identified</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S17</title><p><bold>KEGG enrichment analysis of positively selected genes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S18</title><p><bold>KEGG enrichment analysis of genes located in the inversion regions of Chr1 in sika deer</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S19</title><p><bold>KEGG enrichment analysis of genes located in the inversion regions of Chr28 in sika deer</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S20</title><p><bold>Summary of the distribution of alleles on homologous chromosomes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S21</title><p><bold>Summary of structural variation between two haplotypes</bold></p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e129\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0130\" fn-type=\"supplementary-material\"><p id=\"p0220\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.11.001\" id=\"ir030\">https://doi.org/10.1016/j.gpb.2022.11.001</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["1"], "surname": ["Bubenik", "Bubenik"], "given-names": ["G.A.", "A.B."], "part-title": ["Horns, pronghorns, and antlers"], "year": ["1990"], "publisher-name": ["Springer"], "publisher-loc": ["New York"]}, {"label": ["10"], "surname": ["Yu", "Yang", "Xing"], "given-names": ["M.", "F.", "X."], "article-title": ["Advances on the chromosome of cervid in China"], "source": ["China Animal Husbandary Veterinary Med"], "volume": ["39"], "year": ["2012"], "fpage": ["65"], "lpage": ["68"]}, {"label": ["11"], "surname": ["Tang", "Zhang", "Dong", "Xing"], "given-names": ["L.", "R.", "S.", "X."], "article-title": ["Research progress in Cervidae\u2019s chromosome"], "source": ["Special Wild Econ Animal Plant Res"], "volume": ["42"], "year": ["2020"], "fpage": ["61"], "lpage": ["64+89"]}, {"label": ["14"], "surname": ["Barto\u0161", "Bubenik"], "given-names": ["L.", "G.A."], "article-title": ["Relationships between rank-related behaviour, antler cycle timing and antler growth in deer: behavioural aspects"], "source": ["Anim Prod Sci"], "volume": ["51"], "year": ["2011"], "fpage": ["303"], "lpage": ["310"]}, {"label": ["20"], "surname": ["Guo", "Zheng"], "given-names": ["Y.", "H."], "article-title": ["On the geological distribution, taxonomic status of species and evolutionary history of sika deer in China"], "source": ["Acta Theriol Sinica"], "volume": ["20"], "year": ["2000"], "fpage": ["168"], "lpage": ["179"]}, {"label": ["31"], "surname": ["Li"], "given-names": ["W."], "article-title": ["Mutational analysis of the "], "italic": ["ppp2r1a", "ppp2r1"], "source": ["Nanchang University"], "year": ["2014"]}]
{ "acronym": [], "definition": [] }
76
CC BY
no
2024-01-14 23:41:54
Genomics Proteomics Bioinformatics. 2023 Jun 15; 21(3):470-482
oa_package/00/5f/PMC10787017.tar.gz
PMC10787019
36775057
[ "<title>Introduction</title>", "<p id=\"p0005\">The “relict” plants consist of the remaining population of species that were widely distributed previously but are restricted to limited geographic regions currently. The severe population bottleneck is likely caused by large-scale environmental changes (such as global dramatic temperature decline) that have a fundamental impact on the ecosystem of the previously abundant species ##REF##19137952##[1]##. Evidence reveals that the population dynamics are recorded in the population genomes ##REF##27293186##[2]##. Recently developed sequencing technologies provide a practical approach to uncover the disaster during long-term evolutionary history ##REF##21753753##[3]##, ##REF##25848749##[4]##. However, how relict plants survived from previous environmental changes and flourish in the new territory remains unclear.</p>", "<p id=\"p0010\"><italic>Cyclocarya paliurus</italic> (Batal.) Iljinskaja (wheel wingnut), the sole species in the genus <italic>Cyclocarya</italic> Iljinskaja (Juglandaceae), is not only a well-known multi-function tree species ##UREF##0##[5]##, but also has the character of heterodichogamy, a transitional form in the evolution of plants from monoecism to dioecism ##UREF##1##[6]##. Previous studies have indicated that its leaves are often used in traditional Chinese medicine to treat hypertension and diabetes due to its high biological activity and favorable safety ##UREF##2##[7]##. Furthermore, the antihyperglycemic tea of <italic>C</italic>. <italic>paliurus</italic> was the first health tea approved by Food and Drug Administration (FDA) in 1999 ##REF##32458846##[8]##. These lines of evidence show that <italic>C</italic>. <italic>paliurus</italic> leaves contain multiple bioactive compounds, including triterpenoids, flavonoids, phenolic acids, steroids, and polysaccharides. These compounds protect humans against chronic diseases owing to their antidiabetic, antioxidant, and antimicrobic properties ##UREF##1##[6]##.</p>", "<p id=\"p0015\">Triterpenoids are synthesized from six C5 (isopentenyl diphosphate) units from the common precursor 2,3-oxidosqualene by oxidosqualene cyclases (OSCs) ##REF##23297350##[9]##. These carbon skeletons are further oxidized by cytochrome P450 monooxygenases (P450s) and glycosylated by UDP-dependent glycosyltransferases (UGTs), resulting in diverse triterpenoid structures ##REF##25951908##[10]##, ##REF##28165039##[11]##. Triterpenoids constitute a vast family of natural products that play an important role in significant biological and pharmacological effects, such as cyclocaric acid B extracted from <italic>C</italic>. <italic>paliurus</italic> leaves ##REF##26220631##[12]##. Cyclocaric acid B has a pharmacological activity on diabetes, and it can enhance glucose uptake by involving AMP-activated protein kinase (AMPK) activation and improving insulin sensitivity in adipocytes ##REF##26220631##[12]##. However, the evolutionary history and functions of cyclocaric acid B-related genes remain unknown, although ≥ 40 different triterpenoid compounds have been isolated from <italic>C</italic>. <italic>paliurus</italic> species ##REF##28140736##[13]##. Therefore, elucidation of the biosynthetic pathways leading to the production of cyclocaric acid B is greatly needed for heterologous bioproduction and a high public health priority.</p>", "<p id=\"p0020\">With the importance in pharmaceutical values, a considerable production of <italic>C</italic>. <italic>paliurus</italic> leaves is required for medical use. However, <italic>C</italic>. <italic>paliurus</italic> seedlings can only be propagated from seeds, but its seed quality is deficient with the seed vigor of 0%–10% due to its heterodichogamy ##UREF##3##[14]##. Heterodichogamy in <italic>C</italic>. <italic>paliurus</italic> possesses two temporally complementary morphs, protandry (PA) or protogyny (PG), in monoecious population. The stigma matures before pollen dispersal in PG, whereas pollen scatters before stigma maturation in PA. Hence, the female and male function segregation within PA or PG significantly affects seed filling index and quality. Although heterodichogamy is especially common in Fagales, Magnoliales, Malvales, Laurales, Sapindales, Canellales, Ranunculales, Zingiberales, Trochodendrales, Rosales, Caryophyllales, Malpighiales, and Apiales ##UREF##4##[15]##, the related genetic mechanism is far from well-studied.</p>", "<p id=\"p0025\">The species <italic>C</italic>. <italic>paliurus</italic> is circumscribed with approximately two ploidy levels, including diploid (2<italic>n</italic> = 2<italic>x</italic> = 32) and auto-tetraploid (2<italic>n</italic> = 4<italic>x</italic> = 64), and it is mainly distributed across subtropical mountainous areas in China. Polyploidy or ancient whole-genome duplication (WGD) is a major driver of plant evolution ##REF##31145999##[16]## that contributes to variation in genome size and abundant genetic materials, as well as phenotypic and functional diversification of plants ##REF##27064530##[17]##. Although one polyploid <italic>C</italic>. <italic>paliurus</italic> genome has been reported recently, the collapsed assembly missed haplotypic variations that may underlie important functions ##UREF##5##[18]##. In addition, the exact roles that WGD played in the origin and evolution of <italic>C</italic>. <italic>paliurus</italic> have not been clearly elucidated. Herein, we present three chromosome-scale genomes, containing two diploid <italic>C</italic>. <italic>paliurus</italic> individuals that represent two different flower morphs, protandrous (PA-dip) and protogynous (PG-dip), and one haplotype-resolved genome for auto-tetraploid. Our work uncovers the genetic mechanisms behind the special features of <italic>C</italic>. <italic>paliurus</italic> species, including heterodichogamy, origination, polyploidization, and cyclocaric acid B biosynthesis.</p>" ]
[ "<title>Materials and methods</title>", "<title>Homologous chromosome synapsis analysis of PA-tetra <italic>C</italic>. <italic>paliurus</italic></title>", "<p id=\"p0140\">The male florals at the early stage of meiosis of PA-tetra <italic>C</italic>. <italic>paliurus</italic> were transferred into Carnoy’s fluid (75% methanol and 25% glacial acetic acid) at 4 °C for 24 h under dark condition. Then 5 anthers were transferred to glass slide with 45% glacial acetic acid for 2 min acid hydrolysis. After covering the coverslip, the pollen mother cells were observed using phase contrast microscope, and the effective tablets were stored at −80 °C for 24 h. Then, 100% ethanol was added in materials at room temperature for dehydration of 30 min. Finally, 15 μl DAPI was added, and the tablet was examined by fluorescence microscope (Catalog No. Axioscope A1, Carl Zeiss, Jena, Germany).</p>", "<title>Sequencing and assembly of three <italic>C</italic>. <italic>paliurus</italic> genomes</title>", "<p id=\"p0145\">The <italic>C</italic>. <italic>paliurus</italic> chromosome-level assemblies combined three technologies from single-molecule real-time (SMRT) sequencing with the PacBio Sequel technology, Hi-C, and short reads polished based on Illumina HiSeq sequencing. Briefly, raw data of ∼ 223×, ∼ 115×, and ∼ 221× coverages were generated on the PacBio Sequel II platform for PA-dip, PG-dip, and PA-tetra, respectively. Paired-end reads of ∼ 176×, ∼ 131×, and ∼ 237× coverages were generated on the Illumina NovaSeq 6000 platform for PA-dip, PG-dip, and PA-tetra, respectively (File S1).</p>", "<p id=\"p0150\">The initial contig-level assemblies were accomplished using a series of PacBio assemblers. More specifically, the longest coverage of subreads from PacBio SMRT sequencing was self-corrected using Canu v.1.7 ##REF##28298431##[48]##. Then, error-corrected reads were assembled into genomic contigs using widely-used PacBio assembler Canu v.1.7 ##REF##28298431##[48]## with parameter corOutCoverage = 100. The N50 size, the assembled genome size (<xref rid=\"s0150\" ref-type=\"sec\">Table S2</xref>), and the complete BUSCO ratio (<xref rid=\"s0150\" ref-type=\"sec\">Table S6</xref>) were evaluated to inspect the quality of each round of assemblies. Last, the best results for subsequent analysis were selected through carefully manual inspection. Illumina paired-end reads were further used to polish the PacBio assemblies using Pilon v.1.18 ##REF##25409509##[49]##. Young leaves of <italic>C</italic>. <italic>paliurus</italic> were prepared for Hi-C library construction according to the standard protocol described previously ##REF##22652625##[50]##. The paired-end sequencing libraries were generated from chimeric fragments, followed by Illumina sequencing. The paired-end Hi-C reads were aligned to the contig-level assembly, and mis-joined contigs were then corrected using the 3D-DNA pipeline v.201008 ##REF##28336562##[51]## for abrupt long-range contact pattern detecting. The contigs corrected by Hi-C interactions were successfully linked into 16 pseudo-chromosomes in PG-dip and PA-dip, and 64 pseudo-chromosomes with four sets of haplotypes in PA-tetra <italic>C</italic>. <italic>paliurus</italic> using the ALLHiC pipeline ##REF##31383970##[52]##, following the guideline that was used to assemble an auto-tetraploid sugarcane genome (<ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/tangerzhang/ALLHiC/wiki/ALLHiC%3a-scaffolding-an-auto-polyploid-sugarcane-genome\" id=\"ir010\">https://github.com/tangerzhang/ALLHiC/wiki/ALLHiC:-scaffolding-an-auto-polyploid-sugarcane-genome</ext-link>).</p>", "<title>RNA extraction and sequencing</title>", "<p id=\"p0155\">Total RNA was isolated from stems, leaves, leaf buds, and floral buds using E.Z.N.A Plant RNA Kit (Catalog No. R6827-01, Omega Bio-tek, Doraville, GA), and then purified with RNase-Free DNase I (Catalog No. 2270A, Takara Biotechnology, Dalian, China). Subsequently, 1% agarose gel was used to evaluate the RNA contamination and degradation. The purity was further monitored using ultraviolet spectrophotometer (Catalog No. NP80, Implen, München, Germany). Samples with RNA integrity number (RIN) values higher than 8 were used for downstream complementary DNA (cDNA) library preparation. The cDNA library construction was performed with the NEBNext Ultra RNA Library Prep Kit (Catalog No. E7770, New England BioLabs, Ipswich, MA) according to the manufacturer’s instruction. The Agilent 2100 Bioanalyzer system (Catalog No. G2938A, Agilent, Palo Alto, CA) was used for library quality assessing, and short paired-end reads were generated from the library preparation based on Illumina NovaSeq sequencing platform.</p>", "<title>Repeat annotation</title>", "<p id=\"p0160\">Repetitive sequences were identified in the three <italic>C</italic>. <italic>paliurus</italic> genomes based on the same pipeline. First, RepeatModeler v.2.0.1 (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.repeatmasker.org/RepeatModeler/\" id=\"ir015\">https://www.repeatmasker.org/RepeatModeler/</ext-link>) and RepeatMasker v.4.0.5 (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.repeatmasker.org/\" id=\"ir020\">https://www.repeatmasker.org/</ext-link>) were used for <italic>de novo</italic> prediction of unkown transposable elements (TEs), as well as discovering known TEs. Next, TEclass v.2.1.3 ##REF##19349283##[53]## was further used to categorize the unknown TEs. Then, two pipelines Tandem Repeat Finder (TRF) v.4.07 ##REF##9862982##[54]## and LTR_Finder v.1.05 ##UREF##10##[55]## were used to detect intact LTR-RTs and tandem repeats, respectively. Finally, LTRharvest v1.5.10 ##REF##18194517##[56]## and LTR_retriever ##REF##29233850##[57]## were used to construct a high-quality LTR library.</p>", "<title>Gene annotation</title>", "<p id=\"p0165\">MAKER2 v.2.31.9 computational pipeline ##REF##18025269##[58]## was used to annotate genes in the three <italic>C</italic>. <italic>paliurus</italic> genomes, through a comprehensive strategy from RNA-seq-based prediction, homology-based prediction, and <italic>ab initio</italic> gene prediction. Briefly, RNA-seq data of different tissues of <italic>C</italic>. <italic>paliurus</italic> were assembled by Trinity v.2.6.5 software ##REF##23845962##[59]## with default parameters, genome-guided assembly, and <italic>de novo</italic> assembly. The fragments per kilobase per million (FPKM) expression values of assembled transcripts were quantified by RSEM ##REF##21816040##[60]##, and the transcripts were removed if FPKM less than 1. The PASA v.r09162010 program ##REF##14500829##[61]## was applied to construct a comprehensive transcript library from the filtered transcripts. The almost “full-length” transcripts selected from PASA were aligned to the UniProt protein database, and protein sequences with coverage greater than 95% were reserved as candidate sequences. Afterward, the MAKER2 pipeline was used to integrate coding evidence of three annotation strategies (SNAP v.29–11-2013 ##REF##15144565##[62]##, GeneMark v.4.28 ##REF##16314312##[63]##, and AUGUSTUS v.3.2.3 ##REF##16469098##[64]##) and annotate protein-coding genes. After the first round, the predicated gene models with annotation edit distance (AED) values &lt; 0.2 were selected for model re-training. Finally, gene annotation was improved from the second round of MAKER2. Further, the RNA-seq reads were aligned to reference genomes using HISAT2 v.2.0.4 with default parameters and re-assembled by StringTie v.2.2.0 ##REF##27560171##[65]##. The assembled RNA-seq transcripts and homologous proteins from <italic>O</italic>. <italic>sativa</italic>, <italic>V</italic>. <italic>vinifera</italic>, <italic>Carica papaya</italic>, <italic>Morus notablis</italic>, <italic>Solanum tuberosum</italic>, and <italic>A</italic>. <italic>thaliana</italic> were imported to MAKER2 pipeline. After filtering putative gene models of transposon-derived, a total of 34,699, 35,221, and 90,752 gene models were annotated in PA-dip, PG-dip and PA-tetra <italic>C</italic>. <italic>paliurus</italic> genomes, respectively. BUSCO analyses for PA-dip, PG-dip, and PA-tetra <italic>C</italic>. <italic>paliurus</italic> genomes were performed to evaluate completeness of the protein-coding annotations (<xref rid=\"s0150\" ref-type=\"sec\">Table S6</xref>).</p>", "<title>Phylogenetic tree reconstruction</title>", "<p id=\"p0170\">To identify gene family groups, we analyzed protein-coding genes from 9 species, <italic>C</italic>. <italic>paliurus</italic>, <italic>Carya illinoinensis</italic>, <italic>Juglans nigra</italic>, <italic>P. stenoptera</italic>, <italic>A</italic>. <italic>thaliana</italic>, <italic>Ziziphus jujuba</italic>, <italic>V</italic>. <italic>vinifera</italic>, <italic>Populus trichocarpa</italic>, and <italic>O</italic>. <italic>sativa</italic> genomes. Gene family clustering was performed using OrthoFinder v.2.2.7 ##REF##31727128##[66]## based on 35,221 predicted genes of <italic>C</italic>. <italic>paliurus</italic>, and <italic>O. sativa</italic> was used as outgroup. Phylogenetic tree was constructed for <italic>C</italic>. <italic>paliurus</italic> and 8 other plant species based on coding sequence alignment of 302 single-copy gene families using FastTree v. 2.1.11 software ##REF##19377059##[67]##. The divergence time among 9 species was estimated by the r8s v.1.8.1 program ##REF##12538260##[68]##. For estimation of divergence time, we selected two calibration points from articles and calibrated the age of the nodes between <italic>O. sativa</italic> and <italic>A</italic>. <italic>thaliana</italic> (308–115 MYA), <italic>J. nigra</italic> and <italic>P. stenoptera</italic> (76–36 MYA), and <italic>V. vinifera</italic> and <italic>A</italic>. <italic>thaliana</italic> (135–107 MYA) according to the TimeTree website. The contraction and expansion of the gene families were observed by comparing the differences of cluster size between <italic>C</italic>. <italic>paliurus</italic> and each species using CAFE v.4.2.1 method ##REF##16543274##[69]##.</p>", "<title>Analysis of genome collinear and WGD</title>", "<p id=\"p0175\">For the comparative genomics analysis, the species we chose including <italic>C</italic>. <italic>paliurus</italic>, <italic>P</italic>. <italic>stenoptera</italic>, <italic>J</italic>. <italic>nigra</italic>, and <italic>C</italic>. <italic>illinoinensis</italic> all belong to the family Juglandaceae. The <italic>Z</italic>. <italic>jujuba</italic> shares the same typical feature of heterodichogamy with Juglandaceae. <italic>A</italic>. <italic>thaliana</italic> and <italic>P</italic>. <italic>trichocarpa</italic> were also chosen as the model plants for comparison. <italic>V</italic>. <italic>vinifera</italic> is a basal eudicot that has experienced a known WGT event, without a recent independent WGD. <italic>O</italic>. <italic>sativa</italic> as a monocotyledon, is used as an outgroup. Hence, the genomic information of these plant species are significant for comparative genomics analysis. We performed collinearity searches to identify collinear blocks within <italic>C</italic>. <italic>paliurus</italic> using MCScanX v.1.1.11 ##REF##22217600##[70]##. <italic>Ks</italic> between collinear genes were estimated based on whole-genome duplication integrated analysis (WGDI) v.0.1.6 software ##REF##36307977##[71]## with Yang-Nielsen (YN) model. In brief, the collinear blocks were constructed by performing similarity search for all-against-all protein sequence using BLASTP v.2.8.1 ##REF##9254694##[72]## (cutoff E-value of 1E−10), and then homologous block was built through MCScanX software. Finally, the <italic>Ks</italic> of each homologous gene pair was calculated.</p>", "<title>Analysis of the tetraploidy signatures</title>", "<title>Identification of chromosome-enriched K-mers</title>", "<p id=\"p0180\">To determine whether the genome is auto-tetraploid or allo-tetraploid, we adopted and modified a similar method that was used to study an allo-tetraploid <italic>Miscanthus sinensis</italic> genome ##REF##33116128##[23]## based on counting of chromosome-enriched 13-mers. Briefly, 13-mers were identified across the whole genome using Jellyfish v.2.2.6 ##REF##21217122##[73]##, and only <italic>K</italic>-mers that met the following two conditions were retained: (1) <italic>K</italic>-mers occurring at least 1000 times globally; and (2) <italic>K</italic>-mers that were enriched in any chromosome with at least twofold difference. Applying of the filtering strategy resulted in a total of 11,783 chromosome-enriched 13-mers. We further clustered these selected <italic>K</italic>-mers based on the number of these 13-bp short sequences presenting across the whole genome. The results showed that every homologous chromosome group that comprises 4 haplotypes were grouped together, providing strong evidence of auto-tetraploidy signatures.</p>", "<title>Smudge plot analysis</title>", "<p id=\"p0185\">We also performed the smudge plot analysis ##REF##32188846##[74]## to investigate the polyploid signatures in this tetraploid species. This tool utilized heterozygous paired <italic>K</italic>-mers extracted from raw reads in the sequenced genome, and analyzed the genome structure by comparing the total coverage of paired <italic>K</italic>-mers (<italic>i.e.</italic>, coverage A + coverage B) to the relative coverage of the minor one, <italic>i.e.</italic>, coverage B / (coverage A + coverage B), where A and B are paired heterozygous <italic>K</italic>-mers, A indicates the dominant <italic>K</italic>-mer, and B indicates the minor one.</p>", "<title>Identification of DEGs between PG and PA</title>", "<p id=\"p0190\">Male and female floral buds in various PA and PG individuals were collected at five different stages including (1) S0, physiological differentiation period; (2) S1, dormancy period; (3) S2, germination period; (4) S3, inflorescence elongation period; and (5) S4, maturation period. Three biological replicates of the extracted RNA from flowers (in PA and PG individuals) were sequenced on Illumina NovaSeq platform, and 6-Gb RNA-seq raw data for each sample were generated. Paired-end short reads were aligned to PG-dip <italic>C</italic>. <italic>paliurus</italic> genome using HISAT2 ##REF##25751142##[75]##. The expected number of FPKM fragments mapped were calculated using RSEM v.1.3.0 program ##REF##21816040##[60]##, which was implanted in Trinity package ##REF##23845962##[59]##. Moreover, the DESeq2 R package v.1.30.0 ##REF##25516281##[76]## was applied to identify the DEGs. The clusterProfiler R package v.3.12.0 ##REF##22455463##[77]## was used for GO and KEGG enrichment analyses.</p>", "<title>Genome screening for P450 genes and gene cluster analysis</title>", "<p id=\"p0195\">The hidden Markov model (HMM) profile for the P450 genes (PF00067) was obtained from the Pfam database (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ebi.ac.uk/interpro/set/all/entry/pfam/\" id=\"ir025\">https://www.ebi.ac.uk/interpro/set/all/entry/pfam/</ext-link>). Then, the P450 genes were identified using the HMMER v3.3.2 ##UREF##11##[78]## with default parameters by searching against the <italic>C</italic>. <italic>paliurus</italic> genome. According to definite standards with 40% for family variants described by Xiong ##REF##34267359##[79]##, P450 genes were divided into 68 families by alignment with P450 database ##REF##19951895##[80]##. Maximum likelihood phylogenetic trees were constructed using the Randomized Axelerated Maximum Likelihood (RAxML) package v.8.2.11 ##REF##16928733##[81]## with full-length protein sequences.</p>", "<p id=\"p0200\">The general feature format (GFF) files of 42 expanded P450 genes were used to search for gene clusters. The gene clusters were verified by following criteria: (1) one gene cluster should contain at least three adjacent P450 genes; and (2) the gene clusters were ruled out if the distance between adjacent P450s was more than 0.8 Mb.</p>", "<title>Identification of expressed genes and triterpenoid compounds for <italic>C. paliurus</italic></title>", "<p id=\"p0205\">Leaves in various PA-dip and PA-tetra individuals were collected in May and September, respectively. Three biological replicates of the extracted RNA were sequenced on Illumina NovaSeq platform, and 6-Gb RNA-seq raw data for each sample were generated. Paired-end short reads were aligned to PA-dip <italic>C</italic>. <italic>paliurus</italic> genome using HISAT2. Meanwhile, the same leaf samples were prepared for ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis. UPLC-MS/MS system (UPLC, SHIMADZU Nexera X2; MS/MS, Applied Biosystems 4500 Q TRAP, Waters, Milford, MA) was used to analyze the differences in triterpenoid accumulation between diploid and tetraploid plant leaves. Sample extraction details are described in File S1. The UPLC operation parameters were as follows: chromatographic separation was carried out using an Agilent SB-C18 Analytical high-performance liquid chromatography (HPLC) Column (2.1 mm × 100 mm, 1.8 µm); the mobile phase consisted of ultrapure water (A) and acetonitrile (B), which both contained 0.1% formic acid. Gradient elution was as follows: original ratio of 5% B; B ratio linearly increased to 95% within 9 min and maintained for 1 min; B ratio decreased to 5% during 10–11.1 min and kept for 2.9 min. The flow rate was kept at 0.35 ml/min, temperature 40 °C, and injection volume 4 µl. The electrospray ionization (ESI)-triple quadrupole-linear ion trap (Q TRAP)-MS system used for MS experiment. The operating parameters of the ESI source were as follows: positive ion spray voltage (IS) 5500 V and negative ion mode − 4500 V; source temperature 550 °C; curtain gas (CUR) 25 psi, ion source gas I (GSI) 50 psi, and gas II (GSII) 60 psi, respectively. The 10 μmol/l and 100 μmol/l polypropylene glycol solutions were, respectively, implemented for mass calibration and instrument tuning in linear ion trap (LIT) modes and triple quadrupole (QQQ).</p>", "<title>Population genetic structure</title>", "<p id=\"p0210\">More than coverage of 10× per sample for tetraploid and diploid <italic>C</italic>. <italic>paliurus</italic> were generated from 74 and 35 billion 150-bp Illumina short reads, respectively. Clean data were obtained by removing adapters and low-quality sequences (Q &lt; 30) from paired-end raw reads, followed by aligning against the reference genome of PA-dip <italic>C</italic>. <italic>paliurus</italic> by BWA v.0.7.17 ##REF##19451168##[82]## with default parameters. The variant calling was carried out by GATK v.4.0.3.0 ##REF##20644199##[83]## following the best practice workflow. The general variants were identified for each individual using GATK HaplotypeCaller, and then combined by GenotypeGVCFs function to a single variant calling file. This two-step approach was carried out to ensure variant accuracy, which included re-genotyping and quality recalibration in the combined VCF file. SNPs were then identified using SAMtools/BCFtools with default parameters based on alignments of all Illumina short reads. SNPs were filtered by following parameters: (1) SNPs were only present in one of the two pipelines (SAMtools/BCFtools and GATK); (2) SNPs with read depth more than 1000 or less than 5; (3) non-biallelic SNPs; (4) SNPs with missing rate more than 40%; (5) SNPs in repeat regions; and (6) SNPs having less then 5-bp distance with nearby variant sites. A phylogenetic gene tree was constructed based on SNPs in the single-copy genes regions. Two popular programs (RAxML ##REF##24451623##[84]## with GTRCAT model and IQ-TREE ##REF##25371430##[85]## with self-estimated best substitution model) were applied to construct the maximum likelihood tree. Ancestral population structure among nine <italic>C</italic>. <italic>paliurus</italic> populations was estimated from ancestral population sizes <italic>K</italic> = 1–5 by ADMIXTURE software v.1.3.0, and the population size with the smallest cross-validation error (<italic>K</italic> = 2) was determined. ADMIXTURE analysis was performed following the parameter standard errors, which were estimated by bootstrapping (bootstrap = 200).</p>", "<title>Identification of selective sweeps</title>", "<p id=\"p0215\">To identify selective sweeps, SweeD v.3.0 ##UREF##12##[86]## program was used to identify regions that display significant variations in the SFS by the composite likelihood ratio (CLR) statistic. We allowed 0.3% with maximum missing data in per site, and top 5% as the threshold to screen candidate selective sweeps. Ten diploid and 35 tetraploid individuals were compared to PA-dip and PA-tetra reference genomes, respectively.</p>" ]
[ "<title>Results</title>", "<title>Assembly and annotation of three <italic>C</italic>. <italic>paliurus</italic> genomes</title>", "<p id=\"p0030\">We sequenced and assembled three <italic>C</italic>. <italic>paliurus</italic> genomes, including two diploid and one tetraploid individuals (##FIG##0##Figure 1##; ##TAB##0##Table 1##, Tables S1–S4). The two diploid <italic>C</italic>. <italic>paliurus</italic> individuals represent two different reproduction types in hermaphroditism, PA-dip and PG-dip, whereas the tetraploid form is protandrous (PA-tetra). Karyotype analysis identified 32 chromosomes in the diploid genomes and 64 in the tetraploid genome (<xref rid=\"s0150\" ref-type=\"sec\">Figure S1</xref>). Taking the male florals of PA-tetra <italic>C</italic>. <italic>paliurus</italic> as experimental materials, the homologous chromosome synapsis at the early stage of meiosis in pollen mother cells of PA-tetra <italic>C</italic>. <italic>paliurus</italic> was studied. Multivalent (quadrivalent) phenomena were observed in pollen mother cells (<xref rid=\"s0150\" ref-type=\"sec\">Figure S2</xref>), strongly indicating that the PA-tetra is an auto-tetraploid. Using diploid <italic>Pterocarya stenoptera</italic> (600 Mb) as an internal reference, we estimated the genome size of PA-dip, PG-dip, and PA-tetra <italic>C</italic>. <italic>paliurus</italic> by flow cytometry (FCM) to be about 606 Mb (1C, the total number of DNA base pairs in one copy of the haploid genome), 659 Mb (1C), and 2460 Mb (1C = 1230 Mb), respectively (<xref rid=\"s0150\" ref-type=\"sec\">Figure S3</xref>). A total of 134.9 Gb, 75.5 Gb, and 271.8 Gb subreads were generated on the PacBio Sequel II platform, comprising ∼ 223×, ∼ 115×, and ∼ 221× coverages of the estimated genome sizes (by FCM, 1C) for PA-dip, PG-dip, and PA-tetra, respectively (##TAB##0##Table 1##, <xref rid=\"s0150\" ref-type=\"sec\">Table S1</xref>). The initial contigs were assembled using Canu assembler, resulting in three contig-level assemblies with N50 sizes of ∼ 1.9 Mb in PA-dip, ∼ 1.4 Mb in PG-dip, and ∼ 431 kb in PA-tetra (##TAB##0##Table 1##, <xref rid=\"s0150\" ref-type=\"sec\">Table S2</xref>). The assembled genome sizes were 586.62 Mb for PA-dip and 583.45 Mb for PG-dip, accounting for 96.8% and 88.5% of estimated genome size by FCM (<xref rid=\"s0150\" ref-type=\"sec\">Figure S3</xref>), respectively, while 2.38-Gb sequences were assembled in PA-tetra, almost four times of the haploid size (##TAB##0##Table 1##; <xref rid=\"s0150\" ref-type=\"sec\">Table S2</xref>). The chromosome-level assemblies were achieved using high-throughput chromatin conformation capture (Hi-C) technology (<xref rid=\"s0150\" ref-type=\"sec\">Table S3</xref>). For the diploid PA and PG genomes, 543.53 Mb (92.65%) and 553.87 Mb (94.93%) of sequences were integrated into 16 pseudo-chromosomes, respectively (##FIG##0##Figure 1##G; ##TAB##0##Table 1##, Table S4). The PA-tetra genome comprised 64 pseudo-chromosomes with four sets of monoploid chromosomes using ALLHiC phasing algorithm that anchored 2.17 Gb (91.08%) of genomic sequences, representing a haplotype-resolved assembly of the tetraploid species (##FIG##0##Figure 1##G, <xref rid=\"s0150\" ref-type=\"sec\">Figure S4</xref>; ##TAB##0##Table 1##, <xref rid=\"s0150\" ref-type=\"sec\">Table S4</xref>).</p>", "<p id=\"p0035\">We identified 12,737,788 haplotypic single nucleotide polymorphisms (SNPs) among the haplotype-resolved A/B/C/D homologous chromosomes, affecting 5152 functional genes (<xref rid=\"s0150\" ref-type=\"sec\">Table S5</xref>). These genes were significantly enriched in some primary biological pathways, such as aminoacyl-tRNA and fatty acid biosyntheses, glycerolipid metabolism, mitochondrial genome maintenance, and single strand break repair (<xref rid=\"s0150\" ref-type=\"sec\">Figure S5</xref>). We further assessed the quality of genome assemblies, showing more than 95.2% of Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness (<xref rid=\"s0150\" ref-type=\"sec\">Table S6</xref>). Comparison with the previously published <italic>C</italic>. <italic>paliurus</italic> genome shows an improved BUSCO completeness (95.2% <italic>vs.</italic> 91%) with well-resolved duplicated genes (<italic>i.e.</italic>, allelic genes; BUSCO duplication 82.3% <italic>vs.</italic> 8.4% in <xref rid=\"s0150\" ref-type=\"sec\">Table S6</xref>) ##UREF##5##[18]##. Our assessment using Illumina short reads showed at least 98.89% of global mapping ratio and 93.72% of properly paired reads (<xref rid=\"s0150\" ref-type=\"sec\">Table S7</xref>). Comparison among the three genomes revealed high levels of syntenic relationship with a large number of genes (26,760) located in the syntenic regions (##FIG##0##Figure 1##G). The Hi-C contact heatmaps also confirmed the high consistency of genome structure and quality, which also indicates improved chromosome-scale assemblies in comparison with the previously published genome ##UREF##5##[18]## (<xref rid=\"s0150\" ref-type=\"sec\">Figures S6–S8</xref>).</p>", "<p id=\"p0040\">We annotated 34,699 protein-coding genes in PA-dip and 35,221 protein-coding genes in PG-dip. The initial annotation of the tetraploid genome resulted in 90,752 gene models; however, this number mixed the concept of genes and allelic genes. To identify allelic genes that have at least one base substitution, we adopted the same strategy in our previously published sugarcane genome ##REF##30297971##[19]##, leading to 34,633 allele-defined protein-coding genes in the tetraploid genome (<xref rid=\"s0150\" ref-type=\"sec\">Tables S8 and S9</xref>). Our assessment of the annotation showed 96.2%, 96.2%, and 94.4% of completeness for PA-dip, PG-dip, and PA-tetra, respectively, according to the 1375 conserved genes in BUSCO assessed using embryophyta_odb10 database (<xref rid=\"s0150\" ref-type=\"sec\">Table S10</xref>).</p>", "<p id=\"p0045\">A total of 282.25 Mb (48.1% of the assembled genome), 316.95 Mb (54.3%), and 1,154.35 Mb (48.4%) repetitive sequences were identified in the PA-dip, PG-dip, and PA-tetra genomes, respectively, showing a slight increase in PG-dip genome (<xref rid=\"s0150\" ref-type=\"sec\">Table S11</xref>). The ratio of repetitive elements in the previously reported assembly by Zheng et al. ##UREF##5##[18]## (14.94%) is much lower than our results, possibly due to a large proportion of collapsed sequences. Retroelements account for approximately three-quarters of the repetitive sequences, ranging from 35.7% to 37.3% in the three genomes. However, in contrast to other published plant genomes, such as pineapple ##REF##31570895##[20]##, sugarcane ##REF##30297971##[19]##, and banyan tree ##REF##33035453##[21]##, long interspersed nuclear element (LINE) is the most prominent family in <italic>C</italic>. <italic>paliurus</italic>, spanning from 12.16% to 12.59% of the assembled genomes. In comparison, <italic>Copia</italic> and <italic>Gypsy</italic> account for only ∼ 5.47% and ∼ 5.94% of the assembled genomes on average in <italic>C</italic>. <italic>paliurus</italic> genomes (<xref rid=\"s0150\" ref-type=\"sec\">Table S11</xref>).</p>", "<title>An additional WGD event in the auto-tetraploid genome</title>", "<p id=\"p0050\">Maximum likelihood tree using 302 single-copy gene families from nine plant species reconstructed the phylogenetic relationship among <italic>C</italic>. <italic>paliurus</italic> and related species. The estimated divergence time between <italic>C</italic>. <italic>paliurus</italic> and <italic>P</italic>. <italic>stenoptera</italic> was approximately 46.07 million years ago (MYA) (##FIG##1##Figure 2##A), consistent with the previously reported divergence time of different genera of Juglandaceae ##UREF##6##[22]##. Analysis of the gene families showed that a large number of families experienced expansion (285) and contraction (264) compared with <italic>P. stenoptera</italic> (##FIG##1##Figure 2##A)<italic>.</italic> In addition, we found 1738 gene families specific to the <italic>C</italic>. <italic>paliurus</italic> genome, while 9917 gene families were shared in the selected species, demonstrating evolutionary conservation <bold>(</bold>##FIG##1##Figure 2##B<bold>)</bold>.</p>", "<p id=\"p0055\">The distribution of synonymous substitution rate (<italic>Ks</italic>) of each homologous gene pair within <italic>C</italic>. <italic>paliurus</italic> showed three peaks (##FIG##1##Figure 2##C), representing three WGD events. In addition to the ancient whole-genome triplication (WGT) event shared with grape, <italic>C</italic>. <italic>paliurus</italic> experienced two recent WGDs. Synteny analysis between PA-dip and PG-dip validated the early WGD (<italic>i.e.</italic>, WGD1), dating back to ∼ 67.6–50.7 MYA (##FIG##1##Figure 2##C, <xref rid=\"s0150\" ref-type=\"sec\">Figure S9</xref>). Most of the duplicated chromosomes maintained high levels of syntenic relationship and completeness compared with their counterparts. However, several structural variations were observed (<xref rid=\"s0150\" ref-type=\"sec\">Figure S9</xref>), <italic>e.g.</italic>, an inversion between chromosome 4 (Chr4) and Chr16 and a large deletion in Chr8 compared with Chr10, indicating the diploidization process in the diploid <italic>C</italic>. <italic>paliurus</italic> after the early WGD. The most recent WGD event (<italic>i.e.</italic>, WGD2) happened in ∼ 11.2–10.5 MYA and contributed to the tetraploidy in <italic>C</italic>. <italic>paliurus</italic> species (##FIG##1##Figure 2##C and D). To check whether each of two WGDs made specific contribution to specific gene family expansion in <italic>C</italic>. <italic>paliurus</italic>, we counted 1351 and 2024 genes, which experienced WGD1 and WGD2 events, respectively. Functional enrichment analysis showed that the genes involved in WGD1 event were significantly enriched in ribosomal subunit assembly, mannosyltransferase activity, and <italic>N</italic>-glycan biosynthesis, and the genes involved in WGD2 event were mostly enriched in terpene biosynthesis, such as sesquiterpenoid, triterpenoid, and monoterpenoid biosyntheses (<xref rid=\"s0150\" ref-type=\"sec\">Figure S10</xref>). Meanwhile, the genomic dot plots between <italic>C</italic>. <italic>paliurus</italic> and <italic>Vitis vinifera</italic> validated that tetraploid <italic>C</italic>. <italic>paliurus</italic> experienced two WGD events during the polyploidy evolution (<xref rid=\"s0150\" ref-type=\"sec\">Figures S11 and S12</xref>). We analyzed the timing of long terminal repeat retrotransposon (LTR-RT) insertions and found that LTR bursts occurred at ∼ 1.5 MYA across all the three genomes (<xref rid=\"s0150\" ref-type=\"sec\">Figure S13</xref>) after the divergence between tetraploid and diploid genomes (∼ 11.2–10.5 MYA). Collectively, the large tetraploid genome size is attributed to the most recent WGD (WGD2), rather that the expansion of repeats with the LTR bursts. The fully phased haplotypes facilitate us to investigate the evolution of polyploidy in <italic>C</italic>. <italic>paliurus</italic>. According to the method described by Mitros et al. ##REF##33116128##[23]## that depended on clustering of chromosome-specific <italic>K</italic>-mers (<italic>K</italic> = 13), we found that four haplotypes within each homologous group were consistently partitioned into a same branch (<xref rid=\"s0150\" ref-type=\"sec\">Figure S14</xref>), indicating a similar evolutionary history of the four haplotypes. In addition, the smudge pot analysis using heterozygous <italic>K-</italic>mer pairs extracted from Illumina sequencing reads suggests a highly heterozygous tetraploidy evidenced by the dominant component of AAAB pattern, accounting for 57% of tested <italic>K</italic>-mer pairs (<xref rid=\"s0150\" ref-type=\"sec\">Figure S4</xref>D). These lines of evidence collectively suggest that PA-tetra is likely an auto-tetraploid species with a high heterozygosity of 1.97% (<xref rid=\"s0150\" ref-type=\"sec\">Figure S4</xref>C).</p>", "<title>Expansion of P450 gene families is associated with elevated triterpenoid biosynthesis</title>", "<p id=\"p0060\">Evidence has shown that triterpenoids, sterols, flavones, and phenol acids are enriched in <italic>C</italic>. <italic>paliurus</italic> leaves ##REF##29679877##[24]##, which is possibly associated with the expansion of specific gene families related to the biosynthesis of these secondary metabolites. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses showed that many of the expanded genes (##FIG##1##Figure 2##A) were enriched in sesquiterpene, terpene, monoterpenoid, and triterpenoid biosynthesis pathways (<xref rid=\"s0150\" ref-type=\"sec\">Figures S15 and S16</xref>). For instance, we found that 15% (42/280 in total) of P450 genes expanded, among which 23 genes were clustered on Chr1, Chr4, and Chr12 (<xref rid=\"s0150\" ref-type=\"sec\">Figure S17</xref>). Phylogenetic analysis further identified that, among the 42 expanded P450 genes, 16 genes belong to the CYP89 family that participates in biosynthesis of tetracyclic triterpenoids ##REF##27892922##[25]##, 18 genes belong to the CYP706 family that possibly contributes to the increased flavonoids ##REF##27458469##[26]##, and six genes belong to the CYP82 family (<xref rid=\"s0150\" ref-type=\"sec\">Figure S18</xref>; <xref rid=\"s0150\" ref-type=\"sec\">Table S12</xref>).</p>", "<title>Genes associated with the heterodichogamy in <italic>C</italic>. <italic>paliurus</italic></title>", "<p id=\"p0065\">The most typical feature of <italic>C</italic>. <italic>paliurus</italic> is heterodichogamy with female and male functionally separated within PA or PG individuals, promoting outbreeding in an independent population. To investigate the genes triggering heterodichogamy in <italic>C</italic>. <italic>paliurus</italic>, we performed a comparative transcriptome analysis for the floral buds of PG and PA samples, respectively. These samples contained two tissue types (female and male floral buds) at five different developmental stages, namely from S0 to S4 ##REF##31627470##[27]##.</p>", "<p id=\"p0070\">Pairwise comparison between PG and PA female samples (PG-F <italic>vs.</italic> PA-F) identified 958 differentially expressed genes (DEGs) that were consistently up-regulated or down-regulated in at least two stages. Similarly, 2373 DEGs were found between PA and PG male samples (PA-M <italic>vs.</italic> PG-M) (<xref rid=\"s0150\" ref-type=\"sec\">Figure S19</xref>A and B). Functional analysis revealed that these DEGs were enriched in a series of biological processes involving in floral organ formation and development (<xref rid=\"s0150\" ref-type=\"sec\">Figures S19</xref>C and D, S20, and S21). Notably, many of up-regulated DEGs (128/855 in PG-F and 58/1539 in PA-M) were related to hormone biosynthesis and signaling pathways, indicating that hormones may contribute to the heterodichogamous morphs with asynchronous flowering. We further tested endogenous hormone contents in PA and PG floral buds, including gibberellin (GA<sub>3</sub>)<sub>,</sub> auxin (IAA), and abscisic acid (ABA). The results displayed similar levels of IAA and ABA at each of the five stages especially at S0, an initial differential stage of floral buds (<xref rid=\"s0150\" ref-type=\"sec\">Figure S22</xref>). However, significantly increased levels of GA<sub>3</sub> in PG samples were detected at S0 stage compared with PA (<xref rid=\"s0150\" ref-type=\"sec\">Figure S22</xref>), indicating that GA<sub>3</sub> content likely plays a crucial role in regulating floral bud physiological differentiation and is responsible for the asynchronous flowering.</p>", "<p id=\"p0075\">To investigate the co-expression networks during floral bud development, we identified co-expressed gene sets via weighted gene co-expression network analysis (WGCNA) package based on the 22 RNA sequencing (RNA-seq) datasets (<xref rid=\"s0150\" ref-type=\"sec\">Figure S23</xref>). After filtering genes with low expression, a total of 20,829 genes were retained, distributing in 26 modules (<xref rid=\"s0150\" ref-type=\"sec\">Figures S23 and S24</xref>). We observed that genes in three modules (darkorange: 47 genes; pink: 912 genes; red: 1244 genes) showed a high correlation (R<sup>2</sup> ≥ 0.56, <italic>P</italic> ≤ 0.007, Pearson test) with GA<sub>3</sub> content (<xref rid=\"s0150\" ref-type=\"sec\">Figures S25 and S26</xref>). In addition to “regulation of hormone and gibberellin biosynthetic process”, these genes were also functionally enriched in signal transduction, response to stimulus and stress, and biological regulation (<xref rid=\"s0150\" ref-type=\"sec\">Figures S27 and S28</xref>).</p>", "<p id=\"p0080\">Key hub genes including transcription factor (TF)-coding genes were identified in the WGCNA analysis. For instance, <italic>Trihelix-1</italic> (CpaF1st06806), involved in endogenous hormone signaling and flower development ##REF##20717979##[28]##, and <italic>ERF066</italic> (CpaF1st15865), responsible for embryo development and stress signal transduction ##REF##16832061##[29]##, have the most edges (342 and 279, respectively) (<xref rid=\"s0150\" ref-type=\"sec\">Figure S25</xref>E) in the pink module. In red module, the top two most frequently connected hub genes, <italic>ERF090</italic> (CpaF1st01445) and <italic>WRKY55</italic> (CpaF1st00113) (<xref rid=\"s0150\" ref-type=\"sec\">Figure S25</xref>F), were identified that may play important roles in regulating the development of floral organs ##REF##9553044##[30]## and phytohormone-mediated signal transduction process ##REF##15047897##[31]##.</p>", "<title>Dosage effect contributes to enhanced photosynthesis and increased accumulation of terpenoids</title>", "<p id=\"p0085\">Investigation of the morphology, anatomical structure, and photosynthetic capacity of the leaves of seedlings showed enhanced photosynthesis and accelerated plant growth in the tetraploid <italic>C</italic>. <italic>paliurus</italic>. We observed that a series of growth indices in the tetraploid plants were significantly higher than that in diploid individuals (<italic>P</italic> &lt; 0.01, Duncan’s test), including seedling size, leaf area, length of compound leaves (<xref rid=\"s0150\" ref-type=\"sec\">Figure S29</xref>; <xref rid=\"s0150\" ref-type=\"sec\">Table S13</xref>), thickness of leaf tissues (upper and lower epidermal cells, palisade mesophyll, sponge tissue, and blade), stomatal size, stomatal density (##FIG##2##Figure 3##A, <xref rid=\"s0150\" ref-type=\"sec\">Figures S30 and S31</xref>), chlorophyll content (##FIG##2##Figure 3##B), and net photosynthetic rate (Pn; ##FIG##2##Figure 3##C). In addition, we also detected three growth indices including blade aspect ratio, leaf moisture content, and leaf specific weight, which were significantly lower in the tetraploid individuals than those in diploid ones (Table S13).</p>", "<p id=\"p0090\">To investigate genes underlying the functional impact of polyploidization, we identified 691 genes that showed significantly elevated expression in the tetraploid samples compared to diploid ones (fold change ≥ 2 and <italic>P</italic> ≤ 0.05) (<xref rid=\"s0150\" ref-type=\"sec\">Figure S32</xref>), which were considered as dosage-effect genes. Furthermore, functional annotation showed that these genes were abundantly enriched in some primary biological pathways (<xref rid=\"s0150\" ref-type=\"sec\">Figure S33</xref>). Notably, genes, which are involved in carbohydrate, starch, sucrose, alanine, aspartate, and glutamate metabolism, phosphatidylinositol signaling system, and ion channels, play vital roles in photosynthesis, and are indispensable for plant growth, development, and stress responses ##REF##23558902##[33]##, ##REF##24489071##[34]##. We also explicitly investigated the <italic>Arabidopsis thaliana</italic> key homologous proteins in the photosynthetic pathway. Carbonic anhydrase (CA), phosphoenolpyruvate carboxylase kinase (PPCK), ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), fructose-1,6-bisphosphatase (FBP), and sedoheptulose-1,7-bisphosphatase (SBPASE) had significantly higher expression levels in tetraploid samples than those in diploid ones (<italic>P</italic> ≤ 0.05) (<xref rid=\"s0150\" ref-type=\"sec\">Figure S34</xref>). Meanwhile, we identified 759 dosage-effect genes with higher expression in diploid samples than in tetraploid ones (fold change ≥ 2 and <italic>P</italic> ≤ 0.05). GO and KEGG functional enrichment analyses showed that many of the dosage-effect genes were enriched in regulation of DNA recombination, maltose metabolic process, cysteine and methionine metabolism, and amino sugar and nucleotide sugar metabolism pathways (<xref rid=\"s0150\" ref-type=\"sec\">Figure S35</xref>).</p>", "<p id=\"p0095\">Interestingly, we also noticed that many of the dosage-effect genes were significantly enriched in sesquiterpenoid and triterpenoid biosynthesis and terpenoid metabolism (<italic>P</italic> ≤ 0.05) (<xref rid=\"s0150\" ref-type=\"sec\">Figure S33</xref>), and likely contributed to the increased accumulation of some triterpenoid components in the PA-tetra (##FIG##2##Figure 3##D). Furthermore, we observed that 22 dosage-effect genes belong to the P450 gene family based on basic local alignment search tool (BLAST) results in public databases and phylogenetic analysis (<xref rid=\"s0150\" ref-type=\"sec\">Figures S36 and S37</xref>; File S1). Among them, three P450 subfamilies (CYP716A, CYP72A, and CYP71A) might be vitally important in the biosynthesis of cyclocaric acid B (##FIG##2##Figure 3##E) via modification of different C positions. Previous studies have reported that CYP716A12 and CYP716A1 can catalyze the oxidation at the C-28 position of β-amyrin, forming the triterpene oleanolic acid ##REF##22039103##[35]##, ##REF##26801524##[36]##, while the maslinic acid might be hydroxylated by CYP71A16 and CYP72A397 specifically at C-23 position into the triterpene arjunolic acid ##REF##23570231##[37]##, ##REF##29186583##[38]##. Our study identified two homologous genes in the CYP716A subfamily, two in the CYP71A subfamily, and three in the CYP72A subfamily, showing dosage effects in the tetraploid <italic>C</italic>. <italic>paliurus</italic> (##FIG##2##Figure 3##E). In addition, they are likely the key genes contributing to the biosynthesis pathway of cyclocaric acid B (a specific triterpene to <italic>C</italic>. <italic>paliurus</italic>).</p>", "<title>Population genetics uncovers evolutionary history</title>", "<p id=\"p0100\">To explore the population structure and evolutionary history of the <italic>C</italic>. <italic>paliurus</italic> populations, we resequenced 45 individuals, including 10 diploid and 35 tetraploid individuals native to the south of China, and one walnut species (<italic>Juglans regia</italic>) as an outgroup (##FIG##3##Figure 4##A; <xref rid=\"s0150\" ref-type=\"sec\">Table S14</xref>). Based on our stringent filtering criteria (see Materials and methods), we identified 3,886,832 variants [3,545,162 SNPs and 341,670 insertions/deletions (Indels)] from the diploid population, while identified 26,674,995 variants (23,076,276 SNPs and 3,598,719 Indels) from the tetraploid population. We also identified that the diploid and tetraploid populations contained 3845 and 38,899 Indels in genic regions, as well as 3753 and 23,764 synonymous variants and 5503 and 35,241 nonsynonymous variants, respectively (<xref rid=\"s0150\" ref-type=\"sec\">Table S15</xref>).</p>", "<p id=\"p0105\">A phylogeny of these <italic>C</italic>. <italic>paliurus</italic> individuals collected from nine geographic locations partitioned these samples into two distinct groups (##FIG##3##Figure 4##B). The ten diploid samples were clustered in the first group, and most closely related to the outgroup <italic>J</italic>. <italic>regia</italic>. The remaining 35 tetraploid samples were represented in the second group. Both principal component analysis (PCA) and ADMIXTURE analysis supported the population structure (##FIG##3##Figure 4##C and D). These results indicated a single origin of the last WGD event in <italic>C</italic>. <italic>paliurus</italic> species rather than multiple origins observed in other polyploid species, such as sugarcane ##REF##30297971##[19]##.</p>", "<p id=\"p0110\">To identify the candidate genes responsible for coordinated local adaptation, we further analyzed selective sweeps based on the SweeD analysis in both diploid and auto-tetraploid genomes. A total of 25.88 Mb and 165.18 Mb genomic sequences were under purifying selection in diploid and tetraploid genomes, respectively (<xref rid=\"s0150\" ref-type=\"sec\">Figure S38</xref>). These selectively swept regions were evenly distributed in 16 chromosomes of PA-dip and 64 chromosomes of PA-tetra <italic>C</italic>. <italic>paliurus</italic>, with a number of them showing high levels of selective sweeps (<xref rid=\"s0150\" ref-type=\"sec\">Figure S38</xref>). These swept genomic regions overlapped with 1528 protein-coding genes in diploid, and 4812 allele-defined genes in the tetraploid group. Global GO and KEGG functional enrichment analyses also revealed that 114 and 568 of these swept genes respectively in diploid and tetraploid groups were involved in important functions, such as secondary metabolism, regulation of DNA recombination, and maltose metabolic process (<xref rid=\"s0150\" ref-type=\"sec\">Figures S39–S42</xref>).</p>", "<p id=\"p0115\">Among these swept genes, 262 were shared between the diploid and tetraploid genomes, and also located in the syntenic regions. In addition, the selectively swept genes specific to tetraploid were mostly enriched in terpene synthase activity and terpene biosynthesis (<xref rid=\"s0150\" ref-type=\"sec\">Figures S43 and S44</xref>), probably caused by stronger environmental adaptation ##REF##31304957##[39]## and stress tolerance ##REF##33036280##[40]## than diploid. Further, three genes, CpaM1st41668, CpaM1st05982, and CpaM1st08040, were verified as orthologs of the <italic>A</italic>. <italic>thaliana</italic> genes <italic>FAR1-related sequence</italic> (<italic>FRS10</italic>), <italic>Arabidopsis response regulator 1</italic> (<italic>ARR1</italic>), and <italic>Phytochrome C</italic> (<italic>PHYC</italic>), respectively, which were associated with general environmental variables such as light regulation, temperature, and precipitation ##REF##33846635##[41]##.</p>", "<p id=\"p0120\">The reconstruction with the ancestral alleles from the diploid <italic>C</italic>. <italic>paliurus</italic> reference genome was used to estimate the site frequency spectrum (SFS) for 45 <italic>C</italic>. <italic>paliurus</italic> individuals using analysis of next generation sequencing data (ANGSD) and to generate a stairway plot elucidating effective population size (<italic>Ne</italic>) history over time. With an estimated mutation rate of 2 × 10<sup>−9</sup> per generation and a generation time of 8 years, the stairway plot revealed two population bottlenecks over deep time (<xref rid=\"s0150\" ref-type=\"sec\">Figure S45</xref>). An early <italic>Ne</italic> bottleneck (dating back to ∼ 4.5–3.0 MYA) appeared during the upper Pliocene, consistent with the known events of environment change that boundary between the Pliocene and Miocene, was a regional transition from the warmer to the cooler stages ##UREF##7##[42]##. The last <italic>Ne</italic> drop (dating back to ∼ 0.6–0.16 MYA) corresponded with the great extinction event at the Pleistocene glaciation ##UREF##8##[43]##, followed by a rapid population expansion. Facilitated by the comparison of the demographic bottlenecks in three <italic>Camellia sinensis</italic> genomes, we uncovered similar bottlenecks in <italic>C</italic>. <italic>paliurus</italic> (0.6–0.16 MYA) and <italic>C</italic>. <italic>sinensis</italic> (2.5–0.7 MYA), both coinciding with known periods of environmental change ##REF##34267370##[44]##.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0125\"><italic>C</italic>. <italic>paliurus</italic> is well-known as the sweet tea tree and traditionally used as an herbal medicine ##REF##32289423##[45]##. The diverse ploidy and heterodichogamy in this species make it an ideal model to investigate the functional impact of WGDs and the development of flowers. We have generated three references, including two diploid and one haplotype-resolved tetraploid genomes, by incorporating the newly developed sequencing technologies and chromosome phasing algorithm. Facilitated by the comparison of these genomes and 45 resequenced individuals, we are able to investigate the evolutionary history and uncover functional genes underlying environmental adaptation as well as factors contributing to enhanced photosynthesis and the biosynthesis of cyclocaric acid B, one of the active components for the treatment of hypertension and diabetes ##REF##26220631##[12]##.</p>", "<p id=\"p0130\">Studies have shown that <italic>Cyclocarya</italic> is an ancient genus, likely originating in the late Paleocene and becoming extinct in the early Miocene except for <italic>C</italic>. <italic>paliurus</italic> from the subtropical China ##REF##28140736##[13]##. The remaining <italic>C</italic>. <italic>paliurus</italic> is a relict plant species within the genus, serving as an excellent model to study the adaptive evolution of relict plants. Our population analysis uncovered two bottlenecks in the species, with each coinciding with dramatic climate changes. However, the rapid demographic decline was recovered by population expansion as shown in the stairway plot, posing questions about how this species survived during the long-term evolutionary history. Increasing evidence has shown that WGD is a pivotal contributor to adaptation in angiosperms ##REF##31678615##[46]##. Two rounds of WGDs after the ancient WGT event shared by eudicots were observed in <italic>C</italic>. <italic>paliurus</italic>, occurring at ∼ 67.6–50.7 MYA and ∼ 11.2–10.5 MYA, respectively. Population genetics analysis clustered the 10 diploid and 35 tetraploid resequenced individuals into two distinct groups, indicating one single origination of the latest WGD event rather than multiple WGD events in a different location. Comparison between the auto-tetraploid and diploid genomes showed that the dosage effect after the most recent WGD involved genes contributing to adaptive evolution and improvement of photosynthesis, such as genes involved in the terpenoid metabolic biosynthetic pathways and the carbohydrate, starch, and sucrose metabolism. This is highlighted by the biosynthesis of cyclocaric acid B, which showed a significant increase in the auto-tetraploid genome compared with the diploid <italic>C</italic>. <italic>paliurus</italic>, attributing to elevated copy numbers of CYP716A, CYP72A, and CYP71A subfamily genes by WGDs. We also observed that the Pn, stomatal size, and chlorophyll content in the leaves of tetraploid <italic>C</italic>. <italic>paliurus</italic> were significantly higher than those of diploid, which is a benefit to improve its growth and environment adaptability. Moreover, combining the experimental phenomenon, the pollen viability of diploid <italic>C</italic>. <italic>paliurus</italic> is significantly lower than that in tetraploid (<xref rid=\"s0150\" ref-type=\"sec\">Figure S46</xref>). In conclusion, we propose that the tetraploid <italic>C</italic>. <italic>paliurus</italic> is more superior on the physiological and ecological characteristics than diploid.</p>", "<p id=\"p0135\">As a typical heterodichogamy species, <italic>C</italic>. <italic>paliurus</italic> possesses two complementary morphs with asynchronous flowering, which may effectively prevent selfing, reduce intramorph inbreeding, and heavily contribute to the pattern of genetic diversity in the process of species evolution ##UREF##9##[47]##. Our results uncovered that GA<sub>3</sub> content plays an important role in the asynchronous flowering, which was also evidenced by up-regulated expression of GA-related genes in PG-F and PA-M. In addition to GA-related signaling pathway, co-expression network analysis identified that hub genes, including <italic>Trihelix-1</italic>, <italic>ERF066</italic>, <italic>ERF090</italic>, and <italic>WRKY55</italic>, likely contribute to heterodichogamy trait in <italic>C</italic>. <italic>paliurus</italic>.</p>" ]
[]
[ "<p id=\"np010\">Equal contribution.</p>", "<p><bold><italic>Cyclocarya paliurus</italic></bold> is a relict plant species that survived the last glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B. Here, we presented three <italic>C</italic>. <italic>paliurus</italic> genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative genomic analysis revealed two rounds of recent <bold>whole-genome duplication</bold> events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of <bold>triterpenoids</bold>. <bold>Re</bold><bold>sequencing</bold> analysis of 45 <italic>C</italic>. <italic>paliurus</italic> individuals uncovered two bottlenecks, consistent with the known events of environmental changes, and many selectively swept genes involved in critical biological functions, including plant defense and secondary metabolite biosynthesis. We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes, in particular gibberellin-related genes, associated with the heterodichogamy in <italic>C</italic>. <italic>paliurus</italic> species. Our study sheds light on evolutionary history of <italic>C</italic>. <italic>paliurus</italic> and provides <bold>genomic</bold> resources to study the medicinal herbs.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Kai Ye</p>" ]
[ "<title>Data availability</title>", "<p id=\"p9955\">The whole-genome sequencing raw data including Illumina short reads, PacBio long reads, Hi-C interaction reads, and transcriptome data have been deposited in the Genome Sequence Archive ##REF##34400360##[87]## at the National Genomics Data Center (NGDC), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS) / China National Center for Bioinformation (CNCB) (GSA: CRA004671), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa/\" id=\"PC_linkiWn7hy5HcK\">https://ngdc.cncb.ac.cn/gsa/</ext-link>. The genome assemblies and annotations have been deposited in the Genome Warehouse ##REF##34175476##[88]## at the NGDC, BIG, CAS / CNCB (GWH: GWHBKKW00000000, GWHBKKX00000000, and GWHBKKY00000000), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gwh/\" id=\"PC_linkyA3cIZThUE\">https://ngdc.cncb.ac.cn/gwh/</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0220\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0230\"><bold>Yinquan Qu:</bold> Investigation, Methodology, Formal analysis, Visualization, Writing – original draft, Writing – review &amp; editing. <bold>Xulan Shang:</bold> Resources, Methodology, Writing – original draft. <bold>Ziyan Zeng:</bold> Visualization, Methodology. <bold>Yanhao Yu:</bold> Resources, Formal analysis. <bold>Guoliang Bian:</bold> Resources, Data curation. <bold>Wenling Wang:</bold> Formal analysis. <bold>Li Liu:</bold> Visualization, Formal analysis. <bold>Li Tian:</bold> Formal analysis. <bold>Shengcheng Zhang:</bold> Formal analysis. <bold>Qian Wang:</bold> Resources. <bold>Dejin Xie:</bold> Formal analysis. <bold>Xuequn Chen:</bold> Formal analysis. <bold>Zhenyang Liao:</bold> Formal analysis. <bold>Yibin Wang:</bold> Formal analysis. <bold>Jian Qin:</bold> Formal analysis. <bold>Wanxia Yang:</bold> Resources. <bold>Caowen Sun:</bold> Resources. <bold>Xiangxiang Fu:</bold> Methodology, Resources, Writing – original draft, Writing – review &amp; editing, Supervision. <bold>Xingtan Zhang:</bold> Methodology, Formal analysis, Writing – original draft, Writing – review &amp; editing. <bold>Shengzuo Fang:</bold> Conceptualization, Methodology, Resources, Writing – original draft, Writing – review &amp; editing, Supervision. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0245\">The following are the Supplementary material to this article:</p>", "<p id=\"p0250\">\n\n</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<p id=\"p0270\">\n\n</p>", "<p id=\"p0275\">\n\n</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<p id=\"p0325\">\n\n</p>", "<p id=\"p0330\">\n\n</p>", "<p id=\"p0335\">\n\n</p>", "<p id=\"p0340\">\n\n</p>", "<p id=\"p0345\">\n\n</p>", "<p id=\"p0350\">\n\n</p>", "<p id=\"p0355\">\n\n</p>", "<p id=\"p0360\">\n\n</p>", "<p id=\"p0365\">\n\n</p>", "<p id=\"p0370\">\n\n</p>", "<p id=\"p0375\">\n\n</p>", "<p id=\"p0380\">\n\n</p>", "<p id=\"p0385\">\n\n</p>", "<p id=\"p0390\">\n\n</p>", "<p id=\"p0395\">\n\n</p>", "<p id=\"p0400\">\n\n</p>", "<p id=\"p0405\">\n\n</p>", "<p id=\"p0410\">\n\n</p>", "<p id=\"p0415\">\n\n</p>", "<p id=\"p0420\">\n\n</p>", "<p id=\"p0425\">\n\n</p>", "<p id=\"p0430\">\n\n</p>", "<p id=\"p0435\">\n\n</p>", "<p id=\"p0440\">\n\n</p>", "<p id=\"p0445\">\n\n</p>", "<p id=\"p0450\">\n\n</p>", "<p id=\"p0455\">\n\n</p>", "<p id=\"p0460\">\n\n</p>", "<p id=\"p0465\">\n\n</p>", "<p id=\"p0470\">\n\n</p>", "<p id=\"p0475\">\n\n</p>", "<p id=\"p0480\">\n\n</p>", "<p id=\"p0485\">\n\n</p>", "<p id=\"p0490\">\n\n</p>", "<p id=\"p0495\">\n\n</p>", "<p id=\"p0500\">\n\n</p>", "<p id=\"p0505\">\n\n</p>", "<p id=\"p0510\">\n\n</p>", "<p id=\"p0515\">\n\n</p>", "<p id=\"p0520\">\n\n</p>", "<p id=\"p0525\">\n\n</p>", "<p id=\"p0530\">\n\n</p>", "<p id=\"p0535\">\n\n</p>", "<p id=\"p0540\">\n\n</p>", "<p id=\"p0545\">\n\n</p>", "<p id=\"p9545\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0235\">This work was funded by the <funding-source id=\"gp035\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/100016163</institution-id><institution>National Natural Science Foundation</institution></institution-wrap></funding-source> of China (Grant Nos. 31971642, 32271859, 32071750, 31470637, and 32222019). This work was also supported by the <funding-source id=\"gp040\">Key R&amp;D Program of Jiangsu Province</funding-source> (Grant No. BE2019388) and the <funding-source id=\"gp045\">Priority Academic Program Development of Jiangsu Higher Education Institutions</funding-source> (PAPD), China.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Morphology and genome duplications of <italic>C</italic>.</bold><bold><italic>paliurus</italic></bold><bold>A.</bold> Imparipinnate leaves. <bold>B.</bold> Mature fruits. <bold>C.</bold> Female and male flowers of PA-dip. <bold>D.</bold> Female and male flowers of PG-dip. <bold>E.</bold> Fruit wings that start to spread. <bold>F.</bold> Tetraploid plant. <bold>G.</bold> Genomic alignments between the basal angiosperm <italic>A. trichopoda</italic> and the basal eudicot <italic>V</italic>. <italic>vinifera</italic>, as well as PG-dip, PA-dip, and PA-tetra <italic>C</italic>. <italic>paliurus</italic> are shown. The conserved collinear blocks are shown as the gray lines in the background, and the green lines indicate cases in each round of WGD. <italic>C. paliurus</italic>, <italic>Cyclocarya paliurus</italic>; <italic>A. trichopoda</italic>, <italic>Amborella trichopoda</italic>; <italic>V. vinifera</italic>, <italic>Vitis vinifera</italic>; WGD, whole-genome duplication; PA-tetra, the protandrous tetraploid <italic>C. paliurus</italic>; Chr, chromosome; PG-dip, the protogynous diploid <italic>C. paliurus</italic>; PA-dip, the protandrous diploid <italic>C. paliurus</italic>.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Phylogenetic and comparative analys</bold><bold>e</bold><bold>s of <italic>C. paliurus</italic></bold></p><p><bold>A.</bold> Phylogenetic relationship of <italic>C</italic>. <italic>paliurus</italic>, <italic>C</italic>. <italic>illinoinensis</italic>, <italic>J</italic>. <italic>nigra</italic>, <italic>P</italic>. <italic>stenoptera</italic>, <italic>A</italic>. <italic>thaliana</italic>, <italic>Z</italic>. <italic>jujuba</italic>, <italic>V</italic>. <italic>vinifera</italic>, <italic>P</italic>. <italic>trichocarpa</italic>, and <italic>O</italic>. <italic>sativa</italic>. The divergence time among different plant species is labeled at the bottom. <bold>B.</bold> Venn diagram of orthologous and species-specific gene families in different plant genomes. <bold>C.</bold> Evolutionary analysis of the diploid and tetraploid <italic>C</italic>. <italic>paliurus</italic> genomes with the distribution of <italic>Ks</italic> values of orthologs<italic>.</italic><bold>D.</bold> Synteny analysis between PA-tetra and PA-dip genomes. “monoploid” indicates a reference genome assembly with only one representative haplotype retained, whereas “haplotype” indicates fully phased genome with all the four haplotypes. <italic>C. illinoinensis</italic>, <italic>Carya illinoinensis</italic>; <italic>J. nigra</italic>, <italic>Juglans nigra</italic>; <italic>P. stenoptera</italic>, <italic>Pterocarya stenoptera</italic>; <italic>A. thaliana</italic>, <italic>Arabidopsis thaliana</italic>; <italic>Z. jujuba</italic>, <italic>Ziziphus jujuba</italic>; <italic>P. trichocarpa</italic>, <italic>Populus trichocarpa</italic>; <italic>O. sativa</italic>, <italic>Oryza sativa</italic>; <italic>Ks</italic>, synonymous substitution rate; MYA, million years ago.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Dosage</bold><bold>effect contributes to increased growth adaptability and accumulation of terpenoids</bold></p><p><bold>A.</bold> Scanning electron microscopy of stomata in diploid and tetraploid <italic>C</italic>. <italic>paliurus</italic> leaves. <bold>B.</bold> Comparison of chlorophyll content between diploid and tetraploid <italic>C</italic>. <italic>paliurus</italic> individuals. Statistical significance (<italic>n</italic> = 5) was determined using two-sided Student’s <italic>t</italic>-test. Error bars indicate mean ± SD of indicated replicates. **, <italic>P</italic> &lt; 0.01. <bold>C.</bold> Comparison of Pn between diploid and tetraploid <italic>C</italic>. <italic>paliurus</italic> individuals. ***, <italic>P</italic> &lt; 0.001. <bold>D.</bold> Heatmap showing the accumulation patterns of triterpenoids among the four samples. Sept_diploid indicates diploid samples collected in September; Sept_tetraploid indicates tetraploid samples collected in September; May_diploid indicates diploid samples collected in May; and May_tetraploid indicates tetraploid samples collected in May. <bold>E.</bold> Expression profiles of genes associated with cyclocaric acid B synthesis in <italic>C</italic>. <italic>paliurus</italic> tender and mature leaves for different ploidies. The scale ranging from blue (low) to red (high) indicates the expression magnitude of the FPKM values. The genes of CYP72A subfamily are shown in blue. The functions of the CYP716A14v2 and CYP716C subfamilies were identified by Miettinen and colleagues ##REF##28165039##[11]## and Moses and colleagues ##REF##25576188##[32]##, ##REF##28165039##[11]##. SL, stomatal length; SA, stomatal aperture; SW, stomatal width; mag, magnification; WD, working distance; HV, high voltage; AM, ante meridiem; PM, post meridiem; SD, standard deviation; Pn, net photosynthetic rate; FPP, farnesyl pyrophosphate; SQS, squalene synthase; SQE, squalene epoxidase; bAS, β-amyrin synthesis; FPKM, fragments per kilobase per million.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Phylogenetic splits among <italic>C</italic>. <italic>paliurus</italic> populations</bold></p><p><bold>A.</bold> Dispersion of 45 individuals sampled from 9 sites (a–i) across most of the geographic range of <italic>C</italic>. <italic>paliurus</italic>. Populations are plotted with dots color-coded based on dispersion by latitude and longitude. Yellow stars represent the co-presence of diploid and auto-tetraploid distributions, blue stars represent only auto-tetraploid distribution, and purple star represents the outgroup (<italic>Juglans regia</italic>). More details are shown in <xref rid=\"s0150\" ref-type=\"sec\">Table S14</xref>. The world map was constructed from <ext-link ext-link-type=\"uri\" xlink:href=\"http://bzdt.ch.mnr.gov.cn/index.html\" id=\"PC_linkZ3yIRRA6RW\">http://bzdt.ch.mnr.gov.cn/index.html</ext-link>. <bold>B.</bold> A phylogeny for <italic>C</italic>. <italic>paliurus</italic> individuals estimated from SNPs in neutrally evolving sites. <bold>C.</bold> PCA showing clear separation between diploid and auto-tetraploid populations. <bold>D.</bold> Top: CV plot displaying CV error <italic>vs.</italic> <italic>K</italic>. <italic>K</italic> = 2 is the best fit. Bottom: ADMIXTURE plot for <italic>C</italic>. <italic>paliurus</italic> showing the distribution of genetic clusters (<italic>K</italic> = 2, 3, and 4). <italic>K</italic> = 2 (representing the divergence within diploid and auto-tetraploid clades) indicates the smallest CV error. SNP, single nucleotide polymorphism; PCA, principal component analysis; CV, cross-validation.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"t0005\"><label>Table 1</label><caption><p><bold>Summary on genome assembly and annotation of <italic>C</italic></bold><bold><italic>.</italic></bold><bold><italic>paliurus</italic></bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th colspan=\"2\" align=\"left\"><bold>Sequencing</bold></th><th><bold>PA-dip</bold></th><th><bold>PG-dip</bold></th><th><bold>PA-tetra</bold></th></tr></thead><tbody><tr><td rowspan=\"3\">Illumina paired-end sequencing</td><td>Raw data (Gb)</td><td>106.7</td><td>86</td><td>291.7</td></tr><tr><td>Coverage (×)</td><td>176</td><td>131</td><td>237</td></tr><tr><td>Sequencing depth (×)</td><td>178</td><td>143</td><td>243</td></tr><tr><td rowspan=\"3\">PacBio Sequel II sequencing</td><td>Raw data (Gb)</td><td>134.9</td><td>75.5</td><td>271.8</td></tr><tr><td>Coverage (×)</td><td>223</td><td>115</td><td>221</td></tr><tr><td>Sequencing depth (<bold>×</bold>)</td><td>225</td><td>125</td><td>226</td></tr><tr><td rowspan=\"3\">Hi-C sequencing</td><td>Raw data (Gb)</td><td>65.4</td><td>68</td><td>264</td></tr><tr><td>Coverage (×)</td><td>108</td><td>103</td><td>215</td></tr><tr><td>Sequencing depth (<bold>×</bold>)</td><td>109</td><td>113</td><td>220</td></tr><tr><td rowspan=\"2\">Contig-level assembly and annotation</td><td>Total length of contigs (Mb)</td><td>586.62</td><td>583.45</td><td>2380.95</td></tr><tr><td>Contig N50 (bp)</td><td>1,928,354</td><td>1,389,753</td><td>430,910</td></tr><tr><td>Monoploid/haplotype-resolved chromosome-level genome assembly</td><td>Total length of chromosome-level assembly (Mb)</td><td>543.53</td><td>553.87</td><td>2168.65</td></tr><tr><td colspan=\"2\">BUSCO completeness of assembly (%)</td><td>95.2</td><td>96.4</td><td>95.5</td></tr><tr><td colspan=\"2\">Total number of protein-coding genes anchored on the chromosomes</td><td>34,699</td><td>35,221</td><td>34,633</td></tr><tr><td colspan=\"2\">BUSCO completeness of annotation (%)</td><td>96.2</td><td>96.2</td><td>94.4</td></tr><tr><td colspan=\"2\">Number of genes with 4 alleles</td><td>−</td><td>−</td><td>9362</td></tr><tr><td colspan=\"2\">Number of genes with 3 alleles</td><td>−</td><td>−</td><td>10,262</td></tr><tr><td colspan=\"2\">Number of genes with 2 alleles</td><td>−</td><td>−</td><td>7509</td></tr><tr><td colspan=\"2\">Number of genes with 1 alleles</td><td>−</td><td>−</td><td>7500</td></tr><tr><td colspan=\"2\">Number of unanchored genes/alleles</td><td>−</td><td>−</td><td>588</td></tr></tbody></table></table-wrap>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0305\"><caption><title>Supplementary File 1</title><p><bold>Supplementary information and methods</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0300\"><caption><title>Supplementary Figure S1</title><p><bold>Chromosome karyotypes of <italic>C. paliurus</italic> A.</bold> PA-dip. <bold>B.</bold> PG-dip. <bold>C.</bold> PA-tetra.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0295\"><caption><title>Supplementary Figure S2</title><p><bold>The phenomena of homologous chromosome</bold><bold>synapsis at the early stage of meiosis Ⅰ in PA-tetra <italic>C. paliurus</italic></bold> A total of 11 pollen mother cells were selected to observe and the red rounds represent the quadrivalent.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0290\"><caption><title>Supplementary Figure S3</title><p><bold>Using flow cytometry to estimate genome size of <italic>C</italic>. <italic>paliurus</italic> A.</bold> PG-dip. <bold>B.</bold> PA-dip. <bold>C.</bold> PA-tetra. The <italic>P</italic>. <italic>stenoptera</italic> genome (2n = 2× = ∼ 600 Mb) and PA-tetra <italic>C</italic>. <italic>paliurus</italic> were used as an internal reference standard.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0285\"><caption><title>Supplementary Figure S4</title><p><bold><italic>K-mer</italic> (21-mer) distribution and estimation of genome size and heterozygosity of <italic>C. paliurus</italic> A.</bold> PG-dip. <bold>B.</bold> PA-dip. <bold>C.</bold> PA-tetra. <bold>D.</bold> Total coverage of the k-mer pair (A + B) in PA-tetra <italic>C. paliurus</italic>.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0280\"><caption><title>Supplementary Figure S5</title><p><bold>Functional enrichment analysis of selected genes involved in haplotypic variations in PA-tetra genome A.</bold> GO. <bold>B.</bold> KEGG. GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0275\"><caption><title>Supplementary Figure S6</title><p><bold>Genome-wide analysis of chromatin interactions at 150-kb resolution in PA-dip genome</bold> The colored bar on the right represents the strength of interaction.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0270\"><caption><title>Supplementary Figure S7</title><p><bold>Genome-wide analysis of chromatin interactions at 150-kb resolution in PG-dip genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0265\"><caption><title>Supplementary Figure S8</title><p><bold>Genome-wide analysis of chromatin interactions at 150-kb resolution in PA-tetra genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0260\"><caption><title>Supplementary Figure S9</title><p><bold>Synteny analysis between PA-dip and PG-dip genomes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0255\"><caption><title>Supplementary Figure S10</title><p><bold>Functional enrichment analysis of selected genes involved in WGD1 and WGD2 events A.</bold> GO enrichment analysis of selected genes involved in WGD1 event. <bold>B.</bold> KEGG enrichment analysis of selected genes involved in WGD1 event. <bold>C.</bold> GO enrichment analysis of selected genes involved in WGD2 event. <bold>D.</bold> KEGG enrichment analysis of selected genes involved in WGD2 event.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0250\"><caption><title>Supplementary Figure S11</title><p><bold>Synteny analysis between PA-dip and</bold><italic><bold>V. vinifera</bold></italic> <bold>genomes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0245\"><caption><title>Supplementary Figure S12</title><p><bold>Synteny analysis between PA-tetra and</bold><italic><bold>V. vinifera</bold></italic> <bold>genomes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0240\"><caption><title>Supplementary Figure S13</title><p><bold>Comparison of timing of LTR-RT insertions among PA-tetra, PA-dip, and PG-dip genomes</bold> LTR-RT, long terminal repeat retrotransposon.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0235\"><caption><title>Supplementary Figure S14</title><p><bold>Clustering of counts of</bold><italic><bold>K-mers</bold></italic> <bold>(</bold><italic><bold>K</bold></italic> <bold>= 13) enables the consistent partitioning of four haplotypes in each homologous chromosome into same group</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0230\"><caption><title>Supplementary Figure S15</title><p><bold>GO enrichment analysis of genes experienced expansion in</bold><italic><bold>C. paliurus</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0225\"><caption><title>Supplementary Figure S16</title><p><bold>KEGG pathway analysis of genes experienced expansion in</bold><italic><bold>C. paliurus</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0220\"><caption><title>Supplementary Figure S17</title><p><bold>The P450 clusters of expanded genes are arranged on Chr1, Chr4, and Chr12</bold> P450, cytochrome P450 monooxygenase.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0215\"><caption><title>Supplementary Figure S18</title><p><bold>Phylogenic analysis of P450 families</bold> The yellow and blue branches indicate the sequences from <italic>Arabidopsis</italic> and <italic>C. paliurus</italic>, respectively. The dots represent P450 genes. The outermost arc indicates the P450 gene family.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0210\"><caption><title>Supplementary Figure S19</title><p><bold>Identification and functional enrichment of DEGs between PG and PA <italic>C. paliurus</italic> at five flowering time stages (S0–S4) A</bold>. Venn diagrams of DEGs in the female floral buds (PG-F vs. PA-F). <bold>B.</bold> Venn diagrams of DEGs in the male floral buds (PA-M vs. PG-M). <bold>C.</bold> GO enrichment of the 958 DEGs in female floral buds (PG-F vs. PA-F). <bold>D.</bold> GO enrichment of the 2373 DEGs in male floral buds (PA-M vs. PG-M). In all subsequent figures, PG-F means female floral buds of PG, PA-F means female floral buds of PA, PG-M means male floral buds of PG, and PA-M means male floral buds of PA. FC, fold change; DEGs, differentially expressed genes; PG, protogyny; PA, protandry.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0205\"><caption><title>Supplementary Figure S20</title><p>.<bold>KEGG enrichment of the 958 DEGs in female floral buds (PG-F <italic>vs.</italic> PA-F) at five flowering time stages (S0–S4)</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0200\"><caption><title>Supplementary Figure S21</title><p><bold>KEGG enrichment of the 2373 DEGs in male floral buds (PA-M <italic>vs.</italic> PG-M) at five flowering time stages (S0–S4)</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0195\"><caption><title>Supplementary Figure S22</title><p><bold>Hormone contents of <italic>C. paliurus</italic> during five flower differentiation and development stages A.</bold> Identification of GA3 level in female and male floral buds from PG or PA type. <bold>B.</bold> Identification of ABA level in female and male floral buds from PG or PA type. <bold>C.</bold> Identification of IAA level in female and male floral buds from PG or PA type. FW, fresh weight; GA3, gibberellin; ABA, abscisic acid; IAA, auxin.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0190\"><caption><title>Supplementary Figure S23</title><p><bold>Hierarchical clustering tree (dendrogram) of genes based on co-expression network analysis in PG and PA individuals (female flora buds, male flora buds, female leaves, and male leaves) during five development stages</bold> Each individual’s value is the average of the expression of three replicate samples. PG-L means leaves of PG and PA-L means leaves of PA.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0185\"><caption><title>Supplementary Figure S24</title><p><bold>Co-expression modules identified by weighted gene co-expression network analysis (WGCNA)</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0180\"><caption><title>Supplementary Figure S25</title><p><bold>Functions and networks of co-expression module genes A.</bold> Module–trait relationships. The column indicate GA<sub>3</sub>, and the rows indicate the different modules. The red and blue colors indicate positive and negative correlations, respectively. The correlation coefficient (<italic>r</italic>) and <italic>P</italic> value (<italic>P</italic>) are displayed in each cell. <bold>B.</bold> Eigengene expression profiles in the darkorange module. <bold>C.</bold> Eigengene expression profiles in the pink module. <bold>D.</bold> Eigengene expression profiles in the red module. <bold>E.</bold> Construction of the correlation network of the pink module. <bold>F.</bold> Construction of the correlation network of the red module. The large circles represent transcription factors. The color is determined by the edge number of the gene.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0175\"><caption><title>Supplementary Figure S26</title><p><bold>Expression profiles of three modules and GA3 contents during five stages</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0170\"><caption><title>Supplementary Figure S27</title><p><bold>GO enrichment of three modules (darkorange, red, and pink) genes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0165\"><caption><title>Supplementary Figure S28</title><p><bold>KEGG enrichment of the three modules (darkorange, red, and pink) genes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0160\"><caption><title>Supplementary Figure S29</title><p><bold>The morphological difference between diploid and tetraploid <italic>C. paliurus</italic> A.</bold> Compound leaf. <bold>B.</bold> Singe leaf. <bold>C.</bold> Seedlings.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0155\"><caption><title>Supplementary Figure S30</title><p><bold>The comparison of leaf thickness and stomatal density between diploid and tetraploid <italic>C. paliurus</italic> based on scanning electron microscopy A.</bold> Leaf thickness of diploid sample. <bold>B.</bold> Leaf thickness of tetraploid sample. <bold>C.</bold> Stomatal density of diploid sample. <bold>D.</bold> Stomatal density of tetraploid sample. U-ep, upper epidermal cells; L-ep, lower epidermal cells; Pal, palisade mesophyll; Sp, sponge tissue.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0150\"><caption><title>Supplementary Figure S31</title><p><bold>Quantification of anatomical structure values in different ploidy <italic>C. paliurus</italic> A.</bold> Thickness of leaf tissues. <bold>B.</bold> Stomatal size of leaf. <bold>C.</bold> Stomatal density. **, <italic>P</italic> value &lt; 0.01.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0145\"><caption><title>Supplementary Figure S32</title><p><bold>Heatmap showing the expression patterns of 691 dosage-effect genes among tetraploid and diploid samples</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0140\"><caption><title>Supplementary Figure S33</title><p><bold>KEGG pathway enrichment analysis of up-regulated genes in tetraploid samples</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0135\"><caption><title>Supplementary Figure S34</title><p><bold>Heatmap showing the expression patterns of photosynthesis</bold>-<bold>related genes</bold> CA, carbonic anhydrase; PPCK, phosphoenolpyruvate carboxylase kinase; Rubisco, ribulose-1,5-bisphosphate carboxylase/oxygenase; FBP, fructose-1,6-bisphosphatase; SBPASE, sedoheptulose-1,7-bisphosphatase.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0130\"><caption><title>Supplementary Figure S35</title><p><bold>Functional enrichment analysis of dosage compensation effect genes in</bold><italic><bold>C. paliurus</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0125\"><caption><title>Supplementary Figure S36</title><p><bold>Heatmap showing the expression patterns of P450 family genes of dosage</bold><bold>effect genes across four samples</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0120\"><caption><title>Supplementary Figure S37</title><p><bold>Phylogenetic tree of P450 gene family in multiple species, including <italic>C. paliurus</italic>, <italic>Centella asiatica</italic>, <italic>Avicennia marina</italic>, <italic>Lagerstroemia speciosa, Moreua rubra</italic>, <italic>J. regia</italic>, <italic>Prunus duscis, A. thaliana</italic>, <italic>Kalopanax truncatula</italic>, <italic>Barbarea vulgaris</italic>, <italic>Chenopodium quinoa</italic>, <italic>Lotus japonicus</italic>, <italic>Quercus suber</italic>, <italic>Kalopanax septemlobus</italic>, <italic>and Quercus lobata</italic></bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0115\"><caption><title>Supplementary Figure S38</title><p><bold>Distribution of selective sweep regions in <italic>C. paliurus</italic> genome A.</bold> Diploid. <bold>B.</bold> Tetraploid. CLR, composite likelihood ratio.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0110\"><caption><title>Supplementary Figure S39</title><p><bold>GO enrichment analysis of genes under strong selective sweep in diploid</bold><italic><bold>C. paliuru</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0105\"><caption><title>Supplementary Figure S40</title><p><bold>KEGG pathway analysis of genes under strong selective sweep in diploid <italic>C. paliurus</italic></bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0100\"><caption><title>Supplementary Figure S41</title><p><bold>GO enrichment analysis of genes under strong selective sweep in tetraploid</bold><italic><bold>C. paliurus</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0095\"><caption><title>Supplementary Figure S42</title><p><bold>KEGG pathway analysis of genes under strong selective sweep in tetraploid</bold><italic><bold>C. paliurus</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0090\"><caption><title>Supplementary Figure S43</title><p><bold>Venn diagrams of selective genes in diploid and tetraploid</bold><italic><bold>C. paliurus</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0085\"><caption><title>Supplementary Figure S44</title><p><bold>GO and KEGG enrichment of selective genes specific to tetraploid</bold><italic><bold>C. paliurus</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0080\"><caption><title>Supplementary Figure S45</title><p><bold>Demographic history of <italic>C. paliurus</italic></bold> Historical effective population size for <italic>C. paliurus</italic> beginning from 8 million years ago to present. Stairway plot showing that the <italic>C. paliurus</italic> population has undergone bottlenecks during two known periods of major climate upheaval: the Pleistocene (purple) and the Pliocene (blue). Ne, effective population size.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0075\"><caption><title>Supplementary Figure S46</title><p><bold>The comparison of pollen viability between diploid and tetraploid</bold><italic><bold>C. paliurus</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0070\"><caption><title>Supplementary Table S1</title><p><bold>Sequencing information for the assemblies</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0065\"><caption><title>Supplementary Table S2</title><p><bold>Contig-level assemblies</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Table S3</title><p><bold>Statistics of Hi-C mapping</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Table S4</title><p><bold>Chromosome-level genome assemblies</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Table S5</title><p><bold>Characteristics of genetic variation compared with monoploid genome in PA-tetra</bold><italic><bold>C. paliurus</bold></italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S6</title><p><bold>BUSCO assessment of genome assemblies</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S7</title><p><bold>Statistics of Illumina short reads remapped to the assemblies</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S8</title><p><bold>Allele annotation in auto-tetraploid</bold><italic><bold>C. paliurus</bold></italic> <bold>genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S9</title><p><bold>Genes number of the three</bold><italic><bold>C. paliurus</bold></italic> <bold>genomes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S10</title><p><bold>BUSCO analysis of annotation completeness</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S11</title><p><bold>Repeat annotation of the three</bold><italic><bold>C. paliurus</bold></italic> <bold>genomes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S12</title><p><bold>The expanded P450s families in the</bold><italic><bold>C. paliurus</bold></italic> <bold>genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S13</title><p><bold>Comparison of growth indices between diploid and tetraploid</bold><italic><bold>C. paliurus</bold></italic> <bold>seedling, one year after stumping</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S14</title><p><italic><bold>C. paliurus</bold></italic> <bold>and outgroup (</bold><italic><bold>Juglans regia</bold></italic><bold>) species used for the population genomics analysis</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m9905\"><caption><title>Supplementary Table S15</title><p>Summary of genetic variations in <italic>C. paliurus</italic> populations</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p><italic>Note</italic>: Monoploid genome assembly and annotation were performed for PA-dip and PG-dip; haplotype-resolved chromosome-level genome assembly and annotation were performed fo PA-tetra. Only one allele was retained if the allelic genes had the exact same coding sequences. PA-tetra, the protandrous tetraploid <italic>C</italic>. <italic>paliurus</italic>; PG-dip, the protogynous diploid <italic>C</italic>. <italic>paliurus</italic>; PA-dip, the protandrous diploid <italic>C</italic>. <italic>paliurus</italic>; Hi-C, high-throughput chromatin conformation capture; BUSCO, Benchmarking Universal Single-Copy Orthologs.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"d35e508\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0145\" fn-type=\"supplementary-material\"><p id=\"p0240\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2023.02.001\" id=\"ir030\">https://doi.org/10.1016/j.gpb.2023.02.001</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["5"], "surname": ["Qin", "Yue", "Fang", "Qian", "Zhou", "Shang"], "given-names": ["J.", "X.", "S.", "M.", "S.", "X."], "article-title": ["Responses of nitrogen metabolism, photosynthetic parameter and growth to nitrogen fertilization in "], "italic": ["Cyclocarya paliurus"], "source": ["Forest Ecol Manag"], "volume": ["502"], "year": ["2021"], "object-id": ["119715"]}, {"label": ["6"], "surname": ["Mao", "Fu", "Huang", "Chen", "Qu"], "given-names": ["X.", "X.X.", "P.", "X.L.", "Y.Q."], "article-title": ["Heterodichogamy, pollen viability, and seed set in a population of polyploidy "], "italic": ["Cyclocarya paliurus"], "source": ["Forests"], "volume": ["10"], "year": ["2019"], "fpage": ["347"]}, {"label": ["7"], "surname": ["Zhou", "Quek", "Shang", "Fang"], "given-names": ["M.", "S.Y.", "X.", "S."], "article-title": ["Geographical variations of triterpenoid contents in "], "italic": ["Cyclocarya paliurus"], "source": ["Ind Crop Prod"], "volume": ["162"], "year": ["2021"], "object-id": ["113314"]}, {"label": ["14"], "surname": ["Fu", "Feng", "Shang", "Yang", "Fang"], "given-names": ["X.", "L.", "X.", "W.", "S."], "article-title": ["Observation of morphological and anatomical characters on staminate and pistillate flower differentiation in "], "italic": ["Cyclocarya paliurus"], "source": ["J Nanjing Forest Univ Sci Ed"], "volume": ["35"], "year": ["2011"], "fpage": ["17"], "lpage": ["22"]}, {"label": ["15"], "surname": ["Endress"], "given-names": ["P.K."], "article-title": ["Structural and temporal modes of heterodichogamy and similar patterns across angiosperms"], "source": ["Bot J Linn Soc"], "volume": ["193"], "year": ["2020"], "fpage": ["5"], "lpage": ["18"]}, {"label": ["18"], "surname": ["Zheng", "Xiao", "Su", "Chen", "Chen", "Chen"], "given-names": ["X.H.", "H.B.", "J.Q.", "D.", "J.N.", "B.H."], "article-title": ["Insights into the evolution and hypoglycemic metabolite biosynthesis of autotetraploid "], "italic": ["Cyclocarya paliurus"], "source": ["Ind Crop Prod"], "volume": ["173"], "year": ["2021"], "object-id": ["114154"]}, {"label": ["22"], "surname": ["Sun"], "given-names": ["T."], "part-title": ["The response of land plants to environmental change"], "year": ["2005"], "publisher-name": ["A postdoctoral final report. Institute of Botany"], "publisher-loc": ["Chinese Academy of Sciences"]}, {"label": ["42"], "surname": ["Zheng", "Powell", "An", "Zhou", "Dong"], "given-names": ["H.", "C.M.", "Z.", "J.", "G."], "article-title": ["Pliocene uplift of the northern Tibetan Plateau"], "source": ["Geology"], "volume": ["28"], "year": ["2000"], "fpage": ["715"], "lpage": ["718"]}, {"label": ["43"], "surname": ["Paillard"], "given-names": ["D."], "article-title": ["The timing of Pleistocene glaciations from a simple multiple-state climate model"], "source": ["Nature"], "volume": ["391"], "year": ["1998"], "fpage": ["378"], "lpage": ["381"]}, {"label": ["47"], "surname": ["Bai", "Zeng", "Zhang"], "given-names": ["W.N.", "Y.F.", "D.Y."], "article-title": ["Mating patterns and pollen dispersal in a heterodichogamous tree, "], "italic": ["Juglans mandshurica"], "source": ["New Phytol"], "volume": ["176"], "year": ["2010"], "fpage": ["699"], "lpage": ["707"]}, {"label": ["55"], "surname": ["Xu", "Wang"], "given-names": ["Z.", "H."], "article-title": ["LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons"], "source": ["Nucleic Acids Res"], "volume": ["35"], "year": ["2007"], "fpage": ["265"], "lpage": ["268"]}, {"label": ["78"], "surname": ["Prakash", "Jeffryes", "Bateman", "Finn"], "given-names": ["A.", "M.", "A.", "R.D."], "article-title": ["The HMMER web server for protein sequence similarity search"], "source": ["Curr Protoc Bioinformatics"], "volume": ["60:3.15.1\u201323"], "year": ["2017"]}, {"label": ["86"], "surname": ["Pavlidis", "\u017divkovi\u0107", "Stamatakis", "Alachiotis"], "given-names": ["P.", "D.", "A.", "N."], "article-title": ["SweeD: likelihood-based detection of selective sweeps in thousands of genomes"], "source": ["Mol Biol Evol"], "volume": ["3"], "year": ["2013"], "fpage": ["2224"], "lpage": ["2234"]}]
{ "acronym": [], "definition": [] }
88
CC BY
no
2024-01-14 23:41:55
Genomics Proteomics Bioinformatics. 2023 Jun 11; 21(3):455-469
oa_package/8d/97/PMC10787019.tar.gz
PMC10787021
36470576
[ "<title>Introduction</title>", "<p id=\"p0005\">The transition of jawless to jawed vertebrates lays a foundation for the evolution of vertebrates, which was accompanied by many morphological and phenotypic innovations, especially jaws and the adaptive immune system ##REF##24402279##[1]##. As ancient jawed vertebrates, the fish constitutes a highly diverse and evolutionarily successful class found in both marine and freshwater habitats ##REF##30598796##[2]##. The jawed fishes belong to two clades, the cartilaginous fishes (Chondrichthyes) and bony vertebrates (Osteichthyes), which diverged about 450 million years ago (MYA) ##REF##20551041##[3]##. Cartilaginous fishes are the most basal group of living fishes, which contain about 1000 living species ##UREF##0##[4]##. Except for a few published genome information of Chondrichthyes ##REF##33545088##[5]##, ##UREF##1##[6]##, ##REF##33911273##[7]##, too few genetic data in this important taxonomic position are available for scientists to further study the evolution of chordates and the origin of hard bone formation.</p>", "<p id=\"p0010\">The white-blotched river stingray (<italic>Potamotrygon leopoldi</italic>), also known as Xingu River ray, is a freshwater cartilaginous fish native to the Xingu River basin in Brazil ##REF##29660124##[8]##. The Xingu River is a geographical part of the Amazon River basin, which was inundated by sea during the Pleistocene Epoch. The ancestor of this stingray experienced the transition from marine to freshwater environment. <italic>P</italic>. <italic>leopoldi</italic> belongs to the family Potamotrygonidae in the order Myliobatiformes composed of a group of cartilaginous fishes most-closely related to sharks ##UREF##2##[9]##. The species under the family Potamotrygonidae all live in the tropical and subtropical regions of South America ##UREF##2##[9]##. Unlike the freshwater stingrays in Africa, Asia, and Australia, which belong to the family Dasyatidae, most Potamotrygonidae species live strictly in freshwater, whereas most Dasyatidae species are saltwater dwellers ##UREF##3##[10]##, ##REF##27470808##[11]##. Except a few widespread members, most river stingrays typically reside in and are confined to a single river basin ##UREF##3##[10]##. For its unique appearance (<italic>e.g.</italic>, white spots on black skin) and distinct behavior (<italic>e.g.</italic>, swimming-maneuvering capabilities), <italic>P</italic>. <italic>leopoldi</italic> becomes a pricy pet fish popular in home- and office-based aquaria. Till now, no fish species from the family Potamotrygonidae has been extensively studied at the genome level. Whole-genome data of a Potamotrygonidae member and its comparative analysis with other available fish genomes might help us further reveal the evolutionary features unique to Potamotrygonidae and provide insights into the ancestral state of gnathostome-specific morphological characters and physiological systems. Therefore, <italic>P. leopoldi</italic> provides an excellent model for studying evolution and niche adaptation of freshwater cartilaginous fishes.</p>", "<p id=\"p0015\">In this study, we assembled a 4.11-Gb genome of a male stingray, <italic>P</italic>. <italic>leopoldi</italic>, using the whole-genome shotgun (WGS) approach and based on a raw data collection with a total of 370.97× genome coverage, generated from Pacific Biosciences (PacBio) single molecule real time sequencing (SMRT), Illumina HiSeq2000, and 10X Genomics sequencing platforms. We subsequently compared its genome to other five representative fish genomes (<italic>Cyprinus carpio</italic>, <italic>Lepisosteus oculatus</italic>, <italic>Latimeria chalumnae</italic>, <italic>Danio rerio</italic>, and <italic>Callorhinchus milii</italic>) and one chordate genome (<italic>Branchiostoma floridae</italic>), to capture its unique evolutionary features and molecular basis. Our results indicate that <italic>P</italic>. <italic>leopoldi</italic> is one of the slowest-evolving fish species, even within the cartilaginous fish lineage. The transcriptomic data, obtained from six tissues of <italic>P</italic>. <italic>leopoldi</italic>, shed further lights into highly diversified gene expression profiles among fish lineages, as opposed to the highly coordinated gene expression among mammalian tissues. The knockdown experiment in the fish model reveals the possible genetic foundation for the divergence of hard and cartilaginous skeleton formations. Together, our results start from the <italic>P</italic>. <italic>leopoldi</italic> genome sequencing to the experimental model, providing novel clues for niche adaptation and skeleton formation in the evolutionary history of fish.</p>" ]
[ "<title>Materials and methods</title>", "<title><italic>P</italic>. <italic>leopoldi</italic> sample</title>", "<p id=\"p0100\">A mature male <italic>P</italic>. <italic>leopoldi</italic> individual was acquired from an aquarium in China in January, 2018. It was the descendant of captive <italic>P</italic>. <italic>leopoldi</italic> breeding population. The fish was killed in a humane way, and the experimental procedure was performed in accordance with the guidelines of the Animal Care Committee at the Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. Its skin, heart, blood, muscle, liver, and brain were used for DNA and RNA preparation and sequencing library construction.</p>", "<title>Genome sequencing and assembly</title>", "<p id=\"p0105\">The genomic DNA of <italic>P</italic>. <italic>leopoldi</italic> was sequenced by WGS strategy. Based on the genome features, three different lengths (230 bp, 350 bp, and 450 bp) of DNA inserts were produced. The Illumina HiSeq2000 platform (San Diageo, CA) was used to sequence these reads by the paired-end sequencing method with the read length of 150 bp in order to capture the whole-genome data. A total of 17 DNA libraries were constructed, and the total amount of sequencing data was 882.2 Gb with a coverage of 200.95×. The PacBio SMRT platform yielding an average read length of 20 kb (Menlo Park, CA) was also used to generate 270.51-Gb data, equivalent to a genome coverage of 61.61×. Additionally, a 10X Genomics library was constructed, coupled with the Illumina sequencing platform in a read length of 150 bp, yielding 475.93-Gb data, equivalent to a genome coverage of 108.41×. PacBio long reads were utilized to perform <italic>de novo</italic> assembly. Around 31 million subreads were used for the assembly with FALCON (v0.3.0) to generate contigs ##REF##27749838##[37]##. Primary contigs were polished using Quiver5. The scaffolds were built based on 10X Genomics data. Sequence data were generated using the 10X Genomics GemCode platform (Pleasanton, CA), and the error-corrected contigs were used as input for scaffolding to obtain the primary assembly. After scaffolding, shotgun sequences were used to close gaps between contigs. Paired-end clean reads from the Illumina platform were aligned to the assembly with BWA ##REF##19451168##[38]##. Contigs or scaffolds shorter than 10 kb were excluded from the analysis to avoid spurious misassembly. Gaps in contigs and scaffolds were closed with subreads. To survey the characteristics of the genome, a total of ∼ 140-Gb next-generation sequencing data equivalent to a genome coverage of 33× were generated. Adaptor sequences, polymerase chain reaction (PCR) duplicates, and low-quality sequences were removed from the raw data to generate high-quality sequences. <italic>K</italic>-mer statistics of the high-quality sequences were calculated by Jellyfish (v2.2.7) with the parameters of “-G 2 -m 17” ##REF##21217122##[39]##. GenomeScope 2.0 (<ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/tbenavi1/genomescope2.0\" id=\"ir005\">https://github.com/tbenavi1/genomescope2.0</ext-link>) ##REF##32188846##[40]## was used to estimate the size, heterozygosity rate, and repeat content of the <italic>P</italic>. <italic>leopoldi</italic> genome. Finally, the completeness of the assembly was assessed through BUSCO analysis (v5.2.1; <ext-link ext-link-type=\"uri\" xlink:href=\"https://busco.ezlab.org/\" id=\"ir010\">https://busco.ezlab.org/</ext-link>) and CEG analysis (<ext-link ext-link-type=\"uri\" xlink:href=\"https://korflab.ucdavis.edu/Datasets/cegma/\" id=\"ir015\">https://korflab.ucdavis.edu/Datasets/cegma/</ext-link>).</p>", "<title>Genome annotation</title>", "<p id=\"p0110\">Repeat elements were annotated with both homology annotation and <italic>de novo</italic> prediction. RepeatMasker and RepeatProteinMask (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.repeatmasker.org/RepeatProteinMask.html\" id=\"ir020\">https://www.repeatmasker.org/RepeatProteinMask.html</ext-link>) were used to search the assembled genome against Repbase for known repeat elements ##UREF##5##[41]##, ##REF##26045719##[42]##. LTR-FINDER and RepeatModeler (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.repeatmasker.org/RepeatModeler.html\" id=\"ir025\">https://www.repeatmasker.org/RepeatModeler.html</ext-link>) were used to <italic>de novo</italic> develop repeat element library ##REF##17485477##[43]##. After the library was established, RepeatMasker was further used to detect species-specific repeat elements. Tandem repeats were also searched with Tandem Repeats Finder in the assembled <italic>P</italic>. <italic>leopoldi</italic> genome ##REF##9862982##[44]##. Overlapping transposable elements belonging to the same type of repeats were integrated together.</p>", "<p id=\"p0115\">Protein-coding genes were predicted through combination of <italic>de novo</italic> annotation, homology annotation, and transcriptome-based annotation. AUGUSTUS, GlimmerHMM, SNAP (<ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/KorfLab/SNAP\" id=\"ir030\">https://github.com/KorfLab/SNAP</ext-link>), Geneid, and GENSCAN (<ext-link ext-link-type=\"uri\" xlink:href=\"https://hollywood.mit.edu/GENSCAN.html\" id=\"ir035\">https://hollywood.mit.edu/GENSCAN.html</ext-link>) software packages were used to <italic>de novo</italic> predict protein-coding genes in the <italic>P. leopoldi</italic> genome ##REF##16845043##[45]##, ##REF##15145805##[46]##, ##REF##30332532##[47]##. For homology annotation, the protein sequences from Japanese puffer (<italic>Takifugu rubripes</italic>), rice fish (<italic>Oryzias latipes</italic>), Nile tilapia (<italic>Oreochromis niloticus</italic>), Atlantic cod (<italic>Gadus morhua</italic>), elephant shark (<italic>C</italic>. <italic>milii</italic>), green spotted puffer (<italic>Tetraodon nigroviridis</italic>), zebrafish (<italic>D</italic>. <italic>rerio</italic>), amphioxus (<italic>B</italic>. <italic>floridae</italic>), three-spined stickleback (<italic>Gasterosteus aculeatus</italic>), and coelacanth (<italic>L</italic>. <italic>chalumnae</italic>) were used to search the homologous genes in <italic>P</italic>. <italic>leopoldi</italic> genome with BLAST and GeneWise ##REF##2231712##[48]##, ##REF##15123596##[49]##. For transcriptome-based annotation, the RNA-seq reads from <italic>P</italic>. <italic>leopoldi</italic> skin, heart, blood, muscle, liver, and brain were mapped and assembled with PASA and Cufflinks ##REF##14500829##[50]##, ##REF##22383036##[51]##. EVidenceModeler (EVM) was employed to integrate the gene sets from three annotation methods into a complete and non-redundant gene set ##REF##18190707##[52]##. Finally, PASA was used to correct the EVM annotation result with untranslated region (UTR) and alternative splicing information.</p>", "<p id=\"p0120\">Function annotation was performed through comparing the annotated protein-coding genes with the known protein banks. The final gene set was blasted against four common protein banks, Swiss-Prot (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.uniprot.org/\" id=\"ir040\">https://www.uniprot.org/</ext-link>), NR (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ncbi.nlm.nih.gov/protein\" id=\"ir045\">https://www.ncbi.nlm.nih.gov/protein</ext-link>), KEGG (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.genome.jp/kegg/\" id=\"ir050\">https://www.genome.jp/kegg/</ext-link>), and InterPro (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ebi.ac.uk/interpro/\" id=\"ir055\">https://www.ebi.ac.uk/interpro/</ext-link>). InterProScan was used to integrate the functional results from four protein banks ##REF##24451626##[53]##.</p>", "<p id=\"p0125\">The tRNA genes were identified by tRNAscan-SE software with eukaryote parameters ##REF##31020551##[54]##. The rRNA fragments were predicted by aligning to whale shark and <italic>C</italic>. <italic>milii</italic> template rRNA sequences using BLASTN at E-value of 1 × 10<sup>–10</sup>\n##REF##26250111##[55]##. The miRNA and snRNA genes were predicted using Infernal software by searching against the Rfam database (release 9.1) ##REF##15608160##[56]##.</p>", "<title>Orthology analysis</title>", "<p id=\"p0130\">We first compiled the complete proteomes of 25 fish and one chordate genomes. The proteome data of 13 selected organisms, including blind cave fish (<italic>Astyanax mexicanus</italic>), zebrafish (<italic>D</italic>. <italic>rerio</italic>), Atlantic cod (<italic>G</italic>. <italic>morhua</italic>), three-spined stickleback (<italic>G</italic>. <italic>aculeatus</italic>), coelacanth (<italic>L</italic>. <italic>chalumnae</italic>), spotted gar (<italic>L</italic>. <italic>oculatus</italic>), Nile tilapia (<italic>O</italic>. <italic>niloticus</italic>), rice fish (<italic>O</italic>. <italic>latipes</italic>), sea lamprey (<italic>P</italic>. <italic>marinus</italic>), Amazon molly (<italic>Poecilia formosa</italic>), Japanese puffer (<italic>T</italic>. <italic>rubripes</italic>), green spotted puffer (<italic>T</italic>. <italic>nigroviridis</italic>), and platyfish (<italic>Xiphophorus maculatus</italic>), were obtained from the Ensembl database (release 83, <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ensembl.org/\" id=\"ir060\">https://www.ensembl.org/</ext-link>). The proteome data of other 11 selected organisms, including elephant shark (<italic>C</italic>. <italic>milii</italic>), tongue sole (<italic>Cynoglossus semilaevis</italic>), common carp (<italic>C</italic>. <italic>carpio</italic>), northern pike (<italic>Esox lucius</italic>), channel catfish (<italic>Ictalurus punctatus</italic>), turquoise killifish (<italic>Nothobranchius furzeri</italic>), coho salmon (<italic>Oncorhynchus kisutch</italic>), rainbow trout (<italic>Oncorhynchus mykiss</italic>), Japanese flounder (<italic>Paralichthys olivaceus</italic>), guppy (<italic>Poecilia reticulate</italic>), and Atlantic salmon (<italic>Salmo salar</italic>), were downloaded from the National Center for Biotechnology Information (NCBI) database (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ncbi.nlm.nih.gov/\" id=\"ir065\">https://www.ncbi.nlm.nih.gov/</ext-link>). The proteome of <italic>B</italic>. <italic>floridae</italic> was download from JGI Genome Portal (<ext-link ext-link-type=\"uri\" xlink:href=\"https://genome.jgi.doe.gov/portal/\" id=\"ir070\">https://genome.jgi.doe.gov/portal/</ext-link>). Proteins shorter than 100 amino acids were discarded and, for alternatively spliced genes, only the longest splice variant of each gene was retained.</p>", "<p id=\"p0135\">Orthologous protein groups were determined by OrthoFinder (v2.3.3) with blast search and default parameters ##REF##26243257##[57]##. This procedure led to 2792 orthologous groups with at least one representative protein from aforementioned 25 species plus <italic>P</italic>. <italic>leopoldi</italic>. To maximize orthology, these orthologous groups were filtered with an in-house Perl script to provide a subset group that contained strict one-to-one orthologous proteins from each species. We eventually retained 212 one-to-one orthologous groups for phylogenomic analysis.</p>", "<title>Phylogenomic analysis and estimation of divergence time</title>", "<p id=\"p0140\">Protein sequences in each of the 212 one-to-one orthologous groups were aligned using MUSCLE and ClustalW, and the resulting alignments were combined by M-Coffee to produce the multiple sequence alignments (MSA) ##REF##15034147##[58]##, ##REF##17846036##[59]##, ##REF##16556910##[60]##. We used an in-house Perl script to remove gaps, and the final MSA contained 48,202 amino acid sites. FastTree 2.1 was used to construct the maximum likelihood tree for the final MSA with Jones–Taylor–Thornton (JTT) and category mixture model (CAT) models ##REF##20224823##[61]##. MRBAYES 3.2.6 was used to construct the Bayesian tree for the final MSA with JTT and invgamma models ##REF##11524383##[62]##. We ran the Markov chain Monte Carlo (MCMC) algorithm for 500,000 generations with 4 chains. Bayesian trees were sampled every 100 generations, and the first 25% of trees were excluded from the analysis as burn-in. The Bayesian tree was summarized after the average standard deviation of split frequencies below 0.01. RAxML was used to constructed a maximum likelihood tree using the JTT model with gamma distribution ##REF##24451623##[63]##. Then, MCMCtree was used to predict the divergence time of 26 species ##REF##17483113##[64]##. The intervals of the divergence time between different species were obtained from the TimeTree database ##REF##17021158##[65]##.</p>", "<title>Identification of Hox gene clusters</title>", "<p id=\"p0145\">Forty-nine unique <italic>Hox</italic> genes obtained from a previous study were used as queries to conduct BLAST search (threshold of E-value 1 × 10<sup>−20</sup>) against seven species, including <italic>P</italic>. <italic>leopoldi</italic>, <italic>C</italic>. <italic>carpio</italic>, <italic>L</italic>. <italic>oculatus</italic>, <italic>L</italic>. <italic>chalumnae</italic>, <italic>D</italic>. <italic>rerio</italic>, <italic>C</italic>. <italic>milii</italic>, and <italic>B</italic>. <italic>floridae</italic>, respectively ##REF##29684203##[16]##, ##REF##2231712##[48]##. The Hidden Markov mode (HMM) profile for the homeodomain was used to identify the potential homeodomain containing genes from these genomes with HMMER 3.2.1 (<ext-link ext-link-type=\"uri\" xlink:href=\"https://hmmer.janelia.org/\" id=\"ir075\">https://hmmer.janelia.org/</ext-link>) ##UREF##6##[66]##, as well. All of the obtained genes were further validated using SMART database to determine whether the protein sequences contain homeodomains ##REF##29040681##[67]##.</p>", "<title>Gene family expansion and contraction estimation and selective pressure analysis</title>", "<p id=\"p0150\">Gene family expansion and contraction were analyzed by CAFE (v3.1) using the same seven species in the identification of Hox gene clusters ##REF##16543274##[68]##. After filtering the genes encoding proteins shorter than 100 amino acids and with low sequence complexity, we collected a total of 205,728 genes from seven selected species. OrthoFinder (v2.3.3) was used to classify these genes into orthologous groups based on their sequence similarity. Each orthologous group is actually a gene family. We calculated the probability of each orthologous group by 10,000 Monte Carlo random samplings and estimated the lambda value based on the maximum likelihood model, which represents the rate of expansion and contraction of each gene family. A branch with <italic>P</italic> &lt; 0.05 was considered to have gene amplification and contraction over evolutionary time scales.</p>", "<p id=\"p0155\">PAML was used to estimate the selective pressure of selected genes. Both branch and branch-site mode were applied to detected the selective pressure in <italic>P</italic>. <italic>leopoldi</italic>\n##REF##17483113##[64]##. PAL2NAL was utilized for alignment nucleotide sequences based on protein alignment ##REF##16845082##[69]##. The likelihood ratio tests (LRTs) of M1a <italic>vs.</italic> M2a were employed to examine the selective pressure of each site among selected genes.</p>", "<title>Transcriptome analysis</title>", "<p id=\"p0160\">Total RNA from six <italic>P</italic>. <italic>leopoldi</italic> tissues (skin, heart, blood, muscle, liver, and brain) was prepared using the Qiagen RNeasy Kit (Catalog No. 75142, Qiagen, Düsseldorf, Germany) according to the manufacturer’s instructions, and RNA-seq libraries were constructed according to a standard protocol for the Illumina novaseq6000 sequencing platform (San Diageo, CA) with 100-bp paired-end reads. The reads were aligned onto the assembled <italic>P</italic>. <italic>leopoldi</italic> reference genome with STAR ##REF##23104886##[70]##.</p>", "<p id=\"p0165\">Other RNA-seq data of the brain, heart, muscle, and liver from three fish species, <italic>L</italic>. <italic>oculatus</italic>, <italic>D</italic>. <italic>rerio</italic>, and <italic>C</italic>. <italic>milii</italic>, were retrieved from the NBCI Sequence Read Archive (SRA). The raw RNA-seq data were filtered using Trimmomatic 0.32 to generate clean reads ##REF##24695404##[71]##. Per base sequence qualities of filtered fastq files were checked with FastQC (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.bioinformatics.babraham.ac.uk/projects/fastqc/\" id=\"ir080\">https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</ext-link>). The Ensembl genome of each species was used as a reference genome, and filtered reads were aligned onto the references using STAR ##REF##23104886##[70]##.</p>", "<p id=\"p0170\">RSEM was used to quantify expressed genes into TPM values ##REF##21816040##[72]##. R package DEGseq was used to detect DEGs ##REF##19855105##[73]##. One-to-one orthologous genes between <italic>P</italic>. <italic>leopoldi</italic> and <italic>D</italic>. <italic>rerio</italic> and web-based DAVID Bioinformatics Resources were used for GO annotation ##REF##17784955##[74]##.</p>", "<title>Examination of bone formation-related gene families</title>", "<p id=\"p0175\">The <italic>BMP</italic> and <italic>BMPR</italic> genes of zebrafish were used as query to search the BMP and BMPR gene families in <italic>P</italic>. <italic>leopoldi</italic>, <italic>C</italic>. <italic>carpio</italic>, <italic>L</italic>. <italic>oculatus</italic>, <italic>L</italic>. <italic>chalumnae</italic>, <italic>C</italic>. <italic>milii</italic>, and <italic>B</italic>. <italic>floridae</italic>. Other bone formation-related gene families were examined as follows. The zebrafish orthologous genes were used to annotate each gene family. The gene family with the keyword of “bone”, “calcium”, or “vitamin D” was kept as the bone formation-related candidate gene family for further examination. These bone formation-related candidate gene families were manually checked with literature evidence in order to find the target genes for knockdown experiment.</p>", "<title><italic>gc</italic> gene knockdown in zebrafish</title>", "<p id=\"p0180\"><italic>D</italic>. <italic>rerio</italic> (AB strain) was provided by an in-house <italic>D</italic>. <italic>rerio</italic> Core Facility (CAS Center for Excellence in Molecular Cell Science), and all experimental protocols were approved by the Institutional Animal Care and Use Committee. Two sgRNAs (gc-e4: 5′-GCTCAATGCCTGGATGCTTGGT-3′; gc-e8: 5′-TCGGTTTGGATTCATCGCAGGT-3′) were designed to target the sequences in the exon 4 and exon 8 of the <italic>gc</italic> gene in zebrafish, respectively, based on the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) design website CCTop (<ext-link ext-link-type=\"uri\" xlink:href=\"https://crispr.cos.uni-heidelberg.de/index.html\" id=\"ir085\">https://crispr.cos.uni-heidelberg.de/index.html</ext-link>) and CHOPCHOP (<ext-link ext-link-type=\"uri\" xlink:href=\"https://chopchop.cbu.uib.no/\" id=\"ir090\">https://chopchop.cbu.uib.no/</ext-link>). DNA templates for sgRNAs were produced by annealing and elongating a forward primer containing T7 promoter, guide sequence, and a reverse primer encoding the standard chimeric sgRNA scaffold ##REF##26048245##[75]## (Table S14). DNA templates were purified, and sgRNAs were <italic>in vitro</italic> synthesized and purified. Cas9 RNP complexes were prepared with Cas9 protein and sgRNAs as previously described ##REF##29974860##[76]##. The RNPs were injected into one-cell-stage <italic>D</italic>. <italic>rerio</italic> embryos. Each embryo was injected with a 1-nl mix containing ∼ 5 μM Cas9 and 1 μg/μl (31 μM) sgRNA.</p>", "<p id=\"p0185\"><italic>D</italic>. <italic>rerio</italic> larvae were processed for bone staining with Alizarin Red S using a modified protocol ##REF##17510811##[77]##. Briefly, larvae of 6 days post-fertilization (dpf) were fixed in 4% paraformaldehyde (w/v, pH 7.4) overnight at 4 °C, washed in 1% KOH for 5 min, and bleached in 3% H<sub>2</sub>O<sub>2</sub>/0.5% KOH for 40 min. All specimens were initially stained with 0.05% Alizarin Red S in 70% ethanol overnight, and soaked thoroughly with 25% glycerol/0.1% KOH, 50% glycerol/0.1% KOH, and 75% glycerol/0.1% KOH sequentially. All specimens were stored in 80% glycerol/H<sub>2</sub>O.</p>" ]
[ "<title>Results</title>", "<title><italic>P</italic>. <italic>leopoldi</italic> with a draft genome assembly of 4.11 Gb</title>", "<p id=\"p0020\">We constructed a total of 17 sequencing libraries using genomic DNA extracted from a male <italic>P</italic>. <italic>leopoldi</italic>, and acquired raw data from three sequencing platforms, PacBio SMRT, Illumina HiSeq2000, and 10X Genomics, with coverages of 61.61×, 200.95×, and 108.41×, respectively (Table S1). After stringent filtering and redundancy checking, 1628.63-Gb sequence data were used for a scaffold-based <italic>de novo </italic>genome assembly. The initial combined assembly was based on the data from PacBio long reads. Illumina paired-end data and 10X Genomics data were used for error correction. The DNA composition of the assembled contigs was of 41.97% GC content (Table S2). The genome size estimated by <italic>K</italic>-mer analysis using Illumina paired-end data was about 4.11 Gb in size with 0.79% heterozygosity (Table S3). The read-to-genome alignment rate is 98.48% with a coverage of 98.74% in the assembly (Table S4). The final assembly consisted of 16,227 contigs and 13,238 scaffolds, with a contig N50 of 3937 kb and a scaffold N50 of 5675 kb in size (Table S5). The completeness of the <italic>P</italic>. <italic>leopoldi</italic> genome was estimated to achieve 91.8% (3081/3354) coverage using the Benchmarking Universal Single-Copy Orthologs (BUSCO) method. We mapped 248 core eukaryotic genes (CEGs) to the scaffolds, and 90% of them are found in the predicted exons, based on BLAST-like alignment tool (BLAT) scores. Additionally, Merqury gave the accuracy in consensus base calling with 99.9% (Q30) for the genome assembly (##TAB##0##Table 1##). Taken together, the BUSCO results, CEG results, and mapping quality indicate that our genome assembly is highly accurate and nearly complete.</p>", "<title>More than 90% of <bold><italic>P</italic></bold>. <bold><italic>leopoldi</italic></bold> genes have known functions</title>", "<p id=\"p0025\">The <italic>P</italic>. <italic>leopoldi</italic> genome assembly contains more than 71% repetitive content based on <italic>de novo</italic> and sequence homology analyses (<xref rid=\"s0155\" ref-type=\"sec\">Figure S1</xref>; Tables S6 and S7), which is much higher than that of white shark (58.5%) ##REF##30782839##[12]##. A total of 23,240 protein-coding genes were predicted with high-confidence by combining <italic>de novo</italic> and homologous gene prediction methods with the transcriptomic data and orthologs from other fish genomes (Table S8). This gene number seems higher than that of elephant shark but lower than that in white shark ##REF##24402279##[1]##, ##REF##30782839##[12]##. We assigned preliminary functions to 23,030 (99.1%) protein-coding genes using BLASTp against protein databases including Swiss-Prot, Non-Redundant Protein Sequence Database (NR), Kyoto Encyclopedia of Genes and Genomes (KEGG), and InterPro (<xref rid=\"s0155\" ref-type=\"sec\">Figure S2</xref>; Table S9), and also assigned Gene Ontology (GO) terms to 21,040 (90.5%) protein-coding genes (Table S9). In addition, the orthologs of these protein-coding genes were also analyzed in other fish species (Table S10). Moreover, non-coding genes including microRNAs (miRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), and small nuclearRNAs (snRNAs) are also identified accordingly (Table S11).</p>", "<title><bold><italic>P</italic></bold>. <italic>leopoldi</italic> split from bony fish about 381 MYA and has the slowest evolutionary rate among fish species</title>", "<p id=\"p0030\">A phylogenomic tree of <italic>P</italic>. <italic>leopoldi</italic> and 24 other fish species was constructed using 212 one-to-one orthologous genes with 48,202 amino acid sites, with <italic>B</italic>. <italic>floridae</italic> (a chordate) as the outgroup. A jawless fish, sea lamprey (<italic>Petromyzon marinus</italic>), was basal to cartilaginous and bony fishes, and there was a conspicuous split between cartilaginous and bony fishes (##FIG##0##Figure 1##). Both maximum likelihood and Bayesian trees showed exactly the same topology (<xref rid=\"s0155\" ref-type=\"sec\">Figures S3 and S4</xref>). <italic>P</italic>. <italic>leopoldi</italic> was grouped with <italic>C</italic>. <italic>milii</italic>, forming the Chondrichthyes clade, whereas 22 other bony fishes were clustered as the Osteichthyes clade (<xref rid=\"s0155\" ref-type=\"sec\">Figure S5</xref>). This result is consistent with the traditional taxonomic classification of fishes. A MCMCtree-based divergence time estimation indicated that the split of the other fish species from the class Cyclostomata (<italic>P</italic>. <italic>marinus</italic>) occurred ∼ 533 MYA (##FIG##0##Figure 1##, <xref rid=\"s0155\" ref-type=\"sec\">Figure S6</xref>), and the splits between Chondrichthyes and Osteichthyes and between the superorder Batoidea (<italic>P</italic>. <italic>leopoldi</italic>) and Selachimorpha (<italic>C</italic>. <italic>milii</italic>) are ∼ 381 MYA and ∼ 96 MYA, respectively.</p>", "<p id=\"p0035\">We also calculated the evolutionary rates as total substitution rate per site for each species, using the same set of orthologous genes as in our phylogenomic analysis (##TAB##1##Table 2##). <italic>P</italic>. <italic>leopoldi</italic> had the lowest amino acid substitution rate among 26 species. Tajima’s relative rate tests confirmed that its evolutionary rate was significantly slower than those of <italic>B</italic>. <italic>floridae</italic>, <italic>P</italic>. <italic>marinus</italic>, <italic>L</italic>. <italic>chalumnae</italic>, and <italic>D</italic>. <italic>rerio</italic>, but similar to the other cartilaginous fish, such as <italic>C</italic>. <italic>milii</italic> (Table S12). However, Tajima’s relative rate tests also showed that <italic>L</italic>. <italic>oculatus</italic> exhibited a slower evolutionary rate than <italic>P</italic>. <italic>leopoldi</italic> when using amphioxus or sea lamprey as the outgroup. Thus, the results above suggest that <italic>P</italic>. <italic>leopoldi</italic> is one of the slowest evolving fishes.</p>", "<title>Specific genes/expanded gene families found in <bold><italic>P</italic></bold>. <bold><italic>leopoldi</italic></bold></title>", "<p id=\"p0040\">To explore the evolutionary features of <italic>P</italic>. <italic>leopoldi</italic>, we performed an orthology analysis, by comparing its protein-coding genes with those of <italic>B</italic>. <italic>floridae</italic>, <italic>C</italic>. <italic>milii</italic>, <italic>L</italic>. <italic>chalumnae</italic>, <italic>L</italic>. <italic>oculatus</italic>, <italic>C</italic>. <italic>carpio</italic>, and <italic>D</italic>. <italic>rerio</italic> (##FIG##1##Figure 2##A). After filtering the genes encoding proteins shorter than 100 amino acids and having low sequence complexity from the predicted 23,240 protein-coding gene pool, we kept a total of 18,894 stingray protein-coding genes for orthology analysis. Among these kept <italic>P</italic>. <italic>leopoldi</italic> genes, 12,219, 4347, and 292 of them are chordate orthologs (shared with those of <italic>B</italic>. <italic>floridae</italic>), bony fish orthologs (shared with those of 5 other bony fishes), and cartilaginous fish orthologs (shared with those of <italic>C</italic>. <italic>milii</italic>), respectively. In addition, 2036 of them are <italic>P</italic>. <italic>leopoldi</italic>-specific genes (no homologous relationship with the other six species). Notably, <italic>C</italic>. <italic>carpio</italic> has four rounds of genome duplication and possesses a very large number of protein-coding genes (55,756) ##REF##25240282##[13]##.</p>", "<p id=\"p0045\">Next, we examined gene family expansions and contractions across seven selected species using a total of 205,728 protein-coding genes. According to their homologous relationships, these genes could be classified into 14,818 gene families, and 7830 out of these gene families experienced multiple expansion or contraction events in one or several selected species. A total of 56 gene families were significantly expanded and 14 families were significantly contracted in <italic>P</italic>. <italic>leopoldi</italic> only. GO analysis showed that the expanded and contracted gene families in  <italic>P</italic>. <italic>leopoldi</italic> had different biological emphases (<xref rid=\"s0155\" ref-type=\"sec\">Figure S7</xref>). The expanded gene families were primarily related to the immune system like defense response to virus (Bonferroni corrected <italic>P</italic> &lt; 0.05), whereas the contracted gene families were more enriched with cellular component such as crystallin and lectin (Bonferroni corrected <italic>P</italic> &lt; 0.05). Among the <italic>P</italic>. <italic>leopoldi</italic> gene families that experienced expansion, two of them, immunoglobulin heavy constant delta (IGHD) gene family and T-cell receptor alpha/delta variable (TRAV/TRDV) gene family, are important constituents of the vertebrate immune system (##FIG##1##Figure 2##B and C). Interestingly, their expansions were <italic>P</italic>. <italic>leopoldi</italic>-specific and not found in elephant shark, suggesting their possible roles in freshwater niche adaption. They were also under purifying selection tested with the branch model in PAML (data not shown).</p>", "<title>Eleven <bold><italic>Hox</italic></bold> genes are missing in <bold><italic>P</italic></bold>. <bold><italic>leopoldi</italic></bold> Hox gene clusters</title>", "<p id=\"p0050\">The distinct body shape of <italic>P</italic>. <italic>leopoldi</italic> is assumed to have genetic basis, attributable to its Hox gene clusters that exhibit striking spatial collinearity and drive morphologic diversification of almost all metazoans. Due to the contribution of whole-genome duplication events among vertebrates (especially in teleost fishes) and lineage-specific secondary losses, the number of Hox gene clusters or genes varies greatly among vertebrates ##REF##19805301##[14]##. As shown in ##FIG##2##Figure 3##, Hox gene clusters range from one in cephalochordate <italic>B</italic>. <italic>floridae</italic> to 13 in <italic>C</italic>. <italic>carpio</italic> in number ##REF##20520839##[15]##, ##REF##29684203##[16]##, and there are 33 <italic>Hox</italic> genes belonging to four putative Hox clusters (A, B, C, and D) in <italic>P</italic>. <italic>leopoldi</italic> within single scaffolds. Therefore, <italic>P</italic>. <italic>leopoldi</italic> retains the majority of 2R Hox cluster duplicates. Compared with <italic>C</italic>. <italic>milii</italic>, <italic>P</italic>. <italic>leopoldi</italic> possesses fewer <italic>Hox</italic> genes, especially in the HoxC cluster. Totally, <italic>P. leopoldi</italic> lacks <italic>HoxA4</italic>, <italic>HoxA5</italic>, and <italic>HoxA6</italic> in the HoxA cluster, <italic>HoxB6</italic> in the HoxB cluster, <italic>HoxC1</italic>, <italic>HoxC3</italic>, <italic>HoxC4</italic>, <italic>HoxC5</italic>, <italic>HoxC12</italic>, and <italic>HoxC13</italic> in the HoxC cluster, and <italic>HoxD4</italic> in the HoxD cluster. This difference in <italic>Hox</italic> gene composition may contribute greatly to stingray’s body shape differences compared with <italic>C</italic>. <italic>milii</italic>. Moreover, there are seven <italic>Hox</italic> genes lost in <italic>P</italic>. <italic>leopoldi</italic> but present in all other fishes, including <italic>HoxA5</italic>, <italic>HoxB6</italic>, <italic>HoxC3</italic>, <italic>HoxC4</italic>, <italic>HoxC5</italic>, <italic>HoxC13</italic>, and <italic>HoxD4</italic>. We thus assume that such <italic>Hox</italic> gene diversity between <italic>P</italic>. <italic>leopoldi</italic> and other fish species may genetically explain its specific body morphology.</p>", "<title>Diversified tissue expression profiles in <bold><italic>P</italic></bold>. <bold><italic>leopoldi</italic></bold></title>", "<p id=\"p0060\">To document its tissue-associated genes and evaluate their possible functions, we acquired RNA sequencing (RNA-seq) data from six <italic>P</italic>. <italic>leopoldi</italic> tissues. First, we identified each tissue’s differentially expressed genes (DEGs) by comparing its expression profile with the rest five ones. After normalization based on transcripts per kilobase million (TPM), 3559, 4482, 1806, 2347, 1703, and 2328 DEGs were identified in the blood, brain, heart, liver, muscle, and skin of <italic>P</italic>. <italic>leopoldi</italic>, respectively. Among these DEGs, 87, 2281, 184, 537, 388, and 641 genes were up-regulated, whereas 3472, 2201, 1622, 1810, 1315, and 1687 were down-regulated in the blood, brain, heart, liver, muscle, and skin, respectively. Up-regulated DEGs were all tissue-specific, and no shared up-regulated genes were found in the brain, heart, liver, muscle, and skin (##FIG##3##Figure 4##A). GO analysis showed that each tissue’s up-regulated DEGs were faithful to their tissue’s function (##TAB##2##Table 3##). In the six tissues of <italic>P</italic>. <italic>leopoldi</italic>, down-regulated DEGs shared many overlapping parts among six tissues, and exhibited a similar expression background of antibiotics biosynthesis, catalytic activity, and metabolic process (<xref rid=\"s0155\" ref-type=\"sec\">Figure S8</xref>). Compared to <italic>C</italic>. <italic>milii</italic>, <italic>L</italic>. <italic>oculatus</italic>, and <italic>D</italic>. <italic>rerio</italic>, about one third of the up-regulated DEGs in each tissue were <italic>P</italic>. <italic>leopoldi</italic>-specific (38/87 in blood, 738/2281 in brain, 65/184 in heart, 180/537 in liver, 132/388 in muscle, and 212/641 in skin), and thus their possible functions remain to be discovered in stingray (##FIG##3##Figure 4##B).</p>", "<p id=\"p0065\">Next, we compared the expression profiles of 3738 one-to-one orthologs in four tissues (brain, heart, liver, and muscle) between <italic>P</italic>. <italic>leopoldi</italic>, <italic>C</italic>. <italic>milii</italic>, <italic>L</italic>. <italic>oculatus</italic>, and <italic>D</italic>. <italic>rerio</italic>, and performed the principal component analysis (PCA) to investigate the expression patterns for the four tissues across the four fishes. The PCA result showed a scattered expression pattern for each of the four tissues across four fishes (##FIG##3##Figure 4##C). Our data were separated neither by tissue nor by species. In mammals, expression analyses have shown that the same tissues from different species tend to cluster together ##REF##22012392##[17]##, proposing that the same tissues in different mammals usually perform similar physiological functions. In fishes, the diverged expression pattern of the same tissues suggests a probably much more diversified physiology or a much longer evolutionary history, both of which are not mutually exclusive.</p>", "<title><bold><italic>P</italic></bold>. <bold><italic>leopoldi</italic></bold> lacks the <bold><italic>gc</italic></bold> gene for hard skeleton formation</title>", "<p id=\"p0070\">As a cartilaginous fish, <italic>P</italic>. <italic>leopoldi</italic> already has a complex skeleton structure providing support for its body and internal organs. How hard skeleton emerged in vertebrates and what is the genetic basis for bone formation remain to be investigated. We systematically compared the bone formation-related gene families between cartilaginous and bony fish genomes. First, we examined the bone morphogenetic protein (BMP) gene family and BMP receptor (<italic>BMPR</italic>) genes among seven selected species. It is known that both BMPs and their receptors play an essential role in skeleton formation. Generally, <italic>BMP</italic> genes are classified into eight different clusters according to their phylogenetic relationships (##FIG##4##Figure 5##A). Cartilaginous and bony fishes have the representative genes in all eight clusters. <italic>P</italic>. <italic>leopoldi</italic> does not have the <italic>bmp15</italic> gene, whereas <italic>C</italic>. <italic>milii</italic> has. Compared with fish species, <italic>B</italic>. <italic>floridae</italic> does not have the <italic>bmp3</italic>, <italic>bmp9</italic>, <italic>bmp10</italic>, <italic>bmp15</italic>, and <italic>bmp16</italic> genes. As to <italic>BMPR</italic> genes ##REF##8702914##[18]##, both types I and II are present in both cartilaginous and bony fishes, but <italic>B</italic>. <italic>floridae</italic> misses <italic>BMPR</italic> type II (Table S13). Our analyses suggest that BMPs and their receptors are less likely to answer the question whether the skeleton is made of cartilage or hard bone, because both cartilaginous and bony fishes have all representative <italic>BMP</italic> and <italic>BMPR</italic> genes. Second, we examined the presence or absence of other bone formation-related genes between cartilaginous and bony fishes. After scrutinizing the candidate gene list involved in skeleton formation from six fish species, we found that the <italic>gc</italic> gene, encoding vitamin D-binding protein (VDBP), is present in bony fishes but absent in cartilaginous fishes. <italic>L</italic>. <italic>chalumnae</italic>, <italic>L</italic>. <italic>oculatus</italic>, <italic>C</italic>. <italic>carpio</italic>, and <italic>D</italic>. <italic>rerio</italic> have 2, 1, 3, and 1 copies of <italic>gc</italic>, respectively. We hypothesize that VDBP may be involved in the bone formation process for bony fishes. <italic>D</italic>. <italic>rerio</italic> is a widely used model organism for studies of bone development and formation ##REF##14623232##[19]##. To verify the possible function of the <italic>gc</italic> gene in bone formation, we designed two small guide RNAs (sgRNAs), gc-e4 and gc-e8, against the exon 4 and exon 8 of the <italic>gc</italic> gene, respectively ##REF##24179142##[20]##, using  a sgRNA against the enhanced green fluorescent protein (<italic>EGFP</italic>) gene as a scrambled control. As shown in ##FIG##4##Figure 5##B and C, embryos injected with control ribonucleoproteins (RNPs) displayed normal bone formation, whereas embryos injected with RNPs against the <italic>gc</italic> gene displayed incomplete craniofacial skeleton mineralization. The results support our hypothesis that the <italic>gc</italic> gene is involved in hard skeleton formation.</p>" ]
[ "<title>Discussion</title>", "<title>The evolutionary features of the genome and Hox gene clusters of <italic>P</italic>. <italic>leopoldi</italic></title>", "<p id=\"p0075\">The genomic data of <italic>P</italic>. <italic>leopoldi</italic> provide us an information bonanza for understanding fish evolution, especially the split between cartilaginous and bony fishes. Our phylogenomic analysis showed that Chondrichthyes and Osteichthyes were two parallel monophyletic groups and the split between them can be dated back to 381 MYA, which is less than the estimation of 450 MYA based on mitochondrial genome ##REF##20551041##[3]##. The discrepancy between our result and the mitogenomic estimation could be caused by the different evolutionary rates of nuclear genome and mitochondrial genome. Mitochondrion has a particularly high mutation rate and a much diversified evolutionary spectrum across species ##REF##18752353##[21]##. The non-unified estimations of split time can be explained by different data sources. Generally, the evolutionary rate of elasmobranchs is much lower than that in mammals ##REF##1579163##[22]##, ##REF##10406116##[23]##, and the Chondrichthyes also shows a slower evolutionary rate than the Osteichthyes. In this study, <italic>P</italic>. <italic>leopoldi</italic>, <italic>C</italic>. <italic>milii</italic>, and two basal bony fish species (<italic>L</italic>. <italic>chalumnae</italic> and <italic>L</italic>. <italic>oculatus</italic>) evolved much slower than the other fish species (##FIG##0##Figure 1##). These four fish species also did not experience the third round of genome duplication (3R) which happened in the ray-finned fish lineage ##REF##15014147##[24]##, ##REF##12618368##[25]##. This result supports the hypothesis that the 3R might promote the teleost in a higher rate of sequence evolution ##REF##24402279##[1]##, ##REF##23598338##[26]##, ##REF##19095434##[27]##, and suggests that cartilaginous and ancient bony fishes might have been well adapted to their niches. In <italic>P</italic>. <italic>leopoldi</italic>, <italic>C</italic>. <italic>milii</italic>, <italic>L</italic>. <italic>chalumnae</italic>, and <italic>L</italic>. <italic>oculatu</italic>, the substratum (the number of genes) for evolution to work on was limited and therefore slow evolution is expected. Although <italic>P</italic>. <italic>leopoldi</italic> genome was not assembled at the chromosomal level, the completeness of the genome has achieved 91.8% coverage estimated by the BUSCO methoed. <italic>P</italic>. <italic>leopoldi</italic> has four Hox gene clusters containing 33 genes, the smallest number of <italic>Hox</italic> genes among six fish species analyzed in our study (##FIG##2##Figure 3##). <italic>C</italic>. <italic>milii</italic>, <italic>L</italic>. <italic>chalumnae</italic>, <italic>L</italic>. <italic>oculatus</italic>, <italic>C</italic>. <italic>carpio</italic>, and <italic>D</italic>. <italic>rerio</italic> have 45, 42, 34, 62, and 49 <italic>Hox</italic> genes, respectively. Moreover, <italic>P</italic>. <italic>leopoldi</italic> lacks <italic>HoxA5</italic>, <italic>HoxB6</italic>, <italic>HoxC3</italic>, <italic>HoxC4</italic>, <italic>HoxC5</italic>, <italic>HoxC13</italic>, and <italic>HoxD4</italic> presented in the other five fish species. <italic>P</italic>. <italic>leopoldi</italic> has a disc-like body, whereas most fish species usually have a streamline body. The <italic>Hox</italic> gene difference between <italic>P</italic>. <italic>leopoldi</italic> and the other fish species may help to explain why <italic>P</italic>. <italic>leopoldi</italic> has a simple body design with large pectoral fins and a whip-like tail. However, our study does not provide the answer for which <italic>Hox</italic> gene contributes to what morphological alteration in stingray’s body plan.</p>", "<title>The expansion of two immune-related gene families in <italic>P</italic>. <italic>leopoldi</italic></title>", "<p id=\"p0080\">Our gene family analysis showed that 56 gene families were significantly expanded in <italic>P</italic>. <italic>leopoldi</italic>. Many of them encode protiens involved in immune and stress response, such as heat shock proteins (HSPs), cytochrome P450 (CYP450), and inhibitors of apoptosis (IAPs). Two expanded gene families, IGHD and TRAV/TRDV, were found to be directly related to the immune system (##FIG##1##Figure 2##). Immunoglobulins are membrane-bound or secreted glycoproteins produced by B lymphocytes. Immunoglobulin D (IgD) is made up of two heavy chains of the delta class, and two light chains. IgD is present in species ranging from fish to mammal, suggests that IgD has important immunological functions. IgD has been reported to be able to bind to basophils and mast cells and induce antimicrobial factors, which contributes to immune surveillance and inflammation under pathological conditions ##REF##20727035##[28]##. T-cell receptor alpha (TCRα) recognizes peptides that are bound to major histocompatibility complex (MHC) molecules, and TCR delta (TCRδ) recognizes antigens directly, both of which are considered as a bridge between the innate and adaptive immune system. TCRα and TCRδ cDNA sequences have been identified in the nurse shark ##REF##16549799##[29]##, as well as in other vertebrates. The existence of TCRs in sharks suggests that the adaptive immune system evolved in cartilaginous fish has the same fundamental major components as those existing in vertebrates such as humans ##REF##11125480##[30]##. Our studies of TCR expansion in <italic>P. leopoldi</italic> help elucidate that the <italic>V</italic> genes of TCRs have evolved for 500 million years, and indicate their role in the diversification of the pre-immune repertoire. The natural habitat of <italic>P</italic>. <italic>leopoldi</italic> is Xingu River basin, and the phylogenetic relationship of stingrays shows that the family Potamotrygonidae evolved from the sea-dwelling ancestors ##REF##25867639##[31]##. The fact that stingrays can transit from marine environment to pathogen rich freshwater suggests that stingrays should have a complex immune system. The expansion of immune system-related genes (##FIG##1##Figure 2##) suggests that <italic>P</italic>. <italic>leopoldi</italic> could require specific immune responses for pathogens and antigens in new niches, although there has been no evidence that these two gene families are directly involved in freshwater habitat adaptation. Usually, genes related to immune response are evolutionarily active to coup with the constant-evolving pathogens ##REF##30620335##[32]##. When a gene family expanded through duplication event, some duplicated genes would be free from their function constraint. The old genes performed the normal function, and the new one would go through the neo-functionalization or sub-functionalization process ##REF##19015656##[33]##. Thus, their selection pressure tends to be positive, as well. However, our selective pressure analysis showed that these two gene families were under negative selection, a sign of function constraint. It indicates that their functions were rapidly fixed after the gene family expansion. One possible explanation for this phenomenon is that <italic>P</italic>. <italic>leopoldi</italic> fast adapted to its new niche in Xingu River and its immune system had to rapidly deal with new enemy after its ancestor migrated from the Atlantic Ocean to the Amazon River system. Furthermore, the fact that <italic>P</italic>. <italic>leopoldi</italic> no longer migrated to the other niches renders the functions of these expanded genes important for its survival in order to deal with fixed microbial enemy. Thus, these two expanded gene families were negatively selected. Surely, the argument mentioned above is our hypothesis and needs to be verified in the other fish species whose ancestor migrated to river from ocean.</p>", "<title>The gene expression silhouette of <bold><italic>P</italic></bold>. <bold><italic>leopoldi</italic></bold> tissues</title>", "<p id=\"p0085\">Expression profile comparison among six <italic>P</italic>. <italic>leopoldi</italic> tissues demonstrates that its brain has a much wider expression spectrum than the other tissues (##FIG##3##Figure 4##), and the result is consistent with that of mammalian organs. In mammals, the central nervous system has more specifically expressed genes than the heart and liver ##REF##25679776##[34]##. Compared with mammals, there are more species-specific genes expressed in <italic>P</italic>. <italic>leopoldi</italic> in each of the analyzed tissues ##REF##22012392##[17]##. The brain-specific modules are enriched with genes involved in typical processes as for central nervous system development (Benjamini–Hochberg corrected <italic>P</italic> &lt; 0.05), and thus define common neural tissue functions. Furthermore, the same tissues from different fish species exhibited a much more diversified expression pattern than that observed in mammals. The earliest mammal appeared around 225 MYA, and our analysis showed that fishes emerged at least 533 MYA ##UREF##4##[35]##. As fishes have a much longer evolutionary history than mammals, a greater divergence for fishes at both expression and sequence levels is expected. We are only able to identify 3738 one-to-one orthologous genes among white-blotched river stingray, elephant shark, coelacanth, and zebrafish, which is much less than 5636 amniotic one-to-one orthologous genes identified among nine endothermic species in a previous study ##REF##22012392##[17]##. Therefore, the long fish evolutionary history may explain the non-unified expression profiles of their tissues at least in part. Our analysis of tissue transcriptomes from all representative fish lineages refines previous hypotheses and provides a new viewpoint for the evolution of chordate tissue functions.</p>", "<title>Absence of VDBP in <italic>P</italic>. <italic>leopoldi</italic></title>", "<p id=\"p0090\">Skeleton is an essential part of vertebrate body, which can be made of hard bone or cartilage only. For bone, two cell types, osteoblast and osteocyte, contribute to the formation and mineralization, but cartilage has only one cell type called chondrocyte ##REF##8702914##[18]##, ##REF##14623232##[19]##. Therefore, the emergence of hard skeleton in vertebrates must have engaged complex cellular processes and multiple genetic inventions. We searched the <italic>P</italic>. <italic>leopoldi</italic> gene inventory for the ones known to be involved in bone formation in osteichthyans. All gene families involved in skeleton formation seem to be present, except the <italic>gc</italic> gene which encodes VDBP. Our analyses of <italic>BMP</italic> and <italic>BMPR</italic> genes show that both cartilaginous and bony fishes have all representative members of these two gene families (##FIG##4##Figure 5##A; Table S13). The slight difference in <italic>BMP</italic> and <italic>BMPR</italic> genes between the two fish lineages is insufficient to explain the major departures in their skeletons. One major difference between bones and cartilages is whether calcium phosphate is present in their extracellular matrix or not. A previous study has reported that secreted calcium-binding phosphoproteins (SCPP) are involved in the bone formation in <italic>D</italic>. <italic>rerio</italic>\n##REF##24402279##[1]##. The analysis of <italic>C</italic>. <italic>milii</italic> genome has reported the lack of genes encoding SCPP in cartilaginous fishes, which explains the absence of bone in their endoskeleton ##REF##24402279##[1]##. Our study further demonstrates that VDBP may also take part in the bone formation process (##FIG##4##Figure 5##B and C). Vitamin D promotes the absorption of calcium through the intestines ##REF##15585788##[36]##. Together, our result and that of a previous study both suggest that genes responsible for calcium metabolism are essential for the hard skeleton formation in bony fishes. Because cartilaginous and bony fishes evolved in parallel, several crucial genes alone may sufficiently exclude the hard skeleton from cartilaginous fishes, albeit under ongoing studies.</p>" ]
[ "<title>Conclusion</title>", "<p id=\"p0095\">In this study, we report the assembly and analysis of a draft genome of <italic>P</italic>. <italic>leopoldi</italic>, a cartilaginous freshwater fish. Because cartilaginous fishes constitute a critical outgroup for understanding the evolution and diversity of bony vertebrates, the whole-genome analysis shows that the <italic>P</italic>. <italic>leopoldi</italic> genome is evolving significantly slower than other vertebrates. The transcriptomic data shed lights into highly diversified gene expression profiles among fish lineages, as opposed to the coordinated gene expression among mammalian tissues. The expansion of immune-related gene families IGHD and TRAV/TRDV suggests that the diversification of the pre-immune repertoire in cartilaginous fishes could play a role in the evolution of an adaptive immune system. Our study further demonstrates that VDBP may partly explain the absence of hard bone in their endoskeleton. Together, our results starting from the <italic>P</italic>. <italic>leopoldi</italic> genome to the experimental model provide novel clues for niche adaptation and skeleton formation in the evolutionary history of fishes.</p>" ]
[ "<p id=\"np010\">Equal contribution.</p>", "<p>The <bold>white-blotched river stingray</bold> (<bold><italic>Potamotrygon leopoldi</italic></bold>) is a cartilaginous fish native to the Xingu River, a tributary of the Amazon River system. As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available, <italic>P</italic>. <italic>leopoldi</italic> provides the evolutionary details in fish phylogeny, <bold>niche adaptation</bold>, and skeleton formation. In this study, we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds, with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size. Our analysis shows that <italic>P</italic>. <italic>leopoldi</italic> is a slow-evolving fish that diverged from elephant sharks about 96 million years ago. Moreover, two gene families related to the immune system (immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes) exhibit expansion in <italic>P</italic>. <italic>leopoldi</italic> only. We also identified the Hox gene clusters in <italic>P</italic>. <italic>leopoldi</italic> and discovered that seven <italic>Hox</italic> genes shared by five representative fish species are missing in <italic>P</italic>. <italic>leopoldi</italic>. The RNA sequencing data from <italic>P</italic>. <italic>leopoldi</italic> and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to mammals. Our functional studies suggest that lack of the <italic>gc</italic> gene encoding <bold>vitamin D-binding protein</bold> in cartilaginous fishes (both <italic>P</italic>. <italic>leopoldi</italic> and <italic>Callorhinchus milii</italic>) could partly explain the absence of hard bone in their endoskeleton. Overall, this genome resource provides new insights into the niche adaptation, body plan, and skeleton formation of <italic>P. leopoldi</italic>, as well as the genome evolution in cartilaginous fishes.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Kai Ye</p>" ]
[ "<title>Data availability</title>", "<p id=\"p0190\">The raw sequencing data reported in this study have been deposited in the Genome Sequence Archive ##REF##34400360##[78]## at the National Genomics Data Center (NGDC), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS) / China National Center for Bioinformation (CNCB) (GSA: CRA003264) , and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa\" id=\"ir095\">https://ngdc.cncb.ac.cn/gsa</ext-link>. The whole-genome sequence data and its annotation file in GFF format in this study have been deposited in the Genome Warehouse ##REF##34175476##[79]## at the NGDC, BIG, CAS / CNCB (GWH: GWHAOTN00000000), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gwh\" id=\"ir100\">https://ngdc.cncb.ac.cn/gwh</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0195\">Xiang Zhang is the CEO of Shanghai Nanmulin Biotechnology Company Limited and pays for the sequencing of <italic>P</italic>. <italic>leopoldi</italic>. All the other authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0200\"><bold>Jingqi Zhou:</bold> Methodology, Formal analysis, Visualization, Funding acquisition, Writing – original draft, Writing – review &amp; editing. <bold>Ake Liu:</bold> Methodology, Formal analysis, Visualization, Data curation. <bold>Funan He:</bold> Methodology, Formal analysis, Visualization. <bold>Yunbin Zhang:</bold> Formal analysis, Validation. <bold>Libing Shen:</bold> Conceptualization, Writing – original draft, Writing – review &amp; editing, Supervision. <bold>Jun Yu:</bold> Conceptualization, Writing – review &amp; editing, Supervision. <bold>Xiang Zhang:</bold> Conceptualization, Resources, Funding acquisition, Writing – review &amp; editing, Supervision. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0215\">The following are the Supplementary data to this article:</p>", "<p id=\"p0220\">\n\n</p>", "<p id=\"p0225\">\n\n</p>", "<p id=\"p0230\">\n\n</p>", "<p id=\"p0235\">\n\n</p>", "<p id=\"p0240\">\n\n</p>", "<p id=\"p0245\">\n\n</p>", "<p id=\"p0250\">\n\n</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<p id=\"p0270\">\n\n</p>", "<p id=\"p0275\">\n\n</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0205\">We especially thank Mr. Qiuyuan Hua of Wenzhou Hua Qiuyuan Fishery Company Limited, who provided the sample fish for this study. This study is financially supported by the National Natural Science Foundation of China (Grant No. 31801049), the Major Science and Technology Innovation Program of Shanghai Municipal Education Commission, China (Grant No. 2019-01-07-00-01-E00059), and the Shanghai Nanmulin Biotechnology Company Limited.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Phylogeny of white-blotched river stingray and other 25 selected species</bold>. The phylogenomic tree was constructed with FastTree and MRBAYES using 212 one-to-one orthologous genes. <italic>B</italic>. <italic>flo</italic> (amphioxus) was used to root the tree. The 25 fishes are <italic>P</italic>. <italic>mar</italic> (<italic>Petromyzon</italic> <italic>marinus</italic>; sea lamprey), <italic>C</italic>. <italic>mil</italic> (<italic>Callorhinchus milii</italic>; elephant shark), <italic>P</italic>. <italic>leo</italic> (<italic>Potamotrygon leopoldi</italic>; white-blotched river stingray), <italic>L</italic>. <italic>cha</italic> (<italic>Latimeria chalumnae</italic>; coelacanth), <italic>L</italic>. <italic>ocu</italic> (<italic>Lepisosteus oculatu</italic>; spotted gar), <italic>I</italic>. <italic>pun</italic> (<italic>Ictalurus punctatus</italic>; channel catfish), <italic>A</italic>. <italic>mex</italic> (<italic>Astyanax mexicanus</italic>; blind cave fish), <italic>C</italic>. <italic>car</italic> (<italic>Cyprinus carpio</italic>; common carp), <italic>D</italic>. <italic>rer</italic> (<italic>Danio rerio</italic>; zebrafish), <italic>E</italic>. <italic>luc</italic> (<italic>Esox lucius</italic>; northern pike), <italic>S</italic>. <italic>sal</italic> (<italic>Salmo salar</italic>; Atlantic salmon), <italic>O</italic>. <italic>kis</italic> (<italic>Oncorhynchus kisutch</italic>; coho salmon), <italic>O</italic>. <italic>myk</italic> (<italic>Oncorhynchus mykiss</italic>; rainbow trout), <italic>G</italic>. <italic>mor</italic> (<italic>Gadus morhua</italic>; Atlantic cod), <italic>G</italic>. <italic>acu</italic> (<italic>Gasterosteus aculeatus</italic>; three-spined stickleback), <italic>T</italic>. <italic>nig</italic> (<italic>Tetraodon nigroviridis</italic>; green spotted puffer), <italic>T</italic>. <italic>rub</italic> (<italic>Takifugu rubripes</italic>; Japanese puffer), <italic>C</italic>. <italic>sem</italic> (<italic>Cynoglossus semilaevis</italic>; tongue sole), <italic>P</italic>. <italic>oli</italic> (<italic>Paralichthys olivaceus</italic>; Japanese flounder), <italic>O</italic>. <italic>nil</italic> (<italic>Oreochromis niloticus</italic>; Nile tilapia), <italic>O</italic>. <italic>lat</italic> (<italic>Oryzias latipes</italic>; rice fish), <italic>N</italic>. <italic>fur</italic> (<italic>Nothobranchius furzeri</italic>; turquoise killifish), <italic>X</italic>. <italic>mac</italic> (<italic>Xiphophorus maculatus</italic>; platyfish), <italic>P</italic>. <italic>ret</italic> (<italic>Poecilia reticulate</italic>; guppy), and <italic>P</italic>. <italic>for</italic> (<italic>Poecilia formosa</italic>; Amazon molly). Magenta indicates the Chondrichthyes lineage and sky blue indicates the Osteichthyes lineage. Divergence time is shown in million years. MYA, million years ago.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Gene orthology and family analyses for seven species</bold>. <bold>A.</bold> Gene orthology comparison among <italic>B</italic>. <italic>floridae</italic> (amphioxus), <italic>C</italic>. <italic>milii</italic> (elephant shark), <italic>P</italic>. <italic>leopoldi</italic> (white-blotched river stingray), <italic>L</italic>. <italic>chalumnae</italic> (coelacanth), <italic>L</italic>. <italic>oculatus</italic> (spotted gar), <italic>C</italic>. <italic>carpio</italic> (common carp), and <italic>D</italic>. <italic>rerio</italic> (zebrafish). <bold>B.</bold> Expansion and contraction of the IGHD gene family among seven species. <bold>C.</bold> Expansion and contraction of the TRAV/TRDV gene family among seven species. Number in red indicates the number of expanded genes; number in green indicates the number of contracted genes; number in the parenthesis indicates the total number of expanded and contracted genes. IGHD, immunoglobulin heavy constant delta; TRAV/TRDV, T-cell receptor alpha/delta variable.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Comparison of Hox gene clusters among seven fish species</bold>. The <italic>Hox</italic> genes were identified from <italic>B</italic>. <italic>floridae</italic> (amphioxus), <italic>C</italic>. <italic>milii</italic> (elephant shark), <italic>P</italic>. <italic>leopoldi</italic> (white-blotched river stingray), <italic>L</italic>. <italic>chalumnae</italic> (coelacanth),  <italic>L</italic>. <italic>oculatus</italic> (spotted gar), <italic>C</italic>. <italic>carpio</italic> (common carp), and <italic>D</italic>. <italic>rerio</italic> (zebrafish).</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Transcriptome analyses of</bold><italic><bold>P</bold></italic><bold>.</bold><italic><bold>leopoldi</bold></italic><bold>and other three fishes</bold>. <bold>A.</bold> Venn diagram flower plot of up-regulated genes in six tissues of <italic>P</italic>. <italic>leopoldi</italic>. <bold>B.</bold> Venn diagram flower plot of up-regulated genes specific in <italic>P</italic>. <italic>leopoldi</italic> compared to <italic>C. milii</italic>, <italic>L. oculatus</italic>, and <italic>D. rerio</italic>. <bold>C.</bold> PCA of the expression levels of 3738 one-to-one orthologous genes in the brain, heart, liver, and muscle of <italic>P.</italic> <italic>leopoldi</italic>, <italic>C</italic>. <italic>milii</italic>, <italic>L</italic>. <italic>oculatus</italic>, and <italic>D</italic>. <italic>rerio.</italic> PC, principal component; PCA, principal component analysis.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Analyses of bone formation-related genes among seven selected species</bold>. <bold>A.</bold> Phylogenetic analysis of BMP gene family among seven selected species. <bold>B.</bold> Alizarin Red S staining of 6-dpf control zebrafish. WT represents embryos without injection; EGFP represents embryos injected with RNPs against <italic>EGFP</italic>. <bold>C.</bold> Alizarin Red S staining of 6-dpf <italic>gc</italic>-knockdown zebrafish. gc-e4 represents embryos injected with RNPs against exon 4 of the <italic>gc</italic> gene; gc-e8 represents embryos injected with RNPs against exon 8 of the <italic>gc</italic> gene. WT, wild-type; dpf, days post-fertilization; BMP, bone morphogenetic protein; RNP, ribonucleoprotein; EGFP, enhanced green fluorescent protein.</p></caption></fig>", "<fig id=\"f0030\" position=\"anchor\"><label>Supplementary Figure S1</label><caption><p><bold>The distribution of tandem repeat sequences in white-blotched river stingray genome</bold> X-axis is the divergence of stingray’s tandem repeat sequences to the TE sequences in the Repbase database. SINE, short interspersed element; LINE, long interspersed element; LTR, long terminal repeat; TE, transposon element.</p></caption></fig>", "<fig id=\"f0035\" position=\"anchor\"><label>Supplementary Figure S2</label><caption><p><bold>Venn diagram of the function annotation for white-blotched river stingray’s protein-coding genes using four protein databases</bold> NR, Non-Redundant Protein Sequence Database; KEGG, Kyoto Encyclopedia of Genes and Genomes.</p></caption></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary Figure S3</label><caption><p><bold>The maximum likelihood tree of white-blotched river stingray and 25 selected species with statistical support values</bold> AMX for blind cave fish. DAR for zebrafish. GMO for Atlantic cod. GAC for three-spined stickleback. LAC for coelacanth. LOC for spotted gar. ONI for Nile tilapia. ORL for rice fish. PMA for sea lamprey. PFO for Amazon molly. TRU for Japanese puffer. TNI for green spotted puffer. XMA for platyfish. CMI for elephant shark. CSE for tongue sole. CCA for common carp. ELU for northern pike. IPU for channel catfish. NFU for turquoise killifish. OKI for coho salmon. OMY for rainbow trout. POL for Japanese flounder. PRE for guppy. SSA for Atlantic salmon. BRF for amphioxus. PLE for white-blotched river stingray. Branch length is proportional to the substitution rate.</p></caption></fig>", "<fig id=\"f0045\" position=\"anchor\"><label>Supplementary Figure S4</label><caption><p><bold>The Bayesian tree of white-blotched river stingray and 25 selected species with posterior probability support</bold> AMX for blind cave fish. DAR for zebrafish. GMO for Atlantic cod. GAC for three-spined stickleback. LAC for coelacanth. LOC for spotted gar. ONI for Nile tilapia. ORL for rice fish. PMA for sea lamprey. PFO for Amazon molly. TRU for Japanese puffer. TNI for green spotted puffer. XMA for platyfish. CMI for elephant shark. CSE for tongue sole. CCA for common carp. ELU for northern pike. IPU for channel catfish. NFU for turquoise killifish. OKI for coho salmon. OMY for rainbow trout. POL for Japanese flounder. PRE for guppy. SSA for Atlantic salmon. BRF for amphioxus. PLE for white-blotched river stingray. Branch length is proportional to substitution rate.</p></caption></fig>", "<fig id=\"f0050\" position=\"anchor\"><label>Supplementary Figure S5</label><caption><p><bold>The species tree of 25 selected fishes and one chordate</bold></p></caption></fig>", "<fig id=\"f0055\" position=\"anchor\"><label>Supplementary Figure S6</label><caption><p><bold>The MCMCtree for estimating the divergence time of white-blotched river stingray and 25 selected species</bold> AMX for blind cave fish. DAR for zebrafish. GMO for Atlantic cod. GAC for three-spined stickleback. LAC for coelacanth. LOC for spotted gar. ONI for Nile tilapia. ORL for rice fish. PMA for sea lamprey. PFO for Amazon molly. TRU for Japanese puffer. TNI for green spotted puffer. XMA for platyfish. CMI for elephant shark. CSE for tongue sole. CCA for common carp. ELU for northern pike. IPU for channel catfish. NFU for turquoise killifish. OKI for coho salmon. OMY for rainbow trout. POL for Japanese flounder. PRE for guppy. SSA for Atlantic salmon. BRF for amphioxus. PLE for white-blotched river stingray. The numbers adjacent to the nodes are divergence time which is shown in million years.</p></caption></fig>", "<fig id=\"f0060\" position=\"anchor\"><label>Supplementary Figure S7</label><caption><p><bold>GO enrichment analyses for expanded and contracted gene families identified in white-blotched river stingray</bold> GO, Gene Ontology.</p></caption></fig>", "<fig id=\"f0065\" position=\"anchor\"><label>Supplementary Figure S8</label><caption><p><bold>Upset plot of down-regulated genes in six tissues of white-blotched river stingray</bold></p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"t0005\"><label>Table 1</label><caption><p><bold>Merqury metrics for drafts of the <italic>P</italic>. <italic>leopoldi</italic> genome</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Metric</bold></th><th><bold>Genome</bold></th></tr></thead><tbody><tr><td>Consensus quality value</td><td align=\"left\">37.53</td></tr><tr><td>Assembly error rate (%)</td><td align=\"left\">&lt; 0.01</td></tr><tr><td><italic>K</italic>-mer completeness (%)</td><td align=\"left\">96.51</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0010\"><label>Table 2</label><caption><p><bold>Amino acid substitution rate in 26 fish species</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Species</bold></th><th><bold>Number of substitutions per site</bold></th></tr></thead><tbody><tr><td>Amphioxus</td><td align=\"char\">0.408705</td></tr><tr><td>Sea lamprey</td><td align=\"char\">0.277635</td></tr><tr><td>Elephant shark</td><td align=\"char\">0.252635</td></tr><tr><td>White-blotched river stingray</td><td align=\"char\">0.250005</td></tr><tr><td>Coelacanth</td><td align=\"char\">0.265845</td></tr><tr><td>Spotted gar</td><td align=\"char\">0.250345</td></tr><tr><td>Channel catfish</td><td align=\"char\">0.338655</td></tr><tr><td>Blind cave fish</td><td align=\"char\">0.364285</td></tr><tr><td>Zebrafish</td><td align=\"char\">0.329255</td></tr><tr><td>Common carp</td><td align=\"char\">0.353285</td></tr><tr><td>Northern pike</td><td align=\"char\">0.329085</td></tr><tr><td>Atlantic salmon</td><td align=\"char\">0.321695</td></tr><tr><td>Rainbow trout</td><td align=\"char\">0.328565</td></tr><tr><td>Coho salmon</td><td align=\"char\">0.335825</td></tr><tr><td>Atlantic cod</td><td align=\"char\">0.381235</td></tr><tr><td>Three-spined stickleback</td><td align=\"char\">0.363065</td></tr><tr><td>Green spotted puffer</td><td align=\"char\">0.410095</td></tr><tr><td>Japanese puffer</td><td align=\"char\">0.394355</td></tr><tr><td>Nile tilapia</td><td align=\"char\">0.358895</td></tr><tr><td>Rice fish</td><td align=\"char\">0.407615</td></tr><tr><td>Turquoise killifish</td><td align=\"char\">0.388785</td></tr><tr><td>Platyfish</td><td align=\"char\">0.388865</td></tr><tr><td>Amazon molly</td><td align=\"char\">0.397335</td></tr><tr><td>Guppy</td><td align=\"char\">0.393995</td></tr><tr><td>Tongue sole</td><td align=\"char\">0.391035</td></tr><tr><td>Japanese flounder</td><td align=\"char\">0.359955</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0015\"><label>Table 3</label><caption><p><bold>GO enrichment analysis of up-regulated tissue-specific genes in</bold><bold><italic>P</italic>. <italic>leopoldi</italic></bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Category</bold></th><th><bold>GO term</bold></th><th><bold><italic>P</italic> value</bold></th></tr></thead><tbody><tr><td><bold>Blood</bold></td><td/><td/></tr><tr><td>GOTERM_BP_DIRECT</td><td>Erythrocyte development</td><td>6.62 × 10<sup>−6</sup></td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Embryonic hemopoiesis</td><td>3.41 × 10<sup>−5</sup></td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Erythrocyte differentiation</td><td>6.48 × 10<sup>−5</sup></td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Hemopoiesis</td><td>7.09 × 10<sup>−4</sup></td></tr><tr><td><bold>Brain</bold></td><td/><td/></tr><tr><td>GOTERM_BP_DIRECT</td><td>Central nervous system development</td><td>8.02 × 10<sup>−4</sup></td></tr><tr><td>INTERPRO</td><td>Neurotransmitter-gated ion-channel</td><td>0.001797</td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Ganglioside biosynthetic process</td><td>0.002529</td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Neuropeptide signaling pathway</td><td>0.012035</td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Neural crest cell migration</td><td>0.016101</td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Hindbrain development</td><td>0.027042</td></tr><tr><td><bold>Heart</bold></td><td/><td/></tr><tr><td>GOTERM_BP_DIRECT</td><td>Cardiac muscle cell differentiation</td><td>2.46 × 10<sup>−5</sup></td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Heart morphogenesis</td><td>6.17 × 10<sup>−4</sup></td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Heart looping</td><td>9.05 × 10<sup>−4</sup></td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Heart development</td><td>0.005143</td></tr><tr><td><bold>Liver</bold></td><td/><td/></tr><tr><td>GOTERM_BP_DIRECT</td><td>Liver development</td><td>7.39 × 10<sup>−4</sup></td></tr><tr><td>GOTERM_MF_DIRECT</td><td>Oxidoreductase activity</td><td>1.54 × 10<sup>−11</sup></td></tr><tr><td>KEGG_PATHWAY</td><td>Glycine, serine and threonine metabolism</td><td>0.007413</td></tr><tr><td>KEGG_PATHWAY</td><td>Fatty acid degradation</td><td>8.55 × 10<sup>−5</sup></td></tr><tr><td><bold>Muscle</bold></td><td/><td/></tr><tr><td>GOTERM_BP_DIRECT</td><td>Muscle organ development</td><td>1.76 × 10<sup>−5</sup></td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Skeletal muscle tissue development</td><td>7.32 × 10<sup>−5</sup></td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Myofibril assembly</td><td>2.78 × 10<sup>−4</sup></td></tr><tr><td>INTERPRO</td><td>Myogenic basic muscle-specific protein</td><td>4.65 × 10<sup>−4</sup></td></tr><tr><td>GOTERM_BP_DIRECT</td><td>Skeletal muscle cell differentiation</td><td>0.00223</td></tr><tr><td>UP_KEYWORDS</td><td>Myogenesis</td><td>0.003216</td></tr><tr><td><bold>Skin</bold></td><td/><td/></tr><tr><td>GOTERM_BP_DIRECT</td><td>Ectodermal placode formation</td><td>0.068466</td></tr><tr><td>GOTERM_CC_DIRECT</td><td>Melanosome</td><td>0.015904</td></tr></tbody></table></table-wrap>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0070\"><caption><title>Supplementary Table S1</title><p><bold>Statistics of genome sequencing data of white-blotched river stingray</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0065\"><caption><title>Supplementary Table S2</title><p><bold>Base content statistics of white-blotched river stingray genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Table S3</title><p><bold>Characteristic statistics of genome assembly</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Table S4</title><p><bold>Reads coverage statistics of white-blotched river stingray genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Table S5</title><p><bold>Genome assembly results of white-blotched river stingray</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S6</title><p><bold>Statistical results of repeated sequences in white-blotched river stingray genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S7</title><p><bold>Statistics of repeated sequence classification in white-blotched river stingray genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S8</title><p><bold>Basic statistical information for gene structure prediction</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S9</title><p><bold>The gene function annotation using different methods</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S10</title><p><bold>Gene structures in eleven fish species</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S11</title><p><bold>Statistics of non-coding RNAs in white-blotched river stingray genome</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S12</title><p><bold>Evolutionary rate evaluated by Tajima’s rate tests among 26 species</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S13</title><p><bold>The number of BMPs and BMP receptors in seven species</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S14</title><p><bold>Primer sequences used to generate sgRNAs used in this study</bold></p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e793\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0150\" fn-type=\"supplementary-material\"><p id=\"p0210\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.11.005\" id=\"ir105\">https://doi.org/10.1016/j.gpb.2022.11.005</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["4"], "surname": ["Compagno", "Hamlett"], "given-names": ["L.J.V.", "W.C."], "part-title": ["Checklist of living elasmobranches"], "source": ["editor. Sharks, skates, and rays: the biology of elasmobranch fishes"], "year": ["1999"], "publisher-name": ["Johns Hopkins University Press"], "publisher-loc": ["Baltimore"], "fpage": ["471"], "lpage": ["498"]}, {"label": ["6"], "mixed-citation": ["Zhang Y, Gao H, Li H, Guo J, Ouyang B, Wang M, et al. The white-spotted bamboo shark genome reveals chromosome rearrangements and fast-evolving immune genes of cartilaginous fish. iScience 2020;23:101754."]}, {"label": ["9"], "surname": ["Carrier", "Musick", "Heithaus"], "given-names": ["J.C.", "J.A.", "M.R."], "article-title": ["Sharks and their relatives II\u202f: biodiversity, adaptive physiology, and conservation"], "source": ["J Fish Biol"], "volume": ["79"], "year": ["2011"], "fpage": ["308"], "lpage": ["309"]}, {"label": ["10"], "surname": ["Duncan", "Fernandes"], "given-names": ["W.P.", "M.N."], "article-title": ["Physicochemical characterization of the white, black, and clearwater rivers of the Amazon Basin and its implications on the distribution of freshwater stingrays (Chondrichthyes, Potamotrygonidae)"], "source": ["PanamJAS"], "volume": ["5"], "year": ["2010"], "fpage": ["454"], "lpage": ["464"]}, {"label": ["35"], "surname": ["Datte"], "given-names": ["P.M."], "article-title": ["Earliest mammal with transversely expanded upper molar from the Late Triassic (Carman) Tiki Formation, South Rewa Gondwana Basin, India"], "source": ["J Vertebr Paleontol"], "volume": ["25"], "year": ["2005"], "fpage": ["200"], "lpage": ["207"]}, {"label": ["41"], "mixed-citation": ["Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics 2009;Chapter 4:Unit 4.10."]}, {"label": ["66"], "surname": ["Prakash", "Jeffryes", "Bateman", "Finn"], "given-names": ["A.", "M.", "A.", "R.D."], "article-title": ["The HMMER web server for protein sequence similarity search"], "source": ["Curr Protoc Bioinformatics"], "volume": ["60"], "year": ["2017"], "fpage": ["3"]}]
{ "acronym": [], "definition": [] }
79
CC BY
no
2024-01-14 23:41:55
Genomics Proteomics Bioinformatics. 2023 Jun 5; 21(3):501-514
oa_package/03/32/PMC10787021.tar.gz
PMC10787022
37100237
[ "<title>Introduction</title>", "<p id=\"p0005\">High-quality genome assembly establishes a reference for exploring the evolutionary history and genetic mechanisms of complex traits and facilitates molecular breeding and genomics studies. Fast-growing sequencing technologies and algorithm innovations have promoted breakthroughs in both animal and plant genomes to date. However, assemblies of plant genomes are much more challenging than those of animal genomes, because most animal genomes are diploid and contain fewer repetitive sequences compared to plant genomes ##REF##16892970##[1]##, ##REF##30519250##[2]##. In contrast, plant genomes span several orders of magnitude in size, vary in ploidy and heterozygosity levels, and contain a large number of different types of repeats (35%–90% of the genome) ##REF##30239695##[3]##. Since the first plant genome release for the model plant <italic>Arabidopsis thaliana</italic> in 2000 ##REF##11130711##[4]##, more than 800 plant genomes have been published to date, including the genomes of eudicots, monocots, gymnosperms, ferns, lycophytes, bryophytes, charophytes, and chlorophytes ##UREF##0##[5]##. However, most of these published plant genomes are simple genomes characterized by &lt; 0.8% heterozygosity, and/or &lt; 60% repetitive sequences, whereas chromosome-scale assemblies of plant genomes with highly repetitive sequences, high heterozygosity, or polyploid genomes are incredibly scarce.</p>", "<p id=\"p0010\">Resolving highly repetitive sequences is meaningful for understanding genome evolution and for mining functional elements. For instance, many plants are dioecious with a newly evolved Y chromosome. The suppressed recombination region in the Y chromosome accumulates a large number of mobile elements, which could account for more than 90% of the examined region ##REF##21526970##[6]##, ##UREF##1##[7]##, ##REF##33782581##[8]##. Although some sex determination factors have been identified in a few plant species, including papaya ##REF##22869747##[9]##, poplar ##REF##32483326##[10]##, and fig trees ##REF##33035453##[11]##, the assembly of highly repetitive sequences poses notable challenges, hindering the discovery of sex determination mechanisms in a massive number of dioecious plants. In addition, nearly 80% of plants have undergone whole-genome duplication(s), and many of them still maintain polyploidy with a high level of heterozygosity among haplotypes ##REF##16892970##[1]##. Polyploidy is considered the main force of plant evolution ##REF##30519250##[2]##, contributing to many well-known crops that humans rely on for survival, including wheat (<italic>Triticum aestivum</italic>), rape (<italic>Brassica napus</italic>), upland cotton (<italic>Gossypium hirsutum</italic>), peanut (<italic>Arachis hypogaea</italic>), strawberry (<italic>Fragaria ananassa</italic>), potato (<italic>Solanum tuberosum</italic>), banana (<italic>Musa</italic> spp.), and sugarcane (<italic>Saccharum officinarum</italic>).</p>", "<p id=\"p0015\">Given the importance of these plant species, complex plant genome sequencing has been an emerging frontier in the genomics field. Recently, single-molecule sequencing (SMS) technologies and haplotype assembly algorithms have efficiently generated chromosome-scale and haplotype-phased complex genome assemblies for a few species, including potato ##REF##32989320##[12]##, ##REF##35026436##[13]##, ##REF##35733345##[14]##, ##REF##35767385##[15]##, ##REF##35241824##[16]##, sugarcane ##REF##30297971##[17]##, ##REF##35654976##[18]##, and alfalfa ##REF##31570895##[19]##. Herein, we summarize the challenges of complex genome assembly, the advantages of SMS platforms, and newly developed assembly algorithms in complex plant genome assembly, aiming to provide a comprehensive reference facilitating future genome projects.</p>" ]
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[ "<title>Discussion and future prospects</title>", "<p id=\"p0150\">Deciphering complex plant genomes is of significance in understanding the basic biological mechanisms, including the discovery of key genes or structural variants related to resistance ##REF##28154240##[117]##, ##UREF##15##[118]## and sex determination ##REF##33035453##[11]##. Additionally, benefitting from the development of phasing algorithms, comparative analysis between/among haplotypes in highly heterozygous or polyploid genomes identifies abundant allelic variations, which provide a genetic basis for studying fundamental biological questions about heterosis and allelic imbalance.</p>", "<p id=\"p0155\">In this review, we describe some examples of complex plant genome projects and many tools being used to address the complexity of genome assembly. We recommend that ∼ 30× HiFi and ∼ 100× Hi-C sequencing are necessary for high-quality assemblies of complex genomes. Contigs with high continuity and accuracy can be assembled and phased by a widely used HiFi assembler, Hifiasm ##REF##35332338##[96]##, ##REF##33526886##[97]##. Chromosomal-scale assembly can be achieved using a series of Hi-C scaffolders, including 3D-DNA for diploid genomes and ALLHiC for polyploid genomes. In addition, a significantly improved gapless or T2T assembly requires additional ultralong ONT reads based on several successful cases ##REF##34171480##[27]##, ##REF##34171481##[109]##, ##REF##35748695##[110]##, ##UREF##14##[111]##, ##REF##34487862##[112]##, ##REF##35655433##[113]##. If parents or derived population materials exist, resequencing of these materials can obviously improve haplotype results. However, there is no all-powerful method applicable to all genomes and the optimal genome assembly sometimes needs testing of different pipelines.</p>", "<p id=\"p0160\">Indeed, dozens of plant species that are economically important have ultracomplex genomes, leaving their genomic sequences under ongoing development. A typical example is modern hybrid sugarcane (<italic>Saccharum</italic> spp. hybrids), a widely cultivated crop of sugar and bioenergy production ##UREF##16##[119]##. The nuclear genome of modern hybrid sugarcane is composed of subgenomes originally from <italic>S. officinarum</italic> (an octoploid species, with a basic chromosome number of 10, 2<italic>n</italic> = 80) and <italic>S. spontaneum</italic> (varied ploidy levels between 5× and 16×, a basic chromosome number of 8, 2<italic>n</italic> = 40–128). The hybrid sugarcane genome is much more complicated due to the uneven inheritance of genetic materials from its progenitors through interspecific crosses and one or more subsequent backcrosses ##UREF##17##[120]##, ##UREF##18##[121]##. Modern hybrid sugarcane has a basic chromosome number of 10. However, its complexity resides in the mixture of aneuploid and homo(eo)logous chromosomes, which results in 10 uneven homo(eo)logous chromosome groups of the modern hybrid sugarcane genome carrying a total number of chromosomes ranging from 100 to 130 ##REF##8849904##[122]##, ##REF##29868072##[123]##. It means that there are 8–14 homo(eo)logous copies for most genes in the hybrid sugarcane genome ##REF##29868072##[123]##, ##UREF##19##[124]##. The state-of-the-art Hi-C scaffolding technology loses its power on ultracomplex genomes mostly owing to an extremely low level of uniquely mapped short reads. The recently proposed Pore-C method, which integrates single-molecule long-read sequencing and three-dimensional chromatin conformation capture technology, is able to detect multiway interactions among different genomic regions and distinguish highly similar genomic sequences ##REF##35637420##[125]##. The experimental innovation promises an effective approach to avoid multiple alignment in polyploid genomes, likely solving the ultracomplex sugarcane genome assembly.</p>" ]
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[ "<p>Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, <bold>complex plant genome</bold> assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to <bold>sequencing technology</bold>, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Kai Ye</p>" ]
[ "<title>Challenges of complex genome assembly</title>", "<title>High repetitive sequence content</title>", "<p id=\"p0020\">Repetitive sequences that are similar or identical to sequences elsewhere in the genome represent an important and pervasive part of the dark matter of genomes ##UREF##2##[20]##, ##REF##31767853##[21]##. Many plant genomes are filled with repetitive sequences, including various satellites, rDNA, short interspersed nuclear elements, long interspersed nuclear elements, long terminal repeat (LTR) retrotransposons, and DNA transposons ##REF##26514350##[22]##. For instance, the total repetitive sequences account for ∼ 85% in maize genome ##REF##19965430##[23]## and in the wheat genome ##UREF##3##[24]##, and 74%–80% in the tea plant genome ##REF##28231512##[25]##. These different types of repetitive sequences contain anywhere from two copies to millions of copies, ranging from 1–2 bases (mono- and dinucleotide repeats) to millions of bases ##UREF##2##[20]##, ##REF##30061735##[26]##. These repeat-rich regions usually involve many important genetic functional regions, namely, telomeres, centromeres, multicopy genes, and non-recombining and highly heterochromatic chromosomes such as the Y and W sex chromosomes ##REF##33035453##[11]##, ##REF##34171480##[27]##. Given that these regions play essential roles in the function and evolution of the genome ##REF##17506661##[28]##, ##REF##21041622##[29]##, ##REF##19029538##[30]##, ##REF##19189423##[31]##, the need to precisely assemble them has become a hurdle in complex genome studies.</p>", "<p id=\"p0025\">However, repetitive sequences with hundreds or thousands of repeat units are widely distributed in genomes and cover an ultralong genomic region (such as nest LTRs, which can span 20–200 kb) that cannot be spanned by even long reads generated by SMS. In assemblies with short reads (35–800 bp) as input, nearly identical tandem repeats usually fold into fewer copies (<italic>i.e.</italic>, collapsed assembly, ##FIG##0##Figure 1##A), making it difficult to determine the true number of copies. Similarly, unzipping two identical interspersed repeat units from the assembly graph can produce false joins with flanking unique sequences, leading to chimeric and fragmented contigs (##FIG##0##Figure 1##B). Due to improvements in the length of SMS reads, many repeat regions can now be well resolved, except for the extremely long and complex repeat regions. However, the high level of sequencing errors in SMS reads poses challenges to accurately distinguish minor variants among repetitive sequences from sequencing errors. On the one hand, low-frequency genetic variants with frequencies lower than the sequencing error rate may be mistaken for sequencing error, leading to the underestimation of low-frequency genetic variations. On the other hand, the sequencing error will be mistaken for the genetic variants, resulting in misassembly when sequencing errors are not corrected (##FIG##0##Figure 1##C).</p>", "<title>High heterozygosity</title>", "<p id=\"p0030\">In low-heterozygosity species, the variations between the two haplotypes are mainly small-scale. These small-scale variations enable accurate alignment during assembly, resulting in consensus sequences (##FIG##1##Figure 2##A). However, genomes with high heterozygosity contain many large-scale structural variations between the two haplotypes, leading to assembly ‘bubbles’ that represent redundant allelic sequences (##FIG##1##Figure 2##B). Many plants have high genome heterozygosity due to distant hybridization and self-incompatibility. Therefore, the assembly of these highly heterozygous genomes usually generates a larger size than the estimated size of the haploid genome.</p>", "<title>Polyploidy</title>", "<p id=\"p0035\">Plant polyploidizations originate either from whole-genome duplication of a single species (autopolyploidy) or interspecific hybridization followed by chromosome doubling (allopolyploidy) ##REF##19575590##[32]##, ##UREF##4##[33]##. The assembly of allopolyploid genomes is less complex, and the first wave of polyploid genome assemblies has mainly involved allopolyploid crops, such as rape (<italic>B. napus</italic>), cotton (<italic>G. hirsutum</italic>), and peanut (<italic>A</italic>. <italic>hypogaea</italic>). It is relatively easy to distinguish subgenomes originating from different ancestral species because they have maintained a large proportion of genetic variations during their long evolutionary history. However, autopolyploid organisms consisting of more than two homologous sets of chromosomes pose significant challenges in genome assembly and haplotype phasing due to the high similarity between homologous chromosomes ##REF##31908732##[34]##.</p>", "<p id=\"p0040\">For example, the autotetraploid genome has four similar haplotypes that contain a large proportion of nearly identical sequences. Linking these identical sequences has a tendency to generate chimeric contigs with switch errors or false duplications (##FIG##2##Figure 3##A). These chimeric contigs confuse high-throughput/resolution chromosome conformation capture (Hi-C) signals, resulting in erroneous scaffolds that mess up sequences from different haplotypes (##FIG##2##Figure 3##B). In addition, nearly identical homologous sequences between different haplotypes cannot be accurately distinguished, leaving many collapsed contigs (##FIG##2##Figure 3##C). Furthermore, these collapsed contigs generate Hi-C links with phased contigs belonging to different haplotypes, resulting in superlong and erroneous scaffolds (##FIG##2##Figure 3##D).</p>", "<title>Technical innovations in complex genome assembly</title>", "<title>Evolution of sequencing platforms</title>", "<p id=\"p0045\">Earlier plant genome assemblies were generated using Sanger sequencing and next-generation sequencing (NGS) technologies combined with the minimum tiling path, the overlap layout consensus, or <italic>de Bruijn</italic> graph approaches ##UREF##5##[35]##, ##UREF##6##[36]##, ##REF##31981929##[37]##, ##REF##8752207##[38]## for species such as <italic>A</italic>. <italic>thaliana</italic>\n##REF##11130711##[4]##, <italic>Oryza sativa</italic>\n##REF##11935018##[39]##, ##REF##11935017##[40]##, <italic>Carica papaya</italic>\n##REF##18432245##[41]##, <italic>G. max</italic>\n##REF##20075913##[42]##, and <italic>Populus trichocarpa</italic>\n##UREF##7##[43]##. Although widely used in many genome projects, these sequencing technologies have limited power to overcome assembly challenges in complex genomes due to the limited length of short reads (&lt; 1000 bp) and inevitable GC bias. For instance, sequencing a 2.3-Gb maize genome relied on the construction of 16,848 bacterial artificial chromosome (BAC) libraries. This process was highly labor intensive and generated a fragmented assembly with more than 10% of genomic sequences missing ##REF##19965430##[23]##.</p>", "<p id=\"p0050\">The subsequent SMS technologies advanced by Pacific Biosciences (<italic>i.e.</italic>, PacBio) and Oxford Nanopore Technology (ONT) companies were able to generate long reads that could span the kilobase- or even megabase-level repetitive regions along chromosomes. The first plant genome (<italic>Oropetium thomaeum</italic>) assembled based on only PacBio long reads demonstrated the ability of genome assembly in terms of contiguity and completeness ##REF##31981929##[37]##, ##REF##26560029##[44]##. In addition, the maize B73 genome assembled by PacBio data had a 52-fold increase in contig continuity with reduced assembly errors in the centromeric region compared with the previous version ##REF##19965430##[23]## and greatly facilitated the annotation of functional genes and the evolutionary analysis of transposons ##REF##28605751##[45]##. Although SMS technologies have made revolutionary advancements in the assembly of complex plant genomes, they suffer from a higher sequencing error rate, ranging from 5% to 20% ##REF##29713083##[46]##. To address this issue, PacBio adopts the circular consensus sequencing model to generate long high-fidelity (HiFi) reads by reading multiple passes of a single template molecule ##REF##31406327##[47]##. This strategy achieves a read accuracy of more than 99.8% but at the cost of read length.</p>", "<title>Experimental approaches for genome scaffolding</title>", "<p id=\"p0055\">The reconstruction of chromosomes is an ultimate goal in genome assembly, aiming to determine the orientation and orders of contigs globally. This step, called scaffolding, is vital for many downstream analyses and applied tasks, including the identification of genome-wide genotype–phenotype associations, marker-assisted breeding, and chromosome evolution analysis. Genetic maps were widely applied to early genome projects for genome scaffolding, such as <italic>Arabidopsis</italic>\n##REF##11130711##[4]## and rice genomes ##REF##11935018##[39]##, ##REF##11935017##[40]##. It successfully solved some complex genome assemblies, including that of the hexaploid bread wheat genome ##REF##25637298##[48]##.</p>", "<p id=\"p0060\">During the past decade, fruitful achievements have been made in experimental approaches for genome scaffolding, including BioNano optical maps using a light microscope-based technique to capture the physical locations of selected enzymes and a chromatin conformation capture technique (Hi-C) based on proximity ligation of chromatin. These two novel scaffolding approaches can quickly and accurately reconstruct the chromosomes for some complex plant genomes. Despite the limitation of sparse enzyme sites and the requirement of extraction of long DNA molecules ##REF##32802277##[49]##, BioNano technology has shown its power in chromosomal-scale genome assembly in some plant genome projects, such as that of sorghum ##REF##30451840##[50]##. Hi-C technology can construct linkage information between contigs by detecting long-distance DNA interactions and has become routine for most genome projects. Applying Hi-C has resulted in the successful assembly of dozens or even hundreds of genomes, especially some complex polyploid genomes, such as those of sugarcane ##REF##30297971##[17]## and alfalfa ##REF##32427850##[51]##.</p>", "<title>Strategies for monoploid assembly in diploid genomes</title>", "<p id=\"p0065\">Most diploid genome projects aim to generate ‘consensus’ sequences (<italic>i.e.</italic>, monoploid assembly) to represent a reference genome for a given species (##FIG##1##Figure 2##A). This goal can be easily achieved for some plant genomes with extremely low heterozygosity, such as those of <italic>Arabidopsis</italic> and rice. However, the assembly of heterozygous genomes requires additional processes to solve ‘bubbles’ representing redundant sequences in initial contigs, which contain a large proportion of allelic contigs that originate from homologous chromosomes. Thus, three main strategies have been designed to classify these redundant contigs: read depth (RD)-, whole genome alignment comparison (WGAC)-, and <italic>K</italic>-mer-based strategies.</p>", "<p id=\"p0070\">The RD-based strategy identifies collapsed and redundant sequences by investigating the sequencing depth of mapped reads. The RDplot of the initial contigs in a highly heterozygous genome usually shows a bimodal distribution. Suppose collapsed or haplotype-fused contigs have a 1× RD. In that case, redundant contigs will only have approximately 0.5× RD, because redundant sequences will evenly distribute total reads due to the sequence similarity of two redundant contigs (##FIG##3##Figure 4##A). As a typical example, purge_haplotigs software ##REF##30497373##[52]## utilizes the RD-based strategy for identifying and removing these redundant sequences from a heterozygous assembly and eventually retains primary contigs to construct the monoploid genome (##FIG##3##Figure 4##A). The RD-based strategy has been successfully applied to several highly heterozygous genomes, namely, golden buckwheat (<italic>Fagopyrum dibotrys</italic>) ##REF##35701896##[53]##, red clover (<italic>Trifolium pratense</italic> L.) ##REF##35820796##[54]##, lilacs (<italic>Syringa oblata</italic> L.) ##REF##35673966##[55]##, and carnation (<italic>Dianthus caryophyllus</italic>) ##REF##35247284##[56]##. However, the RD-based strategy consumes time and money due to the need for large-scale global alignment of genome sequences.</p>", "<p id=\"p0075\">In contrast, several software programs, such as Pseudohaploid ##REF##31570895##[19]##, purge_dups ##REF##31971576##[57]##, and Redundans ##REF##27131372##[58]##, implement the WGAC-based strategy to identify allelic contigs that have a high level of similarity and overlapping sequences. The long alignment chains detected by pairwise comparison between assembled contigs are considered redundant homologous regions. Only one copy of these homologous regions with a longer size was eventually retained as a representative haplotype (##FIG##3##Figure 4##B). However, the WGAC-based strategy is also time-consuming due to the global contig pairwise comparison.</p>", "<p id=\"p0080\">To efficiently detect redundant contigs in complex genomes, a <italic>K</italic>-mer-based strategy named Khaper was proposed ##REF##29713083##[46]##. The basic concept of Khaper is to search for common low- and medium-frequency <italic>K</italic>-mers via pairwise comparison between contigs and to identify potential allelic contigs if they share a high proportion of low- and medium-frequency <italic>K</italic>-mers (##FIG##3##Figure 4##C). Because it does not rely on genome-wide sequence alignment, Khaper significantly saves central processing unit (CPU) time and solves the problems of time consumption and overutilization of computational resources in removing the redundancy process of large genomes with high heterozygosity ##REF##29713083##[46]##.</p>", "<title>Toward haplotype-resolved assembly</title>", "<p id=\"p0085\">Most reference genomes for diploid and polyploid organisms stay at the ‘monoploid’ level, which represents ‘mosaic’ sequences that mix two or more homologous chromosomes. Unzipping accurate haplotypes in a polyploid genome is beset with difficulties. In the case of an <italic>n</italic>-ploid organism, <italic>n</italic> − 1 haplotypes must be computed before the haplotype of interest can be inferred. For a pair of single-nucleotide polymorphisms (SNPs) in a polyploid, there are theoretically <italic>n</italic>! connection possibilities. Recently, upgraded sequencing technologies and innovations in algorithms and strategies have provided the basis for assembling highly heterozygous diploid and polyploid genomes at the haplotype level rather than at the monoploid level.</p>", "<p id=\"p0090\">To date, the built-in heuristic algorithms of multiple reference-based or <italic>de novo</italic> phasing tools have been systematically summarized ##REF##31908732##[34]##, ##UREF##8##[59]##, ##UREF##9##[60]##. However, many have been developed for the human genome and have not been applied well to plant genome assembly. Here, to explore effectual phased tools and strategies for assembling complex plant genomes, we have summarized the recently published haplotype-resolved assemblies in plant genomes. We have further divided these assembly approaches into two strategies: reference-based variant phasing and <italic>de novo</italic> assembly-based haplotype phasing (##TAB##0##Table 1##) ##REF##32989320##[12]##, ##REF##32427850##[51]##, ##REF##35733345##[14]##, ##REF##35767385##[15]##, ##REF##35241824##[16]##, ##REF##30297971##[17]##, ##REF##35654976##[18]##, ##REF##34980919##[61]##, ##REF##28827752##[62]##, ##REF##35785503##[63]##, ##UREF##10##[64]##, ##UREF##11##[65]##, ##REF##35548270##[66]##, ##REF##35799188##[67]##, ##REF##33139952##[68]##, ##REF##35333302##[69]##, ##REF##35717499##[70]##, ##REF##34661327##[71]##, ##REF##33605092##[72]##, ##REF##37128067##[73]##, ##REF##33175097##[74]##, ##REF##34354044##[75]##, ##REF##33931633##[76]##, ##REF##34267370##[77]##, ##REF##33866024##[78]##, ##REF##34990066##[79]##, ##REF##32673760##[80]##, ##REF##35033678##[81]##, ##REF##35655434##[82]##, ##REF##35122338##[83]##, ##REF##34792565##[84]##, ##REF##31334758##[85]##, ##REF##31649061##[86]##, ##REF##33118252##[87]##, ##REF##33372615##[88]##, ##REF##31324816##[89]##, ##REF##33128049##[90]##.</p>", "<title>Reference-based variant phasing</title>", "<p id=\"p0095\">In reference-based variant phasing, a high-quality genome is required as the reference to distinguish different haplotypes based on long-range linked allelic variants through alignments of sequencing reads against the reference genome using different phasing algorithms, including minimum error correction ##REF##27280382##[91]##, weighted minimum letter flip ##UREF##8##[59]##, maximum fragment cut ##UREF##12##[92]##, and polyploid balanced optimal partition ##REF##27531103##[93]## as different frameworks ##REF##31908732##[34]##, ##UREF##8##[59]##, ##UREF##9##[60]##. More than 20 reference-based variant phasing tools have been developed (<xref rid=\"s0095\" ref-type=\"sec\">Table S1</xref>). However, only HapCUT2 ##REF##27940952##[94]## and Ranbow ##REF##32469863##[95]## were effectively used in haplotype-resolved genome assemblies of <italic>Litchi chinensis</italic> (diploid) ##REF##34980919##[61]## and <italic>Ipomoea batatas</italic> (hexaploid) ##REF##28827752##[62]## (##TAB##0##Table 1##). HapCUT2 utilizes advanced hybrid phasing programs and can handle chromosome-scale phasing using multiple types of sequencing data, including HiFi, 10X Genomics linked reads, and Hi-C reads ##REF##27940952##[94]##. In contrast, Ranbow is designed for haplotype reconstruction of the polyploid genome using a graph-based algorithm and can integrate all types of small variants in bi- and multiallelic sites to reconstruct haplotypes ##REF##32469863##[95]##. Although the reference-based variant phasing strategy shows its ability with less computational consumption, it also has drawbacks that limit its application to a wide range of complex genomes. The accuracy of this strategy is affected by a series of factors, including the quality of the reference genome, read length, sequencing depth, sequencing errors, and repeats. For instance, most plant genomes contain a large proportion of repetitive sequences, leading to ambiguous read mapping and inaccurate identification of variants. In addition, reference-based variant phasing tools mostly ignore large-scale allelic variants due to the inefficacy of identifying structural variations based on read mapping.</p>", "<title><italic>De novo</italic> assembly-based haplotype phasing</title>", "<p id=\"p0100\">In contrast to reference-based variant phasing, which mainly retains single-nucleotide allelic variants, <italic>de novo</italic> assembly-based haplotype phasing tends to be more comprehensive. It can produce a noncollapsed haplotype-phased assembly, covering large types of allelic variants, such as indels and structural variants ##REF##31908732##[34]##.</p>", "<p id=\"p0105\">Most of the phased plant genomes published to date were completed by relying on <italic>de novo</italic> phased contigs followed by Hi-C scaffolding (<italic>i.e.</italic>, <italic>de novo</italic> phased contig tools + Hi-C scaffolding). Briefly, allelic contigs are initially assembled and phased by allele-aware algorithms implemented in PacBio assemblers (<italic>e.g.</italic>, Hifiasm ##REF##35332338##[96]##, ##REF##33526886##[97]##, Canu ##REF##32801147##[98]##, and FALCON-Unzip ##REF##27749838##[99]##). The phased contigs are subsequently subjected to Hi-C scaffolding tools (such as LACHESIS ##REF##24185095##[100]##, 3D-DNA ##REF##28336562##[101]##, FALCON-Phase ##REF##33911078##[102]##, and ALLHiC ##REF##31383970##[103]##), achieving haplotype construction at the chromosome level (##TAB##0##Table 1##). Hifiasm and Canu use haplotype-aware graphs with reads as nodes and read overlaps as edges to assemble all contigs from different haplotypes ##REF##33526886##[97]##, ##REF##32801147##[98]##. In heterozygous diploid genomes, Hifiasm can solve haplotype-aware graphs based on Hi-C reads that provide long-range links between contigs, in which step allelic contigs are fully separated into two haplotypes ##REF##35332338##[96]##, ##REF##33526886##[97]##. In contrast, Canu requires postprocessing to assign contigs to haplotypes with tools such as Purge_dups ##REF##31971576##[57]##, FALCON-Phase ##REF##33911078##[102]##, and ALLHiC ##REF##31383970##[103]## to split contigs into different haplotypes ##REF##32801147##[98]##. The widely used Hi-C scaffolding programs in haplotype-resolved genome assembly include 3D-DNA and ALLHiC. Benefiting from the fully separated allelic contigs in Hifiasm, 3D-DNA takes contigs from each haplotype as inputs and implements scaffolding algorithms in highly homozygous diploid genomes. However, it has limited power to work with the assembled allelic contigs that are not separated into haplotypes in the polyploid genomes. ALLHiC uses a novel pruning step to remove Hi-C links between phased contigs and collapsed regions as well as allelic Hi-C signals based on a customized allelic contig table ##REF##31383970##[103]##. Removing the interference of Hi-C links allows the phased contigs to be accurately partitioned according to the strength of the Hi-C links. However, ALLHiC depends heavily on the initial assembly quality, a phenomenon that is known as “garbage in, garbage out” ##REF##31383970##[103]##.</p>", "<p id=\"p0110\">Recently, trio-binning-based diploid phasing algorithms for trio sequencing data have been developed, including TrioCanu ##UREF##13##[104]##, Hifiasm + trio ##REF##33526886##[97]##, and WHdenovo ##REF##31860070##[105]##. The long sequencing reads of an F<sub>1</sub> hybrid with a high level of heterozygosity are first partitioned into paternal and maternal read sets based on the unique parental Kmers ##UREF##13##[104]##. The two read sets are assembled separately into two haploid genomes, with each representing a parental genome. Although trio-binning-based algorithms perform exceptionally well in terms of continuity and accuracy of phased contigs, they have limited application to complex plant genomes due to a lack of parental data. In addition, genomic regions that are heterozygous in both parents cannot be phased ##REF##31908732##[34]##.</p>", "<p id=\"p0115\">Genetic maps have been widely used in early genome projects for chromosome construction. Additionally, they demonstrate an ability to carry out haplotype phasing by resequencing hundreds of individuals in a derived population (<italic>e.g.</italic>, a selfing population). In a heterozygous diploid potato (RH), all contigs were assembled from high-quality long reads and 10X Genomics linked reads. Then, each contig was regarded as a molecular marker, and the copy number (0, 1, 2) of the contig in each progeny was inferred based on the distribution of each individual read number, corresponding to the genotype (aa, Aa, AA). The genotype matrix of all contigs in the selfing population allowed the contigs to be divided into 24 linkage groups corresponding to 12 chromosome pairs using traditional genetic mapping strategies. Finally, the long reads and 10X Genomics linked reads for each linkage group were retrieved and reassembled to generate an improved scaffold assembly ##REF##32989320##[12]##. Bao et al. recently introduced this approach into the tetraploid potato genome and assembled the haplotype-resolved genome of a tetraploid cultivated potato ##REF##35733345##[14]##. In addition, gamete binning, a method based on single-cell sequencing of hundreds of haploid gamete genomes, enables the separation of long sequencing reads (such as HiFi reads) into two haploid-specific read sets. After the independent assembly of reads for each haplotype, contigs were scaffolded to the chromosomal level using a genetic map derived from recombination patterns within the same gamete genomes ##REF##33372615##[88]##. Gamete binning has been efficiently used to infer genome-wide haplotypes in diploid pear, apricot tree, tea plant, and tetraploid potato ##REF##35332665##[106]##, ##REF##31649061##[86]##, ##REF##33118252##[87]##, ##REF##33372615##[88]##. However, the construction of the genetic map relies on extensive meiotic recombination, which often means genotyping hundreds of recombined genomes, leading to doubling of sequencing costs relative to other strategies. Moreover, the separation of gametes is severely limited by the level of the experimental technique and by specific seasons. In addition, developing derived populations is time-consuming and costly and may pose significant challenges if the individuals show long juvenility or sterility ##REF##30297971##[17]##.</p>", "<title>Implications of haplotype-resolved genome assembly</title>", "<p id=\"p0120\">In the era of NGS, the compromise method is to use sequence-derived haploid materials or to tolerate chimeric heterozygous regions to construct a reference genome. Therefore, most reference genomes for diploid and polyploid organisms stay at the ‘monoploid’ level, which represents ‘mosaic’ sequences from more than two homologous chromosomes yet fails to capture allelic variants that are diploid or polyploid in nature and that may be associated with compound heterozygotes, dosage effects, homeolog silencing, heterosis, population genetics, and species evolution ##REF##31908732##[34]##. The functional and evolutionary study of polyploids would require a full dissection of the different allele sequences. Accurate haplotype-resolved genome assembly is essential for analyzing haplotypic structural variants and allele-specific expression for complex traits, such as heterosis and genomic imprinting. Additionally, a better understanding of haplotypic variations is key to designing advanced breeding strategies, especially for overcoming severe inbreeding depression or for improving crop yield. Recently, several research groups have generated haplotype-resolved genome assemblies for several important plant species, including sugarcane ##REF##30297971##[17]##, banyan tree ##REF##33035453##[11]##, tea plant ##REF##34267370##[77]##, and potato ##REF##32989320##[12]##, ##REF##35026436##[13]##, ##REF##35733345##[14]##, ##REF##35767385##[15]##, ##REF##35241824##[16]##. These studies not only established references for the assembly of complex genomes but also provided new insights into genome evolution and biological questions concerning these horticulture or crop plants.</p>", "<p id=\"p0125\">The application of the most advanced SMS sequencing and Hi-C technologies has successfully anchored an autotetraploid sugarcane genome onto 32 chromosomes ##REF##30297971##[17]##. Based on a high-quality phased genome, a syntenic analysis confirmed two rounds of whole-genome duplication events in the sugarcane species. The reduction in chromosome bases from 10 to 8 in <italic>Saccharum spontaneum</italic> compared with sorghum has resulted from two chromosome fissions and two fusions.</p>", "<p id=\"p0130\">The Tieguanyin tea cultivar has been cultivated for approximately 300 years, and its genome accumulates a large number of somatic mutations, including deleterious mutations, during the long-term asexual reproduction process. This process increases the genetic load and reduces adaptability. However, our knowledge of dealing with genetic load in the context of vegetatively propagated crops is limited. A fully phased assembly genome provides two sets of alleles that allow the precise study of the allele-specific expression pattern in multiple tissues. The authors found that asexually propagated individuals prefer ancestral or beneficial alleles rather than deleterious mutations to maintain plant growth and development as well as adaptability to the environment ##REF##34267370##[77]##.</p>", "<p id=\"p0135\">Potato (<italic>S</italic>. <italic>tuberosum</italic> L.) is one of the most important tuber crops, but its genetic improvement is slow due to tetrasomic inheritance and clonal propagation ##REF##35241824##[16]##. Asexual propagation through tubers is prone to the accumulation of deleterious mutations and has a higher cost than seed propagation ##REF##34171306##[107]##. However, the decline in selfing caused by deleterious mutations is an obstacle in potato seed propagation. To address this problem, Zhou et al. identified dispersed deleterious mutations and differentially expressed alleles based on a phase diploid genome, which provides operational targets for eradicating harmful alleles or for the accumulation of beneficial alleles through recombination ##REF##32989320##[12]##. This study has subsequently resulted in a breakthrough in potato breeding, leading to vigorous inbred-line-based F<sub>1</sub> hybrids with strong heterosis ##REF##34171306##[107]##. Based on the haplotype-resolved genome of a tetraploid potato cultivar (Otava), Sun et al. found that only 53.6% of the genes have all four haplotypes, and some of the four haplotypes for one gene are identical. Thus, there are only 3.2 haplotypes and 1.9 distinct alleles per gene, suggesting that potato yield and resistance can still be further improved by increasing the allelic diversity of the tetraploid genome because heterosis itself is based on nonadditive interactions of different alleles ##REF##35241824##[16]##. In addition, there were benefits from the phased assembly of tetraploid potato; deleterious mutations between homologous chromosomes were systematically identified; and the mutual shielding of deleterious mutations and functional gene complementation between parents were further reported ##REF##35733345##[14]##. In another phased assembly report on tetraploid potato, researchers analyzed the number and roles of deleterious and dysfunctional genes in the four haplotypes across six tetraploid cultivated potatoes. The autotetraploid potato is a clonally propagated species that undergoes limited meiosis. Its dysfunctional and harmful alleles are not eliminated, which significantly increases the difficulty of breeding. Using phased deleterious and dysfunctional gene information will help breeders create the best allele combination in the F<sub>1</sub> potato generation, thereby improving potato yield and quality ##REF##35026436##[13]##.</p>", "<p id=\"p0140\"><italic>Ficus hispida</italic> is a dioecious plant species, but its sex determination mechanism is a mystery owing to the lack of assembly of sex chromosomes, making it impossible to directly compare the sequence differences between the X and Y chromosomes. To investigate sex determination, our previous study on <italic>Ficus</italic> genomes proposed a novel pipeline, sex phase, to separate X and Y chromosomes by utilizing resequencing reads from individuals of known sex ##REF##33035453##[11]##. The comparative analysis of the phased sex chromosomes highlighted important structural variations between the X and Y chromosomes, including chromosome size (22.6 Mb in Y <italic>vs.</italic> 21.9 Mb in X) and a genomic inversion between 0.61 Mb and 1.57 Mb on the Y chromosome. Importantly, one protein-coding gene, <italic>AGAMOUS 2</italic> (<italic>AG2</italic>), in the sex-determining region, whose ortholog is essential for the development of the stamen and the carpel in <italic>Arabidopsis</italic>\n##REF##17981996##[108]##<italic>,</italic> is present in male individuals but absent in females. Furthermore, PCR amplification of three representative species of the dioecious subgenera confirmed that the <italic>AG2</italic> gene is likely a dominant sex-determining factor across the <italic>Ficus</italic> genus.</p>", "<title>The era of telomere-to-telomere assembly</title>", "<p id=\"p0145\">A more challenging task is to generate gapless or telomere-to-telomere (T2T) assemblies of complex plant genomes. Recently, the goal of near-T2T assemblies has been achieved in rice ##REF##34171480##[27]##, ##REF##34171481##[109]##, ##REF##35748695##[110]##, <italic>Arabidopsis</italic>\n##UREF##14##[111]##, ##REF##34487862##[112]##, ##REF##35655433##[113]##, banana ##REF##34493830##[114]##, and watermelon ##REF##35746868##[115]##. These near-T2T assemblies not only provide the opportunity to update the knowledge of megabase-scale tandemly repeated satellite arrays and epigenetic organization in centromeres, but also indicate that the plant genome has entered the T2T era ##REF##34171480##[27]##, ##UREF##14##[111]##. In sequencing techniques and assembly strategies, these near-T2T genomes all used recent assembly algorithms such as Hicanu and Hifiasm to complete primary contig assembly and fill gaps with high-precision HiFi reads. The remaining gaps were then filled twice with the superlong ONT reads or BAC reads, and the gap sequences were finally corrected and polished with HiFi reads. Alternatively, Rautiainen et al. developed a hybrid genome assembly pipeline (Verkko) for T2T assembly by integrating HiFi and ultralong ONT reads, showing its power to generate the T2T assembly for human genomes ##REF##36797493##[116]##. However, the accumulated experience in these model-like plants to complete the T2T assemblies of the complex plant genomes remains a long way to go before completely solving the high heterozygosity, high repeat sequence content, and high ploidy problems of complex plant genomes.</p>", "<title>Competing interests</title>", "<p id=\"p0165\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0170\"><bold>Weilong Kong:</bold> Investigation, Methodology, Formal analysis, Visualization, Writing – original draft, Writing – review &amp; editing. <bold>Yibin Wang:</bold> Formal analysis, Visualization. <bold>Shengcheng Zhang:</bold> Formal analysis, Visualization. <bold>Jiaxin Yu:</bold> Formal analysis. <bold>Xingtan Zhang:</bold> Conceptualization, Methodology, Resources, Writing – original draft, Writing – review &amp; editing, Supervision. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0185\">The following are the Supplementary data to this article:</p>", "<title>Acknowledgments</title>", "<p id=\"p0175\">This work was supported by the National Natural Science Foundation of China (Grant No. 32222019) and the National Key R&amp;D Program of China (Grant No. 2021YFF1000900). We would like to thank Profs. Jue Ruan and Tao Zhao, who provided many valuable ideas in manuscript preparation.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>The assembly of highly repetitive sequences</bold></p><p><bold>A.</bold> A collapsed assembly error example in tandem repeats. A tandem repeat containing two copies (R1 and R2) separates unique sequences S1 and S2. <bold>B.</bold> Chimeric or fragmented assembly errors in long segmental repeats among different chromosomal regions. S1, S2, S3, and S4 indicate unique sequences, and R1 and R2 represent two identical long segmental repeats. <bold>C.</bold> The impact of sequencing errors on the assembly of highly similar repeats.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>The</bold><bold>impact of high heterozygosity</bold><bold>on genome assembly</bold></p><p><bold>A.</bold> Consensus sequence assembly of a low-heterozygosity genome. Small-scale variations (such as SNPs) in different haplotype sequences can be aligned during assembly and then assembled into consensus sequences. <bold>B.</bold> Bubble structures of highly heterozygous genomes. Large-scale structural variations from different haplotype sequences affect the sequence alignment to form ‘bubbles’ representing redundant allelic sequences and fail to form consensus sequences. SNP, single-nucleotide polymorphism.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Challenges of polyploid genome assembly</bold></p><p><bold>A.</bold> Illustration of chimeric contig assembly errors in an autotetraploid genome, including switch errors and false duplications. <bold>B.</bold> Incorrect Hi-C clustering of chimeric contigs leads to multiple misassemblies. <bold>C.</bold> Illustration of collapsed contig assembly errors in an autotetraploid genome. <bold>D.</bold> The collapsed contig generates Hi-C links with all contigs belonging to four haplotypes, resulting in a superlong and erroneous scaffold. Hap, haplotype; Hi-C, high-throughput/resolution chromosome conformation capture.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Three strategies for identifying redundant contigs</bold></p><p><bold>A.</bold> With the RD-based strategy, redundant or phased contigs are approximately one-half of the mapped RD of collapsed or haplotype-fused contigs due to the bisected RD and the extreme similarity between redundant contigs. Based on the RD of contigs, phased contigs and collapsed contigs can be accurately identified, and the redundant phased contigs will be filtered. <bold>B.</bold> With WGAC-based strategy, contigs with long-scale alignment are identified as redundant contigs, and only the longer one is selected to leave in the monoploid genome. <bold>C.</bold> In the <italic>K</italic>-mer-based strategy, more than 40× Illumina or BGI short reads are first used to build the <italic>K</italic>-mer data pool. Then, low- and medium-frequency <italic>K</italic>-mers are mapped to assembled contigs. Redundant contigs share a high proportion of low- and medium-frequency <italic>K</italic>-mers, and relatively long contigs are finally selected to leave in the monoploid genome. RD, read depth; WGAC, whole genome alignment comparison.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"t0005\"><label>Table 1</label><caption><p><bold>Summary of available haplotype-resolved plant genome assemblies</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Phasing strategy</bold></th><th><bold>Species</bold></th><th><bold>Karyotype</bold></th><th><bold>Sequencing platform</bold></th><th><bold>Tool</bold><bold>or strateg</bold><bold>y</bold></th><th><bold>Ref.</bold></th></tr></thead><tbody><tr><td colspan=\"6\"><bold>Reference-based variant phasing</bold></td></tr><tr><td rowspan=\"2\"/><td><italic>Litchi chinensis</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 30</td><td>Illumina + PacBio + 10X Genomics</td><td>HapCUT2</td><td>##REF##34980919##[61]##</td></tr><tr><td><italic>Ipomoea batatas</italic></td><td>2<italic>n</italic> = 6<italic>x</italic> = 90</td><td>Illumina</td><td>Ranbow</td><td>##REF##28827752##[62]##</td></tr><tr><td colspan=\"6\"><bold><italic>De novo</italic></bold><bold>assembly-based haplotype phasing</bold></td></tr><tr><td rowspan=\"24\"><italic>De novo</italic> phased contig tools + Hi-C scaffolding</td><td><italic>Bletilla striata</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 32</td><td>HiFi + Hi-C</td><td>HiFiasm + LACHESIS</td><td>##REF##35785503##[63]##</td></tr><tr><td><italic>Bupleurum chinense</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 12</td><td>Illumina + HiFi + Hi-C</td><td>HiFiasm + 3D-DNA</td><td>##UREF##10##[64]##</td></tr><tr><td><italic>Suaeda glauca</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 18</td><td>HiFi + Hi-C</td><td>HiFiasm + 3D-DNA</td><td>##UREF##11##[65]##</td></tr><tr><td><italic>Cynodon dactylon</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 36</td><td>Illumina + PacBio + Bionano + Hi-C</td><td>HiFiasm + 3D-DNA</td><td>##REF##35548270##[66]##</td></tr><tr><td><italic>Populus tomentosa</italic></td><td>2<italic>n</italic> = 3<italic>x</italic> = 57</td><td>Illumina + HiFi + Hi-C</td><td>HiFiasm + 3D-DNA</td><td>##REF##35799188##[67]##</td></tr><tr><td><italic>Malus domestica</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 34</td><td>Illumina + 10X Genomics + HiFi</td><td>HiFiasm + DeNovoMAGIC</td><td>##REF##33139952##[68]##</td></tr><tr><td><italic>Manihot esculenta</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 36</td><td>Illumina + HiFi + Hi-C</td><td>HiFiasm + ALLHiC</td><td>##REF##35333302##[69]##</td></tr><tr><td><italic>Pogostemon cablin</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 64</td><td>Illumina + PacBio + Hi-C</td><td>Canu + 3D-DNA</td><td>##REF##35717499##[70]##</td></tr><tr><td><italic>Manihot esculenta</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 36</td><td>Illumina + PacBio + Hi-C</td><td>FALCON + FALCON_unzip + FALCON-Phase</td><td>##REF##34661327##[71]##</td></tr><tr><td><italic>Humulus lupulus</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 20</td><td>Illumina + PacBio + Hi-C</td><td>FALCON + FALCON-unzip</td><td>##REF##33605092##[72]##</td></tr><tr><td><italic>Vanilla planifolia</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 28</td><td>Illumina + ONT</td><td>Miniasm + FALCON-Phase + LACHESIS</td><td>##REF##37128067##[73]##</td></tr><tr><td><italic>Hydrangea macrophylla</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 36</td><td>Illumina + PacBio + Hi-C</td><td>FALCON + FALCON_unzip + FALCON-Phase</td><td>##REF##33175097##[74]##</td></tr><tr><td><italic>Zingiber officinale</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 22</td><td>Illumina + PacBio + Hi-C</td><td>FALCON-Phase + 3D-DNA</td><td>##REF##34354044##[75]##</td></tr><tr><td><italic>Saccharum spontaneum</italic></td><td>1<italic>n</italic> = 4<italic>x</italic> = 32</td><td>Illumina + BACs + PacBio + Hi-C</td><td>Canu + ALLHiC</td><td>##REF##30297971##[17]##</td></tr><tr><td><italic>Saccharum spontaneum</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 40</td><td>HiFi + Hi-C</td><td>Canu + ALLHiC + 3D-DNA</td><td>##REF##35654976##[18]##</td></tr><tr><td><italic>Camellia sinensis</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 30</td><td>HiFi + Hi-C</td><td>HiFiasm + ALLHiC</td><td>##REF##33931633##[76]##</td></tr><tr><td><italic>Solanum tuberosum</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 48</td><td>HiFi + Hi-C</td><td>HiFiasm + ALLHiC</td><td>##REF##35767385##[15]##</td></tr><tr><td><italic>Camellia sinensis</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 30</td><td>Illumina + PacBio + Hi-C</td><td>Canu + ALLHiC</td><td>##REF##34267370##[77]##</td></tr><tr><td><italic>Manihot esculenta</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 36</td><td>PacBio + Hi-C</td><td>Canu + Wtdbg + ALLHiC</td><td>##REF##33866024##[78]##</td></tr><tr><td><italic>Dendrocalamus latiflorus</italic></td><td>2<italic>n</italic> = 6<italic>x</italic> = 70</td><td>Illumina + PacBio + Hi-C</td><td>Falcon + ALLHiC</td><td>##REF##34990066##[79]##</td></tr><tr><td><italic>Medicago sativa</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 32</td><td>Illumina + HiFi + Hi-C</td><td>Canu + ALLHiC</td><td>##REF##32427850##[51]##</td></tr><tr><td><italic>Medicago sativa</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 32</td><td>PacBio + Bionano + Hi-C</td><td>Canu + MECAT + ALLHiC</td><td>##REF##32673760##[80]##</td></tr><tr><td><italic>Medicago sativa</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 32</td><td>PacBio + Hi-C</td><td>Canu + ALLHiC</td><td>##REF##35033678##[81]##</td></tr><tr><td><italic>Artemisia annua</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 18</td><td>Illumina + PacBio + Bionano + Hi-C</td><td>Canu + HiFiasm + FALCON + LACHESIS</td><td>##REF##35655434##[82]##</td></tr><tr><td rowspan=\"3\">Trio-binning-based <italic>de novo</italic> phasing</td><td><italic>Ananas comosus</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 50</td><td>PacBio + ONT + Hi-C + Illumina</td><td>Trio-binning</td><td>##REF##35122338##[83]##</td></tr><tr><td><italic>Cerasus</italic> × <italic>kanzakura</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 16</td><td>Illumina + PacBio</td><td>Trio-binning</td><td>##REF##34792565##[84]##</td></tr><tr><td><italic>Cerasus</italic> × <italic>yedoensis</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 16</td><td>Illumina + PacBio</td><td>Trio-binning</td><td>##REF##31334758##[85]##</td></tr><tr><td rowspan=\"8\">Genetic map-based <italic>de novo</italic> phasing</td><td><italic>Pyrus bretschneideri</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 34</td><td>BACs + SCS</td><td>Gamete binning</td><td>##REF##31649061##[86]##</td></tr><tr><td><italic>Solanum tuberosum</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 48</td><td>HiFi + SCS</td><td>Gamete binning</td><td>##REF##35241824##[16]##</td></tr><tr><td><italic>Camellia sinensis</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 30</td><td>SCS</td><td>Gamete binning</td><td>##REF##33118252##[87]##</td></tr><tr><td><italic>Prunus armeniaca</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 16</td><td>PacBio + SCS</td><td>Gamete binning</td><td>##REF##33372615##[88]##</td></tr><tr><td><italic>Solanum tuberosum</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 24</td><td>ONT + 10X Genomics + HiFi + Hi-C + Illumina for self-population</td><td>Population resequencing</td><td>##REF##32989320##[12]##</td></tr><tr><td><italic>Solanum tuberosum</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 48</td><td>HiFi + Hi-C + Illumina for self-population</td><td>Population resequencing</td><td>##REF##35733345##[14]##</td></tr><tr><td><italic>Vitis riparia</italic></td><td>2<italic>n</italic> = 2<italic>x</italic> = 38</td><td>Illumina + PacBio + 10X Genomics + GBS data</td><td>Population resequencing</td><td>##REF##31324816##[89]##</td></tr><tr><td><italic>Zoysia japonica</italic></td><td>2<italic>n</italic> = 4<italic>x</italic> = 20</td><td>PacBio + GBS data</td><td>Population resequencing (PolyGembler)</td><td>##REF##33128049##[90]##</td></tr></tbody></table></table-wrap>" ]
[]
[]
[]
[]
[]
[ "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S1</title><p><bold>Programs and approaches for haplotype-resolved assembly</bold></p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p><italic>Note</italic>: Hi-C, high-throughput/resolution chromosome conformation capture; PacBio, Pacific Biosciences; ONT, Oxford Nanopore Technologies; GBS, genotyping-by-sequencing; BAC, bacterial artificial chromosome; SCS, single-cell sequencing; HiFi, high fidelity.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"d35e744\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0090\" fn-type=\"supplementary-material\"><p id=\"p0180\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2023.04.004\" id=\"ir005\">https://doi.org/10.1016/j.gpb.2023.04.004</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["5"], "surname": ["Sun", "Shang", "Zhu", "Fan", "Guo"], "given-names": ["Y.Q.", "L.G.", "Q.H.", "L.J.", "L.B."], "article-title": ["Twenty years of plant genome sequencing: achievements and challenges"], "source": ["Trends Plant Sci"], "volume": ["27:391\u2013401"], "year": ["2022"]}, {"label": ["7"], "surname": ["Carey", "Lovell", "Jenkins", "Leebens-Mack", "Schmutz", "Wilson"], "given-names": ["S.B.", "J.T.", "J.", "J.", "J.", "M.A."], "article-title": ["Representing sex chromosomes in genome assemblies"], "source": ["Cell Genom"], "volume": ["2"], "year": ["2022"], "object-id": ["100132"]}, {"label": ["20"], "surname": ["Treangen", "Salzberg"], "given-names": ["T.J.", "S.L."], "article-title": ["Repetitive DNA and next-generation sequencing: computational challenges and solutions"], "source": ["Nat Rev Genet"], "volume": ["13"], "year": ["2012"], "fpage": ["36"], "lpage": ["46"]}, {"label": ["24"], "surname": ["Appels", "Eversole", "Feuillet", "Keller", "Rogers", "Stein"], "given-names": ["R.", "K.", "C.", "B.", "J.", "N."], "article-title": ["Shifting the limits in wheat research and breeding using a fully annotated reference genome"], "source": ["Science"], "volume": ["361"], "year": ["2018"], "fpage": ["eaar719"]}, {"label": ["33"], "surname": ["Spoelhof", "Soltis", "Soltis"], "given-names": ["J.P.", "P.S.", "D.E."], "article-title": ["Pure polyploidy: closing the gaps in autopolyploid research"], "source": ["J Syst Evol"], "volume": ["55"], "year": ["2017"], "fpage": ["340"], "lpage": ["352"]}, {"label": ["35"], "surname": ["Michael", "Jackson"], "given-names": ["T.P.", "S."], "article-title": ["The first 50 plant genomes"], "source": ["Plant Genome"], "volume": ["6"], "year": ["2013"], "fpage": ["1"]}, {"label": ["36"], "surname": ["Rizzi", "Beretta", "Patterson", "Pirola", "Previtali", "Della Vedova"], "given-names": ["R.", "S.", "M.", "Y.", "M.", "G."], "article-title": ["Overlap graphs and "], "italic": ["de Bruijn", "de novo"], "source": ["Quant Biol"], "volume": ["7"], "year": ["2019"], "fpage": ["278"], "lpage": ["292"]}, {"label": ["43"], "mixed-citation": ["Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, et al. 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{ "acronym": [], "definition": [] }
125
CC BY
no
2024-01-14 23:41:55
Genomics Proteomics Bioinformatics. 2023 Jun 25; 21(3):427-439
oa_package/3a/bc/PMC10787022.tar.gz
PMC10787024
36435453
[ "<title>Introduction</title>", "<p id=\"p0005\">The palm family (Arecaceae) consists of ∼ 2600 species belonging to over 180 genera ##UREF##0##[1]##. Over 90% of the diversity within this family is distributed in the tropical region of the world by adaptive radiation ##REF##21679405##[2]##. The Arecaceae is the third most economically important family of plants, after grasses and legumes ##UREF##1##[3]##. The African oil palm (<italic>Elaeis guineensis</italic>) is the most economically important of the Arecaceae, with a global production of ∼ 74 million metric tons of vegetable oil (FAOSTAT, <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.fao.org/faostat\" id=\"PC_linkm8DUr3kidq\">https://www.fao.org/faostat</ext-link>, accessed at 2021/05/03). African oil palm is native to West Africa from Angola northward to Gambia ##UREF##2##[4]##. It was introduced to Southeast Asia in the 1840s, and has been naturalized since then ##UREF##2##[4]##. Oil palm is the most productive oil plant and produces over 35% of vegetable oils with a market value of over $40 billion (EPOA, <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.palmoilandfood.eu/en/palm-oil-production\" id=\"PC_linkm8DUr3kidw\">https://www.palmoilandfood.eu/en/palm-oil-production</ext-link>, accessed at 2022/05/10). Although the oil yield has improved from ∼ 2.0 tons/ha/yr to the current ∼ 4.0 tons/ha/yr in the past 100 years, there is still great potential to further improve the oil yield and other economical traits ##UREF##2##[4]##. In addition, the oil palm industry is seriously threatened by diseases caused by the <italic>Ganoderma</italic> species, resulting in losses of up to 80% of yield in some plantation areas ##UREF##2##[4]##. Improvement of economically important traits using various approaches, including conventional and molecular breeding, is critically important in the oil palm industry.</p>", "<p id=\"p0010\">A high-quality genome assembly is necessary for both molecular breeding to accelerate genetic improvement and understanding species’ evolution. Despite the need to better understand oil palm genomics, only draft genome sequences are available. The completeness and quality of the published genome assemblies are still to be improved ##REF##27426468##[5]##, ##REF##23883927##[6]##, ##REF##33152992##[7]##. Only ∼ 60% of the 1.8-Gb estimated genome sequences were assembled, and ∼ 45% of sequences were anchored to genetic maps in <italic>Pisifera</italic> genome version EG5.1 and/or PMv6 ##REF##23883927##[6]##, ##REF##33152992##[7]##. These draft genome sequences supply important resourses to initiate molecular breeding to accelerate the genetic improvement. However, due to the limited completeness, fragmentation of scaffolds, and incomplete annotations, their applications in genome-wide association studies, comparative genomics, and structural variation analysis in the oil palm species and their related species are limited. Therefore, further improvement of the draft genome of oil palm is essential for molecular breeding in order to improve economic traits and understand the evolution of palms through comparative genomics ##REF##37309424##[8]##.</p>", "<p id=\"p0015\">Here, we report a high-quality chromosome-level genome assembly of <italic>E. guineensis</italic>. Comparative genomic analysis revealed that transposon burst was responsible for genome size expansion in palms. We found evidence that highly tandemly repeated pathogenesis-related (PR) proteins played an important role in defense responses to <italic>Ganoderma</italic> infection. Whole-genome resequencing of 72 trees from West Africa and Southeast Asia revealed the population structure and lower genetic variations of oil palms in Southeast Asia. Signatures of local adaptation in the genome of oil palm was also found. The novel genomic resources and insights gained from this study will contribute to the understanding of palm evolution and accelerate the genetic improvement of oil palm.</p>" ]
[ "<title>Materials and methods</title>", "<title>Genome sequencing and assembly in oil palm</title>", "<p id=\"p0100\">The same <italic>Dura</italic> tree, previously sequenced with Illumina platform ##REF##27426468##[5]##, was sequenced using Single-Molecule Real-Time (SMRT) technology to improve the genome assembly. Genomic DNA was isolated using MagAttract HMW DNA Kit (Catalog No. 67563, Qiagen, Düsseldorf, Germany). Two 20-kb libraries were constructed and sequenced for &gt; 150× coverage on PacBio Sequel II Sequencer (Pacific Biosciences, Menlo Park, CA) by BGI (Hong Kong, China). Flye v2.8 ##REF##30936562##[43]## was used to assemble the genome (-g 1.8 g -m 10,000 --asm-coverage 50 -i 3). Cleaned paired-end reads of 300-bp insert libraries and ∼ 100× coverage from Illumina sequencing ##REF##27426468##[5]## were used to polish the genome with Pilon ##REF##25409509##[44]##.</p>", "<title>Construction of high-density linkage maps</title>", "<p id=\"p0105\">For construction of high-density linkage maps, five F<sub>2</sub> families consisting of a total of 978 progenies were used for RAD sequencing. DNA was isolated from leaves of each tree using DNeasy Plant Mini Kit (Catalog No. 69104, Qiagen). DNA was digested with <italic>Pst</italic>I-HF restriction enzymes (Catalog No. R3140L, New England Biolabs, Ipswich, MA), and RAD libraries were constructed as described in our previous study ##REF##28558657##[45]##. The libraries were sequenced for 150-bp single-end reads on NextSeq500 platform (Illumina, San Diego, CA). Raw reads were cleaned with process_radtags (-r -c -q -t 130) in Stacks package ##REF##23701397##[46]##. Cleaned reads of ∼ 7.3 million for each sample were aligned to the aforementioned reference genome with BWA-MEM ##REF##19451168##[47]## with default parameters. Aligned reads were assembled and called for SNPs with Stacks package ##REF##23701397##[46]##, according to our previous study ##REF##28558657##[45]##. Only one SNP from each RAD tag was kept. SNPs that were present in &gt; 90% individuals within each family and showed Mendelian segregation distortion of &gt; 0.05 in Chi-squared test were retained. Linkage mapping was carried out using Lep-MAP3 ##REF##29036272##[48]##, with a logarithm of the odds score (LOD) of &gt; 10 for linkage group assignment.</p>", "<title>Construction of chromosomal-level genome assemblies of palms</title>", "<p id=\"p0110\">RAD tags that were incorporated into the five high-density linkage maps were aligned to the contigs to assign genomic coordinates. Chimeric contigs were determined by linkage maps, which are not likely to have among-chromosome grouping errors ##REF##27993155##[49]##. Contigs with more than four markers mapped to different linkage groups, were considered as chimeric and were then split at the longest gaps between mismatched fragments. The program ALLMAPS ##REF##25583564##[50]## was then employed to anchor contigs to linkage maps, with default parameters. Centromere positions were estimated based on the distribution of recombination rates along individual chromosomes. Recombination rates, measured as ρ = 4Ner per kb, were estimated using LDhat ##REF##15105499##[51]##. Completeness of genome was examined by mapping to BUSCO v3.0.1 database ##REF##26059717##[52]##.</p>", "<title>Repeat and genome annotations</title>", "<p id=\"p0115\">RepeatModeler (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.repeatmasker.org\" id=\"PC_linkULB2eekSss\">https://www.repeatmasker.org</ext-link>) was first used to build a custom repeat library of the studied species. RepeatMasker ##UREF##6##[53]## was then employed to identify repetitive sequences based on the custom repeat library and Repbase database ##REF##16093699##[54]##. Tandem repeats were further annotated using Tandem Repeats Finder ##REF##9862982##[55]##. Finally, we combined and filtered these repetitive sequences to obtain the nonredundant repeat annotations of the genome based on the coordinates. Assessment of the intact LTR retrotransposons was carried out using LTR_retriever ##REF##29233850##[56]##. Demographic history of the TEs was inferred by investigation on the most abundant LTRs. One hundred LTRs were randomly selected from 40 random subfamilies of <italic>Copia</italic>. Full sequences were extracted and aligned with MUSCLE ##REF##15034147##[57]##. The distribution of pairwise sequence similarity within a family was used to estimate the temporal dynamics of TE activity.</p>", "<p id=\"p0120\">Genome was annotated with MAKER2 pipeline ##REF##24306534##[58]##. Genome sequences were first soft-masked using RepeatMasker ##UREF##6##[53]##, based on the aforementioned repetitive libraries. Cleaned mRNA sequencing reads of multiple organs from our previous study ##REF##27426468##[5]## were assembled with Trinity ##REF##21572440##[59]## and used for evidence-based annotation. For <italic>ab initio</italic> gene model prediction, protein sequences of <italic>E. guineensis</italic> EG5.1 ##REF##23883927##[6]## and EGv2 ##REF##27426468##[5]##, date palm Barhee BC4 ##REF##31615981##[9]##, and coconut HainanTall ##UREF##7##[60]## were used as evidence. SNAP ##REF##15144565##[61]## and AUGUSTUS ##REF##14534192##[62]## were iteratively used to train gene models. Predicated gene models that contained TE domains and were not supported by transcripts were filtered. Cleaned gene models were then annotated by BLAST to Non-Redundant Protein Sequence Database and RefSeq databases with BLASTP (E-value &lt; 1E–10).</p>", "<title>Evolutionary analysis</title>", "<p id=\"p0125\">Homologous blocks within and between species of interest were determined by pairwise whole-genome alignment with LASTZ ##UREF##8##[63]## and all-versus-all BLASTP search with Ortholog-Finder at gene level ##REF##26782935##[64]##. Putative one-to-one orthologs and paralogs from a pair of homologous blocks between oil palm and date palm and within oil palm, respectively, were aligned using MUSCLE ##REF##15034147##[57]##. Coding sequences were then aligned with the guidance of corresponding protein alignments. DNA alignments were further polished using trimAl ##REF##19505945##[65]##. <italic>Ks</italic> was estimated between a pair of homologous genes using KaKs_Calculator ##REF##17531802##[66]##. Local duplicated genes were identified by analyzing the results of all-versus-all BLASTP search as described above, based on their genomic coordinates. To estimate the sequence divergence of LTR retrotransposons, 100 members from each of the randomly selected 30 <italic>Copia</italic> subfamilies were randomly selected and pairwise aligned, according to a previous study ##REF##27088604##[15]##. Pairwise sequence divergence was estimated and compared with that of homologous genes to infer the relative evolution time ##REF##27088604##[15]##.</p>", "<title>Transcriptome analysis</title>", "<p id=\"p0130\">To compare the expression patterns of homologous genes, RNA-seq reads of various parts from oil palm in our previous studies ##REF##33277563##[30]##, ##REF##28348403##[67]##, ##REF##29169327##[68]## and from date palm ##REF##28330456##[69]## were reanalyzed. Raw reads were cleaned with process_shortreads in Stacks package with default parameters, to remove adaptors and low-quality reads. Cleaned reads were then aligned, with default parameters, to the reference genome using STAR ##REF##23104886##[70]##. Uniquely mapped reads were counted to calculate gene expression level based on genome annotations, using the program HTSeq-count ##REF##25260700##[71]##. Gene expression level was then quantified as the number of fragments per kilobase of transcript per million mapped reads (FPKM). Heatmapper ##REF##27190236##[72]## was used to visualize the clusters and relative expression of genes.</p>", "<title>Analysis of <bold><italic>VIRESCENS</italic></bold> in palms</title>", "<p id=\"p0135\">The presence of anthocyanins across palms was examined by measurement of the absorption spectrum of exocarp extracts in 1% acidified methanol, according to a previous method ##REF##24978855##[21]##. Equal exocarp material (100 mg) for each palm were used for extraction and the spectrum of UV absorption was measured from 240 nm to 700 nm with a 10-nm interval. Sequences of <italic>VIRESCENS</italic> across the studied palms were amplified either by amplification of genomic DNA or complementary DNA (cDNA), using primers designed according to sequence homology among oil palm, date palm, and coconut and primer walking (<xref rid=\"s0130\" ref-type=\"sec\">Table S16</xref>). Coding sequences were predicted based on oil palm <italic>VIRESCENS</italic> gene ##REF##24978855##[21]##. Predicted protein sequences were aligned using MUSCLE ##REF##15034147##[57]##, and a phylogenetic tree was constructed using IQ-TREE2 ##REF##32011700##[73]##, under the model of HIV between-patient matrix HIV-Bm with a proportion of invariable sites (HIVb+I) with 1000 bootstrap replications. The relative expression of <italic>VIRESCENS</italic> was examined using reverse transcription polymerase chain reaction (RT-PCR). In brief, total RNA extraction and cDNA synthesis were carried out according to our previous study ##REF##33277563##[30]##. cDNA corresponding to 50 ng of total RNA was used as template for amplification using gene-specific primers, and the housekeeping gene, <italic>ACTB</italic>, was used as a reference, with the following PCR condition: 94 °C for 5 min, followed by 35 cycles of 94 °C for 30 s, 60 °C for 30 s, and 72 °C for 30 s, and a final extension of 72 °C for 5 min. RT-PCR products were examined by running 2% agarose gel.</p>", "<title>Characterization of PR proteins</title>", "<p id=\"p0140\">Protein sequences of all PR family members of different plant species ##REF##27189060##[27]## were used as baits to search the genomes of oil palm, date palm, coconut, and banana, with BLASTP (E-value &lt; 1E–5). Protein sequences were extracted and manually curated, and were then sorted and classified based on protein domains, according to a previous study ##REF##27189060##[27]##. Genomic coordinates of <italic>PR</italic> genes in oil palm were extracted from annotation files to study the distribution and duplication patterns. Protein sequences of PR family members of interest were aligned using MUSCLE ##REF##15034147##[57]##. Alignments were refined using trimAl ##REF##19505945##[65]##. Phylogenetic trees were constructed using IQ-TREE2 ##REF##32011700##[73]##, under automatically searched mutation model (JTT+R4).</p>", "<p id=\"p0145\">Functions of PR proteins in disease resistance were studied by analyzing the RNA-seq data set of oil palm seedlings infected with <italic>G</italic>. <italic>boninense</italic> inoculums at 3, 7, and 11 dpi ##REF##30594134##[25]##. Processing of raw sequencing reads, alignment to reference genome, and count of mapped reads were carried out as described above. Normalization of transcripts and identification of DEGs were performed using DESeq2 ##REF##25516281##[74]##. Genes with a fold change &gt; 2 and a significant cutoff value of 0.005, corresponding to 0.1 after false discovery rate (FDR) corrections, were considered as DEGs.</p>", "<title>Whole-genome resequencing and variant calling</title>", "<p id=\"p0150\">A total of 72 trees from West Africa (50) and Southeast Asia (22) were selected for sequencing. Libraries of 550-bp inserts were constructed using Truseq DNA PCR-Free Kit (Catalog No. 20015963, Illumina) and sequenced on NextSeq500 (Illumina). Raw reads were filtered as described above. Cleaned reads were aligned against reference genome using BWA-MEM ##REF##19451168##[47]##, and variants were called using the Picard/GATK v4.0 best practices workflows ##REF##21478889##[75]##. We further filtered SNPs with the parameters: “QD &lt; 2.0 || DP &gt; 5 || FS &gt; 60.0 || MQ &lt; 40.0 || MQRankSum &lt; −12.5 || ReadPosRankSum &lt; −8.0 || SOR &gt; 4.0”. Only SNPs were retained for further analysis, and those with missing data across populations &gt; 20 were also removed.</p>", "<title>Genetic diversity and population structure analyses</title>", "<p id=\"p0155\">Population genetic diversity indexes including <italic>π</italic>, Tajima’s <italic>D</italic>, and <italic>F</italic><sub>ST</sub> were estimated using VCFtools ##REF##21653522##[76]##. Population structure was analyzed with PCA using PLINK2 ##REF##17701901##[77]##. Genetic clusters from ancestry were inferred using ADMIXTURE ##REF##21682921##[78]##, with the number of clusters ranging from 2 to 10. Cross-validation error was estimated to determine the most likely number of ancestral populations. LD between SNPs within populations (R<sup>2</sup>) was estimated using PopLDdecay (-MAF 0.02, -Het 0.88, -Miss 0.25) ##REF##30321304##[79]##.</p>", "<title>Identification of signatures of selection</title>", "<p id=\"p0160\">Signatures of selection between populations were inferred using <italic>F</italic><sub>ST</sub>, <italic>ϴ</italic><sub><italic>π</italic></sub>, and Tajima’s <italic>D</italic> statistics within the Southeast Asian samples. These estimates were calculated in sliding window size of 100 kb with a window size step of 50 kb. Genomic regions consistently within top 5% of windows for <italic>F</italic><sub>ST</sub> and π, and bottom 5% of windows for Tajima’s <italic>D</italic> in the empirical distribution, were considered as outliers under putative selection. Protein-coding genes in outlier regions were considered under putative selection. Protein sequences were extracted and annotated against <italic>Arabidopsis</italic> protein database (Ensembl TAIR10) using BLASTP with an E-value cutoff &lt; 1E–10. Metascape ##REF##30944313##[80]## was employed to perform Gene Ontology enrichment analysis, with <italic>Arabidopsis</italic> as reference, using default parameters. DEGs responding to drought stress ##REF##33277563##[30]## and fungal infection as described above were used to infer signatures of selection under putative stresses.</p>" ]
[ "<title>Results and discussion</title>", "<title>Chromosomal-level genome of African oil palm</title>", "<p id=\"p0020\">Over 150× coverage of long reads was assembled into 4752 contigs, with a total length of 1.7 Gb, covering 94.5% of the estimated genome (1.8 Gb) (<xref rid=\"s0130\" ref-type=\"sec\">Table S1</xref>). Contig N50 and the longest contig reached up to 2.168 Mb and 12.851 Mb, respectively. We constructed five high-density linkage maps in five F<sub>2</sub> populations, with the number of mapped markers ranging from 12,068 to 19,581 (<xref rid=\"s0130\" ref-type=\"sec\">Figure S1</xref>; <xref rid=\"s0130\" ref-type=\"sec\">Table S2</xref>). Anchoring contigs to these high-density genetic maps, based on a total number of 60,989 informative segregating markers, resulted in 16 pseudochromosomes consisting of 91.6% of assembled sequences and with length ranging from 37.784 Mb to 160.148 Mb, and 59.7% of assembled sequences were oriented (<xref rid=\"s0130\" ref-type=\"sec\">Figure S2</xref>; Tables S1, S3, and S4). Genome completeness analysis assessed with Benchmarking Universal Single-Copy Orthologs (BUSCO) showed that 95.8% of the core genes were found in the genome and 93.3% were complete (<xref rid=\"s0130\" ref-type=\"sec\">Table S5</xref>). Mapping of assembled transcripts and <italic>de novo</italic> assembled restriction-site associated DNA (RAD) tags showed that 98.8% and 97.5% were matched to the genome assembly, respectively. We annotated long terminal repeats (LTRs). The LTR assembly index (LAI) was estimated to be 15.453 ± 2.968 (mean ± standard deviation). This genome assembly significantly increases the total length of assembled sequences by ∼ 61% (contig length from ∼ 1057 Mb to ∼ 1701 Mb), N50 contig size of ∼ 233 folds, N50 scaffold size of ∼ 80 folds, and total length of sequences anchored on pseudochromosomes of ∼ 2.4 folds, compared with previous draft genome sequences (<xref rid=\"s0130\" ref-type=\"sec\">Table S1</xref>) ##REF##27426468##[5]##, ##REF##23883927##[6]##, ##REF##33152992##[7]##. A chromosomal-level genome is necessary for comparative genomic analysis to study genome duplications and understand the genomic architecture of adaptive radiation of palms. Date palm (<italic>Phoenix dactylifera</italic>) Barhee BC4 is one of the most impressive assemblies in palms, in which &lt; 50% of sequences were anchored to pseudochromosomes ##REF##31615981##[9]##. Although diverged ∼ 65 million years ago (MYA) ##REF##23883927##[6]##, we observed a high level of conserved chromosome synteny between oil palm and date palm (##FIG##0##Figure 1##), indicating that the chromosomal-level genome of oil palm can be used for comparative genomic analysis. Taken together, our genome assembly showed high genome coverage, high assembly accuracy, long sequence continuity, and high completeness of both genes and repetitive elements. Therefore, it will be a vital contribution to studies on genetics, genomics, and breeding in palm species.</p>", "<title>Annotation of the African oil palm genome</title>", "<p id=\"p0025\">Repetitive sequences accounted for ∼ 74% of the genome assembly of oil palm (<xref rid=\"s0130\" ref-type=\"sec\">Table S6</xref>), significantly higher than that previously observed in the incomplete genome assembly of this species (∼ 57%) ##REF##23883927##[6]## and that in date palm (∼ 39%) ##REF##31615981##[9]##. LTRs took up 55.79% of the genome. <italic>Copia</italic> is the largest class of LTRs, followed by the <italic>Gypsy</italic> superfamily, representing 39.46% and 17.19% of the assembled genome sequences, respectively (<xref rid=\"s0130\" ref-type=\"sec\">Table S7</xref>). The proportions of the two LTR superfamilies are also much higher than those in date palm (∼ 14% for <italic>Copia</italic> and ∼ 4% for <italic>Gypsy</italic>) ##REF##31615981##[9]##. We observed that the distribution pattern of repetitive sequences was negatively correlated to that of the recombination rate (<italic>R</italic> = −0.412, <italic>P</italic> &lt; 1 × 10<sup>−4</sup>) and the gene density (<italic>R</italic> = −0.794, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>), but positively correlated to the distribution pattern of GC content (<italic>R</italic> = 0.932, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>) (##FIG##0##Figure 1##A–E). In date palm, we observed the same correlation patterns between the repetitive sequences and gene density (<italic>R</italic> = −0.856, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>) and between the repetitive sequences and GC content (<italic>R</italic> = 0.403, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>) (##FIG##0##Figure 1##A–E) as in oil palm, which addresses how transposon dynamics has significantly shaped the genomic architecture of palms. We observed that the distribution of <italic>Copia</italic> was highly correlated with that of the overall repetitive sequences (<italic>R</italic> = 0.952, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>), whereas <italic>Gypsy</italic> were more likely randomly distributed across the genome (<italic>R</italic> = 0.107, <italic>P</italic> &lt; 0.05) (##FIG##0##Figure 1##F and G). Our data indicate that palms have a much higher copy number of <italic>Copia</italic> compared with <italic>Gypsy</italic>, contradicting most other plant genomes, which show higher <italic>Gypsy</italic> content ##REF##31615981##[9]##. Previous studies have reported that retrotransposons in plants play important roles in genome size, genome structure remodeling, gene function, and genome evolution ##REF##10690416##[10]##. Therefore, it is highly possible that <italic>Copia</italic> may play an important role in the evolution of palms.</p>", "<p id=\"p0030\">Gene annotations based on RNA sequencing (RNA-seq), <italic>ab initio</italic> predictions, plant protein-coding genes, and protein domains, predicted 33,447 protein-coding genes. Of these genes, 29,293 (87.58%) were annotated with known proteins or domains (<xref rid=\"s0130\" ref-type=\"sec\">Table S1</xref>). Over 95% of predicted genes showed an annotation edit distance (AED) value of &lt; 0.5, indicating high-quality annotations of the genome (<xref rid=\"s0130\" ref-type=\"sec\">Figure S3</xref>). Median gene length was ∼ 5.2 kb, slightly higher than those of previous oil palm and date palm assemblies of ∼ 4.7 kb and ∼ 4.2 kb, respectively ##REF##23883927##[6]##, ##REF##31615981##[9]##. In addition, more than 98% of the annotated genes were mapped to the 16 chromosome sequences, indicating that this genome assembly represents a nearly complete protein-coding genome and is useful in future genetic and genomic studies. Functional enrichment analysis revealed that gene families showing expansions in oil palm were more involved in stress responses to pathogens and regulation of osmotic stresses (<xref rid=\"s0130\" ref-type=\"sec\">Figures S4 and S5</xref>).</p>", "<title>Transposon burst leads to genome expansion and gene diversification in palms</title>", "<p id=\"p0035\">The variation in genome size across eukaryotes is tremendous and is associated with species diversity ##REF##17090588##[11]##. Polyploidy and transposon expansion are the two major forces driving genome size variation, providing essential resources for evolutionary innovations by generating novel genetic variations and altering gene expression patterns ##UREF##3##[12]##. Thus, it is necessary to unravel these mechanisms in order to better understand adaptive radiation and successful ecological dominance of the taxa. Genome size of palms varies from ∼ 800 Mb to ∼ 3 Gb ##REF##31028709##[13]##. Oil palm and date palm show a striking difference in genome size, with the predicted size of 1.8 Gb and 800 Mb, respectively, providing an excellent system to study genome size variation. Monocots share a common whole-genome duplication (WGD) event at ∼ 150 MYA ##REF##25082857##[14]##. The other paleopolyploid event, exclusively for the ancestor of all palms, occurred at ∼ 75 MYA, resulting in the paleotetraploidy of all palms ##REF##23883927##[6]##, ##REF##31028709##[13]##. We observed large conserved syntenic blocks between homologous chromosome pairs throughout the whole genome (<xref rid=\"s0130\" ref-type=\"sec\">Figure S6</xref>), allowing for examination of the effects of WGD events on genome evolution. Distribution of synonymous substitution rate (<italic>Ks</italic>), estimated based on 4292 and 2793 pairs of homologous genes from syntenic blocks in oil palm and date palm, respectively, revealed a major peak at ∼ 0.32, corresponding to the recent WGD at ∼ 75 MYA that was shared by all palms (##FIG##1##Figure 2##A and B) ##REF##31028709##[13]##. A more recent <italic>Ks</italic> peak was observed at ∼ 0.22 for orthologous gene pairs, indicating the divergence between oil palm and date palm at ∼ 65 MYA ##REF##23883927##[6]##. Here, the divergence of the whole-genome-wide homologous genes supports the conclusion that all palms have experienced two WGD events before adaptive radiation ##REF##31028709##[13]##.</p>", "<p id=\"p0040\">We did not find notable evidence of gene loss in date palm in contrast to oil palm, leading to another hypothesis that transposon proliferation drives genome size expansion and speciation of palms. LTRs are the richest transposable elements (TEs) in both species, with a total length of ∼ 950 Mb and ∼ 200 Mb ##REF##31615981##[9]## for oil palm and date palm, respectively. Difference in LTR content explains ∼ 80.3% of the genome size variation between the two species. Among LTRs, <italic>Copia</italic> is the most abundant superfamily for both species and accounts for ∼ 52.3% of total genome size variation (<xref rid=\"s0130\" ref-type=\"sec\">Table S7</xref>). We examined the historical dynamics of each subfamily of <italic>Copia</italic>. Pairwise sequence divergence within each subfamily presented two peaks with sequence similarity of ∼ 82% and ∼ 92%, respectively, in oil palm (##FIG##1##Figure 2##C). In comparison, two peaks of sequence divergence in date palm at ∼ 84% and ∼ 93% were only slightly visible (##FIG##1##Figure 2##D). In particular, the peak of higher similarity was remarkably inflated in oil palm, suggesting a recent transposon burst in oil palm relative to date palm. We compared the sequence divergence between <italic>Copia</italic> and homologous genes that mark the last WGD and diversification. Homologs in conserved syntenic blocks within each species presented a consistent peak with a similarity of ∼ 86%, whereas the divergence of homologs between species was ∼ 92%, marking the WGD and diversification events, respectively (<xref rid=\"s0130\" ref-type=\"sec\">Figure S7</xref>). The first wave of transposon burst, overlapping with the last WGD event, is suggested to be caused by rediploidization due to elevated genomic stress soon after WGD ##REF##27088604##[15]##. Under the assumption of comparable sequence evolutionary rates ##REF##27088604##[15]##, the second wave of transposon burst coincides with the time of divergence between the two palms, suggesting that transposon burst and differential dynamics play an important role in the diversification of palms. Large-scale transposon proliferation and movement may drive chromosome rearrangements, variation of recombination, and gene diversification, and eventually lead to speciation ##REF##20541961##[16]##.</p>", "<p id=\"p0045\">Transposon dynamics can affect genome-wide expression patterns and promote divergence by epigenetic regulation ##REF##19847266##[17]##. We identified 9786 intact LTRs throughout the genome. Approximately 33.8% of the intact LTRs showed an estimated insertion time of &lt; 1 MYA (<xref rid=\"s0130\" ref-type=\"sec\">Figure S8</xref>), within which 21.8% were in or within 5-kb distance to gene features (<xref rid=\"s0130\" ref-type=\"sec\">Figure S9</xref>). We hypothesized that young intact LTRs closely linked to genes can affect gene expression patterns. First, we compared the expression levels of 273 pairs of paralogous genes from conserved syntenic blocks of oil palm, in which only one of a pair of genes is closely linked to a young intact LTR. However, the expression levels of genes linked to LTRs were only slightly reduced (but not significantly) in almost all 12 examined tissues (<xref rid=\"s0130\" ref-type=\"sec\">Figure S10</xref>; <xref rid=\"s0130\" ref-type=\"sec\">Table S8</xref>). These paralogs diverged since the last WGD at ∼ 75 MYA ##REF##25082857##[14]## and likely have functionally diverged in depth. Thus, the effects of LTRs on linked genes are likely underestimated in these anciently duplicated genes. As expected, these paralogous genes presented a more diverse expression pattern than the recent locally duplicated genes (<xref rid=\"s0130\" ref-type=\"sec\">Figure S11</xref>). We further examined the effects of intact LTRs on 103 pairs of locally duplicated genes with a younger duplication time (<italic>Ks</italic>, 0.15 ± 0.07). Interestingly, genes linked to LTRs showed significantly lower expression levels as compared with their adjacent paralogs, in most of the examined samples (##FIG##1##Figure 2##E). Similar results were reported in the tea plant (<italic>Camellia sinensis</italic> var. <italic>sinensis</italic>) ##REF##32353625##[18]##. These findings highlight the importance of LTRs in promoting transcriptional diversification of duplicated genes by epigenetic suppression of closely linked genes, which finally contributes to genome divergence.</p>", "<title>Sequence variations in the <bold><italic>VIRESCENS</italic></bold> gene may be related to fruit colors in palms</title>", "<p id=\"p0050\">For decades, it has been hypothesized that fruit color had evolved to increase visual conspicuousness, and is subjected to selection by seed dispersing animals ##UREF##4##[19]##. In tropical palms, fruit color evolution is suggested to have interactions with frugivores ##REF##32198956##[20]##. However, the genomic basis of adaptive evolution of fruit color in palms is still unclear. <italic>VIRESCENS</italic> encodes a R2R3-MYB transcription factor, which controls the accumulation of anthocyanins in fruit exocarp of palms, leading to deep violet to black fruit colors ##REF##24978855##[21]##. The dark pigments of the exocarp reduce the visual conspicuousness in contrast with red, orange, and yellow pigmented fruits, which are caused by carotenoids and carotenes, making it less attractive to herbivorous animals. Thus, genes controlling the accumulation of anthocyanins in the exocarp tend to be under selection by seed dispersing animals.</p>", "<p id=\"p0055\">It has been found that loss-of-function mutants of <italic>VIRESCENS</italic> in both oil palm and date palm is associated with loss of anthocyanins in exocarp, leading to conspicuousness of fruit colors ##REF##31615981##[9]##, ##REF##24978855##[21]##. To examine the hypothesis, we cloned and analyzed the <italic>VIRESCENS</italic> gene of four additional palms: coconut, Christmas palm (<italic>Adonidia merrillii</italic>), Macarthur palm (<italic>Ptychosperma macarthurii</italic>), and golden cane palm (<italic>Dypsis lutescens</italic>). First, we measured the absorption spectrum of exocarp extracts and found that all four palms were deficient in anthocyanin accumulation in ripe fruit exocarp in contrast to the oil palm <italic>VIRESCENS</italic> fruit (wild-type) which had a high concentration of anthocyanins (##FIG##2##Figure 3##A and B). All coconut assemblies, including Catigan Green Dwarf ##REF##31167834##[22]##, <italic>Cn. tall</italic>, and <italic>Cn. dwarf</italic>\n##REF##34736486##[23]##, were observed to harbor the complete <italic>VIRESCENS</italic> locus (##FIG##2##Figure 3##C). Interestingly, sequence analysis showed that the <italic>VIRESCENS</italic> gene in these genome sequences was consistently disrupted by an insertion of a highly repetitive region including ∼ 60 simple repeats and ∼ 50 LTRs, leading to loss of partial exon 1 and the whole exon 2 (##FIG##2##Figure 3##C). Disruption of <italic>VIRESCENS</italic> in coconut genome likely explains its green exocarp even in the ripe fruit. In Macarthur palm, we found a premature termination codon in the exon 3 of <italic>VIRESCENS</italic>, resulting in a predicted truncation of 34 amino acids in the C-terminal relative to the sequence of wild-type oil palm (##FIG##2##Figure 3##D). As predicted in both oil palm and date palm, the truncated 34 amino acids are overlapping with the transcriptional activation domain of R2R3-MYB transcription factor (<xref rid=\"s0130\" ref-type=\"sec\">Figure S12</xref>), and loss of this domain leads to deficiency in the regulation of anthocyanin accumulation ##REF##24978855##[21]##. In contrast, we did not identify evidence of loss-of-function mutations in the coding sequences of <italic>VIRESCENS</italic> for both Christmas palm and golden cane palm (<xref rid=\"s0130\" ref-type=\"sec\">Figure S12</xref>). However, the expression of this gene was undetectable in the ripe fruit exocarp of both palms (##FIG##2##Figure 3##E), implying that sequence variations in the regulation regions may have silenced <italic>VIRESCENS</italic> in these lineages. Taken together, our data suggest that variations in the <italic>VIRESCENS</italic> gene might be related to the conspicuousness of fruit colors in palms. Therefore, the <italic>VIRESCENS</italic> gene might be under selection by frugivores.</p>", "<title>Duplication of <italic>PR</italic> genes and their crucial roles in response to <bold><italic>Ganoderma boninense</italic></bold> infection in oil palm</title>", "<p id=\"p0060\">PR proteins, subgrouped into functionally different groups in plants, play critical roles in host defense to viral and fungal infections ##UREF##5##[24]##. To date, little is known about the mechanism of these proteins responding to pathogen infections. We discovered 505 <italic>PR</italic> genes from 16 families in oil palm genome, among which 483 were mapped in 16 chromosomes (##FIG##3##Figure 4##A; <xref rid=\"s0130\" ref-type=\"sec\">Table S9</xref>). We found 319, 382, and 427 <italic>PR</italic> genes in date palm, coconut, and banana genome sequences, respectively. The size of gene families in oil palm was well correlated with that in date palm, coconut, and banana (<italic>R</italic> &gt; 0.92, <italic>P</italic> &lt; 1 × 10<sup>−4</sup>) (<xref rid=\"s0130\" ref-type=\"sec\">Figure S13</xref>), showing no significant evidence of expansion for a specific family. In oil palm, most of the <italic>PR</italic> genes presented in tandem duplications (##FIG##3##Figure 4##A). We defined a tandem array as a region within which genomic distance between any two adjacent <italic>PR</italic> genes was &lt; 100 kb. We discovered 70 tandem arrays, with the number of <italic>PR</italic> genes in each ranging from 2 to 23. Over 64.4% (312) of <italic>PR</italic> genes were found to be located in tandem arrays. The largest tandem array was located at Chr1, consisting of 23 members of PR16 family (##FIG##3##Figure 4##A). We observed that ∼ 97% of <italic>PR</italic> genes in individual tandem arrays were resulted from tandem duplications, whereas the remaining ∼ 3% were from translocation or ancient duplication and divergence. Interestingly, we did not find obvious evidence that these tandem arrays were distributed between a pair of conserved syntenic chromosome blocks. These data suggest that <italic>PR</italic> genes are hyperactive in birth and death, as well as translocations, and may have frequently reorganized their genomic locations.</p>", "<p id=\"p0065\">To understand more about the mechanism of pathogen defense in oil palm, we analyzed the genome-wide expression pattern of <italic>PR</italic> genes against the infection by <italic>G</italic>. <italic>boninense</italic> (<xref rid=\"s0130\" ref-type=\"sec\">Table S10</xref>) published by others ##REF##30594134##[25]##. We found that 84 (16.7%) <italic>PR</italic> genes were among the reported differentially expressed genes (DEGs) in root transcriptomes post infection (<xref rid=\"s0130\" ref-type=\"sec\">Figures S14 and S15</xref>; <xref rid=\"s0130\" ref-type=\"sec\">Table S11</xref>). The remaining <italic>PR</italic> genes may be induced in other tissues or involved in responses to the other pathogens. In detail, 59, 47, and 39 <italic>PR</italic> genes were detected as DEGs at 3, 7, and 11 days post infection (dpi), respectively (<xref rid=\"s0130\" ref-type=\"sec\">Figures S14 and S15</xref>). Thirty-eight (45.2%) DEGs were located in 10 tandem arrays, and distributed across seven chromosomes: Chr1, Chr4, Chr5, Chr6, Chr7, Chr11, and Chr14 (##FIG##3##Figure 4##A). DEGs in four (Chr1:PR1 members, Chr1:PR16 members, Chr7:PR16 members, and Chr14:PR10 members) and three (Chr4:PR7 members, Chr4:PR8 members, and Chr11:PR5 members) tandem arrays were consistently up- and down-regulated, respectively (##FIG##3##Figure 4##A). Analysis of DEGs in individual families (<italic>e</italic>.<italic>g</italic>., <italic>PR</italic> genes in PR5, PR9, and PR16 families) did not always show a consistent expression pattern (##FIG##3##Figure 4##B), suggesting neofunctionalization of the differentially expressed <italic>PR</italic> genes. Notably, DEGs belonging to the PR16 family were largely located in two tandem arrays at Chr1 and Chr7, in which all DEGs were up-regulated (##FIG##3##Figure 4##C), implying that these <italic>PR</italic> genes are subfunctionalized and involved in additive resistance to <italic>G</italic>. <italic>boninense</italic>\n##REF##28338077##[26]##. Phylogenetic analysis revealed three major genetic clusters (Clades 1–3) in PR16 family, and the identified DEGs were all from the subclade 4, the youngest subclade of Clade 3 (<xref rid=\"s0130\" ref-type=\"sec\">Figure S16</xref>). Regarding another tandem array at Chr10, we found that PR16 members were from different subclades of Clade 3, and showed a chimeric pattern of organization. In this tandem array, <italic>PR</italic> genes of subclades 1 and 3 as a unit were repeatedly organized (<xref rid=\"s0130\" ref-type=\"sec\">Figure S17</xref>), as observed in some other plants, <italic>i.e.</italic>, <italic>Theobroma cacao</italic> and <italic>Manihot esculenta</italic>\n##REF##27189060##[27]##, ##REF##31996126##[28]##, suggesting that <italic>PR</italic> genes have diverged prior to tandem duplications over evolutionary time. Taken together, our results reveal the crucial roles of large tandem arrays of <italic>PR</italic> genes in defense responses, particularly those consisting of evolutionary closely related <italic>PR</italic> genes. <italic>PR</italic> genes in chimeric tandem arrays or showing expression pattern shifts could have diverged over evolutionary time and likely been neofunctionalized and/or subfunctionalized.</p>", "<title>Population structure of the African oil palm</title>", "<p id=\"p0070\">We first examined the population structure of oil palms based on 4,410,076 single nucleotide polymorphisms (SNPs) generated by whole-genome resequencing of 72 trees (##FIG##4##Figure 5##A; <xref rid=\"s0130\" ref-type=\"sec\">Table S12</xref>). Both principal component analysis (PCA) and admixture analysis showed that the oil palms in Southeast Asia have clearly differentiated from their ancestral African ones except for those from Singapore and Malaysia, where most of the oil palms were either assigned into the African cluster or differentiated into an intermediate cluster between the African and Southeast Asian clusters (##FIG##4##Figure 5##B and C), since the first introduction in the 1840s ##UREF##2##[4]##. Within Africa, oil palms from the Ivory Coast are strikingly differentiated from the remaining trees. Oil palms from Ghana, Nigeria, Cameroon, and Angola formed into the other cluster, in which pairwise differentiation among locations is limited, with an overall pairwise differentiation (<italic>F</italic><sub>ST</sub>) of ∼ 0.05 (<xref rid=\"s0130\" ref-type=\"sec\">Table S13</xref>). The localized oil palms of Southeast Asia showed considerable differentiation among each other. Admixture analysis suggested the most likely number of genetic clusters to be three, followed by two (<xref rid=\"s0130\" ref-type=\"sec\">Figure S18</xref>). In agreement with PCA, admixture analysis showed evidence of a mixture of genetic clusters between the oil palms of Southeast Asia and Africa. The mixture occurred only in the oil palms of Singapore and Malaysia from Southeast Asia, implying repeated introduction of oil palms to Southeast Asia, likely as a result of escape of commercial cultivation or frequent commercial trade in the studied area.</p>", "<p id=\"p0075\">Introduction of species would lead to loss of genetic diversity, as a result of founder effects and local selection in the new habitats. We examined the genetic diversity between African and Southeast Asian oil palms. Compared with their ancestral populations, oil palms in Southeast Asia showed significantly reduced genetic diversity, measured in nucleotide diversity (<italic>π</italic>: 0.0008 <italic>vs.</italic> 0.0011, <italic>P</italic> &lt; 1 × 10<sup>−48</sup>, <italic>t</italic>-test) (##FIG##4##Figure 5##D), suggesting a recent bottleneck and/or local selection during establishment of the Southeast Asian populations. We also observed significantly more negative Tajima’s <italic>D</italic> in the Southeast Asian oil palms, in comparison to the African oil palms (<italic>P</italic> &lt; 1 × 10<sup>−72</sup>, <italic>t</italic>-test) (##FIG##4##Figure 5##E), suggesting elevated positive selection in the localized Southeast Asian oil palms. We further estimated the linkage disequilibrium (LD) and found that LD decayed to half of the maximum within 10 kb in the oil palms of Africa, faster than that in Southeast Asia with a value of 30 kb (##FIG##4##Figure 5##F). This scale of LD allows for effectively identifying signatures of selection using genome-wide SNPs.</p>", "<title>Adaptive evolution of the African oil palm</title>", "<p id=\"p0080\">To identify signatures of selection during introduction, we conducted a whole-genome scan for candidate regions between African and Southeast Asian oil palms. Both PCA and admixture analysis showed that the 72 oil palms were split into two major genetic clusters (##FIG##4##Figure 5##B and C). <italic>F</italic><sub>ST</sub> and the ratio of <italic>π</italic> values between ancestral and introduced populations (<italic>ϴ<sub>π</sub></italic>) scans identified 127 consistent genomic regions under putative selection, with a total length of ∼ 23 Mb (1.3%) and containing 488 predicted protein-coding genes (##FIG##5##Figure 6##A and B). Sixty-four out of the 127 regions deviated from neutrality by Tajima’s <italic>D</italic> analysis. A total of 317 genes were identified in those regions. Only the consistent results of these genomic scans were considered for further analysis to obtain a confident and reliable result (<xref rid=\"s0130\" ref-type=\"sec\">Table S14</xref>). Gene Ontology enrichment analysis showed that these genes were more involved in stress responses, such as response to ultraviolet (UV), regulation of autophagy, and response to oxidative stress (<xref rid=\"s0130\" ref-type=\"sec\">Figure S19</xref>A). Enrichment analysis against the protein family database Pfam revealed that a notably large proportion of protein families were related to stress responses and disease defense, such as the GDA1/CD39 family, cytochrome P450, monooxygenase, and heme peroxidase. In addition, proteins belonging to the protein families of ZIP Zinc transporter, sodium/hydrogen, and transmembrane domain of ABC transporters that are related to ion transport were also enriched (<xref rid=\"s0130\" ref-type=\"sec\">Figure S19</xref>B). Three genes (two homologs of <italic>WRKY70</italic> and <italic>WRKY24</italic>) from the WRKY transcription factor family were under putative selection. Genes of this family have been extensively shown to be related to abiotic stress in both model plants and oil palm ##REF##29228032##[29]##. These results suggest that genomic regions under putative selection play an important role in the adaptive evolution of oil palm.</p>", "<p id=\"p0085\">As the genes under putative selection are more involved in stress responses, in particular to pathogen infection and ion homeostasis, we separately analyzed these genes in correlation with DEGs responsible for resistance to <italic>G</italic>. <italic>boninense</italic> infection as described above and drought stress in our previous study ##REF##33277563##[30]##. Out of the 317 genes, 22 known protein-coding genes were revealed to be DEGs for drought stress, in which 12 and 10 genes were up- and down-regulated, respectively (##FIG##5##Figure 6##A; <xref rid=\"s0130\" ref-type=\"sec\">Table S15</xref>). Interestingly, we identified a selected region located at Chr5:105910001–110488835 bp with a length of ∼ 4.5 Mb, in which 13 (14.3%) out of 91 genes were DEGs, significantly higher than the ratio under null hypothesis of 4.3% throughout the whole genome. Most of these genes have been verified to be responsible for drought resistance in model plants, such as <italic>4CL2</italic>, <italic>CYP75A1</italic>, <italic>APY2</italic>, <italic>NAC68</italic>, <italic>CHX15</italic>, <italic>TBL33</italic>, and <italic>TBL34</italic>\n##REF##24631264##[31]##, ##REF##22445067##[32]##, ##REF##19368667##[33]##, ##REF##27864442##[34]##. Some of these genes under putative selection were also revealed to be responsible for heat stress, like <italic>LBD36</italic>, <italic>NAC68</italic>, <italic>YCF20</italic>, <italic>4CL2</italic>, and <italic>CYP75A1</italic>\n##REF##16453765##[35]##, ##REF##25426130##[36]##, ##REF##30938465##[37]##.</p>", "<p id=\"p0090\">Among the putatively selected genes, 17 known protein-coding genes were identified as DEGs against <italic>G</italic>. <italic>boninense</italic> infection, in which 3 and 14 were up- and down-regulated, respectively (##FIG##5##Figure 6##B; <xref rid=\"s0130\" ref-type=\"sec\">Table S15</xref>). Some of these genes have been shown to associate with disease resistance in model plant species, such as <italic>BEL1</italic>, <italic>PUB41</italic>, <italic>SAP12</italic>, <italic>CSE</italic>, <italic>NAC6</italic>8, <italic>PBL1</italic>, and <italic>PYL4</italic>\n##REF##22445067##[32]##, ##REF##24474812##[38]##, ##REF##15377756##[39]##, ##REF##27037613##[40]##, ##REF##29081783##[41]##. Interestingly, most of these genes were down-regulated against infection, implying a potential for decreased disease resistance in the oil palms of Southeast Asia; therefore, up-regulation of these genes may enhance disease resistance ##REF##29081783##[41]##, ##REF##30814258##[42]##. Three genes, <italic>CSE</italic>, <italic>NAC68</italic>, and <italic>CYP75A1</italic>, were observed to be responsible for both drought tolerance and fungal resistance, suggesting that these genes play common roles in stress responses. Further functional studies of these genes could provide more useful insights into the adaptive evolution of the African oil palm and supply valuable resources for selective breeding of the species.</p>" ]
[ "<title>Results and discussion</title>", "<title>Chromosomal-level genome of African oil palm</title>", "<p id=\"p0020\">Over 150× coverage of long reads was assembled into 4752 contigs, with a total length of 1.7 Gb, covering 94.5% of the estimated genome (1.8 Gb) (<xref rid=\"s0130\" ref-type=\"sec\">Table S1</xref>). Contig N50 and the longest contig reached up to 2.168 Mb and 12.851 Mb, respectively. We constructed five high-density linkage maps in five F<sub>2</sub> populations, with the number of mapped markers ranging from 12,068 to 19,581 (<xref rid=\"s0130\" ref-type=\"sec\">Figure S1</xref>; <xref rid=\"s0130\" ref-type=\"sec\">Table S2</xref>). Anchoring contigs to these high-density genetic maps, based on a total number of 60,989 informative segregating markers, resulted in 16 pseudochromosomes consisting of 91.6% of assembled sequences and with length ranging from 37.784 Mb to 160.148 Mb, and 59.7% of assembled sequences were oriented (<xref rid=\"s0130\" ref-type=\"sec\">Figure S2</xref>; Tables S1, S3, and S4). Genome completeness analysis assessed with Benchmarking Universal Single-Copy Orthologs (BUSCO) showed that 95.8% of the core genes were found in the genome and 93.3% were complete (<xref rid=\"s0130\" ref-type=\"sec\">Table S5</xref>). Mapping of assembled transcripts and <italic>de novo</italic> assembled restriction-site associated DNA (RAD) tags showed that 98.8% and 97.5% were matched to the genome assembly, respectively. We annotated long terminal repeats (LTRs). The LTR assembly index (LAI) was estimated to be 15.453 ± 2.968 (mean ± standard deviation). This genome assembly significantly increases the total length of assembled sequences by ∼ 61% (contig length from ∼ 1057 Mb to ∼ 1701 Mb), N50 contig size of ∼ 233 folds, N50 scaffold size of ∼ 80 folds, and total length of sequences anchored on pseudochromosomes of ∼ 2.4 folds, compared with previous draft genome sequences (<xref rid=\"s0130\" ref-type=\"sec\">Table S1</xref>) ##REF##27426468##[5]##, ##REF##23883927##[6]##, ##REF##33152992##[7]##. A chromosomal-level genome is necessary for comparative genomic analysis to study genome duplications and understand the genomic architecture of adaptive radiation of palms. Date palm (<italic>Phoenix dactylifera</italic>) Barhee BC4 is one of the most impressive assemblies in palms, in which &lt; 50% of sequences were anchored to pseudochromosomes ##REF##31615981##[9]##. Although diverged ∼ 65 million years ago (MYA) ##REF##23883927##[6]##, we observed a high level of conserved chromosome synteny between oil palm and date palm (##FIG##0##Figure 1##), indicating that the chromosomal-level genome of oil palm can be used for comparative genomic analysis. Taken together, our genome assembly showed high genome coverage, high assembly accuracy, long sequence continuity, and high completeness of both genes and repetitive elements. Therefore, it will be a vital contribution to studies on genetics, genomics, and breeding in palm species.</p>", "<title>Annotation of the African oil palm genome</title>", "<p id=\"p0025\">Repetitive sequences accounted for ∼ 74% of the genome assembly of oil palm (<xref rid=\"s0130\" ref-type=\"sec\">Table S6</xref>), significantly higher than that previously observed in the incomplete genome assembly of this species (∼ 57%) ##REF##23883927##[6]## and that in date palm (∼ 39%) ##REF##31615981##[9]##. LTRs took up 55.79% of the genome. <italic>Copia</italic> is the largest class of LTRs, followed by the <italic>Gypsy</italic> superfamily, representing 39.46% and 17.19% of the assembled genome sequences, respectively (<xref rid=\"s0130\" ref-type=\"sec\">Table S7</xref>). The proportions of the two LTR superfamilies are also much higher than those in date palm (∼ 14% for <italic>Copia</italic> and ∼ 4% for <italic>Gypsy</italic>) ##REF##31615981##[9]##. We observed that the distribution pattern of repetitive sequences was negatively correlated to that of the recombination rate (<italic>R</italic> = −0.412, <italic>P</italic> &lt; 1 × 10<sup>−4</sup>) and the gene density (<italic>R</italic> = −0.794, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>), but positively correlated to the distribution pattern of GC content (<italic>R</italic> = 0.932, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>) (##FIG##0##Figure 1##A–E). In date palm, we observed the same correlation patterns between the repetitive sequences and gene density (<italic>R</italic> = −0.856, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>) and between the repetitive sequences and GC content (<italic>R</italic> = 0.403, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>) (##FIG##0##Figure 1##A–E) as in oil palm, which addresses how transposon dynamics has significantly shaped the genomic architecture of palms. We observed that the distribution of <italic>Copia</italic> was highly correlated with that of the overall repetitive sequences (<italic>R</italic> = 0.952, <italic>P</italic> &lt; 1 × 10<sup>−6</sup>), whereas <italic>Gypsy</italic> were more likely randomly distributed across the genome (<italic>R</italic> = 0.107, <italic>P</italic> &lt; 0.05) (##FIG##0##Figure 1##F and G). Our data indicate that palms have a much higher copy number of <italic>Copia</italic> compared with <italic>Gypsy</italic>, contradicting most other plant genomes, which show higher <italic>Gypsy</italic> content ##REF##31615981##[9]##. Previous studies have reported that retrotransposons in plants play important roles in genome size, genome structure remodeling, gene function, and genome evolution ##REF##10690416##[10]##. Therefore, it is highly possible that <italic>Copia</italic> may play an important role in the evolution of palms.</p>", "<p id=\"p0030\">Gene annotations based on RNA sequencing (RNA-seq), <italic>ab initio</italic> predictions, plant protein-coding genes, and protein domains, predicted 33,447 protein-coding genes. Of these genes, 29,293 (87.58%) were annotated with known proteins or domains (<xref rid=\"s0130\" ref-type=\"sec\">Table S1</xref>). Over 95% of predicted genes showed an annotation edit distance (AED) value of &lt; 0.5, indicating high-quality annotations of the genome (<xref rid=\"s0130\" ref-type=\"sec\">Figure S3</xref>). Median gene length was ∼ 5.2 kb, slightly higher than those of previous oil palm and date palm assemblies of ∼ 4.7 kb and ∼ 4.2 kb, respectively ##REF##23883927##[6]##, ##REF##31615981##[9]##. In addition, more than 98% of the annotated genes were mapped to the 16 chromosome sequences, indicating that this genome assembly represents a nearly complete protein-coding genome and is useful in future genetic and genomic studies. Functional enrichment analysis revealed that gene families showing expansions in oil palm were more involved in stress responses to pathogens and regulation of osmotic stresses (<xref rid=\"s0130\" ref-type=\"sec\">Figures S4 and S5</xref>).</p>", "<title>Transposon burst leads to genome expansion and gene diversification in palms</title>", "<p id=\"p0035\">The variation in genome size across eukaryotes is tremendous and is associated with species diversity ##REF##17090588##[11]##. Polyploidy and transposon expansion are the two major forces driving genome size variation, providing essential resources for evolutionary innovations by generating novel genetic variations and altering gene expression patterns ##UREF##3##[12]##. Thus, it is necessary to unravel these mechanisms in order to better understand adaptive radiation and successful ecological dominance of the taxa. Genome size of palms varies from ∼ 800 Mb to ∼ 3 Gb ##REF##31028709##[13]##. Oil palm and date palm show a striking difference in genome size, with the predicted size of 1.8 Gb and 800 Mb, respectively, providing an excellent system to study genome size variation. Monocots share a common whole-genome duplication (WGD) event at ∼ 150 MYA ##REF##25082857##[14]##. The other paleopolyploid event, exclusively for the ancestor of all palms, occurred at ∼ 75 MYA, resulting in the paleotetraploidy of all palms ##REF##23883927##[6]##, ##REF##31028709##[13]##. We observed large conserved syntenic blocks between homologous chromosome pairs throughout the whole genome (<xref rid=\"s0130\" ref-type=\"sec\">Figure S6</xref>), allowing for examination of the effects of WGD events on genome evolution. Distribution of synonymous substitution rate (<italic>Ks</italic>), estimated based on 4292 and 2793 pairs of homologous genes from syntenic blocks in oil palm and date palm, respectively, revealed a major peak at ∼ 0.32, corresponding to the recent WGD at ∼ 75 MYA that was shared by all palms (##FIG##1##Figure 2##A and B) ##REF##31028709##[13]##. A more recent <italic>Ks</italic> peak was observed at ∼ 0.22 for orthologous gene pairs, indicating the divergence between oil palm and date palm at ∼ 65 MYA ##REF##23883927##[6]##. Here, the divergence of the whole-genome-wide homologous genes supports the conclusion that all palms have experienced two WGD events before adaptive radiation ##REF##31028709##[13]##.</p>", "<p id=\"p0040\">We did not find notable evidence of gene loss in date palm in contrast to oil palm, leading to another hypothesis that transposon proliferation drives genome size expansion and speciation of palms. LTRs are the richest transposable elements (TEs) in both species, with a total length of ∼ 950 Mb and ∼ 200 Mb ##REF##31615981##[9]## for oil palm and date palm, respectively. Difference in LTR content explains ∼ 80.3% of the genome size variation between the two species. Among LTRs, <italic>Copia</italic> is the most abundant superfamily for both species and accounts for ∼ 52.3% of total genome size variation (<xref rid=\"s0130\" ref-type=\"sec\">Table S7</xref>). We examined the historical dynamics of each subfamily of <italic>Copia</italic>. Pairwise sequence divergence within each subfamily presented two peaks with sequence similarity of ∼ 82% and ∼ 92%, respectively, in oil palm (##FIG##1##Figure 2##C). In comparison, two peaks of sequence divergence in date palm at ∼ 84% and ∼ 93% were only slightly visible (##FIG##1##Figure 2##D). In particular, the peak of higher similarity was remarkably inflated in oil palm, suggesting a recent transposon burst in oil palm relative to date palm. We compared the sequence divergence between <italic>Copia</italic> and homologous genes that mark the last WGD and diversification. Homologs in conserved syntenic blocks within each species presented a consistent peak with a similarity of ∼ 86%, whereas the divergence of homologs between species was ∼ 92%, marking the WGD and diversification events, respectively (<xref rid=\"s0130\" ref-type=\"sec\">Figure S7</xref>). The first wave of transposon burst, overlapping with the last WGD event, is suggested to be caused by rediploidization due to elevated genomic stress soon after WGD ##REF##27088604##[15]##. Under the assumption of comparable sequence evolutionary rates ##REF##27088604##[15]##, the second wave of transposon burst coincides with the time of divergence between the two palms, suggesting that transposon burst and differential dynamics play an important role in the diversification of palms. Large-scale transposon proliferation and movement may drive chromosome rearrangements, variation of recombination, and gene diversification, and eventually lead to speciation ##REF##20541961##[16]##.</p>", "<p id=\"p0045\">Transposon dynamics can affect genome-wide expression patterns and promote divergence by epigenetic regulation ##REF##19847266##[17]##. We identified 9786 intact LTRs throughout the genome. Approximately 33.8% of the intact LTRs showed an estimated insertion time of &lt; 1 MYA (<xref rid=\"s0130\" ref-type=\"sec\">Figure S8</xref>), within which 21.8% were in or within 5-kb distance to gene features (<xref rid=\"s0130\" ref-type=\"sec\">Figure S9</xref>). We hypothesized that young intact LTRs closely linked to genes can affect gene expression patterns. First, we compared the expression levels of 273 pairs of paralogous genes from conserved syntenic blocks of oil palm, in which only one of a pair of genes is closely linked to a young intact LTR. However, the expression levels of genes linked to LTRs were only slightly reduced (but not significantly) in almost all 12 examined tissues (<xref rid=\"s0130\" ref-type=\"sec\">Figure S10</xref>; <xref rid=\"s0130\" ref-type=\"sec\">Table S8</xref>). These paralogs diverged since the last WGD at ∼ 75 MYA ##REF##25082857##[14]## and likely have functionally diverged in depth. Thus, the effects of LTRs on linked genes are likely underestimated in these anciently duplicated genes. As expected, these paralogous genes presented a more diverse expression pattern than the recent locally duplicated genes (<xref rid=\"s0130\" ref-type=\"sec\">Figure S11</xref>). We further examined the effects of intact LTRs on 103 pairs of locally duplicated genes with a younger duplication time (<italic>Ks</italic>, 0.15 ± 0.07). Interestingly, genes linked to LTRs showed significantly lower expression levels as compared with their adjacent paralogs, in most of the examined samples (##FIG##1##Figure 2##E). Similar results were reported in the tea plant (<italic>Camellia sinensis</italic> var. <italic>sinensis</italic>) ##REF##32353625##[18]##. These findings highlight the importance of LTRs in promoting transcriptional diversification of duplicated genes by epigenetic suppression of closely linked genes, which finally contributes to genome divergence.</p>", "<title>Sequence variations in the <bold><italic>VIRESCENS</italic></bold> gene may be related to fruit colors in palms</title>", "<p id=\"p0050\">For decades, it has been hypothesized that fruit color had evolved to increase visual conspicuousness, and is subjected to selection by seed dispersing animals ##UREF##4##[19]##. In tropical palms, fruit color evolution is suggested to have interactions with frugivores ##REF##32198956##[20]##. However, the genomic basis of adaptive evolution of fruit color in palms is still unclear. <italic>VIRESCENS</italic> encodes a R2R3-MYB transcription factor, which controls the accumulation of anthocyanins in fruit exocarp of palms, leading to deep violet to black fruit colors ##REF##24978855##[21]##. The dark pigments of the exocarp reduce the visual conspicuousness in contrast with red, orange, and yellow pigmented fruits, which are caused by carotenoids and carotenes, making it less attractive to herbivorous animals. Thus, genes controlling the accumulation of anthocyanins in the exocarp tend to be under selection by seed dispersing animals.</p>", "<p id=\"p0055\">It has been found that loss-of-function mutants of <italic>VIRESCENS</italic> in both oil palm and date palm is associated with loss of anthocyanins in exocarp, leading to conspicuousness of fruit colors ##REF##31615981##[9]##, ##REF##24978855##[21]##. To examine the hypothesis, we cloned and analyzed the <italic>VIRESCENS</italic> gene of four additional palms: coconut, Christmas palm (<italic>Adonidia merrillii</italic>), Macarthur palm (<italic>Ptychosperma macarthurii</italic>), and golden cane palm (<italic>Dypsis lutescens</italic>). First, we measured the absorption spectrum of exocarp extracts and found that all four palms were deficient in anthocyanin accumulation in ripe fruit exocarp in contrast to the oil palm <italic>VIRESCENS</italic> fruit (wild-type) which had a high concentration of anthocyanins (##FIG##2##Figure 3##A and B). All coconut assemblies, including Catigan Green Dwarf ##REF##31167834##[22]##, <italic>Cn. tall</italic>, and <italic>Cn. dwarf</italic>\n##REF##34736486##[23]##, were observed to harbor the complete <italic>VIRESCENS</italic> locus (##FIG##2##Figure 3##C). Interestingly, sequence analysis showed that the <italic>VIRESCENS</italic> gene in these genome sequences was consistently disrupted by an insertion of a highly repetitive region including ∼ 60 simple repeats and ∼ 50 LTRs, leading to loss of partial exon 1 and the whole exon 2 (##FIG##2##Figure 3##C). Disruption of <italic>VIRESCENS</italic> in coconut genome likely explains its green exocarp even in the ripe fruit. In Macarthur palm, we found a premature termination codon in the exon 3 of <italic>VIRESCENS</italic>, resulting in a predicted truncation of 34 amino acids in the C-terminal relative to the sequence of wild-type oil palm (##FIG##2##Figure 3##D). As predicted in both oil palm and date palm, the truncated 34 amino acids are overlapping with the transcriptional activation domain of R2R3-MYB transcription factor (<xref rid=\"s0130\" ref-type=\"sec\">Figure S12</xref>), and loss of this domain leads to deficiency in the regulation of anthocyanin accumulation ##REF##24978855##[21]##. In contrast, we did not identify evidence of loss-of-function mutations in the coding sequences of <italic>VIRESCENS</italic> for both Christmas palm and golden cane palm (<xref rid=\"s0130\" ref-type=\"sec\">Figure S12</xref>). However, the expression of this gene was undetectable in the ripe fruit exocarp of both palms (##FIG##2##Figure 3##E), implying that sequence variations in the regulation regions may have silenced <italic>VIRESCENS</italic> in these lineages. Taken together, our data suggest that variations in the <italic>VIRESCENS</italic> gene might be related to the conspicuousness of fruit colors in palms. Therefore, the <italic>VIRESCENS</italic> gene might be under selection by frugivores.</p>", "<title>Duplication of <italic>PR</italic> genes and their crucial roles in response to <bold><italic>Ganoderma boninense</italic></bold> infection in oil palm</title>", "<p id=\"p0060\">PR proteins, subgrouped into functionally different groups in plants, play critical roles in host defense to viral and fungal infections ##UREF##5##[24]##. To date, little is known about the mechanism of these proteins responding to pathogen infections. We discovered 505 <italic>PR</italic> genes from 16 families in oil palm genome, among which 483 were mapped in 16 chromosomes (##FIG##3##Figure 4##A; <xref rid=\"s0130\" ref-type=\"sec\">Table S9</xref>). We found 319, 382, and 427 <italic>PR</italic> genes in date palm, coconut, and banana genome sequences, respectively. The size of gene families in oil palm was well correlated with that in date palm, coconut, and banana (<italic>R</italic> &gt; 0.92, <italic>P</italic> &lt; 1 × 10<sup>−4</sup>) (<xref rid=\"s0130\" ref-type=\"sec\">Figure S13</xref>), showing no significant evidence of expansion for a specific family. In oil palm, most of the <italic>PR</italic> genes presented in tandem duplications (##FIG##3##Figure 4##A). We defined a tandem array as a region within which genomic distance between any two adjacent <italic>PR</italic> genes was &lt; 100 kb. We discovered 70 tandem arrays, with the number of <italic>PR</italic> genes in each ranging from 2 to 23. Over 64.4% (312) of <italic>PR</italic> genes were found to be located in tandem arrays. The largest tandem array was located at Chr1, consisting of 23 members of PR16 family (##FIG##3##Figure 4##A). We observed that ∼ 97% of <italic>PR</italic> genes in individual tandem arrays were resulted from tandem duplications, whereas the remaining ∼ 3% were from translocation or ancient duplication and divergence. Interestingly, we did not find obvious evidence that these tandem arrays were distributed between a pair of conserved syntenic chromosome blocks. These data suggest that <italic>PR</italic> genes are hyperactive in birth and death, as well as translocations, and may have frequently reorganized their genomic locations.</p>", "<p id=\"p0065\">To understand more about the mechanism of pathogen defense in oil palm, we analyzed the genome-wide expression pattern of <italic>PR</italic> genes against the infection by <italic>G</italic>. <italic>boninense</italic> (<xref rid=\"s0130\" ref-type=\"sec\">Table S10</xref>) published by others ##REF##30594134##[25]##. We found that 84 (16.7%) <italic>PR</italic> genes were among the reported differentially expressed genes (DEGs) in root transcriptomes post infection (<xref rid=\"s0130\" ref-type=\"sec\">Figures S14 and S15</xref>; <xref rid=\"s0130\" ref-type=\"sec\">Table S11</xref>). The remaining <italic>PR</italic> genes may be induced in other tissues or involved in responses to the other pathogens. In detail, 59, 47, and 39 <italic>PR</italic> genes were detected as DEGs at 3, 7, and 11 days post infection (dpi), respectively (<xref rid=\"s0130\" ref-type=\"sec\">Figures S14 and S15</xref>). Thirty-eight (45.2%) DEGs were located in 10 tandem arrays, and distributed across seven chromosomes: Chr1, Chr4, Chr5, Chr6, Chr7, Chr11, and Chr14 (##FIG##3##Figure 4##A). DEGs in four (Chr1:PR1 members, Chr1:PR16 members, Chr7:PR16 members, and Chr14:PR10 members) and three (Chr4:PR7 members, Chr4:PR8 members, and Chr11:PR5 members) tandem arrays were consistently up- and down-regulated, respectively (##FIG##3##Figure 4##A). Analysis of DEGs in individual families (<italic>e</italic>.<italic>g</italic>., <italic>PR</italic> genes in PR5, PR9, and PR16 families) did not always show a consistent expression pattern (##FIG##3##Figure 4##B), suggesting neofunctionalization of the differentially expressed <italic>PR</italic> genes. Notably, DEGs belonging to the PR16 family were largely located in two tandem arrays at Chr1 and Chr7, in which all DEGs were up-regulated (##FIG##3##Figure 4##C), implying that these <italic>PR</italic> genes are subfunctionalized and involved in additive resistance to <italic>G</italic>. <italic>boninense</italic>\n##REF##28338077##[26]##. Phylogenetic analysis revealed three major genetic clusters (Clades 1–3) in PR16 family, and the identified DEGs were all from the subclade 4, the youngest subclade of Clade 3 (<xref rid=\"s0130\" ref-type=\"sec\">Figure S16</xref>). Regarding another tandem array at Chr10, we found that PR16 members were from different subclades of Clade 3, and showed a chimeric pattern of organization. In this tandem array, <italic>PR</italic> genes of subclades 1 and 3 as a unit were repeatedly organized (<xref rid=\"s0130\" ref-type=\"sec\">Figure S17</xref>), as observed in some other plants, <italic>i.e.</italic>, <italic>Theobroma cacao</italic> and <italic>Manihot esculenta</italic>\n##REF##27189060##[27]##, ##REF##31996126##[28]##, suggesting that <italic>PR</italic> genes have diverged prior to tandem duplications over evolutionary time. Taken together, our results reveal the crucial roles of large tandem arrays of <italic>PR</italic> genes in defense responses, particularly those consisting of evolutionary closely related <italic>PR</italic> genes. <italic>PR</italic> genes in chimeric tandem arrays or showing expression pattern shifts could have diverged over evolutionary time and likely been neofunctionalized and/or subfunctionalized.</p>", "<title>Population structure of the African oil palm</title>", "<p id=\"p0070\">We first examined the population structure of oil palms based on 4,410,076 single nucleotide polymorphisms (SNPs) generated by whole-genome resequencing of 72 trees (##FIG##4##Figure 5##A; <xref rid=\"s0130\" ref-type=\"sec\">Table S12</xref>). Both principal component analysis (PCA) and admixture analysis showed that the oil palms in Southeast Asia have clearly differentiated from their ancestral African ones except for those from Singapore and Malaysia, where most of the oil palms were either assigned into the African cluster or differentiated into an intermediate cluster between the African and Southeast Asian clusters (##FIG##4##Figure 5##B and C), since the first introduction in the 1840s ##UREF##2##[4]##. Within Africa, oil palms from the Ivory Coast are strikingly differentiated from the remaining trees. Oil palms from Ghana, Nigeria, Cameroon, and Angola formed into the other cluster, in which pairwise differentiation among locations is limited, with an overall pairwise differentiation (<italic>F</italic><sub>ST</sub>) of ∼ 0.05 (<xref rid=\"s0130\" ref-type=\"sec\">Table S13</xref>). The localized oil palms of Southeast Asia showed considerable differentiation among each other. Admixture analysis suggested the most likely number of genetic clusters to be three, followed by two (<xref rid=\"s0130\" ref-type=\"sec\">Figure S18</xref>). In agreement with PCA, admixture analysis showed evidence of a mixture of genetic clusters between the oil palms of Southeast Asia and Africa. The mixture occurred only in the oil palms of Singapore and Malaysia from Southeast Asia, implying repeated introduction of oil palms to Southeast Asia, likely as a result of escape of commercial cultivation or frequent commercial trade in the studied area.</p>", "<p id=\"p0075\">Introduction of species would lead to loss of genetic diversity, as a result of founder effects and local selection in the new habitats. We examined the genetic diversity between African and Southeast Asian oil palms. Compared with their ancestral populations, oil palms in Southeast Asia showed significantly reduced genetic diversity, measured in nucleotide diversity (<italic>π</italic>: 0.0008 <italic>vs.</italic> 0.0011, <italic>P</italic> &lt; 1 × 10<sup>−48</sup>, <italic>t</italic>-test) (##FIG##4##Figure 5##D), suggesting a recent bottleneck and/or local selection during establishment of the Southeast Asian populations. We also observed significantly more negative Tajima’s <italic>D</italic> in the Southeast Asian oil palms, in comparison to the African oil palms (<italic>P</italic> &lt; 1 × 10<sup>−72</sup>, <italic>t</italic>-test) (##FIG##4##Figure 5##E), suggesting elevated positive selection in the localized Southeast Asian oil palms. We further estimated the linkage disequilibrium (LD) and found that LD decayed to half of the maximum within 10 kb in the oil palms of Africa, faster than that in Southeast Asia with a value of 30 kb (##FIG##4##Figure 5##F). This scale of LD allows for effectively identifying signatures of selection using genome-wide SNPs.</p>", "<title>Adaptive evolution of the African oil palm</title>", "<p id=\"p0080\">To identify signatures of selection during introduction, we conducted a whole-genome scan for candidate regions between African and Southeast Asian oil palms. Both PCA and admixture analysis showed that the 72 oil palms were split into two major genetic clusters (##FIG##4##Figure 5##B and C). <italic>F</italic><sub>ST</sub> and the ratio of <italic>π</italic> values between ancestral and introduced populations (<italic>ϴ<sub>π</sub></italic>) scans identified 127 consistent genomic regions under putative selection, with a total length of ∼ 23 Mb (1.3%) and containing 488 predicted protein-coding genes (##FIG##5##Figure 6##A and B). Sixty-four out of the 127 regions deviated from neutrality by Tajima’s <italic>D</italic> analysis. A total of 317 genes were identified in those regions. Only the consistent results of these genomic scans were considered for further analysis to obtain a confident and reliable result (<xref rid=\"s0130\" ref-type=\"sec\">Table S14</xref>). Gene Ontology enrichment analysis showed that these genes were more involved in stress responses, such as response to ultraviolet (UV), regulation of autophagy, and response to oxidative stress (<xref rid=\"s0130\" ref-type=\"sec\">Figure S19</xref>A). Enrichment analysis against the protein family database Pfam revealed that a notably large proportion of protein families were related to stress responses and disease defense, such as the GDA1/CD39 family, cytochrome P450, monooxygenase, and heme peroxidase. In addition, proteins belonging to the protein families of ZIP Zinc transporter, sodium/hydrogen, and transmembrane domain of ABC transporters that are related to ion transport were also enriched (<xref rid=\"s0130\" ref-type=\"sec\">Figure S19</xref>B). Three genes (two homologs of <italic>WRKY70</italic> and <italic>WRKY24</italic>) from the WRKY transcription factor family were under putative selection. Genes of this family have been extensively shown to be related to abiotic stress in both model plants and oil palm ##REF##29228032##[29]##. These results suggest that genomic regions under putative selection play an important role in the adaptive evolution of oil palm.</p>", "<p id=\"p0085\">As the genes under putative selection are more involved in stress responses, in particular to pathogen infection and ion homeostasis, we separately analyzed these genes in correlation with DEGs responsible for resistance to <italic>G</italic>. <italic>boninense</italic> infection as described above and drought stress in our previous study ##REF##33277563##[30]##. Out of the 317 genes, 22 known protein-coding genes were revealed to be DEGs for drought stress, in which 12 and 10 genes were up- and down-regulated, respectively (##FIG##5##Figure 6##A; <xref rid=\"s0130\" ref-type=\"sec\">Table S15</xref>). Interestingly, we identified a selected region located at Chr5:105910001–110488835 bp with a length of ∼ 4.5 Mb, in which 13 (14.3%) out of 91 genes were DEGs, significantly higher than the ratio under null hypothesis of 4.3% throughout the whole genome. Most of these genes have been verified to be responsible for drought resistance in model plants, such as <italic>4CL2</italic>, <italic>CYP75A1</italic>, <italic>APY2</italic>, <italic>NAC68</italic>, <italic>CHX15</italic>, <italic>TBL33</italic>, and <italic>TBL34</italic>\n##REF##24631264##[31]##, ##REF##22445067##[32]##, ##REF##19368667##[33]##, ##REF##27864442##[34]##. Some of these genes under putative selection were also revealed to be responsible for heat stress, like <italic>LBD36</italic>, <italic>NAC68</italic>, <italic>YCF20</italic>, <italic>4CL2</italic>, and <italic>CYP75A1</italic>\n##REF##16453765##[35]##, ##REF##25426130##[36]##, ##REF##30938465##[37]##.</p>", "<p id=\"p0090\">Among the putatively selected genes, 17 known protein-coding genes were identified as DEGs against <italic>G</italic>. <italic>boninense</italic> infection, in which 3 and 14 were up- and down-regulated, respectively (##FIG##5##Figure 6##B; <xref rid=\"s0130\" ref-type=\"sec\">Table S15</xref>). Some of these genes have been shown to associate with disease resistance in model plant species, such as <italic>BEL1</italic>, <italic>PUB41</italic>, <italic>SAP12</italic>, <italic>CSE</italic>, <italic>NAC6</italic>8, <italic>PBL1</italic>, and <italic>PYL4</italic>\n##REF##22445067##[32]##, ##REF##24474812##[38]##, ##REF##15377756##[39]##, ##REF##27037613##[40]##, ##REF##29081783##[41]##. Interestingly, most of these genes were down-regulated against infection, implying a potential for decreased disease resistance in the oil palms of Southeast Asia; therefore, up-regulation of these genes may enhance disease resistance ##REF##29081783##[41]##, ##REF##30814258##[42]##. Three genes, <italic>CSE</italic>, <italic>NAC68</italic>, and <italic>CYP75A1</italic>, were observed to be responsible for both drought tolerance and fungal resistance, suggesting that these genes play common roles in stress responses. Further functional studies of these genes could provide more useful insights into the adaptive evolution of the African oil palm and supply valuable resources for selective breeding of the species.</p>" ]
[ "<title>Conclusion</title>", "<p id=\"p0095\">We sequenced and assembled a chromosome-level genome of the African oil palm. The genome assembly is of high completeness and continuity, which will serve as a good reference genome for oil palm. Comparative genomic analysis reveals that historical transposon expansion, but not WGD, explains genome size variation of palms, providing essential resources for adaptive radiation. Sequence analysis of the <italic>VIRESCENS</italic> gene in palms suggests that DNA variations in this gene may be related to fruit colors. Moreover, highly tandemly repeated <italic>PR</italic> genes play an important role in defense responses to <italic>Ganoderma</italic> infection. Analysis of genetic variation between the ancestral African and recently introduced Southeast Asian oil palms identified signatures of selection, particularly on the introduced oil palms. Genes under putative selection are remarkably associated with stress responses, providing insights into adaptation to new habitats. The novel genomic resources and insights gained from this study could be exploited for comparative genomics, evolutionary studies, and genetic improvement of palms.</p>" ]
[ "<p id=\"np010\">Equal contribution.</p>", "<p>The palm family (Arecaceae), consisting of ∼ 2600 species, is the third most economically important family of plants. The African <bold>oil palm</bold> (<italic>Elaeis guineensis</italic>) is one of the most important palms. However, the <bold>genome</bold> sequences of palms that are currently available are still limited and fragmented. Here, we report a high-quality chromosome-level reference genome of an oil palm, <italic>Dura</italic>, assembled by integrating long reads with ∼ 150× genome coverage. The assembled genome was 1.7 Gb in size, covering 94.5% of the estimated genome, of which 91.6% was assigned into 16 pseudochromosomes and 73.7% was repetitive sequences. Relying on the conserved synteny with oil palm, the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level. Transposon burst, particularly long terminal repeat retrotransposons, following the last whole-genome duplication, likely explains the genome size variation across palms. Sequence analysis of the <bold><italic>VIRESCENS</italic></bold> gene in palms suggests that DNA variations in this gene are related to fruit colors. Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to <italic>Ganoderma</italic>. Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses, suggesting adaptation to stresses in the new habitat. The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the <bold>evolution</bold> of palms.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Peng Cui</p>" ]
[ "<title>Data availability</title>", "<p id=\"p0165\">Raw sequencing reads generated in this study have been deposited in the DNA Data Bank of Japan SRA database (BioProject ID: PRJDB11628) which are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ddbj.nig.ac.jp\" id=\"PC_linkYniKykTfZF\">https://www.ddbj.nig.ac.jp</ext-link>, and also have been deposited in the Genome Sequence Archive ##REF##34400360##[81]## at the National Genomics Data Center (NGDC), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS) / China National Center for Bioinformation (CNCB) (GSA: CRA008676) which are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa\" id=\"PC_linkULB2eekSAb\">https://ngdc.cncb.ac.cn/gsa</ext-link>. The chromosomal-level genome sequences of oil palm can be accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://genhua.tll.org.sg/\" id=\"PC_linkRLuTYct3eY\">https://genhua.tll.org.sg/</ext-link>, and also have been deposited in the China National GeneBank DataBase (CNGBdb: CNA0047477) which are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://db.cngb.org\" id=\"PC_linkqwO1LTLOpJ\">https://db.cngb.org</ext-link>, and the Genome Warehouse ##REF##34175476##[82]## at the NGDC, BIG, CAS / CNCB (GWH: GWHBKAS00000000) which are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gwh\" id=\"PC_linkm8DUr3kidj\">https://ngdc.cncb.ac.cn/gwh</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0175\">Yuzer Alfiko, Rahmadsyah Rahmadsyah, Sigit Purwantomo, and Antonius Suwanto are current employees of Wilmar International Ltd. All the other authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0170\"><bold>Le Wang:</bold> Methodology, Software, Formal analysis, Visualization, Writing – original draft, Writing – review &amp; editing. <bold>May Lee:</bold> Resources, Methodology, Formal analysis. <bold>Zi Yi Wan:</bold> Resources, Methodology, Formal analysis. <bold>Bin Bai:</bold> Resources, Methodology, Formal analysis. <bold>Baoqing Ye:</bold> Software, Formal analysis. <bold>Yuzer Alfiko:</bold> Resources, Methodology. <bold>Rahmadsyah Rahmadsyah:</bold> Resources, Methodology. <bold>Sigit Purwantomo:</bold> Resources, Methodology. <bold>Zhuojun Song:</bold> Resources, Formal analysis. <bold>Antonius Suwanto:</bold> Resources, Supervision. <bold>Gen Hua Yue:</bold> Conceptualization, Supervision, Resources, Funding acquisition, Writing – review &amp; editing. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0190\">The following are the Supplementary material to this article:</p>", "<p id=\"p0195\">\n\n</p>", "<p id=\"p0200\">\n\n</p>", "<p id=\"p0205\">\n\n</p>", "<p id=\"p0210\">\n\n</p>", "<p id=\"p0215\">\n\n</p>", "<p id=\"p0220\">\n\n</p>", "<p id=\"p0225\">\n\n</p>", "<p id=\"p0230\">\n\n</p>", "<p id=\"p0235\">\n\n</p>", "<p id=\"p0240\">\n\n</p>", "<p id=\"p0245\">\n\n</p>", "<p id=\"p0250\">\n\n</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<p id=\"p0270\">\n\n</p>", "<p id=\"p0275\">\n\n</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<p id=\"p0325\">\n\n</p>", "<p id=\"p0330\">\n\n</p>", "<p id=\"p0335\">\n\n</p>", "<p id=\"p0340\">\n\n</p>", "<p id=\"p0345\">\n\n</p>", "<p id=\"p0350\">\n\n</p>", "<p id=\"p0355\">\n\n</p>", "<p id=\"p0360\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0180\">This work was supported by the Internal Funds of the <funding-source id=\"gp005\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100010730</institution-id><institution>Temasek Life Sciences Laboratory</institution></institution-wrap></funding-source>, Singapore (Grant No. 5020) and <funding-source id=\"gp010\">Wilmar International</funding-source>, Singapore (Grant No. 9200). We thank other lab members for technical supports.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Global view of genomic features of oil palm and genomic synteny with date palm</bold></p><p><bold>A.</bold> Length of individual pseudochromosomes (Mb). <bold>B.</bold> Distribution pattern of recombination rate throughout individual chromosomes. <bold>C.</bold> Distribution pattern of GC content throughout individual chromosomes, estimated in 500-kb window. <bold>D.</bold> Distribution pattern of gene density throughout individual chromosomes, estimated in 500-kb window. <bold>E.</bold> Distribution pattern of repetitive sequences throughout individual chromosomes, estimated in 500-kb window. <bold>F.</bold> Distribution pattern of LTR retrotransposon superfamily <italic>Copia</italic> throughout individual chromosomes, estimated in 500-kb window. <bold>G.</bold> Distribution pattern of LTR retrotransposon superfamily <italic>Gypsy</italic> throughout individual chromosomes, estimated in 500-kb window. <bold>H.</bold> Conserved syntenic blocks between a pair of homologous chromosomes of oil palm and date palm. Chr, chromosome; LTR, long terminal repeat.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Transposon expansion drives genome evolution of palms</bold></p><p><bold>A.</bold> A phylogram showing historical WGD events in palms. <bold>B.</bold> Distribution of <italic>Ks</italic> between a pair of homologous genes between oil palm and date palm (speciation) and separately within oil palm and date palm (WGD). <bold>C.</bold> Pairwise transposon divergence throughout 30 randomly selected subfamilies of LTR retrotransposon superfamily <italic>Copia</italic> in oil palm. Two major peaks at an average similarity of ∼ 82% and ∼ 92% are revealed. <bold>D.</bold> Pairwise transposon divergence throughout 30 randomly selected subfamilies of LTR retrotransposon superfamily <italic>Copia</italic> in date palm. Two major peaks at an average similarity of ∼ 84% and ∼ 93% are only slightly visible. <bold>E.</bold> Comparison of the relative expression levels between a pair of locally duplicated genes throughout 12 examined samples. Only one of each pair of paralogous genes shows intact LTR insertion in gene feature. KD1.5, KD2.5, and KD3.5 indicate kernel samples at 1.5, 2.5, and 3.5 months after fertilization, respectively, while MD1.5, MD2.5, MD3.5, MD4.5, and MD5.5 indicate mesocarp samples at 1.5, 2.5, 3.5, 4.5, and 5.5 months after fertilization, respectively. Flower_m and Flowe_f represent male and female flowers, respectively. *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; ns, not significant (paired <italic>t</italic>-test). WGD, whole-genome duplication; <italic>Ks</italic>, synonymous substitution rate; FPKM, fragments per kilobase of transcript per million mapped reads; <italic>E. guineensis</italic>, <italic>Elaeis guineensis</italic>; <italic>P. dactylifera</italic>, <italic>Phoenix dactylifera</italic>; <italic>O. sativa</italic>, <italic>Oryza sativa</italic>; <italic>M. acuminata</italic>, <italic>Musa acuminata.</italic></p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Variations of the <italic>VIRESCENS</italic> gene in palms</bold></p><p><bold>A.</bold> Color of exocarp extracts in 1% acidified methanol across oil palm, coconut, Macarthur palm, Christmas palm, and golden cane palm. Oil palm <italic>VIRESCENS</italic> fruit type containing anthocyanins showed a dark purple color. <bold>B.</bold> UV absorption spectrum of exocarp extracts in 1% acidified methanol across palms. Oil palm <italic>VIRESCENS</italic> fruit type presented an absorbance peak at ∼ 530 nm, consistent with the absorption of anthocyanins. <bold>C.</bold> Genomic synteny of the <italic>VIRESCENS</italic> locus among oil palm, date palm, and coconut. Coconut <italic>VIRESCENS</italic> is disrupted by an insertion of a 100-kb highly repetitive sequence, where black and red bars indicate simple repeats and LTR retrotransposons, respectively. <bold>D.</bold> Gene models of the <italic>VIRESCENS</italic> gene in oil palm, Macarthur palm, Christmas palm, and golden cane palm. A premature termination codon was detected in exon 3 of Macarthur palm. <bold>E.</bold> Expression of <italic>VIRESCENS</italic> and <italic>ACTB</italic> (a housekeeping gene as a control) in Macarthur palm, Christmas palm, and golden cane palm, examined using gene-specific primers. Three individuals were examined for each species, and minus indicates negative control. UV, ultraviolet.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Genome-wide distribution and</bold><bold>relative expression of</bold><bold><italic>PR</italic></bold><bold>genes</bold><bold>in oil palm</bold></p><p><bold>A.</bold> Genome-wide distribution of <italic>PR</italic> genes throughout 16 chromosomes. Positions of <italic>PR</italic> genes are shown with vertical bars, and PR gene families are discriminated by colors as shown in (B). The number and family of <italic>PR</italic> genes in tandem arrays are indicated at the top of each array. Red and blue arrows indicate that <italic>PR</italic> genes in a certain tandem array show consistently up- and down-regulation, respectively, whereas green arrow indicates that <italic>PR</italic> genes in a certain tandem array show both up- and down-regulation, against fungal infection. <bold>B.</bold> Pie charts showing the numbers of differentially expressed <italic>PR</italic> genes (up-regulation in red, and down-regulation in blue) throughout 16 PR gene families in oil palm root at 3, 7, and 11 days post fungal infection. <bold>C.</bold> Heatmaps showing the relative expression of <italic>PR</italic> genes that are located in tandem arrays in oil palm root at 3, 7, and 11 days post fungal infection. Tandem arrays, within which <italic>PR</italic> genes show consistently up- and down-regulation, are highlighted with red and blue boxes, respectively, whereas those with <italic>PR</italic> genes showing both up- and down-regulation are highlighted with green boxes. PR, pathogenesis-related.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Population divergence of oil palms</bold></p><p><bold>A.</bold> Sampling locations of the ancestral African oil palms and localized Southeast Asian oil palms. <bold>B.</bold> Population structure between and within African and Southeast Asian oil palms, revealed by PCA. <bold>C.</bold> Genetic clusters of population ancestry between and within African and Southeast Asian oil palms, inferred with admixture analysis. <bold>D.</bold> and <bold>E.</bold> Comparison of <italic>π</italic> and Tajima’s <italic>D</italic> between African and Southeast Asian oil palms, estimated with 100-kb window size. ****, <italic>P</italic> &lt; 0.0001 (<italic>t</italic>-test). <bold>F.</bold> LD decay in African and Southeast Asian oil palms, respectively. PCA, principal component analysis; <italic>π</italic>, nucleotide diversity; LD, linkage disequilibrium; PC, principal component.</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>Signatures</bold><bold>of selection in oil palm</bold></p><p><bold>A.</bold> Manhattan plot of genomic regions under putative selection, revealed by <italic>F</italic><sub>ST</sub> scanning between African and Southeast Asian oil palms. Genome-wide significance threshold at top 5% of windows in the empirical distribution is shown. Genes within outlier regions and identified as DEGs in root transcriptomes against drought stress are highlighted with gene names. Two <italic>NFD4</italic> genes are locally duplicated, and only one is indicated. <bold>B.</bold> Manhattan plot of genomic regions under putative selection, revealed by <italic>ϴ<sub>π</sub></italic> scanning between African and Southeast Asian oil palms. Genes within outlier regions and identified as DEGs in root transcriptomes against fungal infection are highlighted. Two <italic>APY2</italic> genes are locally duplicated, and only one is indicated. DEG, differentially expressed gene; <italic>F</italic><sub>ST</sub>, pairwise differentiation; <italic>ϴ<sub>π</sub></italic>, the ratio of <italic>π</italic> values between ancestral and introduced populations.</p></caption></fig>", "<fig id=\"f0035\" position=\"anchor\"><label>Supplementary Figure S1</label><caption><p>Distribution of SNPs in the five high-density linkage maps of the African oil palm SNPs, single nucleotide polymorphisms; LGs, linkage groups</p></caption></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary Figure S2</label><caption><p>Anchoring contigs to five high-density linkage maps of the African oil palm, using the program ALLMAPS Pearson’s correlation coefficient between each linkage group and the corresponding physical maps is denoted with ρ value</p></caption></fig>", "<fig id=\"f0045\" position=\"anchor\"><label>Supplementary Figure S3</label><caption><p>Distribution of the AED values throughout all predicted protein coding genes of the African oil palm genome AED, annotation edit distance</p></caption></fig>", "<fig id=\"f0050\" position=\"anchor\"><label>Supplementary Figure S4</label><caption><p>Comparison of expanded gene families between the African oil palm and date palm</p></caption></fig>", "<fig id=\"f0055\" position=\"anchor\"><label>Supplementary Figure S5</label><caption><p>Functional enrichment of the expanded gene families in the African oil palm, compared to date palm</p></caption></fig>", "<fig id=\"f0060\" position=\"anchor\"><label>Supplementary Figure S6</label><caption><p>Circos plot of homologous blocks between a pair of chromosome fragments in the African oil palm</p></caption></fig>", "<fig id=\"f0065\" position=\"anchor\"><label>Supplementary Figure S7</label><caption><p>Distribution of pairwise sequence divergence between homologous genes Pairwise sequence divergence was estimated within oil palm and date palm (WGD event), and between oil palm and date palm (speciation event)</p></caption></fig>", "<fig id=\"f0070\" position=\"anchor\"><label>Supplementary Figure S8</label><caption><p>Distribution of estimated LTR insertion time, revealed by LTR_retriever Mya, million years ago</p></caption></fig>", "<fig id=\"f0075\" position=\"anchor\"><label>Supplementary Figure S9</label><caption><p>Distribution of the distance between intact LTRs and predicted protein coding genes</p></caption></fig>", "<fig id=\"f0080\" position=\"anchor\"><label>Supplementary Figure S10</label><caption><p>Comparison of the relative expression level between a pair of homologous genes These pairwise homologous genes were from a pair of conserved chromosome syntenic blocks across 12 examined samples, where only one of each pair of homologous genes show intact LTR insertion in the gene feature. KD1.5, KD2.5, and KD3.5 indicate kernel samples at 1.5, 2.5, and 3.5 months after fertilization, respectively, while MD1.5, MD2.5, MD3.5, MD4.5, and MD5.5 indicate mesocarp samples at 1.5, 2.5, 3.5, 4.5, and 5.5 months after fertilization, respectively. * indicates <italic>P</italic> &lt; 0.05 for paired t-test. ns indicates not significant</p></caption></fig>", "<fig id=\"f0085\" position=\"anchor\"><label>Supplementary Figure S11</label><caption><p>Heatmap shows the relative expression level between a pair of homologous genes These pairwise homologous genes were from a pair of conserved chromosome syntenic blocks across 12 examined samples, where only one of each pair of homologous genes show LTR insertion in the genomic feature (upper figure). The relative expression level between a pair of homologous genes from local duplications across 12 examined samples, where only one of each pair of homologous genes show LTR insertion in the genomic feature (lower figure).</p></caption></fig>", "<fig id=\"f0090\" position=\"anchor\"><label>Supplementary Figure S12</label><caption><p>Alignment of VIRESCENS protein sequences and phylogenetic tree based on aligned protein sequences The studied species involved oil palm, date palm, Macarthur palm, Christmas palm, and golden cane palm. Predicted transcriptional activation domain of R2R3-MYB transcription factor was highlighted in grey shade. Amino acid mutation model of HIVb+I and 1000 bootstrap replications were used for tree construction. Orange (<italic>Citrus trifoliata</italic>) Myb transcription factor (ANI87841.1) was used as outgroup</p></caption></fig>", "<fig id=\"f0095\" position=\"anchor\"><label>Supplementary Figure S13</label><caption><p>Correlation of the number of PR family members between species The correlation was estimated between the African oil palm and date palm, between the African oil palm and coconut, and between the African oil palm and banana</p></caption></fig>", "<fig id=\"f0100\" position=\"anchor\"><label>Supplementary Figure S14</label><caption><p>Identification of DEGs in the root samples DEGs were identified at 3, 7, and 11 days post infection with <italic>Ganoderma boninense</italic> (left) and the number of PRs that are identified as DEGs in these samples (right).</p></caption></fig>", "<fig id=\"f0105\" position=\"anchor\"><label>Supplementary Figure S15</label><caption><p>Total DEGs identified in the root samples DEGs were identified at 3, 7, and 11 days post infection with <italic>Ganoderma boninense</italic> (green dots) and PRs that are identified as DEGs in these samples (red dots).</p></caption></fig>", "<fig id=\"f0110\" position=\"anchor\"><label>Supplementary Figure S16</label><caption><p>Phylogenetic tree of PR16 members and the relative expression of the PRs PRs that were classified into the subclade 4 were highlighted, where red shade indicates consistently up-regulated genes in all infected samples, regardless of statistical power, while plus indicates statistically significant DEGs. ns indicates non up-regulated genes</p></caption></fig>", "<fig id=\"f0115\" position=\"anchor\"><label>Supplementary Figure S17</label><caption><p>Genomic organization of PR16 members from different genetic clusters as revealed in Figure S18, in three tandem arrays at chr1, chr7, and chr10, respectively Different colors indicate different subclades</p></caption></fig>", "<fig id=\"f0120\" position=\"anchor\"><label>Supplementary Figure S18</label><caption><p>Inferring the most likely number of genetic clusters (K) among African and Southeast Asian oil palms, based on cross-validation error CV, cross-validation</p></caption></fig>", "<fig id=\"f0125\" position=\"anchor\"><label>Supplementary Figure S19</label><caption><p>Gene Ontology (A) and Pfam enrichments (B) of the genes under putative selection, consistently identified by <italic>F<sub>ST</sub></italic>, <italic>ϴ<sub>π</sub></italic>, and Tajima’s <italic>D</italic> scans, respectively</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0080\"><caption><title>Supplementary Table S1</title><p>Summary statistics of genome assemblies of oil palm, date palm, and coconut</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0075\"><caption><title>Supplementary Table S2</title><p>Summary statistics of five high-density linkage maps, including the number of SNPs and length of each linkage group</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0070\"><caption><title>Supplementary Table S3</title><p>Summary statistics of SNPs that are mapped to contigs and genomic sequences that are anchored onto the linkage maps and oriented</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0065\"><caption><title>Supplementary Table S4</title><p>Genomic sequences anchored onto 16 linkage groups/pseudochromosomes of the African oil palm genome</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Table S5</title><p>Completeness of oil genome assemblies assessed by BUSCO</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Table S6</title><p>Summary statistics of transposable elements in the African oil palm genome</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Table S7</title><p>Summary statistics of LTR retrotransposon superfamilies in the African oil palm genome and date palm genome</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S8</title><p>RNA sequencing samples used to examine homologous gene expressions in African oil palm genome</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S9</title><p>Summary statistics of PRs identified in the genome of oil palm, date palm, coconut, and banana</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S10</title><p>Root samples of African oil palm at 3, 7, and 11 days post infection with <italic>Ganoderma boninense</italic> and negative controls</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S11</title><p>Differentially expressed PRs from different families at 3, 7, and 11 days post infection with <italic>Ganoderma boninense</italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S12</title><p>African oil palm trees used for whole-genome resequencing and the sequencing coverage, sample location, and date for each tree</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S13</title><p>Pairwise <italic>F<sub>ST</sub></italic> of seven African oil palm samples, based on whole genome resequencing</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S14</title><p>Genes identified under putative selection in the oil palm genome</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S15</title><p>Genes that were identified under putative selection in the genome and to be differentially expressed in transcriptomes of oil palm against drought stress or fungal infection</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S16</title><p>Primers used to amplify and examine the expression of VIRESCENS gene in palms</p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e227\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China</p></fn><fn id=\"s0125\" fn-type=\"supplementary-material\"><p id=\"p0185\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.11.002\" id=\"PC_linkaLOJLrHMuJ\">https://doi.org/10.1016/j.gpb.2022.11.002</ext-link>.</p></fn></fn-group>" ]
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{ "acronym": [], "definition": [] }
82
CC BY
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2024-01-14 23:41:55
Genomics Proteomics Bioinformatics. 2023 Jun 24; 21(3):440-454
oa_package/52/bf/PMC10787024.tar.gz
PMC10787048
0
[ "<title>1. Introduction</title>", "<p>Mandibular fractures are the most commonly encountered type of maxillofacial fractures in children. Condylar fractures account for 39% to 52% of all mandibular fractures according to some papers. They even reach 70% according to some authors [##UREF##0##1##].</p>", "<p>A large head, a thin cortical bone, and a fragile narrow neck are all features of condyle anatomy in children. They increase risks of fracture especially in mandibular trauma contexts [##REF##36846088##2##].</p>", "<p>Condylar fractures are usually caused by an indirect blow to the chin or the mandibular angle. In the absence of pain or the inability to express suffering, lesions can be overlooked and not diagnosed until a complication appears [##UREF##0##1##, ##REF##25937718##3##]. Delayed and inadequate treatment can have serious repercussions, including malocclusion, jaw growth disorders, and facial asymmetry. In some cases, ankylosis can be noted [##REF##19521698##4##].</p>", "<p>Herein, we present the role of imaging modalities in the diagnosis, early detection of possible complications of traumatic fractures involving temporomandibular joints (TMJ), and patients' follow-up.</p>", "<p>This paper also highlights the importance of careful interpretation of radiological examinations in preventing condylar fracture complications, especially in pediatric patients.</p>" ]
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[ "<title>3. Discussion</title>", "<p>In this paper, a chronological CT illustration of TMJ ankylosis which is not commonly found in the literature is presented. The pictures emphasize the importance of radiological archive as a fundamental pillar of medico-legal justification in cases of complications.</p>", "<p>Ankylosis is usually painless. Clinical findings do not reveal any joint sound. Ankylosis can develop secondary to trauma as it causes extravasation of blood into the involved joint, leading to disruption of the fibrocartilage integrity and therefore to an increase in fibrous connective tissue [##UREF##0##1##, ##REF##25937718##3##, ##REF##26546159##5##]. In the present case, the etiology of ankylosis was related to a previous head trauma in which condylar fracture was overlooked.</p>", "<p>The ankylotic mass can be mistaken for a benign fibroosseous tumor (osteochondroma or osteoma) [##REF##36249652##6##, ##UREF##1##7##]. In the present case, the diagnosis of ankylosis was evident given the clinical and radiological context.</p>", "<p>It is important to know that these tumors do not invade the joint space which remains visible. The absence of trauma history or other joint diseases (infectious or autoimmune conditions) can help to differentiate this condition from others.</p>", "<p>Fibrous ankylosis can also resemble bony ankylosis because of the presence of hypomobility. However, it is the presence or absence of the articular space that differentiates them.</p>", "<p>Several classifications were proposed in order to properly assess the extension of ankylosis and therefore to establish an adequate treatment plan, including the surgical method and the nature and quantity of the TMJ reconstruction materials [##REF##11803384##8##–##UREF##3##10##].</p>", "<p>The most known classification of TMJ ankylosis was established by Sawhney, proposing 4 types of pathological alterations of the joint elements. Although it gives an objective insight into the bony surface remodeling, this classification is still insufficient with regard to a precise evaluation of the evolution of ankylosis, which may strongly impact the treatment outcomes.</p>", "<p>It is worth noting that other recognized classifications of TMJ ankylosis are available. The categories of El-Hakim et al. are based on CT scans, dealing with the morphological changes of TMJ anatomical elements as well as the proximity of the ankylosed mass to the adjacent vital structures, especially the maxillary artery, thus allowing the surgeon to elaborate an adequate surgical treatment plan and to achieve better operative results with the fewest complications possible [##REF##11803384##8##]. Another classification aiming to assess the medial displacement of condyles was proposed by He et al. [##UREF##3##10##].</p>", "<p>For our patient, ankylosis was fibrous as a thin joint space was still visible on CT scans. It was classified as Type II according to both classifications.</p>", "<p>In general, panoramic radiographs reveal TMJ deformity and complete absence of the joint space obliterated with a bone formation bridging the ramus and the zygomatic arch [##UREF##0##1##].</p>", "<p>The projection of the superior airways frequently crosses over the condylar neck, producing a thin radiolucent line that may be misleading, especially in the context of trauma.</p>", "<p>In the present case, on the day of the accident, the patient had a nonreadable panoramic due to superimpositions. The panoramic performed 3 years later to further explore the patient's mouth limitation was confronted with the clinical findings, and the diagnosis of ankylosis was then made.</p>", "<p>With high resolution and using multiplanar reconstructions, the CT scan provides further data about the anatomical elements and the surrounding environment of TMJ. It also provides details about the morphological changes as it assesses both the medial and lateral poles as well as the region in-between without overlap [##UREF##0##1##, ##REF##17639206##11##].</p>", "<p>In cases of fibrous ankylosis, CT and CBCT (cone beam computed tomography) usually reveal a limited or absent condylar translation as the joint space is narrowed. Cortical bone may show irregularities. With regard to cases of osseous ankylosis, CT findings include partial or complete obliteration of the joint space by a small or a large osseous mass that may fuse the condyle and the temporal fossa [##UREF##4##12##].</p>", "<p>For our patient, CT was performed because a cerebral lesion was suspected. This tool allowed the visualization of the fractured condyle which was previously overlooked.</p>", "<p>CBCT is less expensive and irradiating than CT, especially for pediatric patients, but it is not used for explorations in emergency cases because children are generally not cooperative, leading to movement artifacts [##UREF##5##13##–##REF##28257487##15##].</p>", "<p>In the present case, the condylar fracture took place in the context of a head trauma. Priority was therefore given to the exploration of possible cerebral lesions, and CT was the tool of choice. Besides, CBCT was not performed as it was not available in our hospitals in the 90s.</p>", "<p>To the best of the authors' knowledge, only few publications have presented a radiological illustration of the evolution of condylar fractures to ankylosis.</p>", "<p>The distance between the ankylotic mass and some important structures, such as the internal maxillary artery, mandibular foramen, lateral pterygoid plate, and external auditory canal, should be considered before any intervention. CT studies have also revealed the involvement of the glenoid fossa, foramen ovale, jugular foramen, and mastoid bone in the ankylotic mass [##UREF##0##1##, ##REF##34621659##16##, ##REF##24268963##17##].</p>", "<p>TMJ ankylosis in children can be a deterrent to normal mandibular growth, especially in the presence of a bilateral problem giving the young patient a “Bird face” appearance. The sequelae become more visible as the child grows [##REF##34621659##16##, ##UREF##6##18##, ##REF##16231529##19##].</p>", "<p>The complications related to TMJ ankylosis include several oral dysfunctions. Moreover, this pathology deeply affects the child's facial skeletal development. Facial dysmorphosis caused by an early traumatic ankylosis can cause psychological stress and therefore negatively impacts the patient's quality of life [##REF##26546159##5##, ##REF##27234304##20##]. Surgical treatment proves to offer an overall improvement in the pediatric patients' welfare, which is confirmed by their caregivers [##REF##31296437##21##, ##UREF##7##22##].</p>", "<p>This therapeutic choice entails risks of injury to the facial nerve, middle meningeal artery, and maxillary artery [##REF##24268963##17##, ##REF##29963424##23##, ##REF##34024006##24##].</p>", "<p>In this case, the patient's maximal mouth opening was severely affected due to ankylosis as it was restricted to 10 mm. This hugely hindered the patient's ability to make mandibular movements and thus to adequately eat various foods (he was only consuming liquid food), resulting in a progressive weight loss of the child. He was incapable of properly communicating with peers at school. As the patient was an infant, mandibular growth was slowed down, leading to both gnathic and dental malocclusion. Indeed, the patient was suffering from a mandibular retrognathism and a unilateral cross-bite of the left posterior teeth. Other complications may include obstructive sleep apnea if ankylosis persists in the long term [##REF##36965445##25##].</p>", "<p>Multidimensional radiological examination of traumatized patients should focus on the search for condylar and subcondylar fractures to avoid risks of ankylosis.</p>", "<p>CT allows a thorough study of the fracture lines and their orientation. Matching the reconstruction plane and the fracture line helps to visualize the fracture in all its length. Narrow window allows visualization of TMJ fracture inflammatory and/or infectious complications in the surrounding soft tissues (thickening/abscess of the lateral pterygoid, medial pterygoid, masseter, and temporal or septation of subcutaneous fat).</p>", "<p>Once TMJ fracture is diagnosed, and particularly in cases of pediatric patients, a multidisciplinary decision to treat should be immediately taken and discussed with the patient's family [##REF##32742104##26##], thus avoiding any possible alterations in the child's facial and overall growth [##REF##26546159##5##, ##UREF##6##18##, ##REF##16231529##19##, ##UREF##8##27##, ##REF##31351367##28##].</p>", "<p>In the present case, if a jaw mobilizer was indicated right after the trauma, ankylosis would have been minimized, if not avoided. Indeed, in the cerebral CT performed right after the trauma, a fracture in the head of the condyle was visible, but it was overlooked.</p>" ]
[ "<title>4. Conclusion</title>", "<p>TMJ ankylosis can have a negative impact on facial growth in young patients and can therefore be a huge impairment to a person's physical and psychological development as many functions can be affected by this disorder, mainly mastication, speech, and swallowing [##REF##36643593##29##].</p>", "<p>The aim of this paper was to show the crucial need for suspecting and establishing the diagnosis of condylar fractures within an adequate timeframe, especially for children having a trauma history, even in the absence of external signs of head injury. This implies the medical responsibility of radiologists, dentists, and other healthcare practitioners involved.</p>", "<p>Any pediatric patient presenting to the dental office or to the emergencies with a head trauma context involving mainly the mandible must be oriented for further exploration of TMJ by CT or CBCT scans. The latter are becoming more available and accurate and are considered more economic, irradiation-wise, and financially-wise.</p>", "<p>It is important to note that early physiotherapy should be immediately indicated to restore normal masticatory activity, continue mandibular growth, and thus prevent ankylosis [##REF##32572708##30##].</p>", "<p>We recommend that traumatized patients engage in physiotherapy as a prophylactic measure even if TMJ radiological examinations are not conclusive.</p>", "<p>A long follow-up period extending until the end of mandibular growth must be associated with surgical treatment in order to detect early signs of recurrence which remains possible due to the high regenerative and remodeling capacity in children [##REF##36643593##29##, ##REF##32176014##31##].</p>" ]
[ "<p>Academic Editor: Pia L. Jornet</p>", "<p>Temporomandibular joint ankylosis is an important entity that dentists and maxillofacial surgeons should know about. It clinically manifests through a permanent limitation of mandibular movements coupled with mouth opening inferior to 3 cm. This serious pathology can have serious functional repercussions, such as mastication problems, speech troubles, eating disorders, and jaw growth hindrance, in addition to the psychological difficulties in coping with such a condition in daily life. Herein, we present a radiological and chronological illustration of the evolution of temporomandibular joint ankylosis following an overlooked traumatic fracture of the mandibular condyle. The present case report involves an 8-year-old patient referred for a gradually evolving mouth opening limitation following a car accident. Tomodensitometry was helpful as it revealed an osseous block between the left temporomandibular joint surfaces, showing an ankylosis. Posttraumatic cerebral computed tomography scan was performed. It revealed an undetected fracture of the left condyle. The aim of this paper was to show how a traumatic ankylosis could have been avoided if enough attention was paid to the interpretation of immediate posttraumatic computed tomography scans. A thorough dental examination must be carried out once vital emergency is over. Early diagnosis of temporomandibular joint trauma is a crucial factor in preventing complications, such as ankylosis and its consequent oral dysfunctions. The dentist must automatically suspect condylar fracture when a child presents a history of head trauma, especially a mandibular trauma. This case should be a reminder that although temporomandibular joints are very often left out in patients' vital emergency first examination, temporomandibular joints/they are still a highly important structure which omission, and thus, dysfunction, if lesions are present, can lead to nonnegligible medico-legal consequences/that temporomandibular joints should be taken into account during patients' vital emergency first examination because if they are neglected, in the presence of lesions, they cause dysfunction, thus leading to nonnegligible medico-legal consequences.</p>" ]
[ "<title>2. Case Presentation</title>", "<p>An 8-year-old boy was referred to the oral radiology department for further exploration of severe mouth opening limitation (10 mm), evolving gradually over the previous 3 years with no history of pain episodes reported by the patient or his parents. The patient's caregivers mentioned that he had a car accident at the age of 5 and that he started to get skinner and skinner since then.</p>", "<p>Radiological explorations were performed. Panoramic radiography did not allow a good visualization of the left TMJ as this area was blurred (##FIG##0##Figure 1##). Computed tomography (CT) scan of TMJs was helpful in showing details of the TMJ osseous structures (Figures ##FIG##1##2## and ##FIG##2##3##). Scans revealed some morphological deformities in the temporal and condylar articular surfaces and irregularities in the joint space in the left TMJ. These findings were in favor of an ankylosis of the left TMJ, probably occurring after the trauma caused by the car accident.</p>", "<p>Anterior cerebral CT scan, performed on the day of the accident, revealed a fracture of the left condyle that was overlooked as the patient reported no pain in that area at that time (##FIG##3##Figure 4##).</p>", "<p>After obtaining a written permission from the patient's parents to use medical records for scientific publication and consent to treatment plan, a surgery involving the left TMJ was carried out under general anesthesia. It consisted in eliminating the bony mass and smoothing both the temporal and condylar articular surfaces, thus recreating the lost joint space which immediately allowed a degree of freedom for the condyle within the articulation.</p>", "<p>Anti-inflammatory medication and muscle relaxers were prescribed and taken over 1 month to avoid postsurgical trismus.</p>", "<p>Physiotherapy was indicated right after the surgery in order to regain normal mouth opening. The patient was asked to perform tasks several times a day, including movements of protrusion, retrusion, lateral deviation, and mouth opening using tongue depressors.</p>", "<p>After 3 months of rehabilitation, the patient regained a maximum interincisal opening reaching 30 mm. He was able to communicate via speech and to eat solid food without any discomfort. His weight ameliorated, and his school results improved remarkably.</p>", "<p>The long-term follow-up could not be carried out as the patient did not show up for check-up sessions.</p>" ]
[ "<title>Conflicts of Interest</title>", "<p>The authors declare no competing interest.</p>" ]
[ "<fig position=\"float\" id=\"fig1\"><label>Figure 1</label><caption><p>Panoramic radiograph showing ankylotic mass on the left condyle blurring the joint space (black arrow).</p></caption></fig>", "<fig position=\"float\" id=\"fig2\"><label>Figure 2</label><caption><p>Axial computed tomography slice in bone rendering showing ankylotic mass (black circle) located laterally to the left condyle.</p></caption></fig>", "<fig position=\"float\" id=\"fig3\"><label>Figure 3</label><caption><p>Frontal computed tomography reconstruction in bone rendering showing alteration in articular surfaces of the lateral aspect of the left temporomandibular joint. Note the persistence of joint space in the medial aspect (hatched black arrow).</p></caption></fig>", "<fig position=\"float\" id=\"fig4\"><label>Figure 4</label><caption><p>Immediate posttraumatic computed tomography scan. Axial slice in bone rendering showing fracture of the medial pole of the left condyle (white circle).</p></caption></fig>" ]
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[{"label": ["1"], "person-group": ["\n"], "surname": ["Kavin", "John", "Venkataraman"], "given-names": ["T.", "R.", "S. S."], "article-title": ["The role of three-dimensional computed tomography in the evaluation of temporomandibular joint ankylosis"], "source": ["\n"], "italic": ["Journal of Pharmacy & Bioallied Sciences"], "year": ["2012"], "volume": ["4"], "issue": ["6"], "fpage": ["217"], "lpage": ["220"], "pub-id": ["10.4103/0975-7406.100207"]}, {"label": ["7"], "person-group": ["\n"], "surname": ["Lucamba", "Grillo", "Jodas", "Teixeira"], "given-names": ["A. J.", "R.", "C. R. P.", "R. G."], "article-title": ["Multiple Gardner syndrome osteomas mimicking temporomandibular ankylosis: case report"], "source": ["\n"], "italic": ["Journal of Maxillofacial and Oral Surgery"], "year": ["2023"], "fpage": ["1"], "lpage": ["4"], "pub-id": ["10.1007/s12663-023-01871-1"]}, {"label": ["9"], "person-group": ["\n"], "surname": ["Braimah", "Taiwo", "Ibikunle"], "given-names": ["R. O.", "A. O.", "A. A."], "article-title": ["Temporomandibular joint ankylosis with maxillary extension: proposal for modification of Sawhney\u2019s classification"], "source": ["\n"], "italic": ["Craniomaxillofacial Trauma & Reconstruction Open"], "year": ["2018"], "volume": ["2"], "issue": ["1"], "pub-id": ["10.1055/s-0038-1666852"]}, {"label": ["10"], "person-group": ["\n"], "surname": ["He", "Zhang", "Xiao", "He", "Zhang"], "given-names": ["L.", "Z.", "E.", "Y.", "Y."], "article-title": ["Pathogenesis of traumatic temporomandibular joint ankylosis: a narrative review"], "source": ["\n"], "italic": ["The Journal of International Medical Research"], "year": ["2020"], "volume": ["48"], "issue": ["11"], "fpage": ["030006052097207"], "lpage": ["030006052097211"], "pub-id": ["10.1177/0300060520972073"]}, {"label": ["12"], "person-group": ["\n"], "surname": ["Tamimi", "Hatcher"], "given-names": ["D.", "D."], "source": ["\n"], "italic": ["Speciality Imaging: Temporomandibular Joint"], "year": ["2016"], "edition": ["1st"], "publisher-loc": ["USA"], "publisher-name": ["Elsevier"]}, {"label": ["13"], "person-group": ["\n"], "surname": ["Rozylo-Kalinowska", "Orhan"], "given-names": ["I.", "K."], "article-title": ["Imaging of the Temporomandibular Joint"], "year": ["2019"], "edition": ["1st"], "publisher-loc": ["Switzerland"], "publisher-name": ["Springer Nature"]}, {"label": ["18"], "person-group": ["\n"], "surname": ["Casanova", "Tuji", "Ortega", "Yoo", "Haiter-Neto"], "given-names": ["M. S.", "F. M.", "A. I.", "H. J.", "F."], "article-title": ["Computed tomography of the TMJ in diagnosis of ankylosis: two case reports"], "source": ["\n"], "italic": ["Medicina Oral, Patolog\u00eda Oral y Cirug\u00eda Bucal"], "year": ["2006"], "volume": ["11"], "issue": ["5"], "fpage": ["413"], "lpage": ["416"]}, {"label": ["22"], "person-group": ["\n"], "surname": ["Prabhu", "Issrani", "Ganji"], "given-names": ["N.", "R.", "K. K."], "article-title": ["Current trends in managing TMJ ankylosis in children\u2013summing it up with a case report"], "source": ["\n"], "italic": ["Journal of Surgical Case Reports"], "year": ["2023"], "volume": ["2023"], "issue": ["2"], "fpage": ["1"], "lpage": ["6"], "pub-id": ["10.1093/jscr/rjac550"]}, {"label": ["27"], "person-group": ["\n"], "surname": ["Raheel", "Ara", "Kishore", "Vikram", "Lowal", "Elfaki"], "given-names": ["S. A.", "S. A.", "N.", "V.", "K. A.", "S. O. M."], "article-title": ["3D virtual planning of temporomandibular joint ankylosis using computed tomography a case report in a 4-year-old female patient"], "source": ["\n"], "italic": ["International Journal of Clinical Dental Science"], "year": ["2015"], "volume": ["6"], "fpage": ["11"], "lpage": ["14"], "pub-id": ["10.15713/ins.ijcds.4"]}]
{ "acronym": [], "definition": [] }
31
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2024-01-14 23:41:55
Case Rep Dent. 2024 Jan 5; 2024:5101486
oa_package/19/ae/PMC10787048.tar.gz
PMC10787049
0
[ "<title>1. Introduction</title>", "<p>Mycoplasma pneumoniae pneumonia (MPP) is a common disease of the respiratory system in children caused by mycoplasma pneumoniae (MP), with an incidence of approximately 10%–40% [##REF##21880587##1##, ##REF##24864174##2##]. MP is one of the most common causes of community-acquired pneumonia in children and adolescents. In recent years, the risk of MP infection has increased in the Chinese population. Epidemiological studies have shown that MPP has an epidemic outbreak every 3-4 years in European countries [##REF##31119869##3##, ##UREF##0##4##]. More than 85% of MP strains among pediatric patients in China have been reported as macrolide-resistant MP, which can potentially cause severe and even extrapulmonary diseases. The global increase in macrolide-resistant MP is of concern due to limited therapeutic options [##REF##21880587##1##]. Based on this fact, MPP is divided into refractory mycoplasma pneumoniae pneumonia (RMPP) and general mycoplasma pneumoniae pneumonia (GMPP) [##REF##28922613##5##]. The prevalence of RMPP in children was 14.30%, with 6.83%, 20.86%, and 40.84% in those aged &lt;4 years, 4–7 years, and ≥7 years, respectively [##UREF##1##6##].</p>", "<p>The clinical presentation and manifestations of RMPP vary widely in different individuals and can affect all organs of the body. Children with RMPP may be complicated by pleural effusion, pulmonary atelectasis, gas accumulation in the mediastinum, pneumothorax, and necrotizing pneumonia. Some children with RMPP may develop respiratory distress, followed by rapid deterioration of their pulmonary functions, even requiring mechanical ventilation or extracorporeal lung support using extracorporeal membrane oxygenation (ECMO) [##REF##33403672##7##], resulting in death. After conventional treatments, a recurrence of pulmonary lesions or a prolonged course of disease may still be observed, contributing to structural and/or functional lung abnormalities manifested by bronchiectasis [##UREF##2##8##]. In fact, these conditions are often associated with recurrent pulmonary infections in children and even exert a significant impact on pulmonary function in adults. To prevent progression and reduce relevant complications, early recognition and diagnosis are crucial for the appropriate treatment of RMPP in patients who are prone to clinical and radiological exacerbations during macrolide therapy. With the increase in the incidence and mortality of RMPP, the prevention of high-risk patients with RMPP has become a major concern in clinical practice [##REF##18656264##9##, ##REF##24486173##10##].</p>", "<p>Currently, the diagnosis of RMPP has been challenging, with few significant features detected in laboratory or radiological evaluations, suggesting that there is no specific tool available for the diagnosis of RMPP [##UREF##3##11##]. Studies have shown that C-reactive protein (CRP), lactate dehydrogenase (LDH), erythrocyte sedimentation rate (ESR), percentage of neutrophils (NEPs), and the percentage of lymphocytes, together with the presence of dense solid pulmonary shadows, were significant predictors of RMPP [##REF##27686558##12##–##UREF##5##15##]. Based on the above, this study was aimed to investigate clinical characteristics and explore biomarkers for early prediction of RMPP in children, providing references for the establishment of an efficient protocol for the early diagnosis of RMPP.</p>" ]
[ "<title>2. Materials and Methods</title>", "<title>2.1. Study Design and Patients</title>", "<p>This is a retrospective study. Children with MPP who were admitted to the Department of Respiratory Medicine, Fujian Children's Hospital, between January 2021 and December 2022 were enrolled. A flowchart of our research is detailed in ##FIG##0##Figure 1##.</p>", "<p>Inclusion criteria were the following: (1) patients aged 6 months-12 years; (2) patients who met the diagnostic criteria for MPP: positive results for the serologic test (positive IgM specific to MP, with IgM antibody titer &gt;1 : 160) and nasopharyngeal secretions were positive for MP using polymerase chain reaction (PCR); and (3) patients who voluntarily underwent chest radiograph and/or CT examination.</p>", "<p>Exclusion criteria were as follows: (1) patients with immunodeficiency diseases; (2) patients with respiratory diseases such as congenital bronchopulmonary dysplasia, pulmonary fibrosis, foreign bodies of the bronchial, asthma, tuberculosis, lung tumors, and noninfectious interstitial lung diseases; (3) patients with tumors, fracture trauma, tissue and organ fibrosis, and other diseases; and (4) patients with problems in specimen collection and incomplete data.</p>", "<p>The study was approved by the Ethics Committee of Fujian Children's Hospital, Fujian Medical University. Patients were appropriately informed about treatment decisions. Informed consent was obtained from all patients.</p>", "<title>2.2. Grouping of Patients</title>", "<p>All patients were divided into 2 groups, including the GMPP group and the RMPP group. The diagnosis of RMPP was based on the presence of persistent fever (≥37.5°C) accompanied by clinical and radiological deterioration after azithromycin treatment for ≥7 days [##REF##18656264##9##, ##UREF##5##15##]. Patients who met the diagnosis of RMPP were allocated into the GMPP group; others were classified into the GMPP group.</p>", "<title>2.3. Data Collection</title>", "<p>In the study, patient information was collected, including baseline clinical characteristics, laboratory results, and radiological findings. Baseline clinical characteristics, including age, sex, month and season of onset, hospital stay, clinical symptoms and signs, and extrapulmonary manifestations, were collected from both groups of children. Within 24 h of admission, all children were tested for respiratory pathogens and 2-3 ml of fasting venous blood was drawn for relevant laboratory tests, including MP-specific antibody titer tests, WBC count, percentage of NEP, CRP, LDH, procalcitonin (PCT), D-dimer, and tumor necrosis factor alpha (TNF-<italic>α</italic>). Imaging examinations mainly included chest radiographs and/or CT throughout the course of the disease, from which the extent of involvement, type of lesions, and intrapulmonary complications such as pulmonary atelectasis, pleural effusion, and pulmonary necrosis were collected.</p>", "<title>2.4. Statistical Analysis</title>", "<p>Statistical analysis was performed using SPSS 23.0. Continuous data with normal distribution were described with mean ± standard deviation (SD), and Student's <italic>t</italic>-test was used for comparison between the groups. Continuous data with a skewed distribution were presented with median and interquartile range (IQR), and the Mann–Whitney <italic>U</italic> test was used for comparison between the groups. Categorical data were expressed as frequency and percentage (%), and the chi-square test was used for comparison between the groups. Laboratory indicators of statistical significance in the comparisons were included as risk factors in the prediction of RMPP by using stepwise backward logistic regression. Receiver operating characteristic (ROC) curves were plotted, and the area under the curve (AUC) was calculated to evaluate the predictive value of laboratory indicators for RMPP. A two-sided <italic>P</italic> &lt; 0.05 was considered as statistically significant.</p>" ]
[ "<title>3. Results</title>", "<title>3.1. Comparison of Clinical Characteristics between the RMPP and GMPP Groups</title>", "<p>In this study, 8 of 476 patients withdrew from the study. A total of 468 children with MPP were included finally, of which 156 (33.33%) were in the RMPP group and 312 were in the GMPP group.</p>", "<p>As shown in ##TAB##0##Table 1##, there were 55.77% males and 51.28% females in the RMPP group, with a mean age of 6.23 ± 2.89 years. RMPP occurs primarily in summer (36.54%) and in autumn (30.13%). However, there were no significant differences between the two groups in terms of sex, age, and season of onset (<italic>P</italic> &gt; 0.05).</p>", "<p>In terms of clinical symptoms, all patients in the RMPP group had fever, and the proportion of shortness of breath was significantly higher in the RMPP group than in the GMPP group (23.08% vs. 6.41%, <italic>P</italic> &lt; 0.001); in contrast, the proportions of runny nose (36.90% vs. 8.50%, <italic>P</italic>=&lt;0.001) and gastrointestinal symptoms (26.92% vs.18.59%, <italic>P</italic>=0.047) in the GMPP group were significantly higher than those in the RMPP group. However, the percentage of cough was as high as 94.87% in the RMPP group and 98.08% in the GMPP group, but their difference was not statistically significant (<italic>P</italic> &gt; 0.05).</p>", "<p>In terms of physical examination, the proportion of three concave signs (manifested as the suprasternal fossa, supraclavicular fossa, and concave intercostal space) was significantly higher in the RMPP group than in the GMPP group (10.90% vs. 2.56%, <italic>P</italic> &lt; 0.001). The proportion of moist rales was 52.56% in the RMPP group and 46.79% in the GMPP group, but their difference was not statistically significant (<italic>P</italic> &gt; 0.05).</p>", "<p>In terms of pulmonary imaging, the proportions of pulmonary consolidation (79.49% vs. 41.99%, <italic>P</italic> &lt; 0.001), pulmonary atelectasis (5.77% vs. 1.6%, <italic>P</italic>=0.013), and pleural effusion (30.77% vs. 2.24%, <italic>P</italic> &lt; 0.001) in the RMPP group were all significantly higher than those in the GMPP group.</p>", "<p>Furthermore, the proportion of extrapulmonary complications in the RMPP group was significantly higher than the GMPP group (37.18% vs. 16.99%, <italic>P</italic> &lt; 0.001).</p>", "<p>Extrapulmonary complications refer to the symptoms and signs of damage to other systems other than the respiratory system, including the digestive system, cardiovascular system, blood system, nervous system, urinary system, skin sores, and joint pain.</p>", "<p>The mean duration of hospital days in the RMPP group was also significantly longer than that of the GMPP group (11.09 ± 4.25 vs. 8.27 ± 3.12, <italic>P</italic> &lt; 0.001).</p>", "<title>3.2. Comparison of Laboratory Indicators between the RMPP and GMPP Groups</title>", "<p>As shown in ##TAB##1##Table 2##, comparisons of laboratory indicators between the RMPP and GMPP groups showed that serum levels of CRP, LDH, PCT, and D-dimer were significantly higher in the RMPP group than in the GMPP group. However, the percentage of NEPs was significantly higher in the GMPP group than in the RMPP group. Differences in WBC count and TNF-<italic>α</italic> between the two groups were not statistically significant (<italic>P</italic> &gt; 0.05).</p>", "<title>3.3. Logistic Regression for Risk Factors of RMPP</title>", "<p>Multiple logistic regression analysis showed that serum levels of D-dimer (OR = 8.169, <italic>P</italic> &lt; 0.001), CRP (OR = 1.146, <italic>P</italic> &lt; 0.001), and LDH (OR = 1.025, <italic>P</italic> &lt; 0.001) were independent risk factors for RMPP. The linear probability model was as follows: logit (<italic>P</italic>) = −16.226 + 2.100<italic>X</italic>1 + 0.136<italic>X</italic>2 + 0.024<italic>X</italic>3 (##TAB##2##Table 3##).</p>", "<title>3.4. Predictive Values of Serum D-Dimer, CRP, and LDH Levels for RMPP Using ROC Curves</title>", "<p>To explore the predictive value of serum D-dimer, CRP, and LDH levels for RMPP, the ROC curves were plotted, and the AUC was calculated. The results showed good predictive values of serum D-dimer, CRP, and LDH levels for RMPP, with AUROC of 0.841, 0.870, and 0.893, respectively (##FIG##1##Figure 2##). The optimal cutoff point was determined according to the Youden index. Specifically, the optimal cutoff point of 1.47 ng/ml for the serum D-dimer level revealed a sensitivity of 64.74% and a specificity of 98.72% for the detection of RMPP, the optimal cutoff point of 39.34 mg/L for the serum CRP level revealed a sensitivity of 60.89% and a specificity of 94.55% for the detection of RMPP, and the optimal cutoff point of 379 IU/L for the serum LDH level revealed a sensitivity of 66.67% and a specificity of 93.91% for the detection of RMPP (##TAB##3##Table 4##).</p>" ]
[ "<title>4. Discussion</title>", "<p>RMPP is usually characterized by a long course of disease, a poor therapeutic efficacy, and numerous complications that can even endanger the lives of children. The present study found that serum levels of D-dimer, CRP, and LDH were independent risk factors for RMPP, which laid a basis for early identification of RMPP and may be of great help in the diagnosis and prognosis of these children.</p>", "<p>As reported, the most common clinical symptoms of RMPP were composed of cough (no sputum at the beginning and small to moderate bloodless sputum later), fever, chills, sore throat, headache, hoarseness, myalgia, and general malaise [##UREF##6##16##] and would worsen after 7 days of macrolide therapy, accompanied by persistent fever, pulmonary exacerbation in radiological findings, and extrapulmonary complications [##REF##24277047##17##]. All of this was consistent with the clinical symptoms of children with RMPP observed in this study. Additionally, we also found that clinical symptoms were more severe in the RMPP group compared to the GMPP group, with fever observed in all children and a percentage of shortness of breath of up to 23.08% in the RMPP group. Furthermore, compared to those with GMPP, the images also presented with more severe manifestations in children with RMPP, with proportions of pulmonary consolidation, pulmonary atelectasis, and pleural effusion of 79.49%, 5.77%, and 30.77%, respectively.</p>", "<p>In this study, 126 children (37.18%) with RMPP had extrapulmonary complications, which was significantly more than those in the GMPP group. Furthermore, the mean duration of hospital stays was 11.09 ± 4.25 in the RMPP group, which was also higher than the GMPP group with statistical significance. The abovementioned findings were in agreement with those reported in previous studies. Gong et al. [##UREF##5##15##] identified that persistent fever (&gt;10 days), pleural effusion, extrapulmonary complications, pulmonary consolidation detected in chest radiography, and CRP &gt; 40 mg/L could be used for early evaluation of RMPP by using a fixed-effects model or a random-effects model. In addition, Choi et al. [##UREF##7##18##] showed that respiratory distress, oxygen saturation &lt;90%/cyanosis, oxygen support during hospitalization, lobar pneumonia on admission, and extrapulmonary complications were independent risk factors for RMPP, which was similar to the results of the present study.</p>", "<p>The pathogenic mechanisms of RMPP are complex and include mainly direct pulmonary cell injury and immune response-induced injury. Currently, RMPP is considered to be related to airway mucus hypersecretion, hypercoagulable state, bacterial or viral infection, and excessive immune response due to the community-acquired respiratory distress syndrome (CARDS) toxin [##REF##31399022##19##, ##REF##34674642##20##]. Based on relevant basic research results and literature reports, this study selected 7 highly correlated biomarkers for the study of RMMP prediction indicators. CRP is one of the important indicators of inflammatory response [##UREF##8##21##], which has been widely used for assessing disease severity and treating inflammatory conditions. In addition, serum D-dimer levels have been recognized as a specific marker of the fibrinolytic system and an indicator of monitoring inflammations and severe infections [##REF##32306492##22##]. The elevated level of D-dimer is possibly attributed to the injury of vascular endothelial cells caused by the excessive inflammatory response, which may be related to the mechanism of pulmonary injury in RMPP. Additionally, increased LDH activity has been found to be associated with pulmonary inflammation and hypoxia. High serum LDH levels showed the potential to predict an inadequate response to glucocorticoid treatment [##REF##28539503##23##].</p>", "<p>In this study, the results of multiple logistic regression analysis showed that serum D-dimer, CRP, and LDH levels were independent risk factors for RMPP; AUROCs for serum D-dimer, CRP, and LDH levels in the prediction of RMPP were all more than 0.8 (0.841, 0.870, and 0.893, respectively), suggesting their good predictive values in RMPP. Although the sensitivity of these cutoffs is lower than 65%, the specificity is higher than 93%, which can effectively exclude non-RMPP patients, thereby reducing the misdiagnosis rate. Similar to these findings, Zhang et al. also observed that the levels of CRP, LDH, and interleukin-6 (IL-6) were significantly higher in patients with RMPP than those with GMPP, indicating that they may be important predictors of RMPP in children and could facilitate the early identification of RMPP [##UREF##8##21##]. Meanwhile, the optimal cutoff points for serum D-dimer, CRP, and LDH levels for detecting RMPP were found to be 1.47 ng/ml, 39.34 mg/L, and 379 IU/L, respectively, which were comparable to the values of a case-control study (2.10 ng/ml, 343.08 mg/L, and 375 IU/L for serum levels of D-dimer, CRP, and LDH, respectively) [##REF##33752670##24##]. Based on the abovementioned results, it could be inferred that serum levels of D-dimer, CRP, and LDH may have a certain value for clinical application.</p>", "<p>There were several limitations in this study. First, as a single-center study, this study may have selection bias compared to multicenter studies. Second, a paired design was not performed and the patients in the RMPP group were not matched with those in the GMPP group for certain parameters, which may affect the statistical efficacy of the results. Finally, no joint prediction using multiple indicators was performed. Therefore, in the future, a multicenter-paired study should be conducted to further study the joint prediction of RMPP based on multiple indicators.</p>" ]
[ "<title>5. Conclusions</title>", "<p>In conclusion, serum levels of D-dimer, CRP, and LDH are independent risk factors for RMPP and have high specific predictive values though low sensitivity for the early identification of RMPP. Early detection of RMPP within 24 hours of hospital admission may guide therapy revision for patients to reduce mortality.</p>" ]
[ "<p>Academic Editor: Chak W. Kam</p>", "<title>Objective</title>", "<p> The study aimed to analyze the clinical characteristics of children with RMPP and to explore the biomarkers for the early prediction of RMPP, thus providing references for the clinical diagnosis and treatment of RMPP in children. </p>", "<title>Methods</title>", "<p> Baseline clinical characteristics, clinical symptoms, physical examination, chest imaging, and laboratory indicators between children with RMPP and general refractory mycoplasma pneumoniae pneumonia (GMPP) were compared. Multiple logistic regression analysis was used to determine independent risk factors for RMPP. ROC curves were adopted to analyze the predictive values of biomarkers. </p>", "<title>Results</title>", "<p> The RMPP group had more severe clinical symptoms and manifestations on imaging (including pleural effusion, pulmonary consolidation, and pulmonary atelectasis), a higher incidence of extrapulmonary complications, and a longer duration of hospital stays. Results of multiple logistic regression analysis showed that serum D-dimer (OR = 8.169, <italic>P</italic> &lt; 0.001), C-reactive protein (CRP) (OR = 1.146, <italic>P</italic> &lt; 0.001), and lactate dehydrogenase (LDH) (OR = 1.025, <italic>P</italic> &lt; 0.001) levels were independent risk factors for RMPP. The area under the receiver operating characteristic curve (AUROC) in RMPP prediction was 0.841, 0.870, and 0.893 for serum levels of D-dimer, CRP, and LDH, respectively (<italic>P</italic> &lt; 0.001), with a cutoff value of 1.47 ng/ml, 39.34 mg/L, and 379 IU/L, respectively. </p>", "<title>Conclusions</title>", "<p> Serum D-dimer, CRP, and LDH levels were related to the severity of mycoplasma pneumoniae pneumonia in children and had potential as biomarkers for the early prediction of RMPP, suggesting great applicative values for the early diagnosis and timely intervention of children with RMPP in clinical practice.</p>" ]
[]
[ "<title>Data Availability</title>", "<p>The data that support the findings of this study are available from the corresponding author upon request.</p>", "<title>Conflicts of Interest</title>", "<p>The authors declare that they have no conflicts of interest.</p>" ]
[ "<fig position=\"float\" id=\"fig1\"><label>Figure 1</label><caption><p>Flowchart of the study group.</p></caption></fig>", "<fig position=\"float\" id=\"fig2\"><label>Figure 2</label><caption><p>ROC curves for D-dimer, CRP, and LDH for the prediction of RMPP.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"tab1\"><label>Table 1</label><caption><p>Comparison of clinical characteristics between the RMPP and GMPP groups (<italic>n</italic> = 468).</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Factors</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">RMPP (<italic>n</italic> = 156)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">GMPP (<italic>n</italic> = 312)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>t</italic>/<italic>χ</italic><sup>2</sup></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>P</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<italic>Sex</italic>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.840</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.359</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Male</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">87 (55.77%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">160 (51.28%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Female</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">69 (44.23%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">152 (48.72%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<italic>Age (years)</italic>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.23 ± 2.89</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.57 ± 3.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.294</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.218</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<italic>Onset season</italic>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.117</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.106</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Spring</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">28 (17.95%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">32 (10.26%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Summer</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">57 (36.54%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">113 (36.22%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Fall</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">47 (30.13%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">111 (35.58%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Winter</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24 (15.38%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">56 (17.95%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Clinical symptoms: fever</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">156 (100%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">249 (79.81%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">36.40</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Clinical symptoms: cough</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">148 (94.87%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">306 (98.08%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.682</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.055</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Clinical symptoms: shortness of breath</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">36 (23.08%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20 (6.41%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27.424</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Clinical symptoms: runny nose</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18 (8.50%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">115 (36.90%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">32.777</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Clinical symptoms: gastrointestinal symptoms</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">29 (18.59%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">84 (26.92%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.943</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.047</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Physical examination: moist rale</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">82 (52.56%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">146 (46.79%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.386</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.239</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Physical examination: three concave sign</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17 (10.90%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8 (2.56%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">14.283</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Lung imaging: lung consolidation</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">124 (79.49%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">131 (41.99%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">58.975</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Pulmonary imaging: atelectasis</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9 (5.77%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5 (1.6%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.222</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.013</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Lung imaging: pleural effusion</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">48 (30.77%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7 (2.24%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">81.599</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Extrapulmonary complications</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">58 (37.18%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">56 (16.99%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20.874</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">In hospital (day)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11.09 ± 4.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.27 ± 3.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.355</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab2\"><label>Table 2</label><caption><p>Comparison of laboratory indicators between the RMPP and GMPP groups (<italic>n</italic> = 468).</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Index</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">RMPP (<italic>n</italic> = 156)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">GMPP (<italic>n</italic> = 312)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>t</italic>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>P</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WBC (×10<sup>9</sup>/L)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.76 ± 3.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.02 ± 4.52</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.727</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.467</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">NEP (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">58.69 ± 13.59</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">63.54 ± 14.07</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−3.597</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">CRP (mg/L)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">42.13 ± 10.21</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">26.04 ± 9.15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17.233</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LDH (IU/L)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">414.79 ± 72.76</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">292.98 ± 57.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">19.749</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCT (ng/mL)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.14 ± 0.09</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.11 ± 0.07</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.648</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">D-dimer (ng/ml)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.06 ± 1.08</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.83 ± 0.39</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17.795</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">TNF-<italic>α</italic></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.19 ± 0.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.07 ± 0.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.557</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.120</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab3\"><label>Table 3</label><caption><p>Logistic regression analysis for risk factors of RMPP.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"2\" colspan=\"1\">Index</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">\n<italic>B</italic>\n</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">S.E</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">Wald <italic>χ</italic><sup>2</sup></th><th align=\"center\" rowspan=\"2\" colspan=\"1\">\n<italic>P</italic>\n</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">Exp (B)</th><th align=\"center\" colspan=\"2\" rowspan=\"1\">95% CI</th></tr><tr><th align=\"center\" rowspan=\"1\" colspan=\"1\">Lower bound</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Upper bound</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">D-dimer (<italic>x</italic>1)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.100</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.374</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31.595</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.169</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.169</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.927</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">CRP (<italic>x</italic>2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.136</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.023</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">34.378</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.146</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.146</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.095</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LDH (<italic>x</italic>3)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.024</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.004</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">39.565</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.025</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.025</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.017</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab4\"><label>Table 4</label><caption><p>Predictive values of serum D-dimer, CRP, and LDH levels for RMPP.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Index</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cut off value</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Sensitivity (%)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Specificity (%)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">AUC</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Std. error</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">95% CI</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>P</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">D-dimer</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.47</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">64.74</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">98.72</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.841</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.022</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.798–0.884</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">CRP</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">39.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">60.89</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">94.55</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.870</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.017</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.837–0.903</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LDH</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">379.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">66.67</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">93.91</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.893</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.015</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.864–0.923</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr></tbody></table></table-wrap>" ]
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[{"label": ["4"], "person-group": ["\n"], "surname": ["Wang", "Lin"], "given-names": ["X.", "X."], "article-title": ["Analysis of clinical related factors of severe mycoplasma pneumoniae pneumonia in children based on imaging diagnosis"], "source": ["\n"], "italic": ["Computational and Mathematical Methods in Medicine"], "year": ["2022"], "volume": ["2022"], "fpage": ["8"], "pub-id": ["4852131", "10.1155/2022/4852131"]}, {"label": ["6"], "person-group": ["\n"], "surname": ["Gao", "Yin", "Hu"], "given-names": ["L.-W.", "J.", "Y.-H."], "article-title": ["The epidemiology of paediatric Mycoplasma pneumoniae pneumonia in North China: 2006 to 2016"], "source": ["\n"], "italic": ["Epidemiology and Infection"], "year": ["2019"], "volume": ["147"], "pub-id": ["10.1017/s0950268819000839", "2-s2.0-85070842811"]}, {"label": ["8"], "person-group": ["\n"], "surname": ["You", "Jwa", "Yang", "Kil", "Lee"], "given-names": ["S. Y.", "H. J.", "E. A.", "H. R.", "J. H."], "article-title": ["Effects of methylprednisolone pulse therapy on refractory Mycoplasma pneumoniae pneumonia in children"], "source": ["\n"], "italic": ["Allergy, Asthma and Immunology Research"], "year": ["2014"], "volume": ["6"], "issue": ["1"], "fpage": ["22"], "lpage": ["26"], "pub-id": ["10.4168/aair.2014.6.1.22", "2-s2.0-84891801140"]}, {"label": ["11"], "person-group": ["\n"], "surname": ["Bajantri", "Venkatram", "Diaz-Fuentes"], "given-names": ["B.", "S.", "G."], "article-title": ["Mycoplasma pneumoniae: a potentially severe infection"], "source": ["\n"], "italic": ["Journal of Clinical Medicine and Research"], "year": ["2018"], "volume": ["10"], "issue": ["7"], "fpage": ["535"], "lpage": ["544"], "pub-id": ["10.14740/jocmr3421w"]}, {"label": ["13"], "person-group": ["\n"], "surname": ["Huang", "Huang", "Jiang", "Zhang", "Yan", "Huang"], "given-names": ["L.", "X.", "W.", "R.", "Y.", "L."], "article-title": ["Independent predictors for longer radiographic resolution in patients with refractory Mycoplasma pneumoniae pneumonia: a prospective cohort study"], "source": ["\n"], "italic": ["BMJ Open"], "year": ["2018"], "volume": ["8"], "issue": ["12"], "pub-id": ["10.1136/bmjopen-2018-023719", "2-s2.0-85058870499"]}, {"label": ["15"], "person-group": ["\n"], "surname": ["Gong", "Sun", "Chen", "Chen"], "given-names": ["H.", "B.", "Y.", "H."], "article-title": ["The risk factors of children acquiring refractory Mycoplasma pneumoniae pneumonia: a meta-analysis"], "source": ["\n"], "italic": ["Medicine"], "year": ["2021"], "volume": ["100"], "issue": ["11"], "pub-id": ["10.1097/md.0000000000024894"]}, {"label": ["16"], "person-group": ["\n"], "surname": ["Kumar"], "given-names": ["S."], "article-title": ["Mycoplasma pneumoniae: a significant but underrated pathogen in paediatric community-acquired lower respiratory tract infections"], "source": ["\n"], "italic": ["Indian Journal of Medical Research"], "year": ["2018"], "volume": ["147"], "issue": ["1"], "fpage": ["p. 23"], "pub-id": ["10.4103/ijmr.ijmr_1582_16", "2-s2.0-85046726760"]}, {"label": ["18"], "person-group": ["\n"], "surname": ["Choi", "Chung", "Lee"], "given-names": ["Y. J.", "E. H.", "E."], "article-title": ["Clinical characteristics of macrolide-refractory Mycoplasma pneumoniae pneumonia in Korean children: a multicenter retrospective study"], "source": ["\n"], "italic": ["Journal of Clinical Medicine"], "year": ["2022"], "volume": ["11"], "issue": ["2"], "fpage": ["p. 306"], "pub-id": ["10.3390/jcm11020306"]}, {"label": ["21"], "person-group": ["\n"], "surname": ["Zhang", "Zhou", "Li", "Yang", "Wu", "Chen"], "given-names": ["Y.", "Y.", "S.", "D.", "X.", "Z."], "article-title": ["The clinical characteristics and predictors of refractory Mycoplasma pneumoniae pneumonia in children"], "source": ["\n"], "italic": ["PLoS One"], "year": ["2016"], "volume": ["11"], "issue": ["5"], "pub-id": ["10.1371/journal.pone.0156465", "2-s2.0-84973493555"]}]
{ "acronym": [], "definition": [] }
24
CC BY
no
2024-01-14 23:41:55
Emerg Med Int. 2024 Jan 5; 2024:9328177
oa_package/0c/a8/PMC10787049.tar.gz
PMC10787050
0
[ "<title>1. Introduction</title>", "<p>Effective glycemic control is required to delay or prevent the development of microvascular and macrovascular complications in patients with type 2 diabetes mellitus (T2DM) [##REF##18784090##1##]. However, as the disease progresses, most patients are unlikely to achieve sustained glycemic control without treatment intensification, and combination therapy with various antidiabetic agents is often necessary [##REF##19336687##2##].</p>", "<p>Metformin is the most widely used first-line antidiabetic drug according to multiple guidelines for the treatment of T2DM [##REF##36507650##3##, ##REF##34352984##4##]. Sodium-glucose cotransporter 2 (SGLT2) inhibitors improve glycemic control by blocking glucose reabsorption in the proximal convoluted tubules of the kidney and increasing glycosuria. Beyond their glucose-lowering effects, SGLT2 inhibitors have been associated with beneficial effects such as weight loss and decreases in blood pressure [##REF##24622320##5##]. The combination of metformin and SGLT2 inhibitors has been shown to improve glycemic control and weight loss and to reduce cardiovascular and renal risks in patients with T2DM. Given its demonstrated ability to protect cardiovascular and renal function independent of glucose control in high-risk patients, this combination therapy has been increasingly recommended, particularly for patients with T2DM who also have atherosclerotic cardiovascular disease, heart failure, or renal disease [##REF##36507650##3##, ##REF##34352984##4##, ##REF##36727161##6##].</p>", "<p>When glucose control remains insufficient despite combined treatment with metformin and SGLT2 inhibitors, the dose of metformin can be increased, or another class of antidiabetic medication can be added. Some patients are unable to tolerate metformin, and metformin-associated gastrointestinal adverse events (AEs) such as diarrhea and nausea may depend on metformin dosage [##REF##27987248##7##]. Dipeptidyl peptidase-4 (DPP4) inhibitors are widely used antidiabetic medications that block the action of the DPP4 enzyme, which breaks down incretin hormones and improves glucose control via glucose-dependent secretion of insulin and suppression of glucagon [##REF##17098089##8##]. DPP4 inhibitors are often used as second- or third-line therapies for T2DM because of their ease of use, low risk of hypoglycemia, weight neutrality, and favorable tolerability [##REF##30242726##9##]. Combined treatment with DPP4 inhibitors and SGLT2 inhibitors is an attractive option given their complementary mechanisms of action and the demonstrated effectiveness and tolerability of the combination in patients with T2DM [##REF##28332871##10##, ##REF##28356718##11##]. Gemigliptin is a potent and selective DPP4 inhibitor that has been investigated in combination with various antidiabetic drugs, including metformin, metformin plus sulfonylureas, and insulin [##REF##27766241##12##].</p>", "<p>Triple-combination treatment with DPP4 inhibitors added to metformin plus SGLT2 inhibitors may exhibit synergism with complementary actions, thereby offering an effective therapeutic option. However, no studies have compared their effects with the uptitration of metformin, which is another option for patients with uncontrolled T2DM despite treatment with metformin and SGLT2 inhibitors. Accordingly, this study is aimed at comparing the efficacy and safety of gemigliptin add-on versus metformin dose escalation in patients with T2DM inadequately controlled using metformin and SGLT2 inhibitors.</p>" ]
[ "<title>2. Methods</title>", "<title>2.1. Study Design and Participants</title>", "<p>This investigator-initiated, multicenter, randomized, open-label, and active-controlled trial was conducted across eight sites in Korea from July 2019 to February 2022 (CRIS_number: KCT0003520).</p>", "<p>We enrolled patients who met the following criteria: (a) presence of T2DM, (b) age 20–75 years, (c) body mass index (BMI) of 18.5–40 kg/m<sup>2</sup>, (d) poor glycemic control (7.0% ≤ HbA1c ≤ 10%), and (e) treatment with a stable dose of 1,000–2,000 mg metformin in combination with SGLT2 inhibitors (10 mg dapagliflozin, 10 mg or 25 mg empagliflozin, or 50 mg ipragliflozin) for at least 8 weeks. The key exclusion criteria were as follows: (a) history of type 1 diabetes; (b) acute metabolic complications of diabetes within the past 6 months; (c) history of cardiovascular diseases such as myocardial infarction or angina, percutaneous transluminal coronary angioplasty, or stroke within 6 months before screening; (d) history of allergy or hypersensitivity to DPP4 inhibitors; (e) use of prohibited concomitant medications (systemic corticosteroids, antiobesity drugs, cyclosporine, etc.) within the previous 4 weeks; (f) drug or alcohol abuse within 3 months prior to screening; (g) aspartate aminotransferase (AST) or alanine aminotransferase (ALT) level 3 times higher than the upper limit of the normal range; and (h) estimated glomerular filtration rate &lt; 45 mL/min/1.73 m<sup>2</sup> before screening.</p>", "<p>Eligible participants were randomized 1 : 1 to receive gemigliptin 50 mg/day as an add-on (GEM group) or metformin 500 mg/day escalation (MET group) for 24 weeks. Computer-generated randomization was used, and allocation concealment was achieved using sealed opaque envelopes that were sequentially numbered and kept in a locked cabinet until the time of randomization. Concomitant baseline antidiabetic regimens were maintained throughout the study period. The following baseline data were collected: demographic characteristics, medical and medication histories, physical examination results, fasting plasma glucose (FPG), HbA1c, fasting insulin, lipid profiles (total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides), and laboratory test results for safety (levels of blood creatinine, AST, ALT, complete blood count, and urinalysis). The postprandial glucose (PPG) level was recorded as the average 2-hour PPG after every meal during the 3 days prior to the visit using the self-monitored blood glucose (SMBG) levels of the patients. The homeostasis model assessment of insulin resistance (HOMA-IR) ([fasting insulin (<italic>μ</italic>U/mL) × fasting glucose (mmol/L)]/22.5) value was calculated as an index of insulin resistance, and the HOMA of <italic>β</italic>-cell function (HOMA-<italic>β</italic>) ([20 × fasting insulin (<italic>μ</italic>U/mL)/fasting glucose (mmol/L)] − 3.5) value was calculated as an index of beta cell function. Follow-up visits were scheduled 12 and 24 weeks after enrollment. At each visit, body weight, vital signs, HbA1c, FPG levels, PPG levels, and AEs were assessed. Fasting insulin, lipid profiles, urine albumin-to-creatinine ratio, serum ketone bodies (acetoacetate, total ketone, and <italic>β</italic>-hydroxybutyric acid), and laboratory values for safety were assessed at baseline and week 24.</p>", "<p>Patients were withdrawn during the study under one of the following conditions: drug compliance of less than 80%; HbA1c level of &gt;10.0% at week 12; and withdrawal of consent, at the investigators' discretion, or in certain situations such as significant intercurrent illness or a serious adverse event (SAE) during the trial.</p>", "<p>This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Institutional Review Board (IRB) at each participating site, including the Kyung Hee University Hospital IRB at Gangdong (KHNMC 2018-11-002). All patients provided written informed consent before participating in the study.</p>", "<title>2.2. Outcome Measures</title>", "<p>The primary efficacy endpoint was the change in HbA1c levels from baseline to week 24. The secondary efficacy endpoints were as follows: changes in HbA1c level from baseline to week 12, proportions of participants achieving HbA1c &lt; 6.5% and HbA1c &lt; 7.0% at week 24, changes in FPG and PPG levels at weeks 12 and 24, changes in lipid profiles from baseline to week 24, and changes in HOMA-IR and HOMA-<italic>β</italic> from baseline to week 24. The exploratory endpoints were changes in the urine albumin/creatinine ratio and serum ketone bodies from baseline to week 24.</p>", "<p>Safety was assessed by monitoring the overall incidence of AEs, vital signs, and laboratory and physical examination results. All AEs were recorded and assessed by the investigator to determine their possible relationship with the study interventions. Regarding hypoglycemia, any patient who reported an SMBG level &lt; 70 mg/dL with or without symptoms was considered to have experienced a hypoglycemic episode.</p>", "<title>2.3. Statistical Analysis</title>", "<p>The sample size for the comparison between the MET and GEM groups was determined using a two-sample <italic>t</italic>-test with a targeted power of 80% and a significance level of 0.05. Assuming a treatment difference of 0.5% and a standard deviation of 0.8% [##UREF##0##13##, ##REF##22275444##14##], the calculated sample size, accounting for a 10% anticipated dropout rate, was 37 per group.</p>", "<p>Patients who completed the 24-week treatment period without major protocol deviations were included for the efficacy analyses, and all randomized patients who had been administered the study drug at least once were included for the safety analyses. Baseline demographic and biochemical parameters were summarized using descriptive statistics: continuous variables are reported as the mean and standard deviation or median and interquartile range, while categorical values are reported as counts and percentages. To analyze the efficacy endpoints at weeks 12 and 24, we used the independent <italic>t</italic>-test or Wilcoxon rank-sum test for continuous variables after normality tests with the Shapiro-Wilk test and the <italic>χ</italic><sup>2</sup> test for categorical variables. The HbA1c levels measured repeatedly from baseline to 24 weeks were analyzed using a mixed model for repeated data. Group differences at each time point were analyzed using the Bonferroni post hoc analysis for multiple comparisons. Subgroup analyses of changes in HbA1c levels were performed according to baseline characteristics. An interaction analysis of covariates that affected the 24-week reduction in HbA1c in the GEM group compared with that in the MET group (reference) was conducted using a general linear model adjusted for baseline HbA1c. Safety analyses were performed using Fisher's exact test. Statistical significance was set at <italic>p</italic> &lt; 0.05. SAS9.4 (Statistical Analysis System version, SAS Institute, Cary, NC, USA) and R4.1.0 were used for statistical analyses.</p>" ]
[ "<title>3. Results</title>", "<title>3.1. Baseline Characteristics</title>", "<p>Of the 79 screened patients, 75 were randomized to receive the study medication (38 in the MET group and 37 in the GEM group), 67 of whom completed the study (##FIG##0##Figure 1##).</p>", "<p>The baseline demographic and clinical characteristics were well balanced between the two groups (##TAB##0##Table 1##). The overall mean patient age was 52.36 ± 11.86 years, and the mean BMI was 28.06 ± 4.44 kg/m<sup>2</sup>. The mean duration of T2DM was 7.37 ± 4.90 years, and the mean baseline HbA1c level was 7.59 ± 0.52%. The mean dose of metformin was 1306.72 ± 431.86 mg/day. No significant differences in metabolic parameters, metformin dosage, or use of concomitant medications were observed between the two groups at baseline.</p>", "<title>3.2. Efficacy</title>", "<p>At weeks 12 and 24, the changes in HbA1c levels from baseline were significantly greater in the GEM group than in the MET group (GEM vs. MET = −0.64% ± 0.34% vs. −0.36% ± 0.50%, <italic>p</italic> = 0.009 at week 12; −0.61% ± 0.35% vs. −0.33% ± 0.70%, <italic>p</italic> = 0.045 at week 24; ##TAB##1##Table 2##). When HbA1c repeatedly measured from baseline to 24 weeks were analyzed using a mixed model for repeated data, significant differences were observed between the groups (<italic>p</italic> for group = 0.009, ##FIG##1##Figure 2(a)##). There was a significant difference between two groups at 12 weeks and 24 weeks through the Bonferroni post hoc correction, a multiple comparison test. The proportion of patients who achieved a target HbA1c level of &lt;7.0% at weeks 12 and 24 was greater in the GEM group than in the MET group (GEM vs. MET = 69.7% vs. 35.3%, <italic>p</italic> = 0.005 at week 12; 66.7% vs. 32.3%, <italic>p</italic> = 0.005 at week 24; ##FIG##1##Figure 2(b)##). The proportion of patients achieving a target HbA1c level of &lt;6.5% at week 12 was also greater in the GEM group (24.2% vs. 5.9%, <italic>p</italic> = 0.035; ##FIG##1##Figure 2(b)##). At week 24, the HOMA-<italic>β</italic> value had significantly improved from baseline in the GEM group (GEM vs. MET = 15.60% ± 30.36 vs. −4.48% ± 32.57, <italic>p</italic> = 0.011; ##TAB##1##Table 2##). The changes in FPG and PPG levels from baseline to weeks 12 and 24 were comparable between the groups, as were the changes in lipid profile from baseline to week 24. In the subgroup analyses according to baseline characteristics, a greater reduction in HbA1c levels was observed in the GEM group than in the MET group among patients aged &lt;65 years (-0.36 [CI: -0.67, -0.05]) and those with a T2DM duration &lt; 10 years (-0.45 [CI: -0.79, -0.11]) (##FIG##2##Figure 3##).</p>", "<p>No significant differences in the changes in the UACR or serum ketone bodies were observed (##TAB##1##Table 2##).</p>", "<title>3.3. Safety</title>", "<p>The safety results are summarized in ##TAB##2##Table 3##. There were no SAEs during the study period, and one patient in the GEM group withdrew owing to an AE (urticaria). The AE profiles were similar between the two groups. Hypoglycemia or genital infection was not observed in either group.</p>" ]
[ "<title>4. Discussion</title>", "<p>The present results highlight gemigliptin add-on therapy as an effective treatment of choice compared with escalation of metformin dose in patients with inadequately controlled T2DM despite treatment with metformin and SGLT2 inhibitors, and no significant safety issues were noted. Moreover, the addition of gemigliptin to metformin and SGLT2 inhibitors was shown to improve <italic>β</italic>-cell function.</p>", "<p>T2DM is a multifactorial and progressive disease, and its pathogenesis involves multiple mechanisms. Therefore, combination therapy using various antidiabetic agents with complementary modes of action is recommended [##REF##19336687##2##]. Combined treatment with DPP4 and SGLT2 inhibitors has been proposed as an effective treatment option for T2DM given their complementary mechanisms of action and low risk of hypoglycemia or weight gain [##REF##28332871##10##, ##REF##28356718##11##, ##REF##28322073##15##]. SGLT2 inhibitors increase endogenous glucose production; however, the addition of a DPP4 inhibitor, which inhibits glucose production, can compensate for this increase [##REF##25370334##16##]. In addition, meta-analyses of DPP4 inhibitors or SGLT2 inhibitors have suggested that these drugs exert beneficial effects on glycemic variability [##REF##34575189##17##, ##REF##31527625##18##], and one randomized study reported that SGLT2 inhibitors combined with DPP4 inhibitor therapy strongly reduced glycemic fluctuations when compared with SGLT2 inhibitor monotherapy [##UREF##1##19##]. Moreover, cardiovascular outcome trials have demonstrated the cardiovascular safety of DPP4 inhibitors and the cardiovascular benefits of SGLT2 inhibitors [##REF##28606340##20##]. In another meta-analysis, combined treatment with SGLT2 inhibitors and DPP4 inhibitors enhanced effects on HbA1c reduction (−0.47; 95% CI, −0.58 to −0.37%), exerted a neutral effect on weight (0.19; 95% CI, −0.11 to 0.48 kg), and attenuated the risk of genital infections (0.73; 95% CI, 0.54 to 0.97) versus treatment with SGLT2 inhibitors alone [##UREF##2##21##]. Triple-combination therapy with metformin, DPP4 inhibitors, and SGLT2 inhibitors can target multiple pathophysiological pathways for T2DM, affecting at least six of eight components in the “ominous octet” [##REF##35334083##22##], and appears to strike an appropriate balance among efficacy, safety, and tolerability profiles. In a previous randomized study of triple-combination therapy with metformin, DPP4 inhibitors, and SGLT2 inhibitors, the authors reported a significantly greater reduction in HbA1c at 24 weeks with saxagliptin add-on versus placebo add-on in patients already taking dapagliflozin plus metformin (difference, −0.35% [95% CI −0.52% to −0.18%]) [##REF##26324329##23##].</p>", "<p>In the current study, we compared the effects of gemigliptin with escalation of the metformin dose rather than with those of placebo. A previous meta-analysis demonstrated that an increase in metformin dose resulted in a further modest reduction in HbA1c of 0.26% in trials comparing lower doses with higher doses, up to a metformin dose of 2,000 mg [##REF##22275444##14##]. Another previous randomized study compared the efficacy of combined treatment with the DPP4 inhibitor and metformin with metformin uptitration in Chinese patients with T2DM inadequately controlled with metformin monotherapy. The results indicated that combination therapy with vildagliptin and metformin was more effective in reducing HbA1c levels than metformin uptitration at week 24 (−0.54% vs. −0.40%, difference, 0.15% [95% CI −0.22% −0.07%]) [##REF##27406394##24##]. In the present study, the HbA1c reduction at week 24 was −0.61 ± 0.35% in the GEM group and −0.33 ± 0.70% in the MET group, suggesting a greater hypoglycemic effect of gemigliptin add-on than metformin uptitration. The present study is the first to demonstrate that triple-combination treatment with DPP4 inhibitors, SGTL2 inhibitors, and metformin exerts a better hypoglycemic effect and more effectively protects beta cells than increasing the dose of metformin among patients with T2DM with inadequately controlled disease despite treatment with metformin and SGLT2 inhibitors.</p>", "<p>Our results also revealed improvements in HOMA-<italic>β</italic> as well as HbA1c following the addition of gemigliptin, in accordance with previous findings. In a double-blind randomized controlled trial, initial combination therapy with gemigliptin and metformin produced improvements in HOMA-<italic>β</italic> values when compared with metformin monotherapy [##REF##27619558##25##]. A meta-analysis also reported that gemigliptin was superior to placebo in terms of the effects on HbA1c, FPG, and HOMA-<italic>β</italic> [##UREF##3##26##]. In a study examining the effects of DPP4 and/or SGLT2 inhibitors in the early and advanced phases of diabetes in <italic>db/db</italic> mice, the authors observed that the combination of DPP4 and SGLT2 inhibitors exerted greater beneficial effects on <italic>β</italic>-cell mass and function, especially in the early phase of diabetes rather than an advanced phase [##REF##34373487##27##]. In our subgroup analysis, a reduction in HbA1c levels was significantly greater in the GEM group than in the MET group among patients with younger age or shorter duration of T2DM. Given these findings, intensive combination treatment should be initiated early to prevent the progression of <italic>β</italic>-cell failure.</p>", "<p>Several studies have demonstrated the beneficial effects of DPP4 inhibitors on lipid profiles, and gemigliptin has been reported to slightly decrease total cholesterol, LDL-C, and triglyceride levels [##REF##27766241##12##]. In the present study, the GEM group exhibited a tendency towards decreased triglyceride levels, although the change was not statistically significant.</p>", "<p>There were no significant differences in the incidence of AEs between the two groups in the present study. There were no hypoglycemic events in either group, which is in accordance with the low risk of hypoglycemia noted for metformin, SGTL2 inhibitors, and DPP4 inhibitors. One adverse drug reaction (urticaria) was observed in the GEM group, which is a well-recognized AE associated with DPP4 inhibitors [##REF##23129260##28##]. In this study, there were no gastrointestinal AEs in the MET group, which may be attributed to the fact that the patients were not metformin-naïve before enrollment and underwent gradual dose escalation [##REF##27987248##7##]. Further, no genitourinary tract infections occurred in either group.</p>", "<p>This study had some limitations, including the relatively small number of participants. Because we calculated the sample size based on the primary outcome before the trial, some secondary efficacy outcomes, such as changes in FPG and PPG levels, may not have included enough participants to reveal statistically significant differences. Second, although there was a greater reduction in HbA1c levels in the GEM group, there were no significant differences in FPG or PPG levels between the groups, which may be because 2-hour PPG levels were only examined across 3 days. More precise methods of glucose evaluation, such as 7-point SMBG or continuous glucose monitoring over a longer duration, would have provided a more detailed glucose profile.</p>" ]
[ "<title>5. Conclusions</title>", "<p>In conclusion, the current results highlight gemigliptin add-on therapy as an effective treatment option when compared with metformin dose escalation in patients with T2DM exhibiting inadequate glycemic control using metformin and SGLT2 inhibitors, without safety concerns.</p>" ]
[ "<p>Academic Editor: Mark Yorek</p>", "<title>Background</title>", "<p> We aimed to compare efficacy and safety between gemigliptin add-on and escalation of the metformin dose in patients with inadequately controlled type 2 diabetes mellitus (T2DM) despite treatment with metformin and SGLT2 inhibitors. </p>", "<title>Methods</title>", "<p> This study was a multicenter, randomized, open-label, active-controlled, parallel-group comparative study. Patients with T2DM uncontrolled on metformin and SGLT2 inhibitors were randomized to receive gemigliptin 50 mg as an add-on (GEM group, <italic>n</italic> = 37) or escalation of the metformin dose (500 mg, MET group, <italic>n</italic> = 38) for 24 weeks. The primary endpoint was the change in glycosylated hemoglobin (HbA1c) from baseline to week 24. </p>", "<title>Results</title>", "<p> At weeks 12 and 24, the reduction in HbA1c levels was significantly greater in the GEM group than in the MET group (GEM vs. MET = −0.64% ± 0.34% vs. −0.36% ± 0.50%, <italic>p</italic> = 0.009 at week 12; −0.61% ± 0.35% vs. −0.33% ± 0.70%, <italic>p</italic> = 0.045 at week 24). The proportions of patients who achieved target HbA1c levels of &lt;7.0% at weeks 12 and 24 and &lt;6.5% at week 12 were greater in the GEM group than in the MET group. An index of <italic>β</italic>-cell function was also significantly improved in the GEM group. The safety profiles were similar between the two groups. </p>", "<title>Conclusions</title>", "<p> Gemigliptin add-on therapy may be more effective than metformin dose escalation in patients with T2DM insufficiently controlled using metformin and SGLT2 inhibitors, without safety concerns. This trial is registered with CRIS_number: KCT0003520.</p>" ]
[]
[ "<title>Acknowledgments</title>", "<p>The authors thank the investigators, study participants, and Soo-Jin Chung for the statistical analyses. This study was funded by Daewoong Pharmaceutical Company Limited, Korea, with the initiation of the investigator's proposal.</p>", "<title>Data Availability</title>", "<p>The data used to support the findings of this study are available from the corresponding author upon reasonable request.</p>", "<title>Disclosure</title>", "<p>We acknowledge that a portion of the research presented in this paper was previously exhibited as a poster at the 2022 International Congress of Diabetes and Metabolism (Seoul, Korea; October 6–8, 2022, https://<ext-link xlink:href=\"http://planix.s3.ap-northeast-2.amazonaws.com/ICDM-Abstract-Book.pdf\" ext-link-type=\"uri\">http://planix.s3.ap-northeast-2.amazonaws.com/ICDM-Abstract-Book.pdf</ext-link>). “Daewoong” had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.</p>", "<title>Conflicts of Interest</title>", "<p>The authors declare that there is no conflict of interest regarding the publication of this paper.</p>", "<title>Authors' Contributions</title>", "<p>HJK and IKJ contributed to the design and conduct of the study and the acquisition, analysis, and interpretation of data and drafted the manuscript. JHN, MKM, SHC, SHK, EJR, and KYH conducted the study and the acquisition, analysis, and interpretation of data. All authors have reviewed and approved the final manuscript.</p>" ]
[ "<fig position=\"float\" id=\"fig1\"><label>Figure 1</label><caption><p>Study flowchart.</p></caption></fig>", "<fig position=\"float\" id=\"fig2\"><label>Figure 2</label><caption><p>(a) Changes in HbA1c level from baseline to week 24. When HbA1c repeatedly measured from baseline to 24 weeks were analyzed using a mixed model for repeated data, significant differences were observed between the groups (<italic>p</italic> for group = 0.009). There was a significant difference between the two groups at 12 weeks and 24 weeks through the Bonferroni post hoc correction. Error bars indicate 95% confidence intervals. (b) Proportion of participants achieving HbA1c &lt; 6.5% and HbA1c &lt; 7.0% at weeks 12 and 24.</p></caption></fig>", "<fig position=\"float\" id=\"fig3\"><label>Figure 3</label><caption><p>Subgroup analysis of changes in HbA1c at week 24 according to baseline characteristics. The <italic>p</italic> value reflects the interaction analysis of covariates affecting the 24-week reduction in HbA1c in the GEM group when compared with that in the MET group (reference). Analyses were performed using a general linear model adjusted for baseline HbA1c. Points represent the coefficient estimate, and the error bar shows the 95% confidence interval of the coefficient estimate. <sup>a</sup><italic>p</italic> &lt; 0.05.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"tab1\"><label>Table 1</label><caption><p>Baseline characteristics of the included participants.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"1\" colspan=\"1\"/><th align=\"center\" rowspan=\"1\" colspan=\"1\">Metformin (<italic>n</italic> = 34)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Gemigliptin (<italic>n</italic> = 33)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>p</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Age (y)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">54.12 ± 12.68</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">50.55 ± 10.85</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.220</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Male, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20 (58.82)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">21 (63.64)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.686</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">DM duration (y)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.09 ± 5.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.64 ± 4.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.229</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Weight (kg)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">77.29 ± 14.88</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">78.37 ± 14.30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.762</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI (kg/m<sup>2</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">28.23 ± 4.61</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27.89 ± 4.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.760</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Waist circumference (cm)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">95.44 ± 11.61</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.26 ± 12.95</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.786</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Hypertension, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">23 (67.65)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18 (54.55)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.271</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cardiovascular disease, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4 (11.76)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6 (18.18)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.461</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Dyslipidemia, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">28 (82.35)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24 (72.73)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.345</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Systolic blood pressure (mmHg)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">128.0 ± 9.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">126.8 ± 10.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.613</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Diastolic blood pressure (mmHg)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">78.0 ± 8.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">78.5 ± 8.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.839</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">HbA1c (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.69 ± 0.54</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.48 ± 0.49</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.095</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fasting plasma glucose (mg/dL)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">136.82 ± 20.83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">140.73 ± 20.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.441</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postprandial glucose (mg/dL)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">190.06 ± 35.81</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">191.59 ± 44.32</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.879</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fasting insulin (mIU/L)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10.46 ± 7.07</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.47 ± 5.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.191</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">HOMA-IR</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.52 ± 2.41</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.97 ± 1.92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.306</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">HOMA-<italic>β</italic></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">57.13 ± 44.22</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">41.03 ± 22.80</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.066</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Total cholesterol (mg/dL)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">151.47 ± 33.30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">154.92 ± 31.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.665</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Triglyceride (mg/dL)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">149.50 ± 75.51</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">157.30 ± 85.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.693</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">HDL-C (mg/dL)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">49.32 ± 12.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">51.24 ± 12.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.527</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LDL-C (mg/dL)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">75.70 ± 23</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">76.67 ± 28.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.879</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">eGFR (mL/min/1.73 m<sup>2</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">99.61 ± 21.43</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96.58 ± 17.06</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.501</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">AST (U/L)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">26.26 ± 9.74</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30.12 ± 21.52</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.352</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ALT (U/L)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31.88 ± 16.73</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">32.76 ± 20.55</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.849</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">UACR</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17.8 (34.9)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">511.7 (13.7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.171</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Acetoacetate (<italic>μ</italic>mol/L)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">102.1 (138.2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">121.7 (183.6)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.367</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Total ketone (<italic>μ</italic>mol/L)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">287.3 (254.8)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">315.2 (365.7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.407</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<italic>β</italic>-Hydroxybutyric acid (<italic>μ</italic>mol/L)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">143.2 (171.2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">197.1 (203.3)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.533</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Antidiabetic medication prior to randomization</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> SGLT2 inhibitor</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">  Dapagliflozin, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15 (44.12)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17 (51.52)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.801</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">  Empagliflozin, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15 (44.12)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12 (36.36)</td><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">  Ipragliflozin, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4 (11.76)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4 (12.12)</td><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Metformin dosage (mg/day)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1285.29 ± 441.16</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1328.79 ± 427.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.684</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Concomitant medications</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Antihypertensive drugs, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20 (58.82)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">16 (48.48)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.396</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Antidyslipidemic drugs, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30 (88.24)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">26 (78.79)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.297</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Antiplatelet drugs, <italic>n</italic> (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9 (26.47)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5 (15.15)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.255</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab2\"><label>Table 2</label><caption><p>Study outcomes according to treatment group.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"1\" colspan=\"1\"/><th align=\"center\" rowspan=\"1\" colspan=\"1\">Metformin (<italic>n</italic> = 34)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Gemigliptin (<italic>n</italic> = 33)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>p</italic> value</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">HbA1c (%)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.69 ± 0.54</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.48 ± 0.49</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.095</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.33 ± 0.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.84 ± 0.53</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.003</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.36 ± 0.94</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.87 ± 0.67</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.017</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.36 ± 0.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.64 ± 0.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.009</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.33 ± 0.70</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.61 ± 0.35</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.045</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fasting plasma glucose (mg/dL)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">136.82 ± 20.83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">140.73 ± 20.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.441</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">130.94 ± 22.23</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">132.48 ± 30.40</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.813</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">135.35 ± 30.68</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">128.76 ± 18.97</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.293</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−5.88 ± 19.56</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−8.24 ± 23.62</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.657</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.47 ± 30.07</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−11.97 ± 17.89</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.087</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Postprandial glucose (mg/dL)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">190.06 ± 35.81</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">191.59 ± 44.32</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.879</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">175.22 ± 43.30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">166.18 ± 33.69</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.368</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">170.89 ± 35.49</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">168.71 ± 39.13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.822</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−15.31 ± 31.39</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−22.11 ± 21.73</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.345</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−19.55 ± 32.88</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−22.97 ± 29.27</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.680</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fasting insulin (mIU/L)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10.46 ± 7.07</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.47 ± 5.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.191</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.57 ± 4.60</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.99 ± 7.19</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.781</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.88 ± 5.43</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.52 ± 5.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.075</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">HOMA-IR</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.52 ± 2.41</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.97 ± 1.92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.306</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.21 ± 1.66</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.24 ± 2.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.957</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.31 ± 1.99</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.27 ± 1.98</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.238</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">HOMA-<italic>β</italic></td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">57.13 ± 44.22</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">41.03 ± 22.80</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.066</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">52.65 ± 28.99</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">56.63 ± 41.18</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.649</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−4.48 ± 32.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15.60 ± 30.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.011</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Total cholesterol (mg/dL)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">151.47 ± 33.30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">154.92 ± 31.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.665</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">144.31 ± 31.37</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">147.78 ± 29.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.642</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−7.16 ± 22.69</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">-7.14 ± 18.70</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.996</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Triglyceride (mg/dL)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">149.50 ± 75.51</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">157.30 ± 85.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.693</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">145.35 ± 81.15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">136.09 ± 74.40</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.628</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−4.15 ± 60.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−21.21 ± 55.71</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.234</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">HDL-C (mg/dL)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">49.32 ± 12.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">51.24 ± 12.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.527</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">49.21 ± 13.04</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">51.06 ± 11.13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.534</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.12 ± 5.97</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.18 ± 7.54</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.969</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LDL-C (mg/dL)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">75.70 ± 23.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">76.67 ± 28.36</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.879</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">67.12 ± 25.87</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">71.65 ± 24.16</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.462</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−8.58 ± 18.08</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−5.02 ± 18.13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.424</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">UACR</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17.8 (34.9)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11.7 (13.7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.171</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">19.4 (48.3)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12.8 (10.0)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.107</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.4 (15.7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">-0.3 (12.7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.541</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Acetoacetate (<italic>μ</italic>mol/L)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">102.1 (138.2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">121.7 (183.6)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.367</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">86.2 (120.2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">90 (152.0)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.779</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">-18.4 (159.8)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">-2.4 (244.6)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.817</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Total ketone (<italic>μ</italic>mol/L)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">287.3 (254.8)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">315.2 (365.7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.407</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">231.4 (212.1)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">205.2 (282.2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.827</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">-38.0 (310.6)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">-20.0 (485.7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.640</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<italic>β</italic>-Hydroxybutyric acid (<italic>μ</italic>mol/L)</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Baseline</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">143.2 (171.2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">197.1 (203.3)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.533</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> At week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">121.9 (114.6)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">114.6 (109.8)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.856</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Change from baseline at week 24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">-37.0 (166.4)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">-24.4 (242.8)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.764</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab3\"><label>Table 3</label><caption><p>Adverse events.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"1\" colspan=\"1\"/><th align=\"center\" rowspan=\"1\" colspan=\"1\">Metformin (<italic>n</italic> = 38)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Gemigliptin (<italic>n</italic> = 37)</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Serious adverse events</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Drug withdrawn due to adverse event</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1 (2.70)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Adverse events</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Hypoglycemia</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Pancreatitis</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Genital infection</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Urinary tract infection</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Liver enzyme elevation<sup>a</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Creatinine elevation<sup>b</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1 (2.63)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Leukocytosis<sup>c</sup></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Urticaria</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1 (2.70)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"> Others</td><td rowspan=\"1\" colspan=\"1\"/><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">  Dim eyes</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1 (2.63)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">  Diabetic retinopathy</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1 (2.63)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">  Diabetic neuropathy</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1 (2.70)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">  Herpes zoster</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1 (2.70)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">  Colon polyps</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1 (2.63)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr></tbody></table></table-wrap>" ]
[]
[]
[]
[]
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[ "<table-wrap-foot><fn><p>Values are presented as mean ± standard deviation, median (interquartile range), or number (%). BMI: body mass index; HOMA-IR: homeostasis model assessment of insulin resistance; HOMA-<italic>β</italic>: homeostasis model assessment of <italic>β</italic>-cell function; HDL-C: high-density lipoprotein cholesterol; LDL-C: low-density lipoprotein cholesterol; AST: aspartate aminotransferase; ALT: alanine aminotransferase; UACR: urine albumin-to-creatinine ratio.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>Values are presented as mean ± standard deviation or median (interquartile range). <italic>p</italic> values were applied by independent <italic>t</italic>-test or the Wilcoxon rank-sum test. HOMA-IR: homeostasis model assessment of insulin resistance; HOMA-<italic>β</italic>: homeostasis model assessment of <italic>β</italic>-cell function; HDL-C: high-density lipoprotein cholesterol; LDL-C: low-density lipoprotein cholesterol; UACR: urine albumin-to-creatinine ratio.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>Values are presented as number (%). <sup>a</sup>AST or ALT 3 times higher than the upper limit of the normal range. <sup>b</sup>Creatinine &gt; 1.4 mg/dL. <sup>c</sup>White blood cell count &gt; 10,000/<italic>μ</italic>L. AST: aspartate aminotransferase; ALT: alanine aminotransferase.</p></fn></table-wrap-foot>" ]
[ "<graphic xlink:href=\"JDR2024-8915591.001\" position=\"float\"/>", "<graphic xlink:href=\"JDR2024-8915591.002\" position=\"float\"/>", "<graphic xlink:href=\"JDR2024-8915591.003\" position=\"float\"/>" ]
[]
[{"label": ["13"], "person-group": ["\n"], "surname": ["Rhee", "Lee", "Min"], "given-names": ["E. J.", "W. Y.", "K. W."], "article-title": ["Efficacy and safety of the dipeptidyl peptidase-4 inhibitor gemigliptin compared with sitagliptin added to ongoing metformin therapy in patients with type 2 diabetes inadequately controlled with metformin alone"], "source": ["\n"], "italic": ["Diabetes, Obesity & Metabolism"], "year": ["2013"], "volume": ["15"], "issue": ["6"], "fpage": ["523"], "lpage": ["530"], "pub-id": ["10.1111/dom.12060", "2-s2.0-84877636655"]}, {"label": ["19"], "person-group": ["\n"], "surname": ["Cho", "Nomoto", "Nakamura"], "given-names": ["K. Y.", "H.", "A."], "article-title": ["Favourable effect of the sodium-glucose co-transporter-2 inhibitor canagliflozin plus the dipeptidyl peptidase-4 inhibitor teneligliptin in combination on glycaemic fluctuation: an open-label, prospective, randomized, parallel-group comparison trial (the CALMER study)"], "source": ["\n"], "italic": ["Diabetes, Obesity & Metabolism"], "year": ["2020"], "volume": ["22"], "issue": ["3"], "fpage": ["458"], "lpage": ["462"], "pub-id": ["10.1111/dom.13879", "2-s2.0-85074034386"]}, {"label": ["21"], "person-group": ["\n"], "surname": ["Zhou", "Geng", "Wang", "Huang", "Shen", "Wang"], "given-names": ["Y.", "Z.", "X.", "Y.", "L.", "Y."], "article-title": ["Meta-analysis on the efficacy and safety of SGLT2 inhibitors and incretin based agents combination therapy vs. SGLT2i alone or add-on to metformin in type 2 diabetes"], "source": ["\n"], "italic": ["Diabetes/Metabolism Research and Reviews"], "year": ["2020"], "volume": ["36"], "issue": ["2, article e3223"], "pub-id": ["10.1002/dmrr.3223"]}, {"label": ["26"], "person-group": ["\n"], "surname": ["Oh", "Nguyen", "Yoon", "Ahn", "Kim"], "given-names": ["H.", "H. D.", "I. M.", "B. R.", "M. S."], "article-title": ["Antidiabetic effect of gemigliptin: a systematic review and meta-analysis of randomized controlled trials with Bayesian inference through a quality management system"], "source": ["\n"], "italic": ["Scientific Reports"], "year": ["2021"], "volume": ["11"], "issue": ["1, article 20938"], "pub-id": ["10.1038/s41598-021-00418-z"]}]
{ "acronym": [], "definition": [] }
28
CC BY
no
2024-01-14 23:41:55
J Diabetes Res. 2024 Jan 5; 2024:8915591
oa_package/ae/d7/PMC10787050.tar.gz
PMC10787051
0
[ "<title>1. Introduction</title>", "<p>Ankylosing spondylitis (AS), as a subtype of spondyloarthritis [##UREF##0##1##], is a chronic inflammatory rheumatic disease that is characterized by chronic spinal inflammation, arthritis, gut inflammation, and enthesitis [##REF##20356776##2##]. Patients with fixed and kyphotic deformities caused by AS may face the problems such as impaired horizontal gaze, severe neck pain, and sagittal imbalance [##UREF##1##3##]. A combination of multistep surgery and digital planning is often required in complex AS deformities, which is a real challenge for spine surgeons [##UREF##2##4##]. AS is a considerable burden to patients and society because of deformity, pain, and disability [##REF##30094685##5##].</p>", "<p>Although the exact etiology and pathogenesis of AS are still unknown, mainly five hypotheses, including arthritogenic peptides, an unfolded protein response, human leucocyte antigen (HLA)-B27, homodimer formation, malfunctioning endoplasmic reticulum aminopeptidases, gut inflammation, and dysbiosis to explain the pathogenesis exist [##UREF##3##6##]. Genetic studies suggest that genetic factors account for about 90% of the pathogenesis of AS, and the genetic risk factors involved are major histocompatibility complex (MHC) and non-MHC gene loci [##REF##26974007##7##]. Numerous studies have also shown that immune cell and osteoclast differentiation were crucial mechanisms and findings in the pathogenesis of AS [##UREF##4##8##–##UREF##5##10##].</p>", "<p>Many studies focused on the key genes in the progression of AS by integrated bioinformatics analysis. However, there is no bioinformatics analysis related to the immune infiltration and osteoclast differentiation to analyze the function and regulation of differential genes. Hence, we conducted this investigation to identify the main biomarkers associated with immune infiltration and osteoclast development in the pathological process of AS utilizing bioinformatic techniques.</p>" ]
[ "<title>2. Materials and Methods</title>", "<title>2.1. Data Download</title>", "<p>In our study, microarray data were retrieved from the Gene Expression Omnibus database (<ext-link xlink:href=\"https://www.ncbi.nlm.nih.gov/geo/\" ext-link-type=\"uri\">https://www.ncbi.nlm.nih.gov/geo/</ext-link>) [##REF##23193258##11##] by using keywords “spondylitis, ankylosing” (All Fields) OR “Ankylosing Spondylitis” (all fields). The GPL6947 Illumina HumanHT-12 V3.0 expression bead chip serves as the foundation for this dataset. This chip comprises a total of 32 samples split between two groups. Under the comprehensive consideration, we finally selected GSE25101 as the research object. Patients' information and specimens' source of GSE25101 were outlined in ##TAB##0##Table 1##. The dataset was obtained using R's “GEOquery” package (3.6.3) [##REF##17496320##12##]. The workflow is shown in ##FIG##0##Figure 1##.</p>", "<title>2.2. Differential Expression Analysis</title>", "<p>The “limma” package was applied to standardize and analyze patient and control data differences [##UREF##6##13##]. Differentially expressed genes (DEGs) were selected using the Benjamini–Hochberg adjusted <italic>P</italic> value &lt;0.05.</p>", "<title>2.3. Functional Annotation of DEGs</title>", "<p>Gene ontology (GO) terms include biological process (BP), cellular component (CC), and molecular function (MF). The false discovery rate (FDR) &lt;0.05 was significantly enriched. To reveal the function of the network, the “clusterProfiler” packages were used to perform GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses [##REF##22455463##14##].</p>", "<title>2.4. Construction of Weighted Gene Coexpression Network Analysis (WGCNA)</title>", "<p>WGCNA is a systems biology approach that detects patterns of genetic linkage between diverse samples. Based on connectedness and relationship between genomes and phenotypes, it can reveal highly synergistic genomes, alternative biomarker genes, or therapeutic targets [##UREF##7##15##]. The “hclust” function was initially employed for hierarchical clustering analysis. Then, during module creation, we applied “pickSoftThreshold” to filter the soft thresholds and select the right power levels. To create the coexpression network, we employ the “WGCNA” program. Label each module with a distinct color, and then filter out the modules with the most interconnections. Using the “clusterProfiler” program and Metascape [##UREF##8##16##] (<ext-link xlink:href=\"http://metascape.org\" ext-link-type=\"uri\">http://metascape.org</ext-link>), GO and KEGG analyses were performed on the genes in the modules. The screening criteria for crucial genes were gene significance (GS) &gt; 0.70 and module membership (MM) &gt; 0.80. We intersected the pivotal genes obtained from WGCNA with DEGs associated with osteoclast differentiation to obtain the essential genes. These genes make a significant contribution to the progression of AS.</p>", "<title>2.5. Immune Infiltration Analysis</title>", "<p>The immune cell infiltration matrix was produced by uploading gene expression profile data to CIBERSORT (<ext-link xlink:href=\"https://cibersort.stanford.edu/\" ext-link-type=\"uri\">https://cibersort.stanford.edu/</ext-link>) [##REF##25822800##17##]. To visualize the differences in immune cell infiltration between control and patient groups, two-dimensional PCA clustering maps and violin plots were generated using the “ggplot2” software package. Heat maps of 22 infiltrating immune cells were generated using “pheatmap” (version 1.0.8) software [##UREF##9##18##]. Finally, differences in immune cell infiltration between the high and low-expression groups were analyzed and visualized according to the median expression levels of key genes.</p>", "<title>2.6. RNA Extraction and Reverse Transcription and Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR)</title>", "<p>The peripheral blood was collected from six AS patients and six health volunteers matched by age and sex at the Beijing Chaoyang Hospital, Capital Medical University.</p>", "<p>The inclusion criteria were as follows: (1) the patient was diagnosed with AS, (2) the age of patients ranging from 18 to 35-year old, (3) without osteoporosis or osteopenia, (4) early stage of the AS disease, (5) not associated with infectious diseases, and (6) the patient agrees and signs the informed consent form; The exclusion criteria were as follows: (1) medication was started, (2) with other rheumatic immune diseases, (3) with other chronic diseases, (4) with cancer in any system, (5) history of orthopedic surgery and diseases, and (6) no definite diagnosis of AS. All human specimens were acquired under the approval of the institutional review board of Beijing Chaoyang Hospital, Capital Medical University (2017-KE-67, Beijing, China). Under the guidance of the World Medical Association Declaration of Helsinki, we obtained informed consent from each patient.</p>", "<p>The RNAprep Pure Hi-Blood Kit (Tiangen Biotech, China) was used to perform the reverse transcription of the extracted RNA. Using Nanodrop, the purity and amount of isolated RNA were evaluated. (Thermo Fisher Scientific, USA). cDNA was synthesized using reverse transcriptase (TIANGEN, Beijing, China). On an ABI 7500 Real-Time PCR System (Applied Biosystems), the SYBR Green Real-time PCR Master Mix (TOYOBO, Japan) was employed for quantitative PCR of hub genes. <italic>β</italic>-Actin was utilized as an internal control. All the primers (Sangon, China) used in this study are listed in ##TAB##1##Table 2##. Normalization and calculation of relative mRNA expression were accomplished using the comparative Ct method (2<sup>−<italic>ΔΔ</italic>Ct</sup>). The data are shown as a fold change in expression relative to normal tissue. Comparisons were carried out through a one-way ANOVA, and <italic>P</italic> &lt; 0.05 indicated that there were statistically significant differences.</p>", "<title>2.7. Statistical Analysis</title>", "<p>R software (3.6.3) was utilized to carry out the statistical analysis. Mean ± standard deviation (SD) was calculated for each and every set of numbers. Using the “limma” software tool, the difference in DEGs between control and the patients' groups were determined.</p>" ]
[ "<title>3. Results</title>", "<title>3.1. Research Design Summary</title>", "<p>\n##FIG##0##Figure 1## shows the study's flowchart. Having screened for DEGs in AS using microarray data from the GEO database, we then screened for immune cells linked with AS using CIBERSORT. WGCNA and related techniques were utilized to identify genes focused on immune cells. The relationship between central gene expression and the clinical characteristics of AS was demonstrated using qRT-PCR.</p>", "<title>3.2. DEGs between the Patients and Control Groups</title>", "<p>The data on the expression profiles of the patients and the control group were compared and screened using a threshold of <italic>P</italic> less than 0.05 and a |logFC| value &lt;0.2. We acquired a total of 125 DEGs, 36 of which were upregulated and 89 of which were downregulated among the genes (##FIG##1##Figure 2(a)##).</p>", "<title>3.3. Enrichment Analysis of DEGs</title>", "<p>The KEGG data revealed the enriched pathways for the related genes (##FIG##1##Figure 2(b)##). The findings of the GO analysis revealed that the DEGs were primarily abundant in BPs (##FIG##1##Figure 2(c)##). Intracellular transport, cellular macromolecule localization, the biological process involved in symbiotic interaction, and cell activation involved in immune response were among the substantially enriched BP keywords for the DEGs. Catalytic complex, nuclear protein-containing complex, and ribonucleoprotein complex were among the significantly enriched CC keywords for the DEGs (##FIG##1##Figure 2(d)##). Among the significantly enriched MF keywords for the DEGs, enzyme binding, RNA binding, and transcription factor binding were outlined as the first three (##FIG##1##Figure 2(e)##).</p>", "<title>3.4. Immune Microenvironment Characteristics of AS</title>", "<p>To gain a more comprehensive understanding of the immune environment present in AS, distinct immune cell types were analyzed using the CIBERSORT technique. After deleting cells with an immunological abundance value of “0,” the results showed that 17 different types of immune cells were examined, and it was found that the levels of naive CD4+ T cells and Monocytes were considerably higher in AS (<italic>P</italic> &lt; 0.05; ##FIG##2##Figure 3(a)##). Further research into the CIBERSORT scores revealed a strong positive association between B cells, Tregs, and M2 macrophages. This was illustrated by the correlation-based heatmap (corheatmap), which can be found in ##FIG##2##Figure 3(b)##. On the other hand, the infiltration of CD4+ T cells, NK cells, and M0 macrophages was found to relate to one another negatively. Together, as part of a joint process, the aberrant infiltration of immune cells seen in AS might have particular guiding relevance in the clinical management of the condition.</p>", "<title>3.5. Identification of Immune Cell-Related Genes</title>", "<p>The WGCNA was applied to identify differentially expressed immune cell-related genes and explore the network's phenotype and hub genes (##FIG##3##Figure 4(a)##–##FIG##3##4(c)##). Twenty-five genes were selected by the correlation test. Cytoscape was used to create the interaction network that was comprised of these 25 genes as well as the genes that they were targeting. The WGCNA hub genes were intersected. Different colors were then used to differentiate these DEGs (Figures ##FIG##3##4(b)## and ##FIG##3##4(c)##). One of the four gene modules we assessed was tightly connected with immune cells (##FIG##3##Figure 4(c)##). The blue module had a strong positive correlation of 0.67 with naive CD4+ T cells, and <italic>P</italic> &lt; 0.001 (##FIG##3##Figure 4(d)##). Based on the selection of the 30 most significantly elevated genes and the 33 most important genes, heat maps were generated (##FIG##3##Figure 4(e)##).</p>", "<title>3.6. The Identification of Candidate Biomarkers</title>", "<p>Twenty-five different gene modules were obtained due to the creation of the coexpression matrix (##FIG##3##Figure 4(d)##). Twelve genes satisfied the preselection criteria and were chosen based on relevant tests (Figures ##FIG##4##5(a)## and ##FIG##4##5(b)##). Finally, IGF2R, GRN, SH2D1A, LILRB3, IFNAR1, PLCG2, and TNFRSF1B were identified as key genes. After that, as depicted in Figures ##FIG##4##5(c)## and ##FIG##4##5(d)##, we utilized metascape to collect more information on these genes and analyze their functions. Genes were enriched in essential biological processes, such as inflammatory response, chemokine signaling pathway, cytokine-mediated signaling pathway, regulation of neuroinflammatory response, leukocyte migration, and natural killer cell-mediated cytotoxicity.</p>", "<p>According to the findings, most of the genes significantly enriched in pathways associated with immune response were the blue module.</p>", "<p>We intersected the hub genes screened by WGCNA and the genes in osteoclast differentiation and obtained two genes: IFNAR1 and PLCG2.</p>", "<title>3.7. qRT-PCR Validation of Data</title>", "<p>qRT-PCR experiments were performed to verify the bioinformatics results. The characteristics of patients and healthy volunteers are shown in ##TAB##2##Table 3##. The results revealed that the mRNA expression levels of PLCG2 in AS were significantly higher than that in the normal person (<italic>P</italic>=0.003). The mRNA expression levels of IFNAR1 in AS were significantly lower than that in the normal person (<italic>P</italic> &lt; 0.0001). All of the above results indicate that the outcomes of bioinformatics analysis are very competent and have considerable research value. (Figures ##FIG##5##6(a)## and ##FIG##5##6(b)##).</p>" ]
[ "<title>4. Discussion</title>", "<p>AS is a common chronic inflammatory autoimmune disease in which axial inflammation, bone destruction, and new bone formation are the key events [##UREF##10##19##]. From 2005 to 2019 in China, the total prevalence of AS was 0.29%, among which there were 0.42% in males and 0.15% in females [##REF##32125505##20##]. The mean AS prevalence was 0.24% in Europe, 0.17% in Asia, 0.32% in North America, 0.10% in Latin America, and 0.07% in Africa [##REF##24324212##21##]. The most common symptoms of AS are chronic back pain and spinal stiffness, but peripheral and musculoskeletal manifestations are also frequently present [##UREF##11##22##].</p>", "<p>In this study, we acquired a total of 125 DEGs, 36 of which were upregulated and 89 downregulated among the genes. IGF2R, GRN, SH2D1A, LILRB3, IFNAR1, PLCG2, and TNFRSF1B were identified as key genes enriched in the inflammatory response, chemokine signaling pathway, cytokine-mediated signaling pathway, regulation of neuroinflammatory response, leukocyte migration, and natural killer (NK) cell-mediated cytotoxicity. In terms of the inflammatory response, Guggino et al. [##REF##33452867##23##] evaluated the activation and functional relevance of inflammasome pathways in AS patients and presented that inflammasomes drove type III cytokine production with an IL-1<italic>β</italic>-dependent mechanism in AS patients. The free heavy chain of HLA-B 27 may induce inflammation via T cells, NK cells, and bone marrow cells [##UREF##12##24##]. As is the case with AS, vascular endothelial cells respond to TNF by experiencing various pro-inflammatory alterations. The effectiveness of TNF-blocking medications in the treatment of AS demonstrates that TNF plays an essential part in inflammation [##REF##18161752##25##]. In 17 different types of immune cells, we found naive CD4+ T cells and monocytes were considerably higher in AS. Zheng et al. [##UREF##13##26##] The AS contained a higher proportion of CD8+ T cells, naive CD4+ T cells, and neutrophils among CIBERSORT results. There was a strong positive association between B cells, Tregs, and M2 macrophages, while the infiltration of CD4+ T cells, NK cells, and M0 macrophages was found to relate to one another negatively. Zhang et al. [##UREF##14##27##] reported negative correlations in CD8+ T cells and neutrophils activated memory CD4+ T cells, which was similar to our results. Multiple immune cells control the activity of bone cells and the size of bones through the release of cytokines and signaling pathways. DCs and their subtypes play crucial roles in numerous autoimmune and chronic inflammatory diseases [##REF##28164850##28##]. Increased plasmacytoid DCs have been found in the bone marrow and peripheral blood of AS patients, which has been linked to higher levels of inflammatory cytokines such as trafficking molecules, CCR6 and CCL20, TNF-, IL-6, and IL-23 [##REF##33559242##29##]. The pathophysiology of AS can be better understood if the association between the immune and skeletal systems is further examined.</p>", "<p>The phospholipase C gamma 2 (PLCG2) gene is responsible for encoding phospholipase C<italic>γ</italic>2 [##UREF##15##30##]. PLCG2 can regulate various cells' immune, inflammatory, and allergic responses through NFAT, NF-<italic>κ</italic>B, and MAPK signaling pathways [##UREF##15##30##, ##REF##22000665##31##]. Yu et al. [##REF##15845450##32##] found a point mutation in the mouse PLCG2 gene, which leads to hyperreactive external calcium entry in B cells and expansion of innate inflammatory cells, leading to severe spontaneous inflammation and autoimmunity. In humans, point mutations of PLCG2 can lead to autoimmune inflammation, resulting in arthralgia and inflammatory bowel disease, suggesting that point mutations of PLCG2 are an essential mechanism for inducing immune inflammation [##REF##23000145##33##]. The destruction of bone and cartilage and local osteoporosis are important pathological manifestations of AS, among which osteoclasts play an essential role. Therefore, exploring the genes related to osteoclasts formation is of great significance. Studies have shown that PLCG2 mediator can induce osteoclasts while blocking PLCG2 enzyme activity can limit the development and function of early osteoclasts [##REF##17053833##34##]. Normal bone remodeling requires a balance between the metabolic processes of bone-resorbing cells, osteoclasts, and bone-forming cells [##REF##24363057##35##]. Jeong et al. [##REF##32237724##36##] also found that betulinic acid could significantly inhibit the generation of osteoclasts by inhibiting the phosphorylation of PLCG2. Under the influence of promoting bone resorption factors, the multinucleated osteoclasts were formatted by the fusion and differentiation of monocyte progenitors, which could regulate osteoblast differentiation and bone formation [##REF##18406338##37##].</p>", "<p>IFN can stimulate the differentiation of immune cells and enhance immunological function, which may be an influential variable element in the pathogenesis of AS illness [##REF##28843049##38##]. IFN can play an immunomodulatory role only when it binds to the interferon-<italic>α</italic>/<italic>β</italic> receptor (IFNAR). Studies have shown that IFN-<italic>γ</italic> polymorphisms are positively associated with the risk of AS [##REF##28843049##38##]. Santiago-Raber et al. [##REF##12642605##39##] found in NZB mice that a reduced number of IFN<italic>α</italic>/<italic>β</italic> receptors affected the incidence of immune lupus disease, suggesting the role of IFNAR in rheumatic diseases. However, the mechanism of IFNAR in the immune inflammation of AS remains unclear. It was reported that induction of IFN-B through the STING signaling pathway could restrai osteoclast differentiation and bone resorption, so it is speculated that decreased IFNAR can promote osteoclast differentiation [##REF##30779854##40##].</p>", "<p>In our study, PLCG2 and IFNAR genes were obtained by screening genes meeting the conditions of immune cell infiltration and osteoclast differentiation in AS patients. The above analysis indicated that inhibition of PLCG2 may inhibit the immune inflammatory response and osteoclast formation in patients with AS. In contrast, the increased expression of IFNAR may inhibit the immune inflammatory response and osteoclast formation.</p>", "<p>Limitations of our study still remain. First, we used the GEO database instead of our patient data, and there was unknown bias such as duration of medication, the severity of AS, and race of patients. Second, data validation is not sufficient relatively and qRT-PCR should be used to show the link between hub gene expression and AS clinical characteristics. Based on our existing samples, we will subsequently integrate more samples and conduct in-depth research in peripheral blood, bone tissue, and single cells.</p>" ]
[ "<title>5. Conclusions</title>", "<p>Dysregulation of PLCG2 and IFNAR1 are key factors in disease occurrence and development of AS through regulating immune infiltration and osteoclast differentiation. Investigating the differences between AS and normal samples in immune cell infiltration and osteoclast differentiation would contribute to a better comprehension of the root cause of spondyloarthritis and therapeutic methods.</p>" ]
[ "<p>Academic Editor: Wenyuan Ding</p>", "<title>Objectives</title>", "<p> Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease characterized by chronic spinal inflammation, arthritis, gut inflammation, and enthesitis. We aimed to identify the key biomarkers related to immune infiltration and osteoclast differentiation in the pathological process of AS by bioinformatic methods. </p>", "<title>Methods</title>", "<p> GSE25101 from the Gene Expression Omnibus was used to obtain AS-associated microarray datasets. We performed bioinformatics analysis using R software to validate different expression levels. The purpose of the GO and KEGG enrichment analyses of DEGs was to exclude key genes. Using weighted correlation network analysis (WGCNA), we examined all expression profile data and identified differentially expressed genes. The objective was to investigate the interaction between genetic and clinical features and to identify the essential relationships underlying coexpression modules. The CIBERSORT method was used to make a comparison of the immune infiltration in whole blood between the AS group and the control group. The WGCNA R program from Bioconductor was used to identify hub genes. RNA extraction reverse transcription and quantitative polymerase chain reaction were conducted in the peripheral blood collected from six AS patients and six health volunteers matched by age and sex. </p>", "<title>Results</title>", "<p> 125 DEGs were identified, consisting of 36 upregulated and 89 downregulated genes that are involved in the cell cycle and replication processes. In the WGCNA, modules of MCODE with different algorithms were used to find 33 key genes that were related to each other in a strong way. Immune infiltration analysis found that naive CD4+ T cells and monocytes may be involved in the process of AS. PLCG2 and IFNAR1 genes were obtained by screening genes meeting the conditions of immune cell infiltration and osteoclast differentiation in AS patients among IGF2R, GRN, SH2D1A, LILRB3, IFNAR1, PLCG2, and TNFRSF1B. The results demonstrated that the levels of PLCG2 mRNA expression in AS were considerably higher than those in healthy individuals (<italic>P</italic>=0.003). IFNAR1 mRNA expression levels were considerably lower in AS than in healthy individuals (<italic>P</italic> &lt; 0.0001). </p>", "<title>Conclusions</title>", "<p> Dysregulation of PLCG2 and IFNAR1 are key factors in disease occurrence and development of AS through regulating immune infiltration and osteoclast differentiation. Explaining the differences in immune infiltration and osteoclast differentiation between AS and normal samples will contribute to understanding the development of spondyloarthritis.</p>" ]
[]
[ "<title>Data Availability</title>", "<p>The data of this study are available from the corresponding author.</p>", "<title>Conflicts of Interest</title>", "<p>The authors declare that they have no conflicts of interest.</p>", "<title>Authors' Contributions</title>", "<p>Bo Han and Qiaobo Xie contributed equally to this work.</p>" ]
[ "<fig position=\"float\" id=\"fig1\"><label>Figure 1</label><caption><p>A flow-process chart shows the analysis steps in this study.</p></caption></fig>", "<fig position=\"float\" id=\"fig2\"><label>Figure 2</label><caption><p>Functional annotation of DEGs. (a) DEGs were identified using a volcano plot, where red represents upregulated genes and blue represents downregulated genes. (b) KEGG pathway enrichment analysis for DEGs. (c–e) GO analysis of DEGs in (c) BP, (d) CC, and (e) MF.</p></caption></fig>", "<fig position=\"float\" id=\"fig3\"><label>Figure 3</label><caption><p>Immune infiltration landscape in whole blood. (a) Immune infiltration differences between patients and control group. (b) Correlation matrix of 22 immune cell type proportions. Some of the immune cells had a negative relation, denoted by the color blue, while others had a positive relation, represented by the color red. Compared to the lighter color, the association was much more robust (<italic>P</italic> &lt; 0.05).</p></caption></fig>", "<fig position=\"float\" id=\"fig4\"><label>Figure 4</label><caption><p>Identification of the immune infiltration-related genes in Ankylosing Spondylitis. (a) A clustering tree for the coexpression network module is created. (b) Feature of each combined module's relationship, with distinct colors denoting different parts. Each row represents a module. Each column shows how that module relates to the qualities, and each individual unit consists of both the <italic>P</italic>-value and the correlation coefficient. (c) Genes that belong to the blue module that was selected. (d) The blue portion of the collected genes. (e) A heat map of hub genes.</p></caption></fig>", "<fig position=\"float\" id=\"fig5\"><label>Figure 5</label><caption><p>(a) The hub gene expression levels in different groups. (b) Matrix of expression correlations for each hub gene in AS. (c) The meta scale was used to enhance the functional enrichment of the correlated genes. Symbols “ <sup><italic>∗</italic></sup>”, “ <sup><italic>∗∗</italic></sup>”, and “ns,” respectively, stand for <italic>P</italic> &lt; 0.05, <italic>P</italic> &lt; 0.01, and nonsignificance. (d) Chord plots demonstrate key roles in hub genes. (e) Venn diagram showing the intersection of hub genes in the blue module in WGCNA and genes in the osteoclast differentiation signal pathway.</p></caption></fig>", "<fig position=\"float\" id=\"fig6\"><label>Figure 6</label><caption><p>qRT-PCR validation in the peripheral blood. (a) The mRNA expression levels of PLCG2 in ankylosing spondylitis were significantly higher than that in the normal person (<italic>P</italic>=0.003). (b) The mRNA expression levels of IFNAR1 in ankylosing spondylitis were significantly lower than that in the normal person (<italic>P</italic> &lt; 0.0001). (<italic>P</italic> &lt; 0.05,  <sup><italic>∗∗</italic></sup><italic>P</italic> &lt; 0.01, and  <sup><italic>∗∗∗∗</italic></sup><italic>P</italic> &lt; 0.0001).</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"tab1\"><label>Table 1</label><caption><p>Patients' information and specimens' source of GSE25101.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"1\" colspan=\"1\"/><th align=\"center\" colspan=\"4\" rowspan=\"1\">Patient information</th><th align=\"center\" colspan=\"2\" rowspan=\"1\">Source of specimen</th></tr><tr><th rowspan=\"2\" colspan=\"1\"/><th align=\"center\" rowspan=\"2\" colspan=\"1\">Age (years, mean ± SD)</th><th align=\"center\" colspan=\"2\" rowspan=\"1\">Sex</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">Family history</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">Tissue</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">Cell type</th></tr><tr><th align=\"center\" rowspan=\"1\" colspan=\"1\">Male</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Female</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">AS patients (<italic>n</italic> = 18)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">45.9 ± 12.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Whole blood</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">PBMC</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">AS control (<italic>n</italic> = 16)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Whole blood</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">PBMC</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab2\"><label>Table 2</label><caption><p>PCR primers.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Gene</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Forward primer sequence</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Reverse primer sequence</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">IFNAR1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5′-TGTCCGCAGCCGCAGGTG-3′</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5′-CCCGACAGACTCATCGCTCCTG-3′</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PLCG2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5′-GGACATAGAGCTGGCTTCCC-3′</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5′-GTTCAGTTCTTCTTGCCGCC-3′</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Actin</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5′-ACCGCGAGAAGATGACCCA-3′</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5′-GGATAGCACAGCCTGGATAGCAA-3′</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab3\"><label>Table 3</label><caption><p>The characteristics of patients and healthy volunteers.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Characteristic</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Group AS</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Group control</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>P</italic>\n</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Age (yr)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30.2 ± 4.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">26.5 ± 4.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.21</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Male sex-no. (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5 (83.33)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5 (83.33)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.77</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI (Kg/m<sup>2</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">23.83 ± 4.17</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">23.17 ± 3.87</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.78</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Race-Asian no. (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6 (100)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6 (100)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Positive for HLA-B27-no. (%)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6 (100)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Time (Mons)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.50 ± 3.27</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td></tr></tbody></table></table-wrap>" ]
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{ "acronym": [], "definition": [] }
40
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2024-01-14 23:41:55
Mediators Inflamm. 2024 Jan 5; 2024:3358184
oa_package/5d/2c/PMC10787051.tar.gz
PMC10787052
0
[ "<title>1. Introduction</title>", "<p>In the past, global health priority was on infectious diseases. But with the growth of population, increase in life expectancy, and decrease in mortality, noncommunicable diseases such as musculoskeletal disorders have become common [##REF##27886943##1##, ##REF##11337425##2##]. In this century, according to estimates, the burden of musculoskeletal disorders is very high, and among its common diseases, osteoarthritis, rheumatoid arthritis, gout, low-back pain, and neck pain can be mentioned [##REF##29875522##3##, ##REF##25481420##4##]. In 2019, its age-standardized prevalence was reported as 27.0 per 1000 people [##REF##34980079##5##]. Also, in 2012, 25.5 million Americans were absent from work due to neck pain problems, missing an average of 11.4 days of work [##UREF##0##6##]. Low-back pain is also a common complaint, especially in industrialized societies, with chronic low-back pain reported in 54.0 to 90.0 percent of the adult population. It is considered a public health problem and is the most common complaint among workers in all fields [##UREF##1##7##]. These two disorders are common reasons for visiting medical centers and have a significant impact on individuals, communities, healthcare systems, and businesses [##UREF##2##8##, ##UREF##3##9##]. In Iran, these two disorders are responsible for 11.4% of all years of life with disability [##REF##27258995##10##, ##UREF##4##11##].</p>", "<p>Treatment adherence is very important for the management of patients with low-back and neck pain. Despite the importance of this issue, due to the long course of treatment and the low self-confidence of patients in doing exercises, many patients stop continuing treatment and doing exercises [##REF##26821954##12##, ##REF##28401666##13##]. For this reason, the first and most important step in the management of these two disorders is the continuation and adherence to the treatment along with the participation strategy and correct exercise training, which has been approved in most clinical guidelines [##UREF##5##14##]. Currently, exercise therapy has been introduced as one of the most important treatment methods to reduce disability and improve chronic back and neck pain. It reduces the risk of dangerous diseases and increases life expectancy [##REF##28750310##15##, ##REF##20227641##16##].</p>", "<p>On the other hand, in the management of low-back and neck pain, measuring the clinical effectiveness and evaluating the severity of their pain is a necessity. There are many reliable tools for this, which can be used to determine the severity of the patient's pain and the success rate of the treatment plan [##REF##29787696##17##, ##REF##28753065##18##]. Choosing an outcome measure that is easily scored and provides an objective measure to evaluate the severity of pain is essential in the process of managing low-back and neck pain [##REF##27081203##19##, ##REF##1834753##20##].</p>", "<p>Rehabilitative treatment approaches benefiting from e-health have created a tremendous opportunity to improve patient care and disease management [##REF##28771070##21##]. Electronic health solutions have contributed to the individual's participation in self-care, increased treatment efficiency, and adherence to treatment methods. The mobile application in the field of physiotherapy and rehabilitation causes the following: (a) increasing patients' access to healthcare and health-related information, (b) improving the ability of physiotherapists to diagnose and track neurological and muscular diseases and expand access to online education, and (c) self-management in physiotherapy treatment, which these three factors have facilitated physiotherapy treatment methods [##UREF##6##22##, ##REF##28928110##23##]. Despite a large number of applications in the field of low-back and neck pain management and numerous articles evaluating them [##REF##31867102##24##–##REF##33317134##26##], the lack of an application with an agreed conceptual and content model is a clear information gap. Also, most of the applications in the field of physiotherapy for low-back and neck pain do not use clinical guidelines and valid references for their content [##REF##31867102##24##–##REF##34383379##27##]. For this reason, patients and therapists face challenges in choosing the appropriate evidence-based application [##UREF##7##28##].</p>", "<p>Preparing the conceptual and content model of applications from guidelines and reliable sources is in the direction of evidence-based medical policies as it is one of the most important steps in the design of any information system. In various fields of medicine, we are slowly growing evidence-based development of technologies. For example, Nadri et al. introduced a mobile app for self-care as a complementary approach for cutaneous leishmaniasis. This application provides the best necessary treatment approaches according to user data and based on evidence-based information [##UREF##8##29##]. Also, Ehrler et al., to design a mobile app for bedside nursing care, invited 11 participants to help them choose the most important features to be integrated into the tool with brainstorming sessions [##REF##30973339##30##].</p>", "<p>Considering that the desired goals cannot be achieved with the existing applications, this study tries to meet this need with evidence-based content and validation of this content. Therefore, the present study is aimed at developing a conceptual and content model of a mobile-based application for the management of people with low-back and neck pain.</p>" ]
[ "<title>2. Materials and Methods</title>", "<p>This is a descriptive-analytical study, which was conducted in 2022 as a combination of quantitative and qualitative methods. The study was conducted in two separate stages, which include (1) determining the content and required features and (2) validating the initial content model. ##FIG##0## Figure 1## shows the details of the stages.</p>", "<title>2.1. First Stage: Determining the Content and Required Features</title>", "<p>During the brainstorming sessions, the research team considered three separate steps for this stage. <list list-type=\"order\"><list-item><p>Determining the content of low-back and neck exercises</p></list-item><list-item><p>Determining the appropriate tool to assess the pain intensity of patients</p></list-item><list-item><p>Determining the required features of the application</p></list-item></list></p>", "<p>In the following, the research method is explained in detail in each of these parts.</p>", "<p>Due to the need to use standard and reliable sources whose validity has been confirmed, the research team decided to use reference books to determine low-back and neck exercises and educational materials.</p>", "<p>The second part was related to determining the appropriate tool to assess the severity of patients with low-back and neck pain. Using these tools, patients can assess the severity of their pain and current condition. To find the best tool to use in the application, we tried to extract all the tools available in the assessment of pain intensity using a systematic review. A systematic search was performed using the PRISMA guidelines to retrieve all available studies. Scopus, PubMed, Web of Science, and ScienceDirect were searched along with Google Scholar search engines to extract the valid tools available. The search was performed with the keywords “endpoint”, “physical therapy”, “Neck Pain”, “Low Back Pain”, “Pain Management”, “pain intensity”, and “effect measure”. The inclusion criteria included studies on back or neck pain instruments in English without time limits, and the exclusion criteria included general pain management scales. In the end, the features of these tools were compared to choose the best scale for use in the content model.</p>", "<p>In the third step from the first stage, to determine the required features of the low-back and neck pain application, the research team used the reviewing of existing applications. With this aim, the common features between the apps and those defects were identified. This makes it possible to design a new app by understanding the existing conditions and deficiencies. To identify these features, the Google Play Store was searched based on the keywords “low back pain”, “low back pain”, “lumbago”, “neckache”, and “neck pains”. The applications were reviewed according to the inclusion and exclusion criteria, and eligible cases were included in the study. The inclusion criteria included availability to the public, and no need for an accessory device to perform interventions, updated in 2019 to 2021, providing an exercise solution to encourage the patient to perform daily activities. Exclusion criteria also include providing anatomical, preventive, and diagnostic information without exercise, personalized applications for a specific condition such as pregnant women and people with sciatica pain and back or neck pain due to cancer, apps containing software errors, and apps that provide yoga and relaxation therapy solutions. Eligible apps were installed on mobile phones and evaluated by two members of the research team with the Mobile Application Rating Scale (MARS) questionnaire, and the results were recorded in MS Excel 2019. The results of this section are presented in detail in a separate article and are currently under review in the Journal of Healthcare Engineering.</p>", "<title>2.2. Second Stage: Validation of the Basic Content Model</title>", "<p>After the first stage, a list of the basic content of the app was extracted in all three sections. This was considered a basic content model for the application. To validate and get expert opinions, this model was converted into a questionnaire. The questionnaire included three parts: (1) demographic information of experts, (2) the basic content model of the app, and (3) open questions about the content model. The second part included 40 data elements with three axes of low-back and neck exercises (11 elements), pain intensity assessment tool (10 elements), and required characteristics of the app (19 elements). Each question in the questionnaire has five options based on a 5-point Likert scale: “completely agree =5,” “agree =4,” “I have no opinion=3,” “disagree =2,” and “completely disagree =1.” To determine validity and reliability, it was given to 10 people specializing in physiotherapy and medical informatics. After collecting the questionnaires and analyzing the results, content validity and reliability were obtained as content validity ratio (CVR) = 0.62 and Cronbach's alpha (<italic>α</italic> = 0.66). Content validity assesses whether an instrument covers all relevant aspects of the topic that it is intended to measure. To obtain CVR, experts are asked to determine whether an item is necessary to implement a construct in a set of items or not. A higher score indicates greater panel members' agreement on the necessity of an item in the instrument. Cronbach's alpha is also a method to evaluate reliability by comparing the amount of common variance or covariance among the items that make up an instrument with the amount of overall variance. After determining the validity and reliability, the questionnaire was made available to 15 physiotherapists in medical science universities in Iran and sports medicine specialists in the Sports Medicine Research Center of Tehran University of Medical Sciences by convenience sampling method. The criteria for entering this study were based on user responsiveness, expertise, familiarity with research, and interest in cooperation. 12 specialists (11 physiotherapists and 1 sports medicine specialist) collaborated with the research team. After collecting the questionnaires, SPSS software version 26 was used for data analysis. Data elements in all axes were analyzed based on descriptive statistics indicators such as minimum and maximum score, mean, percentage of content validity ratio, and the degree of interrater reliability.</p>" ]
[ "<title>3. Result</title>", "<title>3.1. Determining the Content and Required Features of the Application</title>", "<p>The results of this stage are shown in three separate parts.</p>", "<title>3.1.1. First Step: Determining the Content Model of Back and Neck Exercises</title>", "<p>The content of exercises and how to display them were considered by the research team and reference books. The main part of the content was determined based on the book <italic>Low Back and Neck Pain: Causes and Conservative Treatment</italic> authored by Paul Williams [##UREF##9##31##]. This book is a resource used to teach the management of low-back and neck pain for undergraduate students of physiotherapy in the Faculty of Rehabilitation at Tehran University of Medical Sciences. In this book, essential exercises for prevention and conservative treatment are presented. ##TAB##0## Table 1## shows the sports exercises selected by the research team from this book along with the description of each exercise.</p>", "<title>3.1.2. Second Part: Determining the Appropriate Tool to Assess the Pain Intensity</title>", "<p>Pain intensity assessment tools were extracted using a systematic review of relevant studies. After extracting the studies, first, all duplicate and unrelated articles were removed from the study and only articles that met the inclusion criteria were left. In summary, the obtained results included 40 articles, and 12 pain intensity assessment tools were extracted from these articles. The PRISMA flow diagram shows the study review process (##FIG##1##Figure 2##).</p>", "<p>After identifying the pain intensity assessment tools, the information on each of them was extracted and compared. ##TAB##1## Table 2## provides comprehensive information on each of these tools.</p>", "<title>3.1.3. The Third Part: Determining the Required Features of the Application</title>", "<p>After examining the apps available in Google Play, 234 neck pain and 246 back pain apps were identified in the initial phase. Of these, 14 apps (8 back pain and 6 neck pain apps) were included in the study based on the inclusion and exclusion criteria. To identify the required features of the application, the content and features of each of the included apps were reviewed. Also, to evaluate more accurately and measure their quality, the evaluation of these programs was done with the MARS questionnaire. Then, the strengths and weaknesses of the apps available in Google Play were extracted. Finally, a series of features were obtained as required features of neck pain and back pain application. The results of this section are shown in ##TAB##2##Table 3##.</p>", "<p>In ##TAB##2##Table 3##, criteria 1 to 3 of the MARS questionnaire examine the presence or absence of desired features in the apps, and criteria 4 to 6 evaluate the quality of the apps. The scores of criteria 4-6 are also obtained from the average scores of two reviewers. The results of the Google Play app reviews showed that there were some essential information elements in some apps, but none of them were evidence-based. However, the “Low back pain relief exercises at home” application with a score of 3.79 scored a higher average score among other applications in terms of compliance with the MARS criteria. Among the neck pain apps, the highest score of 3.58 was related to the Neck &amp; Shoulder Workout (30 days Workout Plan) app. In this app, for 30 days of the month, exclusive sports are designed with animation. However, it should improve aspects such as evidence-based and information quality to increase its impact on users and ensure greater security and privacy.</p>", "<title>3.2. Findings Related to the Validation of the Content Model</title>", "<p>The basic content collected in the first stage was provided to the experts in the form of a questionnaire for validation. ##TAB##3## Table 4## shows the demographic information of the participants at this step. In this survey, most participants were women (66.67 percent), the highest frequency related to the academic rank of assistant professor (41.67 percent), and most participants were from the Tehran University of Medical Sciences (50 percent).</p>", "<p>The survey results are shown in ##TAB##4##Table 5## which is the final content model created in this study. Out of 40 data elements proposed in the questionnaire, 33 elements are considered essential by experts (##TAB##4##Table 5##). All data elements based on exercises and pain intensity assessment scale (CVR &gt; 0.62) remain in the study. Instead, in the axis of the app's features, out of 19 data elements, 7 elements including electronic communication, medication reminder, mental activity tool, physical activity planning, motivational notes, recording the time of three meals, and finding the nearest care centers were excluded, and 12 elements remained.</p>", "<p>Also, the axis of the FRI pain intensity assessment scale attracted favorable opinions with an average score of 100% (CVR = 1). This axis has the highest score among the three axes. The FRI was developed by Feise and Menke in 2001, and its validity and reliability have been confirmed in several languages. It is a 5-point Likert scale from 0 (no pain) to 4 (worst possible pain) [##REF##11148650##43##, ##UREF##13##44##]. The Persian version of this scale was translated by Dr. Ansari et al., in 2012, which has sufficient validity and reliability [##REF##22310090##42##]. The reason for choosing the FRI scale among all pain intensity assessment scales was that the research team chose this scale because of its ease and the need for less time to complete, as well as the existence of various versions in different languages, especially the Persian version.</p>" ]
[ "<title>4. Discussion</title>", "<p>According to the findings, the minimum necessary data elements for the content model of the low-back and neck pain management app are 33 elements, which are determined in the 3 axes of exercises, pain intensity assessment scale, and app features. The results showed that the data elements of the content model, except for some features of the application, were agreed upon by the majority of experts.</p>", "<title>4.1. Data Elements of Content Model Based on Exercises</title>", "<p>The data elements of this axis include 8 exercises for back pain and 3 for neck pain, which are best used as animations in the app. Text instructions, audio, and video files are also recommended for each of the exercises for more clarity on how to do them correctly in the content model. Physiotherapy is usually part of the treatment provided by physical therapists to back pain or neck pain patients. In the current study, 8 exercises for the back and 3 exercises for the neck were determined.</p>", "<p>Dutch clinical guidelines consider patient education and exercise therapy as the main contributions of physiotherapists in the treatment of back pain patients [##UREF##14##45##]. It also showed that physiotherapy compared to other approaches (such as hot packs, massage, stretching, mobilization, short-wave application, ultrasound, stretching exercises, manual therapy exercises, and electrotherapy) becomes more effective [##UREF##14##45##]. The clinical guidelines of the American Medical Association and the American Pain Society for the noninvasive treatment of acute, subacute, and chronic low-back pain have recommended physiotherapy according to the patient's condition [##REF##28192789##46##].</p>", "<p>In the clinical guidelines for neck pain of the American Physical Therapy Association, exercise and patient education are recommended [##UREF##15##47##]. The recommendations of the guidelines confirm the findings of the current study on physiotherapy data [##UREF##13##44##, ##UREF##15##47##]. Also, various studies have investigated the effectiveness of various web-based systems for performing physiotherapy exercise programs at home and the use of apps to train patients, which have had positive results [##REF##26879982##48##, ##REF##28662834##49##].</p>", "<p>In this study, the data elements of exercises are included in the content model in the form of animation to perform correct movements. The experts participating in the validation considered the animated exercises to be effective. They also suggested the use of more exercises in a personalized way for each patient.</p>", "<title>4.2. Data Elements of Pain Intensity Assessment Scale</title>", "<p>The data elements of this axis were selected based on the FRI scale. It is useful for evaluating pain intensity and can report a patient's condition [##REF##11148650##43##, ##UREF##13##44##]. Currently, pain intensity measures are widely used as valuable tools for researchers, physicians, patients, and payers. In the study of Foroutani et al., the responsiveness of the Persian version of the Functional Rating Index in patients with chronic nonspecific neck pain was investigated. This study showed that this scale has a good response and has practical importance for use in the clinic and research [##UREF##16##50##].</p>", "<p>The importance of self-assessment of the health status of the patient or the use of patient-reported outcome measures (PROMs) and reporting provides a valid and reliable justification for the treatment of the patient. The results of measures are also used to analyze the quality of care. Also, with the increasing patients' participation in the care, the use of measures based on the patient's perspective has become increasingly complementary to clinical methods. The results of the use of PROMs in various studies have shown that these tools are essential to demonstrate the value and success of physiotherapy and are an essential tool [##REF##29787696##17##, ##REF##28753065##18##].</p>", "<title>4.3. Data Elements of Application Features</title>", "<p>The elements of this axis were collected by comparing the evaluation results of Google Play apps and were validated by experts. Based on the identification of gaps and strengths, a set of primary data elements was extracted, and finally, the validation results showed that out of 19 elements, only 12 elements with a CVR greater than 0.62 were recognized as essential. The importance of using animation in physiotherapy in a study by Zernicke et al. showed that the use of exercise programs using game consoles for patients with rheumatoid arthritis had similar effects compared to standard exercises at home, so such a program can be an alternative support option for patients with rheumatism [##REF##26728594##51##].</p>", "<p>Chiensriwimol et al. investigated the effectiveness of an exercise simulator for the treatment of a frozen shoulder in a mobile application. The study showed that the use of animation to simulate arm movements in different types of exercises using biofeedback data is effective for the treatment process and physiotherapy because they can remotely monitor and manage the patient's rehabilitation process [##UREF##17##52##]. In Chandra et al.'s study, health technology was used to reduce the difficulties of performing physiotherapy at home and reduce recovery periods. They used a muscle activity sensor connected to a mobile phone to increase the adaptation of sports movements. They argued that health technologies have many capabilities to offer their users, but they should be designed to match the lifestyle and real needs of patients [##UREF##18##53##].</p>", "<p>On the other hand, the importance of patient education as an independent intervention or together with other interventions for people with musculoskeletal pain has been emphasized in several studies. The study of Goff et al. investigated the effect of training patients with knee arthritis in improving pain and function. The results showed that patient education is not an independent treatment and should be combined with physiotherapy to be more effective in statistics and clinical performance than education alone [##REF##34158270##54##]. The results of Ramos-Remus et al.'s study on the education of rheumatic patients showed that patient education is one of the ways to achieve quality improvement in this disease. It is also emphasized that education is not only a program, but it is a strategy [##UREF##19##55##]. The results of the current study also emphasize the importance of using educational videos for conservative and preventive treatment and animations for correct exercises. This is consistent with the results presented in similar articles and promotes education as a special strategy alongside physiotherapy.</p>", "<p>The importance of using reminders to prevent patients from losing motivation to exercise has been investigated in several studies. Jangi et al. conducted a systematic review titled the effect of reminders in physiotherapy, and the results showed that 35% of the studies reported positive effects of reminders [##REF##29387313##56##]. They also concluded that the use of reminders is a useful strategy to improve patients' adherence to exercise programs [##REF##29387313##56##]. This study was consistent with current research and showed that the development of technology and communication offers new ways to increase patient motivation. In the data elements of this content model, there is the use of warning and note setting to perform exercises, which was approved by experts with 100% votes as an essential element.</p>", "<p>The importance of privacy and security of health data is considered sensitive by nature and according to the law, and therefore, it is very important to protect them. As the new capabilities of mobile phones are enhanced and allow millions of applications to take advantage of vast amounts of data, the importance of protecting health data becomes even more important [##UREF##20##57##]. Papageorgiou et al. analyzed the security and privacy of health applications, which showed that most applications do not take into account well-known privacy practices and guidelines, which puts the security of health users' data at risk [##UREF##20##57##]. Also, in another study conducted by Martínez-Pérez et al. to evaluate the privacy of health applications, it was shown that special protection of users' personal health information is important. However, the appropriate methods for doing this are not considered by app designers, and insecure applications are published [##REF##25600193##58##]. In this study, to preserve the privacy of patients in the content model, authentication and other security aspects such as access control have been used, which received 100% of experts' favorable opinions.</p>", "<p>Using health information technology and mobile applications to complete the rehabilitation of low-back and neck pain, which includes physiotherapy, home exercise, and patient education, is effective [##REF##30954161##59##]. Due to the lack of monitoring of low-back pain and neck pain applications, the current study is the first essential step to determine an evidence-based content model with 33 data elements to increase the motivation and adherence of patients to perform correct exercises. Treatment is by mobile health application. Among the advantages of this study are the use of reliable sources to extract the content of the application, the use of special features of the applications, attention to the gaps to solve them, and the validation of the content model by experts.</p>" ]
[ "<title>6. Conclusions</title>", "<p>According to the findings, a content model was presented in 3 axes. The purpose of all the different axes is to increase the patient's willingness to do exercises and the correct way to perform exercises and conservative treatment and check the progress of the treatment. It is possible to improve the course of treatment by providing the possibility of home care performing exercises in a principled manner and making the patient adhere to the continuation of the treatment. It is also possible to improve their communication with the providers through the reports sent by the patient and enable the analysis of the effectiveness of exercises. These goals are possible through approved animated exercises along with instructions on how to perform them, standard pain intensity assessment, and the use of mobile application features. Also, considering the identified gaps in Google Play applications, determining the content model of the application that is based on evidence and validated by experts is useful in improving apps in this field. Developers can use these findings as a basis for designing new applications to manage lower back pain and neck pain.</p>" ]
[ "<p>Academic Editor: Nadeem Sarwar</p>", "<title>Introduction</title>", "<p> As a complementary tool in health, the design of mobile applications to influence care and increase awareness of patients has grown a lot. The purpose of this study is to design and validate the content model of a mobile-based application for managing patients with low-back and neck pain. </p>", "<title>Methods</title>", "<p> This descriptive-analytical study was conducted in two main stages to determine the content model of the application. The first stage consisted of three steps: finding the right exercise, determining the right scale to assess the pain intensity, and determining the appropriate features of the application. In the second stage, data elements collected from the previous stage were prepared in the form of a questionnaire that was given to 12 experts in physical therapy and sports medicine for validation. After collecting the questionnaire, data elements in all parts were analyzed based on the content validity ratio (CVR) and descriptive statistics indicators. </p>", "<title>Result</title>", "<p> The content of the application was prepared in the three axes of exercises for low-back and neck pain, assessment of pain intensity, and features of the application. In the axis of sports exercises, 8 exercises for back pain and 3 exercises for neck pain were included according to the reference books. A Functional Rating Index (FRI) scale with 10 elements was selected in the axis of determining pain intensity. Also, 12 features such as the daily exercise section, using the animation, and using an audio file to explain how to do exercises were included in the model. </p>", "<title>Conclusion</title>", "<p> According to the gaps identified in the existing applications, determining the content model of the application that is based on evidence and according to the opinion of experts is useful in improving the apps. The content model of this study was presented in 3 axes to increase the patient's willingness to do exercises, the correct way to perform exercises, conservative treatment, and check the progress of the treatment. The software developers can use these findings as a basis for designing new apps to manage low-back pain and neck pain.</p>" ]
[ "<title>5. Limitations</title>", "<p>The main limitation of this research is the number of exercises, which should be increased based on acute, subacute, and chronic low-back pain and also based on types of neck pain. Also, exercises should be implemented for each patient in a personalized way. Another limitation was the use of guidelines and articles in English and Persian and not using other languages.</p>" ]
[ "<title>Acknowledgments</title>", "<p>The researchers thank all the people who participated in the research. We are also very grateful to the funders who helped us in the implementation of this research. This study was funded and supported by the Health Professions Education Research Center, Tehran University of Medical Sciences (Grant No. 1400-2-255-54238), and Sports Medicine Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran (Grant No. 1400-1-233-52037).</p>", "<title>Data Availability</title>", "<p>The data used to support the findings of this study are available from the corresponding authors upon request.</p>", "<title>Conflicts of Interest</title>", "<p>YF has received a research grant from the Sports Medicine Research Center and Health Professions Education Research Center for this work. All other authors declare that they have no competing interests.</p>" ]
[ "<fig position=\"float\" id=\"fig1\"><label>Figure 1</label><caption><p>Executive stages and details of study implementation.</p></caption></fig>", "<fig position=\"float\" id=\"fig2\"><label>Figure 2</label><caption><p>PRISMA flow diagram.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"tab1\"><label>Table 1</label><caption><p>Content of low-back and neck pain exercises.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Num</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Exercise picture</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Description</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Num</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Exercise picture</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Description</th></tr></thead><tbody><tr><td align=\"left\" colspan=\"6\" rowspan=\"1\">Low-back pain exercises</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Strengthen the less-used abdominal muscles</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Simultaneous stretching of muscles and nerves and painless walking and strong and short stretching of the low-back muscles and improving the range of motion towards the front of the waist</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Strong contraction of the abdominal muscles</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Stretch on the bar and increase the forward range of motion of the pelvis. Reduce the deflection of the front of the pelvic plate</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Strengthen the weak serine muscles (a group of three muscles that make up the buttocks)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Strengthen the muscles of the legs with special emphasis on the muscles of the front of the thighs (quadriceps muscles) and strengthen the muscles (buttocks) of the serine</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Strong and short low-back muscle stretch and improve the forward range of motion of the waist</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Strengthen leg muscles with special emphasis on front thigh muscles (quadriceps muscles) and strengthen serine muscles</td></tr><tr><td align=\"center\" colspan=\"6\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" colspan=\"6\" rowspan=\"1\">Neck pain exercises</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Strengthen the neck muscles</td><td align=\"center\" rowspan=\"2\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"2\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"2\" colspan=\"1\">Strengthen the neck muscles</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Strengthen the neck muscles</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab2\" content-type=\"sidewaystable\"><label>Table 2</label><caption><p>Comparing pain intensity indexes for low-back pain and neck pain.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Num</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Tool name</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Developer</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Goal</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Items</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Score method</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Description</th></tr></thead><tbody><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Quebec Low Back Pain Disability Scale (QBPDS) [##REF##7732471##32##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Kopec et al. [##REF##7732471##32##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Considering functional limitations related to pain, monitoring patients' progress, and comparing the evolution of LBP individuals in rehabilitation programs</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20 daily activities</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Scoring from 0 means “performing the activity without problems” and 10 means “unable to do”</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Patients should choose the score that best describes their current level of ability in each activity</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Oswestry Disability Index (ODI) [##REF##11074683##33##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Fairbank et al. [##REF##11074683##33##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">The target population of this scale is people who suffer from acute back pain. This scale is used by clinicians and researchers to quantify back pain disability</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10 daily activities</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">They are rated from 0 “I have no pain” to 5 “The pain is the worst possible”</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">It is most effective for persistent severe disability and is published in at least four formats in English and nine languages</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Roland-Morris Disability Questionnaire (RMDQ) [##REF##27081203##19##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Roland-Morrisn et al. [##REF##6222486##34##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">The target population of this scale is very suitable for patients with acute, subacute, or chronic low-back pain with mild to moderate pain</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Scale of 24, 18, and 11 questions</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Average scores</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">This scale is best suited for mild to moderate back pain disability and can be completed in person, electronically, or over the phone</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Chronic Pain Grade Questionnaire (CPGS) [##REF##1408309##35##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Von Korff et al. [##REF##1408309##35##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">For use in all chronic pain conditions including chronic musculoskeletal disorders (MSK) and back pain</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7 indicators</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Based on numerical scores, which are scored from 0 “no pain” and 10 “unbearable pain”</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">This scale was designed before the International Classification of Functioning, Disability, and Health of the World Health Organization (ICF). However, recent studies have shown that this index measures all ICF criteria</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Patient-Specific Functional (PSFS ([##UREF##10##36##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Stratford et al. [##UREF##10##36##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">To provide clinicians with a valid, reliable, responsive, and efficient outcome measure for the management of back pain and neck pain, easy to use, and applicable to a large number of clinical presentations</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11-point Likert indicators of five important activities</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">“0” indicates “unable to perform,” and “10” indicates “ability to perform at previous level”</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">It includes two stages before and after the intervention</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">P4 Screener [##REF##11203035##37##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Cole et al. [##REF##11203035##37##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Attempts were made to improve the “one-dimensional rating scale”</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4 indicators (morning, afternoon, evening, and activity during the last 2 days)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Scores from 0 (no pain) to 10 (highest possible pain level)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ability to complete in less than a minute and analyze in 5 seconds</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Neck Pain Disability Index Questionnaire (NPAD) [##REF##12131066##38##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Goolkasian et al. [##REF##12131066##38##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">This scale is specially prepared for patients with neck pain</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20 indicators</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Points based on numerical scoring</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">It is valid for assessing outcomes in patients with neck pain. It is easy to complete and grade</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Copenhagen Neck Disability Scale (CNFDS) [##UREF##11##39##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Jordan et al. [##UREF##11##39##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">A useful tool for self-care of patients with neck complaints treated with physiotherapy</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Including questions related to headaches, ability to sleep, concentration, and activities of daily living, as well as questions of a psychosocial nature</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Scoring as “yes,” “sometimes,” and “no”</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Available for patients from 20 to 75 years</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Northwick Park Questionnaire (NPQ) [##UREF##12##40##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Northwick Park Hospital</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Objective measurement for outcome assessment and symptom monitoring in patients with acute or chronic neck pain over time</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">The 9th five-part section and the 10th question are related to the comparison of the current status with the status of the last completion time</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Score based on numerical scoring</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Good reliability, high internal consistency, and sensitivity to change</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Neck Disability Index (NDI) [##REF##1834753##20##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vernon et al. [##REF##1834753##20##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Use to evaluate the condition of patients and the evolution process during treatment</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10 six-part sections</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Score based on numerical scoring</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">The target population includes people with chronic neck or upper back pain, radiculopathy, neck injuries, and thoracic disc syndrome</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Bournemouth Questionnaire (BQ) [##REF##10543579##41##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Bolton [##REF##10543579##41##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">The scale is based on ICF dimensions, which also pays attention to the emotional and cognitive aspects of neck pain and back pain. It is designed for patients with nonspecific back or neck pain</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7 questions</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Points from zero to 10 for each question</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">The first version is for measuring different dimensions of pain in patients with back pain, and the second version is for evaluating pain in patients with nonspecific neck pain</td></tr><tr><td align=\"justify\" rowspan=\"1\" colspan=\"1\">12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Functional Rating Index (FRI) [##REF##22310090##42##, ##REF##11148650##43##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Feise and Menke [##REF##11148650##43##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">To assess the condition of the neck, chest, and back, which reduces the need for multiple scales for diseases of the spine</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10 questions</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Points from 0 to 4 for each question</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Adequate validity and reliability, requiring only one minute to complete and approximately 20 seconds for clinician scoring</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab3\" content-type=\"sidewaystable\"><label>Table 3</label><caption><p>Assessment 14 specifically chosen Google Play apps by MARS.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"2\" colspan=\"1\">Num</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">MARS measurement criteria</th><th align=\"center\" rowspan=\"2\" colspan=\"1\">Index</th><th align=\"center\" colspan=\"8\" rowspan=\"1\">Back pain apps</th><th align=\"center\" colspan=\"6\" rowspan=\"1\">Neck pain apps</th></tr><tr><th align=\"center\" rowspan=\"1\" colspan=\"1\">Back pain relief exercises at home</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Back pain exercises 2</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">6-minute back pain relief</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Low-back pain relief exercises</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Lower back pain exercises</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Back pain relief exercises</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Lower back pain and sciatica relief exercises</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Back pain relief exercises at home</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Relieve neck pain</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">My neck</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Neck pain relief exercises</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Neck stretches and exercises</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Neck and shoulder pain relief exercises and stretches</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Neck and shoulder workout</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"10\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"10\" colspan=\"1\">App targets</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Increase happiness/well-being</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Reduce negative emotions</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Depression anxiety/stress</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Anger</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Behavior change</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Alcohol/substance use</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td rowspan=\"1\" colspan=\"1\"/><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td rowspan=\"1\" colspan=\"1\"/><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Goal setting</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Entertainment</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Relationships</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Physical health</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" colspan=\"17\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"11\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"11\" colspan=\"1\">App theoretical background/strategies</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Assessment</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Feedback</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Information</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Education</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Monitoring tracking</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td rowspan=\"1\" colspan=\"1\"/><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Goal setting</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Advice, tip, strategy, and skill training</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Mindfulness</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Meditation</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td rowspan=\"1\" colspan=\"1\"/><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Relaxation</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Gratitude strength-based</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" colspan=\"17\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"6\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"6\" colspan=\"1\">Technical aspects of the app</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Allows sharing (Facebook and Twitter)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td rowspan=\"1\" colspan=\"1\"/><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Has an app community</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Allows password protection</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Requires login</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Sends reminders</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Needs web access to function</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Y</td></tr><tr><td align=\"center\" colspan=\"17\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"4\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"4\" colspan=\"1\">App quality mean score (max score = 5)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Engagement</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.90</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.40</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.80</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.90</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.90</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.10</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Functionality</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.38</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.38</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.38</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.88</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Aesthetics</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.84</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.88</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.44</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.63</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.17</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.17</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.17</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.67</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Information</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.44</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.90</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.43</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.67</td></tr><tr><td align=\"center\" colspan=\"17\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">App subjective quality (max score = 20)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Deal with the user experience with the app questions</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">13.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">14.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17</td></tr><tr><td align=\"center\" colspan=\"17\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">APP-specific</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">The impact of the app on people's attitudes</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">19.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">16</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">25.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">21.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab4\"><label>Table 4</label><caption><p>Demographic distribution of participation.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"center\" colspan=\"2\" rowspan=\"1\">Demographic characteristics</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Frequency</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Percentage</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"3\" colspan=\"1\">Gender</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Male</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">33/33</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Female</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">66/67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Sum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100</td></tr><tr><td align=\"center\" colspan=\"4\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"7\" colspan=\"1\">Organizational affiliation</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Tehran University of Medical Sciences</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">50</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Shahid Beheshti University of Medical Sciences</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">16.6</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Rasht University of Medical Sciences</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.3</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Hamedan University of Medical Sciences</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.3</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Iran University of Medical Sciences</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.3</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Sports and Exercise Medicine Research Center</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.3</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Sum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100</td></tr><tr><td align=\"center\" colspan=\"4\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"7\" colspan=\"1\">Academic rank</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Assistant professor</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">41/6</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Associate professor</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">16/6</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Professor</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">16/6</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Physiotherapy specialist</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8/3</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Fellowship</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8/3</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Sports medicine specialist</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8/3</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Sum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tab5\"><label>Table 5</label><caption><p>The final content model created in this study by 33 data elements.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Axis name</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Number</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Main data elements</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Mean<sup>∗</sup></th><th align=\"center\" rowspan=\"1\" colspan=\"1\">CVR<sup>∗∗</sup></th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"12\" colspan=\"1\">Exercise-based book</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Low-back pain exercise 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/83</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Low-back pain exercise 2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/83</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Low-back pain exercise 3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Low-back pain exercise 4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Low-back pain exercise 5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Low-back pain exercise 6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Low-back pain exercise 7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Low-back pain exercise 8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Neck pain exercise 1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Neck pain exercise 2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/67</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Neck pain exercise 3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/67</td></tr><tr><td align=\"center\" colspan=\"2\" rowspan=\"1\">Total</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/89</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/79</td></tr><tr><td align=\"center\" colspan=\"5\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"11\" colspan=\"1\">Pain intensity rating based on FRI</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Pain intensity</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Sleeping</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Personal care (washing, dressing, etc.)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Travel (driving, etc.)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Work</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Recreation</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Frequency of pain</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Lifting</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Walking</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Standing</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" colspan=\"2\" rowspan=\"1\">Total</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" colspan=\"5\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"13\" colspan=\"1\">Application capability-based app review</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">The daily exercise section and the exercises prescribed by the physiotherapist</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Use animation to show exercises</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Using an audio file to explain how to do exercises</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Playing background music while doing exercises</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/66</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Display the number of exercises performed in the application</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/83</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Increase or decrease the number of exercises</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/83</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/66</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Training for back pain and neck pain</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Using text, audio, and video for daily activities</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Pain intensity assessment with FRI scale</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Report section (number of exercises performed and FRI score)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/92</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/83</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">The ability to send warnings and reminders along with notes</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Access to the application with username and password</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"center\" colspan=\"2\" rowspan=\"1\">Total</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/94</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0/92</td></tr></tbody></table></table-wrap>" ]
[]
[]
[]
[]
[]
[]
[ "<table-wrap-foot><fn><p>\n<sup>∗</sup>Mean: average responses of people regarding the necessity of the item (number between 1 and 5). <sup>∗∗</sup>CVR: the number of experts who declared the item important or very important (scores 4 and 5) divided by the total number of experts.</p></fn></table-wrap-foot>" ]
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M."], "article-title": ["Neck pain"], "source": ["\n"], "italic": ["Journal of Orthopaedic & Sports Physical Therapy"], "year": ["2008"], "volume": ["38"], "issue": ["9"], "fpage": ["A1"], "lpage": ["A34"], "pub-id": ["10.2519/jospt.2008.0303", "2-s2.0-51949093261"]}, {"label": ["50"], "person-group": ["\n"], "surname": ["Foroutani", "Nakhostin Ansari", "Ansari", "Jalaei"], "given-names": ["H.", "N.", "N.", "S."], "article-title": ["Investigating the responsiveness of the Persian version of functional rating index in patients with chronic non-specific neck pain: brief report"], "source": ["\n"], "italic": ["Tehran University Medical Journal TUMS Publications"], "year": ["2018"], "volume": ["76"], "issue": ["7"], "fpage": ["498"], "lpage": ["502"]}, {"label": ["52"], "person-group": ["\n"], "surname": ["Chiensriwimol", "Mongkolnam", "Chan"], "given-names": ["N.", "P.", "J. H."], "article-title": ["Frozen shoulder rehabilitation: exercise simulation and usability study"], "conf-name": ["Proceedings of the Ninth International Symposium on Information and Communication Technology"], "conf-date": ["2018"], "conf-loc": ["New York"]}, {"label": ["53"], "person-group": ["\n"], "surname": ["Chandra", "Oakley", "Silva"], "given-names": ["H.", "I.", "H."], "article-title": ["Designing to support prescribed home exercises: understanding the needs of physiotherapy patients"], "conf-name": ["Proceedings of the 7th Nordic Conference on Human-Computer Interaction: Making Sense Through Design"], "conf-date": ["2018"], "conf-loc": ["New York"]}, {"label": ["55"], "person-group": ["\n"], "surname": ["Ramos-Remus", "Salcedo-Rocha", "Prieto-Parra", "Galvan-Villegas"], "given-names": ["C.", "A. L.", "R. E.", "F."], "article-title": ["How important is patient education?"], "source": ["\n"], "italic": ["Best Practice & Research Clinical Rheumatology"], "year": ["2000"], "volume": ["14"], "issue": ["4"], "fpage": ["689"], "lpage": ["703"], "pub-id": ["10.1053/berh.2000.0107", "2-s2.0-0034543459"]}, {"label": ["57"], "person-group": ["\n"], "surname": ["Papageorgiou", "Strigkos", "Politou", "Alepis", "Solanas", "Patsakis"], "given-names": ["A.", "M.", "E.", "E.", "A.", "C."], "article-title": ["Security and privacy analysis of mobile health applications: the alarming state of practice"], "source": ["\n"], "italic": ["Ieee Access"], "year": ["2018"], "volume": ["6"], "fpage": ["9390"], "lpage": ["9403"], "pub-id": ["10.1109/ACCESS.2018.2799522", "2-s2.0-85041327423"]}]
{ "acronym": [], "definition": [] }
59
CC BY
no
2024-01-14 23:41:55
Int J Telemed Appl. 2024 Jan 5; 2024:8415777
oa_package/50/5b/PMC10787052.tar.gz
PMC10787053
0
[ "<title>1. Introduction</title>", "<p>\n<italic>Salmonella</italic> is a genus that belongs to the family <italic>Enterobacteriaceae</italic>, a Gram-negative facultative anaerobic bacterium, and is regarded as one of the most concerning zoonotic bacteria in the world [##REF##31918736##1##, ##UREF##0##2##]. <italic>Salmonella</italic> is naturally present in the gastrointestinal tracts of many species of animals, including humans, birds, reptiles, and livestock [##UREF##1##3##, ##UREF##2##4##]. The species <italic>S. enterica</italic> is comprised of six subspecies: indica, salamae, enterica, houtenae, arizonae, and diarizonae. It is estimated to have more than 2659 serovars, which are divided into 60 serogroups [##UREF##3##5##, ##UREF##4##6##]. According to the current nomenclature, <italic>Salmonella</italic> spp. is taxonomically classified into two species: <italic>S. bongori</italic> and <italic>S. enterica</italic> [##REF##20093681##7##]. <italic>Salmonella</italic> is generally considered a normal constituent of the reptilian intestinal microbiota with a subclinical presentation [##REF##31918736##1##]. Nevertheless, some reptiles harbor and shed <italic>Salmonella</italic> spp. asymptomatically in their faeces, and up to 90% of them are considered reservoirs for the bacteria [##REF##21660846##8##]. In South Africa, <italic>Salmonella</italic> serovars have previously been documented in farmed crocodiles and a few other, mostly captive reptiles [##REF##9551479##9##]. However, the association of reptile-associated <italic>Salmonella</italic> in South Africa is largely unknown.</p>", "<p>There have even been several outbreaks of human salmonellosis associated with reptiles from various countries [##REF##21660846##8##, ##REF##14711697##10##, ##REF##19841114##11##]. Assessing the risk of humans being infected through direct contact with reptiles becomes challenging due to the lack of a robust understanding of the natural occurrence of <italic>Salmonella</italic> spp. circulating in reptiles and their propensity to switch hosts [##REF##31918736##1##]. The risk of zoonotic disease is higher with the transmission of multidrug-resistant <italic>Salmonella</italic> spp. strains. The presence of plasmids, transposons, integrons, and insertion sequences can contribute to the development of antibiotic resistance [##REF##30408462##12##, ##REF##35208768##13##]. There have been numerous studies on antibiotic resistance genes identified in <italic>Salmonella</italic> spp. [##REF##30408462##12##–##UREF##5##14##]. Most virulence and resistance genes have been transferred between species by horizontal gene transfer (HGT) [##REF##23554414##15##]. Virulence plasmids, pili, and enterotoxins are among the reported <italic>Salmonella</italic> pathogenicity islands (SPIs) [##UREF##6##16##]. Virulence mechanisms are required to defeat host defense systems, and the development of antimicrobial resistance is required to allow pathogenic bacteria to overcome antimicrobial therapy and adapt to and thrive in competitive and demanding environments [##REF##23554414##15##, ##REF##15207870##17##, ##UREF##7##18##]. The virulence genes contribute to pathogenesis through host cell attachment and overcoming host defense mechanisms [##UREF##5##14##]. Infection and virulence are often associated with antibiotic resistance, as seen in biofilm-producing bacteria or intracellular infections [##REF##23554414##15##, ##UREF##6##16##]. Therefore, the aim of this study was to determine the prevalence of <italic>Salmonella</italic> spp. in various wild reptile species and to evaluate their antimicrobial resistance and virulence gene profiles. The remarkable array of reptile diversity in this region acts as a catalyst for the exploration of antibiotic resistance, with ultimate benefits for reptile conservation.</p>" ]
[ "<title>2. Materials and Methods</title>", "<title>2.1. Field Site</title>", "<p>The Timbavati Private Game Reserve is situated between 24°24′S and 31°21′E. It covers an area of 550 km<sup>2</sup> and is located on the central west border of Kruger National Park. The reserve comprises <italic>Combretum apiculatum</italic>, <italic>Acacia nigrescens</italic>, and <italic>Colophospermum mopane</italic> as the dominant vegetation types, with mostly granite or basalt as the principal soil types [##UREF##8##19##].</p>", "<title>2.2. Collection of Samples</title>", "<p>Samples were collected from wild reptiles (<italic>n</italic> = 19) in the Timbavati Private Game Reserve in the Limpopo Province. Collection consisted of active searching for wild reptiles and their subsequent release after sampling. Snakes were placed in transparent plastic tubes before sampling, while other reptiles were restrained by hand [##UREF##9##20##]. Sterile cotton transport swabs (Transystem™) were used to swab the cloaca of the reptiles and were stored at 4°C during field work [##REF##31695452##21##]. The transport medium provides a nonnutritive environment that maintains the viability of microorganisms while restricting growth until samples can be processed.</p>", "<title>2.3. Isolation, Identification, and Serotyping of <italic>Salmonella</italic> Isolates</title>", "<p>The cloacal swabs were pre-enriched in buffered peptone water (BPW Oxoid, Biolab, South Africa) at 37°C for 24 hours. A loopful of the bacterial cells in buffered peptone water was streaked onto xylose-lysine-deoxycholate agar (Merck, Wadeville, South Africa) and Brilliant Green agar (Scharlau Chemie S.A. Barcelona, Spain). The streaked plates were then incubated at 37°C for 24 hours. The colonies were examined for their morphological appearance on the plate (colonies with or without black centers, colorless, or opaque-white colonies surrounded by pink or red zones on XLD). The suspected <italic>Salmonella</italic> spp. colonies, those with glossy large black centers or almost black colonies, were examined for pure culture isolation on BGA. Between three and five colonies were selected and purified on nutrient agar (Merck, Wadeville, South Africa) and incubated at 37°C for 18 to 24 hours.</p>", "<title>2.4. DNA Extraction and Molecular Identification of <italic>Salmonella</italic> Serovars Using <italic>invA</italic> Gene</title>", "<p>The bacterial genomic DNA was extracted using a genomic DNA extraction kit (Invitrogen, USA) from pure cultures. A NanoDrop spectrophotometer was used to measure the DNA concentrations. For the <italic>invA</italic> gene, PCR was carried out using the forward (GTG AAA TTA TCG CCA CGT TCG GGC AA) and reverse (TCA TCG CAC CGT CAA AGG AAC C) oligonucleotide primers with a reaction volume of 25 <italic>μ</italic>L, containing: 8.5 <italic>μ</italic>L nuclease-free water, 12.5 <italic>μ</italic>L PCR Master Mix, 2 <italic>μ</italic>L template DNA, and 1 <italic>μ</italic>L of each primer utilizing an Engine T100 ThermalTM cycler (BioRad, Singapore). The thermal cycling conditions included an initial step of denaturation at 94°C for 5 minutes, then 30 cycles of denaturation at 94°C for 45 seconds, annealing at 58°C for 45 seconds, and extension at 72°C for 70 minutes, followed by a single, concluding extension step at 72°C for 7 minutes [##REF##35208768##13##].</p>", "<title>2.5. Identification of <italic>Salmonella</italic> Species Using 16S rRNA</title>", "<p>All the positive samples for <italic>inv</italic>A were subjected to 16S rRNA for sequencing. The bacterial universal primers (27F: AGA GTT TGA TCM TGG CTC AG and 1492R: GGT TAC CTT GTT ACG ACT T) targeting the 16S rRNA gene segment were used for molecular identification using PCR. The PCR conditions were as follows: initial denaturation step at 96°C for 4 minutes, followed by 30 cycles of denaturation at 94°C for 30 seconds, annealing at 57°C for 30 seconds, and extension at 72°C for 1 minute, and finally, a single and final extension step at 72°C for 10 minutes [##UREF##10##22##].</p>", "<title>2.6. Sequencing of PCR Amplicons</title>", "<p>The PCR products were sequenced at Inqaba Biotechnical Industries (Pty) Ltd., Pretoria, South Africa. The FintchTV [##UREF##11##23##] was used to edit the base pairs of the sequence chromatograms. Sequence identity was evaluated using the nucleotide Basic Local Alignment Search Tool nucleotide (BLASTn) on the NCBI website (<ext-link xlink:href=\"https://blast.ncbi.nlm.nih.gov/Blast.cg\" ext-link-type=\"uri\">https://blast.ncbi.nlm.nih.gov/Blast.cg</ext-link>). The generated <italic>16S</italic> rRNA gene sequences were submitted to the GenBank database and assigned with the accession numbers as follows: OP683334–OP683363.</p>", "<title>2.7. Detection of Virulence Genes among <italic>Salmonella</italic> Serovars</title>", "<p>All <italic>Salmonella</italic> spp. isolates were subjected to PCR screening for 17 (Supplementary <xref rid=\"supplementary-material-1\" ref-type=\"sec\">Table S1</xref>) virulence genes [##UREF##6##16##, ##UREF##12##24##]. A PCR mix (25 <italic>μ</italic>L) was used, consisting of 8.5 <italic>μ</italic>L nuclease-free water, 12.5 <italic>μ</italic>L PCR, 2X DreamTaq Green Master Mix (Thermo-Fisher Scientific, South Africa), 2 <italic>μ</italic>L template DNA, and 1 <italic>μ</italic>L of each primer. The following PCR parameters were applied: 94°C for 5 minutes, 30 cycles of 94°C for 45 seconds, annealing temperatures (for each gene as shown in Supplementary <xref rid=\"supplementary-material-1\" ref-type=\"sec\">Table S1</xref>) for 45 seconds, and 72°C for 1 minute; and 72°C for 10 minutes.</p>", "<title>2.8. Antimicrobial Susceptibility Testing</title>", "<p>Based on the guidelines of the Clinical and Laboratory Standards Institute (CLSI 2023) [##UREF##13##25##], <italic>Salmonella</italic> isolates were tested for their antimicrobial susceptibility to 13 different antimicrobial agents using the Kirby–Bauer disc diffusion method on Mueller–Hinton Agar (Oxoid Ltd., Basingstoke, UK). Antibiotics used in this study were streptomycin (30 <italic>μ</italic>g), ciprofloxacin (5 <italic>μ</italic>g), nalidixic acid (30 <italic>μ</italic>g), gentamicin (10 <italic>μ</italic>g), and kanamycin (30 <italic>μ</italic>g). Resistance to two or more antimicrobials of different classes was considered to be multidrug-resistant (MDR) [##UREF##14##26##].</p>", "<title>2.9. Detection of Antibiotic Resistance Genes</title>", "<p>All the <italic>Salmonella</italic> spp. were tested for the presence of quinolone (<italic>qnrA</italic>, <italic>qnrS</italic>, <italic>parC</italic>, and <italic>aac</italic>(<italic>6</italic>′)<italic>-Ib-cr</italic>) and aminoglycoside (<italic>strA</italic>, <italic>strB</italic>, and <italic>aac</italic>(<italic>6</italic>′)-<italic>Ib</italic>) resistance genes [##REF##24630248##27##–##UREF##15##29##]. Antibiotic resistance genes were detected using the primers and annealing temperatures as shown in Supplementary <xref rid=\"supplementary-material-1\" ref-type=\"sec\">Table S2</xref>.</p>" ]
[ "<title>3. Results</title>", "<title>3.1. Occurrence of <italic>Salmonella</italic> Serovars in Reptiles Using <italic>invA</italic> and 16S rRNA</title>", "<p>A total of 19 samples were collected from lizards (<italic>n</italic> = 6), snakes (<italic>n</italic> = 3), chameleons (<italic>n</italic> = 7), and tortoises (<italic>n</italic> = 3). From these, a total of 30 <italic>Salmonella</italic> spp. isolates were recovered from the various reptile species (##TAB##0##Table 1##). Based on nucleotide BLAST results of 16S rRNA sequences detected, <italic>Salmonella</italic> serovars/species were <italic>S</italic>. Salamae (<italic>n</italic> = 9; 30%), <italic>S</italic>. <italic>enterica</italic> (<italic>n</italic> = 5; 16.7%), <italic>S</italic>. Typhimurium (<italic>n</italic> = 4; 13.3%), <italic>S</italic>. Indiana (<italic>n</italic> = 4; 13.3%), and one for <italic>Salmonella enterica</italic> subsp. <italic>enterica</italic> serovar Abony, <italic>S. enterica</italic> subsp. <italic>enterica</italic> serovar Houtenae, <italic>S. enterica</italic> subsp. <italic>enterica</italic> serovar Waycross, <italic>S. enterica</italic> subsp. <italic>enterica</italic> serovar Typhi, <italic>S. enterica</italic> subsp. <italic>enterica</italic> serovar Kentucky, <italic>S. enterica</italic> subsp. <italic>enterica</italic> serovar Newlands, <italic>S. enterica</italic> subsp. <italic>enterica</italic> serovar Worthington, and <italic>S. enterica</italic> subsp. <italic>enterica</italic> serovar Paratyphi C.</p>", "<title>3.2. Detection Rate and Distribution of Virulence Genes in Various Serotypes</title>", "<p>A total of 30 <italic>Salmonella</italic> spp. isolates harbored either one or more different virulence genes investigated in this study, with sixteen out of seventeen virulence genes detected in this study (##FIG##0##Figure 1##). The distribution of virulence genes among each <italic>Salmonella</italic> isolate is shown on the heatmap (##FIG##1##Figure 2##). The majority of these isolates harbored the following genes; <italic>pag</italic>N (<italic>n</italic> = 30; 100%), <italic>hil</italic>A (<italic>n</italic> = 29; 96.7%), <italic>ssr</italic>B (<italic>n</italic> = 29; 96.7%), <italic>prg</italic>H (<italic>n</italic> = 26; 86.7%), <italic>mar</italic>T (<italic>n</italic> = 26; 86.7%), <italic>mgt</italic>C (<italic>n</italic> = 22; 73.3%), <italic>bap</italic>A (<italic>n</italic> = 21; 70%), <italic>pag</italic>C (<italic>n</italic> = 20; 66.7%), <italic>sip</italic>B (<italic>n</italic> = 19; 63.3%), <italic>cdt</italic>B (<italic>n</italic> = 17; 56.7%), <italic>vex</italic>A (<italic>n</italic> = 12; 40%), <italic>nlp</italic>I (<italic>n</italic> = 14; 46.7%), <italic>pef</italic>A (<italic>n</italic> = 9; 30%), <italic>oaf</italic>A (<italic>n</italic> = 2; 6.7%), <italic>spv</italic>R (<italic>n</italic> = 2; 6.7%), and <italic>sop</italic>B (<italic>n</italic> = 1; 3.3%). The <italic>spv</italic>B gene was not detected in any of the 30 isolates.</p>", "<title>3.3. Antibiotic Susceptibility and Resistant Genes of <italic>Salmonella</italic> Isolates</title>", "<p>\n<italic>Salmonella</italic> isolates in this study had the highest antibiotic resistance rates against nalidixic acid (13; 43.3%) (95% CI: 0.25 ± 0.62), kanamycin (13; 43.3%) (95% CI: 0.25 ± 0.62), streptomycin (5; 16.7%) (95% CI: 0.03 ± 0.31), and ciprofloxacin (1; 3.3%) (95% CI: −0.03 ± 0.0.10) using antibiotic disk diffusion assays (DDA). All 30 (95% CI: 0 ± 0) <italic>Salmonella</italic> isolates were susceptible to gentamicin. Out of the 30 isolates, nine (30%) <italic>Salmonella</italic> serovars harbored more than one antibiotic resistance gene. The distribution of the antibiotic resistance genes for each <italic>Salmonella</italic> isolate is shown on the heatmap (##FIG##1##Figure 2##). PCR was carried out for <italic>Salmonella</italic> isolates to screen for eight antibiotic resistance genes (ARGs). Out of 30 <italic>Salmonella</italic> isolates, the prevalence of the ARGs: <italic>strA</italic>, <italic>strB</italic>, <italic>qnrA</italic>, <italic>qnrS</italic>, <italic>parC</italic>, <italic>aadA</italic>, <italic>aac</italic>(<italic>6ˊ</italic>)-<italic>Ib</italic>, and <italic>aac(6ˊ)-Ib-cr</italic> genes was 10; 33.3%, 2; 6.7%, 5; 16.7, 4; 13.3%, 3; 10%, 7; 23.3%, 2; 6.7%, and 3; 10%, respectively. Among <italic>Salmonella</italic> serovars strains, the presence of the quinolones (<italic>qnr</italic>A, <italic>qnr</italic>S, and <italic>par</italic>C) genes correlated with phenotypic susceptibility.</p>" ]
[ "<title>4. Discussion</title>", "<p>Reptiles carry zoonotic pathogens that cause a variety of infectious diseases in both humans and other animals [##UREF##4##6##]. They are becoming increasingly appealing as pets and are popular attractions at wildlife education centers [##UREF##9##20##]. Although the clinical relevance of <italic>Salmonella</italic> infections in wild and captive reptiles is poorly understood, it is believed that the majority of infections results in an asymptomatic carrier condition and do not cause disease in reptiles [##UREF##4##6##]. <italic>S. enterica</italic> subsp. <italic>enterica</italic> serovar Houtenae has been associated with abdominal abscesses in a severely diseased captive African fat-tailed gecko [##UREF##16##30##].</p>", "<p>Our study confirmed that reptiles are reservoirs of multiple <italic>Salmonella</italic> serovars. There were a number of <italic>Salmonella</italic> serovars detected in different reptiles that are of public health concern and included <italic>S</italic>. <italic>enterica</italic>, <italic>S</italic>. Typhimurium, <italic>S</italic>. Indiana, <italic>S</italic>. Houtenae, <italic>S</italic>. Waycross, <italic>S</italic>. Typhi <italic>S</italic>. Kentucky, <italic>S</italic>. Newlands, <italic>S</italic>. Worthington, and <italic>S</italic>. Paratyphi C [##REF##32349343##31##–##UREF##19##34##].</p>", "<p>From a host-reservoir perspective, chameleons (<italic>Chamaeleo dilepis</italic>) were the most frequently infected with <italic>Salmonella</italic> serovars, i.e., <italic>S</italic>. <italic>enterica</italic>, <italic>S</italic>. Indiana, <italic>S</italic>. Salamae, <italic>S</italic>. Typhi, and <italic>S</italic>. Kentucky. The prevalence rates of <italic>Salmonella</italic> serovars among chameleons, lizards, snakes, and tortoises were 36.8%, 31.6%, 15.8%, and 15.8%, respectively. These findings differ in terms of the frequency of <italic>Salmonella</italic> spp. occurrence in various sectors of captive reptiles in Europe. Higher (76.9%) prevalences of <italic>Salmonella</italic> spp. were recorded in pet snakes, lizards, and tortoises from Poland [##UREF##3##5##], 64.5% in snakes and lizards from Norwegian zoos [##REF##31918736##1##], and 32.6% in domestic snakes, chameleons, and lizards from central Europe [##UREF##20##35##], 43.28% of the pet reptiles carried from Western Romania [##UREF##21##36##], and 50.0% of the lizard from Fernando de Noronha Archipelago (Brazil) [##UREF##22##37##]. The current study is one of the few studies to isolate <italic>Salmonella</italic> serovars from wild reptiles.</p>", "<p>The majority of salmonellosis illnesses are associated with a wide range of serotypes of <italic>S</italic>. <italic>enterica</italic> subsp. <italic>enterica</italic> (I) and are primarily transmitted through tainted food and water [##UREF##16##30##, ##REF##22885752##38##–##UREF##24##40##]. In some parts of the world, pet reptiles provide a significant source of protein for human populations, and in so doing, a transmission route for <italic>Salmonella</italic> is established. All reptiles are exploited for human consumption, but turtles are heavily exploited, while crocodiles, snakes, and lizards may be important locally [##UREF##25##41##, ##UREF##26##42##]. Indeed, there have been numerous reports of reptile-associated salmonellosis in humans, especially in children [##UREF##9##20##, ##UREF##27##43##, ##REF##22835051##44##].</p>", "<p>\n<italic>Salmonella</italic> pathogenicity island 1 is essential for the interaction between <italic>Salmonella</italic> and host cells. <italic>Salmonella</italic> invades epithelial cells through SPI-1 (44). Two SPI-1 genes that encode components of the SPI-1 T3SS apparatus, <italic>invF</italic> and <italic>sicA</italic>, are directly regulated by the <italic>OmpR</italic>/<italic>ToxR</italic> transcriptional regulator HilA [##UREF##28##45##, ##REF##11442828##46##]. Moreover, enterocolitis and human intestinal epithelial cell invasion may be influenced by the regulation of virulence factors including <italic>HilA</italic>, <italic>invA</italic>, and SPI-1 effectors such as <italic>SipA</italic> and <italic>SopABD</italic> [##REF##20822940##47##, ##REF##29045813##48##].</p>", "<p>\n<italic>Salmonella's</italic> intracellular pathogenicity cycle begins with the invasion of intestinal epithelial cells, controlled by the <italic>invA</italic> gene [##REF##30936672##49##]. <italic>Salmonella</italic>-specific gene sequences encode the <italic>InvA</italic> protein that is essential for gut epithelial invasion [##REF##34712421##50##]. The results showed that all <italic>Salmonella</italic> isolates tested positive for the <italic>invA</italic> gene. This is in agreement with the findings of previous studies (12, 13, 21, 22, 37, and 49). It is not surprising because <italic>InvA</italic> is used for molecular identification of these <italic>Salmonella</italic> isolates [##REF##32818228##51##]. Virulence gene profiles showed that all the <italic>Salmonella</italic> serovars isolated in this study were positive for <italic>pag</italic>N, <italic>hil</italic>A, <italic>ssr</italic>B, <italic>prg</italic>H, and <italic>mar</italic>T (100%), (96.7%), (96.7%), (86.7%), and (86.7%), respectively. Similar genes were detected in <italic>Salmonella</italic> species isolated from retail beef samples in selected KwaZulu-Natal municipality areas and in livestock production systems (cattle, sheep, goats, pigs, ducks, and chickens) in the Eastern Cape and KwaZulu-Natal provinces of South Africa [##UREF##29##52##, ##REF##31405078##53##].</p>", "<p>Virulence plasmid operons (<italic>spvRABCD</italic>) are expressed by intracellular environments in host cells and are involved in survival, intracellular growth, and macrophage death [##REF##30143595##54##, ##REF##38023281##55##]. The <italic>spv</italic>R gene was detected in one (3.3%) sample. This observation was different from the findings of a study conducted by Derakhshandeh et al. [##REF##24426086##56##] on humans, where they reported that the prevalence of <italic>spv</italic>B, <italic>spv</italic>C, and <italic>spv</italic>R genes was 26 (43.3%), 44 (73.3%), and 28 (46.6%), respectively. The study on humans and animals reported in 2008 by Amini et al. [##UREF##30##57##] showed that the <italic>spv</italic>B and <italic>spv</italic>C genes were detected in 90% of the isolates. In the current study, the <italic>spv</italic>B gene was not detected in any of the 30 isolates. In Burkina Faso, Nikiema et al. [##UREF##31##58##] detected <italic>spvR</italic> and <italic>spvC</italic> genes at 36.8% and 48.1%, respectively, from 106 <italic>Salmonella</italic> isolates (77 human stools and 14 sandwiches). The <italic>spvC</italic> gene resides on plasmids and plays an important role in adhesion and systemic infection of host cells [##REF##20039795##59##]. The <italic>SipC</italic> protein also targets F-actin, which is critical for the internalization and invasion of pathogens [##REF##34712421##50##]. In consideration of the low level of detection of the <italic>spv</italic> gene in wild reptiles, there is a need to expand the surveillance to a broader host range over a larger geographical area.</p>", "<p>Of the 17 virulence genes screened in this study, 13 are located on <italic>Salmonella</italic> pathogenicity islands (SPIs). All <italic>Salmonella</italic> isolates in this study exhibited high detection rates for virulence genes located on the SPIs, indicating the genes were widely distributed. The SPI-1 genes <italic>sip, hil</italic>, and <italic>prg</italic> encode regulators that produce T3SS effector proteins, assist in <italic>Salmonella</italic> colonization and invasion of intestinal epithelial cells, and can trigger macrophage necrosis and inflammatory responses [##UREF##6##16##].</p>", "<p>Several researchers have recently reported the presence of antibiotic residues in reptiles and antibiotic-resistant bacteria [##UREF##3##5##–##REF##20093681##7##, ##UREF##32##60##]. However, drug resistance in reptiles is relatively uncommon in reptile-associated <italic>Salmonella</italic> [##UREF##32##60##]. Although the prevalence of antimicrobial resistance was not very high in this study, <italic>S</italic>. Worthington had the widest range of antibiotic resistance (60%). High antibiotic resistance prevalence was observed for nalidixic acid (43.3%) and kanamycin (43.3%). In comparison to <italic>Salmonella</italic> isolates in water samples in the Philippines, resistance to kanamycin was higher at 75.4% [##UREF##33##61##]. On the other hand, there is a reported high (95.4%) nalidixic acid resistance by <italic>Salmonella</italic> isolates obtained from broiler and layer chicken farms [##UREF##34##62##]. Thirty-three isolates (33.3%) of <italic>Salmonella</italic> serovars were resistant to at least one antimicrobial drug. Similar findings were reported in studies involving <italic>Salmonella</italic> serovars isolated from reptiles from Taiwan, Trinidad, and Malaysia and their sensitivity to aminoglycosides and quinolones [##REF##20093681##7##, ##REF##10813610##63##, ##UREF##35##64##]. In the same study by Chen et al. [##REF##20093681##7##], as well as a study from Lithuania, <italic>Salmonella</italic> serovars isolates from reptiles most frequently displayed resistance to streptomycin and tetracycline [##UREF##4##6##, ##REF##20093681##7##], and in a study from Poland, the highest antibiotic resistance was detected against streptomycin [##UREF##9##20##]. In a study conducted by Dégi et al. [##UREF##36##65##] in Romania, <italic>Salmonella</italic> serovars isolated from reptiles were resistant to ceftriaxone, ciprofloxacin, vancomycin, cefoxitin, pristinamycin, ampicillin/sulbactam, and gentamicin. In contrast to our results, Abrahão et al. [##UREF##22##37##] have reported 13.3% of isolates from lizard resistant to colistin in Brazil. Given this growing evidence for antibiotic resistance, the importance of reptile-associated <italic>Salmonella</italic> spp. infections to medical research and public health should not be overlooked.</p>", "<p>\n<italic>Salmonella enterica</italic> subsp. <italic>enterica</italic> serovar isolates from this study were resistant to aminoglycosides and quinolone classes of antibiotics. The same antibiotic resistance gene profiles were detected in <italic>Salmonella</italic> serovars isolated from other animals, including commercial chickens, as well as humans in South Africa [##UREF##37##66##–##UREF##39##70##]. Similar antibiotic resistance genes (<italic>strA</italic>, <italic>strB</italic>, and <italic>aadA</italic>) were also detected in reptiles in Poland [##UREF##9##20##]. Both <italic>strA</italic> and <italic>strB</italic> genes encode aminoglycoside-3″-phosphotransferase (APH(3″)-Ib) and aminoglycoside-6-phosphotransferase (APH(6)-Id) proteins that confer streptomycin resistance, respectively [##UREF##40##71##].</p>", "<p>Strains typically pose a high risk for the spread of resistance genes to other microbiota as well as for the treatment of infections [##REF##34737424##72##]. Antimicrobial resistance is rapidly developing and spreading due to interactions between human, animal, and environmental factors [##UREF##38##67##]. There was a correlation between the presence of the quinolones (<italic>qnrA</italic>, <italic>qnrS</italic>, and <italic>parC</italic>) genes and the phenotypic susceptibility of the <italic>Salmonella</italic> serovar strains. Fluoroquinolones are widely used in veterinary practice, but no data involving the incidence of resistance exist [##REF##20409393##69##]. Further research is needed to investigate the possible relationships of microorganism transfer between reptiles and other hosts.</p>", "<title>4.1. Limitation of the Study</title>", "<p>The main drawback of dealing with wild reptiles is how difficult it is to obtain more specimen samples. When it comes to reptile research and surveys, Africa is far less advanced than other continents [##UREF##41##73##]. Areas where reptiles occur in South Africa are usually remote and challenging to work with and sample in, which creates a sampling bias at times, which makes it very difficult for the collection of wild datasets [##UREF##42##74##]. In Barends et al. [##UREF##42##74##] work in what is irrefutably the most famous park or reserve in South Africa (Kruger National Park) to examine reptile species presence within the 1 km resolution, 92% of KNP would be considered “data deficient” for reptile occurrence. As mentioned in our methods section, Timbavati borders KNP and has the same “big five” (lion, leopard, rhino, buffalo, and elephant) dangers for field researchers in terms of sampling [##UREF##8##19##, ##UREF##42##74##].</p>" ]
[ "<title>5. Conclusions</title>", "<p>According to our knowledge, this is the first study reporting on the occurrence, antibiotic resistance, and virulence profiles of <italic>Salmonella</italic> serovars from wild reptiles in South Africa. Chameleons had the highest infection rates for <italic>Salmonella</italic> serovars, followed by lizards, snakes, and turtles. Reptiles can serve as a reservoir for pathogenic bacteria such as <italic>Salmonella</italic>; hence, precautions should be taken when caring for and transporting them, as well as when keeping them in close contact with other animals. There is optimism for effective antibiotic therapy in the case of infection due to the low level of drug resistance of the reptile <italic>Salmonella</italic> serovars detected in the current study. The findings highlight the need for educational efforts aimed at reducing reptile-related infections. As previous literature cited in this study has mentioned that the prevalence of <italic>Salmonella</italic> appears higher in captive reptiles elsewhere in the world, we suggest the next logical step would be an investigation of <italic>Salmonella</italic> prevalence in captive reptiles in the South African pet trade, and with a particular focus on nonnative popular species.</p>" ]
[ "<p>Academic Editor: Todd R. Callaway</p>", "<p>Reptiles are carriers of an array of microorganisms, including significant zoonotic bacteria of the genus <italic>Salmonella</italic>, which cause a disease referred to as salmonellosis that affects both animals and humans. This study investigated the occurrence of <italic>Salmonella</italic> serovars in wild reptiles at Timbavati Private Game Reserve in Limpopo Province, South Africa, and examined their virulence and antimicrobial resistance gene profiles. A total of 19 wild reptiles were sampled, which resulted in 30 presumptive <italic>Salmonella</italic> isolates. The isolates were identified using polymerase chain reaction (PCR) by amplifying the <italic>invA</italic> gene and were further confirmed by <italic>16S</italic> rRNA gene sequencing. <italic>Salmonella</italic> serovars were detected in chameleons (36.8%), lizards (31.6%), snakes (15.8%), and tortoises (15.8%). The use of 16S rRNA gene sequencing revealed that <italic>Salmonella enterica</italic> subsp. <italic>enterica</italic> serovar Salamae (30%), <italic>S</italic>. <italic>enterica</italic> subsp. <italic>enterica</italic> (16.7%), <italic>S</italic>. <italic>enterica</italic> subsp. <italic>enterica</italic> serovar Typhimurium (13.3%), and <italic>S</italic>. <italic>enterica</italic> subsp. <italic>enterica</italic> serovar Indiana (13.3%) were the four most common subspecies among the investigated 30 isolates. Detected virulence genes included <italic>pag</italic>N (100%), <italic>hil</italic>A (96.7%), <italic>ssr</italic>B (96.7%), <italic>prg</italic>H (86.7%), and <italic>mar</italic>T (86.7%). The isolates exhibited resistance to nalidixic acid (43.3%) and kanamycin (43.3%), followed by streptomycin (16.7%) and ciprofloxacin (3.3%). Antibiotic-resistant genes were detected as follows: <italic>strA</italic>, <italic>strB</italic>, <italic>qnrA</italic>, <italic>qnrS</italic>, <italic>parC</italic>, <italic>aadA</italic>, <italic>aac</italic>(<italic>6</italic>′)-<italic>Ib</italic>, and <italic>aac</italic>(<italic>6</italic>′)<italic>-Ib-cr</italic> at 33.3%, 6.7%, 16.7, 13.3%, 10%, 23.3%, 6.7%, and 10%, respectively. The findings highlight the necessity of educational initiatives aimed at reducing reptile-related infections. Effective antibiotic treatment appears promising for infection, given the minimal drug resistance observed in reptile <italic>Salmonella</italic> serovars in the current study.</p>" ]
[]
[ "<title>Acknowledgments</title>", "<p>We would like to thank the Timbavati Private Nature Reserve ecologist and intern students for facilitating our research and providing logistical support. The authors would also like to Thank Mr. Howard Walker for permission to collect reptile samples on his property. Open access funding was enabled and organized by SANLiC Gold.</p>", "<title>Data Availability</title>", "<p>The data that support the findings of this study are made available from the corresponding author upon reasonable request.</p>", "<title>Disclosure</title>", "<p>A collection permit for reptiles was obtained from Limpopo Economic Development, Environment and Tourism (ZA/LP/44171/2022), and Section 20 clearance for working with animal parasites and pathogens was obtained from the Dept. of Agriculture Land Reform and Rural Development.</p>", "<title>Conflicts of Interest</title>", "<p>The authors declare that there are no conflicts of interest.</p>", "<title>Authors' Contributions</title>", "<p>LNM conceptualized the study, contributed to data curation, performed investigation, proposed the methodology, provided the resources, performed visualization, and wrote the original draft. TR and CW conceptualized the study, contributed to data curation, performed investigation, proposed the methodology, provided the resources, and performed visualization. KEL conceptualized the study, contributed to data curation, proposed the methodology, and wrote, reviewed, and edited the article. CP performed validation, performed formal analysis, and reviewed and edited the article. OT performed validation and reviewed and edited the article. All authors have read and agreed to the published version of the manuscript.</p>", "<title>Supplementary Materials</title>" ]
[ "<fig position=\"float\" id=\"fig1\"><label>Figure 1</label><caption><p>Distribution of virulence genes in different <italic>Salmonella</italic> serovars recovered from reptiles in South Africa.</p></caption></fig>", "<fig position=\"float\" id=\"fig2\"><label>Figure 2</label><caption><p>Heatmap showing the clustering of the antibiotic resistance profiles in the <italic>Salmonella</italic> isolates. Light blue and dark blue indicate the absence and presence of antibiotic and resistance genes, respectively, (<ext-link xlink:href=\"https://www.chiPlot.online/#9\" ext-link-type=\"uri\">https://www.chiPlot.online/#9</ext-link> (accessed on 17 June 2023)).</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"tab1\"><label>Table 1</label><caption><p>\n<italic>Salmonella</italic> spp. serovars identification from different reptile species.</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Reptile group</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Species (<italic>n</italic>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>Salmonella</italic> serovars</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Number of <italic>Salmonella</italic>isolates</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"3\" colspan=\"1\">Lizard</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>Metabosorus validis</italic> (2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>S</italic>. Salamae, <italic>S</italic>. Houtenae, and <italic>S</italic>. Salamae</td><td rowspan=\"3\" align=\"center\" colspan=\"1\">10/30 (33%)</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>Chondrodactylus turneri</italic> (2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>S</italic>. Waycross and <italic>S</italic>. Indiana</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>Trachylepis striata</italic> (2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>S</italic>. Typhimurium, <italic>S</italic>. Salamae, and <italic>S</italic>. Salamae</td></tr><tr><td align=\"left\" colspan=\"4\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"3\" colspan=\"1\">Snake</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>Philothamnus semivariegatus</italic> (2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>S</italic>. Worthington</td><td rowspan=\"3\" align=\"center\" colspan=\"1\">3/30 (10%)</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>Bitis arietans</italic> (1)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>S.</italic> Typhimurium and S. Indiana</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>Dispholidus typus</italic> (1)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"> </td></tr><tr><td align=\"left\" colspan=\"4\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Tortoise</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>Stigmochelys pardalis</italic> (3)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>S</italic>. Newlands and <italic>S. enterica</italic></td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2/30 (6.7%)</td></tr><tr><td align=\"left\" colspan=\"4\" rowspan=\"1\">\n<hr/>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Chameleon</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>Chamaeleo dilepis</italic> (7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic>S</italic>. <italic>enterica</italic>, <italic>S</italic>. Indiana, <italic>S</italic>. Salamae, <italic>S.</italic> Typhi, and <italic>S</italic>. Kentucky</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15/30 (50%)</td></tr></tbody></table></table-wrap>" ]
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[ "<supplementary-material id=\"supp-1\" position=\"float\" content-type=\"local-data\"><label>Supplementary Materials</label><caption><p>Supplementary Table S1. Oligonucleotide primers used for detection of virulence associated genes of <italic>Salmonella</italic> isolates. Supplementary Table S2. List of antibiotic resistance genes primers and conditions used in this study.</p></caption></supplementary-material>" ]
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[ "<graphic xlink:href=\"IJMICRO2024-5213895.001\" position=\"float\"/>", "<graphic xlink:href=\"IJMICRO2024-5213895.002\" position=\"float\"/>" ]
[ "<media xlink:href=\"5213895.f1.docx\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
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2024-01-14 23:41:55
Int J Microbiol. 2024 Jan 5; 2024:5213895
oa_package/64/08/PMC10787053.tar.gz
PMC10787057
37973555
[ "<title>Introduction</title>", "<p>Crystalline heterometallic compounds are compositional diverse and functional complexes allowing performances superior to their parent compound and arising synergistic properties.<sup>[</sup>\n##REF##22990593##\n1\n##, ##UREF##0##\n2\n##\n<sup>]</sup> In addition, the accurate and periodic distribution of metal ions throughout a lattice of crystalline compounds enables the customized atomically precise structural regulation for specific performance, which could not realized in macroscopic nanomaterials. So far, the developed mixed‐metal approach mainly includes one‐step self‐assembly based on hard‐soft acid‐base theory,<sup>[</sup>\n##UREF##1##\n3\n##, ##UREF##2##\n4\n##, ##REF##29119626##\n5\n##, ##UREF##3##\n6\n##, ##UREF##4##\n7\n##, ##REF##29719954##\n8\n##\n<sup>]</sup> and post‐synthetic metalation (redox).<sup>[</sup>\n##REF##22990593##\n1\n##, ##REF##24736674##\n9\n##, ##REF##24831234##\n10\n##, ##REF##28350434##\n11\n##\n<sup>]</sup> The first method involves the use of mixed‐donor ligands that discriminate between two types of metal ions through differential binding affinities. The latter post‐synthetic metalation aims to improve performance by adding other metals to the parent homometallic structures. In addition to these two methods, there is an uncommon stepwise method of using metal clusters as raw materials and then combining them with target metals. One successful example is the employ of Cr<sub>3</sub> oxo cluster to make a series of heterometallic frameworks.<sup>[</sup>\n##UREF##5##\n12\n##, ##UREF##6##\n13\n##\n<sup>]</sup> This approach overcomes the limitation of complications arising from the competitive reaction of multiple metals with ligands in a one‐pot synthesis. In practice, however, it requires stable, dissolvable predesigned building blocks making it a daunting challenge and relatively unexplored.</p>", "<p>Cluster chemistry is an effective way to solve the problem of controllable preparation of heterometallic materials. By studying the predesigned cluster two‐step assembly behavior, we can reverse and generalize to the one‐step synthesis method, which combines the advantages of independent control of the stepwise method and the exploration range and rate of one‐step method (<bold>Scheme</bold> ##FIG##0##\n1\n##). Based on these considerations and our research on rare earth and aluminum oxo clusters,<sup>[</sup>\n##REF##30299080##\n14\n##, ##UREF##7##\n15\n##, ##REF##33443999##\n16\n##\n<sup>]</sup> we report one/two‐step synthesis of heterotrimetallic compounds based on predesigned Al<sub>4</sub>Ln<sub>4</sub> metallocycles as high‐performance Lewis acid catalysts. Our stepwise design thinking includes: (1) First introducing rare earth metal ions with strong Lewis acid on the aluminum molecular ring to synthesize the heterometallic ring; (2) Modify the surface ligand of the heterometallic ring to manufacture coordination anchors and Lewis base sites; (3) Use coordination‐drive self‐assembly with the pre‐modified heterometallic ring incorporating the third metal ion; (4) Establish a general, controllable one‐step method that can be applied to more modified ligands and a broad range of other third metals. Through the step‐by‐step structural regulation of introducing rare earth metals, modifying surface ligands, and introducing third metals, we have successfully achieved a gradual “structural manufacturing” and stepwise improvement in the catalytic efficiency in cyanosilylation of aldehydes.</p>" ]
[ "<title>Materials and Methods</title>", "<p>All the reagents and solvents were purchased commercially and were used without further purification. Aluminum isopropoxide (Al(O<sup>i</sup>Pr)<sub>3</sub>) and methylamine ethanol solution (40%, 120 µL) were acquired from Aladdin Chemical Reagent Shanghai. N‐propyl alcohol (HO<sup>n</sup>Pr), N, N‐dimethylformamide (DMF), and sodium benzoate was bought from Sinopharm Chemical Reagent Beijing. Isonicotinic acid (HIN), N‐methyldiethanolamine (H<sub>2</sub>mdea) were purchased from Adamas‐beta. 4‐(4‐pyridy) benzoic acid (Hpyba) was acquired from Jilin Chinese Academy of Sciences‐Yanshen Technology Co., Ltd.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Synthesis and Characterization</title>", "<p>A series of heterobimetallic rings and corresponding heterotrimetallic framework compounds were synthesized via amino‐polyalcohol solvothermal synthesis. Rare‐earth‐metal ions are well‐known as hard Lewis acids and N‐methyldiethanolamine (H<sub>2</sub>mdea) has proven to be an effective mixed‐donor ligand widely used in the synthesis of its heterometallic properties.<sup>[</sup>\n##UREF##8##\n17\n##, ##REF##35926139##\n18\n##, ##UREF##9##\n19\n##\n<sup>]</sup> Herein, aluminum isopropoxide, europium nitrate, and sodium benzoate were sonicated in a 1:1:2 stoichiometric ratio in a H<sub>2</sub>mdea/DMF mixture to obtain a colorless clarified solution. The reaction was carried out at 120 °C for 4 days to obtain colorless blocky crystals of compound Al<sub>4</sub>Eu<sub>4</sub>(BA)<sub>8</sub>(mdea)<sub>8</sub> (<bold>AlOC‐130</bold>) (<bold>Figure</bold> ##FIG##1##\n1a##), and the reaction system always remained clarified (Figure ##SUPPL##0##S1a##, Supporting Information). We systematically investigated the effects of reaction time and temperature on crystal yield and morphology. It was found that a large number of microcrystals started to appear after 36 h of reaction (Figure ##SUPPL##0##S1b##, Supporting Information), and the yield of crystals increased rapidly between 72 and 96 h of reaction time (Figure ##SUPPL##0##S2##, Supporting Information). Its crystallinity was also studied in the temperature range of 80 to 120 °C (Figure ##SUPPL##0##S3##, Supporting Information). The results show that the reaction starts at 90 °C with the precipitation of a small number of crystals (Figure ##SUPPL##0##S4##, Supporting Information).</p>", "<p>In order to verify the universality of the synthesis of this type of cluster and meanwhile as a precursor for later coordination‐driven assembly, we replaced benzoate with isonicotinic acid (HIN) and successfully isolated colorless strip crystals of compound [Al<sub>4</sub>Eu<sub>4</sub>(IN)<sub>8</sub>(mdea)<sub>8</sub>(H<sub>2</sub>O)]·2H<sub>2</sub>O (<bold>AlOC‐131</bold>) (Figure ##FIG##1##1b##). In order to prefabricate sufficient clusters as precursors, we performed scale‐up synthesis experiments and managed to obtain 1.12 g of crystal samples for a one‐batch reaction (Figure ##SUPPL##0##S5##, Supporting Information). Trace amounts of organic amines play an important role in such heterometallic ring reaction systems reported.<sup>[</sup>\n##REF##35926139##\n18\n##, ##REF##25476806##\n20\n##, ##UREF##10##\n21\n##, ##REF##27859837##\n22\n##\n<sup>]</sup> It is worth noting that the synthesis of infinite structures based on heterometallic clusters can be obtained by a two‐step method using prefabricated clusters as precursors and a one‐step method (Figure ##FIG##1##1##). Copper is selected as the third metal due to its well‐known coordination tendency and affinity toward nitrogen donors. When cuprous was introduced into the mother liquor of <bold>AlOC‐131</bold>, we successfully obtained yellow needle‐like crystals of Al<sub>4</sub>Eu<sub>4</sub>Cu<sub>4</sub>I<sub>4</sub>(IN)<sub>8</sub>(mdea)<sub>8</sub> (<bold>AlOC‐132</bold>). After verifying that this stepwise coordination‐driven self‐assembly method is feasible, we tried a one‐pot synthesis method to obtain a higher yield of <bold>AlOC‐132</bold>. Another expansion example is the isolation of yellow columnar crystals of Al<sub>4</sub>Eu<sub>4</sub>Cu<sub>4</sub>I<sub>4</sub>(pyba)<sub>8</sub>(mdea)<sub>8</sub> (<bold>AlOC‐133</bold>, Hpyba = 4‐(4‐pyridyl) benzoic acid). Diversification of synthesis methods toward cluster‐based heterometallic materials paves the way for in‐depth studying of their properties.</p>", "<p>\n<bold>AlOC‐130</bold> and <bold>AlOC‐131</bold> are stable in the air for up to one year, which may be related to the protection of organic ligand shells and the immobilization of alcohol amines with multiple chelation sites (Figures ##SUPPL##0##S6## and ##SUPPL##0##S7##, Supporting Information). In addition, the heterometallic rings are thermally stable up to 350 °C, which is a significant improvement over the previously reported aluminum molecular rings (Figures ##SUPPL##0##S15–S20##, Supporting Information).<sup>[</sup>\n##UREF##7##\n15\n##\n<sup>]</sup> All the above compounds are stable in organic solvents (Figures ##SUPPL##0##S12–S14## and Tables ##SUPPL##0##S1,S2##, Supporting Information). The generalizability of the compounds toward heavy rare earth ions was confirmed by powder X‐ray diffraction (PXRD) and Fourier transform infrared (FT‐IR) of the isomeric structures (Figures ##SUPPL##0##S10,S11## and ##SUPPL##0##S21–S24##, Supporting Information). As shown in Figures ##SUPPL##0##S25–S28## (Supporting Information), the presence of cuprous ions significantly narrows the bandgap of the compound (3.4–1.8 eV change in bandgap from colorless to yellow crystals). The presence of multi‐metal centers in the compounds was confirmed by energy dispersive spectroscopy (EDS) (Figures ##SUPPL##0##S29–S32##, Supporting Information) and their atomically precise structural information has been unambiguously revealed by single crystal X‐ray diffraction (SCXRD) (<bold>Table</bold> ##TAB##0##\n1\n##). The EDS‐mapping patterns of the heterometallic compounds show a uniform distribution of Al, Ln, Cu, C, N, O, and I atoms in the crystals (Figures ##SUPPL##0##S33–S36##, Supporting Information). The bond valence sum (BVS) indicates that the valence states of the heterotrimetallic Al, Eu, and Cu in the compound are 3+, 3+, and 1+, respectively (Tables ##SUPPL##0##S3–S6##, Supporting Information).</p>", "<p>Compound Al<sub>4</sub>Eu<sub>4</sub> is heterobimetallic molecular ring crystallizing in the tetragonal space group <italic toggle=\"yes\">P</italic>‐42<sub>1</sub>c (<bold>Figure</bold> ##FIG##2##\n2a##). The neutral octanuclear ring consists of an alternating arrangement of four Al<sup>3+</sup> and four Eu<sup>3+</sup> ions bridged by eight fully deprotonated mdea<sup>2−</sup> and eight benzoates (Figure ##SUPPL##0##S38a##, Supporting Information). Such alternating arrangement is different from the “Dy<sub>4</sub>‐square‐within‐a‐Ga<sub>4</sub>‐square”,<sup>[</sup>\n##REF##27184869##\n23\n##\n<sup>]</sup> “Tower‐Like” Ln<sub>4</sub>Cr<sub>4</sub>\n<sup>[</sup>\n##REF##30094883##\n24\n##\n<sup>]</sup> and the square [Fe<sub>4</sub>Gd<sub>4</sub>],<sup>[</sup>\n##REF##27184869##\n23\n##\n<sup>]</sup> but is similar to the wheel‐like Sc<sub>4</sub>Gd<sub>4</sub> (Figures ##SUPPL##0##S39–S41##, Supporting Information).<sup>[</sup>\n##REF##35926139##\n18\n##\n<sup>]</sup> Compared with the boat‐shape side‐view of the Sc<sub>4</sub>Gd<sub>4</sub>, Al<sub>4</sub>Eu<sub>4</sub> can be viewed as a chair‐shape with a dihedral angle of 40.17<sup>o</sup> (Figure ##SUPPL##0##S38b##, Supporting Information). Space‐filling diagram of Al<sub>4</sub>Eu<sub>4</sub> reveals that the size of this molecule is ca. 2.1 nm in length and ca. 0.8 nm in thickness (Figure ##FIG##2##2a##).</p>", "<p>The two pincer‐like mdea<sup>2−</sup> ligands chelate one rare earth ion and benzoic acid further connects Al and Eu ions. Each Al<sup>3+</sup> takes the standard six‐connected octahedral geometry (Figure ##SUPPL##0##S42a##, Supporting Information), consisting of oxygen from two carboxylic acid ligands and four mdea<sup>2−</sup> (Figure ##SUPPL##0##S42b##, Supporting Information). Each rare earth ion, on the other hand, is octa‐ligated consisting of two N and six O (Figure ##SUPPL##0##S42c##, Supporting Information), and they come from two mdea<sup>2−</sup> that take the µ<sub>3</sub>‐η<sup>2</sup>:η<sup>1</sup>:η<sup>2</sup> coordination pattern and two carboxylic acid ligands that take the µ<sub>2</sub>‐η<sup>1</sup>:η<sup>1</sup> coordination pattern (Figure ##SUPPL##0##S42d,e##, Supporting Information). As shown in Figure ##FIG##2##2b##, the heterobimetallic molecular rings are stacked in tetragonal arrays through <italic toggle=\"yes\">π</italic>–<italic toggle=\"yes\">π</italic> interactions of aromatic ligands (Figure ##SUPPL##0##S44##, Supporting Information). The distance between the heterometallic rings in the unit cell ranges from 9.88–23.67 Å (Figure ##SUPPL##0##S45a##, Supporting Information). The total solvent‐accessible volumes of <bold>AlOC‐130</bold> as calculated by PLATON are 5.1%.</p>", "<p>Bifunctional isonicotinic acid linkers were introduced as both potential coordination anchors for the subsequent coordination assembly (pyridine nitrogen (<italic toggle=\"yes\">N</italic>\n<sub>py</sub>) coordination sites) and potential adsorption sites for catalytic substrates. The isonicotinic acid‐modified compound <bold>AlOC‐131</bold> (Figure ##FIG##2##2c##) crystallizes in the monoclinic space group <italic toggle=\"yes\">P2<sub>1</sub>/n</italic>. The reduced symmetry is due to a local change in the coordination environment of the Al ions. As shown in Figure ##FIG##2##2d##, there is terminal isonicotinic acid and the nearest vacancy is occupied by a water molecule, generating strong hydrogen bonding interactions (O—H—O, 2.657 Å) within the molecular ring (Figure ##SUPPL##0##S47##, Supporting Information). Instead of the <italic toggle=\"yes\">π</italic>–<italic toggle=\"yes\">π</italic> interactions, these rings are interconnected by hydrogen bonding interactions ranging from 2.71 to 3.40 Å (Figure ##SUPPL##0##S47d##; Table ##SUPPL##0##S8##, Supporting Information). The distances between the heterometallic rings in the unit cell of the compound <bold>AlOC‐131</bold> were in the interval 17.36–27.60 Å (Figure ##SUPPL##0##S45b##, Supporting Information) and the total solvent‐accessible volumes of <bold>AlOC‐131</bold> as calculated by PLATON are 14.1%.</p>", "<p>Compound <bold>AlOC‐132</bold> is a mesoporous 3D framework consisting of above mentioned similar Al<sub>4</sub>Eu<sub>4</sub> heterometallic ring with Cu<sub>2</sub>I<sub>2</sub> units (<bold>Figure</bold> ##FIG##3##\n3\n##; Figures ##SUPPL##0##S48,S49##, Supplementary Movie ##SUPPL##1##S1##). Notably, aluminum's defect site in the pristine discrete cluster of <bold>AlOC‐131</bold> disappeared and its connections are obviously different from our previously reported homometallic Al<sub>8</sub> ring reducing from 12 to 8 (Figure ##SUPPL##0##S50##, Supporting Information).<sup>[</sup>\n##UREF##11##\n25\n##\n<sup>]</sup> Through the use of coordination‐driven self‐assembly, we isolated the infinite porous compound <bold>AlOC‐132</bold> derived from <bold>AlOC‐131</bold> cluster precursor. The eight isonicotinic acids on each heterobimetallic ring are connected to the surrounding eight heterobimetallic rings via Cu<sub>2</sub>I<sub>2</sub> units to generate a 4,8‐connected <italic toggle=\"yes\">scu</italic> net (Figure ##SUPPL##0##S51##, Supporting Information). Mesoporous 1D channels, relatively small channels and microporous cages co‐exist in the structure (dimensions 3.07<sup>*</sup>3.07 nm<sup>2</sup>, 1.25<sup>*</sup>2.28<sup>*</sup>2.28 nm<sup>3</sup> and 1.33<sup>*</sup>1.09 nm<sup>2</sup>, respectively) (Figure ##FIG##3##3c,d##). The type I square channel comprises heterometallic rings at the four vertices and four Cu<sub>2</sub>I<sub>2</sub> on the prongs connected by ligands running along the <italic toggle=\"yes\">c</italic>‐axis (Figure ##SUPPL##0##S53a##, Supporting Information). The type II rhombic channel interleaved with the type I channel is made up of alternating heterometallic rings and Cu<sub>2</sub>I<sub>2</sub> sections distributed at the apex running along the <italic toggle=\"yes\">b</italic>‐axis (Figure ##SUPPL##0##S53b##, Supporting Information). The type III basket‐liked cavity involves two heterometallic rings at the apex and four Cu<sub>2</sub>I<sub>2</sub> sections at the waist (Figure ##SUPPL##0##S53c##, Supporting Information). The distance between the heterometallic rings in the porous framework varied from 12.54 to 22.40 Å (Figure ##SUPPL##0##S54##, Supporting Information). The total solvent‐accessible volumes of <bold>AlOC‐132</bold> as calculated by PLATON are 61.8%.</p>", "<p>To verify the universality of the assembly method and obtain an expanded pore structure, we introduced an elongated version of the Hpyba ligand. However, the result turned out that compound <bold>AlOC‐133</bold> was isolated in the form of a stable double‐interpenetrated version due to the lack of suitable support for such macropores (Figure ##FIG##3##3##). Nevertheless, the coordination‐driven self‐assembly did work well. The use of lengthened flexible pyba<sup>−</sup> maintains the same number of connections as that in <bold>AlOC‐132</bold>, albeit with an increase in the dihedral angle of the inorganic {Al<sub>4</sub>Ln<sub>4</sub>} cluster (from 29.41<sup>o</sup> to 47.76<sup>o</sup>) (Figures ##SUPPL##0##S55,S56##, Supporting Information). The elongated version of the organic ligand with flexibility on each heterobimetallic ring undergoes torsion to connect to the other eight heterobimetallic rings to form an interpenetrating 4,8‐connected 2 (1 + 1) interpenetrating <italic toggle=\"yes\">scu</italic> net (Figures ##SUPPL##0##S58–S60##, Supplementary Movie ##SUPPL##2##S2##). It should be noted that the situation of cavities changes accordingly (Figure ##FIG##3##3g##). First, the large square channel with dimensions of 4.05<sup>*</sup>4.05 nm<sup>2</sup> was divided into four smaller channels with sizes of 2.05<sup>*</sup>2.05 nm<sup>2</sup> (Figure ##SUPPL##0##S61a##, Supporting Information). Second, the size of the microporous channels is smaller (size 0.92<sup>*</sup>1.48 nm<sup>2</sup> vs 1.33<sup>*</sup>1.09 nm<sup>2</sup>) (Figure ##SUPPL##0##S61b##, Supporting Information). Then, the cage cavity is wider in dimension (size 1.25<sup>*</sup>2.28<sup>*</sup>2.28 nm<sup>3</sup> vs 1.82<sup>*</sup>2.90<sup>*</sup>2.90 nm<sup>3</sup>) (Figure ##SUPPL##0##S61c##, Supporting Information). PLATON calculations reveal that the porosity of <bold>AlOC‐133</bold> (64.1%) is still slightly higher than that of <bold>AlOC‐132</bold> (61.8%) even though it is interpenetrated. Hence, we establish a controllable synthesis route toward a specific topological framework. These channels and pores in compounds <bold>AlOC‐132</bold> and <bold>AlOC‐133</bold> are sufficient to accommodate the benzaldehyde substrate (4.34<sup>*</sup>2.43 Å<sup>2</sup>) in the subsequent catalytic process.</p>", "<title>The Catalytic Activity of Heterometallic Ring Compounds</title>", "<p>The cyanylation of carbonyl compounds with TMSCN, a typical Lewis acid‐catalyzed reaction, is an important reaction in organic synthesis for the formation of C—C bonds to produce cyanohydrin derivatives.<sup>[</sup>\n##UREF##12##\n26\n##, ##REF##19209946##\n27\n##, ##REF##26651389##\n28\n##, ##UREF##13##\n29\n##\n<sup>]</sup> While there are many materials used to catalyze this reaction including organic small molecules,<sup>[</sup>\n##UREF##14##\n30\n##, ##UREF##15##\n31\n##\n<sup>]</sup> metal complexes<sup>[</sup>\n##REF##29235696##\n32\n##, ##UREF##16##\n33\n##, ##UREF##17##\n34\n##\n<sup>]</sup>, and crystalline materials,<sup>[</sup>\n##REF##26086918##\n35\n##, ##UREF##18##\n36\n##\n<sup>]</sup> among them crystalline materials with well‐defined structural information can provide insight into the catalytic mechanism at the atomic level. Crystalline materials are mainly focused on metal‐organic frameworks (MOFs),<sup>[</sup>\n##REF##18399629##\n37\n##\n<sup>]</sup> covalent organic frameworks (COFs)<sup>[</sup>\n##REF##30226522##\n38\n##\n<sup>]</sup>, and polyoxometalates (POMs).<sup>[</sup>\n##REF##29932201##\n39\n##\n<sup>]</sup> However, much of the work reported so far shows the structure of the catalyst or a single metal as the active site, neither of which provides insight into the catalytic mechanism. In our previous work, the binding of substrates to the aluminum‐based molecular rings during catalysis was tried and successfully confirmed.<sup>[</sup>\n##REF##37234899##\n40\n##\n<sup>]</sup> Considering the abundance of metal nodes (Al, Eu, and Cu as Lewis acid sites) and the porous nature of these heterometallic rings and their framework materials, they are potential Lewis acid catalysts and shed more light on the reaction from a multi‐metallic synergistic perspective. Hence, we chose cyanylation of benzaldehyde as a typical probe for Lewis acid‐catalyzed reactions.</p>", "<p>Quantitative product yields were obtained by catalyzing the reaction of benzaldehyde (0.5 mmol) with TMSCN (1 mmol) in CH<sub>2</sub>Cl<sub>2</sub> with 1.5 mol.% of AlOCs catalyst loading at room temperature under inert conditions for 2 h (<bold>Table</bold> ##TAB##1##\n2\n##). As shown in Table ##TAB##1##2## entries 1–3, aromatic ligands alone have little effect on the reaction (Figure ##SUPPL##0##S62##, Supporting Information). To clarify the catalytic active center, we synthesized a structural similar homometallic molecular ring <bold>AlOC‐79</bold> modified by isonicotinic acids (<bold>Figure</bold> ##FIG##4##\n4\n##; Figure ##SUPPL##0##S63##, Supporting Information). Compound <bold>AlOC‐79</bold> is a ten‐membered ring with an organic shell environment similar to <bold>AlOC‐131</bold>. We can see from the catalytic result that it did not catalyze as well as either of the heterometallic rings (<bold>AlOC‐130</bold> to <bold>AlOC‐133</bold>), suggesting that the introduction of lanthanide metal ions as Lewis acid sites enhances the catalysis (Table ##TAB##1##2## entry 4). The catalytic effects of the heterometallic molecular rings and their framework were in the order of <bold>AlOC‐130</bold>&lt; <bold>AlOC‐131</bold>&lt; <bold>AlOC‐132</bold>&lt; <bold>AlOC‐133</bold> (88.0%, 95.5%, 98.2%, and 99.9%, respectively) (Table ##TAB##1##2## entries 5–8). It is worth mentioning that the reaction was highly selective and no by‐products were observed (Figures ##SUPPL##0##S64–S67##, Supporting Information). The improved effect of <bold>AlOC‐131</bold> compared with <bold>AlOC‐130</bold> resulted from the presence of N‐substituted aromatic ring that facilitates binding the substrate to the catalyst. In addition, the coordination mode of the organic ligand also affects the catalytic reaction to some extent.<sup>[</sup>\n##REF##26086918##\n35\n##, ##REF##27010759##\n41\n##\n<sup>]</sup> As described in the structure section and shown in Figure ##SUPPL##0##S68## (Supporting Information), the emergence of a terminal isonicotinic and the local defect of the attack of water molecules on Al ions make it increase the Lewis base site and easier to contact with the substrate. The isostructural lanthanide series <bold>AlOC‐131‐Ln</bold> has a considerable catalytic effect, indicating the synergistic effect of Lewis acid site and surface ligand modification (Figure ##SUPPL##0##S69##, Supporting Information).</p>", "<p>The substrate range for the aldehyde cyanosilylation reaction was investigated using <bold>AlOC‐130</bold> as an example (Figure ##SUPPL##0##S70##, Supporting Information). Under standard conditions, when aromatic aldehydes with electronic effect substituents (electron‐donating ‐OCH<sub>3</sub>, electron‐withdrawing ‐CF<sub>3</sub>) or heterocyclic aldehydes were employed, the corresponding products were obtained in high yields after 2 h (85%–95%), which suggests that the reaction is broad tolerance to various substrates. However, 1‐naphthaldehyde and ketone obtained lower catalytic efficiency even after prolonged reaction time (24 h) (30%–40%), which may be related to the spatial site resistance of the substrates.</p>", "<p>Moreover, the catalytic effect of the heterotrimetallic compounds <bold>AlOC‐132</bold> and <bold>AlOC‐133</bold> are superior to those of the heterometallic molecular rings <bold>AlOC‐130</bold> and <bold>AlOC‐131</bold> not only in terms of yield but also in the rate of conversion, which is better illustrated by the presence of the pores structures and triple‐metal centers (Figure ##SUPPL##0##S71##, Supporting Information).<sup>[</sup>\n##UREF##18##\n36\n##, ##REF##30226522##\n38\n##, ##REF##29790543##\n42\n##\n<sup>]</sup> One possible reason for the rapid complete conversion (0.5 h) of the substrate catalyzed by the compound <bold>AlOC‐133</bold> includes the highest porosity throughout these series of compounds (5.1%, 14.1%, 61.8%, and 64.1% for <bold>AlOC‐30</bold> to <bold>AlOC‐133</bold>, respectively).<sup>[</sup>\n##REF##18399629##\n37\n##\n<sup>]</sup> Another reason is the presence of more regular 1D channels and favorable cavity environments (abundant aromatic walls and iodine atoms pointing toward the channel favor the formation of <italic toggle=\"yes\">π</italic>–<italic toggle=\"yes\">π</italic> interactions and O—H—I hydrogen bonding, respectively, with the substrate benzaldehyde) (Figures ##SUPPL##0##S72–S75##, Supporting Information). To investigate the Lewis acid properties of the heterometallic ring and its framework compounds, we performed pyridine FT‐IR spectroscopy. As shown in Figure ##SUPPL##0##S76## (Supporting Information), the pyridine FT‐IR pattern exhibited three signal peaks at 1039, 1047, and ≈1059 cm<sup>−1</sup> corresponding to the adsorption of pyridine on the Lewis acid sites.<sup>[</sup>\n##REF##21597609##\n43\n##, ##UREF##19##\n44\n##, ##UREF##20##\n45\n##, ##UREF##21##\n46\n##\n<sup>]</sup> As expected, the amount of Lewis acid sites increases with the order of catalytic effect. Hence, the synergy of the multiple Lewis acid sites, the pore cavity and the microenvironment are conducive to a good catalytic effect. Their performances are significantly better than those of lanthanide‐based polyoxometalates and MOFs (Table ##SUPPL##0##S9##, Supporting Information),<sup>[</sup>\n##REF##29932201##\n39\n##, ##UREF##22##\n47\n##, ##REF##29749730##\n48\n##\n<sup>]</sup> although their catalytic effect is inferior to those of monomer organo‐aluminum with flexible active sites.<sup>[</sup>\n##UREF##14##\n30\n##, ##REF##28580996##\n49\n##, ##UREF##23##\n50\n##\n<sup>]</sup>\n</p>" ]
[ "<title>Results and Discussion</title>", "<title>Synthesis and Characterization</title>", "<p>A series of heterobimetallic rings and corresponding heterotrimetallic framework compounds were synthesized via amino‐polyalcohol solvothermal synthesis. Rare‐earth‐metal ions are well‐known as hard Lewis acids and N‐methyldiethanolamine (H<sub>2</sub>mdea) has proven to be an effective mixed‐donor ligand widely used in the synthesis of its heterometallic properties.<sup>[</sup>\n##UREF##8##\n17\n##, ##REF##35926139##\n18\n##, ##UREF##9##\n19\n##\n<sup>]</sup> Herein, aluminum isopropoxide, europium nitrate, and sodium benzoate were sonicated in a 1:1:2 stoichiometric ratio in a H<sub>2</sub>mdea/DMF mixture to obtain a colorless clarified solution. The reaction was carried out at 120 °C for 4 days to obtain colorless blocky crystals of compound Al<sub>4</sub>Eu<sub>4</sub>(BA)<sub>8</sub>(mdea)<sub>8</sub> (<bold>AlOC‐130</bold>) (<bold>Figure</bold> ##FIG##1##\n1a##), and the reaction system always remained clarified (Figure ##SUPPL##0##S1a##, Supporting Information). We systematically investigated the effects of reaction time and temperature on crystal yield and morphology. It was found that a large number of microcrystals started to appear after 36 h of reaction (Figure ##SUPPL##0##S1b##, Supporting Information), and the yield of crystals increased rapidly between 72 and 96 h of reaction time (Figure ##SUPPL##0##S2##, Supporting Information). Its crystallinity was also studied in the temperature range of 80 to 120 °C (Figure ##SUPPL##0##S3##, Supporting Information). The results show that the reaction starts at 90 °C with the precipitation of a small number of crystals (Figure ##SUPPL##0##S4##, Supporting Information).</p>", "<p>In order to verify the universality of the synthesis of this type of cluster and meanwhile as a precursor for later coordination‐driven assembly, we replaced benzoate with isonicotinic acid (HIN) and successfully isolated colorless strip crystals of compound [Al<sub>4</sub>Eu<sub>4</sub>(IN)<sub>8</sub>(mdea)<sub>8</sub>(H<sub>2</sub>O)]·2H<sub>2</sub>O (<bold>AlOC‐131</bold>) (Figure ##FIG##1##1b##). In order to prefabricate sufficient clusters as precursors, we performed scale‐up synthesis experiments and managed to obtain 1.12 g of crystal samples for a one‐batch reaction (Figure ##SUPPL##0##S5##, Supporting Information). Trace amounts of organic amines play an important role in such heterometallic ring reaction systems reported.<sup>[</sup>\n##REF##35926139##\n18\n##, ##REF##25476806##\n20\n##, ##UREF##10##\n21\n##, ##REF##27859837##\n22\n##\n<sup>]</sup> It is worth noting that the synthesis of infinite structures based on heterometallic clusters can be obtained by a two‐step method using prefabricated clusters as precursors and a one‐step method (Figure ##FIG##1##1##). Copper is selected as the third metal due to its well‐known coordination tendency and affinity toward nitrogen donors. When cuprous was introduced into the mother liquor of <bold>AlOC‐131</bold>, we successfully obtained yellow needle‐like crystals of Al<sub>4</sub>Eu<sub>4</sub>Cu<sub>4</sub>I<sub>4</sub>(IN)<sub>8</sub>(mdea)<sub>8</sub> (<bold>AlOC‐132</bold>). After verifying that this stepwise coordination‐driven self‐assembly method is feasible, we tried a one‐pot synthesis method to obtain a higher yield of <bold>AlOC‐132</bold>. Another expansion example is the isolation of yellow columnar crystals of Al<sub>4</sub>Eu<sub>4</sub>Cu<sub>4</sub>I<sub>4</sub>(pyba)<sub>8</sub>(mdea)<sub>8</sub> (<bold>AlOC‐133</bold>, Hpyba = 4‐(4‐pyridyl) benzoic acid). Diversification of synthesis methods toward cluster‐based heterometallic materials paves the way for in‐depth studying of their properties.</p>", "<p>\n<bold>AlOC‐130</bold> and <bold>AlOC‐131</bold> are stable in the air for up to one year, which may be related to the protection of organic ligand shells and the immobilization of alcohol amines with multiple chelation sites (Figures ##SUPPL##0##S6## and ##SUPPL##0##S7##, Supporting Information). In addition, the heterometallic rings are thermally stable up to 350 °C, which is a significant improvement over the previously reported aluminum molecular rings (Figures ##SUPPL##0##S15–S20##, Supporting Information).<sup>[</sup>\n##UREF##7##\n15\n##\n<sup>]</sup> All the above compounds are stable in organic solvents (Figures ##SUPPL##0##S12–S14## and Tables ##SUPPL##0##S1,S2##, Supporting Information). The generalizability of the compounds toward heavy rare earth ions was confirmed by powder X‐ray diffraction (PXRD) and Fourier transform infrared (FT‐IR) of the isomeric structures (Figures ##SUPPL##0##S10,S11## and ##SUPPL##0##S21–S24##, Supporting Information). As shown in Figures ##SUPPL##0##S25–S28## (Supporting Information), the presence of cuprous ions significantly narrows the bandgap of the compound (3.4–1.8 eV change in bandgap from colorless to yellow crystals). The presence of multi‐metal centers in the compounds was confirmed by energy dispersive spectroscopy (EDS) (Figures ##SUPPL##0##S29–S32##, Supporting Information) and their atomically precise structural information has been unambiguously revealed by single crystal X‐ray diffraction (SCXRD) (<bold>Table</bold> ##TAB##0##\n1\n##). The EDS‐mapping patterns of the heterometallic compounds show a uniform distribution of Al, Ln, Cu, C, N, O, and I atoms in the crystals (Figures ##SUPPL##0##S33–S36##, Supporting Information). The bond valence sum (BVS) indicates that the valence states of the heterotrimetallic Al, Eu, and Cu in the compound are 3+, 3+, and 1+, respectively (Tables ##SUPPL##0##S3–S6##, Supporting Information).</p>", "<p>Compound Al<sub>4</sub>Eu<sub>4</sub> is heterobimetallic molecular ring crystallizing in the tetragonal space group <italic toggle=\"yes\">P</italic>‐42<sub>1</sub>c (<bold>Figure</bold> ##FIG##2##\n2a##). The neutral octanuclear ring consists of an alternating arrangement of four Al<sup>3+</sup> and four Eu<sup>3+</sup> ions bridged by eight fully deprotonated mdea<sup>2−</sup> and eight benzoates (Figure ##SUPPL##0##S38a##, Supporting Information). Such alternating arrangement is different from the “Dy<sub>4</sub>‐square‐within‐a‐Ga<sub>4</sub>‐square”,<sup>[</sup>\n##REF##27184869##\n23\n##\n<sup>]</sup> “Tower‐Like” Ln<sub>4</sub>Cr<sub>4</sub>\n<sup>[</sup>\n##REF##30094883##\n24\n##\n<sup>]</sup> and the square [Fe<sub>4</sub>Gd<sub>4</sub>],<sup>[</sup>\n##REF##27184869##\n23\n##\n<sup>]</sup> but is similar to the wheel‐like Sc<sub>4</sub>Gd<sub>4</sub> (Figures ##SUPPL##0##S39–S41##, Supporting Information).<sup>[</sup>\n##REF##35926139##\n18\n##\n<sup>]</sup> Compared with the boat‐shape side‐view of the Sc<sub>4</sub>Gd<sub>4</sub>, Al<sub>4</sub>Eu<sub>4</sub> can be viewed as a chair‐shape with a dihedral angle of 40.17<sup>o</sup> (Figure ##SUPPL##0##S38b##, Supporting Information). Space‐filling diagram of Al<sub>4</sub>Eu<sub>4</sub> reveals that the size of this molecule is ca. 2.1 nm in length and ca. 0.8 nm in thickness (Figure ##FIG##2##2a##).</p>", "<p>The two pincer‐like mdea<sup>2−</sup> ligands chelate one rare earth ion and benzoic acid further connects Al and Eu ions. Each Al<sup>3+</sup> takes the standard six‐connected octahedral geometry (Figure ##SUPPL##0##S42a##, Supporting Information), consisting of oxygen from two carboxylic acid ligands and four mdea<sup>2−</sup> (Figure ##SUPPL##0##S42b##, Supporting Information). Each rare earth ion, on the other hand, is octa‐ligated consisting of two N and six O (Figure ##SUPPL##0##S42c##, Supporting Information), and they come from two mdea<sup>2−</sup> that take the µ<sub>3</sub>‐η<sup>2</sup>:η<sup>1</sup>:η<sup>2</sup> coordination pattern and two carboxylic acid ligands that take the µ<sub>2</sub>‐η<sup>1</sup>:η<sup>1</sup> coordination pattern (Figure ##SUPPL##0##S42d,e##, Supporting Information). As shown in Figure ##FIG##2##2b##, the heterobimetallic molecular rings are stacked in tetragonal arrays through <italic toggle=\"yes\">π</italic>–<italic toggle=\"yes\">π</italic> interactions of aromatic ligands (Figure ##SUPPL##0##S44##, Supporting Information). The distance between the heterometallic rings in the unit cell ranges from 9.88–23.67 Å (Figure ##SUPPL##0##S45a##, Supporting Information). The total solvent‐accessible volumes of <bold>AlOC‐130</bold> as calculated by PLATON are 5.1%.</p>", "<p>Bifunctional isonicotinic acid linkers were introduced as both potential coordination anchors for the subsequent coordination assembly (pyridine nitrogen (<italic toggle=\"yes\">N</italic>\n<sub>py</sub>) coordination sites) and potential adsorption sites for catalytic substrates. The isonicotinic acid‐modified compound <bold>AlOC‐131</bold> (Figure ##FIG##2##2c##) crystallizes in the monoclinic space group <italic toggle=\"yes\">P2<sub>1</sub>/n</italic>. The reduced symmetry is due to a local change in the coordination environment of the Al ions. As shown in Figure ##FIG##2##2d##, there is terminal isonicotinic acid and the nearest vacancy is occupied by a water molecule, generating strong hydrogen bonding interactions (O—H—O, 2.657 Å) within the molecular ring (Figure ##SUPPL##0##S47##, Supporting Information). Instead of the <italic toggle=\"yes\">π</italic>–<italic toggle=\"yes\">π</italic> interactions, these rings are interconnected by hydrogen bonding interactions ranging from 2.71 to 3.40 Å (Figure ##SUPPL##0##S47d##; Table ##SUPPL##0##S8##, Supporting Information). The distances between the heterometallic rings in the unit cell of the compound <bold>AlOC‐131</bold> were in the interval 17.36–27.60 Å (Figure ##SUPPL##0##S45b##, Supporting Information) and the total solvent‐accessible volumes of <bold>AlOC‐131</bold> as calculated by PLATON are 14.1%.</p>", "<p>Compound <bold>AlOC‐132</bold> is a mesoporous 3D framework consisting of above mentioned similar Al<sub>4</sub>Eu<sub>4</sub> heterometallic ring with Cu<sub>2</sub>I<sub>2</sub> units (<bold>Figure</bold> ##FIG##3##\n3\n##; Figures ##SUPPL##0##S48,S49##, Supplementary Movie ##SUPPL##1##S1##). Notably, aluminum's defect site in the pristine discrete cluster of <bold>AlOC‐131</bold> disappeared and its connections are obviously different from our previously reported homometallic Al<sub>8</sub> ring reducing from 12 to 8 (Figure ##SUPPL##0##S50##, Supporting Information).<sup>[</sup>\n##UREF##11##\n25\n##\n<sup>]</sup> Through the use of coordination‐driven self‐assembly, we isolated the infinite porous compound <bold>AlOC‐132</bold> derived from <bold>AlOC‐131</bold> cluster precursor. The eight isonicotinic acids on each heterobimetallic ring are connected to the surrounding eight heterobimetallic rings via Cu<sub>2</sub>I<sub>2</sub> units to generate a 4,8‐connected <italic toggle=\"yes\">scu</italic> net (Figure ##SUPPL##0##S51##, Supporting Information). Mesoporous 1D channels, relatively small channels and microporous cages co‐exist in the structure (dimensions 3.07<sup>*</sup>3.07 nm<sup>2</sup>, 1.25<sup>*</sup>2.28<sup>*</sup>2.28 nm<sup>3</sup> and 1.33<sup>*</sup>1.09 nm<sup>2</sup>, respectively) (Figure ##FIG##3##3c,d##). The type I square channel comprises heterometallic rings at the four vertices and four Cu<sub>2</sub>I<sub>2</sub> on the prongs connected by ligands running along the <italic toggle=\"yes\">c</italic>‐axis (Figure ##SUPPL##0##S53a##, Supporting Information). The type II rhombic channel interleaved with the type I channel is made up of alternating heterometallic rings and Cu<sub>2</sub>I<sub>2</sub> sections distributed at the apex running along the <italic toggle=\"yes\">b</italic>‐axis (Figure ##SUPPL##0##S53b##, Supporting Information). The type III basket‐liked cavity involves two heterometallic rings at the apex and four Cu<sub>2</sub>I<sub>2</sub> sections at the waist (Figure ##SUPPL##0##S53c##, Supporting Information). The distance between the heterometallic rings in the porous framework varied from 12.54 to 22.40 Å (Figure ##SUPPL##0##S54##, Supporting Information). The total solvent‐accessible volumes of <bold>AlOC‐132</bold> as calculated by PLATON are 61.8%.</p>", "<p>To verify the universality of the assembly method and obtain an expanded pore structure, we introduced an elongated version of the Hpyba ligand. However, the result turned out that compound <bold>AlOC‐133</bold> was isolated in the form of a stable double‐interpenetrated version due to the lack of suitable support for such macropores (Figure ##FIG##3##3##). Nevertheless, the coordination‐driven self‐assembly did work well. The use of lengthened flexible pyba<sup>−</sup> maintains the same number of connections as that in <bold>AlOC‐132</bold>, albeit with an increase in the dihedral angle of the inorganic {Al<sub>4</sub>Ln<sub>4</sub>} cluster (from 29.41<sup>o</sup> to 47.76<sup>o</sup>) (Figures ##SUPPL##0##S55,S56##, Supporting Information). The elongated version of the organic ligand with flexibility on each heterobimetallic ring undergoes torsion to connect to the other eight heterobimetallic rings to form an interpenetrating 4,8‐connected 2 (1 + 1) interpenetrating <italic toggle=\"yes\">scu</italic> net (Figures ##SUPPL##0##S58–S60##, Supplementary Movie ##SUPPL##2##S2##). It should be noted that the situation of cavities changes accordingly (Figure ##FIG##3##3g##). First, the large square channel with dimensions of 4.05<sup>*</sup>4.05 nm<sup>2</sup> was divided into four smaller channels with sizes of 2.05<sup>*</sup>2.05 nm<sup>2</sup> (Figure ##SUPPL##0##S61a##, Supporting Information). Second, the size of the microporous channels is smaller (size 0.92<sup>*</sup>1.48 nm<sup>2</sup> vs 1.33<sup>*</sup>1.09 nm<sup>2</sup>) (Figure ##SUPPL##0##S61b##, Supporting Information). Then, the cage cavity is wider in dimension (size 1.25<sup>*</sup>2.28<sup>*</sup>2.28 nm<sup>3</sup> vs 1.82<sup>*</sup>2.90<sup>*</sup>2.90 nm<sup>3</sup>) (Figure ##SUPPL##0##S61c##, Supporting Information). PLATON calculations reveal that the porosity of <bold>AlOC‐133</bold> (64.1%) is still slightly higher than that of <bold>AlOC‐132</bold> (61.8%) even though it is interpenetrated. Hence, we establish a controllable synthesis route toward a specific topological framework. These channels and pores in compounds <bold>AlOC‐132</bold> and <bold>AlOC‐133</bold> are sufficient to accommodate the benzaldehyde substrate (4.34<sup>*</sup>2.43 Å<sup>2</sup>) in the subsequent catalytic process.</p>", "<title>The Catalytic Activity of Heterometallic Ring Compounds</title>", "<p>The cyanylation of carbonyl compounds with TMSCN, a typical Lewis acid‐catalyzed reaction, is an important reaction in organic synthesis for the formation of C—C bonds to produce cyanohydrin derivatives.<sup>[</sup>\n##UREF##12##\n26\n##, ##REF##19209946##\n27\n##, ##REF##26651389##\n28\n##, ##UREF##13##\n29\n##\n<sup>]</sup> While there are many materials used to catalyze this reaction including organic small molecules,<sup>[</sup>\n##UREF##14##\n30\n##, ##UREF##15##\n31\n##\n<sup>]</sup> metal complexes<sup>[</sup>\n##REF##29235696##\n32\n##, ##UREF##16##\n33\n##, ##UREF##17##\n34\n##\n<sup>]</sup>, and crystalline materials,<sup>[</sup>\n##REF##26086918##\n35\n##, ##UREF##18##\n36\n##\n<sup>]</sup> among them crystalline materials with well‐defined structural information can provide insight into the catalytic mechanism at the atomic level. Crystalline materials are mainly focused on metal‐organic frameworks (MOFs),<sup>[</sup>\n##REF##18399629##\n37\n##\n<sup>]</sup> covalent organic frameworks (COFs)<sup>[</sup>\n##REF##30226522##\n38\n##\n<sup>]</sup>, and polyoxometalates (POMs).<sup>[</sup>\n##REF##29932201##\n39\n##\n<sup>]</sup> However, much of the work reported so far shows the structure of the catalyst or a single metal as the active site, neither of which provides insight into the catalytic mechanism. In our previous work, the binding of substrates to the aluminum‐based molecular rings during catalysis was tried and successfully confirmed.<sup>[</sup>\n##REF##37234899##\n40\n##\n<sup>]</sup> Considering the abundance of metal nodes (Al, Eu, and Cu as Lewis acid sites) and the porous nature of these heterometallic rings and their framework materials, they are potential Lewis acid catalysts and shed more light on the reaction from a multi‐metallic synergistic perspective. Hence, we chose cyanylation of benzaldehyde as a typical probe for Lewis acid‐catalyzed reactions.</p>", "<p>Quantitative product yields were obtained by catalyzing the reaction of benzaldehyde (0.5 mmol) with TMSCN (1 mmol) in CH<sub>2</sub>Cl<sub>2</sub> with 1.5 mol.% of AlOCs catalyst loading at room temperature under inert conditions for 2 h (<bold>Table</bold> ##TAB##1##\n2\n##). As shown in Table ##TAB##1##2## entries 1–3, aromatic ligands alone have little effect on the reaction (Figure ##SUPPL##0##S62##, Supporting Information). To clarify the catalytic active center, we synthesized a structural similar homometallic molecular ring <bold>AlOC‐79</bold> modified by isonicotinic acids (<bold>Figure</bold> ##FIG##4##\n4\n##; Figure ##SUPPL##0##S63##, Supporting Information). Compound <bold>AlOC‐79</bold> is a ten‐membered ring with an organic shell environment similar to <bold>AlOC‐131</bold>. We can see from the catalytic result that it did not catalyze as well as either of the heterometallic rings (<bold>AlOC‐130</bold> to <bold>AlOC‐133</bold>), suggesting that the introduction of lanthanide metal ions as Lewis acid sites enhances the catalysis (Table ##TAB##1##2## entry 4). The catalytic effects of the heterometallic molecular rings and their framework were in the order of <bold>AlOC‐130</bold>&lt; <bold>AlOC‐131</bold>&lt; <bold>AlOC‐132</bold>&lt; <bold>AlOC‐133</bold> (88.0%, 95.5%, 98.2%, and 99.9%, respectively) (Table ##TAB##1##2## entries 5–8). It is worth mentioning that the reaction was highly selective and no by‐products were observed (Figures ##SUPPL##0##S64–S67##, Supporting Information). The improved effect of <bold>AlOC‐131</bold> compared with <bold>AlOC‐130</bold> resulted from the presence of N‐substituted aromatic ring that facilitates binding the substrate to the catalyst. In addition, the coordination mode of the organic ligand also affects the catalytic reaction to some extent.<sup>[</sup>\n##REF##26086918##\n35\n##, ##REF##27010759##\n41\n##\n<sup>]</sup> As described in the structure section and shown in Figure ##SUPPL##0##S68## (Supporting Information), the emergence of a terminal isonicotinic and the local defect of the attack of water molecules on Al ions make it increase the Lewis base site and easier to contact with the substrate. The isostructural lanthanide series <bold>AlOC‐131‐Ln</bold> has a considerable catalytic effect, indicating the synergistic effect of Lewis acid site and surface ligand modification (Figure ##SUPPL##0##S69##, Supporting Information).</p>", "<p>The substrate range for the aldehyde cyanosilylation reaction was investigated using <bold>AlOC‐130</bold> as an example (Figure ##SUPPL##0##S70##, Supporting Information). Under standard conditions, when aromatic aldehydes with electronic effect substituents (electron‐donating ‐OCH<sub>3</sub>, electron‐withdrawing ‐CF<sub>3</sub>) or heterocyclic aldehydes were employed, the corresponding products were obtained in high yields after 2 h (85%–95%), which suggests that the reaction is broad tolerance to various substrates. However, 1‐naphthaldehyde and ketone obtained lower catalytic efficiency even after prolonged reaction time (24 h) (30%–40%), which may be related to the spatial site resistance of the substrates.</p>", "<p>Moreover, the catalytic effect of the heterotrimetallic compounds <bold>AlOC‐132</bold> and <bold>AlOC‐133</bold> are superior to those of the heterometallic molecular rings <bold>AlOC‐130</bold> and <bold>AlOC‐131</bold> not only in terms of yield but also in the rate of conversion, which is better illustrated by the presence of the pores structures and triple‐metal centers (Figure ##SUPPL##0##S71##, Supporting Information).<sup>[</sup>\n##UREF##18##\n36\n##, ##REF##30226522##\n38\n##, ##REF##29790543##\n42\n##\n<sup>]</sup> One possible reason for the rapid complete conversion (0.5 h) of the substrate catalyzed by the compound <bold>AlOC‐133</bold> includes the highest porosity throughout these series of compounds (5.1%, 14.1%, 61.8%, and 64.1% for <bold>AlOC‐30</bold> to <bold>AlOC‐133</bold>, respectively).<sup>[</sup>\n##REF##18399629##\n37\n##\n<sup>]</sup> Another reason is the presence of more regular 1D channels and favorable cavity environments (abundant aromatic walls and iodine atoms pointing toward the channel favor the formation of <italic toggle=\"yes\">π</italic>–<italic toggle=\"yes\">π</italic> interactions and O—H—I hydrogen bonding, respectively, with the substrate benzaldehyde) (Figures ##SUPPL##0##S72–S75##, Supporting Information). To investigate the Lewis acid properties of the heterometallic ring and its framework compounds, we performed pyridine FT‐IR spectroscopy. As shown in Figure ##SUPPL##0##S76## (Supporting Information), the pyridine FT‐IR pattern exhibited three signal peaks at 1039, 1047, and ≈1059 cm<sup>−1</sup> corresponding to the adsorption of pyridine on the Lewis acid sites.<sup>[</sup>\n##REF##21597609##\n43\n##, ##UREF##19##\n44\n##, ##UREF##20##\n45\n##, ##UREF##21##\n46\n##\n<sup>]</sup> As expected, the amount of Lewis acid sites increases with the order of catalytic effect. Hence, the synergy of the multiple Lewis acid sites, the pore cavity and the microenvironment are conducive to a good catalytic effect. Their performances are significantly better than those of lanthanide‐based polyoxometalates and MOFs (Table ##SUPPL##0##S9##, Supporting Information),<sup>[</sup>\n##REF##29932201##\n39\n##, ##UREF##22##\n47\n##, ##REF##29749730##\n48\n##\n<sup>]</sup> although their catalytic effect is inferior to those of monomer organo‐aluminum with flexible active sites.<sup>[</sup>\n##UREF##14##\n30\n##, ##REF##28580996##\n49\n##, ##UREF##23##\n50\n##\n<sup>]</sup>\n</p>" ]
[ "<title>Conclusion</title>", "<p>In summary, we have demonstrated the stepwise and controllable synthesis of mesoporous heterotrimetallic compounds based on predesigned metallocycles. This synthesis strategy can be extended to a broad range of metals and a handful of bifunctional linkers like pyrazolecarboxylate, imidazolecarboxylate, etc and their derivatives. It is worth mentioning that multi‐metallic centers in heterometallic rings and their framework compounds can serve as Lewis acid sites and are potentially excellent catalysts. Among them, the heterometallic molecular ring exhibits better catalytic activity compared to the homometallic aluminum molecular ring. And the porous heterotrimetallic framework with regular 1D channels, abundant aromatic walls, and larger cavity sizes showed a superior catalytic effect than the heterobimetallic molecular ring. This work provides methods to guide heterometallic molecular ring synthesis, surface modification, and designable assembly to produce porous framework materials and contributes to understanding catalytic reaction mechanisms from various perspectives of multi‐metallic centers, pore environments. In addition, such porous polymetallic frameworks may have broad applications in selective separation and photo(electro)catalysis.</p>" ]
[ "<title>Abstract</title>", "<p>The motivation for making heterometallic compounds stemmed from their emergent synergistic properties and enhanced capabilities for applications. However, the atomically precisely controlled synthesis of heterometallic compounds remains a daunting challenge of the complications that arise when applying several metals and linkers. Herein, a stepwise and controlled method is reported for the accurate addition of second and third metals to homometallic aluminum macrocycles based on the synergistic coordination and hard‐soft acid‐base theory. These heterometallic compounds showed a good Lewis acid catalytic effect, and the addition of hetero‐metals significantly improved the catalytic effect and rate, among that the conversion rate of compound AlOC‐133 reached 99.9% within half an hour. This method combines both the independent controllability of stepwise assembly with the universality of one‐step methods. Based on the large family of clusters, the establishment of this method paves the way for the controllable and customized molecular‐level synthesis of heterometallic materials and creates materials customized for preferential application.</p>", "<p>Here, a stepwise controllable method is developed to construct materials customized for the preferential catalytic application. Mesoporous heterotrimetallic framework compounds are obtained using a predesigned Al<sub>4</sub>Ln<sub>4</sub> heterodimetallic molecular ring. In addition, the catalytic effect on aldehydes is progressively improved by structurally introducing rare‐earth metals and surface ligand modifications, as well as by introducing a third metal to generate a mesoporous structure.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6798-cit-0052\">\n<string-name>\n<given-names>D.</given-names>\n<surname>Luo</surname>\n</string-name>, <string-name>\n<given-names>C.‐H.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>Y.‐B.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>S.‐T.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>W.‐H.</given-names>\n<surname>Fang</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Zhang</surname>\n</string-name>, <article-title>Stepwise and Controllable Synthesis of Mesoporous Heterotrimetallic Catalysts Based on Predesigned Al<sub>4</sub>Ln<sub>4</sub> Metallocycles</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305833</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305833</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Synthesis of the Predesigned Heterobimetallic Clusters and Extended Porous Heterotrimetallic Networks</title>", "<p>Colorless strips <bold>AlOC‐130</bold> crystals were synthesized by amino‐polyalcohol solvothermal synthesis reaction of aluminum isopropoxide (204 mg, 1 mmol), europium nitrate hexahydrate (60 mg, 0.13 mmol), and sodium benzoate (150 mg, 1 mmol) in a solvent mixture containing N‐methyldiethanolamine (2.5 mL) and DMF (2.5 mL) at 120 °C for 4 days. When sodium benzoate was substituted with isonicotinic acid, colorless bulk crystals of compound <bold>AlOC‐131</bold> were isolated. Yellow needle‐like <bold>AlOC‐132</bold> and yellow columnar crystals of <bold>AlOC‐133</bold> were obtained by adding n‐propanol suspension of cuprous iodide to the above system by HIN and lengthened Hpyba ligand, respectively. For a more detailed synthesis process please refer to the Electronic Supporting Information (ESI).</p>", "<title>X‐ray Crystallography</title>", "<p>Single crystal X‐ray diffraction data of AlOCs were collected on Hybrid Pixel Array detector equipped with Ga‐Kα radiation (λ = 1.3405 Å) at about 100 K. The structures were solved with the dual‐direct methods using ShelxT and refined with the full‐matrix least‐squares technique based on F<sup>2</sup> using the SHELXL.<sup>[</sup>\n##UREF##24##\n51\n##\n<sup>]</sup> Non‐hydrogen atoms were refined anisotropically. Hydrogen atoms were added theoretically, riding on the concerned atoms and refined with fixed thermal factors. All absorption corrections were performed using the multi‐scan program. The crystals of the compounds <bold>AlOC‐132</bold> and <bold>AlOC‐133</bold> are so small that high angle diffraction is weak. Some of the atoms on the chelating ligand N‐methyldiethanolamine could not be fixed. Despite many attempts, it ended up with failure. Their presence has also been confirmed by a variety of other characterizations including FT‐IR, EDS, and so on. The obtained crystallographic data are summarized in Tables ##SUPPL##0##S10,S11## (Supporting Information).</p>", "<title>General Procedure of Cyanosilylation</title>", "<p>The mixture of aldehyde, trimethylsilyl cyanide (TMSCN) and CH<sub>2</sub>Cl<sub>2</sub> was added to the schlenk tube (0.5 mmol aldehyde, 1 mmol TMSCN and 5 mL CH<sub>2</sub>Cl<sub>2</sub>), where AlOCs had been introduced in advance. The mixture was stirred (200 rpm) at room temperature for 2 h, under N<sub>2</sub> atmosphere. Yields were determined by <sup>1</sup>H‐NMR analysis using CH<sub>2</sub>Br<sub>2</sub> as an internal standard.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>Research reported in this publication was supported by the National Natural Science Foundation of China (22371278, 92061104), the Funding of Fujian Provincial Chemistry Discipline Alliance, the National Key Research and Development Project (2022YFA1503900), the Natural Science Foundation of Fujian Province (2021J06035) and the Youth Innovation Promotion Association CAS (Y2021081).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6798-fig-0005\"><label>Scheme 1</label><caption><p>The synthetic strategy toward the mesoporous heterometallic compounds.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6798-fig-0001\"><label>Figure 1</label><caption><p>One‐step and two‐step synthesis strategy of heterometallic pore structures based on predesigned ring compounds. (The inset is a photograph of their crystals under a microscope, the scale bar is 100 µm).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6798-fig-0002\"><label>Figure 2</label><caption><p>Molecular structures of heterobimetallic molecular rings. a) Ball‐and‐stick and space‐filling modeling diagram of the compound <bold>AlOC‐130</bold>. b) Stacking diagram of the compound <bold>AlOC‐130</bold> c) Ball‐and‐stick and space‐filling modeling diagram of the compound <bold>AlOC‐131</bold>. d) Stacking diagram of the compound <bold>AlOC‐131</bold>. Hydrogen atoms are omitted for clarity. Color code: Al, green; Eu: pink; C, gray; O, red; N, and blue. Black lines represent unit cells. Non‐metal atoms have been omitted for clarity of the schematic.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6798-fig-0003\"><label>Figure 3</label><caption><p>The molecular structures of mesoporous heterotrimetallic compounds. Ball‐and‐stick diagram of the {Al<sub>4</sub>Ln<sub>4</sub>} unit in the a) compound <bold>AlOC‐132,</bold> and e) compound <bold>AlOC‐133</bold>. Stacking diagram of b) compound <bold>AlOC‐132</bold> and f) compound <bold>AlOC‐133</bold> along [001] direction. Different colors indicate different layers of the interspersed structure. Cavities in the c) compound <bold>AlOC‐132</bold> and g) compound <bold>AlOC‐133</bold>. Perspective view of void space of d) compound <bold>AlOC‐132</bold> and h) compound <bold>AlOC‐133</bold> along <italic toggle=\"yes\">c</italic>‐axis. Hydrogen and some non‐metal atoms are omitted for clarity. Color code: Al, green; Eu: pink; Cu, blue; I: violet; C, gray; O, red; N, blue.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6798-fig-0004\"><label>Figure 4</label><caption><p>The molecular structure and supramolecular packing diagram of AlOC‐79.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6798-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Summary of heterometallic rings compounds: crystal data and structure refinement results.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">compounds</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">formula<xref rid=\"advs6798-tbl1-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">sp.gr.</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">a</italic> (Å)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">b</italic> (Å)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">c</italic> (Å)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">V</italic> (Å)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">R</italic>\n<sub>int</sub>\n<xref rid=\"advs6798-tbl1-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">CCDC<xref rid=\"advs6798-tbl1-note-0003\" ref-type=\"table-fn\">\n<sup>c)</sup>\n</xref>\n</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>AlOC‐130</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Al<sub>4</sub>Eu<sub>4</sub>(BA)<sub>8</sub>(mdea)<sub>8</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">P</italic>‐42<sub>1</sub>c</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">23.3687(10)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">23.3687(10)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.8818(10)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5396.41(7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.0386</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2288338</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>AlOC‐131</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[Al<sub>4</sub>Eu<sub>4</sub>(IN)<sub>8</sub>(mdea)<sub>8</sub> (H<sub>2</sub>O)]·2H<sub>2</sub>O</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">P</italic>2<sub>1</sub>/n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18.9563(2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">21.8313(2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27.7034(4)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11447.5(2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.0592</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2288339</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>AlOC‐132</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Al<sub>4</sub>Eu<sub>4</sub>Cu<sub>4</sub>I<sub>4</sub>(IN)<sub>8</sub>(mdea)<sub>8</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">I</italic>4/mmm</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31.674 (4)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31.674 (4)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">25.087 (5)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">25169(7)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.0998</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2288340</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>AlOC‐133</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Al<sub>4</sub>Eu<sub>4</sub>Cu<sub>4</sub>I<sub>4</sub>(pyba)<sub>8</sub>(mdea)<sub>8</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">C</italic>mcm</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">41.3594(17)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17.9180(8)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40.8506(15)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30273(2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.1618</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2288341</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6798-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Comparison of benzaldehyde cyanosilylation reactions catalyzed by different catalysts.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th colspan=\"4\" align=\"center\" rowspan=\"1\">\n\n</th></tr><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Entry<xref rid=\"advs6798-tbl2-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Catalytic</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Time (h)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Yield (%)<xref rid=\"advs6798-tbl2-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HIN<xref rid=\"advs6798-tbl2-note-0003\" ref-type=\"table-fn\">\n<sup>c)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">None</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Hpyba<xref rid=\"advs6798-tbl2-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">None</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">BA<xref rid=\"advs6798-tbl2-note-0005\" ref-type=\"table-fn\">\n<sup>e)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">None</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AlOC‐79<xref rid=\"advs6798-tbl2-note-0006\" ref-type=\"table-fn\">\n<sup>f)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">70.1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<bold>AlOC‐130</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">88.0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<bold>AlOC‐131</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">95.5</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<bold>AlOC‐132</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">98.2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<bold>AlOC‐133</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">99.9</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
[]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
[]
[]
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[ "<supplementary-material id=\"advs6798-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6798-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplementary Movie 1</p></caption></supplementary-material>", "<supplementary-material id=\"advs6798-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplementary Movie 2</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6798-tbl1-note-0001\"><label>\n<sup>a)</sup>\n</label><p>Abbreviations: BA = benzoic acid; IN = isonicotinic acid; mdea = N‐methyldiethanolamine; pyba = 4‐(4‐pyridy)benzoic acid;</p></fn><fn id=\"advs6798-tbl1-note-0002\"><label>\n<sup>b)</sup>\n</label><p>Crystallographic data of the structures were solved with direct methods using OLEX2 v1.2 © OlexSys Ltd. 2004 – 2023. Detailed X‐ray crystallographic data are provided in Tables ##SUPPL##0##S10,S11## (Supporting Information);</p></fn><fn id=\"advs6798-tbl1-note-0003\"><label>\n<sup>c)</sup>\n</label><p>CCDC numbers are applied from the Cambridge Crystallographic Data Centre database. The crystal under investigation showed no significant intensity at a high angle and the increasing flexibility of the lengthened carbon chain compromising the data quality and the model obtained.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"advs6798-tbl2-note-0001\"><label>\n<sup>a)</sup>\n</label><p>Reaction conditions: catalyst 1.5 mol%, aldehyde 0.5 mmol, TMSCN 1 mmol, and CH<sub>2</sub>Cl<sub>2</sub> as solvent, temperature (303 K) under N<sub>2</sub>;</p></fn><fn id=\"advs6798-tbl2-note-0002\"><label>\n<sup>b)</sup>\n</label><p>Yields were determined by <sup>1</sup>H NMR using CH<sub>2</sub>Br<sub>2</sub> as an internal standard;</p></fn><fn id=\"advs6798-tbl2-note-0003\"><label>\n<sup>c)</sup>\n</label><p>HIN = isonicotinic acid;</p></fn><fn id=\"advs6798-tbl2-note-0004\"><label>\n<sup>d)</sup>\n</label><p>Hpyba = 4‐(4‐pyridy) benzoic acid;</p></fn><fn id=\"advs6798-tbl2-note-0005\"><label>\n<sup>e)</sup>\n</label><p>BA = benzoic acid;</p></fn><fn id=\"advs6798-tbl2-note-0006\"><label>\n<sup>f)</sup>\n</label><p>A ring of aluminum molecules protected by isonicotinic acid and ethoxy (Figure ##FIG##4##4##, Figure ##SUPPL##0##S63##, Supporting Information).<sup>[</sup>\n##UREF##11##\n25\n##\n<sup>]</sup>\n</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2305833-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305833-s002.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305833-s003.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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Technol."], "year": ["2020"], "volume": ["10"], "fpage": ["1699"]}, {"label": ["47"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["M.", "A.", "B.", "J.", "J.", "T.", "Z.", "G.", "X."], "surname": ["Gustafsson", "Bartoszewicz", "Mart\u00edn\u2010Matute", "Sun", "Grins", "Zhao", "Li", "Zhu", "Zou"], "source": ["Chem. Mater."], "year": ["2010"], "volume": ["22"], "fpage": ["3316"]}, {"label": ["50"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n"], "given-names": ["S.", "M.", "B.", "S."], "surname": ["Rawat", "Bhandari", "Prashanth", "Singh"], "source": ["ChemCatChem"], "year": ["2020"], "volume": ["12"], "fpage": ["2407"]}, {"label": ["51"], "mixed-citation": ["\n"], "string-name": ["\n"], "given-names": ["G. M."], "surname": ["Sheldrick"], "source": ["Acta Cryst."], "year": ["2015"], "volume": ["71"], "fpage": ["3"]}]
{ "acronym": [], "definition": [] }
51
CC BY
no
2024-01-14 23:41:55
Adv Sci (Weinh). 2023 Nov 16; 11(2):2305833
oa_package/cd/05/PMC10787057.tar.gz
PMC10787058
37967351
[ "<title>Introduction</title>", "<p>Breast and prostate cancers are the two most prevalent types worldwide with over 1 million deaths globally each year, predominantly due to metastatic disease.<sup>[</sup>\n##UREF##0##\n1\n##\n<sup>]</sup> Tumor metastasis is one of the most critical events in cancer development, after which five‐year patient survival rates in the UK decreases from 90–98% when diagnosed at Stage I‐II, to 26% at Stage IV for breast cancer, and 99% to 30% at equivalent stages for prostate cancer.<sup>[</sup>\n##UREF##1##\n2\n##\n<sup>]</sup> One of the most common sites for tumor metastasis is bone, with over 450,000 patients currently suffering from this condition in the US.<sup>[</sup>\n##REF##15084698##\n3\n##\n<sup>]</sup> Indeed, it is the preferred site for breast and prostate cancer metastasis,<sup>[</sup>\n##REF##21701513##\n4\n##\n<sup>]</sup> with 65−75% of patients with metastases developing skeletal lesions that account for &gt;80% of all cases of metastatic bone disease.<sup>[</sup>\n##REF##11417967##\n5\n##, ##REF##26539296##\n6\n##\n<sup>]</sup> Recent research has shown that metastatic spread occurs early in breast cancer development,<sup>[</sup>\n##REF##27974799##\n7\n##, ##REF##18167340##\n8\n##\n<sup>]</sup> and disseminated tumor cells are present in bone marrow by the time primary tumors are diagnosed.<sup>[</sup>\n##UREF##2##\n9\n##\n<sup>]</sup> Once metastatic tumors develop in bone, the median survival time is 1–4 years,<sup>[</sup>\n##REF##11417967##\n5\n##\n<sup>]</sup> indicating that metastasis is now a common cause of death and suffering in breast and prostate cancer patients.<sup>[</sup>\n##REF##21593787##\n10\n##\n<sup>]</sup> Despite this, the mechanisms by which metastatic tumors develop in bone from disseminated tumor cells, and the interactions between bone cells and cancer cells, remain poorly understood.</p>", "<p>Much research into the effects of metastatic cancer cells in bone has focussed on the marrow, and interactions with the array of bone cell types found there.<sup>[</sup>\n##REF##21593787##\n10\n##\n<sup>]</sup> However, osteocytes represent &gt;90% of bone cells,<sup>[</sup>\n##REF##22552701##\n11\n##\n<sup>]</sup> are spread throughout mineralized bone tissue and are known to be the primary regulator of this environment, orchestrating the behavior of other bone cells in response to mechanical loading.<sup>[</sup>\n##UREF##3##\n12\n##\n<sup>]</sup> Despite their important regulatory role, osteocyte interactions with cancer cells have only recently begun to be explored. Initial conditioned media experiments showed that signals secreted by osteocytes could alter proliferation and migration in a range of breast and prostate cancer cells,<sup>[</sup>\n##REF##26977015##\n13\n##\n<sup>]</sup> Their importance has been further demonstrated in breast cancer through the application of mechanical loading, showing that conditioned media from osteocytes stimulated using oscillatory fluid flow can reduce the trans‐endothelial migration of triple‐negative MDA‐MB‐231 breast cancer cells, possibly through signaling to osteoclasts and endothelial cells as intermediaries.<sup>[</sup>\n##REF##29384215##\n14\n##, ##REF##30417549##\n15\n##\n<sup>]</sup> Additional research into oestrogen receptor‐positive MCF‐7 breast cancer cells observed increased proliferation and migration when treated with conditioned media of mechanically stimulated osteocytes, identifying CXCL1/2 as a potential mechanism.<sup>[</sup>\n##REF##33310182##\n16\n##\n<sup>]</sup> A significant recent advance in the field of cancer research is the development of microfluidic platforms<sup>[</sup>\n##REF##36765593##\n17\n##\n<sup>]</sup> designed to replicate extravasation of MDA‐MB‐231 cells in the presence of osteocytes, demonstrated reduced extravasation with mechanical stimulation of the bone cells.<sup>[</sup>\n##UREF##4##\n18\n##\n<sup>]</sup> In a similar manner, our group has recently observed increased invasive behavior in both breast and prostate cancer cells when osteocytes were mechanically stimulated in an organ‐chip model of metastatic bone disease.<sup>[</sup>\n##REF##34200761##\n19\n##\n<sup>]</sup> However, almost no research has investigated the cytokine crosstalk between cancer cells and osteocytes in co‐culture, which is perhaps more representative of an established metastatic tumor microenvironment.</p>", "<p>It is clear that osteocytes are emerging as a key regulator of metastasis in breast cancer, and possibly also in prostate cancer. However, the molecular mechanisms through which osteocytes regulate cancer cells remain unknown. Even less is known about how a developing mass of tumor cells affects osteocytes, with possible consequences for modulation of cancer cell behavior and downstream bone remodeling. Therefore, the objective of this study is to take a step‐wise approach, selectively adjusting conditioned media and co‐culture studies to replicate osteocyte‐ and cancer‐dominated environments found in vivo, teasing apart the mechanisms through which breast and prostate cancer cells interact with bone cells and the bone microenvironment to form metastatic tumors.</p>" ]
[]
[ "<title>Results</title>", "<title>Osteocyte Conditioned Media, but Not Co‐Culture, Suppresses Proliferation and Increases Migration in Both Breast and Prostate Cancer Cells</title>", "<p>We first examined the effect of osteocyte conditioned media (CM) on cancer cell behavior and compared this with the effect of osteocytes in co‐culture (Co‐C) with the cancer cells. We suggest that the conditioned media experiments are more representative of early metastasis where there are insufficient cancer cell numbers to regulate the osteocytes, while co‐culture maybe more representative of established metastatic colonies (see schematic in <bold>Figure</bold>\n##FIG##0##\n1A##). Addition of conditioned media from osteocytes resulted in significantly reduced proliferation, of up to 26%, in both of the breast cancer cell lines and both of the prostate cancer cell lines (Figure ##FIG##0##1B##). In contrast, conditioned media resulted in large increases in migration (up to 144%) in each cancer cell type (Figure ##FIG##0##1C##). Hence, secreted factors from osteocytes push cancer cells into a more migratory, anti‐proliferative phenotype. While a small, but significant, increase in invasion of MDA‐MB‐231 breast cancer cells was observed with conditioned media and co‐culture, no significant changes were observed in other cell lines with regard to invasion (Figure ##FIG##0##1D##). This pattern continued in other experiments and thus the remaining invasion results have been included in Figure ##SUPPL##0##S1## (Supporting Information)</p>", "<p>In contrast, co‐culture with osteocyte cells made no significant difference to either proliferation or migration behavior of cancer cells, when compared to control cancer cells in standard media. This indicates the osteocyte regulation of cancer cells, as seen with conditioned media, is blocked by the cancer cells, suggesting changes in crosstalk between the two cell populations as metastatic colonies develop.</p>", "<title>Osteocyte Regulation of Breast and Prostate Cancer Cell Proliferation and Migration is Inhibited by TGF‐β Released from Cancer Cells</title>", "<p>The observation that osteocyte regulation of cancer cells is absent in co‐culture suggests soluble factors from cancer cells may be responsible for suppressing this osteocyte behavior. A prime candidate for mediating this crosstalk was transforming growth factor (TGF‐β), known to be secreted by many cancer cell types. Indeed, we found significant amounts of TGF‐β were released by all four cancer cell lines tested here, with 2.4 to 4.3 fold increases compared to standard control media (<bold>Figure</bold>\n##FIG##1##\n2A##, with concentrations in Figure ##SUPPL##0##S2##, Supporting Information). To test the involvement of TGF‐β in regulating this behavior, we pre‐treated osteocytes with TGF‐β and then collected conditioned media, with this treatment inhibiting the decreased proliferation and increased migration stimulated by osteocyte conditioned media (Figure ##FIG##1##2B##). To further test this, a knockdown of TGF‐β receptor I in osteocytes in co‐culture was performed via siRNA transfection (confirmation of knockdown in Figure ##SUPPL##0##S3##, Supporting Information). Osteocyte TGF‐β receptor I knockdown in co‐culture resulted in significantly decreased cancer cell proliferation (by up to 24%, Figure ##FIG##1##2C##) and significantly increased cancer cell migration (by up to 149%, Figure ##FIG##1##2C##; Figure ##SUPPL##0##S3## Supporting Information), when compared to both non‐transfected and scrambled transfected controls. The behavior of cancer cells in co‐culture with osteocytes lacking TGF‐β receptor I, is strikingly similar to that observed in conditioned media in Figure ##FIG##0##1##. Together, these results indicate that cancer cell secretion of TGF‐β blocks the osteocyte regulation of cancer cell proliferation and migration.</p>", "<title>TGF‐β Secreted by Breast and Prostate Cancer Cells Reduces Expression of Osteocyte Primary Cilia and IFT88</title>", "<p>We next determined the effect of cancer cell‐secreted TGF‐β on the osteocytes as a first step to identifying the mechanism through which osteocytes regulate cancer cells. The primary cilium, a slender organelle typically protruding from the cell surface (shown via confocal and SR‐SIM images in <bold>Figure</bold>\n##FIG##2##\n3A##), is a key chemosignaling nexus present in almost all mammalian cells, with the notable exception of proliferating cancer cells where it is instead associated with increased drug resistance.<sup>[</sup>\n##REF##29874589##\n20\n##\n<sup>]</sup> In osteocytes, it is known to govern a range of important pathways, including Wnt, Hedgehog and mechanosignaling.<sup>[</sup>\n##UREF##5##\n21\n##\n<sup>]</sup> In standard cell culture, 40–60% of osteocytes expressed a primary cilium, with lengths of ≈3–4 µm (<bold>Figure</bold>\n##FIG##3##\n4\n##). Immunofluorescence imaging of osteocytes demonstrated that TGF‐β reduced osteocyte primary cilia prevalence and length, in agreement with findings reported in other cell types.<sup>[</sup>\n##REF##30038235##\n22\n##, ##REF##28271209##\n23\n##, ##REF##25828538##\n24\n##\n<sup>]</sup> Furthermore, conditioned media from each cancer cell line also induced similar changes in cilia expression with shorter cilia and prevalence decreased to 20% (Figure ##FIG##3##4##; Figure ##SUPPL##0##S4##, Supporting Information). Similarly, cancer cells also down‐regulated cilia expression in osteogenically‐differentiated human MSCs (Figure ##SUPPL##0##S5##, Supporting Information). Cancer cell conditioned media also induced decreased mechanosensitivity in osteocytes as measured by cyclooxygenase‐2 (COX‐2) mRNA expression, an important regulator of downstream osteogenic signaling (Figure ##SUPPL##0##S6A##, Supporting Information). Using siRNA for intraflagellar transport protein 88 (IFT88) to knockdown osteocyte primary cilia, we found that this disrupted osteocyte mechanosensitivity did indeed abrogate the mechano‐regulated control of breast cancer cell proliferation, as we observed previously.<sup>[</sup>\n##REF##34200761##\n19\n##\n<sup>]</sup> However, no effect on prostate cancer cells was observed (Figure ##SUPPL##0##S6B##, Supporting Information). Reduction in cilia expression caused by TGF‐β or cancer cell conditioned media was also associated with rounding of osteocytes, as measured by significant changes in circularity and cell area (Figure ##FIG##3##4##; Figures ##SUPPL##0##S4## and ##SUPPL##0##S7##, Supporting Information). These changes in morphology suggest reduced actin tension, which has previously been shown to inhibit cilia expression.<sup>[</sup>\n##REF##33392209##\n25\n##\n<sup>]</sup> TGF‐β treatment also reduced osteocyte expression of the intraflagellar transport gene, IFT88 (<bold>Figure</bold>\n##FIG##4##\n5\n##), which controls ciliagenesis as demonstrated in various cell types including osteoblasts and chondrocytes.<sup>[</sup>\n##REF##30038235##\n22\n##, ##REF##28271209##\n23\n##, ##REF##25828538##\n24\n##\n<sup>]</sup> We then sought to block TGF‐β regulation of osteocyte primary cilia expression using either small molecule inhibitor of TGF‐β receptor I or siRNA transfection. The effectiveness of both approaches was confirmed by the complete inhibition of any changes in cilia length or prevalence induced by TGF‐β treatment (Figure ##FIG##4##5##). Disruption of TGF‐β receptor I was then shown to inhibit the effect of cancer cell conditioned media on osteocyte cilia expression (Figure ##FIG##4##5##). Thus, we demonstrate that cancer cells suppress the expression of osteocyte primary cilia/IFT88 via the release of TGF‐β.</p>", "<title>Osteocyte Primary Cilia/IFT88 are Required for Regulation of Cancer Cell Proliferation and Migration</title>", "<p>We have shown that the disruption of cancer cell proliferation and migration by osteocytes is suppressed by release of TGF‐β from cancer cells, and that TGF‐β also disrupts osteocyte cilia and IFT88 expression (Figures ##FIG##3##4## and ##FIG##4##5##). We, therefore, sought to determine whether the inhibition of osteocyte regulation of cancer cell behavior was due to the reduced expression of osteocyte cilia/IFT88 or via another TGF‐β‐mediated pathway. To achieve this we employed a knockdown of osteocyte primary cilia via IFT88 siRNA transfection as confirmed by confocal immunofluorescence, qPCR, and western blot (Figure ##SUPPL##0##S8##, Supporting Information). This resulted in reduced cilia expression without any significant changes in cell morphology (Figure ##SUPPL##0##S9##, Supporting Information). Conditioned media from osteocytes transfected with scrambled siRNA significantly reduced cancer cell proliferation and increased migration compared to that seen in cancer cells alone (<bold>Figure</bold>\n##FIG##5##\n6A,B##). This response occurred in the two breast cancer cell lines and in the two prostate cancer cell lines, mirroring the effect of conditioned media from non‐transfected osteocytes (Figure ##FIG##0##1##). However, this response was blocked when using conditioned media from osteocytes transfected with siRNA to IFT88, with significant differences between the response between IFT88 siRNA and scrambled control (Figure ##FIG##5##6A,B##). Consequently, there were no statistically significant differences in proliferation or migration compared to cancer cells alone. Thus, these effects of conditioned media from osteocytes with IFT88/cilia knockdown, replicate the behavior seen in co‐culture (Figure ##FIG##0##1##).</p>", "<title>Disruption of Osteocyte Primary Cilia Inhibits TNF‐α Release, which Modulates Cancer Cell Behavior</title>", "<p>We have now shown that osteocytes suppress cancer cell proliferation and increase migration and that this response is blocked by cancer cell secretion of TGF‐β. In this final section, we sought to identify the paracrine signaling mechanism through which osteocytes regulate cancer cell behavior. We have shown that this signaling is blocked by inhibition of osteocyte primary cilia/IFT88 expression via cancer cell secretion of TGF‐β. Therefore, a cytokine array of 32 standard pro‐inflammatory targets was used to compare media from TGF‐β treated and IFT88 KD osteocytes with their respective vehicle or scrambled siRNA controls (<bold>Figure</bold>\n##FIG##6##\n7A,B\n##; Figures ##SUPPL##0##S10## and ##SUPPL##0##S11##, Supporting Information). A protein‐protein interaction (PPI) network of the targets present in the cytokine array was generated using STRING<sup>[</sup>\n##REF##12519996##\n26\n##\n<sup>]</sup> indicating a cluster of interacting proteins (Figure ##SUPPL##0##S12##, Supporting Information), four of which were highly differentially expressed in our cytokine arrays. Interleukin 10 (IL‐10) and tumor necrosis factor alpha (TNF‐α) demonstrated &gt;1.5‐fold changes in secretion that were similar in both TGF‐β treated and IFT88 KD osteocytes as shown in the heatmap in Figure ##FIG##6##7A##. Subsequent analysis of TNF‐α via an ELISA confirmed this similarity in behavior (Figure ##FIG##6##7C##; Figure ##SUPPL##0##S13##, Supporting Information). By contrast, interleukin 6 (IL‐6) and vascular endothelial growth factor (VEGF) demonstrated the least similar responses between the two groups.</p>", "<p>When these four pro‐inflammatory factors were added to cancer cells, TNF‐α was the only cytokine to cause a decrease in proliferation alongside an increase in migration (Figure ##FIG##5##6D,E##). The similarity of this pattern of behavior to that induced by osteocyte conditioned media, implicates TNF‐α as a potential cytokine secreted by osteocytes to regulate cancer cell proliferation and migration. This was confirmed via addition of a TNF‐α small‐molecule inhibitor to osteocyte conditioned media, which significantly inhibited the decreased cancer cell proliferation and increased migration such that there were no significant differences compared to cancer cells alone (<bold>Figure</bold>\n##FIG##7##\n8A##).</p>", "<p>Thus, we suggest the following bi‐direction or feedback mechanism regulating cancer cell behavior as shown schematically in <bold>Figure</bold>\n##FIG##8##\n9\n##:\n<list list-type=\"simple\" id=\"advs6797-list-0001\"><list-item><p>‐TNF‐α is secreted by osteocytes, which in early metastasis, vastly outnumber cancer cells, suppressing proliferation of breast and prostate cancer cells, while encouraging migration (Figure ##FIG##8##9A##).</p></list-item><list-item><p>‐This behavior is dependent on osteocyte primary cilia and associated IFT88, which are inhibited in established metastatic colonies by increased TGF‐β secreted by the higher number of cancer cells (Figure ##FIG##8##9B##).</p></list-item><list-item><p>‐This disruption of the cilia/IFT88 expression blocks TNF‐α secretion from osteocytes, thereby switching off both the inhibition of cancer cell proliferation and the up‐regulation of migration.</p></list-item><list-item><p>‐Hence, increased numbers of cancer cells produce more TGF‐β, further disabling osteocyte TNF‐α secretion in a positive feedback loop reducing cancer cell migration and increasing proliferation, thereby accelerating metastatic tumor growth.</p></list-item></list>\n</p>", "<p>This hypothesis is further corroborated by RNAseq studies publicly available as part of “The Cancer Genome Atlas (TCGA)” and analyzed using KMPlot<sup>[</sup>\n##REF##34309564##\n27\n##\n<sup>]</sup> in which there is a trend of lower rates of disease‐free survival in breast and prostate cancer patients with low expression of TNF‐α receptors (Figure ##SUPPL##0##S14A##, Supporting Information). These data indicate a selective advantage for cancer cells that cannot sense this osteocyte signaling. Similarly, gene transcription data from previous metastatic databases analyzed using TNMPlot<sup>[</sup>\n##REF##33807717##\n28\n##\n<sup>]</sup> showed a trend of decreased expression of TNF‐α receptors in metastatic tissue compared to primary breast or prostate tumors (Figure ##SUPPL##0##S14B##, Supporting Information), matching with our feedback mechanism hypothesis.</p>", "<p>This hypothesis is used to develop a simple numerical model of metastatic cancer cell growth as presented in Figure ##FIG##7##8C##. Taking the average doubling rate of the cancer cells via fold change in proliferation observed over 24 and 48 h periods, and applying an ≈20% suppression of proliferation observed via osteocytes, we have modeled an estimated cell growth curve (Figure ##FIG##8##9C##). This predicts an initial slow growth rate of cancer cells up to a tipping point, beyond which growth rate accelerates as osteocyte suppression is attenuated by cancer cells.</p>", "<p>More complex in vitro models, such as organ‐on‐a‐chip models composed of all‐human cells and incorporating a more complex 3D tumor microenvironment, will strengthen further analysis of this novel mechanism.<sup>[</sup>\n##REF##36765593##\n17\n##\n<sup>]</sup> Therefore, we have constructed tumor spheroids from the cancer cell lines and tested the effects of both the mouse osteocyte cell line and osteogenically‐differentiated human MSCs on their proliferation, finding no significant difference in spheroid growth between the mouse and human cells (Figure ##FIG##7##8B,C##). A trend toward increased proliferation was observed when the MCF‐7 spheroids were stimulated with human MSC conditioned media, which may arise from the fact that, while these cells are osteogenically differentiated they cannot be fully pushed down the differentiation pathway toward terminally differentiated osteocytes. While we have not explored endothelial to mesenchymal transition (EMT) in this study, this process may play a role in some of the changes seen in our model. To further explore these questions, we have now built upon our previous organ‐on‐a‐chip model of cancer cells and osteocytes<sup>[</sup>\n##REF##34200761##\n19\n##\n<sup>]</sup> to build an all‐human organ‐chip model of 3D suspended osteogenically‐differentiated human MSCs and 3D spheroids of human cancer cells (Figure ##FIG##8##9D,E##). Future work with this new bone metastasis organ‐chip model will allow further investigation and therapeutic testing in a more complex 3D human tumor microenvironment.</p>" ]
[ "<title>Discussion</title>", "<p>This study presents a novel cytokine mechanism, common to both breast and prostate cancer, whereby osteocytes can suppress cancer cell proliferation via TNF‐α secretion. This anti‐proliferative mechanism is primary cilium‐ or IFT88‐dependent, and can be suppressed by TGF‐β released by cancer cells. These findings present the intriguing prospect of a positive feedback loop, whereby breast and prostate cancer cells disable this anti‐cancer mechanism to encourage further proliferation of cancer cells, greater production of TGF‐β, and further knockdown of osteocyte regulation. These mechanisms present new therapeutic targets to prevent further growth of bone metastatic tumors, including potential ciliotherapies.</p>", "<p>This study used MLO‐Y4 osteocyte‐like cells of mouse origin, with breast (MDA‐MB‐231 and MCF‐7) and prostate (PC‐3 and LNCaP) cancer cells of human origin. Despite the limitations provided by the species difference, these cancer cell lines are very well‐established and have been studied extensively in mouse models of cancer cell metastasis.<sup>[</sup>\n##REF##27867497##\n29\n##, ##REF##23580590##\n30\n##\n<sup>]</sup> A key limitation of the MLO‐Y4 cell line is low sclerostin expression, which prevents us from investigating the effect of this pathway in bone metastasis. However, MLO‐Y4 cells are the most well‐understood osteocyte cell‐line.<sup>[</sup>\n##REF##23612223##\n31\n##\n<sup>]</sup> The use of these established cell lines provided greater reproducibility than would be possible with human primary cells, which are terminally differentiated and would have been difficult to obtain in the quantities required for this study. In the absence of terminally differentiated primary human osteocytes, we repeated a number of experiments using osteogenically‐differentiated primary human MSCs, finding no significant difference between our results and those from the MLO‐Y4 cell line. The approach of sequential conditioning and co‐culture is less physiologically representative than an in vivo system, but allowed us to isolate effects and investigate specific molecular interactions between two cell types. Moreover, the use of conditioned media and transwell co‐culture means only soluble factors could have an impact on our observations, and this is more representative than direct contact with osteocytes, which are dispersed and embedded in the bone matrix. Finally, there are well‐accepted limitations of 2D monolayer cultures as being unrepresentative of the tumor microenvironment, and so we have replicated a number of our findings in 3D spheroids of cancer cell lines, and have developed a fully human organ‐on‐a‐chip model to test this mechanism in a more physiologically relevant microenvironment.</p>", "<p>Osteocyte regulation of cancer cell behavior has been observed previously, with conditioned media found to alter proliferation, migration, invasion, and extravasation of cancer cells.<sup>[</sup>\n##REF##26977015##\n13\n##, ##REF##29384215##\n14\n##, ##REF##30417549##\n15\n##, ##REF##33310182##\n16\n##, ##UREF##4##\n18\n##, ##REF##34200761##\n19\n##\n<sup>]</sup> A recent study has begun the important work of explaining these changes, proposing a potential CXCL1/2‐mediated mechanism through which osteocytes may regulate proliferation of breast cancer cells.<sup>[</sup>\n##REF##33310182##\n16\n##\n<sup>]</sup> However, a general mechanism through which osteocytes control both breast and prostate cancer cell behaviors remains unknown. Our experiments demonstrated a range of pro‐inflammatory cytokines expressed by osteocytes, with TNF‐α presenting as the candidate mostly likely to explain the patterns of decreased proliferation and increased migration resulting from osteocyte conditioned media. Thus, we identify a new mechanism through which invading cancer cells, initially entering an environment regulated by osteocytes, progressively corrupt this environment through disruption of osteocyte signaling. Indeed, this inhibition of cancer cell proliferation by osteocytes may play a role in the observed dormancy of breast and prostate cancer cells before establishing metastatic colonies in bone tissue.<sup>[</sup>\n##REF##19147774##\n32\n##, ##REF##8931609##\n33\n##, ##REF##25801619##\n34\n##\n<sup>]</sup>\n</p>", "<p>It is particularly interesting that this anti‐proliferative signaling can be shut down via soluble TGF‐β, which was secreted in large quantities by all four breast and prostate cancer cell lines. As mentioned above, osteocytes may encourage an apparently dormant state for metastatic cells via TNF‐α, a theory supported by trends of higher recurrence‐free survival in patients with higher TNF‐α receptor expression in the TCGA.<sup>[</sup>\n##REF##34309564##\n27\n##\n<sup>]</sup> In our working model of this mechanism the invading metastatic cancer cells produce TGF‐β, initially in small quantities, which begins to shut down this anti‐cancer mechanism upon contact with osteocyte TGF‐β receptors. This would be exacerbated via cancer cells upregulating osteoclast activity through other established pathways,<sup>[</sup>\n##REF##15734993##\n35\n##, ##REF##11375413##\n36\n##\n<sup>]</sup> releasing TGF‐β sequestered in the surrounding bone matrix and further flooding the microenvironment with TGF‐β.<sup>[</sup>\n##REF##23951413##\n37\n##\n<sup>]</sup> Therefore, we speculate that a tipping point could be reached, with sufficient TGF‐β present to shut down the anti‐cancer TNF‐α mechanism locally, resulting in cancer cell proliferation, tumor growth and secretion of yet more TGF‐β, setting off a proliferative positive feedback loop. Elucidating this molecular mechanism presents the opportunity of inhibiting this feedback loop through disruption of the TGF‐β pathway. Indeed, it is well‐established that TGF‐β is crucial for development of bone metastases in vivo<sup>[</sup>\n##REF##9916131##\n38\n##\n<sup>]</sup> and small molecule TGF‐β inhibitors as adjuvant therapy have been shown to reduce EMT in a mouse model metastatic breast cancer<sup>[</sup>\n##REF##20442777##\n39\n##\n<sup>]</sup> with the prospect that further inhibition could shut down this mechanism. Alternatively, interventions to increase TNF‐α secretion by osteocytes or other cells in the bone environment could cause a similar therapeutic effect.</p>", "<p>Osteocytes regulate bone homeostasis in response to mechanical loading via a range of mechanosensing mechanisms,<sup>[</sup>\n##UREF##6##\n40\n##, ##REF##25399300##\n41\n##, ##REF##23567965##\n42\n##\n<sup>]</sup> including integrin attachments,<sup>[</sup>\n##UREF##7##\n43\n##, ##UREF##8##\n44\n##, ##REF##22675160##\n45\n##\n<sup>]</sup> their glycocalyx,<sup>[</sup>\n##REF##27203269##\n46\n##, ##REF##14610310##\n47\n##\n<sup>]</sup> and the primary cilium.<sup>[</sup>\n##REF##21899847##\n48\n##, ##REF##21810408##\n49\n##\n<sup>]</sup> Thus, changes in osteocyte behavior induced by TGF‐β from cancer cells may disturb bone biology, with disruptions to osteocyte regulation of bone remodeling linked to age‐related degeneration<sup>[</sup>\n##REF##34161267##\n50\n##\n<sup>]</sup> osteoporosis,<sup>[</sup>\n##REF##34171514##\n51\n##, ##REF##34826091##\n52\n##, ##REF##25863050##\n53\n##\n<sup>]</sup> osteoarthritis<sup>[</sup>\n##REF##23815527##\n54\n##\n<sup>]</sup> and osteogenesis imperfecta.<sup>[</sup>\n##REF##28548288##\n55\n##\n<sup>]</sup> In particular, it is well‐established that primary cilia are key to normal osteocyte function, mechanoresponsiveness and regulation of other bone cell types,<sup>[</sup>\n##UREF##9##\n56\n##\n<sup>]</sup> and thus the cancer cell‐induced changes in osteocyte cilia we observed will likely also affect bone biology, such as the disruption of mechanosensitivity observed here. We have demonstrated here, for the first time, an additional role for osteocyte primary cilia and the associated IFT88 pathway, in controlling TNF‐α secretion and altering metastatic cancer cell behavior. Decreased expression and length of osteocyte cilia correlated with restoration of cancer cell proliferation. This presents the intriguing prospect that metastatic bone disease could in fact be treated as an osteocyte ciliopathy, with the potential to inhibit development and growth of metastatic lesions, and associated deterioration of bone tissue, via drugs that increase osteocyte primary cilia expression, such as fenoldopam.<sup>[</sup>\n##UREF##10##\n57\n##, ##REF##35230705##\n58\n##, ##UREF##11##\n59\n##\n<sup>]</sup> Further research is required to solidify this link, as the effect resulting from TGF‐β may be associative rather than causative, but these findings present a promising new therapeutic target for metastatic bone disease.</p>", "<p>In conclusion, this study presents a novel anti‐cancer mechanism inherent in osteocytes, by far the most abundant bone cell type. We show that osteocytes suppress proliferative behavior in both breast and prostate cancer cells via secretion of soluble TNF‐α. However, this mechanism can be inhibited by cancer cells through secretion of TGF‐β, reducing osteocyte primary cilia and IFT88 expression, which downregulates TNF‐α secretion. These findings reveal a previously unknown mechanism regulates cancer cell proliferation and migration common to both breast and prostate bone metastases. This presents promising therapeutic targets, with the potential to reduce metastatic bone tumor growth in cancer patients.</p>" ]
[]
[ "<title>Abstract</title>", "<p>Bone metastases are a common cause of suffering in breast and prostate cancer patients, however, the interaction between bone cells and cancer cells is poorly understood. Using a series of co‐culture, conditioned media, human cancer spheroid, and organ‐on‐a‐chip experiments, this study reveals that osteocytes suppress cancer cell proliferation and increase migration via tumor necrosis factor alpha (TNF‐α) secretion. This action is regulated by osteocyte primary cilia and associated intraflagellar transport protein 88 (IFT88). Furthermore, it shows that cancer cells block this mechanism by secreting transforming growth factor beta (TGF‐β), which disrupts osteocyte cilia and IFT88 gene expression. This bi‐directional crosstalk signaling between osteocytes and cancer cells is common to both breast and prostate cancer. This study also proposes that osteocyte inhibition of cancer cell proliferation decreases as cancer cells increase, producing more TGF‐β. Hence, a positive feedback loop develops accelerating metastatic tumor growth. These findings demonstrate the importance of cancer cell‐osteocyte signaling in regulating breast and prostate bone metastases and support the development of therapies targeting this pathway.</p>", "<p>This study identifies a previously unknown molecular mechanism common to both breast and prostate cancer cells, whereby they hijack bone cells to stimulate growth of bone metastases. This cell crosstalk is investigated, finding that osteocytes inherently suppress cancer cell proliferation. This is regulated by the osteocyte's primary cilium, which cancer cells can knock down to stimulate bone metastases.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6797-cit-0068\">\n<string-name>\n<given-names>S. W.</given-names>\n<surname>Verbruggen</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Nolan</surname>\n</string-name>, <string-name>\n<given-names>M. P.</given-names>\n<surname>Duffy</surname>\n</string-name>, <string-name>\n<given-names>O. M.</given-names>\n<surname>Pearce</surname>\n</string-name>, <string-name>\n<given-names>C. R.</given-names>\n<surname>Jacobs</surname>\n</string-name>, <string-name>\n<given-names>M. M.</given-names>\n<surname>Knight</surname>\n</string-name>, <article-title>A Novel Primary Cilium‐Mediated Mechanism Through which Osteocytes Regulate Metastatic Behavior of Both Breast and Prostate Cancer Cells</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305842</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305842</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Experimental Design</title>", "<p>An array of cell culture experiments were designed in order to investigate the differences between early metastases, in which osteocyte signaling and regulation of the bone marrow environment likely dominates, and established metastases, in which the large numbers of cancer cells in a lesion likely results in crosstalk with osteocytes. Thus, conditioned media studies were used to mimic the one‐way signaling in early metastasis, while transwell co‐cultures were used to replicate the cytokine crosstalk via soluble factors in established metastases, as outlined in Figure ##FIG##0##1A##.</p>", "<title>Cell Culture Conditions</title>", "<p>The human breast cancer cell lines MDA‐MB‐231 and MCF‐7, and human prostate cancer cell lines PC3 and LNCaP were obtained from the American Type Culture collection (ATCC), and were routinely maintained in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% foetal bovine serum (FBS), and 100 U mL<sup>−1</sup> penicillin and 100 µg mL<sup>−1</sup> streptomycin (all Sigma–Aldrich). The MLO‐Y4 osteocyte‐like mouse cell line was a kind gift from Professor L. Bonewald (University of Missouri, Kansas City, USA) and were cultured on collagen‐coated surfaces (rat tail collagen type I, 0.15 mg mL<sup>−1</sup>) with α‐modified essential medium (α‐MEM, Gibco) supplemented with 2.5% FBS, 2.5% iron supplemented calf serum (CS, HyClone Laboratories, Logan, UT, USA), and 100 U mL<sup>−1</sup> penicillin and 100 µg mL<sup>−1</sup> streptomycin (all Sigma–Aldrich). hMSC's were routinely sub‐cultured in DMEM Glutamax (ThermoFisher 21885‐025) and supplemented with 10% FBS and 5% Penicillin/Streptomycin. Cells were differentiated at 5 × 10<sup>3</sup> cell cm<sup>−2</sup> in αMEM media supplemented with 10% FBS, 5% Penicillin/Streptomycin, 100 nM Dexamethasone, 5 µM Ascorbic Acid and 10 mM B‐glycerophosphate for a period of 21 days with media changed every 2–3 days. All cells were maintained at 37 ˚C, with 5% CO<sub>2</sub> and 95% humidity.</p>", "<p>In all cases, conditioned media (CM) from MLO‐Y4 cells was applied to cancer cells at a 1:1 ratio. Un‐cultured MLO‐Y4 standard media was applied at a 1:1 ratio to cancer cells in control groups, to remove any variability from combining different media types. The same technique was applied when adding cancer cell CM to osteocytes or hMSCs. Unless otherwise stated, each CM experiment contained three sample wells and was repeated on three separate occasions, resulting in <italic toggle=\"yes\">n</italic> = 9 samples per group. In all co‐culture experiments, osteocytes were seeded at the same density as CM experiments and cultured for the same length of time, sharing the same total volume of media with the cancer cells.</p>", "<title>3D Cell Cultures</title>", "<p>MCF‐7 and PC3 cells were cultured as spheroids using the 3D on‐top assay as described in detail in Bissell et al.<sup>[</sup>\n##REF##17396127##\n60\n##\n<sup>]</sup> In brief, Matrigel was defrosted overnight and a thin layer of Matrigel was used to coat the cell culture plastic. Cells were seeded at .25 × 10<sup>5</sup> cells cm<sup>−2</sup> using 100 µL of Matrigel and incubated at 37 °C for 20 min. Cells were then overlaid with a 2% Matrigel supplemented media. Spheroids were cultured for a period of 12 days with a control or hMSC conditioned media (1:1 ratio) that was refreshed every 2–3 days. Spheroids were tracked and imaged using the Lumascope 720 and spheroid area was measured using the polygon tool in Fiji‐ImageJ.</p>", "<title>Organ‐on‐a‐Chip Model</title>", "<p>The Emulate S1 chip was activated as per the standardized Emulate Inc protocol. Following the 21 days hMSC differentiation cells were trypsinized using 0.05% trypsin. Cancer spheroids were harvested from Matrigel after 12 days using a 5 m<sc>m</sc> EDTA‐PBS solution. The hMSC and cancer spheroids were then combined into a 1 mg mL<sup>−1</sup> collagen‐I rat tail solution and seeded into the bottom channel of the Emulate S1 chip. The gel was allowed to set for 30 min before connecting the chips. The standard flow rate of 30 µL h<sup>−1</sup> was applied to the top channel, while no flow was applied to the bottom channel.</p>", "<title>Fluid Shear Stress Experiments</title>", "<p>Mechanical loading was applied to the MLO‐Y4 cells using oscillatory fluid flow generated by culturing cells in rectangular flasks (82 mm × 92 mm; 10 mL of media) on a rocking platform that oscillated at a frequency of 0.5 Hz and with an amplitude of 1.5 cm for 24 h after an initial 24 h static period post‐seeding. This system has been shown to generate spatiotemporal fluid‐flow induced maximal shear stress of ≈0.1 Pa across a layer of cells<sup>[</sup>\n##REF##21810408##\n49\n##, ##REF##20185133##\n61\n##\n<sup>]</sup> that is partially representative of that experienced by osteocytes within the lacunar network in bone (0.01–1 Pa).<sup>[</sup>\n##REF##23567965##\n42\n##, ##REF##27203269##\n46\n##, ##REF##8051194##\n62\n##, ##REF##20715178##\n63\n##\n<sup>]</sup> In all experiments, CM was collected after 24 h of fluid shear or un‐sheared static culture conditions.</p>", "<title>Proliferation Assay</title>", "<p>The proliferation of the cultured cells was assessed using the AlamarBlue cell viability assay that detected redox reduction during cell growth. Cancer cells were seeded onto 24 well plates at a density of 25 × 10<sup>3</sup> cells cm<sup>‐</sup>\n<sup>2</sup> At the experimental endpoint, 50 µL of the AlamarBlue reagent (Life Technologies, Eugene, OR, USA) was added to each well containing cells and 500 µL of culture medium. Cells were then incubated for 3 h at 37 ˚C. The fluorescence was measured with a Synergy 4 multi‐mode microplate reader (BioTek Instruments, Winooski, VT, USA) with excitation at 544 nm and emission at 590 nm. The fluorescence value was proportional to the number of viable cells.</p>", "<title>Migration Assay</title>", "<p>Cancer cells were seeded into a 24‐well plate at a density of 50 × 10<sup>3</sup> cells cm<sup>−2</sup> and allowed to form a monolayer that was then scratched with a P200 pipette tip to create a linear wound ≈200 µm wide. Migration of the cells into the wounding gap was monitored by light microscopy serial time‐lapse imaging using a Lumascope LS720 imaging system (Etaluma Inc., Carlsbad, CA, USA) with a 20× objective. The percentage of wound gap closure was measured using a plugin for ImageJ software (National Institutes of Health, Bethesda, MD, USA) as previously described.<sup>[</sup>\n##REF##25482647##\n64\n##\n<sup>]</sup>\n</p>", "<title>Invasion Assay</title>", "<p>An in vitro Matrigel invasion assay was used to assess the invasiveness of cancer cells<sup>[</sup>\n##UREF##12##\n65\n##\n<sup>]</sup> Briefly, transwell inserts (8‐µm pores) for 24‐well plates were pre‐coated with 50 µL/insert of 1 mg mL<sup>−1</sup> Matrigel (Corning Inc., Corning, NY, USA), for 1 h at 37 ˚C. Subsequently, cancer cells were seeded into the upper chamber of each insert at 75 × 10<sup>3</sup> cells cm<sup>−2</sup> in 250 µL basal medium. Control medium or CM, 500 µL, was added to each well (lower chamber) under the inserts. After incubation for 24 h, cells that had penetrated the Matrigel‐coated membrane and adhered to the other side of the inserts were dissociated with Trypsin (Sigma–Aldrich) for 7 min at 37 ˚C. A total of 250 mL of media was then added to neutralize the Trypsin. AlamarBlue was then added to the solution containing invaded cells, with the assay performed as described for proliferation above.</p>", "<title>Enzyme‐Linked Immunosorbent Assay (ELISA)</title>", "<p>TGF‐β secretion by cancer cells, and TNF‐α secretion by osteocytes, was quantified via enzyme‐linked immunosorbent assay (ELISA), according to manufacturer's instructions (Catalogue numbers 501 129 049 and BMS607‐3, respectively; both Invitrogen Life Technologies, Eugene, OR, USA). Control and conditioned media were added to a coated Corning ELISA plate. Samples were washed three times and incubated with horseradish peroxidase‐conjugated secondary antibody for 1 h at room temperature. Horseradish peroxidase detection reagent was added, the samples were incubated at room temperature for 30 min, and absorbance was measured at 450 nm.</p>", "<title>Immunocytochemistry and Microscopy</title>", "<p>For primary cilia imaging and analysis, MLO‐Y4 cells cultured on collagen I‐coated glass‐bottom 24‐well plates (Mattek) were fixed in 10% formalin and treated with anti‐acetylated α‐tubulin primary antibody, 1:1, from a C3B9 hybridoma cell line (Sigma–Aldrich). Cilia were visualized with Alexa‐Fluor 488 secondary antibody, 1:1000 (Life Technologies) and imaged with a 100× oil objective on a Leica DMi8 epifluorescence microscope. Nuclei were stained with DAPI (Life Technologies), and F‐actin was stained with phalloidin (Santa Cruz Biotech). Cell area, and circularity, and cilia incidence and length were analyzed using ImageJ software.</p>", "<title>Confocal Microscopy</title>", "<p>Imaging of the organ‐chip was performed at 20× on a Zeiss 710 ELYRA PS.1 confocal microscope using an EC PlanNeofluar10×/0.3 M27 objective (Zeiss, Oberkochen, Germany). Confocal z‐sections were made throughout the cell depth (approximately 20 sections) using 5 µm step size with an image format of 2048 × 2048 yielding a pixel size of 0.415 µm × 0.415 µm (image size ≈850 µm × 850 µm).</p>", "<title>Super‐Resolution Structured Illumination Microscopy</title>", "<p>Cells imaged for super‐resolution structured illumination microscopy were cultured on coverslips, fixed with 10% formalin, and underwent permeabilization with both 0.5% Triton X‐100 and Methanol. The ciliary axoneme was detected using a mouse acetylated α‐tubulin antibody (1:2000, Sigma–Aldrich). The basal body was observed using rabbit pericentrin (1:500, Abcam), and the intraflagellar transport protein, homolog 88, was detected using an IFT88 polyclonal rabbit antibody (1:1000, Proteintech). Slides were mounted using ProLong Antifade mountant (Invitrogen) and imaged using the Zeiss 710 ELYRA PS.1 microscope (Carl Zeiss, Oberkochen, Germany) with a 63×/1.4 NA objective.</p>", "<title>Cytokine Array</title>", "<p>Cytokines present in osteocyte CM were assessed using an Abcam mouse cytokine antibody array (ab133994, Abcam) according to manufacturer's instructions. Image Studio Lite was used to quantitate cytokine spots as per manufacturer's instructions, measured using Li‐Cor Odyssey imaging system. Raw densitometry data was extracted by identifying a single exposure with a high signal to noise ratio, measuring the density of each spot using circles of equal size dimensions, and determining the summed signal density across the entire circle for each spot. Background signal was then subtracted and data was normalized based on positive control signals for each array. A negative control of uncultured standard media and a positive control of osteocytes treated with lipopolysaccharide (LPS), known to stimulate an inflammatory response in osteocytes<sup>[</sup>\n##REF##31904537##\n66\n##\n<sup>]</sup> were included.</p>", "<title>Western Blotting</title>", "<p>Cells were lysed in RIPA lysis buffer (Sigma) with complete protease inhibitor cocktail (Sigma) and PhosSTOP (Sigma). Lysates were denatured by boiling for 5 min with SDS loading buffer, separated on a 14‐10% Bis Tris gel (Invitrogen) and transferred to polyvinylidene difluoride (PVDF) membrane. Membranes were activated using 100% methanol prior to transfer and were subsequently blocked using 5% BSA at room temperature for 1 h. Primary antibodies were used at 4 °C overnight at a 1:1000 dilution (TGF‐β Receptor 1: Abcam, IFT88: Proteintech, β‐Actin: Abcam). Following incubation and membrane washing with 1x TBS‐T, secondary HRP conjugated antibodies were used at room temperature for 1 h. Protein bands were detected using an enhanced chemiluminescence substrate enhancer solution that was applied to the membrane directly before scanning using either the GE healthcare chemidoc system or the Li‐Cor Odyssey imaging system.</p>", "<title>Cell Treatments</title>", "<p>Cell lines were treated with the following where relevant prior to downstream assays: 10 µg mL<sup>−1</sup> TGF‐β Receptor 1 small molecule inhibitor (LY 364 947, Tocris), 5 ng mL<sup>−1</sup> recombinant human TGF‐β1 (240‐B‐002, R&amp;D Systems), 10 ng mL<sup>−1</sup> Lipopolysaccharide (LPS) solution (00‐4976‐93, Invitrogen), 10 ng mL<sup>−1</sup> recombinant human TNF‐α (PHC3015, Gibco), 10 ng mL<sup>−1</sup> recombinant human IL‐6 (PHC0064, Gibco), 10 ng mL<sup>−1</sup> recombinant human IL‐10 (PHC0104, Gibco), 10 ng mL<sup>−1</sup> recombinant human VEGF‐A (PHC9394, Gibco), 1 ng mL<sup>−1</sup> TNF‐α Receptor small molecule inhibitor (CAS 1049741‐03‐8, Calbiochem, Sigma–Aldrich).</p>", "<title>RNA Interference</title>", "<p>Gene silencing was performed by siRNA mediated knockdown and compared to scramble siRNA control (Life Technologies). For TGF‐β receptor 1 disruption, cells were transfected with 20 µM TGF‐βR1 siRNA (5′‐CGAACAGAAGUUAAGGCCAAAUAUU‐3′). For primary cilia disruption, cells were transfected with 20 µM IFT88 siRNA (5′‐CCAGAAACAGATGAGGACGACCTTT‐3′) or scrambled siRNA control using Lipofectamine 2000 (Life Technologies) as previously described<sup>[</sup>\n##REF##20371630##\n67\n##\n<sup>]</sup> Any gross effects were not observed on cellular morphology for all siRNA treatments.</p>", "<title>RNA Extraction</title>", "<p>RNA was extracted from cells using the RNeasy Plus Minikit (Qiagen) as per manufacturer instructions. RNA was quantified using a Nanodrop Spectrophotometer (Thermo scientific) and all RNA was stored at −80 °C. Using the Quantitech reverse transcription kit (Qiagen) 1 µg of total RNA was synthesised into cDNA and stored at −20 °C.</p>", "<title>RT‐qPCR</title>", "<p>Real time PCR was performed using TaqMan gene expression assay kits (Thermo Fisher) and the Quant Studio 7 flex real time PCR system (Thermo Fisher). Gene expression was analyzed by quantitative real‐time PCR using primers and probes (Life Technologies) for analysis of intraflagellar transport 88, <italic toggle=\"yes\">IFT88</italic> (Mm00493675_m1); cyclooxygenase‐2, <italic toggle=\"yes\">COX‐2</italic> (Mm00478374_m1) and <italic toggle=\"yes\">GAPDH</italic> (4 351 309). <italic toggle=\"yes\">GAPDH</italic> was used as a housekeeping gene endogenous control and relative fold change in gene expression was calculated using the 2<sup>−ΔΔCT</sup> method.</p>", "<title>Gene Expression and Protein Interaction Database Analyses</title>", "<p>A protein‐protein interaction (PPI) network was generated from experiments and datasets only, using the high confidence setting on STRING (Search Tool for the Retrieval of Interacting Genes/Proteins).<sup>[</sup>\n##REF##12519996##\n26\n##\n<sup>]</sup> Clustering analysis was performed using the Markov Cluster Algorithm (MCL) with the highest inflation parameter (10), indicating a cluster of highly interacting proteins among cytokine array targets.</p>", "<p>Kaplan–Meir plots of recurrence‐free survival in patients with high or low expression of the TNFRSF1A gene were generated from The Cancer Genome Atlas (TCGA) using KMPlotter.<sup>[</sup>\n##REF##34309564##\n27\n##\n<sup>]</sup> Analysis was performed on the Pan‐Cancer DNA repositories, using n = 980 breast cancer and <italic toggle=\"yes\">n</italic> = 492 prostate cancer samples.</p>", "<p>A comparison of RNA expression of the TNFRSF1A gene between normal, primary tumor and mestastatic tumor samples was performed on databases of tumor samples using the TNMPlot tool<sup>[</sup>\n##REF##33807717##\n28\n##\n<sup>]</sup> that compared data from the Gene Expression Omnibus of the National Centre for Biotechnology Information (NCBI‐GEO), The Cancer Genome Atlas (TCGA), the Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and the Genotype‐Tissue Expression (GTEx).</p>", "<title>Statistical Analysis</title>", "<p>As described in figure legends, the statistical analyses were performed using GraphPad Prism 5 (GraphPad Software). Statistical significance compared between groups indicated by horizontal lines as follows: light gray, <italic toggle=\"yes\">p</italic> &lt; 0.05; dark gray, <italic toggle=\"yes\">p</italic> &lt; 0.01; black, <italic toggle=\"yes\">p</italic> &lt; 0.001; by one‐way ANOVA with Bonferroni post‐hoc test. As indicated in the figure legends, experiments were repeated independently multiple times and similar results were obtained.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>S.W.V., C.R.J., and M.M.K. performed conceptualization. S.W.V., J.N., M.P.D., and M.M.K. performed methodology. S.W.V., J.N., and M.P.D. performed the investigation. S.W.V. and J.N. performed visualization. O.M.T.P., C.R.J., and M.M.K. performed supervision. S.W.V. wrote the original draft. S.W.V., J.N., M.P.D., O.M.P.T., and M.M.K. performed review and editing.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors would like to thank Prof. X. Edward Guo, Dr. Clare Thompson and Dr. Angus Wann for useful insights and discussions. This work has been funded by the following research grants: European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie grant agreement No. 748305 (SWV); National Institutes of Health (NIH) grant R01AR062177 (MPD, CRJ); and Engineering and Physical Sciences Research Council – Cancer Research UK (EPSRC‐CRUK) Multidisciplinary Award C56133/A29455 (JN, OMTP, MMK). Additional support was provided via the Queen Mary+Emulate Organs‐on‐chips Centre (<ext-link xlink:href=\"http://www.cpm.qmul.ac.uk/emulate\" ext-link-type=\"uri\">www.cpm.qmul.ac.uk/emulate</ext-link>). This work forms part of the research portfolio of the National Institute for Health Research Barts Biomedical Research Centre (NIHR203330).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available in the supplementary material of this article.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6797-fig-0001\"><label>Figure 1</label><caption><p>Osteocyte conditioned media inhibited proliferation and increased migration of breast and prostate cancer cells, with absence of this effect in co‐culture suggesting the existence of a feedback mechanism in vivo. A) Schematic of conditioned media model of early metastasis, and co‐culture model of late metastasis. Fold‐change in B) proliferation, C) migration and D) invasion of breast (MDA‐MD‐231 &amp; MCF‐7) and prostate (PC‐3 &amp; LNCaP) cancer cell lines, after 48 h in conditioned media or co‐culture with the MLO‐Y4 osteocyte‐like cell line (<italic toggle=\"yes\">n</italic> = 9). Bar charts represent mean ± standard deviation. Statistically significant differences indicated by horizontal lines based on one‐way ANOVA with Bonferroni post‐hoc test (light gray <italic toggle=\"yes\">p</italic> &lt; 0.05, dark gray <italic toggle=\"yes\">p</italic> &lt; 0.01, black <italic toggle=\"yes\">p</italic> &lt; 0.001).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6797-fig-0002\"><label>Figure 2</label><caption><p>TGF‐β, secreted by breast and prostate cancer cells, blocks the disruption of cancer cells via osteocyte conditioned media. Similarly, knockdown of osteocyte TGF‐β receptor I in co‐culture resulted in similar effects to normal osteocyte conditioned media, inhibiting proliferation and increasing migration of breast and prostate cancer cells, indicating TGF‐β plays a role in feedback loop. A) Fold‐increases in TGF‐β secretion by cancer cell lines compared to standard culture media, as measured by ELISA. Fold‐change in B) proliferation and migration of breast (MDA‐MD‐231 &amp; MCF‐7) and prostate (PC‐3 &amp; LNCaP) cancer cell lines, after 48 h in osteocyte CM, with or without TGF‐β pre‐treatment (<italic toggle=\"yes\">n</italic> = 9). Data normalized to untreated control cancer cells. Quantification of C) proliferation and migration of breast and prostate cancer cell lines, after 48 h in co‐culture (Co‐C) with osteocytes in which TGF‐β receptor I has been knocked down with siRNA (TGFβR KD) (<italic toggle=\"yes\">n</italic> = 9). Data normalized to co‐culture with non‐transfected osteocytes and shown alongside scrambled controls (SCRAM). Bar charts represent mean ± standard deviation. Statistically significant differences indicated by horizontal lines based on one‐way ANOVA with Bonferroni post‐hoc test (light gray <italic toggle=\"yes\">p</italic> &lt; 0.05, dark gray <italic toggle=\"yes\">p</italic> &lt; 0.01, black <italic toggle=\"yes\">p</italic> &lt; 0.001).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6797-fig-0003\"><label>Figure 3</label><caption><p>Osteocyte primary cilia expression was reduced in co‐culture with breast and prostate cancer cells. A) Schematic of the osteocyte primary cilium demonstrating how IFT88 binds to motor proteins to construct the axoneme. Imaging performed using confocal microscopy (nuclei = blue, DAPI; F‐actin cytoskeleton = red, phalloidin; axoneme = green, acetylated α‐tubulin) and super‐resolution Structured Illumination Microscopy (SR‐SIM) (centrosome/basal body = magenta, pericentrin; axoneme = green, acetylated α‐tubulin). B,C) Primary cilia expression in osteocytes (control) and the effect of co‐culture with each breast and prostate cancer cell line (Co‐C). Quantification of B) cilia incidence and C) cilia length. Bar charts represent mean ± standard deviation for <italic toggle=\"yes\">n</italic> = 9 technical replicates. Statistically significant differences indicated by horizontal lines based on one‐way ANOVA with Bonferroni post‐hoc test (light gray <italic toggle=\"yes\">p</italic> &lt; 0.05, dark gray <italic toggle=\"yes\">p</italic> &lt; 0.01, black <italic toggle=\"yes\">p</italic> &lt; 0.001). Data points for each replicate indicate the incidence based &gt;200 cells and median values for cilia length based on 100 cilia.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6797-fig-0004\"><label>Figure 4</label><caption><p>Conditioned media from breast and prostate cancer cells reduced osteocyte primary cilia expression. This effect was inhibited by disruption of TGF‐β receptor I via small molecule inhibitor or siRNA. (A‐B) Primary cilia expression in osteocytes (control) and the effect of cancer cell conditioned media (CC‐CM) from cancer cells. Conditioned media was applied either on its own (+CC‐CM) or after pre‐treatment with TGF‐β receptor I small‐molecule inhibitor (+CC‐CM +TGF‐βR Inhib) or following siRNA knockdown of TGF‐β receptor I (+CM +TGF‐βR KD). Quantification of A) cilia incidence and B) cilia length. Bar charts represent mean ± standard deviation for <italic toggle=\"yes\">n</italic> = 9 technical replicates. Statistically significant differences indicated by horizontal lines based on one‐way ANOVA with Bonferroni post‐hoc test (light gray <italic toggle=\"yes\">p</italic> &lt; 0.05, dark gray <italic toggle=\"yes\">p</italic> &lt; 0.01, black <italic toggle=\"yes\">p</italic> &lt; 0.001). Data points for each replicate indicate the incidence based &gt;200 cells and median values for cilia length based on &gt;100 cilia.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6797-fig-0005\"><label>Figure 5</label><caption><p>TGF‐β, released by breast and prostate cancer cells, significantly reduced expression of osteocyte primary cilia and IFT88. A) Immunofluorescent images of osteocytes (nuclei = blue, DAPI; primary cilia = green, acetylated α‐tubulin; F‐actin cytoskeleton = red, phalloidin), showing shorter and fewer primary cilia (indicated by white arrows) with addition of TGF‐β. B,C) This effect was reversed by either the addition of a TGF‐β receptor I small‐molecule inhibitor (TGF‐βR Inhib) or knockdown of TGF‐β receptor I via siRNA transfection (TGF‐βR KD) (<italic toggle=\"yes\">n</italic> = 9). D) Super‐resolution Structured Illumination Microscopy (SR‐SIM) images of IFT88 present in an osteocyte cilium, showing E) the intensity profile along the axoneme (IFT88 = magenta; axoneme = green, acetylated α‐tubulin). F) TGF‐β treatment of osteocytes also decreased expression of IFT88 (<italic toggle=\"yes\">n</italic> = 1) as measured by qPCR, when compared to vehicle‐treated controls. Bar charts represent mean ± standard deviation. Statistically significant differences indicated by horizontal lines based on one‐way ANOVA with Bonferroni post‐hoc test (light gray <italic toggle=\"yes\">p</italic> &lt; 0.05, dark gray <italic toggle=\"yes\">p</italic> &lt; 0.01, black <italic toggle=\"yes\">p</italic> &lt; 0.001).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6797-fig-0006\"><label>Figure 6</label><caption><p>Knockdown of osteocyte primary cilia/IFT88 altered cancer cell behavior via conditioned media to match control and co‐culture conditions. Fold‐change in A) proliferation and B) migration of breast (MDA‐MD‐231 &amp; MCF‐7) and prostate (PC‐3 &amp; LNCaP) cancer cell lines, after 48 h in standard control media, conditioned media from MLO‐Y4s transfected with scrambled (SCRAM O‐CM) or IFT88 (IFT88 KD O‐CM) siRNA (<italic toggle=\"yes\">n</italic> = 9). Bar charts represent mean ± standard deviation. Statistically significant differences indicated by horizontal lines based on one‐way ANOVA with Bonferroni post‐hoc test (light gray <italic toggle=\"yes\">p</italic> &lt; 0.05, dark gray <italic toggle=\"yes\">p</italic> &lt; 0.01, black <italic toggle=\"yes\">p</italic> &lt; 0.001).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6797-fig-0007\"><label>Figure 7</label><caption><p>Knockdown of osteocyte primary cilia, via IFT‐88 siRNA or TGF‐β treatment, inhibited production of TNF‐α (highlighted in red), a cytokine that decreased proliferation and increased migration in cancer cells. A,B) Cytokine targets were selected based on significant change relative to control CM in a cytokine array of 32 inflammatory proteins (only those with a greater than 25% change shown), for both the most similar (IL‐10 and TNF‐α) and least similar (IL‐6 and VEGF) expression changes. C) An ELISA confirmed significant decreases in TNF‐α concentration in MLO‐Y4 CM with IFT88 siRNA knockdown or TGF‐β treatment. Fold change in D) proliferation and E) migration in breast (MDA‐MD‐231 &amp; MCF‐7) and prostate (PC‐3 &amp; LNCaP) cancer cell lines, after 24 h treatment with selected inflammatory cytokines (<italic toggle=\"yes\">n</italic> = 3). Bar charts represent mean ± standard deviation. Statistically significant differences indicated by horizontal lines based on one‐way ANOVA with Bonferroni post‐hoc test (light gray <italic toggle=\"yes\">p</italic> &lt; 0.05, dark gray <italic toggle=\"yes\">p</italic> &lt; 0.01, black <italic toggle=\"yes\">p</italic> &lt; 0.001).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6797-fig-0008\"><label>Figure 8</label><caption><p>Pre‐treatment of cancer cells with a TNF‐α Inhibitor blocks the effect of osteocyte conditioned media on cancer cells, replicating the effect of co‐culture, and effects measured in monolayer culture are replicated using 3D cancer spheroids. A) Fold‐change in proliferation and migration of breast (MDA‐MD‐231 &amp; MCF‐7) and prostate (PC‐3 &amp; LNCaP) cancer cell lines, after 48 h in osteocyte CM or with pre‐treatment with a TNF‐α small molecule inhibitor (<italic toggle=\"yes\">n</italic> = 9,3). B) 3D spheroids generated using MCF‐7 and PC‐3 cells were monitored over 12 days, finding C) that similar effects on proliferation were measured whether conditioned media was from mouse MLO‐Y4 osteocyte cell line or osteogenically‐differentiated human MSCs. Bar charts represent mean ± standard deviation. Statistically significant differences indicated by horizontal lines based on one‐way ANOVA with Bonferroni post‐hoc test (light gray <italic toggle=\"yes\">p</italic> &lt; 0.05, dark gray <italic toggle=\"yes\">p</italic> &lt; 0.01, black <italic toggle=\"yes\">p</italic> &lt; 0.001) or by asterisks using the same test (** <italic toggle=\"yes\">p</italic> &lt; 0.05, **** <italic toggle=\"yes\">p</italic> &lt; 0.0001).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6797-fig-0009\"><label>Figure 9</label><caption><p>TNF‐α secreted by osteocytes inhibits proliferation and encourages migration in breast and prostate cancer cells, with this inherent anti‐cancer mechanism dependent on IFT88/primary cilium expression. TGF‐β secretion by cancer cells blocks this mechanism, allowing further proliferation of cancer cells and potentially reaching a tipping point beyond which tumor growth accelerates. A) Working model of osteocyte‐cancer cell interactions in early metastasis when few cancer cells are present, followed by a working model of B) a larger tumor in established metastasis, with potential activated/inhibited signaling identified. C) Model of cancer cell proliferation under the influence of osteocyte signaling, with the proposed feedback loop leading to a tipping point after which cell growth accelerates. D) Schematic of a microfluidic organ‐on‐a‐chip model of human breast and prostate cancer metastases developed using the Emulate Inc. platform to further test this mechanism, and E) associated confocal microscopy images showing the human cancer cell spheroids suspended in hydrogel within the organ‐chip. F) Co‐culture of the cancer cell spheroids alongside osteogenically‐differentiated human MSCs, with nuclei immunostained for DAPI (blue), cell cytoskeleton by phalloidin for F‐actin (magenta), and cancer cells are selectively stained with EpCAM and shown as a z‐stack (green), with hMSCs visible in the merged image as cells not expressing EpCAM.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6797-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6797-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"advs6797-note-0001\"><p>The authors would like to dedicate this work to Prof. Chris Jacobs, who sadly passed away before it was completed after a long battle with cancer. Chris was personally excited about this work as it was a departure from his traditional expertise to tackle the problem of metastases, which had become all too familiar to him. Chris was a giant in the field of cell biomechanics, but also an excellent mentor and friend. He will be greatly missed, but remembered through his impressive legacy of scientific contributions and those he mentored.</p></fn></fn-group>" ]
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[ "<media xlink:href=\"ADVS-11-2305842-s002.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305842-s001.xlsx\"><caption><p>Click here for additional data file.</p></caption></media>" ]
[{"label": ["1"], "mixed-citation": ["\n"], "collab": ["GLOBOCAN 2020"], "article-title": ["Estimated Cancer Incidence, Mortality and Prevalence Worldwide in 2020"], "ext-link": ["https://gco.iarc.fr/"]}, {"label": ["2"], "mixed-citation": ["\n"], "collab": ["\n"], "italic": ["Cancer Research UK"], "ext-link": ["https://www.cancerresearchuk.org/health\u2010professional/cancer\u2010statistics\u2010for\u2010the\u2010uk"]}, {"label": ["9"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["S.", "F. D.", "B.", "W.", "M. P.", "R. C.", "G.", "I. J.", "B.", "G.", "J. Y.", "C.", "D.", "G.", "E. F.", "G.", "B.", "T.", "G. Y.", "J.", "A.", "K."], "surname": ["Braun", "Vogl", "Naume", "Janni", "Osborne", "Coombes", "Schlimok", "Diel", "Gerber", "Gebauer", "Pierga", "Marth", "Oruzio", "Wiedswang", "Solomayer", "Kundt", "Strobl", "Fehm", "Wong", "Bliss", "Vincent\u2010Salomon", "Pantel"], "source": ["New Engl. Joutnal Med."], "year": ["2005"], "volume": ["353"], "fpage": ["793"]}, {"label": ["12"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["E.", "G.", "P.", "G.", "F.p", "L."], "surname": ["Birmingham", "Niebur", "Mchugh", "Shaw", "Barry", "Mcnamara"], "source": ["Eur. Cells Mater."], "year": ["2012"], "volume": ["23"], "fpage": ["13"]}, {"label": ["18"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["X.", "K.", "D.", "Q.", "L.", "Y.\u2010H. V.", "D.", "N.", "L.", "E. W. K.", "L."], "surname": ["Mei", "Middleton", "Shim", "Wan", "Xu", "Ma", "Devadas", "Walji", "Wang", "Young", "You"], "source": ["Integr. Biol."], "year": ["2019"], "volume": ["11"], "fpage": ["119"]}, {"label": ["21"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n"], "given-names": ["S. W.", "L. M.", "S. W."], "surname": ["Verbruggen", "McNamara", "Verbruggen"], "source": ["Bone Mechanobiology in Health and Disease"], "person-group": ["\n"], "publisher-name": ["Academic Press"], "publisher-loc": ["Massachusetts, USA"], "year": ["2018"]}, {"label": ["40"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n"], "given-names": ["M. B.", "W.\u2010Y.", "R.", "O."], "surname": ["Schaffler", "Cheung", "Majeska", "Kennedy"], "source": ["Calcified Tissue Int."], "year": ["2014"], "volume": ["94"], "fpage": ["5"]}, {"label": ["43"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n"], "given-names": ["L. M.", "R. J.", "S.", "V.", "M. B."], "surname": ["Mcnamara", "Majeska", "Weinbaum", "Friedrich", "Schaffler"], "source": ["Anat. Rec."], "year": ["2009"], "volume": ["292"], "fpage": ["355"]}, {"label": ["44"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n"], "given-names": ["Y.", "L. M.", "M. B.", "S."], "surname": ["Wang", "McNamara", "Schaffler", "Weinbaum"], "source": ["Proc. Natl. Acad. Sci. USA"], "year": ["2007"], "volume": ["104"], "elocation-id": ["15946"]}, {"label": ["56"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n"], "given-names": ["S. W.", "A.", "G. C."], "surname": ["Verbruggen", "Sittichokechaiwut", "Reilly"], "article-title": ["Osteocytes and Primary Cilia. Current Osteoporosis Reports"], "year": ["2023"], "pub-id": ["10.1007/s11914-023-00819-1"]}, {"label": ["57"], "mixed-citation": ["\n"], "string-name": ["\n", "\n"], "given-names": ["M.", "C.r"], "surname": ["Spasic", "Jacobs"], "source": ["Eur. Cells Mater."], "year": ["2017"], "volume": ["33"], "fpage": ["158"]}, {"label": ["59"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n"], "given-names": ["M. M.", "M. P.", "S. W.", "C. R."], "surname": ["Sutton", "Duffy", "Verbruggen", "Jacobs"], "source": ["Cells Tissues Organs"], "year": ["2023"], "volume": ["1"], "fpage": ["1"]}, {"label": ["65"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n"], "given-names": ["C. R.", "N.", "M.", "L. V."], "surname": ["Justus", "Leffler", "Ruiz\u2010Echevarria", "Yang"], "source": ["J Vis Exp"], "year": ["2014"], "volume": ["88"], "elocation-id": ["51046"]}]
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67
CC BY
no
2024-01-14 23:41:55
Adv Sci (Weinh). 2023 Nov 15; 11(2):2305842
oa_package/73/00/PMC10787058.tar.gz
PMC10787059
37973557
[ "<title>Introduction</title>", "<p>Colorectal cancer (CRC) is a lethal cancer with a high fatality rate worldwide.<sup>[</sup>\n##REF##32133645##\n1\n##\n<sup>]</sup> Approximately 2 million people suffer from this cancer, with almost 900 000 deaths related to CRC occurring annually, with a growing trend in some countries.<sup>[</sup>\n##REF##31631858##\n2\n##, ##REF##33538338##\n3\n##\n<sup>]</sup> Due to limitations in early diagnosis, a significant number of patients are in the advanced stage when diagnosed. Almost 20% of these patients have liver metastases (CRLM). Liver metastasis is the most common form of metastasis in CRC and is the leading cause of death in patients with CRC.<sup>[</sup>\n##REF##32133645##\n1\n##, ##REF##31631858##\n2\n##\n<sup>]</sup>\n</p>", "<p>With early detection through screening and with continuous improvement in treatment methods, including surgery, radiotherapy, chemotherapy, and targeted therapy, the overall survival rate of CRC patients has improved greatly in recent years, as compared with the past.<sup>[</sup>\n##REF##31631858##\n2\n##, ##UREF##0##\n4\n##, ##REF##34526356##\n5\n##\n<sup>]</sup> Systemic chemotherapy with 5‐fluorouracil (5‐FU) combined with oxaliplatin or irinotecan (CPT‐11) has always played a key role in adjuvant therapy for CRC, improving survival in patients with resected CRC.<sup>[</sup>\n##REF##10744089##\n6\n##, ##REF##15051767##\n7\n##\n<sup>]</sup> For CRLM patients, surgical resection is considered to be the preferred treatment modality,<sup>[</sup>\n##REF##35004967##\n8\n##, ##REF##25392845##\n9\n##\n<sup>]</sup> which may provide better survival benefits for patients when combined with systemic chemotherapy.<sup>[</sup>\n##REF##27380959##\n10\n##, ##REF##30380461##\n11\n##, ##REF##26417845##\n12\n##, ##REF##33575295##\n13\n##\n<sup>]</sup>\n</p>", "<p>Nevertheless, CRC has high levels of heterogeneity,<sup>[</sup>\n##REF##27922044##\n14\n##\n<sup>]</sup> and chemotherapy efficacy remains limited. Therefore, individualized treatment plans, particularly for patients with metastatic CRC, have become increasingly important and urgent. Unfortunately, given the post‐metastatic intratumoral heterogeneity, combined with the apparent individual heterogeneity of the tumor, the choice of individualized chemotherapy drugs remains an intractable problem. Efficient and accurate drug screening models remain lacking in clinical practice.</p>", "<p>Patient‐derived xenograft (PDX) models have been identified as a superior model system for translational research, as they maintain the characteristics of the original heterogeneous patient tumor.<sup>[</sup>\n##REF##25185190##\n15\n##\n<sup>]</sup> PDX models have been shown to be useful for predicting drug sensitivity or resistance of tumors to improve guidance for therapies for patients.<sup>[</sup>\n##REF##33212364##\n16\n##, ##REF##30151914##\n17\n##\n<sup>]</sup> However, PDX is time‐consuming, has a low success rate, and requires many resources. In recent years, the patient‐derived tumor organoid model (PDTO) has been extensively studied as a preclinical cancer model for drug screening.<sup>[</sup>\n##REF##28757181##\n18\n##, ##REF##31171691##\n19\n##, ##REF##29366522##\n20\n##\n<sup>]</sup> Yao et al. demonstrated that organoids derived from patients with advanced rectal cancer can be used reliably as predictive models of response to chemoradiation and could potentially be used as a companion tool for rectal cancer treatment.<sup>[</sup>\n##REF##31761724##\n21\n##\n<sup>]</sup> In addition, Ganesh et al. indicated that PDTO could serve as a reliable tool for predicting chemoradiation response by establishing a murine endoluminal rectal cancer model.<sup>[</sup>\n##REF##31591597##\n22\n##\n<sup>]</sup> These studies have proven the physiological and predictive superiority of the PDTO platform over conventional methods, such as monolayer cell culture and PDX. Despite this, major problems with PDTO, which include the lack of standardized methods, complexity of organoid cultures, and reproducibility of manipulation, cannot be ignored.<sup>[</sup>\n##UREF##1##\n23\n##, ##REF##30981763##\n24\n##\n<sup>]</sup>\n</p>", "<p>In addition to these popular models, 3D‐bioprinting (3DP) models have become a novel biotechnique implicated by many emerging studies, which can rapidly establish in vitro “organs” with complex 3D architecture by using living cells in bioink and can simulate the microenvironment in vivo.<sup>[</sup>\n##REF##26724184##\n25\n##, ##REF##32407108##\n26\n##\n<sup>]</sup> Furthermore, complex multicellular bioprinting is possible.<sup>[</sup>\n##UREF##2##\n27\n##, ##REF##25093879##\n28\n##\n<sup>]</sup> This frontier biotechnology has been applied to reconstruct several tissues and organs in vitro, such as the heart,<sup>[</sup>\n##REF##31371612##\n29\n##\n<sup>]</sup> vessels,<sup>[</sup>\n##REF##27552316##\n30\n##\n<sup>]</sup> skin,<sup>[</sup>\n##UREF##3##\n31\n##\n<sup>]</sup> and bone.<sup>[</sup>\n##UREF##4##\n32\n##\n<sup>]</sup> We previously successfully established a hepatorganoid model of HepRG cells using 3DP technology and demonstrated that transplanting 3DP hepatorganoids could prolong the survival of mice with liver failure. <sup>[</sup>\n##REF##32434830##\n33\n##\n<sup>]</sup> In cancer research, cancer models established by the 3DP biotechnique represent a substantial improvement over traditional 2D models, which can restore the tumor microenvironment by mimicking space complexity and facilitating physiologically relevant cell‐cell and cell‐bioink interactions.<sup>[</sup>\n##REF##26216543##\n34\n##\n<sup>]</sup> 3DP tumor models have been applied in disease modeling and drug screening in a number of studies.<sup>[</sup>\n##REF##33741496##\n35\n##, ##REF##28501712##\n36\n##, ##REF##31918229##\n37\n##\n<sup>]</sup> We previously established a 3DP model of hepatocellular carcinoma cell lines that made drug screening possible.<sup>[</sup>\n##REF##32582546##\n38\n##\n<sup>]</sup> We also utilized patient‐derived tumor cells to print a 3DP tumor model and demonstrated that the 3DP tumor model could be applied in individualized therapy as a potential clinical tool.<sup>[</sup>\n##REF##32599574##\n39\n##, ##REF##33007612##\n40\n##\n<sup>]</sup>\n</p>", "<p>In this study, we applied 3DP technology to establish patient‐derived CRC and CRLM models and demonstrated that 3DP tumor models maintained the specific biomarkers and characteristic mutation profiles of their parent tumors. Drug testing revealed marked tumor heterogeneity, including inter‐tumor heterogeneity among different patients and heterogeneity between primary and paired metastatic tumors within the same patient. We correlated the drug response data of CRLM 3DP models with patients’ clinical outcomes after neoadjuvant chemotherapy (NAC) and demonstrated that the 3DP cancer model could be a reliable and highly efficient platform for the individualized treatment of cancer.</p>" ]
[]
[ "<title>Results</title>", "<title>Construction of CRC Patient‐Derived 3DP Model</title>", "<p>This study enrolled 40 patients undergoing surgery for CRC in a clinical trial (ClinicalTrials.gov identifier NCT04755907), with informed patient consent (<bold>Figure</bold>\n##FIG##0##\n1A##). Patients’ baseline characteristics are shown in Table ##SUPPL##0##S1## (Supporting Information). All tumors were adenocarcinomas, based on pathology.</p>", "<p>CRC 3DP models of 37 specimens were established and stably cultured. Two specimens could not be successfully established due to microbial contamination. One specimen was insufficient for cell extraction. Due to specimen size limitations, PDTOs were established in seven of 37 cases, passaged in Matrigel, and cultured in organoid medium, as previously described. Additionally, due to the limitation of specimen sizes, not all CRC 3DP models underwent primary cell extraction, whole‐exome sequencing (WES), and histopathological analysis. Specimens from seven patients underwent WES, and 37 underwent drug tests (Figure ##FIG##0##1A##).</p>", "<p>Tumor cells were isolated as described previously and resuspended in gelatin (Gel)‐sodium alginate (SA) bioink for printing. The entire printing process was conducted inside the modeling chamber of the high‐precision 3D cell printer (SPP1603, SUNP) under a controlled temperature and sterile environment. The 6 mm × 6 mm × 1.2 mm grid‐like 3D structures obtained are shown in Figure ##SUPPL##0##S1A## (Supporting Information). Primary CRC cells demonstrated a significant proliferative capacity, with over 85% of the cells maintaining viability in the 3DP models for a period of 2 weeks (Figure ##SUPPL##0##S1B,C##, Supporting Information).</p>", "<title>Histological and Genomic Features of CRC 3DP Models</title>", "<p>The Gel‐SA composite bioink system is one of the most widely used low‐cost natural biomaterials in the field of micro‐extrusion‐based 3D bioprinting.<sup>[</sup>\n##UREF##5##\n41\n##, ##REF##34940707##\n42\n##\n<sup>]</sup> Notably, it boasts high grid porosity and remarkable cell compatibility. Through calcium ion crosslinking, it acquires controlled mechanical properties to prevent cell settling.<sup>[</sup>\n##UREF##6##\n43\n##, ##REF##32481829##\n44\n##\n<sup>]</sup> Numerous studies, including our previous research, have extensively validated the exceptional biocompatibility and highly controllable printability of this ink.<sup>[</sup>\n##REF##32434830##\n33\n##, ##REF##33007612##\n40\n##, ##REF##35288311##\n45\n##, ##REF##31173833##\n46\n##\n<sup>]</sup> Within this context, we observed that primary tumor cells derived from CRC patients could proliferate into a diverse and irregular 3D sphere morphology within the porous microenvironment of the Gel‐SA bioink, akin to the behavior of tumor organoids (tumoroids) in PDTO, which similarly display a spontaneous assembly into various morphologies (Figure ##FIG##0##1B##; Figure ##SUPPL##0##S2A##, Supporting Information; and Supplemental Videos). Significantly, the tumoroid‐like structures within the 3DP model exhibited a relatively consistent size within the porous Gel‐SA bioink, a stark contrast to the organoids in PDTO that showcased substantial variations (Figure ##SUPPL##0##S2B##, Supporting Information).</p>", "<p>Hematoxylin and eosin (HE) staining unveiled that certain tumoroid‐like structures within the 3DP model formed 3D structures with enclosed cavities or solid forms (Figure ##FIG##0##1C##). This architectural feature potentially resembles the glandular cavity‐like structures observed in some parental tumors (Figure ##FIG##0##1C##). PDTO specimens demonstrated significantly greater morphological diversity, a finding in line with prior research,<sup>[</sup>\n##REF##31761724##\n21\n##\n<sup>]</sup> including solid, thin cyst wall, and thick cyst wall structures (Figure ##FIG##0##1B,C##; Figure ##SUPPL##0##S2A##, Supporting Information). Similar to CRC PDTO,<sup>[</sup>\n##REF##31761724##\n21\n##, ##REF##31591597##\n22\n##\n<sup>]</sup> CRC 3DP models also could retain the biomarkers of the primary tumors from which they were derived. Biomarker expression analysis by immunofluorescence revealed that biomarkers detected in CRC tumors including CK7, CDX2, β‐catenin, Ki‐67, CK20, and pan‐cytokeratin (CK‐pan) were all significantly expressed in both CRC PDTOs and CRC 3DP models (Figure ##FIG##0##1D##; Figure ##SUPPL##0##S2C##, Supporting Information). These similarities in biomarker staining patterns suggest that the 3DP models and organoids both could retain the specific histopathological features of the parental tumors.</p>", "<p>In previous studies, we revealed that 3DP tumor models derived from cancer patients recapitulate the genomic mutation profiles of corresponding tumors.<sup>[</sup>\n##REF##33007612##\n40\n##\n<sup>]</sup> To demonstrate that 3DP models derived from patients with CRC recapitulated the genomic profiles of the paired tumor tissues, seven 3DP models (P3, P6, P10, P11, P13, P15, and P18) at day 10 post‐bioprinting were subjected to WES along with their corresponding tumor tissues. As previous studies have revealed that PDTO maintains the genomic alterations of corresponding tumors.<sup>[</sup>\n##REF##31761724##\n21\n##, ##REF##28052255##\n47\n##, ##REF##25957691##\n48\n##\n<sup>]</sup> WES was also conducted on five PDTOs derived from P10, P11, P13, P15, and P18. Analysis of the results showed that the concordance of single nucleotide variations (SNVs) was well retained by the 3DP models with original tumor tissues for all tested specimens (<bold>Figure</bold>\n##FIG##1##\n2A##). Analysis of the proportion of SNVs and insertions/deletions (indels) within each group further demonstrated mutual similarity (Figure ##FIG##1##2B##). In addition, the concordance of exonic variants between the 3DP models and paired tumor tissues was comparable to that between the PTDO models and corresponding tumor tissues (Figure ##FIG##1##2B##).</p>", "<p>More than 60 significantly mutated genes in CRC were selected from a recent study involving a large CRC cohort in the Chinese population<sup>[</sup>\n##REF##35487942##\n49\n##\n<sup>]</sup> and other previous studies.<sup>[</sup>\n##REF##27149842##\n50\n##, ##REF##22810696##\n51\n##, ##REF##29316426##\n52\n##\n<sup>]</sup> SNVs of these significantly mutated genes were analyzed, and mutations observed in at least one sample were shown (Figure ##FIG##1##2C##). The results illustrated that the CRC 3DP models retained the SNV spectrum of the significantly mutated genes in the original tumor tissues, although a few gains or losses were observed. Gene mutations associated with the Wnt signaling pathway were consistently observed in the 3DP model and PDTO of all seven specimens, and the mutation rate of APC was 100%. Significantly, in our results, seven CRC 3PD models retained a 94.2% overlap of the most frequent CRC gene mutational variants and their matching PDTOs also reached a high overlap rate (94.3%) (Figure ##FIG##1##2D##).</p>", "<title>Chemotherapy Drugs Test of CRC 3DP Model</title>", "<p>5‐FU, CPT‐11, and oxaliplatin are first‐line adjuvant chemotherapy drugs for CRC. We individually treated CRLM 3DP models in vitro with 5‐FU, CPT‐11, or oxaliplatin. We found that the relative cell viability of the CRC 3DP models was significantly different at 72 h after dosing (Figure ##SUPPL##0##S3##, Supporting Information). The single chemotherapy agent sensitivity of the 37 CRC 3DP models to 5‐FU, CPT‐11, and oxaliplatin was presented by a normalized area under the dose‐response curve (AUC) calculated from each dose‐response curve (<bold>Figure</bold>\n##FIG##2##\n3A##). CRC 3D models derived from patients exhibited significant heterogeneity in their responses to single drug stimulation of 5‐FU, CPT‐11, or oxaliplatin, including heterogeneous responses of the same model to different drugs and heterogeneity across different models to the same drug. Such significant heterogeneity is represented by the wide range of normalized AUC values (0.2‐1.0) depicted in the heatmaps (Figure ##FIG##2##3B##).</p>", "<title>CRLM Patient‐Derived 3DP Model Establishment and Development</title>", "<p>We further included 31 patients who underwent CRLM surgery in the aforementioned clinical trial, with informed patient consent (<bold>Figure</bold>\n##FIG##3##\n4A##); their baseline characteristics are shown in <bold>Table</bold>\n##SUPPL##0##\nS2\n## (Supporting Information). The pathological type of all the tumors was adenocarcinoma.</p>", "<p>Tumor cells were isolated as described previously and were resuspended in Gel‐SA bio ink for printing. CRLM 3DP models of the 29 specimens were established and stably cultured. Simultaneously, eight PDTOs were successfully established and passaged in Matrigel. The main reason for the failure of the two specimens was insufficient tumor cell extraction. Unlike the CRC specimens, none of the CRLM specimens were contaminated with microorganisms. The cell viability assay demonstrated that primary CRLM cells remained viable in the 3D‐printed model over 2 weeks (Figure ##SUPPL##0##S4A##, Supporting Information). Live and dead cell staining assays showed that most primary tumor cells (over 85%) remained alive within 2 weeks in 3DP models (Figure ##SUPPL##0##S4B##, Supporting Information).</p>", "<p>Bright‐field images and HE staining revealed that primary CRLM cells formed tumoroid‐like structures in the CRLM 3DP model, exhibiting similar morphological features to the CRC 3DP model. In comparison with CRLM PDTOs, significant differences were observed in terms of morphology (Figure ##FIG##3##4B,C##; Figure ##SUPPL##0##S5A##, Supporting Information). Much like the tumoroid‐like sphere sizes observed in the CRC 3DP model, the CRLM 3DP models also displayed remarkable consistency. Over a short period, these models exhibited relatively minor variations in cell sphere sizes, with the majority falling within the range of approximately 50 to 100 µm (Figure ##SUPPL##0##S5B##, Supporting Information). Additionally, the CRLM 3DP models also retained the biomarkers of the primary tumors from which they were derived. Immunofluorescence biomarker expression analysis revealed that 3DP CRLM models, CRLM organoids, and paired parental tumors exhibited similar staining patterns for CK7, CDX2, β‐catenin, Ki‐67, CK20, and CK‐pan (<bold>Figure</bold>\n##FIG##4##\n5A##; Figure ##SUPPL##0##S5C##, Supporting Information). The fluorescence expression of Ki67 in PDTOs was more prominent compared to that in the corresponding tumor tissues and 3DP models.</p>", "<p>Similarly, to demonstrate that 3DP models derived from patients with CRLM recapitulated the genomic profiles of the paired tumor tissues, seven CRLM 3DP models (LM3, LM6, LM8, LM10, LM11, LM14, and LM15) in long‐term culture were subjected to WES, along with their corresponding tumor tissues. Analysis of the proportion of SNVs and indels indicated that the mutations in the original tumor tissues were retained by the CRLM 3DP models, and the concordance of mutations between 3DP models and the paired tumor tissues was comparable to that between PTDOs and the corresponding tumor tissues (Figure ##FIG##4##5B##).</p>", "<p>Then, SNVs of significantly mutated genes of CRLM were analyzed using the above‐selected significantly mutated CRC genes. The results illustrated that the CRLM 3DP models also retained the SNV spectrum in the significantly mutated genes in the original tumor tissues, despite that there existed a few gains or losses of SNVs. (Figure ##FIG##4##5C##). Consistent with the analysis results of the CRC 3DP models, CRLM 3DP models retained a high (95.2%; 93.2% for CRLM PDTOs) overlap with the most frequent mutational variants in the parent tumor (Figure ##FIG##4##5D##). In addition, the expected levels of mutations in the WNT pathway were observed in CRLM 3DP model and PDTO cultures.</p>", "<title>Responses of CRLM 3DP Models to Chemical Drugs that Correlate with Clinical Responses</title>", "<p>Furthermore, drug sensitivity assays were performed on CRLM 3DP models from 24 patients to assess their response to 5‐FU, CPT‐11, and oxaliplatin. The normalized AUC, calculated from the dose‐response curves (Figures ##SUPPL##0##S6## and ##SUPPL##0##S7A##, Supporting Information), was used to quantify the sensitivity of these models to each chemotherapy agent. Moreover, the heatmap analysis (<bold>Figure</bold>\n##FIG##5##\n6A##) reveals significant heterogeneity in the response of different CRLM 3DP models to various chemotherapy agents as well. In a clinical context, NAC was administered to 20 patients with CRLM. Ten patients underwent FOLFOX (chemotherapy regimen of 5‐FU, and oxaliplatin) regimen chemotherapy; five patients received XELOX (chemotherapy regimen of capecitabine (5‐FU) and oxaliplatin) regimen; two patients underwent pre‐treatment with FOLFIRI (chemotherapy regimen of 5‐FU, CPT‐11, and leucovorin calcium), and two patients underwent pre‐treatment with FOLFOXIRI (chemotherapy regimen of 5‐FU, CPT‐11, oxaliplatin and leucovorin calcium). One patient (LM29) who had undergone curative resection for primary colorectal cancer, presented with hepatic metastasis upon post‐treatment evaluation following a complete course of adjuvant monotherapy with 5‐FU. This case is categorized as a CRLM patient who received preoperative adjuvant monotherapy with 5‐FU.</p>", "<p>To investigate the correlation between the results of in vitro drug sensitivity tests and the responses of CRLM patients to NAC, we ranked all the normalized AUC values of the drug tests from the highest to the lowest (Figure ##FIG##5##6B##). For each patient who received NAC, the lowest normalized AUC values of the drugs used in the treatment were highlighted with annotations indicating clinical outcomes. As shown in Figure ##FIG##5##6B##, there were no overlaps among the lowest AUC values of patients considered to show disease control (partial response, PR, and stable disease, SD) and disease progression (PD) in the clinic. Furthermore, we utilized the Jenks Natural Breaks algorithm to classify data points into groups. To avoid overfitting, the classification that generated the minimum number of breaks to obtain a goodness‐of‐fit greater than 90% was adopted (Figure ##SUPPL##0##S7B##, Supporting Information). Based on this, all normalized AUC values were segregated into four groups. A Jenks break of 0.690 allowed the classification of normalized AUC values for discriminating the 3DP models as sensitive or resistant in drug tests. If any drug used in the treatment generated a normalized AUC value lower than 0.690, the 3DP model was regarded as sensitive to that regimen. 3DP models were designated as resistant to the clinical regimen only if all drugs yielded a normalized AUC higher than 0.690 (Figure ##FIG##5##6B##).</p>", "<p>For instance, the CRLM 3DP models from LM1, LM19, and LM25 were all triple‐resistant, and the patients had a poor response. LM29 demonstrated resistance to 5‐FU and CPT‐11 while exhibiting sensitivity to oxaliplatin. However, the patient underwent adjuvant treatment with 5‐FU monotherapy, leading to the rapid emergence of hepatic metastases. CRLM 3DP models from LM2 and LM17 were triple‐sensitive, and the two patients achieved a good clinical response. Patient LM24 displayed sensitivity to both medications (5‐FU and oxaliplatin) included in the treatment regimen (XELOX) and achieved a favorable clinical response.</p>", "<p>The 3DP models derived from patients who achieved a stable clinical response demonstrated sensitivity to at least one of the medications included in the treatment regimen. Figure ##FIG##5##6C## summarizes the patients’ treatment regimens, clinical outcomes, and CRLM 3DP model responses to drug tests. In our findings, patients with CRLM who did not show disease progression were sensitive to at least one chemotherapeutic agent in the chemotherapy regimen they received. These results demonstrated that the responses of the 3DP CRLM model to the drug tests matched well with the clinical outcomes of the corresponding patients.</p>", "<title>Different Drug Responses Between Primary Colorectal Cancer and its Metastases</title>", "<p>Among the CRC and CRLM patients included in this study, we obtained primary and metastatic specimens from seven CRC patients with synchronous liver metastases (P17/LM5, P19/LM6, P21/LM8, P22/LM14, P24/LM16, P33/LM18, and P40/LM23). As presented in Figure ##FIG##5##6D##, one patient (P19/LM6) did not receive NAC, one patient (P24/LM16) received the XELOX regimen, one patient (P33/LM18) received the FOLFIRI regimen, and other four patients (P17/LM5, P21/LM8, P2/LM14, and P40 /LM23) were treated with the FOLFOX regimen. The responses of these seven pairs of tumors 3DP models in drug tests demonstrated that the drug response of the primary CRC tumors and liver metastases show marked heterogeneity between primary and metastases in the same chemotherapy regimen, even to a single agent in the regimen (Figure ##FIG##5##6D##).</p>" ]
[ "<title>Discussion</title>", "<p>The heterogeneity of patients with advanced cancer is considered to be the principal reason for the failure of cancer drug therapies.<sup>[</sup>\n##REF##27922044##\n14\n##\n<sup>]</sup> The selection of sensitive drugs among the many existing treatment options for individualized treatment is a challenge for oncologists. With the development of 3DP technology, the establishment of a tumor model by 3DP holds great promise in cancer research, particularly for personalized cancer treatment.<sup>[</sup>\n##REF##26216543##\n34\n##, ##REF##33493799##\n53\n##\n<sup>]</sup> To date, relevant research in oral cancer,<sup>[</sup>\n##REF##29857831##\n54\n##\n<sup>]</sup> breast cancer,<sup>[</sup>\n##REF##30616234##\n55\n##\n<sup>]</sup> colorectal cancer,<sup>[</sup>\n##REF##34869264##\n56\n##\n<sup>]</sup> and lung cancer<sup>[</sup>\n##UREF##7##\n57\n##\n<sup>]</sup> has shown that 3DP technology can be a novel platform to study tumor development and shows the potential to accelerate cancer research dramatically.<sup>[</sup>\n##REF##26216543##\n34\n##, ##REF##33741496##\n35\n##, ##REF##28501712##\n36\n##\n<sup>]</sup>\n</p>", "<p>In contrast to immortalized cancer cell lines, individualized patient‐derived tumor cells have been broadly employed in high‐throughput screening of drug candidates and cancer biomarkers, because they retain tumor heterogeneity and genomic features.<sup>[</sup>\n##REF##32855097##\n58\n##\n<sup>]</sup> Efficient, rapid, and practical generation of 3D models is imperative when handling freshly isolated patient‐derived tumor cells. We employed an automated 3D bioprinting platform that successfully executed this strategy. We have further enhanced the optimization of a proven Gel‐SA bioink‐based 3D model system by designing a refined, intricate, mesh‐like 3D structure using a computer platform (Figure ##SUPPL##0##S1A##, Supporting Information). This has enabled us to efficiently create sufficiently homogenized 3D tumor models in a short duration. Herein, we employed a high‐precision bioprinter to successfully establish patient‐derived personalized models for both CRC and CRLM. Notably, this marks the pioneering achievement of establishing patient‐derived CRC/CRLM tumor models through 3D biotechnology, achieving a remarkable success rate of 93.0%. The entire workflow, commencing from the surgical procedure to the bioprinting of the 3DP tumor model, takes less than 2 hours. Our findings underscore the good viability of primary tumor cells within the 3D bioink configuration and their excellent activity prior to commencing in vitro treatments.</p>", "<p>Our investigation revealed that primary tumor cells within the 3DP models have the capacity to generate 3D structures, encompassing both enclosed cavities and solid formations (Figures ##FIG##0##1C## and ##FIG##3##4C##). This phenomenon potentially corresponds to the histomorphological traits of the parental tumor; however, a broader sample size is warranted to firmly establish this connection. Due to the excellent printability of this specific bioink and the precision of the bioprinter, the tumor volume in 3DP models exhibits minimal variation and a uniform distribution, resulting in outstanding reproducibility. In contrast to PDTO, which exhibits substantial variability in construction methods and organoid sizes, and lacks standardized protocols, resulting in significant labor and material expenses,<sup>[</sup>\n##UREF##1##\n23\n##, ##REF##30981763##\n24\n##\n<sup>]</sup> the 3DP tumor model offers distinct advantages. These include its cost‐effectiveness, efficient modeling process, higher success rate, ability to maintain cell viability, and reduced time requirements for procedures. Moreover, 3DP technology can be utilized to create diverse cell models that accurately assemble the immune microenvironment in vitro, thereby making the 3DP tumor model even more promising for individualized drug prediction and cancer research.</p>", "<p>In our study, the establishment of 3DP tumor models requires a substantial quantity of primary tumor cells. This aligns with the cellular density prerequisites for constructing 3D biofabricated tissue engineering models (round from 1 to 10 million cells/ml).<sup>[</sup>\n##REF##25093879##\n59\n##, ##UREF##8##\n60\n##\n<sup>]</sup> Utilizing micro‐extrusion‐based bioprinting allows for the rapid creation of bio‐models containing high‐density cells that can function effectively within a short timeframe, closely mimicking native tissues. Additionally, both excessively low and high cellular densities can affect the physicochemical properties of the bioink.<sup>[</sup>\n##UREF##6##\n43\n##, ##REF##31785543##\n61\n##, ##UREF##9##\n62\n##\n<sup>]</sup> Specifically, for our investigation involving 3D bioprinting primary tumor cells sourced from patients, maintaining a concentration of 3 to 5 million cells per milliliter in our bioink is appropriate. This concentration promotes the optimal growth status for primary tumor cells within a short time window, facilitating reliable and accurate drug testing outcomes. Presently, a primary limitation in achieving successful 3DP tumor establishment is the restricted yield of cells obtained from specimens. Consequently, we refrained from utilizing tumor specimens procured via biopsy forceps.</p>", "<p>Our existing results illustrated that the patient‐derived tumor 3DP model can retain the biomarkers and genomic characterization of original tumors. Drug response results from 37 CRC 3DP models and 24 CRLM 3DP models illustrated notable inter‐patient heterogeneity of CRC and CRLM, which may be more pronounced than previously realized. The preservation of heterogeneity suggests that the 3DP models can be applied to predict individualized therapies.</p>", "<p>Recently, Mo et al. established a living biobank with 50 organoids derived from paired CRC and CRLM lesions, with an overall success rate of 80.6%. Their results showed that CRLM PDTOs have excellent potential for predicting the chemosensitivity and clinical prognosis of patients.<sup>[</sup>\n##UREF##10##\n63\n##\n<sup>]</sup> In our CRLM study, 20 patients with CRLM received NAC. Based on our analysis of the drug test results, we determined that the drug responses of the tested 3DP models had correlation with the clinical outcomes of the corresponding CRLM patients who underwent NAC. During the analysis, we adopted an approach from a recent study by classifying the AUC derived from the dose‐response curve,<sup>[</sup>\n##REF##34789479##\n64\n##\n<sup>]</sup> which was then translated into clinical information. The chosen predictor AUC avoided disregard of the potential clinical utility of chemotherapeutics as much as possible. We did not use combinations of drugs in the 3DP model because it was difficult to determine the combined drug concentration in vitro. The clinical response of most combination drug therapies can be explained by monotherapy,<sup>[</sup>\n##REF##29245013##\n65\n##, ##REF##34983746##\n66\n##\n<sup>]</sup> however, the potential difference between combination therapy and independent single‐drug therapies in the 3DP tumor model deserves further study.</p>", "<p>It is worth noting that the primary tumor and metastases in the same patient may respond differently to the same chemotherapy regimen. Mo et al. demonstrated that primary and metastatic lesions from the same patient were heterogeneous in molecular fingerprints, but the majority results of drug sensitivity in vitro were highly consistent. In our study, we obtained primary tumor and metastatic specimens from seven patients with synchronous liver metastases from CRC and performed the same drug response tests. Drug test results are expressed in the predictor AUC as previously described. We found that CRC patients with synchronous liver metastases demonstrated different responses to single chemotherapy drug between the primary tumors and metastases. This indicated tumor‐to‐tumor heterogeneity between the primary tumors and metastases which could not be ignored. We found that the primary and metastatic lesions of four patients who received NAC had different pathological regression responses. In our results, the metastatic lesions of these four patients all showed good pathological responses relatively, whereas the primary lesions did not respond considerably. These results illustrated that the existing heterogeneity in chemotherapy drug test results and clinical treatment responses between primary and metastatic lesions of part patients are important issues that should be taken into account in precision medicine. Due to the limitations of the specimen size, we were able to perform drug tests only for paired primary and metastatic lesions. WES was not performed to analyze the differential gene profiles that may exist between the primary and metastatic foci.</p>" ]
[ "<title>Conclusion</title>", "<p>In conclusion, we have successfully established a 3DP tumor model for patients with CRC/CRLM, which, to our knowledge, has not been reported previously. We demonstrated that this model could maintain the biological and genetic features of the original tumor, and importantly, we found a significant correlation between clinical outcomes in patients with CRLM and individual 3DP tumor model drug sensitivity tests, considering the significant tumor heterogeneity. The next generation of individualized treatment will likely involve a more precise medicine model, which requires incorporating the heterogeneity of the patient population into every step of the diagnosis‐treatment cascade. While individualized treatment of advanced malignancies, including CRLM, is currently relatively ambiguous, our findings indicate that the patient‐derived cancer 3DP model has the potential to serve as a platform to enhance precision cancer treatment and expedite the clinical development of new drugs. However, given the relatively small sample size in our study, further studies are required to test this method in a larger patient population.</p>" ]
[ "<title>Abstract</title>", "<p>Methods accurately predicting the responses of colorectal cancer (CRC) and colorectal cancer liver metastasis (CRLM) to personalized chemotherapy remain limited due to tumor heterogeneity. This study introduces an innovative patient‐derived CRC and CRLM tumor model for preclinical investigation, utilizing 3d‐bioprinting (3DP) technology. Efficient construction of homogeneous in vitro 3D models of CRC/CRLM is achieved through the application of patient‐derived primary tumor cells and 3D bioprinting with bioink. Genomic and histological analyses affirm that the CRC/CRLM 3DP tumor models effectively retain parental tumor biomarkers and mutation profiles. In vitro tests evaluating chemotherapeutic drug sensitivities reveal substantial tumor heterogeneity in chemotherapy responses within the 3DP CRC/CRLM models. Furthermore, a robust correlation is evident between the drug response in the CRLM 3DP model and the clinical outcomes of neoadjuvant chemotherapy. These findings imply a significant potential for the application of patient‐derived 3DP cancer models in precision chemotherapy prediction and preclinical research for CRC/CRLM.</p>", "<p>The study showcases the establishment of patient‐derived 3D bioprinting models for colorectal cancer and its liver metastases. These models highly retain parent tumor biomarkers and mutation profiles, revealing substantial heterogeneity. Crucially, drug testing correlates strongly with clinical response, highlighting the great potential of 3D bioprinting tumor model as a preclinical platform for personalized cancer therapy.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6802-cit-0073\">\n<string-name>\n<given-names>H.</given-names>\n<surname>Sun</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Sun</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Ke</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>B.</given-names>\n<surname>Jin</surname>\n</string-name>, <string-name>\n<given-names>P.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Jiang</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Zhao</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Sun</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Sun</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Pang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>B.</given-names>\n<surname>Wu</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Zhao</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Sang</surname>\n</string-name>, <string-name>\n<given-names>B.</given-names>\n<surname>Xing</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>P.</given-names>\n<surname>Huang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Mao</surname>\n</string-name>, <article-title>Prediction of Clinical Precision Chemotherapy by Patient‐Derived 3D Bioprinting Models of Colorectal Cancer and Its Liver Metastases</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304460</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304460</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Participants and Specimens</title>", "<p>Patients with CRC/CRLM were recruited from an observational clinical trial (ClinicalTrials.gov identifier: NCT04755907) in four medical centers: Peking Union Medical College Hospital, Cancer Hospital Chinese Academy of Medical Sciences, Beijing Cancer Hospital, and China‐Japan Friendship Hospital. The enrollment criteria included age ≥ 18 years, clinical diagnosis of CRC/CRLM, and feasibility of surgical treatment. CRC and CRLM were confirmed by postoperative pathological diagnosis in all participants. Written informed consent was obtained from all the patients prior to tissue acquisition. The study was conducted in accordance with recognized ethical guidelines and received approval from the Ethics Review Committee of Peking Union Medical College Hospital (Approval No. JS‐2475).</p>", "<p>The specimens were transported on ice in DMEM/F12 (Gibco, Billings, MT, USA) medium with primocin (0.2%) (InvivoGen, San Diego, CA, USA), antibiotic‐antimycotic (1%) (Gibco), and RHOK inhibitor Y‐27632 (10 µ<sc>m</sc>) (Sigma–Aldrich, St Louis, MO, USA), and arrived at the laboratory as soon as possible after surgery. Upon arrival, each specimen was swiftly divided into several parts according to size for primary cell extraction, WES, or histopathological analysis.</p>", "<title>Cell Isolation, Bioprinting, and Culture</title>", "<p>Specimens for tumor cell isolation and culture were washed in cold phosphate buffered solution (PBS) with primocin (0.2%), antibiotic‐antimycotic (1%), and Y‐27632 (10 µ<sc>m</sc>) for 5 min × 3 min to avoid contamination by microorganisms and were then minced into pieces smaller than 3 mm, on ice. Then, the specimen fragments, in cold PBS, were transferred to a 15 mL centrifuge tube and centrifuged at 100 × <italic toggle=\"yes\">g</italic> for 3 min until the supernatant became clear. Minced tissues were incubated in digestion medium (DEME/F12 medium supplemented with collagenase II (1.5 mg mL<sup>−1</sup>) (Gibco), dispase type II (1 mg mL<sup>−1</sup>) (Sigma–Aldrich), hyaluronidase (20 µg mL<sup>−1</sup>) (Sigma–Aldrich), Y27632 (10 µ<sc>m</sc>), antibiotic‐antimycotic (1%), and primocin(0.2%)) at 37 °C on an orbital shaker at 37 °C for 30–60 min and were shaken manually every 15 min. Tumor cells were collected after filtering through a 100‐µm cell strainer (Biosharp, San Diego, CA, USA), centrifuged at 300 × <italic toggle=\"yes\">g</italic> for 5 min, and resuspended in 3DP culture medium after cell counting for bioprinting.</p>", "<p>To formulate the bioink, Gel and SA were mixed evenly with the cell suspension in proportion: Briefly, bioink was mixed well with the cell suspension, 4% SA (Sigma–Aldrich), and 12% Gel (Sigma–Aldrich) at a volume ratio of 2:1:2, resulting in a final concentration of tumor cells of 5 × 10<sup>6</sup> cells mL<sup>−1</sup> and the final concentration of Gel and SA was 4.8% and 0.8%. The bioink cell/biomaterial mixture was drawn into a 3 mL syringe (BD, Franklin Lakes, NJ, USA) with a 23 G needle. After incubating at 4 °C for 30 min until ink gels were formed, the syringe was set into a 3D bioprinter (Cherry Hill, NJ, USA). The temperature of the nozzle and the chamber was set to 20 and 10 °C, respectively. The 3DP model was designed as layer‐by‐layer grids with a size of 6 mm × 6 mm × 1.2 mm (layer height was 0.2 mm and line width was 0.8 mm) and was printed using an extrusion speed of 1.5 mm<sup>3</sup> s<sup>−1</sup>. The printing process was conducted within 2 h, during which the 3D bioprinting models were collected in 48‐well plates on the chamber platform.</p>", "<p>Fresh 3DP grids were immersed in calcium chloride solution (3%) for 2 min to cross‐link the SA, thus providing better physical strength, and then washed with Hank's Balanced Salt Solution (HBSS) (Gibco). Each 3DP model was cultured in 500 µl 3DP medium, which was composed of advanced DMEM/F12 (Gibco), B27 supplement (1×) (Life Technologies, Carlsbad, CA, USA), N2 supplement (1×) (Life Technologies), GlutaMAX (2 m<sc>m</sc>) (Gibco), HEPES (10 m<sc>m</sc>) (Gibco), recombinant EGF (50 ng mL<sup>−1</sup>) (PeproTech, Rocky Hill, NJ, USA), N‐acetyl‐L‐cysteine(1 m<sc>m</sc>) (Sigma–Aldrich), Prostaglandin E2 (10 n<sc>m</sc>) (Sigma–Aldrich), A8301 (500 n<sc>m</sc>) (Tocris Bioscience, Bristol, UK), SB202190 (3 ε<sc>m</sc>) (Sigma–Aldrich), Gastrin I (10 n<sc>m</sc>) (Sigma–Aldrich), primocin (0.2%), antibiotic‐antimycotic (1%), and Y27632 (10 µ<sc>m</sc>). The 3DP medium was refreshed every 3 days. To assess the viability of the 3DP CRLM models, Calcein‐AM (CAM, Sigma–Aldrich) and propidium iodide (PI, Sigma–Aldrich) staining were performed on days 1, 3, 6, 10, and 14 after bioprinting. This staining method allows for the discrimination of viable cells, which were labeled green, from dead cells, which were labeled red. Additionally, the CellTiter‐Glo 3D Cell Viability Assay (Promega, Madison, WI, USA) was used to evaluate the cell viability of the CRC 3DP model.</p>", "<p>To establish PDTOs, the tumor cell pellet was suspended in Matrigel and promptly inoculated into preheated 24‐well flat‐bottomed cell culture plates (Costar, Washington, DC, USA) in a dome shape, using 50 µL volume per well. After a 10‐min incubation at 37 °C in 5% CO<sub>2</sub>, the wells were covered with 500 µL of 3DP medium. PDTOs were maintained by refreshing the medium every 3 days, while monitoring and capturing images of the organoids at specific time points using a microscope. Organoid passaging was performed every 1–2 weeks based on their density. Initially, organoids were dissociated using TrypLETM Express (GIBCO) and mechanically sheared through bovine serum albumin‐coated (1%) pipette tips, followed by multiple centrifugation washes at 300 × <italic toggle=\"yes\">g</italic> until the Matrigel was cleared. The organoid fragments were then resuspended in Matrigel and seeded as described above. Cryopreservation of organoids was conducted using a serum‐free medium (NCM Biotech, Jiangsu, China), and upon recovery, the medium was supplemented with Y27632 (10 m<sc>m</sc>) for culture.</p>", "<title>HE, and Immunofluorescence Staining</title>", "<p>Fresh specimens were fixed with paraformaldehyde (PFA) (4%) (Sigma–Aldrich). PDTOs and 3DP models were collected and fixed in 10% formaldehyde calcium (Solarbio, Beijing, China) overnight after culturing for 10 days. After embedding in paraffin, specimens were sectioned into 5‐µm‐thick slices and subsequently stained with HE following standard procedures.</p>", "<p>For immunofluorescence, fresh tumor specimens were fixed in PFA (4%) overnight, dehydrated using a gradient of sucrose solution, embedded in Tissue‐Tek O.C.T. compound (Sakura Finetek, Torrance, CA, USA), and cut into 5‐µm‐thick slices. PDTOs and 3DP models were harvested 10 days after manufacturing, dissociated gently, and seeded in chambered cell culture slides coated with Gel (3%), where they were cultured overnight in 3DP culture medium. They were handled using standard immunofluorescence procedures. Briefly, the tissue sections were fixed in 4% PFA for 15 min. Dissociated units of 3DP CRC/CRLM models and PDTOs on chambered cell culture slides were fixed in 10% formaldehyde for 15 min. Then, all samples were permeabilized with Triton X‐100 (0.3%) (Sigma–Aldrich) for 20 min at room temperature, blocked in 1% bovine serum albumin (Sigma–Aldrich) for 30 min at room temperature, and incubated with primary antibodies in blocking buffer at 4 °C overnight. Rabbit anti‐CK20 (1:200, Abcam, Cambridge, MA, USA), mouse anti‐CK7 (1:200, Abcam), rabbit anti‐CDX2 (1:200, Abcam), rabbit anti‐β‐catenin (1:200, Abcam), mouse anti‐Ki‐67 (1:200, Abcam), and mouse anti‐CK‐pan (1:200, Abcam) were used as primary antibodies for immunohistochemical staining. The 3DP models and sections were then incubated with goat anti‐rabbit IgG Alexa Fluor 488 (1:300, Abcam) and goat anti‐mouse IgG Alexa Fluor 594 (1:300, Abcam) for 2 h at room temperature. 4′,6‐Diamidino‐2‐phenylindole (DAPI) (20 µ<sc>m</sc>, Sigma–Aldrich) was used to label the nuclei at room temperature. The stained sections were mounted in an anti‐fade solution containing DAPI (Abcam). The samples were then washed with HBSS. Stained cells and sections were observed under a laser scanning confocal microscope (Nikon A1, Tokyo, Japan).</p>", "<title>Whole‐Exome Sequencing and Mutation Analysis</title>", "<p>DNA from CRC/CRLM specimens and corresponding CRC/CRLM 3DP models and PDTOs of patients was extracted using the TIANamp Genomic DNA Kit (Tiangen Biotech, Beijing, China) following the manufacturer's protocol after culturing for 10 days. Prior to library construction, the extracted DNA was strictly tested as follows: i) detection of DNA purity using a NanoPhotometer spectrophotometer (IMPLEN, Westlake Village, CA, USA); ii) quantification of DNA concentration using the Qubit DNA Assay Kit in a Qubit 2.0 Fluorometer (Life Technologies); iii) evaluation of DNA degradation and contamination on agarose gels (1%). The whole exome was captured using the Agilent SureSelect Human All Exon V6 platform (Agilent, Santa Clara, CA, USA) and sequencing was performed on an Illumina HiSeq 4000‐PE150 (Illumina, San Diego, CA, USA).</p>", "<p>Reads were aligned to the human reference genome (GRCh37/HG19) using the Burrows‐Wheeler Aligner (BWA, version 0.7.9a).<sup>[</sup>\n##REF##19451168##\n67\n##\n<sup>]</sup> Local realignment and base quality score recalibration were performed using the Genome Analysis Toolkit (GATK),<sup>[</sup>\n##REF##20644199##\n68\n##\n<sup>]</sup> with duplicate reads removed using Picard. SNVs and indels were simultaneously called with the HaplotypeCaller of GATK (v3.3.0).</p>", "<title>Drug Tests and Cell Viability Assay</title>", "<p>Drug treatment in the 3DP models was conducted on day 6, the time‐point of the second medium change. 5‐FU (Selleck), CPT‐11 (Selleck), and oxaliplatin (Selleck), three drugs commonly applied as chemotherapy of CRC/CRLM, were tested in the 3DP CRC/CRLM models, as single agents. Drugs were added to 500 µL culture medium according to a set concentration gradient (100, 50, 10, 1, and 0 µ<sc>m</sc>), and the drug‐containing culture medium was refreshed every 24 h for 72 h. Cell viability was detected using the CellTiter‐Glo 3D Cell Viability Assay (Promega, Madison, WI, USA), according to the manufacturer's instructions.</p>", "<title>Clinical Information for Outcome Evaluation of Patients Who Underwent Chemotherapy Treatment</title>", "<p>Patients received standard treatment according to the guidelines for CRC/CRLM after multidisciplinary consultation. Some participants who were potentially eligible for surgical treatment were recommended to receive neoadjuvant therapy before surgery, while others underwent surgery without NAC. The most widely used regimens of (neo) adjuvant chemotherapy for CRC and CRLM patients included FOLFOX, FOLFIRI, FOLFOXIRI, and XELOX.</p>", "<p>Clinical responses to NAC for CRLM were evaluated based on radiological examinations by attending physicians, independent of the laboratory work. Chemotherapy responses of CRLM patients were classified as PR, SD, or PD used to evaluate CRLM tumor response in this study, according to the Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. PR and SD were both classified as disease control. Tumor and node staging for all resected specimens were conducted according to the 7th American Joint Committee on Cancer TNM staging manual.</p>", "<p>For CRC, tumor regression grade (TRG) was mainly used to evaluate the clinical response of patients to NAC in this study. All tumor slides were examined at the microscope by independent pathologists. To compare tumor response between paired specimens from the same patient, tumor regression was scored in CRC after NAC using a modified Mandard protocol<sup>[</sup>\n##REF##8194005##\n69\n##\n<sup>]</sup> that can also be applied to CRLM.<sup>[</sup>\n##REF##17060484##\n70\n##\n<sup>]</sup> The modified Mandard protocol was based on the presence of residual tumor cells and the extent of fibrosis, which were defined as follows: TRG 1, complete regression with no residual tumor; TRG 2, presence of rare residual cancer cells; TRG 3, presence of larger numbers of residual cancer cells with predominant fibrosis; TRG 4, residual cancer outgrowing the fibrosis; and TRG 5, absence of regressive changes. TRG was associated with prognosis in patients receiving preoperative chemotherapy.<sup>[</sup>\n##REF##17060484##\n70\n##\n<sup>]</sup> Considering the degree of tumor regression and survival benefit of the patients, the patients were divided into two groups. Tumors with TRG 1, 2, or 3 tended to show a good response to NAC, and those with TRG 4 or 5 tended to show a poor response to NAC.</p>", "<title>Statistical Analysis</title>", "<p>Cell viability of the 3DP models after drug treatment was normalized to the mean of the untreated controls. Dose‐response curves of drug testing were fitted using weighted n‐parameter logistic regression in the R package “nplr”.<sup>[</sup>\n##UREF##11##\n71\n##\n<sup>]</sup> The AUC was inferred according to Simpson's rule, and the normalized AUC was obtained by dividing the corresponding AUC value by the maximum area for each concentration range.</p>", "<p>To understand the correlation between the results of drug testing and the patients’ clinical responses, normalized AUC values of CRLM 3DP models were ordered and then clustered into groups according to the Jenks Natural Breaks algorithm.<sup>[</sup>\n##UREF##12##\n72\n##\n<sup>]</sup> The number of breaks was defined as the minimum that reached a goodness‐of‐fit exceeding 90%. By minimizing intragroup variance and maximizing intergroup variance, this algorithm identified cutoff values to discriminate drug tests as sensitive or resistant in this study as well as in previous research.<sup>[</sup>\n##REF##34789479##\n64\n##\n<sup>]</sup> Relevant analyses between lab drug testing and the clinical responses were performed using the R package “jenks” in the “classInt”. All statistical analyses were conducted using R software version 4.0.1 (<ext-link xlink:href=\"http://www.r-project.org\" ext-link-type=\"uri\">www.r‐project.org</ext-link>).</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>H.S., L.S., X.K., and L.L. contributed equally to this work. Y.M., H.Y., and P.H. conceived, designed, and supervised the study, obtained funding and provided administrative, technical, or material support. H.S., L.S., X.K., and L.L. contributed to the development of methodology. L.S., L.L., C.L., and B.J. contributed to the analysis and interpretation of data. H.S. and X.K. contributed to the writing of the manuscript. P.W., Z.J., H.Z., Z.Y., Y.S., J.L., Y.W., M.S., M.P., Y.H.W., B.W., H.T.Z., X.S., and B.X. contributed to the acquisition of data and material. Y.M., H.Y., P.H., H.T.Z., and X.S. contributed to the review and revision of the manuscript. All authors read and approved the final manuscript.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank all patients who participated in this study. This work was supported by the Ministry of Science and Technology of China (2019YFA0801501), National High‐Level Hospital Clinical Research Funding (2022‐PUMCH‐B‐034), Chinese Academy of Medical Sciences Initiative for Innovative Medicine (2021‐I2M‐1‐058, 2022‐I2M‐2‐003), Chinese Academy of Medical Sciences Start‐up Grants (2021‐RC310‐004, 2020‐RC310‐007), Tianjin Natural Science Foundation for Distinguished Young Scholars (21JCJOJCO0030), National Natural Science Foundation of China (31970687, 32271470, 82300754), and Beijing‐Tianjin‐Hebei Basic Research Cooperation Special Project (22JCZXJC00200).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6802-fig-0001\"><label>Figure 1</label><caption><p>Study process and histopathological characterization of CRC 3DP models. A) The study process in primary colorectal cancer. A total of 40 patients undergoing surgery for CRC were enrolled, and 3DP models were successfully established and stably cultured for 37 patients. B) Bright‐field images of CRC 3DP models and CRC PDTOs on day 6 after production. Scale bar = 100 µm. C) HE staining comparing CRC 3DP models with corresponding organoids and parental tumors. Scale bar of tumor, 100 µm. Organoid and 3DP scale bars, 20 µm. D) CRC 3DP models and corresponding organoids and parent tumors were co‐stained with CK20 (green), CK7 (red), CDX2 (green), CK‐pan (red), β‐catenin (red), Ki‐67 (green) to examine the profiles of CRC biomarkers. DAPI was used to visualize nuclei (blue). Scale bar of tumor staining = 50 µm. Scale bars of 3DP and organoids staining = 20 µm.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6802-fig-0002\"><label>Figure 2</label><caption><p>Genetic alteration profiles of CRC 3DP models and corresponding primary tumors. A) The concordance of single‐nucleotide variants (SNVs) of CRC 3DP models and CRC PDTOs with original tumor tissues. B) Proportions of exonic variants observed in all tested samples (T, tumor; P, 3DP; O, PDTO). C) Spectrum of SNVs in the most frequently mutated genes of CRC. Each row represented a driver gene, and each column represented the mutational profile of CRC 3DP models, CRC PDTOs, and parental tumors (T, tumor; P, 3DP; O, PDTO).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6802-fig-0003\"><label>Figure 3</label><caption><p>Drug responses of CRC 3DP models. A) The sensitivity of 37 CRC 3DP models to the chemotherapeutic drugs 5‐fluorouracil (5‐FU), irinotecan (CPT‐11), and oxaliplatin was assessed by determining the normalized area under the curve (AUC) from the corresponding dose‐response curves. B) Heatmap showing drug responses in CRC 3DP models of 37 patients. The responses to drug tests were presented as the AUC.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6802-fig-0004\"><label>Figure 4</label><caption><p>Establishment of the CRLM 3DP model. A) Study process in liver metastases. 31 patients undergoing CRLM surgery were enrolled. CRLM 3DP models of the 29 specimens were established. Drug responses were tested in 24 3DP CRLM models, among which 20 patients received neoadjuvant chemotherapy. B) Bright‐field images of CRLM 3DP models and PDTOs. Scale bar = 100 µm. C) HE staining of CRLM 3DP models, corresponding organoids, and parental tumors. Scale bar of tumor, 100 µm. Organoid and 3DP scale bars, 20 µm.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6802-fig-0005\"><label>Figure 5</label><caption><p>Histological and genetic mutational characterization of CRLM 3DP models. A) CRLM 3DP models and corresponding organoids and parent tumors were co‐stained with CK20 (green), CK7 (red), CDX2 (green), CK‐pan (red), β‐catenin (red), Ki‐67(green) to examine the profiles of CRC biomarkers. DAPI was used to visualize nuclei (blue). Scale bar of tumor staining = 50 µm. Scale bars of 3DP and organoids staining = 20 µm. B) Proportions of exonic variants for all tested samples (T, tumor; P, 3DP; O, PDTO). C) Spectrum of SNVs in the most frequently mutated genes of CRLM. Each row represents a driver gene, and each column represents the mutational profile of CRLM 3DP models, PDTOs, and parental tumors (T, tumor; P, 3DP; O, PDTO). D) Bar plots present the concordance among the SNVs of the most frequently mutated genes identified in CRLM 3DP models, PDTOs, and corresponding primary tumors.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6802-fig-0006\"><label>Figure 6</label><caption><p>Correlation of CRLM 3DP models drug responses to clinical responses of neoadjuvant therapy. A) Heatmap showing drug responses in CRLM 3DP models of 24 patients. The responses to drug tests were presented as the normalized area under AUC. B) Correlation between normalized AUC values of drug tests and disease control of CRLM patients. All the normalized AUC values were shown as circles and ranked from the highest to the lowest. For each patient who received neoadjuvant chemotherapy, only the lowest AUC value of drugs used in the clinical regimen was highlighted, with the clinical response superimposed on the corresponding circle. Blue, yellow, and red denote PR, SD, and PD, respectively. The dotted line represents the cutoff value (0.690) of the normalized AUC values, which was generated by the Jenks natural breaks algorithm, classifying the CRLM 3DP models into sensitive or resistant to the drug. C) The normalized AUC values of each patient with known clinical response to neoadjuvant therapy. The dotted line symbolizes the cutoff value (0.690) for the classification of normalized AUC values. The pound sign represented the drug used in the patients’ chemotherapy regimens, and the regimens in clinic were shown at the bottom. D) Heatmap presents different drug responses and clinic outcomes between CRC primary lesions and their paired liver metastases.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6802-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6802-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 1</p></caption></supplementary-material>", "<supplementary-material id=\"advs6802-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 2</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2304460-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304460-s003.wmv\" mimetype=\"video\" mime-subtype=\"x-ms-wmv\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304460-s002.wmv\" mimetype=\"video\" mime-subtype=\"x-ms-wmv\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
72
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 16; 11(2):2304460
oa_package/d0/25/PMC10787059.tar.gz
PMC10787060
37985922
[ "<title>Introduction</title>", "<p>To achieve a carbon‐neutral society, there is an urgent need to develop materials for CO<sub>2</sub> capture and storage. Porous coordination networks (PCNs), also known as metal–organic frameworks (MOFs), which are composed of organic multidentate ligands combined with metal ions, have attracted attention as promising candidates because of their readily modifiable structures and tunable pore environments. Previous efforts to improve the affinity of networks for CO<sub>2</sub> focused on increasing the number of point interactions with the adsorbed molecules by incorporating open metal sites,<sup>[</sup>\n##REF##22908934##\n1\n##, ##REF##22805561##\n2\n##\n<sup>]</sup> amino groups,<sup>[</sup>\n##UREF##0##\n3\n##, ##REF##22475173##\n4\n##, ##REF##28669181##\n5\n##\n<sup>]</sup> or inorganic fluorinated anions<sup>[</sup>\n##UREF##1##\n6\n##, ##REF##27388208##\n7\n##\n<sup>]</sup> into their structures. Additionally, PCNs with flexible structures were also explored for this application. They rely on structural transformations that are induced by pressure changes and can be selectively triggered by CO<sub>2</sub>, including gate opening<sup>[</sup>\n##UREF##2##\n8\n##, ##REF##16332040##\n9\n##, ##REF##17854181##\n10\n##, ##REF##22575013##\n11\n##, ##REF##32747638##\n12\n##, ##REF##30679369##\n13\n##, ##REF##37454124##\n14\n##\n<sup>]</sup> and rotation dynamics of ligands.<sup>[</sup>\n##UREF##3##\n15\n##, ##REF##33705119##\n16\n##, ##REF##28507686##\n17\n##\n<sup>]</sup>\n</p>", "<p>Although there has been considerable progress in improving CO<sub>2</sub> uptake capacities and selectivity,<sup>[</sup>\n##UREF##4##\n18\n##, ##REF##31863992##\n19\n##, ##REF##22204561##\n20\n##, ##REF##28555216##\n21\n##, ##UREF##5##\n22\n##\n<sup>]</sup> the possibility of its long‐term storage inside PCNs under ambient conditions has received comparatively less attention since the interactions between the adsorbed gas and the network are typically facilitated by weak intermolecular interactions (physisorption). Therefore, to prevent gas diffusion outside, functional groups that can form stronger covalent bonds with CO<sub>2</sub> molecules (chemisorption) need to be introduced. However, because of the high stability of the resultant chemical bonds, CO<sub>2</sub> desorption and sorbent regeneration can be energy intensive, as in the case of amino‐based liquids which are commonly used to capture CO<sub>2</sub> in industrial settings.</p>", "<p>In this study, we present an alternative approach for trapping CO<sub>2</sub> inside PCNs. An interpenetrated network containing isolated voids between two adjacent nets was constructed. Even though these voids cannot be directly accessed, stretchable transient channels resembling “magic doors” could appear, enabling the material to adsorb CO<sub>2</sub> and exclude N<sub>2</sub>. Once confined inside, CO<sub>2</sub> did not exhibit any strong interactions with the pore interior and the same mechanism was impeding its diffusion to the outside. As a result, the network could retain CO<sub>2</sub> for more than one week while being kept on a bench.</p>" ]
[]
[ "<title>Results and Discussions</title>", "<p>To obtain the desired material, a ligand (<bold>L</bold>) based on a pseudo‐tetrahedral bimesityl skeleton<sup>[</sup>\n##UREF##6##\n23\n##, ##REF##31180667##\n24\n##\n<sup>]</sup> decorated with four pyrimidine groups was developed (<bold>Figure</bold> ##FIG##0##\n1a##; Figures ##SUPPL##0##S2## and ##SUPPL##0##S3##, Supporting Information). Because of its steric bulk and orientation of nitrogen atoms around pyrimidine rings, the coordination directions are bent at an angle against the center–vertex axes. Therefore, the coordination of this ligand was expected to create PCNs with highly compact convergent structures featuring small pores. The reaction of <bold>L</bold> with CuI in the presence of KI and PPh<sub>3</sub> in the CH<sub>3</sub>CN/H<sub>2</sub>O/EtOH solvent mixture under solvothermal conditions yielded two distinct crystal morphologies, yellow plates and yellow prisms. Single crystal X‐ray diffraction analysis (SCXRD) revealed that the former crystals corresponded to a 2D network with the molecular formula of {[(Cu<sub>2</sub>I<sub>2</sub>)(<bold>L</bold>)]·solvent}<sub>n</sub> (<bold>1</bold>). On the other hand, the prisms were a different polymorph, {[(Cu<sub>4</sub>I<sub>4</sub>)(<bold>L</bold>)]·solvent}<sub>n</sub> (<bold>2</bold>), with a 3D interpenetrated structure. The two PCNs always crystallized together as a mixture during the synthesis. However, because of differences in their crystal densities, 1.782 and 2.086 g cm<sup>−3</sup> for <bold>1</bold> and <bold>2</bold>, respectively, pure samples could be obtained by the density separation method.<sup>[</sup>\n##REF##21541391##\n25\n##\n<sup>]</sup>\n</p>", "<p>The structure of network <bold>1</bold> consisted of Cu<sub>2</sub>I<sub>2</sub> dimers connected by four pyrimidine groups from four separate ligands forming staggered 2D layers (Figure ##SUPPL##0##S4##, Supporting Information). In comparison, network <bold>2</bold> had a diamondoid‐type structure containing Cu<sub>4</sub>I<sub>4</sub> cubane clusters as connector nodes (Figure ##FIG##0##1b−d##). Because each Cu ion coordinated to only one nitrogen atom in each pyrimidine ring, the resultant network was highly distorted limiting the degree of interpenetration to only two nets. This material possessed closed pores with dimensions of 5.2 × 4.9 × 4.9 Å. However, the size of the maximum aperture between each pore was only 2.4 × 1.5 Å, which was too small for any molecule to pass through. Nevertheless, acetonitrile molecules were present in the pores of the as‐synthesized crystal of <bold>2</bold> (Figure ##SUPPL##0##S5##, Supporting Information), which could be removed by heating at 473 K for 12 h under vacuum without loss of crystallinity, suggesting that some diffusion pathways could exist for the guest escape to occur (vide infra). The crystallinity of network samples was assessed by powder X‐ray diffraction (PXRD). The measured patterns (Figures ##SUPPL##0##S8## and ##SUPPL##0##S9##, Supporting Information) matched closely with the simulated patterns from the single crystal structures, thus confirming their phase purity. Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were performed, revealing that networks <bold>1</bold> and <bold>2</bold> were stable up to 400 °C at which point the ligand began to decompose (Figure ##SUPPL##0##S10a–c##, Supporting Information). A smaller weight decrease was observed at ≈250 °C, which was due to the evaporation of solvent (MeCN) from the pores.</p>", "<p>These results prompted us to investigate the possibility of adsorbing different gases into the two networks. First, N<sub>2</sub> isotherms measured at 77 and 298 K showed no appreciable uptakes in both structures (<bold>Figure</bold> ##FIG##1##\n2a##; Figures ##SUPPL##0##S11## and ##SUPPL##0##S12b##, Supporting Information). Additionally, network <bold>1</bold> displayed only a negligible uptake capacity for CO<sub>2</sub> at 298 K (Figure ##SUPPL##0##S11a##, Supporting Information). These results indicated that the pores in its structure are not accessible to small gas molecules in the measured pressure range. In contrast, network <bold>2</bold> adsorbed CO<sub>2</sub> at several temperatures, reaching close to one molecule per void, indicating a complete saturation (Figure ##FIG##1##2a##; Figure ##SUPPL##0##S12##, Supporting Information). The material could be fully regenerated and reused for up to five cycles without any loss of uptake capacity (Figure ##SUPPL##0##S13##, Supporting Information). Furthermore, the CO<sub>2</sub> sorption isotherm showed hysteresis between adsorption and desorption branches, suggesting some degree of guest trapping.<sup>[</sup>\n##UREF##2##\n8\n##\n<sup>]</sup> The Clausius–Clapeyron equation, which is typically employed for calculation of the isosteric heat of adsorption for gases,<sup>[</sup>\n##REF##32661527##\n26\n##\n<sup>]</sup> could not be applied to the sorption data of network <bold>2</bold> because of the crossing over of isotherms measured at different temperatures. Unexpectedly, the CO<sub>2</sub> isotherm measured at 195 K showed almost no uptake (Figure ##SUPPL##0##S12##, Supporting Information), suggesting that some energy barrier was blocking its entry (vide infra). Since desorption only began at low pressures, it was speculated that the loaded material might retain CO<sub>2</sub> even if exposed to ambient air. To test this hypothesis, infrared spectroscopy (IR) was performed. The crystals of <bold>2@activated</bold> were sealed in 1 atm of CO<sub>2</sub> for 1 day ensuring a complete saturation of the available pores to give <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub>. Its IR spectrum contained a strong absorption band at 2340 cm<sup>−1</sup>, indicating the presence of physisorbed CO<sub>2</sub> (Figure ##SUPPL##0##S14##, Supporting Information).<sup>[</sup>\n##REF##26851930##\n27\n##, ##UREF##7##\n28\n##\n<sup>]</sup> This interpretation was additionally corroborated by the TGA‐DSC measurement, which revealed a gradual weight loss in the 70–200 °C temperature range matching the weight of ≈1 CO<sub>2</sub> molecule per 1 formula unit of network <bold>2</bold> (Figure ##SUPPL##0##S10d##, Supporting Information). The crystals of <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub> were left in the air while monitoring changes in the IR peak over time. Remarkably, the IR signal was still present after 1 week (Figure ##FIG##1##2b##). Following the peak evolution with time (Figures ##SUPPL##0##S15## and ##SUPPL##0##S16##, Supporting Information) showed a quick drop in intensity in the first 5 h, which then stabilized at ≈12% of the initial absorption even after &gt; 60 h. To the best of our knowledge, such long‐term trapping ability has not been reported in other coordination networks where CO<sub>2</sub> interaction is limited to physisorption. As a comparison, the same experiment was performed on the CO<sub>2</sub>‐loaded HKUST‐1 framework ([Cu<sub>3</sub>(BTC)<sub>2</sub>], BTC = 1,3,5‐benzenetricarboxylic acid), however, no IR signal from the adsorbed CO<sub>2</sub> was detected (Figure ##SUPPL##0##S17##, Supporting Information). This means that the gas molecules quickly escaped the pores as soon as the powder was exposed to the air and before it could be transferred into the IR cell, thus further emphasizing the unique trapping ability of network <bold>2</bold>.</p>", "<p>To elucidate the structural changes accompanying the CO<sub>2</sub> adsorption and visualize the encapsulated gas molecules, SCXRD analysis was performed. X‐ray diffraction data of <bold>2@activated</bold> and <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub> were collected at 90 and 298 K. Comparing the crystal structures before and after CO<sub>2</sub> adsorption, the network backbone did not experience any changes, regardless of the measurement temperature (<bold>Figure</bold> ##FIG##2##\n3a##). At the same time, the pores remained isolated and inaccessible. The 90 K structure of <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub> contained electron density in the center of the void, which was assigned to the CO<sub>2</sub> molecule (Figure ##FIG##2##3b,c##). The representative short distances between the network and each atom of CO<sub>2</sub> were Cu(network)···O(CO<sub>2</sub>) = 4.39(2) Å, I(network)···O(CO<sub>2</sub>) = 4.20(2) Å, C(network) ···O(CO<sub>2</sub>) = 3.39(2) Å, and N(network)···O(CO<sub>2</sub>) = 3.53(2) Å. None of these contacts could be attributed to any bond formation. Therefore, the CO<sub>2</sub> adsorption into network <bold>2</bold> was facilitated primarily by the weak secondary interactions. These findings were further corroborated by in situ PXRD of network <bold>2</bold> collected in a CO<sub>2</sub> atmosphere (Figure ##SUPPL##0##S18##, Supporting Information). The diffraction patterns displayed almost no change after the adsorption, which matched the single crystal results. Interestingly, the opening of channels, as CO<sub>2</sub> was diffusing through the network (vide infra), also could not be observed in the collected data, indicating that they appeared at random locations in the crystal without the creation of any long‐range order.</p>", "<p>The fact that no obvious structural changes were observed in network <bold>2</bold> before and after CO<sub>2</sub> encapsulation indicated that the aperture between the pores opened only momentarily allowing the guest molecule to pass through. This effect could also be responsible for the lack of N<sub>2</sub> uptake. To further explore these structural dynamics, the adsorption behavior of <bold>2</bold> was simulated with PreFerred Potential (PFP)<sup>[</sup>\n##REF##35637178##\n29\n##\n<sup>]</sup> version 3.0.0 on Matlantis.<sup>[</sup>\n##UREF##8##\n30\n##\n<sup>]</sup> First, the enthalpies of adsorption (Δ<italic toggle=\"yes\">H</italic>\n<sub>ads</sub>) were calculated. Optimizing structures with and without guest molecules, and comparing their energy states, generated Δ<italic toggle=\"yes\">H</italic>\n<sub>ads</sub> values of − 40 and − 26 kJ mol<sup>−1</sup> at 300 K for CO<sub>2</sub> and N<sub>2</sub>, respectively. When the calculations were performed without dispersion force correction, the Δ<italic toggle=\"yes\">H</italic>\n<sub>ads</sub> values were close to 0 kJ mol<sup>−1</sup>. This result is consistent with the fact that the interaction between the network and CO<sub>2</sub> is dominated by weak dispersion forces. Furthermore, the Δ<italic toggle=\"yes\">H</italic>\n<sub>ads</sub> values obtained from this simulation suggested that CO<sub>2</sub> was physisorbed by the network.</p>", "<p>The optimized location of CO<sub>2</sub> inside network <bold>2</bold> was at the center of the pore (Figure ##SUPPL##0##S19##, Supporting Information) matching the single crystal structure (Figure ##FIG##2##3a##, Supporting Information). The CO<sub>2</sub> molecule had a limited degree of mobility and was trapped in a steep potential energy well bound by the pore walls. This behavior can explain the relatively high strength of CO<sub>2</sub> physisorption despite the lack of strongly interacting groups. Considering the CO<sub>2</sub>/N<sub>2</sub> selectivity, the simulated enthalpy of adsorption for CO<sub>2</sub> was 14 kJ mol<sup>−1</sup> larger than for N<sub>2</sub>. This trend is consistent with other PCNs since the higher polarizability and quadrupole moment of CO<sub>2</sub> molecule typically leads to higher interaction energies.<sup>[</sup>\n##REF##22204561##\n20\n##\n<sup>]</sup> However, this enthalpy difference alone was not sufficient to account for the complete lack of N<sub>2</sub> uptake.</p>", "<p>Next, the diffusion path of CO<sub>2</sub> through the network was evaluated. The initial state consisted of one CO<sub>2</sub> molecule enclosed inside a pore of a unit cell. Whereas in the final state, the same molecule was relocated into an adjacent closed pore. The motion coordinates were linearly interpolated into seven separate intermediate states, and the Nudged Elastic Band (NEB) method<sup>[</sup>\n##UREF##9##\n31\n##\n<sup>]</sup> was used to optimize their structures. The results demonstrated that CO<sub>2</sub> could move from one closed pore to another without disrupting the network connectivity (<bold>Figure</bold> ##FIG##3##\n4a##; Movie ##SUPPL##2##S1##, Supporting Information). In the transition state, the CuI cubane cluster and the coordinated pyrimidine ring were slightly twisted, opening up a passage between the neighboring pores, which was akin to a “magic door” opening up and creating a soft stretchable channel. After CO<sub>2</sub> passed through the channel, the “magic door” closed behind and the network backbone returned to the initial state. In the process, the size of the aperture increased from 1.7 × 2.1 to 2.5 × 2.6 Å in the fully open state, sufficient for CO<sub>2</sub> to pass through. This transition state was more energetically unstable than the initial and final states. Therefore, for CO<sub>2</sub> to diffuse through the network, it must overcome an energy barrier, which can be considered an activation energy (<italic toggle=\"yes\">E</italic>\n<sub>a</sub>), while crossing between the pores. Similar simulations were performed for N<sub>2</sub>, and the <italic toggle=\"yes\">E</italic>\n<sub>a</sub> values for CO<sub>2</sub> and N<sub>2</sub> were calculated to be 55 and 67 kJ mol<sup>−1</sup>, respectively. The reason for this difference was attributed to the larger kinetic diameter of N<sub>2</sub> (3.6 Å) compared to CO<sub>2</sub> (3.3 Å).<sup>[</sup>\n##UREF##10##\n32\n##\n<sup>]</sup> This effect could explain the difference in maximum uptakes of the two gases. Furthermore, since gas adsorption and desorption processes in network <bold>2</bold> were constrained by sizable activation energy barriers, it significantly prolonged the equilibration time between the pore and the outside environment, thus allowing the network to retain CO<sub>2</sub> for extended periods.</p>" ]
[ "<title>Results and Discussions</title>", "<p>To obtain the desired material, a ligand (<bold>L</bold>) based on a pseudo‐tetrahedral bimesityl skeleton<sup>[</sup>\n##UREF##6##\n23\n##, ##REF##31180667##\n24\n##\n<sup>]</sup> decorated with four pyrimidine groups was developed (<bold>Figure</bold> ##FIG##0##\n1a##; Figures ##SUPPL##0##S2## and ##SUPPL##0##S3##, Supporting Information). Because of its steric bulk and orientation of nitrogen atoms around pyrimidine rings, the coordination directions are bent at an angle against the center–vertex axes. Therefore, the coordination of this ligand was expected to create PCNs with highly compact convergent structures featuring small pores. The reaction of <bold>L</bold> with CuI in the presence of KI and PPh<sub>3</sub> in the CH<sub>3</sub>CN/H<sub>2</sub>O/EtOH solvent mixture under solvothermal conditions yielded two distinct crystal morphologies, yellow plates and yellow prisms. Single crystal X‐ray diffraction analysis (SCXRD) revealed that the former crystals corresponded to a 2D network with the molecular formula of {[(Cu<sub>2</sub>I<sub>2</sub>)(<bold>L</bold>)]·solvent}<sub>n</sub> (<bold>1</bold>). On the other hand, the prisms were a different polymorph, {[(Cu<sub>4</sub>I<sub>4</sub>)(<bold>L</bold>)]·solvent}<sub>n</sub> (<bold>2</bold>), with a 3D interpenetrated structure. The two PCNs always crystallized together as a mixture during the synthesis. However, because of differences in their crystal densities, 1.782 and 2.086 g cm<sup>−3</sup> for <bold>1</bold> and <bold>2</bold>, respectively, pure samples could be obtained by the density separation method.<sup>[</sup>\n##REF##21541391##\n25\n##\n<sup>]</sup>\n</p>", "<p>The structure of network <bold>1</bold> consisted of Cu<sub>2</sub>I<sub>2</sub> dimers connected by four pyrimidine groups from four separate ligands forming staggered 2D layers (Figure ##SUPPL##0##S4##, Supporting Information). In comparison, network <bold>2</bold> had a diamondoid‐type structure containing Cu<sub>4</sub>I<sub>4</sub> cubane clusters as connector nodes (Figure ##FIG##0##1b−d##). Because each Cu ion coordinated to only one nitrogen atom in each pyrimidine ring, the resultant network was highly distorted limiting the degree of interpenetration to only two nets. This material possessed closed pores with dimensions of 5.2 × 4.9 × 4.9 Å. However, the size of the maximum aperture between each pore was only 2.4 × 1.5 Å, which was too small for any molecule to pass through. Nevertheless, acetonitrile molecules were present in the pores of the as‐synthesized crystal of <bold>2</bold> (Figure ##SUPPL##0##S5##, Supporting Information), which could be removed by heating at 473 K for 12 h under vacuum without loss of crystallinity, suggesting that some diffusion pathways could exist for the guest escape to occur (vide infra). The crystallinity of network samples was assessed by powder X‐ray diffraction (PXRD). The measured patterns (Figures ##SUPPL##0##S8## and ##SUPPL##0##S9##, Supporting Information) matched closely with the simulated patterns from the single crystal structures, thus confirming their phase purity. Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were performed, revealing that networks <bold>1</bold> and <bold>2</bold> were stable up to 400 °C at which point the ligand began to decompose (Figure ##SUPPL##0##S10a–c##, Supporting Information). A smaller weight decrease was observed at ≈250 °C, which was due to the evaporation of solvent (MeCN) from the pores.</p>", "<p>These results prompted us to investigate the possibility of adsorbing different gases into the two networks. First, N<sub>2</sub> isotherms measured at 77 and 298 K showed no appreciable uptakes in both structures (<bold>Figure</bold> ##FIG##1##\n2a##; Figures ##SUPPL##0##S11## and ##SUPPL##0##S12b##, Supporting Information). Additionally, network <bold>1</bold> displayed only a negligible uptake capacity for CO<sub>2</sub> at 298 K (Figure ##SUPPL##0##S11a##, Supporting Information). These results indicated that the pores in its structure are not accessible to small gas molecules in the measured pressure range. In contrast, network <bold>2</bold> adsorbed CO<sub>2</sub> at several temperatures, reaching close to one molecule per void, indicating a complete saturation (Figure ##FIG##1##2a##; Figure ##SUPPL##0##S12##, Supporting Information). The material could be fully regenerated and reused for up to five cycles without any loss of uptake capacity (Figure ##SUPPL##0##S13##, Supporting Information). Furthermore, the CO<sub>2</sub> sorption isotherm showed hysteresis between adsorption and desorption branches, suggesting some degree of guest trapping.<sup>[</sup>\n##UREF##2##\n8\n##\n<sup>]</sup> The Clausius–Clapeyron equation, which is typically employed for calculation of the isosteric heat of adsorption for gases,<sup>[</sup>\n##REF##32661527##\n26\n##\n<sup>]</sup> could not be applied to the sorption data of network <bold>2</bold> because of the crossing over of isotherms measured at different temperatures. Unexpectedly, the CO<sub>2</sub> isotherm measured at 195 K showed almost no uptake (Figure ##SUPPL##0##S12##, Supporting Information), suggesting that some energy barrier was blocking its entry (vide infra). Since desorption only began at low pressures, it was speculated that the loaded material might retain CO<sub>2</sub> even if exposed to ambient air. To test this hypothesis, infrared spectroscopy (IR) was performed. The crystals of <bold>2@activated</bold> were sealed in 1 atm of CO<sub>2</sub> for 1 day ensuring a complete saturation of the available pores to give <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub>. Its IR spectrum contained a strong absorption band at 2340 cm<sup>−1</sup>, indicating the presence of physisorbed CO<sub>2</sub> (Figure ##SUPPL##0##S14##, Supporting Information).<sup>[</sup>\n##REF##26851930##\n27\n##, ##UREF##7##\n28\n##\n<sup>]</sup> This interpretation was additionally corroborated by the TGA‐DSC measurement, which revealed a gradual weight loss in the 70–200 °C temperature range matching the weight of ≈1 CO<sub>2</sub> molecule per 1 formula unit of network <bold>2</bold> (Figure ##SUPPL##0##S10d##, Supporting Information). The crystals of <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub> were left in the air while monitoring changes in the IR peak over time. Remarkably, the IR signal was still present after 1 week (Figure ##FIG##1##2b##). Following the peak evolution with time (Figures ##SUPPL##0##S15## and ##SUPPL##0##S16##, Supporting Information) showed a quick drop in intensity in the first 5 h, which then stabilized at ≈12% of the initial absorption even after &gt; 60 h. To the best of our knowledge, such long‐term trapping ability has not been reported in other coordination networks where CO<sub>2</sub> interaction is limited to physisorption. As a comparison, the same experiment was performed on the CO<sub>2</sub>‐loaded HKUST‐1 framework ([Cu<sub>3</sub>(BTC)<sub>2</sub>], BTC = 1,3,5‐benzenetricarboxylic acid), however, no IR signal from the adsorbed CO<sub>2</sub> was detected (Figure ##SUPPL##0##S17##, Supporting Information). This means that the gas molecules quickly escaped the pores as soon as the powder was exposed to the air and before it could be transferred into the IR cell, thus further emphasizing the unique trapping ability of network <bold>2</bold>.</p>", "<p>To elucidate the structural changes accompanying the CO<sub>2</sub> adsorption and visualize the encapsulated gas molecules, SCXRD analysis was performed. X‐ray diffraction data of <bold>2@activated</bold> and <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub> were collected at 90 and 298 K. Comparing the crystal structures before and after CO<sub>2</sub> adsorption, the network backbone did not experience any changes, regardless of the measurement temperature (<bold>Figure</bold> ##FIG##2##\n3a##). At the same time, the pores remained isolated and inaccessible. The 90 K structure of <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub> contained electron density in the center of the void, which was assigned to the CO<sub>2</sub> molecule (Figure ##FIG##2##3b,c##). The representative short distances between the network and each atom of CO<sub>2</sub> were Cu(network)···O(CO<sub>2</sub>) = 4.39(2) Å, I(network)···O(CO<sub>2</sub>) = 4.20(2) Å, C(network) ···O(CO<sub>2</sub>) = 3.39(2) Å, and N(network)···O(CO<sub>2</sub>) = 3.53(2) Å. None of these contacts could be attributed to any bond formation. Therefore, the CO<sub>2</sub> adsorption into network <bold>2</bold> was facilitated primarily by the weak secondary interactions. These findings were further corroborated by in situ PXRD of network <bold>2</bold> collected in a CO<sub>2</sub> atmosphere (Figure ##SUPPL##0##S18##, Supporting Information). The diffraction patterns displayed almost no change after the adsorption, which matched the single crystal results. Interestingly, the opening of channels, as CO<sub>2</sub> was diffusing through the network (vide infra), also could not be observed in the collected data, indicating that they appeared at random locations in the crystal without the creation of any long‐range order.</p>", "<p>The fact that no obvious structural changes were observed in network <bold>2</bold> before and after CO<sub>2</sub> encapsulation indicated that the aperture between the pores opened only momentarily allowing the guest molecule to pass through. This effect could also be responsible for the lack of N<sub>2</sub> uptake. To further explore these structural dynamics, the adsorption behavior of <bold>2</bold> was simulated with PreFerred Potential (PFP)<sup>[</sup>\n##REF##35637178##\n29\n##\n<sup>]</sup> version 3.0.0 on Matlantis.<sup>[</sup>\n##UREF##8##\n30\n##\n<sup>]</sup> First, the enthalpies of adsorption (Δ<italic toggle=\"yes\">H</italic>\n<sub>ads</sub>) were calculated. Optimizing structures with and without guest molecules, and comparing their energy states, generated Δ<italic toggle=\"yes\">H</italic>\n<sub>ads</sub> values of − 40 and − 26 kJ mol<sup>−1</sup> at 300 K for CO<sub>2</sub> and N<sub>2</sub>, respectively. When the calculations were performed without dispersion force correction, the Δ<italic toggle=\"yes\">H</italic>\n<sub>ads</sub> values were close to 0 kJ mol<sup>−1</sup>. This result is consistent with the fact that the interaction between the network and CO<sub>2</sub> is dominated by weak dispersion forces. Furthermore, the Δ<italic toggle=\"yes\">H</italic>\n<sub>ads</sub> values obtained from this simulation suggested that CO<sub>2</sub> was physisorbed by the network.</p>", "<p>The optimized location of CO<sub>2</sub> inside network <bold>2</bold> was at the center of the pore (Figure ##SUPPL##0##S19##, Supporting Information) matching the single crystal structure (Figure ##FIG##2##3a##, Supporting Information). The CO<sub>2</sub> molecule had a limited degree of mobility and was trapped in a steep potential energy well bound by the pore walls. This behavior can explain the relatively high strength of CO<sub>2</sub> physisorption despite the lack of strongly interacting groups. Considering the CO<sub>2</sub>/N<sub>2</sub> selectivity, the simulated enthalpy of adsorption for CO<sub>2</sub> was 14 kJ mol<sup>−1</sup> larger than for N<sub>2</sub>. This trend is consistent with other PCNs since the higher polarizability and quadrupole moment of CO<sub>2</sub> molecule typically leads to higher interaction energies.<sup>[</sup>\n##REF##22204561##\n20\n##\n<sup>]</sup> However, this enthalpy difference alone was not sufficient to account for the complete lack of N<sub>2</sub> uptake.</p>", "<p>Next, the diffusion path of CO<sub>2</sub> through the network was evaluated. The initial state consisted of one CO<sub>2</sub> molecule enclosed inside a pore of a unit cell. Whereas in the final state, the same molecule was relocated into an adjacent closed pore. The motion coordinates were linearly interpolated into seven separate intermediate states, and the Nudged Elastic Band (NEB) method<sup>[</sup>\n##UREF##9##\n31\n##\n<sup>]</sup> was used to optimize their structures. The results demonstrated that CO<sub>2</sub> could move from one closed pore to another without disrupting the network connectivity (<bold>Figure</bold> ##FIG##3##\n4a##; Movie ##SUPPL##2##S1##, Supporting Information). In the transition state, the CuI cubane cluster and the coordinated pyrimidine ring were slightly twisted, opening up a passage between the neighboring pores, which was akin to a “magic door” opening up and creating a soft stretchable channel. After CO<sub>2</sub> passed through the channel, the “magic door” closed behind and the network backbone returned to the initial state. In the process, the size of the aperture increased from 1.7 × 2.1 to 2.5 × 2.6 Å in the fully open state, sufficient for CO<sub>2</sub> to pass through. This transition state was more energetically unstable than the initial and final states. Therefore, for CO<sub>2</sub> to diffuse through the network, it must overcome an energy barrier, which can be considered an activation energy (<italic toggle=\"yes\">E</italic>\n<sub>a</sub>), while crossing between the pores. Similar simulations were performed for N<sub>2</sub>, and the <italic toggle=\"yes\">E</italic>\n<sub>a</sub> values for CO<sub>2</sub> and N<sub>2</sub> were calculated to be 55 and 67 kJ mol<sup>−1</sup>, respectively. The reason for this difference was attributed to the larger kinetic diameter of N<sub>2</sub> (3.6 Å) compared to CO<sub>2</sub> (3.3 Å).<sup>[</sup>\n##UREF##10##\n32\n##\n<sup>]</sup> This effect could explain the difference in maximum uptakes of the two gases. Furthermore, since gas adsorption and desorption processes in network <bold>2</bold> were constrained by sizable activation energy barriers, it significantly prolonged the equilibration time between the pore and the outside environment, thus allowing the network to retain CO<sub>2</sub> for extended periods.</p>" ]
[ "<title>Conclusion</title>", "<p>In conclusion, two coordination networks with isolated voids were obtained using the same starting materials. Despite the presence of seemingly inaccessible pores in these structures, network <bold>2</bold> was able to selectively capture and store CO<sub>2</sub>. Interestingly, the structural changes before and after gas uptake were negligible, and the pores remained closed. This behavior is in stark contrast to the common gating effect reported for PCNs, where the adsorption of gases induces a dramatic phase transition, and the open and closed states can be easily distinguished and characterized. The accompanying transitions often generate significant mechanical stress that can cause irreversible damage to the network structures.<sup>[</sup>\n##REF##26397165##\n33\n##\n<sup>]</sup> Simulations using Matlantis revealed that the adsorption properties of <bold>2</bold> were controlled by what we termed a “magic door” mechanism, which facilitated channel formation between the pores through minor adjustments in the network structure allowing the passage of CO<sub>2</sub> molecules. The activation energy barrier requirement for this process could rationalize the high CO<sub>2</sub>/N<sub>2</sub> selectivity, as well as the remarkable ability of the network to retain CO<sub>2</sub> while exposed to the atmosphere (Figure ##FIG##3##4b##). These results provide useful insights for future design strategies focusing on isolated voids inside PCNs that can remain sealed after gas encapsulation, thus bringing new perspectives for the development of CO<sub>2</sub> sorbents.</p>" ]
[ "<title>Abstract</title>", "<p>A coordination network containing isolated pores without interconnecting channels is prepared from a tetrahedral ligand and copper(I) iodide. Despite the lack of accessibility, CO<sub>2</sub> is selectively adsorbed into these pores at 298 K and then retained for more than one week while exposed to the atmosphere. The CO<sub>2</sub> adsorption energy and diffusion mechanism throughout the network are simulated using Matlantis, which helps to rationalize the experimental results. CO<sub>2</sub> enters the isolated voids through transient channels, termed “magic doors”, which can momentarily appear within the structure. Once inside the voids, CO<sub>2</sub> remains locked in limiting its escape. This mechanism is facilitated by the flexibility of organic ligands and the pivot motion of cluster units. In situ powder X‐ray diffraction revealed that the crystal structure change is negligible before and after CO<sub>2</sub> capture, unlike gate‐opening coordination networks. The uncovered CO<sub>2</sub> sorption and retention ability paves the way for the design of sorbents based on isolated voids.</p>", "<p>A coordination network selectively captures and traps CO<sub>2</sub> despite lacking pore accessibility. Neural Network Potential (NNP) simulations show that CO<sub>2</sub> diffusion is enabled by formation of transient channels through slight structural adjustments, which are dubbed “magic doors”. The presence of a guest‐dependent activation energy barrier necessary for this process can explain the adsorption selectivity and CO<sub>2</sub> retention ability of this network.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6887-cit-0034\">\n<string-name>\n<given-names>T.</given-names>\n<surname>Shimada</surname>\n</string-name>, <string-name>\n<given-names>P. M.</given-names>\n<surname>Usov</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Wada</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Ohtsu</surname>\n</string-name>, <string-name>\n<given-names>T.</given-names>\n<surname>Watanabe</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Adachi</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Hashizume</surname>\n</string-name>, <string-name>\n<given-names>T.</given-names>\n<surname>Matsumoto</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Kawano</surname>\n</string-name>, <article-title>Long Time CO<sub>2</sub> Storage Under Ambient Conditions in Isolated Voids of a Porous Coordination Network Facilitated by the “Magic Door” Mechanism</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2307417</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202307417</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was supported by JSPS KAKENHI Grants JP20H04662, JP21K18976, JPMJSP2106, JP23H04878, the JSPS A3 Foresight Program, and ENEOS Corporation. The powder X‐ray diffraction experiments were performed at the RIKEN Materials Science Beamline (BL44B2) of SPring‐8 with the approval of RIKEN (proposal no. 20220021). The single crystal X‐ray diffraction analysis was performed under the approval of the Photon Factory Program Advisory Committee (proposal no. 2021G046, 2022G621).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6887-fig-0001\"><label>Figure 1</label><caption><p>a) Single crystal structure of <bold>L</bold>. The structure of network <bold>2</bold>, b) the voids outlined in dark yellow, c) a single diamondoid‐type net, and d) two interpenetrated nets represented by different colors. C – grey, N – blue, Cu – orange, and I – purple, hydrogen atoms were omitted for clarity.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6887-fig-0002\"><label>Figure 2</label><caption><p>a) Adsorption and desorption isotherms of N<sub>2</sub> and CO<sub>2</sub> for <bold>2@activated</bold> measured at 298 K. b) Time‐dependent IR spectra of <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub> left in the air.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6887-fig-0003\"><label>Figure 3</label><caption><p>a) Adsorption of CO<sub>2</sub> into network <bold>2</bold> showing the single crystal structures of <bold>2@activated</bold> and <bold>2@CO</bold>\n<sub>\n<bold>2</bold>\n</sub>. b) Short contacts between network <bold>2</bold> and a CO<sub>2</sub> molecule. c) CO<sub>2</sub> orientation inside the pore (dark yellow). C – grey, N – blue, Cu – orange, and I – purple, hydrogen atoms were omitted for clarity.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6887-fig-0004\"><label>Figure 4</label><caption><p>a) The diffusion path of CO<sub>2</sub> through network <bold>2</bold> simulated by Matlantis. The accessible pore space is colored dark yellow. The traversing CO<sub>2</sub> molecule is shown using space‐filling model. C – grey, N – blue, O – red, Cu – orange, and I – purple, hydrogen atoms were omitted for clarity. b) Comparison of adsorption energy diagrams for chemisorption and physisorption processes to the mechanism investigated in the present work.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6887-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6887-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6887-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 1</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2307417-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2307417-s003.zip\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2307417-s002.gif\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
33
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 20; 11(2):2307417
oa_package/47/48/PMC10787060.tar.gz
PMC10787061
37953381
[ "<title>Introduction</title>", "<p>Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with diverse clinical manifestations and unpredictable disease courses, which affects more than 6 million people in the world.<sup>[</sup>\n##REF##18305268##\n1\n##\n<sup>]</sup> The various organ involvements of SLE patients cause a profound effect on their health‐related life quality, the delayed diagnosis of which would lead to organ damage accrual and retard the survival improvement.<sup>[</sup>\n##REF##32367037##\n2\n##\n<sup>]</sup> However, due to the complexity and heterogenicity of SLE,<sup>[</sup>\n##REF##32988843##\n3\n##\n<sup>]</sup> the underlying pathogenic mechanism has not been fully elucidated, restricting the discovery of reliable biomarkers for its diagnosis and related metabolic pathway analysis.</p>", "<p>Metabolic fingerprints correlate with other omics (e.g., genomics and proteomics), as metabolites are the end products of gene expression.<sup>[</sup>\n##REF##27708401##\n4\n##\n<sup>]</sup> Addressing the delayed diagnosis and high cost of current genomic and proteomic biomarkers,<sup>[</sup>\n##REF##33397992##\n5\n##\n<sup>]</sup> metabolic biomarkers provide a more distal characterization of pathological and physiological processes, which are more sensitive to the slight variations of health status.<sup>[</sup>\n##UREF##0##\n6\n##\n<sup>]</sup> In addition, the translational use of metabolic biomarkers in concert with genomic and proteomic markers may change the way of biomarker utility in SLE. However, the manner how SLE hallmarks (metabolic disorders, organ injuries, and autoimmunity abnormality, etc.) affect metabolites is still unknown.<sup>[</sup>\n##REF##24692585##\n7\n##\n<sup>]</sup> The limited exploration of SLE metabolic fingerprint attributes to two key factors: 1) lack of a large sample cohort to exclude the individual difference, and 2) absence of advanced metabolic detection tool.</p>", "<p>Serum detection assays promise SLE diagnostics owing to their minimal invasiveness and desirable adaptability for large‐scale clinic use, superior to the conventional methods (e.g., biopsy and physical examination).<sup>[</sup>\n##REF##32678093##\n8\n##\n<sup>]</sup> Current analytic tools for serum metabolic analysis mainly include nuclear molecular resonance (NMR) spectroscopy and mass spectrometry (MS).<sup>[</sup>\n##REF##32179679##\n9\n##\n<sup>]</sup> Superior to the NMR of suboptimal sensitivity and limited identification capability, MS affords high sensitivity and favorable biomarker identification ability assisted by tandem MS. Mainly, laser desorption/ionization (LDI) MS enables fast analysis speed, low sample consumption, and cost‐effective expenses by nano‐assisted solid‐gas transition,<sup>[</sup>\n##REF##27708401##\n4\n##, ##REF##21518695##\n10\n##\n<sup>]</sup> promising to be a powerful analytical tool in the coming era of precision medicine. Herein, we acquired serum metabolic fingerprints (SMFs) of 915 individuals by nano‐assisted LDI MS (<bold>Scheme</bold>\n##FIG##0##\n1A##), which could be deciphered by sparse learning for SLE diagnosis and metabolic biomarker panel construction (Scheme ##FIG##0##1B##).</p>" ]
[]
[ "<title>Results</title>", "<title>Serum Metabolic Fingerprint Analysis</title>", "<p>We carried out the metabolic measurement of 1 µL of native serum from each sample in a microarray manner (Figure ##FIG##1##1B##), without any complex pretreatment. For a typical LDI MS detection, we loaded the serum sample microarray with ferric particles as the matrix (see Methods in Supporting Information, Figure ##SUPPL##0##1C##). Notably, the ferric particles demonstrated nanoscale surface roughness for selective metabolite enrichment and stable crystalline structure eliminating the conventional sweet‐spot searching (Figure ##SUPPL##0##S1##, Supporting Information). These ferric particles can be ideal for LDI MS due to the fine water dispersity (polydispersity index (PDI) &lt; 0.3, Figure ##SUPPL##0##S2A##, Supporting Information) for matrix use, negative surface charge (zeta potential, Figure ##SUPPL##0##S2B##, Supporting Information) for cation adduct,<sup>[</sup>\n##REF##27708401##\n4\n##, ##REF##32678093##\n8\n##, ##REF##30296378##\n12\n##\n<sup>]</sup> strong light absorption in the ultraviolet range (Figure ##SUPPL##0##S2C##, Supporting Information) for laser energy transfer during LDI process.<sup>[</sup>\n##REF##29172460##\n13\n##\n<sup>]</sup> Besides, the preparation of ferric particles is scalable and capable of &gt; 150 000 tests per batch (Figure ##SUPPL##0##S2D##, Supporting Information) since only 1 µg of ferric particles is required per LDI MS detection (Figure ##FIG##1##1C##). Consequently, nano‐assisted LDI MS achieved the original data acquisition within 1 minute per individual. The typical MS spectra acquired for SLE and HC were exhibited in Figure ##FIG##1##1D##.</p>", "<p>A blueprint of SLE patients and HCs displayed in Figure ##FIG##1##1E## summarized the SMFs of 731 individuals (SLE/HC, 357/374) in the discovery cohort. Notably, the mass to charge (<italic toggle=\"yes\">m/z</italic>) features were focused on the low mass range of small metabolites (<italic toggle=\"yes\">m/z</italic> of 100–1000), considering the desirable detection selectivity (dealing with high concentrations of salts/proteins in Figure ##SUPPL##0##S3##, Supporting Information) and sensitivity (dealing with low concentrations of small metabolites in Figure ##SUPPL##0##S4##, Supporting Information). Specifically, from the raw mass spectrum containing ≈ 120 000 <italic toggle=\"yes\">m/z</italic> data points per sample, the SMF of 908 <italic toggle=\"yes\">m/z</italic> features was obtained by searching the local maxima. We also examined the intra‐similarity of mass spectra using cosine correlation analysis, confirming the high similarity within the SLE/HC group (≈90% SLE patients/HCs with similarity score &gt; 0.9, Figure ##SUPPL##0##S5##, Supporting Information). Therefore, our platform features fast analytical speed (&lt; 1 minute per individual) and high‐throughput (908 <italic toggle=\"yes\">m/z</italic> features within the ≈120 000 data points of raw mass spectra) for achieving the large cohort extraction of SMFs, laying the solid foundation for following the SLE diagnostic model construction.</p>", "<title>Diagnosis by Machine Learning</title>", "<p>We diagnosed SLE patients from HCs by machine learning of the SMFs (<bold>Figure</bold>\n##FIG##2##\n2\n##). Based on the sufficient sample size demonstrated by power analysis (Figure ##SUPPL##0##S6##, Supporting Information),<sup>[</sup>\n##REF##21720319##\n14\n##\n<sup>]</sup> we studied the diagnostic performance of SMFs in identifying SLE patients from HCs by using different machine learning methods. In the discovery cohort, the sparse learning of SMFs achieved the diagnostic AUC of 0.950 with a 95% confidence interval (CI) of 0.935‐0.965 (Figure ##FIG##2##2A## and Table ##SUPPL##0##S3##, Supporting Information), the performance of which remained stable as changing model numbers (Figure ##SUPPL##0##S7## and Table ##SUPPL##0##S4##, Supporting Information). The employed parameters of the sparse learning were determined by the iterative optimization process (Figure ##SUPPL##0##S8##, Supporting Information), which was based on the literature with slight modifications.<sup>[</sup>\n##REF##32678093##\n8a\n##\n<sup>]</sup> Notably, the SLE patients could be differentiated from HCs with a sensitivity/specificity of 86.0%/92.0% (Figure ##FIG##2##2B##). In contrast, other machine learning methods only afforded the limited AUC of 0.486‐0.544 (<italic toggle=\"yes\">p</italic> &lt; 0.05, Figure ##FIG##2##2A##, and Table ##SUPPL##0##S3##, Supporting Information).</p>", "<p>We also conducted the machine learning methods on the SMFs of an independent validation cohort. Specifically, sparse learning of SMFs achieved the diagnostic AUC of 0.992 with 95% CI of 0.983‐1.000 for diagnosing SLE patients from HCs, higher than the AUC of 0.450‐0.533 afforded by other machine learning methods (<italic toggle=\"yes\">p</italic> &lt; 0.05, Figure ##FIG##2##2C##, and Table ##SUPPL##0##S3##, Supporting Information). Accordingly, SMFs by sparse learning achieved the sensitivity/specificity of 89.0%/100.0% (Figure ##FIG##2##2D##), much higher than other machine learning methods (sensitivity/specificity of 44.1%−61.3%/34.1%−65.9%, <italic toggle=\"yes\">p</italic> &lt; 0.05, Table ##SUPPL##0##S3##, Supporting Information). We also investigated the performance of major organ involvements in SLE (Table ##SUPPL##0##S5##, Supporting Information), and the results showed limited specificity. This could be due to the fact that the majority of SLE patients have multi‐organ involvement (Figure ##SUPPL##0##S9##, Supporting Information), and the biomarkers selected based on multi‐organ involvement have limited effectiveness in distinguishing patients with involvement of different organs. For disease activity, while the SMFs failed to distinguish the SLE patients with low disease activity (SLEDAI ≤ 6) and high disease activity (SLEDAI &gt; 6), the established model maintained the diagnostic performance (AUC of 0.898) in identifying the SLE patients with low disease activity (Figure ##SUPPL##0##S10##, Supporting Information). Briefly, the superiority of SMFs by sparse learning has been demonstrated for SLE diagnosis due to its high consistency exhibited in the discovery and validation cohort.</p>", "<title>Construction of SLE Metabolic Biomarker Panel</title>", "<p>We expected to identify the unique metabolic pattern of SLE patients from the massive features, thus providing insights for elucidating related pathological mechanisms. We identified a biomarker panel of 4 metabolites (imidazoleacetic acid, 2‐hydroxyadipic acid, glucose, and pseudouridine) for SLE based on the optimized diagnostic model by measuring the contribution of each <italic toggle=\"yes\">m/z</italic> feature within SMFs (<bold>Figure</bold>\n##FIG##3##\n3A## and Table ##SUPPL##0##S6##, Supporting Information).</p>", "<p>The identification and validation for the 4 high‐contribution <italic toggle=\"yes\">m/z</italic> features within SMFs were conducted by an LC‐ESI‐HRMS<sup>2</sup> metabolic analysis for an independent validation cohort (SLE/HC, 14/13). Specifically, the information on <italic toggle=\"yes\">m/z</italic> and fold changes of intensities can serve as identifier to match the <italic toggle=\"yes\">m/z</italic> features within different mass spectrometry platform of the same compound. Next, the high‐contribution <italic toggle=\"yes\">m/z</italic> features within LDI‐MS were annotated to metabolites (imidazoleacetic acid, 2‐hydroxyadipic acid, glucose and pseudouridine) according to the matched <italic toggle=\"yes\">m/z</italic> features within LC‐MS/MS via accurate mass and MS/MS matching with the human metabolome database (<ext-link xlink:href=\"https://hmdb.ca\" ext-link-type=\"uri\">https://hmdb.ca</ext-link>, Table ##SUPPL##0##S7##, Supporting Information).<sup>[</sup>\n##REF##23161693##\n15\n##\n<sup>]</sup> Meanwhile, the LC‐MS/MS result, consistent with the LDI‐MS result, verified that the biomarkers were reliable.</p>", "<p>Sparse learning of biomarker panel reached an enhanced diagnostic AUC of 0.800–0.877 (Figure ##FIG##3##3B,C##, and Table ##SUPPL##0##S8##, Supporting Information). It was critical to combine the 4 metabolic biomarkers as a biomarker panel for presenting the unique metabolic pattern of SLE, as these biomarkers showed limited diagnostic performances when singly applied (AUC of 0.66‐0.81/0.58‐0.83 in discovery/validation cohort, Figure ##SUPPL##0##S11## and Table ##SUPPL##0##S9##, Supporting Information). Notably, the 4 potential biomarkers did not show correlation with SLEDAI, which suggested that the biomarkers are geared towards the diagnosis of SLE patients but have limited capability in assessing disease activity (Table ##SUPPL##0##S10##, Supporting Information). Moreover, the validity of the above metabolic panel (4 metabolic biomarkers) was illustrated by maintaining the diagnostic performance of whole profiling of SMFs (908 <italic toggle=\"yes\">m/z</italic> features) with slight AUC loss (&lt;0.1, Figure ##FIG##2##2##).</p>", "<p>In patients with rheumatoid arthritis (RA), features associated with systemic lupus erythematosus (SLE) are commonly observed and both RA and SLE are systemic autoimmune diseases, sharing some similar clinical features and underlying pathogenesis.<sup>[</sup>\n##REF##19004043##\n16\n##\n<sup>]</sup> We also investigated the potential metabolic biomarkers regarding the variations in SLE patients compared to HCs or a small cohort of rheumatoid arthritis (RA) patients as disease controls. Compared to HCs, these four potential biomarkers were all up‐regulated in SLE patients by affording the fold change of 1.09‐2.30 (Figure ##FIG##3##3D##, Figure ##SUPPL##0##S12## and Tables ##SUPPL##0##S11## and ##SUPPL##0##S12##, Supporting Information). The established metabolic biomarkers showed significant differences between SLE and RA patients (357/27, Figure ##FIG##3##3E##, Tables ##SUPPL##0##S13## and ##SUPPL##0##S14##, Supporting Information, <italic toggle=\"yes\">p</italic> &lt; 0.05). Also, the SLE and RA patients could be assembled into two clusters by applying the unsupervised cluster method of principal component analysis (PCA) (Figure ##FIG##3##3F##, Tables ##SUPPL##0##S13## and ##SUPPL##0##S14##, Supporting Information), suggesting their different metabolic patterns in distal metabolic fingerprints. As the medication of RA and SLE was significantly different, we applied the propensity score matching (PSM) to select SLE patients to match the RA patients, which was conducted at a ratio of 1:1 for age, gender, and medication (prednisone, methotrexate, leflunomide, and hydroxychloroquine, Table ##SUPPL##0##S15##, Supporting Information). The PCA analysis demonstrated the limited influence of medication. A similar result was also obtained on 20 patients (SLE/RA, 10/10) with naïve treatment (Figure ##SUPPL##0##S13##, Supporting Information). Considering the small sample size of RA patients, the effect of medication regimens (e.g., corticosteroids) still calls for more future efforts on cohort construction with strict enrollment criteria.</p>", "<p>We constructed a small cohort to evaluate the effect of medications on the diagnostic performance of SMFs in our SLE patients (Table ##SUPPL##0##S16##, Supporting Information). The diagnostic model based on the SLE patients who were treatment naive and HCs showed the AUC of 0.947 (Figure ##SUPPL##0##S14A##, Supporting Information), which maintained the major diagnostic performance based on the large cohort of 915 individuals (AUC of 0.950). The difference in medication exposure could not result in the differentiation between SLE patients (AUC of 0.504, Figure ##SUPPL##0##S14B##, Supporting Information), indicating the limited influence of medication usage in the SLE diagnostic model. We conducted PCA analysis on SLE patients who received different dosages of corticosteroids in the discovery cohort, including 15 individuals who received no corticosteroids, 100 individuals with a daily dosage of less than 20 mg, 104 individuals with a daily dosage between 20 and 40 mg, and 79 individuals with a daily dosage greater than 40 mg. As shown in Figure ##SUPPL##0##S14C## (Supporting Information), no distinct clusters were formed for patients with different medication scenarios, illustrating the minor role of corticosteroids in the SLE diagnostic model. Moreover, there were 27 SLE patients who exhibited complications with diabetes and dyslipidemia, the effect of which on the diagnostic model could be negligible, as shown in Figure ##SUPPL##0##S14D## (Supporting Information). While the above analysis provided indirect insights into medication and complication effects, it is critical to construct a cohort with strict enrollment criteria to rule out the medication effect in the future.</p>" ]
[ "<title>Discussion</title>", "<p>SLE is a progressive autoimmune disease with great heterogeneity. The accurate and in‐time diagnosis of SLE is indispensable for effective treatment and appropriate prognosis. Currently, the clinical diagnosis of SLE relies on three major classification criteria (EULAR/ACR‐2019, SLICC‐2012, and ACR‐1997 criteria) with both clinical criteria and immunological criteria involved. Besides the complexity, there were about 25.6‐30.5% of patients missed as estimated despite the major classification criteria afforded the high diagnostic performance (sensitivity of 85.7‐91.3% and specificity of 93.0‐97.3%).<sup>[</sup>\n##REF##31704720##\n17\n##\n<sup>]</sup> Meanwhile, it is of intense research efforts to develop the alternatives to current classification criteria based on a simple blood test, mainly focusing on the design of assays from nucleic acids and proteins.<sup>[</sup>\n##REF##33397992##\n5\n##, ##REF##16905576##\n18\n##\n<sup>]</sup> Importantly, given a designed cohort like genomic/proteomic approaches to study large series of individuals (&gt; 1000), metabolic approaches would be the next‐generation diagnostic tools, considering that 1) metabolites at the end of pathways reveal the real‐time status of patients with precision; 2) metabolic assay construction is facile and free of expensive or tedious sequencing/immunoassays.</p>", "<p>Notably, the metabolic analysis of metabolites as end‐products has exhibited great potential for profiling complex diseases like cancers. In this study, we conducted the serum metabolic analysis for SLE patients and achieved the identification of SLE patients from HCs with a diagnostic sensitivity of 86.0–89.0% and specificity of 92.0‐100.0% in the cohort of 915 individuals (SLE/HC of 448/467). Compared with the prior serum metabolomic studies in SLE (Table ##SUPPL##0##S17##, Supporting Information), the present study afforded the optimized diagnostic performance and improved credibility due to the advantages in sample volume and study design, detection platform, and statistical algorithms.</p>", "<p>The sample volume and study design are of fundamental significance to the metabolic analysis. In this study, a large cohort of 731 individuals (SLE/HCs, 357/374) was constructed, which is essential to avoid individual differences for SLE metabolic analysis. In addition, 184 individuals were further classified as an independent cohort for verification, thus ensuring credible diagnostic performance. In contrast, the previous studies of SLE metabolic analysis were conducted based on small numbers of individuals (60‐140 individuals, including 30‐80 SLE and 20‐60 controls),<sup>[</sup>\n##REF##16905576##\n18\n##, ##REF##31130958##\n19\n##\n<sup>]</sup> which often lacked an independent validation cohort and could be easily disturbed by individual difference. Similarly, some pilot studies also found promising results on the specific metabolomic signature in LN patients but might run the risk of overfitting due to the limited sample size (20‐110 individuals).<sup>[</sup>\n##UREF##0##\n6\n##, ##REF##32128093##\n20\n##\n<sup>]</sup>\n</p>", "<p>A high‐performance metabolic detection platform is also critical for SLE diagnosis. The mainstream platforms include NMR spectrometry and MS, besides biochemical/immunoassay.<sup>[</sup>\n##UREF##2##\n21\n##\n<sup>]</sup> For NMR, the spins of nuclei interact with the applied magnetic field to characterize atomic species for untargeted detection,<sup>[</sup>\n##UREF##3##\n22\n##\n<sup>]</sup> but the weak interaction energy involved results in low sensitivity. For comparison, MS affords high‐throughput (≈1000 <italic toggle=\"yes\">m/z</italic> features) and high resolution (± 10 mDa) for both targeted and untargeted metabolic detection.<sup>[</sup>\n##REF##27708401##\n4\n##, ##UREF##4##\n23\n##\n<sup>]</sup> However, frequently applied MS techniques of GC/LC‐MS call for a considerate experimental time of 0.5–1 h,<sup>[</sup>\n##REF##21518695##\n10a–c\n##\n<sup>]</sup> sample volume of 30–50 µL,<sup>[</sup>\n##REF##21518695##\n10c\n##\n<sup>]</sup> and prime cost of additional devices and reagents.<sup>[</sup>\n##REF##21518695##\n10\n##, ##UREF##5##\n24\n##\n<sup>]</sup> Accordingly, nano‐assisted LDI MS we developed is 1) fast without tedious sample pretreatment, due to the surface nano‐crevices of the matrix for in situ size‐selective enrichment of small metabolites rather than large molecules (Figure ##SUPPL##0##S1##, Supporting Information); 2) of low sample volume (1 µL of serum per individual), due to the unique LDI process in producing efficient cation adduct at low detection limits (8.8–85.4 pmol, Figure ##SUPPL##0##S4##, Supporting Information); and 3) low‐cost and free of additional devices and reagents, due to the direct recognition of serum microarrays on‐chip (Figure ##FIG##1##1A,B##) in an antibody‐free manner. Notably, compared to reported nano matrix based on metal oxide,<sup>[</sup>\n##UREF##6##\n25\n##\n<sup>]</sup> the ferric particles can offer high production efficiency and easy‐controlled structure, making it suitable for widespread adoption in large‐scale and clinical testing. Therefore, the ferric particle assisted LDI MS tackled the major challenges in metabolic analysis, serving as a promising detection platform.</p>", "<p>A suitable statistical algorithm is essential to interpreting the MS signals for diagnosis due to their complexity (containing ≈120000 data points per SMF). Distinct from the prior metabolomic studies in SLE that adopted the traditional statistical algorithms (eg, principal component analysis (PCA)), sparse learning was applied for SMFs based diagnostic model building towards computer‐aided diagnosis. Sparse learning of the SMFs exhibited a superior diagnostic AUC of 0.950‐0.992 for SLE diagnosis. No performance loss in the independent validation cohort further confirmed the validity of the established diagnostic model (Figure ##FIG##2##2## and Figure ##SUPPL##0##S6##, Supporting Information). The success of sparse learning over other machine learning methods attributes to the sparse regularization and intrinsic sparsity of SMFs (Figure ##SUPPL##0##S7## and Table ##SUPPL##0##S4##, Supporting Information).<sup>[</sup>\n##REF##27708401##\n4a\n##\n<sup>]</sup> For sparse regularization, sparse learning allows to gauge the contributions of these <italic toggle=\"yes\">m/z</italic> features via numeric computation and assign high weights to a limited number of biomarkers with relatively high importance. For intrinsic sparsity, only a few <italic toggle=\"yes\">m/z</italic> features are potentially useful to diagnosis, revealed by that only tens of features (66 <italic toggle=\"yes\">m/z</italic> signals) were selected stably with frequency ≥ 95 and statistical significance (<italic toggle=\"yes\">p</italic> &lt; 0.05) as metabolic biomarkers. Therefore, we achieved the advanced sparse learning‐aided diagnosis of SLE based on the SMFs.</p>", "<p>In clinical practice, employing the fewer selected metabolites as biomarkers is more practical and feasible than attempting to use the entire set of 66 features.<sup>[</sup>\n##REF##24930143##\n26\n##\n<sup>]</sup> We constructed a four‐metabolite panel based on the optimized diagnostic model (66 features), which maintained the diagnostic performance of the whole profiling of SMFs. The panel was further validated in a small cohort of SLE patients versus RA patients. The four metabolites (imidazoleacetic acid, 2‐hydroxyadipic acid, glucose, and pseudouridine) identified in the current study showed certain consistency with previous metabolic profiling or pathogenesis studies and revealed novel discoveries. Glucose was found to be increased in SLE patients by several different metabolic profiling studies.<sup>[</sup>\n##REF##32128093##\n20\n##, ##REF##27441838##\n27\n##\n<sup>]</sup> The alternation of glucose could be raised by the mitochondrial dysfunction and consequent energy abnormality of SLE patients, agreeing with CD4<sup>+</sup> T cells metabolism.<sup>[</sup>\n##UREF##7##\n28\n##\n<sup>]</sup> 2‐Hydroxyadipic acid, an aliphatic acyclic compound, is another biomarker associated with the energy abnormality, which is involved in fatty acid metabolism.<sup>[</sup>\n##REF##20141220##\n29\n##\n<sup>]</sup> Clinically, our group has reported that metformin, originally a medication for diabetes, reduced frequency of major flares in SLE patients,<sup>[</sup>\n##UREF##8##\n30\n##\n<sup>]</sup> indicating that the metabolism of glucose and energy is a promising therapeutic target in SLE. In addition to energy metabolism, the disorder of histamine metabolism was also found to be associated with SLE in the present study, which is mainly involved in immune regulation and allergy.<sup>[</sup>\n##REF##29433511##\n31\n##\n<sup>]</sup> Imidazoleacetic acid is the oxidative product of histamine,<sup>[</sup>\n##REF##26293811##\n32\n##\n<sup>]</sup> an important immunomodulator that regulates allergic inflammatory reactions and other physiological processes.<sup>[</sup>\n##REF##29433511##\n31\n##, ##REF##11956288##\n33\n##\n<sup>]</sup> The abnormality of histamine metabolism in SLE patients has been reported in previous work,<sup>[</sup>\n##REF##16905576##\n18\n##, ##REF##31933894##\n34\n##\n<sup>]</sup> indicating histamine metabolism could be a key factor in the pathogenesis of SLE and other immune diseases. Another interesting biomarker is pseudouridine, also known as 5‐ribosyluracil, associated with the nucleoside metabolism. Previous metabolic profiling studies haven't suggested the abnormality of nucleoside metabolism of SLE, which, however, has been reported to be related to other autoimmune diseases, such as Graves’ disease and Aicardi‐Goutières syndrome.<sup>[</sup>\n##REF##29915201##\n35\n##\n<sup>]</sup> The abnormality of nucleoside metabolism could indicate the dysfunctions for activation and proliferation of immune cells, which demand more complex and energy expensive nucleotide synthesis pathway.<sup>[</sup>\n##REF##28683280##\n36\n##\n<sup>]</sup> Meanwhile, nucleotide metabolism is involved in the regulation of mtDNA‐dependent innate immunity.<sup>[</sup>\n##REF##33903774##\n37\n##\n<sup>]</sup> Our finding suggested that nucleotide metabolism has the potential as a novel target for therapeutic interventions to prevent SLE. Although the biomarker panel identified in this study differed from previous reports, the pathways and biological roles of biomarkers were generally consistent across the present and previous studies, which were mainly involved in the inflammation responses, mitochondrial dysfunction, carbohydrate and lipid metabolism abnormality.<sup>[</sup>\n##REF##16905576##\n18\n##, ##REF##31933894##\n34\n##, ##REF##32259244##\n38\n##\n<sup>]</sup> The different metabolites within the same metabolic pathways were identified as biomarkers across the present and prior studies could be due to different ionization sources. The mass spectrometers with different ionization sources generally produce distinct SMFs in metabolic analysis, which can yield a particular machine learning model, resulting in the difference of high contribution biomarkers. On the other hand, in the present study, the purpose of the construction of biomarker panel is to efficiently identify SLE patients with the use of as few biomarkers as possible, which caused that <italic toggle=\"yes\">m/z</italic> features of some differential metabolites were not selected to the biomarker panel and identified. In clinical practice, employing the 4 selected metabolites as biomarkers is more practical and feasible than attempting to use the entire set of 66 features. These 4 metabolites have demonstrated substantial diagnostic performance and can be readily utilized for diagnostic purposes in a clinical setting. They offer a balance between accuracy and clinical applicability, making them suitable for translation into clinical practice.</p>" ]
[ "<title>Conclusion</title>", "<p>We acquired the SMFs of 915 individuals by nano‐assisted LDI MS and achieved the SLE diagnosis with AUC of 0.950–0.992 by sparse learning of the SMFs. We preliminarily constructed a biomarker panel of 4 metabolites for SLE patients, demonstrating their unique metabolic pattern compared to HCs and RA patients. In parallel to recent genomic and proteomic advances, this work would inspire the pathogenic insights of SLE emerging in metabolomics and shed light on the clinical tool for precision diagnosis and monitoring in the near future.</p>", "<p>There are still several limitations and future research lines to be stated, including that 1) MS system is required to record the SMFs and may hinder its potential application in point‐of‐care (POC) testing; 2) There are opportunities for enhancing cohort collection, including improving the matching between patient and healthy groups, conducting screenings for untreated patients, incorporating disease control groups (such as Sjogren's syndrome), and gathering samples from diverse ethnic backgrounds. These efforts will aid in achieving a more comprehensive understanding of the mechanisms underlying SLE; 4) a combination of multi‐modal information would enhance the outreach and applicability of our approach.</p>" ]
[ "<title>Abstract</title>", "<p>Metabolic fingerprints in serum characterize diverse diseases for diagnostics and biomarker discovery. The identification of systemic lupus erythematosus (SLE) by serum metabolic fingerprints (SMFs) will facilitate precision medicine in SLE in an early and designed manner. Here, a discovery cohort of 731 individuals including 357 SLE patients and 374 healthy controls (HCs), and a validation cohort of 184 individuals (SLE/HC, 91/93) are constructed. Each SMF is directly recorded by nano‐assisted laser desorption/ionization mass spectrometry (LDI MS) within 1 minute using 1 µL of native serum, which contains 908 mass to charge features. Sparse learning of SMFs achieves the SLE identification with sensitivity/specificity and area‐under‐the‐curve (AUC) up to 86.0%/92.0% and 0.950 for the discovery cohort. For the independent validation cohort, it exhibits no performance loss by affording the sensitivity/specificity and AUC of 89.0%/100.0% and 0.992. Notably, a metabolic biomarker panel is screened out from the SMFs, demonstrating the unique metabolic pattern of SLE patients different from both HCs and rheumatoid arthritis patients. In conclusion, SMFs characterize SLE by revealing its unique metabolic pattern. Different regulation of small molecule metabolites contributes to the precise diagnosis of autoimmune disease and further exploration of the pathogenic mechanisms.</p>", "<p>Systemic lupus erythematosus (SLE) with the highest area under the curve value of 0.992 by sparse learning of serum metabolic fingerprints of a large cohort of 915 individuals are characterized. A high‐performance nano‐assisted laser desorption/ionization mass spectrometry is developed for the acquisition of serum metabolic fingerprints within 1 min using 1 µL of each native serum. This work provides a promising assay for SLE precision diagnosis with high throughput and low sample consumption in clinics.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6764-cit-0063\">\n<string-name>\n<given-names>S.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Ding</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Qi</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Huang</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Huang</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Tang</surname>\n</string-name>, <string-name>\n<given-names>N.</given-names>\n<surname>Shen</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Qian</surname>\n</string-name>, <string-name>\n<given-names>Q.</given-names>\n<surname>Guo</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Wan</surname>\n</string-name>, <article-title>Serum Metabolic Fingerprints Characterize Systemic Lupus Erythematosus</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304610</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304610</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Study Design and Population</title>", "<p>This is a cross‐sectional study with a total of 915 individuals, including 448 SLE patients and 467 healthy controls (HCs) (<bold>Figure</bold> ##FIG##1##\n1A## and Tables ##SUPPL##0##S1## and ##SUPPL##0##S2##, Supporting Information). All the patients were recruited from Renji Hospital, School of Medicine, Shanghai Jiao Tong University, from Oct. 1<sup>st</sup>, 2016 to Jun. 30<sup>th</sup>, 2018. All SLE patients fulfilled the classification criteria of 2012 systemic lupus international collaborating clinics (SLICC).<sup>[</sup>\n##UREF##1##\n11\n##\n<sup>]</sup> For the HCs, 467 healthy volunteers, who showed no signs of arthralgia, heart failure, renal failure, autoimmune disease, inflammatory conditions, and other major diseases, were included in this study. All the participants gave their written informed consents before the beginning of the study. This research was conducted in accordance with the Declaration of Helsinki and approved by the institutional ethics committee of Renji Hospital (RA‐2019‐156), School of Medicine, Shanghai Jiao Tong University.</p>", "<p>Specifically, 731 individuals (357 SLE patients and 374 age‐ and sex‐matched HCs) were randomly employed as the discovery ##SUPPL##0##cohort## for SLE diagnostic model building (Table ##SUPPL##0##S1##, Supporting Information). The other 184 individuals (91 SLE patients and 93 age‐ and sex‐matched HCs) ##SUPPL##0##were## applied as the independent validation cohort for verifying the SLE diagnostic model (Table ##SUPPL##0##S1##, Supporting Information). No significant differences of age and sex were discovered between the discovery and validation cohort for SLE patients, ensuring the effective validation results (<italic toggle=\"yes\">p</italic> &gt; 0.05, Table ##SUPPL##0##S2##, Supporting Information).</p>", "<p>The organ involvements of 448 SLE patients were confirmed based on their medical history and pathological examinations, including 228 with renal involvement, 203 with mucocutaneous involvement, 134 with hematological involvement, 123 with musculoskeletal involvement, and 87 with cardiorespiratory involvement. In addition, a small RA queue was collected for disease controls, and a separate queue (SLE/HC, 14, 13) for metabolic marker detection under the same ethics committee (RA‐2019‐156). All the participants gave their written informed consents before the beginning of the study.</p>", "<p>This research was conducted following the Declaration of Helsinki and approved by the institutional ethics committee of Renji Hospital (RA‐2019‐156), School of medicine, Shanghai Jiao Tong University.</p>", "<title>Conflict of Interest</title>", "<p>The authors have filed patents using the nano‐assisted LDI MS methods to detect and diagnose SLE patients.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>S.L., H.D., and Z.Q. contributed equally to this work. The authors express the gratitude to the patients and healthy volunteers who made this work possible. The authors are grateful for the financial support from Project 2022YFC2502800 by Natioanl Key R&amp;D Program of China, Projects 22074044, 22122404, 81971771, and 82001709 by National Natural Science Foundation of China, Project KF2105 by State Key Laboratory of Oncogenes and Related Genes, Projects 2017YFE0124400, 2017YFC0909000, 2021YFF0703500, and 2021YFA0910104 by Ministry of Science and Technology of the People's Republic of China, and Project 2021‐01‐07‐00‐02‐E00083 by Shanghai Institutions of Higher Learning. This work was also sponsored by the Shanghai Rising‐Star Programme (19QA1404800), Innovation Group Project of Shanghai Municipal Health Commission (2019CXJQ03), Innovation Research Plan by the Shanghai Municipal Education Commission (ZXWF082101), and Programme for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning. Renji Hospital Biobank was funded by the National Human Genetic Resources Sharing Service Platform (2005DKA21300).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6764-fig-0004\"><label>Scheme 1</label><caption><p>Nano‐assisted acquisition of serum metabolic fingerprints (SMFs) and systemic lupus erythematosus (SLE) diagnosis by sparse learning. A) Experimental process of laser desorption/ionization mass spectrometry (LDI MS) detection. 1 µL of native serum per individual was mixed with ferric particles for LDI MS detection. The mass to charge (<italic toggle=\"yes\">m/z)</italic> features of sodium ion (Na<sup>+</sup>) and potassium ion (K<sup>+</sup>) adducts were recorded under the irradiation of Nd:YAG laser (355 nm). B) Sparse learning of SMFs was conducted for SLE metabolic analysis. The SMFs of SLE patients and healthy controls (HCs) in the discovery cohort were first applied in 5‐fold cross‐validation with 20 rounds, yielding 100 diagnostic models for verification of receiver operating characteristic (ROC) curves. The optimized model was obtained by assessing ROC curves of above 100 models. Then an independent validation cohort was applied to the optimized model to obtain the blind test result. Specific <italic toggle=\"yes\">m/z</italic> features were also screened out as biomarkers and constructed as a biomarker panel for analysis.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6764-fig-0001\"><label>Figure 1</label><caption><p>SMF extraction by nano‐assisted LDI MS. A) Sample characteristics and study design of 915 individuals, including 731 in the discovery cohort and 184 in the validation cohort. The SMF acquisition process is shown in (B,C). B) The serum samples were collected from SLE patients and HCs according to standard protocols (see Methods for more details) with only 1 µL of serum per individual loaded on the plate. C) The matrix suspension was mixed with serum sample for direct LDI MS detection. D) Typical MS spectra of an SLE patient and a healthy volunteer with <italic toggle=\"yes\">m/z</italic> of 100–400. E) The blueprint consists of 731 SMFs in the discovery cohort, each of which contains 908 <italic toggle=\"yes\">m/z</italic> features.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6764-fig-0002\"><label>Figure 2</label><caption><p>Differentiation of SLE from HCs by machine learning methods. A) ROC curves based on the 731 SMFs (SLE/HC, 357/374) in the discovery cohort, using sparse learning (AUC of 0.950), decision tree (AUC of 0.486), logistic regression (AUC of 0.489), supporting vector machine (SVM, AUC of 0.498), K‐nearest neighbors (kNN, AUC of 0.544), and random forest (AUC of 0.513). B) The scatter plot of probability in the discovery cohort is based on the optimized diagnostic model of sparse learning. C) ROC curve based on the 184 SMFs (SLE/HC, 91/93) in the validation cohort, using sparse learning (AUC of 0.992), decision tree (AUC of 0.533), logistic regression (AUC of 0.527), SVM (AUC of 0.450), kNN (AUC of 0.523), and random forest (AUC of 0.499). D) The scatter plot of probability in the validation cohort is based on the optimized diagnostic model of sparse learning. Every dot in (B) and (D) represents one individual in this study.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6764-fig-0003\"><label>Figure 3</label><caption><p>Construction of metabolic biomarker panel of SLE. A) Workflow for constructing the metabolic biomarker panel. After the pretreatment of raw mass spectra (containing 120 000 data points), the SMF of 908 <italic toggle=\"yes\">m/z</italic> features was extracted, yielding 66 <italic toggle=\"yes\">m/z</italic> signals through the feature selection process, thus identifying 4 biomarkers. B) The ROC curves by sparse learning of the 4 biomarkers in the discovery cohort (red line) and validation cohort (black line). C) The scatter plot of probability in discovery cohort based on the optimized diagnostic model of SMFs. D) The intensity plot of SLE patients (in pink) and HCs (in green) is based on the 4 biomarkers, according to five independent LDI MS experiments. E) The intensity plot of 357 SLE patients (in pink) and 27 rheumatoid arthritis (RA) patients (in yellow) based the 4 biomarkers, according to five independent LDI MS experiments (* represents <italic toggle=\"yes\">p</italic> &lt; 0.05, ** represents <italic toggle=\"yes\">p</italic> &lt; 0.01, *** represents <italic toggle=\"yes\">p</italic> &lt; 0.001, and **** represented <italic toggle=\"yes\">p</italic> &lt; 0.0001). F) The scores plot of SLE patients and RA patients by principal component analysis (PCA).</p></caption></fig>" ]
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[ "<media xlink:href=\"ADVS-11-2304610-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
38
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 12; 11(2):2304610
oa_package/d4/c6/PMC10787061.tar.gz
PMC10787062
37985567
[ "<title>Introduction</title>", "<p>To counteract worsening climate change and mounting energy shortfalls, solid oxide fuel cells (SOFCs) have emerged as a promising power generation technology because of their high efficiency and eco‐friendliness.<sup>[</sup>\n##REF##36546885##\n1\n##\n<sup>]</sup> Unlike low‐temperature fuel cells, SOFCs operating at high temperatures offer a distinct feature of fuel flexibility, allowing direct conversion of the chemical energy in available hydrocarbons, ammonia, and complex fuels into electricity.<sup>[</sup>\n##UREF##0##\n2\n##\n<sup>]</sup> However, owing to high activity for catalyzing the cleavage of C−H bonds, traditional Ni‐based ceramic anodes of SOFCs readily suffer from carbon coking when directly using hydrocarbons as fuels, causing the decreased active sites and the corresponding performance degradation.<sup>[</sup>\n##REF##36440888##\n3\n##\n<sup>]</sup> Moreover, the volume change during redox cycles and the Ni coarsening during the long‐term operation of Ni‐based ceramic anodes also restrict the energy efficiency and operating life of SOFCs.<sup>[</sup>\n##UREF##1##\n4\n##\n<sup>]</sup>\n</p>", "<p>In response, enormous efforts have been devoted to developing alternative anode materials to Ni‐based cermets for hydrocarbon‐fueled SOFCs. Particularly, perovskite oxides (general formula of ABO<sub>3</sub>)<sup>[</sup>\n##UREF##2##\n5\n##\n<sup>]</sup> with mixed ionic‐electronic conduction, such as doped‐SrTiO<sub>3‐δ</sub> (ST),<sup>[</sup>\n##REF##36121444##\n6\n##\n<sup>]</sup> La<sub>0.75</sub>Sr<sub>0.25</sub>Cr<sub>0.5</sub>Mn<sub>0.5</sub>O<sub>3‐δ</sub> (LSCM),<sup>[</sup>\n##REF##12692533##\n7\n##\n<sup>]</sup> PrBaMn<sub>2</sub>O<sub>5+δ</sub> (PBM)<sup>[</sup>\n##REF##25532072##\n8\n##\n<sup>]</sup> and Sr<sub>2</sub>Fe<sub>1.5</sub>Mo<sub>0.5</sub>O<sub>6‐δ</sub> (SFM),<sup>[</sup>\n##REF##20941791##\n9\n##\n<sup>]</sup> and their derivatives, show great potentials as anodes for hydrocarbon fueled SOFCs because of their high carbon deposition‐resistance and excellent structural stability. Nevertheless, the sluggish kinetics of perovskite oxides toward hydrocarbon conversion, which are typically lower than the common Ni‐based ceramic anodes, restricts their large‐scale commercialization in SOFCs.</p>", "<p>Actually, developing a single‐phase material that meets all the requirements of the anode for hydrocarbon‐fueled SOFCs is challenging. Instead, the rational design of composite electrodes, where each component serves its specific functionality, is likely a more promising approach. For example, combining perovskite oxide with an oxygen ionic conductor (e.g., doped CeO<sub>2</sub>) not only facilitated the oxygen ionic transfer but also stabilized the interfacial contact of anode/electrolyte, eventually resulting in a remarkable decrease in polarization resistance.<sup>[</sup>\n##UREF##3##\n10\n##\n<sup>]</sup> Constructing a metal‐oxide heterointerface represents another viable approach to promote the intrinsic activity of electrocatalysts. Particularly, in situ exsolution has emerged as an advanced strategy to precisely manipulate the metal‐oxide heterointerface,<sup>[</sup>\n##REF##24153368##\n11\n##\n<sup>]</sup> compared to the conventional infiltration method involving multiple and unmanageable deposition and heat treatment processes.<sup>[</sup>\n##REF##34793177##\n12\n##\n<sup>]</sup> Of paramount significance, the exsolved heterointerface showcases distinctive advantages, including metal‐oxide heterointerface for synergistic electrocatalysis, the strong metal‐oxide interaction for curtailing carbon deposition and metal nanoparticles agglomeration, and reversible structure during redox cycling.<sup>[</sup>\n##UREF##4##\n13\n##\n<sup>]</sup> For instance, the single cell with a CoFe exsolved Sr<sub>2</sub>Fe<sub>1.5‐x</sub>Co<sub>x</sub>Mo<sub>0.5</sub>O<sub>6‐δ</sub> anode demonstrated a peak power density of 0.27 W cm<sup>−2</sup> at 800 °C for 130 h using CH<sub>4</sub> as the fuel.<sup>[</sup>\n##REF##32149494##\n14\n##\n<sup>]</sup> A RuFe exsolved SrTi<sub>0.3</sub>Fe<sub>0.7</sub>Ru<sub>0.07</sub>O<sub>3‐δ</sub> anode showed a high coking resistance in steam/ethanol mixtures.<sup>[</sup>\n##UREF##5##\n15\n##\n<sup>]</sup> The crucial descriptors involved in regulating the morphology and performance of exsolved heterointerface have been revealed, including exsolved metal component determined by exsolution energy, defect tailoring of perovskite host, and phase transformation of perovskite host et al.<sup>[</sup>\n##REF##28656965##\n16\n##\n<sup>]</sup> Therefore, introducing oxygen ionic conductor and constructing a metal‐oxide heterointerface are effective solutions to boost the performance of perovskite anodes. However, developing a heterogeneous anode with well‐tailored components and morphology to simultaneously achieve high intrinsic activity and fast oxygen ionic conduction is a significant challenge.</p>", "<p>Herein, we highlight a smart dual‐exsolved self‐assembled anode enabling efficient and robust CH4‐fueled SOFCs. The initial heterogeneous anode, comprising Ru incorporated Sr<sub>2</sub>Fe<sub>1.5</sub>Mo<sub>0.5</sub>O<sub>6‐δ</sub> (SFM) and Ru incorporated Gd<sub>0.1</sub>Ce<sub>0.9</sub>O<sub>2‐δ</sub> (GDC) phases, is self‐assembled by a one‐pot method. It has been reported that Ru element demonstrates reversible dissolution and exsolution capabilities in both SFM perovskite<sup>[</sup>\n##REF##34580312##\n17\n##\n<sup>]</sup> and CeO<sub>2</sub> fluorite<sup>[</sup>\n##UREF##6##\n18\n##\n<sup>]</sup> lattices. As expected, Ru metal is in situ exsolved on both Ru‐SFM and Ru‐GDC surfaces induced by a reducing atmosphere during the actual operation of SOFCs, creating Ru@Ru‐SFM/Ru‐GDC dual‐exsolved self‐assembled anode. Unlike conventional mechanical mixing composite anodes, the self‐assembled anode promises an enlarged three‐phase boundary benefitting electrocatalysis.<sup>[</sup>\n##REF##34172742##\n19\n##\n<sup>]</sup> Furthermore, leveraging the cooperation of oxygen ionic conductor and the creation of exsolved heterointerfaces, the single cell using the Ru@Ru‐SFM/Ru‐GDC anode delivers high peak power densities of 1.03 and 0.63 W cm<sup>−2</sup> at 800 °C under humidified H<sub>2</sub> and CH<sub>4</sub>, far exceeding the referenced SFM/GDC anode. Using humidified CH<sub>4</sub> as fuel, this anode demonstrates remarkable durability for 200 h without apparent carbon deposition. As revealed by DFT calculations, the heterointerfaces of Ru@Ru‐SFM and Ru@Ru‐GDC exhibit smaller energy barriers compared to SFM, denoting higher intrinsic activities for CH<sub>4</sub> conversion.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Morphology and Structure</title>", "<p>\n<bold>Figure</bold> ##FIG##0##\n1a## illustrates the structural change for the formation of the dual‐exsolved self‐assembled Ru@Ru‐SFM/Ru‐GDC electrocatalyst. Using a facile one‐pot method, mixed metal salts are self‐assembled into Ru‐incorporated SFM and Ru‐incorporated GDC phases. Notably, when the anode exposed to a reducing atmosphere in actual operating, metallic Ru is segregated onto both Ru‐SFM and Ru‐GDC surfaces simultaneously, receiving the Ru@Ru‐SFM/Ru‐GDC anode. Figure ##FIG##0##1b## provides the X‐ray diffraction (XRD) patterns of SFM/GDC, Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts. Similar to SFM/GDC electrocatalyst, the Ru‐incorporated Ru‐SFM/Ru‐GDC electrocatalyst exhibits a composition comprising a cubic perovskite phase and a cubic fluorite phase.<sup>[</sup>\n##UREF##7##\n20\n##\n<sup>]</sup> Characteristic peaks corresponding to individual RuO<sub>2</sub> are absent, suggesting the potential Ru doping into the SFM and GDC lattices. After reduction, an additional peak (≈43.7°) emerges in the Ru@Ru‐SFM/Ru‐GDC electrocatalyst, well indexed to the phase of Ru (PDF #97‐065‐0568). Concurrently, shifts in the peaks representative of the perovskite and fluorite phases toward lower angles are observed, implying that the lattice expansion is likely induced via the presence of low‐valence metal cations and the generation of oxygen vacancies after reduction. As shown in hydrogen temperature programmed reduction (H<sub>2</sub>‐TPR, Figure ##SUPPL##0##S1##, Supporting Information), an obvious hydrogen consumption peak ≈282 °C likely corresponds to the exsolution of metallic Ru.</p>", "<p>To gain insights into the morphology of the Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts, scanning electron microscopy (SEM) and high‐resolution transmission electron microscopy (HRTEM) analysis were performed. The SEM image reveals a smooth surface of submicron Ru‐SFM/Ru‐GDC particles. (Figure ##FIG##0##1c##). After being exposed to a reducing atmosphere, large amounts of nano‐sized particles are decorated on the surface of the Ru‐SFM/Ru‐GDC backbone (Figure ##FIG##0##1d##). Analysis of the HRTEM image for Ru‐SFM/Ru‐GDC (Figure ##SUPPL##0##S2##, Supporting Information) indicates lattice spacing of 0.226 and 0.163 nm, which are well indexed to the (220) plane of Ru‐SFM and (311) plane of Ru‐GDC, respectively. Energy dispersive spectrometer (EDS) mapping further demonstrates that the anode self‐assembles into Ru‐SFM and Ru‐GDC phases, and the Ru element is uniformly distributed in the Ru‐SFM and Ru‐GDC backbones.</p>", "<p>In contrast, a collection of spherical nanoparticles is deeply anchored onto the surfaces of Ru‐SFM/Ru‐GDC backbones after reduction (<bold>Figure</bold> ##FIG##1##\n2a##). Of note, this strongly anchored configuration induced by in situ exsolution promises a potent metal‐oxide interaction that offers the potential to inhibit carbon deposition and the agglomeration of exsolved nanoparticles. Beyond Ru‐SFM (220) and Ru‐GDC (311) planes in the backbone, the lattice spacing of surface exsolved nanoparticles is 0.233 nm, fairly agreeing with the (100) plane of metallic Ru (Figure ##FIG##1##2b,c##). In addition, the average particle sizes of exsolved Ru nanoparticles on Ru‐SFM and Ru‐GDC surfaces are ≈2.73 and ≈3.62 nm (Figure ##SUPPL##0##S3##, Supporting Information), respectively. EDS elemental distribution mapping analysis further validates the presence of Ru@Ru‐SFM (Figure ##FIG##1##2d##) and Ru@Ru‐GDC (Figure ##FIG##1##2e##) heterointerfaces. These results affirm that the fabrication of Ru@Ru‐SFM/Ru‐GDC electrocatalyst has been successfully achieved through the integrated methodology of self‐assembly and dual‐exsolution.</p>", "<p>To assess the influence of exsolution on elemental chemical states, X‐ray photoelectron spectroscopy (XPS) measurements were conducted on Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts. <bold>Figure</bold> ##FIG##2##\n3a## shows that the peak leak centered at 463.8 eV is well assigned to the Ru<sup>4+</sup> state in the Ru‐SFM/Ru‐GDC electrocatalyst.<sup>[</sup>\n##REF##34580312##\n17\n##\n<sup>]</sup> It is noteworthy that a new peak located at 461.3 eV is recorded in Ru@Ru‐SFM/Ru‐GDC electrocatalyst, confirming the exsolution of metallic Ru after reduction. Contrasting outcomes are observed for other metal ions such as Fe (Figure ##FIG##2##3b##), Mo (Figure ##FIG##2##3c##), and Ce (Figure ##FIG##2##3d##), where their reduced average valence states are established post reduction (Table ##SUPPL##0##S1##, Supporting Information), accompanied by the absence of their metallic states. For instance, the Fe<sup>3+</sup>:Fe<sup>2+</sup> valence ratio in Ru‐SFM/Ru‐GDC reduces from 57.5%:42.5% to 39.0%:61.0% in Ru@Ru‐SFM/Ru‐GDC. These findings bolster the contention that the exsolved particles predominantly constitute metallic Ru rather than alloy.</p>", "<p>The reduction in metal ion valence state always corresponds with the generation of oxygen vacancies to maintain electrical neutrality. The O 1s XPS spectra of Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts are categorized into the oxygen species of carbonate/hydroxyl oxygen (CO<sub>3</sub>\n<sup>2−</sup>/OH<sup>−</sup>) centered at 531.2 eV, adsorbed oxygen (O<sub>2</sub>\n<sup>2−</sup>/O<sup>−</sup>) centered at 529.5 eV, lattice oxygen (O<sub>lat.</sub>) centered at 528.5 eV (Figure ##FIG##2##3e##).<sup>[</sup>\n##UREF##8##\n21\n##\n<sup>]</sup> The elevated adsorbed oxygen: lattice oxygen ratio following reduction indicates a higher concentration of oxygen vacancies in the Ru@Ru‐SFM/Ru‐GDC electrocatalyst compared to Ru‐SFM/Ru‐GDC (Table ##SUPPL##0##S1##, Supporting Information). Furthermore, electron paramagnetic resonance (EPR) analysis reveals a heightened peak intensity for Ru@Ru‐SFM/Ru‐GDC (Figure ##FIG##2##3f##), also indicating a greater abundance of oxygen vacancies than in Ru‐SFM/Ru‐GDC.<sup>[</sup>\n##UREF##9##\n22\n##\n<sup>]</sup> The created oxygen vacancies facilitate rapid oxygen mobility and contribute to the oxidative conversion of hydrocarbons.<sup>[</sup>\n##REF##37399582##\n23\n##\n<sup>]</sup> Remarkably, the structure change is reversible during redox cycles. As confirmed by XRD, SEM, and XPS (Figures ##SUPPL##0##S4##–##SUPPL##0##S6## and Table ##SUPPL##0##S2##, Supporting Information), the exsolved Ru nanoparticels are redissolved into Ru‐SFM/Ru‐GDC lattice after reoxidation, and Ru nanoparticels can be exsolved again after rereduction (Figures ##SUPPL##0##S7##–##SUPPL##0##S9## and Table ##SUPPL##0##S2##, Supporting Information). Such good reversibility of exsolution/dissolution suggests the structural flexibility of dual‐exsolved self‐assembled electrocatalyst.</p>", "<title>Enhanced Electrochemical Performance</title>", "<p>Electrochemical impedance spectra (EIS) of anodes were examined using symmetric cells (Figure ##SUPPL##0##S10##, Supporting Information) at 800 °C in 5% H<sub>2</sub>‐Ar atmosphere, to comprehend the impact of Ru dual‐exsolution on electrochemical processes. As shown in Figure ##SUPPL##0##S11##, Supporting Information, the Ru@Ru‐SFM/Ru‐GDC anode exhibits smaller polarization resistances (<italic toggle=\"yes\">R</italic>\n<sub>p</sub>) and lower activation energy compared to the SFM/GDC anode. This suggests an accelerated reaction kinetics for H<sub>2</sub> oxidation after dual‐exsolution. Furthermore, distribution of relaxation time (DRT) analysis exhibits that the impedance spectra consist of distinct high‐frequency polarization (HF), medium‐frequency polarization (MF), and low‐frequency polarization (LF) arcs, corresponding respectively to charge transfer, ion surface exchange and transmission, and gas absorption/desorption processes.<sup>[</sup>\n##UREF##10##\n24\n##\n<sup>]</sup> Both LF‐R<sub>p</sub> and MF‐R<sub>p</sub> significantly decreases, implying that the ion surface exchange and transmission, and gas absorption/desorption are accelerated by dual‐exsolution of metallic Ru.</p>", "<p>To evaluate the practical viability of the Ru@Ru‐SFM/Ru‐GDC electrocatalyst as a potential anode for SOFCs, single SOFCs with an asymmetric architecture of porous Ru@Ru‐SFM/Ru‐GDC (anode) || dense LSGM (electrolyte) || porous PBSCF/GDC (cathode) were prepared (<bold>Figure</bold> ##FIG##3##\n4a##). For comparison, SOFCs employing a SFM/GDC anode were also investigated. The compositional purities of the synthetic LSGM electrolyte and PBSCF/GDC composite cathode are confirmed by XRD analysis (Figure ##SUPPL##0##S12##, Supporting Information). As depicted in Figure ##FIG##3##4b##, the Ru@Ru‐SFM/Ru‐GDC anode, ≈23 µm in thickness, and the PBSCF/GDC cathode, ≈23 µm in thickness, are both screen‐printed on opposing sides of a ≈230 µm thick LSGM electrolyte. Remarkably, using the smart self‐assembly approach results in the fabrication of a submicron‐structured Ru‐SFM/Ru‐GDC skeleton (Figure ##FIG##3##4c##). The following in situ dual‐exsolution of nanoscale metallic Ru onto such submicron skeleton yields a hierarchical anode structure characterized by abundant heterointerfaces conducive to electrocatalytic activity. According to BET analyses (Table ##SUPPL##0##S3##, Supporting Information), the dual‐exsolved Ru‐SFM/Ru‐GDC anode exhibits a higher surface area of 8.80 m<sup>2</sup> g<sup>−1</sup> than that of unexsolved SFM/GDC anode (6.38 m<sup>2</sup> g<sup>−1</sup>). Additionally, the robust contact in the interface of electrolyte and anode ensures high structural stability and rapid ion transport.</p>", "<p>Using humidified H<sub>2</sub> (≈3% H<sub>2</sub>O) as the fuel, the peak power densities (PPD) of 0.65, 0.34, and 0.16 W cm<sup>−2</sup> are achieved on the SFM/GDC single cell at operating temperatures of 800, 750, and 700 °C (<bold>Figure</bold> ##FIG##4##\n5a##). In contrast, the Ru@Ru‐SFM/Ru‐GDC single cell exhibits superior performance, with PPD values of 1.03, 0.71, and 0.44 W cm<sup>−2</sup> at 800, 750, and 700 °C (Figure ##FIG##4##5b##), respectively. This enhanced performance of the Ru@Ru‐SFM/Ru‐GDC single cell can be primarily attributed to its lower polarization resistance (<italic toggle=\"yes\">R</italic>\n<sub>p</sub>) compared to the SFM/GDC single cell (0.073 vs. 0.134 Ω cm<sup>2</sup> at 800 °C), as demonstrated in Figure ##FIG##4##5c,d##. In view of almost the same electrolyte and cathode materials, the reduced R<sub>p</sub> indicates that the anodic reaction kinetics associated with H<sub>2</sub> oxidation is significantly enhanced by dual‐exsolution, in line with the results of symmetrical cells. In addition, compared to single cells using other high performing perovskite anodes, the PPD of the single cell featuring the Ru@Ru‐SFM/Ru‐GDC anode surpasses most of the reported ones (Table ##SUPPL##0##S4##, Supporting Information).</p>", "<p>When transitioning to the direct utilization of humidified CH<sub>4</sub> (≈3% H<sub>2</sub>O), the PPD of the SFM/GDC single cell is 0.32 W cm<sup>−2</sup> at 800 °C (<bold>Figure</bold> ##FIG##5##\n6a##), while the Ru@Ru‐SFM/Ru‐GDC single cell achieves a higher PPD of 0.63 W cm<sup>−2</sup> at the same temperature (Figure ##FIG##5##6b##). The R<sub>p</sub> of the Ru@Ru‐SFM/Ru‐GDC single cell (0.22 Ω cm<sup>2</sup> at 800 °C) is remarkably lower than that of the SFM/GDC single cell (0.58 Ω cm<sup>2</sup> at 800 °C) (Figure ##FIG##5##6c##), denoting that the Ru@Ru‐SFM/Ru‐GDC anode offers a much higher electrocatalytic activity toward CH<sub>4</sub> conversion. According to DRT analysis, three characteristic peaks in the HF, MF, and LF ranges are identified (Figure ##FIG##5##6d##). Among them, the LF‐R<sub>p</sub> is dramatically reduced, indicative of the significantly enhanced CH<sub>4</sub> absorption/dissociation kinetics after Ru dual‐exsolution.<sup>[</sup>\n##UREF##17##\n33\n##\n<sup>]</sup>\n</p>", "<title>Carbon Deposition Tolerance</title>", "<p>The galvanostatic test of the Ru@Ru‐SFM/Ru‐GDC anode based single cell was conducted at 800 °C, applying a constant current density of 1.0 A cm<sup>−2</sup>. As depicted in Figure ##FIG##5##6e##, the cell voltage remains consistently stable at ≈0.59 V for 200 h. Of note, the PPD and durability of the CH<sub>4</sub> fueled single cell using the Ru@Ru‐SFM/Ru‐GDC anode favorably rival most of previously reported perovskite anodes, as illustrated in Figure ##FIG##5##6f## and Table ##SUPPL##0##S5## (Supporting Information). No Raman carbon peaks, including the D‐band at 1357 cm<sup>−1</sup> and G‐band at 1585 cm<sup>−1</sup>, are detected on the Ru@Ru‐SFM/Ru‐GDC anode after the extensive long‐term stability test (<bold>Figure</bold> ##FIG##6##\n7a##), demonstrating the exceptional resistance of the Ru@Ru‐SFM/Ru‐GDC anode to carbon deposition during CH<sub>4</sub> exposure. Moreover, the original phase structure of the Ru@Ru‐SFM/Ru‐GDC anode is almost not changed after long‐term CH<sub>4</sub> operation, as shown in Figure ##FIG##6##7b##. XPS analyses in Figure ##FIG##6##7c## and Figure ##SUPPL##0##S13## (Supporting Information), confirm the consistent existence of metallic Ru within the Ru@Ru‐SFM/Ru‐GDC anode.</p>", "<p>In addition, the morphology of the Ru@Ru‐SFM/Ru‐GDC anode after long‐term durability test was investigated by SEM and TEM. This self‐assembled anode retains its highly porous submicron structure without the presence of discernible carbon deposits (Figure ##FIG##6##7d##). It is worth noting that the exsolved nanoparticles firmly anchor onto the Ru‐SFM/Ru‐GDC substrate without agglomeration, as shown in Figure ##FIG##6##7e,f##. These findings indicate that the nano‐heterointerfaces in the Ru@Ru‐SFM/Ru‐GDC anode maintain excellent structural stability throughout CH<sub>4</sub> operation, likely owing to the strong metal‐support interaction created by the exsolution approach.<sup>[</sup>\n##UREF##15##\n31\n##\n<sup>]</sup>\n</p>", "<title>Mechanism of CH<sub>4</sub> Conversion</title>", "<p>Experimental characterizations have substantiated the occurrence of dual exsolution, resulting in the formation of Ru@Ru‐SFM and Ru@Ru‐GDC heterointerfaces, which significantly improve the activity of CH<sub>4</sub> conversion. Consequently, we conducted density functional theory (DFT) calculations to elucidate the underlying mechanism governing CH<sub>4</sub> conversion over dual‐exsolved heterointerfaces. Theoretical modes of pristine SFM (001), Ru cluster@Ru‐SFM (001), and Ru cluster@Ru‐GDC (111) are built, as depicted in <bold>Figure</bold> ##FIG##7##\n8a–c##, respectively. A widely accepted pathway and corresponding free energy profiles of CH<sub>4</sub> conversion are illustrated in Figure ##FIG##7##8d##.<sup>[</sup>\n##UREF##18##\n34\n##\n<sup>]</sup> The relevant reaction intermediates adsorbed on SFM, Ru@Ru‐SFM, and Ru@Ru‐GDC are respectively depicted in Figures ##SUPPL##0##S14##–##SUPPL##0##S16## (Supporting Information). These calculations conclusively establish that the CH<sub>4</sub> activation as the formation of CH<sub>3</sub>* is the rate‐determining step. Existing literatures had also corroborated that the initial dehydrogenation process was mainly the rate determining step for hydrocarbon conversion.<sup>[</sup>\n##REF##37399582##\n23\n##, ##UREF##11##\n25\n##\n<sup>]</sup> Afterward, the CH<sub>4</sub> conversion process shows a downhill energy trend. It is evident that the calculated energy barriers of Ru@Ru‐SFM (0.22 eV), and Ru@Ru‐GDC (0.40 eV) heterointerfaces are lower than that of pristine SFM (0.52 eV), endowing them with higher intrinsic activities toward CH<sub>4</sub> conversion.</p>", "<p>Figure ##FIG##7##8e## provides the calculated partial density of states (DOS) of SFM, Ru@Ru‐SFM, and Ru@Ru‐GDC. One can see that the specific orbital contributions of Ru@Ru‐SFM, and Ru@Ru‐GDC heterointerfaces around the Fermi level are richer than that of pristine SFM. Compared with the pristine SFM, the Ru@Ru‐SFM, and Ru@Ru‐GDC heterointerfaces substantially facilitate the CH<sub>4</sub> adsorption/activation by effectively weakening the C−H bond,<sup>[</sup>\n##REF##37399582##\n23\n##\n<sup>]</sup> promoting the activities toward CH<sub>4</sub> conversion. Moreover, it has been revealed that the synergistic effect of Lewis acid (perovskite oxide) and Lewis base (exsolved metal) contributes to CH<sub>4</sub> dehydrogenation process.<sup>[</sup>\n##REF##35638132##\n35\n##\n<sup>]</sup> Herein, the Lewis acid‐Lewis base pairs of exsolved Ru@Ru‐SFM perovskite oxide and exsolved Ru@Ru‐GDC fluorite oxide<sup>[</sup>\n##REF##29482317##\n36\n##\n<sup>]</sup> follow the same mechanism.</p>", "<p>Beyond high intrinsic activities of heterointerfaces, the Ru@Ru‐SFM/GDC anode, prepared by an integrated approach combining self‐assembly and dual‐exsolution, exhibits a nano@submicron hierarchical structure, ensuring a high density of heterointerfaces. Furthermore, the introduction of GDC can enhance the oxygen ionic conductivity of the anode, significantly expanding the electrochemical active area from the anode/electrolyte near‐interface to the anode bulk.<sup>[</sup>\n##UREF##19##\n37\n##\n<sup>]</sup> This combination of high intrinsic activity, high density of active sites, and high oxygen ionic conduction establishes Ru@Ru‐SFM/Ru‐GDC as a prominent anode material with outstanding electrochemical performance for CH<sub>4</sub> fueled SOFCs.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Morphology and Structure</title>", "<p>\n<bold>Figure</bold> ##FIG##0##\n1a## illustrates the structural change for the formation of the dual‐exsolved self‐assembled Ru@Ru‐SFM/Ru‐GDC electrocatalyst. Using a facile one‐pot method, mixed metal salts are self‐assembled into Ru‐incorporated SFM and Ru‐incorporated GDC phases. Notably, when the anode exposed to a reducing atmosphere in actual operating, metallic Ru is segregated onto both Ru‐SFM and Ru‐GDC surfaces simultaneously, receiving the Ru@Ru‐SFM/Ru‐GDC anode. Figure ##FIG##0##1b## provides the X‐ray diffraction (XRD) patterns of SFM/GDC, Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts. Similar to SFM/GDC electrocatalyst, the Ru‐incorporated Ru‐SFM/Ru‐GDC electrocatalyst exhibits a composition comprising a cubic perovskite phase and a cubic fluorite phase.<sup>[</sup>\n##UREF##7##\n20\n##\n<sup>]</sup> Characteristic peaks corresponding to individual RuO<sub>2</sub> are absent, suggesting the potential Ru doping into the SFM and GDC lattices. After reduction, an additional peak (≈43.7°) emerges in the Ru@Ru‐SFM/Ru‐GDC electrocatalyst, well indexed to the phase of Ru (PDF #97‐065‐0568). Concurrently, shifts in the peaks representative of the perovskite and fluorite phases toward lower angles are observed, implying that the lattice expansion is likely induced via the presence of low‐valence metal cations and the generation of oxygen vacancies after reduction. As shown in hydrogen temperature programmed reduction (H<sub>2</sub>‐TPR, Figure ##SUPPL##0##S1##, Supporting Information), an obvious hydrogen consumption peak ≈282 °C likely corresponds to the exsolution of metallic Ru.</p>", "<p>To gain insights into the morphology of the Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts, scanning electron microscopy (SEM) and high‐resolution transmission electron microscopy (HRTEM) analysis were performed. The SEM image reveals a smooth surface of submicron Ru‐SFM/Ru‐GDC particles. (Figure ##FIG##0##1c##). After being exposed to a reducing atmosphere, large amounts of nano‐sized particles are decorated on the surface of the Ru‐SFM/Ru‐GDC backbone (Figure ##FIG##0##1d##). Analysis of the HRTEM image for Ru‐SFM/Ru‐GDC (Figure ##SUPPL##0##S2##, Supporting Information) indicates lattice spacing of 0.226 and 0.163 nm, which are well indexed to the (220) plane of Ru‐SFM and (311) plane of Ru‐GDC, respectively. Energy dispersive spectrometer (EDS) mapping further demonstrates that the anode self‐assembles into Ru‐SFM and Ru‐GDC phases, and the Ru element is uniformly distributed in the Ru‐SFM and Ru‐GDC backbones.</p>", "<p>In contrast, a collection of spherical nanoparticles is deeply anchored onto the surfaces of Ru‐SFM/Ru‐GDC backbones after reduction (<bold>Figure</bold> ##FIG##1##\n2a##). Of note, this strongly anchored configuration induced by in situ exsolution promises a potent metal‐oxide interaction that offers the potential to inhibit carbon deposition and the agglomeration of exsolved nanoparticles. Beyond Ru‐SFM (220) and Ru‐GDC (311) planes in the backbone, the lattice spacing of surface exsolved nanoparticles is 0.233 nm, fairly agreeing with the (100) plane of metallic Ru (Figure ##FIG##1##2b,c##). In addition, the average particle sizes of exsolved Ru nanoparticles on Ru‐SFM and Ru‐GDC surfaces are ≈2.73 and ≈3.62 nm (Figure ##SUPPL##0##S3##, Supporting Information), respectively. EDS elemental distribution mapping analysis further validates the presence of Ru@Ru‐SFM (Figure ##FIG##1##2d##) and Ru@Ru‐GDC (Figure ##FIG##1##2e##) heterointerfaces. These results affirm that the fabrication of Ru@Ru‐SFM/Ru‐GDC electrocatalyst has been successfully achieved through the integrated methodology of self‐assembly and dual‐exsolution.</p>", "<p>To assess the influence of exsolution on elemental chemical states, X‐ray photoelectron spectroscopy (XPS) measurements were conducted on Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts. <bold>Figure</bold> ##FIG##2##\n3a## shows that the peak leak centered at 463.8 eV is well assigned to the Ru<sup>4+</sup> state in the Ru‐SFM/Ru‐GDC electrocatalyst.<sup>[</sup>\n##REF##34580312##\n17\n##\n<sup>]</sup> It is noteworthy that a new peak located at 461.3 eV is recorded in Ru@Ru‐SFM/Ru‐GDC electrocatalyst, confirming the exsolution of metallic Ru after reduction. Contrasting outcomes are observed for other metal ions such as Fe (Figure ##FIG##2##3b##), Mo (Figure ##FIG##2##3c##), and Ce (Figure ##FIG##2##3d##), where their reduced average valence states are established post reduction (Table ##SUPPL##0##S1##, Supporting Information), accompanied by the absence of their metallic states. For instance, the Fe<sup>3+</sup>:Fe<sup>2+</sup> valence ratio in Ru‐SFM/Ru‐GDC reduces from 57.5%:42.5% to 39.0%:61.0% in Ru@Ru‐SFM/Ru‐GDC. These findings bolster the contention that the exsolved particles predominantly constitute metallic Ru rather than alloy.</p>", "<p>The reduction in metal ion valence state always corresponds with the generation of oxygen vacancies to maintain electrical neutrality. The O 1s XPS spectra of Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts are categorized into the oxygen species of carbonate/hydroxyl oxygen (CO<sub>3</sub>\n<sup>2−</sup>/OH<sup>−</sup>) centered at 531.2 eV, adsorbed oxygen (O<sub>2</sub>\n<sup>2−</sup>/O<sup>−</sup>) centered at 529.5 eV, lattice oxygen (O<sub>lat.</sub>) centered at 528.5 eV (Figure ##FIG##2##3e##).<sup>[</sup>\n##UREF##8##\n21\n##\n<sup>]</sup> The elevated adsorbed oxygen: lattice oxygen ratio following reduction indicates a higher concentration of oxygen vacancies in the Ru@Ru‐SFM/Ru‐GDC electrocatalyst compared to Ru‐SFM/Ru‐GDC (Table ##SUPPL##0##S1##, Supporting Information). Furthermore, electron paramagnetic resonance (EPR) analysis reveals a heightened peak intensity for Ru@Ru‐SFM/Ru‐GDC (Figure ##FIG##2##3f##), also indicating a greater abundance of oxygen vacancies than in Ru‐SFM/Ru‐GDC.<sup>[</sup>\n##UREF##9##\n22\n##\n<sup>]</sup> The created oxygen vacancies facilitate rapid oxygen mobility and contribute to the oxidative conversion of hydrocarbons.<sup>[</sup>\n##REF##37399582##\n23\n##\n<sup>]</sup> Remarkably, the structure change is reversible during redox cycles. As confirmed by XRD, SEM, and XPS (Figures ##SUPPL##0##S4##–##SUPPL##0##S6## and Table ##SUPPL##0##S2##, Supporting Information), the exsolved Ru nanoparticels are redissolved into Ru‐SFM/Ru‐GDC lattice after reoxidation, and Ru nanoparticels can be exsolved again after rereduction (Figures ##SUPPL##0##S7##–##SUPPL##0##S9## and Table ##SUPPL##0##S2##, Supporting Information). Such good reversibility of exsolution/dissolution suggests the structural flexibility of dual‐exsolved self‐assembled electrocatalyst.</p>", "<title>Enhanced Electrochemical Performance</title>", "<p>Electrochemical impedance spectra (EIS) of anodes were examined using symmetric cells (Figure ##SUPPL##0##S10##, Supporting Information) at 800 °C in 5% H<sub>2</sub>‐Ar atmosphere, to comprehend the impact of Ru dual‐exsolution on electrochemical processes. As shown in Figure ##SUPPL##0##S11##, Supporting Information, the Ru@Ru‐SFM/Ru‐GDC anode exhibits smaller polarization resistances (<italic toggle=\"yes\">R</italic>\n<sub>p</sub>) and lower activation energy compared to the SFM/GDC anode. This suggests an accelerated reaction kinetics for H<sub>2</sub> oxidation after dual‐exsolution. Furthermore, distribution of relaxation time (DRT) analysis exhibits that the impedance spectra consist of distinct high‐frequency polarization (HF), medium‐frequency polarization (MF), and low‐frequency polarization (LF) arcs, corresponding respectively to charge transfer, ion surface exchange and transmission, and gas absorption/desorption processes.<sup>[</sup>\n##UREF##10##\n24\n##\n<sup>]</sup> Both LF‐R<sub>p</sub> and MF‐R<sub>p</sub> significantly decreases, implying that the ion surface exchange and transmission, and gas absorption/desorption are accelerated by dual‐exsolution of metallic Ru.</p>", "<p>To evaluate the practical viability of the Ru@Ru‐SFM/Ru‐GDC electrocatalyst as a potential anode for SOFCs, single SOFCs with an asymmetric architecture of porous Ru@Ru‐SFM/Ru‐GDC (anode) || dense LSGM (electrolyte) || porous PBSCF/GDC (cathode) were prepared (<bold>Figure</bold> ##FIG##3##\n4a##). For comparison, SOFCs employing a SFM/GDC anode were also investigated. The compositional purities of the synthetic LSGM electrolyte and PBSCF/GDC composite cathode are confirmed by XRD analysis (Figure ##SUPPL##0##S12##, Supporting Information). As depicted in Figure ##FIG##3##4b##, the Ru@Ru‐SFM/Ru‐GDC anode, ≈23 µm in thickness, and the PBSCF/GDC cathode, ≈23 µm in thickness, are both screen‐printed on opposing sides of a ≈230 µm thick LSGM electrolyte. Remarkably, using the smart self‐assembly approach results in the fabrication of a submicron‐structured Ru‐SFM/Ru‐GDC skeleton (Figure ##FIG##3##4c##). The following in situ dual‐exsolution of nanoscale metallic Ru onto such submicron skeleton yields a hierarchical anode structure characterized by abundant heterointerfaces conducive to electrocatalytic activity. According to BET analyses (Table ##SUPPL##0##S3##, Supporting Information), the dual‐exsolved Ru‐SFM/Ru‐GDC anode exhibits a higher surface area of 8.80 m<sup>2</sup> g<sup>−1</sup> than that of unexsolved SFM/GDC anode (6.38 m<sup>2</sup> g<sup>−1</sup>). Additionally, the robust contact in the interface of electrolyte and anode ensures high structural stability and rapid ion transport.</p>", "<p>Using humidified H<sub>2</sub> (≈3% H<sub>2</sub>O) as the fuel, the peak power densities (PPD) of 0.65, 0.34, and 0.16 W cm<sup>−2</sup> are achieved on the SFM/GDC single cell at operating temperatures of 800, 750, and 700 °C (<bold>Figure</bold> ##FIG##4##\n5a##). In contrast, the Ru@Ru‐SFM/Ru‐GDC single cell exhibits superior performance, with PPD values of 1.03, 0.71, and 0.44 W cm<sup>−2</sup> at 800, 750, and 700 °C (Figure ##FIG##4##5b##), respectively. This enhanced performance of the Ru@Ru‐SFM/Ru‐GDC single cell can be primarily attributed to its lower polarization resistance (<italic toggle=\"yes\">R</italic>\n<sub>p</sub>) compared to the SFM/GDC single cell (0.073 vs. 0.134 Ω cm<sup>2</sup> at 800 °C), as demonstrated in Figure ##FIG##4##5c,d##. In view of almost the same electrolyte and cathode materials, the reduced R<sub>p</sub> indicates that the anodic reaction kinetics associated with H<sub>2</sub> oxidation is significantly enhanced by dual‐exsolution, in line with the results of symmetrical cells. In addition, compared to single cells using other high performing perovskite anodes, the PPD of the single cell featuring the Ru@Ru‐SFM/Ru‐GDC anode surpasses most of the reported ones (Table ##SUPPL##0##S4##, Supporting Information).</p>", "<p>When transitioning to the direct utilization of humidified CH<sub>4</sub> (≈3% H<sub>2</sub>O), the PPD of the SFM/GDC single cell is 0.32 W cm<sup>−2</sup> at 800 °C (<bold>Figure</bold> ##FIG##5##\n6a##), while the Ru@Ru‐SFM/Ru‐GDC single cell achieves a higher PPD of 0.63 W cm<sup>−2</sup> at the same temperature (Figure ##FIG##5##6b##). The R<sub>p</sub> of the Ru@Ru‐SFM/Ru‐GDC single cell (0.22 Ω cm<sup>2</sup> at 800 °C) is remarkably lower than that of the SFM/GDC single cell (0.58 Ω cm<sup>2</sup> at 800 °C) (Figure ##FIG##5##6c##), denoting that the Ru@Ru‐SFM/Ru‐GDC anode offers a much higher electrocatalytic activity toward CH<sub>4</sub> conversion. According to DRT analysis, three characteristic peaks in the HF, MF, and LF ranges are identified (Figure ##FIG##5##6d##). Among them, the LF‐R<sub>p</sub> is dramatically reduced, indicative of the significantly enhanced CH<sub>4</sub> absorption/dissociation kinetics after Ru dual‐exsolution.<sup>[</sup>\n##UREF##17##\n33\n##\n<sup>]</sup>\n</p>", "<title>Carbon Deposition Tolerance</title>", "<p>The galvanostatic test of the Ru@Ru‐SFM/Ru‐GDC anode based single cell was conducted at 800 °C, applying a constant current density of 1.0 A cm<sup>−2</sup>. As depicted in Figure ##FIG##5##6e##, the cell voltage remains consistently stable at ≈0.59 V for 200 h. Of note, the PPD and durability of the CH<sub>4</sub> fueled single cell using the Ru@Ru‐SFM/Ru‐GDC anode favorably rival most of previously reported perovskite anodes, as illustrated in Figure ##FIG##5##6f## and Table ##SUPPL##0##S5## (Supporting Information). No Raman carbon peaks, including the D‐band at 1357 cm<sup>−1</sup> and G‐band at 1585 cm<sup>−1</sup>, are detected on the Ru@Ru‐SFM/Ru‐GDC anode after the extensive long‐term stability test (<bold>Figure</bold> ##FIG##6##\n7a##), demonstrating the exceptional resistance of the Ru@Ru‐SFM/Ru‐GDC anode to carbon deposition during CH<sub>4</sub> exposure. Moreover, the original phase structure of the Ru@Ru‐SFM/Ru‐GDC anode is almost not changed after long‐term CH<sub>4</sub> operation, as shown in Figure ##FIG##6##7b##. XPS analyses in Figure ##FIG##6##7c## and Figure ##SUPPL##0##S13## (Supporting Information), confirm the consistent existence of metallic Ru within the Ru@Ru‐SFM/Ru‐GDC anode.</p>", "<p>In addition, the morphology of the Ru@Ru‐SFM/Ru‐GDC anode after long‐term durability test was investigated by SEM and TEM. This self‐assembled anode retains its highly porous submicron structure without the presence of discernible carbon deposits (Figure ##FIG##6##7d##). It is worth noting that the exsolved nanoparticles firmly anchor onto the Ru‐SFM/Ru‐GDC substrate without agglomeration, as shown in Figure ##FIG##6##7e,f##. These findings indicate that the nano‐heterointerfaces in the Ru@Ru‐SFM/Ru‐GDC anode maintain excellent structural stability throughout CH<sub>4</sub> operation, likely owing to the strong metal‐support interaction created by the exsolution approach.<sup>[</sup>\n##UREF##15##\n31\n##\n<sup>]</sup>\n</p>", "<title>Mechanism of CH<sub>4</sub> Conversion</title>", "<p>Experimental characterizations have substantiated the occurrence of dual exsolution, resulting in the formation of Ru@Ru‐SFM and Ru@Ru‐GDC heterointerfaces, which significantly improve the activity of CH<sub>4</sub> conversion. Consequently, we conducted density functional theory (DFT) calculations to elucidate the underlying mechanism governing CH<sub>4</sub> conversion over dual‐exsolved heterointerfaces. Theoretical modes of pristine SFM (001), Ru cluster@Ru‐SFM (001), and Ru cluster@Ru‐GDC (111) are built, as depicted in <bold>Figure</bold> ##FIG##7##\n8a–c##, respectively. A widely accepted pathway and corresponding free energy profiles of CH<sub>4</sub> conversion are illustrated in Figure ##FIG##7##8d##.<sup>[</sup>\n##UREF##18##\n34\n##\n<sup>]</sup> The relevant reaction intermediates adsorbed on SFM, Ru@Ru‐SFM, and Ru@Ru‐GDC are respectively depicted in Figures ##SUPPL##0##S14##–##SUPPL##0##S16## (Supporting Information). These calculations conclusively establish that the CH<sub>4</sub> activation as the formation of CH<sub>3</sub>* is the rate‐determining step. Existing literatures had also corroborated that the initial dehydrogenation process was mainly the rate determining step for hydrocarbon conversion.<sup>[</sup>\n##REF##37399582##\n23\n##, ##UREF##11##\n25\n##\n<sup>]</sup> Afterward, the CH<sub>4</sub> conversion process shows a downhill energy trend. It is evident that the calculated energy barriers of Ru@Ru‐SFM (0.22 eV), and Ru@Ru‐GDC (0.40 eV) heterointerfaces are lower than that of pristine SFM (0.52 eV), endowing them with higher intrinsic activities toward CH<sub>4</sub> conversion.</p>", "<p>Figure ##FIG##7##8e## provides the calculated partial density of states (DOS) of SFM, Ru@Ru‐SFM, and Ru@Ru‐GDC. One can see that the specific orbital contributions of Ru@Ru‐SFM, and Ru@Ru‐GDC heterointerfaces around the Fermi level are richer than that of pristine SFM. Compared with the pristine SFM, the Ru@Ru‐SFM, and Ru@Ru‐GDC heterointerfaces substantially facilitate the CH<sub>4</sub> adsorption/activation by effectively weakening the C−H bond,<sup>[</sup>\n##REF##37399582##\n23\n##\n<sup>]</sup> promoting the activities toward CH<sub>4</sub> conversion. Moreover, it has been revealed that the synergistic effect of Lewis acid (perovskite oxide) and Lewis base (exsolved metal) contributes to CH<sub>4</sub> dehydrogenation process.<sup>[</sup>\n##REF##35638132##\n35\n##\n<sup>]</sup> Herein, the Lewis acid‐Lewis base pairs of exsolved Ru@Ru‐SFM perovskite oxide and exsolved Ru@Ru‐GDC fluorite oxide<sup>[</sup>\n##REF##29482317##\n36\n##\n<sup>]</sup> follow the same mechanism.</p>", "<p>Beyond high intrinsic activities of heterointerfaces, the Ru@Ru‐SFM/GDC anode, prepared by an integrated approach combining self‐assembly and dual‐exsolution, exhibits a nano@submicron hierarchical structure, ensuring a high density of heterointerfaces. Furthermore, the introduction of GDC can enhance the oxygen ionic conductivity of the anode, significantly expanding the electrochemical active area from the anode/electrolyte near‐interface to the anode bulk.<sup>[</sup>\n##UREF##19##\n37\n##\n<sup>]</sup> This combination of high intrinsic activity, high density of active sites, and high oxygen ionic conduction establishes Ru@Ru‐SFM/Ru‐GDC as a prominent anode material with outstanding electrochemical performance for CH<sub>4</sub> fueled SOFCs.</p>" ]
[ "<title>Conclusion</title>", "<p>In summary, we have developed a novel Ru@Ru‐SFM/Ru‐GDC anode of SOFCs by a dual‐exsolution and self‐assembly approach, which delivers remarkable activity for CH<sub>4</sub> conversion and high tolerance to carbon deposition. The Ru@Ru‐SFM/Ru‐GDC anode based single cell delivers a high peak power density of 0.63 W cm<sup>−2</sup> at 800 °C and a remarkable durability for 200 h with humidified CH<sub>4</sub> as fuel, favorably rivalling most reported perovskite‐based anodes for CH<sub>4</sub> fueled SOFCs. Experimental findings and DFT calculations reveal that the high electrochemical performance is primarily attributed to the unique hierarchical architecture with high oxygen ionic conduction, rich heterointerfaces and high intrinsic activity with low energy barrier for CH<sub>4</sub> conversion. The innovative integration of self‐assembly and dual exsolution in the Ru@Ru‐SFM/Ru‐GDC anode offers a promising solution for high‐performance hydrocarbon fueled SOFCs, which might also guide the design of heterointerfaces for various electrocatalysis.</p>" ]
[ "<title>Abstract</title>", "<p>Perovskite oxides have emerged as alternative anode materials for hydrocarbon‐fueled solid oxide fuel cells (SOFCs). Nevertheless, the sluggish kinetics for hydrocarbon conversion hinder their commercial applications. Herein, a novel dual‐exsolved self‐assembled anode for CH<sub>4</sub>‐fueled SOFCs is developed. The designed Ru@Ru‐Sr<sub>2</sub>Fe<sub>1.5</sub>Mo<sub>0.5</sub>O<sub>6‐δ</sub>(SFM)/Ru‐Gd<sub>0.1</sub>Ce<sub>0.9</sub>O<sub>2‐δ</sub>(GDC) anode exhibits a unique hierarchical structure of nano‐heterointerfaces exsolved on submicron skeletons. As a result, the Ru@Ru‐SFM/Ru‐GDC anode‐based single cell achieves high peak power densities of 1.03 and 0.63 W cm<sup>−2</sup> at 800 °C under humidified H<sub>2</sub> and CH<sub>4</sub>, surpassing most reported perovskite‐based anodes. Moreover, this anode demonstrates negligible degradation over 200 h in humidified CH<sub>4</sub>, indicating high resistance to carbon deposition. Density functional theory calculations reveal that the created metal‐oxide heterointerfaces of Ru@Ru‐SFM and Ru@Ru‐GDC have higher intrinsic activities for CH<sub>4</sub> conversion compared to pristine SFM. These findings highlight a viable design of the dual‐exsolved self‐assembled anode for efficient and robust hydrocarbon‐fueled SOFCs.</p>", "<p>To achieve efficient and robust CH<sub>4</sub> fueled solid oxide fuel cells, a hierarchical Ru@Ru‐Sr<sub>2</sub>Fe<sub>1.5</sub>Mo<sub>0.5</sub>O<sub>6‐δ</sub> (SFM)/Ru‐Gd<sub>0.1</sub>Ce<sub>0.9</sub>O<sub>2‐δ</sub> (GDC) anode is developed by an innovative integration of self‐assembly and dual exsolution. The single cell using this anode delivers a high peak power density of 0.63 W cm<sup>−2</sup> at 800 °C and a remarkable stability for 200 h using humidified CH<sub>4</sub> as fuel.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6888-cit-0071\">\n<string-name>\n<given-names>F.</given-names>\n<surname>Hu</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Ling</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Huang</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Zhao</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Gui</surname>\n</string-name>, <string-name>\n<given-names>B.</given-names>\n<surname>He</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Zhao</surname>\n</string-name>, <article-title>Smart Dual‐Exsolved Self‐Assembled Anode Enables Efficient and Robust Methane‐Fueled Solid Oxide Fuel Cells</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2306845</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202306845</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Powder Preparation</title>", "<p>The raw materials were analytically pure and were purchased by Sinopharm Chemical Reagent Co., Ltd. Ru@Ru‐Sr<sub>2</sub>Fe<sub>1.5</sub>Mo<sub>0.5</sub>O<sub>6‐δ</sub>(SFM)/Ru‐Gd<sub>0.1</sub>Ce<sub>0.9</sub>O<sub>2‐δ</sub>(GDC) anode was prepared by an elegant one‐pot self‐assembly approach. The molar doping levels of pretailored Ru in SFM and GDC were 10% and 5%, respectively. The mass ratio of Ru‐SFM: Ru‐GDC was ≈6:4. Citric acid monohydrate and glycolic acid as complexing agents were first introduced into deionized water, followed by introducing stoichiometric quantities of Sr(NO<sub>3</sub>)<sub>2</sub>, Fe(NO<sub>3</sub>)<sub>3</sub>•9H<sub>2</sub>O, (NH<sub>4</sub>)<sub>6</sub>Mo<sub>7</sub>O<sub>24</sub>•4H<sub>2</sub>O, Gd(NO<sub>3</sub>)<sub>3</sub>•6H<sub>2</sub>O, Ce(NO<sub>3</sub>)<sub>3</sub>•6H<sub>2</sub>O, and Ru(NO<sub>3</sub>)•xH<sub>2</sub>O. The obtained homogeneous precursor solution was stirred continuously at ≈80 °C for 3 h to generate a viscous gel. The gel was then heat‐treated at 300 °C for 1 h in an oven to obtain a spongy powder. Such precursor was calcined in air at 1100 °C for 3 h to acquire the self‐assembled Ru‐SFM/Ru‐GDC composite anode. The dual‐exsolved self‐assembled Ru@Ru‐SFM/Ru‐GDC composite anode was in situ created via the emergence of Ru metal nanoparticles on the surface of Ru‐SFM/Ru‐GDC substrate during H<sub>2</sub> or CH<sub>4</sub> fuel cell operation at high temperatures. Additionally, La<sub>0.8</sub>Sr<sub>0.2</sub>Ga<sub>0.8</sub>Mg<sub>0.2</sub>O<sub>3‐δ</sub> (LSGM) electrolyte, PrBa<sub>0.5</sub>Sr<sub>0.5</sub>Co<sub>1.5</sub>Fe<sub>0.5</sub>O<sub>5+δ</sub> (PBSCF)/GDC cathode, and compared SFM/GDC anode were prepared using the similar one‐pot method.</p>", "<title>Cell Fabrication and Measurement</title>", "<p>Electrolyte‐supporting single cell with a sandwich structure of Ru‐SFM/Ru‐GDC anode || LSGM electrolyte || PBSCF/GDC cathode was fabricated. The LSGM disk was prepared by dry‐pressing and sintering at 1400 °C for 5 h in air, with the thickness of ≈230 µm for the single cell. The anode and cathode inks were separately obtained by dispersing terpineol solution with the respective powders (anode and cathode) at a mass ratio of 1:2. The inks were screen‐printed on opposing sides of the LSGM electrolyte, followed by calcination at 1050 °C for 3 h to fabricate the Ru‐SFM/Ru‐GDC || LSGM || PBSCF/GDC single cell. Ag paste was uniformly applied on the anode and cathode as the current collector. Glass ceramics was applied as the sealing material to prevent gas leakage.</p>", "<p>The Ru‐SFM/Ru‐GDC anode was in situ reduced at 800 °C during SOFC operation in H<sub>2</sub> or CH<sub>4</sub> atmosphere. During fuel cell operation, humidified (3% H<sub>2</sub>O) with H<sub>2</sub> or CH<sub>4</sub> was fed to the anode at 20 mL min<sup>−1</sup>, while the PBSCF/GDC cathode was exposed to static air. Electrochemical measurements of the single cells were conducted from 800, 750, and 700 °C, including current–voltage and power density curves, along with electrochemical impedance spectroscopy (EIS) in a 1 MHz to 0.1 Hz frequency range. The distribution of relaxation time (DRT) method was utilized to fit the EIS data. Stability testing of the fuel cell was performed at a constant current density of 1.0 A cm<sup>−2</sup> and 800 °C using the humidified CH<sub>4</sub> as the fuel.</p>", "<title>Materials Characterization</title>", "<p>X‐ray diffraction (XRD, Bruker D8‐Focus) was used to determine the phase structures of the as‐prepared powders. Morphology of powders and single cell were conducted by scanning electron microscopy (SEM, Hitachi SU‐8010), high‐resolution transmission electron microscopy (HRTEM, Titan G260‐300). X‐ray photoelectron spectroscopy (XPS, Kratos Axis Ultra DLD) using an Al Kα X‐ray source was applied to analyze the surface chemical states, with the C 1s peak at 284.8 eV as a calibration standard. Electron paramagnetic resonance (EPR, Bruker‐A300) was used to assess the oxygen vacancy concentration. Temperature‐programmed reduction of H<sub>2</sub> (H<sub>2</sub>‐TPR) profiles was recorded on a Micromeritics Chemisorption Analyzer (Auto Chem II 2920) over room temperature to 900 °C. Raman spectra were collected by Alpha 300‐R Raman spectrometer in the range of 1000–2000 cm<sup>−1</sup>. Specific surface areas of Ru@Ru‐SFM/Ru‐GDC and SFM/GDC anodes were analyzed by Barrette–Emmett–Teller (BET) with the apparatus of ASAP 2020HD88.</p>", "<title>Theoretical Calculation</title>", "<p>The Vienna Ab Initio Simulation Package (VASP)<sup>[</sup>\n##REF##36546885##\n1\n##\n<sup>]</sup> was used to perform density functional theory (DFT) calculations within the generalized gradient approximation (GGA‐PBE) formalism.<sup>[</sup>\n##UREF##0##\n2\n##\n<sup>]</sup> The projected augmented wave (PAW) method<sup>[</sup>\n##REF##36440888##\n3\n##\n<sup>]</sup> described ionic cores and valence electrons using a plane wave basis set with a 450 eV kinetic energy cutoff. Partial occupancies of Kohn–Sham orbitals were permitted via Gaussian smearing (width 0.05 eV). Electronic energies were considered converged below 10<sup>−5</sup> eV changes. Geometry optimizations were deemed complete when forces were below 0.05 eV Å<sup>−1</sup>. Grimme's DFT‐D3 methodology accounted for dispersion interactions. The gamma point sampled the Brillouin zone during structural optimizations, with bottom atomic layers fixed and the remainder relaxed. SFM (001) surface, Ru cluster@Ni‐SFM (001) and Ru cluster@Ni‐GDC (111) were built for CH<sub>4</sub> conversion, respectively. The free energy of a gas phase molecule or an adsorbate on the surface was calculated by the equation <italic toggle=\"yes\">G</italic> = <italic toggle=\"yes\">\n<underline underline-style=\"single\">E</underline>\n</italic> + ZPE − TS, where <italic toggle=\"yes\">E</italic> is the total energy, ZPE is the zero‐point energy, <italic toggle=\"yes\">T</italic> is the temperature in kelvin (298.15 K is set here), and <italic toggle=\"yes\">S</italic> is the entropy. The standard hydrogen electrode (SHE) model<sup>[</sup>\n##UREF##1##\n4\n##\n<sup>]</sup> was adopted in the calculations of Gibbs free energy changes (Δ<italic toggle=\"yes\">G</italic>) of all reaction steps, which was used to evaluate the reaction barrier.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was supported by the financial support from the National Natural Science Foundation of China (No. 22075256 and No. 21975229), the Natural Science Foundation of Zhejiang Province (No. LY23E020004 and No. LY23B030004), and the Shenzhen Science and Technology Program (No. JCYJ20220530162403008).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6888-fig-0001\"><label>Figure 1</label><caption><p>a) Schematic illustration of structure evolution of dual‐exsolved self‐assembled Ru@Ru‐SFM/Ru‐GDC electrocatalyst, b) powder XRD patterns of SFM/GDC, Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts, SEM images of c) Ru‐SFM/Ru‐GDC and d) Ru@Ru‐SFM/Ru‐GDC electrocatalysts.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6888-fig-0002\"><label>Figure 2</label><caption><p>a) HRTEM image of total Ru@Ru‐SFM/Ru‐GDC electrocatalyst, b) selected Ru@Ru‐SFM particle, c) selected Ru@Ru‐GDC particle, EDS mapping of d) selected Ru@Ru‐SFM particle, e) selected Ru@Ru‐GDC particle.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6888-fig-0003\"><label>Figure 3</label><caption><p>XPS spectra of a) Ru 3p, b) Fe 2p, c) Mo 3d, d) Ce 3d, e) O 1s, and f) EPR spectra of Ru‐SFM/Ru‐GDC and Ru@Ru‐SFM/Ru‐GDC electrocatalysts.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6888-fig-0004\"><label>Figure 4</label><caption><p>a) Schematic diagram illustrating H<sub>2</sub> or CH<sub>4</sub> fueled SOFCs, SEM cross‐sectional views of b) electrolyte supported single cell and c) Ru@Ru‐SFM/Ru‐GDC anode.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6888-fig-0005\"><label>Figure 5</label><caption><p>I−V and I−P curves of the H<sub>2</sub> fueled single cells using a) SFM/GDC anode and b) Ru@Ru‐SFM/Ru‐GDC anode, EIS curves of the H<sub>2</sub> fueled single cells using c) SFM/GDC anode and d) Ru@Ru‐SFM/Ru‐GDC anode.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6888-fig-0006\"><label>Figure 6</label><caption><p>\n<italic toggle=\"yes\">I−V</italic> and <italic toggle=\"yes\">I−P</italic> curves of the CH<sub>4</sub> fueled single cells using a) SFM/GDC anode and b) Ru@Ru‐SFM/Ru‐GDC anode, c) EIS curves and d) DRT analysis, e) cell potential as function of elapsed time for the Ru@Ru‐SFM/Ru‐GDC single cell, f) comparison of the peak power densities of CH<sub>4</sub> fueled single cells (Sr<sub>2</sub>Fe<sub>1.5</sub>Mo<sub>0.5</sub>O<sub>6–δ</sub> (SFM),<sup>[</sup>\n##REF##20941791##\n9a\n##\n<sup>]</sup> Sr<sub>2</sub>ZnMoO (R‐SZMO),<sup>[</sup>\n##UREF##11##\n25\n##\n<sup>]</sup> Co@Sr<sub>2</sub>Fe<sub>1.3</sub>Co<sub>0.2</sub>Mo<sub>0.5</sub>O<sub>6‐δ</sub> (Co@SFCM),<sup>[</sup>\n##UREF##12##\n26\n##\n<sup>]</sup> CoNiMo/Sr<sub>2</sub>FeMoO<sub>6–δ</sub> (CNM/SFM),<sup>[</sup>\n##UREF##13##\n27\n##\n<sup>]</sup> CoFe@La<sub>0.5</sub>Ba<sub>0.5</sub>Mn<sub>0.8</sub>Fe<sub>0.1</sub>Co<sub>0.1</sub>O<sub>3‐δ</sub> (CoFe@LBMFC),<sup>[</sup>\n##REF##30668911##\n28\n##\n<sup>]</sup> Pr<sub>6</sub>O<sub>11</sub>‐PrBaMn<sub>2</sub>O<sub>5+δ</sub> (Pr‐PBMO),<sup>[</sup>\n##UREF##14##\n29\n##\n<sup>]</sup> Ni@La<sub>0.4</sub>Sr<sub>0.4</sub>Ti<sub>0.85</sub>Ru<sub>0.07</sub>Ni<sub>0.08</sub>O<sub>3−δ</sub> ([email protected]),<sup>[</sup>\n##REF##36106728##\n30\n##\n<sup>]</sup> Ni@(La<sub>0.2</sub>Sr<sub>0.8</sub>)<sub>0.925</sub>Ti<sub>0.55</sub>Mn<sub>0.35</sub>Ni<sub>0.1</sub>O<sub>3‐δ</sub> (Ni@LSTMN),<sup>[</sup>\n##UREF##15##\n31\n##\n<sup>]</sup> NiFe@La<sub>0.6</sub>Ce<sub>0.1</sub>Sr<sub>0.3</sub>Fe<sub>0.9</sub>Ni<sub>0.1</sub>O<sub>3‐δ</sub> (NiFe@CLSFNi),<sup>[</sup>\n##UREF##16##\n32\n##\n<sup>]</sup> FeCoNiCuAl‐Sm<sub>0.2</sub>Ce<sub>0.8</sub>O<sub>2</sub> (FeCoNiCuAl‐SDC)<sup>[</sup>\n##UREF##17##\n33\n##\n<sup>]</sup>).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6888-fig-0007\"><label>Figure 7</label><caption><p>a) Raman spectrum, b) XRD pattern, c) XPS Ru 3p spectrum, d) SEM image, TEM images of e) selected Ru@Ru‐SFM particle and f) selected Ru@Ru‐GDC particle for the Ru@Ru‐SFM/Ru‐GDC anode after long‐term durability testing.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6888-fig-0008\"><label>Figure 8</label><caption><p>Theoretical modes of pristine a) SFM, b) Ru@Ru‐SFM, and c) Ru@Ru‐GDC, d) free‐energy profiles of CH<sub>4</sub> conversion, e) density of states for SFM, Ru@Ru‐SFM, and Ru@Ru‐GDC.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6888-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2306845-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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Energy"], "year": ["2018"], "volume": ["3"], "fpage": ["1042"]}, {"label": ["37"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n"], "given-names": ["Y. L.", "B. B.", "Z. Y.", "H. J. M.", "C. R."], "surname": ["Wang", "Hu", "Zhu", "Bouwmeester", "Xia"], "source": ["J. Mater. Chem. A"], "year": ["2014"], "volume": ["2"], "fpage": ["136"]}]
{ "acronym": [], "definition": [] }
37
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 20; 11(2):2306845
oa_package/0f/04/PMC10787062.tar.gz
PMC10787063
37847914
[ "<title>Introduction</title>", "<p>Nature has long served as a model template for the design of many man‐made products and technologies. For instance, marine animals possess a sensory system that has been highly optimized over millions of years of evolution, allowing them to display remarkable survival hydrodynamics.<sup>[</sup>\n##UREF##0##\n1\n##\n<sup>]</sup> Given the fact that most marine animals inhabit conditions comprising murky waters, the presence of sensory organs finely attuned to the tiniest of flow disturbances (often on the order of µm s<sup>−1</sup>) allows them to perform impressive tasks such as hunting prey, escaping from predators, and schooling in synchronization as part of a group in low visibility conditions. The study of the sensory biology of such organisms can inspire elegant solutions for engineering problems. For instance, the lateral line organ of fish, consisting of an array of hair‐like microstructures both on the skin (‘superficial neuromasts’) and under the skin (‘canal neuromasts’), is responsible for helping fish sense flow velocities as low as 18–38 µm s<sup>−1</sup> in the frequency range of 10–20 Hz.<sup>[</sup>\n##REF##567787##\n2\n##, ##UREF##1##\n3\n##\n<sup>]</sup> These neuromast sensors enable the fish to detect objects in their vicinity and effectively map their hydrodynamic surroundings.<sup>[</sup>\n##UREF##2##\n4\n##\n<sup>]</sup> Similarly, crocodiles possess an array of dome‐shaped pressure receptors on their face that are highly sensitive to waves on the water surface (force sensing thresholds ≈0.08 mN and displacements ≈3.9 µm<sup>[</sup>\n##REF##23136155##\n5\n##\n<sup>]</sup>), allowing them to detect tiny stimuli, e.g. generated by a single water droplet, without the use of vision or audition.<sup>[</sup>\n##REF##12015589##\n6\n##\n<sup>]</sup> Finally, seals, the focus of this paper, possess an exquisite capability of long‐distance prey tracking as we will detail.</p>", "<p>In their seminal behavioral experiments performed two decades ago, Dehnhardt et al.<sup>[</sup>\n##REF##11441183##\n7\n##\n<sup>]</sup> showed that harbor seals (with no visual or auditory cues) were able to follow the hydrodynamic trail of a robotic submarine even when the submarine had a 20 second head start. Using their results, Dehnhardt et al.<sup>[</sup>\n##REF##11441183##\n7\n##\n<sup>]</sup> estimated that the seal might be able to track herring swimming up to 180 m away, if the background noise from the surroundings and the aging of the fish trail were assumed to be negligible. Such an impressive ability is made possible by the whiskers on the seal's snout that function not only as active touch receptors but also as ultrasensitive flow sensors, displaying a flow sensing threshold as low as 0.25 mm s<sup>−1</sup> at a stimulus frequency of 50 Hz.<sup>[</sup>\n##UREF##3##\n8\n##\n<sup>]</sup> Owing to the highly innervated whisker follicles,<sup>[</sup>\n##UREF##4##\n9\n##\n<sup>]</sup> seals are able to detect the flow signatures in the wake of prey that swim ahead of them, even when the prey has swum by several seconds before (<bold>Figure</bold> ##FIG##0##\n1a##). In addition to the high innervation density, several seal species of the <italic toggle=\"yes\">Phocidae</italic> family, such as the harbor seal (<italic toggle=\"yes\">Phoca vitulina</italic>, Figure ##FIG##0##1b##), grey seal (<italic toggle=\"yes\">Halichoerus grypus</italic>, Figure ##FIG##0##1c##), harp seal (<italic toggle=\"yes\">Pagophilus groenlandicus</italic>), ringed seal (<italic toggle=\"yes\">Pusa hispida</italic>), and spotted seal (<italic toggle=\"yes\">Phoca largha</italic>),<sup>[</sup>\n##UREF##5##\n10\n##\n<sup>]</sup> display undulations along the length of their whiskers (Figure ##FIG##0##1d##) that are believed to play a major role in their exceptional hydrodynamic trail tracking capabilities.</p>", "<p>Seals swim at speeds on the order of ≈1.3 m s<sup>−1[</sup>\n##REF##17766306##\n11\n##\n<sup>]</sup> (Re ≈ 1460 assuming a characteristic dimension of 1 mm for the whisker) and are capable of detecting flow disturbances lower than 1 mm s<sup>−1</sup>.<sup>[</sup>\n##UREF##6##\n12\n##\n<sup>]</sup> This exquisite ability to sense perturbances up to 1000× lower than the seal's swimming speed implies that the whisker must first be able to minimize any vibrations (‘noise’) induced by its own swimming to be able to make itself sensitive to the vortices (‘signal’) left behind in the wake of its prey. A common source of noise for high‐aspect ratio bluff bodies (such as seal whiskers) placed in a uniform flow is the transverse vibration induced by a flow instability in the wake forming behind the body due to flow separation at the sharp curves of the bluff body. The flow instability gives rise to alternating sign vortices on either side of the structure that excite the structure at the same frequency as that of the vortex shedding, causing what is commonly termed as vortex‐induced vibration (VIV). It has been postulated that the undulating geometry of seal whiskers (essentially a tapered cantilever beam having an elliptical cross‐section with periodically varying major and minor axes) is responsible for VIV suppression, allowing the whiskers to experience a significantly high signal‐to‐noise ratio (SNR) in their function as flow sensors.</p>", "<p>The premise of biomimetic sensing is predicated upon the study of the underlying physical principles governing the exquisite sensing capabilities of animals, with a view to replicating their morphology, functionality, and performance in man‐made sensors. Unlike the well‐studied fish lateral line system mentioned earlier, the understanding of the seal whisker sensing system is relatively nascent and has thus been the focus of multidisciplinary studies over the past decade,<sup>[</sup>\n##REF##34699729##\n13\n##\n<sup>]</sup> with a particular emphasis on the effect of undulations in the whisker morphology on VIV suppression.<sup>[</sup>\n##REF##20639428##\n14\n##, ##UREF##7##\n15\n##, ##UREF##8##\n16\n##, ##UREF##9##\n17\n##\n<sup>]</sup> Due to the twin difficulties of limited access to seal whiskers and performing vibration and fluid flow measurements at the small scale of the seal whisker (cross‐sectional dimensions &lt; 1 mm), several researchers also used approaches such as physical modeling (e.g., by performing experiments on scaled‐up whisker‐like structures<sup>[</sup>\n##UREF##6##\n12\n##, ##UREF##10##\n18\n##, ##UREF##11##\n19\n##, ##UREF##12##\n20\n##\n<sup>]</sup>) and numerical modeling<sup>[</sup>\n##UREF##13##\n21\n##, ##UREF##14##\n22\n##, ##UREF##15##\n23\n##, ##REF##31342935##\n24\n##, ##UREF##16##\n25\n##\n<sup>]</sup> to study the effect of undulations on VIV. The insights gleaned from these studies can be valuable in realizing bioinspired engineering applications such as underwater flow sensing,<sup>[</sup>\n##UREF##17##\n26\n##\n<sup>]</sup> biomimetic wind turbine designs with drag force reduction,<sup>[</sup>\n##UREF##18##\n27\n##\n<sup>]</sup> and vibration‐reducing cables in offshore structures.<sup>[</sup>\n##UREF##19##\n28\n##\n<sup>]</sup> In particular, it is of great interest to understand which design parameter (or combination of parameters) of the undulating whisker geometry (Figure ##FIG##0##1e##) contributes the most to its VIV suppression, since this can have useful consequences for the biomimetic design of low‐noise underwater structures. Further, reliable and accurate knowledge of the geometric and material characteristics of seal whiskers can greatly aid in deciphering the mechanisms via which the whiskers interact with (and become sensitive to) flow vortices during hydrodynamic trail following.<sup>[</sup>\n##REF##34699729##\n13\n##\n<sup>]</sup>\n</p>", "<p>In this paper, we performed a comprehensive form‐function characterization of grey and harbor seal whiskers with respect to their morphology, material properties, and VIV response in a uniform water flow. The whisker geometry was studied using both 2D and 3D measurement techniques to quantify the undulations and taper in the whiskers. Material properties were measured using first‐of‐its‐kind nanoindentation measurements to estimate the Young's modulus and flexural rigidity of the whiskers. The internal structure of the whiskers was observed using optical and scanning electron microscopy to clearly delineate, for the first time, three different regions in the transverse cross‐section. Further, we compared the vibration characteristics of grey and harbor seal whiskers with those of a similarly‐sized circular cylinder to study the effect of undulations on VIV suppression. Microelectromechanical systems (MEMS) piezoelectric sensors and 3D‐printed piezoresistive sensors were developed to measure the VIV of the whiskers and a comparable circular cylinder in uniform water flow. Similarly, transient fluid‐structure interaction (FSI) simulations were conducted using finite element modeling (FEM) to simulate the vibration response of the whisker and the cylinder in a steady flow, representing an advancement over previous numerical approaches in the literature that only focused on modeling the fluid flow around a rigid whisker structure, neglecting its flexibility. The results of our exhaustive study indicate that the dimensionless ratio of undulation wavelength to mean whisker diameter (<italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub>) in phocid seals may have evolved to be in the optimal range of 4.4–4.6, enabling an order‐of‐magnitude reduction in vortex‐induced vibrations compared to a similarly‐shaped cylinder. This result can help explain the minimal self‐induced noise of seal whiskers that endows phocid seals with an exquisite hydrodynamic trail following capability. Our findings further highlight the importance of the dimensionless <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio in the biomimetic design of seal whisker‐inspired vibration‐resistant structures, such as marine risers, wake detection sensors for submarines, and other underwater structures prone to VIV.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Morphometrics</title>", "<p>The geometry of both the harbor and grey seal whiskers features undulations along their length. The whisker is, in essence, a tapered beam with an elliptical cross section whose major and minor axes vary periodically along its length. 2D outlines of ten harbor seal whiskers and ten grey seal whiskers, obtained after optical microscopy and image processing (<bold>Figure</bold> ##FIG##1##\n2a,b##), indicated consistent profiles in the observed length of 30 mm along both the XZ and YZ views as shown in Figure ##FIG##1##2c–f##. In general, substantial consistency was found between our geometric measurements and previous studies in the literature<sup>[</sup>\n##UREF##5##\n10\n##, ##UREF##9##\n17\n##, ##REF##28840853##\n29\n##\n<sup>]</sup> for the harbor seal whisker. Measurements of the grey seal whisker, on the other hand, were found to be much rarer, with only one study<sup>[</sup>\n##UREF##5##\n10\n##\n<sup>]</sup> that reported morphometrics. Our measurements and their comparison with the literature are summarized in <bold>Table</bold> ##TAB##0##\n1\n##.</p>", "<p>The measurements shown in Table ##TAB##0##1## only provided 2D information of the width of the whisker and neglected its thickness. To capture the 3D undulating morphology of the seal whisker from 2D measurements, Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> proposed a geometric framework comprising a total of seven parameters (<italic toggle=\"yes\">a</italic>, <italic toggle=\"yes\">b, k</italic>, <italic toggle=\"yes\">l</italic>, <italic toggle=\"yes\">M</italic>, <italic toggle=\"yes\">α</italic>, and <italic toggle=\"yes\">β</italic> as defined in Figure ##FIG##0##1e##). Here, the undulating whisker is approximated as a 3D surface that encloses two periodically recurring ellipses. The primary axis of the initial ellipse (with semi‐major axis denoted as <italic toggle=\"yes\">a</italic> and semi‐minor axis as <italic toggle=\"yes\">b</italic>) is established by connecting adjacent crests along the upper and lower profiles of the whisker. Conversely, the primary axis of the subsequent ellipse (with semi‐major axis referred to as <italic toggle=\"yes\">k</italic> and semi‐minor axis as <italic toggle=\"yes\">l</italic>) is established by connecting adjacent troughs along the upper and lower profiles of the whisker. These two ellipses exhibit inclinations (assumed to be constant in this framework) with respect to the longitudinal axis of the whisker, characterized by angles <italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic>, respectively. The alternating repetition of these ellipses (maintaining a separation distance of <italic toggle=\"yes\">M</italic>) along the longitudinal axis can be readily transformed into a 3D surface representation of the whisker using computer‐aided design (CAD) software packages. This geometric framework has been used by researchers for reporting whisker undulation measurements<sup>[</sup>\n##REF##20639428##\n14\n##, ##REF##28840853##\n29\n##\n<sup>]</sup> and to develop 3D models of the seal whisker for experimental<sup>[</sup>\n##UREF##6##\n12\n##\n<sup>]</sup> and numerical<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup> studies. Using the knowledge of the coordinates of the relevant points from microscopy and image processing, we measured <italic toggle=\"yes\">a</italic>, <italic toggle=\"yes\">k</italic>, <italic toggle=\"yes\">M</italic>, <italic toggle=\"yes\">α</italic>, and <italic toggle=\"yes\">β</italic> from the XZ view, while <italic toggle=\"yes\">b</italic> and <italic toggle=\"yes\">l</italic> were measured from the YZ view according to the definitions given in Figure ##FIG##0##1e##. <bold>Table</bold> ##TAB##1##\n2\n## lists the parameters measured in this study and compares them with the measurements of Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> (who used photogrammetry) and Rinehart et al.<sup>[</sup>\n##REF##28840853##\n29\n##\n<sup>]</sup> (who used computed tomography scanning) for harbor seal whiskers. The measured parameters for grey seal whiskers are also listed in Table ##TAB##1##2##; however, for this seal species, no corresponding studies were found in the literature for comparison.</p>", "<p>It must be noted that Hanke et al.’s framework<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> assumed constant angles of inclination (<italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic>) for the two ellipses shown in Figure ##FIG##0##1e##. In reality, however, the angles can vary over a wide range.<sup>[</sup>\n##REF##28840853##\n29\n##\n<sup>]</sup> As shown in Table ##TAB##1##2##, our <italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic> measurements yielded considerable variations for both seal species (histograms indicating the spread in <italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic> values are shown in Figure ##SUPPL##0##S1## of the Supporting Information), agreeing with Rinehart et al.’s<sup>[</sup>\n##REF##28840853##\n29\n##\n<sup>]</sup> observations. Due to the large spread in the measurements, the concept of an average <italic toggle=\"yes\">α</italic> or <italic toggle=\"yes\">β</italic> is not physically meaningful, but has nonetheless been reported in Table ##TAB##1##2## for the sake of completeness. Finally, although the dimensions of the harbor and grey seal whiskers measured in our study (Tables ##TAB##0##1## and ##TAB##1##2##) were different, with the grey seal whisker being wider and thicker than the harbor seal whisker, it is interesting to note that the ratios of wavelength (<italic toggle=\"yes\">λ</italic> ≡ 2<italic toggle=\"yes\">M</italic>) to mean diameter (<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≡ <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mfrac><mml:mrow><mml:mi>a</mml:mi><mml:mo>+</mml:mo><mml:mi>b</mml:mi><mml:mo>+</mml:mo><mml:mi>k</mml:mi><mml:mo>+</mml:mo><mml:mi>l</mml:mi></mml:mrow><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:math>) of both species of whiskers were similar, viz. <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 4.4 ± 0.7 for the harbor seal whisker and <italic toggle=\"yes\">λ</italic>/ <italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 4.6 ± 0.8 for the grey seal whisker. The implications of this ratio on the VIV suppression of whiskers will be discussed later.</p>", "<p>Although the model of Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> allows for an easy construction of a 3D model using only 2D measurements of the whisker along the XZ and YZ views, it is an idealized surface model that neglects several important geometric parameters such as the taper and curvature of whiskers which play a major role in determining their frequency response.<sup>[</sup>\n##UREF##20##\n30\n##, ##UREF##21##\n31\n##\n<sup>]</sup> To gain a more complete picture of the whisker morphometry, we also 3D‐scanned one harbor and one grey seal whisker using blue light scanning technology (<bold>Figure</bold> ##FIG##2##\n3a,b##). The resulting digital model (in the form of a .STP file) could be easily viewed in a CAD software such as Autodesk Netfabb which facilitated measurements along successive transverse cross‐sections of the whisker (Figure ##FIG##2##3c##). A video rendering of the scanned harbor and grey seal whisker models is available in the Supporting Information (Movies ##SUPPL##1##S1a## and ##SUPPL##2##S1b##, respectively), showing close‐up 3D views of the undulations along both the width and the thickness of the whiskers. Measurement planes normal to the whisker axis were defined at intervals of every 0.5 mm along the whisker length, and the major and minor axis dimensions (approximating each cross‐section as an ellipse) were measured as a function of the whisker length, allowing us to quantify the taper of the whisker. It must be noted that the major and minor axis dimensions measured in the 3D‐scanned model refer to the transverse cross‐section of the whisker normal to its axis, and are hence different from the parameters (<italic toggle=\"yes\">a</italic>, <italic toggle=\"yes\">b</italic>, <italic toggle=\"yes\">k</italic>, <italic toggle=\"yes\">l</italic>) of Hanke et al.’s<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> framework which referred to the dimensions of inclined ellipses (Figure ##FIG##0##1e##). As seen in Figure ##FIG##2##3d,e##, the semi‐major axis (i.e., half width) of both the grey and harbor seal whiskers oscillated about a mean value that remained constant (≈0.6 mm for the grey seal and ≈0.55 mm for the harbor seal whisker) for more than half the whisker length, after which it started tapering off rapidly near the whisker tip. On the other hand, the semi‐minor axis (i.e., half thickness) of both whiskers was seen to oscillate about a linearly decreasing mean value, indicating a uniform taper from the whisker base to its tip. The cross‐sectional area also showed a linear decrease from base to tip for both whiskers (Figure ##FIG##2##3d,e##). The whisker taper in both cases was thus seen to be primarily due to the linear decrease in their thickness, with little contribution from the variation in the width of the whisker. Although the 3D morphometric results presented here were obtained only from one whisker each of a harbor and a grey seal (statistical analysis of five 3D‐scanned harbor and grey seal whiskers is currently underway and will be the subject of future work), the preliminary information reported here can still be used to inform more realistic models of seal whiskers. For instance, Shatz et al.<sup>[</sup>\n##UREF##20##\n30\n##\n<sup>]</sup> calculated the fundamental frequencies of undulating harp seal whiskers by assuming them to be rectangular beams with uniformly tapering width and thickness. The accuracy of such models can be improved by using the morphometric observations from this study, e.g. that the width of the rectangular beam remains constant for over half the whisker length and only starts tapering near the tip of the whisker.</p>", "<title>Material Properties</title>", "<p>The polished transverse cross‐section of the grey seal whisker revealed an internal microstructure comprising three distinct regions distinguishable under the optical microscope (<bold>Figure</bold> ##FIG##3##\n4a,b##): the outermost cortex region resembled a smooth shell, the outer medulla appeared darker and comprised an oval region with multiple offshoots, and the inner medulla appeared at the center of the cross‐section and appeared darkest under the optical microscope. A detailed discussion on the internal structure can be found in the Supporting Information Text and Figure ##SUPPL##0##S2## (Supporting Infomation). Nanoindentation tests (Figure ##FIG##3##4c##) revealed a gradation in the Young's modulus values along the radial direction of the elliptical cross‐section. The outermost cortex region was found to be the stiffest (6.39 ± 0.46 GPa), followed by the outer medullar region (5.03 ± 0.67 GPa). The inner medullar region was almost half as stiff as the cortex (3.53 ± 1.57 GPa). Interestingly, the standard deviation in the modulus values of the inner medulla was observed to be much higher, with some tests resulting in elastic moduli as low as 0.4 GPa (near the geometric center of the cross‐section), suggesting the possibility of soft tissue in this region. Further, as seen in Figure ##FIG##3##4d##, a slight decrease in the moduli was observed for all three regions from the proximal tip to the distal tip. The average Young's modulus average exhibited a slight decrease (from 6.1 GPa at the proximal end to 5.6 GPa at the distal end) over the length of the whisker as shown in Figure ##FIG##3##4e##. The comparison of our measurements with the aforementioned literature data is summarized in <bold>Table</bold> ##TAB##2##\n3\n##. Although the spread in the reported Young's modulus values in the literature is high, this is not unexpected given the variety of methods (with their concomitant assumptions) employed in the literature, as listed in Table ##TAB##2##3##. For instance, the measurement of <italic toggle=\"yes\">E</italic> using a tensile test, implemented either using DMA<sup>[</sup>\n##REF##24871073##\n32\n##\n<sup>]</sup> or microtesting,<sup>[</sup>\n##UREF##20##\n30\n##\n<sup>]</sup> is complicated by the fact that a whisker is not shaped like a typical tensile sample, thus making it difficult to convert the measured force into stress due to the non‐uniformity of the cross‐sectional area. Similarly, point load bending<sup>[</sup>\n##UREF##21##\n31\n##\n<sup>]</sup> employed to calculate flexural rigidity (<italic toggle=\"yes\">EI</italic>) and elastic modulus (<italic toggle=\"yes\">E</italic>) is an indirect testing method entailing many assumptions (e.g., approximating the whisker geometry as cylindrical with no undulations or taper in order to use elastic beam bending theory) that can introduce errors in the measured properties. The nanoindentation technique employed in this study is a more direct measurement technique that affords higher resolution both within a cross‐section and along the whisker length. This occurs, however, at the cost of destroying the whisker sample through sectioning and polishing. Finally, we note that there also exists a wide variance in the reported Young's modulus values for the relatively more well‐studied rat whisker, with <italic toggle=\"yes\">E</italic> values ranging from 3–4 GPa<sup>[</sup>\n##REF##12878692##\n33\n##, ##REF##21993474##\n34\n##\n<sup>]</sup> to 7.36 GPa<sup>[</sup>\n##UREF##22##\n35\n##\n<sup>]</sup> in the literature.</p>", "<p>An important parameter with respect to the flow sensing performance of the whisker is its flexural rigidity (<italic toggle=\"yes\">EI</italic>), also referred to as bending stiffness. This parameter determines the whisker's bending response due to a tactile and/or hydrodynamic stimulus, and is plotted in Figure ##FIG##3##4f## as a function of distance along the whisker length (see Materials and Methods for more details). As expected, the rigidity was much lesser around the major axis owing to the elliptical shape of the whisker, allowing easier bending about the major (<italic toggle=\"yes\">XX</italic>) than the minor (<italic toggle=\"yes\">YY</italic>) axis. Interestingly, although Equation (##FORMU##1##2##) (see Experimental Section) suggests that the effective flexural rigidity (plotted in Figure ##FIG##3##4f##) contains contributions from all the three regions, viz. the cortex, outer medulla, and inner medulla, it was found that the flexural rigidity of the cortex was the major contributor (up to 98%) to the overall rigidity about the whisker major axis, suggesting that the outer and inner medullar regions did not have a significant effect on the overall bending behavior of the whisker about its major axis. The flexural rigidity about both axes decreased along the length of the whisker due to its taper. However, the decrease in <italic toggle=\"yes\">EI<sub>xx</sub>\n</italic> (indicating resistance to bending about the major axis) was more drastic, reducing by a factor of 5 within only 50% of the whisker length, than the decrease in <italic toggle=\"yes\">EI<sub>yy</sub>\n</italic> (indicating resistance to bending about the minor axis) which was more gradual in nature. The slightly lower rigidity within the initial 10 mm length of the whisker can be attributed to the fact that this portion is typically embedded within the seal muzzle and thus reinforced by the surrounding tissue and the follicle‐sinus complex.<sup>[</sup>\n##UREF##4##\n9\n##\n<sup>]</sup>\n</p>", "<p>Due to similarities in functionality and performance, seal whiskers are often compared to rat whiskers. A major difference that can be surmised from the preceding discussion is in the morphology of the two whiskers — while rat whiskers are smaller and have a conical shape (length ≈10–50 mm, base diameter ≈20–50 µm, and tip diameter ≈5 µm),<sup>[</sup>\n##REF##27260019##\n36\n##\n<sup>]</sup> (phocid) seal whiskers tend to be flattened (i.e., elliptical in cross‐section) and contain 3D undulations along their lengths. The morphological differences exist due to the differences in the nature of loading experienced by the whiskers. While rats use their whiskers for object localization and texture recognition (resulting in point loading at the whisker tip), the function of seal whiskers is geared toward both tactile sensing and hydrodynamic trail following. The latter entails a combination of two different kinds of loading on the whisker: a distributed static load caused by the drag force due to the seal's swimming velocity, and a dynamic concentrated load due to the vortices in the wake of, for instance, prey swimming ahead of it. Although no direct in situ observations of the whisker orientation have been made when the seal is in the process of hunting for prey (Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> mounted a camera on a harbor seal and observed whisker position and movement but not orientation), a whisker is often assumed to be oriented such that its angle of attack (AOA), defined as the angle between the major axis of the elliptical whisker and the velocity of the seal's swimming motion, is 0° to minimize the drag force and VIV.<sup>[</sup>\n##REF##20639428##\n14\n##, ##UREF##9##\n17\n##, ##UREF##23##\n37\n##\n<sup>]</sup> In the AOA = 0° orientation, successive vortical stimuli from the wake of the escaping prey then excite the whisker along the direction of its minor axis, causing the whisker to bend about its major (<italic toggle=\"yes\">XX</italic>) axis. Beem and Triantafyllou<sup>[</sup>\n##UREF##6##\n12\n##\n<sup>]</sup> conducted experiments to study the interactions of a scaled‐up harbor seal whisker (AOA = 0°) with a vortex generator placed upstream, and used dye visualization to observe a “slaloming” mechanism that allowed the whisker‐like structure to be locked‐in to the vortical frequency by swaying between the alternating vortices in the wake street. As the structure oscillated transversely to the forward motion, it was synchronized to first approach the closest oncoming vortex on one side and was further pulled toward it due to the low pressure associated with a vortex; then, as the whisker progressed forward, it moved sidewise approaching the next vortex on the other side, again pulled by its low‐pressure gradient, and so on. This constituted the mechanism of vibrational amplitude amplification and hence energy extraction. Such “wake‐induced vibrations (WIV)”<sup>[</sup>\n##UREF##6##\n12\n##\n<sup>]</sup> allow the seal to be attuned to the tiniest of flow disturbances while following the trail of an escaping prey, even when the prey has swum by several seconds before.<sup>[</sup>\n##REF##11441183##\n7\n##\n<sup>]</sup> Seen in the light of this discussion, we propose that the low flexural rigidity about the major axis (<italic toggle=\"yes\">EI</italic>\n<sub>xx</sub>) shown in Figure ##FIG##3##4f## imparts greater flexibility to the distal half of the whisker, allowing it to effectively slalom its way through a train of incoming vortices. The resulting WIV's are subsequently transduced into a neural signal at the highly innervated whisker base,<sup>[</sup>\n##UREF##4##\n9\n##\n<sup>]</sup> enabling the exquisite ability of the seal to sense flow disturbances up to 1000× lower than its swimming speed. The role of undulations with respect to VIV of grey and harbor seal whiskers is discussed in the next subsection.</p>", "<p>Finally, the density of the whiskers was measured as follows. Ten grey seal whiskers were weighed on a microbalance and their collective volume was subsequently noted by measuring the amount of water displaced by them. The average density (mass divided by volume) was calculated to be 1280 ± 80 kg m<sup>−3</sup> after repeating the mass and volume measurement five times.</p>", "<title>VIV Suppression due to Whisker Undulations</title>", "<p>The undulating whisker morphology of phocid seals, such as the harbor and grey seals, is believed to reduce the VIV phenomenon, resulting in lower noise in the whisker flow sensing system. Prior experiments in the literature conducted with isolated real seal whiskers have produced conflicting results, with some researchers<sup>[</sup>\n##REF##20639428##\n14\n##, ##UREF##7##\n15\n##\n<sup>]</sup> reporting VIV reduction due to the undulations while others<sup>[</sup>\n##UREF##9##\n17\n##\n<sup>]</sup> finding similar vibration behavior in structures with and without undulations. To study the effect of undulations on the VIV behavior of high‐aspect ratio bluff bodies, we compared the VIV signals of three structures: a harbor seal whisker, a grey seal whisker, and a rigid polyvinylchloride (PVC) cylinder, using a piezoelectric sensor. The material (PVC) and diameter (1 mm) of the cylinder were chosen to maintain similar flexural rigidity and Reynold's number to those of the seal whiskers (more details can be found in Materials and Methods), thus ensuring a fair comparison of VIV responses of the three structures. The seal whisker relies upon the bending moment created by flow disturbances to excite its innervated base and generate a neural signal. This mechanotransduction sensing principle was mimicked by fixing the whisker atop a PZT piezoelectric sensing membrane (<bold>Figure</bold> ##FIG##4##\n5a–c##), wherein the whisker vibrations deformed the membrane and generated a measurable electrical voltage. A piezoelectric MEMS sensor developed in our prior work<sup>[</sup>\n##UREF##24##\n38\n##, ##UREF##25##\n39\n##, ##UREF##26##\n40\n##\n<sup>]</sup> was used as the sensing base in this study due to its small size (8 mm × 8 mm) and waterproof design. The self‐powered sensor only responded to dynamic forces due to its piezoelectric sensing principle, making it ideal to measure time‐dependent VIV phenomena. The three structures, viz. the harbor seal whisker, grey seal whisker, and the PVC cylinder, were tested at a water flow speed of 0.4 m s<sup>−1</sup> (Re ≈450 calculated using a characteristic dimension of 1 mm) in a recirculating water tunnel (Figure ##FIG##4##5d##) and the AOA was maintained at 0° for the two seal whiskers. As seen from the time series data of Figure ##FIG##4##5e##, the peak‐to‐peak sensor voltage in the case of the PVC cylinder (≈0.8 V) was up to 6× higher than that of the harbor seal whisker (≈0.12 V) and up to 13× higher than that of the grey seal whisker (≈0.06 V), indicating significantly reduced vibrations for the undulating whiskers as compared to the smooth cylinder.</p>", "<p>The experiments described above represented an indirect method of deducing VIV through the piezoelectric sensor output. In order to gain more insight into the vibration response of the three structures placed in uniform water flow, an FEM model was constructed in COMSOL Multiphysics (Figure ##FIG##4##5f##). The simulation results (Figure ##FIG##4##5g##) reinforced the experimentally observed trend (Figure ##FIG##4##5e##), namely that the transverse vibration amplitudes for the cylinder were the highest, followed by the harbor and grey seal whiskers, respectively. Interestingly, both the experimental and numerical results suggested that the grey seal whiskers were able to suppress VIV better than the harbor seal whiskers at the tested flow speed. This trend of VIV response (grey seal whisker &lt; harbor seal whisker &lt; cylinder) can be understood in light of a recent study by Lyons et al.<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup> that used a factorial design of numerical experiments to perform a comprehensive study of the effect of varying geometric parameters describing the harbor seal whisker undulations on <italic toggle=\"yes\">C</italic>\n<sub>D</sub> and <italic toggle=\"yes\">C</italic>\n<sub>L</sub>. Although the researchers<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup> constructed the “baseline” harbor seal whisker geometry using an erroneous value of wavelength (see footnote to Table ##TAB##1##2##), the study nonetheless shed light on the relative importance of independent geometric parameters on the resulting VIV performance of the whisker. Lyons et al.<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup> found that the aspect ratio or slenderness (<mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>γ</mml:mi><mml:mo>:</mml:mo><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>a</mml:mi><mml:mi>cos</mml:mi><mml:mi>α</mml:mi><mml:mo>+</mml:mo><mml:mi>k</mml:mi><mml:mi>cos</mml:mi><mml:mi>β</mml:mi></mml:mrow><mml:mrow><mml:mi>b</mml:mi><mml:mo>+</mml:mo><mml:mi>l</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>), undulation wavelength (<mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>λ</mml:mi><mml:mo>:</mml:mo><mml:mo>=</mml:mo><mml:mn>2</mml:mn><mml:mi>M</mml:mi></mml:mrow></mml:mrow></mml:math>), and undulation amplitude along the width (<mml:math id=\"jats-math-5\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant=\"normal\">c</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>a</mml:mi><mml:mi>cos</mml:mi><mml:mi>α</mml:mi><mml:mo>−</mml:mo><mml:mi>k</mml:mi><mml:mi>cos</mml:mi><mml:mi>β</mml:mi><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:mrow><mml:mi>b</mml:mi><mml:mo>+</mml:mo><mml:mi>l</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>) were the (non‐dimensional) parameters that had the largest effect on <italic toggle=\"yes\">C</italic>\n<sub>L</sub> and, by extension, on VIV. The sixteen numerical experiments conducted by the researchers provided some indication of how VIV suppression capabilities can change in two undulating structures with different geometric parameters. For instance, there existed a geometry (labeled ‘EL2’<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup>) that had higher <italic toggle=\"yes\">γ</italic>, <italic toggle=\"yes\">λ</italic>, and lower <italic toggle=\"yes\">A</italic>\n<sub>C</sub> values compared to the baseline harbor seal whisker geometry and exhibited a lower <italic toggle=\"yes\">C</italic>\n<sub>L</sub> than the baseline geometry. Using the definitions and terminology of Lyons et al., our measurements (Tables ##TAB##0##1## and ##TAB##1##2##) revealed that the grey seal whisker also had greater <italic toggle=\"yes\">γ</italic> and <italic toggle=\"yes\">λ</italic> and lower <italic toggle=\"yes\">A</italic>\n<sub>C</sub> values compared to the harbor seal whisker (see Supporting Text and Table ##SUPPL##0##S1## of the Supporting Information for additional details). Similar to the “EL2” design of Lyons et al., the grey seal whisker also exhibited lower VIV compared to the harbor seal whisker, thus providing qualitative validation of the VIV trend (grey seal whisker &lt; harbor seal whisker &lt; cylinder) observed in our experiments and simulation results (Figure ##FIG##4##5e,g##).</p>", "<p>The presence of undulations in a high‐aspect ratio bluff body, such as a cylinder, disrupts the spatial coherence of the downstream Kármán vortex street<sup>[</sup>\n##UREF##6##\n12\n##\n<sup>]</sup> and thus reduces the VIV experienced by the body. The exact relationship between the geometry of the undulating body and the reduction in VIV is complex and has been a focus of recent studies.<sup>[</sup>\n##UREF##15##\n23\n##, ##REF##31342935##\n24\n##, ##UREF##27##\n41\n##\n<sup>]</sup> For instance, it is of interest to understand which geometric parameters in the whisker's undulating geometry are most relevant to VIV suppression. The manyfold reduction in the VIV response of both harbor and grey seal whiskers compared to a circular cylinder (Figure ##FIG##4##5e,g##) hinted that the whisker undulations might be optimized for VIV suppression. Interestingly, although the dimensions of the harbor and grey seal whiskers are clearly different (see Tables ##TAB##0##1## and ##TAB##1##2##), both undulation geometries displayed similar <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> values, viz. 4.4 and 4.6, respectively. Further, the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> values reported in the literature for other phocid seal species, e.g. 4.55 (after correcting for the error mentioned in the footnote of Table ##TAB##1##2##) for harbor seal whiskers<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> and 4.6 for elephant seal whiskers,<sup>[</sup>\n##REF##28840853##\n29\n##\n<sup>]</sup> are also in the vicinity of our <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> measurements for grey and harbor seal whiskers, suggesting the importance of the dimensionless <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio toward VIV suppression.</p>", "<p>To explore this hypothesis, we tested the VIV response of 3D‐printed whisker‐like geometries (scaled up 10×) of varying <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios for both harbor and grey seal whiskers. The experiments were conducted in a recirculating water flume (Re ≈1350–1600, similar to the Re experienced by real seal whiskers during foraging), as shown in <bold>Figure</bold> ##FIG##5##\n6a–d##. The whisker structures were mounted on a 3D‐printed piezoresistive cantilever sensor featuring a serpentine graphene nanoplatelet (GNP) strain gauge near its fixed end (Figure ##FIG##5##6a,b##). The harbor seal whisker geometry (<italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 4.4) and grey seal whisker geometry (<italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 4.6) were used as the baseline models respectively, while the other models were constructed by varying the wavelength to generate a total of eight undulating whisker‐like models with the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio varying from 1 to 7 for each species. Three representative examples are shown in Figure ##FIG##5##6a,b## pertaining to the harbor seal whisker study. The resulting VIV response (as measured by the graphene‐based cantilever sensor in mV) as a function of <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> (Figure ##FIG##5##6e##) displayed a local minimum around <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 4.4–4.6 for both the harbor and grey seal whiskers. The “optimal <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio” hypothesis was also tested using the FSI model described earlier, wherein similar numerical experiments were conducted to gauge the VIV response (nondimensional tip displacement, <italic toggle=\"yes\">d</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub>) of whisker structures of varying <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios (Figure ##FIG##5##6f##). Both the harbor and grey seal whisker curves (Figure ##FIG##5##6f##) displayed a similar qualitative trend: a local maximum around <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 3–4, a local minimum around <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 4.4–5, followed by a local maximum again around <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 5–6. The qualitative differences in the experimental (Figure ##FIG##5##6e##) and FEM (Figure ##FIG##5##6f##) results can be attributed to the differences in how the experiments and FEM models were set up: the experiments (with scaled‐up whiskers) were conducted at Re ≈ 1350–1600 while the simulations were at Re ≈ 135; the 3D‐printed whiskers were partially submerged in the water due to physical constraints, whereas the whisker models were completely submerged in the water domain in the simulations; and so on.</p>", "<p>Remarkably, both our experiments and numerical FSI simulations indicated that the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio of 4.4–4.6, <italic toggle=\"yes\">viz</italic>. the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio possessed by harbor and grey seal whiskers respectively, was optimal for VIV suppression. Undulating structures are known to disrupt the 2D wake structure (comprising spanwise vortices as experienced by a smooth cylinder) via the production of streamwise vorticity components, resulting in a 3D wake structure. It is probable that at the optimal <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio of 4.4–4.6, the streamwise vorticity components generated at the saddle and nodal planes of the undulating geometry are ideally situated for distorting the spanwise vorticity and maintaining the stability of the 3D wake structure far downstream of the undulating structure. In other words, the interplay between neighboring streamwise vortices at the optimal <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio prevent the spanwise vortex sheets from curling up into mature vortex structures.<sup>[</sup>\n##UREF##28##\n42\n##\n<sup>]</sup> The resulting increase in the vortex formation length can significantly reduce VIV of the whisker structure. A complete mechanistic explanation of this optimality is outside the scope of the current work, and is the subject of current and future work.</p>", "<p>Further, our results are in broad agreement with comparable numerical<sup>[</sup>\n##UREF##27##\n41\n##, ##UREF##28##\n42\n##\n<sup>]</sup> and experimental<sup>[</sup>\n##UREF##29##\n43\n##\n<sup>]</sup> studies conducted in the literature. As an example, Chen et al.<sup>[</sup>\n##UREF##29##\n43\n##\n<sup>]</sup> recently reported that for harbor seal whisker‐inspired structures (scaled up 70×), an optimal <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 4–5 resulted in a 93% reduction in the RMS of the aerodynamic lift coefficient in wind tunnel tests (Re = 38000). Our numerical and experimental data, combined with the fact that similar <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios (in the range 4.4–4.6) have been observed in the whiskers of other phocid seals,<sup>[</sup>\n##REF##20639428##\n14\n##, ##REF##28840853##\n29\n##\n<sup>]</sup> provide strong evidence that the undulating whisker geometry may have been optimized by the process of evolution to minimize VIV‐generated noise, allowing the phocid seal to become finely attuned to the hydrodynamic signals in the wake of escaping prey. These novel findings also highlight the importance of the nondimensional <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D<sub>m</sub>\n</italic> ratio in the design of VIV‐resistant bioinspired structures for engineering applications in the future.</p>", "<p>It must be noted that the undulating geometry of phocid seal whiskers is comprised of many other geometric factors, in addition to the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio. It is, for instance, of great interest to understand the functional role of the ellipse inclinations (<italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic>) in the whisker geometry, since this staggered waviness is unique to the phocid seal whisker. Further, VIV suppression is one half of the story, and the reaction of the whisker to the wake of the escaping prey (e.g., by a frequency lock‐in with the dominant frequencies of the wake<sup>[</sup>\n##REF##34699729##\n13\n##\n<sup>]</sup>) to maximize its “wake‐induced vibration” is a key consideration in understanding the evolutionary benefits of the phocid seal whisker structure – this will be the focus of a forthcoming publication.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Morphometrics</title>", "<p>The geometry of both the harbor and grey seal whiskers features undulations along their length. The whisker is, in essence, a tapered beam with an elliptical cross section whose major and minor axes vary periodically along its length. 2D outlines of ten harbor seal whiskers and ten grey seal whiskers, obtained after optical microscopy and image processing (<bold>Figure</bold> ##FIG##1##\n2a,b##), indicated consistent profiles in the observed length of 30 mm along both the XZ and YZ views as shown in Figure ##FIG##1##2c–f##. In general, substantial consistency was found between our geometric measurements and previous studies in the literature<sup>[</sup>\n##UREF##5##\n10\n##, ##UREF##9##\n17\n##, ##REF##28840853##\n29\n##\n<sup>]</sup> for the harbor seal whisker. Measurements of the grey seal whisker, on the other hand, were found to be much rarer, with only one study<sup>[</sup>\n##UREF##5##\n10\n##\n<sup>]</sup> that reported morphometrics. Our measurements and their comparison with the literature are summarized in <bold>Table</bold> ##TAB##0##\n1\n##.</p>", "<p>The measurements shown in Table ##TAB##0##1## only provided 2D information of the width of the whisker and neglected its thickness. To capture the 3D undulating morphology of the seal whisker from 2D measurements, Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> proposed a geometric framework comprising a total of seven parameters (<italic toggle=\"yes\">a</italic>, <italic toggle=\"yes\">b, k</italic>, <italic toggle=\"yes\">l</italic>, <italic toggle=\"yes\">M</italic>, <italic toggle=\"yes\">α</italic>, and <italic toggle=\"yes\">β</italic> as defined in Figure ##FIG##0##1e##). Here, the undulating whisker is approximated as a 3D surface that encloses two periodically recurring ellipses. The primary axis of the initial ellipse (with semi‐major axis denoted as <italic toggle=\"yes\">a</italic> and semi‐minor axis as <italic toggle=\"yes\">b</italic>) is established by connecting adjacent crests along the upper and lower profiles of the whisker. Conversely, the primary axis of the subsequent ellipse (with semi‐major axis referred to as <italic toggle=\"yes\">k</italic> and semi‐minor axis as <italic toggle=\"yes\">l</italic>) is established by connecting adjacent troughs along the upper and lower profiles of the whisker. These two ellipses exhibit inclinations (assumed to be constant in this framework) with respect to the longitudinal axis of the whisker, characterized by angles <italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic>, respectively. The alternating repetition of these ellipses (maintaining a separation distance of <italic toggle=\"yes\">M</italic>) along the longitudinal axis can be readily transformed into a 3D surface representation of the whisker using computer‐aided design (CAD) software packages. This geometric framework has been used by researchers for reporting whisker undulation measurements<sup>[</sup>\n##REF##20639428##\n14\n##, ##REF##28840853##\n29\n##\n<sup>]</sup> and to develop 3D models of the seal whisker for experimental<sup>[</sup>\n##UREF##6##\n12\n##\n<sup>]</sup> and numerical<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup> studies. Using the knowledge of the coordinates of the relevant points from microscopy and image processing, we measured <italic toggle=\"yes\">a</italic>, <italic toggle=\"yes\">k</italic>, <italic toggle=\"yes\">M</italic>, <italic toggle=\"yes\">α</italic>, and <italic toggle=\"yes\">β</italic> from the XZ view, while <italic toggle=\"yes\">b</italic> and <italic toggle=\"yes\">l</italic> were measured from the YZ view according to the definitions given in Figure ##FIG##0##1e##. <bold>Table</bold> ##TAB##1##\n2\n## lists the parameters measured in this study and compares them with the measurements of Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> (who used photogrammetry) and Rinehart et al.<sup>[</sup>\n##REF##28840853##\n29\n##\n<sup>]</sup> (who used computed tomography scanning) for harbor seal whiskers. The measured parameters for grey seal whiskers are also listed in Table ##TAB##1##2##; however, for this seal species, no corresponding studies were found in the literature for comparison.</p>", "<p>It must be noted that Hanke et al.’s framework<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> assumed constant angles of inclination (<italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic>) for the two ellipses shown in Figure ##FIG##0##1e##. In reality, however, the angles can vary over a wide range.<sup>[</sup>\n##REF##28840853##\n29\n##\n<sup>]</sup> As shown in Table ##TAB##1##2##, our <italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic> measurements yielded considerable variations for both seal species (histograms indicating the spread in <italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic> values are shown in Figure ##SUPPL##0##S1## of the Supporting Information), agreeing with Rinehart et al.’s<sup>[</sup>\n##REF##28840853##\n29\n##\n<sup>]</sup> observations. Due to the large spread in the measurements, the concept of an average <italic toggle=\"yes\">α</italic> or <italic toggle=\"yes\">β</italic> is not physically meaningful, but has nonetheless been reported in Table ##TAB##1##2## for the sake of completeness. Finally, although the dimensions of the harbor and grey seal whiskers measured in our study (Tables ##TAB##0##1## and ##TAB##1##2##) were different, with the grey seal whisker being wider and thicker than the harbor seal whisker, it is interesting to note that the ratios of wavelength (<italic toggle=\"yes\">λ</italic> ≡ 2<italic toggle=\"yes\">M</italic>) to mean diameter (<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≡ <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mfrac><mml:mrow><mml:mi>a</mml:mi><mml:mo>+</mml:mo><mml:mi>b</mml:mi><mml:mo>+</mml:mo><mml:mi>k</mml:mi><mml:mo>+</mml:mo><mml:mi>l</mml:mi></mml:mrow><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:math>) of both species of whiskers were similar, viz. <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 4.4 ± 0.7 for the harbor seal whisker and <italic toggle=\"yes\">λ</italic>/ <italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 4.6 ± 0.8 for the grey seal whisker. The implications of this ratio on the VIV suppression of whiskers will be discussed later.</p>", "<p>Although the model of Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> allows for an easy construction of a 3D model using only 2D measurements of the whisker along the XZ and YZ views, it is an idealized surface model that neglects several important geometric parameters such as the taper and curvature of whiskers which play a major role in determining their frequency response.<sup>[</sup>\n##UREF##20##\n30\n##, ##UREF##21##\n31\n##\n<sup>]</sup> To gain a more complete picture of the whisker morphometry, we also 3D‐scanned one harbor and one grey seal whisker using blue light scanning technology (<bold>Figure</bold> ##FIG##2##\n3a,b##). The resulting digital model (in the form of a .STP file) could be easily viewed in a CAD software such as Autodesk Netfabb which facilitated measurements along successive transverse cross‐sections of the whisker (Figure ##FIG##2##3c##). A video rendering of the scanned harbor and grey seal whisker models is available in the Supporting Information (Movies ##SUPPL##1##S1a## and ##SUPPL##2##S1b##, respectively), showing close‐up 3D views of the undulations along both the width and the thickness of the whiskers. Measurement planes normal to the whisker axis were defined at intervals of every 0.5 mm along the whisker length, and the major and minor axis dimensions (approximating each cross‐section as an ellipse) were measured as a function of the whisker length, allowing us to quantify the taper of the whisker. It must be noted that the major and minor axis dimensions measured in the 3D‐scanned model refer to the transverse cross‐section of the whisker normal to its axis, and are hence different from the parameters (<italic toggle=\"yes\">a</italic>, <italic toggle=\"yes\">b</italic>, <italic toggle=\"yes\">k</italic>, <italic toggle=\"yes\">l</italic>) of Hanke et al.’s<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> framework which referred to the dimensions of inclined ellipses (Figure ##FIG##0##1e##). As seen in Figure ##FIG##2##3d,e##, the semi‐major axis (i.e., half width) of both the grey and harbor seal whiskers oscillated about a mean value that remained constant (≈0.6 mm for the grey seal and ≈0.55 mm for the harbor seal whisker) for more than half the whisker length, after which it started tapering off rapidly near the whisker tip. On the other hand, the semi‐minor axis (i.e., half thickness) of both whiskers was seen to oscillate about a linearly decreasing mean value, indicating a uniform taper from the whisker base to its tip. The cross‐sectional area also showed a linear decrease from base to tip for both whiskers (Figure ##FIG##2##3d,e##). The whisker taper in both cases was thus seen to be primarily due to the linear decrease in their thickness, with little contribution from the variation in the width of the whisker. Although the 3D morphometric results presented here were obtained only from one whisker each of a harbor and a grey seal (statistical analysis of five 3D‐scanned harbor and grey seal whiskers is currently underway and will be the subject of future work), the preliminary information reported here can still be used to inform more realistic models of seal whiskers. For instance, Shatz et al.<sup>[</sup>\n##UREF##20##\n30\n##\n<sup>]</sup> calculated the fundamental frequencies of undulating harp seal whiskers by assuming them to be rectangular beams with uniformly tapering width and thickness. The accuracy of such models can be improved by using the morphometric observations from this study, e.g. that the width of the rectangular beam remains constant for over half the whisker length and only starts tapering near the tip of the whisker.</p>", "<title>Material Properties</title>", "<p>The polished transverse cross‐section of the grey seal whisker revealed an internal microstructure comprising three distinct regions distinguishable under the optical microscope (<bold>Figure</bold> ##FIG##3##\n4a,b##): the outermost cortex region resembled a smooth shell, the outer medulla appeared darker and comprised an oval region with multiple offshoots, and the inner medulla appeared at the center of the cross‐section and appeared darkest under the optical microscope. A detailed discussion on the internal structure can be found in the Supporting Information Text and Figure ##SUPPL##0##S2## (Supporting Infomation). Nanoindentation tests (Figure ##FIG##3##4c##) revealed a gradation in the Young's modulus values along the radial direction of the elliptical cross‐section. The outermost cortex region was found to be the stiffest (6.39 ± 0.46 GPa), followed by the outer medullar region (5.03 ± 0.67 GPa). The inner medullar region was almost half as stiff as the cortex (3.53 ± 1.57 GPa). Interestingly, the standard deviation in the modulus values of the inner medulla was observed to be much higher, with some tests resulting in elastic moduli as low as 0.4 GPa (near the geometric center of the cross‐section), suggesting the possibility of soft tissue in this region. Further, as seen in Figure ##FIG##3##4d##, a slight decrease in the moduli was observed for all three regions from the proximal tip to the distal tip. The average Young's modulus average exhibited a slight decrease (from 6.1 GPa at the proximal end to 5.6 GPa at the distal end) over the length of the whisker as shown in Figure ##FIG##3##4e##. The comparison of our measurements with the aforementioned literature data is summarized in <bold>Table</bold> ##TAB##2##\n3\n##. Although the spread in the reported Young's modulus values in the literature is high, this is not unexpected given the variety of methods (with their concomitant assumptions) employed in the literature, as listed in Table ##TAB##2##3##. For instance, the measurement of <italic toggle=\"yes\">E</italic> using a tensile test, implemented either using DMA<sup>[</sup>\n##REF##24871073##\n32\n##\n<sup>]</sup> or microtesting,<sup>[</sup>\n##UREF##20##\n30\n##\n<sup>]</sup> is complicated by the fact that a whisker is not shaped like a typical tensile sample, thus making it difficult to convert the measured force into stress due to the non‐uniformity of the cross‐sectional area. Similarly, point load bending<sup>[</sup>\n##UREF##21##\n31\n##\n<sup>]</sup> employed to calculate flexural rigidity (<italic toggle=\"yes\">EI</italic>) and elastic modulus (<italic toggle=\"yes\">E</italic>) is an indirect testing method entailing many assumptions (e.g., approximating the whisker geometry as cylindrical with no undulations or taper in order to use elastic beam bending theory) that can introduce errors in the measured properties. The nanoindentation technique employed in this study is a more direct measurement technique that affords higher resolution both within a cross‐section and along the whisker length. This occurs, however, at the cost of destroying the whisker sample through sectioning and polishing. Finally, we note that there also exists a wide variance in the reported Young's modulus values for the relatively more well‐studied rat whisker, with <italic toggle=\"yes\">E</italic> values ranging from 3–4 GPa<sup>[</sup>\n##REF##12878692##\n33\n##, ##REF##21993474##\n34\n##\n<sup>]</sup> to 7.36 GPa<sup>[</sup>\n##UREF##22##\n35\n##\n<sup>]</sup> in the literature.</p>", "<p>An important parameter with respect to the flow sensing performance of the whisker is its flexural rigidity (<italic toggle=\"yes\">EI</italic>), also referred to as bending stiffness. This parameter determines the whisker's bending response due to a tactile and/or hydrodynamic stimulus, and is plotted in Figure ##FIG##3##4f## as a function of distance along the whisker length (see Materials and Methods for more details). As expected, the rigidity was much lesser around the major axis owing to the elliptical shape of the whisker, allowing easier bending about the major (<italic toggle=\"yes\">XX</italic>) than the minor (<italic toggle=\"yes\">YY</italic>) axis. Interestingly, although Equation (##FORMU##1##2##) (see Experimental Section) suggests that the effective flexural rigidity (plotted in Figure ##FIG##3##4f##) contains contributions from all the three regions, viz. the cortex, outer medulla, and inner medulla, it was found that the flexural rigidity of the cortex was the major contributor (up to 98%) to the overall rigidity about the whisker major axis, suggesting that the outer and inner medullar regions did not have a significant effect on the overall bending behavior of the whisker about its major axis. The flexural rigidity about both axes decreased along the length of the whisker due to its taper. However, the decrease in <italic toggle=\"yes\">EI<sub>xx</sub>\n</italic> (indicating resistance to bending about the major axis) was more drastic, reducing by a factor of 5 within only 50% of the whisker length, than the decrease in <italic toggle=\"yes\">EI<sub>yy</sub>\n</italic> (indicating resistance to bending about the minor axis) which was more gradual in nature. The slightly lower rigidity within the initial 10 mm length of the whisker can be attributed to the fact that this portion is typically embedded within the seal muzzle and thus reinforced by the surrounding tissue and the follicle‐sinus complex.<sup>[</sup>\n##UREF##4##\n9\n##\n<sup>]</sup>\n</p>", "<p>Due to similarities in functionality and performance, seal whiskers are often compared to rat whiskers. A major difference that can be surmised from the preceding discussion is in the morphology of the two whiskers — while rat whiskers are smaller and have a conical shape (length ≈10–50 mm, base diameter ≈20–50 µm, and tip diameter ≈5 µm),<sup>[</sup>\n##REF##27260019##\n36\n##\n<sup>]</sup> (phocid) seal whiskers tend to be flattened (i.e., elliptical in cross‐section) and contain 3D undulations along their lengths. The morphological differences exist due to the differences in the nature of loading experienced by the whiskers. While rats use their whiskers for object localization and texture recognition (resulting in point loading at the whisker tip), the function of seal whiskers is geared toward both tactile sensing and hydrodynamic trail following. The latter entails a combination of two different kinds of loading on the whisker: a distributed static load caused by the drag force due to the seal's swimming velocity, and a dynamic concentrated load due to the vortices in the wake of, for instance, prey swimming ahead of it. Although no direct in situ observations of the whisker orientation have been made when the seal is in the process of hunting for prey (Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> mounted a camera on a harbor seal and observed whisker position and movement but not orientation), a whisker is often assumed to be oriented such that its angle of attack (AOA), defined as the angle between the major axis of the elliptical whisker and the velocity of the seal's swimming motion, is 0° to minimize the drag force and VIV.<sup>[</sup>\n##REF##20639428##\n14\n##, ##UREF##9##\n17\n##, ##UREF##23##\n37\n##\n<sup>]</sup> In the AOA = 0° orientation, successive vortical stimuli from the wake of the escaping prey then excite the whisker along the direction of its minor axis, causing the whisker to bend about its major (<italic toggle=\"yes\">XX</italic>) axis. Beem and Triantafyllou<sup>[</sup>\n##UREF##6##\n12\n##\n<sup>]</sup> conducted experiments to study the interactions of a scaled‐up harbor seal whisker (AOA = 0°) with a vortex generator placed upstream, and used dye visualization to observe a “slaloming” mechanism that allowed the whisker‐like structure to be locked‐in to the vortical frequency by swaying between the alternating vortices in the wake street. As the structure oscillated transversely to the forward motion, it was synchronized to first approach the closest oncoming vortex on one side and was further pulled toward it due to the low pressure associated with a vortex; then, as the whisker progressed forward, it moved sidewise approaching the next vortex on the other side, again pulled by its low‐pressure gradient, and so on. This constituted the mechanism of vibrational amplitude amplification and hence energy extraction. Such “wake‐induced vibrations (WIV)”<sup>[</sup>\n##UREF##6##\n12\n##\n<sup>]</sup> allow the seal to be attuned to the tiniest of flow disturbances while following the trail of an escaping prey, even when the prey has swum by several seconds before.<sup>[</sup>\n##REF##11441183##\n7\n##\n<sup>]</sup> Seen in the light of this discussion, we propose that the low flexural rigidity about the major axis (<italic toggle=\"yes\">EI</italic>\n<sub>xx</sub>) shown in Figure ##FIG##3##4f## imparts greater flexibility to the distal half of the whisker, allowing it to effectively slalom its way through a train of incoming vortices. The resulting WIV's are subsequently transduced into a neural signal at the highly innervated whisker base,<sup>[</sup>\n##UREF##4##\n9\n##\n<sup>]</sup> enabling the exquisite ability of the seal to sense flow disturbances up to 1000× lower than its swimming speed. The role of undulations with respect to VIV of grey and harbor seal whiskers is discussed in the next subsection.</p>", "<p>Finally, the density of the whiskers was measured as follows. Ten grey seal whiskers were weighed on a microbalance and their collective volume was subsequently noted by measuring the amount of water displaced by them. The average density (mass divided by volume) was calculated to be 1280 ± 80 kg m<sup>−3</sup> after repeating the mass and volume measurement five times.</p>", "<title>VIV Suppression due to Whisker Undulations</title>", "<p>The undulating whisker morphology of phocid seals, such as the harbor and grey seals, is believed to reduce the VIV phenomenon, resulting in lower noise in the whisker flow sensing system. Prior experiments in the literature conducted with isolated real seal whiskers have produced conflicting results, with some researchers<sup>[</sup>\n##REF##20639428##\n14\n##, ##UREF##7##\n15\n##\n<sup>]</sup> reporting VIV reduction due to the undulations while others<sup>[</sup>\n##UREF##9##\n17\n##\n<sup>]</sup> finding similar vibration behavior in structures with and without undulations. To study the effect of undulations on the VIV behavior of high‐aspect ratio bluff bodies, we compared the VIV signals of three structures: a harbor seal whisker, a grey seal whisker, and a rigid polyvinylchloride (PVC) cylinder, using a piezoelectric sensor. The material (PVC) and diameter (1 mm) of the cylinder were chosen to maintain similar flexural rigidity and Reynold's number to those of the seal whiskers (more details can be found in Materials and Methods), thus ensuring a fair comparison of VIV responses of the three structures. The seal whisker relies upon the bending moment created by flow disturbances to excite its innervated base and generate a neural signal. This mechanotransduction sensing principle was mimicked by fixing the whisker atop a PZT piezoelectric sensing membrane (<bold>Figure</bold> ##FIG##4##\n5a–c##), wherein the whisker vibrations deformed the membrane and generated a measurable electrical voltage. A piezoelectric MEMS sensor developed in our prior work<sup>[</sup>\n##UREF##24##\n38\n##, ##UREF##25##\n39\n##, ##UREF##26##\n40\n##\n<sup>]</sup> was used as the sensing base in this study due to its small size (8 mm × 8 mm) and waterproof design. The self‐powered sensor only responded to dynamic forces due to its piezoelectric sensing principle, making it ideal to measure time‐dependent VIV phenomena. The three structures, viz. the harbor seal whisker, grey seal whisker, and the PVC cylinder, were tested at a water flow speed of 0.4 m s<sup>−1</sup> (Re ≈450 calculated using a characteristic dimension of 1 mm) in a recirculating water tunnel (Figure ##FIG##4##5d##) and the AOA was maintained at 0° for the two seal whiskers. As seen from the time series data of Figure ##FIG##4##5e##, the peak‐to‐peak sensor voltage in the case of the PVC cylinder (≈0.8 V) was up to 6× higher than that of the harbor seal whisker (≈0.12 V) and up to 13× higher than that of the grey seal whisker (≈0.06 V), indicating significantly reduced vibrations for the undulating whiskers as compared to the smooth cylinder.</p>", "<p>The experiments described above represented an indirect method of deducing VIV through the piezoelectric sensor output. In order to gain more insight into the vibration response of the three structures placed in uniform water flow, an FEM model was constructed in COMSOL Multiphysics (Figure ##FIG##4##5f##). The simulation results (Figure ##FIG##4##5g##) reinforced the experimentally observed trend (Figure ##FIG##4##5e##), namely that the transverse vibration amplitudes for the cylinder were the highest, followed by the harbor and grey seal whiskers, respectively. Interestingly, both the experimental and numerical results suggested that the grey seal whiskers were able to suppress VIV better than the harbor seal whiskers at the tested flow speed. This trend of VIV response (grey seal whisker &lt; harbor seal whisker &lt; cylinder) can be understood in light of a recent study by Lyons et al.<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup> that used a factorial design of numerical experiments to perform a comprehensive study of the effect of varying geometric parameters describing the harbor seal whisker undulations on <italic toggle=\"yes\">C</italic>\n<sub>D</sub> and <italic toggle=\"yes\">C</italic>\n<sub>L</sub>. Although the researchers<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup> constructed the “baseline” harbor seal whisker geometry using an erroneous value of wavelength (see footnote to Table ##TAB##1##2##), the study nonetheless shed light on the relative importance of independent geometric parameters on the resulting VIV performance of the whisker. Lyons et al.<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup> found that the aspect ratio or slenderness (<mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>γ</mml:mi><mml:mo>:</mml:mo><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>a</mml:mi><mml:mi>cos</mml:mi><mml:mi>α</mml:mi><mml:mo>+</mml:mo><mml:mi>k</mml:mi><mml:mi>cos</mml:mi><mml:mi>β</mml:mi></mml:mrow><mml:mrow><mml:mi>b</mml:mi><mml:mo>+</mml:mo><mml:mi>l</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>), undulation wavelength (<mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>λ</mml:mi><mml:mo>:</mml:mo><mml:mo>=</mml:mo><mml:mn>2</mml:mn><mml:mi>M</mml:mi></mml:mrow></mml:mrow></mml:math>), and undulation amplitude along the width (<mml:math id=\"jats-math-5\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>A</mml:mi><mml:mi mathvariant=\"normal\">c</mml:mi></mml:msub><mml:mo>:</mml:mo><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>a</mml:mi><mml:mi>cos</mml:mi><mml:mi>α</mml:mi><mml:mo>−</mml:mo><mml:mi>k</mml:mi><mml:mi>cos</mml:mi><mml:mi>β</mml:mi><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:mrow><mml:mi>b</mml:mi><mml:mo>+</mml:mo><mml:mi>l</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>) were the (non‐dimensional) parameters that had the largest effect on <italic toggle=\"yes\">C</italic>\n<sub>L</sub> and, by extension, on VIV. The sixteen numerical experiments conducted by the researchers provided some indication of how VIV suppression capabilities can change in two undulating structures with different geometric parameters. For instance, there existed a geometry (labeled ‘EL2’<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup>) that had higher <italic toggle=\"yes\">γ</italic>, <italic toggle=\"yes\">λ</italic>, and lower <italic toggle=\"yes\">A</italic>\n<sub>C</sub> values compared to the baseline harbor seal whisker geometry and exhibited a lower <italic toggle=\"yes\">C</italic>\n<sub>L</sub> than the baseline geometry. Using the definitions and terminology of Lyons et al., our measurements (Tables ##TAB##0##1## and ##TAB##1##2##) revealed that the grey seal whisker also had greater <italic toggle=\"yes\">γ</italic> and <italic toggle=\"yes\">λ</italic> and lower <italic toggle=\"yes\">A</italic>\n<sub>C</sub> values compared to the harbor seal whisker (see Supporting Text and Table ##SUPPL##0##S1## of the Supporting Information for additional details). Similar to the “EL2” design of Lyons et al., the grey seal whisker also exhibited lower VIV compared to the harbor seal whisker, thus providing qualitative validation of the VIV trend (grey seal whisker &lt; harbor seal whisker &lt; cylinder) observed in our experiments and simulation results (Figure ##FIG##4##5e,g##).</p>", "<p>The presence of undulations in a high‐aspect ratio bluff body, such as a cylinder, disrupts the spatial coherence of the downstream Kármán vortex street<sup>[</sup>\n##UREF##6##\n12\n##\n<sup>]</sup> and thus reduces the VIV experienced by the body. The exact relationship between the geometry of the undulating body and the reduction in VIV is complex and has been a focus of recent studies.<sup>[</sup>\n##UREF##15##\n23\n##, ##REF##31342935##\n24\n##, ##UREF##27##\n41\n##\n<sup>]</sup> For instance, it is of interest to understand which geometric parameters in the whisker's undulating geometry are most relevant to VIV suppression. The manyfold reduction in the VIV response of both harbor and grey seal whiskers compared to a circular cylinder (Figure ##FIG##4##5e,g##) hinted that the whisker undulations might be optimized for VIV suppression. Interestingly, although the dimensions of the harbor and grey seal whiskers are clearly different (see Tables ##TAB##0##1## and ##TAB##1##2##), both undulation geometries displayed similar <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> values, viz. 4.4 and 4.6, respectively. Further, the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> values reported in the literature for other phocid seal species, e.g. 4.55 (after correcting for the error mentioned in the footnote of Table ##TAB##1##2##) for harbor seal whiskers<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> and 4.6 for elephant seal whiskers,<sup>[</sup>\n##REF##28840853##\n29\n##\n<sup>]</sup> are also in the vicinity of our <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> measurements for grey and harbor seal whiskers, suggesting the importance of the dimensionless <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio toward VIV suppression.</p>", "<p>To explore this hypothesis, we tested the VIV response of 3D‐printed whisker‐like geometries (scaled up 10×) of varying <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios for both harbor and grey seal whiskers. The experiments were conducted in a recirculating water flume (Re ≈1350–1600, similar to the Re experienced by real seal whiskers during foraging), as shown in <bold>Figure</bold> ##FIG##5##\n6a–d##. The whisker structures were mounted on a 3D‐printed piezoresistive cantilever sensor featuring a serpentine graphene nanoplatelet (GNP) strain gauge near its fixed end (Figure ##FIG##5##6a,b##). The harbor seal whisker geometry (<italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 4.4) and grey seal whisker geometry (<italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 4.6) were used as the baseline models respectively, while the other models were constructed by varying the wavelength to generate a total of eight undulating whisker‐like models with the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio varying from 1 to 7 for each species. Three representative examples are shown in Figure ##FIG##5##6a,b## pertaining to the harbor seal whisker study. The resulting VIV response (as measured by the graphene‐based cantilever sensor in mV) as a function of <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> (Figure ##FIG##5##6e##) displayed a local minimum around <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 4.4–4.6 for both the harbor and grey seal whiskers. The “optimal <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio” hypothesis was also tested using the FSI model described earlier, wherein similar numerical experiments were conducted to gauge the VIV response (nondimensional tip displacement, <italic toggle=\"yes\">d</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub>) of whisker structures of varying <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios (Figure ##FIG##5##6f##). Both the harbor and grey seal whisker curves (Figure ##FIG##5##6f##) displayed a similar qualitative trend: a local maximum around <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 3–4, a local minimum around <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 4.4–5, followed by a local maximum again around <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 5–6. The qualitative differences in the experimental (Figure ##FIG##5##6e##) and FEM (Figure ##FIG##5##6f##) results can be attributed to the differences in how the experiments and FEM models were set up: the experiments (with scaled‐up whiskers) were conducted at Re ≈ 1350–1600 while the simulations were at Re ≈ 135; the 3D‐printed whiskers were partially submerged in the water due to physical constraints, whereas the whisker models were completely submerged in the water domain in the simulations; and so on.</p>", "<p>Remarkably, both our experiments and numerical FSI simulations indicated that the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio of 4.4–4.6, <italic toggle=\"yes\">viz</italic>. the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio possessed by harbor and grey seal whiskers respectively, was optimal for VIV suppression. Undulating structures are known to disrupt the 2D wake structure (comprising spanwise vortices as experienced by a smooth cylinder) via the production of streamwise vorticity components, resulting in a 3D wake structure. It is probable that at the optimal <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio of 4.4–4.6, the streamwise vorticity components generated at the saddle and nodal planes of the undulating geometry are ideally situated for distorting the spanwise vorticity and maintaining the stability of the 3D wake structure far downstream of the undulating structure. In other words, the interplay between neighboring streamwise vortices at the optimal <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio prevent the spanwise vortex sheets from curling up into mature vortex structures.<sup>[</sup>\n##UREF##28##\n42\n##\n<sup>]</sup> The resulting increase in the vortex formation length can significantly reduce VIV of the whisker structure. A complete mechanistic explanation of this optimality is outside the scope of the current work, and is the subject of current and future work.</p>", "<p>Further, our results are in broad agreement with comparable numerical<sup>[</sup>\n##UREF##27##\n41\n##, ##UREF##28##\n42\n##\n<sup>]</sup> and experimental<sup>[</sup>\n##UREF##29##\n43\n##\n<sup>]</sup> studies conducted in the literature. As an example, Chen et al.<sup>[</sup>\n##UREF##29##\n43\n##\n<sup>]</sup> recently reported that for harbor seal whisker‐inspired structures (scaled up 70×), an optimal <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 4–5 resulted in a 93% reduction in the RMS of the aerodynamic lift coefficient in wind tunnel tests (Re = 38000). Our numerical and experimental data, combined with the fact that similar <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios (in the range 4.4–4.6) have been observed in the whiskers of other phocid seals,<sup>[</sup>\n##REF##20639428##\n14\n##, ##REF##28840853##\n29\n##\n<sup>]</sup> provide strong evidence that the undulating whisker geometry may have been optimized by the process of evolution to minimize VIV‐generated noise, allowing the phocid seal to become finely attuned to the hydrodynamic signals in the wake of escaping prey. These novel findings also highlight the importance of the nondimensional <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D<sub>m</sub>\n</italic> ratio in the design of VIV‐resistant bioinspired structures for engineering applications in the future.</p>", "<p>It must be noted that the undulating geometry of phocid seal whiskers is comprised of many other geometric factors, in addition to the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio. It is, for instance, of great interest to understand the functional role of the ellipse inclinations (<italic toggle=\"yes\">α</italic> and <italic toggle=\"yes\">β</italic>) in the whisker geometry, since this staggered waviness is unique to the phocid seal whisker. Further, VIV suppression is one half of the story, and the reaction of the whisker to the wake of the escaping prey (e.g., by a frequency lock‐in with the dominant frequencies of the wake<sup>[</sup>\n##REF##34699729##\n13\n##\n<sup>]</sup>) to maximize its “wake‐induced vibration” is a key consideration in understanding the evolutionary benefits of the phocid seal whisker structure – this will be the focus of a forthcoming publication.</p>" ]
[ "<title>Conclusion</title>", "<p>The results presented in this paper offer experimental and numerical evidence to underscore the crucial role played by the undulating seal whisker's <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio in the seal's exceptional hydrodynamic trail following feats. Further, the geometric and material property measurements reported here are expected to contribute toward more accurate and comprehensive biomechanical models of the grey and harbor seal whiskers, which will help shed light on the FSI mechanisms that enable the ultrahigh flow sensitivity exhibited by seal whiskers. The identification of <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> as an important dimensionless design parameter for VIV suppression will also help guide the design of bioinspired vibration‐resistant structures and high signal‐to‐noise ratio flow sensors for engineering applications.</p>" ]
[ "<title>Abstract</title>", "<p>Seals are well‐known for their remarkable hydrodynamic trail‐following capabilities made possible by undulating flow‐sensing whiskers that enable the seals to detect fish swimming as far as 180 m away. In this work, the form‐function relationship in the undulating whiskers of two different phocid seal species, viz. harbor and gray seals, is studied. The geometry and material properties of excised harbor and grey seal whiskers are systematically characterized using blue light 3D scanning, optical and scanning electron microscopy, and nanoindentation. The effect of the undulating geometry on the whiskers’ vibration in uniform water flow is studied using both experimental (piezoelectric MEMS and 3D‐printed piezoresistive sensors developed in‐house) and numerical (finite element method) techniques. The results indicate that the dimensionless ratio of undulation wavelength to mean whisker diameter (<italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub>) in phocid seals may have evolved to be in the optimal range of 4.4–4.6, enabling an order‐of‐magnitude reduction in vortex‐induced vibrations (compared to a similarly‐shaped circular cylinder) and, consequently, an enhanced flow sensing capability with minimal self‐induced noise. The results highlight the importance of the dimensionless <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio in the biomimetic design of seal whisker‐inspired vibration‐resistant structures, such as marine risers and wake detection sensors for submarines.</p>", "<p>Phocid seal whiskers possess a unique undulating geometry that reduces vortex‐induced vibrations (VIV) and helps the seal track its prey. In this work, the form‐function relationships in harbor and grey seal whiskers are studied. The results indicate that the wavelength‐to‐mean diameter ratio (<italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub>) of the undulating whiskers may have evolved to possess an optimal value of 4.5 to minimize VIV.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6641-cit-0054\">\n<string-name>\n<given-names>A. M.</given-names>\n<surname>Kamat</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Zheng</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Bos</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Cao</surname>\n</string-name>, <string-name>\n<given-names>M. S.</given-names>\n<surname>Triantafyllou</surname>\n</string-name>, <string-name>\n<given-names>A. G. P.</given-names>\n<surname>Kottapalli</surname>\n</string-name>, <article-title>Undulating Seal Whiskers Evolved Optimal Wavelength‐to‐Diameter Ratio for Efficient Reduction in Vortex‐Induced Vibrations</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304304</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304304</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Morphometry of Seal Whiskers</title>", "<p>Multiple whiskers were excised during the necropsy of deceased grey (two: one male and one female) and harbor (four: three female and one male) seals at the Zeehondencentrum (Pieterburen, the Netherlands). The harbor seals were puppies (age ≈ 10 days to 1–2 years) while the grey seals were adults. Ten whiskers each from both the grey and harbor seals were used for the geometric measurements, and were chosen based on similarity in lengths to ensure meaningful statistical data, since seal whiskers usually span a range of lengths depending upon their position on the seal's muzzle. The whiskers were fixed on to a microscopic glass slide using putty and observed under an optical microscope (Olympus VANOX‐T AH‐2) at a 25× magnification. Micrographs were obtained along two views according to the coordinate system defined in Figure ##FIG##0##1e##: the XZ view (when the wider dimension of the whisker was parallel to the microscopic slide) and the YZ view (when the narrower dimension of the whisker was parallel to the microscopic slide). Since a seal whisker usually exhibits curvature, the whole length of the whisker typically does not lie in a single plane. Hence, measurements were only conducted on the middle “planar” portion of whiskers encompassing around eight undulating wavelengths (≈30–35 mm length) per whisker. Successive optical micrographs in this portion were obtained along the length of the whiskers and later stitched together using the Adobe Illustrator CC 2018 software. The micrograph was analyzed using an open‐source image processing software (Fiji<sup>[</sup>\n##REF##22743772##\n44\n##\n<sup>]</sup>) which automatically identified the 2D coordinates of all the local maxima and minima of the undulations.</p>", "<p>For the 3D measurements, two representative seal whiskers (one each from grey and harbor seals) were 3D scanned using the GOM ATOS III Triple Scan 8M blue light scanning system. The scanner featured an 8‐megapixel dual camera system, with a 90 mm lens for the cameras and a 120 mm projector lens. The machine was used in the “SO MV60” preset configuration that entailed a scan volume of 60 mm × 45 mm × 35 mm and a measurement accuracy of 17 µm. A thin coating (≈10 µm) of chalk spray was applied to the whisker using an airbrush prior to the 3D scanning to enhance its reflectance. 0.4 mm photogrammetric targets were used. The GOM ATOS Professional software was used to create the main meshing per scan and per side using photogrammetry, and the software Geomagic Wrap was used to assemble these sections into one model. The 3D scanning and reverse engineering processes were performed by a local company (GEOSCAN, the Netherlands), resulting in a digital computer‐aided design (CAD) model of the harbor and grey seal whiskers.</p>", "<title>Internal Structure and Material Properties</title>", "<p>A grey seal whisker was sectioned into twenty‐four parts (each ≈5 mm long) and the cross sections were cold‐mounted in a transparent epoxy resin (EpoFix, Streurs). The resin was allowed to cure overnight at room temperature which ensured that the whiskers were not subjected to any high temperature or pressure typically associated with sample mounting processes. The transverse cross sections were then ground with successively finer sandpaper and polished with diamond paste (Struers) to a final roughness of ≈1 µm. Optical (Olympus VANOX‐T AH‐2) and scanning electron (Philips ESEM‐XL30) micrographs were obtained to observe the internal microstructure of the whiskers at magnifications of 50–200×. Further, nine polished cross sections along the whisker length (three near the whisker base, three in the middle, and three near the whisker tip) were subjected to nanoindentation testing (MTS Nanoindenter XP) to measure the Young's modulus. In these tests, the polished cross sections were loaded and unloaded using a Berkovich indenter in the “depth‐controlled” mode up to a depth of 0.5 µm, and the Young's modulus was calculated from the slope of the force‐displacement curve during the unloading stage using the Oliver‐Pharr method.<sup>[</sup>\n##UREF##30##\n45\n##\n<sup>]</sup> A hold time of 3 s was applied at the maximum depth before unloading to allow the biological material to reach equilibrium and to ensure that the biological material's creep rate did not affect the modulus calculation.<sup>[</sup>\n##UREF##31##\n46\n##\n<sup>]</sup> Nanoindentation tests were conducted in three cross‐sections near the proximal end, three near the center, and three near the distal end of the grey seal whisker, resulting in a total of 43 measurements in the cortex, 58 measurements in the outer medulla, and 35 measurements in the inner medulla distributed over nine different polished transverse cross sections of the grey seal whisker.</p>", "<title>Calculation of Average Elastic Modulus and Flexural Rigidity Profiles</title>", "<p>Using the area fractions of each region (Figure ##FIG##3##4b##), the average Young's modulus (<italic toggle=\"yes\">E</italic>\n<sub>avg</sub>) can be estimated using the rule of mixtures as follows:\nwhere <italic toggle=\"yes\">A</italic> is the area fraction, <italic toggle=\"yes\">E</italic> is the Young's modulus, and the subscripts <italic toggle=\"yes\">c</italic>, <italic toggle=\"yes\">om</italic>, and <italic toggle=\"yes\">im</italic> refer to the cortex, outer medullar and inner medullar regions in the whisker cross‐section, respectively. The resulting weighted average indicated a slight decrease (from 6.1 GPa at the proximal end to 5.6 GPa at the distal end) in the Young's modulus over the length of the whisker as shown in Figure ##FIG##3##4e##.</p>", "<p>The effective flexural rigidity, (<italic toggle=\"yes\">EI</italic>)<italic toggle=\"yes\">\n<sub>eff</sub>\n</italic>, at a given location along the whisker's length is the cumulative effect of the individual rigidities of the three regions:\n\n</p>", "<p>\n<italic toggle=\"yes\">E<sub>c</sub>\n</italic>, <italic toggle=\"yes\">E<sub>om</sub>\n</italic>, and <italic toggle=\"yes\">E<sub>im</sub>\n</italic> were obtained from Figure ##FIG##3##4d##, while the corresponding moments of inertia of the three regions can be calculated by approximating their boundaries as ellipses. If <italic toggle=\"yes\">p</italic> and <italic toggle=\"yes\">q</italic> denote the semi‐major and semi‐minor axes of the elliptical boundaries defining a given region, then the corresponding moments of inertia of the three regions are:\n\n\n\n\n\nwhere the subscripts <italic toggle=\"yes\">XX</italic> and <italic toggle=\"yes\">YY</italic> refer to the moment of inertia computed about the major and minor axes, respectively. Using the major and minor axis measurements of the three regions from the transverse cross‐sections (Figure ##FIG##3##4a##) and the knowledge of the Young's modulus measurement of each region (Figure ##FIG##3##4d##), the flexural rigidity about both the major (<italic toggle=\"yes\">XX</italic>) and minor (<italic toggle=\"yes\">YY</italic>) axis of bending was calculated using Equations (##FORMU##1##2##)–(##FORMU##6##5##) and is plotted in Figure ##FIG##3##4f## as a function of distance along the whisker length.</p>", "<title>Experimental Measurements of VIV Using Piezoelectric MEMS Sensor</title>", "<p>The structure of the MEMS sensor comprised a 27 µm thick piezoelectric PZT sensing plate bonded to a 20 µm thick device layer of a silicon on insulator (SOI) wafer with a 0.2 µm oxide layer, resulting in a total thickness of 47.2 µm. The membrane displayed a resonant frequency of 23.3 kHz<sup>[</sup>\n##UREF##24##\n38\n##\n<sup>]</sup> which was orders of magnitude higher than typical seal whisker resonant frequencies that are in the range of 20–200 Hz.<sup>[</sup>\n##UREF##20##\n30\n##\n<sup>]</sup> The sensor was fabricated using MEMS microfabrication processes that included SOI substrate‐PZT layer bonding using spin‐on cytop polymer, chemical‐mechanical‐polishing, sputter deposition of the top and bottom electrodes sandwiching the sensing membrane, patterning of the electrode interconnects and pads, wet etching of the PZT layer to contact the bottom electrode, and releasing the diaphragm structure using the anisotropic deep reactive ion etching (DRIE).<sup>[</sup>\n##UREF##24##\n38\n##\n<sup>]</sup>\n</p>", "<p>The 35 mm long whiskers and cylinder were glued on to the piezoelectric membrane using nonconductive epoxy (EPO‐TEK H70E) and subsequently cured in a furnace for 90 min at 80 °C. The whisker vibrations caused buckling of the piezoelectric membrane, generating charges at the top and bottom Au electrodes (Figure ##FIG##4##5a##). Cladded copper wires were connected to the Au electrodes on the membrane using conductive epoxy (EPOTEK H20E) to establish electrical connections to the external data acquisition circuit (Figure ##FIG##4##5c##). Finally, nonconductive epoxy was used to seal all the electrical contacts to ensure robust and waterproof connections.</p>", "<p>The whisker/cylinder flow sensors were then tested in a recirculating water flow tank that had a circular test section of inner diameter 102 mm (Figure ##FIG##5##6a##). In order to eliminate the effect of the whisker curvature, 35 mm long straight segments of the whiskers (featuring around 10 undulations) were tested. The material and geometric properties of the PVC cylinder (Young's modulus = 2.43 – 4 GPa<sup>[</sup>\n##UREF##32##\n47\n##\n<sup>]</sup> and diameter = 1 mm) resulted in a flexural rigidity of 120 – 190 N‐mm<sup>2</sup> that was similar to the rigidity of the whiskers (Figure ##FIG##3##4f##) tested in the experiment. Moreover, the characteristic dimension of the cylinder (1 mm diameter) was close to the mean diameter given in Table ##TAB##1##2## (<italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 0.80 ±0.14 mm for the harbor seal and <italic toggle=\"yes\">D</italic>\n<sub>m</sub> = 0.96 ±0.07 mm for the grey seal whisker), ensuring comparable Reynolds (Re) numbers for all three flow‐structure interactions. The whisker‐on‐sensor system was glued to a 3D printed fixture (Figure ##FIG##4##5b,c##) that could be easily screwed into an opening in the recirculating water flow tank. A water flow speed of 0.4 m s<sup>−1</sup> (Re ≈ 450) was chosen since this was high enough to cause downstream vortex shedding and yet low enough to ensure that the structure (whiskers and/or cylinder) did not separate from the sensing membrane. The sensor output was acquired (via the cladded copper wires mentioned above) using the NI‐DAQ USB‐6003 (National Instruments) and recorded in the NI Signal Express software at a sampling frequency of 10 kHz, and a band pass filter between 0–200 Hz was applied to the resulting data to eliminate the high‐frequency noise and focus on the frequency range relevant to seal whisker vibrations.<sup>[</sup>\n##UREF##20##\n30\n##\n<sup>]</sup> Each experiment was repeated around seven times to ensure repeatability in the results.</p>", "<title>Experimental Measurements of Optimal <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> Ratios Using 3D‐Printed Piezoresistive Sensor</title>", "<p>To investigate the effect of the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio on VIV suppression, CAD models of the harbor and grey seal whisker structures were first constructed using the geometric framework proposed by Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> Parameters <italic toggle=\"yes\">a</italic>, <italic toggle=\"yes\">b</italic>, <italic toggle=\"yes\">k</italic>, <italic toggle=\"yes\">l</italic>, <italic toggle=\"yes\">α</italic>, and <italic toggle=\"yes\">β</italic> (Figure ##FIG##0##1e## and Table ##TAB##1##2##) were maintained the same, and the parameter <italic toggle=\"yes\">M</italic> (Figure ##FIG##0##1e##) was changed to obtain whisker‐like structures with varying <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios equaling 1, 2, 3, 4, 4.4 (harbor seal) or 4.6 (grey seal), 5, 6, and 7 (Figure ##FIG##5##6a##). The whisker models were then scaled up (10×) in dimensions, with the total length of the structure being 150 mm. The eight structures were 3D‐printed using the stereolithography method (Formlabs Form 3, ‘Grey Pro’ material, Figure ##FIG##5##6b##). The whisker structure to be tested was mounted on the free end of a 3D‐printed cantilever sensor (Figure ##FIG##5##6c##) that featured a serpentine graphene nanoplatelets (GNP) strain gauge near its fixed end. The details of the design and fabrication of the GNP‐based cantilever sensor and its high gauge factor and stable piezoresistive behavior as measured in the past work.<sup>[</sup>\n##UREF##12##\n20\n##, ##REF##31262009##\n48\n##, ##REF##33217747##\n49\n##, ##UREF##33##\n50\n##\n<sup>]</sup> To eliminate errors and uncertainty arising out of sensor‐to‐sensor variability, the same cantilever sensor was used for all the tests, and the whisker‐sensor assembly was designed in a way that the whisker to be tested could be easily mounted and dismounted from the cantilever sensor's free end (Figure ##FIG##5##6a–c##), thus ensuring a fair comparison between the VIV responses across the varying <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios.</p>", "<p>During the tests, the GNP‐based cantilever sensor was located above a recirculating water flume (5L Loligo Systems swim tunnel), with the whisker structure immersed into the water (Figure ##FIG##5##6d##). The whisker was oriented such that its major axis was parallel to the oncoming flow of 0.15 m s<sup>−1</sup> speed, i.e., at AOA = 0°. The VIV of the whisker excited the GNP‐based cantilever at the same frequency. The GNP sensor output was obtained using a voltage divider circuit equipped with a low‐pass RC filter, and data were sampled at a rate of 5 kHz using the NI‐DAQ USB‐6289 equipment and the NI Signal Express software. The fast Fourier transform (FFT) operation was conducted upon the resulting time series data, and the VIV response of the whisker structure was quantified by noting the dominant peak in the frequency domain, where the magnitude of the peak indicated the severity of the VIV phenomenon for each whisker structure (three examples are shown in Figure ##SUPPL##0##S5##, Supporting Information). The structures showed a peak at a frequency of ≈3 Hz, agreeing with theoretical estimate for vortex shedding frequency (≈3.15 Hz) computed using <mml:math id=\"jats-math-14\" display=\"inline\"><mml:mrow><mml:mfrac><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo>×</mml:mo><mml:msub><mml:mi>U</mml:mi><mml:mi>∞</mml:mi></mml:msub></mml:mrow><mml:mi>D</mml:mi></mml:mfrac></mml:mrow></mml:math> in which <italic toggle=\"yes\">St</italic> is the Strouhal number (0.21 for the expected Reynolds number range), <italic toggle=\"yes\">U<sub>∞</sub>\n</italic> is the free stream velocity (0.15 m s<sup>−1</sup>, Re ≈1350–1600), and <italic toggle=\"yes\">D</italic> is the characteristic cross‐sectional dimension of the scaled‐up whisker (≈10 mm). The test for each whisker structure was repeated ten times, and the spectral peak of the sensor (characterizing the VIV response) was plotted as a function of the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio as shown in Figure ##FIG##5##6e##.</p>", "<title>FEM Modeling of VIV Using COMSOL Multiphysics</title>", "<p>To gain more insight into the flow‐whisker interactions leading to whisker vibrations and VIV, FEM simulations were conducted using the coupled fluid‐structure interaction (FSI) module of COMSOL Multiphysics by placing a circular cylinder (diameter 0.6 mm), harbor seal whisker model, and grey seal whisker model in a uniform water flow of 0.2 m s<sup>−1</sup> (Re ≈ 135). The CAD models of the seal whiskers were constructed directly in COMSOL Multiphysics using the framework of Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> and the measurements given in Table ##TAB##1##2##. Each time‐dependent simulation lasted one second which was long enough to neglect any effect of initial transients. The structures were located in a flow domain (water) of dimensions 40 mm × 25 mm × 10 mm (Figure ##FIG##5##6c##), and the fixed end of the cantilevered structures was maintained at a distance of 5 mm away from the side walls and the upstream flow inlet. Note that in reality, the proximal end of the whiskers was embedded in soft material, i.e., the seal's muzzle, rather than being rigidly fixed as assumed in the simulations. In the case of the whiskers, the flow direction was along their major axis (i.e., AOA = 0°). A laminar flow model was used to solve the fluid mechanics equations, while linear elasticity was assumed for the deformation of the structures in the coupled FSI model. The wall condition at the structure‐fluid interface was no‐slip, and the surface mesh of the solid structure was made fine to ensure proper representation of surface morphology of the seal whisker.</p>", "<p>The flow domain was divided into six subdomains (Figure ##SUPPL##0##S3a,b##, Supporting Information) that included two rectangular and four trapezoidal regions (inlet and outlet faces are labeled). The trapezoidal subdomains surrounded a rectangular subdomain (3 mm x 3 mm x 30 mm) that contained the structure (i.e., the whiskers or the circular cylinder). This arrangement was chosen to ensure a dense mesh in the fluid domain around the cylinder where the flow separation regions have to be finely resolved. A tetrahedral mesh with a minimum element size of 0.0632 mm and a maximum element size of 0.585 mm was used for the solid domain (i.e., whiskers or cylinder). For the rectangular subdomain surrounding the solid structure, a predefined mesh with a minimum element size of 0.316 mm and a maximum element size of 1.06 mm was used (Figure ##SUPPL##0##S3c##, Supporting Information). Further, a swept mapped mesh was used for the four trapezoidal domains and the downstream rectangular domain. The total number of elements of the meshed simulation domain was on the order of 10<sup>6</sup>.</p>", "<p>The coupled FSI model solved both the governing equations of fluid mechanics (i.e., water flow behavior) and solid mechanics (deformation of structure) together, allowing to directly observe the whisker and cylinder (0.6 mm diameter) displacements in contrast with earlier numerical models in the literature<sup>[</sup>\n##UREF##13##\n21\n##, ##UREF##14##\n22\n##, ##UREF##15##\n23\n##, ##REF##31342935##\n24\n##\n<sup>]</sup> that focused only on the fluid behavior while assuming the solid structure to be rigid. The grey and harbor seal CAD models used in the FSI simulation were constructed using the framework of Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> and the morphometric measurements (Table ##TAB##1##2##). Identical material properties (Young's modulus = 6 GPa, density = 1300 kg/m<sup>3</sup>) were used for all the three solid structures based on the measurements of the grey seal whisker. The three structures were cantilevered at the base and placed in a uniform water flow of 0.2 m s<sup>−1</sup>. The VIV response was observed by plotting the transverse tip displacement normalized by the mean diameter (<italic toggle=\"yes\">d</italic>/<italic toggle=\"yes\">D<sub>m</sub>\n</italic>) as a function of time for a total simulation time of 1 s (Figure ##FIG##4##5g##). The simulation showed that all three structures initially bent in the direction of the flow due to the drag force (Figure ##SUPPL##0##S4##, Supporting Information), after which they started vibrating transversely due to forces exerted by periodic vortex shedding (Movies ##SUPPL##3##S2a–c##, Supporting Information). Unlike the two whiskers, the cylinder also vibrated along the flow direction at a frequency (122 Hz, Figure ##SUPPL##0##S4##, Supporting Information) that was almost double the frequency of transverse vibration (62 Hz, Figure ##FIG##5##6d##) and an amplitude (<italic toggle=\"yes\">d</italic>\n<sub>f</sub>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 0.05, Figure ##SUPPL##0##S4##, Supporting Information) that was a third of the amplitude of the transverse vibration (<italic toggle=\"yes\">d</italic>/<italic toggle=\"yes\">D<sub>m</sub>\n</italic> ≈ 0.14, Figure ##FIG##5##6d##). Such relations between the in‐line and transverse vibrations were remarkably similar to the numbers reported for flexible isolated cylinders placed in uniform flow,<sup>[</sup>\n##UREF##34##\n51\n##\n<sup>]</sup> thus serving as verification of the computational model. Further, the VIV frequency calculated from the simulated tip displacement (≈62 Hz) showed good agreement with the theoretically predicted<sup>[</sup>\n##UREF##35##\n52\n##\n<sup>]</sup> vortex shedding frequency behind the cylinder (≈66 Hz), where the latter was computed using <mml:math id=\"jats-math-15\" display=\"inline\"><mml:mrow><mml:mfrac><mml:mrow><mml:mi>S</mml:mi><mml:mi>t</mml:mi><mml:mo>×</mml:mo><mml:msub><mml:mi>U</mml:mi><mml:mi>∞</mml:mi></mml:msub></mml:mrow><mml:mi>D</mml:mi></mml:mfrac></mml:mrow></mml:math> in which <italic toggle=\"yes\">St</italic> is the Strouhal number (0.21 for the expected Reynolds number range), <italic toggle=\"yes\">U<sub>∞</sub>\n</italic> is the free stream velocity (0.2 m s<sup>−1</sup>), and <italic toggle=\"yes\">D</italic> is the cylinder diameter (0.6 mm).</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>A.M.K. and X.Z. contributed equally to this work. A.M.K. conceptualized and co‐supervised the project, performed the nanoindentation testing and internal structure characterization, conducted data analysis, and wrote the manuscript. X.Z. performed the COMSOL Multiphysics simulations, fabricated the 3D‐printed cantilever sensors, performed the experimental and numerical <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> study, conducted data analysis, and edited the manuscript. J.B. performed the 2D measurements of the whisker geometry, packaged the piezoelectric MEMS sensor and whisker assembly, and conducted VIV suppression testing in the water tunnel. M.C. co‐supervised the project, edited the manuscript, and acquired funding. M.S.T. co‐supervised the project and edited the manuscript. A.G.P.K. conceptualized and co‐supervised the project, fabricated the piezoelectric MEMS sensors, performed internal structure characterization, acquired funding, and edited the manuscript. All the authors contributed to the discussion of results and a critical reading of the manuscript.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors gratefully acknowledge financial support from the European Research Council (ERC‐STG‐101042370, ‘SEALSENSE’; ERC‐CoG‐771687, ‘CORNEA’) and the Netherlands Organization for Scientific Research grant (NWO‐vidi‐14134). The authors express their sincere gratitude to the staff of the Zeehondencentrum (Pieterburen, the Netherlands), especially Ana Rubio Garcia, Sander van Dijk, Anna Salazar Casals, and Margarita Méndez Aróstegui for providing harbor and grey seal whiskers and helping during whisker excision. The authors thank Prof. Antonis Vakis (University of Groningen) and Marijn van Rooij (Ocean Grazer BV) for granting access to the water tunnel facilities, Lucas van Rennes (GEOSCAN) for performing 3D scanning and CAD modeling of the whiskers, and Aubree Jones (University of Rhode Island) for insightful discussions regarding the internal structure of seal whiskers.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available in the supplementary material of this article.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6641-fig-0001\"><label>Figure 1</label><caption><p>Hydrodynamic trail following using undulating whiskers. a) Schematic of a seal tracking a fish by following its hydrodynamic trail, b) harbor seal, c) grey seal, d) optical micrographs of harbor and grey seal whiskers showing undulations in the whisker geometry along with the measurement parameters used to characterize 2D undulations,<sup>[</sup>\n##UREF##5##\n10\n##\n<sup>]</sup> and e) geometric framework proposed by Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> to describe the 3D undulating structure of the whisker. a) Adapted with permisson. Copyright 2021, ColoringAll.com. B,c) Reproduced with permission. Courtesy of the Zeehondencentrum (Pieterburen, NL). e) Reproduced with permission.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> Copyright 2010, The Company of Biologists.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6641-fig-0002\"><label>Figure 2</label><caption><p>2D morphometric measurements of undulating grey and harbor seal whiskers (ten each). Exemplar stitched optical micrographs of a) harbor seal whiskers and b) grey seal whiskers obtained in both the XZ (showing width) and YZ (showing thickness) views. The scale bar (2 mm) applies to all the micrographs shown in (a) and (b). 2D profiles extracted from the micrographs after image processing: c) ten harbor seal whiskers (XZ view), d) ten grey seal whiskers (XZ view), e) ten harbor seal whiskers (YZ view), and f) ten grey seal whiskers (YZ view).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6641-fig-0003\"><label>Figure 3</label><caption><p>3D morphometric measurements of undulating grey and harbor seal whiskers (one each). a) GOM ATOS III Triple Scan 8M blue light scanning system used for 3D scanning of the whisker, b) close‐up view of the whisker in the process of being scanned, c) the resulting 3D surface model of the whisker and transverse cross‐sectional measurements performed in Autodesk Netfabb. The resulting measurements (semi‐major axis, semi‐minor axis, and cross‐sectional area assuming an elliptical cross‐section) as a function of length were plotted for the d) harbor seal whisker and e) grey seal whisker. Images (a) and (b) courtesy of Lucas van Rennes (GEOSCAN, the Netherlands) and reprinted with permission.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6641-fig-0004\"><label>Figure 4</label><caption><p>Internal microstructure and properties of the grey seal whisker. a) Optical micrographs of transverse cross sections along the length of the whisker (seven shown out of a total of 24 cross sections), b) identification of three distinct regions, viz. cortex, outer medulla, inner medulla in the transverse cross sections and their corresponding share of the total cross‐sectional area as a function of distance from the proximal end of the whisker (based on a total of 24 transverse cross‐sections). c) Exemplar load‐displacement curves from the nanoindentation tests for the cortex, inner and outer medullar regions, d) Young's modulus values for the cortex, inner and outer medullar regions calculated from the nanoindentation tests at three different locations along the whisker length. e) Average Young's modulus and f) flexural rigidity values calculated along the whisker length.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6641-fig-0005\"><label>Figure 5</label><caption><p>Effect of whisker undulations on VIV. a) Schematic of whisker affixed to the piezoelectric sensor along with the exploded version of the individual components of the MEMS sensor, b) photographs of whiskers and cylinder attached to the piezoelectric MEMS sensor, and c) close‐up photograph showing the MEMS sensor and electrical connections. d) Schematic of experimental setup to test the VIV response of whiskers and a comparable circular cylinder using the MEMS sensor, e) time‐series data recorded by the piezoelectric sensor for the two whiskers and the cylinder for 1 min, f) COMSOL model setup to simulate fluid‐structure interactions of whiskers and cylinder, g) normalized tip displacements (time series data) simulated using the FEM model for the two whiskers and the cylinder.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6641-fig-0006\"><label>Figure 6</label><caption><p>The importance of the <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratio in VIV suppression. a) Schematic of whisker‐like undulating structures having three different <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios, b) 3D‐printed whisker structures having three different <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios. c) Assembly of the whisker‐like structure and the 3D‐printed piezoresistive cantilever sensor with GNP strain gauge. experimental setup to test the VIV response of whiskers and a comparable circular cylinder using the MEMS sensor. d) Experimental setup to measure VIV of whiskers having different <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios in a recirculating water flume. VIV response as a function of <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ratios determined e) experimentally using piezoresistive cantilever sensor and f) via COMSOL FSI model, offering evidence that <italic toggle=\"yes\">λ</italic>/<italic toggle=\"yes\">D</italic>\n<sub>m</sub> ≈ 4.4–4.6 represents an optimal ratio for minimum self‐induced noise due to VIV for both harbor and grey seal whiskers.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6641-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Comparison of measurements of harbor and grey seal whisker with the literature. The range refers to the standard deviation based on the measurement of 10 whiskers each of harbor and grey seals.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Species</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Source</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Peak‐to‐peak top [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Peak‐to‐peak bottom [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Crest width [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Trough width [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Crest width / Trough width</th></tr></thead><tbody><tr><td rowspan=\"4\" align=\"left\" colspan=\"1\">Harbor seal</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ref. [##UREF##5##10##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.27 ± 0.39</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.26 ± 0.40</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.92 ± 0.13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.73 ± 0.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.26</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ref. [##UREF##9##17##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.88 ± 0.45</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">N/A</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.11 ± 0.88</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.88 ± 0.03</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.27</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ref. [##REF##28840853##29##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.44 ± 0.72</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.45 ± 0.73</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.05 ± 0.24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.83 ± 0.19</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.26</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">This work</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.49 ± 0.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.53 ± 0.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.17 ± 0.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.93 ± 0.19</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.28 ± 0.18</td></tr><tr><td rowspan=\"2\" align=\"left\" colspan=\"1\">Grey seal</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ref. [##UREF##5##10##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.43 ± 0.38</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.41 ± 0.39</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.76 ± 0.13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.63 ± 0.11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.21</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">This work</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.36 ± 0.41</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.41 ± 0.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.39 ± 0.15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.23 ± 0.18</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.13 ± 0.14</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6641-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Comparison of measurements of harbor and grey seal whisker using the geometric framework of Hanke et al.<sup>[</sup>\n##REF##20639428##\n14\n##\n<sup>]</sup> The range refers to the standard deviation based on the measurement of 10 whiskers each of harbor and grey seals.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Species</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Source</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">a</italic> [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">k</italic> [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">b</italic> [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">l</italic> [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">M</italic> [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">α</italic> [°]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">β</italic> [°]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">D<sub>m</sub>\n</italic> [mm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-1\" display=\"inline\"><mml:mrow><mml:mfrac><mml:mrow><mml:mn>2</mml:mn><mml:mi>M</mml:mi></mml:mrow><mml:msub><mml:mi>D</mml:mi><mml:mi>m</mml:mi></mml:msub></mml:mfrac></mml:mrow></mml:math>\n</th></tr></thead><tbody><tr><td rowspan=\"3\" align=\"left\" colspan=\"1\">Harbor seal</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ref. [##REF##20639428##14##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.595</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.475</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.29</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.91<xref rid=\"advs6641-tbl2-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15.27</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">17.60</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.28</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ref. [##REF##28840853##29##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.525 ± 0.118</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.416 ± 0.094</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.178 ± 0.067</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.219 ± 0.083</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.724 ± 0.364</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.299 ± 5.266</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.218 ± 5.838</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.66 ± 0.08</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.26 ± 0.92</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">This work</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.58 ± 0.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.47 ± 0.09</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.25 ± 0.08</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.3 ± 0.09</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.72 ± 0.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.23 ± 13.47</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.07 ± 25.19</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.80 ± 0.14</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.36 ± 0.69</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Grey seal</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">This work</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.7 ± 0.08</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.62 ± 0.09</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.29 ± 0.03</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.33 ± 0.04</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.22 ± 0.27</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.7 ± 16.13</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">13.24 ± 22.61</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.96 ± 0.07</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.63 ± 0.77</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6641-tbl-0003\" content-type=\"Table\"><label>Table 3</label><caption><p>Comparison of measured mechanical properties of seal whiskers with the literature.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"left\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Source</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Seal species</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">E</italic> [GPa]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">EI</italic>\n<sub>xx</sub> [N−mm<sup>2</sup>]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">EI</italic>\n<sub>yy</sub> [N−mm<sup>2</sup>]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Method of measurement</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ref. [##REF##24871073##32##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Harbor</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>2 – 5.5</p>\n<p>(distal – proximal)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>0 – 1800</p>\n<p>(distal – proximal)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">N/A</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">DMA (0.001% and 0.005% strain at different frequencies)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ref. [##UREF##21##31##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Grey</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.9 – 16.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">28 – 34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">95 – 98</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Point load bending test</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ref. [##UREF##20##30##]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Harp</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.8 – 3.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">N/A</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">N/A</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Tensile test (microtester)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">This work</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Grey</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>5.6 – 6.1</p>\n<p>(distal – proximal)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>10 – 519</p>\n<p>(distal – proximal)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>184 – 820</p>\n<p>(distal – proximal)</p>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Nanoindentation</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
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display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mfenced open=\"(\" close=\")\"><mml:mi>EI</mml:mi></mml:mfenced><mml:mi>eff</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mfenced open=\"(\" close=\")\"><mml:mi>EI</mml:mi></mml:mfenced><mml:mi>c</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>EI</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>om</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>EI</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>im</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi>c</mml:mi></mml:msub><mml:msub><mml:mi>I</mml:mi><mml:mi>c</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi>om</mml:mi></mml:msub><mml:msub><mml:mi>I</mml:mi><mml:mi>om</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi>im</mml:mi></mml:msub><mml:msub><mml:mi>I</mml:mi><mml:mi>im</mml:mi></mml:msub></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6641-disp-0003\">\n<label>(3a)</label>\n<mml:math id=\"jats-math-8\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mi>X</mml:mi><mml:mi>X</mml:mi><mml:mo>,</mml:mo><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>π</mml:mi><mml:mn>4</mml:mn></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:msub><mml:mi>p</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:msubsup><mml:mi>q</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow><mml:mn>3</mml:mn></mml:msubsup></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6641-disp-0004\">\n<label>(3b)</label>\n<mml:math id=\"jats-math-9\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mi>Y</mml:mi><mml:mi>Y</mml:mi><mml:mo>,</mml:mo><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>π</mml:mi><mml:mn>4</mml:mn></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:msub><mml:mi>q</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:msubsup><mml:mi>p</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow><mml:mn>3</mml:mn></mml:msubsup></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6641-disp-0005\">\n<label>(4a)</label>\n<mml:math id=\"jats-math-10\" display=\"block\"><mml:mrow><mml:mrow><mml:mspace width=\"0.33em\"/><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mi>X</mml:mi><mml:mi>X</mml:mi><mml:mo>,</mml:mo><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>π</mml:mi><mml:mn>4</mml:mn></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>p</mml:mi><mml:mrow><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:msubsup><mml:mi>q</mml:mi><mml:mrow><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow><mml:mn>3</mml:mn></mml:msubsup><mml:mo>−</mml:mo><mml:msub><mml:mi>p</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:msubsup><mml:mi>q</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow><mml:mn>3</mml:mn></mml:msubsup></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6641-disp-0006\">\n<label>(4b)</label>\n<mml:math id=\"jats-math-11\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mi>Y</mml:mi><mml:mi>Y</mml:mi><mml:mo>,</mml:mo><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>π</mml:mi><mml:mn>4</mml:mn></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>q</mml:mi><mml:mrow><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:msubsup><mml:mi>p</mml:mi><mml:mrow><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow><mml:mn>3</mml:mn></mml:msubsup><mml:mo>−</mml:mo><mml:msub><mml:mi>q</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:msubsup><mml:mi>p</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>m</mml:mi></mml:mrow><mml:mn>3</mml:mn></mml:msubsup></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6641-disp-0007\">\n<label>(5a)</label>\n<mml:math id=\"jats-math-12\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mi>X</mml:mi><mml:mi>X</mml:mi><mml:mo>,</mml:mo><mml:mi>c</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>π</mml:mi><mml:mn>4</mml:mn></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:msub><mml:msubsup><mml:mi>q</mml:mi><mml:mi>c</mml:mi><mml:mn>3</mml:mn></mml:msubsup><mml:mo>−</mml:mo><mml:msub><mml:mi>p</mml:mi><mml:mrow><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:msubsup><mml:mi>q</mml:mi><mml:mrow><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow><mml:mn>3</mml:mn></mml:msubsup></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6641-disp-0008\">\n<label>(5b)</label>\n<mml:math id=\"jats-math-13\" display=\"block\"><mml:mrow><mml:mrow><mml:mspace width=\"0.33em\"/><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mi>Y</mml:mi><mml:mi>Y</mml:mi><mml:mo>,</mml:mo><mml:mi>c</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>π</mml:mi><mml:mn>4</mml:mn></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>q</mml:mi><mml:mi>c</mml:mi></mml:msub><mml:msubsup><mml:mi>p</mml:mi><mml:mi>c</mml:mi><mml:mn>3</mml:mn></mml:msubsup><mml:mo>−</mml:mo><mml:msub><mml:mi>q</mml:mi><mml:mrow><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub><mml:msubsup><mml:mi>p</mml:mi><mml:mrow><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow><mml:mn>3</mml:mn></mml:msubsup></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>" ]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
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[]
[]
[ "<supplementary-material id=\"advs6641-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6641-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 1a</p></caption></supplementary-material>", "<supplementary-material id=\"advs6641-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 1b</p></caption></supplementary-material>", "<supplementary-material id=\"advs6641-supitem-0004\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 2a</p></caption></supplementary-material>", "<supplementary-material id=\"advs6641-supitem-0005\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 2b</p></caption></supplementary-material>", "<supplementary-material id=\"advs6641-supitem-0006\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 2c</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6641-tbl2-note-0001\"><label>\n<sup>a)</sup>\n</label><p>It is likely that the value of <italic toggle=\"yes\">M</italic> was mistakenly underreported (by a factor of 2) in Ref.[##REF##20639428##14##] as pointed out by Beem<sup>[</sup>\n##UREF##36##\n53\n##\n<sup>]</sup> in her PhD dissertation.</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2304304-s002.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304304-s003.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304304-s004.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304304-s006.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304304-s001.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304304-s005.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
53
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Oct 17; 11(2):2304304
oa_package/db/8d/PMC10787063.tar.gz
PMC10787064
37984867
[ "<title>Introduction</title>", "<p>Soft robots are composed of compliant materials that are capable of flexible movement, autonomous behavior, and safer human‐machine interaction. Inspired by biological systems, such systems are designed to mimic the locomotion and performance of soft animals that exist in nature to achieve complex motion in uncertain or constrained environments. In recent decades, a variety of soft robotic systems and devices have been developed,<sup>[</sup>\n##REF##26017446##\n1\n##, ##UREF##0##\n2\n##, ##UREF##1##\n3\n##, ##REF##28539483##\n4\n##, ##UREF##2##\n5\n##\n<sup>]</sup> with a range of milestone works.<sup>[</sup>\n##UREF##3##\n6\n##, ##UREF##4##\n7\n##, ##REF##26160940##\n8\n##, ##REF##33157883##\n9\n##, ##UREF##5##\n10\n##, ##REF##33157852##\n11\n##, ##REF##33658693##\n12\n##\n<sup>]</sup> However, the soft bodies of the robots can be damaged during the operation as a result of mechanical fatigue, punctures, electrical breakdown, and electrochemical corrosion, which can lead to unexpected failure during operation as an associated additional energy consumption and cost. The creation of soft self‐healing robots that are able to self‐repair and heal from structural damage will highly enhance the robustness and sustainability of soft robots.</p>", "<p>A range of self‐healing mechanisms and materials are available to embed within a soft robot. An extrinsic self‐healing process relies on the intervention of pre‐embedded healing agents in polymers, often carried in the form of microcapsules or microvascular fibers, which respond to release the healing agents upon rupture and react to bind damaged surfaces. Intrinsic self‐healing of polymer is possible by exploiting the reversible interactions among the dynamic covalent bonds that are produced by associative or dissociative mechanisms, or non‐covalent bonds with or without external stimulus.<sup>[</sup>\n##REF##32907199##\n13\n##, ##REF##20839257##\n14\n##, ##REF##23864042##\n15\n##, ##UREF##6##\n16\n##, ##UREF##7##\n17\n##, ##UREF##8##\n18\n##, ##UREF##9##\n19\n##, ##UREF##10##\n20\n##, ##UREF##11##\n21\n##, ##UREF##12##\n22\n##, ##UREF##13##\n23\n##\n<sup>]</sup> Comprehensive reviews on the topic of self‐healing polymers and their applications for soft robotics are published.<sup>[</sup>\n##REF##32907199##\n13\n##, ##REF##20839257##\n14\n##, ##REF##23864042##\n15\n##, ##UREF##6##\n16\n##, ##UREF##7##\n17\n##, ##UREF##8##\n18\n##, ##UREF##9##\n19\n##, ##UREF##10##\n20\n##, ##UREF##11##\n21\n##, ##UREF##12##\n22\n##, ##UREF##13##\n23\n##\n<sup>]</sup> Since the intrinsic healing mechanism operates at the molecular level, it has the particular advantage of being able to enable repeated self‐healing of the material.</p>", "<p>Non‐covalent interactions are ubiquitous in nature and biological systems, such as hydrogen bonding, metal‐ligand coordination, or ionic interactions, contributing to protein assembly, structural stability, molecular recognition, mechanical properties, and responsive functions. Inspired by nature, the introduction of non‐covalent interactions into commercial polymers provides a unique potential to develop new functionalities and expand the applications of engineering polymers. As an example, commercial poly (styrene‐butadiene‐styrene) elastomers (SBS) typically exhibit phase‐separated microstructures, where the styrene blocks cluster and act as physical crosslinks for reinforcement and melt‐processibility. By exploiting the vinyl groups of the butadiene blocks of SBS, we have successfully grafted a range of polar groups onto the SBS backbone via one‐step thiol‐ene chemistry and introduced greater levels of polarity to the non‐polar elastomer to intrinsically affect both dielectric and mechanical properties, and in particular to introduce a self‐healing function.<sup>[</sup>\n##UREF##14##\n24\n##, ##UREF##15##\n25\n##, ##UREF##16##\n26\n##\n<sup>]</sup> We have synthesized the methyl thioglycolate grafted SBS (MGSBS) elastomer in our previous work and investigated the reaction conditions including the excess of methyl thioglycolate required for efficient thiol group and vinyl group coupling and minimal interchain crosslinking.<sup>[</sup>\n##UREF##14##\n24\n##\n<sup>]</sup> The excellent self‐healing ability of MGSBS at ambient conditions was demonstrated in the event of mechanical cuts and electrical breakdown.<sup>[</sup>\n##UREF##15##\n25\n##\n<sup>]</sup> After experiencing a dielectric breakdown, the dielectric strength can be recovered by up to 67% of the initial strength, and after mechanical damage, 39% of the initial dielectric strength can be recovered. Firstly, we punctured the elastomer with a needle probe, and the pinhole defects were cleaned and self‐healed at room temperature. To maximize the degree of damage and healing, the pristine elastomer was cut fully through its thickness using a sharp and clean scalpel and healed by applying a small load of 5 N at ambient temperature for 5 min to ensure the damaged surfaces were in good contact and flattened in‐plane. Once the cutting site had healed, the ≈25 mm in length cutting had fully closed, and the healed site could be clearly observed when stretched normally to the cutting direction. The MGSBS had recovered 25% of its strength with a strain of over 100%. According to our investigations, the highest graft ratio of 98.5% of MGSBS led to the highest self‐healing efficiency and highest relative permittivity.<sup>[</sup>\n##UREF##16##\n26\n##\n<sup>]</sup>\n</p>", "<p>Although the range of self‐healing mechanisms of polymers have shown significant potential to empower self‐healing capability to soft robots, only a limited number of publications demonstrate their use in soft robotic devices and applications.<sup>[</sup>\n##UREF##7##\n17\n##, ##UREF##9##\n19\n##, ##UREF##10##\n20\n##\n<sup>]</sup>\n</p>", "<p>A self‐sealing soft gripper that is resistant to punctures was first developed by Shepherd et al. in 2013,<sup>[</sup>\n##REF##24123311##\n27\n##\n<sup>]</sup> by embedding highly fibrillated polyaramid fibers in a silicone elastomer. This allows the fabricated soft actuator or gripper to recover its original shape by physically pressing the punctured surfaces and sealing the hole. Terryn et al. developed a variety of soft self‐healable actuators, grippers, and robotic hands based on thermal reversible Diels‐Alder (DA) reactions (11, 28, 29). These devices could be healed and were able to fully recover performance from macroscopic damages such as scratches, cuts, and ruptures after applying a mild heat treatment (70–90 °C). For example, healing of the actuator was demonstrated when damaged under two dramatic phenomena,<sup>[</sup>\n##REF##33157852##\n11\n##\n<sup>]</sup> namely (i) perforation damage when the device was over‐pressurized at 0.46 bar and (ii) a deep wall cut of ≈4.4 mm in length and a thickness of 0.3 mm. Both forms of damage were successfully healed after 30 h at a maximum healing temperature of 70 °C. To eliminate the need for external heating resources, a soft self‐healable gripper was developed that used a novel Diels‐Alder network with high molecular mobility, which enabled autonomous healing macroscopic damage at room temperature<sup>[</sup>\n##UREF##17##\n28\n##\n<sup>]</sup>; however, this is at the expense of reduced output power and force capabilities of the gripper.</p>", "<p>With the recent development of additive manufacturing technology, 3D‐printed self‐healable robotic devices have been developed.<sup>[</sup>\n##REF##32160110##\n29\n##, ##REF##32264440##\n30\n##, ##UREF##18##\n31\n##\n<sup>]</sup> Roels et al. tested the healability of a 3D‐printed Diels‐Alder‐based gripper.<sup>[</sup>\n##REF##32160110##\n29\n##\n<sup>]</sup> When the fingers of the gripper were subjected to a puncture, cut, and being sliced in half, they could heal after being heat treated at 90 °C for 30 min, and after held at room temperature for 24 h the gripper was able to recover its full performance with only visible scars. Wallin et al. developed a cost‐efficient stereolithography (SLA)‐based fabrication technique to create soft robots.<sup>[</sup>\n##REF##32264440##\n30\n##\n<sup>]</sup> They prototyped fluidic elastomer actuators from a silicone (polydimethylsiloxane) material that was filled with thiol‐ene resins and formed at high resolution (≈50 µm) and at rapid fabrication speeds. The material system allowed rapid self‐healing via sunlight‐induced photopolymerization to recover actuator properties after damage from scratches and punctures. When the membrane of the fluidic elastomer actuators was pierced, the resin was able to flow outward and be exposed to sunlight, thereby leading to photopolymerization and self‐healing of the hole. A micro‐stereolithography system was also used to fabricate soft self‐healable muscles, which were manufactured from a disulfide‐based supramolecular network with healing capacities.<sup>[</sup>\n##UREF##18##\n31\n##\n<sup>]</sup> The muscles were able to recover entirely from being cut in half to fully restore their initial structural integrity and mechanical strengths to 100% after healing for 2 h at 60 °C. The muscle was able to lift a weight ten times its own weight for multiple cycles.</p>", "<p>To enable shape memory effects, Zhang et al. developed thermo‐reversible polyurethanes (PDAPU) with targeted light‐controlled shape memory and self‐healing properties (32). The reactive cross‐linking of aniline trimer (AT) in the PDAPU network formed a homogeneous network with enhanced mechanical properties, good solvent resistance, and highly efficient photothermal capability. The materials were used to print a variety of self‐healable 3D objects including a butterfly, octopus, hand, and flat dog bone, where the self‐healing efficiency was &gt;70%. Zhang et al. developed a double‐network self‐healing shape memory polymer material for high‐resolution (up to 30 µm) light processing‐based 3D printing technology.<sup>[</sup>\n##UREF##20##\n33\n##\n<sup>]</sup> The material was made by incorporating a semicrystalline polycaprolactone (PCL) into a methacrylate‐based shape memory polymer. The PCL linear polymer provided the self‐healing capability by melting PCL in the matrix at 80 °C, with a healing efficiency of &gt;90% for mechanical damage. A damaged 3D‐printed gripper was able to heal at 80 °C for 5 min. The healed gripper was able to perform when driven by the shape memory mechanism and was able to lift a weight of 10 g. To develop self‐healing modular actuators for reconfigurable robots, Gomez et al. developed a vat photopolymerizable self‐healing elastomer which was capable of extreme elongations of up to 1000%.<sup>[</sup>\n##UREF##21##\n34\n##\n<sup>]</sup> The self‐healing elastomer was developed using a combination of thiol/acrylate mixed chain/step‐growth polymerizations and applied a combination of physical processes and dynamic‐bond exchange via thioethers to achieve full self‐healing capability over multiple damage and healing cycles. Soft modular actuators with complex internal cavities and channel networks can be printed with high resolution and the use of 3D‐printed technology provides an effective fabrication tool to open new research areas in the development of multifunctional soft robots with complex geometries, self‐healing, and shape memory capabilities.</p>", "<p>Self‐healable dielectric elastomer actuators (DEAs) have been developed and applied to soft robots to achieve large actuation strain, high bandwidth, high energy density, self‐healing capability, and flexible nature. Zhang et al. reported on the electrical and mechanical self‐healing in high‐performance dielectric actuator which uses a thermoplastic methyl thioglycolate–modified styrene–butadiene–styrene (MG‐SBS) elastomer.<sup>[</sup>\n##UREF##15##\n25\n##\n<sup>]</sup> They investigated the DEAs and characterized the electrical properties and actuator response and healing process before and after healing. The MG‐SBS elastomer shows promising healing capability, which could heal damage from dielectric breakdown, mechanical damage, and a combination of mechanical and electrical damage. This work has benchmarked the feasibility of using MG‐SBS‐based material for creating complex soft robots that provide a range of motion. Soft hydraulically amplified self‐healing electrostatic (HASEL) actuators, which employ a mechanism that couples electrostatic and hydraulic forces to achieve a variety of actuation motions were first developed by Acome et al.<sup>[</sup>\n##REF##29302008##\n35\n##\n<sup>]</sup> The HASEL actuators apply a mechanism that couples electrostatic and hydraulic forces to achieve a variety of actuation modes. The electrohydraulic mechanism is used to activate soft‐matter hydraulic architectures, while the fluidic actuation mechanism is used to realize the muscle‐like performance and self‐sensing abilities of DE actuators. The HASEL actuator exhibited muscle‐like performance and self‐healing capability after being subjected to dielectric breakdown. The use of liquid dielectrics in HASEL actuators allows for immediate recovery of functionality after dielectric breakdown events. The actuators can be used in a stacked configuration to generate high deformation and their response can be adapted to different geometries. The group prototyped two HASEL actuators in both donut and planar geometries. A stack of five donut HASEL actuators was able to achieve a 37% linear strain and large actuation response at frequencies up to 20 Hz. A soft gripper was developed using two stack donut HASEL actuators which were able to successfully grasp delicate objects, such as raspberries and eggs. The advantage of using liquid dielectrics is that they can rapidly return to an insulating state after dielectric damage, which enables HASEL actuators to effectively self‐heal after being subjected to dielectric breakdown. The donut HASEL actuators were able to provide self‐healing for 50 dielectric breakdown events, with the highest breakdown voltage of 29.3 kV. To further improve HASEL performance, Tian et al. developed new HASEL actuators that integrate a bilayer polymer shell for improved properties of high dielectric strength, dielectric permittivity, and elastic modulus.<sup>[</sup>\n##UREF##22##\n36\n##\n<sup>]</sup> The new bilayer HASEL exhibited a strain of 164% at 5 kV and a load‐bearing capability of 620 mN at 6 kV. The high strain, high output load, and self‐healing capability position HASEL actuators as promising candidates for the development of multifunctional soft robotic systems.</p>", "<p>Tang et al. developed a new class of fully soft self‐healable pumps that utilize electrical energy to pump liquid through an electron and ion migration mechanism.<sup>[</sup>\n##REF##33854071##\n37\n##\n<sup>]</sup> A self‐healing liquid based on a dibutyl sebacate‐tung oil solution, where the tung oil was dissolved evenly in the dibutyl sebacate, was used as the liquid medium of the pump. Tung oil was selected as it has excellent solidification properties due to its unique composition, namely oxygen‐linked fatty carboxylate residue and reactive conjugated carbon–carbon double bonds. When the soft pumps were damaged, the self‐healing liquid was exposed to air, and a solid film was formed which solidified, which automatically heals any damage. The self‐healing time is dependent on the temperature, and for a small puncture damage a healing time of ≈6 h at 35 °C and ≈24 h at 24  °C is required. The self‐healable pumps are scalable, which provides opportunities for developing a variety of untethered self‐healable soft robotic devices.</p>", "<p>In this work, we have created a new form of soft intrinsically self‐healable robot using a melt‐extruded MG‐SBS elastomer tube, which enables the robot to autonomically self‐heal from multiple damage events at room temperature after 24 h. We examined the self‐healing performance and efficiency of the robot, robot mechanical characterization, and dynamic performance before and after healing. The robot is designed and actuated using a new micro two‐way SMA (TWSMA) spring actuation system. This new approach provides a route to the creation of future soft robots that have large output force, fast locomotion speed, and self‐healing capabilities. We also demonstrated a scalable and continuous melt‐extrusion process for functional soft robotics development.</p>" ]
[]
[ "<title>Results</title>", "<title>Self‐Healing Mechanism and Performance of Melt‐Extruded MG‐SBS Tubes</title>", "<p>\n<bold>Figure</bold> ##FIG##0##\n1A## shows that the introduction of polar methyl thioglycolate to the butadiene blocks of SBS with a high grafting ratio of 98.5% induced a change in the phase morphology from order to disorder transition (AFM images<sup>[</sup>\n##UREF##16##\n26\n##\n<sup>]</sup>). This indicated that the polar groups have altered the intramolecular interactions and interrupted the clustering of the polystyrene hard domains. As characterized by Raman, real‐time FTIR, and SAXS in our previous work,<sup>[</sup>\n##UREF##14##\n24\n##\n<sup>]</sup> the δ<sup>+</sup> CH<sub>2</sub> or δ<sup>+</sup> CH<sub>3</sub> group on either side of the ester of methyl thioglycolate is able to accept electron charge from the δ‐ aromatic center of styrene, i.e., CH···π interaction, which homogenizes the phase morphology from a sea‐island structure to a more disordered microstructure through the abundant electrostatic interactions along the polymer chains. As the electron density within the aromatic ring decreases, the HC‐CH aromatic bonds experience a weaker pull from the center of the ring, thereby increasing the bond length slightly. A similar interaction is observed in nature to give proteins their secondary structure.<sup>[</sup>\n##REF##19037862##\n39\n##\n<sup>]</sup> The self‐healing behavior of MG‐SBS originates from both the microstructural homogeneity and the dynamic electrostatic interactions among the polymer chains and is enhanced with the grafting ratio.<sup>[</sup>\n##UREF##14##\n24\n##\n<sup>]</sup> Figure ##FIG##0##1B## provides a snapshot of the mechanical and electromechanical properties of SBS and MG‐SBS. The grafting of methyl thioglycolate increased the relative permittivity (<italic toggle=\"yes\">ε<sub>r</sub>\n</italic>) of SBS from <italic toggle=\"yes\">ε<sub>r</sub>\n</italic> = 2.8 to <italic toggle=\"yes\">ε<sub>r</sub>\n</italic> = 11.4 at 10<sup>3</sup> Hz in MG‐SBS. In addition, the MG‐SBS exhibited reduced stiffness and strength as compared to SBS, where the lower Young's modulus of 2.87 ± 0.6 MPa, tensile strength of 3.13 ± 0.12 MPa, and a strain at break of 569 ± 25.9% meet the mechanical property requirements of the high strain crawling robot, in particular, the reduced Young's modulus and lower hysteresis loss of MG‐SBS are advantageous for actuation. The stress relaxation of MG‐SBS is decreased to 78% of its maximum stress value when subjected to a fixed 100% elongation, which is higher than SBS of 55%, indicating the stronger interchain electrostatic interaction preventing polymer chain slippage, which does not exist in SBS.</p>", "<p>Due to the thermoplastic nature of MG‐SBS, it can be continuously melt‐extruded into elastomer tubing at 170–180 °C (Figure ##FIG##0##1C##), where the tubes formed are able to preserve the ambient autonomous self‐healing properties. Due to the advantages of intrinsic healing, which can heal multiple times and does not require the use of encapsulants, and autonomous healing, which requires the application of additional external stimuli, we selected methyl thioglycolate. The grafting of methyl thioglycolate increased the relative permittivity (<italic toggle=\"yes\">ε</italic>\n<sub>r</sub>) of SBS from <italic toggle=\"yes\">ε</italic>\n<sub>r</sub> = 2.8 to <italic toggle=\"yes\">ε</italic>\n<sub>r</sub> = 11.4 at 10<sup>3</sup> Hz in MG‐SBS, while maintaining a low tan δ of 0.01 (where tan δ = dielectric loss/relative permittivity) at 10<sup>3</sup> Hz. Meanwhile, MGSBS exhibited reduced stiffness and strength as compared to SBS, where the lower Young's modulus of 2.87 ± 0.6 MPa, tensile strength of 3.13 ± 0.12 MPa and a strain at break of 569 ± 25.9% is particularly attractive to the requirement the high strain crawling robot, where the reduced Young's modulus (from 51.7 ± 6.4 MPa for SBS to 2.87 ± 0.6 MPa for MG‐SBS) is advantageous for actuation.</p>", "<p>Self‐healing of this material is likely to originate from either the δ+ CH<sub>2</sub> or δ+ CH<sub>3</sub> group on either side of the MG ester, which accepts electron density from the δ‐ aromatic ring, as shown in Figure ##FIG##0##1##. As the electron density within the aromatic ring decreases, the HC‐CH aromatic bonds experience a weaker pull from the center of the ring, increasing the bond length slightly. A similar interaction is observed in nature to give proteins their secondary structure.<sup>[</sup>\n##REF##19037862##\n39\n##\n<sup>]</sup> The mode of operation of the crawling robot leads to deformation of the main elastomer body to strain levels of ≈10%. Therefore, the key healing requirements are recovery of the stiffness of the material and the ability to recover the failure strain to a sufficient level.</p>", "<title>Soft Self‐Healable Robot</title>", "<p>Inspired by the crawling mechanism of the caterpillar, which is also termed a two‐anchor crawling mechanism, the design and architecture of the self‐healable robot are shown in <bold>Figure</bold> ##FIG##1##\n2\n##, which consists of a self‐healing body, a micro two‐way SMA (TWSMA) spring actuator, silicone‐based front and rear feet, and seven supporting feet. The self‐healing robot is designed to manage damage to its outer body not to its actuation system, since the outer body is most susceptible to damage from its local environment. The front and rear feet were cast using silicone rubber, and the supporting feet were 3D‐printed using polylactide (PLA). All feet were adhered to the self‐healing MG‐SBS body with the same gap distance of 15 mm. The length of the self‐healing body of the robot is 138 mm, with a “skin” thickness of 1 mm. A micro SMA spring actuator with a spring diameter of 1.5 mm and a length of 110 mm was arranged along with the body. The designed T‐shaped holes with a diameter of 3 mm in the front and rear feet are used to fix the TWSMA spring and the cable connected to the TWSMA spring, whereas a hole with a diameter of 4 mm on the supporting feet is present to arrange the TWSMA spring. When the TWSMA spring contracts, the distance between the front and rear feet decreases, and since the length of the self‐healing body is constant, a bending deformation is realized.</p>", "<p>The self‐healable robot has two moving feet, the front and rear feet, and seven supporting feet. The moving feet enable the movement of the robot by spontaneously changing the friction force between the feet and the ground surface. The single‐direction mechanism of foot movement is shown in <bold>Figure</bold> ##FIG##2##\n3\n##, where Figure ##FIG##2##3A## shows a wedge‐shaped structure with a frictionless surface and a frictional surface. The frictional surface is made using a silicone rubber with a high friction coefficient, while the frictionless surface with a low friction coefficient is realized by adhering transparent tape onto the silicone rubber surface. When the wedge block moves backward, the wedges deform, and the frictional surface makes contact with the ground, resulting in a significant increase in the contact area. As a result, a large friction force is generated and represents a high friction state. When the wedge block moves forward, only the small tip areas of the wedges deform. The contact surface with the ground is the frictionless surface and the contact area is relatively small, therefore, the generated friction force is small and represents a low friction state, as shown in Figure ##FIG##2##3A##. This use of single‐direction movement structure provides three advantages: i) the switching between the friction state can be realized by the internal actuation force, including the elastic potential energy of the TWSMA spring, the strain energy of the self‐healing body, and the gravitational potential energy of the robot, rather than the introduction of any external actuation forces; ii) the force required for switching the friction state is relatively small, and the forces produced by the robot itself are sufficiently large to change the friction state, including the elastic forces of both the SMA spring and the self‐healable robot body, and the gravity of the robot; iii) the switching time required to change the friction state is short, which can be neglected when controlling the robot. In summary, the friction force for a robot moving backward is much larger than that for moving forward, and the change of the friction force is only dependent on the moving direction. Therefore, by using a single‐directional movement mechanism, the self‐healable robot can effectively move forward.</p>", "<p>To enable efficient movement, the advanced design of the robot feet is implemented on the self‐healing robot with an effective 0 to 90° range frictional contact surface, as shown in Figure ##FIG##2##3B##, while the simplified foot block is shown in Figure ##FIG##2##3A## can achieve single‐direction movement at a horizontal state. When the robot is actuated, the advanced design robot feet rotate from the horizontal state to another angle which, along with the bending of the body, efficiently generates frictional forces during movement to continuously drive the robot forward. Insufficient use of supporting feet can lead to collapse of the robot body due to gravity and the low stiffness of the self‐healing body. The use of too many supporting feet can lead to potential problems, including i) limited deformation due to the close arrangement of the feet and their self‐interference; and ii) the additional weight of the self‐healable robot that can limit robot movement. In our design, seven supporting feet were used based on the simulated results, which suggest the need for optimization between the movement flexibility and the robot weight. In addition, the TWSMA hole on the supporting feet should not interfere with the contraction and relaxation of the TWSMA spring, so the thickness of the supporting feet was designed as 2 mm, and the diameter of the hole is 4 mm, which is much larger than the diameter of the TWSMA spring (1.5 mm) to allow the free of movement.</p>", "<p>Inspired by the crawling mechanism of the caterpillar, which is also termed a two‐anchor crawling mechanism, the actuation mechanism of the self‐healable robot in a single locomotion step is illustrated in Figure ##FIG##2##3C##. A single locomotion step can be divided into two periods, namely the TWSMA heating period and TWSMA cooling period. During the heating period, the TWSMA spring contracts and generates a force to pull the front and rear feet closer, so that the rear foot moves forward and the front foot keeps still due to the high friction force generated by the frictional surface of the wedge‐shape foot; see Stage 1 to Stage 3 in Figure ##FIG##2##3C##. The self‐healing tube is deformed into an inverted U shape, so the elastic potential energy of the TWSMA spring transforms into the gravitational potential energy of the robot and the strain energy of the self‐healing tube. During the cooling period, the TWSMA spring extends, and the self‐healing tube returns to its original shape as a result of the release of the gravitational potential energy and the strain energy; see Stage 3 to Stage 5 in Figure ##FIG##2##3C##. A force generated by these two energies pushes the front foot moving forward, while the rear foot keeps still due to the strong friction resistance. After a heating period and a cooling period of the TWSMA spring, the self‐healable robot can move forward over a distance, which is defined as the moving distance per step.</p>", "<title>Robot Performance</title>", "<p>To investigate the self‐healing capability of the robot, we cut and damaged the robot twice during characterization. The robot was autonomically healed successfully after the introduction of two damage events, as shown in <bold>Figure</bold> ##FIG##3##\n4A## where the status and performance of the original and healed robot after the first damage and the second damage are shown. In the undamaged state, the average velocity of the original robot was 21.6 cm/min (= 18 mm <sup>−1</sup>step) and the maximum height of the robot, as defined in Figure ##FIG##3##4B##, was 24.22 mm. The middle height equals the maximum height for an undamaged robot. The locomotion of the original robot is shown in Movie ##SUPPL##1##S1## (Supporting Information). The first damage was introduced by cutting with scissors in the middle position of the robot body. After the introduction of damage, the two parts of the robot were placed together for 24 h at room temperature to automatically self‐heal. The locomotion of the healed robot after the first damage is shown in Movie ##SUPPL##2##S2## (Supporting Information), where the average velocity decreases to 11.7 cm/min (= 9.75 mm <sup>−1</sup>step). After healing from the initial introduction of damage, the self‐healable body forms an M shape when it is actuated by the micro SMA, instead of the original inverted U shape. This is because the elastic modulus of the material in the cutting location after healing is smaller than that of the original so the deformation at the healed location is larger than that of the rest of the self‐healable body. The middle and maximum heights are used to characterize the robot's performance, as shown in Figure ##FIG##3##4B##. The middle and maximum heights of the healed robot are 18.12 and 20.09 mm, respectively. The M shape deformation of the healed body decreases the maximum height and the average velocity of the robot, but the robot continues to function with good performance with good physical crawling heights of 75%–83% of the original height, and with an average crawling speed of 54% of the original speed.</p>", "<p>To investigate the robustness and repeatability of the self‐healing performance, a second level of damage was conducted by introducing two scissor cuts at the positions of 1/4 and 3/4 of the self‐healable body. Three separated body parts were placed together for 24 h at room temperature for self‐healing. The locomotion of the robot after the second damage and 24 h self‐healing process are shown in Movie ##SUPPL##3##S3## (Supporting Information). The robot successfully recovered from the damage, where the average velocity was 16 cm/min (= 13.33 mm <sup>−1</sup>step). The middle height of the robot is 20.1 mm, and the maximum height is 23.42 mm, which are very close to the original undamaged states. The robot functions with good physical crawling heights of 83%–96% of the original height, and with an average crawling speed of 74% of the original speed. When actuated, the robot is almost fully recovered to the original inverted U shape, as shown in Figure ##FIG##3##4A##.</p>", "<title>Mechanical Properties of Micro SMA Spring Actuators</title>", "<p>The mechanical properties of micro SMA spring actuators are shown in <bold>Figure</bold> ##FIG##4##\n5A##, where the temperature, force, and length of the actuator were used to characterize the properties. The SMA length reflects the compression and extension processes of the actuator, whereas the signal indicates the heating (signal = 1) and cooling (signal = 0) states. The micro SMA spring actuator begins to heat at 20 s, and the temperature and force of the SMA spring are increased. The SMA spring needed to be heated for 30 s to reach the maximum temperature of 115 °C. The output force of the SMA spring increased from 0 to 1.04 N within 4 s and reached its steady state with a measured temperature of 55 °C. The SMA actuator was continually heated and began to compress at 75 s until reaching a zero‐output force at 126 s, and then returned to its original length at 175 s. After the compression and extension process, the micro SMA spring actuator stopped heating and started cooling at room temperature of 23 °C. During the cooling process, the output force decreased from 1.11 N to 0 in 5 s and the temperature dropped from 129 °C to 75 °C. The temperature of the SMA spring requires 60 s decreasing to return to room temperature.</p>", "<p>The temperature and force during the heating and cooling processes are shown in Figure ##FIG##4##5B,C##. Compared to the cooling process, the temperature fluctuated to a greater extent during the heating process from 30 to 60 s, which was a result of the stress‐induced martensite (SIM) transformation.<sup>[</sup>\n##UREF##24##\n40\n##\n<sup>]</sup> When the micro SMA is fully heated, its crystal structure transforms from martensite into austenite, and the transformation from austenite into martensite is achieved by cooling the SMA. The stress‐induced martensite transformation is an alternative method to achieve the structural transformation from austenite into martensite. During the heating process, the length of the micro SMA spring actuator was maintained constant in a tensile testing machine, which led to an increased output force, so that the actuator was stressed. While some martensite formation was induced by the stress‐induced transformation, the continual heating of the micro SMA actuator led to the martensite formed by the applied stress ultimately transforming to the austenite phase due to a temperature‐induced transformation. The competition between the stress‐induced transformation (from austenite to martensite) and the temperature‐induced transformation (from martensite to austenite) led to a fluctuation of temperature during the heating process, as shown in Figure ##FIG##4##5B##. Compared with the slow change of the temperature, the force changed rapidly during the heating and cooling process (see Figure ##FIG##4##5C##). The output force of the micro SMA spring actuators is related to the phase ratio between martensite and austenite phases of the SMAs, where the relationship between the spring length and force during compression and extension is shown in Figure ##FIG##4##5D##.</p>", "<p>The stiffness of the SMA spring is 0.040 N mm<sup>−1</sup> during compression and 0.043 N mm<sup>−1</sup> during extension. The small difference in stiffness (0.003 N mm<sup>−1</sup>) is a result of the phase ratio of the martensite and austenite, which is dependent on the stress and temperature.<sup>[</sup>\n##UREF##25##\n41\n##\n<sup>]</sup> The stress history experienced by the micro SMA spring actuator induces a stress‐induced martensite transformation, leading to the phase ratio difference and a very small difference in stiffness. The stress history is defined as the process of the stress suffered by the SMA spring from the initial start to the present. When the SMA spring is fully heated, the martensite is almost transformed into austenite, and the effect of temperature is reduced. However, the stiffness difference (0.003 N mm<sup>−1</sup>) is small and does not significantly affect the performance of SMA springs.</p>", "<p>For the robot to operate repeatedly the shape memory effect needs to operate repeatedly and ideally provide a reversible spontaneous shape change during cooling and heating without any need to apply external stress. Figure ##FIG##4##5E## shows the two‐way properties of the micro SMA spring actuator, where the contraction and extension processes are shown in Movie ##SUPPL##4##S4## (Supporting Information). There was no external force acting on the micro SMA spring actuator during the processes, and the spring was free to move and unstressed. The phase transformation between the martensite and austenite phase were therefore a result of the change in temperature. The spring length at zero force is the length of the micro SMA spring without any external force acting on it, which is temperature‐dependent. Before the heating process, the spring length is 134 mm and during the heating process, the spring length contracts rapidly from 134 mm to 80 mm in 2 s due to the phase transformation from the martensite to austenite phase. During the cooling process, the spring length spontaneously extends to 133 mm in 10 s as it transforms from the austenite to martensite phase. The original length of the micro SMA spring actuator was almost recovered after being fully heated and cooled down to room temperature. During the two‐way SMA (TWSMA) training preparation, the micro SMA spring actuator generated permanent deformation by a plastic strain, which makes it possible to obtain a reversible spontaneous shape change during cooling and heating processes without any external stress. As a result, the TWSMA is able to memorize its shape at both high and low temperatures to provide a mechanism for robot motion. In Figure ##FIG##4##5D##, the contraction and extension of the micro SMA spring actuator were controlled by the tensile machine, resulting in external stress acting on it. After being fully heated, the spring length at zero force with an external stress is 109 mm, which is larger than 80 mm (see Figure ##FIG##4##5E##) without an external load. This length difference is caused by the stress history suffered by the micro SMA spring actuator. With regard to actuator performance, the effective working range of the actuator with stress was 109–135 mm, which is smaller than the stress‐free micro SMA (80–134 mm). A challenge of using a TWSMA is that the strain can rapidly deteriorate at high temperatures or when subjected to a high external force.<sup>[</sup>\n##UREF##26##\n42\n##\n<sup>]</sup> Therefore, the micro SMA spring actuator was selected for use at low temperatures and low external force conditions within the soft robot.</p>", "<title>Self‐Healable Robot Characterizisatation</title>", "<title>Robot Geometry Definition</title>", "<p>The analytical model of the self‐healable robot is shown in <bold>Figure</bold> ##FIG##5##\n6A##. The length of the TWSMA spring is defined as <italic toggle=\"yes\">l<sub>SMA</sub>\n</italic>, which is changed upon heating or cooling of the TWSMA spring. The body length of the self‐healable robot is constant and defined as <italic toggle=\"yes\">L</italic>. The difference in height between the TWSMA spring and the self‐healing tube is constant and defined as <italic toggle=\"yes\">φ</italic>. According to the actuation mechanism of the self‐healable robot in a single step, the front foot remains still on heating the TWSMA spring, whereas the rear foot remains still on cooling the TWSMA spring. Therefore, the origin at point <italic toggle=\"yes\">O</italic> is defined as the bottom‐right or bottom‐left points when heating or cooling the TWSMA spring, respectively. A Cartesian coordinate system is established based on the origin, and another bottom point is defined as point <italic toggle=\"yes\">A</italic>, as shown in Figure ##FIG##5##6B,C##. The horizontal distance between point <italic toggle=\"yes\">O</italic> and point <italic toggle=\"yes\">A</italic> is defined as <italic toggle=\"yes\">d</italic>, whereas the height difference between point <italic toggle=\"yes\">O</italic> and the vertex of the self‐healing tube is defined as <italic toggle=\"yes\">h</italic>. The center of mass of the robot is set to the center of the rectangle as point <italic toggle=\"yes\">M</italic>.</p>", "<p>When the robot is actuated during the heating process, point A moves toward the <italic toggle=\"yes\">x</italic>+ direction with a velocity of <italic toggle=\"yes\">v</italic> and the rectangle body geometry deforms into an inverted “U” shape. To simplify the geometry, the deformed sides of both the TWSMA spring and the self‐healing body are assumed to be two concentric arcs. The radius and the angle of the TWSMA spring arc are <italic toggle=\"yes\">R</italic> and <italic toggle=\"yes\">θ</italic>. Therefore, we have\n\n\nwhere <italic toggle=\"yes\">θ</italic> ranges from 0 to π.</p>", "<title>Robot Dynamic Model</title>", "<p>The model is analyzed using the law of conservation of energy. Four energies related to the robot locomotion are: i) the elastic potential energy of the TWSMA spring <italic toggle=\"yes\">E</italic>\n<sub>SMA</sub> ii) the strain energy of the self‐healing body <italic toggle=\"yes\">E</italic>\n<sub>tube</sub> iii) the gravitational potential energy <italic toggle=\"yes\">E</italic>\n<sub>g</sub>, and iv) the kinetic energy <italic toggle=\"yes\">E</italic>\n<sub>v</sub>. During the heating process, a part of the elastic potential energy of the TWSMA is transformed into strain energy and gravitational potential energy, and the remaining energy is converted into kinetic energy\n\n</p>", "<p>Similarly, the relationship during the cooling process of the TWSMA spring is given as:\n\n</p>", "<p>The kinetic energy <italic toggle=\"yes\">E</italic>\n<sub>v</sub> is related to the average velocity of the robot, as shown in Equation (##FORMU##5##6##)\nwhere <italic toggle=\"yes\">m</italic> is the mass of the robot. The average velocity of the robot is:\n\n</p>", "<p>With the velocity and energy relationship derivations presented in the Supplementary Materials, the average velocity of the robot is given by:\n\n</p>", "<p>We define a function <italic toggle=\"yes\">f<sub>v</sub>\n</italic>(θ)\n\n</p>", "<p>As the angle <italic toggle=\"yes\">θ</italic> increases during heating process but decreases during the cooling process, a sign function is used to calculate the direction of <italic toggle=\"yes\">θ</italic>. It is defined the angle <italic toggle=\"yes\">θ</italic> equals 0 when the robot is unactuated. Combining ##FORMU##6##Equations (7–##, ##FORMU##8##9##), an ordinary differential equation (ODE) for the dynamic model of the self‐healable robot can be established\n\n</p>", "<title>Robot Elastic Potential Energy</title>", "<p>The elastic potential energy of the robot TWSMA spring body is\nwhere <italic toggle=\"yes\">k</italic> is the stiffness and <italic toggle=\"yes\">l</italic>\n<sub>0</sub> is the length of spring at zero force. According to Equation (##FORMU##10##11##), the elastic potential energy is related to the real‐time length of the TWSMA spring <italic toggle=\"yes\">l</italic>\n<sub>SMA</sub> (<italic toggle=\"yes\">l<sub>SMA</sub>\n</italic> = θ<italic toggle=\"yes\">R</italic>), and the material properties of the TWSMA spring. The properties of the TWSMA spring depend on the ratio between the martensite and austenite phases, which is a function of temperature and stress.<sup>[</sup>\n##UREF##27##\n43\n##, ##UREF##28##\n44\n##\n<sup>]</sup> Here we considered that the properties of the TWSMA spring are dominated by the temperature with a neglected effect on stress. For a TWSMA spring with a constant <italic toggle=\"yes\">l</italic>\n<sub>SMA</sub>, increasing <italic toggle=\"yes\">k</italic> and decreasing <italic toggle=\"yes\">l</italic>\n<sub>0</sub> results in a higher force. During the heating process, the TWSMA spring temperature increases from room temperature (≈23 °C) to the maximum (102 °C) and the output force increases from 0 to the maximum (1.04 N); the condition of cooling is the opposite (see Figure ##FIG##4##5##). Therefore, we have\n\n</p>", "<p>The related stiffness <italic toggle=\"yes\">k</italic> and the zero‐force length <italic toggle=\"yes\">l</italic>\n<sub>0</sub> at the maximum force are <italic toggle=\"yes\">k</italic>\n<sub>∞</sub> and <italic toggle=\"yes\">l</italic>\n<sub>0,∞</sub>. The output force of the TWSMA spring at the temperature <italic toggle=\"yes\">T</italic> is <italic toggle=\"yes\">F</italic>\n<sub>T</sub>, the related stiffness is <italic toggle=\"yes\">k</italic>\n<sub>T</sub> and the zero‐force length is <italic toggle=\"yes\">l</italic>\n<sub>0,T</sub>. A linear relationship is assumed and given by Equation (##FORMU##12##13##):\n\n</p>", "<p>During the heating process, the heating temperature is controlled to allow only a part of the martensite phase to transform into austenite. The experimental force and temperature results are in Figure ##FIG##4##5B,C## were used to establish the relationship between the force and temperature. They are separately fitted by two following models,\n\n\n</p>", "<p>The fitting parameters of force are <italic toggle=\"yes\">A</italic> = 1.052 N, <italic toggle=\"yes\">t</italic>\n<sub>0</sub> = 1.3 s, and <italic toggle=\"yes\">p</italic> = 4.158, whereas that of temperature are <italic toggle=\"yes\">T</italic>\n<sub>0</sub> = 23 °C, <italic toggle=\"yes\">T</italic>\n<sub>1</sub> = 96.63 °C, and <italic toggle=\"yes\">t</italic>\n<sub>1</sub> = 8.304 s. Before conducting the cooling process, both martensite and austenite phases exist in the TWSMA spring body, and the austenite phase transforms into martensite upon cooling. However, the transformation kinetics of the phase ratio is difficult to accurately predict during real‐time motion. After the TWSMA spring was fully heated, only the austenite existed and the output force of the TWSMA spring during the cooling process decreased from the maximum of 1.11 N to zero in 5 s (see Figure ##FIG##4##5C##). The temperature of the TWSMA at 5 s is 72 °C, which is sufficient to transform martensite into austenite during heating (see Figure ##FIG##4##5B##). Here, it is assumed that the change rate of the spring force during cooling <italic toggle=\"yes\">k</italic>\n<sub>cooling</sub> is defined as:\nwhere <italic toggle=\"yes\">k</italic>\n<sub>cooling</sub> is assumed to be a constant and fitted by the force result during the cooling process, which is −0.2217 N/s.</p>", "<title>Strain Energy</title>", "<p>When the self‐healing body deforms, it stores strain energy that is related to the deformation of the robot body. Due to the large deformation and the nonlinearity of the constitutive model of the self‐healing tube, it is difficult to solve the analytical solutions for the strain energy. Finite element analysis models were developed for analyzing the strain energy of the self‐healing body. A two parameters Mooney‐Rivlin model was used as the constitutive model of the self‐healing tube, and the model is given as,\n\n</p>", "<p>The parameters <italic toggle=\"yes\">C</italic>\n<sub>10</sub> and <italic toggle=\"yes\">C</italic>\n<sub>01</sub> were fitted by uniaxial extension experiment data. The equation of uniaxial extensional stress is\nwhere <italic toggle=\"yes\">λ</italic> is the ratio of the final and initial lengths in the principal directions. The fitting results of the parameters <italic toggle=\"yes\">C</italic>\n<sub>10</sub> and <italic toggle=\"yes\">C</italic>\n<sub>01</sub> are 0.167 and 0.0475 MPa, as shown in <bold>Figure</bold> ##FIG##6##\n7A##. The finite element model (FEM) was conducted in ANSYS 2021 R1, where the <italic toggle=\"yes\">fixed point</italic> and the <italic toggle=\"yes\">free‐moving point</italic> of the robot body are defined as shown in Figure ##FIG##6##7B##. FEM modeling is\n\n</p>", "<p>The strain energy used in the dynamic model is calculated by using spline interpolation based on the FEM results.</p>", "<title>Gravitational Potential Energy</title>", "<p>The gravitational potential energy is calculated by using the average rising height of the robot\n\n</p>", "<p>The average raising height during the heating or cooling process is,\n\n</p>", "<title>Model Evaluation</title>", "<p>The model of the self‐healable robot is evaluated analytically and experimentally. The length of the self‐healing robotic body <italic toggle=\"yes\">L</italic> is 110 mm, the high difference <italic toggle=\"yes\">φ</italic> is 7 mm, and the mass of the robot is 4 g, as shown in <bold>Figure</bold> ##FIG##7##\n8A##. For the TWSMA spring properties, the stiffness <italic toggle=\"yes\">k</italic>\n<sub>∞</sub> is 0.04 N mm<sup>−1</sup> and the zero‐force length <italic toggle=\"yes\">l</italic>\n<sub>0,∞</sub> is 89 mm after the TWSMA is fully heated. A pulse width modulation (PWM) waveform with a period of 5 s consisting of a heating time of 1.8 s and a cooling time of 3.2 s is used to control the TWSMA spring. A K‐type polyimide flat film thermocouple was attached to the TWSMA spring to measure the temperature, as shown in Figure ##FIG##7##8A## and in Movie ##SUPPL##5##S5## (Supporting Information). Figure ##FIG##7##8B## shows the experimental temperature which was used for the ordinary differential equation (ODE) dynamic model to calculate the elastic potential energy. The TWSMA spring was arranged at room temperature before 15 s. After 15 s, the TWSMA spring was actuated by using the pulse‐width modulation (PWM) driven signal, and the temperature started to increase. The temperature output performs a zigzag shape with a period of 5 s. The elastic potential energy ESMA, strain energy Etube, and gravitational potential energy <italic toggle=\"yes\">E</italic>\n<sub>g</sub> obtained by calculating ODE dynamic model are shown in Figure ##FIG##7##8C##. The kinetic energy <italic toggle=\"yes\">E</italic>\n<sub>v</sub> of the robot is small and was not plotted. For the self‐healable robot, the elastic potential energy <italic toggle=\"yes\">E</italic>\n<sub>SMA</sub> is the dominant energy. During the heating process, most of the elastic potential energy <italic toggle=\"yes\">E</italic>\n<sub>SMA</sub> is transformed into the gravitational potential energy <italic toggle=\"yes\">E</italic>\n<sub>g</sub>, the minority of energy is transformed into the strain energy <italic toggle=\"yes\">E</italic>\n<sub>tube</sub>, and limited energy is transformed into the kinetic energy <italic toggle=\"yes\">E</italic>\n<sub>v</sub>.</p>", "<p>The simulated and experimental results of robot performance including robot height, length, and position during the movement are shown in Figure ##FIG##7##8D–F##. The TWSMA spring was actuated at 15 s, and the maximum temperature in the first PWM‐driven period (15–20 s) was 32 °C, which is insufficient to transform the martensite phase into the austenite phase, resulting in the force generated by the TWSMA spring is insufficient to actuate the soft‐healable robot. After the second PWM period (20–25 s), the change in the energies and robot motion can be observed. All three energies <italic toggle=\"yes\">E</italic>\n<sub>g</sub>, <italic toggle=\"yes\">E</italic>\n<sub>SMA,</sub> and Etube increased with the temperature, and the difference between elastic potential energy <italic toggle=\"yes\">E</italic>\n<sub>SMA</sub> and gravitational potential energy <italic toggle=\"yes\">E</italic>\n<sub>g</sub> became larger; see Figure ##FIG##7##8C##. This is because of the decrease in robot length, and more elastic potential energy ESMA is transformed into strain energy <italic toggle=\"yes\">E</italic>\n<sub>tube</sub>. As shown in Figure ##FIG##7##8D,E##, the simulated robot height and length agreed well with the experimental results, which can effectively predict the motion trend and characteristics. Some differences occurred at the minimum and maximum heights and lengths, and this is because the deformation of silicone moving feet was not considered and included in the robot dynamic model. The robot's position is defined based on the center point of the robot body. As shown in Figure ##FIG##7##8F##, the robot was accelerated from 0–40 s, and the moving velocity tended to remain steady after 40 s. From 40 s – 60 s, the simulated average moving velocity is 24.24 cm/min, while the experimental average moving velocity is 14.2 cm/min. The velocity difference is caused by using the thin and light flat film thermocouple which can hinder the movement of the robot during the experiments. For comparison, the average velocity of the robot achieved in the robot's original state without attaching the film thermocouple to the robot is 21.6 cm/min, which is similar to the simulated results. The small velocity difference could be a result of a skidding effect. During the heating or cooling processes, the status of the front or rear feet is considered stationary; however the friction force of the silicone rubber is not infinite, so the front and rear feet may skid, depending on the surface, when the robot moves. The success of the model provides analytical tools to analyze the motion of the robot theoretically and accurately without the need to conduct more complex case‐dependent computational finite element models.</p>", "<title>Self‐Healing Efficiency</title>", "<p>The mechanical and electrical properties of the MG‐SBS self‐healing tube and its repeated recoveries were examined. Self‐healing efficiency can be quantified by comparing the healed properties with the original properties. We examine here the self‐healing efficiency of the materials after both mechanical damages. A tensile bar specimen was cut in half, and then we placed the two surfaces back in contact and left at room temperature for 72 h. The recovered mechanical properties are elongation at break 116%, stress 0.8 MPa, and stiffness of 10.85 MPa, as compared to the original specimen which has an elongation at break of 569%, a stress of 3.13 MPa and a stiffness of 2.87 MPa, a self‐healing efficiency of 39% was obtained. The self‐healing capacity ensures that our new self‐healable robot is able to recover from mechanical damage with good performance, in particular the stiffness and elongation to break.</p>", "<p>\n<bold>Figure</bold> ##FIG##8##\n9A## shows the complex impedance response of the initial (uncut) material and its response with healing time after the cut surfaces were placed in contact with each other. The elastomer exhibits a classical semi‐circle impedance response which represents a parallel arrangement of a resistor (<italic toggle=\"yes\">R</italic>) and capacitance (<italic toggle=\"yes\">C</italic>), where the intersection of the semi‐circle arc with the Z’‐axis at a low frequency corresponds to the overall resistance. Figure ##FIG##8##9B## also shows the AC conductivity and phase angle with frequency for the uncut elastomer, and during healing. At low frequencies (0.1–10 Hz) the AC conductivity is relatively frequency independent, indicating the material is behaving as a conductor; this agrees with the phase angle approaching 0° in this low‐frequency range. At higher frequencies (&gt;10 Hz), the material behaves as a capacitor, where the AC conductivity becomes frequency dependent and the phase angle approaches −90°, since an AC current lags AC voltage by 90°. As there is a limited difference between the capacitive impedance response of the uncut material and healed material at high frequencies (Figure ##FIG##8##9B##), it can be assumed that the capacitance, and therefore permittivity, does not change significantly during healing and any changes in impedance are dominated by changes in conductivity and electrical transport across the healing interface.</p>", "<p>Figure ##FIG##8##9A## indicates that the uncut material has the smallest semi‐circle intersection point and resistance, which corresponds to the highest conductivity in Figure ##FIG##8##9B##. On placing the cut surfaces in contact, there is a rapid recovery of the low frequency (0.1 Hz) conductivity from 6.3 × 10<sup>−5</sup> S m<sup>−1</sup> to 2.6 × 10<sup>−5</sup> m<sup>−1</sup>, and this corresponds to an increase in the intersection of the semi‐circle to the Z’‐axis in Figure ##FIG##8##9A## (“initial cut”). During the initial 24 h of self‐healing, the intersection points of the semi‐circle increase, where there is a small decrease in the low‐frequency conductivity to 1.5 ×10<sup>−5</sup> m<sup>−1</sup>. The initial rapid recovery is likely to be due to rapid electrostatic interactions during the healing processes of surface rearrangement and surface approach, with subsequent wetting of the surfaces by a phase of lower conductivity greater than the initial material as the healing process continues. As the healing time progresses from 24 h to 192 h (8 days) the semi‐circle intersection point then decreases (Figure ##FIG##8##9A##) and the AC conductivity approaches that of the initial uncut material to a value of 4.5 × 10<sup>−5</sup> m<sup>−1</sup>. This may be due to longer healing time allowing greater diffusion and randomization of material at the fracture site, so that the healed regions become more representative of the initial material, as the mechanism of Wool. The initial rapid recovery of electrical response, in particular the AC conductivity and phase angle, indicates that the material provides sufficient self‐healing via electrostatic bonding and a degree of diffusion to achieve the necessary degree of self‐healing for recovery of mechanical properties.</p>" ]
[ "<title>Discussion</title>", "<p>We have created a soft crawling robot that can self‐heal autonomously to its full performance at room temperature after being significantly damaged. The innovative design of the robot integrates a micro TWSMA spring actuation system and a self‐healing dielectric elastomer MG‐SBS.</p>", "<p>The thermoplastic nature of the MG‐SBS elastomer material allows continuous manufacturing of intrinsically self‐healing MG‐SBS tubes by scalable industrial melt extrusion process, which expands the applicability of self‐healing robots for practical applications. The introduction of organic polar groups to commodity SBS thermoplastic elastomers increased the relative permittivity (<italic toggle=\"yes\">ε</italic>\n<sub>r</sub>) of SBS from <italic toggle=\"yes\">ε</italic>\n<sub>r</sub> = 2.8 to <italic toggle=\"yes\">ε</italic>\n<sub>r</sub> = 11.4 at 10<sup>3</sup> Hz, meanwhile, the highly grafted polar groups along the polymer backbones enhanced the intramolecular interactions and interrupted the polystyrene clustering, so that induced the phase morphology transition from original ordered structure to more disorder morphology. This explains the enhanced extensibility (569 ± 25.9%), reduced Young's modulus (2.87 ± 0.6 MPa), and autonomous ambient self‐healing via the abundant electrostatic interactions among the polymer chains. The intrinsic self‐healing nature of the material as a result of electrostatic interactions allows repeated recovery of the required elastic modulus and strain to failure at room temperature after 24 h, with a low hysteresis loss. The rapid self‐healing is also observed in terms of recovery of electrical properties, in particular the rapid recovery of AC conductivity and phase.</p>", "<p>A two‐anchor crawling mechanism is applied to the robot for locomotion. Taking advantage of the controllable heating and cooling processes of TWSMA spring actuation system, the movement and speed of the robot are controllable by adjusting the PWM control signal. In addition, the advanced optimized moving feet were developed to maximize the moving efficiency. The structure and the geometry of the robot feet can be applied to a variety of soft crawlers in different scales.</p>", "<p>The performance of the self‐healable robot was validated in experiments. The measured deformation (maximum and middle heights) and crawling speed of the robot resulting from heating and cooling period of TWSMA agree with the analytical modeling results. Some expected velocity discrepancies can be caused by the attachment of the thermocouple on the robot during the experiments, and the skidding effect of the feet on the experiment platform surface. The self‐healing capacity of the robot was verified by healing from significant repetitive cutting damages. The robot was cut into half and three separate parts and fully recovered after 24 h at room temperature. Small weak scars can be seen after cutting and healing due to the change of modulus at the cutting positions but they do not significantly affect the robot performance. The self‐healing tube and the robot are easy to conduct and cost‐efficient to provide autonomous healing without the need for external stimuli. This material combination and integration enable high‐performance soft robots with autonomic self‐healing capability without external stimulus, which is novel in the field. We created the analytical models for the self‐healable robot which can effectively predict the characteristics and dynamics of the robot, without conducting complex computation‐inefficient finite element models. This can be a valuable tool for the future design, analysis, and optimization of soft crawlers.</p>", "<p>In summary, this study presents a new methodology for the design and actuation of self‐healable robots. The MGSBS‐based geometry can be used for a variety of soft robotic applications and increases the life span of the soft components and robots, while the TWSMA spring actuator can be applied as a new integrated actuation system to soft robots using its two‐way memory effect. Our demonstration has successfully proven the concepts that can be developed for high technology readiness levels applications, such as exploration robots and industrial robots under uncertain and extreme environments, which can improve the sustainability of robots and generate research impact.</p>" ]
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[ "<title>Abstract</title>", "<p>Soft robotic bodies are susceptible to mechanical fatigue, punctures, electrical breakdown, and aging, which can result in the degradation of performance or unexpected failure. To overcome these challenges, a soft self‐healing robot is created using a thermoplastic methyl thioglycolate–modified styrene–butadiene–styrene (MG‐SBS) elastomer tube fabricated by melt‐extrusion, to allow the robot to self‐heal autonomously at room temperature. After repeated damage and being separated into several parts, the robot is able to heal its stiffness and elongation to break to enable almost complete recovery of robot performance after being allowed to heal at room temperature for 24 h. The self‐healing capability of the robot is examined across the material scale to robot scale by detailed investigations of the healing process, healing efficiency, mechanical characterization of the robot, and assessment of dynamic performance before and after healing. The self‐healing robot is driven by a new micro two‐way shape‐memory alloy (TWSMA) spring actuator which achieved a crawling speed of 21.6 cm/min, equivalent to 1.57 body length per minute. An analytical model of the robot is created to understand the robot dynamics and to act as an efficient tool for self‐healing robot design and optimization. This work therefore provides a new methodology to create efficient, robust, and damage‐tolerant soft robots.</p>", "<p>Soft robotic bodies are susceptible to mechanical fatigue, punctures, electrical breakdown, and aging. A soft self‐healing robot is created using a thermoplastic MG‐SBS elastomer tube fabricated by melt‐extrusion, to allow the robot to self‐heal autonomously at room temperature. After repeated damage and being separated into several parts, the robot is able to heal and enable almost complete recovery of robot performance.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6801-cit-0048\">\n<string-name>\n<given-names>X.</given-names>\n<surname>Liang</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Yuan</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Wan</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Gao</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Bowen</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Pan</surname>\n</string-name>, <article-title>Soft Self‐Healing Robot Driven by New Micro Two‐Way Shape Memory Alloy Spring</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305163</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305163</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Micro SMA Spring Actuator</title>", "<p>The Micro SMA could be categorized into two characteristics: one‐way SMA (OWSMA) and two‐way SMA (TWSMA). The OWSMA retained a deformation after removing the external force and recovered to its initial state when being heated. The TWSMA could memorize its state at both low and high temperatures. Considering that the force generated by the gravitational potential energy and the strain energy of the self‐healable robot was insufficient to extend and deform the OWSMA spring during the cooling period (see stage 3 to stage 5 in Figure ##FIG##2##3C##), the TWSMA spring was determined to use to create the robot to mimic the locomotion of caterpillars. This was a first in the design of soft self‐healing robots. Perkins concluded that the TWSME was a result of a macroscopic non‐uniform residual stress field, so a non‐uniform plastic deformation was a necessary condition to obtain a TWSME.<sup>[</sup>\n##UREF##29##\n45\n##\n<sup>]</sup> Schroeder proposed that the growth of detwinned martensite was related to characteristics of the two‐way shape memory.<sup>[</sup>\n##UREF##30##\n46\n##\n<sup>]</sup> Wada and Liu proved that the dislocation structures created by martensite pre‐deformation were beneficial for generating a better TWSME experimentally.<sup>[</sup>\n##UREF##31##\n47\n##\n<sup>]</sup> Therefore, a large pre‐deformation method was used to prepare the TWSMA spring in other work (see <bold>Figure</bold> ##FIG##9##\n10A##). The original length of the SMA spring was 10 mm. The original SMA spring was pre‐extended at room temperature, and the length of the extended spring was defined as extended length. After pre‐extension, the extended SMA spring was heated without an external load for 1 min by applying a 5 V power supply; during this time, the SMA spring contracted significantly. Finally, the SMA spring was cooled to room temperature, and the TWSMA spring was realized. The length difference between heated and cooled states was defined as the working range. The relationship between the extended length and the working range is shown in Figure ##FIG##9##10B##. With an increase in the extended length, the working range increases significantly. The data was fitted by using a power model\nwhere <italic toggle=\"yes\">a</italic> and <italic toggle=\"yes\">b</italic> are 2.5 × 10<sup>−5</sup> and 2.65. The extended length of the TWSMA spring was 180 mm.</p>", "<title>Self‐Healing Materials—Materials</title>", "<p>Styrene‐butadiene‐styrene (SBS), Vector 8508A, was a linear triblock copolymer from Dexco. It had a 29 wt.% styrenic content, a diblock content of &lt;1 wt.%, a density of 0.41 g/cm<sup>3</sup> (ASTM D1895), a melt flow rate of 12 g 10 min<sup>−1</sup> (ASTM D1238) and recommended processing conditions of between 180 °C – 225 °C. General reagents methyl thioglycolate (MG, 95%) was purchased from Sigma‐Aldrich.</p>", "<title>Self‐Healing Materials—Manufacturing Self‐Healing Tube</title>", "<p>The methyl thioglycolate‐modified SBS (MG‐SBS) was detailed in our previous work.<sup>[</sup>\n##UREF##14##\n24\n##\n<sup>]</sup> The MGSBS pellets were fed into a single‐screw extrusion machine (Collin Germany) tubes for melt‐extrusion of elastomer tubes. The processing temperature was set as 150, 170, 180, and 175 °C from the feeding zone to the die (inner diameter of 6 mm, external diameter of 7 mm), extrusion rate was 30 rpm.</p>", "<title>Experimental Preparation and Measurement—Robot Feet Preparation and Fabrication</title>", "<p>The single‐direction robotic feet were manufactured by molding. The molds and cores were 3D‐printed using PLA, and the detailed design can be found in Supplementation. After assembling the mold, the mixing silicone liquid rubber (Ecoflex 00–30, Smooth‐on) was poured into the mold and placed at room temperature at 23 °C. The silicone rubber was cured completely after 4 h. Finally, the single‐direction feet were removed from the mold.</p>", "<title>Experimental Preparation and Measurement—Tensile Testing and Temperature Measurement of Micro SMA</title>", "<p>Tensile testing was conducted using a tensile testing machine Instron 3369. During the tensile test experiments, four steps were performed: i) The SMA spring was heated by a 5 V power supply and kept at the same length for 1 min. ii) The SMA spring was compressed with a speed of 0.5 mm <sup>−1</sup>s until its output force reached zero. iii) The SMA spring was extended to its original length with a speed of 0.5 mm <sup>−1</sup>s. iv) The SMA spring was kept at the same length and cooled for 2 min.</p>", "<p>A K‐type polyimide flat film thermocouple (TC Direct) was attached to the TWSMA spring to measure its real‐time temperature. A thermocouple module (NI‐9213, National Instruments) carried by a compact‐DAQ chassis (USB‐9162, National Instruments) was used to record the temperature data. The data acquisition program was based on LabVIEW, and the sampling frequency was 20 Hz.</p>", "<title>Experimental Preparation and Measurement—SMA Robot Controller</title>", "<p>An Arduino microcontroller board (Mega‐2560) was used to generate the PWM signal with a period of 5 s. The output signal drives a relay module to switch the heating and cooling modes for the TWSMA spring.</p>", "<title>Experimental Preparation and Measurement—Electrical Characterisation</title>", "<p>The electrical properties of the materials during self‐healing were determined using a Solartron 1260 Impedance Analyser with a Solartron 1296 Dielectric Interface. The sample was electroded with silver paint and the complex impedance of the materials was measured from 0.1 Hz to 103 Hz at 3 V peak to peak in an air‐conditioned laboratory at 16 °C. The sample was initially tested, then cut using a clean razor blade, and tested immediately after placing the two cut surfaces back in contact with each other. The sample was then periodically tested as it self‐healed for up to 192 h.</p>", "<p>The AC conductivity (admittance) was determined using Equation (##FORMU##22##23##),\nwhere <italic toggle=\"yes\">Z</italic>′ and <italic toggle=\"yes\">Z</italic>″ are the real and imaginary parts of the impedance, respectively, <italic toggle=\"yes\">A</italic> is the area of the materials and <italic toggle=\"yes\">t</italic> is the thickness. The phase angle (<italic toggle=\"yes\">θ</italic>) between current and voltage was determined from Equation (##FORMU##23##24##):\n\n</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>M.P. and C.W. conceptualized the idea. X.R.L., M.P., and C.W. designed the methodology. The investigation involved X.R.L., C.G.Y, X.L.G., and C.B. M.P. managed funding acquisition and project administration. M.P., C.W., and C.B. did the supervision. X.R.L., M.P., C.W., and C.B. wrote the first draft, and X.R.L., C.G.Y., M.P., C.W., and CB reviewed and edited it.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank the polymer extrusion support from Prof A. Kelly and P. Coates from the University of Bradford, UK. The authors also thank Leverhulme Research Fellowship RF‐2020‐503, The Leverhulme Trust UK. The Alumni Fund F1920A‐RS02, University of Bath UK for the funding.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0001\"><label>Figure 1</label><caption><p>A) Modification of commodity SBS via one‐step thiol‐ene click chemistry to obtain MG‐SBS, AFM images showing the microstructure development,<sup>[</sup>\n##UREF##16##\n26\n##\n<sup>]</sup> schematic showing the self‐healing mechanism of MG‐SBS; B) physical properties of SBS and MG‐SBS, and C) continuous melt‐extrusion of MG‐SBS to produce tubes for soft‐robot application.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0002\"><label>Figure 2</label><caption><p>Architecture of the soft self‐healable robot. A) 3D model B) robot prototype C) fully actuated and deformed robot.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0003\"><label>Figure 3</label><caption><p>Mechanism of moving feet of the robot and robot locomotion A) Structure of single‐direction movement block and its mechanism when it moves backward and forward. B) Structures of the novel advanced rear and front feet and their statuses from the moving stage 1 to 4 during locomotion C) actuation mechanism of the self‐healable robot in a single locomotion step.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0004\"><label>Figure 4</label><caption><p>A) Schematic of the original and damaged robot and its self‐healing performance. B) Middle height, maximum height, and average velocity of the robot under different states.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0005\"><label>Figure 5</label><caption><p>Properties of the micro SMA spring actuator. A) Temperature and force responses of the micro SMA spring actuator. Heating process (signal = 1) was achieved using a 5 V power supply and the cooling process (signal = 0) was achieved by placing the micro SMA spring at room temperature (≈23 °C). B) Temperature and force C) during the heating and cooling processes. D) Relationship between the force and length of the SMA spring during the compression and extension processes. E) Two‐way SMA effect and training preparation.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0006\"><label>Figure 6</label><caption><p>A) Geometry model of the self‐healable robot. Model definition of the situations when B) heating and C) cooling the TWSMA spring.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0007\"><label>Figure 7</label><caption><p>A) Experimental results and fitting curves based on the two‐parameter Mooney‐Rivlin model. B) Finite element analysis model and strain energy of the self‐healing robotic body.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0008\"><label>Figure 8</label><caption><p>Analytical and experimental robot energies and mechanical properties A) Thermocouple attached to the self‐healable robot and B) the temperature of the TWSMA spring. C) Elastic potential energy ESMA, strain energy Etube, and gravitational potential energy <italic toggle=\"yes\">E</italic>\n<sub>g</sub> calculated by the dynamic model. D) Height, E) length, and F) position validated in experiments.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0009\"><label>Figure 9</label><caption><p>A) Complex impedance response of MG‐SBS with healing time B) Frequency dependence of AC conductivity (upper image) and phase angle (lower image) with healing time.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6801-fig-0010\"><label>Figure 10</label><caption><p>A) Preparation of a two‐way micro SMA actuator and B) The relationship between extended length and working range.</p></caption></fig>" ]
[]
[ "<disp-formula id=\"advs6801-disp-0001\">\n<label>(1)</label>\n<mml:math id=\"jats-math-1\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>R</mml:mi><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>L</mml:mi><mml:mi>θ</mml:mi></mml:mfrac><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mi>φ</mml:mi></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0002\">\n<label>(2)</label>\n<mml:math id=\"jats-math-2\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>d</mml:mi><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mn>2</mml:mn><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mfrac><mml:mi>L</mml:mi><mml:mi>θ</mml:mi></mml:mfrac><mml:mo>−</mml:mo><mml:mi>φ</mml:mi></mml:mrow></mml:mfenced><mml:mi>sin</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mi>θ</mml:mi><mml:mn>2</mml:mn></mml:mfrac></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0003\">\n<label>(3)</label>\n<mml:math id=\"jats-math-3\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>h</mml:mi><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>L</mml:mi><mml:mi>θ</mml:mi></mml:mfrac><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi>cos</mml:mi><mml:mfrac><mml:mi>θ</mml:mi><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:mfenced><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:mi>φ</mml:mi><mml:mi>cos</mml:mi><mml:mfrac><mml:mi>θ</mml:mi><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0004\">\n<label>(4)</label>\n<mml:math id=\"jats-math-4\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>S</mml:mi><mml:mi>M</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mi>u</mml:mi><mml:mi>b</mml:mi><mml:mi>e</mml:mi></mml:mrow></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi>g</mml:mi></mml:msub></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0005\">\n<label>(5)</label>\n<mml:math id=\"jats-math-5\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mi>u</mml:mi><mml:mi>b</mml:mi><mml:mi>e</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi>g</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>S</mml:mi><mml:mi>M</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0006\">\n<label>(6)</label>\n<mml:math id=\"jats-math-6\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mi>m</mml:mi><mml:msup><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>¯</mml:mo></mml:mover><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0007\">\n<label>(7)</label>\n<mml:math id=\"jats-math-7\" display=\"block\"><mml:mrow><mml:mrow><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>¯</mml:mo></mml:mover><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msqrt><mml:mfrac><mml:mrow><mml:mn>2</mml:mn><mml:mfenced separators=\"\" open=\"|\" close=\"|\"><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>S</mml:mi><mml:mi>M</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:msub><mml:mo>−</mml:mo><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mi>u</mml:mi><mml:mi>b</mml:mi><mml:mi>e</mml:mi></mml:mrow></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi>g</mml:mi></mml:msub></mml:mrow></mml:mfenced></mml:mrow></mml:mfenced></mml:mrow><mml:mi>m</mml:mi></mml:mfrac></mml:msqrt></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0008\">\n<label>(8)</label>\n<mml:math id=\"jats-math-8\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>¯</mml:mo></mml:mover><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msup><mml:mi>θ</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mo>·</mml:mo><mml:msqrt><mml:mrow><mml:mspace width=\"-0.16em\"/><mml:mfrac><mml:mrow><mml:msup><mml:msup><mml:mi>d</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mn>2</mml:mn></mml:msup><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced></mml:mrow><mml:mn>4</mml:mn></mml:mfrac><mml:mo linebreak=\"badbreak\">+</mml:mo><mml:mfrac><mml:mrow><mml:msup><mml:msup><mml:mi>h</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mn>2</mml:mn></mml:msup><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced></mml:mrow><mml:mrow><mml:msup><mml:mi>d</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:msup><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>−</mml:mo><mml:mi>φ</mml:mi></mml:mrow></mml:mfenced><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mfrac><mml:mspace width=\"-0.16em\"/><mml:msup><mml:mfenced separators=\"\" open=\"[\" close=\"]\"><mml:mspace width=\"-0.16em\"/><mml:mrow><mml:msup><mml:mi>R</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mi>arc</mml:mi><mml:mi>sin</mml:mi><mml:mspace width=\"-0.16em\"/><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mspace width=\"-0.16em\"/><mml:mfrac><mml:mi>d</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi>R</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"-0.16em\"/></mml:mfenced><mml:mo>−</mml:mo><mml:mfrac><mml:mi>d</mml:mi><mml:mn>2</mml:mn></mml:mfrac><mml:msqrt><mml:mrow><mml:msup><mml:mi>R</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mo>−</mml:mo><mml:mfrac><mml:msup><mml:mi>d</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mn>4</mml:mn></mml:mfrac></mml:mrow></mml:msqrt></mml:mrow></mml:mfenced><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:msqrt></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0009\">\n<label>(9)</label>\n<mml:math id=\"jats-math-9\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msqrt><mml:mrow><mml:mspace width=\"-0.16em\"/><mml:mfrac><mml:mrow><mml:msup><mml:msup><mml:mi>d</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mn>2</mml:mn></mml:msup><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced></mml:mrow><mml:mn>4</mml:mn></mml:mfrac><mml:mo linebreak=\"badbreak\">+</mml:mo><mml:mfrac><mml:mrow><mml:msup><mml:msup><mml:mi>h</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mn>2</mml:mn></mml:msup><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced></mml:mrow><mml:mrow><mml:msup><mml:mi>d</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:msup><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mi>h</mml:mi><mml:mo>−</mml:mo><mml:mi>φ</mml:mi></mml:mrow></mml:mfenced><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mfrac><mml:mspace width=\"-0.16em\"/><mml:msup><mml:mfenced separators=\"\" open=\"[\" close=\"]\"><mml:mspace width=\"-0.16em\"/><mml:mrow><mml:msup><mml:mi>R</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mi>arc</mml:mi><mml:mi>sin</mml:mi><mml:mspace width=\"-0.16em\"/><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mspace width=\"-0.16em\"/><mml:mfrac><mml:mi>d</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi>R</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"-0.16em\"/></mml:mfenced><mml:mo>−</mml:mo><mml:mfrac><mml:mi>d</mml:mi><mml:mn>2</mml:mn></mml:mfrac><mml:msqrt><mml:mrow><mml:msup><mml:mi>R</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mo>−</mml:mo><mml:mfrac><mml:msup><mml:mi>d</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mn>4</mml:mn></mml:mfrac></mml:mrow></mml:msqrt></mml:mrow></mml:mfenced><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:msqrt></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0010\">\n<label>(10)</label>\n<mml:math id=\"jats-math-10\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msup><mml:mi>θ</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mover accent=\"true\"><mml:mi>v</mml:mi><mml:mo>¯</mml:mo></mml:mover><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced></mml:mrow></mml:mfrac><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">s</mml:mi><mml:mi>g</mml:mi><mml:mi>n</mml:mi></mml:mrow><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>S</mml:mi><mml:mi>M</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:msub><mml:mo>−</mml:mo><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mi>u</mml:mi><mml:mi>b</mml:mi><mml:mi>e</mml:mi></mml:mrow></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi>g</mml:mi></mml:msub></mml:mrow></mml:mfenced></mml:mrow></mml:mfenced></mml:mrow><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:mfenced open=\"(\" close=\")\"><mml:mi>θ</mml:mi></mml:mfenced></mml:mrow></mml:mfrac><mml:msqrt><mml:mrow><mml:mspace width=\"-0.16em\"/><mml:mfrac><mml:mrow><mml:mn>2</mml:mn><mml:mfenced separators=\"\" open=\"|\" close=\"|\"><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>S</mml:mi><mml:mi>M</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:msub><mml:mo>−</mml:mo><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mi>u</mml:mi><mml:mi>b</mml:mi><mml:mi>e</mml:mi></mml:mrow></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi>g</mml:mi></mml:msub></mml:mrow></mml:mfenced></mml:mrow></mml:mfenced></mml:mrow><mml:mi>m</mml:mi></mml:mfrac></mml:mrow></mml:msqrt></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0011\">\n<label>(11)</label>\n<mml:math id=\"jats-math-11\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mi>S</mml:mi><mml:mi>M</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msup><mml:mi>x</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mi>k</mml:mi><mml:msup><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>l</mml:mi><mml:mrow><mml:mi>S</mml:mi><mml:mi>M</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:msub><mml:mo>−</mml:mo><mml:msub><mml:mi>l</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:mrow></mml:mfenced><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0012\">\n<label>(12)</label>\n<mml:math id=\"jats-math-12\" display=\"block\"><mml:mrow><mml:mrow><mml:munder><mml:mi>lim</mml:mi><mml:mrow><mml:mi>T</mml:mi><mml:mo>→</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi>max</mml:mi></mml:msub></mml:mrow></mml:munder><mml:msub><mml:mi>F</mml:mi><mml:mrow><mml:mi>S</mml:mi><mml:mi>M</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>F</mml:mi><mml:mi>∞</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:munder><mml:mi>lim</mml:mi><mml:mrow><mml:mi>T</mml:mi><mml:mo>→</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi>r</mml:mi><mml:mi>o</mml:mi><mml:mi>o</mml:mi><mml:mi>m</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:munder><mml:msub><mml:mi>F</mml:mi><mml:mrow><mml:mi>S</mml:mi><mml:mi>M</mml:mi><mml:mi>A</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0013\">\n<label>(13)</label>\n<mml:math id=\"jats-math-13\" display=\"block\"><mml:mrow><mml:mrow><mml:mfrac><mml:msub><mml:mi>F</mml:mi><mml:mi>T</mml:mi></mml:msub><mml:msub><mml:mi>F</mml:mi><mml:mi>∞</mml:mi></mml:msub></mml:mfrac><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:msub><mml:mi>k</mml:mi><mml:mi>T</mml:mi></mml:msub><mml:msub><mml:mi>k</mml:mi><mml:mi>∞</mml:mi></mml:msub></mml:mfrac><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:mi>L</mml:mi><mml:mo>−</mml:mo><mml:msub><mml:mi>l</mml:mi><mml:mrow><mml:mn>0</mml:mn><mml:mo>,</mml:mo><mml:mi>T</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mi>L</mml:mi><mml:mo>−</mml:mo><mml:msub><mml:mi>l</mml:mi><mml:mrow><mml:mn>0</mml:mn><mml:mo>,</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0014\">\n<label>(14)</label>\n<mml:math id=\"jats-math-14\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>F</mml:mi><mml:mfenced open=\"(\" close=\")\"><mml:mi>t</mml:mi></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi>A</mml:mi><mml:mfenced separators=\"\" open=\"[\" close=\"]\"><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mrow><mml:mn>1</mml:mn><mml:mo>+</mml:mo><mml:msup><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mi>t</mml:mi><mml:mo>/</mml:mo><mml:msub><mml:mi>t</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:mrow></mml:mfenced><mml:mi>p</mml:mi></mml:msup></mml:mrow></mml:mfrac></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0015\">\n<label>(15)</label>\n<mml:math id=\"jats-math-15\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:mfenced open=\"(\" close=\")\"><mml:mi>t</mml:mi></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mo>−</mml:mo><mml:mi>t</mml:mi><mml:mo>/</mml:mo><mml:msub><mml:mi>t</mml:mi><mml:mn>1</mml:mn></mml:msub></mml:mrow></mml:msup></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0016\">\n<label>(16)</label>\n<mml:math id=\"jats-math-16\" display=\"block\"><mml:mrow><mml:mrow><mml:mfrac><mml:mrow><mml:mi>d</mml:mi><mml:mi>F</mml:mi></mml:mrow><mml:mrow><mml:mi>d</mml:mi><mml:mi>t</mml:mi></mml:mrow></mml:mfrac><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mrow><mml:mi>c</mml:mi><mml:mi>o</mml:mi><mml:mi>o</mml:mi><mml:mi>l</mml:mi><mml:mi>i</mml:mi><mml:mi>n</mml:mi><mml:mi>g</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0017\">\n<label>(17)</label>\n<mml:math id=\"jats-math-17\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>W</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mn>10</mml:mn></mml:msub><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>−</mml:mo><mml:mn>3</mml:mn></mml:mrow></mml:mfenced><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mn>01</mml:mn></mml:msub><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo>−</mml:mo><mml:mn>3</mml:mn></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0018\">\n<label>(18)</label>\n<mml:math id=\"jats-math-18\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:mn>11</mml:mn></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mn>2</mml:mn><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mn>10</mml:mn></mml:msub><mml:mo>+</mml:mo><mml:mfrac><mml:msub><mml:mi>C</mml:mi><mml:mn>01</mml:mn></mml:msub><mml:mi>λ</mml:mi></mml:mfrac></mml:mrow></mml:mfenced><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mi>λ</mml:mi><mml:mo>−</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:msup><mml:mi>λ</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mfrac></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0019\">\n<label>(19)</label>\n<mml:math id=\"jats-math-19\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mi>tube</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>f</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mi>u</mml:mi><mml:mi>b</mml:mi><mml:mi>e</mml:mi></mml:mrow></mml:msub><mml:mfenced open=\"(\" close=\")\"><mml:mi>d</mml:mi></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0020\">\n<label>(20)</label>\n<mml:math id=\"jats-math-20\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mi>g</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi>m</mml:mi><mml:mi>g</mml:mi><mml:mover accent=\"true\"><mml:mi>h</mml:mi><mml:mo>¯</mml:mo></mml:mover></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0021\">\n<label>(21)</label>\n<mml:math id=\"jats-math-21\" display=\"block\"><mml:mrow><mml:mrow><mml:mover accent=\"true\"><mml:mi>h</mml:mi><mml:mo>¯</mml:mo></mml:mover><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mi>d</mml:mi></mml:mfrac><mml:msubsup><mml:mo>∫</mml:mo><mml:mrow><mml:mo>−</mml:mo><mml:mi>d</mml:mi></mml:mrow><mml:mn>0</mml:mn></mml:msubsup><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>p</mml:mi></mml:msub><mml:mi>d</mml:mi><mml:msub><mml:mi>x</mml:mi><mml:mi>p</mml:mi></mml:msub></mml:mrow><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mfrac><mml:msup><mml:mi>R</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mi>d</mml:mi></mml:mfrac><mml:mi>arc</mml:mi><mml:mi>sin</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mi>d</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi>R</mml:mi></mml:mrow></mml:mfrac></mml:mfenced><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mfrac><mml:msqrt><mml:mrow><mml:mn>4</mml:mn><mml:msup><mml:mi>R</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mo>−</mml:mo><mml:msup><mml:mi>d</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:msqrt><mml:mn>4</mml:mn></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0022\">\n<label>(22)</label>\n<mml:math id=\"jats-math-22\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>y</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi>a</mml:mi><mml:msup><mml:mi>x</mml:mi><mml:mi>b</mml:mi></mml:msup></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0023\">\n<label>(23)</label>\n<mml:math id=\"jats-math-23\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>σ</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:msup><mml:mi>Z</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mrow><mml:msup><mml:msup><mml:mi>Z</mml:mi><mml:mo>′</mml:mo></mml:msup><mml:mn>2</mml:mn></mml:msup><mml:mo>+</mml:mo><mml:msup><mml:msup><mml:mi>Z</mml:mi><mml:mrow><mml:mo>′</mml:mo><mml:mo>′</mml:mo></mml:mrow></mml:msup><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mfrac><mml:mo>·</mml:mo><mml:mfrac><mml:mi>t</mml:mi><mml:mi>A</mml:mi></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6801-disp-0024\">\n<label>(24)</label>\n<mml:math id=\"jats-math-24\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>θ</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msup><mml:mi>tan</mml:mi><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msup><mml:mi>Z</mml:mi><mml:mrow><mml:mo>′</mml:mo><mml:mo>′</mml:mo></mml:mrow></mml:msup><mml:mo>/</mml:mo><mml:msup><mml:mi>Z</mml:mi><mml:mo>′</mml:mo></mml:msup></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>" ]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
[]
[]
[]
[ "<supplementary-material id=\"advs6801-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6801-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 1</p></caption></supplementary-material>", "<supplementary-material id=\"advs6801-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 2</p></caption></supplementary-material>", "<supplementary-material id=\"advs6801-supitem-0004\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 3</p></caption></supplementary-material>", "<supplementary-material id=\"advs6801-supitem-0005\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 4</p></caption></supplementary-material>", "<supplementary-material id=\"advs6801-supitem-0006\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 5</p></caption></supplementary-material>" ]
[]
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[ "<media xlink:href=\"ADVS-11-2305163-s003.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305163-s002.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305163-s005.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305163-s006.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305163-s004.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305163-s001.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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M."], "surname": ["Shepherd", "Ilievski", "Choi", "Morin", "Stokes", "Mazzeo", "Chen", "Wang", "Whitesides"], "source": ["Multigait soft robot"], "publisher-name": ["PNAS"], "publisher-loc": ["Washington, DC"], "year": ["2011"], "volume": ["108"], "elocation-id": ["20400"]}, {"label": ["7"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["M. T.", "R. F.", "B.", "K. C.", "M.", "M.", "R. J.", "G. M."], "surname": ["Tolley", "Shepherd", "Mosadegh", "Galloway", "Wehner", "Karpelson", "Wood", "Whitesides"], "source": ["Soft Robot"], "year": ["2014"], "volume": ["1"], "fpage": ["213"]}, {"label": ["10"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n"], "given-names": ["S. I.", "R. J.", "C."], "surname": ["Rich", "Wood", "Majidi"], "source": ["Nat. 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Inter."], "year": ["2018"], "volume": ["10"], "elocation-id": ["38438"]}, {"label": ["25"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["Y.", "C.", "R.", "J.", "M.", "P.", "T.", "C.", "C."], "surname": ["Zhang", "Ellingford", "Zhang", "Roscow", "Hopkins", "Keogh", "Mcnally", "Bowen", "Wan"], "source": ["Adv. Funct. Mater."], "year": ["2019"], "volume": ["29"], "elocation-id": ["1808431"]}, {"label": ["26"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["C.", "R.", "A. M.", "Y.", "O. B.", "H.", "P.", "C.", "C."], "surname": ["Ellingford", "Zhang", "Wemyss", "Zhang", "Brown", "Zhou", "Keogh", "Bowen", "Wan"], "source": ["Acs. Appl. Mater. Inter."], "year": ["2020"], "volume": ["12"], "fpage": ["7595"]}, {"label": ["28"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n"], "given-names": ["S.", "J.", "E.", "G.", "B."], "surname": ["Terryn", "Brancart", "Roels", "Van Assche", "Vanderborght"], "source": ["IEEE Robot. Autom. Mag."], "year": ["2020"], "volume": ["27"], "fpage": ["44"]}, {"label": ["31"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n"], "given-names": ["K.", "A.n", "H.", "Y.", "Q."], "surname": ["Yu", "Xin", "Du", "Li", "Wang"], "source": ["NPG Asia Mater"], "year": ["2019"], "volume": ["11"], "fpage": ["7"]}, {"label": ["32"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["Y.", "X.\u2010Y.u", "M.", "C.", "J.", "Z. L."], "surname": ["Zhang", "Yin", "Zheng", "Moorlag", "Yang", "Wang"], "source": ["J. Mater. Chem. 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{ "acronym": [], "definition": [] }
47
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 20; 11(2):2305163
oa_package/80/77/PMC10787064.tar.gz
PMC10787065
37974523
[ "<title>Introduction</title>", "<p>Experiments designed to exploit quantum technologies for applications can be extremely challenging. Fragile quantum states must be delicately manipulated, whilst minimizing sources of decoherence, in order to preserve a quantum advantage. This often necessitates cutting‐edge experimental physics, including precise and complex optical assemblies,<sup>[</sup>\n##UREF##0##\n1\n##, ##REF##34767431##\n2\n##\n<sup>]</sup> strong vector magnetic fields,<sup>[</sup>\n##REF##34047600##\n3\n##\n<sup>]</sup> high‐speed microwave delivery,<sup>[</sup>\n##REF##12066177##\n4\n##\n<sup>]</sup> and compatibility with extremely low temperature environments.<sup>[</sup>\n##UREF##1##\n5\n##\n<sup>]</sup> Emerging quantum technologies based on hybrid quantum systems<sup>[</sup>\n##REF##25737558##\n6\n##\n<sup>]</sup> combine research from two or more experimental settings: such as coupling spins in silicon to superconducting resonators and qubits,<sup>[</sup>\n##UREF##2##\n7\n##, ##REF##34912088##\n8\n##\n<sup>]</sup> interfacing remote NV centers in diamond with photonic qubits,<sup>[</sup>\n##REF##35614248##\n9\n##\n<sup>]</sup> and using nanomechanics to interface with spins<sup>[</sup>\n##UREF##3##\n10\n##\n<sup>]</sup> or superconducting qubits.<sup>[</sup>\n##UREF##4##\n11\n##\n<sup>]</sup>\n</p>", "<p>As these proof‐of‐principle devices become more sophisticated and start to scale in size and complexity, established lab infrastructure such as translation stages and solenoid coils will no longer provide the flexibility, speed, and precision to meet these constrained<sup>[</sup>\n##REF##36754957##\n12\n##\n<sup>]</sup> and sometimes competing experimental requirements. In contrast, the field of robotics has long adapted to operate robots in challenging conditions, such as at the microscale<sup>[</sup>\n##UREF##5##\n13\n##\n<sup>]</sup> or in very low temperature environments.<sup>[</sup>\n##UREF##6##\n14\n##\n<sup>]</sup> Robotics can provide more flexible and adaptable approaches than traditional methods, which would speed up the deployment of quantum technology across applications. With sophisticated software stacks and well‐developed open‐source hardware, the deployment of robotics in a diverse range of experimental settings in the chemical and biological sciences has become increasingly feasible.<sup>[</sup>\n##REF##30022133##\n15\n##, ##REF##36289227##\n16\n##\n<sup>]</sup>\n</p>", "<p>Here, we introduce and validate the idea of robot‐assisted quantum technology. Specifically, we employ the use of a robotic arm to hold a strong permanent magnet to meet a requirement in spin‐based sensing: aligning an external magnetic field along the magnetic dipole axis of an arbitrarily oriented spin system (<bold>Figure</bold> ##FIG##0##\n1a##). We demonstrate that this method has significant advantages where traditional techniques for generating vector fields, such as mounting the magnet on a fixed axis translation stage, or using a three‐axis Helmholtz coil, are infeasible owing to the tight physical constraints of the surrounding optomechanical apparatus. While this work focuses on a specific use case for robotics in quantum technology, the methods developed here can be easily adapted and extended to other experimental settings.</p>", "<title>Problem Statement and Requirements</title>", "<p>Spin‐based magnetometers operate by mapping local perturbations in their environment to shifts in the transition (magnetic resonance absorption) frequency of the spin system.<sup>[</sup>\n##UREF##7##\n17\n##\n<sup>]</sup> The NV center in diamond, an atom‐like defect comprising a nitrogen atom and neighboring vacancy site,<sup>[</sup>\n##UREF##8##\n18\n##\n<sup>]</sup> is the prototypical solid state quantum sensor on account of its optically accessible spin state, which allows optical manipulation and readout of its spin state at room temperature (optically detected magnetic resonance or ODMR). NV center magnetometers have rapidly advanced over the past decade and have reached maturity as a quantum magnetometer, with nanotesla (nT) sensitivities at nanoscale resolutions.<sup>[</sup>\n##REF##24801494##\n19\n##, ##UREF##9##\n20\n##\n<sup>]</sup> As magnetic dipole–dipole interactions are weak and confined to the near field, near‐surface NV centers are required to image fields from individual spins.<sup>[</sup>\n##UREF##10##\n21\n##\n<sup>]</sup> Nanoscale inclusions of diamond, or nanodiamond, are used to host the spin probe in hot and wet biochemical surroundings in applications such as protein<sup>[</sup>\n##REF##23738579##\n22\n##, ##REF##26847544##\n23\n##\n<sup>]</sup> or cell detection.<sup>[</sup>\n##REF##21552253##\n24\n##, ##REF##34929080##\n25\n##\n<sup>]</sup> Nanodiamonds typically contribute an additional energy term Π to the NV center Hamiltonian <italic toggle=\"yes\">H</italic>, from lattice strain and local charges<sup>[</sup>\n##UREF##11##\n26\n##, ##REF##30608732##\n27\n##\n<sup>]</sup>\nwhere <bold>B</bold>\n<sub>⊥</sub> = (<italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>) and <bold>S</bold>\n<sub>⊥</sub> = (<italic toggle=\"yes\">S</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, <italic toggle=\"yes\">S</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>) are the transverse magnetic field and Pauli spin terms, with <italic toggle=\"yes\">z</italic> defined as the axis comprising the NV center along the diamond lattice. In Figure ##FIG##0##1b##, the energy term Π leads to a frequency splitting of size 2Π (shown in gray), making the NV center transition frequencies robust to magnetic field fluctuations to first order. A bias field <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> is thus required bring to the NV center into the regime (<italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> ≫ Π/γ) where the transitions are linearly dependent on the magnetic field, which corresponds to the highest sensitivity. Given that nanodiamonds typically display Π ≈ 10 MHz,<sup>[</sup>\n##UREF##12##\n28\n##\n<sup>]</sup> this requires a moderate <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> magnetic field of 5 mT aligned to the NV axis. A misaligned magnetic field (with a residual <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub> or <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> component) would lead to a mixing of the energy eigenstates, which would result in a reduction of both the fluorescence and contrast (SNR) of the spin‐dependent optical readout.<sup>[</sup>\n##UREF##13##\n29\n##\n<sup>]</sup> Magnetic fields of 5 mT significantly degrade the spin coherence time (<italic toggle=\"yes\">T</italic>\n<sub>2</sub>) of the NV center when misaligned by 5° as they cause nearby nuclear spins to precess.<sup>[</sup>\n##UREF##14##\n30\n##, ##UREF##15##\n31\n##\n<sup>]</sup>\n</p>", "<p>To date, the established method to align a static magnetic field to an arbitrarily oriented spin is using three perpendicular wire coils<sup>[</sup>\n##REF##23396312##\n32\n##, ##UREF##16##\n33\n##, ##UREF##17##\n34\n##\n<sup>]</sup> or sets of coils in the Helmholtz configuration.<sup>[</sup>\n##UREF##12##\n28\n##, ##UREF##18##\n35\n##, ##UREF##19##\n36\n##\n<sup>]</sup> The configuration is convenient for producing vector magnetic fields, after calibration, as the current in each coil can be ratioed to produce a desired orientation. Typically, these systems operate at 1 mT and use hundreds of wire turns, with field strengths limited by Ohmic heating and sample distance. Proximal microcoils can cause significant heating, which has adverse implications for sensitive samples, such as in biosensing.<sup>[</sup>\n##UREF##20##\n37\n##, ##UREF##21##\n38\n##\n<sup>]</sup> Fields can be significantly increased with the use of superconducting solenoids, but with added costs and constraints.</p>", "<p>The constraint of requiring coils at three axes around the sample severely restricts optical or mechanical degrees of freedom. An alternative method is to place and orient a strong neodymium permanent magnet (NdFeB) in the vicinity of the sample. The advantage here is that the small magnet can produce much larger field strengths than the coil. It is less restrictive in its physical footprint, so it can be combined with optical assemblies and cryogenics. The magnets are aligned using linear<sup>[</sup>\n##REF##32182080##\n39\n##, ##UREF##22##\n40\n##, ##REF##32167360##\n41\n##\n<sup>]</sup> or rotational translation stages.<sup>[</sup>\n##UREF##23##\n42\n##, ##UREF##24##\n43\n##\n<sup>]</sup> The physical limitations of these stages preclude the alignment of certain orientation spin‐based systems.<sup>[</sup>\n##UREF##24##\n43\n##\n<sup>]</sup> Typically, the magnet is positioned once and is aligned along a set diamond crystalline axis because the calibration process is cumbersome. This precludes the use of nanodiamonds where each site may have a random dipole orientation,<sup>[</sup>\n##REF##36776813##\n44\n##\n<sup>]</sup> eliminating important applications such as inspecting spatially separated regions or tracking dynamic events in liquid environments. When alignment is not possible, it results in a reduction in sensor performance.<sup>[</sup>\n##UREF##25##\n45\n##\n<sup>]</sup> In general, misaligned magnetic fields have severe implications for spin mixing, flipping, and limited coherence across a range of spin‐based systems.<sup>[</sup>\n##UREF##26##\n46\n##, ##UREF##27##\n47\n##, ##REF##25437256##\n48\n##\n<sup>]</sup>\n</p>", "<p>We propose to combine the convenience and control of coils with the small footprint and strength of a permanent magnet in developing a robotically controlled vectorial field alignment system. Our approach has the following advantages: 1) Increased precision and control: The robot manipulates the magnet with a high degree of accuracy, ensuring precise alignment of the generated magnetic field. For our application, this means better than 5° accuracy.<sup>[</sup>\n##UREF##14##\n30\n##\n<sup>]</sup> 2) Fast alignment: By employing a robot to move and position the magnet across optimal trajectories, alignment should be more efficient than manual techniques. 3) Long‐term stability: Employing closed‐loop feedback with sufficient torque against gravity will maintain position securely for extended periods, ensuring stable alignment during experiments. 4) Enhanced reproducibility: A robust algorithm can align and realign the magnet between sample exchanges or across multiple sites of interrogation. The robot consistently produces a given orientation field for different sample geometries. 5) Scalability: the robot has an adaptable routine that is able to suit a wide range of experimental configurations and constraints. One can also easily extend to scenarios where two fields with specific orientations need to be simultaneously applied, for instance, an in‐plane and an out‐of‐plane field.</p>", "<p>To position a magnet at a desired location in 3D space with respect to a point of interest, allowing for rotation about two axes to achieve magnetic field orientation, we require a robot with at least five degrees of freedom. The robot must be capable of handling a moderate payload in order to carry enough magnet mass to produce an appreciable field (10 mT) at a distance. It should also be readily available with a well‐developed software interface and be economical to meet the requirements of use outside the robotics community. In the following section, we will evaluate the use of robotics for the described task.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Workspace Analysis</title>", "<p>Workspace analysis is essential for robotic control and application, as it evaluates the space the robot can access and manipulate with its end‐effector, constrained by the robot's kinematic configuration. This analysis helps to identify the robot's suitability for specific tasks and environments. Key aspects include the reachable workspace volume (total 3D space the robot's end‐effector can reach), workspace boundaries (limits of reachable space), and dexterity within this workspace (ability to precisely orient the end‐effector).<sup>[</sup>\n##UREF##28##\n49\n##\n<sup>]</sup> In this section, we perform workspace analysis on a magnet carrying robotic arm to evaluate its performance in generating vector magnetic fields.</p>", "<p>The robotic arm consists of a set of rigid bodies called links, connected by joints, with each joint driven by a motor actuator. An end‐effector, in this case, a permanent magnet, is attached to the end link. The arm is an open chain robot, with the position and orientation of the end‐effector uniquely determined from the joint positions. The common configuration comprises of six joints, providing six degrees of freedom (DoF). For our experiments, we use a <italic toggle=\"yes\">Niryo NED 2</italic> robot owing to its well‐documented open source stack, and ready availability. The arm has a moderate payload of 300 g, and is thus capable of lifting 40 cm<sup>3</sup> of NdFeB, which can generate a surface magnetic field of ≈ 800 mT (see Figure ##SUPPL##0##S1##, Supporting Information). For ease of adoption, we select a cylindrical magnetic source with a radial hole, through which it can be fixed by a screw to the tool shaft. As shown in Figure ##FIG##0##1c##, the robot is first set up by translating the tool center point (TCP) along the <italic toggle=\"yes\">x</italic>‐axis of its end‐effector, coaxial with the magnetization axis of the magnet (Figure ##FIG##0##1a##). This translation sets the distance, and hence strength, of the magnet from the point of interrogation.</p>", "<p>To create a set vector field, the robot uses the robot operating system (ROS) kinematic processor<sup>[</sup>\n##UREF##29##\n50\n##\n<sup>]</sup> to position its joints in order to compute the desired pose. The robot pose comprises the location and orientation of the TCP relative to a global coordinate frame. Rigid robots possess six state variables (<italic toggle=\"yes\">x</italic>, <italic toggle=\"yes\">y</italic>, <italic toggle=\"yes\">z</italic>, α<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>), where the latter three coordinates are angles of rotation about the <italic toggle=\"yes\">x</italic>, <italic toggle=\"yes\">y</italic>, and <italic toggle=\"yes\">z</italic>‐axes, respectively. The inverse kinematics problem is to find the joint position given a desired pose. In Table ##SUPPL##0##S1##, Supporting Information, we give the Denavit–Hartenberg (D–H) representation for the kinematics of this robot. In principle, by fixing <italic toggle=\"yes\">x</italic>, <italic toggle=\"yes\">y</italic>, and <italic toggle=\"yes\">z</italic> at the NV center location, the vector orientation of an applied magnetic field can be modified by varying α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> of the pose. In our scheme, the cylindrical magnet is symmetric about α<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, so this degree of freedom is left unused. In Figure ##FIG##0##1c##, we simulate in RViz, a visualization software for ROS, that the robot is sufficiently dexterous in positioning its joints to achieve a range of orientations, whereby the magnet is rotated around a stationary point with varying α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>. In Figure ##SUPPL##0##S2##, Supporting Information, we calculate the full workspace volume and dexterity within this volume.</p>", "<title>Magnetic Vector Reconstruction</title>", "<p>The goal of controlling the pose angle is to create a desired magnetic vector field at a given sample location. For experimental verification, we position a 3‐axis Hall sensor at the point of interest in order to measure the field generated from the combined system of the robotic arm and its permanent magnet end‐effector. We set the robot approximately collinear with the sensor axis which is observed using a camera with a zoom lens. In <bold>Figure</bold> ##FIG##1##\n2a##, we see the effect of adding magnets to the structure up to 70% of the payload by setting the robot along an arc trajectory from horizontal to vertical, by rotating the desired pose from α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = 0 to α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = π/2 with the distance between the sample and magnet surface fixed.</p>", "<p>Commonly, in robotics, camera data is processed to extract information on the desired pose.<sup>[</sup>\n##UREF##5##\n13\n##\n<sup>]</sup> Here, the three‐axis Hall sensor provides rich additional vector information, which, coupled with the known dependence of the magnetic field on position, allows the pose to be measured with higher precision than is visually observable. We fit the data with a closed form expression of the magnetic field observed from the cylindrical magnet,<sup>[</sup>\n##UREF##30##\n51\n##\n<sup>]</sup> using the pose variables as fitting parameters. We fit a constant 15° offset in α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and observe this in the <italic toggle=\"yes\">x</italic>–<italic toggle=\"yes\">z</italic> crossing point of the sensor and the robot, which for an aligned system would occur at 45° (marked by a dashed line in Figure ##FIG##1##2a##). Additionally, for this trajectory, we would expect no <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> field to be measured. The non‐zero <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> component is well fit to the varying non‐zero α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> occurring when each magnet is added. This offset results in a non‐linear relation between the number of magnets added and the observed strength. With an initial calibration trajectory to record this magnetic field information, fine alignment can be achieved either by physically adjusting the robot or by modifying the coordinate frame to correct for the observed misalignment error.</p>", "<p>Following this initial trajectory, in Figure ##FIG##1##2b##, we observe that by scanning through a dictionary of poses, varying only α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>, we are able to traverse a set of <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>B</mml:mi><mml:mtext>abs</mml:mtext></mml:msub><mml:mover accent=\"true\"><mml:mi mathvariant=\"bold\">n</mml:mi><mml:mo>^</mml:mo></mml:mover><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>y</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>z</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> points on the sphere where <italic toggle=\"yes\">B</italic>\n<sub>abs</sub> is an approximately constant scalar and <mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi mathvariant=\"bold\">n</mml:mi><mml:mo>^</mml:mo></mml:mover></mml:mrow></mml:math> is the unit normal vector. In the image plots, we see the measured <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, and <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> over each pose α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> compared to the designed field. There is a small percentage of white pixels representing poses within the workspace that were unachievable by the kinematic processor. The robot scans in a meander, alternating +<italic toggle=\"yes\">z</italic>, −<italic toggle=\"yes\">z</italic>, and artefacts of this are seen through scan lines in the measured data. Overall, we measure high angular accuracy with a mean error of 2.9° and mode error of 2.3° and confirm that the robotic arm is able to produce desired field orientations with a high accuracy. In measuring the field components against the designed pose, this accuracy captures uncertainty in the motor actuators, the corresponding pose of the robot, the analytical model of the field generated, and the field measured by the Hall sensor. This measurement confirms alignment is achievable with this system over all vector orientations below the target 5° threshold.</p>", "<title>Field Amplitude Control</title>", "<p>For a set vector orientation and magnet mass, some ODMR applications require tuning of the magnetic field amplitude, for instance so that the spin resonance frequency matches a microwave resonator.<sup>[</sup>\n##UREF##31##\n52\n##, ##UREF##32##\n53\n##\n<sup>]</sup> The field amplitude can be controlled by tuning the distance between the magnet and the sample position. However, the magnetic field fall‐off with <italic toggle=\"yes\">r</italic> distance is highly non‐linear, characterized by the Biot–Savart 1/<italic toggle=\"yes\">r</italic>\n<sup>3</sup> relation. In addition, the robotic arm performs non‐linear displacement, requiring dual movement of two rotational joints per linear step of the end effector.</p>", "<p>We observe in Figure ##FIG##1##2c## that the displacement of the magnet away from the Hall sensor is sufficiently linear to produce a 1/<italic toggle=\"yes\">x</italic>\n<sup>3</sup> response in <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>. Because the magnetic field generated by the permanent magnet is large, it can be positioned sufficiently far away from the sensor so that the 10 mm 1/<italic toggle=\"yes\">r</italic>\n<sup>3</sup> trajectory can be subsampled within the 0.5 mm resolution of the robot (lines shown in the top panel) to create a desired response <italic toggle=\"yes\">B</italic>(<italic toggle=\"yes\">r</italic>). In the middle panel, we observe that we can create a linear field response between 0 and 10 mT through this method. In the bottom panel, we observe the error in this sampling technique is typically lower than 0.1 mT. However, as expected, this error increases for close distances to the sensor as the available resolution to subsample the 1/<italic toggle=\"yes\">r</italic>\n<sup>3</sup> field diminishes.</p>", "<title>Collision‐Free Motion Planning</title>", "<p>With operation validated in an unconstrained environment, we move to navigating the robot around complicated lab infrastructure. By evaluating intersections with its environment, the robot is able to compute collisions in the ROS simulation using LBKPiece from the Open Motion Planning Library to traverse a tree of possible trajectories to achieve a given pose goal.<sup>[</sup>\n##UREF##33##\n54\n##\n<sup>]</sup>\n</p>", "<p>We take two experimental setups in our lab, a cryostat with an optical window and a scanning stage confocal microscope (see <bold>Figure</bold> ##FIG##2##\n3a##), and add their spatial meshes in simulation to the robot environment. For these complex geometries, it would not be possible to position three‐axis Helmholtz coils for magnetic field alignment due to the competing requirements for optical access to the sample and the need to move the sample in 3D. Single microcoils or a permanent magnet mounted on a stage would have limitations in terms of achievable proximity to the sample.</p>", "<p>With the available kinematics of the 6 DoF robotic arm, the position of the magnet with respect to the sample is far less constrained. In Figure ##FIG##2##3a##, using LBKPiece, we simulate that a chosen subset of poses can be traversed with access to the top and back sides of the cryostat, oriented around the TCP located at the sample mount, generating a −<italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, +<italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, −<italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> sphere segment (one‐eighth) without collisions. However, we observe that for the scanning stage confocal microscope, only a subset of any sphere segment is achievable. Poses that cannot be accessed without collision are shown with red dots and form a significant part of the subset. From this simulation, it is evident that there would have limited success of the robot in the magnetization‐axis‐aligned configuration described in Figure ##FIG##0##1c##.</p>", "<title>Designing Collision‐Free Field Vectors</title>", "<p>An important consideration at this point is that the set of poses in this configuration only make a small subset of the possible joint configurations of the robot and therefore possible magnetic field vectors. By moving the TCP defined in Figure ##FIG##0##1c## from the NV center to the magnet, we give free control over its orientation and position, with access to the fringing fields of the magnetic source. Our hypothesis is that there exists a set of collision‐free poses that would produce a full set of magnetic vectors. This idea makes use of the magnetic inverse problem in field sensing: even if a pose cannot be reached, the desired field can be obtained because there is a non‐unique mapping between the field and the pose.<sup>[</sup>\n##UREF##34##\n55\n##\n<sup>]</sup> Our algorithm is laid out in Figure ##FIG##1##2b##. First, the unreachable set of poses in the constrained environment is found. For each such pose (Figure ##FIG##1##2b(i)##), the TCP is translated along <italic toggle=\"yes\">x</italic> to the magnet center and the magnet is then linearly translated in either <italic toggle=\"yes\">y</italic> or <italic toggle=\"yes\">z</italic> to a new reachable pose (Figure ##FIG##1##2b(ii)##). Next, the new pose is rotated in α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> or α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> to obtain the same vector field orientation as the original pose (Figure ##FIG##1##2b(iii)##). Finally, the magnet is translated along <italic toggle=\"yes\">x</italic> to recover the original magnitude (Figure ##FIG##1##2b(iv)##).</p>", "<p>To calculate the vector rotation in Figure ##FIG##1##2b(iii)##, we can approximate the magnet with a dipole, for which the inverse magnetostatic expression is known.<sup>[</sup>\n##UREF##34##\n55\n##\n<sup>]</sup> For a powerful permanent magnet, the arm can be withdrawn at sufficient distances so that this dipole approximation becomes valid. The orientation of a unit dipole <mml:math id=\"jats-math-5\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>m</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> at a vector <mml:math id=\"jats-math-6\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>r</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> to create a field at the sensor location <mml:math id=\"jats-math-7\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>B</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> is given by\nwhere μ<sub>0</sub> is the vacuum permeability.</p>", "<p>In Figure ##FIG##2##3c##, we model the <italic toggle=\"yes\">z</italic> displaced magnet and find that the field observed at the sample location (green dot) has a significantly modified orientation (first panel). We can use Equation (##FORMU##1##2##) to calculate the dipole orientation <mml:math id=\"jats-math-9\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>m</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> to find <mml:math id=\"jats-math-10\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>B</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> (middle panel). We then rotate the magnet to be coaxial with the calculated dipole orientation and recover the desired field vector <mml:math id=\"jats-math-11\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>B</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> with high accuracy, minimizing <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> (last panel). In Figure ##FIG##2##3d##, we show that in the physical experiment, the off‐axial field component is indeed minimized when set to the calculated 26° angle, and that this algorithm succeeds within the pose resolution limit of the robot.</p>", "<p>As well as correcting orientation, for some applications it is important to maintain the field amplitude. This final step in Figure ##FIG##2##3b(iv)## is achieved by using the known 1/<italic toggle=\"yes\">r</italic>\n<sup>3</sup> Biot–Savart relation of Figure ##FIG##1##2c## to scale the amplitude, translating the magnet in <italic toggle=\"yes\">x</italic>. To capture both the orientation and amplitude, we define a Gaussian kernel similarity function between the target field vector <italic toggle=\"yes\">B</italic>\n<sub>1</sub> and the replacement vector <italic toggle=\"yes\">B</italic>\n<sub>2</sub>, as this is well bounded between 0 (least similar) and 1 (most similar):\nwith <italic toggle=\"yes\">d</italic> = 3. We experimentally implement each step of the algorithm in Figure ##FIG##2##3e## and see that the final vector achieves a high similarity to the target vector with <italic toggle=\"yes\">S</italic> = 0.95. This can also be seen by comparing the histograms of the measured field components in Figure ##FIG##2##3e(i,iv)##. Here, the final amplitude correcting step maintains the desired field orientation. We have evidenced that by using this algorithm, it is possible to systematically replace unreachable poses with reachable poses with the same field vector. The full dexterity offered by the robotic links combined with the inverse problem of magnetostatics make this system a powerful tool for setting arbitrary‐strength magnetic field vectors in highly constrained environments. We note that this model works in standard laboratories without the presence of ferromagnets. Field distortions in the presence of iron or nickel objects should be calculated if present.</p>", "<title>Experimental Setting of an NV Center Confocal Microscope</title>", "<p>Following validation with the Hall sensor, we now move to a full experimental setting in order to evaluate the performance of the robot for aligning a spin based quantum sensor. We see in <bold>Figure</bold> ##FIG##3##\n4a,b## that this requires navigating a highly complex environment with many sensitive optical and mechanical instruments.</p>", "<p>In the technique described in the previous section, the collision‐free positions found in simulation can be downloaded to the physical robot. This requires a fine alignment between the simulation and the real world performance, which could be achieved using the approach described in Figure ##FIG##1##2a##. In a highly constrained environment, we find sensor‐driven fine angular alignment is difficult to achieve as the initial calibration trajectories contain poses that cannot be verified as collision‐free until this alignment has succeeded. In a future iteration, additional sensor data could enrich this information using machine vision or ultrasound to map the collision surroundings.</p>", "<p>A fast and pragmatic approach in an experimental setting is to <italic toggle=\"yes\">teach</italic> the robot a set of collision‐free poses. We do this by switching the torque on each motor off momentarily, allowing the joints to move freely. Now, the operator can grasp the magnet and guide the robotic arm to a desired location within the geometry, avoiding collision. Whilst doing this, the user can monitor the magnetic field produced at the sample location with the Hall sensor. When a desired field is registered, the torque and closed loop feedback can be switched on, locking the magnet in its set position. The corresponding coordinates (either the pose or the joint angles) can be registered along with the measured magnetic field. Through this method, the user can hunt and find locations where, for instance, <italic toggle=\"yes\">z</italic> is the dominant field component. These poses can be used to gather information to calibrate the source to its experimental surroundings. We can both compare the taught poses with the simulation to calculate collisions and with the dipole field model, we can locally modify the taught position to achieve the desired magnetic field vectors.</p>", "<p>As a proof‐of‐principle experiment, we teach the robot a trajectory across the confocal microscope shown in Figure ##FIG##3##4a##. We can then demonstrate that traversing this trajectory repeatably affects the NV center spin based sensor. In Figure ##FIG##3##4c##, we use the confocal microscope to locate a collection of milled solid immersion lenses in a polycrystalline diamond sample,<sup>[</sup>\n##UREF##35##\n56\n##\n<sup>]</sup> observing a bright NV center in the central lens (Figure ##FIG##3##4d##). With the robot arm at its home position, 10 cm away from the sample, we perform ODMR on this NV center (see Experimental Section for experimental details). As defined in Equation (##FORMU##0##1##), we observe a small 3.7030 MHz splitting due to an intrinsic Π = 1.8515 MHz, about the central <italic toggle=\"yes\">D</italic> = 2.8704 GHz, shown in Figure ##FIG##3##4e##. In moving the TCP near the NV center site, with the robot end effector in the vicinity of the experimental setup, we observe a large 100 MHz splitting in the ODMR spectra (green plot) from the presence of the permanent magnet. Typically, the NV center must be optically aligned to the photon detector within 500 nm using a piezo stage and the ability to engage and disengage the robot whilst performing ODMR indicates it is suitable to use in this highly sensitive experiment.</p>", "<title>Robotic Vectorial Field Alignment of a Single Spin Sensor</title>", "<p>In Figure ##FIG##3##4f##, we repeat the ODMR for a set of robot poses along a collision‐free trajectory with α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = 20 ° at 5 ° increments in α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> (Trajectory 1). Each data point was averaged over 5 min. The peak resonances show a smooth increase in splitting from <italic toggle=\"yes\">D</italic> as the magnet is moved in front of the objective. The same path is traversed at 2° increments in α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> (Trajectory 2) and resonance data shows the same splitting trend, indicating that the trajectory‐induced splitting is reproducible. The fitted resonances can be used to extract the polar angle between the NV axis and the magnetic field of interrogation, from the zero‐field parameters <italic toggle=\"yes\">D</italic> and Π (see Experimental Section for details).<sup>[</sup>\n##REF##18833276##\n57\n##\n<sup>]</sup> This gives a value of 61.0 ± 0.3° for Trajectory 1 and 61.8 ± 0.2° for Trajectory 2.<sup>[</sup>\n##REF##18833276##\n57\n##\n<sup>]</sup> This small polar angle change over the 25 ° range in α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> indicates that the NV center is near aligned with the world coordinate <italic toggle=\"yes\">z</italic>‐axis.</p>", "<p>In Figure ##FIG##3##4g##, by replacing the diamond sample with the Hall sensor and focusing the objective at the center of the sensor area, we can map the field components generated by the trajectory. This alignment step co‐locates the relative pose between the sensor and the robot as described in Figure ##SUPPL##0##S3##, Supporting Information. We see that the <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub> and <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> components cross, as expected for varying α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>. We find the Hall field amplitude |<italic toggle=\"yes\">B</italic>| in excellent agreement with the ODMR sensed field amplitude (see Figure ##SUPPL##0##S3##, Supporting Information). For the trajectory chosen, the robot TCP is not yet fully aligned with the NV or Hall sensor area. We see that in contrast to Figure ##FIG##1##2b##, the trajectory does not conserve |<italic toggle=\"yes\">B</italic>|, with a large increasing <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> component, and this is the main contribution to the increased splitting between the two resonances in Figure ##FIG##3##4f##.</p>", "<p>Using the amplitude data, we can normalize each splitting to isolate the field component ratios (see Experimental Section). In Figure ##FIG##3##4g##, this normalization results in the appearance of a dip from both trajectories, with the phase and contrast of the dip giving an estimation of the NV's orientation. The low contrast, non‐zero minima in α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> indicates the NV center is near aligned with the world coordinate <italic toggle=\"yes\">z</italic>‐axis as previously discussed. We find that both datasets can be well fitted with the characteristic equation<sup>[</sup>\n##UREF##17##\n34\n##\n<sup>]</sup> to find α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = 64.1 ± 0.4°, α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = 97.6 ± 0.7° for Trajectory 1 and α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = 62.9 ± 0.8°, α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = 97.9 ± 1.4° for Trajectory 2. In this, we have shown that vectorial field alignment can be achieved with robotic trajectories of as little as six steps. This is especially useful for ODMR, where collecting each spectra takes on the order of minutes.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Workspace Analysis</title>", "<p>Workspace analysis is essential for robotic control and application, as it evaluates the space the robot can access and manipulate with its end‐effector, constrained by the robot's kinematic configuration. This analysis helps to identify the robot's suitability for specific tasks and environments. Key aspects include the reachable workspace volume (total 3D space the robot's end‐effector can reach), workspace boundaries (limits of reachable space), and dexterity within this workspace (ability to precisely orient the end‐effector).<sup>[</sup>\n##UREF##28##\n49\n##\n<sup>]</sup> In this section, we perform workspace analysis on a magnet carrying robotic arm to evaluate its performance in generating vector magnetic fields.</p>", "<p>The robotic arm consists of a set of rigid bodies called links, connected by joints, with each joint driven by a motor actuator. An end‐effector, in this case, a permanent magnet, is attached to the end link. The arm is an open chain robot, with the position and orientation of the end‐effector uniquely determined from the joint positions. The common configuration comprises of six joints, providing six degrees of freedom (DoF). For our experiments, we use a <italic toggle=\"yes\">Niryo NED 2</italic> robot owing to its well‐documented open source stack, and ready availability. The arm has a moderate payload of 300 g, and is thus capable of lifting 40 cm<sup>3</sup> of NdFeB, which can generate a surface magnetic field of ≈ 800 mT (see Figure ##SUPPL##0##S1##, Supporting Information). For ease of adoption, we select a cylindrical magnetic source with a radial hole, through which it can be fixed by a screw to the tool shaft. As shown in Figure ##FIG##0##1c##, the robot is first set up by translating the tool center point (TCP) along the <italic toggle=\"yes\">x</italic>‐axis of its end‐effector, coaxial with the magnetization axis of the magnet (Figure ##FIG##0##1a##). This translation sets the distance, and hence strength, of the magnet from the point of interrogation.</p>", "<p>To create a set vector field, the robot uses the robot operating system (ROS) kinematic processor<sup>[</sup>\n##UREF##29##\n50\n##\n<sup>]</sup> to position its joints in order to compute the desired pose. The robot pose comprises the location and orientation of the TCP relative to a global coordinate frame. Rigid robots possess six state variables (<italic toggle=\"yes\">x</italic>, <italic toggle=\"yes\">y</italic>, <italic toggle=\"yes\">z</italic>, α<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>), where the latter three coordinates are angles of rotation about the <italic toggle=\"yes\">x</italic>, <italic toggle=\"yes\">y</italic>, and <italic toggle=\"yes\">z</italic>‐axes, respectively. The inverse kinematics problem is to find the joint position given a desired pose. In Table ##SUPPL##0##S1##, Supporting Information, we give the Denavit–Hartenberg (D–H) representation for the kinematics of this robot. In principle, by fixing <italic toggle=\"yes\">x</italic>, <italic toggle=\"yes\">y</italic>, and <italic toggle=\"yes\">z</italic> at the NV center location, the vector orientation of an applied magnetic field can be modified by varying α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> of the pose. In our scheme, the cylindrical magnet is symmetric about α<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, so this degree of freedom is left unused. In Figure ##FIG##0##1c##, we simulate in RViz, a visualization software for ROS, that the robot is sufficiently dexterous in positioning its joints to achieve a range of orientations, whereby the magnet is rotated around a stationary point with varying α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>. In Figure ##SUPPL##0##S2##, Supporting Information, we calculate the full workspace volume and dexterity within this volume.</p>", "<title>Magnetic Vector Reconstruction</title>", "<p>The goal of controlling the pose angle is to create a desired magnetic vector field at a given sample location. For experimental verification, we position a 3‐axis Hall sensor at the point of interest in order to measure the field generated from the combined system of the robotic arm and its permanent magnet end‐effector. We set the robot approximately collinear with the sensor axis which is observed using a camera with a zoom lens. In <bold>Figure</bold> ##FIG##1##\n2a##, we see the effect of adding magnets to the structure up to 70% of the payload by setting the robot along an arc trajectory from horizontal to vertical, by rotating the desired pose from α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = 0 to α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = π/2 with the distance between the sample and magnet surface fixed.</p>", "<p>Commonly, in robotics, camera data is processed to extract information on the desired pose.<sup>[</sup>\n##UREF##5##\n13\n##\n<sup>]</sup> Here, the three‐axis Hall sensor provides rich additional vector information, which, coupled with the known dependence of the magnetic field on position, allows the pose to be measured with higher precision than is visually observable. We fit the data with a closed form expression of the magnetic field observed from the cylindrical magnet,<sup>[</sup>\n##UREF##30##\n51\n##\n<sup>]</sup> using the pose variables as fitting parameters. We fit a constant 15° offset in α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and observe this in the <italic toggle=\"yes\">x</italic>–<italic toggle=\"yes\">z</italic> crossing point of the sensor and the robot, which for an aligned system would occur at 45° (marked by a dashed line in Figure ##FIG##1##2a##). Additionally, for this trajectory, we would expect no <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> field to be measured. The non‐zero <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> component is well fit to the varying non‐zero α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> occurring when each magnet is added. This offset results in a non‐linear relation between the number of magnets added and the observed strength. With an initial calibration trajectory to record this magnetic field information, fine alignment can be achieved either by physically adjusting the robot or by modifying the coordinate frame to correct for the observed misalignment error.</p>", "<p>Following this initial trajectory, in Figure ##FIG##1##2b##, we observe that by scanning through a dictionary of poses, varying only α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>, we are able to traverse a set of <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>B</mml:mi><mml:mtext>abs</mml:mtext></mml:msub><mml:mover accent=\"true\"><mml:mi mathvariant=\"bold\">n</mml:mi><mml:mo>^</mml:mo></mml:mover><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>y</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mi>z</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> points on the sphere where <italic toggle=\"yes\">B</italic>\n<sub>abs</sub> is an approximately constant scalar and <mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi mathvariant=\"bold\">n</mml:mi><mml:mo>^</mml:mo></mml:mover></mml:mrow></mml:math> is the unit normal vector. In the image plots, we see the measured <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, and <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> over each pose α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> compared to the designed field. There is a small percentage of white pixels representing poses within the workspace that were unachievable by the kinematic processor. The robot scans in a meander, alternating +<italic toggle=\"yes\">z</italic>, −<italic toggle=\"yes\">z</italic>, and artefacts of this are seen through scan lines in the measured data. Overall, we measure high angular accuracy with a mean error of 2.9° and mode error of 2.3° and confirm that the robotic arm is able to produce desired field orientations with a high accuracy. In measuring the field components against the designed pose, this accuracy captures uncertainty in the motor actuators, the corresponding pose of the robot, the analytical model of the field generated, and the field measured by the Hall sensor. This measurement confirms alignment is achievable with this system over all vector orientations below the target 5° threshold.</p>", "<title>Field Amplitude Control</title>", "<p>For a set vector orientation and magnet mass, some ODMR applications require tuning of the magnetic field amplitude, for instance so that the spin resonance frequency matches a microwave resonator.<sup>[</sup>\n##UREF##31##\n52\n##, ##UREF##32##\n53\n##\n<sup>]</sup> The field amplitude can be controlled by tuning the distance between the magnet and the sample position. However, the magnetic field fall‐off with <italic toggle=\"yes\">r</italic> distance is highly non‐linear, characterized by the Biot–Savart 1/<italic toggle=\"yes\">r</italic>\n<sup>3</sup> relation. In addition, the robotic arm performs non‐linear displacement, requiring dual movement of two rotational joints per linear step of the end effector.</p>", "<p>We observe in Figure ##FIG##1##2c## that the displacement of the magnet away from the Hall sensor is sufficiently linear to produce a 1/<italic toggle=\"yes\">x</italic>\n<sup>3</sup> response in <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>. Because the magnetic field generated by the permanent magnet is large, it can be positioned sufficiently far away from the sensor so that the 10 mm 1/<italic toggle=\"yes\">r</italic>\n<sup>3</sup> trajectory can be subsampled within the 0.5 mm resolution of the robot (lines shown in the top panel) to create a desired response <italic toggle=\"yes\">B</italic>(<italic toggle=\"yes\">r</italic>). In the middle panel, we observe that we can create a linear field response between 0 and 10 mT through this method. In the bottom panel, we observe the error in this sampling technique is typically lower than 0.1 mT. However, as expected, this error increases for close distances to the sensor as the available resolution to subsample the 1/<italic toggle=\"yes\">r</italic>\n<sup>3</sup> field diminishes.</p>", "<title>Collision‐Free Motion Planning</title>", "<p>With operation validated in an unconstrained environment, we move to navigating the robot around complicated lab infrastructure. By evaluating intersections with its environment, the robot is able to compute collisions in the ROS simulation using LBKPiece from the Open Motion Planning Library to traverse a tree of possible trajectories to achieve a given pose goal.<sup>[</sup>\n##UREF##33##\n54\n##\n<sup>]</sup>\n</p>", "<p>We take two experimental setups in our lab, a cryostat with an optical window and a scanning stage confocal microscope (see <bold>Figure</bold> ##FIG##2##\n3a##), and add their spatial meshes in simulation to the robot environment. For these complex geometries, it would not be possible to position three‐axis Helmholtz coils for magnetic field alignment due to the competing requirements for optical access to the sample and the need to move the sample in 3D. Single microcoils or a permanent magnet mounted on a stage would have limitations in terms of achievable proximity to the sample.</p>", "<p>With the available kinematics of the 6 DoF robotic arm, the position of the magnet with respect to the sample is far less constrained. In Figure ##FIG##2##3a##, using LBKPiece, we simulate that a chosen subset of poses can be traversed with access to the top and back sides of the cryostat, oriented around the TCP located at the sample mount, generating a −<italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>, +<italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, −<italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> sphere segment (one‐eighth) without collisions. However, we observe that for the scanning stage confocal microscope, only a subset of any sphere segment is achievable. Poses that cannot be accessed without collision are shown with red dots and form a significant part of the subset. From this simulation, it is evident that there would have limited success of the robot in the magnetization‐axis‐aligned configuration described in Figure ##FIG##0##1c##.</p>", "<title>Designing Collision‐Free Field Vectors</title>", "<p>An important consideration at this point is that the set of poses in this configuration only make a small subset of the possible joint configurations of the robot and therefore possible magnetic field vectors. By moving the TCP defined in Figure ##FIG##0##1c## from the NV center to the magnet, we give free control over its orientation and position, with access to the fringing fields of the magnetic source. Our hypothesis is that there exists a set of collision‐free poses that would produce a full set of magnetic vectors. This idea makes use of the magnetic inverse problem in field sensing: even if a pose cannot be reached, the desired field can be obtained because there is a non‐unique mapping between the field and the pose.<sup>[</sup>\n##UREF##34##\n55\n##\n<sup>]</sup> Our algorithm is laid out in Figure ##FIG##1##2b##. First, the unreachable set of poses in the constrained environment is found. For each such pose (Figure ##FIG##1##2b(i)##), the TCP is translated along <italic toggle=\"yes\">x</italic> to the magnet center and the magnet is then linearly translated in either <italic toggle=\"yes\">y</italic> or <italic toggle=\"yes\">z</italic> to a new reachable pose (Figure ##FIG##1##2b(ii)##). Next, the new pose is rotated in α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> or α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> to obtain the same vector field orientation as the original pose (Figure ##FIG##1##2b(iii)##). Finally, the magnet is translated along <italic toggle=\"yes\">x</italic> to recover the original magnitude (Figure ##FIG##1##2b(iv)##).</p>", "<p>To calculate the vector rotation in Figure ##FIG##1##2b(iii)##, we can approximate the magnet with a dipole, for which the inverse magnetostatic expression is known.<sup>[</sup>\n##UREF##34##\n55\n##\n<sup>]</sup> For a powerful permanent magnet, the arm can be withdrawn at sufficient distances so that this dipole approximation becomes valid. The orientation of a unit dipole <mml:math id=\"jats-math-5\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>m</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> at a vector <mml:math id=\"jats-math-6\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>r</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> to create a field at the sensor location <mml:math id=\"jats-math-7\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>B</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> is given by\nwhere μ<sub>0</sub> is the vacuum permeability.</p>", "<p>In Figure ##FIG##2##3c##, we model the <italic toggle=\"yes\">z</italic> displaced magnet and find that the field observed at the sample location (green dot) has a significantly modified orientation (first panel). We can use Equation (##FORMU##1##2##) to calculate the dipole orientation <mml:math id=\"jats-math-9\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>m</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> to find <mml:math id=\"jats-math-10\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>B</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> (middle panel). We then rotate the magnet to be coaxial with the calculated dipole orientation and recover the desired field vector <mml:math id=\"jats-math-11\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>B</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mrow></mml:math> with high accuracy, minimizing <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> (last panel). In Figure ##FIG##2##3d##, we show that in the physical experiment, the off‐axial field component is indeed minimized when set to the calculated 26° angle, and that this algorithm succeeds within the pose resolution limit of the robot.</p>", "<p>As well as correcting orientation, for some applications it is important to maintain the field amplitude. This final step in Figure ##FIG##2##3b(iv)## is achieved by using the known 1/<italic toggle=\"yes\">r</italic>\n<sup>3</sup> Biot–Savart relation of Figure ##FIG##1##2c## to scale the amplitude, translating the magnet in <italic toggle=\"yes\">x</italic>. To capture both the orientation and amplitude, we define a Gaussian kernel similarity function between the target field vector <italic toggle=\"yes\">B</italic>\n<sub>1</sub> and the replacement vector <italic toggle=\"yes\">B</italic>\n<sub>2</sub>, as this is well bounded between 0 (least similar) and 1 (most similar):\nwith <italic toggle=\"yes\">d</italic> = 3. We experimentally implement each step of the algorithm in Figure ##FIG##2##3e## and see that the final vector achieves a high similarity to the target vector with <italic toggle=\"yes\">S</italic> = 0.95. This can also be seen by comparing the histograms of the measured field components in Figure ##FIG##2##3e(i,iv)##. Here, the final amplitude correcting step maintains the desired field orientation. We have evidenced that by using this algorithm, it is possible to systematically replace unreachable poses with reachable poses with the same field vector. The full dexterity offered by the robotic links combined with the inverse problem of magnetostatics make this system a powerful tool for setting arbitrary‐strength magnetic field vectors in highly constrained environments. We note that this model works in standard laboratories without the presence of ferromagnets. Field distortions in the presence of iron or nickel objects should be calculated if present.</p>", "<title>Experimental Setting of an NV Center Confocal Microscope</title>", "<p>Following validation with the Hall sensor, we now move to a full experimental setting in order to evaluate the performance of the robot for aligning a spin based quantum sensor. We see in <bold>Figure</bold> ##FIG##3##\n4a,b## that this requires navigating a highly complex environment with many sensitive optical and mechanical instruments.</p>", "<p>In the technique described in the previous section, the collision‐free positions found in simulation can be downloaded to the physical robot. This requires a fine alignment between the simulation and the real world performance, which could be achieved using the approach described in Figure ##FIG##1##2a##. In a highly constrained environment, we find sensor‐driven fine angular alignment is difficult to achieve as the initial calibration trajectories contain poses that cannot be verified as collision‐free until this alignment has succeeded. In a future iteration, additional sensor data could enrich this information using machine vision or ultrasound to map the collision surroundings.</p>", "<p>A fast and pragmatic approach in an experimental setting is to <italic toggle=\"yes\">teach</italic> the robot a set of collision‐free poses. We do this by switching the torque on each motor off momentarily, allowing the joints to move freely. Now, the operator can grasp the magnet and guide the robotic arm to a desired location within the geometry, avoiding collision. Whilst doing this, the user can monitor the magnetic field produced at the sample location with the Hall sensor. When a desired field is registered, the torque and closed loop feedback can be switched on, locking the magnet in its set position. The corresponding coordinates (either the pose or the joint angles) can be registered along with the measured magnetic field. Through this method, the user can hunt and find locations where, for instance, <italic toggle=\"yes\">z</italic> is the dominant field component. These poses can be used to gather information to calibrate the source to its experimental surroundings. We can both compare the taught poses with the simulation to calculate collisions and with the dipole field model, we can locally modify the taught position to achieve the desired magnetic field vectors.</p>", "<p>As a proof‐of‐principle experiment, we teach the robot a trajectory across the confocal microscope shown in Figure ##FIG##3##4a##. We can then demonstrate that traversing this trajectory repeatably affects the NV center spin based sensor. In Figure ##FIG##3##4c##, we use the confocal microscope to locate a collection of milled solid immersion lenses in a polycrystalline diamond sample,<sup>[</sup>\n##UREF##35##\n56\n##\n<sup>]</sup> observing a bright NV center in the central lens (Figure ##FIG##3##4d##). With the robot arm at its home position, 10 cm away from the sample, we perform ODMR on this NV center (see Experimental Section for experimental details). As defined in Equation (##FORMU##0##1##), we observe a small 3.7030 MHz splitting due to an intrinsic Π = 1.8515 MHz, about the central <italic toggle=\"yes\">D</italic> = 2.8704 GHz, shown in Figure ##FIG##3##4e##. In moving the TCP near the NV center site, with the robot end effector in the vicinity of the experimental setup, we observe a large 100 MHz splitting in the ODMR spectra (green plot) from the presence of the permanent magnet. Typically, the NV center must be optically aligned to the photon detector within 500 nm using a piezo stage and the ability to engage and disengage the robot whilst performing ODMR indicates it is suitable to use in this highly sensitive experiment.</p>", "<title>Robotic Vectorial Field Alignment of a Single Spin Sensor</title>", "<p>In Figure ##FIG##3##4f##, we repeat the ODMR for a set of robot poses along a collision‐free trajectory with α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = 20 ° at 5 ° increments in α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> (Trajectory 1). Each data point was averaged over 5 min. The peak resonances show a smooth increase in splitting from <italic toggle=\"yes\">D</italic> as the magnet is moved in front of the objective. The same path is traversed at 2° increments in α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> (Trajectory 2) and resonance data shows the same splitting trend, indicating that the trajectory‐induced splitting is reproducible. The fitted resonances can be used to extract the polar angle between the NV axis and the magnetic field of interrogation, from the zero‐field parameters <italic toggle=\"yes\">D</italic> and Π (see Experimental Section for details).<sup>[</sup>\n##REF##18833276##\n57\n##\n<sup>]</sup> This gives a value of 61.0 ± 0.3° for Trajectory 1 and 61.8 ± 0.2° for Trajectory 2.<sup>[</sup>\n##REF##18833276##\n57\n##\n<sup>]</sup> This small polar angle change over the 25 ° range in α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> indicates that the NV center is near aligned with the world coordinate <italic toggle=\"yes\">z</italic>‐axis.</p>", "<p>In Figure ##FIG##3##4g##, by replacing the diamond sample with the Hall sensor and focusing the objective at the center of the sensor area, we can map the field components generated by the trajectory. This alignment step co‐locates the relative pose between the sensor and the robot as described in Figure ##SUPPL##0##S3##, Supporting Information. We see that the <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub> and <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> components cross, as expected for varying α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>. We find the Hall field amplitude |<italic toggle=\"yes\">B</italic>| in excellent agreement with the ODMR sensed field amplitude (see Figure ##SUPPL##0##S3##, Supporting Information). For the trajectory chosen, the robot TCP is not yet fully aligned with the NV or Hall sensor area. We see that in contrast to Figure ##FIG##1##2b##, the trajectory does not conserve |<italic toggle=\"yes\">B</italic>|, with a large increasing <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> component, and this is the main contribution to the increased splitting between the two resonances in Figure ##FIG##3##4f##.</p>", "<p>Using the amplitude data, we can normalize each splitting to isolate the field component ratios (see Experimental Section). In Figure ##FIG##3##4g##, this normalization results in the appearance of a dip from both trajectories, with the phase and contrast of the dip giving an estimation of the NV's orientation. The low contrast, non‐zero minima in α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> indicates the NV center is near aligned with the world coordinate <italic toggle=\"yes\">z</italic>‐axis as previously discussed. We find that both datasets can be well fitted with the characteristic equation<sup>[</sup>\n##UREF##17##\n34\n##\n<sup>]</sup> to find α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = 64.1 ± 0.4°, α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = 97.6 ± 0.7° for Trajectory 1 and α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = 62.9 ± 0.8°, α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> = 97.9 ± 1.4° for Trajectory 2. In this, we have shown that vectorial field alignment can be achieved with robotic trajectories of as little as six steps. This is especially useful for ODMR, where collecting each spectra takes on the order of minutes.</p>" ]
[ "<title>Conclusion</title>", "<p>Our results show that an industrially designed robotic arm can be adapted to operate around sensitive optomechanical samples and setups. The presented modality produces stable and controllable magnetic fields that are capable of manipulating and aligning a single solid state quantum spin sensor. This is an important step in the use of robotics to replace axial stages and bulky field coils for experimental physics and in developing quantum technologies, where we have evidenced the benefit of the innate flexibility and configurability of robotic arms in highly constrained environments.</p>", "<p>The next step in this work is to generate on‐demand magnetic fields using a sophisticated algorithm that maps the traversable space given geometrical parameters, making use of the collision‐free techniques described. With this, a set of control points can be found, considering application‐specific criteria such as the field magnitude, linearization, or the time taken to move between points.</p>", "<p>Robotics, unlike solenoid coils, produce minimal local heat. This makes them suited for sensitive samples, and algorithms could be designed for tracking quantum sensors in motion under cell uptake, a difficult task where the spin sensor orientation changes over time.<sup>[</sup>\n##REF##23619694##\n58\n##, ##REF##28317922##\n59\n##\n<sup>]</sup> For further flexibility, the cylindrical magnet could be replaced with a rectangular magnet fixed perpendicular to its magnetic axis, with the unused roll degree of freedom in the robotic wrist providing rapid field orientation.</p>", "<p>Beyond an off‐the‐shelf design, an application‐specific robot could further maximize efficiency, precision, and control. This could have a larger payload whilst having a smaller form factor, for instance. We can extend this to the use of multiple robots to generate gradient magnetic fields. Without our approach, we find a 99% field uniformity over millimeter volumes (see Figure ##SUPPL##0##S1##, Supporting Information). However, this is significantly less than Helmholtz coils, which maintain this uniformity over their central volume (&gt; cm<sup>3</sup>). To combat this, multiple robots could be combined to increase uniformity over large areas. As well as a range of solid‐state sensors, the alignment of atoms and ions in cold and vacuum environments can be explored with these form factors. A probe‐like flux concentrator appended to the end‐effector could achieve higher field strengths at distant locations, although the presence of this ferromagnet would have to be robustly modeled.<sup>[</sup>\n##REF##33117992##\n60\n##\n<sup>]</sup>\n</p>", "<p>In addition, the robot‐driven orientation presented can be extended to aligning quantum objects with a range of parameters, including electric and light fields. Here, the end effector would be an electrode, or in optics, a laser or mirror surface. Following this proof‐of‐principle work, the adaptability of robots in combination with sophisticated software could provide ruggedness for alignment in demanding real‐world environments where quantum technologies are emerging, such as point to point quantum key distribution (QKD)<sup>[</sup>\n##UREF##36##\n61\n##\n<sup>]</sup> and quantum range finding.<sup>[</sup>\n##REF##33379552##\n62\n##\n<sup>]</sup>\n</p>" ]
[ "<title>Abstract</title>", "<p>Developing practical quantum technologies will require the exquisite manipulation of fragile systems in a robust and repeatable way. As quantum technologies move toward real world applications, from biological sensing to communication in space, increasing experimental complexity introduces constraints that can be alleviated by the introduction of new technologies. Robotics has shown tremendous progress in realizing increasingly smart, autonomous, and highly dexterous machines. Here, a robotic arm equipped with a magnet is demonstrated to sensitize an NV center quantum magnetometer in challenging conditions unachievable with standard techniques. Vector magnetic fields are generated with 1° angular and 0.1 mT amplitude accuracy and determine the orientation of a single stochastically‐aligned spin‐based sensor in a constrained physical environment. This work opens up the prospect of integrating robotics across many quantum degrees of freedom in constrained settings, allowing for increased prototyping speed, control, and robustness in quantum technology applications.</p>", "<p>Robotic arms consist of sets of links that allow arbitrary positioning and orientation of an end tool. This study shows such a technique can be used to align vector spin‐based quantum sensors with high accuracy by positioning a permanent magnet. The flexibility demonstrated is important for emerging quantum sensing applications in physically constrained environments.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6788-cit-0064\">\n<string-name>\n<given-names>J. A.</given-names>\n<surname>Smith</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>K. C.</given-names>\n<surname>Balram</surname>\n</string-name>, <article-title>Robotic Vectorial Field Alignment for Spin‐Based Quantum Sensors</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304449</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304449</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Magnetic Field Modeling</title>", "<p>Magnetic field calculations in this work were performed using the closed form expressions presented in the Magpylib package.<sup>[</sup>\n##UREF##30##\n51\n##\n<sup>]</sup> The hollow cylindrical magnet was modeled by subtracting an inner cylindrical magnetic source of opposite magnetization from the outer cylindrical magnet source.</p>", "<title>Robotic Modeling</title>", "<p>The Niryo NED 2 robot geometry was specified in the unified robot description format (URDF). Here, the end‐effector geometry file specified in the URDF was replaced with the geometry of the magnet tool. For the collision‐free motion path finding, the experimental setups were modeled in FreeCad, and the geometry file of the robot base was replaced. The robot was simulated in an ROS environment and controlled using the Python wrapper PyNiryo2.</p>", "<title>Experimental Setup</title>", "<p>The magnetic field measurements in this work were made using the Infineon TLE493D‐P2B6MS2GO 3D magnetic sensor fitted on a compact platform mount or in the described confocal microscope. For the ODMR measurements, the NV center was excited by a CW 532 nm laser (gem 532; Laser Quantum). A confocal microscope was used to image the collected count rate. Using a 0.9 NA microscope objective, the excitation beam was highly focused on the sample, producing a nearly diffraction‐limited spot (&lt; 1 <mml:math id=\"jats-math-13\" display=\"inline\"><mml:mrow><mml:mi>μ</mml:mi></mml:mrow></mml:math>m diameter). The NV center PL was collected through the same lens and separated from the excitation path by the use of a dichroic mirror before detection by single photon avalanche diodes (SPADs) (SPCM‐AQRH‐12‐FC; Excelitas). By scanning the position of the sample, a map of the detected count rate was generated, from which the position of the NV center and its maximum count rate could be found. ODMR was performed under CW excitation using a Rohde and Schwarz SMB100A microwave source driving a custom loop antenna PCB on which the sample was mounted.</p>", "<title>Spin Sensor Modeling</title>", "<p>The spin transitions presented in Figure ##FIG##0##1b## were calculated by solving the Hamiltonian eigenstates in QuTiP.<sup>[</sup>\n##UREF##37##\n63\n##\n<sup>]</sup> Other calculations used the NV spin energies characteristic polynomial presented in Balasubramanian et al., whereas the polar angle θ between the field and the NV center was found using the solution given in that work.<sup>[</sup>\n##REF##18833276##\n57\n##\n<sup>]</sup> The polynomial could be solved and least‐squared fitted to the experimental data to find the NV orientation <mml:math id=\"jats-math-14\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msubsup><mml:mi>α</mml:mi><mml:mi>y</mml:mi><mml:mi>NV</mml:mi></mml:msubsup><mml:mo>,</mml:mo><mml:msubsup><mml:mi>α</mml:mi><mml:mi>z</mml:mi><mml:mi>NV</mml:mi></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math>,<sup>[</sup>\n##UREF##17##\n34\n##\n<sup>]</sup>\nwhere <mml:math id=\"jats-math-16\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>γ</mml:mi><mml:mo>=</mml:mo><mml:mo form=\"prefix\">arccos</mml:mo><mml:mo stretchy=\"false\">(</mml:mo><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>cos</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msubsup><mml:mi>α</mml:mi><mml:mi>z</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msubsup><mml:mo>−</mml:mo><mml:msubsup><mml:mi>α</mml:mi><mml:mi>z</mml:mi><mml:mi>NV</mml:mi></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mi>cos</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msubsup><mml:mi>α</mml:mi><mml:mi>y</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msubsup><mml:mo>−</mml:mo><mml:msubsup><mml:mi>α</mml:mi><mml:mi>y</mml:mi><mml:mi>NV</mml:mi></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math> with a known <mml:math id=\"jats-math-17\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>α</mml:mi><mml:mi>y</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msubsup></mml:mrow></mml:math> and <mml:math id=\"jats-math-18\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>α</mml:mi><mml:mi>z</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msubsup></mml:mrow></mml:math> set by the robot, <italic toggle=\"yes\">D</italic> and Π fitted from the zero‐field data, and β = γ<sub>e</sub>|<italic toggle=\"yes\">B</italic>| where γ<sub>e</sub> is the gyromagnetic ratio and |<italic toggle=\"yes\">B</italic>| is the external magnetic field amplitude. In the trajectories presented, and the separation between resonances ν(<italic toggle=\"yes\">i</italic>), |<italic toggle=\"yes\">B</italic>| was not conserved. For this fit, a constant |<italic toggle=\"yes\">B</italic>| must be obtained, so it must first be normalized using the field magnitude data. For this, the higher resolution Hall data was sub‐sampled to reduce noise (see Figure ##SUPPL##0##S3##, Supporting Information) and obtain normalized splittings ν<sub>\n<italic toggle=\"yes\">n</italic>\n</sub>(<italic toggle=\"yes\">i</italic>) for each measurement point <italic toggle=\"yes\">i</italic> where:\nand leave the non‐physical <italic toggle=\"yes\">B</italic> in the characteristic equation as the third free parameter in the fit to this data.</p>", "<title>Statistical Analysis</title>", "<p>Raw Hall data and confocal photoluminescence data were presented as collected. ODMR data was processed using Python. Spectra was two‐point resampled by summing adjacent bins in Numpy to aid fitting. LMFit was used to fit Gaussian centroids. LMFit was then used to sinusoid‐fit the centroids. For this, Numpy was used to normalize the trajectory using the Hall data as described in the previous section. All data was visualized using Matplotlib in Python.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank Jorge Monroy‐Ruz for building the NV center confocal microscope used in this experiment. The authors thank Jorge Monroy‐Ruz, Hao‐Cheng Weng, Wyatt Vine, and John G. Rarity for useful discussions. The authors acknowledge funding support from the Engineering and Physical Sciences Research Council (EPSRC) grant QC:SCALE EP/W006685/1.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6788-fig-0001\"><label>Figure 1</label><caption><p>Experimental setup and working principles. A) Placing a permanent magnet near the NV center magnetometer produces a magnetic field of a known orientation, defined along its axis (field lines in white). B) One use case here is to change the spin resonance of the magnetometer to operate at its most sensitive regime (linear with respect to detected field) away from the zero‐field splitting (marked in gray). As observed, field along the NV center <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> affects this response, whereas transverse components only contribute unwanted performance degradation. The field <italic toggle=\"yes\">B</italic>\n<sub>ext</sub> should therefore be approximately aligned to the NV center magnetic dipole orientation <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>. C) The 6 DoF robot is used to orient the magnet in complex surroundings. The robot base is located at the world origin (<italic toggle=\"yes\">x</italic>‐axis indicated in red, <italic toggle=\"yes\">y</italic>‐axis indicated in green, <italic toggle=\"yes\">z</italic>‐axis in blue). The tool center point (TCP axis marked) is translated along the <italic toggle=\"yes\">x</italic>‐axis of the end effector axis (marked) to set the required field strength. The TCP coordinates (<italic toggle=\"yes\">x</italic>, <italic toggle=\"yes\">y</italic>, <italic toggle=\"yes\">z</italic>, α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>) are then set to the NV center position and rotated around the <italic toggle=\"yes\">y</italic> and <italic toggle=\"yes\">z</italic> axes, that is, varying α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> and α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> of the TCP, to form a defined vector from the end effector to the TCP (shown in yellow). The robot position at a range of different (α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>) is shown in the inset diagrams. Through this method, the highly‐dexterous robot can create fields with arbitrary field strengths and orientations and align the TCP axis with the NV axis to produce the desired <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6788-fig-0002\"><label>Figure 2</label><caption><p>Robot arm generates arbitrary vector magnetic fields. A) A permanent magnet of varying mass is placed in the tool (left panel). A Hall sensor measures the <italic toggle=\"yes\">x</italic>–<italic toggle=\"yes\">z</italic> trajectory of the field produced by the arm (right panel). The trajectory is well‐fitted using a model of the field generated by the cylindrical magnet, noting a 15 ° offset in the <italic toggle=\"yes\">x</italic>–<italic toggle=\"yes\">z</italic> crossing from the expect 45° (shown with dotted line) and a varying non‐zero offset in <italic toggle=\"yes\">y</italic>, with this offset resulting in a non‐linear trend in the field registered with increasing magnetic mass. This initial measurement and model can be used for fine alignment calibration. B) The arm can create a field over the full <italic toggle=\"yes\">x</italic>–<italic toggle=\"yes\">y</italic>–<italic toggle=\"yes\">z</italic> sphere segment (one‐eighth) with 3° accuracy. White pixels in the image plots (circled in red) indicate the few unreachable positions. C) The distance <italic toggle=\"yes\">r</italic> from the end effector to the tool center point (TCP) produces a field strength fall off in <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub> proportional to 1/<italic toggle=\"yes\">r</italic>\n<sup>3</sup> (top panel), from which points (shown by vertical lines) can be then sampled (middle panel) to create a linear field response with high accuracy (bottom panel).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6788-fig-0003\"><label>Figure 3</label><caption><p>Motion planning in experimental settings. A) We model two experimental settings: a cryostat with optical access and a confocal microscope. Plotted are the simulated collisions with the robot (in red) and avoided collisions (in blue) over the fixed position varied (α<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>, α<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>) poses. For the confocal, we observe a limited reachable workspace subset. B) We develop an algorithm to replace these unreachable poses with collision‐free poses. The procedure follows: i) a desired field vector is measured in a forbidden position; ii) displacement puts the magnet in an allowed position; iii) angular orientation sets the correct field vector; and iv) a further displacement corrects the field magnitude. C) Using a dipole source to calculate the rotation, we can deterministically rotate the magnet and recover the <mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>B</mml:mi><mml:mo>^</mml:mo></mml:mover></mml:mrow></mml:math> vector (title bar) at the observer (green dot). D) The designed rotation matches experimentally in minimizing the transverse field at 26°. E) Measuring with the 3D Hall sensor at each stage following panels in (B), the final vector well matches the initial vector (quantified by the similarity function <italic toggle=\"yes\">S</italic> defined in the text).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6788-fig-0004\"><label>Figure 4</label><caption><p>Robot‐assisted magnetometry: A) Image of confocal microscope setup showing robotic arm in position. B) Optically accessed cryostat with robotic arm in position. C) Confocal image of NV center located in diamond lens (mounted in setup shown in A). D) Photoluminescence scan in <italic toggle=\"yes\">z</italic> of above. E) Optically detected magnetic resonance (ODMR) showing zero‐field magnetic field splitting of associated spin in blue when the robot arm is ≈10 cm from the sensor and strong 100 MHz splitting in green when the robot arm is proximal to the spin sensor. F) Fitted peak resonance for robot trajectory in 5° increments (large circles) and 2° increments (small circles), indicating movement is stable and repeatable. G) Hall sensor data shows the <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub> and <italic toggle=\"yes\">B</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> crossover in trajectory. Normalizing splitting between resonances by <italic toggle=\"yes\">B</italic> magnitude reveals σ<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> dependence in Trajectory 1 (black) and Trajectory 2 (blue), indicative of angular alignment.</p></caption></fig>" ]
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[ "<disp-formula id=\"advs6788-disp-0001\">\n<label>(1)</label>\n<mml:math id=\"jats-math-1\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>H</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi>D</mml:mi><mml:msubsup><mml:mi>S</mml:mi><mml:mi>z</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:mi mathvariant=\"normal\">Π</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:msubsup><mml:mi>S</mml:mi><mml:mi>x</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>−</mml:mo><mml:msubsup><mml:mi>S</mml:mi><mml:mi>y</mml:mi><mml:mn>2</mml:mn></mml:msubsup></mml:mfenced><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:mi>γ</mml:mi><mml:msub><mml:mi mathvariant=\"bold\">B</mml:mi><mml:mo>⊥</mml:mo></mml:msub><mml:mo>·</mml:mo><mml:msub><mml:mi mathvariant=\"bold\">S</mml:mi><mml:mo>⊥</mml:mo></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:mi>γ</mml:mi><mml:msub><mml:mi>B</mml:mi><mml:mi>z</mml:mi></mml:msub><mml:msub><mml:mi>S</mml:mi><mml:mi>z</mml:mi></mml:msub></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6788-disp-0002\">\n<label>(2)</label>\n<mml:math id=\"jats-math-8\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>m</mml:mi><mml:mo>⃗</mml:mo></mml:mover><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:mn>6</mml:mn><mml:mi>π</mml:mi></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:mfrac><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mover accent=\"true\"><mml:mi>B</mml:mi><mml:mo>⃗</mml:mo></mml:mover><mml:mo>·</mml:mo><mml:mover accent=\"true\"><mml:mi>r</mml:mi><mml:mo>⃗</mml:mo></mml:mover><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mfenced separators=\"\" open=\"|\" close=\"|\"><mml:mover accent=\"true\"><mml:mi>r</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mfenced><mml:mover accent=\"true\"><mml:mi>r</mml:mi><mml:mo>⃗</mml:mo></mml:mover><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mfrac><mml:mrow><mml:mn>4</mml:mn><mml:mi>π</mml:mi></mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:mfrac><mml:msup><mml:mfenced separators=\"\" open=\"|\" close=\"|\"><mml:mover accent=\"true\"><mml:mi>r</mml:mi><mml:mo>⃗</mml:mo></mml:mover></mml:mfenced><mml:mn>3</mml:mn></mml:msup><mml:mover accent=\"true\"><mml:mi>B</mml:mi><mml:mo>⃗</mml:mo></mml:mover><mml:mo>,</mml:mo></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6788-disp-0003\">\n<label>(3)</label>\n<mml:math id=\"jats-math-12\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>S</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi>exp</mml:mi><mml:mfrac><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>B</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo>−</mml:mo><mml:msub><mml:mi>B</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:msup><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:mn>2</mml:mn><mml:msup><mml:mi>d</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mfrac></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6788-disp-0004\">\n<label>(4)</label>\n<mml:math id=\"jats-math-15\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msup><mml:mi>x</mml:mi><mml:mn>3</mml:mn></mml:msup><mml:mo linebreak=\"badbreak\">−</mml:mo><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:msup><mml:mi>D</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mn>3</mml:mn></mml:mfrac><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msup><mml:mi mathvariant=\"normal\">Π</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mo>+</mml:mo><mml:msup><mml:mi>β</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mfenced><mml:mi>x</mml:mi><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mfrac><mml:msup><mml:mi>β</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mn>2</mml:mn></mml:mfrac><mml:mi>D</mml:mi><mml:mi>cos</mml:mi><mml:mn>2</mml:mn><mml:mi>γ</mml:mi></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo linebreak=\"badbreak\">−</mml:mo><mml:mfrac><mml:mi>D</mml:mi><mml:mn>6</mml:mn></mml:mfrac><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mn>4</mml:mn><mml:msup><mml:mi mathvariant=\"normal\">Π</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mo>+</mml:mo><mml:msup><mml:mi>β</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mfenced></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd/><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo linebreak=\"badbreak\">+</mml:mo><mml:mfrac><mml:mrow><mml:mn>2</mml:mn><mml:msup><mml:mi>D</mml:mi><mml:mn>3</mml:mn></mml:msup></mml:mrow><mml:mn>27</mml:mn></mml:mfrac><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6788-disp-0005\">\n<label>(5)</label>\n<mml:math id=\"jats-math-19\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:msub><mml:mi>ν</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:mi>ν</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>B</mml:mi><mml:mtext>Hall</mml:mtext></mml:msub><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>i</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow></mml:mrow></mml:mfrac><mml:mi>max</mml:mi><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>B</mml:mi><mml:mtext>Hall</mml:mtext></mml:msub><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>" ]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
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[ "<supplementary-material id=\"advs6788-supl-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[]
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[ "<media xlink:href=\"ADVS-11-2304449-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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Adv Sci (Weinh). 2023 Nov 17; 11(2):2304449
oa_package/e6/6a/PMC10787065.tar.gz
PMC10787066
37946710
[ "<title>Introduction</title>", "<p>Yes‐Associated Protein (YAP) is a mechanically activated downstream effector of the Hippo pathway,<sup>[</sup>\n##REF##21654799##\n1\n##\n<sup>]</sup> which plays a critical role in embryogenesis by controlling the size and shape of organs through the proliferation of embryonic parenchymal cells, such as cardiomyocytes and hepatocytes.<sup>[</sup>\n##REF##17980593##\n2\n##, ##REF##21512031##\n3\n##\n<sup>]</sup> Similar to its paralog protein TAZ, which is encoded by the WWTR1 gene, YAP acts in a pleiotropic fashion by interacting with tissue‐ and stage‐specific transcription factors,<sup>[</sup>\n##REF##35012640##\n4\n##, ##REF##21262812##\n5\n##\n<sup>]</sup> primarily those of the TEAD family.<sup>[</sup>\n##REF##25287865##\n6\n##, ##REF##30050119##\n7\n##, ##REF##30566373##\n8\n##, ##REF##30026699##\n9\n##\n<sup>]</sup> YAP is commonly overexpressed in many solid tumors including breast, lung, colorectal, pancreatic, and liver carcinomas, as well as melanoma and glioma, during their growth, progression and metastasis.<sup>[</sup>\n##REF##31308148##\n10\n##, ##REF##28951564##\n11\n##, ##REF##27300434##\n12\n##, ##REF##31270418##\n13\n##\n<sup>]</sup> YAP has been shown to promote tumor survival by driving tumor immune evasion through the activation of PD‐L1 transcription and by rewiring macrophage response to a pro‐tumor phenotype.<sup>[</sup>\n##REF##31174841##\n14\n##\n<sup>]</sup> Additionally, it appears to inhibit autophagy‐related cell death,<sup>[</sup>\n##REF##31337986##\n15\n##\n<sup>]</sup> and drive tumor resistance to targeted therapy and chemotherapy, supposedly through the stimulation of pro‐survival and anti‐apoptotic genes.<sup>[</sup>\n##REF##31174841##\n14\n##\n<sup>]</sup> YAP overexpression has been linked to poor prognosis and survival in patients with breast cancer, as well as in other tumor types.<sup>[</sup>\n##UREF##0##\n16\n##, ##REF##30006603##\n17\n##\n<sup>]</sup>\n</p>", "<p>Our group has recently demonstrated that YAP‐mediated activation of cell adhesion genes drives the stiffening of CAL51 triple‐negative breast cancer (TNBC) cells.<sup>[</sup>\n##REF##28504269##\n18\n##\n<sup>]</sup> TNBC defines a subtype of breast cancer characterized by aggressive behavior, frequent relapses, and resistance to chemotherapy.<sup>[</sup>\n##REF##31548545##\n19\n##, ##REF##33812473##\n20\n##\n<sup>]</sup> We have subsequently shown that targeting YAP via mechanical, pharmacological, or genetic strategies prevents breast cancer cells from undergoing epithelial‐to‐mesenchymal transition (EMT) and migration, favoring instead the acquisition of a terminally differentiated phenotype of adipocytes.<sup>[</sup>\n##REF##30904599##\n21\n##\n<sup>]</sup>\n</p>", "<p>Increased extracellular matrix (ECM) stiffness is a common feature of solid tumors,<sup>[</sup>\n##REF##18654431##\n22\n##, ##REF##29541636##\n23\n##\n<sup>]</sup> and the expression of EMT transition markers is often used to gauge the aggressiveness of breast cancer.<sup>[</sup>\n##REF##19909494##\n24\n##\n<sup>]</sup> Interestingly, YAP hyperactivation has been recently discovered to play a key role in enabling cancer‐associated fibroblasts (CAFs) to induce tumor stroma stiffening and promote malignant cell invasion and metastatization.<sup>[</sup>\n##REF##23708000##\n25\n##\n<sup>]</sup> Given its dual role in CAFs and tumor cells as both a mechanosensitive protein and a proto‐oncogene, YAP is now viewed as a critical component in the positive feedback loop that leads to stroma stiffening and cancer dissemination. Recently, manipulating the mechanical properties of cells or substrates has been proposed as a plausible strategy to control nanoparticle binding and internalization, hence paving the way to using nanoparticles for the mechanotargeting of primary or metastatic cancer cells.<sup>[</sup>\n##UREF##1##\n26\n##, ##REF##29797358##\n27\n##\n<sup>]</sup> Considering this, understanding the interactions between biological systems and nanomaterials has become a major goal of nanomedicine, with the aim of designing nanomaterials that can effectively interact with living cells.<sup>[</sup>\n##REF##31695150##\n28\n##, ##UREF##2##\n29\n##\n<sup>]</sup>\n</p>", "<p>The design and effectiveness of nanomedicines for cancer therapy depend on various physicochemical properties of the nanocarrier, including its size, shape, stiffness, and surface chemistry.<sup>[</sup>\n##UREF##3##\n30\n##, ##REF##18697944##\n31\n##\n<sup>]</sup> Much research has focused on optimizing these properties to enhance cell‐nanoparticle interaction and improve anti‐cancer drug delivery.<sup>[</sup>\n##REF##20138662##\n32\n##, ##REF##32426455##\n33\n##\n<sup>]</sup> Notwithstanding significant advances in understanding bio‐nano interactions over the last 20 years, much remains unknown about the exact mechanisms underlying cell‐nanoparticle interactions.<sup>[</sup>\n##REF##33597736##\n34\n##\n<sup>]</sup> Nevertheless, unveiling the processes responsible for these interactions at the molecular level may lead to the development of new strategies for enhancing nanoparticle delivery to specific cells of interest.<sup>[</sup>\n##REF##31932672##\n35\n##\n<sup>]</sup>\n</p>", "<p>Despite YAP is being proposed as a target for novel treatments,<sup>[</sup>\n##REF##25772357##\n36\n##, ##REF##27262779##\n37\n##\n<sup>]</sup> its response to nanoparticles internalization and its potential role in their trafficking has never been investigated. In the present study, we used TNBC cells to unveil the role of YAP in cell‐nanoparticle interactions and show its potential in regulating nanoparticle internalization via the control of membrane organization and cell mechanics. We demonstrate that YAP is responsible for the transcription of genes regulating cell‐matrix interactions, ECM deposition, and endocytic pathways in breast cancer cells, and show that its inhibition boosts the internalization of nanoparticles. Finally, we delineate how the intracellular delivery of doxorubicin‐loaded liposomes can be enhanced by pharmacologically tampering with YAP activity. In conclusion, by identifying Hippo effector as a determinant of cell‐nanoparticle interaction, we propose its inhibition as a viable therapeutic strategy for improving nanodrug delivery to triple‐negative breast cancer cells.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>YAP Depletion Affects the Mechanical, Physical Properties, and the Membrane Organization of CAL51 TNBC Cells</title>", "<p>We first investigated the effect of YAP depletion on the morphology of CAL51 TNBC cells, which are characterized by constitutively high levels of YAP expression and activity.<sup>[</sup>\n##REF##30904599##\n21\n##\n<sup>]</sup> Using CRISPR/CAS9 technology, we generated a stable YAP‐deficient mutant CAL51 cell line (described in Ref. [##REF##28504269##18##]), and confirmed YAP depletion through confocal microscopy (<bold>Figure</bold> ##FIG##0##\n1A##) and western blot analyses (Figure ##FIG##0##1B##). Next, we used atomic force microscopy (AFM) to determine the effect of YAP depletion on the mechanical properties of CAL51 cells and found a significant reduction in Young's modulus in YAP ‐/‐ cells (Figure ##FIG##0##1C##). Moreover, compared to CAL51 WT cells, YAP ‐/‐ cells displayed reduced surface area, both as determined by actin coverage and membrane extension (Figure ##FIG##0##1D,E##), as well as perturbed cell morphology, resulting from their inability to spread over the adhesion surface (Figure ##FIG##0##1F##; see Figures ##SUPPL##0##S1## and ##SUPPL##0##S2##, Supporting Information). These changes were due to the failure of the mutant cells to assemble focal adhesions and form proper cytoskeleton (Figure ##FIG##0##1G##).<sup>[</sup>\n##REF##28504269##\n18\n##, ##REF##33116297##\n38\n##\n<sup>]</sup> Importantly, YAP depletion did not affect the proliferation and viability of CAL51 TNBC cells (see Figure ##SUPPL##0##S3##, Supporting Information).</p>", "<p>Given the striking change in morphology and mechanics exhibited by YAP ‐/‐ CAL51 cells compared to the wild‐type control, we analyzed their membrane structure using Correlative Probe and Electron Microscopy (CPEM) by LiteScope. This technique combines AFM and scanning electron microscope (SEM) to characterize 3D surface in situ, estimate surface roughness, and perform height/depth profiling with precise AFM tip navigation.<sup>[</sup>\n##UREF##4##\n39\n##\n<sup>]</sup> The analysis demonstrated that YAP depletion and the following decrease in membrane tension led to the remodeling of the plasma membrane in CAL51 TNBC cells and the emergence of dynamic features connected with extensive cellular reorganization (Figure ##FIG##0##1H,I##). Previous literature has reported the appearance of various membrane structures including blebs and vacuole‐like dilations upon the reduction of cell strain.<sup>[</sup>\n##REF##20858416##\n40\n##\n<sup>]</sup> In YAP ‐/‐ cells, we observed the emergence of ripple‐like deformations (Figure ##FIG##0##1J##), which increased the roughness of the cell membrane, as quantified through height irregularity (<italic toggle=\"yes\">R</italic>\n<sub>q</sub>, Figure ##FIG##0##1K##).</p>", "<title>YAP Transcriptional Activity Controls the Expression of Genes Involved in Membrane Organization and Endocytosis in CAL51 TNBC Cells</title>", "<p>Given the substantial effects that YAP depletion played on the structure of cell membrane, we hypothesized that the changes in the membrane of YAP ‐/‐ cells might be reflected in their transcriptional landscape. We adopted RNA sequencing (RNA‐seq) to investigate the regulation of genes encoding for proteins involved in plasma membrane organization (see Figure ##SUPPL##0##S4##, Supporting Information). Overall, RNA‐seq revealed a total of 4219 differentially expressed genes in YAP ‐/‐ cells compared to WT CAL51 cells, with 1925 of them being downregulated and 2294 upregulated following YAP depletion (see Figure ##SUPPL##0##S4a–c##, Supporting Information). The most represented gene ontology (GO) annotations were connected to ECM organization, cell migration, and cell adhesion in WT cells (see Figure ##SUPPL##0##S4d##, Supporting Information), while genes related to integral components of the plasma membrane were found among the cellular components in YAP ‐/‐ counterpart (see Figure ##SUPPL##0##S4e##, Supporting Information).</p>", "<p>In line with our findings regarding cell membrane organization (Figures ##FIG##0##1H–M##), we detected the presence of amphiphysin I (<italic toggle=\"yes\">AMPH1</italic>) among the genes being affected the most by YAP depletion. <italic toggle=\"yes\">AMPH1</italic> encodes for a protein that senses and generates membrane curvatures, is implicated in clathrin‐mediated endocytosis,<sup>[</sup>\n##REF##22184226##\n41\n##\n<sup>]</sup> and was significantly upregulated in CAL51 YAP ‐/‐ cells (log2Fc 7.69, <italic toggle=\"yes\">P</italic> &lt; 0.05, <bold>Figure</bold> ##FIG##1##\n2A##). Together with <italic toggle=\"yes\">AMPH1</italic>, several genes contributing to plasma membrane assembly that were overexpressed in WT CAL51 may explain the differences in cell membrane organization (Figure ##FIG##1##2A##). These include <italic toggle=\"yes\">RFTN1</italic> (log2Fc 2.79), <italic toggle=\"yes\">EHD2</italic> (log2Fc 2.4), <italic toggle=\"yes\">MYOC</italic> (log2Fc 5.83) and <italic toggle=\"yes\">PITPNM1</italic> (log2Fc 2.86).<sup>[</sup>\n##REF##12805216##\n42\n##, ##REF##17233914##\n43\n##, ##REF##18855004##\n44\n##, ##REF##11909959##\n45\n##\n<sup>]</sup>\n</p>", "<p>GO enrichment analysis identified several molecular functions being differentially regulated that were connected to plasma membrane network components, with high scores for lipid raft organization, localization, and assembly (see Figure ##SUPPL##0##S5a##, Supporting Information). Interestingly, lipid rafts, responsible for membrane heterogeneity, strongly impacts the stability and functionality of the plasma membrane at the nanoscale, thus directly supporting high sub‐compartmentalization and intrinsic organization.<sup>[</sup>\n##REF##20044567##\n46\n##\n<sup>]</sup> In addition, STRING PPI analysis yielded a highly clustered network containing 68 nodes and 384 edges for WT CAL51, while 54 nodes and 39 edges were identified for YAP‐depleted cells (Figure ##FIG##1##2B##). WT CAL51 cells showed a significantly higher number of interactors and interconnections between the key elements of the membrane organization network compared to YAP ‐/‐ cells, possibly indicating a higher degree of membrane complexity. The cluster coefficients for both conditions were quite similar (0.394 for WT and 0.5 for YAP ‐/‐). More importantly, RNA‐seq analysis revealed the differential expression of genes encoding proteins involved in endocytosis (Figure ##FIG##1##2C##; see Figure ##SUPPL##0##S5b##, Supporting Information), a process that appears to be dysregulated in tumors.<sup>[</sup>\n##REF##33262521##\n47\n##\n<sup>]</sup> Therefore, the RNA‐seq analysis was extended to examine the expression of transcripts involved in the trafficking of intracellular organelles and endocytic pathways in YAP ‐/‐ cells compared to CAL51 WT cells. This comparison led to the identification of differentially expressed genes involved in caveolae‐mediated endocytosis (Figure ##FIG##1##2D##), clathrin‐mediated endocytosis (Figure ##FIG##1##2E##), and macropinocytosis (Figure ##FIG##1##2F##). While the number of differentially regulated genes in the caveolae‐mediated pathway was similar between WT and YAP ‐/‐ cells (11 in WT and 8 in YAP ‐/‐, although YAP ‐/‐ cells displayed overall higher upregulation; see Figure ##SUPPL##0##S5b##, Supporting Information), clathrin‐related and macropinocytosis‐related genes showed the most striking difference, with more genes of the clathrin‐mediated pathway upregulated in YAP ‐/‐ cells (5 genes in YAP ‐/‐ vs 1 gene in WT) and more genes of the macropinocytosis‐mediated pathway upregulated in WT cells (1 gene in YAP ‐/‐ vs 3 genes in WT).</p>", "<p>To further corroborate these findings, we performed a GO enrichment analysis on the genes involved in endocytosis that were differentially expressed in WT and YAP ‐/‐ cells. The analysis revealed significant differences between WT and YAP ‐/‐ cells in annotations for the negative and positive regulators of endocytosis (see Figures ##SUPPL##0##S6## and ##SUPPL##0##S7##, Supporting Information). For the negative regulators (GO:0045806), WT cells showed high scores for the regulation of endocytic vesicles (<italic toggle=\"yes\">P</italic> = 0.001) and early endosomes (<italic toggle=\"yes\">P</italic> = 0.002) compared to YAP ‐/‐ cells (<italic toggle=\"yes\">P</italic> = 0.13 for endocytic vesicles, <italic toggle=\"yes\">P</italic> = 0.03 for early endosomes), whereas YAP ‐/‐ cells yielded high scores for endosomal recycling genes (<italic toggle=\"yes\">P</italic> = 0.014). These findings indicate that YAP depletion in triple‐negative breast cancer cells lead to the downregulation of transcripts that encode proteins responsible for inhibiting the endocytic pathways (see Figure ##SUPPL##0##S6##, Supporting Information). The positive regulators (GO:0045807), on the other hand, were more abundant in the absence of YAP: relative to WT CAL51, YAP ‐/‐ cells showed significant scores for the terms positive regulators of the endocytic vesicle (<italic toggle=\"yes\">P</italic> = 3.11×10<sup>−5</sup> in YAP ‐/‐ vs <italic toggle=\"yes\">P</italic> = 0.006 in WT) and cytoplasmic vesicle membrane (<italic toggle=\"yes\">P</italic> = 0.000476 in YAP ‐/‐ vs <italic toggle=\"yes\">P</italic> = 0.02 in WT), while CAL51 WT had high scores for collagen‐containing extracellular matrix (<italic toggle=\"yes\">P</italic> = 7.56×10<sup>−5</sup>) and secretory granule lumen (<italic toggle=\"yes\">P</italic> = 0.00035; see Figure ##SUPPL##0##S7##, Supporting Information). Taken together, these results indicate that YAP depletion in CAL51 TNBC cells determines an alteration in the genes involved in endocytosis.</p>", "<title>YAP Regulates the Entry of Nanoparticles in CAL51 TNBC Cells</title>", "<p>Encouraged by these findings, we hypothesized that YAP might play a role in the internalization of nanoparticles and nanodrugs. We figured this might explain how Hippo pathway effector promotes TNBC resistance to chemotherapy.<sup>[</sup>\n##REF##33069769##\n48\n##\n<sup>]</sup> To test this hypothesis, we treated WT and CAL51 YAP ‐/‐ cells with inert polystyrene (PS) nanoparticles (NPs), which have been widely used in bio‐nano interaction studies due to their tunable size and ease of functionalization.<sup>[</sup>\n##REF##21344890##\n49\n##, ##REF##31573181##\n50\n##\n<sup>]</sup> Carboxylated PS nanoparticles with 200 and 900 nm diameter (PS200 and PS900) were first labeled with carboxytetramethylrhodamine using EDC chemistry and characterized via transmission electron microscopy (TEM), spectrofluorometer, and dynamic light scattering (DLS) (see Figure ##SUPPL##0##S8a–e##, Supporting Information). Next, WT and YAP ‐/‐ CAL51 cells were incubated with PS200 and PS900, and nanoparticle binding to the cells evaluated using flow cytometry and confocal microscopy. Our flow cytometry results showed that already after 4 h incubation, PS nanoparticles could be found preferentially bound to YAP ‐/‐ CAL51 cells as compared to their WT counterparts (<bold>Figure</bold> ##FIG##2##\n3A##; see Figures ##SUPPL##0##S9## and ##SUPPL##0##S10a##, Supporting Information). This effect was independent of the nanoparticle size and could be further confirmed by confocal analysis. Through this analysis, we – in fact – showed that a higher number of nanoparticles co‐localized with the membrane of YAP ‐/‐ compared to WT cells (Figure ##FIG##2##3B,C##; see Figure ##SUPPL##0##S10b##, Supporting Information). Interestingly, CPEM analysis allowed us to visualize the detailed morphology of the nanoparticles in contact with CAL51 cells, further corroborating these findings. In WT cells, NPs were bound to the external face of the membrane but not yet internalized after 4 h (see Figure ##SUPPL##0##S11a##, Supporting Information). They in fact appeared bright on SEM and AFM imaging in CAL51 WT and showed limited co‐localization with the cell membrane (see the height profile of the area at the nanoparticle‐membrane binding site in Figure ##SUPPL##0##S11b##, Supporting Information). On the contrary, at the same time‐point NPs were already surrounded by an organic coating attributable to plasma membrane in cells in which YAP had been depleted (see Figure ##SUPPL##0##S11c##, Supporting Information). This result indicated that the nanoparticles were embedded in the cell membrane, as revealed by the reduction of the height profile at the nanoparticle‐membrane binding site (see Figure ##SUPPL##0##S11d##, Supporting Information).</p>", "<p>We next focused on investigating whether the striking difference in particle interaction with cell membrane could be due to the changes in membrane curvature, actin dynamics, and cell mechanosensing as induced by YAP activity.<sup>[</sup>\n##REF##28504269##\n18\n##, ##REF##23122885##\n51\n##\n<sup>]</sup> Hence, we reduced the nanoparticle dosage and increased the incubation time, and found enhanced nanoparticle internalization over time in YAP ‐/‐ CAL51, regardless of dose and time (see Figure ##SUPPL##0##S12a##, Supporting Information). No significant change was observed in YAP localization in WT cells after nanoparticle binding, suggesting no direct impact on intracellular protein shuttling (see Figure ##SUPPL##0##S12b##, Supporting Information). However, a marked decrease in membrane stiffness was noted in WT CAL51 after 4 h of incubation with nanoparticles, but no such change was seen in YAP‐depleted cells (Figure ##FIG##2##3D##). Although the effect of nanoparticles on the cell membrane properties is debated, with responses possibly dependent not only on the nanoparticle size but also their composition,<sup>[</sup>\n##REF##30971727##\n52\n##\n<sup>]</sup> our data suggest that the reduction in membrane rigidity in WT CAL51 did not enhance nanoparticle internalization over time, as YAP ‐/‐ cells exhibited higher binding and internalization in all conditions tested. This was likely due to a stronger impact of YAP depletion on cell membrane stiffness than the physical effects of nanomaterial interactions alone. Furthermore, z‐stack confocal images and TEM micrographs confirmed the internalization of particles in both WT and YAP ‐/‐ cells (see Figure ##SUPPL##0##S13a,b##, Supporting Information), although a higher number of particles was found to bind and co‐localize with the cell membrane in the absence of YAP.</p>", "<p>Next, we treated WT and CAL51 YAP ‐/‐ cells with inhibitors selective for each type of endocytosis to study the impact of YAP on the route of nanoparticle internalization in CAL51 TNBC cells. In particular, the cells were pre‐treated for 2 h with cytochalasin D, chlorpromazine, and nystatin to inhibit macropinocytosis, caveolin‐mediated, and clathrin‐mediated endocytosis, respectively.<sup>[</sup>\n##REF##32426455##\n33\n##\n<sup>]</sup> The cells were then incubated with PS200 and PS900 for 4 h. The live/dead assay was used to confirm no significant effect on cell viability under the chosen treatment conditions (see Figure ##SUPPL##0##S14##, Supporting Information). The obtained results showed that PS200 primarily entered the cells through clathrin‐mediated endocytosis, while PS900 primarily did so through macropinocytosis (see Figure ##SUPPL##0##S15a,b##, Supporting Information), which was in line with previous findings for similar‐sized nanoparticles.<sup>[</sup>\n##REF##35986441##\n53\n##\n<sup>]</sup> After internalization, the particles followed classical endocytic pathways and accumulated in lysosomes within 8 h of incubation (see Figure ##SUPPL##0##S15c##, Supporting Information). These endocytic processes were not affected by the absence of YAP, suggesting that the protein per se does not impact endocytosis pathways but rather affects the dynamics of cell‐nanoparticle association and internalization.</p>", "<p>To evaluate the potential of manipulating tumor cell mechanosensing to enhance nanoparticle delivery in a heterogeneous and complex milieu, we co‐cultured WT CAL51 cells with YAP ‐/‐ cells in a 1:1 ratio. The latter had been previously labeled with 7‐amino‐4‐chloromethylcoumarin (CellTracker). The co‐culture was incubated with either PS200 or PS900 for 4 h. In line with our cell morphology data (Figure ##FIG##0##1##), YAP ‐/‐ cells had a lower total surface area compared to the parental line due to their tendency to spread less on the substrate (see Figure ##SUPPL##0##S16a,b##, Supporting Information). Interestingly, despite the lower area exposed, YAP‐depleted cells bound and internalized a significantly higher number of nanoparticles, as revealed by flow cytometry and confocal analysis (Figure ##FIG##2##3E,F##; see Figure ##SUPPL##0##S16c##, Supporting Information). Indeed, z‐projection confocal images showed consistent preferential co‐localization of nanoparticles within the membrane of YAP ‐/‐ CAL51 cells (see Figure ##SUPPL##0##S17a,b##, Supporting Information). This result contradicts previous studies linking a higher cell surface area with a higher internalization rate,<sup>[</sup>\n##REF##30971727##\n52\n##, ##REF##23484640##\n54\n##\n<sup>]</sup> and suggests that YAP mechanosensing and cell mechanics outplay cell surface area in nanoparticle binding.</p>", "<p>Next, we tested whether the internalization of nanoparticles was affected by their surface coating and charge. These parameters are crucial in bio‐nano interaction studies and have been extensively studied to optimize nanoparticle design for efficient targeting or escape from specific cell types for improved therapy delivery.<sup>[</sup>\n##REF##33277608##\n55\n##\n<sup>]</sup> To determine the impact of nanoparticle surface properties on the differential internalization rate seen in CAL51 cells with or without YAP, PS nanoparticles were coated with the metal phenolic network (MPN) to alter their physicochemical properties, such as surface charge and free energy.<sup>[</sup>\n##REF##23846899##\n56\n##\n<sup>]</sup> Briefly, the MPN coating was applied to the surface of 5‐((5‐Aminopentyl)thioureidyl)fluorescein‐labeled PS200 and PS900 nanoparticles by the assembly of tannic acid (TA) and FeCl<sub>3</sub> according to a previously described protocol.<sup>[</sup>\n##REF##31573181##\n50\n##\n<sup>]</sup> The application of the MPN coating formed PS200‐MPN and PS900‐MPN (Figure ##FIG##2##3G##; see Figure ##SUPPL##0##S18a##, Supporting Information), and the success of the coating was confirmed using a spectrophotometer and dynamic light scattering (DLS) analysis (see Figure ##SUPPL##0##S18b–e##, Supporting Information). To examine cell‐nanoparticle interactions, WT and YAP ‐/‐ CAL51 cells were incubated with PS200‐MPN and PS900‐MPN for 4 h. Flow cytometry and confocal analysis revealed higher binding and internalization in YAP ‐/‐ cells compared to WT cells, supporting the previous results observed using non‐coated PS200 and PS900 nanoparticles (<bold>Figure</bold> ##FIG##3##\n4H–J##; see Figure ##SUPPL##0##S19a,b##, Supporting Information). Our findings indicate that despite coating the particles with MPN, the binding and internalization trends remain consistent with those observed for the uncoated particles and that the influence of cell mechanobiology, specifically the protein YAP, supersedes the properties of the materials in cell–nanoparticle interactions process.</p>", "<p>Analog internalization pattern between the two cell lines was observed by testing fluid‐phase endocytosis and macropinocytosis with fluorescent dextran (Dx‐FITC) and pHrodo‐zymosan respectively (see Figure ##SUPPL##0##S20a,b##, Supporting Information), and in free‐serum conditions where protein corona effect is ruled out (see Figure ##SUPPL##0##S21a,b##, Supporting Information).</p>", "<p>Compellingly, similar results were obtained in tumorigenic HEK293 WT or YAP‐depleted cells (see Figures ##SUPPL##0##S22## and ##SUPPL##0##S23##, Supporting Information), while no differences in nanoparticles binding and internalization was observed in a non‐cancer cell line model of iPSC‐induced fibroblasts in presence or absence of YAP, indicating the selectivity of YAP role for regulating this process in carcinogenic cells (see Figure ##SUPPL##0##S24##, Supporting Information).</p>", "<p>The transcriptional activity of YAP requires its shuttling to the cell nucleus, where it acts as co‐activator by interacting with context‐specific transcription factors.<sup>[</sup>\n##REF##19371381##\n57\n##\n<sup>]</sup> To determine the role of YAP in repressing nanoparticle uptake in TNBC cells, YAP ‐/‐ cells were transfected with a YAP hyperactive mutant (YAP‐S6A). The mutant form of YAP carries a set of mutations in its sequence that converts the residues S61, S109, S127, S128, S131, S136, S164, and S381 into alanine residues. These mutations render the protein non‐phosphorylatable and, consequently, resistant to inactivation and/or degradation. The shuttling of the YAP‐S6A mutant protein to the nucleus is not inhibited via phosphorylation by the upstream Hippo pathway effectors LATS1/2 and MOB1 (Figure ##FIG##2##3K##). A mock vector was used as control. The transfection was first verified by quantifying the expression of YAP protein using western blot and confocal imaging (Figure ##FIG##2##3L,M##). The YAP‐S6A‐ or mock‐transduced CAL51 cells were then incubated with PS200 and PS900 nanoparticles. In line with the hypothesis that YAP presence in the nucleus represses nanoparticle uptake, YAP‐S6A cells exhibited reduced nanoparticle uptake after 4 h of incubation compared to YAP ‐/‐ cells transfected with a mock vector (Figure ##FIG##2##3N##). Interestingly, transfecting YAP‐S6A in WT cells (YAP +/+ CAL51; see Figure ##SUPPL##0##S25a##, Supporting Information) did not induce any significant change in nanoparticle uptake (see Figure ##SUPPL##0##S25b–f##, Supporting Information). This result could be explained by the fact that parental CAL51 cells already expressed a very high basal level of YAP, and the expression of a hyperactive mutant YAP‐S6A did not induce any noticeable change in cell morphology (see Figure ##SUPPL##0##S25d##, Supporting Information), adhesion (see Figure ##SUPPL##0##S25e##, Supporting Information), or transcription. RT‐qPCR further corroborated this hypothesis, showing no change in mRNA levels of CYR61 and CTGF, the two main transcriptional targets of YAP, in YAP +/+ CAL51 compared to WT cells (see Figure ##SUPPL##0##S25f##, Supporting Information).</p>", "<p>These findings indicate that YAP activity affects cell‐nanoparticle interactions and point at YAP as potential regulator of nanoparticles internalization.</p>", "<title>Substrate Stiffness Hinders Nanoparticle Uptake through YAP</title>", "<p>The stiffness of the tumor stroma has been reported to impact YAP intracellular localization and transcriptional activity,<sup>[</sup>\n##REF##23708000##\n25\n##\n<sup>]</sup> which correlates with the ability of cancer cells to metastasize, leading to treatment resistance and poor prognosis.<sup>[</sup>\n##REF##33037194##\n58\n##\n<sup>]</sup> YAP intracellular shuttling and transcriptional activity are controlled by the mechanical properties of the surrounding microenvironment, with cells grown on soft substrates (<italic toggle=\"yes\">E</italic>&lt;5 kPa) exhibiting cytosolic YAP localization while the protein moves to the nucleus on stiffer substrates (<italic toggle=\"yes\">E</italic>&gt;10 kPa).<sup>[</sup>\n##REF##33990464##\n59\n##\n<sup>]</sup> Additionally, the sensitivity of YAP to ECM components such as collagen and fibronectin has been previously documented,<sup>[</sup>\n##REF##30026699##\n9\n##\n<sup>]</sup> with fibronectin accumulation during ECM remodeling triggering YAP nuclear shuttling, independently of substrate stiffness.<sup>[</sup>\n##REF##28504269##\n18\n##, ##REF##26216901##\n60\n##\n<sup>]</sup> To investigate the influence of substrate stiffness and ECM composition on nanoparticle internalization in TNBC CAL51 cells through YAP, WT and YAP ‐/‐ cells were cultured on tissue culture polystyrene (TCPS, Young's modulus in GPa range) or soft surfaces (PDMS) with a defined Young's modulus of 2 kPa coated with either collagen or fibronectin. Confocal microscopy was used to quantify YAP subcellular localization in TNBC cells in response to substrate stiffness or ECM composition. First, we found that in the presence of collagen, the soft substrate hindered YAP nuclear localization, while the presence of fibronectin reversed this effect and restored YAP shuttling to the nucleus of cells grown on a soft substrate (<bold>Figure</bold> ##FIG##3##\n4A,B##). This indicated that the biochemical cues from fibronectin were able to overcome the effects of the mechanical properties of the substrate under the given experimental conditions. We then investigated the relationship among substrate stiffness, YAP activity and nanoparticle uptake in TNBC cells by incubating cells cultured on soft or stiff substrates with PS200 and PS900 nanoparticles for 4 h. Our results showed that CAL51 WT cells grown on 2 kPa soft substrate coated with collagen (low YAP activity) exhibited increased nanoparticle uptake, whereas this phenomenon was not observed on stiff PSS or 2 kPa substrates coated with fibronectin (high YAP activity, Figure ##FIG##3##4C–F##). Conversely, YAP ‐/‐ CAL51 cells showed no change in nanoparticle internalization on either PSS or 2 kPa substrates coated with collagen or fibronectin (see Figure ##SUPPL##0##S26##, Supporting Information). These results suggest that YAP mechanical displacement from the nucleus could be an effective way to augment nanoparticle uptake in TNBC cells.</p>", "<title>YAP Promotes ECM Network Deposition and Affects Cell‐Nanoparticle Interactions in a 3D In Vitro Model of TNBC</title>", "<p>The efficiency of endocytosis is tightly linked to the composition of the ECM that surrounds cells. We hypothesized that the increase in nanoparticle uptake measured in YAP ‐/‐ cells could be explained by a less structured ECM in these cells. We first performed an RT<sup>2</sup>‐profiler PCR array and found that many genes related to ECM‐cell adhesion were significantly upregulated in WT cells compared to YAP ‐/‐ cells (<bold>Figure</bold> ##FIG##4##\n5A##; see Figure ##SUPPL##0##S27a,b##, Supporting Information). Some of these genes are known to be directly regulated by YAP transcriptional activity, such as CTGF (CCN2). To get a deeper insight into how YAP regulates the ECM landscape, we explored network connectivity and ontological interconnections between ECM components identified in both WT and YAP ‐/‐ cells using the STRING protein‐protein interaction (PPI) database with a score threshold of 0.4.<sup>[</sup>\n##REF##25352553##\n61\n##\n<sup>]</sup> The STRING PPI analysis yielded a highly clustered network containing 39 nodes and 336 edges and with a clustering coefficient of 0.74 for WT CAL51, indicating a significant high number of interactions (Figure ##FIG##4##5B##). On the opposite, the analysis of YAP ‐/‐ CAL51 cells showed a network with fewer connections, containing 38 nodes and 165 edges, and with a lower clustering coefficient of 0.49 (see Figure ##SUPPL##0##S27c##, Supporting Information). As expected, the GO enrichment analysis revealed significant differences in the molecular function of the ECM network between WT and YAP ‐/‐ cells. While the former cells had high scores for annotations related to ECM and extracellular structure organization (<italic toggle=\"yes\">P</italic> = 2.46×10<sup>−12</sup>) (Figure ##FIG##4##5C##), the latter displayed low scores for annotations related to ECM (<italic toggle=\"yes\">P</italic> = 0.0043) and extracellular structure organization (<italic toggle=\"yes\">P</italic> = 0.0078) (see Figure ##SUPPL##0##S27d##, Supporting Information). Interestingly, the analysis also revealed that YAP depletion led to the dysregulation of several classes of ECM transcripts associated with cancer or known to promote tumor growth (see Figure ##SUPPL##0##S28a,b##, Supporting Information).<sup>[</sup>\n##REF##25381661##\n62\n##\n<sup>]</sup>\n</p>", "<p>Next, we aimed to validate the hypothesis that reduced ECM deposition in YAP ‐/‐ cells was responsible for increased nanoparticle uptake. We established a 3D cell culture system, which resembles the complex and heterogeneous tumor microenvironment more closely than a 2D monolayer.<sup>[</sup>\n##REF##31904048##\n63\n##, ##REF##28646905##\n64\n##\n<sup>]</sup> We generated 3D spheroids of both WT and YAP ‐/‐ CAL51cells and investigated nanoparticle uptake using this experimental model. Briefly, the cells were seeded onto round‐bottom ultra‐low attachment plates and spun to promote their aggregation. As expected, after 5 days of culture, the spheroids obtained from WT or YAP ‐/‐ cells showed distinct morphologies similar to what previously described (Figure ##FIG##4##5D##; see Figure ##SUPPL##0##S29a##, Supporting Information).<sup>[</sup>\n##REF##28504269##\n18\n##\n<sup>]</sup>\n</p>", "<p>Then, we investigated YAP expression in WT spheroids and found that YAP was evenly distributed in both the cytoplasm and nucleus of the cells (Figure ##FIG##4##5E##). The live/dead assay confirmed that the cells were viable, with no detectable sign of cell death in either WT or YAP ‐/‐ spheroids (see Figure ##SUPPL##0##S29b##, Supporting Information). We then incubated WT and YAP ‐/‐ spheroids with PS200 and PS900 nanoparticles and quantified nanoparticle binding using flow cytometry and confocal imaging. After 4 h of incubation, we found that YAP ‐/‐ CAL51 spheroids exhibited significantly higher nanoparticle binding than WT spheroids (Figure ##FIG##4##5F–H##). This result was also confirmed using different nanoparticle concentrations and incubation times (see Figure ##SUPPL##0##S29c,d##, Supporting Information). Next, we stained WT and YAP ‐/‐ CAL51 spheroids with antibodies directed against relevant ECM proteins. The confocal microscopy analysis demonstrated that CAL51 WT cells produced a rich and multicomponent ECM composed of various proteins such as collagen, CTGF, fibronectin, laminin, and periostin, all contributing to the spheroid assembly. In contrast, YAP ‐/‐ depletion determined a stark reduction in the expression of the same ECM proteins (Figure ##FIG##4##5I##; see Figure ##SUPPL##0##S30##, Supporting Information). Considering these results, targeting YAP may serve as a promising strategy for improving nanoparticle uptake into solid tumors by tuning cell membrane properties and decreasing ECM deposition.</p>", "<title>YAP Targeting Improves Nanomedicine Delivery to TNBC Cells</title>", "<p>After demonstrating that YAP depletion can be leveraged to increase nanoparticle uptake in TNBC CAL51 cells, we next aimed to demonstrate the therapeutic benefits of combining nanoparticle treatment with YAP targeting. To assess the efficiency of drug delivery, we chose liposomes (<bold>Figure</bold> ##FIG##5##\n6A##; see Figure ##SUPPL##0##S31a,b##, Supporting Information), as they have a long history of success since Doxil,<sup>[</sup>\n##REF##20044567##\n46\n##\n<sup>]</sup> the first nano drug that reached the market, and have been recently used in nanoformulations to treat cancer and other diseases.<sup>[</sup>\n##REF##34394960##\n65\n##, ##REF##34715546##\n66\n##, ##REF##35189345##\n67\n##\n<sup>]</sup> We used a doxorubicin‐loaded liposomal formulation (Doxo‐NP) and evaluated its drug delivery efficiency in both WT and YAP ‐/‐ cells. Flow cytometry analysis showed significantly higher fluorescence intensity in YAP ‐/‐ compared to WT CAL51cells after 4‐hour incubation with different concentrations of Doxo‐NP (Figure ##FIG##5##6B##; see Figure ##SUPPL##0##S31c##, Supporting Information). Confocal imaging confirmed a higher association of nanoparticles with YAP ‐/‐ cells (Figure ##FIG##5##6C,D##; see Figure ##SUPPL##0##S31d##, Supporting Information). Results from the WT and YAP ‐/‐ CAL51 co‐culture and 3D spheroid experiments were also consistent (see Figures ##SUPPL##0##S31e## and ##SUPPL##0##S32a,b##, Supporting Information).</p>", "<p>Next, we extended the treatment to 24 h and used confocal imaging to show that doxorubicin accumulated more in the nuclei of YAP ‐/‐ cells as compared to WT cells (Figure ##FIG##5##6E–G##). Additionally, we performed western blot analysis 48 h post‐treatment with antibodies directed against cPARP and γ‐H2AX and detected increased expression of both proteins in YAP ‐/‐ CAL51 cells following Doxo‐NP treatment. This effect was blunted in WT cells treated with the same NPs (Figure ##FIG##5##6H##). High toxicity was observed in YAP ‐/‐ cells at 24‐ and 48‐hours post‐treatment, with a considerably lower number of live cells per well compared to WT CAL51 (Figure ##FIG##5##6I,J##).</p>", "<p>Finally, we investigated if the pharmacological inhibition of YAP could be exploited to enhance Doxo‐NP uptake in TNBC CAL51 cells. To this purpose, small molecule CA3 (1 µ<sc>m</sc>) was used to inhibit YAP activity in breast tumor cells for 12 h and showed no significant toxicity (see Figure ##SUPPL##0##S33a##, Supporting Information).<sup>[</sup>\n##REF##29167315##\n68\n##\n<sup>]</sup> Confocal images showed that CA3 treatment caused YAP to shuttle from the nucleus to the cytoplasm (Figure ##FIG##5##6K##; see Figure ##SUPPL##0##S34##, Supporting Information), which was confirmed by the western blot analysis, revealing CA3‐induced phosphorylation of YAP (Figure ##FIG##5##6L##; see Figure ##SUPPL##0##S33b##, Supporting Information). Importantly, treatment with CA3 followed by a 4‐hour incubation with Doxo‐NP significantly increased nanoparticle binding and internalization (Figure ##FIG##5##6M##; see Figure ##SUPPL##0##S33c##, Supporting Information). It also increased the toxicity of the treatment with the nanoformulation with respect to the nanodrug alone, due to increased nanoparticle internalization and drug release (see Figure ##SUPPL##0##S33d##, Supporting Information). Interestingly, the same effect of YAP inhibition by CA3, in terms of nanoparticle‐cell association, was observed on another TNBC cell line, MDA‐MB‐231 (see Figure ##SUPPL##0##S35a,b##, Supporting Information).</p>", "<p>In light of these results, the inhibition of YAP using suitable drugs may be a promising strategy to improve cancer cell toxicity when combined with nanomedicine for the treatment of TNBC.</p>" ]
[ "<title>Results and Discussion</title>", "<title>YAP Depletion Affects the Mechanical, Physical Properties, and the Membrane Organization of CAL51 TNBC Cells</title>", "<p>We first investigated the effect of YAP depletion on the morphology of CAL51 TNBC cells, which are characterized by constitutively high levels of YAP expression and activity.<sup>[</sup>\n##REF##30904599##\n21\n##\n<sup>]</sup> Using CRISPR/CAS9 technology, we generated a stable YAP‐deficient mutant CAL51 cell line (described in Ref. [##REF##28504269##18##]), and confirmed YAP depletion through confocal microscopy (<bold>Figure</bold> ##FIG##0##\n1A##) and western blot analyses (Figure ##FIG##0##1B##). Next, we used atomic force microscopy (AFM) to determine the effect of YAP depletion on the mechanical properties of CAL51 cells and found a significant reduction in Young's modulus in YAP ‐/‐ cells (Figure ##FIG##0##1C##). Moreover, compared to CAL51 WT cells, YAP ‐/‐ cells displayed reduced surface area, both as determined by actin coverage and membrane extension (Figure ##FIG##0##1D,E##), as well as perturbed cell morphology, resulting from their inability to spread over the adhesion surface (Figure ##FIG##0##1F##; see Figures ##SUPPL##0##S1## and ##SUPPL##0##S2##, Supporting Information). These changes were due to the failure of the mutant cells to assemble focal adhesions and form proper cytoskeleton (Figure ##FIG##0##1G##).<sup>[</sup>\n##REF##28504269##\n18\n##, ##REF##33116297##\n38\n##\n<sup>]</sup> Importantly, YAP depletion did not affect the proliferation and viability of CAL51 TNBC cells (see Figure ##SUPPL##0##S3##, Supporting Information).</p>", "<p>Given the striking change in morphology and mechanics exhibited by YAP ‐/‐ CAL51 cells compared to the wild‐type control, we analyzed their membrane structure using Correlative Probe and Electron Microscopy (CPEM) by LiteScope. This technique combines AFM and scanning electron microscope (SEM) to characterize 3D surface in situ, estimate surface roughness, and perform height/depth profiling with precise AFM tip navigation.<sup>[</sup>\n##UREF##4##\n39\n##\n<sup>]</sup> The analysis demonstrated that YAP depletion and the following decrease in membrane tension led to the remodeling of the plasma membrane in CAL51 TNBC cells and the emergence of dynamic features connected with extensive cellular reorganization (Figure ##FIG##0##1H,I##). Previous literature has reported the appearance of various membrane structures including blebs and vacuole‐like dilations upon the reduction of cell strain.<sup>[</sup>\n##REF##20858416##\n40\n##\n<sup>]</sup> In YAP ‐/‐ cells, we observed the emergence of ripple‐like deformations (Figure ##FIG##0##1J##), which increased the roughness of the cell membrane, as quantified through height irregularity (<italic toggle=\"yes\">R</italic>\n<sub>q</sub>, Figure ##FIG##0##1K##).</p>", "<title>YAP Transcriptional Activity Controls the Expression of Genes Involved in Membrane Organization and Endocytosis in CAL51 TNBC Cells</title>", "<p>Given the substantial effects that YAP depletion played on the structure of cell membrane, we hypothesized that the changes in the membrane of YAP ‐/‐ cells might be reflected in their transcriptional landscape. We adopted RNA sequencing (RNA‐seq) to investigate the regulation of genes encoding for proteins involved in plasma membrane organization (see Figure ##SUPPL##0##S4##, Supporting Information). Overall, RNA‐seq revealed a total of 4219 differentially expressed genes in YAP ‐/‐ cells compared to WT CAL51 cells, with 1925 of them being downregulated and 2294 upregulated following YAP depletion (see Figure ##SUPPL##0##S4a–c##, Supporting Information). The most represented gene ontology (GO) annotations were connected to ECM organization, cell migration, and cell adhesion in WT cells (see Figure ##SUPPL##0##S4d##, Supporting Information), while genes related to integral components of the plasma membrane were found among the cellular components in YAP ‐/‐ counterpart (see Figure ##SUPPL##0##S4e##, Supporting Information).</p>", "<p>In line with our findings regarding cell membrane organization (Figures ##FIG##0##1H–M##), we detected the presence of amphiphysin I (<italic toggle=\"yes\">AMPH1</italic>) among the genes being affected the most by YAP depletion. <italic toggle=\"yes\">AMPH1</italic> encodes for a protein that senses and generates membrane curvatures, is implicated in clathrin‐mediated endocytosis,<sup>[</sup>\n##REF##22184226##\n41\n##\n<sup>]</sup> and was significantly upregulated in CAL51 YAP ‐/‐ cells (log2Fc 7.69, <italic toggle=\"yes\">P</italic> &lt; 0.05, <bold>Figure</bold> ##FIG##1##\n2A##). Together with <italic toggle=\"yes\">AMPH1</italic>, several genes contributing to plasma membrane assembly that were overexpressed in WT CAL51 may explain the differences in cell membrane organization (Figure ##FIG##1##2A##). These include <italic toggle=\"yes\">RFTN1</italic> (log2Fc 2.79), <italic toggle=\"yes\">EHD2</italic> (log2Fc 2.4), <italic toggle=\"yes\">MYOC</italic> (log2Fc 5.83) and <italic toggle=\"yes\">PITPNM1</italic> (log2Fc 2.86).<sup>[</sup>\n##REF##12805216##\n42\n##, ##REF##17233914##\n43\n##, ##REF##18855004##\n44\n##, ##REF##11909959##\n45\n##\n<sup>]</sup>\n</p>", "<p>GO enrichment analysis identified several molecular functions being differentially regulated that were connected to plasma membrane network components, with high scores for lipid raft organization, localization, and assembly (see Figure ##SUPPL##0##S5a##, Supporting Information). Interestingly, lipid rafts, responsible for membrane heterogeneity, strongly impacts the stability and functionality of the plasma membrane at the nanoscale, thus directly supporting high sub‐compartmentalization and intrinsic organization.<sup>[</sup>\n##REF##20044567##\n46\n##\n<sup>]</sup> In addition, STRING PPI analysis yielded a highly clustered network containing 68 nodes and 384 edges for WT CAL51, while 54 nodes and 39 edges were identified for YAP‐depleted cells (Figure ##FIG##1##2B##). WT CAL51 cells showed a significantly higher number of interactors and interconnections between the key elements of the membrane organization network compared to YAP ‐/‐ cells, possibly indicating a higher degree of membrane complexity. The cluster coefficients for both conditions were quite similar (0.394 for WT and 0.5 for YAP ‐/‐). More importantly, RNA‐seq analysis revealed the differential expression of genes encoding proteins involved in endocytosis (Figure ##FIG##1##2C##; see Figure ##SUPPL##0##S5b##, Supporting Information), a process that appears to be dysregulated in tumors.<sup>[</sup>\n##REF##33262521##\n47\n##\n<sup>]</sup> Therefore, the RNA‐seq analysis was extended to examine the expression of transcripts involved in the trafficking of intracellular organelles and endocytic pathways in YAP ‐/‐ cells compared to CAL51 WT cells. This comparison led to the identification of differentially expressed genes involved in caveolae‐mediated endocytosis (Figure ##FIG##1##2D##), clathrin‐mediated endocytosis (Figure ##FIG##1##2E##), and macropinocytosis (Figure ##FIG##1##2F##). While the number of differentially regulated genes in the caveolae‐mediated pathway was similar between WT and YAP ‐/‐ cells (11 in WT and 8 in YAP ‐/‐, although YAP ‐/‐ cells displayed overall higher upregulation; see Figure ##SUPPL##0##S5b##, Supporting Information), clathrin‐related and macropinocytosis‐related genes showed the most striking difference, with more genes of the clathrin‐mediated pathway upregulated in YAP ‐/‐ cells (5 genes in YAP ‐/‐ vs 1 gene in WT) and more genes of the macropinocytosis‐mediated pathway upregulated in WT cells (1 gene in YAP ‐/‐ vs 3 genes in WT).</p>", "<p>To further corroborate these findings, we performed a GO enrichment analysis on the genes involved in endocytosis that were differentially expressed in WT and YAP ‐/‐ cells. The analysis revealed significant differences between WT and YAP ‐/‐ cells in annotations for the negative and positive regulators of endocytosis (see Figures ##SUPPL##0##S6## and ##SUPPL##0##S7##, Supporting Information). For the negative regulators (GO:0045806), WT cells showed high scores for the regulation of endocytic vesicles (<italic toggle=\"yes\">P</italic> = 0.001) and early endosomes (<italic toggle=\"yes\">P</italic> = 0.002) compared to YAP ‐/‐ cells (<italic toggle=\"yes\">P</italic> = 0.13 for endocytic vesicles, <italic toggle=\"yes\">P</italic> = 0.03 for early endosomes), whereas YAP ‐/‐ cells yielded high scores for endosomal recycling genes (<italic toggle=\"yes\">P</italic> = 0.014). These findings indicate that YAP depletion in triple‐negative breast cancer cells lead to the downregulation of transcripts that encode proteins responsible for inhibiting the endocytic pathways (see Figure ##SUPPL##0##S6##, Supporting Information). The positive regulators (GO:0045807), on the other hand, were more abundant in the absence of YAP: relative to WT CAL51, YAP ‐/‐ cells showed significant scores for the terms positive regulators of the endocytic vesicle (<italic toggle=\"yes\">P</italic> = 3.11×10<sup>−5</sup> in YAP ‐/‐ vs <italic toggle=\"yes\">P</italic> = 0.006 in WT) and cytoplasmic vesicle membrane (<italic toggle=\"yes\">P</italic> = 0.000476 in YAP ‐/‐ vs <italic toggle=\"yes\">P</italic> = 0.02 in WT), while CAL51 WT had high scores for collagen‐containing extracellular matrix (<italic toggle=\"yes\">P</italic> = 7.56×10<sup>−5</sup>) and secretory granule lumen (<italic toggle=\"yes\">P</italic> = 0.00035; see Figure ##SUPPL##0##S7##, Supporting Information). Taken together, these results indicate that YAP depletion in CAL51 TNBC cells determines an alteration in the genes involved in endocytosis.</p>", "<title>YAP Regulates the Entry of Nanoparticles in CAL51 TNBC Cells</title>", "<p>Encouraged by these findings, we hypothesized that YAP might play a role in the internalization of nanoparticles and nanodrugs. We figured this might explain how Hippo pathway effector promotes TNBC resistance to chemotherapy.<sup>[</sup>\n##REF##33069769##\n48\n##\n<sup>]</sup> To test this hypothesis, we treated WT and CAL51 YAP ‐/‐ cells with inert polystyrene (PS) nanoparticles (NPs), which have been widely used in bio‐nano interaction studies due to their tunable size and ease of functionalization.<sup>[</sup>\n##REF##21344890##\n49\n##, ##REF##31573181##\n50\n##\n<sup>]</sup> Carboxylated PS nanoparticles with 200 and 900 nm diameter (PS200 and PS900) were first labeled with carboxytetramethylrhodamine using EDC chemistry and characterized via transmission electron microscopy (TEM), spectrofluorometer, and dynamic light scattering (DLS) (see Figure ##SUPPL##0##S8a–e##, Supporting Information). Next, WT and YAP ‐/‐ CAL51 cells were incubated with PS200 and PS900, and nanoparticle binding to the cells evaluated using flow cytometry and confocal microscopy. Our flow cytometry results showed that already after 4 h incubation, PS nanoparticles could be found preferentially bound to YAP ‐/‐ CAL51 cells as compared to their WT counterparts (<bold>Figure</bold> ##FIG##2##\n3A##; see Figures ##SUPPL##0##S9## and ##SUPPL##0##S10a##, Supporting Information). This effect was independent of the nanoparticle size and could be further confirmed by confocal analysis. Through this analysis, we – in fact – showed that a higher number of nanoparticles co‐localized with the membrane of YAP ‐/‐ compared to WT cells (Figure ##FIG##2##3B,C##; see Figure ##SUPPL##0##S10b##, Supporting Information). Interestingly, CPEM analysis allowed us to visualize the detailed morphology of the nanoparticles in contact with CAL51 cells, further corroborating these findings. In WT cells, NPs were bound to the external face of the membrane but not yet internalized after 4 h (see Figure ##SUPPL##0##S11a##, Supporting Information). They in fact appeared bright on SEM and AFM imaging in CAL51 WT and showed limited co‐localization with the cell membrane (see the height profile of the area at the nanoparticle‐membrane binding site in Figure ##SUPPL##0##S11b##, Supporting Information). On the contrary, at the same time‐point NPs were already surrounded by an organic coating attributable to plasma membrane in cells in which YAP had been depleted (see Figure ##SUPPL##0##S11c##, Supporting Information). This result indicated that the nanoparticles were embedded in the cell membrane, as revealed by the reduction of the height profile at the nanoparticle‐membrane binding site (see Figure ##SUPPL##0##S11d##, Supporting Information).</p>", "<p>We next focused on investigating whether the striking difference in particle interaction with cell membrane could be due to the changes in membrane curvature, actin dynamics, and cell mechanosensing as induced by YAP activity.<sup>[</sup>\n##REF##28504269##\n18\n##, ##REF##23122885##\n51\n##\n<sup>]</sup> Hence, we reduced the nanoparticle dosage and increased the incubation time, and found enhanced nanoparticle internalization over time in YAP ‐/‐ CAL51, regardless of dose and time (see Figure ##SUPPL##0##S12a##, Supporting Information). No significant change was observed in YAP localization in WT cells after nanoparticle binding, suggesting no direct impact on intracellular protein shuttling (see Figure ##SUPPL##0##S12b##, Supporting Information). However, a marked decrease in membrane stiffness was noted in WT CAL51 after 4 h of incubation with nanoparticles, but no such change was seen in YAP‐depleted cells (Figure ##FIG##2##3D##). Although the effect of nanoparticles on the cell membrane properties is debated, with responses possibly dependent not only on the nanoparticle size but also their composition,<sup>[</sup>\n##REF##30971727##\n52\n##\n<sup>]</sup> our data suggest that the reduction in membrane rigidity in WT CAL51 did not enhance nanoparticle internalization over time, as YAP ‐/‐ cells exhibited higher binding and internalization in all conditions tested. This was likely due to a stronger impact of YAP depletion on cell membrane stiffness than the physical effects of nanomaterial interactions alone. Furthermore, z‐stack confocal images and TEM micrographs confirmed the internalization of particles in both WT and YAP ‐/‐ cells (see Figure ##SUPPL##0##S13a,b##, Supporting Information), although a higher number of particles was found to bind and co‐localize with the cell membrane in the absence of YAP.</p>", "<p>Next, we treated WT and CAL51 YAP ‐/‐ cells with inhibitors selective for each type of endocytosis to study the impact of YAP on the route of nanoparticle internalization in CAL51 TNBC cells. In particular, the cells were pre‐treated for 2 h with cytochalasin D, chlorpromazine, and nystatin to inhibit macropinocytosis, caveolin‐mediated, and clathrin‐mediated endocytosis, respectively.<sup>[</sup>\n##REF##32426455##\n33\n##\n<sup>]</sup> The cells were then incubated with PS200 and PS900 for 4 h. The live/dead assay was used to confirm no significant effect on cell viability under the chosen treatment conditions (see Figure ##SUPPL##0##S14##, Supporting Information). The obtained results showed that PS200 primarily entered the cells through clathrin‐mediated endocytosis, while PS900 primarily did so through macropinocytosis (see Figure ##SUPPL##0##S15a,b##, Supporting Information), which was in line with previous findings for similar‐sized nanoparticles.<sup>[</sup>\n##REF##35986441##\n53\n##\n<sup>]</sup> After internalization, the particles followed classical endocytic pathways and accumulated in lysosomes within 8 h of incubation (see Figure ##SUPPL##0##S15c##, Supporting Information). These endocytic processes were not affected by the absence of YAP, suggesting that the protein per se does not impact endocytosis pathways but rather affects the dynamics of cell‐nanoparticle association and internalization.</p>", "<p>To evaluate the potential of manipulating tumor cell mechanosensing to enhance nanoparticle delivery in a heterogeneous and complex milieu, we co‐cultured WT CAL51 cells with YAP ‐/‐ cells in a 1:1 ratio. The latter had been previously labeled with 7‐amino‐4‐chloromethylcoumarin (CellTracker). The co‐culture was incubated with either PS200 or PS900 for 4 h. In line with our cell morphology data (Figure ##FIG##0##1##), YAP ‐/‐ cells had a lower total surface area compared to the parental line due to their tendency to spread less on the substrate (see Figure ##SUPPL##0##S16a,b##, Supporting Information). Interestingly, despite the lower area exposed, YAP‐depleted cells bound and internalized a significantly higher number of nanoparticles, as revealed by flow cytometry and confocal analysis (Figure ##FIG##2##3E,F##; see Figure ##SUPPL##0##S16c##, Supporting Information). Indeed, z‐projection confocal images showed consistent preferential co‐localization of nanoparticles within the membrane of YAP ‐/‐ CAL51 cells (see Figure ##SUPPL##0##S17a,b##, Supporting Information). This result contradicts previous studies linking a higher cell surface area with a higher internalization rate,<sup>[</sup>\n##REF##30971727##\n52\n##, ##REF##23484640##\n54\n##\n<sup>]</sup> and suggests that YAP mechanosensing and cell mechanics outplay cell surface area in nanoparticle binding.</p>", "<p>Next, we tested whether the internalization of nanoparticles was affected by their surface coating and charge. These parameters are crucial in bio‐nano interaction studies and have been extensively studied to optimize nanoparticle design for efficient targeting or escape from specific cell types for improved therapy delivery.<sup>[</sup>\n##REF##33277608##\n55\n##\n<sup>]</sup> To determine the impact of nanoparticle surface properties on the differential internalization rate seen in CAL51 cells with or without YAP, PS nanoparticles were coated with the metal phenolic network (MPN) to alter their physicochemical properties, such as surface charge and free energy.<sup>[</sup>\n##REF##23846899##\n56\n##\n<sup>]</sup> Briefly, the MPN coating was applied to the surface of 5‐((5‐Aminopentyl)thioureidyl)fluorescein‐labeled PS200 and PS900 nanoparticles by the assembly of tannic acid (TA) and FeCl<sub>3</sub> according to a previously described protocol.<sup>[</sup>\n##REF##31573181##\n50\n##\n<sup>]</sup> The application of the MPN coating formed PS200‐MPN and PS900‐MPN (Figure ##FIG##2##3G##; see Figure ##SUPPL##0##S18a##, Supporting Information), and the success of the coating was confirmed using a spectrophotometer and dynamic light scattering (DLS) analysis (see Figure ##SUPPL##0##S18b–e##, Supporting Information). To examine cell‐nanoparticle interactions, WT and YAP ‐/‐ CAL51 cells were incubated with PS200‐MPN and PS900‐MPN for 4 h. Flow cytometry and confocal analysis revealed higher binding and internalization in YAP ‐/‐ cells compared to WT cells, supporting the previous results observed using non‐coated PS200 and PS900 nanoparticles (<bold>Figure</bold> ##FIG##3##\n4H–J##; see Figure ##SUPPL##0##S19a,b##, Supporting Information). Our findings indicate that despite coating the particles with MPN, the binding and internalization trends remain consistent with those observed for the uncoated particles and that the influence of cell mechanobiology, specifically the protein YAP, supersedes the properties of the materials in cell–nanoparticle interactions process.</p>", "<p>Analog internalization pattern between the two cell lines was observed by testing fluid‐phase endocytosis and macropinocytosis with fluorescent dextran (Dx‐FITC) and pHrodo‐zymosan respectively (see Figure ##SUPPL##0##S20a,b##, Supporting Information), and in free‐serum conditions where protein corona effect is ruled out (see Figure ##SUPPL##0##S21a,b##, Supporting Information).</p>", "<p>Compellingly, similar results were obtained in tumorigenic HEK293 WT or YAP‐depleted cells (see Figures ##SUPPL##0##S22## and ##SUPPL##0##S23##, Supporting Information), while no differences in nanoparticles binding and internalization was observed in a non‐cancer cell line model of iPSC‐induced fibroblasts in presence or absence of YAP, indicating the selectivity of YAP role for regulating this process in carcinogenic cells (see Figure ##SUPPL##0##S24##, Supporting Information).</p>", "<p>The transcriptional activity of YAP requires its shuttling to the cell nucleus, where it acts as co‐activator by interacting with context‐specific transcription factors.<sup>[</sup>\n##REF##19371381##\n57\n##\n<sup>]</sup> To determine the role of YAP in repressing nanoparticle uptake in TNBC cells, YAP ‐/‐ cells were transfected with a YAP hyperactive mutant (YAP‐S6A). The mutant form of YAP carries a set of mutations in its sequence that converts the residues S61, S109, S127, S128, S131, S136, S164, and S381 into alanine residues. These mutations render the protein non‐phosphorylatable and, consequently, resistant to inactivation and/or degradation. The shuttling of the YAP‐S6A mutant protein to the nucleus is not inhibited via phosphorylation by the upstream Hippo pathway effectors LATS1/2 and MOB1 (Figure ##FIG##2##3K##). A mock vector was used as control. The transfection was first verified by quantifying the expression of YAP protein using western blot and confocal imaging (Figure ##FIG##2##3L,M##). The YAP‐S6A‐ or mock‐transduced CAL51 cells were then incubated with PS200 and PS900 nanoparticles. In line with the hypothesis that YAP presence in the nucleus represses nanoparticle uptake, YAP‐S6A cells exhibited reduced nanoparticle uptake after 4 h of incubation compared to YAP ‐/‐ cells transfected with a mock vector (Figure ##FIG##2##3N##). Interestingly, transfecting YAP‐S6A in WT cells (YAP +/+ CAL51; see Figure ##SUPPL##0##S25a##, Supporting Information) did not induce any significant change in nanoparticle uptake (see Figure ##SUPPL##0##S25b–f##, Supporting Information). This result could be explained by the fact that parental CAL51 cells already expressed a very high basal level of YAP, and the expression of a hyperactive mutant YAP‐S6A did not induce any noticeable change in cell morphology (see Figure ##SUPPL##0##S25d##, Supporting Information), adhesion (see Figure ##SUPPL##0##S25e##, Supporting Information), or transcription. RT‐qPCR further corroborated this hypothesis, showing no change in mRNA levels of CYR61 and CTGF, the two main transcriptional targets of YAP, in YAP +/+ CAL51 compared to WT cells (see Figure ##SUPPL##0##S25f##, Supporting Information).</p>", "<p>These findings indicate that YAP activity affects cell‐nanoparticle interactions and point at YAP as potential regulator of nanoparticles internalization.</p>", "<title>Substrate Stiffness Hinders Nanoparticle Uptake through YAP</title>", "<p>The stiffness of the tumor stroma has been reported to impact YAP intracellular localization and transcriptional activity,<sup>[</sup>\n##REF##23708000##\n25\n##\n<sup>]</sup> which correlates with the ability of cancer cells to metastasize, leading to treatment resistance and poor prognosis.<sup>[</sup>\n##REF##33037194##\n58\n##\n<sup>]</sup> YAP intracellular shuttling and transcriptional activity are controlled by the mechanical properties of the surrounding microenvironment, with cells grown on soft substrates (<italic toggle=\"yes\">E</italic>&lt;5 kPa) exhibiting cytosolic YAP localization while the protein moves to the nucleus on stiffer substrates (<italic toggle=\"yes\">E</italic>&gt;10 kPa).<sup>[</sup>\n##REF##33990464##\n59\n##\n<sup>]</sup> Additionally, the sensitivity of YAP to ECM components such as collagen and fibronectin has been previously documented,<sup>[</sup>\n##REF##30026699##\n9\n##\n<sup>]</sup> with fibronectin accumulation during ECM remodeling triggering YAP nuclear shuttling, independently of substrate stiffness.<sup>[</sup>\n##REF##28504269##\n18\n##, ##REF##26216901##\n60\n##\n<sup>]</sup> To investigate the influence of substrate stiffness and ECM composition on nanoparticle internalization in TNBC CAL51 cells through YAP, WT and YAP ‐/‐ cells were cultured on tissue culture polystyrene (TCPS, Young's modulus in GPa range) or soft surfaces (PDMS) with a defined Young's modulus of 2 kPa coated with either collagen or fibronectin. Confocal microscopy was used to quantify YAP subcellular localization in TNBC cells in response to substrate stiffness or ECM composition. First, we found that in the presence of collagen, the soft substrate hindered YAP nuclear localization, while the presence of fibronectin reversed this effect and restored YAP shuttling to the nucleus of cells grown on a soft substrate (<bold>Figure</bold> ##FIG##3##\n4A,B##). This indicated that the biochemical cues from fibronectin were able to overcome the effects of the mechanical properties of the substrate under the given experimental conditions. We then investigated the relationship among substrate stiffness, YAP activity and nanoparticle uptake in TNBC cells by incubating cells cultured on soft or stiff substrates with PS200 and PS900 nanoparticles for 4 h. Our results showed that CAL51 WT cells grown on 2 kPa soft substrate coated with collagen (low YAP activity) exhibited increased nanoparticle uptake, whereas this phenomenon was not observed on stiff PSS or 2 kPa substrates coated with fibronectin (high YAP activity, Figure ##FIG##3##4C–F##). Conversely, YAP ‐/‐ CAL51 cells showed no change in nanoparticle internalization on either PSS or 2 kPa substrates coated with collagen or fibronectin (see Figure ##SUPPL##0##S26##, Supporting Information). These results suggest that YAP mechanical displacement from the nucleus could be an effective way to augment nanoparticle uptake in TNBC cells.</p>", "<title>YAP Promotes ECM Network Deposition and Affects Cell‐Nanoparticle Interactions in a 3D In Vitro Model of TNBC</title>", "<p>The efficiency of endocytosis is tightly linked to the composition of the ECM that surrounds cells. We hypothesized that the increase in nanoparticle uptake measured in YAP ‐/‐ cells could be explained by a less structured ECM in these cells. We first performed an RT<sup>2</sup>‐profiler PCR array and found that many genes related to ECM‐cell adhesion were significantly upregulated in WT cells compared to YAP ‐/‐ cells (<bold>Figure</bold> ##FIG##4##\n5A##; see Figure ##SUPPL##0##S27a,b##, Supporting Information). Some of these genes are known to be directly regulated by YAP transcriptional activity, such as CTGF (CCN2). To get a deeper insight into how YAP regulates the ECM landscape, we explored network connectivity and ontological interconnections between ECM components identified in both WT and YAP ‐/‐ cells using the STRING protein‐protein interaction (PPI) database with a score threshold of 0.4.<sup>[</sup>\n##REF##25352553##\n61\n##\n<sup>]</sup> The STRING PPI analysis yielded a highly clustered network containing 39 nodes and 336 edges and with a clustering coefficient of 0.74 for WT CAL51, indicating a significant high number of interactions (Figure ##FIG##4##5B##). On the opposite, the analysis of YAP ‐/‐ CAL51 cells showed a network with fewer connections, containing 38 nodes and 165 edges, and with a lower clustering coefficient of 0.49 (see Figure ##SUPPL##0##S27c##, Supporting Information). As expected, the GO enrichment analysis revealed significant differences in the molecular function of the ECM network between WT and YAP ‐/‐ cells. While the former cells had high scores for annotations related to ECM and extracellular structure organization (<italic toggle=\"yes\">P</italic> = 2.46×10<sup>−12</sup>) (Figure ##FIG##4##5C##), the latter displayed low scores for annotations related to ECM (<italic toggle=\"yes\">P</italic> = 0.0043) and extracellular structure organization (<italic toggle=\"yes\">P</italic> = 0.0078) (see Figure ##SUPPL##0##S27d##, Supporting Information). Interestingly, the analysis also revealed that YAP depletion led to the dysregulation of several classes of ECM transcripts associated with cancer or known to promote tumor growth (see Figure ##SUPPL##0##S28a,b##, Supporting Information).<sup>[</sup>\n##REF##25381661##\n62\n##\n<sup>]</sup>\n</p>", "<p>Next, we aimed to validate the hypothesis that reduced ECM deposition in YAP ‐/‐ cells was responsible for increased nanoparticle uptake. We established a 3D cell culture system, which resembles the complex and heterogeneous tumor microenvironment more closely than a 2D monolayer.<sup>[</sup>\n##REF##31904048##\n63\n##, ##REF##28646905##\n64\n##\n<sup>]</sup> We generated 3D spheroids of both WT and YAP ‐/‐ CAL51cells and investigated nanoparticle uptake using this experimental model. Briefly, the cells were seeded onto round‐bottom ultra‐low attachment plates and spun to promote their aggregation. As expected, after 5 days of culture, the spheroids obtained from WT or YAP ‐/‐ cells showed distinct morphologies similar to what previously described (Figure ##FIG##4##5D##; see Figure ##SUPPL##0##S29a##, Supporting Information).<sup>[</sup>\n##REF##28504269##\n18\n##\n<sup>]</sup>\n</p>", "<p>Then, we investigated YAP expression in WT spheroids and found that YAP was evenly distributed in both the cytoplasm and nucleus of the cells (Figure ##FIG##4##5E##). The live/dead assay confirmed that the cells were viable, with no detectable sign of cell death in either WT or YAP ‐/‐ spheroids (see Figure ##SUPPL##0##S29b##, Supporting Information). We then incubated WT and YAP ‐/‐ spheroids with PS200 and PS900 nanoparticles and quantified nanoparticle binding using flow cytometry and confocal imaging. After 4 h of incubation, we found that YAP ‐/‐ CAL51 spheroids exhibited significantly higher nanoparticle binding than WT spheroids (Figure ##FIG##4##5F–H##). This result was also confirmed using different nanoparticle concentrations and incubation times (see Figure ##SUPPL##0##S29c,d##, Supporting Information). Next, we stained WT and YAP ‐/‐ CAL51 spheroids with antibodies directed against relevant ECM proteins. The confocal microscopy analysis demonstrated that CAL51 WT cells produced a rich and multicomponent ECM composed of various proteins such as collagen, CTGF, fibronectin, laminin, and periostin, all contributing to the spheroid assembly. In contrast, YAP ‐/‐ depletion determined a stark reduction in the expression of the same ECM proteins (Figure ##FIG##4##5I##; see Figure ##SUPPL##0##S30##, Supporting Information). Considering these results, targeting YAP may serve as a promising strategy for improving nanoparticle uptake into solid tumors by tuning cell membrane properties and decreasing ECM deposition.</p>", "<title>YAP Targeting Improves Nanomedicine Delivery to TNBC Cells</title>", "<p>After demonstrating that YAP depletion can be leveraged to increase nanoparticle uptake in TNBC CAL51 cells, we next aimed to demonstrate the therapeutic benefits of combining nanoparticle treatment with YAP targeting. To assess the efficiency of drug delivery, we chose liposomes (<bold>Figure</bold> ##FIG##5##\n6A##; see Figure ##SUPPL##0##S31a,b##, Supporting Information), as they have a long history of success since Doxil,<sup>[</sup>\n##REF##20044567##\n46\n##\n<sup>]</sup> the first nano drug that reached the market, and have been recently used in nanoformulations to treat cancer and other diseases.<sup>[</sup>\n##REF##34394960##\n65\n##, ##REF##34715546##\n66\n##, ##REF##35189345##\n67\n##\n<sup>]</sup> We used a doxorubicin‐loaded liposomal formulation (Doxo‐NP) and evaluated its drug delivery efficiency in both WT and YAP ‐/‐ cells. Flow cytometry analysis showed significantly higher fluorescence intensity in YAP ‐/‐ compared to WT CAL51cells after 4‐hour incubation with different concentrations of Doxo‐NP (Figure ##FIG##5##6B##; see Figure ##SUPPL##0##S31c##, Supporting Information). Confocal imaging confirmed a higher association of nanoparticles with YAP ‐/‐ cells (Figure ##FIG##5##6C,D##; see Figure ##SUPPL##0##S31d##, Supporting Information). Results from the WT and YAP ‐/‐ CAL51 co‐culture and 3D spheroid experiments were also consistent (see Figures ##SUPPL##0##S31e## and ##SUPPL##0##S32a,b##, Supporting Information).</p>", "<p>Next, we extended the treatment to 24 h and used confocal imaging to show that doxorubicin accumulated more in the nuclei of YAP ‐/‐ cells as compared to WT cells (Figure ##FIG##5##6E–G##). Additionally, we performed western blot analysis 48 h post‐treatment with antibodies directed against cPARP and γ‐H2AX and detected increased expression of both proteins in YAP ‐/‐ CAL51 cells following Doxo‐NP treatment. This effect was blunted in WT cells treated with the same NPs (Figure ##FIG##5##6H##). High toxicity was observed in YAP ‐/‐ cells at 24‐ and 48‐hours post‐treatment, with a considerably lower number of live cells per well compared to WT CAL51 (Figure ##FIG##5##6I,J##).</p>", "<p>Finally, we investigated if the pharmacological inhibition of YAP could be exploited to enhance Doxo‐NP uptake in TNBC CAL51 cells. To this purpose, small molecule CA3 (1 µ<sc>m</sc>) was used to inhibit YAP activity in breast tumor cells for 12 h and showed no significant toxicity (see Figure ##SUPPL##0##S33a##, Supporting Information).<sup>[</sup>\n##REF##29167315##\n68\n##\n<sup>]</sup> Confocal images showed that CA3 treatment caused YAP to shuttle from the nucleus to the cytoplasm (Figure ##FIG##5##6K##; see Figure ##SUPPL##0##S34##, Supporting Information), which was confirmed by the western blot analysis, revealing CA3‐induced phosphorylation of YAP (Figure ##FIG##5##6L##; see Figure ##SUPPL##0##S33b##, Supporting Information). Importantly, treatment with CA3 followed by a 4‐hour incubation with Doxo‐NP significantly increased nanoparticle binding and internalization (Figure ##FIG##5##6M##; see Figure ##SUPPL##0##S33c##, Supporting Information). It also increased the toxicity of the treatment with the nanoformulation with respect to the nanodrug alone, due to increased nanoparticle internalization and drug release (see Figure ##SUPPL##0##S33d##, Supporting Information). Interestingly, the same effect of YAP inhibition by CA3, in terms of nanoparticle‐cell association, was observed on another TNBC cell line, MDA‐MB‐231 (see Figure ##SUPPL##0##S35a,b##, Supporting Information).</p>", "<p>In light of these results, the inhibition of YAP using suitable drugs may be a promising strategy to improve cancer cell toxicity when combined with nanomedicine for the treatment of TNBC.</p>" ]
[ "<title>Conclusion</title>", "<p>Due to its pro‐tumorigenic role as an oncogene, YAP has been proposed as a target to halt cancer progression.<sup>[</sup>\n##REF##24336504##\n69\n##\n<sup>]</sup> In this study, we showed that YAP depletion in the TNBC cell line CAL51 significantly alters the mechanical properties, surface area and adhesion of the cells. Moreover, we demonstrated that YAP controls the genetic landscape of CAL51 cells by impacting the transcription of genes involved in membrane organization and endocytosis. RNA‐seq analysis revealed differential expression of several genes involved in cell‐substrate adhesion, actin‐membrane linkage, ECM production, contraction, membrane tension and organization in YAP ‐/‐ relative to CAL51 WT cells. Notably, we observed that YAP depletion determines the upregulation of several genes that positively regulate endocytosis and that may contribute to the internalization of nanoparticles. Recent studies have shown a connection between YAP and the endocytic machinery in the cytoplasm.<sup>[</sup>\n##REF##31806419##\n70\n##\n<sup>]</sup> These interactions have long been linked to protein turnover via a degradation pathway alternative to the Hippo pathway, LATS1/2 phosphorylation, and proteasome. However, as our understanding of the feedback between the plasma membrane domain and mechanosensing effectors advances, the cytoplasmic pool of YAP directly interacting with proteins of the membrane, vesicles, and organelles may uncover novel and unexpected functions related to the control of organelles trafficking. Our findings suggest that YAP may play a leading role in the regulation of endocytic processes; however, its role in the homeostasis of cytoplasmic vesicles and organelles remains unclear and warrants further investigation of the molecular pathways underlying these interactions.</p>", "<p>Throughout the study, we found that YAP knockout led to changes in cell physical and biological properties, resulting in increased nanoparticle uptake that was exclusively linked to YAP activity, not the size or surface coating of the nanoparticles. Additionally, in a co‐culture system, where WT and YAP ‐/‐ CAL51 cells were seeded together, cells in which the Hippo effector had been genetically depleted showed a higher association rate with nanoparticles compared to WT cells, suggesting a possible mechanotargeting effect where cell mechanics plays a key role in bio‐nano interactions. While the substrate and cell mechanics are often intertwined in nanoparticle uptake processes,<sup>[</sup>\n##REF##33429644##\n71\n##\n<sup>]</sup> our study shows that YAP activity overrides substrate mechanics in controlling nanoparticle internalization. Indeed, irrespective of the Young's modulus of the surface where the cells were grown, YAP activity was the key determinant in nanoparticle uptake. Specifically, an increase in YAP activity through cell‐ECM interactions such as integrin‐fibronectin did not enhance nanoparticle uptake even on low‐stiffness substrates. Furthermore, in 3D spheroid cultures, the mechanical state of cell‐cell interaction greatly depended on ECM production and deposition, which could, in turn, impact nanoparticle association and penetration within the spheroids. As a result, nanoparticles tend to associate more with spheroids derived from YAP ‐/‐ than WT cells. These data indicate that the intracellular activity of YAP and related mechanosensing proteins, not substrate mechanics, play an active role in nanoparticle internalization.</p>", "<p>Our findings show that cell mechanobiology contributes to cell‐nanoparticle interactions, and the functions of its principal pathways and effectors may improve nanoparticle delivery to cancer cells. The mechanobiology pathways identified here may be leveraged to ameliorate the design of nanoparticles, focusing on the development and characterization of nanomaterials that are able to interact with the cell membrane in more efficient ways. Although the role of YAP‐paralog protein TAZ (WWTR1) would be worth investigating in the context of breast cancer cell–nanoparticle interaction, in the present work, we have decided to focus exclusively on YAP due to our previous results that have shown that the latter exerts a stronger effect on cell adhesion to the extracellular matrix.<sup>[</sup>\n##REF##28504269##\n18\n##\n<sup>]</sup>\n</p>", "<p>However, considering that breast cancer, and cancer in general, is a complex disease, the role of YAP in TNBC and other cancers should be evaluated on a case‐by‐case basis. In our study, we propose that in cases where disease stratification is feasible, and YAP is found to be overexpressed, combining its inhibition with nanomedicine could offer a novel strategy to enhance therapeutic effectiveness. It is likely that other mechanosensing proteins play a significant role in regulating cell–nanoparticle interactions in different cell types or cancer cells, and further studies are necessary to elucidate these aspects.</p>", "<p>From a clinical perspective, several mechanotherapeutic drugs are currently under evaluation in clinical trials and are expected to be used in combination with other therapies, such as chemotherapy, targeted therapies, and immunotherapies.<sup>[</sup>\n##REF##31375797##\n72\n##\n<sup>]</sup> The inhibition of YAP through appropriate drugs may represent a promising strategy when combined with nanomedicine administration to enhance the toxicity against cancer cells, similar to the approaches using Onivyde, a liposomal formulation of irinotecan used in combination with free leucovorin and 5‐fluorouracil for metastatic pancreatic cancer,<sup>[</sup>\n##REF##27219482##\n73\n##\n<sup>]</sup> and Apealea, a micellar formulation of paclitaxel administered in combination with carboplatin for the treatment of ovarian cancer.<sup>[</sup>\n##REF##31432461##\n74\n##\n<sup>]</sup> Noteworthy, recently, the co‐delivery of lipid nanoparticles (LNP) carrying FAK siRNA and CRISPR‐PD‐L1 has been demonstrated to be effective in reducing the extracellular matrix deposition and stiffness of cancer cells upon continuous administrations.<sup>[</sup>\n##REF##35551240##\n75\n##\n<sup>]</sup> This approach increases the delivery of LNPs, together with the transfection efficiency, and effectively induces the knock‐down of immune checkpoints.<sup>[</sup>\n##REF##35551240##\n75\n##\n<sup>]</sup>\n</p>", "<p>To summarize, in this study we have demonstrated that YAP co‐transcriptional activity hinders nanoparticle binding and internalization. As we explored along the paper, several reasons may account for this association and can be ascribed to the role of YAP in: i) directing the transcription of genes involved in cell adhesion and mechanosensing; ii) affecting the genetic landscape of endocytic pathways by transcriptionally suppressing proteins involved in endocytosis; iii) perturbing cell membrane tension and organization, thus promoting its deformation and facilitating the formation of endocytic vesicles; iv) producing an abundant and dense ECM network that may ultimately hamper nanoparticle diffusion.</p>", "<p>In conclusion, by genetically, mechanically, or pharmacologically targeting YAP, we show that it is possible to increase nanoparticle association and internalization in TNBC cells, highlighting the role of mechanobiology in shaping the fate of bio‐nano interactions in cancer cells. We demonstrate that blocking YAP activity may be used to increase the delivery of nano drugs, paving the way for novel combinatorial therapies suited to tackle cancer tumorigenicity while simultaneously enhancing the delivery of anti‐cancer nanotherapeutics. This work opens up new avenues for selectively tuning cell‐nanoparticle interactions by targeting molecular processes that differentiate between cancer cells and their healthy counterpart, thus improving both the delivery and specificity of nanotherapy. To assess the pre‐clinical and clinical value of such nanotherapies, we propose an alternative fundamental mechanism for nanoparticle entry into the cells. A deeper understanding of the cell mechanobiology pathways in bio‐nano interactions and the search for new targets and drugs to modulate their functions could accelerate the development of advanced next‐generation nanotherapies that would address the challenges posed by nanomedicine concerning targeted and selective drug delivery.</p>" ]
[ "<title>Abstract</title>", "<p>Interactions between living cells and nanoparticles are extensively studied to enhance the delivery of therapeutics. Nanoparticles size, shape, stiffness, and surface charge are regarded as the main features able to control the fate of cell‐nanoparticle interactions. However, the clinical translation of nanotherapies has so far been limited, and there is a need to better understand the biology of cell‐nanoparticle interactions. This study investigates the role of cellular mechanosensitive components in cell‐nanoparticle interactions. It is demonstrated that the genetic and pharmacologic inhibition of yes‐associated protein (YAP), a key component of cancer cell mechanosensing apparatus and Hippo pathway effector, improves nanoparticle internalization in triple‐negative breast cancer cells regardless of nanoparticle properties or substrate characteristics. This process occurs through YAP‐dependent regulation of endocytic pathways, cell mechanics, and membrane organization. Hence, the study proposes targeting YAP may sensitize triple‐negative breast cancer cells to chemotherapy and increase the selectivity of nanotherapy.</p>", "<p>The inhibition of Yeas‐associated protein (YAP) in TNBC cells affects the organization of plasma membrane, reduces the extracellular matrix (ECM) deposition, impacts their adhesion ability, and increases the endocytosis rate. Thus, targeting cell mechanobiology may be leveraged to optimize cell‐nanoparticle interactions. Ultimately, these changes contribute cooperatively to promote the delivery of nanomedicines to cancer cells and improve the therapeutic efficiency.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6692-cit-0076\">\n<string-name>\n<given-names>M.</given-names>\n<surname>Cassani</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Fernandes</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Oliver‐De La Cruz</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Durikova</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Vrbsky</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Patočka</surname>\n</string-name>, <string-name>\n<given-names>V.</given-names>\n<surname>Hegrova</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Klimovic</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Pribyl</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Debellis</surname>\n</string-name>, <string-name>\n<given-names>P.</given-names>\n<surname>Skladal</surname>\n</string-name>, <string-name>\n<given-names>F.</given-names>\n<surname>Cavalieri</surname>\n</string-name>, <string-name>\n<given-names>F.</given-names>\n<surname>Caruso</surname>\n</string-name>, <string-name>\n<given-names>G.</given-names>\n<surname>Forte</surname>\n</string-name>, <article-title>YAP Signaling Regulates the Cellular Uptake and Therapeutic Effect of Nanoparticles</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2302965</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202302965</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<p>Detailed experimental methods can be found in <italic toggle=\"yes\">Supporting information</italic>.</p>", "<title>Statistical Analysis</title>", "<p>Results are based on at least three replicates, and the data are presented as the mean ± s.d. The calculations were performed using GraphPad Prism v. 6.0 (San Diego, USA). For single‐cell analysis, a minimum of 100 cells per sample were considered. Along the manuscript, the following statistical tests have been used: Unpaired <italic toggle=\"yes\">t</italic>‐test with Welch's correction; Kruskal–Wallis one‐way ANOVA followed by post‐hoc Dunn's multiple comparisons test; two‐way ANOVA followed by Sidak's or Tukey's multiple comparisons test. The appropriate statistical test was applied to the data as indicated in the figure captions for each experiment. All data are presented as mean ± standard deviation (S.D.). A P &lt; 0.05 was considered statistically significant as denoted with asterisks [(*) <italic toggle=\"yes\">p</italic> ≤ 0.05, (**) <italic toggle=\"yes\">p</italic> ≤ 0.01, (***) <italic toggle=\"yes\">p</italic> ≤ 0.001].</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>M.C. and G.F. conceptualized the idea for the study. M.C., S.F., J.O.D.L.C., J.V., V.H., M.P., S.K., J.P., and D.D. designed the methodology. M.C. and S.F. performed investigation. M.C. visualized the idea for the study. M.C. and G.F. performed supervision and wrote the original draft. M.C., S.F., F.C., and G.F. wrote, reviewed, and edited the final manuscript.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors are grateful to František Foret for granting the access to its facility at the Department of Bioanalytical Instrumentation of the institute of analytical chemistry of Brno. The authors thank Jana Bartoňová, Stefania Pagliari, and Vladimír Vinarský for scientific advice and technical assistance. The authors thank Roberto Marotta and Federico Catalano of the Electron Microscopy Facility, Fondazione Istituto Italiano Di Tecnologia for technical assistance. The authors acknowledge the CF Genomics of CEITEC supported by the NCMG research infrastructure (LM2018132 funded by MEYS CR) Bioinformatics for their support with obtaining scientific data presented in this paper. The authors also acknowledge CIISB, Instruct‐CZ Centre of Instruct‐ERIC EU consortium, funded by MEYS CR infrastructure project LM2023042 and European Regional Development Fund‐Project “UP CIISB” (No. CZ.02.1.01/0.0/0.0/18_046/0015974), is gratefully acknowledged for the financial support of the measurements at the CF Nanobiotechnology. The authors also thank Romana Vlčková, Hana Dulová, and Jana Vašíčková for their support on continuation of the study. The authors thank Ilya Demchenko from Insight Editing London for editorial support of the manuscript. Marco Cassani, an iCARE‐2 fellow, has received funding from Fondazione per la Ricerca sul Cancro (AIRC) and the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska‐Curie Grant Agreement No. 800924. Giancarlo Forte was supported by the European Regional Development Fund—Project ENOCH (No. CZ.02.1.01/0.0/0.0/16_019/0000868). Jorge Oliver‐De La Cruz and Soraia Fernandes were supported by the European Social Fund and European Regional Development Fund‐Project MAGNET (CZ.02.1.01/0.0/0.0/15_003/0000492). This work was supported by Marie Curie H2020‐MSCA‐IF‐2020 MSCA‐IF‐GF “MecHA‐Nano”, Grant Agreement No 101031744. This work was also supported by Ministry of Health of the Czech Republic, grant no. NU23J‐08‐00035.</p>", "<p>Open access publishing facilitated by The University of Melbourne, as part of the Wiley ‐ The University of Melbourne agreement via the Council of Australian University Librarians.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6692-fig-0001\"><label>Figure 1</label><caption><p>YAP depletion affects CAL51 adhesion, mechanics, morphology, and membrane properties. A) Representative confocal images depicting YAP expression in WT or YAP ‐/‐ CAL51 cells. Cells were stained for YAP (AF555, red), and nuclei were counterstained with DAPI (blue). Scale bar: 50 µm. The green dashed line box shows higher magnification pictures. Scale bar: 10 µm. B) Western blot analysis showing the levels of YAP protein in WT or YAP ‐/‐ CAL51 cells. β‐tubulin was used for protein loading normalization. C) Dot plot representation of the Young's modulus analysis of WT or YAP ‐/‐ CAL51 cells as measured by atomic force microscopy (AFM). WT CAL51: <italic toggle=\"yes\">n</italic> = 80; YAP ‐/‐ CAL51: <italic toggle=\"yes\">n</italic> = 10. Statistical analysis was performed by unpaired t‐test with Welch's correction; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. D) Dot plot analysis of WT or YAP ‐/‐ CAL51 total membrane area. Cells were stained with Alexa Fluor 488‐labeled wheat germ agglutinin (WGA‐488, green). <italic toggle=\"yes\">n</italic> &gt; 100 cells. Statistical analysis was performed by unpaired <italic toggle=\"yes\">t</italic>‐test with Welch's correction; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. E) Dot plot analysis of WT or YAP ‐/‐ CAL51 cell surface area calculated based on the total actin coverage of the cells. Cells were stained with Alexa Fluor 488‐labeled Phalloidin (Pha‐488, green). <italic toggle=\"yes\">n</italic> &gt; 100. Statistical analysis was performed by unpaired <italic toggle=\"yes\">t</italic>‐test with Welch's correction; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. F) CAL51 WT (left) and YAP ‐/‐ cells (right) 3D reconstruction. Cells were stained with DAPI and WGA‐488 (green). Scale bar: 20 µm. G) Representative confocal images of WT or YAP ‐/‐ CAL51 cells stained for nuclei (DAPI, blue) and actin (Pha‐488, green, top), vinculin (AF488, green, middle), and membrane (WGA‐647, red, bottom), respectively. Scale bar: 20 µm. The insets display high‐magnification images. Scale bar: 10 µm. Correlative Probe and Electron Microscopy (CPEM) imaging of CAL51 WT (H) and CAL51 YAP ‐/‐ (I) cells. AFM and SEM images are shown. White dashed line boxes indicate the detail of the magnifications shown as AFM and SEM images on the right of each main micrograph. J) Plot displaying the profile of the membrane roughness as determined for WT (red) and YAP ‐/‐ (blue) CAL51 cells in the region highlighted in the SEM images on the right (red dashed line, top for CAL51 WT; blue dashed line, bottom for YAP ‐/‐ CAL51). The roughness profile was calculated on the deconvolved images. Scale bar: 0.5 µm. K) Mean square roughness of the height irregularity (<italic toggle=\"yes\">R</italic>\n<sub>q</sub>) measured on WT (red) and YAP ‐/‐ (blue) CAL51cells. <italic toggle=\"yes\">n</italic> = 20. Statistical analysis was performed by unpaired t‐test with Welch's correction; <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6692-fig-0002\"><label>Figure 2</label><caption><p>YAP depletion alters the expression of genes related to membrane organization and endocytosis pathways. A) Heatmap of the relative expression of significantly regulated genes associated with the membrane organization network in YAP ‐/‐ and WT CAL51 cells. <italic toggle=\"yes\">n</italic> = 4 (P adj &lt; 0.05, log2Fc &gt; ǀ2ǀ). B) STRING PPI network of differently expressed proteins involved in membrane organization in WT (top) and YAP ‐/‐ CAL51 (bottom) cells obtained from Cytoscape (P adj &lt; 0.05, log2Fc &gt; ǀ2ǀ, confidence cutoff 0.4). C) Graphical representation of the main mechanisms of endocytosis, i.e., caveolae‐related endocytosis, clathrin‐related endocytosis, and macropinocytosis, investigated in the present study. D) Heatmap of genes involved in endocytosis pathways for caveolae‐related genes. E) heatmap of genes involved in clathrin‐mediated endocytosis pathways. F). Heatmap of genes involved in macropinocytosis (P adj &lt; 0.05, log2Fc &gt; ǀ1ǀ).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6692-fig-0003\"><label>Figure 3</label><caption><p>YAP knockout promotes nanoparticle binding and internalization in CAL51 TNBC cells. A) 4‐hour cellular uptake of PS200 and PS900 in WT (red) and YAP ‐/‐ CAL51 (blue). Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 3; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. B) Nanoparticle intensity per cell after 4 h of incubation of CAL51 WT and YAP ‐/‐ cells with PS200 and PS900. Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 3; <sup>***</sup> indicates <italic toggle=\"yes\">p</italic> &lt; 0.001. <italic toggle=\"yes\">n</italic> &gt; 100 cells. C) Confocal images of WT (top) and YAP ‐/‐ (bottom) CAL51 cells after 4 h of incubation with PS200 and PS900. Cells were stained with WGA‐488 (green) and/or DAPI (blue). Magnified images are displayed inside the red dashed line boxes for each cell and particle type. Scale bar: 25 and 10 µm. D) Young's modulus analysis of WT (top) and YAP ‐/‐ (bottom) cells after 4 h of incubation with PS200 and PS900, as measured by atomic force microscopy (AFM). Statistical analysis was performed using the Kruskal–Wallis one‐way ANOVA followed by Dunn's multiple comparisons test. WT CAL51: <italic toggle=\"yes\">n</italic> = 80; YAP ‐/‐ CAL51: <italic toggle=\"yes\">n</italic> = 10; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001; ns, non‐significant. E) 4‐hour cellular uptake of PS200 and PS900 in a co‐culture of WT (red) and YAP ‐/‐ (blue) CAL51. Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 3; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. F) Confocal images of WT and YAP ‐/‐ cells co‐culture in the presence of PS200 and PS900 for 4 h. White dashed line indicates CAL51 YAP ‐/‐ cells. Grey arrows indicate particles co‐localized with YAP ‐/‐ cells (encircled by white dashed lines), while green arrows indicate particles in contact with WT cells (encircled by green dashed lines). CAL51 YAP ‐/‐ cells are stained with 7‐amino‐4‐chloromethylcoumarin (grey) and whole cell population with WGA‐488 (green). Scale bar: 10 µm. G) The surface properties of PS200 and PS900 were modified by MPN coating, using tannic acid and FeCl<sub>3</sub>. H) 4‐hour cellular uptake of PS200‐MPN and PS900‐MPN for WT (red) and YAP ‐/‐ (blue) CAL51. Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 3; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. I,J) Confocal images of WT (top) and YAP ‐/‐ (bottom) CAL51 cells after 4 h of incubation with PS200 (I) and PS900 (J). Cells are stained with WGA‐647 (red) and DAPI (blue). The particles are displayed in green. Magnified images are displayed inside red dashed line boxes for each cell and particle type. Scale bar: 50 and 10 µm. K) Schematic representation of the phosphorylation‐mediated repression of YAP translocation to the nucleus by kinases involved in different pathways, mainly Hippo pathway (LATS1/2 kinases and scaffolding protein MOB1). Due to substitutions of serine residues with alanine residues in six different positions (S61A, S109A, S127A, S128A, S131A, S136A, S164A, and S381A), YAP‐S6A cannot be phosphorylated by upstream kinases, thus is constitutively active in the cell nucleus. L) Western blot analysis of the levels of YAP protein in CAL51 YAP ‐/‐ and in cells transfected with a plasmid carrying a copy of the YAPS6A gene. β‐tubulin was used for protein loading normalization. M) Confocal images of YAP ‐/‐ (CTRL) and YAPS6A CAL51. Cells were stained with DAPI (blue) and YAP (AF555, red). Scale bar: 10 µm. N) 4‐hour cellular uptake of PS200 and PS900 in YAP ‐/‐ (blue) and YAPS6A (red) CAL51. Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 3; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6692-fig-0004\"><label>Figure 4</label><caption><p>Substrate mechanics impairs nanoparticle uptake through YAP. A) Confocal images of CAL51 WT cells grown on a stiff polystyrene substrate coated with collagen (left) or fibronectin (right). Cells were stained with DAPI (blue), Pha‐488 (green), and YAP (AF555, red). Magnified images are displayed inside gray dashed line boxes. Scale bar: 50 and 10 µm. B) Confocal images of WT CAL51 cells grown on a 2 kPa soft substrate coated with collagen (left) or fibronectin (right). Cells were stained with DAPI (blue), Pha‐488 (green), and YAP (AF555, red). Magnified images are displayed inside gray dashed line boxes. Scale bar: 50 and 10 µm. C) 4‐hour cellular uptake of PS200 (light gray) and PS900 (dark gray) in WT cells grown on a stiff polystyrene substrate coated with collagen or fibronectin. Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 3; ns, non‐significant. D) 4‐hour cellular uptake of PS200 (light gray) and PS900 (dark gray) in WT CAL51 grown on a 2 kPa soft substrate coated with collagen or fibronectin. Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 3; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. E) Schematic representation of the mechanism proposed for the differences found in nanoparticle uptake in WT CAL51 cells grown on polystyrene substrates. The cells are well‐spread and attached to the surface, with high YAP nuclear localization. F) Schematic representation of the mechanism proposed for the differences found in nanoparticle uptake in WT CAL51 cells grown on soft substrates. When cells are grown on a soft substrate with a molecular‐mechanical inert coating such as collagen, YAP shuttles out of the nucleus in an inactive state, and cells appear round and poorly spread. This decrease in YAP activity leads to a significant increase in nanoparticle uptake. Conversely, fibronectin coating outplays soft stiffness substrates, activates YAP and restores the mechanical properties. Nanoparticle uptake is reduced similar to what happens on stiff polystyrene.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6692-fig-0005\"><label>Figure 5</label><caption><p>YAP knockdown affects nanoparticle binding and ECM deposition in 3D CAL51 spheroids. A) Heatmap representing the changes in expression for ECM and cell adhesion molecules in YAP ‐/‐ compared to WT CAL51 cells, as obtained from RT<sup>2</sup>‐profiler PCR array analysis (P adj &lt; 0.05, fold change 2). B) STRING PPI network of differently expressed ECM proteins in CAL51 WT obtained from Cytoscape (P adj &lt; 0.05, log2Fc &gt; ǀ2ǀ, confidence cutoff 0.4). C) Bar plot representation of common enriched biological processes and pathways related to ECM network from the ENRICHR database, showing the most significantly upregulated genes in WT compared to YAP ‐/‐ CAL51 cells (P adj &lt; 0.05, log2Fc &gt; ǀ2ǀ). D) Z‐projection images of WT (left) and YAP ‐/‐ CAL51 (right) spheroids after 5 days of culture. Cells are stained with WGA‐488 (green) and DAPI (blue). Scale bar: 200 µm. E) Confocal images of the spheroids derived from WT and YAP ‐/‐ cells. Cells were stained with DAPI (blue) and YAP (AF555, red). Scale bar: 10 µm. F) 4‐hour cellular uptake of PS200 and PS900 in WT (red) and YAP ‐/‐ (blue) CAL51 spheroids. Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 5; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. G) Confocal images of the spheroids derived from WT CAL51 cells incubated with PS200 (left) and PS900 (right) for 4 h. H) Representative confocal images of the spheroids derived from YAP‐/‐ CAL51 cells incubated with PS200 (left) and PS900 (right) for 4 h. Cells were stained with WGA‐488 (green) and DAPI (blue). Nanoparticles are shown in red. Scale bar: 100 µm. I) Representative confocal images of the indicated ECM components for the spheroids derived from WT (left) and YAP ‐/‐ (right) CAL51 cells. Collagen type 1 alpha (Col1A), collagen type III alpha 1 (Col3A1), connective tissue growth factor (CTGF), and periostin are stained with 2nd antibody labeled with AF‐555 (red); fibronectin and laminin are stained with II‐antibody labeled with AF‐488 (green). Scale bar: 25 µm.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6692-fig-0006\"><label>Figure 6</label><caption><p>Pharmacological and genetic targeting of YAP increases the internalization of doxorubicin‐loaded liposomes and improves drug delivery in TNBC CAL51 cells. A) Graphical representation of doxorubicin‐loaded liposome (Doxo‐NP) formulation used for drug delivery. B) Median fluorescence intensity (MFI) of Doxo‐NP uptake in WT (red) and YAP ‐/‐ (blue) CAL51 as a function of nanoparticle concentration after 4‐hour incubation. Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 3; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. C) Nanoparticle intensity per cell after a 4‐hour incubation of WT and YAP ‐/‐ CAL51 cells with Doxo‐NP. Statistical analysis was performed using the unpaired <italic toggle=\"yes\">t</italic>‐test with Welch's correction. <italic toggle=\"yes\">n</italic> &gt; 120; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. D) Confocal images of WT (top) and YAP ‐/‐ (bottom) CAL51 cells after 4‐hour incubation with Doxo‐NP. Cells were stained with DAPI (blue). Nanoparticles are displayed in red. Magnified images are shown inside white dashed line boxes. Scale bar: 10 and 5 µm. E) Representative confocal images of WT (top) and YAP ‐/‐ (bottom) CAL51 cells at 24 h after 4‐hour incubation with Doxo‐NP. Cells were stained with DAPI (blue). Doxorubicin is displayed in red. Scale bar: 20 µm. F) Dot plot representation of doxorubicin intensity per cell at 24 h after a 4‐hour incubation of WT and YAP ‐/‐ cells with Doxo‐NP. Statistical analysis was performed using the unpaired <italic toggle=\"yes\">t</italic>‐test with Welch's correction. <italic toggle=\"yes\">n</italic> &gt; 100; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. G) A plot profile of doxorubicin intensity (red) co‐localized with the nucleus (blue, DAPI) of WT (top) and YAP ‐/‐ (bottom) CAL51 cells. On the right, confocal images show a detailed view of the region chosen for the intensity plots (white line) in WT (top) and YAP ‐/‐ (bottom) cells. Scale bar: 10 µm. H) Western blot showing the levels of cleaved PARP (cPARP) and histone H2AX (γ‐H2A.X) in WT (left) and YAP ‐/‐ (right) CAL51 cells untreated (CTRL) or treated with Doxo‐NP for 4 h and collected for the analysis 48 h post‐treatment. β‐tubulin was used for protein loading normalization. I) Representative confocal images of WT (top) and YAP ‐/‐ (bottom) CAL51cells after 4 h of incubation with Doxo‐NP and 24 and 48 h after treatment with the nanoparticles. Nuclei were stained with DAPI. Scale bar: 100 µm. J) Cell proliferation plot expressed as number of cells per surface area for WT (red line and circle) and YAP ‐/‐ (blue line and squares) CAL51cells at 0, 24, and 48 h after 4‐hour Doxo‐NP treatment. Statistical analysis was performed using the two‐way ANOVA followed by Sidak's multiple comparisons test. <italic toggle=\"yes\">n</italic> = 3; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001. K) Representative confocal images of untreated (CTRL, left) or CA3‐treated WT cells (1 µ<sc>m</sc> CA3, left) for 12 h. Cells were stained with YAP (AF555, red) and the nuclei were counterstained with DAPI (blue) and. The cell perimeter and cell nuclei are highlighted with a dashed white line and a dashed blue line respectively, in magnified images (bottom). Scale bar: 50 and 10 µm. L) Western blot showing the levels of YAP and phospho‐YAP (p‐YAP) in WT CAL51 untreated (CTRL) or treated with 0.5 and 1 µ<sc>m</sc> CA3 inhibitor for 12 h. β‐tubulin was used for protein loading normalization. M) MFI after a 4‐hour incubation of CAL51 WT cells with Doxo‐NP without treatment (red) or after treatment with 1 µ<sc>m</sc> CA3 inhibitor for 12 h (grey). Statistical analysis was performed using the unpaired t‐test with Welch's correction. <italic toggle=\"yes\">n</italic> = 5; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6692-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6692-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2302965-s002.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2302965-s001.xlsx\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
75
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 9; 11(2):2302965
oa_package/58/fc/PMC10787066.tar.gz
PMC10787067
38015024
[ "<title>Introduction</title>", "<p>PDAC is a highly aggressive and refractory disease with a poor 5‐year survival.<sup>[</sup>\n##REF##32113937##\n1\n##\n<sup>]</sup> According to the Global Cancer Statistics 2020, a total of 495773 new cases and 466003 deaths were reported, ranking PDAC the 14th in incidence and 7th in mortality (4.7% of all cancer‐caused deaths) globally.<sup>[</sup>\n##REF##33538338##\n2\n##\n<sup>]</sup> PDAC may arise from multiple triggers, including tobacco smoking, diabetes mellitus, obesity, dietary factors, alcohol abuse, ethnicity, family history, and genetic factors,<sup>[</sup>\n##REF##30905320##\n3\n##, ##REF##30834048##\n4\n##\n<sup>]</sup> but its pathogenic mechanisms remain incompletely understood.</p>", "<p>Covalent modifications on histone tails play fundamental roles in regulating chromatin structure and controlling transcriptional activity.<sup>[</sup>\n##REF##10638745##\n5\n##, ##REF##14970850##\n6\n##\n<sup>]</sup> Histone lysine methylation has been established as a central modification in the epigenetic regulation of eukaryotic genomes.<sup>[</sup>\n##REF##12067650##\n7\n##, ##REF##16919862##\n8\n##, ##REF##20442736##\n9\n##\n<sup>]</sup> During this modification, the lysine residues on histones H3 or H4, such as H3K4, H3K9, H3K27 and H4K20, are mono‐, di‐ or tri‐methylated.<sup>[</sup>\n##REF##16261189##\n10\n##\n<sup>]</sup> Emerging evidence has highlighted that histone lysine methylation is dynamically regulated by both histone lysine methyltransferases (KMTs) and demethylases (KDMs).<sup>[</sup>\n##REF##16630806##\n11\n##, ##REF##17410086##\n12\n##, ##REF##17218267##\n13\n##, ##REF##19234061##\n14\n##, ##REF##21141727##\n15\n##, ##REF##31582846##\n16\n##, ##REF##31287209##\n17\n##\n<sup>]</sup> Catalyzed by KMT2D and removed by LSD1,<sup>[</sup>\n##REF##28669924##\n18\n##, ##REF##28699367##\n19\n##\n<sup>]</sup> H3K4me1 serves as a powerful epigenetic component during transcriptional control. Genome‐wide ChIP‐seq analysis has uncovered that H3K4me1 predominantly deposits at a large set of distal enhancers or promoters, with a highly dynamic correlation with cell‐type‐specific gene expression profiles.<sup>[</sup>\n##REF##23473601##\n20\n##, ##REF##29273804##\n21\n##, ##REF##32432110##\n22\n##\n<sup>]</sup> H3K4me1 function as a binding site for epigenetic regulators or factors associated with gene transcription, including chromatin remodelers, histone acetyltransferases, and transcription factors.<sup>[</sup>\n##REF##29273804##\n21\n##, ##REF##24368734##\n23\n##, ##REF##24656132##\n24\n##\n<sup>]</sup> Yu et al. have found that H3K27me3‐H3K4me1 transition plays a key role in lineage differentiation by regulating the expression of tissue specific genes.<sup>[</sup>\n##REF##36991495##\n25\n##\n<sup>]</sup> Moreover, H3K4me1 and H3K27ac have been reported to initiate the activation of LINC00969, thereby inhibiting the transcription/post‐transcription of NLRP3, promoting the acquired gefitinib resistance, and suppressing the pyrodeath of lung cancer.<sup>[</sup>\n##REF##37156816##\n26\n##\n<sup>]</sup> Furthermore, Larsson et al. have uncovered that the H3K4me1 level falls to induce transcriptional dysregulation in multiple pathways, thus promoting colorectal cancer development.<sup>[</sup>\n##UREF##0##\n27\n##\n<sup>]</sup>\n</p>", "<p>EBF2, a transcription factor with basic helix‐loop‐helix (bHLH) domain, participates in the differentiation and function of brown and beige adipocytes.<sup>[</sup>\n##REF##23499423##\n28\n##, ##REF##25197048##\n29\n##\n<sup>]</sup> Stine et al. have reported that subcutaneous white adipose tissue or primary adipose cell cultures from EBF2 knockout mouse fail to trigger thermogenic programming in response to adrenergic stimulation.<sup>[</sup>\n##REF##26844207##\n30\n##\n<sup>]</sup> Conversely, EBF2 if its expression is restored in adipose tissues, can robustly stimulate beige adipocyte formation in the white adipose tissue of mice.<sup>[</sup>\n##REF##26844207##\n30\n##\n<sup>]</sup> Genome‐wide ChIP‐seq mapping and analysis have revealed that EBF2 preferentially moves to the enhancer regions of brown fat‐specific genes, thereby increasing RNA polymerase II and H3K27ac mark occupancies on brown fat‐selective cis elements.<sup>[</sup>\n##REF##28446594##\n31\n##\n<sup>]</sup> Having established that EBF2 regulates chromatin accessibility, Shapira et al. further uncovered that EBF2 cooperates with ATP‐dependent BAF (SWI/SNF) chromatin remodeling complexes to regulate chromatin structure.<sup>[</sup>\n##REF##28428261##\n32\n##\n<sup>]</sup> However, the roles of EBF2 and its associated molecules in PDAC pathogenesis remain unknown.</p>", "<p>In this study, we identified EBF2 as an H3K4me1‐binding protein. Through RNA‐seq and ChIP‐seq analyses, we teased out KLLN as a direct target of KMT2D and EBF2 in PDAC cells, and further verified that KMT2D and EBF2 cooperatively inhibited the proliferation, migration, and invasion of PDAC cells through upregulating KLLN. These findings reveal a novel pathologic mechanism underlying PDAC progression and provide potential therapeutic targets for PDAC treatment.</p>" ]
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[ "<title>Results</title>", "<title>EBF2 is Identified as the H3K4me1‐Binding Protein</title>", "<p>Unmodified histone 3 (H3), H3K4me1 peptides were incubated with nuclear extract of SW1990 cells, separated by SDS‐PAGE gel, and subjected to mass spectrometry. Factors specifically associating with H3K4me1 were screened by peptide pulldown coupled with mass spectrometry analysis. Mass spectrometry‐based proteomic analysis yielded a plethora of putative H3K4me1‐associated proteins, including many known histone or DNA modifiers, readers, and chromatin remodelers (Table ##SUPPL##0##S1##, Supporting Information). Given that KMT2D executes its antitumor function via catalyzing the formation of H3K4me1 in pancreatic cancer, we explored the genes associated with H3K4me1. Seven genes were identified in mass spectrometry and bioinformatic analysis, all significantly downregulated in pancreatic cancer (GEO data, GSE32676),<sup>[</sup>\n##REF##30337373##\n33\n##\n<sup>]</sup> including TSPYL2, TSR1, METAP2, CYR61, EBF2, CIRBP, and TGFBR3. Among them, EBF2, a transcription factor, had a helix‐loop‐helix structure (<bold>Figure</bold> ##FIG##0##\n1A##). Using biotin‐labeled peptides and protein extracts from SW1990 and PANC‐1 cells, the pull‐down assay confirmed the preferential binding of EBF2 to H3K4me1 over H3K4me3 in vitro (Figure ##FIG##0##1B##).</p>", "<p>The CDS region of EBF2 gene was inserted into pET‐28a plasmid to express recombinant His‐tagged EBF2 fusion protein (His‐EBF2) in <italic toggle=\"yes\">E. coli</italic> (Figure ##FIG##0##1C##). We observed that purified His‐EBF2 was pulled down by H3K4me1 peptide, but not by H3K4me3 (Figure ##FIG##0##1C##). The MST assay suggested that His‐EBF2 directly bound to H3K4me1 peptide with a dissociation constant (Kd) of 7.37 ± 0.377 µ<sc>m</sc> (Figure ##FIG##0##1D##). The ITC assay also showed a strong affinity of His‐EBF2 to H3K4me1 peptide (Figure ##FIG##0##1E##; Ka = 7.11 × 10<sup>5</sup> ± 1.48 × 10<sup>5</sup> mol<sup>−1</sup>), implying that EBF2 can specifically recognize H3K4me1. To gain insight into this recognition, we analyzed the crystal structure of human EBF2 in complex with a H3K4me1‐containing histone H3 tail peptide. Molecular docking showed that H3K4me1 nestled tightly in a pocket on the surface, which contained hydrophobic side chains of His239 (H239) of EBF2 (Figure ##SUPPL##0##S1A##, Supporting Information). Co‐IP on SW1990 cells showed that the ability of EBF2‐H239A to bind H3K4me1 was significantly weaker than that of EBF2‐WT (Figure ##SUPPL##0##S1B##, Supporting Information). This indicated that H239 is the site for H3K4me1 binding to EBF2 protein. We further examined the expression of EBF2 in PDAC and adjacent tissues. Immunofluorescence staining showed lower protein levels of EBF2 and H3K4me1 in PDAC tissues than in adjacent tissues (Figure ##FIG##0##1F##). Both EBF2 and H3K4me1 marks were co‐localized in the nuclei of PDAC or adjacent cells. Western blot analysis confirmed the reduction of EBF2 expression in PDAC tissues (Figure ##FIG##0##1G##), both in the nucleus and cytoplasm (Figure ##SUPPL##0##S1C##, Supporting Information). These data demonstrated EBF2 as an H3K4me1‐associated protein, and the low expression of EBF2 in PDAC tissues supported that EBF2 may play a critical role in PDAC progression.</p>", "<title>EBF2 Inhibits the Proliferation and Metastasis of PDAC Cells</title>", "<p>To evaluate the expression of EBF2 in PDAC tissues, a tissue microarray (TMA) was constructed, which comprised 90 pairs of PDAC and corresponding adjacent normal tissue samples. The TMA was subjected to IHC staining, showing that EBF2 was mainly located in the nuclei of both normal and PDAC tumor cells (<bold>Figure</bold> ##FIG##1##\n2A##). H scores revealed that the protein level of EBF2 was significantly downregulated in PDAC tissues as compared to that in the normal tissues (Figure ##FIG##1##2B##). The expression level of EBF2 was negatively correlated with tumor stage, lymph node metastasis, and distal metastasis in PDAC patients (Figure ##FIG##1##2C–E##). Kaplan–Meier survival curves showed that a lower EBF2 expression was significantly associated with a worse survival (Figure ##FIG##1##2F##).</p>", "<p>To evaluate the effect of EBF2 on the biological behavior of PDAC cells, SW1990 and PANC‐1 cell lines stably expressing EBF2 shRNA were obtained by puromycin screening. EBF2 depletion in SW1990 and PANC‐1 cells were confirmed by qPCR and Western blot (Figure ##FIG##1##2G,H##; Figure ##SUPPL##0##S1D,E##, Supporting Information). CCK‐8, EdU incorporation, colony‐formation, and Transwell assays were applied to assess the effects of EBF2 on cell proliferation, migration, and invasion of PDAC cells in vitro. EBF2‐depleted SW1990 and PANC‐1 cells exhibited more pronounced proliferation, migration, and invasion than control cells (Figure ##FIG##1##2I–L##; Figure ##SUPPL##0##S1F–I##, Supporting Information). Furthermore, silencing EBF2 significantly facilitated the growth of SW1990‐luc xenografts in vivo (Figure ##FIG##1##2M–O##). To examine the metastatic behavior of SW1990 cells in vivo, EBF2‐depleted SW1990‐luc cells were injected into the tail veins of BALB/c mice. Through live‐imaging observations, we found that EBF2 deficiency promoted the formation of metastatic foci in the lungs of mice (Figure ##FIG##1##2P,Q##). H&amp;E staining showed that both liver and lung metastases increased in mice injected with EBF2‐depleted SW1990‐luc cells (Figure ##SUPPL##0##S1J,K##, Supporting Information). These data were consistent with the association of EBF2 downregulation with PDAC progression.</p>", "<title>KMT2D Expression is Positively Correlated with EBF2 Expression in PDAC Tissues and KMT2D Depletion Induces the Phenotype of EBF2 Knockout</title>", "<p>KMT2D, also known as ALR/MLL4, catalyzes the formation of H3K4me1 on promoters or enhancers to regulate cell‐type‐specific gene expression and cell fate transition.<sup>[</sup>\n##REF##28669924##\n18\n##, ##REF##32432110##\n22\n##, ##REF##24656132##\n24\n##\n<sup>]</sup> However, the clinical significance and biological roles of KMT2D in PDAC remain to be clarified. Through IHC staining, we found that KMT2D was significantly downregulated in PDAC tissues (<bold>Figure</bold> ##FIG##2##\n3A,B##), and negatively correlated with tumor stage, lymph node metastasis, and distal metastasis in PDAC patients (Figure ##FIG##2##3C–E##). Kaplan–Meier survival curves show that KMT2D downregulation predicted a poor survival (Figure ##FIG##2##3F##). Subsequent Spearman correlation analysis demonstrated that KMT2D expression was positively correlated with EBF2 expression in PDAC tissues (n = 90, r = 0.5002, <italic toggle=\"yes\">p</italic> &lt; 0.0001) (Figure ##FIG##2##3G##).</p>", "<p>We established SW1990 and PANC‐1 cell lines with stable KMT2D knockdown to evaluate the role of KMT2D in PDAC (Figure ##FIG##2##3H,I##; Figure ##SUPPL##0##S2A,B##, Supporting Information). CCK‐8, EdU incorporation, colony‐formation, and Transwell assays uncovered that knockdown of KMT2D significantly enhanced the proliferation, migration, and invasion of SW1990‐luc and PANC‐1 cells (Figure ##FIG##2##3J–M##; Figure ##SUPPL##0##S2C–F##, Supporting Information), which mimics the phenotype caused by EBF2 depletion. In vivo results demonstrated that knockdown of KMT2D significantly promoted the growth of SW1990‐luc xenografts (Figure ##FIG##2##3N–P##), as well as the formation of metastatic foci in mouse lungs (Figure ##FIG##2##3Q,R##; Figure ##SUPPL##0##S2G,H##, Supporting Information). These results revealed that KMT2D could attenuate PDAC growth and metastasis.</p>", "<title>KLLN is a Common Transcriptional Target of KMT2D and EBF2 in PDAC Cells</title>", "<p>Next, we sought to elucidate the roles of KMT2D‐ and EBF2‐regulated H3K4me1 through profiling the gene transcription in PDAC cells with H3K4me1 activation by GSK‐LSD1 or EBF2 overexpression (EBF2‐OE). GSK‐LSD1, as a selective inhibitor of KDM1A/LSD1, can increase H3K4me1 level via blocking the histone H3K4 demethylase activity of KDM1A/LSD1.<sup>[</sup>\n##REF##29395062##\n34\n##, ##REF##29997151##\n35\n##, ##REF##30514804##\n36\n##, ##REF##35198054##\n37\n##\n<sup>]</sup> RNA‐seq revealed that the upregulation of EBF2 or H3K4me1 causes transcriptional alterations in SW1990 cells. These differentially expressed genes (DEGs) were overlapped genes between EBF2‐OE and GSK‐LSD1‐treated SW1990 cells. A total of 17 upregulated genes were screened by RNA‐seq (<bold>Figure</bold> ##FIG##3##\n4A##). Among them, we selected KLLN for further investigation, for that it has been identified as a p53‐dependent tumor suppressor or an inducer of S and G2 phase checkpoint control.<sup>[</sup>\n##REF##18385383##\n38\n##, ##REF##23446638##\n39\n##\n<sup>]</sup> Gene Set Enrichment Analysis (GSEA) revealed that these DEGs were enriched for genes regulated by p53 (Figure ##FIG##3##4B##). The qPCR and Western blot assays validated the significant upregulation of KLLN mRNA and protein levels in EBF2‐OE and GSK‐LSD1‐treated SW1990 cells (Figure ##FIG##3##4C–F##). Moreover, qPCR and Western blot assays verified that the mRNA and protein levels of KLLN significantly downregulated in KMT2D‐ or EBF2‐depleted SW1990 and PANC‐1 cells (Figure ##SUPPL##0##S3A–D##, Supporting Information). ChIP‐qPCR assay was further performed to examine the binding of KMT2D, H3K4me1, and EBF2 at the promoter of KLLN gene in SW1990 cells. A series of oligonucleotide primers were designed for sequencing the proximal promoter region of the KLLN gene (−1831 to TSS). ChIP‐qPCR results revealed significant KMT2D, H3K4me1, and EBF2 signals in the promoter region of KLLN gene, especially the −500 bp upstream region (Figure ##SUPPL##0##S3E##, Supporting Information). EBF2 knockdown (EBF2‐KD) markedly blocked the binding of EBF2, but not H3K4me1 in SW1990 cells (Figure ##SUPPL##0##S3F##, Supporting Information). Interestingly, KMT2D knockdown (KMT2D‐KD) also significantly inhibited the bindings of KMT2D, H3K4me1, and EBF2 in SW1990 cells (Figure ##SUPPL##0##S3G##, Supporting Information).</p>", "<p>To further explore the genome‐wide occupancy of KMT2D‐dependent H3K4me1 and EBF2, we performed ChIP‐seq and CUT&amp;Tag analyses using SW1990 cells. ChIP‐seq revealed a prominent reduction in KMT2D, H3K4me1, and EBF2 signals at the transcription start site (TSS) and promoter regions of genes in KMT2D‐depleted (KMT2D‐KD) cells (Figure ##SUPPL##0##S3H–J##, Supporting Information). These results were validated by the CUT&amp;Tag data (Figure ##SUPPL##0##S3K–M##, Supporting Information). IHC staining exhibited that KLLN was also significantly downregulated in PDAC tissues (Figure ##FIG##3##4G,H##), and its expression was negatively correlated with tumor stage, lymph node metastasis, and distal metastasis in PDAC patients (Figure ##FIG##3##4I–K##). Kaplan–Meier survival curves showed that patients with a low expression of KLLN exhibited a poor survival (Figure ##FIG##3##4L##). Spearman correlation analysis (Figure ##FIG##3##4M,N##) showed that KLLN expression was positively correlated with KMT2D (n = 90, r = 0.6838, <italic toggle=\"yes\">p</italic> &lt; 0.0001) or EBF2 expression in PDAC tissues (n = 90, r = 0.7541, <italic toggle=\"yes\">p</italic> &lt; 0.0001). Western blot analysis and IHC staining further verified that KLLN downregulation in KMT2D‐ or EBF2‐depleted xenograft tissues was accompanied by increased Ki67 expression (Figure ##FIG##3##4O,P##). These data indicated that KLLN was regulated by both KMT2D and EBF2.</p>", "<title>GSK‐LSD1 Inhibits the Proliferation, Migration and Invasion of PDAC Cells</title>", "<p>To evaluate the performance of KMT2D‐mediated H3K4me1 in the proliferation, migration, and invasion of PDAC cells, we constructed KMT2D‐C, KMT2D<sub>fusion</sub>, and methyltransferase activity‐deficient mutant KMT2D<sub>fusion</sub> C1523A (mKMT2D<sub>fusion</sub>) plasmids, as previously reported (<bold>Figure</bold> ##FIG##4##\n5A##).<sup>[</sup>\n##REF##23249737##\n40\n##\n<sup>]</sup> We then transfected these plasmids into SW1990 and PANC‐1 cells, finding that KMT2D<sub>fusion</sub> overexpression activated the expression of H3K4me1 and KLLN, while mKMT2D<sub>fusion</sub> did not (Figure ##FIG##4##5B##; Figure ##SUPPL##0##S4A##, Supporting Information). Colony formation and Transwell assays showed that KMT2D<sub>fusion</sub> significantly impeded the proliferation, migration, and invasion of SW1990 and PANC‐1 cells in vitro (Figure ##FIG##4##5C,D##; Figure ##SUPPL##0##S4B,C##, Supporting Information).</p>", "<p>Western blot analysis showed that GSK‐LSD1 increased the levels of H3K4me1 and KLLN in a concentration‐dependent manner (Figure ##FIG##4##5E##; Figure ##SUPPL##0##S4D##, Supporting Information), and significantly inhibited the proliferation, migration, and invasion of SW1990 and PANC‐1 cells (Figure ##FIG##4##5F–H##; Figure ##SUPPL##0##S4E–G##, Supporting Information). Consistently, in vivo experiments showed that GSK‐LSD1‐treated mice presented significantly smaller sizes of SW1990‐luc xenografts compared to control mice (Figure ##FIG##4##5I–K##). The upregulation of H3K4me1 and KLLN in these metastatic foci was verified by Western blot and IHC analyses (Figure ##FIG##4##5L,M##). Subsequently, a patient‐derived xenograft (PDX) model of PDAC was successfully established, and the tumor growth was monitored under different treatments. Compared with control mice, GSK‐LSD1‐treated mice developed remarkably smaller tumors in which the expression of H3K4me1 was significantly upregulated. Notably, GSK‐LSD1 therapy exhibited more favorable effects than Gemcitabine, which was a commonly used medication for PDAC patients (Figure ##FIG##4##5N,O##). To prove the linkage between EBF2 and H3K4me1, we performed Co‐IP in SW1990 cells. As shown in Figure ##FIG##4##5P##, GSK‐LSD1 treatment increased H3K4me1 level without affect EBF2 expression, and co‐immunoprecipitated more EBF2, which may be due to the upregulation of H3K4me1. To explore whether GSK‐LSD1 fulfills its tumor‐suppressing role by upregulating KLLN, rescue experiments were performed. As shown in Figure ##FIG##4##5Q–S## and Figure ##SUPPL##0##S4H–J## (Supporting Information), knockdown of KLLN markedly attenuated the tumor‐suppressive phenotype of GSK‐LSD1 in SW1990 and PANC‐1 cells.</p>", "<title>KMT2D and EBF2 Cooperate to Activate the Expression of KLLN</title>", "<p>To gain insight into the molecular mechanisms by which KMT2D and EBF2 regulate KLLN, we manipulated the expression of KMT2D or EBF2 in SW1990 and PANC‐1 cells, and determined the expression of KLLN by Western blot. Interestingly, the cells co‐expressing KMT2D<sub>fusion</sub> and EBF2 exhibited a greater KLLN activity than those transfected with KMT2D<sub>fusion</sub> or EBF2 alone, suggesting KMT2D and EBF2 might cooperate to activate the expression of KLLN in SW1990 (<bold>Figure</bold> ##FIG##5##\n6A,B##) and PANC‐1 cells (Figure ##SUPPL##0##S5A,B##, Supporting Information). When EBF2 was knocked down (EBF2‐KD), KMT2D<sub>fusion</sub> imposed a weaker effect on the expression of KLLN in SW1990 (Figure ##FIG##5##6C,D##) and PANC‐1 cells (Figure ##SUPPL##0##S5C,D##, Supporting Information), indicating that EBF2 mediated this cooperative effect.</p>", "<p>To determine the effect of KMT2D and EBF2 on cell phenotype, we manipulated the expression of KMT2D or EBF2 in SW1990 and PANC‐1 cells and assessed their proliferation, migration, and invasion in vitro. Compared with KMT2D‐C or mKMT2D<sub>fusion</sub> control, KMT2D<sub>fusion</sub> overexpression significantly inhibited the proliferation, migration, and invasion of SW1990 and PANC‐1 cells. Moreover, the cells co‐expressing KMT2D<sub>fusion</sub> and EBF2 exhibited a greater inhibitory effect on the proliferation, migration, and invasion of SW1990 and PANC‐1 cells than those transfected with KMT2D<sub>fusion</sub> or EBF2 alone (Figure ##FIG##5##6E–G##; Figure ##SUPPL##0##S5E–G##, Supporting Information).</p>", "<p>Rescue experiments were also performed to testify whether the tumor suppressive effect of KMT2D and EBF2 is mediated by KLLN. As shown in Figure ##FIG##5##6H–K## and Figure ##SUPPL##0##S5H–K## (Supporting Information), knockdown of KMT2D or EBF2 enhanced the proliferation, migration, and invasion of SW1990 and PANC‐1 cells. Interestingly, rescuing KLLN expression significantly reversed the phenotypic changes of SW1990 and PANC‐1 cells induced by KMT2D or EBF2 knockdown. Taken together, KMT2D and EBF2 might inhibit the proliferation, migration, and invasion of PDAC cells through targeting KLLN. Colony formation and Transwell assays indicated that EBF2 overexpression significantly abolished the promotive effects of KMT2D on the proliferation, migration, and invasion of SW1990 cells, but knockdown of KMT2D plus EBF2, compared to KMT2D or EBF2 knockdown alone, enhanced those processes of SW1990 cells (Figure ##SUPPL##0##S6A–D##, Supporting Information). Taken together, KMT2D and EBF2 inhibited the proliferation, migration, and invasion of PDAC cells through targeting KLLN.</p>" ]
[ "<title>Discussion</title>", "<p>In the present study, we reveal that H3K4me1 is recognized by EBF2, a transcription factor with a helix‐loop‐helix structure. Our results demonstrate that, through interacting with KMT2D‐dependent H3K4me1 and epigenetically upregulating KLLN (also known as killin), EBF2 inhibits PDAC cell proliferation, migration, and invasion.</p>", "<p>H3K4me1 is an evolutionarily conserved histone modification, catalyzed by the COMPASS‐like methyltransferase family, including KMT2C and KMT2D.<sup>[</sup>\n##REF##32432110##\n22\n##, ##REF##24368734##\n23\n##, ##REF##24656132##\n24\n##\n<sup>]</sup> H3K4me1 demarcates the boundaries of active enhancers or promoters, thus limiting the recruitment of effectors or modulators.<sup>[</sup>\n##REF##28483418##\n41\n##\n<sup>]</sup> Therefore, factors that can specifically recognize H3K4me1 would facilitate histone modification in epigenetic regulation. Previous studies in <italic toggle=\"yes\">Arabidopsis</italic> have reported that the CW domain of histone methyltransferase SDG8, a zinc‐binding domain with conserved cysteines and tryptophans, was responsible for binding H3K4me1.<sup>[</sup>\n##REF##14607086##\n42\n##, ##REF##29496997##\n43\n##\n<sup>]</sup> However, a crystal structure analysis has revealed that the hydrophobic, narrow pocket of the CW domain of SDG8 bring about steric hindrance that prohibits the binding of highly methylated lysine.<sup>[</sup>\n##REF##29496997##\n43\n##\n<sup>]</sup> In line with this, the CW domains in mammalian MORC1, MORC2, and LSD2 proteins are unable to recognize any methylated H3K4 peptides, whereas those of mammalian ZCWPW1, ZCWPW2, MORC3, and MORC4 can bind to unmethylated or tri‐methylated H3K4.<sup>[</sup>\n##REF##20826339##\n44\n##, ##REF##26933034##\n45\n##, ##REF##28818372##\n46\n##\n<sup>]</sup> Local et al. have revealed that the PHD2 domain of Double PHD fingers 3 (DPF3) enables the preferential recognition of H3K4me1 over H3K4me3, thereby facilitating the recruitment of BRG1‐associated factor (BAF) chromatin remodeling complex to enhancers in mammalian cells.<sup>[</sup>\n##REF##29255264##\n47\n##\n<sup>]</sup> Through mass spectrometry‐based proteomic analysis and in vitro peptide/protein interaction assays, we here identified that transcription factor EBF2 can pinpoint H3K4me1, and distinguish it from H3K4me3. A previous study has shown that EBF2 physically acts on the chromatin remodeler Brahma‐Related Gene 1 (BRG1) and the BAF chromatin remodeling complex in brown adipocytes.<sup>[</sup>\n##REF##28428261##\n32\n##\n<sup>]</sup> However, ChIP analysis revealed that EBF2 binding to brown fat genes, such as UCP1, was not interrupted by DPF3 or BRG1 deficiency, suggesting that EBF2 binding precedes BAF‐mediated chromatin remodeling. Notably, structural and functional analyses uncovered that EBF1, another member of the EBF family, could recognize nucleosome‐enriched DNA to increase chromatin accessibility through its C‐terminal domain.<sup>[</sup>\n##REF##24097267##\n48\n##, ##REF##26982363##\n49\n##\n<sup>]</sup> Taken together, EBF proteins can directly contact with chromatin in gene regulation. Although the DNA‐binding domain of EBF2 shares 92% of its amino acid sequences with EBF1,<sup>[</sup>\n##REF##11578857##\n50\n##, ##REF##20876732##\n51\n##\n<sup>]</sup> future studies are required to explore whether EBF2 directly binds to nucleosomal DNA or histone modifications, particularly H3K4me1.</p>", "<p>KMT2D, also known as ALR/MLL4, catalyzes the formation of H3K4me1 on promoters or enhancers of cell‐type‐specific genes to regulate gene expression and cell fate transition.<sup>[</sup>\n##REF##28669924##\n18\n##, ##REF##23249737##\n40\n##, ##REF##28483418##\n41\n##\n<sup>]</sup> Multiple studies have dug into the roles of KMT2D in the initiation and progression of various cancers. For example, loss of KMT2D in the early stage can collaborate with the upregulation of Bcl‐2 oncogene to facilitate lymphoma development.<sup>[</sup>\n##REF##26366710##\n52\n##, ##REF##26366712##\n53\n##\n<sup>]</sup> Lung‐specific KMT2D loss significantly promotes lung tumorigenesis and pro‐tumorigenic programming in mice, including glycolysis, supporting its role as a tumor suppressor.<sup>[</sup>\n##REF##32243837##\n54\n##\n<sup>]</sup> In line with these studies, the function analysis in the present study uncovered that knockdown of KMT2D dramatically boosted the proliferation, migration, and invasion of PDAC cells. However, recent studies have also suggested that KMT2D greatly enhanced the proliferation, invasion, and tumor formation of gastric cancer or prostate cancer cells,<sup>[</sup>\n##REF##33853662##\n55\n##, ##REF##25516281##\n56\n##\n<sup>]</sup> implying that KMT2D acts on the tumor in either a promotive or a suppressive manner. Given that KMT2D catalyzes the formation of H3K4me1 on cell‐type‐specific gene enhancers or promoters, we hypothesized that its function is largely dependent on the H3K4me1‐binding factors. This hypothesis was supported by our function analysis that knockdown of KMT2D copied the phenotype caused by EBF2 in vitro and in vivo.</p>", "<p>KLLN is located in 10q23.31 and originally identified as a target of p53 involved in the S‐phase regulation.<sup>[</sup>\n##REF##18385383##\n38\n##\n<sup>]</sup> Bennett et al. have shown that the KLLN promoter is hypermethylated in patients with Cowden syndrome without germline mutations in PTEN.<sup>[</sup>\n##REF##20979621##\n57\n##\n<sup>]</sup> As the first predisposition gene for such syndrome, KLLN confers a high risk of breast, thyroid, and other cancers.<sup>[</sup>\n##REF##20979621##\n57\n##\n<sup>]</sup> KLLN downregulation is significantly associated with high Gleason scores, indicating KLLN as a diagnostic or prognostic biomarker for advanced prostate carcinomas.<sup>[</sup>\n##UREF##1##\n58\n##\n<sup>]</sup> In breast cancer cells, Sankunny et al. have demonstrated that KLLN mediated DNA damage‐induced apoptosis through the pathway of p53 phosphorylation and acetylation.<sup>[</sup>\n##REF##19451168##\n59\n##\n<sup>]</sup> Wang et al. have reported that transcription factor KLLN induces cell cycle arrest and apoptosis in breast cancer cells by directly promoting the transcription of TP53 and TP73.<sup>[</sup>\n##REF##31036827##\n60\n##\n<sup>]</sup> KLLN may act as a tumor suppressor and regulates cell cycle and apoptosis in diverse cancers. In the present study, we found that KLLN was downregulated in PDAC tissues, and rescuing its expression largely reversed the phenotype changes caused by EBF2 or KMT2D knockdown. These findings suggest that KLLN serves as a critical effector downstream KMT2D and EBF2 in the regulation of PDAC progression. Nevertheless, we could not rule out the possibility that KMT2D and EBF2 may target other genes to regulate PDAC progression. There are still limitations in this study. In particular, the enrichment of EBF2 and H3K4me1 in the KLLN promoter region was not very significant in the ChIP‐seq and CUT&amp;Tag data. This may due to the low expression of KMT2D, EBF2, and H3K4me1 in PDAC cells or the decrease of measurement sensitivity caused by random errors or interference. These factors can thereby culminate an unstable targeting outcome for individual gene. For defining the regulation of KMT2D, EBF2, and H3K4me1 in PDAC, the future studies are required to validate and characterize the enrichment of EBF2 and H3K4me1 in the KLLN promoter region by using other highly sensitive novel technologies.</p>", "<p>In conclusion, we screened out EBF2 as a novel H3K4me1‐binding protein. EBF2 and KMT2D work together to regulate H3K4me1, posing strong activation on KLLN and inhibition on PDAC progression (<bold>Figure</bold> ##FIG##6##\n7\n##). The interplay between H3K4me1 histone modification and KLLN transcription could be exploited to design novel therapeutic strategies for PDAC.</p>", "<title>Abbreviations</title>", "<p>KMT2D: Histone‐lysine N‐methyltransferase 2D; H3K4me1: Monomethylation of histone H3 at Lysine 4; EBF2: Early B‐cell factor 2;KLLN: Killin, p53 regulated DNA replication inhibitor; PDAC: Pancreatic cancer; TSS: transcription start site; LSD1: lysine‐specific demethylase 1; KMTs: histone lysine methyltransferases; KDMs: histone lysine demethylases; shRNA: Short hairpin RNA; siRNA: Small interfering RNA; H&amp;E: Hematoxylin and eosin; SDS‐page; sodium dodecyl sulfate‐polyacrylamide gel electrophoresis; IPTG: isopropyl‐β‐D‐thiogalactoside; MST: Microscale thermophoresis; ITC: Isothermal titration calorimetry; RNA‐seq: qPCR: Quantitative real‐time PCR; RNA sequencing; CCK‐8: Cell Counting Kit‐8; EdU: 5‐Ethynyl‐2′‐deoxyuridine; ChIP: Chromatin immunoprecipitation; ChIP‐seq: Chromatin immunoprecipitation sequencing; Cleavage Under Targets and Tagmentation (CUT&amp;Tag); IHC immunohistochemical; PDX: Patient‐derived xenograft; DEGs: Differentially expressed genes; GSEA: Gene Set Enrichment Analysis; Brg1: Brahma‐related gene 1; BAF: BRG1‐associated factor; DPF3: Double PHD fingers 3.</p>" ]
[]
[ "<title>Abstract</title>", "<p>Mono‐methylation of histone H3 on Lys 4 (H3K4me1), which is catalyzed by histone‐lysine N‐methyltransferase 2D (KMT2D), serves as an important epigenetic regulator in transcriptional control. In this study, the authors identify early B‐cell factor 2 (EBF2) as a binding protein of H3K4me1. Combining analyses of RNA‐seq and ChIP‐seq data, the authors further identify killin (KLLN) as a transcriptional target of KMT2D and EBF2 in pancreatic ductal adenocarcinoma (PDAC) cells. KMT2D‐dependent H3K4me1 and EBF2 are predominantly over‐lapped proximal to the transcription start site (TSS) of KLLN gene. Comprehensive functional assays show that KMT2D and EBF2 cooperatively inhibit PDAC cells proliferation, migration, and invasion through upregulating KLLN. Such inhibition on PDAC progression is also achieved through increasing H3K4me1 level by GSK‐LSD1, a selective inhibitor of lysine‐specific demethylase 1 (LSD1). Taken together, these findings reveal a new mechanism underlying PDAC progression and provide potential therapeutic targets for PDAC treatment.</p>", "<p>EBF2 is a novel H3K4me1‐binding protein. EBF2 and KMT2D cooperatively regulate H3K4me1, leading to epigenetically activation of KLLN expression and strongly inhibition of PDAC progression. Such inhibition on PDAC progression is also achieved through increasing H3K4me1 level by GSK‐LSD1, a selective inhibitor of LSD1. These findings reveal a novel pathologic mechanism underlying PDAC progression and provide potential therapeutic targets for PDAC treatment.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6859-cit-0067\">\n<string-name>\n<given-names>B.</given-names>\n<surname>Yao</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Xing</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Meng</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Zhou</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Qu</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Jin</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Yuan</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Zen</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Ma</surname>\n</string-name>, <article-title>EBF2 Links KMT2D‐Mediated H3K4me1 to Suppress Pancreatic Cancer Progression via Upregulating KLLN</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2302037</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202302037</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Cell Culture</title>", "<p>Human pancreatic cancer cell lines SW1990 and PANC‐1 were purchased from the American Type Culture Collection (ATCC, USA), and cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco, USA) or Roswell Park Memorial Institute 1640 medium (RPMI‐1640; Gibco) supplemented with 10% fetal calf serum (FCS; Wisent, Canada) and penicillin‐streptomycin solution (100 µg mL<sup>−1</sup>; Beyotime, China) in a humidified chamber with 5% CO<sub>2</sub> at 37 °C.</p>", "<title>Cell Transfection and siRNA Interference Assays</title>", "<p>SiRNAs against KMT2D and EBF2 were synthesized by GenePharma (Shanghai, China). SW1990 and PANC‐1 cells were transfected with oligonucleotides or indicated plasmids using Lipofectamine 2000 (Invitrogen, USA) according to the manufacturer's instructions. The sequences of siRNAs included KMT2D siRNA‐1: 5′‐GAGUCGAACUUUACUGUCUCC‐3′; KMT2D siRNA‐2: 5′‐CCACUCUCAUCAAAUCCGACA‐3′. EBF2 siRNA‐1: 5′‐GAGGUGACAUUAUCUUAUA‐3′; EBF2 siRNA‐2: 5′‐GCACUCACUACAAGUUACA‐3′.</p>", "<title>Mass Spectrometry</title>", "<p>C‐terminal biotin‐tagged 19 amino acid N‐terminal peptides of H3, H3K4me1, and H3K4me3 were incubated with nuclear extract of SW1990 cells, and then with high‐capacity streptavidin agarose (Thermo Scientific, USA) for immunoprecipitation. The product was separated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) with silver staining. Protein bands of interest were excised and subjected to electrospray‐ion trap tandem mass spectrometry (LCQ‐Deca, Finnigan).</p>", "<title>Plasmid Construction, Recombinant Protein Expression and Purification</title>", "<p>His‐EBF2 plasmid was constructed by inserting the CDS of EBF2 into PET‐28a vector, transformed into <italic toggle=\"yes\">E. coli</italic> BL21 (DE3), and cultured with isopropyl‐β‐D‐thiogalactoside (IPTG; Beyotime) at 16 °C for 12 h, until the optical density (OD600) reached 0.5–0.6. BL21 cells were collected and sonicated in cold PBS buffer, and His‐fusion proteins were purified with High Affinity Nickel beads (Genscript, Nanjing, China). The purity of His‐fusion proteins was evaluated by SDS‐PAGE.</p>", "<title>Microscale Thermophoresis (MST) Assay</title>", "<p>Purified recombinant EBF2 proteins were labeled with Monolith NT‐647‐NHS. Labeled proteins were used at a concentration of 100 n<sc>m</sc> in PBS containing 0.05% Tween‐20 (pH 7.4). All the concentrations of H3, H3K4me1, and H3K4me3 peptides ranged from 10 n<sc>m</sc> to 500 µ<sc>m</sc>. The combined solution of labeled proteins and peptides was incubated for 5 min and transferred into silicon‐treated capillaries. Thermophoresis was measured for 30 s on a NanoTemper Monolith NT.115 (NanoTemper Technologies GMBH, Germany) using LED power of 60% and 20%. Dissociation constants were calculated by NanoTemper Analysis 1.5.41 software using the mass action equation (Kd formula).</p>", "<title>Isothermal Titration Calorimetry (ITC) Assay</title>", "<p>A MicroCal ITC‐200 system (Malvern Instruments Ltd., UK) was used for ITC assay. Briefly, the synthesized peptides (Genscript) and proteins were all subjected to extensive dialysis against PBS. Peptides at a concentration of 1 m<sc>m</sc> were loaded into the ITC syringe, and proteins at a concentration of 100 µ<sc>m</sc> into the ITC cell. Then, every 2 µL of peptide was automatically injected into the cell at 25 °C. The results of binding isotherms were analyzed using the Origin 7.0 software package (Origin Lab).</p>", "<title>Immunofluorescence (IF) and Confocal Microscopy</title>", "<p>IF was performed on 5 µ<sc>m</sc> sections of tissue specimens following the manufacturer's protocol. PDAC and adjacent tissues were fixed with 4% formaldehyde for 24 h at room temperature. Having been washed three times with PBS containing 0.1% Triton X‐100, incubated with primary antibodies (H3K4me1 and EBF2) for 1 h at room temperature, washed again, incubated with secondary antibodies for 1 h at room temperature, stained with DAPI (Sigma, USA), and visualized by confocal scanning microscopy (Olympus FV10i, Japan).</p>", "<title>Protein Extraction and Western Blot Analysis</title>", "<p>SW1990 and PANC‐1 cells were isolated using lysate buffer containing protease inhibitors. Samples containing equal amounts of protein were separated by SDS‐PAGE. After electrophoresis, the proteins were transferred to a PVDF membrane (Millipore, Billerica, MA, USA) and blocked with 5% skim milk for 2 h at room temperature. An overnight incubation of membranes was made at 4 °C with primary antibodies against KMT2D (1:1000; Affinity, China), EBF2 (1:1000; Affinity), and KLLN (1:1000; Abcam, USA). After washing with 1× TBST for three times, a 2 h incubation of membranes was implemented with horseradish peroxidase (HRP)‐gemeled Affinipure Goat Anti‐Rabbit IgG (H + L) (1:10000; ProteinTech, China) or Peroxidase‐gemeled Affinipure Goat Anti‐Mouse IgG (H+L) (1:10000; ProteinTech) at room temperature. Proteins were visualized by chemiluminescence using an ECL kit (Thermo Fisher).</p>", "<title>Co‐Immunoprecipitation Assay (Co‐IP)</title>", "<p>Co‐immunoprecipitation assay was performed as described previously.<sup>[</sup>\n##REF##29269867##\n61\n##\n<sup>]</sup> Briefly, SW1990 cells were transfected with indicated constructs or treated with GSK‐LSD1, washed with cold phosphate buffered saline (PBS), and lysed with cold cell lysis buffer. Then, the lysates were incubated with appropriate specific antibodies or normal rabbit IgG at 4 °C overnight in constant rotation, followed by the addition of protein A/G Sepharose beads and incubation for 2 h at 4 °C. The beads were then washed five times by the lysis buffer. Bead‐bound proteins were resolved by SDS‐PAGE and detected by immunoblotting using indicated antibodies.</p>", "<title>RNA Isolation and Quantitative Real‐Time PCR (qPCR)</title>", "<p>Total RNA was extracted from cultured cells using RNAiso plus (Takara, Japan). cDNA was synthesized from every 1 µg of total RNA in reverse transcription reactions with Hifair III 1st Strand cDNA Synthesis SuperMix for qPCR (Cat No. 11 141; Yeasen, Shanghai, China). qPCR was performed with Hieff qPCR SYBR Green Master Mix (Yeasen) using a Roche LightCycler 96 Real‐Time PCR System. Cycling conditions were set at 94 °C for 15 s, 60 °C for 1 min, and 72 °C for 30 s. Each reaction was performed in triplicate. The primer sequences were as follows: KMT2D‐F: 5′‐GCTGGCTGGTGAGGATAAAG‐3′; KMT2D‐R: 5′‐CAGTTACAGAGAGCACAACGC‐3′; EBF2‐F: 5′‐CATGTCATCAAGTCCCACCG‐3′; EBF2‐R: 5′‐TTACATCGGGGGTACAACAAG‐3′; KLLN‐F: 5′‐GTTGAGTGGAAAGTACGGAACG‐3’; KLLN‐R: 5′‐TGTGGGTGCTTGTGTAACCAG‐3′. β‐actin‐F: 5′‐CCTAGAAGCATTTGCGGTGG‐3′; β‐actin‐R: 5′‐GAGCTACGAGCTGCCTGACG‐3′.</p>", "<title>RNA Sequencing (RNA‐Seq) Assay</title>", "<p>Total RNA was isolated from cells using RNAiso plus (Takara). The quantity and integrity of RNA were separately evaluated using the K5500 (Beijing Kaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA). Briefly, the mRNA was enriched by OligodT NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA), and then fragmented into ≈200 bp. Subsequently, the RNA fragments were subjected to first and second strand cDNA synthesis, followed by adaptor ligation and enrichment according to instructions of NEBNext Ultra RNA Library Prep Kit for Illumina. The purified library products were evaluated by the Agilent 2200 TapeStation and Qubit (Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired‐end 150 bp (Ribobio, China). The clean reads were acquired after discarding low‐quality reads or those containing adapter and ploy‐N. HISAT2 was employed to calibrate clean reads to human reference genome hg38 with default parameters. HTSeq was used to convert aligned short reads into read counts for each gene model. Differential gene expression was assessed by DESeq2 using read counts as input.<sup>[</sup>\n##REF##33793001##\n62\n##\n<sup>]</sup> The Benjamini–Hochberg multiple test correction method was employed. Genes with significant upregulation under indicated conditions (fold change &gt; 1.5, <italic toggle=\"yes\">p</italic> &lt; 0.05) were visualized using heat maps.<sup>[</sup>\n##UREF##1##\n63\n##\n<sup>]</sup> RNA‐seq data sets were available (GEO accession number GSE237363).</p>", "<title>CCK‐8, EdU Incorporation, Colony Formation, and Transwell Assays</title>", "<p>Cell proliferation was determined by Cell Counting Kit‐8 (CCK‐8, Yeasen) and EdU Cell Proliferation Assay kit (Ribobio, Guangzhou, China). Colony formation was observed by staining with 0.1% crystal violet (Sangon Biotechnologies Inc., Shanghai, China). Cell migration and invasion were assessed using 8 µ<sc>m</sc> pore Transwell chambers with (for invasion assay) or without Matrigel (for migration assay). For migration assay, 5 × 10<sup>4</sup> SW1990 or 3 × 10<sup>4</sup> PANC‐1 cells were seeded into the upper chamber of the Transwell apparatus (Corning, USA) in serum‐free medium, and the medium supplemented with 10% FBS was added to the bottom chamber. For invasion assay, 10 × 10<sup>4</sup> SW1990 or 6 × 10<sup>4</sup> PANC‐1 cells were seeded into the upper Corning BioCoat Matrigel invasion chamber. After 24 h, the cells on the upper surface that had not passed through the polycarbonate filter were removed using a moistened cotton swab; the cells having migrated to the lower membrane surface were fixed in 100% methanol for 10 min, stained with 0.4% crystal violet for 15 min, and counted under a microscope (Nikon, Japan) at ×100 magnification. The cells were manually counted using Image J software. Three independent experiments were performed.</p>", "<title>Chromatin Immunoprecipitation (ChIP)</title>", "<p>ChIP was performed with SW1990 cells using Cell Signaling Technology ChIP kit (CST, USA). Normal rabbit IgG served as the control. ChIP samples were analyzed by qPCR using the FastStart Universal SYBR Green Master. The primer sequences for ChIP were as follows: Primer 1‐F: 5′‐CTCCCGCCCGAGCCCACGG‐3′; Primer 1‐R: 5′‐AGGCGAGGGAGATGAGAGAC‐3′. Primer 2‐F: 5′‐CGTGTTGGAGGCAGTAGAAG‐3′; Primer 2‐R: 5′‐GGCACCTCCCGCTCCTGGAG‐3′. Primer 3‐F: 5′‐CTACTCAATATCCATTCTATG‐3′; Primer 3‐R: 5′‐CAACTTTGAACTGTATGTAG‐3′.</p>", "<title>ChIP‐Seq Data Processing and Analysis</title>", "<p>ChIP‐seq was performed using modified ChIP and ChIP‐seq protocols previously described.<sup>[</sup>\n##REF##23386643##\n64\n##\n<sup>]</sup> ChIP samples were sequenced and analyzed for H3K4me1 and EBF2 by Shanghai Jiayin Biotechnology Co., Ltd (Shanghai, China). The Raw data of fastq format were first processed through in‐house perl scripts. Next, the clean data were obtained by removing reads containing adapter, reads containing ploy‐N, and low‐quality data from raw data. All the downstream analyses were based on high‐quality clean data. Then, using the bwa program, the clean reads were aligned to the reference genome sequences.<sup>[</sup>\n##UREF##2##\n65\n##\n<sup>]</sup> ChIP‐seq data sets were available (GEO accession number GSE237364).</p>", "<title>Cleavage Under Targets and Tagmentation (CUT&amp;Tag)</title>", "<p>CUT&amp;Tag was performed according to the instruction of Hyperactive Universal CUT &amp; Tag Assay Kit for Illumina Pro (Cat No. TD904; Vazyme, Nanjing, China). TruePrep Index Kit V4 (Cat No. TD204; Vazyme) was used for index‐labeled DNA library preparation. Paired‐end sequencing was provided by LC Bio (Hangzhou, China).<sup>[</sup>\n##REF##23418309##\n66\n##\n<sup>]</sup> CUT&amp;Tag data sets were available (GEO accession number GSE237365).</p>", "<title>Clinical Samples and Immunohistochemical (IHC) Staining</title>", "<p>PDAC and tumor adjacent tissues were obtained from the Second Affiliated Hospital of Nanjing Medical University. Ninety pairs of ductal adenocarcinoma and adjacent normal pancreatic tissue sections (HPanA180Su03) were obtained from Shanghai Outdo Biotech (National Human Genetic Resources Sharing Service Platform with code No. XT20‐021, Shanghai, China), under the approval by the Ethics Committee of Shanghai Outdo Biotech. IHC staining was performed on paraffin‐embedded sections of biopsies from ductal adenocarcinoma patients and controls according to standard protocols (CST). Briefly, the sections were incubated with primary antibodies, including anti‐EBF2 (1:100 dilution; Affinity), anti‐KMT2D (1:100 dilution; Abcam), anti‐KLLN (1:100 dilution; Abcam), followed by incubation with horseradish peroxidase‐conjugated goat anti‐rabbit secondary antibodies. Antibody binding was visualized using a 2‐Solution DAB Kit (Invitrogen). All pancreatic cancer tissue sections were examined by two experienced pathologists, and the EBF2, KMT2D or KLLN stained in the tissue was scored independently using the H‐score system by two pathologists blinded to the clinical data. Rare discordance in scoring was resolved by re‐examination and consultation between the pathologists. The intensity of immunostaining (category A) was documented as 0–3: 0, negative; 1, weak; 2, moderate; 3, strong. For the Pearson correlation scatter plot of molecules in ductal adenocarcinoma, the H score was calculated by adding the multiplication product of the different staining intensities in category A (0–3) with the percentage of positive cells, i.e., H score (0–300 scale)  =  3 × (% at 3+) + 2 × (% at 2+) + 1 × (% at 1+). The clinical features of patients are listed in Additional file 1: Table ##SUPPL##0##S2## (Supporting Information). In the survival analysis, the overall survival was stratified by expression of the gene of interest and presented as Kaplan–Meier plots. The between‐group difference in the overall survival was evaluated by the log‐rank test. The correlation between EBF2, KMT2D, and KLLN expression in ductal adenocarcinoma was assessed via Pearson correlation analysis.</p>", "<title>Subcutaneous Tumorigenesis Model</title>", "<p>BALB/c nude mice (4 weeks old) were purchased from the Animal Core Facility of Nanjing Medical University. Every 1 × 10<sup>6</sup> SW1990‐luc cells (SW1990 cells labeled with luciferase) were suspended in 100 µL of PBS and Matrigel (Corning) mixture, then subcutaneously injected into the right forelimb of nude mice. The length and width of tumor were measured every 2 or 3 days. Tumor volume was calculated using the formula: Volume  =  0.5 × length × width<sup>2</sup>. Luciferase signals in nude mice were measured at the first and fourth week after injection. The mice were sacrificed at 30 days for in vivo proliferation assay. Mice were anesthetized with isoflurane gas and sacrificed by cervical dislocation. Tumor tissues of these mice were collected for further analyses.</p>", "<title>Lung Metastasis Model</title>", "<p>BALB/c nude mice (5 weeks old) were purchased from the Animal Core Facility of Nanjing Medical University. About 1 × 10<sup>5</sup> SW1990‐luc cells were suspended in 100 µL of PBS and injected into the caudal vein of nude mice. Luciferase signals in nude mice were measured weekly. The mice were anesthetized with isoflurane gas and sacrificed at 30 days by cervical dislocation for in vivo metastasis assay. Lung and liver samples were collected for further analyses.</p>", "<title>Patient‐Derived Xenograft (PDX) Model</title>", "<p>A PDX model was established by implanting tumor fragments into immunodeficient nude mice. Tumor fragments were derived from a female PDAC patient with stage II ductal adenocarcinoma, who underwent surgery at the Second Affiliated Hospital of Nanjing Medical University. Informed consent was obtained from each patient, and all procedures involving human samples were approved by the Ethics Committee of the Second Affiliated Hospital of Nanjing Medical University.</p>", "<title>Bioluminescence Imaging</title>", "<p>Luciferase signals from D‐luciferin (Cat No. MB1834; MeilunBio, Dalian, China) were measured using IVIS Spectrum (PerkinElmer, USA) at indicated concentrations. The luciferase signal activity was quantitated using the software provided by the manufacturer.</p>", "<title>Statistical Analysis</title>", "<p>Statistical analysis was implemented on the GraphPad Prism 8.0 software (GraphPad Inc., La Jolla, CA, USA). Unless otherwise specified, data were collected from at least three independent experiments and expressed as mean ±SEM. Two‐group comparison of experiments data was accomplished through the Student's <italic toggle=\"yes\">t</italic>‐test, and multiple‐group comparison by the ANOVA test. One‐way ANOVA was used to compare data of more than two groups under one treatment, whereas two‐way ANOVA to compare data of more than two groups under more than one treatment. Survival curves were constructed using the Kaplan–Meier method and analyzed by the log‐rank test. The correlations analysis was based on Pearson's correlation. The sample size of each experimental group was shown in each figure as the number of dots. <italic toggle=\"yes\">p</italic> &lt; 0.05 was considered statistically significant: <sup>*</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01.</p>", "<title>Ethics Approval and Consent to Participate</title>", "<p>Written informed consent was obtained from all patients. The study was approved by the Ethics Committee of Nanjing Medical University (2021‐KY‐096‐01 and SHYJS‐CP‐1901009).</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>B.Y. and M.X. contributed equally to this work. The authors thank the patients, clinical investigators, and staff who participated in this study. This study was supported by grants from the National Natural Science Foundation of China (No. 82072484, 82002989, 82373058 and 82372749), the Natural Science Foundation in University of Jiangsu Province (No. 20KJB310006), the Major Projects of Science and Technology Development Fund of Nanjing Medical University (No. NMUD2019004) and the Natural Science Foundation of Jiangsu Province (BK20231261).</p>", "<title>Data Availability Statement</title>", "<p>The datasets used in the current study are available from the corresponding author on reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6859-fig-0001\"><label>Figure 1</label><caption><p>EBF2 is identified as an H3K4me1‐binding protein. A) Venn diagram showing the overlapping genes that were associated with H3K4me1 and significantly reduced in pancreatic cancer (GEO data, GSE32676). B) Peptide pull‐down assay to determine the interactions between H3, H3K4me1, or H3K4me3 peptides and EBF2 in vitro. C) Peptide pull‐down assay performed with purified His‐EBF2 fusion protein and H3, H3K4me1, or H3K4me3 peptides (right); Coomassie blue staining with SDS‐PAGE gel for the purified His‐EBF2 fusion protein expressed in <italic toggle=\"yes\">E. coli</italic> (left). D) MST assay confirming the direct interactions between His‐EBF2 and H3, H3K4me1, or H3K4me3 peptides. Kd = 7.37 ± 0.377 µ<sc>m</sc>. E) ITC binding curve of His‐EBF2 fusion protein with H3K4me1 peptide. Ka = 7.11 × 10<sup>5</sup> ± 1.48 × 10<sup>5</sup> mol<sup>−1</sup>. F) Immunofluorescence staining of EBF2 protein in PDAC and adjacent tissues. G) Western blot analysis for EBF2 protein level in PDAC and adjacent tissues.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6859-fig-0002\"><label>Figure 2</label><caption><p>EBF2 is downregulated in PDAC tissues and inhibits cell proliferation and metastasis. A) H&amp;E and IHC staining of EBF2 protein in PDAC and adjacent normal tissues. Scale bar, 10 µm. B) H scores of EBF2 in PDAC and adjacent normal tissues. C–E) Correlations of EBF2 expression with tumor stage (C), lymph node metastasis (D), and distal metastasis (E) in PDAC patients. Data in B–E are presented as mean ± SEM, <sup>*</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by Student's <italic toggle=\"yes\">t</italic>‐test. F) Kaplan–Meier plot of overall survival in 90 patients with PDAC, stratified by EBF2 expression (Log‐rank test, <italic toggle=\"yes\">p</italic> &lt; 0.0001). G, H) The mRNA (G) and protein (H) levels of EBF2 in SW1990 cells treated with EBF2 shRNAs (EBF2‐KD) or negative control (SCR) verified by qPCR and Western blot assays. Data in G are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by one‐way ANOVA test. I–L) CCK‐8 (I), EdU incorporation (J), colony‐formation (K) and Transwell (L) assays were performed to assess the effects of EBF2 knockdown on the proliferation, migration, and invasion of SW1990 cells in vitro. Data in I–L are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by two‐way ANOVA (I) and one‐way ANOVA (J–L) test. M) Images of subcutaneous tumor xenografts in SCR and EBF2‐KD mice. N) The tumor growth curves of xenografts were plotted in SCR and EBF2‐KD mice. O) BALB/c nude mice with subcutaneous tumor xenografts in SCR and EBF2‐KD group were imaged with in vivo imaging system at different time points. P) BALB/c nude mice injected with SCR and EBF2‐KD SW1990 cells via tail vein were imaged by in vivo imaging system at different time points. Data in N–P are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by two‐way ANOVA test (n = 5). Q) Representative images of lung metastasis loci in SCR and EBF2‐KD mice. Data in Q are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by Student's <italic toggle=\"yes\">t</italic>‐test (n = 5).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6859-fig-0003\"><label>Figure 3</label><caption><p>KMT2D expression is positively correlated with EBF2 expression in PDAC tissues and copies the phenotype caused by EBF2. A) H&amp;E and IHC staining of KMT2D protein in PDAC and adjacent normal tissues. Scale bar, 10 µm. B) H score of KMT2D in PDAC and adjacent normal tissues. C–E) Correlations of KMT2D expression with tumor stage (C), lymph node metastasis (D), and distal metastasis (E) of PDAC patients. Data in B–E are presented as mean ± SEM, <sup>*</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by Student's <italic toggle=\"yes\">t</italic>‐test. F) Kaplan–Meier plot of overall survival in 90 patients with PDAC, stratified by KMT2D expression (Log‐rank test, <italic toggle=\"yes\">p</italic> &lt; 0.01). G) Spearman correlation analysis of KMT2D and EBF2 levels in PDAC tissues (n = 90, r = 0.5002, <italic toggle=\"yes\">p</italic> &lt; 0.0001). H, I) The mRNA (H) and protein (I) levels of KMT2D in SW1990 cells verified by qPCR and Western blot assays. Data in H are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by one‐way ANOVA test. J–M) EdU incorporation (J), colony‐formation (K), CCK‐8 (L), and Transwell (M) assays assessed the effects of KMT2D knockdown on the proliferation, migration, and invasion of SW1990 cells in vitro. Data in J–M are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by two‐way ANOVA (L) and one‐way ANOVA (J, K, and M) test. N) Images of subcutaneous tumor xenografts in KMT2D knockdown (KMT2D‐KD) and control (SCR) mice. O) The tumor growth curves of xenografts were plotted in SCR and KMT2D‐KD mice. P) BALB/c nude mice with subcutaneous tumor xenografts in SCR and EBF2‐KD group were imaged with in vivo imaging system at different time points. Q) BALB/c nude mice injected with SCR and EBF2‐KD SW1990 cells through the tail vein were imaged by in vivo imaging system at different time points. Data in O–Q are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by two‐way ANOVA test (n = 5). R) Representative images of lung metastasis loci in SCR and KMT2D‐KD mice. Data in R are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by Student's <italic toggle=\"yes\">t</italic>‐test (n = 5).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6859-fig-0004\"><label>Figure 4</label><caption><p>KLLN is a common transcriptional target of KMT2D and EBF2 in PDAC cells. A) Heatmaps from RNA‐seq data showing overlapping of differentially expressed genes (DEGs) of SW1990‐luc cells with EBF2 overexpression (EBF2‐OE) or H3K4me1 activation by GSK‐LSD1. B) Gene Set Enrichment Analysis (GSEA) reveals that the DEGs are enriched in genes regulated by p53. C, D) The mRNA (C) and protein (D) levels of EBF2 and KLLN in negative control (Vector) and EBF2 overexpressed (EBF2‐OE) SW1990 cells verified by qPCR and Western blot analysis. Data in C are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by Student's <italic toggle=\"yes\">t</italic>‐test. E,F) The mRNA (E) and protein (F) levels of KLLN in negative control (Vector) and GSK‐LSD1‐treated SW1990 cells verified by qPCR and Western blot analysis. Data in E are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by Student's <italic toggle=\"yes\">t</italic>‐test. G) H&amp;E and IHC staining of KLLN protein in PDAC and adjacent normal tissues. Scale bar, 10 µm. H) H score of KLLN in PDAC and tumor adjacent tissues. I–K) Correlations of KLLN expression with tumor stage (I), lymph node metastasis (J), and distal metastasis (K) in PDAC patients. Data in I–K are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by Student's <italic toggle=\"yes\">t</italic>‐test. L) Kaplan–Meier plot of overall survival of 90 patients with PDAC, stratified by KLLN expression (Log‐rank test, <italic toggle=\"yes\">p</italic> = 0.001). M) Spearman correlation analysis of KMT2D and KLLN levels in PDAC tissues (n = 90, r = 0.6838, <italic toggle=\"yes\">p</italic> &lt; 0.0001). N) Spearman correlation analysis of EBF2 and KLLN levels in PDAC tissues (n = 90, r = 0.7541, <italic toggle=\"yes\">p</italic> &lt; 0.0001). O) Western blot analysis of KLLN and H3K4me1 levels in SCR, KMT2D‐KD, or EBF2‐KD xenografts. P) H&amp;E and IHC staining of KLLN and Ki67 in SCR, KMT2D‐KD, or EBF2‐KD xenografts. Scale bar, 20 µm.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6859-fig-0005\"><label>Figure 5</label><caption><p>GSK‐LSD1 inhibits the proliferation, migration, and invasion of PDAC cells. A) Diagram of flag‐tagged KMT2D‐C, KMT2Dfusion and mKMT2Dfusion plasmid models. B) Western blot analysis of KLLN and H3K4me1 levels in SW1990 cells transfected with KMT2D‐C, KMT2D<sub>fusion,</sub> and mKMT2D<sub>fusion</sub>. C, D) Colony‐formation (C) and Transwell (D) assays of SW1990 cells transfected with KMT2D‐C, KMT2D<sub>fusion,</sub> and mKMT2D<sub>fusion</sub>. Data in C and D are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by one‐way ANOVA test. E) Western blot analysis of H3K4me1 and KLLN levels in SW1990 cells treated with 0, 1, 10, or 100 µ<sc>m</sc> GSK‐LSD1. F–H) Colony‐formation (F), CCK‐8 (G), and Transwell (H) assays of SW1990 cells treated with Vehicle and GSK‐LSD1. Data in F–H are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by Student's <italic toggle=\"yes\">t</italic>‐test (F and H), two‐way ANOVA test (G). I, J) BALB/c nude mice injected with SW1990‐luc cells were treated with Vehicle or GSK‐LSD1, and imaged at different time points by in vivo imaging system. Data in J are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by two‐way ANOVA test (n = 5). K) Images of subcutaneous tumor xenografts in Vehicle and GSK‐LSD1 mice. L,M) Western blot (L) and IHC staining (M) analysis of KLLN and H3K4me1 levels in control or GSK‐LSD1‐treated lung metastasis tissues. N) Images of patient‐derived xenograft (PDX) models treated with vehicle, gemcitabine, or GSK‐LSD1. Data in N are presented as mean ± SEM, <sup>*</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by two‐way ANOVA test (n = 5). O) IHC staining analysis of KLLN and H3K4me1 levels in PDX tumors treated with vehicle, gemcitabine, or GSK‐LSD1. P) Co‐IP assay of proteins immunoprecipitated with H3K4me1 antibodies from lysates of SW1990 cells treated with vehicle control and GSK‐LSD1. Q–S) CCK‐8 (Q), colony‐formation (R) and Transwell (S) assays were used to detect the proliferation, migration, and invasion of control, GSK‐LSD1, and GSK‐LSD1+KLLN SW1990 cells. Data in Q–S are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by two‐way ANOVA test (Q) and one‐way ANOVA test (R and S).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6859-fig-0006\"><label>Figure 6</label><caption><p>KMT2D and EBF2 cooperate to regulate the expression of KLLN. A) Western blot of KLLN and H3K4me1 in SW1990 cells transfected with KMT2D‐C, KMT2D<sub>fusion</sub>, or EBF2. B) Western blot of KLLN and H3K4me1 in SW1990 cells transfected with mKMT2D<sub>fusion</sub>, KMT2D<sub>fusion</sub> or EBF2. C) Western blot of KLLN and H3K4me1 in SW1990 cells transfected with KMT2D‐C, KMT2D<sub>fusion</sub> or EBF2‐KD. D) Western blot of KLLN and H3K4me1 in SW1990 cells transfected with mKMT2D<sub>fusion</sub>, KMT2D<sub>fusion</sub>, or EBF2‐KD. β‐actin and H3 were used as loading control. E–G) Colony‐formation (E), migration (F), and invasion (G) of SW1990 cells treated with KMT2D‐C, KMT2D<sub>fusion</sub>, mKMT2D<sub>fusion</sub>, EBF2, KMT2D<sub>fusion</sub>+EBF2, mKMT2D<sub>fusion</sub>+EBF2. H,I) Colony‐formation assays (H) and Transwell (I) assays of SW1990 cells transfected with control (NC), KMT2D‐KD or KMT2D‐KD + KLLN. J‐K) Colony‐formation assays (J) and Transwell (K) assays of SW1990 cells transfected with control (NC), EBF2‐KD or EBF2‐KD+KLLN. Scale bar,100 µm. Data in E–K are presented as mean ± SEM, <sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 by one‐way ANOVA test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6859-fig-0007\"><label>Figure 7</label><caption><p>A diagram of EBF2 interacting with KMT2D‐mediated H3K4me1 to suppress pancreatic cancer progression.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6859-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2302037-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
[{"label": ["27"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["C.", "L.", "L.", "T.", "S.", "L. Q.", "M. A.", "N.", "K.", "K.", "T."], "surname": ["Larsson", "Cordeddu", "Siggens", "Pandzic", "Kundu", "He", "Ali", "Pristovsek", "Hartman", "Ekwall", "Sjoblom"], "source": ["Clin. Epigenet."], "year": ["2020"], "volume": ["12"], "fpage": ["74"]}, {"label": ["63"], "mixed-citation": ["\n"], "string-name": ["\n"], "given-names": ["K. L."], "surname": ["Bennett"], "source": ["JAMA, J. Am. Med. Assoc."], "year": ["2010"], "volume": ["304"], "fpage": ["2724"]}, {"label": ["65"], "mixed-citation": ["\n"], "string-name": ["\n", "\n"], "given-names": ["M.", "C."], "surname": ["Sankunny", "Eng"], "source": ["Cell Death Discov."], "year": ["2018"], "volume": ["4"], "fpage": ["31"]}]
{ "acronym": [], "definition": [] }
66
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 28; 11(2):2302037
oa_package/13/ef/PMC10787067.tar.gz
PMC10787068
37983591
[ "<title>Introduction</title>", "<p>Mitochondria are the metabolic and signaling organelles that sense cellular and environmental changes to reprogram intraorganellar pathways for proper adaptation to pathologies such as ischemia and disrupted energy metabolism.<sup>[</sup>\n##REF##22424226##\n1\n##\n<sup>]</sup> Dysregulation of mitochondrial function is a common feature of many human diseases, including cancer and metabolic disorders.<sup>[</sup>\n##REF##22424226##\n1\n##, ##REF##28792006##\n2\n##\n<sup>]</sup> Tumor necrosis factor receptor‐associated protein 1 (TRAP1), a mitochondrial paralog of 90 kDa heat shock protein (Hsp90), reprograms cancer cell metabolism to adapt to the harsh tumor environment.<sup>[</sup>\n##REF##24731398##\n3\n##\n<sup>]</sup> In this process, TRAP1 reprograms cellular energetics, cellular redox pathways, calcium homeostasis, and cell death signaling by interacting with the mitochondrial substrate proteins that modulate these processes in cancer cells.<sup>[</sup>\n##REF##24731398##\n3\n##, ##REF##30683653##\n4\n##\n<sup>]</sup> Considering its broad impacts on mitochondrial pathways, TRAP1 could play a role in the onset and progression of human diseases that involve altered mitochondrial function.</p>", "<p>The retina is the most metabolically demanding tissue of the body due to its high neuronal density, and thus is vulnerable to energetic insufficiencies caused by ischemia, changes in the availability of metabolic substrates, and mitochondrial dysfunction.<sup>[</sup>\n##REF##32712136##\n5\n##\n<sup>]</sup> Adaptive responses involving mitochondrial pathways are necessary to maintain the function of retinal cells, especially under stress conditions.<sup>[</sup>\n##REF##32712136##\n5\n##, ##REF##30665952##\n6\n##\n<sup>]</sup> Retinal ischemia and metabolic stress contribute to the pathologies of devastating sight‐threatening diseases such as retinopathy of prematurity (ROP) and proliferative diabetic retinopathy (PDR).<sup>[</sup>\n##REF##22455417##\n7\n##\n<sup>]</sup> Thus, we speculated that TRAP1 could be dysregulated in these disease conditions, reprogramming mitochondrial pathways as a maladaptive compensatory response in ischemic retinopathies, although the role of TRAP1 in these contexts has not been reported.</p>", "<p>Cellular adaptation to low oxygen levels involves the stabilization of hypoxia‐inducible factors including HIF1α, which is regulated by the oxygen‐sensing enzyme prolyl hydroxylase (PHD).<sup>[</sup>\n##REF##32144406##\n8\n##\n<sup>]</sup> However, retinal ischemia, a common causative mechanism of ocular disease, prompts compensatory stabilization of HIF1α and subsequent elevation of angiogenic and vascular permeability factors such as vascular endothelial growth factor (VEGF), which contribute to retinal vascular hyperpermeability and pathological neovascularization.<sup>[</sup>\n##REF##28724805##\n9\n##\n<sup>]</sup> Therefore, intravitreal injection of anti‐VEGF therapies is effective in treating neovascularization and pathologic vascular leakage in ROP and PDR.<sup>[</sup>\n##REF##28724805##\n9\n##, ##REF##33469209##\n10\n##\n<sup>]</sup> However, these pathologies can recur after anti‐VEGF therapy in some patients, and anti‐VEGF therapies for the treatment of ROP have raised concerns that anti‐VEGF drugs may cross the blood‐retinal barrier (BRB), potentially posing risks to premature infants.<sup>[</sup>\n##REF##33469209##\n10\n##, ##REF##27506484##\n11\n##\n<sup>]</sup> Furthermore, in DR patients, repeated intravitreal injections are not only painful, but can also cause major vision‐threatening complications such as endophthalmitis.<sup>[</sup>\n##REF##29891901##\n12\n##\n<sup>]</sup> These limitations underscore the urgent clinical need to develop alternative therapeutic targets by identifying novel regulatory mechanisms of disease.</p>", "<p>In the present study, we identified a novel and previously unreported function of TRAP1 in maintaining HIF1α stability in ischemic retinopathies. Pharmacologic and genetic inhibition of TRAP1 elevated cytoplasmic calcium to activate the calcium‐dependent protease calpain‐1, which triggers HIF1α degradation independently of PHD to suppress BRB breakdown and pathologic retinal neovascularization. Collectively, our findings suggest that TRAP1 could be a promising therapeutic target for the treatment of HIF1α‐dependent vascular diseases, laying the groundwork for future translational studies.</p>" ]
[]
[ "<title>Results</title>", "<title>TRAP1 is Required for Development of Pathologic Microvascular Changes in Retinopathy</title>", "<p>To investigate the involvement of TRAP1 in the pathologic process of ischemic retinopathy, we used the oxygen‐induced retinopathy (OIR) mouse model of ROP<sup>[</sup>\n##REF##19816419##\n13\n##\n<sup>]</sup> (<bold>Figure</bold> ##FIG##0##\n1A##). In OIR mice at postnatal day 17 (P17), mRNA and protein levels of TRAP1 were significantly higher than those of age‐matched controls (Figure ##FIG##0##1B,C##). Immunohistochemical staining of OIR mouse retinas revealed elevated TRAP1 levels throughout the entire areas of the inner plexiform layer (IPL) and outer plexiform layer (OPL) (Figure ##FIG##0##1D##), which were enriched in mitochondria, as demonstrated by staining for mitochondrial inner membrane proteins (Figure ##SUPPL##0##S1##, Supporting Information), suggesting mitochondrial alterations in diseased retinal cells.</p>", "<p>To investigate the contribution of TRAP1 to retinal vascular pathologies, gene‐trap <italic toggle=\"yes\">Trap1</italic> knockout (KO) mice were generated (Figure ##SUPPL##0##S2A,B##, Supporting Information) and analyzed in the OIR model. In <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR retinas, both neovascular tuft formation and vaso‐obliteration were considerably lower than in <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> OIR mice (Figure ##FIG##0##1E##), indicating <italic toggle=\"yes\">Trap1</italic> ablation decreased retinal vascular pathogenesis. Consequently, the Hypoxyprobe‐positive area was significantly smaller in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice than in <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> OIR mice (Figure ##FIG##0##1F##). Meanwhile, the retinal vascular structures of <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mice were comparable at P5, P12, and P36 (Figure ##SUPPL##0##S3A–C##, Supporting Information) and at P12 in OIR mice (Figure ##SUPPL##0##S3D##, Supporting Information), demonstrating that TRAP1 deletion alone did not affect normal physiological vascular development or hyperoxic vessel regression in neonatal mouse retinas.</p>", "<title>TRAP1‐HIF1α Crosstalk is Essential for the Pathogenesis of Ischemic Retinopathy</title>", "<p>OIR mice exhibited retinal hypoxia (Figure ##FIG##0##1F##) and elevated expression of HIF1α (Figure ##FIG##0##1C##), a master transcription factor that upregulates the expression of key angiogenic factors such as VEGF and angiopoietin‐like 4 (ANGPTL4) to induce aberrant retinal angiogenesis.<sup>[</sup>\n##REF##31403471##\n15\n##\n<sup>]</sup> Retinal expression and nuclear localization of HIF1α were much lower in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice than in <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> OIR mice (<bold>Figure</bold> ##FIG##1##\n2A##). At 6 h after transfer from a hyperoxic chamber to room air, the level of Hypoxyprobe staining was comparably strong in OIR <italic toggle=\"yes\">Trap</italic>1<sup>+/+</sup> and <italic toggle=\"yes\">Trap</italic>1<sup>−/−</sup> mice at P12 (Figure ##FIG##1##2B##), indicating that retinal hypoxia occurs in OIR mice at P12 regardless of their TRAP1 status. However, only the <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> retinas exhibited HIF1α degradation (Figure ##FIG##1##2C##), suggesting that TRAP1 ablation promoted oxygen‐independent degradation of HIF1α. Consequently, expression of the angiogenic factors VEGF and ANGPTL4 was reduced in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice (Figure ##FIG##1##2D,E##). Interestingly, knockout of TRAP1expression in OIR mice decreased angiogenic factor levels to those similar to control mice, but without completely eliminating their expression (Figure ##FIG##1##2E##).</p>", "<p>The strong positive VEGF staining of glutamine synthetase‐positive cells (Figure ##SUPPL##0##S4A##, Supporting Information) suggested that Müller cells express angiogenic factors, as previously reported,<sup>[</sup>\n##REF##20530741##\n14\n##, ##REF##7846076##\n16\n##\n<sup>]</sup> In primary mouse Müller cells and the human Müller cell line MIO‐M1 exposed to hypoxia, siRNA‐mediated depletion of TRAP1 induced degradation of HIF1α protein without affecting its mRNA level and reduced expression of HIF1α‐regulated angiogenic factors (Figure ##SUPPL##0##S4B–E##, Supporting Information). Further, HIF1α expression also increased TRAP1 expression in Müller cells subjected to hypoxia (Figure ##SUPPL##0##S5A–C##, Supporting Information), as reported previously,<sup>[</sup>\n##REF##33934112##\n17\n##\n<sup>]</sup> indicating positive reciprocal regulation exists between HIF1α and TRAP1. Collectively, these data indicate that TRAP1 is essential for HIF1α stabilization and subsequent angiogenic factor expression in the hypoxic retina.</p>", "<title>TRAP1‐Dependent Stabilization of HIF1α in a Diabetic Mouse Model</title>", "<p>Retinal hypoxia, activation of HIF1α, and consequent expression of angiogenic factors are crucial for the development of diabetic retinopathy.<sup>[</sup>\n##REF##31403471##\n15\n##, ##REF##34364890##\n18\n##\n<sup>]</sup> Thus, to further investigate TRAP1‐dependent retinal vascular changes in vivo, retinal hypoxia and HIF1α stabilization were examined in a streptozotocin (STZ)‐induced mouse model of type 1 diabetes<sup>[</sup>\n##REF##27114552##\n19\n##\n<sup>]</sup> (Figure ##SUPPL##0##S6A,B##, Supporting Information). Despite the lack of noticeable neovascularization, STZ mice exhibited severe retinal hypoxia, as revealed by Hypoxyprobe staining (<bold>Figure</bold> ##FIG##2##\n3A##), and increased TRAP1 and HIF1α expression (Figure ##SUPPL##0##S6C–E##, Supporting Information), indicating hypoxia in the retinas of these mice similar to that in the retinas of OIR mice. Consistent with the observations in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice, the nuclear expression of retinal HIF1α and subsequent expression of VEGF and ANGPTL4 were significantly reduced to physiological levels in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> STZ mice (Figure ##SUPPL##0##S7A–C##, Supporting Information). Interestingly, the retinas of diabetic <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> STZ mice showed significantly lower capillary degeneration and subsequently higher vascular densities than those of <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> STZ mice (Figure ##FIG##2##3B##; Figure ##SUPPL##0##S7D##, Supporting Information).</p>", "<p>Furthermore, it has been reported that retinal abnormalities, such as glial dysfunction, immune cell activation, vascular degeneration, and increased cell death, begin to develop even before massive vascular abnormalities appear in both DR rodent models and human patients.<sup>[</sup>\n##REF##33469209##\n10\n##, ##REF##20530741##\n14\n##\n<sup>]</sup> In <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> STZ mice, Müller glial cells were activated, as evidenced by elevated glial fibrillary acidic protein (GFAP) expression, whereas in <italic toggle=\"yes\">Trap1<sup>−</sup>\n</italic>\n<sup>/−</sup> STZ mice their activation was suppressed (Figure ##SUPPL##0##S8A##, Supporting Information). Immune activation, characterized by an increase in the population of activated amoeboid microglia with elevated pro‐inflammatory cytokine expression, was observed in <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> STZ mice; this activation was completely reversed in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> STZ mice (Figure ##SUPPL##0##S8B,C##, Supporting Information). Furthermore, retinal thickness, indicative of retinal neurodegeneration in diabetes,<sup>[</sup>\n##REF##9519752##\n20\n##\n<sup>]</sup> was decreased in <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup>, but not in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup>, STZ mice (Figure ##FIG##2##3C##). Consistently, the massive retinal cell death and increased hypoxia observed in <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> STZ mice were dramatically reversed in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> STZ mice (Figure ##FIG##2##3A,D##). Collectively, the data strongly suggest that TRAP1 contributes to the development of retinal abnormalities in type 1 diabetic STZ mice, and that loss of TRAP1 reverses these abnormalities in vivo.</p>", "<title>TRAP1 Inhibition Restores the BRB in Ischemic Retinopathy</title>", "<p>Among HIF1α‐regulated cytokines, angiopoietin‐2 (ANG2) promotes the pathologic angiogenic functions of VEGF, and is implicated in the detachment and loss of pericytes (PCs) from endothelial cells (ECs), leading to BRB breakdown and increased vascular permeability.<sup>[</sup>\n##REF##35396185##\n21\n##\n<sup>]</sup> These histopathologic features were observed in both OIR and STZ wild‐type mice (<bold>Figure</bold> ##FIG##3##\n4A–F##). Expression of ANG2 was elevated in OIR and STZ mouse retinas, and was significantly reduced in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mice at both the mRNA and protein levels; however, ANG1 expression was unaffected by <italic toggle=\"yes\">Trap1</italic> ablation in OIR and STZ mice (Figure ##SUPPL##0##S9A–F##, Supporting Information). Consequently, in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR and STZ mice, the ratio of PCs to ECs and expression of the adherens junction protein VE‐cadherin were restored (Figure ##FIG##3##4A–D##), indicating that TRAP1 inhibition restored PC‐EC integrity. Restoration of BRB integrity was further demonstrated by decreased extravasations of fibrinogen exudates and red blood cells (Figure ##FIG##3##4E,F##; Figure ##SUPPL##0##S10A,B##, Supporting Information). Similarly, fluorescein angiography and fluorescein‐dextran permeability analyses revealed that the elevated retinal vascular leakages observed in <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> STZ mice were reduced in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mice (Figure ##SUPPL##0##S11A,B##, Supporting Information).</p>", "<p>To further examine the PC‐EC interaction, cocultures of human umbilical vein endothelial cells (HUVECs) and human brain vascular pericytes (HBVPs) were treated with conditioned media (CM) collected from MIO‐M1 cells exposed to hypoxia (Figure ##SUPPL##0##S12A##, Supporting Information). CM obtained from cells treated with TRAP1‐targeting siRNA reduced tube formation areas and increased the PC‐EC ratio compared with CM obtained from cells treated with control siRNA (Figure ##SUPPL##0##S12B–D##, Supporting Information). Similarly, treatment with CM obtained from MIO‐M1 cells depleted of ANG2 or HIF1α using siRNAs reduced tube formation areas and elevated the PC‐EC ratio (Figure ##SUPPL##0##S12E–G##, Supporting Information). Collectively, these results indicate that TRAP1 inhibition not only suppresses retinal neovascularization but also restores the BRB in mice with ischemic retinopathy, potentially by decreasing ANG2 expression.</p>", "<p>Depletion of TRAP1 using siRNAs resulted in decreases in the levels of various angiogenic factors released from hypoxic Müller cells. The angiogenic factors included monocyte chemoattractant protein‐1 (MCP‐1), granulocyte macrophage colony‐stimulating factor (GM‐CSF), heparin‐binding EGF‐like growth factor (HB‐EGF), chemokine ligand 16 (CXCL16), interleukin‐8 (IL‐8), and pentraxin 3 (PTX‐3) (Figure ##SUPPL##0##S13A–C##, Supporting Information). Since these factors are also increased in DR patients and implicated in the pathogenesis of retinopathy,<sup>[</sup>\n##REF##29565290##\n22\n##\n<sup>]</sup> the reduced retinal pathogenesis observed upon TRAP1 inhibition might be associated with decreases in the levels of these factors, as well as those of VEGF, ANGPTL4, and ANG2.</p>", "<title>TRAP1 Inhibition Activates Calpain‐1 to Trigger HIF1α Proteolysis</title>", "<p>TRAP1 elevates the cellular concentration of succinate, leading to inhibition of PHD and subsequent stabilization of HIF1α, by inactivating succinate dehydrogenase (SDH) in cancer cells.<sup>[</sup>\n##REF##23747254##\n23\n##\n<sup>]</sup> However, TRAP1‐HIF1α regulation in the retina does not involve SDH and PHD because it was unaffected by treatment with a large excess of succinate (Figure ##SUPPL##0##S14A##, Supporting Information), the PHD inhibitor dimethyloxalylglycine (DMOG), and a HIF1α mutant (P402A and P564A) lacking PHD hydroxylation sites (Figure ##SUPPL##0##S14B##, Supporting Information). 17‐Dimethyl‐aminothylamino‐17‐demethoxy‐geldanamycin (DMAG), which inhibits cytoplasmic, but not mitochondrial Hsp90s,<sup>[</sup>\n##REF##25785725##\n24\n##\n<sup>]</sup> did not affect the stability of HIF1α, indicating that the regulatory mechanism is mitochondria‐specific,<sup>[</sup>\n##REF##18809331##\n25\n##\n<sup>]</sup> (Figure ##SUPPL##0##S14C##, Supporting Information).</p>", "<p>Interestingly, the proteasome inhibitor MG132 completely blocked HIF1α degradation triggered by TRAP1 inhibition, but lactacystin did not (Figure ##SUPPL##0##S14D,E##, Supporting Information). Prior studies have reported that calpains, which are calcium‐activated proteases, are inhibited by MG132 but not by lactacystin,<sup>[</sup>\n##REF##11514224##\n26\n##\n<sup>]</sup> and can proteolyze HIF1α independently of PHD.<sup>[</sup>\n##REF##16421254##\n27\n##\n<sup>]</sup> Further, TRAP1 inhibition increases mitochondrial calcium discharge by increasing cyclophilin D (CypD) activity to trigger opening of the mitochondrial permeability transition pore (mPTP).<sup>[</sup>\n##REF##24731398##\n3\n##, ##REF##30683653##\n4\n##, ##REF##31956271##\n28\n##\n<sup>]</sup> Together, these data suggest that TRAP1 regulation of HIF1α is mediated by calcium and calpains.</p>", "<p>TRAP1 inhibition elevated the cytoplasmic calcium concentration and calpain enzyme activity (<bold>Figure</bold> ##FIG##4##\n5A,B##). Subsequently, among the ubiquitously expressed isoforms, calpain‐1, but not calpain‐2, was activated as indicated by calpain autolysis (Figure ##FIG##4##5C##).<sup>[</sup>\n##REF##11893336##\n29\n##\n<sup>]</sup> However, the expression of calpain‐1 was unaffected (Figure ##FIG##4##5D##). Previous reports suggest that calpain‐1 is activated in the micromolar range of calcium concentration and calpain‐2 near the millimolar range.<sup>[</sup>\n##REF##11914728##\n30\n##\n<sup>]</sup> Consistently, compared with the substantial calcium release triggered by thapsigargin from the ER, TRAP1 inhibition only modestly increased cytoplasmic calcium levels (Figure ##FIG##4##5A,E##), which was fully reversed by inhibition of CypD by siRNAs (Figure ##FIG##4##5C,E##), indicating the involvement of mitochondrial calcium discharge via the mPTP in HIF1α degradation.</p>", "<p>Both HIF1α degradation and calpain‐1 activation were fully reversed by treatment with CypD‐targeting siRNAs, a calcium chelator (1,2‐bis (o‐aminophenoxy) ethane‐<italic toggle=\"yes\">N</italic>, <italic toggle=\"yes\">N</italic>, <italic toggle=\"yes\">N</italic>', <italic toggle=\"yes\">N</italic>'‐tetraacetic acid (BAPTA)), and a calpain inhibitor (ALLN) (Figure ##FIG##4##5C,F,G##), further confirming that the mechanism is dependent on mitochondrial calcium/calpain‐1. TRAP1 inhibition increased calpain‐1 staining in mitochondria‐enriched perinuclear regions (<bold>Figure</bold> ##FIG##5##\n6A##), further supporting the notion that calpain‐1 was activated by the discharge of mitochondrial calcium. Similarly, the active (cleaved) forms of calpain‐1 were elevated in OIR and STZ retinas isolated from <italic toggle=\"yes\">TRAP1</italic>\n<sup>−/−</sup> mice, but not in control retinas or OIR and STZ retinas isolated from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> mice (Figure ##FIG##5##6B,C##). Proteolytic enzyme activity of calpain was also elevated in OIR and STZ retinas isolated from <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mice, but not in control retinas or OIR and STZ retinas isolated from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> mice (Figure ##FIG##5##6D,E##). Finally, siRNA‐mediated depletion of calpain‐1 abolished HIF1α degradation in MIO‐M1 cells, but treatment with calpain‐2‐targeting siRNA did not (Figure ##FIG##5##6F,G##), confirming the pathway is calpain‐1‐dependent. These data indicate that TRAP1 inhibition activates calpain‐1 to destabilize HIF1α by inducing mild mitochondrial calcium release into the cytosol (Figure ##FIG##5##6H##).</p>", "<p>Given that TRAP1 is implicated in the generation of mitochondrial reactive oxygen species (ROS),<sup>[</sup>\n##REF##25785725##\n24b\n##\n<sup>]</sup> resulting in the stabilization of HIF1α,<sup>[</sup>\n##REF##15369676##\n31\n##\n<sup>]</sup> we analyzed retinal ROS production using dihydroethidium (DHE) staining. The levels of DHE staining were comparable between <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mouse retinas from both STZ and OIR models (Figure ##SUPPL##0##S15A,B##, Supporting Information), indicating the retinal ROS production is not affected by TRAP1 expression.</p>", "<title>Pharmacological Inhibition of TRAP1 Alleviates Vascular Pathologies in OIR Mice</title>", "<p>Among representative allosteric and orthosteric TRAP1 inhibitors,<sup>[</sup>\n##REF##25785725##\n24\n##, ##REF##34758612##\n32\n##\n<sup>]</sup> MitoQ was more than 10‐fold higher potency than gamitrinib in inducing the degradation of HIF1α (<bold>Figure</bold> ##FIG##6##\n7A,B##). Treatment with MitoQ or gamitrinib did not affect HIF1α expression, the cytosolic calcium concentration, or calpain‐1 activation in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> cells (Figure ##SUPPL##0##S16A–C##, Supporting Information), indicating that it induces HIF1α degradation in a TRAP1‐specific manner. Similar to the phenotype of <italic toggle=\"yes\">Trap1</italic> KO mice, intravitreal injection of MitoQ dramatically reduced both avascular and neovascular tuft areas in OIR mice (Figure ##SUPPL##0##S17A,B##, Supporting Information). Furthermore, topically applied MitoQ showed potent activity, and its effects were comparable with those observed in <italic toggle=\"yes\">Trap1</italic> KO mice (Figure ##SUPPL##0##S17C,D##, Supporting Information), indicating that MitoQ was efficiently delivered to the posterior segment of the eye.</p>", "<p>TRAP1 inhibitors derived from MitoQ, SB‐U014, and SB‐U015, are more effective in inhibiting TRAP1 than MitoQ and lack antioxidant activity.<sup>[</sup>\n##REF##34758612##\n32\n##\n<sup>]</sup> These derivatives induced HIF1α degradation more strongly than MitoQ (Figure ##FIG##6##7A,B##). The IC<sub>50</sub> values of SB‐U014, SB‐U015, and MitoQ were 0.040, 0.041, and 0.077 µM, respectively. SB‐U014, SB‐U015, and MitoQ elicited cytotoxic effects on mouse primary Müller cells at concentrations of 27, 32, and 22 µM, respectively; therefore, there were several hundred‐fold (295–773‐fold) differences between the therapeutic and toxic doses (<bold>Table</bold> ##TAB##0##\n1\n##; Figure ##SUPPL##0##S18A##, Supporting Information). This indicates that the safety margins of all these drugs are very high, and that of SB‐U015 is highest. Topically applied MitoQ, SB‐U014, and SB‐U015 reduced the extent of avascular and neovascular tuft areas in OIR mice (Figure ##FIG##6##7C,D##).</p>", "<p>Following topical administration of SB‐U015 to mice and rabbits, the peak drug concentration (C<sub>max</sub>) was reached at 0.83 and 1.5 h (T<sub>max</sub>), respectively. The C<sub>max</sub> and area under the concentration‐time curve to last measurement (AUC<sub>last</sub>) values were 1.8‐ and 2‐fold higher in rabbit retina than in P12 mouse retina, respectively (<bold>Table</bold> ##TAB##1##\n2\n##). These data suggest that topically administered SB‐U015 can be sufficiently delivered to the retina irrespective of ocular size and anatomy. Furthermore, all drugs were nonirritants in the reconstructed human cornea epithelial model according to the OECD guidelines for test chemicals (Figure ##SUPPL##0##S18B## and Table ##SUPPL##0##S1##, Supporting Information), and there was no noticeable histologic abnormality after topical application of TRAP1 inhibitors based on hematoxylin and eosin (H&amp;E) staining (Figure ##SUPPL##0##S18C##, Supporting Information), suggesting that topical application of the drugs is safe.</p>", "<p>Collectively, these data demonstrate that TRAP1 inhibitors can be developed as therapeutic agents to treat ischemic retinopathy, alleviating pathological angiogenesis and restoring the normal vascular architecture via topical application.</p>" ]
[ "<title>Discussion</title>", "<p>HIF1α is a transcription factor that contributes to the pathogenesis of ischemic retinopathy by up‐regulating expression of proangiogenic factors.<sup>[</sup>\n##REF##26113211##\n33\n##\n<sup>]</sup> The present study demonstrated that mitochondrial chaperone TRAP1 is necessary for HIF1α‐dependent retinal pathogenesis in mouse models of ischemic retinopathy. Genetic and pharmacologic inhibition of TRAP1 triggered calpain‐1 activation and subsequent HIF1α degradation in both ischemic OIR and diabetic STZ mice, which not only suppressed pathologic neovascularization but also restored BRB integrity and microvascular structure without any recognizable adverse effects. Our data collectively indicate that TRAP1 is a novel druggable target to treat HIF1α‐driven ischemic retinopathies, and that small molecule inhibitors of TRAP1, such as MitoQ and SB‐U015, could be utilized to develop potent therapeutics with well‐tolerated topical administration.</p>", "<p>In the ischemic retina, TRAP1 altered mitochondrial signaling by inhibiting CypD, the master regulator of mPTPs, and subsequently decreasing mPTP opening.<sup>[</sup>\n##REF##24731398##\n3\n##, ##REF##30683653##\n4\n##\n<sup>]</sup> Although the molecular components are controversial, there are at least two types of mPTPs, namely, a reversible low conductance pore with physiological functions and an irreversible high conductance pore involved in cell death.<sup>[</sup>\n##REF##34880425##\n34\n##\n<sup>]</sup> In many cancer cells, TRAP1 inhibition triggers opening of high conductance pores by activating CypD, which results in massive calcium discharge, leading to mitochondrial dysfunction and cell death.<sup>[</sup>\n##REF##24731398##\n3\n##, ##REF##30683653##\n4\n##\n<sup>]</sup> However, in retinal cells, TRAP1 inhibition seems to trigger opening of the low conductance mPTP and a small amount of mitochondrial calcium discharge because it does not elicit cytotoxic effects; activates calpain‐1, which requires a low micromolar concentration of calcium; and does not activate calpain‐2, which requires a high micromolar to millimolar concentration of calcium.<sup>[</sup>\n##REF##11893336##\n29\n##\n<sup>]</sup> Due to the diffusive nature and relatively low level of calcium released upon TRAP1 inhibition, calpain‐1 was elevated (and probably activated) primarily near to mitochondria. This is reminiscent of the recruitment of calpains to the endoplasmic reticulum and Golgi where the local calcium concentration is elevated for their efficient activation.<sup>[</sup>\n##REF##32848200##\n35\n##\n<sup>]</sup> Collectively, our data suggest that spatiotemporal regulation of calpain‐1 is coordinated by mPTP opening and mitochondrial calcium discharge in the hypoxic retina. Thus, in diseased hypoxic retinal cells, expression of TRAP1 is induced to close mPTPs and maintain mitochondrial calcium storage, which is essential for activation of HIF1α and development of retinopathy.</p>", "<p>To induce OIR, mouse pups are reared in a hyperoxic chamber (P7‐P12, 75% O<sub>2</sub>), which mimics oxygen exposure in preterm infants in neonatal intensive care.<sup>[</sup>\n##REF##22455417##\n7\n##, ##REF##19816419##\n13\n##\n<sup>]</sup> Thus, the OIR model has been widely used to study ROP and develop therapeutic interventions,<sup>[</sup>\n##REF##19816419##\n13a\n##\n<sup>]</sup> suggesting that TRAP1 inhibitors could be used to develop therapeutics for ROP acting via novel mechanisms. In addition, OIR mimics pathologic retinal neovascularization that is driven by hypoxia and aberrant expression of angiogenic factors in proliferative DR .<sup>[</sup>\n##REF##28724805##\n9\n##\n<sup>]</sup> Mice with STZ‐induced diabetes exhibited retinal hypoxia and HIF1α activation similar to those observed in OIR mice, which likely contributed to early vascular pathologies characteristic of non‐proliferative DR, such as vascular hyperpermeability and capillary degeneration.<sup>[</sup>\n##REF##22455417##\n7a\n##\n<sup>]</sup> Therefore, further research into the functions of TRAP1 in the progression of DR could lead to the development of novel treatments for early and advanced stages of DR based on TRAP1 inhibitors.</p>", "<p>Laser photocoagulation surgery, which permanently destroys peripheral retinal vessels, is currently the standard of care for severe ROP in preterm infants.<sup>[</sup>\n##REF##22455417##\n7c\n##\n<sup>]</sup> Intravitreal injection of anti‐VEGF drugs has recently been combined with laser photocoagulation therapy to improve the treatment outcome by minimizing irreversible loss of the visual field due to peripheral retinal ablation.<sup>[</sup>\n##REF##21323540##\n36\n##\n<sup>]</sup> However, because VEGF plays an important role in vascular development of the retina and other tissues in preterm infants, the potential ocular and systemic side effects of intravitreally administered anti‐VEGF drugs cannot be ignored.<sup>[</sup>\n##REF##27506484##\n11\n##, ##UREF##0##\n37\n##\n<sup>]</sup> Contrastingly, TRAP1 inhibition is unlikely to pose a risk for these side effects, as expression of angiogenic factors, including VEGF, ANGPTL4, and ANG2, was only suppressed partially to physiological levels in OIR mice. Consistently, vascular regression, which can be caused by complete inhibition of angiogenic factors, was not observed in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mice. This finding indicates that TRAP1 did not affect basal expression of angiogenic factors during physiologic retinal vascular development. Collectively, TRAP1 inhibition suppresses only aberrant angiogenic factors produced by stabilized HIF1α in the diseased ischemic retina. This intervention can thus enable normalization of vascular structure by restoring balanced expression of angiogenic factors in OIR mice. Thus, TRAP1 should be further evaluated as a novel therapeutic target for development of safe and effective ROP interventions that do not present the concerns of vascular disruption induced by laser surgery and VEGF inactivation.</p>", "<p>Intravitreal injection of anti‐VEGF drugs has also been widely performed as a standard of care for diabetic retinopathies such as diabetic macular edema and PDR.<sup>[</sup>\n##REF##22455417##\n7\n##, ##REF##28724805##\n9\n##\n<sup>]</sup> However, targeting VEGF alone has several limitations. Specifically, some patients are refractory to anti‐VEGF drugs,<sup>[</sup>\n##REF##28724805##\n9\n##, ##REF##25692915##\n38\n##\n<sup>]</sup> and repeated therapy, especially of DR patients, can lead to tissue atrophy and ischemia.<sup>[</sup>\n##REF##18607560##\n39\n##\n<sup>]</sup> Drug irresponsiveness can arise, at least in part, due to other HIF1α‐inducible factors such as ANGPTL4 and ANG2,<sup>[</sup>\n##REF##33469209##\n10\n##\n<sup>]</sup> leading to neovascularization and BRB deterioration in the absence of VEGF. Consistently, combined neutralization of such proangiogenic factors has better efficacy than VEGF monotherapy in animal disease models,<sup>[</sup>\n##UREF##1##\n40\n##\n<sup>]</sup> and a bispecific antibody drug, faricimab, has recently been approved for the treatment of ocular diseases.<sup>[</sup>\n##REF##35396185##\n21b\n##\n<sup>]</sup> These considerations support the proposition that a TRAP1 inhibition strategy could be effective for the treatment of ischemic retinopathies, which would inactivate the upstream master regulator HIF1α to simultaneously block pathological up‐regulation of multiple angiogenic regulators.</p>", "<p>Currently, no ophthalmic preparations are available for the treatment of retinal diseases, which is likely due to poor drug delivery to the posterior segment. Thus, more research will be required to understand the factors affecting the efficiency of drug delivery to the retina to develop optimal and effective ophthalmic solutions. To this end, in this study, we compared the ocular pharmacokinetics of the most potent TRAP1 inhibitor SB‐U015 in mice and rabbits. The results revealed that rabbits accumulated more SB‐U015 in their retinas than mice after topical administration, indicating that the drug can reach the retina irrespective of eyeball size and anatomy. These findings suggest that eye drop application of TRAP1 inhibitors has the potential to achieve effective drug concentrations in human retinas, providing a noninvasive treatment option for ischemic retinopathies.</p>", "<p>In this study, the mitochondrial chaperone TRAP1 was identified and validated as a target protein for development of effective therapeutics for ischemic retinopathies with a novel mode of action. Furthermore, considering that small molecules have high tissue penetration and improved stability compared with large molecular weight antibody drugs, TRAP1 inhibitors could be not only formulated as noninvasive ophthalmic solutions as shown here, but also combined with various drug delivery systems such as drug‐loaded contact lens and long‐lasting implants to avoid or reduce patient treatment burdens associated with repeated intravitreal injections.</p>" ]
[]
[ "<title>Abstract</title>", "<p>Activation of hypoxia‐inducible factor 1α (HIF1α) contributes to blood‐retinal barrier (BRB) breakdown and pathological neovascularization responsible for vision loss in ischemic retinal diseases. During disease progression, mitochondrial biology is altered to adapt to the ischemic environment created by initial vascular dysfunction, but the mitochondrial adaptive mechanisms, which ultimately contribute to the pathogenesis of ischemic retinopathy, remain incompletely understood. In the present study, it is identified that expression of mitochondrial chaperone tumor necrosis factor receptor‐associated protein 1 (TRAP1) is essential for BRB breakdown and pathologic retinal neovascularization in mouse models mimicking ischemic retinopathies. Genetic <italic toggle=\"yes\">Trap1</italic> ablation or treatment with small molecule TRAP1 inhibitors, such as mitoquinone (MitoQ) and SB‐U015, alleviate retinal pathologies via proteolytic HIF1α degradation, which is mediated by opening of the mitochondrial permeability transition pore and activation of calcium‐dependent protease calpain‐1. These findings suggest that TRAP1 can be a promising target for the development of new treatments against ischemic retinopathy, such as retinopathy of prematurity and proliferative diabetic retinopathy.</p>", "<p>This study reveals that the mitochondrial chaperone TRAP1 is vital for stabilizing HIF1α, a key transcription factor in pathologic microvascular changes in ischemic retinopathies. Therefore, inhibiting TRAP1 genetically or pharmacologically alleviates retinal vascular pathologies by inducing HIF1α proteolytic degradation, indicating that TRAP1 can be a promising target for the development of therapies for ischemic retinopathy.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6878-cit-0072\">\n<string-name>\n<given-names>S.‐Y.</given-names>\n<surname>Kim</surname>\n</string-name>, <string-name>\n<given-names>N. G.</given-names>\n<surname>Yoon</surname>\n</string-name>, <string-name>\n<given-names>J. Y.</given-names>\n<surname>Im</surname>\n</string-name>, <string-name>\n<given-names>J. H.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Kim</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Jeon</surname>\n</string-name>, <string-name>\n<given-names>Y. J.</given-names>\n<surname>Choi</surname>\n</string-name>, <string-name>\n<given-names>J.‐H.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>A.</given-names>\n<surname>Uemura</surname>\n</string-name>, <string-name>\n<given-names>D. H.</given-names>\n<surname>Park</surname>\n</string-name>, <string-name>\n<given-names>B. H.</given-names>\n<surname>Kang</surname>\n</string-name>, <article-title>Targeting the Mitochondrial Chaperone TRAP1 Alleviates Vascular Pathologies in Ischemic Retinopathy</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2302776</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202302776</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Chemicals and Antibodies</title>", "<p>All chemicals were purchased from Sigma (Burlington, MA, USA) unless indicated otherwise. DMOG, ALLN (calpain inhibitor), lactacystin, and thapsigargin were purchased from Cayman (Ann Arbor, MI, USA). MitoQ and 17‐DMAG were purchased from MedChemExpress (Monmouth Junction, NJ, USA) and LC laboratories (Woburn, MA, USA), respectively. Antibodies against TRAP1 (#612344), HIF1α (#610958), CD31 (#550274), VE‐cadherin (#555289), Ter119 (#561033), Hsp90 (#610418), and Hsp70 (#610607) were purchased from BD Biosciences (San Jose, CA, USA). Isolectin B4 (IB4) conjugated with Alexa Fluor 488 (#I21411) and antibodies against TRAP1 (#PA5‐27596), calpain‐1 (#MA3‐940), and PDGFR‐β (#14‐1402‐82) were purchased from Invitrogen (Waltham, MA, USA). Antibodies against HIF1α (#NB 100–479), and VEGF (#NB 100–664) were purchased from Novus Biologicals (Centennial, CO, USA). Anti‐collagen IV (#ab19808), anti‐TRAP1 (#ab151239), anti‐F4/80 (#ab6640), and anti‐GFAP (ab#53554) antibodies were purchased from Abcam (Cambridge, UK). Antibodies against calpain‐2 (#2539) and cleaved caspase‐3 (#9664) were purchased from Cell Signaling Technology (Danvers, MA, USA). Antibodies against β‐actin (#MP 691001) and glutamine synthetase (#MAB302) were purchased from Millipore (Burlington, MA, USA). Antibodies against ANG2 (#MAB 098–100) and VEGF (#AF‐493‐SP) were purchased from R&amp;D Systems (Minneapolis, MN, USA). Antibodies against ANGPTL4 (#LS‐C331822‐100; Lifespan Bioscience; Seattle, WA, USA), Chk1 (#sc‐8408; Santa Cruz; Dallas, TX, USA), CypD (#AP1035; Calbiochem; San Diego, CA, USA), and fibrinogen (#F8512; Sigma) were obtained from the indicated suppliers.</p>", "<title>Animal Models of Retinopathy</title>", "<p>All animal experiments except ocular pharmacokinetic analyses in rabbits were approved by the Institutional Animal Care and Use Committee (IACUC) of the Ulsan National Institution of Science and Technology (IACUC‐UNIST20‐01, IACUC‐UNIST21‐21, and IACUC‐UNIST21‐30). The rabbit ocular pharmacokinetic experiment was approved by the IACUC of Knotus (KNOTUS IACUC 22‐KE‐0109) and conducted in Knotus (Republic of Korea). Animals were housed in a room with constant humidity (40–60%) and temperature (20–25°C) under a 12 h light‐dark cycle. Mice were given free access to food and water.</p>", "<p>To induce OIR (Figure ##FIG##0##1A##), mouse pups were exposed to 75% oxygen at postnatal day 7 (P7) until P12 together with their mothers in a hyperoxic chamber (InVivo Cabinet Model 15; Coy Laboratory; Grass Lake, MI, USA). Hyperoxia‐exposed pups were returned to room air at P12 with nursing mothers until P17. At P17, mice were sacrificed, and eyes were enucleated.</p>", "<p>\n<italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mice were designed and generated by the UC Davis Mouse Biology Program. The <italic toggle=\"yes\">Trap1</italic> locus was genotyped using the following primers: 5′‐GAGGAGTGGTATTGGAAGTATGGAC‐3′ and 5′‐AGTAGCTTTCCCTTATATACAGAATGCC‐3′ for the wild‐type allele, and 5′‐AGTTCAATGCAAGACTTCTGCCAAGG‐3′ and 5′‐GAGATGGCGCAACGCAATTAAT‐3′ for the <italic toggle=\"yes\">Trap1</italic> KO allele (Figure ##SUPPL##0##S2A##, Supporting Information).</p>", "<p>For the STZ mouse model of type 1 diabetes (Figure ##SUPPL##0##S6A##, Supporting Information), STZ (75 mg/kg/day) was intraperitoneally injected into 8‐week‐old male C57BL/6J mice for 5 days. The fasting blood glucose levels of mice were measured every week with a glucometer to monitor development and maintenance of diabetes. Mice with glucose levels of 350 mg dl<sup>−1</sup> or higher were deemed diabetic. Mouse eyes were collected and analyzed at 16 weeks after STZ treatment.</p>", "<title>Intravitreal Injection and Topical Treatment of Drugs in OIR Mice</title>", "<p>For intravitreal injection, MitoQ was injected into the vitreous cavity using a Nanoliter 2000 microinjector (World Precision Instruments; Sarasota, FL, USA) fitted with glass capillary pipettes under anesthesia. In total, 1 µl MitoQ (0.1 mg/ml) was delivered into the right eye of an OIR mouse once at P12. The contralateral eye was injected with vehicle (0.1% DMSO prepared in distilled water) as a control. For topical treatment, 10 µl drug dissolved in 80% Liposic (Bauch Health Companies Inc.; Laval, Canada) was applied to the right eye, and vehicle was applied to the contralateral left eye for 1 min, and then residual drugs were wiped out. Mice were treated with the drugs once or thrice daily from P12 to P17.</p>", "<title>Immunohistochemistry and Hypoxyprobe Staining</title>", "<p>For hypoxic tissue staining, 60 mg/kg Hypoxyprobe (Burlington, MA, USA) was intravenously and intraperitoneally injected into STZ and OIR mice, respectively. After 90 min, mice were intracardially perfused with phosphate‐buffered saline (PBS), and eyes were harvested and fixed with 4% paraformaldehyde (PFA) overnight at 4°C. STZ mouse eyes underwent slide staining after production of paraffin blocks, and OIR mouse eyes underwent whole‐mount staining. Paraffin‐embedded tissue sections were analyzed by immunohistochemistry using a Rabbit and Mouse Specific HRP/DAB (ABC) Detection IHC Kit (Abcam) according to the manufacturer's instructions. Paraffin sections were dewaxed, rehydrated, and treated with the hydrogen peroxide block for 10 min, followed by heat‐induced antigen retrieval in 10 m<sc>m</sc> sodium citrate (pH 6.0) using a pressure cooker. Tissue slides were blocked with blocking solution followed by the Hypoxyprobe primary antibody overnight at 4 °C. The next day, slides were incubated with biotinylated goat antipolyvalent and streptavidin peroxidase, and then the DAB substrate reaction was performed. Tissue slides were scanned with a slide scanner microscope (Olympus; Tokyo, Japan) and analyzed using ImageJ.</p>", "<title>Fluorescein Angiography and Fluorescein‐Dextran Permeability Analyses</title>", "<p>For angiographic analysis of retinal vascular leakage, 100 µl of 1% fluorescein sodium (Sigma) was intraperitoneally injected into age matched control and 16‐week‐old STZ mice, respectively. Mice were anesthetized with intraperitoneal injection of 2.5% avertin (250 mg/kg). Isopto Atropine drops (Alcon, Geneva, Switzerland) were used for dilation, followed by the application of GenTeal Tears (Alcon) for lubrication of mouse eyes. Retinal vessel leakage was imaged by an iVivo Funduscope (OcuScience, Henderson, NV, USA), and quantified using ImageJ.</p>", "<p>For fluorescein‐dextran permeability analysis, mice were anesthetized with an intraperitoneal injection of 2.5% avertin (250 mg/kg), followed by the injection of 100 µl fluorescein‐dextran (1.25 mg/mouse, Sigma) into the left ventricle. After 5 min, eyes were collected, fixed in 4% PFA for 2 h on ice, and whole‐mounted onto glass slides after dissection. Fluorescence images were acquired using an LSM980 confocal microscope (Zeiss) and analyzed with ImageJ.</p>", "<title>Immunostaining of Whole‐Mount Retinas</title>", "<p>Fixed eyes were dissected to isolate retinas under a microscope. Subsequently, flattened retinas were blocked, permeabilized, and exposed to primary and secondary antibodies as described for immunofluorescence staining. Retinas were immersed in mounting medium. Fluorescence images were acquired using an Axio Zoom fluorescence microscope (Zeiss; Oberkochen, Germany) or a LSM780 or LSM980 confocal microscope (Zeiss). Image analyses were performed with a Zeiss image analyzer.</p>", "<title>Immunofluorescence Staining</title>", "<p>After heat‐induced antigen retrieval, tissue slides were permeabilized with PBS containing 1% Triton X‐100 for 1 h; blocked with PBS containing 5% fetal bovine serum (FBS), 5% bovine serum albumin (BSA), and 0.3% Triton X‐100 for 1 h at room temperature (RT); incubated with primary antibodies overnight at 4°C; and stained with Alexa Fluor‐labeled secondary antibodies (Invitrogen) for 1 h at RT. After incubation, the slides were stained with DAPI (Invitrogen) for 5 min at RT and immersed in mounting medium (Vector Laboratories; Newark, CA, USA). Images were acquired using a LSM780 confocal microscope (Zeiss). Image analyses were performed with Zeiss image analyzer.</p>", "<title>Dihydroethidium (DHE) Staining</title>", "<p>After heat‐induced antigen retrieval, tissue slides were blocked with PBS containing 5% fetal bovine serum (FBS), 5% bovine serum albumin (BSA), and 0.3% Triton X‐100 for 1 h at room temperature (RT). After blocking, the slides were incubated with 5 µM DHE (Invitrogen) in 1XPBS solution for 30 min at 37 °C in dark, stained with DAPI (Invitrogen) for 5 min at RT, and then immersed in mounting medium (Vector Laboratories; Newark, CA, USA). 10 m<sc>m</sc>\n<italic toggle=\"yes\">N</italic>‐acetyl cysteine (NAC; Sigma) was used to eliminate ROS as a negative control. Images were acquired using an LSM780 confocal microscope (Zeiss) and analyzed using a Zeiss image analyzer.</p>", "<title>Cell Culture and Knockdown Experiments</title>", "<p>The human Müller cell line MIO‐M1 was a gift from Prof. S. Yoshida (University of Kurume, Kurume, Fukuoka, Japan), and was cultured in DMEM‐low glucose (Sigma) supplemented with 10% FBS (Gibco; Waltham, MA, USA) and 1% penicillin‐streptomycin (Gibco). GFP‐expressing HUVECs (Angio‐Proteomie; Boston, MA, USA) were cultured in EGM medium (Lonza; Basel, Switzerland). HBVPs (Sciencell; Carlsbad, CA, USA) were cultured in pericyte media (Sciencell). All cell lines were cultured as recommended by the manufacturer and incubated at 37 °C with 5% CO<sub>2</sub>. For knockdown experiments, siRNAs were transfected using G‐fectin (Genolution; Seoul, Republic of Korea) as instructed by the supplier. siRNAs targeting TRAP1, HIF1α, calpain‐1, calpain‐2, and CypD were synthesized by Genolution as follows:\n\n</p>", "<title>Generation of <italic toggle=\"yes\">Trap1</italic> Knockout (KO) Cell Lines</title>", "<p>MIO‐M1 <italic toggle=\"yes\">Trap1</italic> KO cell lines were generated using CRISPR/Cas9‐derived RNA‐guided endonucleases (Toolgen; Seoul, Republic of Korea). MIO‐M1 cells were co‐transfected with the Cas9 vector and TRAP1‐sgRNA expression vector (sgRNA sequence 1; 5′‐CTCGGCCTGGAACTCATGTTTGG‐3′ and sequence 2; 5′‐AGCTTTTGGACATTGTTGCCCGG‐3′) using jetPRIME transfection reagent (Polyplus; Illkirch‐Graffenstaden, France). Transfected cells were selected in culture medium containing 3 mg/ml puromycin (Sigma). Single‐cell colonies were collected using a cloning cylinder (I.D. × H 6.4 mm × 8 mm; Sigma) and analyzed using T7 endonuclease I to confirm <italic toggle=\"yes\">Trap1</italic> KO.</p>", "<title>Flow Cytometric Analysis of Cellular Calcium</title>", "<p>Cells (2 × 10<sup>5</sup>) were cultured on a 6‐well plate, treated with drugs under hypoxia or normoxia for 6 h, and stained with 2 µ<sc>m</sc> Fluo‐4 AM (Invitrogen) for 30 min at RT. Fluorescence signals were detected using a flow cytometer (LSRFortessa; BD Biosciences).</p>", "<title>Isolation of Primary Müller Cells</title>", "<p>Mouse primary Müller cells were isolated as reported previously.<sup>[</sup>\n##UREF##2##\n43\n##\n<sup>]</sup> In brief, retinas were isolated from P5–P7 mice and dissociated using a Papain Dissociation Kit (Worthington Industries; Columbus, OH, USA). Collected retinal cells were incubated on a plate coated with 0.1% gelatin (Sigma), and the culture media (DMEM supplemented with 10% FBS and 1% penicillin‐streptomycin) was changed once every 2 days. Cells were subcultured into a new plate and incubated for another 7 days. Adherent cells were largely primary Müller cells, as confirmed by immunocytochemical analysis using an anti‐glutamine synthetase antibody (Millipore).</p>", "<title>Preparation of CM and the Tube Formation Assay</title>", "<p>To collect CM from MIO‐M1 cells exposed to hypoxia, cells were transfected with siRNAs and incubated for 24 h in normoxia. The media were replaced by fresh DMEM/F12 supplemented with 1% FBS, and cells were incubated for another 24 h under normoxia or 1% O<sub>2</sub> hypoxia chamber (SMA‐30D; Astec; Fukuoka, Japan). The media were collected, centrifuged at 130 g for 5 min, and stored at −80°C as CM (Figure ##SUPPL##0##S12A##, Supporting information). In total, 8 × 10<sup>4</sup> GFP‐expressing HUVECs and 1.6 × 10<sup>4</sup> HBVPs labeled with CellTracker Red CMTPX (Invitrogen) were suspended in CM supplemented with 1% FBS and plated in a 35 mm coverglass‐bottom dish (Spl; Gyeonggi‐do, Republic of Korea) coated with Matrigel (Corning; Corning, NY, USA). Cells were incubated for 6 h to allow tube formation. Images were acquired using a LSM780 confocal microscope and analyzed using a Zeiss image analyzer.</p>", "<title>Proteome Profiler Human Angiogenesis Array</title>", "<p>Proteome profiler arrays for 55 human angiogenesis‐related proteins were used according to the manufacturer's instructions (ARY007; Proteome Profiler Human Cytokine Array Kit, R&amp;D Systems, Minneapolis, MN, USA). A total of 500 µl conditioned media (CM) collected from MIO‐M1 cells exposed to hypoxia was combined with biotinylated antibodies and incubated with the membrane overnight at 4 °C. On the following day, the membrane was washed with 1X wash buffer and subsequently incubated with Streptavidin‐HRP for 30 min. After incubation, the membrane was washed three times and developed using the ECL solution. Analysis was performed using a LAS4000 system (GE Healthcare; Chicago, IL, USA), and pixel density was quantified using ImageJ.</p>", "<title>Western Blotting</title>", "<p>Cells and tissue samples were lysed using RIPA buffer (50 mM Tris, pH 8.0, 150 m<sc>m</sc> NaCl, 1% NP‐40, and 0.25% <italic toggle=\"yes\">N</italic>‐deoxycholate) containing protease and phosphatase inhibitor cocktails (Roche). Lysates were separated by SDS‐PAGE and transferred to PVDF membranes. The membranes were blocked with 10% skim milk prepared in TBST (TBS (50 mM Tris and 150 m<sc>m</sc> NaCl, pH 7.6) containing 0.05% Tween‐20) for 1 h at RT and incubated with primary antibodies in antibody diluent solution (TBS containing 3 m<sc>m</sc> sodium azide and 0.1% BSA) overnight at 4 °C. After washing with TBST, the membranes were incubated with secondary antibodies for 1 h in 10% skim milk prepared in TBST. Finally, the membranes were washed three times with TBST, treated with ECL solution (Bio‐Rad; Hercules, CA, USA), and analyzed using a LAS4000 system (GE Healthcare; Chicago, IL, USA).</p>", "<title>Eye Irritation Test with MCTT HCE</title>", "<p>An eye irritation test was performed using a 3D human corneal epithelial (HCE) model, called MCTT HCE (KeraSkin; Biosolution, Seoul, Republic of Korea), for OECD test guideline 492, following the manufacturer's instructions. In brief, HCE tissues were incubated overnight in medium provided by the supplier. Thereafter, 2 m<sc>m</sc> MitoQ, SB‐U014, and SB‐U015 were applied to the upper epithelial surface of HCE tissues and incubated for 10 min. After removing the drugs by washing the tissues with PBS, the tissues were further incubated for 16 h, and then subjected to the WST‐1 assay for viability assessment and fixed in 4% PFA for histological analysis.</p>", "<title>RNA Extraction and Real Time PCR Analysis</title>", "<p>Tissue samples and cells were treated with TRIzol (Thermo Fisher Scientific, Waltham, MA, USA) and chloroform (Sigma), and total RNA was prepared with an RNA extraction kit (Qiagen; Hilden, Germany). cDNA was synthesized from RNA using a RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific) with oligo dT. cDNA was amplified with the primer sets shown below and qPCR SYBR Green pre‐mix (Enzynomics; Daejeon, Republic of Korea) on a LightCycler 480 system (Roche).</p>", "<title>Sequences of Real Time PCR Primers</title>", "<p>\n\n</p>", "<title>Calpain Activity Assay</title>", "<p>Calpain enzyme activity was measured using a Calpain Activity Assay Kit (Abcam) according to the manufacturer's instructions. In brief, cell and tissue samples were lysed with the extraction buffer provided with the kit. After homogenization and centrifugation of samples, soluble fractions were collected. A mixture of cell lysate, reaction buffer, and calpain substrate (Ac‐LLY‐AFC) was incubated for 1 h at 37 °C. Fluorescence was measured at <italic toggle=\"yes\">λ</italic>\n<sub>ex</sub> = 400 nm and <italic toggle=\"yes\">λ</italic>\n<sub>em</sub> = 500 nm using a microplate reader (Synergy neo; Biotek; Winooski, VT, USA).</p>", "<title>Ocular Pharmacokinetic Analysis after Topical Drug Administration</title>", "<p>The rabbit pharmacokinetic experiment was approved by the IACUC of Knotus (KNOTUS IACUC 22‐KE‐0109) and conducted in Knotus (Republic of Korea). The mouse pharmacokinetic experiment was approved by the IACUC of UNIST. Male New Zealand white rabbits weighing 2.0–2.5 kg provided by the Hallym animal center (Anyang, Republic of Korea), and C57BL/6J mice at P17 were used for the pharmacokinetic study. For topical treatment, 50 and 10 µl SB‐U015 dissolved in Liposic were topically administered once to both eyes of rabbits and mice, respectively. Residual drugs were wiped out after blinking 2–3 times. Animals were sacrificed at 0, 0.5, 1, 2, and 4 h after drug treatment, and the following samples were immediately prepared: retina for mice and rabbits, and cornea, sclera, aqueous humor, and plasma for rabbits. Collected samples were kept at −80 °C until analysis.</p>", "<p>Plasma and tissue samples were analyzed according to an optimized bioanalytical method. Ocular tissues (retina, cornea, and sclera) were diluted fivefold with acetonitrile and homogenized with a Retsch MM400 instrument (Haan, Germany). Thereafter, 10 µl aliquots of chlorpropamide were added as an internal standard to 50 µl aliquots of plasma, aqueous humor, and diluted ocular tissues, followed by 200 µl aliquots of acetonitrile for protein precipitation. The mixture was vortexed for 10 min and centrifuged at 16 100 g at 4 °C for 10 min. In total, 5 µl of the supernatant was injected into the LC‐MS/MS system.</p>", "<p>The HP 1290 infinity system (Agilent; Santa Clara, CA, USA) was composed of a binary pump, degasser, autosampler, and column oven. A Kinetex C18 column (50 × 2.1 mm, 2.6 µm particle size; Phenomenex; Torrance, CA, USA) was used with a mobile phase consisting of (A) acetonitrile containing 0.1% formic acid and (B) deionized water containing 0.1% formic acid with isocratic mode (A:B = 60:40). The positive ion mode of the Agilent 6430 Triple Quad LC‐MS/MS system (Agilent) linked with ultraperformance liquid chromatography was used. Multiple‐reaction monitoring was used to track the ion transition at m/z 553.2→262.1 for SB‐U015 and m/z 227.0→175.0 for chlorpropamide. MassHunter software (ver 6.0; Agilent) was used to operate LC‐MS/MS and collect data.</p>", "<p>Pharmacokinetic analysis was achieved by noncompartmental analysis using Phoenix WinNonlin 8.1 (Certara; Princeton, NJ, USA). The time (T<sub>max</sub>) taken to reach the peak concentration (<italic toggle=\"yes\">C</italic>\n<sub>max</sub>) was determined directly from the profile of the time‒plasma concentration. The linear‐log trapezoidal rule was applied to calculate the area under the tissue concentration‒time curve from time zero to the last quantification (AUC<sub>last</sub>).</p>", "<title>Statistical Analysis</title>", "<p>All data are presented as mean ± standard error of the mean (SEM) from at least two independent experiments. Statistical analyses were performed using Prism 7 (GraphPad Software; La Jolla, CA, USA). The two‐tailed Student's <italic toggle=\"yes\">t</italic>‐test was performed to compare different groups. <italic toggle=\"yes\">P</italic> &lt; 0.05 was considered statistically significant.</p>", "<title>Conflict of interest</title>", "<p>B.H.K. is the founder of SmartinBio. Inc. Other authors declare that they have no competing interests.</p>", "<title>Author Contributions</title>", "<p>S.Y.K. and N.G.Y. contributed equally to this work. S.Y.K., N.G.Y., D.H.P., and B.H.K. conceived and designed the study. S.Y.K. and N.G.Y. performed most experiments. J.Y.I. generated OIR and STZ mice. Ji Hye Lee contributed to histologic sample preparation. J.K., Y.J.J., and D.H.P. performed OIR mouse experiments. Y.J.C. and Jong‐Hwa Lee performed ocular pharmacokinetics analysis. S.Y.K., N.G.Y., D.H.P., A.U., and B.H.K. analyzed the data. S.Y.K., N.G.Y., D.H.P., and B.H.K. wrote the manuscript with feedback from all authors.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>N.G.Y. is supported by the National Research Foundation (NRF) funded by the Ministry of Science and ICT (MSIT), Republic of Korea (2022R1C1C2010406). D.H.P. is supported by the NRF funded by MSIT (2019R1A2C1084371); the Information Technology Research Center support program funded by MSIT and supervised by the Institute of Information and Communications Technology Planning and Evaluation (IITP) (IITP‐2023‐2020‐0‐01808); the Korea Drug Development Fund (KDDF) funded by MSIT, Ministry of Trade, Industry, and Energy, and Ministry of Health and Welfare (MOHW) (RS‐2021‐DD120784 (HN21C0923000021)); and the Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI) funded by MOHW (HR22C1832). B.H.K. is supported by the NRF (2019R1A2C2086618, 2018R1A5A1024340, 2019M3A9A8065669, and 2022M3E5F2017408) and the KDDF (RS‐2021‐DD120712 (HN21C0882)). Figure ##FIG##5##6H## and the table of contents (ToC) image were created with BioRender.com.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available in the supplementary material of this article.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6878-fig-0001\"><label>Figure 1</label><caption><p>Contribution of TRAP1 to the development of ischemic retinopathy. A) Schematic for the experimental procedures of OIR mice. OIR mice were generated as described in the Experimental Section. P7 mice were exposed to hyperoxia (75% oxygen) for 5 days (vaso‐obliteration), and then returned to room air for 5 days (compensatory neovascularization). At P17, mice were sacrificed for analyses. B) Quantification of TRAP1 mRNA. Retinas collected from OIR mice and age‐matched control mice (RA, room air) were analyzed by quantitative real time PCR (qPCR) (<italic toggle=\"yes\">n</italic> = 6; duplicate experiment of 3 mice/group). C) Quantification of TRAP1 protein levels. Left. RA and OIR mouse retinas were comparatively analyzed by western blotting. Right. The band intensities of TRAP1 were normalized to those of β‐actin in mouse retinas and compared (<italic toggle=\"yes\">n</italic> = 10 mice/group). D) Immunohistochemical staining of TRAP1 in mouse retinas. Mouse retinal sections were stained with an anti‐TRAP1 antibody (red) and DAPI (blue), and analyzed by confocal microscopy. Scale bar, 20 µm and 5 µm (enlarged image). GCL, ganglion cell layer; IPL, inner plexiform layer; INL, inner nuclear layer; OPL, outer plexiform layer; ONL, outer nuclear layer (<italic toggle=\"yes\">n</italic> = 3 mice/RA, <italic toggle=\"yes\">n</italic> = 6 mice/OIR). E) Normalized retinal blood vessels in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice. Left. Retinas collected from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice were flat‐mounted and stained with an anti‐CD31 antibody. Scale bars, 500 µm (top) and 100 µm (bottom). Right. Quantification of neovascular tuft (NVT) and avascular areas. Retinal vessel images (<italic toggle=\"yes\">n</italic> = 9 mice/group) were quantitatively analyzed as reported previously.<sup>[</sup>\n##REF##19816419##\n13a\n##\n<sup>]</sup> F) Hypoxyprobe staining of OIR mouse retinas. Left. Whole‐mounted retinas from OIR mice (P17) were stained with Hypoxyprobe (green) and an anti‐CD31 antibody (red) to visualize hypoxic regions and blood vessels, respectively. Hypoxic areas were significantly decreased in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice relative to <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> OIR mice. Scale bar, 200 µm. Right. Quantification of Hypoxyprobe‐positive areas (n = 7 mice/group). Data information: Data are expressed as mean ± SEM. Student <italic toggle=\"yes\">t</italic>‐test, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> &lt; 0.001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6878-fig-0002\"><label>Figure 2</label><caption><p>Regulation of HIF1α stability and angiogenic factor expression by TRAP1. A) HIF1α expression in P17 OIR mouse retinas. Left. Retinal sections collected from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice were stained with an anti‐HIF1α antibody (red) and DAPI (blue), and imaged by confocal microscopy. Scale bars, 20 µm and 5 µm (inset). Right Quantification of the ratio (%) of HIF1α/DAPI double‐positive areas to DAPI‐positive areas (<italic toggle=\"yes\">n</italic> = 6 mice/group). B) Identification of hypoxic areas in P12 OIR mouse retinas. Left. Whole‐mount retinas were stained with Hypoxyprobe (green) and an anti‐CD31 antibody (red) to visualize hypoxic regions and blood vessels, respectively. Scale bar, 200 µm. Right. Quantification of hypoxic areas. Hypoxyprobe‐positive areas were quantified from the obtained images (<italic toggle=\"yes\">n</italic> = 5 mice/group). C) Expression of HIF1α in P12 control (RA) and OIR mouse retinas. Western blot analysis was performed to measure HIF1α expression in the retinas of <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> RA and OIR mice (<italic toggle=\"yes\">n</italic> = 3 mice/group). D) VEGF and ANGPTL4 expression in mouse P17 OIR retinas. Retinal sections from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice were stained with anti‐VEGF (red) and anti‐ANGPTL4 (green) antibodies, and analyzed by confocal microscopy (<italic toggle=\"yes\">n</italic> = 3 mice/group). Scale bar, 20 µm. E) Quantitation of <italic toggle=\"yes\">Vegf</italic> and <italic toggle=\"yes\">Angptl4</italic> mRNAs in P17 OIR mouse retinas. mRNA levels in control (RA) and OIR <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mouse retinas were analyzed by qPCR and compared (<italic toggle=\"yes\">n</italic> = 6; duplicate experiment of 3 mice/group). Data information: Data are expressed as mean ± SEM. Student <italic toggle=\"yes\">t</italic>‐test, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> &lt; 0.001; ns, not significant.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6878-fig-0003\"><label>Figure 3</label><caption><p>\n<italic toggle=\"yes\">Trap1</italic> KO decreases vascular abnormalities in STZ mice. A) Hypoxyprobe staining of the retinas of 16‐week post‐STZ injection <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mice of 25 weeks old (Figure ##SUPPL##0##S6A##, Supporting information). Left. Retinal sections of <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> STZ mice were analyzed by Hypoxyprobe staining. Scale bar, 50 µm. Right. Quantitation of Hypoxyprobe‐positive areas (<italic toggle=\"yes\">n</italic> = 5 mice/group). B) Decreased retinal capillary degeneration in <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> STZ mice. Left. STZ and control (Con) retinas from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> mice were flat‐mounted and stained with anti‐CD31 (red) and anti‐collagen IV antibodies (green) to visualize blood vessels and basement membranes, respectively. White triangles indicate acellular capillaries. Scale bar, 20 µm. Right. Quantification of acellular capillaries. The number of acellular capillaries was counted in each microscopic field (<italic toggle=\"yes\">n</italic> = 15; 5 mice/group, 3 fields/mouse). C) Thinning of STZ mouse retinas. Left. Retinal sections collected from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> STZ mice were analyzed by H&amp;E staining. Scale bar, 50 µm. Right. Quantification of retinal thickness (control n = 6, STZ <italic toggle=\"yes\">n</italic> = 10 mice/group). D) Cell death in STZ mouse retinas. Left. Retinal sections of <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> STZ mice were analyzed by cleaved caspase‐3 (c‐Casp‐3, red) staining. Scale bar, 20 µm. Right. Quantification of c‐Casp‐3‐positive cells in STZ mouse retinas (control <italic toggle=\"yes\">n</italic> = 3, STZ <italic toggle=\"yes\">n</italic> = 6 mice/group). Data information: Data are expressed as mean ± SEM. Student <italic toggle=\"yes\">t</italic>‐test, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> &lt; 0.001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6878-fig-0004\"><label>Figure 4</label><caption><p>TRAP1 regulation of vascular organization and permeability. A) Pericyte vascular coverage in P17 OIR mouse retinas. Left. Whole‐mount retinas collected from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> P17 OIR mice were stained with an anti‐PDGFR‐β antibody (magenta) and IB4 (green) to label PCs and ECs, respectively, and analyzed by confocal microscopy. Scale bar, 50 µm. Right. The ratio of the PDGFR<sup>+</sup> area to the IB4<sup>+</sup> area was calculated to measure pericyte coverage in vascularized areas (<italic toggle=\"yes\">n</italic> = 5 mice/group). Neovascular tufts were not included in analysis. B) Pericyte coverage in STZ mouse retinas. Left. Whole‐mount retinas collected from STZ mice were analyzed by confocal microscopy as in (A). Scale bar, 20 µm. Right. The number of PCs per millimeter of capillary length was counted (<italic toggle=\"yes\">n</italic> = 15; 5 mice/group, 3 fields/mouse). C) Endothelial junction integrity in P17 OIR mouse retinas. Left. Whole‐mount retinas collected from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice were stained with an anti‐VE‐cadherin antibody to visualize adherens junctions. Scale bars, 20 µm (top) and 5 µm (bottom). Right. The intensities of VE‐cadherin staining were calculated and compared (<italic toggle=\"yes\">n</italic> = 10; 4 mice/group, 2–3 fields/mouse). D) Endothelial junction integrity in STZ mouse retinas. Left. Whole‐mount retinas collected from STZ mice were analyzed by confocal microscopy as in (C). Scale bar, 20 µm (top) and 5 µm (bottom). Right. Quantification of VE‐cadherin staining intensity (<italic toggle=\"yes\">n</italic> = 10; 4 mice/group, 2–3 fields/mouse). E) Vascular leakage in P17 OIR mouse retinas. Left. Whole‐mount retinas collected from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> OIR mice were stained with anti‐fibrinogen (green) and anti‐CD31 (red) antibodies. Scale bars, 50 µm. Right. Quantification of fibrinogen signals (<italic toggle=\"yes\">n</italic> = 5 mice/group, 1 field/mouse). F) Vascular leakage in STZ mouse retinas. Left. Whole‐mount retinas collected from STZ mice were analyzed by confocal microscope as in (E). Scale bars, 10 µm. Right. Quantification of fibrinogen signal (<italic toggle=\"yes\">n</italic> = 4–5; 4 mice/group, 1–2 fields/mouse). Data information: Data are expressed as mean ± SEM. Student <italic toggle=\"yes\">t</italic>‐test, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> &lt; 0.001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6878-fig-0005\"><label>Figure 5</label><caption><p>TRAP1 inhibition induces mPTP opening, mitochondrial calcium discharge, and calpain‐1 activation. A) Visualization of cytoplasmic calcium. Fluo‐4 AM‐labeled MIO‐M1 cells were incubated with the TRAP1 inhibitors gamitrinib and MitoQ<sup>[</sup>\n##REF##34758612##\n32\n##, ##REF##19229106##\n41\n##\n<sup>]</sup> for 6 h or thapsigargin for 30 min under hypoxia, and analyzed by confocal microscopy. Scale bars, 10 µm and 2 µm (inset). B) Calpain activation by TRAP1 inhibitors. MIO‐M1 cells were treated with a TRAP1 inhibitor, 3 µM gamitrinib or 0.5 µ<sc>m</sc> MitoQ, for 6 h under hypoxia (<italic toggle=\"yes\">n</italic> = 4). Enzyme activity was measured using a fluorogenic calpain substrate as described in the Experimental Section. C) Restored HIF1α expression upon CypD inhibition. MIO‐M1 cells were incubated with control or CypD‐targeting siRNAs, treated with the TRAP1 inhibitor MitoQ for 6 h under hypoxia, harvested, and analyzed by western blotting. Black and red arrows indicate pro and autolyzed forms of calpain‐1, respectively. D) <italic toggle=\"yes\">Calpain‐1</italic> mRNA expression upon TRAP1 depletion. MIO‐M1 cells were incubated with TRAP1‐targeting siRNAs for 48 h, exposed to hypoxia for 6 h, harvested, and analyzed by qPCR (<italic toggle=\"yes\">n</italic> = 4). E) Modestly elevated cytosolic calcium by TRAP1 inhibition. After siRNA knockdown of CypD, Fluo‐4 AM‐labeled MIO‐M1 cells were incubated under hypoxic conditions with MitoQ for 6 h. Cells were then analyzed by flow cytometry to detect cytoplasmic calcium. F) Inhibition of HIF1α degradation by calcium chelation. MIO‐M1 cells were incubated with TRAP1 inhibitors, 3 µ<sc>m</sc> gamitrinib, and 0.5 µM MitoQ, and a cell‐permeable calcium chelator, BAPTA (10 µM), for 6 h as indicated under hypoxia and analyzed by western blotting. G) Blocked HIF1α degradation by calpain inhibition. MIO‐M1 cells under hypoxia were incubated with 3 µ<sc>m</sc> gamitrinib, 0.5 µ<sc>m</sc> MitoQ, and 10 µ<sc>m</sc> ALLN (calpain inhibitor) as indicated for 6 h and analyzed by western blotting. Data information: Data are expressed as mean ± SEM. Student <italic toggle=\"yes\">t</italic>‐test, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> &lt; 0.001; ns, not significant.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6878-fig-0006\"><label>Figure 6</label><caption><p>TRAP1 inhibition triggers calcium/calpain‐1‐dependent HIF1α degradation. A) Staining of mitochondria and calpain‐1. MitoTracker‐labeled MIO‐M1 cells were exposed to 3 µ<sc>m</sc> gamitrinib or 0.5 µ<sc>m</sc> MitoQ for 6 h under hypoxia and analyzed by immunocytochemistry with an anti‐calpain‐1 antibody. Scale bars, 10 µm (top) and 5 µm (bottom). B) Calpain autolysis in OIR mouse retinas. Left. Retinas collected from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> (n = 3 mice) and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> (<italic toggle=\"yes\">n</italic> = 4 mice) OIR mice were analyzed by western blotting. Right. Protein band intensities of HIF1α, cleaved calpain‐1, and calpain‐2 were normalized to those of β‐actin and compared. C) Calpain autolysis in STZ mouse retinas. Left. Retinal samples collected from STZ (<italic toggle=\"yes\">n</italic> = 4 mice) and age‐matched control (<italic toggle=\"yes\">n</italic> = 3 mice) mice with the <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> or <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> genotype were analyzed by western blotting. Right. Protein band intensities were analyzed as in (B). D,E) Calpain activity in mouse retinas. Calpain enzyme activities were analyzed in retinas collected from <italic toggle=\"yes\">Trap1</italic>\n<sup>+/+</sup> and <italic toggle=\"yes\">Trap1</italic>\n<sup>−/−</sup> STZ (D, <italic toggle=\"yes\">n</italic> = 8 mice/group) and OIR (E, <italic toggle=\"yes\">n</italic> = 6 mice/group) mice and compared. F) Depletion of calpains by siRNAs. Calpain‐1‐ and calpain‐2‐targeting siRNA‐treated MIO‐M1 cells were incubated with 3 µ<sc>m</sc> gamitrinib or 0.5 µ<sc>m</sc> MitoQ for 6 h under hypoxia and analyzed by western blotting. G) Depletion of calpain‐1 and TRAP1 by siRNAs. MIO‐M1 cells treated with siRNAs as indicated were exposed to hypoxia for 6 h and analyzed by western blotting. H) HIF1α degradation following TRAP1 inhibition. TRAP1 inhibition caused mild mitochondrial calcium discharge into the cytoplasm by opening CypD‐regulated mPTPs. Subsequent activation of calpain‐1 proteolytically degrades HIF1α. Data information: Data are expressed as mean ± SEM. Student <italic toggle=\"yes\">t</italic>‐test, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> &lt; 0.001; ns, not significant.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6878-fig-0007\"><label>Figure 7</label><caption><p>Normalized retinal vascularization upon topical application of TRAP1 inhibitors. A) HIF1α degradation induced by TRAP1 inhibitors. MIO‐M1 cells were incubated with various concentrations of TRAP1 inhibitors as indicated for 6 h under hypoxia and analyzed by western blotting. B) Quantification of HIF1α protein degradation. The HIF1α band intensities in western blot data obtained as in (A) were analyzed and compared. The data are mean ± SEM from four independent experiments. C) Vascular structure of P17 OIR mouse retinas after topical drug application. Vehicle and 2 mM TRAP1 inhibitors were topically administered to the left and right eyes, respectively, of OIR mice at P12 once per day for 5 days. At P17, mice were sacrificed and analyzed by whole‐mount staining with an anti‐CD31 antibody and confocal microscopy. Scale bar, 500 µm. D) Quantification of avascular areas and neovascular tuft. Retinal images collected as in (C) were quantitatively analyzed (<italic toggle=\"yes\">n</italic> = 5 mice/group). Data information: Data are expressed as mean ± SEM. Student <italic toggle=\"yes\">t</italic>‐test, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> &lt; 0.001; <sup>*</sup>\n<italic toggle=\"yes\">P</italic> &lt;0.5.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6878-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Therapeutic index.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Drug</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">HIF1α degradation<xref rid=\"advs6878-tbl1-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref> (IC<sub>50</sub>, µM)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Normal cell cytotoxicity<xref rid=\"advs6878-tbl1-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref> (IC<sub>50</sub>, µM)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Therapeutic index (B/A)</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">MitoQ</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.077 ± 0.016</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22.47 ± 0.46</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">295.81</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">SB‐U014</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.040 ± 0.091</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27.47 ± 0.77</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">694.92</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">SB‐U015</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.041 ± 0.083</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31.78 ± 0.76</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">773.05</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6878-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Ocular pharmacokinetics analysis after topical administration of SB‐U015.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr><th rowspan=\"2\" align=\"left\" colspan=\"1\"/><th align=\"center\" rowspan=\"1\" colspan=\"1\">Mouse</th><th colspan=\"5\" style=\"border-bottom:solid 1px #000000\" align=\"center\" rowspan=\"1\">Rabbit</th></tr><tr style=\"border-bottom:solid 1px #000000\"><th align=\"center\" rowspan=\"1\" colspan=\"1\">Retina</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Retina</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Sclera</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Aqueous humor</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cornea</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Plasma</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">C<sub>max</sub> [ng/g]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">36.5 ± 7.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">65.6 ± 20.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">664.3 ± 122.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3272.4 ± 283.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">AUC<sub>last</sub> [hng/g]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">44.8 ± 6.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">90.9 ± 16.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1697.9 ± 318.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9226.6 ± 637.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">T<sub>max</sub> [h]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.8 ± 0.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.5 ± 0.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.1 ± 0.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.6 ± 0.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">NA</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"anchor\" id=\"jats-table-wrap-1\"><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Species</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Name</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Sequence (5′→3′)</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siTRAP1‐#1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AAACATGAGTTCCAGGCAGAG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siTRAP1‐#2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GCCCGTTCTCTGTACTCAGAA</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siHIF1α‐#1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GGGTTATGAGCCGGAAGAACT</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siHIF1α‐#2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GATGGAAGCACTAGACAAAGT</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siTRAP1‐#1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AAACATGAGTTCCAGGCCGAG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siTRAP1‐#2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CCCGGTCCCTGTACTCAGAAA</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siCalpain‐1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GGAACAACGTGGACCCATA</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siCalpain‐2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CTATTGGCTTCGCGGTCTA</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siCypD‐#1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GGACTCTAATACCTGTTTA</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siCypD‐#2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GGCAGATGTCGTCCCAAAG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siANG2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GTGACTGCCACGGTGAATAAT</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">siHIF1α</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GGCCACATTCACGTATATGAT</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"anchor\" id=\"jats-table-wrap-2\"><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Species</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Name</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Forward (5′→3′)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Reverse (5′→3′)</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">β‐actin</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AGAGCTACGAGCTGCCTGAC</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AGCACTGTGTTGGCGTACAG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TRAP1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AGCGCACTCATCAGGAAACT</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TCAAACTCACGAAGGTGCAG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HIF1α</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GAAAGCGCAAGTCCTCAAAG</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TGGGTAGGAGATGGAGATGC</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ANGPTL4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GGGTCTGGAGGAGGTGCATA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AGTACTGGCCGTTGAGGTTG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VEGF</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CTACCTCCACCATGCCAAGT</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CTCGATTGGATGGCAGTAGC</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ANG1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AGGCTTGGTTTCTCGTCAGA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TCTGCACAGTCTCGAAATGG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ANG2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TGGGATTTGGTAACCCTTC</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AAGTTGGAAGGACCACATG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Human</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Calpain‐1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ACATGGAGGCCATCACTTTC</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GGTCCACGTTGTTCCACTCT</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">β‐actin</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TGTCCACCTTCCAGCAGATGT</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AGCTCAGTAACAGTCCGCCTAG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TRAP1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GAGGAAAGCCAGTTCTGCAC</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GCTCTCCTCCTCCTTGTCCT</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HIF1α</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GGGTACAAGAAACCACCCAT</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GAGGCTGTGTCGACTGAGAA</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ANGPTL4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">GGAAAAGATGCACCCTTCAA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TGCTGGATCTTGCTGTTTTG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VEGF</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TTACTGCTGTACCTCCACC</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ACAGGACGGCTTGAAGATG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ANG1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AGGCTTGGTTTCTCGTCAGA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TCTGCACAGTCTCGAAATGG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ANG2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TCCAAGAGCTCGGTTGCTAT</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">AGTTGGGGAAGGTCAGTGTG</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mouse</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Calpain‐1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">ACATTTTACGAGGGCACCTG</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CTCCCGGTTGTCATAGTCGT</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
[]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
[]
[]
[]
[ "<supplementary-material id=\"advs6878-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6878-tbl1-note-0001\"><label>\n<sup>a)</sup>\n</label><p>IC<sub>50</sub> values of HIF1α protein degradation in MIO‐M1 cells upon TRAP1 inhibitor treatment were analyzed as in Figure ##FIG##6##7A,B## (<italic toggle=\"yes\">n</italic> = 4);</p></fn><fn id=\"advs6878-tbl1-note-0002\"><label>\n<sup>b)</sup>\n</label><p>IC<sub>50</sub> values of the cytotoxic activities of the drugs in primary Müller cells were calculated as in Figure ##SUPPL##0##S18A##, Supporting information (<italic toggle=\"yes\">n</italic> = 4). The therapeutic index<sup>[</sup>\n##REF##22935759##\n42\n##\n<sup>]</sup> was determined as (IC<sub>50</sub> for normal cell cytotoxicity)/(IC<sub>50</sub> for HIF1α degradation). Data information: Data are expressed as mean ± SEM.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"advs6878-tbl2-note-0001\"><p>*NA: Not applicable because the analyte was not detected.</p></fn><fn id=\"advs6878-tbl2-note-0002\"><p>Data information: Data are expressed as mean ± SEM (n = 4) except for plasma (n = 2) and mouse retina (n = 3).</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2302776-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
43
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 20; 11(2):2302776
oa_package/ed/20/PMC10787068.tar.gz
PMC10787069
37939304
[ "<title>Introduction</title>", "<p>Solid‐state quantum sensors have enabled new ways to detect magnetic, electric fields or temperature with extreme sensitivity that approaches the quantum limit.<sup>[</sup>\n##REF##34362736##\n1\n##\n<sup>]</sup> One of the most promising platforms so far has been the Nitrogen Vacancy (NV) center, an optically addressable defect in diamond, due to its exceptional electronic spin properties at room temperatures. The electron spin state can be experimentally detected by the optically detected magnetic resonance technique, which involves sweeping the microwave (MW) frequency while recording the corresponding fluorescence intensities as a function of time.<sup>[</sup>\n##REF##34362736##\n1b\n##\n<sup>]</sup> Customized methods such as confocal‐<sup>[</sup>\n##REF##18833276##\n2\n##\n<sup>]</sup> and widefield‐based<sup>[</sup>\n##REF##20441343##\n3\n##\n<sup>]</sup> fluorescence microscope have served as gold standards for quantum sensing measurements. In particular, the widefield diamond quantum sensing approach allows for parallel readout of spatially resolved NV fluorescence, offering enormous potential in diverse fields.<sup>[</sup>\n##REF##34038091##\n4\n##\n<sup>]</sup> Since the first experimental demonstration,<sup>[</sup>\n##REF##20441343##\n3a\n##\n<sup>]</sup> the NV‐based widefield quantum sensing platform has been rapidly developed and fully exploited in various areas, across biomedical,<sup>[</sup>\n##REF##36551148##\n5\n##\n<sup>]</sup> condensed matter physics<sup>[</sup>\n##REF##34038091##\n4\n##, ##UREF##0##\n6\n##\n<sup>]</sup> and integrated circuit (IC) inspecting.<sup>[</sup>\n##REF##36298930##\n7\n##\n<sup>]</sup> While continuous efforts have been made to improve its measurement accuracy and spatial resolution, the focus has also shifted to the temporal domain to realize ultrafast ODMR. This extension would allow for the monitoring of dynamic signals, such as neuronal action potential<sup>[</sup>\n##REF##27911765##\n8\n##\n<sup>]</sup> and cell‐activity related temperature change,<sup>[</sup>\n##REF##33608613##\n9\n##\n<sup>]</sup> However, this direction is hindered by the challenge of handling the massive amount of data in the form of image frames that needs to be transferred from the camera sensors for further processing.<sup>[</sup>\n##REF##20441343##\n3\n##, ##REF##29604724##\n10\n##\n<sup>]</sup> This data transfer can significantly limit the temporal resolution, which is typically no more than 100 fps<sup>[</sup>\n##UREF##1##\n11\n##\n<sup>]</sup> due to the use of frame‐based image sensors. As a result, the potential for widefield magnetometry in dynamic measurements has only been exploited to a limited extent.</p>", "<p>Several studies have proposed different approaches to improve the temporal resolution in widefield quantum sensing, including down‐sampling method (with potential artefacts introduced),<sup>[</sup>\n##REF##23903748##\n12\n##\n<sup>]</sup> frequency multiplexing<sup>[</sup>\n##UREF##2##\n13\n##\n<sup>]</sup> (with complicated implementation while limited speed‐up), advanced sensing arrays with single‐photon avalanche diodes (SPADs)<sup>[</sup>\n##UREF##3##\n14\n##\n<sup>]</sup> (with complex circuit integration needed), and in‐pixel demodulation with lock‐in cameras<sup>[</sup>\n##REF##35610314##\n15\n##\n<sup>]</sup> (with sacrificed sensing precision). However, the fundamental limitation still lies in the monitored fluorescence intensity changes with image frames associated with a vast amount of data, leading to unsatisfactory performance in widefield quantum sensing. To overcome this bottleneck, we propose using a neuromorphic vision camera<sup>[</sup>\n##REF##33238098##\n16\n##\n<sup>]</sup> to pre‐process fluorescence intensity data near the sensor device, which reduces the data transmitted for post‐processing and significantly enhances the temporal resolution, enabling fast dynamic measurements.</p>", "<p>Unlike traditional sensors that record the light intensity levels, neuromorphic vision sensors process the light intensity change into “spikes” similar to biological vision systems, leading to improved temporal resolution (≈µs) and dynamic range (&gt;120 dB).<sup>[</sup>\n##REF##33238098##\n16\n##, ##REF##20493680##\n17\n##\n<sup>]</sup> This approach is particularly effective in scenarios where image changes are infrequent, such as object tracking<sup>[</sup>\n##UREF##4##\n18\n##\n<sup>]</sup> and autonomous vehicles,<sup>[</sup>\n##UREF##5##\n19\n##\n<sup>]</sup> as it eliminates redundant static background signals. Recently, this technique has gained attention in precision instruments measurements, such as emerging applications including fast‐focusing in light microscope fast‐focusing,<sup>[</sup>\n##UREF##6##\n20\n##\n<sup>]</sup> dynamic magneto‐optic Kerr effect (MOKE) microscopy,<sup>[</sup>\n##UREF##7##\n21\n##\n<sup>]</sup> fast cell flow sorting,<sup>[</sup>\n##UREF##8##\n22\n##\n<sup>]</sup> vibration measurement,<sup>[</sup>\n##UREF##9##\n23\n##\n<sup>]</sup> fast‐tracking of beads,<sup>[</sup>\n##REF##32700715##\n24\n##\n<sup>]</sup> and super‐resolution imaging.<sup>[</sup>\n##REF##36418490##\n25\n##\n<sup>]</sup> Given that the fluorescence intensities encoded by MW spatial‐temporally vary only near the resonance frequency and therefore changes are rare, diamond quantum sensing is an ideal way of leveraging the benefits of this new approach.</p>", "<p>This study, to the best of our knowledge, is the first to describe the application of the neuromorphic vision sensor to perform wide‐field diamond quantum sensing. Specifically, we develop a custom and efficient protocol to process event‐type quantum sensing data, which enables the reconstruction of derivative ODMR spectrum. Our experimental results demonstrate that this new approach takes far less time than conventional frame‐based approaches (140 ms vs. 1.82 s), while achieving similar precision (0.034 MHz vs. 0.031 Mhz) in detecting the ODMR resonance frequency over a field of view (FOV) of 18*18 µm<sup>2</sup>. We showcase its potential in monitoring sub‐second scale laser heating of diamond surface coated with gold nanoparticles, which was previously impossible with conventional approaches. Temperature monitoring with 0.28 s temporal resolution and 0.5 K temperature precision is demonstrated in our experiment. We anticipate that our successful demonstration of the proposed method will revolutionize widefield quantum sensing, significantly improving performance at an affordable cost. Our study also paves the way for the development of intelligent quantum sensors with more advanced in‐sensor processing capabilities,<sup>[</sup>\n##REF##32132692##\n26\n##\n<sup>]</sup> and brings closer the realization of near‐sensor processing with emerging memory‐based electronic synapse devices.<sup>[</sup>\n##REF##30894760##\n27\n##\n<sup>]</sup> These advances hold great promises for further enhancing the performance of widefield quantum sensing, leading to new opportunities in scientific research and practical applications.</p>" ]
[]
[ "<title>Results</title>", "<title>Neuromorphic Widefield Quantum Sensing Concept</title>", "<p>Diamond quantum sensing is facilitated by the NV center, which consists of a nitrogen atom and a nearby vacancy center hosted in diamond lattice. Due to the unique transition between triplets' ground and excited states,<sup>[</sup>\n##REF##34362736##\n1b\n##\n<sup>]</sup> the spin states of NV centers could be readout through the emitted red fluorescence excited with a green laser (<bold>Figure</bold> ##FIG##0##\n1A##). The hallmark of quantum sensing based on NV centers in diamond is to perform the so‐called optically detected magnetic resonance measurements, i.e., the monitored NV fluorescence changing with temporally encoded MW frequency. Specifically, the widefield ODMR measurement records the spatiotemporal NV fluorescence intensity changes in parallel, via a conventional frame‐based sensor which normally operates at a limited framerate. With swept MW frequency, all pixels in the camera sensor synchronously record both regions of interest (i.e., NV fluorescence) as well as the background fluorescence, generating a series of frames with fixed time interval (Figure ##FIG##0##1B##). This inflexible process produces highly redundant data (e.g., of the order of ≈10 MB) for transmission and further process, causing a significant latency (e.g., of the order of ≈10 ms per frame). This makes it difficult to apply widefield diamond quantum sensing in many dynamic processes such as mapping the action potential of a single neuron.<sup>[</sup>\n##REF##27911765##\n8a\n##\n<sup>]</sup>\n</p>", "<p>The proposed widefield quantum sensing approach using a neuromorphic vision sensor aims to address the challenge described above. Instead of simply recording the fluorescence intensities from the frame‐based camera, this method pre‐processes data near the sensor. During widefield ODMR measurement, we observe that the fluorescence intensity only changes in the regions of interest and near the resonance frequency, while the majority of data changes only slightly. As a result, we adopt a neuromorphic event camera that converts the light intensity changes into sparse “change events” or spikes. (Figure ##FIG##0##1C##). This resembles the working principle of photoreceptors in the human retina, which responds only to light intensity changes and converts them into spikes for transmission and processing in neural systems.<sup>[</sup>\n##REF##33238098##\n16\n##, ##UREF##5##\n19\n##\n<sup>]</sup> For example, the working mode in our optical nerve has resulted in only ≈20 Mb s<sup>−1</sup> of data transmission to the visual cortex, while a rate of 20 Gb s<sup>−1</sup> is required for the frame‐based working mode in conventional digital cameras to match the same spatial‐temporal resolution. The compressed data transmission thus results in significantly reduced latency and a high energy efficiency.<sup>[</sup>\n##REF##33238098##\n16\n##, ##UREF##10##\n28\n##\n<sup>]</sup> Likewise, we use a neuromorphic sensor to measure the fluorescence change in parallel, from which a spike is generated only when the temporal fluorescence change surpasses a predefined threshold level. Because the fluorescence only changes significantly near the resonance, the general spikes are inherently sparse. Moreover, the spikes are only generated for the region of interest (ROI) where there exist intensity changes like NV centers modulated (temporally encoded) by MW frequency, further reducing the data transmission and improving the performance in widefield diamond quantum sensing.</p>", "<title>Event‐Based ODMR</title>", "<p>To demonstrate the feasibility of our idea, we performed Monte‐Carlo simulations using a model with stochastic measurements as detailed in Methods. As shown in the upper part of <bold>Figure</bold> ##FIG##1##\n2A##, our numerical simulation reproduced a light intensity that can be well‐fitted with a Lorentz function that is consistent with previous experiments.<sup>[</sup>\n##REF##18833276##\n2\n##, ##UREF##11##\n29\n##\n<sup>]</sup> For the proposed event‐based approach, the simulated signal exhibits the shape of the derivative of a Lorentz function (lower part of Figure ##FIG##1##2A##).</p>", "<p>In fact, the relationship between the original and event‐based ODMR can be well understood and mathematically derived: First, the light intensity is converted to a series of events in our simulation, based on the working process of the proposed neuromorphic sensor.<sup>[</sup>\n##REF##33238098##\n16a\n##\n<sup>]</sup> In this regard, each sensing pixel responds to light intensity changes independently and produces a positive event when the light intensity increase surpasses a predefined threshold <italic toggle=\"yes\">C</italic>\n<sub>th</sub>, and a negative event for a decrease (Figure ##FIG##1##2B##). Therefore, if the threshold value is much smaller than the intensity change, the time interval Δ<italic toggle=\"yes\">t</italic> between two events can approximately describe the derivative of the original spectrum at that point:\n\n</p>", "<p>Equation (##FORMU##0##1##) clearly shows that the fluorescence intensity gradient is encoded as the density of events, as Δ<italic toggle=\"yes\">t</italic> is inversely proportional to the derivative of intensity, as illustrated in Figure ##FIG##1##2B##. To recover the spectrum gradient, we calculate the event density λ<sub>s</sub>(t) by counting the number of simulated events within a certain time range <italic toggle=\"yes\">T</italic>:\n\n</p>", "<p>Finally, the derivative Lorentzian spectrum <mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:mrow><mml:msubsup><mml:mi>I</mml:mi><mml:mi>log</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>f</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> is reconstructed from the <mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:mrow><mml:msubsup><mml:mi>I</mml:mi><mml:mi>log</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>t</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> using an established relationship between time <italic toggle=\"yes\">t</italic> and microwave frequency <italic toggle=\"yes\">f</italic>. This is clearly verified by our simulation results (shown in the lower panel in Figure ##FIG##1##2A##), where the discrete points of summed events can be fitted with the derivative Lorentzian function. The resonance frequency <italic toggle=\"yes\">f</italic>\n<sub>0</sub> can also be determined at the point where the derivative crosses zero value. To describe the quality of the spectrum, the quality metric Q<sub>F</sub> (for original Lorentzian spectrum) and Q<sub>E</sub> (for derivative Lorentzian spectrum) can also be calculated, where Q<sub>F</sub> is defined as the full width at half maximum (FWHM), while Q<sub>E</sub> is defined as the frequency difference of two inflection points of the spectrum. Therefore, our method provides a new route to represent ODMR by the post‐processed events. Consequently, we refer to this new technique as event‐based ODMR measurement. This form of measurement has guided our following experiments.</p>", "<title>Experimental Demonstration of Event‐Based ODMR Measurement</title>", "<p>We have successfully demonstrated our event‐based ODMR measurement concept through experiments and systematically compared its performance with the conventional frame‐based approach. As a benchmark for comparison, we used a highly specialized Electron Multiplying Charged Coupled Device (EMCCD), a typical frame‐based camera used in traditional ODMR measurement. Due to its frame‐based working mode, we swept the MW across 70 discrete frequency points to perform ODMR measurements with a framerate of 38.5 fps or 26 ms per frame (<bold>Figure</bold> ##FIG##2##\n3A##). As a result, the overall measurement time was 1.82 s for one complete ODMR measurement. By contrast, the event camera is not limited by frame rate due to its unique working principle, so we swept the same frequency range in a linear chirp manner (continuously) with only 70 ms, as shown in Figure ##FIG##2##3B##. (As illustrated in the section “Event‐based ODMR measurement” in Experimental Section, we repeat the sweep for 10 loops for one complete ODMR measurement to mitigate the influence of noise events). In fact, the time could be further improved with a trade‐off with the sensing precision (discussed in detail in Figure ##FIG##2##3G##). Indeed, an extreme short time of 3.5 ms, with a degraded yet acceptable precision (0.11 MHz) has been realized in our event‐based experiment. Such a short time is unattainable by frame‐based methods (Figure ##FIG##2##3G##).</p>", "<p>The superior performance of the proposed event‐based ODMR measurement is attributable to its unique working principle, which could be explicitly seen from the raw data format. The frame‐based widefield ODMR measurement generates a series of frames, representing a massive amount of data to transfer during the scanning of full ODMR spectrum across all pixels (Figure ##FIG##2##3C##) in order to maintain the precision of the ODMR measurement. This results in a limited framerate of the camera and increased sensing time. By contrast, the proposed event‐based wide‐field ODMR measurement generates data in the form of sparse events, significantly reducing data transfer and enabling much faster sensing speeds. This feature is evident in our experimental data (Figure ##FIG##2##3D##) during our event‐based wide‐field ODMR measurement. The data consists of a stream of spatial‐temporal events in which the event density and polarity encode the information related to the fluorescence intensity changes. As expected, the detected event density is noticeably concentrated near two turning points, while it is sparse in the off‐resonance region of the measured event‐based ODMR spectrum (insert in Figure ##FIG##2##3F##). A consistent demonstration for this phenomenon can be observed in the recorded video (Movie ##SUPPL##1##S1##, Supporting Information). This can also be verified by the time trace of accumulated number of events in one typical measurement (Figure ##SUPPL##0##S11## (Supporting Information), where the average event number from the central pixel is counted for every 1 ms of the sweep). The event number remains minimal in the off‐resonance frequency region, with only a few events generated due to noise. However, the number increases significantly near the in‐resonance frequency (close to the turning points). These data are consistent with our assumption and further support the improved performance of our method.</p>", "<p>The proposed event‐based ODMR measurement employs a distinct measurement protocol, data representation, and processing method, but still achieves the same resonance frequency as frame‐based ODMR measurements. For conventional frame‐based ODMR measurements, the raw intensity recorded at a specific location, which varies with microwave frequency, can be fitted with a Lorentzian function to extract the resonance frequency (<italic toggle=\"yes\">f<sub>0</sub>\n</italic> = 2869.62 MHz) (Figure ##FIG##2##3E##). By contrast, the event‐based measurement reconstructs the derivative Lorentzian spectrum from the density of events, i.e., the summation of event number over a defined period (Figure ##FIG##2##3F##). By fitting with a derivative Lorentzian function, the resonance frequency can also be extracted, although it appears to exhibit a noticeable deviation (<italic toggle=\"yes\">f</italic>\n<sub>0</sub> = 2872.23 MHz) compared to the EMCCD result. This deviation is caused by the time delay between the event camera and MW source and also the large threshold of the event camera (detailed in Section <xref rid=\"advs6671-sec-0020\" ref-type=\"sec\">2</xref>, Supporting Information) and can be easily compensated for by performing another backward frequency sweep (<italic toggle=\"yes\">f</italic>\n<sub>0</sub> = 2867.03 MHz) and averaging the two results (the corrected resonance frequency <italic toggle=\"yes\">f</italic>\n<sub>0</sub>* = 2869.63 MHz indicated in Figure ##FIG##2##3F##).</p>", "<p>The distinct measurement protocol also results in a different model to describe the trade‐off relationship between the measurement precision <italic toggle=\"yes\">σ</italic> and the sensing time <italic toggle=\"yes\">τ</italic>. We conducted experiments to study this relationship with both frame‐based ODMR measurement using an EMCCD camera and event‐based ODMR measurement using an event camera. Details on precision calculation are provided in the section “Calculation of sensing precision and time” in Experimental Section. From the result in Figure ##FIG##2##3G##, it is evident that precision improves with longer sensing time for both methods. The trade‐off for the frame‐based approach can be explained with the shot‐noise model<sup>[</sup>\n##REF##24801494##\n32\n##\n<sup>]</sup> (<mml:math id=\"jats-math-7\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>σ</mml:mi><mml:mo>∝</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:msubsup><mml:mi>τ</mml:mi><mml:mi>e</mml:mi><mml:mn>0.5</mml:mn></mml:msubsup></mml:mfrac></mml:mrow></mml:mrow></mml:math>), where τ<sub>e</sub> is the total exposure time for one complete ODMR measurement. Our experiment shows that it follows: <mml:math id=\"jats-math-8\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:mrow><mml:mi>E</mml:mi><mml:mi>M</mml:mi><mml:mi>C</mml:mi><mml:mi>C</mml:mi><mml:mi>D</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>0.028</mml:mn><mml:mfrac><mml:mn>1</mml:mn><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mi>τ</mml:mi><mml:mo>−</mml:mo><mml:msub><mml:mi>τ</mml:mi><mml:mi>o</mml:mi></mml:msub></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>0.48</mml:mn></mml:msup></mml:mfrac></mml:mrow></mml:mrow></mml:math>, where τ‐ τ<sub>0</sub> is the exposure time τ<sub>e</sub> in the short noise model, and τ<sub>0</sub> is the overhead for data readout and transmission, so the result is closely aligned with the theoretical model. In our measurement, τ<sub>0</sub> = 1.12s (for readout of 70 frames), which is roughly consistent with the camera's fastest speed (67 fps).<sup>[</sup>\n##UREF##12##\n30\n##\n<sup>]</sup> The fitting curve for our event‐based method follows <mml:math id=\"jats-math-9\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:mrow><mml:mi>e</mml:mi><mml:mi>v</mml:mi><mml:mi>e</mml:mi><mml:mi>n</mml:mi><mml:mi>t</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>0.023</mml:mn><mml:mfrac><mml:mn>1</mml:mn><mml:msup><mml:mi>τ</mml:mi><mml:mn>0.43</mml:mn></mml:msup></mml:mfrac></mml:mrow></mml:mrow></mml:math>. We attribute this root‐inverse property to varying probabilities of event generation (see Section <xref rid=\"advs6671-sec-0080\" ref-type=\"sec\">4</xref>, Supporting Information), rather than the shot‐noise limitation experienced by the EMCCD, given that event camera pixels detect photo‐current rather than integrated photo‐generated charges.<sup>[</sup>\n##UREF##13##\n31\n##\n<sup>]</sup>\n</p>", "<p>A comparison of the results of our event‐based and frame‐based methods clearly demonstrates that the event‐based approach significantly reduces sensing time while maintaining a comparable level of precision. As illustrated in Figure ##FIG##2##3G##, data points derived from the event‐based method fall to the left of those obtained using the EMCCD‐based frame approach. Moreover, the performance of lock‐in camera‐based works realizes either high precision but long sensing time<sup>[</sup>\n##REF##35610314##\n15b\n##\n<sup>]</sup> or a shorter sensing time with significantly degraded precision,<sup>[</sup>\n##REF##35610314##\n15a\n##\n<sup>]</sup> but in general is not competitive with our results. <bold>Table</bold> ##TAB##0##\n1\n## compares the key performance metrics of the event‐based and frame‐based methods, demonstrating that our data reduces the sensing time of the event‐method by more than an order of magnitude (0.14 s vs. 1.82 s) while maintaining a similar sensing precision (0.034 MHz vs. 0.031Mhz). This time‐saving mainly comes from the negligible data readout, as only a few hundred kilobytes of event data need to be transferred after the pre‐processing near the sensor. The data transfer overhead is estimated to be ≈1.7 ms based on 1.6 Gbps camera bandwidth,<sup>[</sup>\n##UREF##13##\n31\n##\n<sup>]</sup> compared to 1.12 s required for the frame‐based method using an EMCCD (consumed mainly by the pixel‐by‐pixel analog‐to‐digital conversion (16bit) and readout).</p>", "<p>The comparison also suggests that our approach has a much higher spatial and temporal signal‐to‐background ratio (SBR<sub>s</sub> and SBR<sub>t</sub>\n<sup>[</sup>\n##REF##30891803##\n33\n##\n<sup>]</sup>) than the conventional method (see Section <xref rid=\"advs6671-sec-0090\" ref-type=\"sec\">5</xref> in Supporting Information for the calculation of these values based on raw events). The higher SBR values are attributable to the unique working mode of the neuromorphic method, which only responds to changed fluorescence. Since the light intensity from background pixels away from the ROI does not change, only rare events are produced by large noise. This helps to reduce data redundancy and also makes it easier to distinguish the ROI from the background area, which is highly desirable in nano‐diamond related applications.<sup>[</sup>\n##REF##33608613##\n9b\n##\n<sup>]</sup> Finally, we note that the event camera can work in a wider dynamic range<sup>[</sup>\n##REF##33238098##\n16a\n##\n<sup>]</sup> and at a much lower cost than the EMCCD camera used for comparison. The performance of our method can, in principle, be further improved by adopting a high‐figure‐of‐merit neuromorphic vision sensor.<sup>[</sup>\n##UREF##14##\n34\n##\n<sup>]</sup>\n</p>", "<title>Widefield Temperature Dynamics Measurement</title>", "<p>To showcase the potential application in monitoring highly dynamic processes, we experimentally demonstrated widefield NV‐based quantum thermometry measurements. The NV‐based quantum thermometry relies on the thermally induced ODMR spectrum shift, which has been recognized as an ultrasensitive platform for various scientific and industrial applications.<sup>[</sup>\n##REF##34038091##\n4\n##, ##REF##23903748##\n12\n##, ##REF##26584676##\n35\n##\n<sup>]</sup> The linear temperature dependence of the resonance frequency which originates from the thermal lattice expansion and temperature dependence of the electron–phonon interaction<sup>[</sup>\n##REF##26584676##\n35\n##, ##REF##20366868##\n36\n##\n<sup>]</sup> is used for transferring resonance frequency into temperature changes (details in “Dynamic temperature measurement” in Experimental Section).</p>", "<p>We began with a static measurement, where the power of the laser used to heat up the sample (<bold>Figure</bold> ##FIG##3##\n4A##) was fixed at specific values, ensuring the system is settled in an equilibrium state. The static temperature distribution was calculated from the ODMR resonance frequency shift. Our experiment revealed a linear relationship between measured temperature and heating laser power, as shown in Figure ##FIG##3##4B##. The measurement precision was below 0.5 K for all measurements (lower panel in Figure ##FIG##3##4B##), and an almost uniform temperature distribution (upper panel in Figure ##FIG##3##4B##) was observed due to the high thermal conductivity of the bulk diamond sample.<sup>[</sup>\n##UREF##15##\n37\n##\n<sup>]</sup>\n</p>", "<p>Based on the static measurement, we further demonstrated the dynamic temperature monitoring, where the temperature is controlled via an electrically‐rotated linear polarizer that tunes the heating laser power (red in Figure ##FIG##3##4A##). By rotating the polarizer at a fixed speed <italic toggle=\"yes\">ω</italic>, the heating laser power irradiating the sample surface will be tuned in a continuous cosine square pattern (Figure ##SUPPL##0##S15A##, Supporting Information), indicating a similar pattern in temperature dynamics, i.e., ΔT = <italic toggle=\"yes\">A</italic>\n<sub>0</sub>\n<italic toggle=\"yes\">cos</italic>\n<sup>2</sup>(ω<italic toggle=\"yes\">t</italic> + φ) + <italic toggle=\"yes\">c</italic>. With the event‐based OMDR measurement, we achieved a temporal resolution of 0.28 s, demonstrating an easy widefield temperature tracking. The periodic temperature change within the FOV is clearly observed in Figure ##FIG##3##4C## (see also Movie ##SUPPL##2##S2##, Supporting Information). The temperature change is consistent with the heating laser power in terms of the cosine square fitting (the center pixel is shown in Figure ##FIG##3##4D## while others in Figure ##SUPPL##0##S15B##, Supporting Information) and the Fourier transform (FT) (Figure ##FIG##3##4E##). The fitting shows a bias from 0 K (reference zero point measured with 0 mW red laser in the static measurement) because of the accumulated heat during continuous laser tuning, which requires more time to be released to reach the equilibrium temperature. The extracted rotation speed from fitting (i.e., ω<sub>meas.</sub> = 0.728 rad s<sup>−1</sup>) is very close to the pre‐set value ω<sub>set</sub> = 0.724 rad s<sup>−1</sup>. Combining measurement from all pixels during the widefield measurement confirms spatially uniform temperature dynamics. By contrast, the results measured with the frame‐based method using an EMCCD show aperiodic and smaller‐range temperature change (lower panel in Figure ##FIG##3##4D##) and also irregular FT (Figure ##FIG##3##4E##), indicating a failure to track the temperature change due to the much longer sensing time (with temporal resolution of 1.82 s). The sensing temporal resolution of our event‐based method can be further improved to 0.14 s at an expense of slightly reduced precision (Figure ##SUPPL##0##S15C##, Supporting Information).</p>", "<p>Interestingly, we also discovered that the measured temperature amplitude using our method decreases with the increased rotation speed of the polarizer (summarized in <bold>Table</bold> ##TAB##1##\n2\n## and Figure ##SUPPL##0##S16##, Supporting Information). This phenomenon is attributable to the long response time for the thermal dynamic property of the gold particles, instead of under‐sampling, which has been verified by the transition measurement with temperature switched by an acousto‐optic modulator (AOM). The periodic temperature switches are reproduced matching the protocol shown in Figure ##SUPPL##0##S17## (Supporting Information). The heating and cooling process of the first cycle is fitted with a first‐order exponential response function, from which we extract a 0.71 s rising and falling time. The first‐order frequency response based on this response time aligns well with the previously mentioned temperature amplitude measured under different rotation speeds (Figure ##SUPPL##0##S18##, Supporting Information), a phenomenon that cannot be observed with the frame‐based method using an EMCCD.</p>" ]
[ "<title>Discussion</title>", "<p>The essence of widefield quantum sensing is to detect changes in the number of photons across space and time, presenting a complex trade‐off problem in both spatial and temporal domains. Our event‐based working process holds the smart pre‐process capability that detects sparse events adaptively in both space and time, thus matching well with the requirement of quantum sensing. Specifically, the neuromorphic pixels work independently and asynchronously, enabling the immediate readout of detected fluorescence change without waiting for the other pixels, which allows for an extremely high time resolution. Moreover, the event data that constitute the time‐varying fluorescence spectrum have an adaptive time interval because events are generated only when the light change surpasses a threshold. This efficient process reduces redundant data and overcomes the limitations of frame rate in the frame‐based approaches, enabling low‐latency ODMR measurements.</p>", "<p>It should be emphasized that our method has significant potential for further development in the future. In addition to its application in dynamic temperature measurement, it can be readily extended to magnetic field sensing, which has implications for the manipulation of magnetic skyrmions,<sup>[</sup>\n##REF##34038091##\n4\n##, ##REF##23900221##\n38\n##\n<sup>]</sup> spin‐assisted super‐resolution imaging,<sup>[</sup>\n##REF##23547791##\n39\n##\n<sup>]</sup> and detection of neuron action potential,<sup>[</sup>\n##REF##34038091##\n4\n##, ##REF##27911765##\n8\n##\n<sup>]</sup> among other possibilities. Furthermore, neural network algorithms<sup>[</sup>\n##REF##26017442##\n40\n##\n<sup>]</sup> could be used to map the raw events back to the original spectrum, as they preserve the derivative function relationship, or directly infer the observables such as temperature and magnetic field, potentially optimizing the precision further. Integration of electronic synapse devices<sup>[</sup>\n##REF##30894760##\n27\n##\n<sup>]</sup> could also enable in‐sensor or near‐sensor algorithm execution,<sup>[</sup>\n##REF##32132692##\n26\n##\n<sup>]</sup> paving the way for the development of intelligent quantum sensors.</p>" ]
[ "<title>Conclusion</title>", "<p>To summarize, we have demonstrated an event‐based quantum sensing method that achieves both low‐latency and high‐accuracy ODMR measurement. A derivative Lorentzian spectrum can be reconstructed from raw events that are transferred from continuous fluorescence change through an event camera. By fitting the equation, the resonance frequency is extracted with comparable precision (0.034 MHz vs. 0.031 MHz) but in a much shorter time (0.14 s vs. 1.82 s) than the results obtained from frame‐based ODMR using an EMCCD. The working principle also offers additional benefits, such as adaptive sampling, higher SBR and a wider dynamic range. Finally. our method is successfully demonstrated in tracking widefield dynamic temperature change with a 0.28 s time resolution.</p>" ]
[ "<title>Abstract</title>", "<p>Despite increasing interest in developing ultrasensitive widefield diamond magnetometry for various applications, achieving high temporal resolution and sensitivity simultaneously remains a key challenge. This is largely due to the transfer and processing of massive amounts of data from the frame‐based sensor to capture the widefield fluorescence intensity of spin defects in diamonds. In this study, a neuromorphic vision sensor to encode the changes of fluorescence intensity into spikes in the optically detected magnetic resonance (ODMR) measurements is adopted, closely resembling the operation of the human vision system, which leads to highly compressed data volume and reduced latency. It also results in a vast dynamic range, high temporal resolution, and exceptional signal‐to‐background ratio. After a thorough theoretical evaluation, the experiment with an off‐the‐shelf event camera demonstrated a 13× improvement in temporal resolution with comparable precision of detecting ODMR resonance frequencies compared with the state‐of‐the‐art highly specialized frame‐based approach. It is successfully deploy this technology in monitoring dynamically modulated laser heating of gold nanoparticles coated on a diamond surface, a recognizably difficult task using existing approaches. The current development provides new insights for high‐precision and low‐latency widefield quantum sensing, with possibilities for integration with emerging memory devices to realize more intelligent quantum sensors.</p>", "<p>A high‐precision and low‐latency widefield diamond quantum sensing method has been demonstrated by utilizing a neuromorphic vision sensor (here an event camera). The resonance frequency of the optical detection magnetic resonance can be extracted from the reconstructed raw event data, leading to 13x improvement in temporal resolution and similar precision in comparison with frame‐based camera.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6671-cit-0090\">\n<string-name>\n<given-names>Z.</given-names>\n<surname>Du</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Gupta</surname>\n</string-name>, <string-name>\n<given-names>F.</given-names>\n<surname>Xu</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Zhou</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Wrachtrup</surname>\n</string-name>, <string-name>\n<given-names>N.</given-names>\n<surname>Wong</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Chu</surname>\n</string-name>, <article-title>Widefield Diamond Quantum Sensing with Neuromorphic Vision Sensors</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304355</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304355</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Sample Preparation</title>", "<p>The diamond sample was bought from Element Six (UK) Ltd. (SC Plate CVD 3.0 × 3.0 × 0.25 mm &lt;100&gt; P2 145‐500‐0549), which contains a uniform distribution of NV centers. The NV concentration of the sample was estimated to be 670 µm<sup>−3</sup> using the home built confocal setup, by comparing the count‐rate to that of a single NV center. On top of the sample, a thin layer of gold nanoparticles was fabricated as follows: Gold nanoparticles were synthesized according to a published process.<sup>[</sup>\n##UREF##16##\n41\n##\n<sup>]</sup> Briefly, mixed solutions of NaOH (5 ml, 0.1 M) and ultrapure water (45 ml) were prepared. Tetrakis(hydroxymethyl)phosphonium chloride (THPC, 67.2 µmol in 1 ml water) was added to the above mix solutions. After 5 mins, HAuCl4 solution (2 ml of a 1% w/w solution in water, 59 µmol) was added under vigorous stirring. The seeding gold colloid solution was obtained. Single‐crystalline bulk diamonds were sonicated in acetone and isopropanol for 5 min each and dried with nitrogen. The diamonds were cleaned and chemically activated by freshly prepared piranha solution (H2SO4/H2O2 = 7:3) at 90 °C for 1 h, rinsed thoroughly with ultrapure water and ethanol, and dried with nitrogen. 1,2‐bis(triethoxysilyl)ethane (10 ul, BTSE), tetraethoxysilicicic acid (20 ul, TEOS) and 3‐aminopropyltriethoxysilane (20 ul, APTES) were slowly added dropwise to a mixture of ethanol (2850 µl), ultrapure water (150 µl) and hydrochloric acid (10 µl), and hydrolyzed for 2 h. After hydrolysis, the cleaned diamonds were placed into the above hydrolysis solution and deposited for 6 h. After the reaction, the diamonds were cleaned with ethanol and dried with nitrogen. Mixed solutions of hydrochloric acid (10 µl) and ultrapure water (1 ml) were prepared. 1 ml seeding gold colloid solution was added the above mix solutions. Diamond with surface amination was placed into the above good colloid solution and deposited overnight. After the reaction, the diamonds were cleaned with ultrapure water and dried with nitrogen and obtained diamond with gold film. A layer of positively charged silica was coated on the diamond surface to enable the adsorption of negatively charged gold nanoparticles based on their electrostatic interaction (Figure ##SUPPL##0##S1##, Supporting Information).<sup>[</sup>\n##UREF##17##\n42\n##\n<sup>]</sup>\n</p>", "<title>Measurement Setup</title>", "<p>Figure ##SUPPL##0##S2A## (Supporting Information) shows the setup it was used for performing ODMR. A 532 nm laser (MGL‐III‐532) to excite the diamond sample (prepared using the procedures mentioned above) was used. After being expanded by a widefield lens, and reflected by a dichroic mirror (DM, cut‐off wavelength 605 nm), the laser illuminated the diamond sample through a microscope objective lens (OL, Olympus UplanSApo, 40x/0.95NA) with a 18 um (FWHM) beam spot. The emitted fluorescence was then collected by the same objective lens. Microwaves (MW) were generated by a custom‐built system shown in Figure ##SUPPL##0##S2C## (Supporting Information), where microwave signals from a RF signal generator (SynthNV PRO, with frequency <italic toggle=\"yes\">f</italic>\n<sub>1</sub> fixed at 2835 MHz) and an arbitrary waveform generator (AWG, Rigol DG5071, with frequency <italic toggle=\"yes\">f</italic>\n<sub>2</sub> swept from 1 to 70 MHz) were mixed through a RF mixer (Mini‐Circuits ZEM‐4300+) to yield the target frequency <italic toggle=\"yes\">f</italic>\n<sub>1</sub>+<italic toggle=\"yes\">f</italic>\n<sub>2</sub>. After further amplification using a microwave amplifier (ZHL‐16W‐43‐s+), the mixed signal was fed on diamond through a waveguide for tuning the NVs’ spin states. The tuned fluorescence was first filtered by the Long‐pass filter (LP, cut‐off wavelength 650 nm), and then detected by an event camera (Prophesee, EVK1‐Gen3.1 VGA) after passing through the tube lens (TL). For comparison, it was built anther optical path in the same system for traditional quantum sensing using EMCCD (Photometrics, Evolve 512 Delta), which could be switched through a flip mirror (FM). Moreover, a series of pulses were generated through a digital pulse generator (Quantum Composer, 8210) to synchronize the MW frequency sweep and the cameras’ measurement.</p>", "<title>Details of Simulation</title>", "<p>In the simulation, the NV electron spin dynamics by including stochastic projective measurements during the protocols to take the continuous ODMR measurement process into account was modeled. Specifically, a weak measurement rate Γ<sub>\n<italic toggle=\"yes\">M</italic>\n</sub> to describe the measurement speed such that the probability of no projective measurement occurring within a short time interval Δ<italic toggle=\"yes\">t</italic> was <mml:math id=\"jats-math-10\" display=\"inline\"><mml:mrow><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mo>−</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi mathvariant=\"normal\">M</mml:mi></mml:msub><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>t</mml:mi></mml:mrow></mml:msup></mml:mrow></mml:math> was used. Between successive projective measurements, the dynamics of the NV electron spins was driven by the NV Hamiltonian that includes the effect of microwave control. When a projective measurement occurred, it would prepare the NV electron to the | <italic toggle=\"yes\">m<sub>s</sub>\n</italic> = 0〉 spin state due to optical initialization and emit a photon with a probability <italic toggle=\"yes\">p</italic>\n<sub>photon</sub> = |〈0|Ψ〉|<sup>2</sup>, where |Ψ〉 is the state just before the projective measurement. The intensity signal <italic toggle=\"yes\">I</italic> is proportional to the counted number of photons.</p>", "<p>The probability distribution of the time <italic toggle=\"yes\">t</italic>\n<sub>2M</sub> between two successive projective measurements was an exponential distribution. This allows us to randomly generate <italic toggle=\"yes\">t</italic>\n<sub>2M</sub> by using a random variate <italic toggle=\"yes\">p</italic>\n<sub>M</sub> drawn from the uniform distribution on the unit interval (0,1) with the relation <mml:math id=\"jats-math-11\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>p</mml:mi><mml:mi mathvariant=\"normal\">M</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:mo>−</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi mathvariant=\"normal\">M</mml:mi></mml:msub><mml:msub><mml:mi>t</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi mathvariant=\"normal\">M</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msup></mml:mrow></mml:mrow></mml:math>. It was set Γ<sub>M</sub> = 1.5 MHz to match the experimental results. To reduce the simulation overhead, that the evolution of each NV electron spin state |Ψ〉 between two successive projective measurements was driven by a simplified two‐level Hamiltonian <mml:math id=\"jats-math-12\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>H</mml:mi><mml:mo>=</mml:mo><mml:mfrac><mml:mi>ℏ</mml:mi><mml:mn>2</mml:mn></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>σ</mml:mi><mml:mi>z</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:mi mathvariant=\"normal\">Ω</mml:mi><mml:msub><mml:mi>σ</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> was assumed, where Ω was the Rabi frequency of microwave control and Δ was the detuning between the microwave frequency and the energy splitting ω<sub>NV</sub> of the NV <italic toggle=\"yes\">m<sub>s</sub>\n</italic> = 0, −1 spin states. σ<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> and σ<sub>\n<italic toggle=\"yes\">x</italic>\n</sub> are Pauli operators with σ<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = |0〉〈0| − | − 1〉〈 − 1|. In the simulation, it was considered 10 000 NV centers where the values of ω<sub>NV</sub> follow a normal distribution with mean value µ = 2π × 2870 MHz and standard deviation σ = 2π × 5.5 MHz. The aforementioned steps were repeated until the continuous ODMR measurement time <italic toggle=\"yes\">T</italic> was reached.</p>", "<p>For the original ODMR, we varied the microwave frequency ω<sub>MW</sub>/(2π) discretely from 2836 to 2905 MHz with a step size of 1 MHz. The measuring time for each frequency is <italic toggle=\"yes\">T</italic>\n<sub>frame</sub> = 10 ms. These values were used in the experiments. The light intensity corresponding to each frequency was obtained by summing up the photons generated by all NV centers within the time <italic toggle=\"yes\">T</italic>\n<sub>frame</sub>. The light intensity was normalized and displayed in the upper panel of Figure ##FIG##1##2A##.</p>", "<p>For the simulation of the event‐based ODMR, the microwave frequency ω<sub>MW</sub>/(2π) in steps of 1 kHz every 1 µ<italic toggle=\"yes\">s</italic> from 2836 to 2905 MHz was changed. According to the time resolution of the event camera, a duration <italic toggle=\"yes\">T</italic>\n<sub>event</sub> = 10 µ<italic toggle=\"yes\">s</italic> was set. The light intensity <italic toggle=\"yes\">I</italic> was defined as the sum of photons emitted by all NV centers in the duration <italic toggle=\"yes\">T</italic>\n<sub>event</sub>. It was then considered the light intensity difference between two adjacent durations Δ<italic toggle=\"yes\">I</italic> = <italic toggle=\"yes\">I</italic>\n<sub>latter</sub> − <italic toggle=\"yes\">I</italic>\n<sub>former</sub>, and compared it with a predefined threshold <italic toggle=\"yes\">c</italic>\n<sub>th</sub> = 1. If Δ<italic toggle=\"yes\">I</italic> ≥ <italic toggle=\"yes\">c</italic>\n<sub>th</sub> (Δ<italic toggle=\"yes\">I</italic> ≤ −<italic toggle=\"yes\">c</italic>\n<sub>th</sub>). We then recorded an event 1 (−1). Since the microwave frequency changes by 1 MHz every 100<italic toggle=\"yes\">T</italic>\n<sub>event</sub> time, it was added up the events generated in this frequency interval, then obtained the events number corresponding to the midpoint frequency of this interval, as shown in the bottom panel of Figure ##FIG##1##2A##.</p>", "<title>Frame‐Based ODMR Measurement</title>", "<p>The frame‐based ODMR was performed following the protocols shown in Figure ##SUPPL##0##S3## (Supporting Information). The 532 nm laser was kept on throughout the measurement to perform a continuous‐wave (CW)‐mode quantum sensing. The MW was swept from <italic toggle=\"yes\">f</italic>\n<sub>1</sub>‐2836 to <italic toggle=\"yes\">f</italic>\n<sub>70</sub>‐2905 MHz with a discrete step of 1 MHz. The time duration for one frequency step is <italic toggle=\"yes\">t</italic>\n<sub>step</sub> (different <italic toggle=\"yes\">t</italic>\n<sub>step</sub> from 26 to 260 ms were tried in the measurement) and the total time for a full sweep cycle is <italic toggle=\"yes\">T</italic> = <italic toggle=\"yes\">t</italic>\n<sub>step</sub>*70. During the stepped sweep, the absolute light intensity was recorded by the EMCCD, yielding a series of frames. The frequency sweep and EMCCD detection were synchronized by sequenced external pulses with the same step time. The frequency‐tuned light intensities were fitted with the Lorentzian function after that the resonance frequency was extracted. The precision of the sensing was evaluated by calculating the standard deviation of resonance frequency from repeated measurements. Here a binning size of 20 by 20 pixels was used for an improved precision, which means the light intensities stored in 20 by 20 pixels are first summarized before being fitted.</p>", "<title>Event‐Based ODMR Measurement</title>", "<p>The event‐based ODMR was performed following the protocols shown in Figure ##SUPPL##0##S4## (Supporting Information). Again, the 532 nm laser was kept constant throughout the measurement. Triggered with an external pulse, the MW frequency was swept linearly from <italic toggle=\"yes\">f</italic>\n<sub>1</sub>‐2836 to <italic toggle=\"yes\">f</italic>\n<sub>70</sub>‐2905 MHz with a period <italic toggle=\"yes\">T</italic> (<italic toggle=\"yes\">T</italic> changes from 3.5 to 140 ms). During frequency sweeping, the fluorescence change was continuously detected by the event camera and a stream of events was output. As discussed in the working principle in the main text, a moving sum method to process those raw events was used and reconstruct the derivative Lorentzian spectrum. Specifically, a window covering 1 MHz MW frequency was used to slide across the full sweeping range, during which all event values generated from this frequency range were summed. The same binning size of 20 by 20 pixels was chosen for processing the raw data as the one used in the frame‐based ODMR. Moreover, the measurement mentioned above was repeated for 10 loops and the outputs were stacked to mitigate the influence of noise events. Finally, the processed results were fitted with the derivative Lorentzian function to extract the resonance frequency. The standard deviation of 10 fittings was calculated to describe the sensing precision.</p>", "<title>Calculation of Sensing Precision and Time</title>", "<p>In traditional quantum sensing, the precision is usually defined as sensitivity: <mml:math id=\"jats-math-13\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>η</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi>δ</mml:mi><mml:msub><mml:mi>B</mml:mi><mml:mrow><mml:mi>m</mml:mi><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:mrow></mml:msub><mml:mo>∗</mml:mo><mml:msqrt><mml:msub><mml:mi>τ</mml:mi><mml:mi>e</mml:mi></mml:msub></mml:msqrt><mml:mo>=</mml:mo><mml:mfrac><mml:msub><mml:mi>σ</mml:mi><mml:msub><mml:mi>f</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:msub><mml:msub><mml:mi>γ</mml:mi><mml:mi>g</mml:mi></mml:msub></mml:mfrac><mml:mo>∗</mml:mo><mml:msqrt><mml:msub><mml:mi>τ</mml:mi><mml:mi>e</mml:mi></mml:msub></mml:msqrt></mml:mrow></mml:mrow></mml:math> for magnetic field sensing or <mml:math id=\"jats-math-14\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>η</mml:mi><mml:mi>T</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mi>δ</mml:mi><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi>m</mml:mi><mml:mi>i</mml:mi><mml:mi>n</mml:mi></mml:mrow></mml:msub><mml:mo>∗</mml:mo><mml:msqrt><mml:msub><mml:mi>τ</mml:mi><mml:mi>e</mml:mi></mml:msub></mml:msqrt><mml:mo>=</mml:mo><mml:mfrac><mml:msub><mml:mi>σ</mml:mi><mml:msub><mml:mi>f</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:msub><mml:mrow><mml:mi>d</mml:mi><mml:mi>D</mml:mi><mml:mo>/</mml:mo><mml:mi>d</mml:mi><mml:mi>T</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:msqrt><mml:msub><mml:mi>τ</mml:mi><mml:mi>e</mml:mi></mml:msub></mml:msqrt></mml:mrow></mml:mrow></mml:math> for temperature measurement, where <mml:math id=\"jats-math-15\" display=\"inline\"><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:msub><mml:mi>f</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:msub></mml:mrow></mml:math>was the standard deviation of measured resonance frequency <italic toggle=\"yes\">f</italic>\n<sub>0</sub>, γ<sub>\n<italic toggle=\"yes\">g</italic>\n</sub> is gyromagnetic ratio,<sup>[</sup>\n##REF##34038091##\n4a\n##\n<sup>]</sup>\n<italic toggle=\"yes\">d</italic>D/<italic toggle=\"yes\">d</italic>T is the thermal susceptibility of the Zero‐Field‐Splitting energy.<sup>[</sup>\n##REF##20366868##\n36\n##, ##REF##23900221##\n38\n##\n<sup>]</sup> Here τ<sub>\n<italic toggle=\"yes\">e</italic>\n</sub>is the exposure time and for traditional‐camera‐based quantum sensing, <mml:math id=\"jats-math-16\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:msub><mml:mi>f</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:msub><mml:mo>∼</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:msqrt><mml:msub><mml:mi>τ</mml:mi><mml:mi>e</mml:mi></mml:msub></mml:msqrt></mml:mfrac></mml:mrow></mml:mrow></mml:math> if the measurement was shot‐noise limited.<sup>[</sup>\n##UREF##10##\n28\n##\n<sup>]</sup> The event camera, however, only measures the change of photo‐current rather than integrating photo‐generated charges, so the concept of exposure time does not apply (or is extremely short considering the pixels response can reach µs level) for an event camera. To make a fair comparison, the precision directly as the standard deviation of extracted <italic toggle=\"yes\">f</italic>\n<sub>0</sub> was defined, which can be calculated as <mml:math id=\"jats-math-17\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:msub><mml:mi>f</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:msqrt><mml:mfrac><mml:mrow><mml:msubsup><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mrow><mml:mi>N</mml:mi><mml:mi>r</mml:mi><mml:mi>e</mml:mi><mml:mi>p</mml:mi><mml:mi>e</mml:mi><mml:mi>a</mml:mi><mml:mi>t</mml:mi></mml:mrow></mml:msubsup><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:msubsup><mml:mi>f</mml:mi><mml:mn>0</mml:mn><mml:mi>i</mml:mi></mml:msubsup><mml:mo>−</mml:mo><mml:mover accent=\"true\"><mml:mi>f</mml:mi><mml:mo>¯</mml:mo></mml:mover></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mrow><mml:mi>r</mml:mi><mml:mi>e</mml:mi><mml:mi>p</mml:mi><mml:mi>e</mml:mi><mml:mi>a</mml:mi><mml:mi>t</mml:mi></mml:mrow></mml:msub></mml:mfrac></mml:msqrt></mml:mrow></mml:mrow></mml:math>, where <mml:math id=\"jats-math-18\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>f</mml:mi><mml:mo>¯</mml:mo></mml:mover></mml:mrow></mml:math>is the mean of <italic toggle=\"yes\">f</italic>\n<sub>0</sub> measured from different repeated sweeps and <italic toggle=\"yes\">N</italic>\n<sub>repeat</sub> is the repeated measurements. Additionally, for a fair sensing speed comparison, the total sensing time τ was used, i.e., the total measurement time consumed before getting the resonance frequency, to represent imaging speed for all the three methods. In general, the shorter the time τ, the higher the sensing speed. In the event camera measurement, the total time <italic toggle=\"yes\">τ</italic> = <italic toggle=\"yes\">T</italic>*<italic toggle=\"yes\">N</italic>\n<sub>loop</sub>*2, where <italic toggle=\"yes\">T</italic> is the time consumed for one single direction sweeping, <italic toggle=\"yes\">N</italic>\n<sub>loop</sub> is the number of looped sweeps for one measurement, and 2 means forward and backward sweeping. For EMCCD, <italic toggle=\"yes\">τ</italic> = <italic toggle=\"yes\">τ</italic>\n<sub>e</sub>+ <italic toggle=\"yes\">τ<sub>o</sub>\n</italic>, where τ<sub>e</sub> is the total exposure time for one complete ODMR sweep. Here, <italic toggle=\"yes\">τ<sub>o</sub>\n</italic> = 1.12s is the data readout and transfer time for the EMCCD was used, and it was this value that limits the further reduction of sensing time cost.</p>", "<p>For the works using lock‐in cameras,<sup>[</sup>\n##REF##35610314##\n15\n##\n<sup>]</sup> the sensing time and precision were transformed from the data provided in the paper. Specifically, for reference 15a, they obtained a magnetic sensitivity of <mml:math id=\"jats-math-19\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>η</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>731</mml:mn><mml:mi>nT</mml:mi><mml:mo>/</mml:mo><mml:msqrt><mml:mrow><mml:mi>H</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:msqrt></mml:mrow></mml:mrow></mml:math> using <italic toggle=\"yes\">τ<sub>e</sub>\n</italic> = 4.8 ms averaging time per frame. According to the definition of sensitivity mentioned above, the standard deviation of extracted <italic toggle=\"yes\">f</italic>\n<sub>0</sub>, <sub>i.e.,</sub> sensing precision is <mml:math id=\"jats-math-20\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:msub><mml:mi>f</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mi>η</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mo>∗</mml:mo><mml:mfrac><mml:msub><mml:mi>γ</mml:mi><mml:mi>g</mml:mi></mml:msub><mml:msqrt><mml:msub><mml:mi>τ</mml:mi><mml:mi>e</mml:mi></mml:msub></mml:msqrt></mml:mfrac><mml:mo>≈</mml:mo><mml:mn>0.29</mml:mn><mml:mspace width=\"0.33em\"/><mml:mi>M</mml:mi><mml:mi>H</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:mrow></mml:math>. Next the sensing time is estimated to be <italic toggle=\"yes\">τ<sub>e</sub>*N</italic>\n<sub>in</sub> = 0.34s, where <italic toggle=\"yes\">N</italic>\n<sub>in</sub>, i.e., the number of frequency steps swept for one ODMR, is assumed to be the same as the measurement as no specific information is provided in the paper. For reference 15b, <mml:math id=\"jats-math-21\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:msub><mml:mi>f</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:mn>0.056</mml:mn><mml:mspace width=\"0.33em\"/><mml:mi>M</mml:mi><mml:mi>H</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:mrow></mml:math> with 10 repeated acquisitions can be extracted from Figure 10 in the paper. They used a demodulation frame rate of 3500 fps to acquire 500 frames per ODMR measurement, so that the sensing time could be calculated as: 1/3500*500*10 = 1.43 s.</p>", "<title>Dynamic Temperature Measurement</title>", "<p>Another red laser (MDL‐III‐637) was added to the initial ODMR system for controlling the temperature of the sample (<bold>Figure</bold> ##FIG##3##\n4A##). As illustrated in the fabrication process, the sample was covered with gold nano‐particles which absorb laser power and can be used for local heating of the diamond sample. Due to the high thermal conductivity of the bulk diamond sample, the local heat will transmit across the sample to reach a thermal equilibrium. Hence, the diamond sample temperature can be controlled by modulating the red laser power. The red laser power was modulated by rotating a linear polarizer (LPNIRE100‐B) mounted on a motorized rotation stage. For incident power I<sub>0</sub> entering the polarizer, the output power is <italic toggle=\"yes\">I</italic>\n<sub>0</sub> cos<sup>2</sup>(<italic toggle=\"yes\">θ</italic>), where <italic toggle=\"yes\">θ</italic> is the angle between the polarization axis of incident laser and polarizer.</p>", "<p>For static measurement, the red laser was set to different power levels (from 0 to the maximum of 240 mW) by rotating the polarizer to different angles. The resonance frequencies <italic toggle=\"yes\">f</italic>\n<sub>0</sub> of different pixels (covering ≈60*60 pixels, i.e., 16*16 µm<sup>2</sup> of the ROI) were extracted and transferred to a temperature difference using <mml:math id=\"jats-math-22\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi mathvariant=\"normal\">T</mml:mi><mml:mo>=</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:msubsup><mml:mi>f</mml:mi><mml:mn>0</mml:mn><mml:mi>p</mml:mi></mml:msubsup><mml:mo>−</mml:mo><mml:msubsup><mml:mi>f</mml:mi><mml:mn>0</mml:mn><mml:mn>0</mml:mn></mml:msubsup></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>/</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mfrac><mml:mrow><mml:mi>d</mml:mi><mml:mi>D</mml:mi></mml:mrow><mml:mrow><mml:mi>d</mml:mi><mml:mi>T</mml:mi></mml:mrow></mml:mfrac><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, where <mml:math id=\"jats-math-23\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>f</mml:mi><mml:mn>0</mml:mn><mml:mi>p</mml:mi></mml:msubsup></mml:mrow></mml:math> and <mml:math id=\"jats-math-24\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>f</mml:mi><mml:mn>0</mml:mn><mml:mn>0</mml:mn></mml:msubsup></mml:mrow></mml:math> are resonance frequencies measured when the red laser power is p and 0 mW (taken as the reference zero temperature which is also used in the dynamic measurement), respectively. And the thermal susceptibility of the Zero‐Field‐Splitting energy <mml:math id=\"jats-math-25\" display=\"inline\"><mml:mrow><mml:mrow><mml:mfrac><mml:mrow><mml:mi>d</mml:mi><mml:mi>D</mml:mi></mml:mrow><mml:mrow><mml:mi>d</mml:mi><mml:mi>T</mml:mi></mml:mrow></mml:mfrac><mml:mo>=</mml:mo><mml:mn>74</mml:mn><mml:mi>k</mml:mi><mml:mi>H</mml:mi><mml:mi>z</mml:mi></mml:mrow></mml:mrow></mml:math>/°C is extracted from the calibration measurement (Figure ##SUPPL##0##S13##, Supporting Information) and then used to calculate the temperature change. The measurement was repeated for 10 times, from which the temperature precision was calculated. For dynamic temperature measurement, the red laser power was continuously changed by rotating the polarizer with the speed ω pre‐determined by a Python program. During measurement, fixed period <italic toggle=\"yes\">P</italic> of 14 and 7 ms were tried to sweep the MW frequency and events of 10 looped sweeps were stacked to extract the resonance frequency. It took 0.28 s/0.14 s (considering forward and backward sweeps) to obtain one temperature distribution. The temporal change of temperature was fitted with function ΔT = <italic toggle=\"yes\">A</italic>\n<sub>0</sub>\n<italic toggle=\"yes\">cos</italic>\n<sup>2</sup>(ω<italic toggle=\"yes\">t</italic> + φ) + <italic toggle=\"yes\">c</italic>, from which the polarizer's rotation speed ω and the temperature change range <italic toggle=\"yes\">A</italic>\n<sub>0</sub> was extracted.</p>", "<title>Statistical Analysis</title>", "<p>In this work, the standard deviation of fitted resonance frequencies/temperatures from 10 repeated measurements was calculated to represent the error range of experimental results.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare the following competing financial interests: A PCT Patent application has been filed with application No. PCT/CN2022/129840.</p>", "<title>Author Contributions</title>", "<p>Z.D., M.G. and F.X. contributed equally to this work. Z.Q.C. and C.L. conceived the idea. Z.Y.D., M.G., F. X., K.Z., J.H.Z. performed the experiments and analyzed data under the supervision of Z.Q.C., C.L., and N.W., Y.Y.L performed the simulations under the supervision of Z.Y.W., Y.Z. and J.W. discussed the results and commented on the manuscript. Z.Y.D., C.L., and Z.Q.C. wrote the manuscript with input from all authors.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank Prof. Edmund Y. Lam and Dr. Hayden K.H. So, for fruitful discussions, and S.Z. for help in surface modification of diamond sample. Z.Q.C. acknowledges financial support provided under the HKSAR Government Research Grants Council (RGC) Research Matching Grant Scheme (Grant No. 207300313); the HKSAR Innovation and Technology Fund (ITF) through the Platform Projects of the Innovation and Technology Support Program (Grant No. ITS/293/19FP); HKU Seed Fund; the Guangdong Special Support Project (2019BT02 × 030); and the Health@InnoHK program of the Innovation and Technology Commission of the HKSAR Government. C.L. acknowledges the HKSAR Government RGC Early Career Scheme (ECS) grant (Grant No. 27210321); NSFC Excellent Young Scientist Fund (Hong Kong and Macau) under Grant 62122005. N.W. acknowledges financial support provided under the HKSAR Government RGC Theme‐based Research Scheme (TRS) grant (Grant No. T45‐701/22‐R). JW acknowledges funding from the EU via the project AMADEUS, the BMBF via the cluster4future QSENS as well as the DFG via the GRK2642 and FOR 2724. YL and ZW acknowledge support from the National Natural Science Foundation of China (Grant No. 12074131) and the Natural Science Foundation of Guangdong Province (Grant No. 2021A1515012030). Y.Z. acknowledges support from the Guangdong Special Support Project (2019BT02 × 030).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6671-fig-0001\"><label>Figure 1</label><caption><p>Concept, design and implementation of widefield quantum sensing. A) Overview of NV‐based widefield quantum sensing: energy level diagram and atomic structure of NV centers; and the experimental apparatus of widefield quantum diamond microscope. L: Laser; DM: Dichroic Mirror; BS: Beam Splitter; M: Mirror; B) A schematic showing the working principle of frame‐based widefield quantum sensing, where a series of frames are output from a frame‐based sensor recording both fluorescence intensity and background signals. C) A schematic showing the working principle of proposed neuromorphic widefield quantum sensing, where the fluorescence changes are converted into sparse spikes through a neuromorphic vision sensor.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6671-fig-0002\"><label>Figure 2</label><caption><p>Theoretical background. A) Simulated ODMR spectrum using conventional frame‐based sensor (green dots) and event‐based sensor (orange dots), with quality described via <italic toggle=\"yes\">Q</italic>\n<sub>F</sub> (upper panel) and Q<sub>E</sub> (lower panel), respectively. QF: full width at half maximum, QE: the frequency difference between two inflection points. The resonance frequency can be extracted by fitting the data with Lorentzian function (brown solid curve) and its derivative (black solid curve), respectively. B) Cartoon showing the conversion from the frame‐based ODMR spectrum into event‐based one through processing the recorded time trace of computed raw events.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6671-fig-0003\"><label>Figure 3</label><caption><p>Experimental demonstration. The measurement protocol, raw datasets and obtained ODMR spectrum (of the central point of ROI) using frame‐based A,C,E) and event‐based sensor B,D,F), respectively. The insert in (F) shows raw event frames (by accumulating events of 1 ms range) at three different frequency points. The spectra in E and F are fitted with the Lorentzian and its derivative functions, respectively, from which the resonance frequency <italic toggle=\"yes\">f</italic>\n<sub>0</sub> is extracted (<italic toggle=\"yes\">f<sub>0</sub>\n</italic>*is the averaged result from forward and backward sweeping as discussed in Section <xref rid=\"advs6671-sec-0020\" ref-type=\"sec\">2</xref> in Supporting Information; Error represents the standard deviation from 10 repeated measurements. The other 9 spectrums can be found in Figures ##SUPPL##0##S6## and ##SUPPL##0##S7##, Supporting Information). G) Comparison of precision σ and required sensing time τ for measurements using event camera (red squares), EMCCD (green circles) and lock‐in camera (blue stars), respectively. The results of event‐ and EMCCD‐ based methods are fitted with <mml:math id=\"jats-math-5\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:mrow><mml:mi>e</mml:mi><mml:mi>v</mml:mi><mml:mi>e</mml:mi><mml:mi>n</mml:mi><mml:mi>t</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>0.023</mml:mn><mml:mfrac><mml:mn>1</mml:mn><mml:msup><mml:mi>τ</mml:mi><mml:mn>0.43</mml:mn></mml:msup></mml:mfrac></mml:mrow></mml:mrow></mml:math> (orange solid) and <mml:math id=\"jats-math-6\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:mrow><mml:mi>E</mml:mi><mml:mi>M</mml:mi><mml:mi>C</mml:mi><mml:mi>C</mml:mi><mml:mi>D</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>0.028</mml:mn><mml:mfrac><mml:mn>1</mml:mn><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mi>τ</mml:mi><mml:mo>−</mml:mo><mml:msub><mml:mi>τ</mml:mi><mml:mi>o</mml:mi></mml:msub></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>0.48</mml:mn></mml:msup></mml:mfrac></mml:mrow></mml:mrow></mml:math> (cyan solid), respectively.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6671-fig-0004\"><label>Figure 4</label><caption><p>Widefield dynamic temperature measurements. A) Setup for dynamic temperature measurement. The main part of the system resembles that shown in Figure ##SUPPL##0##S2A## (Supporting Information), with an additional red laser serving as the heating source tuned by an electrically rotated linear polarizer. B) Static measurement of temperature change versus red laser power for the central point of ROI. C) The spatiotemporal temperature response of the sample measured with event‐based method. D) Cosine temperature change in the central point of ROI measured with event‐based (blue squares) and frame‐based (purple stars) ODMR. Only the event‐based method tracks the true temperature change which can be fitted with the cosine square function. E) Fourier transforms (FTs, magnitude) of the data in D. (the FT of frame‐based results is scaled to 0‐0.1 for a clear comparison). The FT of event‐based results is consistent with that of laser power tuned by the same rotated polarizer.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6671-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Comparison between frame‐based and event‐based ODMR. The sensing time, precision and data amount are compared with their typical values obtained by experiment. SBRs and SBRt stand respectively for spatial and temporal signal‐to‐background ratio, defined in Section <xref rid=\"advs6671-sec-0090\" ref-type=\"sec\">5</xref>, Supporting Information.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Method</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Sensing Time</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Precision</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Data Amount</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Latency</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">SBR<sub>s</sub>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">SBR<sub>t</sub>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Dynamic Range</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Conventional Quantum Sensing (e.g., EMCCD<xref rid=\"advs6671-tbl1-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.82 s</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.031 MHz</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">35 MB</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">26 ms</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">64</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96 dB</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Neuromorphic Quantum Sensing (e.g., Event Camera<xref rid=\"advs6671-tbl1-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.14 s<xref rid=\"advs6671-tbl1-note-0003\" ref-type=\"table-fn\">\n<sup>c)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.034 MHz</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">363 KB</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">220 µs</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">194</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">120 dB</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6671-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Measured rotation speed and temperature change range under different modulation speeds of the polarizer in comparison with the set values.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">ω<sub>set</sub> (rad/s)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">ω<sub>meas.</sub> (rad/s)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">A</italic>\n<sub>0</sub> (K)</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.207</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.206</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.56</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.414</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.415</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.61</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.724</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.728</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.34</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
[ "<disp-formula id=\"advs6671-disp-0001\">\n<label>(1)</label>\n<mml:math id=\"jats-math-1\" display=\"block\"><mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>t</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>I</mml:mi><mml:mi>log</mml:mi></mml:msub><mml:mo>/</mml:mo><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>I</mml:mi><mml:mi>log</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>t</mml:mi></mml:mrow></mml:mfrac></mml:mfenced><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mrow><mml:msubsup><mml:mi>I</mml:mi><mml:mi>log</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mfenced open=\"(\" close=\")\"><mml:mi>t</mml:mi></mml:mfenced></mml:mrow></mml:mfrac><mml:mo linebreak=\"goodbreak\">×</mml:mo><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mspace width=\"0.33em\"/><mml:msub><mml:mi>I</mml:mi><mml:mi>log</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mrow><mml:msubsup><mml:mi>I</mml:mi><mml:mi>log</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mfenced open=\"(\" close=\")\"><mml:mi>t</mml:mi></mml:mfenced></mml:mrow></mml:mfrac><mml:mo linebreak=\"goodbreak\">×</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi>th</mml:mi></mml:msub></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6671-disp-0002\">\n<label>(2)</label>\n<mml:math id=\"jats-math-2\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>λ</mml:mi><mml:mi>s</mml:mi></mml:msub><mml:mfenced open=\"(\" close=\")\"><mml:mi>t</mml:mi></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>T</mml:mi><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi mathvariant=\"normal\">t</mml:mi></mml:mrow></mml:mfrac><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mfrac><mml:mi>T</mml:mi><mml:msub><mml:mi>C</mml:mi><mml:mi>th</mml:mi></mml:msub></mml:mfrac><mml:mo linebreak=\"goodbreak\">×</mml:mo><mml:msubsup><mml:mi>I</mml:mi><mml:mi>log</mml:mi><mml:mo>′</mml:mo></mml:msubsup><mml:mfenced open=\"(\" close=\")\"><mml:mi>t</mml:mi></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>" ]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
[]
[]
[]
[ "<supplementary-material id=\"advs6671-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6671-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 1</p></caption></supplementary-material>", "<supplementary-material id=\"advs6671-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 2</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6671-tbl1-note-0001\"><label>\n<sup>a)</sup>\n</label><p>Evolve 512 Delta Photometrics, price ≈$20000<sup>[</sup>\n##UREF##12##\n30\n##\n<sup>]</sup>;</p></fn><fn id=\"advs6671-tbl1-note-0002\"><label>\n<sup>b)</sup>\n</label><p>EVK1‐Gen 3.1 VGA Prophesee, price ≈$4000<sup>[</sup>\n##UREF##13##\n31\n##\n<sup>]</sup>;</p></fn><fn id=\"advs6671-tbl1-note-0003\"><label>\n<sup>c)</sup>\n</label><p>The calculation considers both forward and backward frequency sweep.</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2304355-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304355-s003.avi\" mimetype=\"video\" mime-subtype=\"x-msvideo\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304355-s002.gif\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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42
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 8; 11(2):2304355
oa_package/88/1d/PMC10787069.tar.gz
PMC10787070
37939308
[ "<title>Introduction</title>", "<p>Antimony chalcogenides (Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub>, 0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1), including antimony sulfide (Sb<sub>2</sub>S<sub>3</sub>), antimony selenide (Sb<sub>2</sub>Se<sub>3</sub>), and antimony selenosulfide (Sb<sub>2</sub>(S,Se)<sub>3</sub>), are widely used as light‐harvesting materials in solar cells due to their low toxicity, excellent chemical stability, and high light absorption coefficients (&gt;10<sup>5</sup> cm<sup>−1</sup> in visible region). The recently developed hydrothermal deposition synthesis of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> thin film has enabled the power conversion efficiency (PCE) of solar cells to exceed 10.7%, indicating its great potential in practical applications with further efficiency improvement.<sup>[</sup>\n##UREF##0##\n1\n##, ##UREF##1##\n2\n##\n<sup>]</sup> Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> consists of 1D (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons, in which Sb─Se is covalently bonded along the c‐axis, while the ribbons interact with each other through weak van der Waals (vdW) force.<sup>[</sup>\n##UREF##2##\n3\n##\n<sup>]</sup> This phenomenon leads to an anisotropic carrier transport property within the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. Carrier transport along ribbons shows high efficiency, but hopping transport across ribbons appears very difficult. The maximum conductivity ratio between the c‐axis and vdW orientations is ≈16. Furthermore, the optical responsiveness ratio between these orientations is estimated to be 15, indicating that the carrier transport in the c‐axis orientation is highly effective.<sup>[</sup>\n##UREF##3##\n4\n##, ##UREF##4##\n5\n##\n<sup>]</sup> The termination end of the (<italic toggle=\"yes\">hk</italic>0) planes in the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons does not necessarily result in the Sb─See bond breakage, thereby essentially decreasing the generation of dangling bonds. This characteristic results in [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films with intrinsically benign grain boundaries that minimize recombination losses, displaying an advantage of quasi‐1D (Q1D) structured materials.<sup>[</sup>\n##UREF##5##\n6\n##\n<sup>]</sup> Both ttheoretical study and extensive experimental investigations show that almost all high‐efficiency Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> solar cells have a high percentage of (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons that are inclined vertically to the substrate.<sup>[</sup>\n##UREF##5##\n6\n##, ##UREF##6##\n7\n##, ##UREF##7##\n8\n##, ##UREF##8##\n9\n##, ##UREF##9##\n10\n##\n<sup>]</sup> For low‐dimensional materials, the surface energy of the crystalline plane parallel to the van der Waals force is always lower than that along the covalent bond direction.<sup>[</sup>\n##UREF##7##\n8\n##\n<sup>]</sup> In terms of energy minimization principle, the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons tend to grow parallel to the substrate to minimize the surface energy,<sup>[</sup>\n##UREF##10##\n11\n##\n<sup>]</sup> making it very challenging to manipulate the growth of [<italic toggle=\"yes\">hk</italic>1]‐oriented (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons.</p>", "<p>Crystal orientation engineering generally refers to the regulation of the nucleation and growth behavior to enable the inorganic compound films to grow along specific crystal planes. Various methods are currently being used to prepare [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films, which are generally solution‐based and vacuum deposition methods. The solution method mainly includes hydrothermal, chemical bath deposition, and spin‐coating methods, while the vacuum method primarily consists of rapid thermal evaporation, close space sublimation, vapor transport deposition, thermal evaporation, and magnetron sputtering deposition approaches.</p>", "<p>The presence of different [<italic toggle=\"yes\">hk</italic>1] film orientations indicates that the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons tilt at different angles to the substrate. Ribbons with a low‐index facet specifically exhibit larger angles to the substrate and tend to grow perpendicular to it, while those with a high‐index facet indicate smaller ribbon angles to the substrate and tend to grow parallel to it. In films, the ribbon tilt angles to the substrate affect the carrier transport efficiency to a great extent. The [001]‐oriented ribbons perpendicular to the substrate particularly exhibit the best carrier transport performance due to their shorter transport distances compared to other [<italic toggle=\"yes\">hk</italic>1]‐oriented ribbons.<sup>[</sup>\n##REF##31755514##\n12\n##, ##UREF##11##\n13\n##, ##UREF##12##\n14\n##, ##UREF##13##\n15\n##\n<sup>]</sup> The electron diffusion length in the [001]‐oriented (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons is approximately five times longer than that in the [221]‐oriented ribbons; thus, the [001] orientation is more conducive to improving the device performance.<sup>[</sup>\n##UREF##14##\n16\n##\n<sup>]</sup> In addition, [001]‐oriented films have a higher growth rate along the ribbon direction, such that when the lateral strain generated between the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons exceeds the tolerance range of the van der Waals forces during deposition, the films tend to transform into a nanorod array, which is a common structure in [001]‐oriented films.<sup>[</sup>\n##REF##30631064##\n17\n##\n<sup>]</sup> The [001]‐oriented nanorod array structured films reduce reflectivity and enhance light harvesting, which is beneficial to the performance of photovoltaic devices.<sup>[</sup>\n##UREF##15##\n18\n##\n<sup>]</sup> This structure has been applied to solar cells and achieved breakthroughs in the PCE.<sup>[</sup>\n##REF##30631064##\n17\n##, ##UREF##16##\n19\n##\n<sup>]</sup> However, the nanorod array structure tends to form rough surface morphology, which leads to the generation of current leakage channels bringing about adverse effects in the open‐circuit voltage (<italic toggle=\"yes\">V</italic>\n<sub>OC</sub>) and the fill factor (FF) of planar‐type solar cells.<sup>[</sup>\n##REF##34569779##\n20\n##, ##UREF##17##\n21\n##\n<sup>]</sup> Therefore, regulating the growth of ribbons to maintain an appropriate tilt angle is more suitable for application in planar heterojunction solar cell devices. Enhancing the lateral growth of ribbons to increase the film compactness and grain size is a key issue when developing [001]‐oriented structured devices. The presence of defects, such as dislocations related to the strain generated during the grain growth in the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films can inhibit the carrier transport along the ribbons. Therefore, developing advanced preparation methods that can better control the strain during the film growth process to fundamentally suppress the dislocation generation may be a promising direction.<sup>[</sup>\n##UREF##18##\n22\n##\n<sup>]</sup>\n</p>", "<p>Controlling crystal orientation is a great challenge in the field of film preparation, and the application of advanced characterization techniques as well as understanding of the underlying mechanisms are essential for the study of crystal orientation.<sup>[</sup>\n##REF##35801858##\n23\n##\n<sup>]</sup> In this review, we first introduce common characterization methods that are used to quantitatively analyze the crystal orientation, including pole figure, orientation distribution map, texture coefficient, and ribbon carrier transport factors. Afterward, we summarize the relevant progress of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> crystal orientation engineering in terms of the orientation regulation methods and mechanisms, mainly analyzing the influence of film growth kinetics and interface lattice matching on the crystal growth orientation. We also discuss the orientation mechanisms of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films from five aspects including growth rate, posttreatment, substrate type, interfacial engineering, and seeding material, as shown in <bold>Figure</bold> ##FIG##0##\n1\n##. Lastly, we provide a brief outlook on the current challenges in crystal orientation engineering of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film for solar cell applications.</p>" ]
[ "<title>Crystallographic Orientation Characterization Methods</title>", "<p>Theoretically, the orientation of each grain in a polycrystalline material is completely disordered and randomly distributed. However, the actual growth process always exhibits an inhomogeneously oriented crystal distribution, i.e., the growth orientation in certain directions significantly increases. This phenomenon is usually considered the preferred orientation. The orientation characteristics of polycrystalline films are described by the crystal texture, while the crystal texture existence indicates that the crystal has anisotropy,<sup>[</sup>\n##UREF##19##\n24\n##\n<sup>]</sup> leading to significant differences in the carrier transport properties between [<italic toggle=\"yes\">hk</italic>1]‐ and [<italic toggle=\"yes\">hk</italic>0]‐oriented Q1D‐Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. The pole figure and texture coefficient based on X‐ray diffraction (XRD), as well as the orientation distribution map based on electron backscatter diffraction (EBSD), are useful techniques to analyze the crystal orientation. These analysis methods obtain information about the crystal structure and orientation from macroscopic at localized regions.<sup>[</sup>\n##UREF##20##\n25\n##\n<sup>]</sup> We will briefly introduce herein the relevant characterization methods used to determine the crystal orientation.</p>", "<title>Pole Figure</title>", "<p>The pole figure is an important means of analyzing and determining the polycrystalline film texture, it is derived from the XRD characterization. Plotting the intensity of each (<italic toggle=\"yes\">hkl</italic>) line relative to the sample coordinates in a stereographic projection enables us to qualitatively understand the crystallite orientation relative to the sample direction. These stereographic projection plots are defined as pole figures.<sup>[</sup>\n##UREF##21##\n26\n##\n<sup>]</sup> In <bold>Figure</bold> ##FIG##1##\n2a##, the sample's direction is defined by the transverse (TD), rolling (RD), and normal (ND) directions, respectively. The pole direction is defined by the radial <italic toggle=\"yes\">α</italic>, azimuthal <italic toggle=\"yes\">β</italic> angles, and tilt angle <italic toggle=\"yes\">χ</italic>. The pole density of point <italic toggle=\"yes\">P</italic> is defined as the point <italic toggle=\"yes\">P</italic>′ projected by a straight line from point <italic toggle=\"yes\">P</italic> to point <italic toggle=\"yes\">S</italic> on the equatorial plane. The pole density in all directions can be mapped onto the equatorial plane through stereographic projection (Figure ##FIG##1##2b##). This method was recently used to analyze the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film orientation.<sup>[</sup>\n##REF##31755514##\n12\n##, ##UREF##13##\n15\n##, ##UREF##22##\n27\n##, ##UREF##23##\n28\n##\n<sup>]</sup> Zhou et al. implemented the XRD pole figure to demonstrate that the grains of Sb<sub>2</sub>Se<sub>3</sub> films prepared by selenizing [003]‐oriented Sb films are mainly [001] preferred orientation.<sup>[</sup>\n##REF##31755514##\n12\n##\n<sup>]</sup> In Figure ##FIG##1##2c##, the XRD pole figure of the (002) plane shows a sharp single pole with a very narrow tilt angle of 10°, providing strong evidence for the highly preferred [001] orientation of the Sb<sub>2</sub>Se<sub>3</sub> film.</p>", "<title>Orientation Distribution Map</title>", "<p>Electron backscatter diffraction (EBSD) is a scanning electron microscopy (SEM) based characterization technique commonly used to investigate the spatially resolved microstructural–crystallographic information of crystalline or polycrystalline materials with a sub‐micrometer resolution.<sup>[</sup>\n##REF##36415914##\n29\n##\n<sup>]</sup> Standard EBSD measurements are performed in the SEM chamber using either a direct electron detector or a conventional fluoroscope and camera (Figure ##FIG##1##2d##).<sup>[</sup>\n##UREF##20##\n25\n##\n<sup>]</sup> A direct detector or phosphor screen very close to the sample allows imaging of backscattered electrons escaping from the sample at a specific Bragg angle, thus determining the orientation of the localized crystal. The resulting diffraction pattern is often referred to as a Kikuchi pattern, and diffraction of the lattice planes results in a series of intersecting bands called Kikuchi lines (Figure ##FIG##1##2e##). Since the Kikuchi bands correspond to the lattice planes, the angle between the bands can be utilized to determine the orientation of the crystal (Figure ##FIG##1##2f##).<sup>[</sup>\n##UREF##24##\n30\n##\n<sup>]</sup> Scanning the beam over the surface of the sample collects patterns pixel by pixel, which can be indexed by comparing them with the simulated patterns, and ultimately results in a microstructure map of the sample, which includes information on crystal orientation, phase, strain, and grain boundaries. As shown in Figure ##FIG##1##2g##, the Sb<sub>2</sub>Se<sub>3</sub> film exhibits randomly oriented grain distribution.<sup>[</sup>\n##UREF##13##\n15\n##\n<sup>]</sup>\n</p>", "<title>Texture Coefficient</title>", "<p>The texture coefficient (<italic toggle=\"yes\">TC</italic>) is a commonly used parameter for quantitatively evaluating the preferred crystal plane orientation. The calculation formula for the <italic toggle=\"yes\">TC</italic> of crystal planes (<italic toggle=\"yes\">hkl</italic>) is as follows: <mml:math id=\"jats-math-1\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:msub><mml:mi>C</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>hkl</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>hkl</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>hkl</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>1</mml:mn><mml:mo>/</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>∑</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>hkl</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mi>r</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>hkl</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>, where <italic toggle=\"yes\">I</italic>\n<sub>(</sub>\n<italic toggle=\"yes\">\n<sub>hkl</sub>\n</italic>\n<sub>)</sub>, <italic toggle=\"yes\">I</italic>\n<sub>r(</sub>\n<italic toggle=\"yes\">\n<sub>hkl</sub>\n</italic>\n<sub>)</sub>, and <italic toggle=\"yes\">n</italic> indicate the intensity obtained from the XRD, intensity referring to the diffraction patterns from the inorganic crystal structure database (ICSD), and the number of diffraction peaks considered, respectively. The calculated <italic toggle=\"yes\">TC</italic> ≈ 1 for all (<italic toggle=\"yes\">hkl</italic>) crystal planes (<italic toggle=\"yes\">TC</italic>\n<sub>(</sub>\n<italic toggle=\"yes\">\n<sub>hkl</sub>\n</italic>\n<sub>)</sub>) indicates that the film comprises randomly oriented grains similar to the information reflected by the ICSD. By contrast, <italic toggle=\"yes\">TC</italic>\n<sub>(</sub>\n<italic toggle=\"yes\">\n<sub>hkl</sub>\n</italic>\n<sub>)</sub> &gt; 1 signifies that the film grows along the given (<italic toggle=\"yes\">hkl</italic>) crystal plane as the preferred orientation, while <italic toggle=\"yes\">TC</italic>\n<sub>(</sub>\n<italic toggle=\"yes\">\n<sub>hkl</sub>\n</italic>\n<sub>)</sub> &lt; 1 denotes that the orientation along the given (<italic toggle=\"yes\">hkl</italic>) crystal plane is suppressed. Therefore, the <italic toggle=\"yes\">TC</italic>\n<sub>(</sub>\n<italic toggle=\"yes\">\n<sub>hkl</sub>\n</italic>\n<sub>)</sub> increase means the film tends to grow along the (<italic toggle=\"yes\">hkl</italic>)‐preferred orientation.<sup>[</sup>\n##UREF##27##\n33\n##\n<sup>]</sup>\n</p>", "<title>Ribbon Carrier Transport Factor</title>", "<p>The <italic toggle=\"yes\">TC</italic> is a convincing indicator for evaluating the films’ crystal orientation. It can also reflect the transport characteristics of carriers for polycrystalline materials. However, films usually contain multiple crystal planes with different [<italic toggle=\"yes\">hk</italic>1] and [<italic toggle=\"yes\">hk</italic>0] orientations. Pattini et al. calculated the ribbon carrier transport (<italic toggle=\"yes\">RCT</italic>) factors for different oriented ribbons to quantitatively evaluate the contribution of different oriented ribbons to the effective carrier transport. The <italic toggle=\"yes\">RCT</italic> is calculated according to <italic toggle=\"yes\">RCT</italic>  =  <italic toggle=\"yes\">TC</italic> × <italic toggle=\"yes\">EVC</italic>, where <italic toggle=\"yes\">EVC</italic> represents the component of the [<italic toggle=\"yes\">hkl</italic>]‐oriented ribbons along the [001] direction. The (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons in Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> are stacked along the c‐axis direction, thereby requiring the ribbons to grow perpendicular to the substrate (i.e., along the [001] direction) to ensure a high‐efficiency carrier transport. The carriers show the worst transport performance when the ribbons are parallel to the substrate (i.e., along the [<italic toggle=\"yes\">hk</italic>0] direction). The ribbons in the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film typically exhibit different orientations, with their angles ranging from 0° to 90° between the ribbons and the surface normal of the film. <bold>Table</bold> ##TAB##0##\n1\n## lists the most common angles between the ribbons and the surface normal along with the effective vertical component of the ribbons defined by the strip angle cosine ranging from 0 ([<italic toggle=\"yes\">hk</italic>0]‐oriented ribbon) to 1 ([001]‐oriented ribbon). <bold>Figure</bold> ##FIG##2##\n3\n## depicts the corresponding crystal planes.<sup>[</sup>\n##UREF##22##\n27\n##, ##UREF##23##\n28\n##\n<sup>]</sup>\n</p>" ]
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[ "<title>Abstract</title>", "<p>The emerging antimony chalcogenide (Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub>, 0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1) semiconductors are featured as quasi‐1D structures comprising (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons, this structural characteristic generates facet‐dependent properties such as directional charge transfer and trap states. In terms of carrier transport, proper control over the crystal nucleation and growth conditions can promote preferentially oriented growth of favorable crystal planes, thus enabling efficient electron transport along (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons. Furthermore, an in‐depth understanding of the origin and impact of the crystal orientation of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films on the performance of corresponding photovoltaic devices is expected to lead to a breakthrough in power conversion efficiency. In fact, there are many studies on the orientation control of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> colloidal nanomaterials. However, the synthesis of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> thin films with controlled facets has recently been a focus in optoelectronic device applications. This work summarizes methodologies that are applied in the fabrication of preferentially oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films, including treatment strategies developed for crystal orientation engineering in each process. The mechanisms in the orientation control are thoroughly analyzed. An outlook on perspectives for the future development of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> solar cells based on recent research and issues on orientation control is finally provided.</p>", "<p>Crystal orientation engineering is critical for regulating the crystal plane‐dependent properties of quasi‐1D antimony chalcogenide materials, which in turn affects device efficiency. The regulation of crystal orientation is influenced by various factors such as growth rate, posttreatment, substrate type, interfacial engineering, and the introduction of seeding materials.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6622-cit-0136\">\n<string-name>\n<given-names>K.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>R.</given-names>\n<surname>Tang</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Zhu</surname>\n</string-name>, <string-name>\n<given-names>T.</given-names>\n<surname>Chen</surname>\n</string-name>, <article-title>Critical Review on Crystal Orientation Engineering of Antimony Chalcogenide Thin Film for Solar Cell Applications</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304963</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304963</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Orientation Control Strategies in Different Deposition Methods</title>", "<p>Researchers exploit various deposition methods to prepare Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films with enhanced [<italic toggle=\"yes\">hk</italic>1] orientation. These methods are mainly classified into two: solution‐processed (e.g., hydrothermal and chemical bath deposition and spin‐coating method) and vacuum deposition (e.g., rapid thermal evaporation, close space sublimation, vapor transport deposition, thermal evaporation, and magnetron sputtering method) methods. This section presents an overview of each deposition method mentioned above and summarizes the approaches for enhancing the [<italic toggle=\"yes\">hk</italic>1] orientation of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films.</p>", "<title>Hydrothermal Deposition</title>", "<p>Hydrothermal deposition is an effective method of using an aqueous solution as the reaction system in a closed reactor (autoclave) to dissolve and recrystallize normally insoluble or poorly soluble substances by heating and pressurizing the reaction system (or autogenous vapor pressure), thereby creating a relatively high‐temperature and ‐pressure reaction environment for completing the inorganic material synthesis and treatment. This method is featured as a simple operation with environmental friendliness and low organic residues.<sup>[</sup>\n##UREF##28##\n34\n##, ##UREF##29##\n35\n##\n<sup>]</sup> Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> prepared through this method shows an improved film quality with flat and compact surface morphology, increased grain size, and reduced defects, which enable the currently highest efficiency of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> solar cells.<sup>[</sup>\n##UREF##0##\n1\n##, ##UREF##1##\n2\n##, ##UREF##30##\n36\n##, ##UREF##31##\n37\n##\n<sup>]</sup> The hydrothermal deposition of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film generally uses antimony potassium tartrate (KSbC<sub>4</sub>H<sub>4</sub>O<sub>7</sub>·0.5H<sub>2</sub>O) as the Sb source, sodium thiosulfate (Na<sub>2</sub>S<sub>2</sub>O<sub>3</sub>) as the S source, and selenourea and sodium selenosulfate (Na<sub>2</sub>SeSO<sub>3</sub>) as the Se sources. <bold>Figure</bold> ##FIG##3##\n4a## presents a schematic of the hydrothermal deposition.</p>", "<p>Several kinds of strategies have been developed to improve the [<italic toggle=\"yes\">hk</italic>1] orientation of hydrothermally deposited Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. It has been observed that introducing additives (e.g., selenourea, thiourea, and ethanol) to the hydrothermal precursor solution is able to regulate the growth rate of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films,<sup>[</sup>\n##UREF##1##\n2\n##, ##UREF##30##\n36\n##, ##REF##33871973##\n38\n##\n<sup>]</sup> the presence of inorganic salts (e.g., Cd<sup>2+</sup>, F<sup>−</sup>, and Cl<sup>−</sup> ions) facilitate the regulation of exposed crystalline planes of a substrate<sup>[</sup>\n##UREF##10##\n11\n##, ##UREF##32##\n39\n##, ##UREF##33##\n40\n##, ##UREF##34##\n41\n##, ##UREF##35##\n42\n##, ##UREF##36##\n43\n##\n<sup>]</sup> and ultimately direct the oriented growth of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. We will discuss the detailed mechanisms in Sections <xref rid=\"advs6622-sec-0170\" ref-type=\"sec\">4.1</xref> and <xref rid=\"advs6622-sec-0250\" ref-type=\"sec\">4.4</xref>.</p>", "<title>Chemical Bath Deposition</title>", "<p>The chemical bath deposition (CBD) method is a solution reaction conducted at a mild temperature (&lt;100 °C) and with atmospheric pressure. The ion release rate in the solution during this process is controlled by a complexation reaction. A chemical reaction occurs when the product of the anion and cation concentrations reaches the solubility product of the two ion types. Figure ##FIG##3##4b## depicts a schematic of the chemical reaction. This method possesses simple operation, low cost, and high capacity features.<sup>[</sup>\n##REF##17487315##\n44\n##\n<sup>]</sup> The reaction condition of the CBD is mild, allowing for better control of the reaction rate and the nucleation process. The CBD method is also beneficial to the formation of a relatively smooth and uniform film morphology.<sup>[</sup>\n##UREF##37##\n45\n##\n<sup>]</sup> Reactants can also be timely added in situ during the reaction process, further increasing the flexibility in the film deposition.<sup>[</sup>\n##UREF##38##\n46\n##\n<sup>]</sup> In 2014, the CBD achieved a 7.5% PCE in the Sb<sub>2</sub>S<sub>3</sub> solar cells, indicating its potential for preparing metal chalcogenide films.<sup>[</sup>\n##UREF##39##\n47\n##\n<sup>]</sup> In recent years, the CBD has made significant contributions to the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> solar cell development. By adding different sulfur (i.e., Na<sub>2</sub>S<sub>2</sub>O<sub>3</sub> and thioacetamide) and selenium (Na<sub>2</sub>SeSO<sub>3</sub> and selenourea) sources to the CBD precursor solutions to deposit Sb<sub>2</sub>S<sub>3</sub> and Sb<sub>2</sub>Se<sub>3</sub>, respectively, the film growth rate and [<italic toggle=\"yes\">hk</italic>1] orientation have been improved, eventually obtaining the highest efficiencies for both the Sb<sub>2</sub>S<sub>3</sub> and Sb<sub>2</sub>Se<sub>3</sub> solar cells.<sup>[</sup>\n##UREF##37##\n45\n##, ##UREF##40##\n48\n##\n<sup>]</sup>\n</p>", "<title>Spin‐Coating Method</title>", "<p>Spin coating is a kind of convenient thin film fabrication method utilizing simple spin‐coater equipment. In film fabrication, a molecular precursor solution of the compound is spin‐coated on a substrate, followed by low‐temperature heating to evaporate the solvent and solidify the film. Further annealing at high temperatures promotes the solid‐state reaction, crystallization, and film formation (Figure ##FIG##3##4c##).<sup>[</sup>\n##UREF##41##\n49\n##\n<sup>]</sup> This film fabrication method has the advantages of simplicity, and convenience, while a major portion of the solution is spun out without utilization.<sup>[</sup>\n##UREF##42##\n50\n##\n<sup>]</sup> Various precursor solution systems, such as hydrazine solution with dissolved Sb, S, and Se powders,<sup>[</sup>\n##REF##26042519##\n51\n##\n<sup>]</sup> butyldithiocarbamate system with dissolved Sb<sub>2</sub>O<sub>3</sub> and Se powders,<sup>[</sup>\n##UREF##43##\n52\n##\n<sup>]</sup> and mixed solvents of <italic toggle=\"yes\">N</italic>, <italic toggle=\"yes\">N</italic>‐dimethylformamide (DMF) and dimethyl sulfoxide (DMSO) for dissolving SbCl<sub>3</sub>, thiourea, and selenourea to form a homogeneous solution, are currently being developed to prepare Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films.<sup>[</sup>\n##UREF##44##\n53\n##\n<sup>]</sup> Notably, by adding a tiny amount of water into the mixed DMF and DMSO solvent to dissolve the Sb, S, and Se precursors, Wu et al. prepared Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1‐x</sub>)<sub>3</sub> films with increased grain size and suppressed deep‐level defects and finally achieved a PCE of 7.42%.<sup>[</sup>\n##UREF##44##\n53\n##\n<sup>]</sup> Various strategies based on spin coating have also been developed to regulate the growth habits of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film to enhance its [<italic toggle=\"yes\">hk</italic>1] orientation. In this regard, the [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>Se<sub>3</sub> nanorod arrays are prepared by dissolving SbCl<sub>3</sub> and Se powder in the mixed solvent of thioglycolic acid, ethanolamine, and 2‐methoxyethanol. The formation mechanism of nanorod arrays is attributed to the adsorption of carboxylate anions as capping agents on the side ends of the (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons inhibiting the lateral growth of ribbons.<sup>[</sup>\n##UREF##45##\n54\n##, ##UREF##46##\n55\n##, ##UREF##47##\n56\n##\n<sup>]</sup> The [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>S<sub>3</sub>\n<sup>[</sup>\n##UREF##48##\n57\n##, ##UREF##49##\n58\n##\n<sup>]</sup> and Sb<sub>2</sub>Se<sub>3</sub>\n<sup>[</sup>\n##UREF##50##\n59\n##\n<sup>]</sup> nanorod arrays are obtained by spin‐coating a seeding material on the substrate. Further mechanistic discussions will be presented in Section <xref rid=\"advs6622-sec-0260\" ref-type=\"sec\">4.5</xref>.</p>", "<title>Rapid Thermal Evaporation</title>", "<p>Sb<sub>2</sub>Se<sub>3</sub> has a melting point of 608 °C with a high saturated vapor pressure of ≈1200 Pa at 550 °C, which enables Sb<sub>2</sub>Se<sub>3</sub> films to be deposited at a high deposition rate through the vapor deposition method. The rapid thermal evaporation (RTE) method can control the deposition rate up to 1 µm min<sup>−1</sup>, which is much higher than that of the conventional thermal evaporation (typically 0.01–0.1 µm min<sup>−1</sup>) and magnetron sputtering (typically 0.01–0.05 µm min<sup>−1</sup>) methods. In 2015, Zhou et al. developed an RTE method for the Sb<sub>2</sub>Se<sub>3</sub> film preparation. During this process, the Sb<sub>2</sub>Se<sub>3</sub> powder can directly be evaporated under a low vacuum pressure of ≈8 mTorr and condensed onto the substrate at gradient temperature to form high‐quality Sb<sub>2</sub>Se<sub>3</sub> film. The distance between the evaporation source and the substrate is controlled at 0.8 cm to achieve a fast deposition rate and a high material utilization ratio. <bold>Figure</bold> ##FIG##4##\n5a## depicts a schematic of the RTE deposition process. Based on the RTE method, a significant [<italic toggle=\"yes\">hk</italic>1]‐oriented growth of the Sb<sub>2</sub>Se<sub>3</sub> film can be achieved through regulation strategies, including the exposure of the specific crystalline planes of the interfacial material<sup>[</sup>\n##UREF##8##\n9\n##, ##UREF##52##\n61\n##\n<sup>]</sup> and the introduction of seeding materials.<sup>[</sup>\n##UREF##7##\n8\n##\n<sup>]</sup>\n</p>", "<title>Close Space Sublimation</title>", "<p>Similar to the RTE method, the close space sublimation (CSS) method has the characteristics of a high deposition rate and a close source–substrate distance. It is one of the promising technologies for large‐scale manufacturing.<sup>[</sup>\n##UREF##53##\n62\n##\n<sup>]</sup> The only difference is that the CSS deposition is completed through solid sublimation and does not undergo the solid melting process like the RTE method.<sup>[</sup>\n##UREF##5##\n6\n##\n<sup>]</sup> The CSS method is widely used in the CdTe solar cell preparation due to its excellent scalability, high throughput, and efficient material utilization.<sup>[</sup>\n##UREF##54##\n63\n##\n<sup>]</sup> In recent years, it has also been used to prepare Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films, exhibiting great potential in obtaining high‐efficiency solar cells. For the first time, Phillips et al.<sup>[</sup>\n##UREF##55##\n64\n##\n<sup>]</sup> and Zeng et al.<sup>[</sup>\n##UREF##56##\n65\n##\n<sup>]</sup> prepared Sb<sub>2</sub>Se<sub>3</sub> and Sb<sub>2</sub>S<sub>3</sub> films using the CSS method, while Li et al. prepared CSS‐deposited Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1‐x</sub>)<sub>3</sub> films by Sb<sub>2</sub>Se<sub>3</sub> and Sb<sub>2</sub>S<sub>3</sub> co‐sublimation.<sup>[</sup>\n##UREF##57##\n66\n##\n<sup>]</sup>\n</p>", "<p>In terms of the orientation control and the solar cell efficiency improvement, selenization has been performed on Mo/W/Pb substrates to induce highly [001]‐oriented (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons. As a result, a significant improvement in the device's performance is achieved.<sup>[</sup>\n##UREF##6##\n7\n##, ##REF##30631064##\n17\n##, ##UREF##16##\n19\n##, ##UREF##58##\n67\n##\n<sup>]</sup> Some other interface regulation methods,<sup>[</sup>\n##UREF##59##\n68\n##\n<sup>]</sup> together with the introduction of seeding materials,<sup>[</sup>\n##UREF##60##\n69\n##\n<sup>]</sup> have also been proven effective in promoting the [<italic toggle=\"yes\">hk</italic>1] orientation of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films.</p>", "<title>Vapor Transport Deposition</title>", "<p>Vapor transport deposition (VTD) is an excellent technique for the mass production of CdTe thin‐film solar cells and has been successfully employed in Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> solar cells. In the VTD, the distance between the substrate and the evaporation source is adjustable, allowing for an independent adjustment of the substrate temperature by changing the distance. Figure ##FIG##4##5b is## a schematic of the VTD. This feature can effectively reduce the inaccurate temperature control caused by the temperature coupling between the evaporation source and the substrate during the film deposition process, which is the problem faced by the RTE and CSS methods. The VTD process also increases the gas‐phase transport distance, which promotes uniform mixing of gas‐phase particles (e.g., Se, Sb, and Sb<sub>x</sub>Se<sub>y</sub>). A VTD device with a larger source–substrate distance will cause sulfur loss in CdS, which is more conducive to obtaining vertically oriented Sb<sub>2</sub>S<sub>3</sub> films.<sup>[</sup>\n##REF##32326702##\n70\n##\n<sup>]</sup> Therefore, most of the high‐efficiency Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> solar cells prepared through the VTD method are based on the CdS substrates,<sup>[</sup>\n##UREF##61##\n71\n##, ##REF##34553903##\n72\n##, ##UREF##62##\n73\n##, ##REF##29872054##\n74\n##\n<sup>]</sup> while those prepared through the RTE and CSS methods are mostly based on metal oxide or Mo substrates.<sup>[</sup>\n##UREF##6##\n7\n##, ##UREF##7##\n8\n##, ##UREF##8##\n9\n##, ##REF##30631064##\n17\n##, ##UREF##16##\n19\n##, ##UREF##54##\n63\n##, ##UREF##60##\n69\n##\n<sup>]</sup> In 2018, Wen et al. prepared highly oriented and improved‐crystallinity Sb<sub>2</sub>Se<sub>3</sub> films using the VTD method, achieving a 7.6% PCE.<sup>[</sup>\n##REF##29872054##\n74\n##\n<sup>]</sup> Zhang et al. developed a vertical VTD (V‐VTD) method to enhance the [<italic toggle=\"yes\">hk</italic>1] orientation of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films prepared through the VTD method. Compared with the traditional VTD, the main improvement in the V‐VTD is the sufficient space between the substrate and the evaporation source that provides a relatively wide regulation range and achieves a preferential [<italic toggle=\"yes\">hk</italic>1] growth orientation of Sb<sub>2</sub>S<sub>3</sub>.<sup>[</sup>\n##UREF##63##\n75\n##\n<sup>]</sup> The orientation filtering<sup>[</sup>\n##UREF##15##\n18\n##\n<sup>]</sup> and postselenization treatment<sup>[</sup>\n##UREF##64##\n76\n##\n<sup>]</sup> strategies are more favorable to the growth of [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1‐x</sub>)<sub>3</sub> films. The detailed mechanisms are discussed in Sections <xref rid=\"advs6622-sec-0200\" ref-type=\"sec\">4.1.3</xref> and <xref rid=\"advs6622-sec-0230\" ref-type=\"sec\">4.2.2</xref>.</p>", "<title>Thermal Evaporation</title>", "<p>Thermal evaporation is a common vacuum method for preparing thin films. In the deposition process, the raw materials are heated in an evaporation boat inside a vacuum chamber to form molecules or atoms, followed by escaping to the substrate surface through the stream flow and solidifying to form films (Figure ##FIG##4##5c##). The thermal evaporation method possesses the characteristics of easy operation, simple deposition mechanism, and high‐purity of the prepared films.<sup>[</sup>\n##UREF##65##\n77\n##\n<sup>]</sup> Notably, the highly saturated vapor pressure of Se makes it prone to loss during the Sb<sub>2</sub>Se<sub>3</sub> film preparation. Zhang et al. annealed thermally evaporated Sb<sub>2</sub>Se<sub>3</sub> films under the H<sub>2</sub>Se and H<sub>2</sub>S atmospheres to compensate for the lost Se. However, the treated films transformed to an unfavorable [<italic toggle=\"yes\">hk</italic>0] orientation.<sup>[</sup>\n##UREF##66##\n78\n##\n<sup>]</sup> Li et al. compensated for the Se loss by coevaporating the Sb<sub>2</sub>Se<sub>3</sub> and Se powders and demonstrated a beneficial effect on the preferred orientation of the deposited Sb<sub>2</sub>Se<sub>3</sub> films.<sup>[</sup>\n##UREF##67##\n79\n##\n<sup>]</sup> The effects of the thermal evaporation conditions, such as the substrate temperature,<sup>[</sup>\n##UREF##68##\n80\n##\n<sup>]</sup> source–substrate distance, and coevaporation sequence,<sup>[</sup>\n##UREF##69##\n81\n##\n<sup>]</sup> on the film orientation have been studied. Accordingly, some interface regulation methods have been found favorable for obtaining [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films.<sup>[</sup>\n##UREF##70##\n82\n##\n<sup>]</sup>\n</p>", "<title>Magnetron Sputtering Deposition</title>", "<p>Magnetron sputtering is a method of ionizing Ar ions under an electric field to rapidly bombard the target and produce gas particles for deposition on a substrate. This method has the features of a large deposition area, fast deposition rate, easy control, and strong film adhesion. Magnetron sputtering is classified into direct current (DC) and radio frequency (RF) magnetron sputtering. In 2017, Liang et al. prepared [221]‐oriented Sb<sub>2</sub>Se<sub>3</sub> nanorod array films through RF magnetron sputtering by sputtering a single Sb<sub>2</sub>Se<sub>3</sub> target with a substrate temperature of 375 °C, achieving a 2.11% PCE.<sup>[</sup>\n##UREF##71##\n83\n##\n<sup>]</sup> They also systematically studied the effect of the substrate temperature on the Sb<sub>2</sub>Se<sub>3</sub> film orientation and demonstrated amorphous films prepared at a substrate temperature below 150 °C.<sup>[</sup>\n##UREF##72##\n84\n##\n<sup>]</sup> Subsequently, they performed a postselenization treatment on the amorphous film to prepare an [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>Se<sub>3</sub> film, obtaining a 6.06% PCE.<sup>[</sup>\n##UREF##73##\n85\n##\n<sup>]</sup> Numerous studies have shown that the postselenization of the prepared Sb thin films is beneficial in preparing Sb<sub>2</sub>Se<sub>3</sub> films with [001]‐preferred orientation.<sup>[</sup>\n##REF##31755514##\n12\n##, ##UREF##11##\n13\n##, ##REF##37126652##\n86\n##, ##UREF##74##\n87\n##, ##UREF##75##\n88\n##, ##UREF##76##\n89\n##, ##UREF##77##\n90\n##\n<sup>]</sup> Figure ##FIG##4##5d## depicts the schematic for this. In 2016, Yuan et al. deposited an Sb film on the Mo substrate through DC magnetron sputtering, followed by a postselenization to prepare the Sb<sub>2</sub>Se<sub>3</sub> thin film, and applied it to the substrate‐structure solar cells. However, the device's efficiency was not high.<sup>[</sup>\n##UREF##78##\n91\n##\n<sup>]</sup> Liang et al. deposited Sb thin films using the RF magnetron sputtering method. This was followed by a postselenization treatment that not only prepared [001]‐oriented Sb<sub>2</sub>Se<sub>3</sub> films, but also improved the solar cell PCE to 6.84% with an open‐circuit voltage higher than 500 mV.<sup>[</sup>\n##UREF##75##\n88\n##\n<sup>]</sup> Furthermore, Liang X et al.<sup>[</sup>\n##UREF##79##\n92\n##\n<sup>]</sup> and Spaggiari et al.<sup>[</sup>\n##UREF##23##\n28\n##\n<sup>]</sup> have verified the effects of the chamber pressure, substrate type, and substrate temperature on the orientation of magnetron‐sputtered Sb<sub>2</sub>Se<sub>3</sub> films, consequently providing theoretical and experimental bases for the further improvement of the film orientation and the device efficiency in the future.</p>", "<title>Mechanisms of the Orientation Regulation</title>", "<p>The kinetic energy of the deposited particles has a modulating effect on the crystal structure, defects, and film orientation.<sup>[</sup>\n##UREF##80##\n93\n##, ##UREF##81##\n94\n##, ##UREF##82##\n95\n##, ##UREF##83##\n96\n##\n<sup>]</sup> The kinetic energy of the particles can be evaluated using the mean free path (<italic toggle=\"yes\">λ</italic>) defined as <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>λ</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow><mml:mrow><mml:msqrt><mml:mn>2</mml:mn></mml:msqrt><mml:mi>π</mml:mi><mml:msup><mml:mi mathvariant=\"normal\">d</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mi>p</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>, where <italic toggle=\"yes\">T</italic> is the temperature; <italic toggle=\"yes\">d</italic> is the molecular diameter; <italic toggle=\"yes\">p</italic> is the pressure; and <italic toggle=\"yes\">k</italic>\n<sub>B</sub> is the Boltzmann constant.<sup>[</sup>\n##UREF##84##\n97\n##\n<sup>]</sup> This equation shows that the evaporation source temperature and the reaction chamber pressure are both factors influencing the kinetic energy of particles. The evaporation source temperature can directly affect the evaporation rates, while the chamber pressure affects the deposition rate of particles reaching the substrate surface via collisions between vapor and chamber gas particles. In the practical deposition process, researchers tend to focus more on the film growth rate. The correlation between the growth and the deposition rates can be defined as the adhesion coefficient related to the substrate temperature, composition, and structure.<sup>[</sup>\n##UREF##85##\n98\n##\n<sup>]</sup> In addition, the posttreatment also has a regulating effect on the film's oriented growth.</p>", "<p>The difference in the polar and nonpolar crystal plane characteristics allows the crystal surface to present completely different atomic stacking orders. For the crystal ZnO shown in <bold>Figure</bold> ##FIG##5##\n6\n##, the Zn and O atoms are uniformly distributed on the nonpolar planes but alternately distributed on the polar ones.<sup>[</sup>\n##UREF##8##\n9\n##\n<sup>]</sup> The different crystal planes exposed on the substrate result in different bonding modes between the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons and the substrate, which played a crucial role in controlling the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film orientation. For the randomly oriented ZnO with exposed nonpolar (100) planes, the uniformly distributed Zn and O atoms on the surface can form Zn─Se and Sb─O bonds with Se and Sb at the ends of (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons, respectively. Thus, the (100)‐oriented ZnO plane can induce [221]‐oriented Sb<sub>2</sub>Se<sub>3</sub> films (Figure ##FIG##5##6a##). In contrast, when the (002) polar plane of ZnO is exposed, only Zn or O atoms are exposed on the surface, thus forming only one type of bonding with the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons. Either the Zn<sup>2+</sup> end forms a Zn─Se bond with the exposed Se atom on the (001) planes of Sb<sub>2</sub>Se<sub>3</sub> or the O<sup>2−</sup> end forms a Sb─O bond with the exposed Sb atom (Figure ##FIG##5##6b##). This interfacial bonding causes a lattice mismatch and results in the generation of dangling bonds and poor adhesion at the interface, depicting a thermodynamic instability that influences the (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons to tend to grow along the [120] orientation.<sup>[</sup>\n##UREF##34##\n41\n##, ##UREF##62##\n73\n##\n<sup>]</sup> Extensive studies developed a series of methods for improving the lattice matching degree between the interfacial material and the [<italic toggle=\"yes\">hk</italic>1]‐oriented ribbons, including matching more suitable substrates, interfacial engineering, and introducing seeding materials.</p>", "<p>This section summarizes the orientation control mechanisms of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films prepared using different methods. <bold>Table</bold> ##TAB##1##\n2\n## presents the deposition methods, regulation mechanism of the oriented films, preferred orientations, <italic toggle=\"yes\">TC</italic>s, device configurations, and device performance (PCE) mentioned in this work.</p>", "<title>Growth Rate</title>", "<p>The film growth rate is influenced by the deposition rate and the adhesion coefficient between the film and the substrate, which can be defined by the formula of <italic toggle=\"yes\">G</italic> = <italic toggle=\"yes\">α</italic>\n<sub>c</sub>\n<italic toggle=\"yes\">R</italic>, where <italic toggle=\"yes\">G</italic> is the growth rate; <italic toggle=\"yes\">α</italic>\n<sub>c</sub> is the adhesion coefficient; and <italic toggle=\"yes\">R</italic> is the deposition rate.<sup>[</sup>\n##UREF##87##\n100\n##\n<sup>]</sup> The surface energy of the (<italic toggle=\"yes\">hk</italic>1) crystal planes of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film is relatively high, resulting in a high growth rate along this orientation and a high adhesion coefficient.<sup>[</sup>\n##REF##30207360##\n117\n##\n<sup>]</sup> On the contrary, the vdW bonding strength along the (<italic toggle=\"yes\">hk</italic>0) crystal plane is weak, resulting in low adhesion to the substrate and a slow growth rate along this direction. When the vapor particles reach the substrate surface with higher kinetic energy, atoms can be rearranged on the substrate surface driven by sufficient energy, making Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film tend to expose high‐energy (<italic toggle=\"yes\">hk</italic>1) crystal planes.<sup>[</sup>\n##UREF##81##\n94\n##\n<sup>]</sup> In other words, increasing the kinetic energy of the deposited particles is beneficial for obtaining highly oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films, which has been demonstrated by multiple groups.</p>", "<title>Particle Kinetic Energy</title>", "<p>For the vacuum deposition methods (e.g., coevaporation,<sup>[</sup>\n##UREF##69##\n81\n##\n<sup>]</sup> RTE,<sup>[</sup>\n##UREF##5##\n6\n##\n<sup>]</sup> CSS,<sup>[</sup>\n##UREF##104##\n118\n##\n<sup>]</sup> VTD,<sup>[</sup>\n##REF##29872054##\n74\n##, ##UREF##63##\n75\n##\n<sup>]</sup> magnetron sputtering,<sup>[</sup>\n##UREF##79##\n92\n##, ##REF##32225231##\n119\n##\n<sup>]</sup> and pulsed laser deposition),<sup>[</sup>\n##UREF##105##\n120\n##\n<sup>]</sup> the strategies developed for regulating the vapor particle kinetic energy (e.g., adjustment of the evaporation source temperature,<sup>[</sup>\n##REF##29872054##\n74\n##, ##UREF##63##\n75\n##, ##UREF##87##\n100\n##\n<sup>]</sup> source–substrate distance,<sup>[</sup>\n##UREF##5##\n6\n##, ##REF##29872054##\n74\n##, ##UREF##69##\n81\n##\n<sup>]</sup> vapor concentration,<sup>[</sup>\n##UREF##86##\n99\n##, ##UREF##88##\n101\n##\n<sup>]</sup> and chamber pressure)<sup>[</sup>\n##REF##37126652##\n86\n##\n<sup>]</sup> demonstrate that an increase in the kinetic energy of the vapor particles can effectively increase the [<italic toggle=\"yes\">hk</italic>1] orientation of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films.</p>", "<p>A similar trend is observed in the solution methods for preparing Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. For example, the rapid hydrothermal deposition is kinetically more favorable to the vertical growth of (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons. Tang et al. prepared Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films using the hydrothermal method. They found that increasing the selenourea ratio in the precursor solution accelerated the film growth and enhanced the [<italic toggle=\"yes\">hk</italic>1] orientation, enabling the efficiency of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> solar cells to exceed 10% for the first time.<sup>[</sup>\n##UREF##30##\n36\n##\n<sup>]</sup> Liu et al. introduced thiourea into the precursor solution of KSbC<sub>4</sub>H<sub>4</sub>O<sub>7</sub>·0.5H<sub>2</sub>O and Na<sub>2</sub>SeSO<sub>3</sub> to complex SbO<sup>+</sup> ions in the Sb<sub>2</sub>Se<sub>3</sub> deposition to inhibit the generation of the Sb<sub>2</sub>O<sub>3</sub> precipitation and promote the Sb<sub>2</sub>Se<sub>3</sub> film growth rate. They prepared an enhanced [<italic toggle=\"yes\">hk</italic>1]‐oriented film, with the corresponding device showing a 7.9% efficiency.<sup>[</sup>\n##REF##33871973##\n38\n##\n<sup>]</sup> Meanwhile, Zhao et al. introduced selenourea as both a complexing agent and a selenium source to the same precursor solution, further promoting the growth rate of Sb<sub>2</sub>Se<sub>3</sub> films using the CBD method. They prepared Sb<sub>2</sub>Se<sub>3</sub> films with [<italic toggle=\"yes\">hk</italic>1]‐preferred orientations, eventually obtaining a 10.57% PCE, which was the highest Sb<sub>2</sub>Se<sub>3</sub> solar cell efficiency at that time.<sup>[</sup>\n##UREF##37##\n45\n##\n<sup>]</sup> Wang et al. used the CBD method and combined different sulfur sources (i.e., Na<sub>2</sub>S<sub>2</sub>O<sub>3</sub> and C<sub>2</sub>H<sub>5</sub>NS) to accelerate the release rate of sulfur ions and the growth rate of Sb<sub>2</sub>S<sub>3</sub> films. These enhanced the growth of the films and their [<italic toggle=\"yes\">hk</italic>1] orientation, resulting in the currently highest PCE of 8% for Sb<sub>2</sub>S<sub>3</sub> solar cells.<sup>[</sup>\n##UREF##40##\n48\n##\n<sup>]</sup>\n</p>", "<p>The obtained results proved that increasing the kinetic energy of the ions deposited in the vacuum or solution deposition system can effectively enhance the [<italic toggle=\"yes\">hk</italic>1] orientation of the thin film, thereby also improving the solar cell device performance. However, particles with excessive energy are detrimental to the film quality and the device performance because they can cause lattice displacement, generate lattice defects, decrease the film crystallinity, and produce pinholes.<sup>[</sup>\n##REF##29872054##\n74\n##, ##UREF##86##\n99\n##, ##UREF##89##\n102\n##\n<sup>]</sup> In addition, a further increase in the film growth rate leads to the whisker formation and secondary nuclei generation, resulting in the film growing in a random orientation.<sup>[</sup>\n##UREF##87##\n100\n##\n<sup>]</sup> Therefore, aside from the particle kinetic energy, other factors (e.g., substrate temperature) must also be considered for the optimal growth of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films.</p>", "<title>Substrate Temperature</title>", "<p>For the vacuum deposition method, the thin‐film nucleation and growth involve a series of kinetic processes, including the particle (atoms or molecules) deposition, re‐evaporation and migration on the substrate, and the subsequent crystal nucleation and growth processes (<bold>Figure</bold> ##FIG##6##\n7a##). The vapor particle adsorption and migration on the crystal surface follow the terrace–ledge–kink model (Figure ##FIG##6##7b##), while the dangling bonds and the surface energy of the crystal planes increase in the order of terraces, ledges, and kinks.<sup>[</sup>\n##UREF##106##\n121\n##\n<sup>]</sup> In the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films, the (<italic toggle=\"yes\">hk</italic>0) crystal planes parallel to the side of the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons have no dangling bonds. Moreover, their corresponding surface energy is low. By contrast, the (<italic toggle=\"yes\">hk</italic>1) planes with a large number of dangling bonds have a high surface energy.<sup>[</sup>\n##UREF##5##\n6\n##\n<sup>]</sup> Therefore, the (<italic toggle=\"yes\">hk</italic>0) planes of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films are likely terraces.<sup>[</sup>\n##UREF##68##\n80\n##\n<sup>]</sup> Park et al. explored the effect of the substrate temperature on the film orientation based on this model. They found that the critical radius of the crystal nucleus, the potential barrier for a stable nucleus formation, the diffusion length, and desorption rate of the adsorbed atoms increase as the substrate temperature increases (Figure ##FIG##6##7c##). The density of the dangling bonds on the crystal facets increases in the order of terrace–ledge–kink, resulting in an increase in the reactivity, and enabling terrace‐adsorbed atoms to easily diffuse to the ledges and kinks. There are no dangling bonds on the (<italic toggle=\"yes\">hk</italic>0) crystal planes, and their surface energy is low. Thus, the adsorbed atoms will diffuse onto the (<italic toggle=\"yes\">hk</italic>1) planes and lead to crystal growth along the [<italic toggle=\"yes\">hk</italic>1] orientation.<sup>[</sup>\n##UREF##68##\n80\n##\n<sup>]</sup>\n</p>", "<p>The adhesion coefficient is related to the substrate properties determining the initial nucleus orientation. For Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub>, the [<italic toggle=\"yes\">hk</italic>1]‐oriented crystal nuclei have a high adhesion coefficient to the substrate, while the [<italic toggle=\"yes\">hk</italic>0]‐oriented nuclei have a small value. The adhesion coefficient and the growth rate of the film vary with the changes in the substrate temperature. Kondrotas et al. systematically summarized the effect of the substrate temperature on the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film orientation (<bold>Figure</bold> ##FIG##7##\n8a–c##).<sup>[</sup>\n##UREF##87##\n100\n##\n<sup>]</sup> The growth rate of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film can be accelerated to a certain extent by increasing the evaporation temperature or decreasing the substrate temperature, consequently resulting in [<italic toggle=\"yes\">hk</italic>1]‐oriented films. Further increasing the growth rate to Region III will lead to the whisker formation and secondary nucleation, thus resulting in a nearly randomly oriented growth. Therefore, the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films deposited within a narrow substrate temperature range exhibit an [<italic toggle=\"yes\">hk</italic>1]‐preferred orientation. This temperature range varies with the substrate types. For example, using CdS, MoSe<sub>2</sub>, and ZnO as substrates tends to induce an [<italic toggle=\"yes\">hk</italic>1]‐preferred orientation of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. Their most appropriate substrate temperature range is usually higher than that of the TiO<sub>2</sub> and Mo substrates which tend to induce the [<italic toggle=\"yes\">hk</italic>0] orientation.<sup>[</sup>\n##UREF##13##\n15\n##, ##REF##34569779##\n20\n##, ##UREF##23##\n28\n##, ##UREF##87##\n100\n##, ##UREF##107##\n122\n##, ##UREF##108##\n123\n##, ##REF##26639125##\n124\n##, ##UREF##109##\n125\n##\n<sup>]</sup> Several groups have used the VTD,<sup>[</sup>\n##UREF##87##\n100\n##\n<sup>]</sup> coevaporation,<sup>[</sup>\n##UREF##68##\n80\n##, ##UREF##69##\n81\n##\n<sup>]</sup> and CSS<sup>[</sup>\n##REF##30631064##\n17\n##\n<sup>,100]</sup> techniques to deposit Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. These works demonstrated the dependence of the optimal substrate temperature window for obtaining [<italic toggle=\"yes\">hk</italic>1] orientation on different substrate types.</p>", "<p>In conclusion, both evaporation and substrate temperature affect the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film orientation, while a low substrate temperature leads to a decrease in the grain size and crystallinity.<sup>[</sup>\n##UREF##87##\n100\n##\n<sup>]</sup> Therefore, one of the optimal growth conditions is to achieve a balanced temperature between the evaporation source and the substrate, such as obtaining Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films with enhanced [<italic toggle=\"yes\">hk</italic>1] orientation and high crystallinity. The above discussion provides insights on improving the deposition parameters to obtain the optimal performance of the vacuum‐deposited Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. Notably, due to TE has a lower evaporation rate than that of CSS, RTE, and VTD technologies, selecting a suitable substrate is more important for it to obtain highly [<italic toggle=\"yes\">hk</italic>1]‐oriented and crystalline Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. We explain the mechanisms of the substrate type influence on the orientations in Section <xref rid=\"advs6622-sec-0240\" ref-type=\"sec\">4.3</xref>.</p>", "<title>Substrate Morphology</title>", "<p>The substrate surface morphology or flatness has a regulatory effect on the morphology and orientation of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. In this regard, Otavio Mendes et al. proposed an “orientation filtering” method for growing [001]‐oriented Sb<sub>2</sub>Se<sub>3</sub> nanorod arrays on the ZnO nanorod array substrate. They demonstrated that the Sb<sub>2</sub>Se<sub>3</sub> grains with [<italic toggle=\"yes\">hk</italic>0] and low‐angle [<italic toggle=\"yes\">hk</italic>1] orientations grow in the ZnO nanorod interstices, while the Sb<sub>2</sub>Se<sub>3</sub> nanorods with the [001] orientation grow at the top of the ZnO nanorods (<bold>Figure</bold> ##FIG##8##\n9a##). The degree of [001] orientation decreases with the increasing ZnO nanorod density. The authors further deposited thin CdS, Al<sub>2</sub>O<sub>3</sub>, and TiO<sub>2</sub> overlayers on the ZnO nanorods, but the morphology and orientation of the grown Sb<sub>2</sub>Se<sub>3</sub> nanorods almost did not change (Figure ##FIG##8##9b,c##). In other words, the formation of the Sb<sub>2</sub>Se<sub>3</sub> nanorod arrays entirely depends on the substrate morphology and the growth kinetics, rather than the substrate type. This study provides a new method for preparing [001]‐oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films.<sup>[</sup>\n##UREF##15##\n18\n##\n<sup>]</sup>\n</p>", "<title>Posttreatment</title>", "<title>Postannealing Process</title>", "<p>Based on the principle of crystal surface energy minimization, the postannealing temperature is considered another non‐negligible factor affecting the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film orientation. Wu et al. investigated the influence of the annealing process on the Sb<sub>2</sub>S<sub>3</sub> film orientation and proposed a possible crystal growth model (<bold>Figure</bold> ##FIG##9##\n10\n##). Compared to the fast‐heating annealing method, the slow‐heating annealing treatment was more conducive to obtaining [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>S<sub>3</sub> films. They suggested that the direct high‐temperature (380 °C) annealing treatment of the precursor film can lead to abnormal grain growth, ultimately exposing more (<italic toggle=\"yes\">hk</italic>0) crystal planes to minimize the surface energy (Figure ##FIG##9##10a,d,e##). On the contrary, when the precursor film was first treated at a low temperature of &lt;300°C, and then heated to 380°C within a certain period, the low‐temperature treatment can stabilize the film morphology and orientation, resulting in the grains growing in a relatively uniform manner in the subsequent high‐temperature annealing, and can maintain the same morphology and orientation as the precursor. The orientation of the hydrothermally deposited Sb<sub>2</sub>S<sub>3</sub> precursor film was more inclined toward [<italic toggle=\"yes\">hk</italic>1] (Figure ##FIG##9##10a–c##), such that the slow‐heating annealing process can increase the [<italic toggle=\"yes\">hk</italic>1]‐preferred orientation of the Sb<sub>2</sub>S<sub>3</sub> films.<sup>[</sup>\n##UREF##91##\n104\n##\n<sup>]</sup>\n</p>", "<p>In addition to the heating process, Yuan et al. found that the cooling process also affects the crystal orientation of the Sb<sub>2</sub>S<sub>3</sub> films. Through a rapid cooling treatment of the RTE‐deposited Sb<sub>2</sub>S<sub>3</sub> film, the (200) crystal plane growth was found suppressed, resulting in better electron transport and a device performance improvement.<sup>[</sup>\n##UREF##110##\n126\n##\n<sup>]</sup> Zhang et al. found that the preferred Sb<sub>2</sub>Se<sub>3</sub> orientation varies with the annealing atmospheres. The Sb<sub>2</sub>Se<sub>3</sub> films annealed in the H<sub>2</sub>S and H<sub>2</sub>Se atmospheres tend to expose (020) and (120) planes, respectively, while those annealed in an inert Ar atmosphere tend to expose (211) and (221) planes.<sup>[</sup>\n##UREF##66##\n78\n##\n<sup>]</sup> Li et al. demonstrated that the posttreatment of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films with potassium iodide in a vacuum annealing environment can enhance the [211] orientation.<sup>[</sup>\n##UREF##90##\n103\n##\n<sup>]</sup>\n</p>", "<title>Selenization Kinetics</title>", "<p>A postselenization approach that allows the Sb<sub>2</sub>Se<sub>3</sub> films to exhibit a [<italic toggle=\"yes\">hk</italic>1]‐oriented growth from the top to the substrate has been presented.<sup>[</sup>\n##REF##31755514##\n12\n##, ##UREF##11##\n13\n##, ##REF##37126652##\n86\n##, ##UREF##74##\n87\n##, ##UREF##75##\n88\n##, ##UREF##76##\n89\n##, ##UREF##77##\n90\n##\n<sup>]</sup> In a tube furnace, when treating the Sb film deposited on the substrate using the Se vapor generated by the Se powder, the diffusion and selenization reactions occur as Se atoms reach the Sb film surface. The selenization reaction is faster than the diffusion reaction; hence, the formed (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbon allows the Se atoms to resist the vdW forces and continuously undergo selenization downward along the [001] direction. This results in Sb<sub>2</sub>Se<sub>3</sub> films with ribbons perpendicular to the substrate.<sup>[</sup>\n##UREF##11##\n13\n##\n<sup>]</sup> The orientation regulation through the postselenization treatment on the absorber layer is mainly driven by the selenization kinetics. Notably, the [001]‐oriented growth can be controlled by balancing the collision rate and the kinetic energy of the Se vapor particles reaching the film surface. Based on this, Wen et al. prepared [001]‐oriented Sb<sub>2</sub>Se<sub>3</sub> films by controlling the vapor pressure to regulate the collision rate and the kinetic energy of the Se vapor particles reaching the Sb film surface. They obtained an efficiency of 8.42% for the flexible Sb<sub>2</sub>Se<sub>3</sub> devices.<sup>[</sup>\n##REF##37126652##\n86\n##\n<sup>]</sup> The orientation control is driven by selenization kinetics; therefore, the substrate type is no longer the main factor affecting the film orientation. Zhou et al. conducted a postselenization treatment on the Sb<sub>2</sub>Se<sub>3</sub> films deposited on MoSe<sub>2</sub>, soda lime glass (SLG), NiO, SiO<sub>2</sub>, and FTO substrates. All the treated films exhibited a [001] orientation consistent with the above‐mentioned conclusions.<sup>[</sup>\n##UREF##11##\n13\n##\n<sup>]</sup>\n</p>", "<p>During the postselenization process, the high‐energy Se vapor may considerably affect the behavior of the adsorbed atoms and the nucleus–substrate interaction, consequently altering the film growth kinetics with specific morphology and orientation. Under the Se atmosphere, the (<italic toggle=\"yes\">hk</italic>1) crystal plane will have a higher growth rate due to the increased energy of the adsorbed atoms, thereby forming preferred [<italic toggle=\"yes\">hk</italic>1] orientation. Liang et al. and Fan et al. successfully transformed the [<italic toggle=\"yes\">hk</italic>0] orientation of the Sb<sub>2</sub>Se<sub>3</sub> films deposited through VTD<sup>[</sup>\n##UREF##64##\n76\n##\n<sup>]</sup> and CSS<sup>[</sup>\n##REF##34569779##\n20\n##\n<sup>]</sup> methods into [<italic toggle=\"yes\">hk</italic>1] orientation through the postselenization treatment. Wang et al. prepared Sb<sub>2</sub>S<sub>3</sub> films on FTO/CdS substrates through TE method and demonstrated the positive effect of the postselenization treatment on the [<italic toggle=\"yes\">hk</italic>1] orientation enhancement.<sup>[</sup>\n##REF##30191479##\n127\n##\n<sup>]</sup> Mavlonov et al. developed a PLD in situ selenization technique for preparing Sb<sub>2</sub>Se<sub>3</sub> films. They achieved an [<italic toggle=\"yes\">hk</italic>1]‐preferred orientation by adjusting the Sb:Se atomic ratio of the target material to 1:3 to render a Se‐rich state.<sup>[</sup>\n##UREF##105##\n120\n##\n<sup>]</sup> Peng et al. prepared Sb<sub>2</sub>S<sub>3</sub> films with preferred [<italic toggle=\"yes\">hk</italic>1] orientation by post‐sulfurizing the Sb films that were deposited on the Mo substrates using pulse electrodeposition. They obtained the highest efficiency of 3.35% for the substrate‐structure Sb<sub>2</sub>S<sub>3</sub> solar cells.<sup>[</sup>\n##UREF##9##\n10\n##\n<sup>]</sup>\n</p>", "<p>In addition to vapor selenization, an effective liquid selenization method has recently been proposed. Yao et al. developed a liquid medium annealing (LMA) method to regulate the Sb<sub>2</sub>S<sub>3</sub> orientation by controlling the Se<sub>2</sub>\n<sup>2−</sup> concentration in the Se<sub>2</sub>\n<sup>2−</sup>–oleylamine complex. Due to the high thermal conductivity and high Se activity in the LMA system, the activated Se<sub>2</sub>\n<sup>2−</sup> anions can react with Sb<sub>2</sub>S<sub>3</sub> to activate the apical bud growth on the (Sb<sub>4</sub>S<sub>6</sub>)<sub>n</sub> ribbons, along with releasing the oleylamine adsorbed on the (<italic toggle=\"yes\">hk</italic>0) plane to facilitate the growth of the [<italic toggle=\"yes\">hk</italic>1] orientation. In this process, the bottom of the Sb<sub>2</sub>S<sub>3</sub> layer undergoes recrystallization to inherit the [<italic toggle=\"yes\">hk</italic>1] orientation of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> seeding material at the top, ultimately obtaining a highly oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film.<sup>[</sup>\n##UREF##2##\n3\n##\n<sup>]</sup>\n</p>", "<title>Substrate Type</title>", "<p>The Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film orientation is strongly dependent on the substrate type. Zhou et al. investigated the effect of the indium‐doped tin oxide (ITO), fluorine‐doped tin oxide (FTO), and boron‐doped zinc oxide (BZO) substrates on the orientation of the CSS‐Sb<sub>2</sub>Se<sub>3</sub> films.<sup>[</sup>\n##UREF##17##\n21\n##\n<sup>]</sup>\n<bold>Figure</bold> ##FIG##10##\n11\n## presents the results. The Sb<sub>2</sub>Se<sub>3</sub> film grown on ITO mainly exhibited an [<italic toggle=\"yes\">hk</italic>0] orientation, while that grown on FTO mainly showed [211] and [221] orientations, indicating that the ribbons grown on FTO were more perpendicular to the substrate than those on ITO. Notably, the Sb<sub>2</sub>Se<sub>3</sub> film deposited on BZO exhibited a highly oriented growth with a distinct (002) crystal plane exposed, indicating that the ribbons grew to be completely perpendicular to the substrate. B doping in BZO can induce the lattice deformation of ZnO, thereby increasing the exposure proportion of nonpolar (110) crystal planes.<sup>[</sup>\n##UREF##111##\n128\n##, ##UREF##112##\n129\n##\n<sup>]</sup> Cao et al. prepared Sb<sub>2</sub>Se<sub>3</sub> nanorod array structured films with a [001] orientation on a BZO substrate.<sup>[</sup>\n##UREF##111##\n128\n##\n<sup>]</sup>\n</p>", "<p>Spaggiari et al. investigated the growth orientation of the Sb<sub>2</sub>Se<sub>3</sub> films deposited by RF sputtering method on SLG, FTO, Mo, ZnO, and CdS substrates.<sup>[</sup>\n##UREF##22##\n27\n##\n<sup>]</sup> They demonstrated that the Sb<sub>2</sub>Se<sub>3</sub> films grown on the CdS and ZnO substrates exhibit superior vertical orientation, while those grown on Mo substrates have the poorest vertical orientation. Kondrotas et al.<sup>[</sup>\n##UREF##87##\n100\n##\n<sup>]</sup> and Zeng et al.<sup>[</sup>\n##UREF##61##\n71\n##\n<sup>]</sup> drew a similar conclusion using the VTD and RTE methods. Valdman et al. demonstrated the epitaxial growth of the [001]‐oriented (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons on the [100]‐oriented mica substrate.<sup>[</sup>\n##UREF##113##\n130\n##\n<sup>]</sup> Wen et al. demonstrated that the CdS grown on mica substrates can induce the growth of [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>Se<sub>3</sub> films. As a result, a flexible Sb<sub>2</sub>Se<sub>3</sub> solar cell based on the mica substrate achieved a high efficiency of 7.15%.<sup>[</sup>\n##UREF##12##\n14\n##\n<sup>]</sup>\n</p>", "<p>Tang et al. analyzed the mechanism of the effect of substrate types on the growth orientation of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films from the bonding energy perspective. The bonding energy of Ti─O (662 kJ mol<sup>−1</sup>) is much stronger than that of Cd–S (196 kJ mol<sup>−1</sup>) and Zn─O (284 kJ mol<sup>−1</sup>); thus, the Sb and Se atoms can hardly bond to the TiO<sub>2</sub> substrate during the film deposition. This results in most (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons lying lateral on the substrate and forming [<italic toggle=\"yes\">hk</italic>0]‐oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films.<sup>[</sup>\n##UREF##7##\n8\n##\n<sup>]</sup> According to the lattice matching mechanism, Deng et al. found that the exposed (101) crystal planes of TiO<sub>2</sub> particle films are favorable to Sb<sub>2</sub>S<sub>3</sub> film growing along the [<italic toggle=\"yes\">hk</italic>1] orientation.<sup>[</sup>\n##UREF##52##\n61\n##\n<sup>]</sup> Dong et al. compared the orientations of the hydrothermally deposited Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films grown on crystalline and amorphous TiO<sub>2</sub> nanoparticle films. They found that the film is more likely to nucleation on amorphous TiO<sub>2</sub> and grow along the [<italic toggle=\"yes\">hk</italic>1]‐preferred orientation by alleviating the lattice mismatch between the amorphous TiO<sub>2</sub> and the [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film. From the crystal surface energy perspective, Wang et al. demonstrated that the low‐energy SnO<sub>2</sub> (110) or TiO<sub>2</sub> (101) facets both tend to coordinate with the Se and Sb atoms, inducing (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons to grow along the [<italic toggle=\"yes\">hk</italic>1] orientation.<sup>[</sup>\n##UREF##92##\n105\n##\n<sup>]</sup>\n</p>", "<title>Interfacial Engineering</title>", "<p>Feasible strategies have been proposed to regulate the crystal plane exposure to improve the lattice matching degree between the interface material and the [<italic toggle=\"yes\">hk</italic>1]‐oriented (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons. A common method for such a purpose is to selectively control the nucleation and growth rates in different directions during crystal growth. Some inorganic or organic additives have been used as the capping agents for selectively adsorbing on the specific crystal planes, thereby regulating the crystal plane exposure.<sup>[</sup>\n##REF##30875200##\n131\n##\n<sup>]</sup> According to the crystal growth theory, the growth rate of the specific crystal planes can be evaluated using surface energies. For CdS, the polar planes with large surface energies (e.g., (101) and (002)) will exhibit high growth rates during the film growth and quickly disappear from the crystal surface, eventually exposing more nonpolar crystal planes (e.g., (100) planes). The Sb and S(e) atoms in the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> precursor films tend to form a chemical bond with S and Cd on the nonpolar (100) plane of CdS, which is favorable for the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons growing along the [<italic toggle=\"yes\">hk</italic>1] direction. In contrast, the S or Cd atoms alternatively distributed on the polar (002) plane of CdS preferentially coordinate with Sb or S(e) atoms of the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons through van der Waals face, enabling the ribbons tend to grow parallel to the substrate.<sup>[</sup>\n##UREF##69##\n81\n##\n<sup>]</sup>\n</p>", "<p>Based on this theory, Jin et al. regulated the exposed planes of CdS films by adding Cd ions to the hydrothermal precursor solution to enhance the [<italic toggle=\"yes\">hk</italic>1]‐oriented growth of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films and ultimately obtained the enhanced device performance.<sup>[</sup>\n##UREF##10##\n11\n##, ##UREF##34##\n41\n##\n<sup>]</sup> Yin et al. reported that the exposed crystal planes of CdS can be adjusted by tuning the sequence of the coevaporation order of S and Sb<sub>2</sub>Se<sub>3</sub>, leading to the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons growing vertically on the CdS substrate and exhibiting an enhancement of the [<italic toggle=\"yes\">hk</italic>1] orientation.<sup>[</sup>\n##UREF##69##\n81\n##\n<sup>]</sup> Li et al. prepared CdS:O films through a molecular beam epitaxial deposition method, and proposed that O atoms have distinct interactions on different crystal planes of CdS. Based on the density functional theory calculations, the O doping in CdS is demonstrated to increase the exposure of nonpolar (100) plane and enhance the [<italic toggle=\"yes\">hk</italic>1] orientation of (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons.<sup>[</sup>\n##UREF##93##\n106\n##\n<sup>]</sup> Pan et al. prepared CdS with an exposed (103) crystal plane using the CSS method. They then demonstrated that this exposed facet can induce the vertical anchoring of the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons prepared by VTD method.<sup>[</sup>\n##UREF##62##\n73\n##\n<sup>]</sup>\n</p>", "<p>Fluoride ions (F<sup>−</sup>) are widely used as capping agents for regulating the growth rate and exposure of the crystal planes due to their unique selective adsorption properties.<sup>[</sup>\n##REF##18509440##\n132\n##\n<sup>]</sup> Shi et al. introduced F<sup>−</sup> into the hydrothermal precursor solution. They proposed that the F<sup>−</sup> could preferentially adsorb on the (101) crystal plane of CdS, increasing the exposure of nonpolar (100) plane of CdS and promoting the [<italic toggle=\"yes\">hk</italic>1]‐preferred orientation of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub>. F<sup>−</sup> can also selectively adsorb on the side of the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons, thereby hindering the lateral growth of the ribbons and promoting their longitudinal growth.<sup>[</sup>\n##UREF##35##\n42\n##\n<sup>]</sup> Chloride ions and carboxylate anions were demonstrated to have similar effects according to Chen et al.<sup>[</sup>\n##UREF##36##\n43\n##\n<sup>]</sup> and Yang et al.<sup>[</sup>\n##UREF##45##\n54\n##\n<sup>]</sup> Based on the high mobility and activity of lithium ions, Mao et al. proposed a strategy for annealing Sb<sub>2</sub>S<sub>3</sub> films in a LiCl molten salt bath. They successfully doped Li into Sb<sub>2</sub>S<sub>3</sub> while enhancing the [<italic toggle=\"yes\">hk</italic>1] orientation. As a result, they achieved a 6.16% PCE, which was the highest value among all inorganic Sb<sub>2</sub>S<sub>3</sub> solar cells at that time.<sup>[</sup>\n##UREF##33##\n40\n##\n<sup>]</sup> They also found that Bi doping can exhibit a similar effect to Li.<sup>[</sup>\n##UREF##32##\n39\n##\n<sup>]</sup>\n</p>", "<p>As mentioned above, the Mo substrate is not favorable for the [<italic toggle=\"yes\">hk</italic>1]‐oriented growth of the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons. By performing a postselenization treatment on the Mo substrate to form a MoSe<sub>2</sub> interfacial layer, Li et al. prepared vertically oriented Sb<sub>2</sub>Se<sub>3</sub> nanorod array films through the CSS and injection vapor deposition (IVD) methods. Using these methods, they obtained the top efficiencies of 9.2% and 10.1%, respectively, for the Sb<sub>2</sub>Se<sub>3</sub> solar cells.<sup>[</sup>\n##REF##30631064##\n17\n##, ##UREF##37##\n45\n##\n<sup>]</sup> Similarly, Liang et al. introduced a WSe<sub>2</sub> layer by selenizing the W back‐contact layer, which reduced the interfacial lattice mismatch with the (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons. They then prepared [001]‐oriented Sb<sub>2</sub>Se<sub>3</sub> nanorod arrays on WSe<sub>2</sub> using the CSS method.<sup>[</sup>\n##UREF##58##\n67\n##\n<sup>]</sup> Subsequently, they evaporated a thin PbSe layer at the buried back‐contact interface on the Mo foil to promote the growth of [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>Se<sub>3</sub> films. As a result, they obtained the highest PCE of 8.43% for the flexible Sb<sub>2</sub>Se<sub>3</sub> solar cells.<sup>[</sup>\n##UREF##6##\n7\n##\n<sup>]</sup>\n</p>", "<p>Note that the surface state of the substrate may also vary during the vacuum deposition process, thereby influencing the orientation of subsequently deposited films. Due to the high saturated vapor pressure of S, the S loss will inevitably occur during the vacuum deposition of CdS films. This will lead to an increase in the Cd<sup>2+</sup> dangling bonds on the CdS surface and ultimately result in different bonding modes with the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. Zeng et al. demonstrated the above conclusion by comparing the different orientation characteristics of Sb<sub>2</sub>S<sub>3</sub> films deposited on CdS substrates using RTE and VTD vacuum methods. The CdS surface was easily surrounded by saturated S vapor due to the closer source–substrate distance of the RTE, resulting in a saturated S state on the film surface. Consequently, only one type of bonding was formed between the (Sb<sub>4</sub>S<sub>6</sub>)<sub>n</sub> ribbons and the CdS surface. This led the ribbons to be parallel to the CdS substrate. However, the source–substrate distance in VTD is relatively large, and S loss is prone to occur during the film deposition. This results in an increase in the Cd dangling bonds on the CdS surface, which is more conducive for obtaining vertically oriented Sb<sub>2</sub>S<sub>3</sub> films.<sup>[</sup>\n##REF##32326702##\n70\n##\n<sup>]</sup>\n</p>", "<p>Researchers have also proposed effective interfacial modification strategies for regulating the absorber layer orientation. The high bonding energy of Sn─O and Ti─O hinders the vertical growth of (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons on SnO<sub>2</sub> and TiO<sub>2</sub> substrates. Based on this issue, Zhou et al. used CdCl<sub>2</sub> to treat the SnO<sub>2</sub> substrate and form a Cd─O bond with bonding energy much lower than Sn─O, thereby inducing the vertical growth of (Sb<sub>4</sub>S<sub>6</sub>)<sub>n</sub> ribbons.<sup>[</sup>\n##UREF##59##\n68\n##\n<sup>]</sup> Meanwhile, Wang et al. treated the TiO<sub>2</sub> substrates using TiCl<sub>4</sub>, consequently enhancing the interfacial bonding between the TiO<sub>2</sub> and Sb<sub>2</sub>Se<sub>3</sub> absorber layers with the introduction of Cl atoms, and promoting the vertical growth of (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons.<sup>[</sup>\n##UREF##97##\n110\n##\n<sup>]</sup> Cai et al. used SbCl<sub>3</sub> to modify the CdS surface, thereby increasing the exposed nonpolar planes of CdS and enhancing the [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>Se<sub>3</sub> films.<sup>[</sup>\n##UREF##70##\n82\n##\n<sup>]</sup> Wang et al. treated the CdS surface with ammonia, enhancing the [<italic toggle=\"yes\">hk</italic>1] orientation of Sb<sub>2</sub>Se<sub>3</sub> films, as well.<sup>[</sup>\n##UREF##96##\n109\n##\n<sup>]</sup> Guo L. et al. prepared CdS:O films by postannealing the CdS at different oxygen partial pressures. They demonstrated that oxygen doping could significantly improve the [<italic toggle=\"yes\">hk</italic>1] orientation of Sb<sub>2</sub>Se<sub>3</sub> and illustrated that the improved orientation can be attributed to the O diffusion between the (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons, forming Sb─O─Se chains and changing the growth orientation of the (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons.<sup>[</sup>\n##UREF##95##\n108\n##\n<sup>]</sup> Furthermore, Guo H. et al. treated the CdS surface with oxygen plasma and demonstrated the beneficial effect of the increased oxygen content on CdS surface on the vertical growth of the Sb<sub>2</sub>Se<sub>3</sub> films.<sup>[</sup>\n##UREF##114##\n133\n##\n<sup>]</sup>\n</p>", "<title>Seeding Material</title>", "<p>According to the film growth theory, the initial seed determines the final film orientation.<sup>[</sup>\n##UREF##7##\n8\n##, ##UREF##91##\n104\n##, ##UREF##101##\n114\n##\n<sup>]</sup> Eliminating dominant [<italic toggle=\"yes\">hk</italic>0]‐oriented seeds and retaining [<italic toggle=\"yes\">hk</italic>1]‐oriented seeds are the key steps to obtain [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films. Due to the weak vdW force that binds the [<italic toggle=\"yes\">hk</italic>0]‐oriented seeds to the substrate, adjusting the substrate heating method can break the adhesion between them.<sup>[</sup>\n##UREF##7##\n8\n##\n<sup>]</sup> Sb<sub>2</sub>S<sub>3</sub> and Sb<sub>2</sub>Se<sub>3</sub> have the same crystal structure; hence, they are often employed as the seeding materials for the oriented growth of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films.<sup>[</sup>\n##UREF##7##\n8\n##, ##UREF##13##\n15\n##, ##UREF##60##\n69\n##, ##UREF##100##\n113\n##, ##UREF##101##\n114\n##, ##UREF##115##\n134\n##\n<sup>]</sup> Some metals<sup>[</sup>\n##UREF##116##\n135\n##\n<sup>]</sup> and metal oxides<sup>[</sup>\n##UREF##49##\n58\n##, ##UREF##98##\n111\n##, ##UREF##99##\n112\n##, ##UREF##102##\n115\n##\n<sup>]</sup> have also been used as crystal seeding materials for regulating the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film orientation.</p>", "<p>Li et al. proposed a “seed screening” strategy for regulating the Sb<sub>2</sub>Se<sub>3</sub> orientation based on the different bonding strengths of the [<italic toggle=\"yes\">hk</italic>0]‐ and [<italic toggle=\"yes\">hk</italic>1]‐oriented (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons with the substrate. In <bold>Figure</bold> ##FIG##11##\n12\n##, a gradient heating method was used to recrystallize the seeding material at high temperatures, thereby removing the [<italic toggle=\"yes\">hk</italic>0]‐oriented Sb<sub>2</sub>Se<sub>3</sub> seeds deposited at the low temperatures and retaining the [<italic toggle=\"yes\">hk</italic>1]‐oriented seeding material. The subsequently deposited Sb<sub>2</sub>Se<sub>3</sub> films grew along the [<italic toggle=\"yes\">hk</italic>1] orientation induced by the seeding material. This regulation method was fundamentally different from the previously mentioned approach of regulating the substrate temperature to control the growth orientation. This technique achieved a 7.62% PCE, which is currently the highest efficiency of the Sb<sub>2</sub>Se<sub>3</sub> solar cells based on TiO<sub>2</sub> substrates.<sup>[</sup>\n##UREF##7##\n8\n##\n<sup>]</sup> Spalatu and Krautmann et al. enhanced the [001] orientation of the subsequently deposited Sb<sub>2</sub>Se<sub>3</sub> films by predepositing a thin Sb<sub>2</sub>Se<sub>3</sub> seeding material on the TiO<sub>2</sub> and CdS substrates using CSS method.<sup>[</sup>\n##UREF##13##\n15\n##, ##UREF##101##\n114\n##\n<sup>]</sup> Amin et al. improved the vertical orientation of subsequently CSS‐deposited Sb<sub>2</sub>Se<sub>3</sub> films by using hydrothermally deposited Sb<sub>2</sub>S<sub>3</sub> as the seeding material on CdS.<sup>[</sup>\n##UREF##100##\n113\n##\n<sup>]</sup> Rijal et al. used pre‐prepared [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>Se<sub>3</sub> as the seeding material and prepared highly [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>Se<sub>3</sub> films on Mo substrate through CSS method, achieving a PCE of 8.5% for the substrate‐structure solar cells.<sup>[</sup>\n##UREF##60##\n69\n##\n<sup>]</sup>\n</p>", "<p>The spatial distance of Ti─O (4.71 nm) on the (101) plane of TiO<sub>2</sub> actually matched well with the spatial distance of S–Sb (4.79 nm) on the (101) plane of Sb<sub>2</sub>S<sub>3</sub>. Thus, a good lattice matching was found between the orthotropic [101]‐oriented Sb<sub>2</sub>S<sub>3</sub> and the anatase [101]‐oriented TiO<sub>2</sub>. Wang et al. developed a seed‐assisted solution method for the pre‐spin coated [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>S<sub>3</sub> seeding material on a polycrystalline TiO<sub>2</sub> nanoparticle film and prepared [<italic toggle=\"yes\">hk</italic>1]‐preferred oriented Sb<sub>2</sub>S<sub>3</sub>\n<sup>[</sup>\n##UREF##48##\n57\n##, ##UREF##49##\n58\n##\n<sup>]</sup> and Sb<sub>2</sub>Se<sub>3</sub>\n<sup>[</sup>\n##UREF##50##\n59\n##\n<sup>]</sup> nanorod array films by repeating the spin‐coating and annealing processes. Based on the above work, Liu et al. prepared [211]–oriented Sb<sub>2</sub>S<sub>3</sub> nanorod array films with Sb<sub>2</sub>Se<sub>3</sub> seeding material. Unlike the Sb<sub>2</sub>S<sub>3</sub> seeding material, which can only induce an [<italic toggle=\"yes\">hk</italic>1]‐oriented growth on the TiO<sub>2</sub> nanoparticle films, the Sb<sub>2</sub>Se<sub>3</sub> seeding material can induce the growth of [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>S<sub>3</sub> films on any substrate.<sup>[</sup>\n##UREF##98##\n111\n##\n<sup>]</sup>\n</p>", "<p>In addition to Sb<sub>2</sub>S<sub>3</sub> and Sb<sub>2</sub>Se<sub>3</sub>, some metal oxides can also serve as seeds for inducing the oriented growth of the films. Wang et al. deposited a thin CeO<sub>2</sub> layer on the CdS surface, which resulted in a smoother surface that induced the vertical growth of the Sb<sub>2</sub>Se<sub>3</sub> grains.<sup>[</sup>\n##UREF##99##\n112\n##\n<sup>]</sup> Zi et al. sputtered an Al<sub>2</sub>O<sub>3</sub> layer between the CdS and Sb<sub>2</sub>Se<sub>3</sub> layers, effectively inhibiting the growth of the [<italic toggle=\"yes\">hk</italic>0]‐oriented (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons and promoting the [<italic toggle=\"yes\">hk</italic>1]‐oriented growth.<sup>[</sup>\n##UREF##102##\n115\n##\n<sup>]</sup> Lin et al. inserted a MoO<sub>2</sub> layer between the Mo substrate and the Sb<sub>2</sub>Se<sub>3</sub> film, consequently promoting the growth of [211]‐oriented (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbons.<sup>[</sup>\n##UREF##103##\n116\n##\n<sup>]</sup> Yang et al. demonstrated the introduction of an additional metal element to serve as a crystal seed for the oriented film preparation. They prepared an Ag:Sb<sub>2</sub>S<sub>3</sub> thin film by sulfurizing the Ag/Sb metal precursor film predeposited on the Mo substrate and applied it as the photocathode. They proved that some AgSbS<sub>2</sub> crystal units were formed in the Ag/Sb bimetallic films during the sulfurization process, which served as the [<italic toggle=\"yes\">hk</italic>1]‐oriented seeding material that promoted the preparation of completely [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>S<sub>3</sub> films. This strategy can be extended to the fabrication of high‐efficiency Sb<sub>2</sub>S<sub>3</sub> solar cells.<sup>[</sup>\n##UREF##116##\n135\n##\n<sup>]</sup>\n</p>", "<title>Summary and Outlook</title>", "<p>In summary, this study first outlined the main factors affecting the orientation of the Q1D Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films and the influence of this orientation on the performance of the corresponding photovoltaic devices from the perspective of crystal orientation engineering. We summarized herein the developed strategies for improving [<italic toggle=\"yes\">hk</italic>1]‐oriented films based on the solution and vacuum deposition methods and thoroughly explained the oriented growth mechanism. The following results were drawn in this work:\n<list list-type=\"order\" id=\"advs6622-list-0001\"><list-item><p>The crystal orientation of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films is mainly influenced by the growth rate. The growth rate in the vacuum deposition methods is mainly influenced by the particle kinetic energy, the growth temperature, and the substrate properties. High‐kinetic energy particles are favorable for the growth of the [<italic toggle=\"yes\">hk</italic>1]‐oriented Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films, while an excessively high growth temperature is unfavorable to the [<italic toggle=\"yes\">hk</italic>1] orientation. The substrate type can affect the film growth rate and the orientation. Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films with a preferential orientation and a high crystallinity can be obtained by combining the abovementioned factors. In addition, different postannealing modes can affect the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film orientation. The postselenization treatment of the Sb thin films is a top‐down method for preparing [001]‐oriented Sb<sub>2</sub>Se<sub>3</sub> films, which is mainly influenced by the selenization kinetics, rather than the substrate properties. Introducing additives into the precursor solution of the solution method can effectively regulate the oriented growth of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film. On the one hand, the additives play an important role in regulating the particle deposition rate to improve the film orientation. On the other hand, they can act as capping agents to adsorb on specific crystalline planes to control their growth rate, thereby regulating the orientation of the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons.</p></list-item><list-item><p>Interfacial lattice matching regulation is an effective method of controlling the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film orientation. The lattice mismatch between the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films and the interfacial materials of the substrate leads to a weak bonding strength of the ribbons to the substrate, which results in the ribbons tending to lay flat on the substrate to minimize the surface energy. Effective interfacial engineering strategies for interfacial materials (e.g., ion selective adsorption and interface treatment for increasing the exposure of nonpolar crystal planes) should be considered to enhance the bonding between the interfacial material and the [<italic toggle=\"yes\">hk</italic>1]‐oriented (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons. Introducing a seeding material between the substrate and the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film can also enhance their lattice matching, thereby inducing the growth of [<italic toggle=\"yes\">hk</italic>1]‐oriented ribbons.</p></list-item></list>\n</p>", "<p>Many feasible methods are currently being developed in the field of crystal orientation engineering. However, the following critical issues must be addressed:\n<list list-type=\"order\" id=\"advs6622-list-0002\"><list-item><p>The current highest efficiency of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> solar cells is obtained through the hydrothermal deposition method. However, the film orientation and crystallinity prepared through this method must be further improved compared to those prepared by the vacuum deposition method. Therefore, improving the crystallinity and the [<italic toggle=\"yes\">hk</italic>1] orientation of the hydrothermally deposited Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films is expected to further improve the device efficiency.</p></list-item><list-item><p>The ways of regulating the optimal coordination between the [001]‐oriented nanorod arrays and the lateral grown [<italic toggle=\"yes\">hk</italic>0]‐oriented grains in the films to simultaneously improve the preferred orientation, compactness, and large grain size of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films is a key issue in developing 1D material‐based photovoltaic devices.</p></list-item><list-item><p>The existence of dislocations in the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films can act as defects to inhibit the carrier transport along the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons. The dislocation formation may be related to the strains generated during the grain growth. Therefore, the development of an advanced growth process that can better control the strain is a promising direction for suppressing these internal dislocations.</p></list-item></list>\n</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>" ]
[ "<title>Acknowledgements</title>", "<p>This work was supported by the National Key Research and Development Program of China (2019YFA0405600), National Natural Science Foundation of China (22005293, U19A2092 and 22275180), Institute of Energy, Hefei Comprehensive National Science Center (Grant No. 21KZS212), and Collaborative Innovation Program of Hefei Science Center, CAS.</p>", "<p>\n<bold>Ke Li</bold> is currently a Ph.D. student at the University of Science and Technology of China (USTC) under the supervision of Professor Tao Chen, his research focuses on the development of a new interfacial engineering method and fabrication of antimony chalcogenide solar cells.</p>", "<p>\n<bold>Rongfeng Tang</bold> obtained her Ph.D. degree in 2019 from the University of Science and Technology of China (USTC) under the supervision of Professor Tao Chen. She joined the Tao Chen Group of USTC in 2019 and is working as an associate researcher. Her research focuses on the synthesis of nanomaterials and the fabrication of solar cells based on antimony chalcogenides semiconductors. She has published over 40 papers in Nature Energy, Advanced Energy Materials, Advanced Functional Materials, and so on.</p>", "<p>\n<bold>Changfei Zhu</bold> obtained his B.S. and Ph.D. degrees both from the University of Science and Technology of China (USTC) in 1984 and 1990, respectively. Afterward, he worked in the Department of Materials Science and Engineering, at USTC. He is working as a full professor now at the Department of Materials Science and Engineering, USTC. His research interests include the fundamental study and application of transitional metal oxide, wide band gap semiconductors, and new concept solar cells. He has published over 180 papers, including Nature Energy, Solar Energy Materials and Solar Cells, Applied Physics Letters, Science Bulletin, and so on.</p>", "<p>\n<bold>Tao Chen</bold> obtained his Ph.D. degree from Nanyang Technological University, Singapore, in 2010. In 2011, he joined the Department of Physics, Chinese University of Hong Kong as a Research Assistant Professor. Since 2015, he has been working in the Department of Materials Science and Engineering, University of Science and Technology of China as a full professor. His work focuses on emerging metal chalcogenides solar cells. He has published over 150 papers including Nature Energy, Nature Communications, Advanced Materials, Energy and Environmental Science, Journal of the American Chemical Society, and so on. He contributed two book chapters in the field of emerging solar cells, he also sits on the Editorial Board Member of Nano Research.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0001\"><label>Figure 1</label><caption><p>Schematic diagram of the currently developed strategies for regulating the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> crystal orientation.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0002\"><label>Figure 2</label><caption><p>a) Schematic diagram of the pole figure measured by X‐ray goniometer. b) Pole figure obtained from 2D mapping of the pole density onto the equatorial plane. Adapted with permission.<sup>[</sup>\n##UREF##21##\n26\n##\n<sup>]</sup> Copyright 2019, International Union of Crystallography. c) XRD pole figure of (002) plane preferred orientation, radial lines (purple) in the pole figure represent the tilt angle <italic toggle=\"yes\">χ</italic> with an increment of 30°. Reproduced with permission.<sup>[</sup>\n##REF##31755514##\n12\n##\n<sup>]</sup> Copyright 2019, the Royal Society of Chemistry. d) Schematic of EBSD setup. Reproduced with permission under the terms of the Creative Commons CC‐BY‐NC license.<sup>[</sup>\n##UREF##25##\n31\n##\n<sup>]</sup> Copyright 2018, Adhyaksa et al., Wiley‐VCH. e) Formation of Kikuchi patterns. Reproduced with permission.<sup>[</sup>\n##UREF##26##\n32\n##\n<sup>]</sup> Copyright 2015, International Union of Crystallography. f) Simulated symmetry patterns for crystals at different orientations. Reproduced with permission under the terms of the Creative Commons CC‐BY license.<sup>[</sup>\n##UREF##20##\n25\n##\n<sup>]</sup> Copyright 2020, Sun et al., Wiley‐VCH. g) EBSD map with orientation distribution of the Sb<sub>2</sub>Se<sub>3</sub> film. Reproduced with permission under the terms of the Creative Commons CC‐BY‐NC‐ND license.<sup>[</sup>\n##UREF##13##\n15\n##\n<sup>]</sup> Copyright 2021, Krautmann et al., Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0003\"><label>Figure 3</label><caption><p>a–h) Graphical representations of the (Sb<sub>4</sub>Se<sub>6</sub>)<sub>n</sub> ribbon inclination (red arrow, Sb<sup>3+</sup> = brown dots, Se<sup>2+</sup> = green dots) corresponding to [001] with respect to the growing surface (blue line) under different grain orientations. Reproduced with permission.<sup>[</sup>\n##UREF##22##\n27\n##\n<sup>]</sup> Copyright 2020, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0004\"><label>Figure 4</label><caption><p>a) Schematic of the hydrothermal deposition of Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> in an autoclave, wherein KSbC<sub>4</sub>H<sub>4</sub>O<sub>7</sub>, Na<sub>2</sub>S<sub>2</sub>O<sub>3</sub>, and selenourea are employed as the Sb, S, and Se sources, respectively. Reproduced with permission.<sup>[</sup>\n##UREF##30##\n36\n##\n<sup>]</sup> Copyright 2020, Springer Nature. b) Schematic illustration of the CBD process based on different sulfur sources. Reproduced with permission.<sup>[</sup>\n##UREF##40##\n48\n##\n<sup>]</sup> Copyright 2022, Wiley‐VCH. c) Schematic illustration of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> film fabrication by spin coating. Reproduced with permission.<sup>[</sup>\n##UREF##51##\n60\n##\n<sup>]</sup> Copyright 2017, Wiley‐VCH.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0005\"><label>Figure 5</label><caption><p>Schematic diagrams of different vacuum deposition methods: a) rapid thermal evaporation (RTE) method and b) vapor transport deposition (VTD) method. Reproduced with permission.<sup>[</sup>\n##UREF##63##\n75\n##\n<sup>]</sup> Copyright 2020, Wiley‐VCH. c) Thermal evaporation (TE) method. Reproduced with permission.<sup>[</sup>\n##UREF##69##\n81\n##\n<sup>]</sup> Copyright 2021, Wiley‐VCH. d) Radio frequency (RF) magnetron sputtering of the Sb film and the subsequent postselenization treatment. Reproduced with permission.<sup>[</sup>\n##UREF##75##\n88\n##\n<sup>]</sup> Copyright 2020, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0006\"><label>Figure 6</label><caption><p>Atomistic model of the [221]‐oriented Sb<sub>2</sub>Se<sub>3</sub> film on the (100) (a) and (002) (b) planes of ZnO. The dotted light magenta lines represent the bond formation leading to a successful charge separation at the interface. The absence of these lines indicates the generation of the dangling bonds causing a recombination loss. + represents the hole, while − represents the electron. The straight arrows represent a smooth carrier separation, while the curvilineal arrows represent the recombination loss. Reproduced with permission.<sup>[</sup>\n##UREF##8##\n9\n##\n<sup>]</sup> Copyright 2017, Springer Nature.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0007\"><label>Figure 7</label><caption><p>a) Nucleation and growth process during the vacuum deposition of thin films. b) Kink–ledge–terrace model for the Sb<sub>2</sub>Se<sub>3</sub> grain growth. c) Functional curve of the total free energy versus the substrate temperature. Reproduced with permission.<sup>[</sup>\n##UREF##68##\n80\n##\n<sup>]</sup> Copyright 2019, the Royal Society of Chemistry.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0008\"><label>Figure 8</label><caption><p>a) Growth rate as a function of the substrate temperature. α<sub>c(</sub>\n<italic toggle=\"yes\">\n<sub>hk</sub>\n</italic>\n<sub>0)</sub> and α<sub>c(</sub>\n<italic toggle=\"yes\">\n<sub>hkl</sub>\n</italic>\n<sub>,</sub>\n<italic toggle=\"yes\">\n<sub>l</sub>\n</italic>\n<sub>≠0)</sub> are the adhesion coefficients on the (<italic toggle=\"yes\">hk</italic>0) and (<italic toggle=\"yes\">hkl</italic>, <italic toggle=\"yes\">l</italic>≠0) surfaces, respectively (dashed lines). b) Scanning electron microscopy images of the Sb<sub>2</sub>Se<sub>3</sub> morphology deposited on the ZnO substrate under the three growth regimes (from top to bottom): T<sub>sub</sub> = 205 °C, T<sub>sour</sub>  =  560 °C; T<sub>sub</sub>  =  243 °C, T<sub>sour</sub>  =  510 °C; and T<sub>sub</sub>  =  275 °C, T<sub>sour</sub>  =  510°C. c) Schematic representation of the Sb<sub>2</sub>Se<sub>3</sub> microstructure grown under the three discussed regimes by the VTD method. The yellow dots depict the initial nuclei. Reproduced with permission.<sup>[</sup>\n##UREF##87##\n100\n##\n<sup>]</sup> Copyright 2019, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0009\"><label>Figure 9</label><caption><p>a) Mechanism of the Sb<sub>2</sub>Se<sub>3</sub> crystal growth on the ZnO‐NW for forming highly (001) oriented films. b) Schematic of the coated nanostructured and flat substrates. c) (002) texture coefficients of Sb<sub>2</sub>Se<sub>3</sub> films with CdS, Al<sub>2</sub>O<sub>3</sub>, and TiO<sub>2</sub> coatings on flat FTO and ZnO‐NW substrates. Reproduced with permission under the terms of the Creative Commons CC‐BY‐NC‐ND license.<sup>[</sup>\n##UREF##15##\n18\n##\n<sup>]</sup> Copyright 2023, Otavio Mendes et al., Wiley‐VCH.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0010\"><label>Figure 10</label><caption><p>Mechanism of the Sb<sub>2</sub>S<sub>3</sub> orientation dependence on the grain growth. Surface texture of the a) Sb<sub>2</sub>S<sub>3</sub> precursor film, b) Sb<sub>2</sub>S<sub>3</sub> film after low‐temperature stabilization treatment, and c) Sb<sub>2</sub>S<sub>3</sub> film after normal grain growth. d, e) Surface texture of the Sb<sub>2</sub>S<sub>3</sub> film undergoing an abnormal grain growth process. Reproduced with permission.<sup>[</sup>\n##UREF##91##\n104\n##\n<sup>]</sup> Copyright 2023, the Royal Society of Chemistry.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0011\"><label>Figure 11</label><caption><p>a) XRD patterns and b) texture coefficients of the diffraction peaks of the Sb<sub>2</sub>Se<sub>3</sub> thin films deposited on the ITO, FTO, and BZO substrates. Reproduced with permission.<sup>[</sup>\n##UREF##17##\n21\n##\n<sup>]</sup> Copyright 2021, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6622-fig-0012\"><label>Figure 12</label><caption><p>Growth model of the Sb<sub>2</sub>Se<sub>3</sub> seed evolution with duration time (left section), Sb<sub>2</sub>Se<sub>3</sub> film growth based on the corresponding seeds (middle section), and Sb<sub>2</sub>Se<sub>3</sub> films with an increased thickness (right section). Reproduced with permission.<sup>[</sup>\n##UREF##7##\n8\n##\n<sup>]</sup> Copyright 2021, Wiley‐VCH.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6622-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Angles between the (Sb<sub>4</sub>S(e)<sub>6</sub>)<sub>n</sub> ribbons and the surface normal and the effective vertical component of the ribbon orientation. Reproduced with permission.<sup>[</sup>\n##UREF##22##\n27\n##\n<sup>]</sup> Copyright 2020, Elsevier.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Crystallographic plane</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Angle between the ribbons and the surface normal [°]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Effective vertical component [EVC]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">(002)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">(211)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">37.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.79</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">(221)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">43.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.72</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">(301)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">45.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.70</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">(041)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">53.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.60</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">(141)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">54.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.58</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">(061)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">63.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.44</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">(<italic toggle=\"yes\">hk</italic>0)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">90</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6622-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Summary of the device configurations, deposition methods, orientation mechanisms, preferred orientations, texture coefficients, and PCE of the Sb<sub>2</sub>(S<sub>x</sub>Se<sub>1−x</sub>)<sub>3</sub> films and solar cell devices.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Device configuration<xref rid=\"advs6622-tbl2-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Deposition method<xref rid=\"advs6622-tbl2-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Orientation regulation mechanism</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Preferred orientation</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Texture coefficient</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">PCE [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Reference</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>(S,Se)<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##1##2##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>(S,Se)<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##30##36##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>Se<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##33871973##38##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>Se<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CBD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]/[301]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##37##45##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>S<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CBD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##40##48##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>Se<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">RTE</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##5##6##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/CdS/Sb<sub>2</sub>(S,Se)<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##86##99##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/CdS/Sb<sub>2</sub>Se<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##87##100##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/CdS/Sb<sub>2</sub>Se<sub>3</sub>/C/Ag</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.09</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##88##101##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/CdS/Sb<sub>2</sub>S<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##89##102##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo/Sb<sub>2</sub>Se<sub>3</sub>/CdS/ZnO/AZO/Al</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TE</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Growth rate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##68##80##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>(S,Se)<sub>3</sub>/PCBM/Ag</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Post‐treatment</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.22</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##90##103##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>S<sub>3</sub>/spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Post‐treatment</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.82</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##91##104##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/TiO<sub>2</sub>/CdS/Sb<sub>2</sub>S<sub>3</sub>/C/Ag</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Post‐treatment</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[041]/[141]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.23</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##2##3##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo/Sb<sub>2</sub>S<sub>3</sub>/CdS/i‐ZnO/AZO/Ni/Al</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">PE + sulfuration</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Post‐treatment</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[111]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.35</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##9##10##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo/Sb<sub>2</sub>Se<sub>3</sub>/CdS/ITO/Ag</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CSS + Selenization</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Selenization kinetics</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.86</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##34569779##20##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo/Sb<sub>2</sub>Se<sub>3</sub>/CdS/ITO/Ag</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD + Selenization</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Selenization kinetics</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[101]/[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.40</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##64##76##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">mica/Mo/Sb<sub>2</sub>Se<sub>3</sub>/CdS/ITO/Ag grid</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TE + Selenization</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Selenization kinetics</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##37126652##86##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/ZnO/Sb<sub>2</sub>Se<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">RTE</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Lattice matching</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##8##9##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/TiO<sub>2</sub>/Sb<sub>2</sub>S<sub>3</sub>/Se‐treated/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">RTE</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Lattice matching</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##52##61##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ag/ITO/epi‐CdS/Sb<sub>2</sub>Se<sub>3</sub>/Au/SU‐8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Lattice matching</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[322]/[422]/[041]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##12##14##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/SnO<sub>2</sub>/TiO<sub>2</sub>/CdS/Sb<sub>2</sub>Se<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Lattice matching</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[041]/[141]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##92##105##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/SnO<sub>2</sub>/CdS/Sb<sub>2</sub>(S,Se)<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.37</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##35##42##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/SnO<sub>2</sub>/CdS/Sb<sub>2</sub>(S,Se)<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[101]/[111]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##34##41##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS:O/Sb<sub>2</sub>(S,Se)<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]/[301]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.59</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##93##106##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/TiO<sub>2</sub>/Sb<sub>2</sub>(S,Se)<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.08</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##94##107##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/CdS:In/Sb<sub>2</sub>S<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##36##43##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/TiO<sub>2</sub>/CdS/Sb<sub>2</sub>S<sub>3</sub>/spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##10##11##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Li‐Sb<sub>2</sub>S<sub>3</sub>/PbS/C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.16</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##33##40##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo/MoSe<sub>2</sub>/Sb<sub>2</sub>Se<sub>3</sub>/CdS/ZnO/AZO</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">IVD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##16##19##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo/MoSe<sub>2</sub>/Sb<sub>2</sub>Se<sub>3</sub>/HR‐ZnO/LR‐ZnO/Ag</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CSS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##30631064##17##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">W/WSe2/Sb<sub>2</sub>Se<sub>3</sub>/CdS/i‐ZnO/AZO</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CSS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.46</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##58##67##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PI/Mo/PbSe/ Sb2Se3/CdS/i‐ZnO/AZO/Ag</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CSS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.43</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##6##7##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS:O/Sb<sub>2</sub>Se<sub>3</sub>/Graphite/Ag</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CSS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##95##108##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/SnO<sub>2</sub>/Sb<sub>2</sub>Se<sub>3</sub>/P3HT/C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CSS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.41</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##59##68##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO//CdS/Sb<sub>2</sub>(S,Se)<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.12</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##62##73##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/CdS/Sb<sub>2</sub>Se<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.48</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##96##109##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/TiO<sub>2</sub>/Sb<sub>2</sub>Se<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]/[301]/[141]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.33</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##97##110##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO/CdS/Sb<sub>2</sub>S<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[121]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.73</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##32326702##70##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>(S,Se)<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TE</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##69##81##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>Se<sub>3</sub>/spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">TE</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Interfacial engineering</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.89</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##70##82##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/TiO<sub>2</sub>/Sb<sub>2</sub>S<sub>3</sub>/PTB7/MoO<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Spin coating</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.18</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##98##111##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/TiO<sub>2</sub>/Sb<sub>2</sub>S<sub>3</sub>/PTB7/MoO<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Spin coating</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##48##57##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/TiO<sub>2</sub>/Sb<sub>2</sub>S<sub>3</sub>/Spiro‐OMeTAD/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Spin coating</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##49##58##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/TiO<sub>2</sub>/Sb<sub>2</sub>Se<sub>3</sub>/PbS/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">RTE</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.62</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##7##8##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/CeO<sub>2</sub>/Sb<sub>2</sub>Se<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">RTE</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.14</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##99##112##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo/Sb<sub>2</sub>Se<sub>3</sub>/CdS/i‐ZnO/AZO/Ag grid</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CSS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]/[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##60##69##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>S<sub>3</sub> seed/Sb<sub>2</sub>Se<sub>3</sub>/Spiro‐OMeTAD/C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CSS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.44</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##100##113##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Sb<sub>2</sub>Se<sub>3</sub>/Au</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">CSS</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##101##114##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FTO/CdS/Al<sub>2</sub>O<sub>3</sub>/Sb<sub>2</sub>Se<sub>3</sub>/C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VTD</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[101]/[211]/[221]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##102##115##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo/Sb<sub>2</sub>Se<sub>3</sub>/CdS/ITO/Ag</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">MS + selenization</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Seeding material</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[211]/[221]/[001]</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.14</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##103##116##]</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
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[ "<table-wrap-foot><fn id=\"advs6622-tbl2-note-0001\"><label>\n<sup>a)</sup>\n</label><p>FTO, fluorine‐doped tin oxide; ITO, indium tin oxide; AZO, aluminum‐doped ZnO; PCBM, [6,6]‐phenyl‐C61‐butyric acid methylester; SU‐8, photoresist; HR‐ZnO, high‐resistance ZnO; LR‐ZnO, low‐resistance ZnO; PI, polyimide; P3HT, poly(3‐hexylthiophene); and PTB7, poly[4,8‐bis(5‐(2ethylhexyl) thiophen‐2‐yl)benzo[1,2‐b;4,5‐b′]dithiophene‐2,6diyl‐alt‐(4‐(2‐ethylhexyl)−3‐fluorothieno[3,4‐b]thiophene‐)−2‐carboxylate‐2‐6‐diyl)];</p></fn><fn id=\"advs6622-tbl2-note-0002\"><label>\n<sup>b)</sup>\n</label><p>HD, hydrothermal deposition; CBD, chemical bath deposition; RTE, rapid thermal evaporation; CSS, close space sublimation; VTD, vapor transport deposition; TE, thermal evaporation; MS, magnetron sputtering; and PE, pulse electrodeposition.</p></fn></table-wrap-foot>" ]
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{ "acronym": [], "definition": [] }
135
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 8; 11(2):2304963
oa_package/f0/fd/PMC10787070.tar.gz
PMC10787071
37949679
[ "<title>Introduction</title>", "<p>Cooling technologies have been important since ancient times, and many novel technologies have been developed. However, most current cooling systems rely on vapor compression, necessitating the use of refrigerants and external energy; and therefore, raising environmental concerns. It is worth noting that ≈10% of energy consumed in the United States is used for cooling the interiors of buildings.<sup>[</sup>\n##UREF##0##\n1\n##\n<sup>]</sup> Ever‐increasing concerns about global warming, and the imperative to achieve net‐zero carbon emissions are driving research to develop ecologically‐benign, energy‐efficient methods to cool buildings, vehicles, industrial equipment, and the human body.</p>", "<p>Passive radiative cooling (RC) may present a future sustainable cooling technology that operates without external energy. By harnessing the coldness of the universe, RC dissipates excessive heat of terrestrial objects to the universe by thermal radiation. This is in sharp contrast to other cooling technologies,<sup>[</sup>\n##UREF##1##\n2\n##, ##UREF##2##\n3\n##\n<sup>]</sup> which mostly deposit heat elsewhere on Earth. Coincidentally, the atmosphere on a cloud‐free day is transparent in the main range of wavelengths (8 ≤ <italic toggle=\"yes\">λ</italic> ≤ 13 µm) emitted by objects that have a temperature of ≈300 K. This range is called the atmospheric window (AW). Thus, thermal radiation emitted by these objects can be dissipated into space without being absorbed by the atmosphere.</p>", "<p>RC exploits a ubiquitous heat transfer process of thermal radiation.<sup>[</sup>\n##UREF##3##\n4\n##\n<sup>]</sup> In the early stage,<sup>[</sup>\n##UREF##4##\n5\n##, ##UREF##5##\n6\n##, ##UREF##6##\n7\n##, ##UREF##7##\n8\n##, ##REF##18204570##\n9\n##, ##UREF##8##\n10\n##, ##UREF##9##\n11\n##\n<sup>]</sup> fundamental studies investigated the emissivity properties,<sup>[</sup>\n##UREF##6##\n7\n##, ##UREF##7##\n8\n##, ##REF##18204570##\n9\n##\n<sup>]</sup> influence of geological location,<sup>[</sup>\n##UREF##10##\n12\n##\n<sup>]</sup> and influence of weather conditions<sup>[</sup>\n##UREF##11##\n13\n##\n<sup>]</sup> on atmospheric transmittance. The research identified several materials, including polymers,<sup>[</sup>\n##UREF##4##\n5\n##\n<sup>]</sup> titanium dioxides,<sup>[</sup>\n##UREF##6##\n7\n##\n<sup>]</sup> silicon nitrides,<sup>[</sup>\n##UREF##12##\n14\n##\n<sup>]</sup> and silicon monoxide<sup>[</sup>\n##UREF##7##\n8\n##\n<sup>]</sup> that have great potential for emitting thermal radiation in the AW. Subsequently, sub‐ambient night‐time RC has been achieved by using these bulk materials.<sup>[</sup>\n##UREF##5##\n6\n##, ##UREF##6##\n7\n##, ##UREF##13##\n15\n##, ##UREF##14##\n16\n##\n<sup>]</sup> However, their use in daytime RC was found to be limited because they absorb a significant amount of sunlight. Therefore, a fundamental challenge is posed for daytime RC, which requires the manipulation of electromagnetic properties to achieve both low absorption in the solar spectrum (0.3 ≤ <italic toggle=\"yes\">λ</italic> ≤ 2.5 µm) and high emittance in the AW.</p>", "<p>Approaches that utilized several materials and structural effects facilitated the development of sub‐ambient daytime RC over the last decade.<sup>[</sup>\n##REF##25428501##\n17\n##, ##REF##23461597##\n18\n##\n<sup>]</sup> In these approaches, structural designs had provided essential ways to engineer electromagnetic properties over such a broad wavelength range, allowing for sub‐ambient daytime RC by suppressing solar absorption and emitting thermal radiation in the AW. The accessibility of full day‐and‐night RC offers even vast opportunities for energy‐efficient applications for buildings,<sup>[</sup>\n##UREF##15##\n19\n##\n<sup>]</sup> vehicles,<sup>[</sup>\n##UREF##16##\n20\n##\n<sup>]</sup> solar cells,<sup>[</sup>\n##UREF##17##\n21\n##\n<sup>]</sup> and for personal thermal management.<sup>[</sup>\n##UREF##18##\n22\n##\n<sup>]</sup> The significant impact and potential of passive RC has spurred researchers to address the remaining practical challenges over the last few years, including implementing novel fabrication methods and practical functionalities. Consequently, a number of review papers<sup>[</sup>\n##UREF##15##\n19\n##, ##UREF##19##\n23\n##, ##UREF##20##\n24\n##, ##UREF##21##\n25\n##, ##UREF##22##\n26\n##, ##UREF##23##\n27\n##, ##UREF##24##\n28\n##, ##UREF##25##\n29\n##, ##UREF##26##\n30\n##, ##UREF##27##\n31\n##\n<sup>]</sup> have also actively been published to comprehensively summarize the latest trends in RC technologies and propose future directions, all aimed at driving technological advancements in this field. For example, several review papers<sup>[</sup>\n##UREF##15##\n19\n##, ##UREF##20##\n24\n##\n<sup>]</sup> have examined the influences of environmental factors on cooling performances, such as climate, temperature, and atmospheric conditions to explore high‐performing radiative coolers. Materials and structural designs have been thoroughly reviewed<sup>[</sup>\n##UREF##21##\n25\n##, ##UREF##22##\n26\n##\n<sup>]</sup> to inspire innovative structural designs or guide suitable choices. Other review papers have focused on aspects of the historical development<sup>[</sup>\n##UREF##28##\n32\n##\n<sup>]</sup> of RC technologies or their integration in specific applications such as buildings,<sup>[</sup>\n##UREF##24##\n28\n##, ##UREF##25##\n29\n##\n<sup>]</sup> solar energy harvesting,<sup>[</sup>\n##UREF##19##\n23\n##, ##UREF##26##\n30\n##\n<sup>]</sup> and personal thermal management.<sup>[</sup>\n##UREF##27##\n31\n##, ##UREF##29##\n33\n##\n<sup>]</sup> Meanwhile, a few have examined various fabrication methods<sup>[</sup>\n##UREF##23##\n27\n##, ##UREF##29##\n33\n##, ##UREF##30##\n34\n##\n<sup>]</sup> for the realization of radiative coolers, but these are often categorized under specific structures and materials. For example, various fabrication methods for organic materials<sup>[</sup>\n##UREF##29##\n33\n##\n<sup>]</sup> and film structures<sup>[</sup>\n##UREF##30##\n34\n##\n<sup>]</sup> have thoroughly been reviewed. However, it is crucial to offer a holistic overview of the diverse fabrication methods that underpin radiative cooler realization, encompassing a wide range of materials and structures. Such an overview is particularly essential to identify potential approaches for real‐world applications and ensure their practical viability.</p>", "<p>In this article, we provide a comprehensive review of RC that covers the entire research landscape, encompassing fundamental concepts, structural designs, device fabrication methods, and emerging strategies and applications for commercialization with the aim of bridging the gap between research and practical implementation. We specifically focus on providing a comprehensive overview of various fabrication methods for RC; while, also exploring potential fabrication methods for practicality and real‐world applications. Through this review, we strive to facilitate a deeper understanding of RC and inspire further advancements in the field. We begin by briefly discussing the fundamentals of RC; then, review several structures and their physical mechanisms. Then, we review various methods to fabricate these structures and introduce potential functionalities and practical applications. We conclude by highlighting the challenges and potential of passive RC.(Figure ##SUPPL##0##S1##, Supporting Information)</p>" ]
[ "<title>Fabrication Method</title>", "<p>Radiative coolers with different structural configurations have been realized by exploiting a variety of micro‐ arnd nano‐processing techniques, including thin‐film deposition, lithography, and effective‐medium formation (<bold>Figure</bold> ##FIG##1##\n2a##). In this section, we provide an overview of recent advances in daytime RC from the point of view of fabrication method (Figure ##FIG##1##2b##). After thoroughly reviewing various fabrication techniques to realize radiative coolers, we then examine potential fabrication methods for practical uses.</p>", "<title>1D Fabrication</title>", "<p>Early studies on daytime RC attempted to extract thermo–optical properties from multilayer structures. Due to their simple design configurations, multilayer structures can readily be fabricated by facile methods. Typically, 1D multilayer structures can be fabricated by sequential thin film processing. Thin film processing is divided into: 1) surface‐processing techniques that either increase the effect or impart functionality to the base material and 2) coating or depositing other substances on the base material. Overall, in this review, thin‐film processing entails coating and deposition into the base material. Multilayer structures can be realized by growing metal and dielectric films on substrates by physical vapor deposition (PVD)<sup>[</sup>\n##UREF##74##\n103\n##\n<sup>]</sup> and chemical vapor deposition (CVD).<sup>[</sup>\n##REF##29384374##\n104\n##, ##REF##19947596##\n105\n##\n<sup>]</sup>\n</p>", "<p>PVD is a set of techniques that deposit target materials onto a substrate by either evaporation or sputtering under a high vacuum (<bold>Figure</bold> ##FIG##2##\n3a##). PVD can be classified into three main methods: electron‐beam evaporation,<sup>[</sup>\n##UREF##75##\n106\n##\n<sup>]</sup> sputtering,<sup>[</sup>\n##UREF##76##\n107\n##\n<sup>]</sup> and thermal evaporation<sup>[</sup>\n##UREF##77##\n108\n##\n<sup>]</sup> depending on the method used to produce the film. PVD can provide a stable process with a simple mechanism to deposit target materials by physical force; thus, it enables low‐temperature deposition under high vacuum and produces high‐purity thin film regardless of the substrate.</p>", "<p>PVD has been widely employed in the field of RC to deposit metallic mirrors, such as Ag, Al, and various inorganic materials, onto both commercial substrates and flexible polymer films.<sup>[</sup>\n##UREF##78##\n109\n##, ##UREF##79##\n110\n##\n<sup>]</sup> These deposited Ag and Al metal mirrors are capable of reflecting the solar spectrum, leading to a significant reduction in <italic toggle=\"yes\">P</italic>\n<sub>sun</sub>, a major contributor to cooling flux loss. Moreover, PVD enables the deposition of IR absorptive inorganic materials including SiO<sub>2</sub>, Si<sub>3</sub>N<sub>4</sub>, and Al<sub>2</sub>O<sub>3</sub> within the same chamber, offering versatility and convenience for RC research. Notably, the pioneering work on sub‐ambient daytime RC utilized multilayer structures composed of dielectrics and metal mirrors, realized through electron beam evaporation (Figure ##FIG##2##3a##).<sup>[</sup>\n##REF##25428501##\n17\n##\n<sup>]</sup> The simplicity and ease of fabrication offered by PVD have spurred numerous research efforts, propelling advancements in the field of RC. However, the need for high vacuum increases the equipment's complexity, and the growth of mean free path (MFP) of evaporative particle can form uneven step coverage, which can yield low adhesion and poor uniformity.</p>", "<p>CVD, on the other hand, uses chemical reactions to grow thin films of the target materials on the substrate from vapor‐phase precursors (Figure ##FIG##2##3b##). CVD can be classified according to the precursor‐decomposition methods, such as: thermal CVD,<sup>[</sup>\n##UREF##80##\n111\n##\n<sup>]</sup> plasma‐enhanced (PE) CVD,<sup>[</sup>\n##UREF##81##\n112\n##\n<sup>]</sup> and atomic layer deposition(ALD). CVD allows large‐area film growth with adequate step coverage by a series of reactions, including diffusion, adsorption, chemical reaction, and desorption over the entire area at a low vacuum. Consequently, CVD allows a more cost‐effective fabrication option compared to PVD, which necessitates the use of a high‐vacuum system. In addition, CVD has high versatility as it enables the growth of various thin films, including ceramics and semiconductors, by utilizing modified precursors. This enables the continuous deposition of several promising inorganic materials for daytime RC, such as SiO<sub>2</sub>, Al<sub>2</sub>O<sub>3</sub>, and Si<sub>3</sub>N<sub>4</sub>, using CVD. In addition, the modulation of precursors and established reactant gases in CVD allows the growth of materials with different absorption peaks, thereby increasing absorption across the broad IR spectral range. Therefore, several multilayer structures for sub‐ambient daytime RC, such as alternating SiO<sub>2</sub>/Si<sub>3</sub>N<sub>4</sub>,<sup>[</sup>\n##UREF##82##\n113\n##\n<sup>]</sup> and a thermal‐emissive polymer with a CVD‐grown high‐/low‐refractive‐index Bragg mirror,<sup>[</sup>\n##UREF##16##\n20\n##\n<sup>]</sup> have been developed using CVD. In addition, by using both PVD and CVD techniques, a radiative cooler with a long lifespan consisting entirely of inorganic materials has also been developed (Figure ##FIG##2##3b##).<sup>[</sup>\n##REF##31990166##\n41\n##\n<sup>]</sup> In a typical CVD process, the vacuum level and temperature should be carefully controlled to adjust the MFP and reaction rate to yield uniform film growth. However, operating at high vacuum results in a longer MFP and compromises the step coverage; while, low vacuum conditions can lead to the overhang phenomenon. It can be overcome by increasing the fabrication temperature at low vacuum to increase the particle mobilities in the film, but the use of low vacuum is subject to impurity problems. Moreover, the use of high‐temperature processes poses limitations when working with flexible polymers.</p>", "<p>ALD can be considered to be a kind of CVD process and can be used to fabricate radiative coolers with high‐purity layers.<sup>[</sup>\n##UREF##44##\n58\n##\n<sup>]</sup> ALD uses a vapor‐phase precursor and a reactive gas alternatively injected to grow atomic layers per cycle, and the repetition of this process forms a film layer. ALD allows formation of uniform step coverage with outstanding adsorption characteristics compared to other processes. By using ALD, the film thickness can be adjusted precisely; however, the atomic‐scale deposition has an extremely slow deposition rate. Consequently, it may not be suitable for growing thick films that are required to have sufficient IR absorptive capabilities over a large area for effective RC.</p>", "<p>1D multilayer structures promoted initial RC studies with simple designs and fabrication methods. Gentle et al.<sup>[</sup>\n##UREF##83##\n114\n##\n<sup>]</sup> utilized commercial reflector films, the ESR film produced by 3 M, with a reflectivity of up to 98%, as mirrors for a scalable daytime RC. Likewise, commercial polymer films with thicknesses of 50–100 µm have demonstrated comparable cooling performance to those fabricated in the laboratory when deposited with reflectors for use in daytime RC. The use of these price‐competitive reflectors or polymer films presents a promising opportunity for the commercialization of daytime radiative coolers. Despite their simple designs, multilayer structures have posed challenges in real‐world applications due to the limited degrees of freedom and the need for reflectors. These disadvantages led researchers to explore other structures of either 2D for enhancing cooling effects or 3D for scalability.</p>", "<title>2D Fabrication</title>", "<p>By leveraging recent advances in nanofabrication techniques, researchers have successfully expanded the exploration of more intricate 2D structures, unlocking additional degrees of freedom and effectively enhancing cooling effect. These advancements have resulted in the creation of various 2D photonic structures that exhibit unprecedented light–matter interactions.<sup>[</sup>\n##UREF##84##\n115\n##\n<sup>]</sup> These artificial 2D structures can be optimized through a series of designs to possess ideal RC optical characteristics, featuring high reflectance of the solar spectrum, along with selectively enhanced AW emission properties.<sup>[</sup>\n##REF##26089358##\n54\n##\n<sup>]</sup> The methods of forming 2D micro‐/nano‐structures can be categorized into top–down and bottom–up approaches. Top–down lithography forms the pattern by using a light source<sup>[</sup>\n##UREF##85##\n116\n##\n<sup>]</sup> or electron beam<sup>[</sup>\n##UREF##86##\n117\n##\n<sup>]</sup> to selectively remove parts of a bulk piece of material (<bold>Figure</bold> ##FIG##3##\n4a,b##). Bottom–up processes stack small materials to form bulk nanostructures (Figure ##FIG##3##4c,d##).</p>", "<p>Top–down approaches have been widely used because they offer high fidelity and controllability. Photolithography is a commonly used top–down fabrication approach in which a light source is projected through a mask onto a photoresist (PR), resulting in the formation of hard mask pattern. Subsequently, the exposed areas are etched away, leaving behind the desired pattern.<sup>[</sup>\n##UREF##85##\n116\n##\n<sup>]</sup> It can be widely used to form the pattern on the substrate or through the post‐process such as the deposition process, which can form a certain pattern composed of target materials. To achieve high‐efficiency RC, promising inorganic materials can be processed using photolithography, enabling precise fabrication of the following microstructures that induce selective IR absorption.</p>", "<p>RC has been achieved using an array of holes patterned by photolithography in glass (Figure ##FIG##3##4a##).<sup>[</sup>\n##REF##26392542##\n62\n##\n<sup>]</sup> A porous structure was formed by UV exposure through a square grid metal mask to form a PR mask. Then, the PR pattern was isotropically etched to form a periodic hole pattern. The periodic hole pattern induced high IR emission due to the impedance matching between the structure and the surrounding air. Subsequently, 2D pillar structures have been developed having similar optical properties to those of the hole array.<sup>[</sup>\n##UREF##87##\n118\n##, ##UREF##88##\n119\n##\n<sup>]</sup> Inspired by natural creatures using photonic crystal to achieve RC, researchers have also explored the use of biomimetic photonic crystals as efficient radiative coolers. Hence, micro‐pyramid structures that mimic natural creatures for daytime RC have been achieved using both photolithography and chemical etching processes.<sup>[</sup>\n##UREF##43##\n56\n##, ##REF##32541048##\n57\n##, ##UREF##89##\n120\n##\n<sup>]</sup> The introduction of isotropic wet‐etching allows the realization of complex structures that are difficult to fabricate using only photolithography. However, photolithography relies on projection of light through a mask; so, the structures are highly dependent on the mask; this dependence imposes a constraint on the degree of freedom of structures that can be fabricated by the method.</p>", "<p>Electron beam lithography (EBL) does not use a mask, thereby, alleviating the constraint associated with mask dependence. EBL uses a concentrated electron beam to scan an E‐beam‐sensitive resist and writes patterns directly.<sup>[</sup>\n##UREF##86##\n117\n##\n<sup>]</sup> EBL allows the generation of features down to &lt; 10 nm by utilizing a nanometer‐sized focused beam to scan along a user‐specified path. EBL has been used to write a conical shape of metal–dielectric alternating layers serving as a broadband IR absorber for RC (Figure ##FIG##1##2b##).<sup>[</sup>\n##UREF##40##\n51\n##\n<sup>]</sup> This conical shape was fabricated by exploiting the physical phenomenon between sidewall deposition and lift‐off.<sup>[</sup>\n##UREF##90##\n121\n##\n<sup>]</sup> Subsequently, a rectangular resonator composed of a metal–dielectric bilayer had been utilized to achieve additional thermal emission.<sup>[</sup>\n##UREF##41##\n52\n##\n<sup>]</sup> In addition, EBL fabrication was also used to demonstrate smart cooling.<sup>[</sup>\n##UREF##91##\n122\n##\n<sup>]</sup> A phase‐change material (e.g., VO<sub>2</sub>) was patterned on several dielectric layers, achieving temperature‐adaptive cooling. However, despite its high resolution, EBL is highly expensive and has low throughput due to its serial scanning nature, significantly limiting its practicality. Therefore, it has often been employed in the laboratory‐scale research to propose and demonstrate new structures for RC.</p>", "<p>On the other hand, bottom–up approaches use materials to stack up using physical and chemical interactions and have been introduced for scalable RC fabrication. These methods can be easily scaled up to large areas by assembling small particles to form the bulk structures. Bottom–up approaches to realize 2D structures for RC have mainly been reported using nanoimprint lithography (NIL) and colloidal lithography (CL).</p>", "<p>NIL creates patterns by placing a polymer resin into a mold and curing it under pressure.<sup>[</sup>\n##UREF##92##\n123\n##, ##REF##36637666##\n124\n##\n<sup>]</sup> NIL has been exploited for a scalable fabrication with high throughput due to the repeatable uses of molds. So far, NIL that uses various forms of resin, including promising inorganic‐nanoparticle‐embedded resins, has been reported, and it is being developed to a highly versatile process technology due to its high throughput.<sup>[</sup>\n##REF##32385266##\n125\n##\n<sup>]</sup> Highly efficient RC has been obtained by using a randomly‐distributed pyramidal inorganic structure that is imprinted from a slurry state and followed by post‐annealing (Figure ##FIG##3##4c##).<sup>[</sup>\n##UREF##93##\n126\n##\n<sup>]</sup> Similarly, a disk array RC has also been successfully realized by exposing photocurable resin on a flexible mirror film to UV light.<sup>[</sup>\n##UREF##94##\n127\n##\n<sup>]</sup> Notably, this fabrication method is compatible with a flexible polymer substrate because the method does not require high temperature or a chemical process. In addition, micro‐/nano‐structure can be transferred through a single‐step, high‐speed production process, indicating the potential for the commercialization of 2D RC.</p>", "<p>CL is another approach to fabricate periodic arrays.<sup>[</sup>\n##REF##23611897##\n128\n##, ##REF##17015295##\n129\n##\n<sup>]</sup> CL exploits the surface–energy interaction between spherical particles and a functionalized substrate. A suspension of spherical particles dispersed in a hydrophilic substrate self‐assembles to form a hexagonal array as the solvent evaporates. CL has been used to realize a simple radiative cooler that has a monolayer of microspheres (Figure ##FIG##3##4d##).<sup>[</sup>\n##UREF##95##\n130\n##\n<sup>]</sup>\n</p>", "<p>Other bottom–up approaches have also been used to fabricate various 2D structures for RC.<sup>[</sup>\n##UREF##96##\n131\n##, ##UREF##97##\n132\n##, ##UREF##98##\n133\n##, ##UREF##99##\n134\n##\n<sup>]</sup> Anodizing uses an electrochemical reaction and is typically used to produce anodic aluminum oxide (AAO) templates.<sup>[</sup>\n##UREF##96##\n131\n##, ##UREF##97##\n132\n##\n<sup>]</sup> By using two‐step electrochemical anodization, a periodic and porous AAO template for RC has been developed.<sup>[</sup>\n##UREF##97##\n132\n##\n<sup>]</sup> In addition to the AAO template, the AAO cooling effect has been further improved by coating it with a layer of ultra‐thin inorganic film grown by ALD. The emitter was then transferred to the Al substrate to reflect the solar spectrum, and thereby, operated under direct sunlight. Similarly, a two‐step anodization process has been used to fabricate a self‐aggregated AAO formed by capillary forces.<sup>[</sup>\n##UREF##98##\n133\n##\n<sup>]</sup> A colorful radiative cooler has been obtained using a bioinspired array of SiO<sub>2</sub> that was realized using a self‐assembled silver island structure.<sup>[</sup>\n##UREF##99##\n134\n##\n<sup>]</sup>\n</p>", "<p>Although 2D fabrication can exhibit dramatic improvement in cooling performance via interesting structures, their intricate fabrication process may lead to increased fabrication costs per unit area. This poses a challenge when it comes to the commercialization of 2D radiative coolers with high performance.</p>", "<title>3D Fabrication</title>", "<p>3D structures such as particles and voids in media are easy to implement using high‐throughput fabrication methods and have been actively used in effective daytime radiative coolers. These structures induce a strong optical scattering effect and can be used to achieve high solar reflection. 3D radiative coolers can be made from materials compatible with high‐throughput fabrication methods and equipment; and are therefore, the most promising candidates for large‐scale applications. Methods to fabricate 3D radiative coolers can be divided into a bottom–up approach that mixes particles (Section <xref rid=\"advs6694-sec-0110\" ref-type=\"sec\">3.3.1</xref>) and a top–down approach that creates voids in the matrix (Section <xref rid=\"advs6694-sec-0120\" ref-type=\"sec\">3.3.2</xref>). Fabrication of particles or voids forms the effective medium by adding particles to a matrix or removing them from it.</p>", "<title>Particle Matrix</title>", "<p>Various methods have been used to convert a particle mixture into the desired form. Pressing uses mechanical pressure to fabricate uniform structures such as film or plate; the method is highly scalable fabrication of devices (<bold>Figure</bold> ##FIG##4##\n5a##) and achieves scalable manufacturing of several radiative coolers. One example<sup>[</sup>\n##REF##28183998##\n135\n##\n<sup>]</sup> is a bi‐layer thermoplastic polymer that contains randomly‐dispersed inorganic particles and is coated on a metal mirror (Figure ##FIG##4##5a##). A composite that contains the particles is pressed between heated upper and lower rolls resulting in a film with uniform thickness. Another similar fabrication method involves the use of a melting press to produce a film‐type radiative cooler made of inorganic–organic composite.<sup>[</sup>\n##UREF##100##\n136\n##\n<sup>]</sup> The scalability of such techniques drives research to find new functionalities and applications, such as a mass‐produced inorganic and polymer mixtures film<sup>[</sup>\n##UREF##101##\n137\n##\n<sup>]</sup> that becomes a greenish color after pressure molding with heated rolls; the colored cooler can be used as an artificial lawn.</p>", "<p>High‐speed coating has also been proposed as a method to produce RC films. Spin‐coating is a fast and simple technique to coat uniform films on a lab scale. Early research<sup>[</sup>\n##UREF##34##\n40\n##\n<sup>]</sup> demonstrated a thin film for RC by spin‐coating a polymer onto a mirror substrate; then, curing the polymer. The productivity of the process could be increased by using simple coatings by mixing a polymer, inorganic particles, and a UV‐curable resin. This composite was spin‐coated on a mirror; then, cured by UV exposure; however, this curing process partially negated the advantage of the rapid fabrication process. To reduce the number of fabrication steps, composites of two inorganic particles in an acrylate binder could produce films without the need for post‐processing<sup>[</sup>\n##UREF##59##\n76\n##\n<sup>]</sup> (Figure ##FIG##4##5b##). The productivity was increased by omitting the UV‐exposure process. Other coating methods have also been used to fabricate radiative coolers. For example, a RC film was developed by using dip‐coating, which exploited the surface tension between the precursor solution and the sample.<sup>[</sup>\n##REF##33974398##\n48\n##\n<sup>]</sup> Improving the scalability of the process was important to drive potential large‐scale applications but should be done without degrading the effectiveness of radiative coolers; hence, a composite film containing hierarchically inorganic core–shell particles has been developed for high effectiveness, obtained by high‐temperature sintering of thin inorganic film.<sup>[</sup>\n##UREF##67##\n85\n##\n<sup>]</sup> Additional backscattering resulting from the core–shell shape contributes to increased cooling effect. Despite its high scattering efficiency, the high‐temperature treatment process can act as a limiting factor for the application and productivity of flexible substrates.</p>", "<p>Composites that include particles can also be applied by casting a slurry; the inorganic particles are dispersed within a composite material. This method uses molds to process slurries into the desired shape and has been presented for mass production. These advantages suggest the potential for the application of RC composite in various exterior materials. Therefore, a RC film is produced<sup>[</sup>\n##UREF##57##\n73\n##, ##REF##33856776##\n74\n##\n<sup>]</sup> by casting slurries composed of polymer‐dissolved solvents with added inorganic particles; ultrasonication promotes the distribution of the particles within the matrix to form a slurry that has effective optical properties. The slurry cast on the mold is converted to a free‐standing film by removing the air bubbles and the solvent. Using tools to disperse the slurry can further accelerate productivity.</p>", "<p>Tape casting, also called blade coating, spreads the slurry through a certain edge to form films. A specific amount of slurry is poured onto a flat tape; then, a blade at a certain height above the flat plate spreads the slurry forward to form a film of a certain thickness (Figure ##FIG##4##5c##). A free‐standing film can be obtained by drying slurry and removing the tape. The possibility of large‐area fabrication by blade coating is first demonstrated<sup>[</sup>\n##UREF##102##\n138\n##\n<sup>]</sup> using a pre‐polymer on a mirror. This possibility has stimulated various subsequent studies. For example, a cooling film was demonstrated using a double layer of inorganic–organic composite that had been deposited by tape casting.<sup>[</sup>\n##UREF##58##\n75\n##\n<sup>]</sup> Similarly, a cooling film was achieved using screen‐printing. These advances suggest that slurries may be widely applicable.<sup>[</sup>\n##REF##32437122##\n139\n##\n<sup>]</sup> A radiative cooler with self‐cleaning functionality, which avoids degraded cooling performance due to surface dust or debris, is obtained by coupling functional groups to hierarchical‐size spherical inorganic particles to induce superhydrophobicity.<sup>[</sup>\n##UREF##103##\n140\n##\n<sup>]</sup> (Figure ##FIG##4##5c##).</p>", "<p>Spray coating can directly coat materials regardless of substrates and surface curvatures (Figure ##FIG##4##5d##). Several spray‐coating methods are reported for practical RC. For example, films that increase optical scattering are obtained by spraying crystal particle‐based suspension on a mirror.<sup>[</sup>\n##UREF##51##\n67\n##\n<sup>]</sup> In addition, cooling coatings are obtained by spraying an inorganic geopolymer<sup>[</sup>\n##REF##33226211##\n87\n##\n<sup>]</sup> (Figure ##FIG##4##5d##). Using periodically moving equipment during the spray process facilitates the uniform formation of inorganic particle films, thereby avoiding unexpected optical responses and achieving expected cooling performance approximating the design. Use of spraying to fabricate RC layers offers great advantages because it can use any type of slurry or matter.</p>", "<title>Void Matrix</title>", "<p>Effective emissive composites with voids that can facilitate solar scattering can induce RC. Fabrication of porous matrix is easily scalable and can support mass production of radiative coolers. A representative process is phase inversion that generates voids by exploiting the discrepancy in the volatilization rates of inter‐solvents during polymerization of a matrix dissolved in solvents (Figure ##FIG##4##5e##). The mechanism of dissolving particles by solvents can also be regarded as a kind of phase inversion.</p>", "<p>Porous RC films have been achieved using hierarchical pores formed by the different volatilization rates of solvents.<sup>[</sup>\n##REF##30262632##\n38\n##\n<sup>]</sup> A porous matrix with random‐sized voids can be formed depending on the solvent evaporation path in the polymer. The matrix can be easily fabricated by coating and drying. A subsequent study<sup>[</sup>\n##UREF##104##\n141\n##\n<sup>]</sup> used self‐assembled multilayer polymer beads as templates to construct periodic porous structures. After the polymer was infiltrated into a template, an annealing process removed the beads to produce a flexible thermal emitter that included periodic voids. Similarly, porous cooling films had been fabricated by dissolving away granulated sugar that had been dispersed in water on the surface of the polymer.<sup>[</sup>\n##UREF##69##\n90\n##\n<sup>]</sup> Recently, a combination of phase inversion method, blade coating, and a roll‐to‐roll process demonstrated scalable manufacturing of a radiative cooler at the meter scale.<sup>[</sup>\n##UREF##105##\n142\n##\n<sup>]</sup>\n</p>", "<p>Fabrication schemes that use more than one material, such as mixing particles<sup>[</sup>\n##REF##33397941##\n89\n##, ##UREF##71##\n92\n##, ##UREF##106##\n143\n##\n<sup>]</sup> or adding functional materials for hybrid cooling,<sup>[</sup>\n##UREF##107##\n144\n##\n<sup>]</sup> have been combined with the phase‐inversion method. For example, a hierarchical porous structure has been used for sub‐ambient RC. The structure can be fabricated by casting a polymer that contains dispersed nanoparticles in self‐assembled hexagonal beads to fabricate layered porous arrays.<sup>[</sup>\n##REF##33397941##\n89\n##\n<sup>]</sup> Subsequent etching of periodic microbeads and nanoparticles yields hierarchical porous arrays. Although two‐step etching achieves high cooling effect, the method has insufficient productivity. Therefore, alternative methods have been proposed that offer high production efficiency with simple processes.</p>", "<p>Mixing particles that have high refractive index into a phase‐inversion precursor can yield a complex porous‐particle structure.<sup>[</sup>\n##UREF##106##\n143\n##\n<sup>]</sup> The hierarchical voids and additional backscattering of high‐index particles contribute to the increase in solar reflection. A strategy that exploits the particle's gravitational sedimentation and phase inversion can achieve a porous‐particle bilayer in a single process;<sup>[</sup>\n##UREF##71##\n92\n##\n<sup>]</sup> this approach yields devices that have higher cooling effect than others that had been produced at similar fabrication speeds. RC has also been achieved using hydrogel‐porous polymer;<sup>[</sup>\n##UREF##107##\n144\n##\n<sup>]</sup> this structure utilized an additional cooling effect caused by the evaporation of moisture absorbed by the hydrogel and could substantially increase the passive cooling effect. The hybrid structure was manufactured using two‐step casting and phase inversion; and therefore, could have high productivity.</p>", "<p>Electrospinning shoots electrically‐charged polymer solutions through jets onto a collector to form a fiber network. This method has been used to fabricate porous‐arranged RC fabrics (Figure ##FIG##4##5f##). Use of a phase inversion precursor in the polymer solutions and electrospinning can acquire additively hierarchical porosity inside the fibers.<sup>[</sup>\n##UREF##73##\n96\n##\n<sup>]</sup> In addition, two‐step processes of electrospinning and emulsion deposition yield a flexible hybrid membrane radiative cooler, and the production is highly effective and scalable.<sup>[</sup>\n##UREF##55##\n71\n##\n<sup>]</sup> Several radiative coolers use natural fibers of silk and further process them. For example, nano‐processed silk has been produced using a scalable coupling‐reagent‐assisted dip coating method.<sup>[</sup>\n##REF##34750560##\n102\n##\n<sup>]</sup> Tetrabutyl titanate was used as a coupling reagent that connects the inorganic nanoparticles of Al<sub>2</sub>O<sub>3</sub> to natural silk, and this combination significantly increases the RC effect. Similarly, artificially‐restructured micro‐scale/nano‐scale silk was produced by electrospinning, and effectively scattered sunlight.<sup>[</sup>\n##UREF##108##\n145\n##\n<sup>]</sup> These methods to fabricate RC fiber are compatible with commercial textile manufacturing equipment and are promising low‐cost, high‐throughput manufacturing methods. Use of evaporation cooling has also been used in fabrics. Functionalized hydrogels and porous fibrous bilayers have been combined to form a hybrid porous network by combining a phase‐separation precursor and hydrogels that contain random pores made by freeze‐thawing and fiber electrospinning.<sup>[</sup>\n##REF##35960798##\n97\n##\n<sup>]</sup> Another bilayer fabric that uses hierarchically‐sized particles was produced using a two‐step electrospinning process.<sup>[</sup>\n##REF##35075910##\n98\n##\n<sup>]</sup> The fabricated fabric was treated in hydrophilic solution to promote additional evaporative cooling. Hierarchically hollow core and shell cooling fibers have been formed by coaxial electrospinning that uses two types of phase separation precursors.<sup>[</sup>\n##REF##34014070##\n99\n##\n<sup>]</sup> Further, an existing electrospinning technique has been combined with a roll‐to‐roll collector to produce nanofibers that had constant thickness and could be produced on meter scale.<sup>[</sup>\n##REF##33199884##\n100\n##\n<sup>]</sup> Melt spinning had also been used to produce cooling fibers that were made from polymer pellets that contained inorganic particles injected by melt extrusion mixing.<sup>[</sup>\n##REF##34353954##\n101\n##\n<sup>]</sup>\n</p>", "<p>Other conventional fabrication methods to achieve RC have used various materials that incorporate porous structures. For example, a ball‐milling method can form uniform polymer micro‐clusters to increase solar reflection.<sup>[</sup>\n##UREF##70##\n91\n##\n<sup>]</sup> Two‐step anodization can increase the porosity of an AAO template (Figure ##FIG##4##5 g##).<sup>[</sup>\n##UREF##109##\n146\n##\n<sup>]</sup> Delignifying and repressing natural wood, a structural material with mesoporous cellulose was developed and showed highly effective RC.<sup>[</sup>\n##REF##31123132##\n147\n##\n<sup>]</sup> Recently, a new approach utilizing 3D direct printing had been applied to develop radiative coolers. The primary technique of 3D printing involved introducing materials into the supply mechanism and extruding them through a nozzle. For example, it could be utilized as a mixed resin consisting of inorganic particles and solvents to enable IR emission and phase conversion.<sup>[</sup>\n##REF##33464912##\n148\n##\n<sup>]</sup> Thanks to this intuitive fabrication mechanism, it was possible to rapidly produce a wide range of shapes without being constrained by pre‐existing structures. Likewise, porous structures could be readily fabricated using a variety of materials and fabrication methods; and therefore, have numerous potential practical uses.</p>", "<title>Expected Method</title>", "<p>With the support of micro‐/nano‐processing, RC technology has achieved rapid advancements in cooling effectiveness and scalability and has been developed in the direction of improving cooling efficiency and fabrication productivity. The research paradigm, which is shifting toward commercialization, can be well‐observed from big (3 M, Gore‐tex Corp., etc.) and emerging venture companies (Radi‐cool, SkyCool System, Foel Inc., etc.) and market movements. RC technology is attracting substantial interest from diverse communities as a promising energy‐saving technology that has high feasibility. However, actual commercialization requires solutions to some remaining challenges. First, the RC effect is generally subject to the material's inherent optical properties. Hence, efforts should be made to develop and optimize materials. Second, to secure economic feasibility, RC technology can be implemented in real‐life only after development of facile fabrication methods that yield a reasonable cooling effect. Recently, optimized material technology in the field of photonics has been reported. Effective manipulation of light requires sub‐wavelength structures that have a high refractive index and low loss. For example, internal chemical reactions can be controlled by adjusting CVD conditions control to develop low‐loss amorphous silicon, which is transparent in the visible regime.<sup>[</sup>\n##UREF##110##\n149\n##\n<sup>]</sup> This technology can be achieved by controlling the process conditions with existing equipment, and the method can be applied to different materials to seek optimized optical characteristics. Currently, these technologies have been applied to several materials and process technologies and have prompted subsequent studies.<sup>[</sup>\n##UREF##111##\n150\n##, ##REF##33090760##\n151\n##\n<sup>]</sup> In addition, this approach of controlling optical properties through process manipulation is not limited to CVD. For instance, the glancing angle deposition enables the development of novel materials. It can create porous films reducing solar absorption through scattering or enabling selective radiation based on their structure. These advancements have potential applications in the field of RC. The recent attempt to enhance light confinement by ALD‐deposited high‐refractive‐index ultrathin film on structured polymer, enabling control of the optical properties of the entire 12‐inch medium, has been reported.<sup>[</sup>\n##REF##36959502##\n152\n##\n<sup>]</sup> This strategy applicable to large areas can be utilized in a manner that contributes to enhancing cooling efficiency by using a novel approach; while, utilizing existing fabrication processes. Alternatively, embedding of TiO<sub>2</sub> NPs, which have high refractive index with low loss can be dispersed in a UV‐curable resin to yield an effective medium,<sup>[</sup>\n##REF##32385266##\n125\n##, ##REF##33385188##\n153\n##\n<sup>]</sup> and the optical properties of the materials can be modulated by adjusting the volume fraction of particles. This fabrication process can replace the high‐cost lithography and ALD processes by using the inexpensive nanoimprint and coating processes. The utilization of inorganic particle‐embedded resin in patterned roll‐to‐roll or roll‐to‐plate processes also offers the potential for the mass production of patterned 2D arrays. Depending on their design, enhanced selective reflection and emission characteristics can be induced, thereby enabling the commercialization of high‐efficiency RC films. We believe that these upcoming technologies are integrated with advanced technology, which may provide a breakthrough toward the commercialization of RC.</p>" ]
[]
[]
[ "<title>Conclusion and Outlook</title>", "<p>RC is a promising new direction in sustainable energy research. Here, we have reviewed progress in research on RC technology, from the early demonstrations to recent advances toward practical applications. We conclude by highlighting the challenges and future potentials of passive RC systems.</p>", "<p>We note that some commercial companies such as 3 M and Gore‐tex Corp have successfully demonstrated the commercial viability of radiative coolers, showcasing the potential for real‐world applications. For instance, 3 M utilized multilayer structures for optical films that can cool the surfaces such as bus shelter roofs throughout the day and night. SkyCool Systems, founded in 2016, have developed a rooftop panel system that can be used as an add‐on to air conditioning and refrigeration systems leveraging the RC technology to reduce energy consumption. Other recently founded companies such as ChillSkyn have developed porous polymer coating and other forms of radiative cooling paint that can be easily applied to various surfaces including metal, plastics, and wood, showcasing its versatility in use. These emerging commercialized products are different from lab‐scale demonstrations in that they are particularly designed and tested to be implemented and produced in large‐scale offering efficient cooling solutions to various markets and industries. These applications include roofing in warehouses, factories, thermal power plants, and data centers as well as common transportations and vehicles used in shipping and deliveries.</p>", "<p>However, in this shifting research paradigm, there are several challenges that need to be addressed to effectively promote the efficient commercialization and widespread implementation of other laboratory research on RC technologies.</p>", "<p>First, low‐cost and ecologically‐benign fabrication methods need to be developed for large‐scale utilization. Although simple and scalable manufacturing methods have been evaluated, some are only compatible with specific materials and structures; further, some cause environmental problems, such as use of hazardous chemicals and emission of volatile organic compounds.<sup>[</sup>\n##UREF##71##\n92\n##, ##REF##33345542##\n93\n##, ##REF##35572754##\n183\n##\n<sup>]</sup> To realize real‐world implementation of radiative coolers, researchers must find suitable materials while developing scalable, cost‐effective, and ecologically‐benign fabrication methods for commercialization. This involves optimizing fabrication techniques, reducing material costs, and streamlining production processes. Second, RC is highly sensitive to humidity and regional climate conditions. Humidity in the air significantly lowers the atmospheric transmission and degrades the heat dissipation of the cooler. Radiative coolers that are robust to surrounding atmospheric condition would greatly improve the efficacy of radiative cooling in many applications. In addition, the establishment of specific standards and regulations for RC technology will provide crucial support for its commercialization, ensuring defined performance metrics, safety guidelines, and overall quality and reliability. Last, integration of RC technologies into existing infrastructure poses another challenge. Radiative coolers need to be seamlessly integrated into buildings, cooling networks, and other relevant systems. Compatibility with different applications and effective integration strategies will be crucial to ensure smooth implementation and maximize the benefits of RC technology.</p>", "<p>While challenges and limitations remain, recent work on functional RC suggests emerging research directions and prospective applications. As explained above, the effectiveness of a radiative cooler has almost reached its limit. To boost the effectiveness of a passive cooling system, a hybrid approach that uses both radiative and evaporative cooling can be used.<sup>[</sup>\n##REF##29296678##\n184\n##, ##UREF##131##\n185\n##, ##REF##35148051##\n186\n##, ##UREF##132##\n187\n##\n<sup>]</sup> This approach could overcome the fundamental difficulties arising from humid atmosphere and significantly increase the efficiency of a passive cooling system by exploiting two different heat transfer mechanisms.</p>", "<p>We anticipate that RC will be used in an increasing range of applications and will have considerable technological impact. Besides the functionalities reviewed in Section <xref rid=\"advs6694-sec-0140\" ref-type=\"sec\">4</xref>, development of radiative coolers with improved self‐cleaning and durability suggests promising applications for surfaces that require long‐term use.<sup>[</sup>\n##REF##35960798##\n97\n##, ##UREF##133##\n188\n##, ##UREF##134##\n189\n##, ##REF##35973997##\n190\n##, ##UREF##135##\n191\n##\n<sup>]</sup> Combining RC concepts with various research in sustainable energy and thermal managing field such as photothermal<sup>[</sup>\n##REF##35439052##\n192\n##\n<sup>]</sup> and vapor condensation<sup>[</sup>\n##REF##33790008##\n193\n##\n<sup>]</sup> offers great functional integration of a device. Improving the availability and reliability of RC would be the next crucial step for the engineers and researchers.</p>", "<p>Beyond simply increasing cooling effect, research in RC is now moving toward practical applications and integration with other thermal management systems. We believe that our review will inspire many researchers of nanotechnology, optics, energy, and other disciplines, and will propel this ecologically‐benign technology toward practical applications in energy saving.</p>" ]
[ "<title>Abstract</title>", "<p>Radiative cooling, a technology that lowers the temperature of terrestrial objects by dissipating heat into outer space, presents a promising ecologically‐benign solution for sustainable cooling. Recent years witness substantial progress in radiative cooling technologies, bringing them closer to commercialization. This comprehensive review provides a structured overview of radiative cooling technologies, encompassing essential principles, fabrication techniques, and practical applications, with the goal of guiding researchers toward successful commercialization. The review begins by introducing the fundamentals of radiative cooling and the associated design strategies to achieve it. Then, various fabrication methods utilized for the realization of radiative cooling devices are thoroughly discussed. This discussion includes detailed assessments of scalability, fabrication costs, and performance considerations, encompassing both structural designs and fabrication techniques. Building upon these insights, potential fabrication approaches suitable for practical applications and commercialization are proposed. Further, the recent efforts made toward the practical applications of radiative cooling technology, including its visual appearance, switching capability, and compatibility are examined. By encompassing a broad range of topics, from fundamental principles to fabrication and applications, this review aims to bridge the gap between theoretical research and real‐world implementation, fostering the advancement and widespread adoption of radiative cooling technology.</p>", "<p>Radiative cooling technologies garner significant interest as ecologically‐benign solutions for future energy sustainability. This comprehensive review offers a well‐organized exploration of radiative cooling, encompassing its foundational design principles, fabrication techniques, potential methods for practical implementation, and real‐world applications. Its overarching aim is to guide researchers seeking successful commercialization within this field.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6694-cit-0194\">\n<string-name>\n<given-names>S.</given-names>\n<surname>So</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Yun</surname>\n</string-name>, <string-name>\n<given-names>B.</given-names>\n<surname>Ko</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Kim</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Noh</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Park</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Park</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Rho</surname>\n</string-name>, <article-title>Radiative Cooling for Energy Sustainability: From Fundamentals to Fabrication Methods Toward Commercialization</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305067</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305067</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Materials and Structure Designs</title>", "<p>RC occurs by energy exchange among the earth, the sun, and the universe. The terrestrial objects’ temperature is det)ermined by the balance among energy absorbed from the Sun (<italic toggle=\"yes\">P</italic>\n<sub>sun</sub>), atmospheric radiation (<italic toggle=\"yes\">P</italic>\n<sub>atm</sub>), the thermal emission of the surface (<italic toggle=\"yes\">P</italic>\n<sub>rad</sub>), and the other heat losses (<italic toggle=\"yes\">P</italic>\n<sub>non − rad</sub>). By taking into account all energy exchange, the net cooling power <mml:math id=\"jats-math-1\" display=\"inline\"><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mrow><mml:mi>net</mml:mi><mml:mo>_</mml:mo><mml:mi>cooling</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math> is given by:<sup>[</sup>\n##REF##25428501##\n17\n##\n<sup>]</sup>\n\n</p>", "<p>Each energy term and ideal radiative coolers are discussed in detail in Note ##SUPPL##0##S1##, Supporting Information.</p>", "<p>RC has been realized and developed by evaluations of various photonic structures and materials. Ideal radiative coolers should not absorb the solar spectrum and should perfectly emit thermal radiation in the AW. To meet these requirements, a wide variety of organic and inorganic materials that exhibit phonon‐polariton resonances in the AW have been used. Natural bulk materials that satisfy these properties were studied in the 1970s and 1980s.<sup>[</sup>\n##UREF##4##\n5\n##, ##UREF##6##\n7\n##, ##UREF##13##\n15\n##, ##UREF##14##\n16\n##, ##UREF##31##\n35\n##, ##UREF##32##\n36\n##\n<sup>]</sup> Most of them are broadband emitters, and their absorption behavior is determined by their bulk material properties. The optical properties of materials commonly used for RC are summarized in <bold>Table</bold> ##TAB##0##\n1\n##.</p>", "<p>To achieve deep sub‐ambient cooling effect under direct sunlight, the radiative cooler must strongly reflect solar radiation and strongly emit in the AW. These requirements cannot be achieved using only bulk materials as their emission spectrum is fixed. Therefore, to delicately control the electromagnetic properties and thereby increase the RC effect, novel structures must be designed, and their underlying physical phenomena must be exploited.</p>", "<p>Recent advances in nanophotonics have provided methods to manipulate electromagnetic properties by using tailored nano‐ and micro‐scale structures. Radiative coolers reported to date can be categorized into four structures: multilayer structures, metamaterials, random particles, and porous structures. Multilayer structures refer to photonic designs in which several materials are stacked in layers (<bold>Figure</bold> ##FIG##0##\n1a##). The sequence of materials and layer thicknesses of these structures are engineered to control the spectral responses of radiative coolers. Metamaterials are artificially‐engineered materials composed of subwavelength structures (Figure ##FIG##0##1b##), which enable delicate manipulation of light–matter interactions, such as triggering electromagnetic resonance and generating an effective gradient refractive index. In contrast to these two structures with precisely defined geometries, random particles (Figure ##FIG##0##1c##) and porous structures (Figure ##FIG##0##1d##) are structural designs with random configurations, which exploit a strong optical‐scattering effect. Depending on the target application and environment, different structure and material design strategies are required. In this section, we introduce these four structures, with focus on their physical mechanisms that are exploited to manipulate electromagnetic properties.</p>", "<title>Multilayers</title>", "<p>A multilayer structure is composed of several materials vertically stacked in layers and can be designed to suppress solar absorption and maximize infrared (IR) emission (Figure ##FIG##0##1e##). This structure can be understood as a 1D photonic crystal in which two materials that have different refractive indices and thicknesses are periodically stacked. The behavior of wave propagation in the media can be described by the dispersion relation; waves in an isotropic, homogeneous, and dispersionless medium exhibit a linear relation between its frequency and momentum; and thus, show straight curves in the photonic band structure; this result implies that any frequency of light can propagate (Figure ##FIG##0##1f##, left). On the contrary, in periodic structures, Bragg scattering occurs and a photonic bandgap is formed; that is, when the wavelength of the incident light is comparable to the lattice constant, multiple reflections at each interface create a destructive interference. Consequently, such periodic structures only allow certain frequencies of light to pass through them without scattering while forbidding the propagation of light that has other frequencies. In the photonic band structure, the allowed modes correspond to a set of frequencies on the band (curves), and the forbidden modes correspond to frequencies within the photonic bandgap (Figure ##FIG##0##1f##, right).</p>", "<p>The strategy of using multilayers for RC is to exploit the combination of multiple material properties and utilize the photonic bandgap effect to manipulate electromagnetic properties. Photonic crystals can be used to design a strong reflector or a highly‐selective band‐pass filter for the target wavelength range by stacking a material that has high refractive index alternately with a material that has low refractive index. An aperiodic or quasi‐periodic structure can also be used by optimizing material sequence and layer thicknesses to maximize interference effect and increase broadband reflection in solar spectrum. With well‐chosen material combinations and optimized thicknesses, the bandgap of the structures can be engineered to have the target reflection/emission spectrum that enables high solar reflectivity and strong thermal radiation. Typically, multilayer radiative coolers are composed of many alternating layers and a metal film at the bottom. The alternating layers are responsible for increasing both reflectance in the solar spectrum and thermal emittance in the AW. The metal film provides high reflection from ultraviolet (UV) to near‐infrared (NIR) because of its high conductivity, which cancels out the incident field. Early breakthrough demonstrations of sub‐ambient RC using multilayer structures<sup>[</sup>\n##REF##25428501##\n17\n##, ##REF##23461597##\n18\n##\n<sup>]</sup> have impelled many research communities to widen the range of material candidates and tailor the effectiveness of the devices by tailoring their configurations.<sup>[</sup>\n##REF##27959339##\n39\n##, ##UREF##34##\n40\n##, ##REF##31990166##\n41\n##, ##UREF##35##\n42\n##, ##UREF##36##\n43\n##, ##UREF##37##\n44\n##, ##REF##30063836##\n45\n##, ##REF##29317637##\n46\n##, ##REF##30184837##\n47\n##, ##REF##33974398##\n48\n##\n<sup>]</sup> Owing to the simplicity of multilayer structures, a variety of optimization algorithms can be used to further increase the cooling effect.<sup>[</sup>\n##UREF##16##\n20\n##, ##REF##31990166##\n41\n##, ##UREF##38##\n49\n##\n<sup>]</sup>\n</p>", "<title>Metamaterials</title>", "<p>Metamaterials are artificially‐engineered materials composed of subwavelength structures. Their subwavelength features allow for delicate manipulation of electromagnetic responses, and thereby, extend the boundaries of material properties far beyond those available in nature.<sup>[</sup>\n##UREF##39##\n50\n##\n<sup>]</sup> Advances in nanofabrication technology have enabled development of photonic designs that use metamaterials to increase absorption within the AW by controlling the light–matter interaction.<sup>[</sup>\n##UREF##40##\n51\n##, ##UREF##41##\n52\n##, ##REF##32917610##\n53\n##, ##REF##26089358##\n54\n##, ##UREF##42##\n55\n##, ##UREF##43##\n56\n##, ##REF##32541048##\n57\n##, ##UREF##44##\n58\n##\n<sup>]</sup>\n</p>", "<p>Thermal emission in the AW can be increased by using metamaterials to induce electromagnetic resonance. The subwavelength structure geometries and the constituent materials can be designed to exhibit large resonance at target frequencies.<sup>[</sup>\n##UREF##39##\n50\n##, ##REF##18518577##\n59\n##, ##UREF##45##\n60\n##\n<sup>]</sup> Numerous studies have tailored resonant optical cavity modes of metallic and dielectric structures. Metallic resonators support plasmonic resonances induced by surface plasmons, which are coherent and collective electron oscillations confined at dielectric–metal surfaces. The strong photon–electron interactions and extreme light confinement can be increased when combined with cavity modes such as Fabry–Pérot resonance in metal–insulator–metal structures (Figure ##FIG##0##1g,h##). In contrast, dielectric resonators support multipolar resonant responses called Mie resonances when their characteristic size is comparable to incident light wavelength (Figure ##FIG##0##1i##). The optical resonances in lossy materials can increase absorption at the corresponding frequency. Therefore, such resonance‐based approaches have been exploited in radiative coolers in various plasmonic<sup>[</sup>\n##UREF##40##\n51\n##, ##REF##32917610##\n53\n##, ##UREF##44##\n58\n##\n<sup>]</sup> and dielectric<sup>[</sup>\n##UREF##41##\n52\n##, ##UREF##46##\n61\n##\n<sup>]</sup> systems. In particular, efficient RC requires effective thermal emission through the AW; so, the broadband absorption must cover the entire range of 8 ≤ <italic toggle=\"yes\">λ</italic> ≤ 13 µm. To this end, the structure geometries can be optimized to exhibit multiple resonance,<sup>[</sup>\n##UREF##41##\n52\n##, ##REF##32917610##\n53\n##\n<sup>]</sup> waveguide modes,<sup>[</sup>\n##UREF##40##\n51\n##, ##UREF##44##\n58\n##\n<sup>]</sup> or exploit high loss materials.<sup>[</sup>\n##UREF##46##\n61\n##\n<sup>]</sup>\n</p>", "<p>Emission in the AW can also be increased by using micro‐patterned surfaces to generate a gradient refractive index (Figure ##FIG##0##1j##). Bio‐inspired pyramid structures,<sup>[</sup>\n##REF##26089358##\n54\n##, ##REF##32541048##\n57\n##\n<sup>]</sup> photonic crystals,<sup>[</sup>\n##REF##26392542##\n62\n##\n<sup>]</sup> or grating patterns<sup>[</sup>\n##UREF##47##\n63\n##, ##UREF##48##\n64\n##\n<sup>]</sup> have been introduced to create an effective index gradient and improve the impedance‐matching condition. The patterned structures can reduce the interface reflection in the mid‐infrared (MIR); and thus, increase the absorption in the AW.</p>", "<p>Radiative coolers that use multilayer structures or metamaterials can be tailored to have strong solar reflection and highly selective emission in the IR range. However, they require intricate fabrication steps such as high‐precision lithography or deposition techniques, which limit large‐scale applications of these devices. For practical use of radiative coolers, simpler methods than these are required.</p>", "<title>Random Particles</title>", "<p>When light traveling in air encounters a particle or a certain object, it interacts with the atoms or molecules of that object. Consequently, the light gets deflected or scattered in different directions. This phenomenon called optical scattering is influenced by various factors such as differences in refractive index, irregular surface, or the size of the particle. By randomly distributing nano/micro‐particles with certain degree of thickness, strong scattering effect is induced which can collectively yield high reflection. In RC technology, particles with high refractive index in the solar spectrum are particularly desirable because optical scattering is driven by the sudden impedance mismatch between the structure and the air (Figure ##FIG##0##1k##, left). By selecting suitable materials and dispersing them in a random configuration to increase both solar reflection and IR emission, effective RC can be realized. Many approaches aimed to maximize the scattering efficiencies of particles by exploiting the influences of size and material parameters (Figure ##FIG##0##1l##).</p>", "<p>Radiative coolers using random particles have been in the limelight for being compatible with scalable, low‐cost, and reliable production. Various inorganic materials have been evaluated for these particles, mostly in paint‐format, that have high particle concentrations.<sup>[</sup>\n##UREF##6##\n7\n##, ##UREF##49##\n65\n##, ##UREF##50##\n66\n##, ##UREF##51##\n67\n##, ##UREF##52##\n68\n##, ##UREF##53##\n69\n##, ##UREF##54##\n70\n##, ##UREF##55##\n71\n##, ##UREF##56##\n72\n##, ##UREF##57##\n73\n##, ##REF##33856776##\n74\n##\n<sup>]</sup> Typically, these structures require binding materials to physically bind the particles together and for good mechanical properties. TiO<sub>2</sub> has a favorable scattering efficiency because it has a high refractive index even compared to typical polymer binders; and therefore, was used in early approaches.<sup>[</sup>\n##UREF##6##\n7\n##, ##UREF##49##\n65\n##, ##UREF##51##\n67\n##, ##UREF##52##\n68\n##\n<sup>]</sup> However, due to its low energy bandgap of 3.0 eV at <italic toggle=\"yes\">λ</italic> &lt; 0.4 µm, it absorbs UV and violet light which together account for 7% of the solar energy;<sup>[</sup>\n##UREF##50##\n66\n##\n<sup>]</sup> and therefore, has limited cooling effect. To mitigate this problem, other UV non‐absorbing materials such as SiO<sub>2</sub>,<sup>[</sup>\n##UREF##54##\n70\n##, ##UREF##55##\n71\n##, ##UREF##56##\n72\n##, ##UREF##58##\n75\n##\n<sup>]</sup> CaCO<sub>3</sub>,<sup>[</sup>\n##UREF##57##\n73\n##\n<sup>]</sup> BaSO<sub>4</sub>,<sup>[</sup>\n##UREF##50##\n66\n##, ##REF##33856776##\n74\n##\n<sup>]</sup> and Al<sub>2</sub>O<sub>3</sub>\n<sup>[</sup>\n##UREF##56##\n72\n##, ##UREF##59##\n76\n##\n<sup>]</sup> have been exploited.</p>", "<p>Paint‐format radiative coolers possessing strong sunlight scattering ability can be used in metal‐free substrates enabling broad range of applications. Hence, strategies to increase the solar reflection of paint‐format coolers have been a major research area. Numerical investigations have sought to optimize the size parameters and size distribution of particles to maximize solar reflection.<sup>[</sup>\n##UREF##52##\n68\n##, ##UREF##60##\n77\n##, ##UREF##61##\n78\n##\n<sup>]</sup> To analyze different particle coating designs with large thickness, various simulation tools such as Monte Carlo simulation,<sup>[</sup>\n##UREF##62##\n79\n##, ##REF##20555520##\n80\n##, ##UREF##63##\n81\n##\n<sup>]</sup> Lattice Boltzman model,<sup>[</sup>\n##UREF##64##\n82\n##, ##UREF##65##\n83\n##\n<sup>]</sup> finite element method,<sup>[</sup>\n##UREF##60##\n77\n##\n<sup>]</sup> and finite‐difference‐time‐domain<sup>[</sup>\n##UREF##66##\n84\n##\n<sup>]</sup> have been used. Other approaches include using multiple materials such as mixing different particles<sup>[</sup>\n##REF##31990166##\n41\n##, ##UREF##56##\n72\n##\n<sup>]</sup> or utilizing core–shell structures<sup>[</sup>\n##UREF##63##\n81\n##, ##UREF##67##\n85\n##\n<sup>]</sup> for complete back‐scattering.</p>", "<title>Porous Structures</title>", "<p>Porous structures, in principle, use the same strategy as random particles of enhancing optical scattering because the pores can be regarded as the inverse of particles. Randomly distributed air voids generate impedance mismatch between the host medium and pores and can effectively scatter the incoming sunlight (Figure ##FIG##0##1k##, middle). Porous structures have primarily been implemented in polymers and polymer composites because the fabrication methods are simple, inexpensive, and scalable.<sup>[</sup>\n##REF##31886998##\n86\n##, ##REF##33226211##\n87\n##, ##UREF##68##\n88\n##, ##REF##33397941##\n89\n##, ##UREF##69##\n90\n##, ##UREF##70##\n91\n##, ##UREF##71##\n92\n##, ##REF##33345542##\n93\n##\n<sup>]</sup> Owing to their molecular vibration modes, polymers generally feature low absorption in the solar spectrum and high absorption in the IR.<sup>[</sup>\n##UREF##72##\n94\n##\n<sup>]</sup> Optimizing the pore size to maximize optical scattering has been a major research goal<sup>[</sup>\n##REF##30262632##\n38\n##, ##REF##33524258##\n95\n##\n<sup>]</sup> as for radiative coolers that use random particles. The scattering‐efficiency spectra of pores depends on their size. Therefore, pores must be fabricated to have hierarchical sizes, from ≈10 nm to ≈10 µm; so that, differently‐sized pores can scatter different wavelength bands to achieve broadband solar reflection from UV to NIR. To produce such polymer structure with broad pore size distribution, a variety of fabrication methods has been proposed and developed such as phase inversion methods using different volatilization rates of solvents, which will be presented in detail in Section <xref rid=\"advs6694-sec-0070\" ref-type=\"sec\">3</xref>.</p>", "<p>Many reports used networks of porous nanofibers as radiative coolers<sup>[</sup>\n##UREF##73##\n96\n##, ##REF##35960798##\n97\n##, ##REF##35075910##\n98\n##, ##REF##34014070##\n99\n##, ##REF##33199884##\n100\n##, ##REF##34353954##\n101\n##, ##REF##34750560##\n102\n##\n<sup>]</sup> (Figure ##FIG##0##1k##, right). The fibers were typically produced using electrospinning, which processed materials such as polymers and silk and could achieve high‐throughput fabrication. These structures have enormous potential in applications such as cooling textiles.</p>", "<p>With the advances in fabrication technology and material investigations, the diversity of prospective applications of RC technology is continuously expanding. The optimal configuration of a radiative cooling system, including the substrate materials, indoor or outdoor environment, and system enclosures, may significantly vary depending on the specific target application. Depending on these conditions, appropriate design and materials of radiative cooler should be carefully chosen.</p>", "<title>Potential Functionalities and Applications of RC</title>", "<p>Despite its short history, the rapid advance of RC technology has promoted its implementation into real‐world applications and even commercialization. However, for practical applications, other aspects of radiative coolers besides the cooling effect and fabrication methods should also be considered. Such aspects include material qualities, visual appearance, switching capability, durability, and compatibility with other fields such as photovoltaic,<sup>[</sup>\n##REF##26392542##\n62\n##, ##UREF##112##\n154\n##\n<sup>]</sup> thermoelectricity,<sup>[</sup>\n##REF##32904365##\n155\n##, ##UREF##113##\n156\n##\n<sup>]</sup> and water harvesting.<sup>[</sup>\n##UREF##114##\n157\n##, ##REF##35622905##\n158\n##\n<sup>]</sup> In this section, recent efforts to address such practical issues are reviewed. First, radiative coolers that can be simply coated on the exterior walls in large‐scale and cooling textiles are summarized. Second, radiative coolers with aesthetic functions are discussed. The realizations of colored or transparent radiative coolers by controlling the spectra in the solar range are covered. Finally, temperature‐adaptive radiative coolers that provide the cooling effect only at high temperatures are reviewed.</p>", "<title>Facile Techniques for Large‐Scale Exterior Coating and Textiles</title>", "<p>To facilitate the implementation of the radiative coolers into practical applications, scalable manufacturing of the coolers, that is, particle–polymer composites coatings<sup>[</sup>\n##REF##28183998##\n135\n##, ##UREF##115##\n159\n##\n<sup>]</sup> and porous polymers,<sup>[</sup>\n##REF##30262632##\n38\n##, ##REF##35402873##\n160\n##, ##UREF##116##\n161\n##\n<sup>]</sup> has been developed. These scalable methods have enabled the application of radiative coolers to large‐scale exterior walls. The radiative coolers in early studies have been designed to exhibit high reflectivity in all solar spectrum and high emissivity in the MIR regime to maximize the outdoor cooling effect (<bold>Figure</bold> ##FIG##5##\n6a##). RC materials satisfying this concept have not only verified their potential to be used for exterior walls but can also be produced in various forms of coatings, paints, and blocks. Polymer mixed micrometer‐sized SiO<sub>2</sub> spheres‐based high‐throughput and cost‐effective roll‐to‐roll method using polymethylpentene (TPX) demonstrated its superior flexibility and scalable fabrication ability that can cover the outdoor structure exterior.<sup>[</sup>\n##REF##28183998##\n135\n##\n<sup>]</sup> A paint‐like facile fabrication of hierarchically porous poly(vinylidene fluoride‐co‐ hexafluoropropylene) coatings improves the convenience of making surface coating due to the ease of spraying onto a wide range of surfaces.<sup>[</sup>\n##REF##30262632##\n38\n##\n<sup>]</sup> A RC wood block with excellent mechanical strength was also introduced by cellulose nanofibers (Figure ##FIG##5##6b##).<sup>[</sup>\n##REF##31123132##\n147\n##\n<sup>]</sup> The ease of manufacturing RC coatings, paints, and block‐type building materials has proven the potential for use in outdoor structures such as real buildings, as verified in the cooling performance evaluation of the actual warehouse size.<sup>[</sup>\n##UREF##117##\n162\n##\n<sup>]</sup>\n</p>", "<p>Another main use of RC is a cooling textile,<sup>[</sup>\n##UREF##18##\n22\n##, ##REF##27701110##\n163\n##, ##UREF##118##\n164\n##, ##REF##33184204##\n165\n##\n<sup>]</sup> which can be used for various purposes such as wearable devices and clothes. In the case of textiles, the common RC concept illustrated in Figure ##FIG##5##6a## is required because the surface temperature under direct sunlight is generally higher than the body temperature. Recently, a radiative cooler made by the nano‐processed silk was proposed by using a molecular bonding design strategy and scalable dip‐coating method. The stand‐alone nano‐processed silk demonstrated 3.5 °C sub‐ambient cooling under direct sunlight and the temperature reduction ≈8 °C compared to the natural silk, verifying its cooling potential.<sup>[</sup>\n##REF##34750560##\n102\n##\n<sup>]</sup> Another large‐scale woven fabric by hierarchical‐morphology design was reported.<sup>[</sup>\n##REF##34353954##\n101\n##\n<sup>]</sup> Randomly dispersed scatters throughout the fabric achieved high reflectivity of 92.4% with high emissivity of 94.5%. The test on a human body covered by woven fabric demonstrated that it could cool down ≈4.8 °C compared to common cotton fabric.</p>", "<title>Coloration and Transparency</title>", "<p>While the concept of RC is typically to control the radiative thermal load of outdoor structures on buildings, automobiles, and clothing, the visual aesthetic is also a significant aspect that cannot be ignored. As the aforementioned approaches perfectly reflect light in the visible range, controlling the thermal load in the colored structure is not achievable. The presence of a reflectance resonance in the visible region, which is inside the solar spectrum, allows a radiative cooler to exhibit color (Figure ##FIG##5##6c##). Including early studies showing the reflection of different peaks using metal oxides in the paint mixture,<sup>[</sup>\n##UREF##119##\n166\n##\n<sup>]</sup> studies for esthetic properties of materials for daytime RC using optimized nanostructures, materials, and photoluminescence; have been reported.<sup>[</sup>\n##UREF##120##\n167\n##, ##REF##35508472##\n168\n##, ##REF##35686917##\n169\n##, ##UREF##121##\n170\n##, ##UREF##122##\n171\n##\n<sup>]</sup> Various research has reported the realization of color by controlling resonance in the visible region using various nanostructures such as multilayers and particles.<sup>[</sup>\n##REF##29317637##\n46\n##, ##UREF##120##\n167\n##, ##REF##35508472##\n168\n##, ##REF##32426464##\n172\n##, ##UREF##123##\n173\n##\n<sup>]</sup> These nanostructures can lead to resonance by adjusting the spacer thickness or scattering properties from the distributed particles.</p>", "<p>However, a tradeoff between color and cooling effect has arisen due to the cooling power loss from the resonance in the visible region.<sup>[</sup>\n##UREF##16##\n20\n##, ##UREF##120##\n167\n##\n<sup>]</sup> Structural optimization for balance between the esthetic function and cooling capacity is inevitably a significant design criterion. Fortunately, the reflection spectrum and the representative color do not obey one‐to‐one correspondence. In other words, it is possible to design two radiative coolers that exhibit the same color but have different cooling effects. Therefore, the sophisticated design of the radiative cooler can bring out the realization of daytime RC while exhibiting an aesthetic effect. The example of a radiative cooler showing the same pink color broke the balance of color and cooling performance and provided a clue to find the optimal design (Figure ##FIG##5##6d##).<sup>[</sup>\n##REF##29317637##\n46\n##\n<sup>]</sup> Experimental results showed that two photonic multilayer structures having similar color could have different net cooling flux. The tunable range was from 680 W m<sup>−2</sup> for all color to 866 W m<sup>−2</sup>, which can be 47.6 °C temperature difference under direct sunlight. This study demonstrated the significant potential of the colored radiative cooler.</p>", "<p>The control of thermal load via spectral manipulation in a specific wavelength region also suggests the possibilities of transparent RC. Transparency also has a great impact on practical applications of RC such as vehicles and buildings. Based on this concept, various efforts to serve two ends between transparency and RC have been reported.<sup>[</sup>\n##UREF##16##\n20\n##, ##UREF##103##\n140\n##, ##UREF##124##\n174\n##\n<sup>]</sup> The first visibly transparent radiative cooler was designed to have high transmissivity only in the visible spectrum while being reflective in the non‐visible solar range (UV and NIR region) and emits its thermal energy in the MIR region (Figure ##FIG##5##6e‐i##). A transparent radiative cooler based on multilayer structure of selective reflector and PDMS emitter layer was investigated.<sup>[</sup>\n##UREF##16##\n20\n##\n<sup>]</sup> The selective reflector partially transmits visible light and reflects undesirable NIR region (from 0.74 to 1.4 µm). The top PDMS layer radiates thermal energy through the AW. Consequently, the maximum temperature reduction of 14.4 °C was achieved during the daytime. In addition to the effort to control the transmittance of only the visible region, a similar concept of transparent RC including the NIR region was reported (Figure ##FIG##5##6e‐ii##).<sup>[</sup>\n##UREF##124##\n174\n##, ##UREF##125##\n175\n##\n<sup>]</sup>\n</p>", "<p>Solar cells are another good application for the transparency of RC.<sup>[</sup>\n##UREF##17##\n21\n##, ##UREF##126##\n176\n##, ##UREF##127##\n177\n##\n<sup>]</sup> Solar cells operated under direct sunlight warm up naturally, which can affect reliability and efficiency.<sup>[</sup>\n##UREF##128##\n178\n##\n<sup>]</sup> Therefore, optimized RC having maximized thermal emission and transparency to sunlight is required. It is ideal to exhibit high emissivity in the MIR region over 4 µm or more while maintaining high transmittance in the solar spectrum.<sup>[</sup>\n##UREF##17##\n21\n##\n<sup>]</sup> Recently, visibly clear and flexible RC materials have been developed (Figure ##FIG##5##6f##) using randomly distributed silica aerogel microparticles in a silicone elastomer.<sup>[</sup>\n##UREF##127##\n177\n##\n<sup>]</sup> The deployment in solar cells demonstrates effective suppression of the temperature increase under solar irradiation, thereby mitigating the performance degradation of solar cells due to the heating issues by satisfying the photonic concept of high transmittance in the overall solar spectral region.</p>", "<title>Temperature Adaptive Regulation</title>", "<p>Various research on RC has been developed based on passive photonic structures. However, it is difficult to judge that passive RC will always work if it has different environments and temperatures according to seasons or regions. At ambient temperature that does not require cooling, an active switchable RC concept, in which the cooling can be turned on and off, is important. The key concept of these active switchable radiative coolers is to control the emissivity of the MIR region. When the emissivity of MIR is high, the cooler is an on‐state because it can emit a lot of heat (Figure ##FIG##5##6 g##); whereas in the opposite case, it is an off‐state due to the limited thermal emission (Figure ##FIG##5##6i##). Since the theoretical proposal of the multilayer structure using a phase change material,<sup>[</sup>\n##REF##30184837##\n47\n##\n<sup>]</sup> various efforts toward such switchable RC systems have been followed.<sup>[</sup>\n##UREF##129##\n179\n##, ##UREF##130##\n180\n##\n<sup>]</sup> These results here lead to new functionalities of RC and can potentially be used in a wide range of applications for the thermal managements of buildings, vehicles, and textiles,<sup>[</sup>\n##REF##30184837##\n47\n##\n<sup>]</sup> with advances in technology for practical use that can meet the photonics standpoint.</p>", "<p>For the development of switchable radiative coolers, it is essential to find temperature‐responsive materials with a transition temperature near room temperature. While doped VO<sub>2</sub> exhibits a transition temperature around room temperature, the desirable transition temperature in the indoor environment is still lower than this.<sup>[</sup>\n##REF##30184837##\n47\n##, ##UREF##98##\n133\n##\n<sup>]</sup> A temperature‐adaptive switchable radiative coating using W<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>V<sub>1−</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>O<sub>2</sub> was developed, and the possibility of achieving the desired transition temperature (≈22 °C) was demonstrated.<sup>[</sup>\n##REF##34914515##\n181\n##\n<sup>]</sup> This active RC material shows switchable thermal emissivity by photonically amplified metal–insulator transition from 0.20 to 0.90 for the ambient temperature changes lower than 15 °C and above 30 °C (Figure ##FIG##5##6 h##). Another problem to be tackled for practical use is that the materials for switchable RC are difficult to fabricate, especially in large scale. Recently, a thermochromic coating based on tungsten‐doped VO<sub>2</sub>‐PMMA/spacer/low‐E stack using a solution process was reported to satisfy the demands of switchable RC function in different temperature.<sup>[</sup>\n##REF##34914526##\n182\n##\n<sup>]</sup> The modulation ability of MIR emissivity of this coating can be adjusted by tuning the spacer thickness and VO<sub>2</sub> weight ratio and doping. Simple solution process by coating giving different emissivity of 0.61 (at high temperature) and 0.21 (at low temperature) regulates RC automatically; while, maintaining visible region transparency and near‐infrared modulation (Figure ##FIG##5##6j##). These temperatures‐adaptive regulations of RC can be utilized in various applications throughout various climatic conditions.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>S.S., J.Y., B.K. and D.L. contributed equally to this work. This work was financially supported by the POSCO‐POSTECH‐RIST Convergence Research Center program funded by POSCO, and the National Research Foundation (NRF) grants (NRF‐2022M3H4A1A02046445, NRF‐2022M3C1A3081312, NRF‐2022M3H4A1A02074314, NRF‐2019R1A2C3003129, NRF‐2019R1A5A8080290, and NRF‐2018M3D1A1058997) funded by the Ministry of Science and ICT (MSIT) of the Korean government. S.S. and M.K. acknowledge the NRF <italic toggle=\"yes\">Sejong</italic> Science fellowships (NRF‐2022R1C1C2009430 and NRF‐2022R1C1C2004662), respectively, funded by the MSIT of the Korean government. S.S. acknowledges the Korea University grant (No. K2317231), the Regional Innovation Strategy (RIS) grant (2021RIS‐004) funded by the Ministry of Education (MOE) of the Korean government, and the Institute of Information &amp; Communications Technology Planning &amp; Evaluation (IITP) grant (No. 2019‐0‐01906, the POSTECH Artificial Intelligence Graduate School program) funded by the MSIT of the Korean government. B.K. acknowledges the NRF Ph.D. fellowship (NRF‐2022R1A6A3A13066244) funded by the MOE of the Korean government. D.L. acknowledges the NRF grant (NRF‐2022R1F1A1065453) funded by the MSIT of the Korean government, and RIS grant (2022RIS‐005) funded by the MOE of the Korean government.</p>", "<p>\n<bold>Sunae So</bold> is an assistant professor at the Department of Electro‐Mechanical Systems Engineering in the Korea University‐Sejong Campus. She received her B.S. in 2016 and Ph.D. in 2022, both in Mechanical Engineering, from the Pohang University of Science and Technology (POSTECH), Korea. From 2022 to 2023, she was as a postdoctoral researcher in the Graduate School of Artificial Intelligence at POSTECH. Her research interests include nanophotonics, optical metamaterials and metasurfaces, and inverse design.</p>", "<p>\n<bold>Jooyeong Yun</bold> received her B.S. (2021) in Mechanical Engiennering at POSTECH. She is currently a graduate student in Mechanical Engineering at POSTECH. Her research interests include nanophotonics, deep learning and computational imaging.</p>", "<p>\n<bold>Byoungsu Ko</bold> received his B.S. (2019) in Mechanical Engineering at the Myongji University, Korea. He is currently a M.S. and Ph.D. integrated candidate under the guidance of Prof. Junsuk Rho at POSTECH. His research interests focus on radiative cooling and tunable metasurfaces.</p>", "<p>\n<bold>Dasol Lee</bold> is currently an assistant professor in Biomedical Engineering at the Yonsei University (Mirae campus). He received his B.S. in Biomedical Engineering from the Yonsei University (Mirae campus), Korea, in 2013; M.S. in Medical System Engineering from the Gwangju Institute of Science and Technology (GIST), Korea, in 2015; and Ph.D. in Mechanical Engineering from POSTECH, in 2021.</p>", "<p>\n<bold>Junsuk Rho</bold> is a <italic toggle=\"yes\">Mu‐Eun‐Jae</italic> endowed chair professor and young distinguished professor in Mechanical Engineering and Chemical Engineering at POSTECH. He received his B.S. (2007) and M.S. (2008) in Mechanical Engineering from the Seoul National University and the University of Illinois, Urbana‐Champaign, respectively. After getting his Ph.D. (2013) in Mechanical Engineering and Nanoscale Science and Engineering from the University of California Berkeley, he worked as a postdoctoral fellow in the Materials Sciences Division at Lawrence Berkeley National Laboratory and was an Ugo Fano Fellow in the Nanoscience and Technology Division at Argonne National Laboratory.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6694-fig-0001\"><label>Figure 1</label><caption><p>Structural designs for RC and their physical mechanisms. a) Multilayers, b) metamaterials, c) random particles, d) porous structures, e) 1D photonic crystals creating allowed and forbidden modes of light propagation, and f) photonic band diagram of bulk material (left) and 1D photonic crystal (right). Frequencies within the photonic bandgap are forbidden modes and cannot propagate into the structure. g) Resonant absorption generated by cavity modes in metamaterials, h) magnetic field intensity profile of Fabry–Pérot resonance in a metal–insulator–metal structure, i) electric dipole and magnetic dipole resonance in dielectric cylinders, j) effective gradient refractive index produced by the patterned surface, k) light scattering caused by random surface and scatterer geometries, and l) scattering efficiency of silicon dioxide microparticles. Scattering efficiency spectrum differs among particle sizes.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6694-fig-0002\"><label>Figure 2</label><caption><p>Overview of the development of RC. a) Structural designs for RC and their fabrication methods, b) timeline of the development of RC technology, categorized by structural designs. Gray: natural materials, yellow: 1D multilayer structure, green: 2D metamaterials, blue: 3D particle and porous structures.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6694-fig-0003\"><label>Figure 3</label><caption><p>Fabrication methods for 1D daytime radiative coolers. a) A thin film deposition is started by ripping target base material off with physical force. b) A thin film is grown on the substrate by reacting between vapor‐phase precursors and reactive gas. Panel (a): Adapted with permission.<sup>[</sup>\n##REF##25428501##\n17\n##\n<sup>]</sup> Nature Springer. Panel (b): Adapted with permission.<sup>[</sup>\n##REF##31990166##\n41\n##\n<sup>]</sup> ACS Publications.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6694-fig-0004\"><label>Figure 4</label><caption><p>Fabrication methods for 1D and 2D daytime radiative coolers. Top–down lithography engraves bulk materials into microstructures and nanostructures. Representative categories top–down lithography use a) UV and b) electron beams. Bottom–up lithography stacks base materials or particles on the substrate by filling or assembling. Representative mechanisms of bottom–up lithography are c) imprint and d) self‐assembled colloidal. Panel (a): Adapted with permission.<sup>[</sup>\n##REF##26392542##\n62\n##\n<sup>]</sup> National Academy of Sciences. Panel (b): Adapted with permission.<sup>[</sup>\n##UREF##40##\n51\n##\n<sup>]</sup> Wiley. Panel (c): Adapted with permission.<sup>[</sup>\n##UREF##93##\n126\n##\n<sup>]</sup> Wiley. Panel (d): Adapted with permission.<sup>[</sup>\n##UREF##95##\n130\n##\n<sup>]</sup>Wiley.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6694-fig-0005\"><label>Figure 5</label><caption><p>Fabrication methods for preparing 3D structures for daytime RC. a) In pressing, a uniform film is molded out by continuous press equipment. b) In coating, a thin film is formed by centrifugal force induced by chuck rotation. c) In casting, a liquid or slurry is poured into a mold to form a shape. Casting methods can be classified as natural spread or machine‐driven. d) In spraying, a jet is used to spread slurry onto a free‐curved surface at high speed. e) In phase inversion, porosity is achieved by randomly‐distributed voids that form as a result of a difference in solvent volatilization rates. f) In electrospinning, an electrically‐charged polymer solution spun through a jet forms a fiber network on a collector. g) In anodizing, a reaction to anodic voltages grows an oxide film on the metal in an electrolyte solution. Mainly, in RC research, anodizing is applied to fabricate porous anodized aluminum oxide (AAO) templates. Panel (a): Adapted with permission.<sup>[</sup>\n##REF##28183998##\n135\n##\n<sup>]</sup> AAAS. Panel (b): Adapted with permission.<sup>[</sup>\n##UREF##59##\n76\n##\n<sup>]</sup> Elsevier. Panel (c): Adapted with permission.<sup>[</sup>\n##UREF##103##\n140\n##\n<sup>]</sup> Elsevier. Panel (d): Adapted with permission.<sup>[</sup>\n##REF##33226211##\n87\n##\n<sup>]</sup> ACS Publications. Panel (e): Adapted with permission.<sup>[</sup>\n##REF##30262632##\n38\n##\n<sup>]</sup> AAAS. Panel (f): Adapted with permission.<sup>[</sup>\n##REF##34750560##\n102\n##\n<sup>]</sup> Nature Portfolio. Panel (g): Adapted with permission.<sup>[</sup>\n##UREF##109##\n146\n##\n<sup>]</sup> Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6694-fig-0006\"><label>Figure 6</label><caption><p>Photonic concepts and applications of RC. a) RC concept having high reflectivity in solar spectral regime and high emissivity in MIR regime. b) RC wood by engineered cellulose nanofibers. c) RC concept having resonance in visible regime for color generation and high reflectivity and emissivity in the other regime. d) Reflectivity spectra of two different RC films in visible regime. Even the two multilayer structures show similar color; the difference of thermal emissivity leads to significant gap of cooling effect. e) RC concept having high transmissivity: e‐i) only in visible regime or e‐ii) in solar spectral region and high emissivity in MIR regime. f) Transparent RC film by SiO<sub>2</sub> aerogel nanoparticles randomly distributed in PDMS. The RC film shows high transparency in solar spectrum regime with high emissivity in MIR regime. g) RC concept having high emissivity in MIR region. h‐i) Schematic and h‐ii,iii) working mechanism of the temperature adaptive radiative cooler. Patterned array of V<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>V<italic toggle=\"yes\">\n<sub>1</sub>\n</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>O<sub>2</sub> blocks in a BaF<sub>2</sub> layer on Ag film represents switchable cooling effect below and above the transition temperature as shown in right side spectra. i) RC concept having low emissivity in MIR region. j) Scalable temperature adaptive radiative cooler by simple solution process based on VO<sub>2</sub>/spacer/low‐E stacked film (inset figure) and its switchable emissivity spectra. Panel (b): Adapted with permission.<sup>[</sup>\n##REF##31123132##\n147\n##\n<sup>]</sup> AAAS. Panel (d): Adapted with permission.<sup>[</sup>\n##REF##29317637##\n46\n##\n<sup>]</sup> Springer Nature. Panel (f): Adapted with permission.<sup>[</sup>\n##UREF##127##\n177\n##\n<sup>]</sup> Wiley. Panel (h): Adapted with permission.<sup>[</sup>\n##REF##34914515##\n181\n##\n<sup>]</sup> AAAS. Panel (j): Adapted with permission.<sup>[</sup>\n##REF##34914526##\n182\n##\n<sup>]</sup> AAAS.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6694-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Optical properties of typically used RC materials. Black: refractive index; red: extinction coefficient. Data obtained from ref. [##UREF##33##37##, ##REF##30262632##38##].</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Solar reflection</td><td colspan=\"4\" align=\"center\" rowspan=\"1\">Metal</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td colspan=\"2\" align=\"center\" rowspan=\"1\">\n<p>\n\n</p>\n</td><td align=\"center\" colspan=\"2\" rowspan=\"1\">\n<p>\n\n</p>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">IR absorption</td><td colspan=\"4\" align=\"center\" rowspan=\"1\">Inorganic materials</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>\n\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>\n\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>\n\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>\n\n</p>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td colspan=\"4\" align=\"center\" rowspan=\"1\">Polymer</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td colspan=\"2\" align=\"left\" rowspan=\"1\">\n<p>\n\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>\n\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>\n\n</p>\n</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
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[ "<supplementary-material id=\"advs6694-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[]
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no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 10; 11(2):2305067
oa_package/1f/fd/PMC10787071.tar.gz
PMC10787072
37946709
[ "<title>Introduction</title>", "<p>The desire for sustainable and clean energy has sparked widespread interest due to the environmental issue created by the depletion of fossil fuel supplies and the production of greenhouse gases.<sup>[</sup>\n##UREF##0##\n1\n##\n<sup>]</sup> For the production of high‐value chemicals, clean biofuels, and degradable new materials, bioelectrocatalysis offers a green, sustainable, and efficient selection.<sup>[</sup>\n##UREF##1##\n2\n##\n<sup>]</sup> Bioelectrocatalysis employs biological system materials as catalysts to catalyze redox reactions on the electrode.<sup>[</sup>\n##UREF##2##\n3\n##\n<sup>]</sup> It is a cross‐field of biocatalysis and electrocatalysis and fully exploits the benefits of mild biocatalysis conditions and low temperature,<sup>[</sup>\n##UREF##3##\n4\n##\n<sup>]</sup> as well as the flexible conversion of electrical to chemical energy.<sup>[</sup>\n##REF##33050699##\n5\n##\n<sup>]</sup> Electrochemical reactions in the biocatalysis process safely deliver redox equivalents required for biocatalysis while consuming electricity provided by renewable resources.<sup>[</sup>\n##UREF##1##\n2\n##\n<sup>]</sup>\n</p>", "<p>The basic functional portion in a bioelectrochemical system is a bioelectrocatalyst,<sup>[</sup>\n##REF##33050699##\n5\n##\n<sup>]</sup> which consists primarily of electroactive microbial cells and oxidoreductase.<sup>[</sup>\n##UREF##1##\n2\n##\n<sup>]</sup> In 1912, Porter proposed to use intact living cells as biocatalysts for bioelectrocatalysis.<sup>[</sup>\n##UREF##4##\n6\n##\n<sup>]</sup> In the 1960s, electrochemists expanded bioelectrocatalysts to isolated oxidoreductases.<sup>[</sup>\n##UREF##5##\n7\n##\n<sup>]</sup> Subsequently, oxidoreductase and electroactive microbial cells were used to trigger enzyme fuel cells and microbial fuel cells (MFCs), respectively.<sup>[</sup>\n##REF##33050699##\n5\n##\n<sup>]</sup> Furthermore, electrochemical enzyme/microbial biosensors and enzyme/microbial electrosynthesis are catalyzed by oxidoreductase and electroactive microbial cells.<sup>[</sup>\n##UREF##6##\n8\n##\n<sup>]</sup> Generally speaking, bioelectrocatalysis technologies have mainly been applied in biosensors, biofuel cells, and bioelectrosynthesis.</p>", "<p>Machine learning (ML) demonstrates a “learning” experience related to artificial intelligence, and it learns and enhances its analysis by applying computing algorithms.<sup>[</sup>\n##UREF##7##\n9\n##\n<sup>]</sup> As a significant subfield of artificial intelligence, ML has been widely used in image analysis, medical diagnosis, network intrusion detection and prediction, and other fields,<sup>[</sup>\n##UREF##8##\n10\n##\n<sup>]</sup> indicating its ability to solve complex problems. Bioelectrocatalysis contains various influencing factors and complex interactions, which are far from the capability of simple controlled experiments. Therefore, ML has been introduced in recent years to analyze complex problems in different subfields of bioelectrocatalysis. For example, ML overcomes the low accuracy issue of traditional methods in biosensors and transforms ordinary biosensors into intelligent biosensors based on decision‐making systems to automatically predict the type or concentration of analytes.<sup>[</sup>\n##REF##33185417##\n11\n##\n<sup>]</sup> ML optimizes the efficiency of MFCs by a low‐cost approach in biofuel cells and thus compensates for the flaw that constrained laboratory circumstances cannot accurately represent the actual situation.<sup>[</sup>\n##REF##33335352##\n12\n##\n<sup>]</sup> For bioelectrosynthesis, it is a development prospect to maximumly introduce protein engineering in enzyme electrosynthesis and combine microbial electrosynthesis with synthetic biology.<sup>[</sup>\n##REF##33050699##\n5\n##\n<sup>]</sup> Although only several works have applied ML in bioelectrosynthesis, it has the potential to boost oxidoreductase and electroactive microbial cell activity. At present, there is progress in the emerging field of bioelectrocatalysis combined with ML, but there is a lack of review to systematically summarize the development of this field.</p>", "<p>This review discusses the research progress of ML in bioelectrocatalysis, including a brief introduction to the ML modeling process for readers who are not majoring in computer sciences and ML applications in bioelectrocatalysis. Based on previous research, the applications of ML in electrochemical (EC) biosensors, MFCs, and microbial electrosynthesis are outlined. Finally, the current problems and prospects of ML in bioelectrocatalysis applications are discussed.</p>" ]
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[ "<title>Abstract</title>", "<p>At present, the global energy crisis and environmental pollution coexist, and the demand for sustainable clean energy has been highly concerned. Bioelectrocatalysis that combines the benefits of biocatalysis and electrocatalysis produces high‐value chemicals, clean biofuel, and biodegradable new materials. It has been applied in biosensors, biofuel cells, and bioelectrosynthesis. However, there are certain flaws in the application process of bioelectrocatalysis, such as low accuracy/efficiency, poor stability, and limited experimental conditions. These issues can possibly be solved using machine learning (ML) in recent reports although the combination of them is still not mature. To summarize the progress of ML in bioelectrocatalysis, this paper first introduces the modeling process of ML, then focuses on the reports of ML in bioelectrocatalysis, and ultimately makes a summary and outlook about current issues and future directions. It is believed that there is plenty of scope for this interdisciplinary research direction.</p>", "<p>Bioelectrocatalysis for clean energy production and organic waste/environmental pollutant treatment has received a great deal of attention from scientists and engineers around the world. The introduction of machine learning (ML) in this field has just started. At present, ML is mainly applied to electrochemical biosensors and microbial fuel cells, and there are already visible achievements.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6660-cit-0101\">\n<string-name>\n<given-names>J.</given-names>\n<surname>Huang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Gao</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Chang</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Peng</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Yu</surname>\n</string-name>, <string-name>\n<given-names>B.</given-names>\n<surname>Wang</surname>\n</string-name>, <article-title>Machine Learning in Bioelectrocatalysis</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2306583</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202306583</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Machine Learning Modeling</title>", "<p>Traditional ML modeling workflow consists mostly of data collection, feature extraction, algorithm design and model training, and model evaluation.<sup>[</sup>\n##REF##35862246##\n13\n##\n<sup>]</sup> The main procedures in developing an ML model are illustrated in <bold>Figure</bold> ##FIG##0##\n1\n##: gathering data to generate a training dataset, generating and choosing mathematical descriptors, selecting a suitable algorithm and establishing the model, and assessing the model's quality and predicting abilities.<sup>[</sup>\n##REF##35862246##\n13\n##\n<sup>]</sup> It should be noted that the recently developed ML method, named deep learning, combines feature extraction and algorithm design to generate an end‐to‐end model.<sup>[</sup>\n##REF##34814265##\n14\n##\n<sup>]</sup>\n</p>", "<p>Here are the steps of traditional ML modeling. The first step is data collection. It is the most critical and time‐consuming process in the whole workflow, and a significant quantity of high‐quality datasets is a prerequisite to guaranteeing reliable prediction.<sup>[</sup>\n##UREF##9##\n15\n##\n<sup>]</sup> The usual approach for creating datasets is to preprocess and clean the original data gathered through experiments or computations, and then encode them into binary values that computers can identify.<sup>[</sup>\n##REF##36116627##\n16\n##\n<sup>]</sup> The second step is feature extraction, including descriptor generation and selection. The third step is algorithm design and model training. Different algorithms perform differently on the same dataset at times. Linear regression, for example, is appropriate for datasets with linear relationships, but it frequently produces inadequate model performance when applied to datasets with nonlinear relationships.<sup>[</sup>\n##REF##36116627##\n16\n##\n<sup>]</sup> Besides, the selection and optimization of hyperparameters affect ML prediction performance.<sup>[</sup>\n##UREF##10##\n17\n##\n<sup>]</sup> The fourth step is model evaluation, which employs various parameters to assess the regression and classification models. These steps are detailed in the sections that follow.</p>", "<title>Data Collection</title>", "<p>Data on the subject of bioelectrocatalysis are primarily gathered from experiments and literature, and sometimes data about the genome are required in this field when analyzing microbes, which is obtained from the National Center for Biotechnology Information (NCBI). The following are some specific examples.</p>", "<p>\n<italic toggle=\"yes\">Data from Experiments</italic>: Shabani et al.<sup>[</sup>\n##UREF##11##\n18\n##\n<sup>]</sup> used support vector regression to determine the association between MFC output voltage and chemical oxygen demand (COD). The data are from experiments that yielded a collection of 48 data points (4 MFC, 4 COD values, each repeated three times). Each repetition signifies that a batch of water is supplied to the MFC, resulting in the output voltage peak. In another case, Fang et al.<sup>[</sup>\n##UREF##12##\n19\n##\n<sup>]</sup> took experimental data as a training set and verification set. They established the relationship of four operating conditions with Coulombic efficiency (CE) and power density.</p>", "<p>\n<italic toggle=\"yes\">Data from Literature</italic>: The dataset used by Cai et al.<sup>[</sup>\n##REF##30909014##\n20\n##\n<sup>]</sup> contained 69 samples of microbial community data from different laboratory‐scale experiments,<sup>[</sup>\n##REF##27701451##\n21\n##\n<sup>]</sup> including 36 samples for acetate feed, 27 samples for wastewater feed, and 6 samples for carbohydrate feed, all of which were combined with ML techniques to predict feed substrates in MFCs.</p>", "<p>\n<italic toggle=\"yes\">Data from NCBI</italic>: Lesnik et al.<sup>[</sup>\n##REF##31790212##\n22\n##\n<sup>]</sup> created an ML model based on genomic data and tested its capacity to predict the resistance and resilience of MFCs. The genome dataset is stored in the NCBI sequence reading file. It includes 1810 amplicon sequence variants (ASVs) and was used as an input to the resistance and resilience classification model. ASV is a specific region in a DNA sequence that contains some variations associated with a specific gene or disease. Using this dataset, it was possible to verify that the decline in the accuracy of the elasticity model may be because elasticity is the product of a more complex interaction involving several genera, including those outside the assumption that it is indeed a potential stability indicator.</p>", "<p>The quantity and quality of the original datasets influence the maximum level of ML performance. Noise data should be minimized and unbiased sampling should be ensured as much as feasible while building the first dataset for the ML model.<sup>[</sup>\n##REF##36116627##\n16\n##, ##UREF##13##\n23\n##\n<sup>]</sup> Moreover, in the process of collecting data about bioelectrocatalysis in the future, text extraction methods based on ML or currently popular large language models (LLMs) should also be considered to obtain data quickly.</p>", "<title>Feature Extraction</title>", "<p>The process of transforming original data into an algorithm is called characterization or feature extraction.<sup>[</sup>\n##REF##30046072##\n24\n##\n<sup>]</sup> It contains two steps, namely, descriptor creation and descriptor selection, both of which determine the quality and interpretability of a model.<sup>[</sup>\n##REF##35862246##\n13\n##\n<sup>]</sup> The chosen descriptors should have clearly defined chemical or physical meanings to effectively define the main characteristics and properties of data, and involve the least amount of computing work.<sup>[</sup>\n##REF##36116627##\n16\n##\n<sup>]</sup> It should be noted that data attributes dictate the top limit of maximum likelihood, whereas the algorithm only brings the model as near to the upper limit as is feasible.<sup>[</sup>\n##UREF##14##\n25\n##\n<sup>]</sup>\n</p>", "<title>Descriptor Generation</title>", "<p>A good descriptor separates objects in the data space and encodes features linked to the modeled and predicted qualities.<sup>[</sup>\n##REF##30046072##\n24\n##, ##UREF##15##\n26\n##\n<sup>]</sup> Although context determines how a descriptor is generated, there are certain universal guidelines.<sup>[</sup>\n##REF##35862246##\n13\n##\n<sup>]</sup> First and foremost, the descriptor sets must give unique information. Second, descriptors should not be excessive. Redundant descriptors have a very low correlation with the modeled characteristics, and their values do not move much in the dataset (namely, low variance).<sup>[</sup>\n##REF##35862246##\n13\n##\n<sup>]</sup> Therefore, they should be deleted to avoid over‐fitting the model and damaging its ability to predict new data attributes.</p>", "<p>In the field of bioelectrocatalysis, descriptors are associated with research purposes. For example, research on the stability analysis of cyclic voltammograms (CV)<sup>[</sup>\n##UREF##16##\n27\n##\n<sup>]</sup> takes the cumulative voltage variance, cumulative current variance, and product as descriptors. Research on the relationship between MFC output voltage and COD<sup>[</sup>\n##REF##23428752##\n28\n##\n<sup>]</sup> takes the maximum peak height (PH), peak area (PA), peak duration (PD), acceleration rate (AR), and sedimentation rate (SR) as descriptors. The descriptors in different kinds of research differ significantly, so it is necessary to summarize descriptors in bioelectrocatalysis.</p>", "<title>Descriptor Selection</title>", "<p>There are two main strategies for descriptor selection: downward selection and dimensionality reduction.<sup>[</sup>\n##REF##35862246##\n13\n##\n<sup>]</sup> For downward selection, several statistical techniques are employed to condense a huge number of descriptors into a manageable quantity. An L1 regularization term is inserted in a regression model, and items with low correlation with the model are penalized by reducing them to zero, which is known as the least absolute shrinkage and selection operator (LASSO).<sup>[</sup>\n##UREF##17##\n29\n##\n<sup>]</sup> After training, each descriptor's relevance is frequently assessed using a tree algorithm like the random forest.<sup>[</sup>\n##REF##29553728##\n30\n##\n<sup>]</sup> Dimensionality reduction is another method, and new descriptors are created by linearly combining the existing descriptors, in which principal component analysis (PCA) is the most popular method.<sup>[</sup>\n##UREF##18##\n31\n##\n<sup>]</sup> PCA establishes the main components or a set of orthogonal vectors as new descriptors to speed up the construction of the ML model,<sup>[</sup>\n##UREF##19##\n32\n##\n<sup>]</sup> but it might also lose some important information from data points.</p>", "<p>Understanding the significance of descriptors is helpful for the initial feature extraction screening. Using Pearson correlation analysis, one may determine the significance of descriptors.<sup>[</sup>\n##REF##33635641##\n33\n##\n<sup>]</sup> For example, Shabani et al.<sup>[</sup>\n##UREF##11##\n18\n##\n<sup>]</sup> extracted five characteristics from each peak: PH, PA, PD, AR, and SR. Then, the dimension of the dataset is reduced by deleting characteristics with low connection to the Pearson correlation coefficient (PCC) between features and COD values, and the number of features is decreased from 5 to 3 (PH, PA, PD).</p>", "<title>Algorithm Design and Model Training</title>", "<p>After determining the optimal feature subset, algorithm design and model training are carried out. The first step is algorithm design. <bold>Figure</bold> ##FIG##1##\n2\n## shows the reported ML algorithms used in bioelectrocatalysis. ML mainly includes unsupervised learning and supervised learning.<sup>[</sup>\n##UREF##20##\n34\n##\n<sup>]</sup> Supervised learning refers to fitting a model to marked data (or a subset of data), in which there are some basic truth attributes, which are usually measured by experiments or assigned by researchers.<sup>[</sup>\n##REF##34518686##\n35\n##\n<sup>]</sup> In contrast, unsupervised learning identifies patterns in unlabeled data without providing basic truth information to the system in the form of predetermined tags.<sup>[</sup>\n##REF##34518686##\n35\n##\n<sup>]</sup> Unsupervised learning algorithms include clustering algorithms and dimension reduction algorithms. A set of data is clustered when its components are similar to one another,<sup>[</sup>\n##REF##35862246##\n13\n##\n<sup>]</sup> and the structure of data is understood by combining similar observations.<sup>[</sup>\n##REF##32128792##\n36\n##\n<sup>]</sup> Dimension reduction is to transform data with a large number of attributes (or dimensions) into low‐dimensional forms while preserving the different relationships between data points<sup>[</sup>\n##REF##34518686##\n35\n##\n<sup>]</sup> for data visualization and deleting features without information.<sup>[</sup>\n##REF##32128792##\n36\n##\n<sup>]</sup> Supervised learning algorithm includes classification algorithm and regression algorithm. Classification means that the output value is classified (assigning data to many categories), and regression means that the output value is digital (a continuous set of values).<sup>[</sup>\n##REF##32128792##\n36\n##\n<sup>]</sup>\n</p>", "<p>The second step is model training. Typically, the available data is split into a training set, a verification set, and a test set.<sup>[</sup>\n##REF##34518686##\n35\n##\n<sup>]</sup> The training set is used directly to train and build different models, the verification set is used to monitor training and select algorithms and hyperparameters, and the test set is used to evaluate the model's performance and predict errors on unused test datasets during training.<sup>[</sup>\n##REF##34518686##\n35\n##, ##REF##32128792##\n36\n##\n<sup>]</sup>\n</p>", "<title>Model Evaluation</title>", "<p>A high‐performing ML model should be able to predict unknown data as well as to fit existing data.<sup>[</sup>\n##REF##36116627##\n16\n##\n<sup>]</sup> The coefficient of determination (R<sup>2</sup>),<sup>[</sup>\n##UREF##12##\n19\n##, ##REF##33901823##\n37\n##\n<sup>]</sup> mean square error (MSE),<sup>[</sup>\n##REF##33335352##\n12\n##, ##UREF##11##\n18\n##, ##REF##33901823##\n37\n##, ##REF##36397204##\n38\n##\n<sup>]</sup> root‐mean‐square error (RMSE)<sup>[</sup>\n##UREF##12##\n19\n##, ##REF##31790212##\n22\n##, ##REF##33901823##\n37\n##, ##REF##36397204##\n38\n##, ##UREF##21##\n39\n##\n<sup>]</sup> and mean average error (MAE)<sup>[</sup>\n##REF##31790212##\n22\n##, ##REF##36397204##\n38\n##\n<sup>]</sup> are commonly used to assess the predictive accuracy of regression models. To examine the variations in prediction performance across different categorization models, accuracy, precision, recall, specificity, and F1 score are commonly utilized.<sup>[</sup>\n##REF##31898477##\n40\n##\n<sup>]</sup> Furthermore, the receiver's operating characteristic (ROC) curve is an essential metric for evaluating the performance of a non‐uniformly distributed sample classifier,<sup>[</sup>\n##REF##34822886##\n41\n##\n<sup>]</sup> with the area under the ROC curve (AUC) quantitatively representing the model's prediction performance.<sup>[</sup>\n##REF##33901823##\n37\n##, ##REF##34525701##\n42\n##\n<sup>]</sup>\n</p>", "<title>Evaluation of Regression Model</title>", "<p>For a dataset of size n, the real value <italic toggle=\"yes\">y<sub>i</sub>\n</italic> (<italic toggle=\"yes\">i</italic> = 1, 2, 3, …, n), average value <mml:math id=\"jats-math-1\" display=\"inline\"><mml:mrow><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>¯</mml:mo></mml:mover></mml:mrow></mml:math>, and the predicted value <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mrow><mml:mover accent=\"true\"><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>^</mml:mo></mml:mover><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>(<italic toggle=\"yes\">i</italic> = 1, 2, 3, …, n) can be used to calculate the evaluation parameters of the regression model, mainly including R<sup>2</sup>, MSE, RMSE, and MAE. The defining characteristics and formulas of these parameters are shown in <bold>Table</bold> ##TAB##0##\n1\n##.</p>", "<p>In bioelectrocatalysis, R<sup>2</sup> is a commonly used evaluation index to judge the accuracy of the model prediction. For example, in the study of Vakilian et al.,<sup>[</sup>\n##REF##33901823##\n37h\n##\n<sup>]</sup> R<sup>2</sup> of different ML algorithms for predicting nitrate concentration was compared. Results show that the R<sup>2</sup> of SVM (0.97 and 0.96 for the prediction of nitrate concentration of plant enzyme and bacterial enzyme, respectively) was higher than DT, NB, RF, ANN, and least‐square support vector machine (LSSVM), indicating its good prediction accuracy and model performance.</p>", "<title>Evaluation of Classification Model</title>", "<p>The confusion matrix is a common format for conveying accuracy evaluation in the form of an n‐by‐n matrix. The four types of confusion matrix metrics are as follows<sup>[</sup>\n##REF##31898477##\n40\n##\n<sup>]</sup>: (1) True Positives (TP): The number of samples with positive predictive values and positive true values. (2) False Negatives (FN): The number of samples with negative predictive values and positive true values. (3) False Positives (FP): The number of samples with positive predictive values and negative true values. (4) True Negatives (TN): The number of samples with negative predictive values and negative true values. Confusion matrix metrics and classification model evaluation methods are shown in <bold>Figure</bold> ##FIG##2##\n3\n##, and the definitions and formulas of the related assessment parameters are shown in <bold>Table</bold> ##TAB##1##\n2\n##.</p>", "<p>Circumstances where the model rightly predicts negative/positive classes are referred to as TN/TP, whereas circumstances where the model wrongly predicts negative/positive classes are referred to as FN/FP. The confusion matrix is used to calculate several assessment parameters, including accuracy (ACC), precision (also known as positive predictive value (PPV)), recall (also called true positive rate (TPR)), specificity (also called true negative rate (TNR), false positive rate (FPR) and false negative rate (FNR), and F1 score.</p>", "<p>TPR and FPR in Table ##TAB##1##2## represent the vertical and horizontal axes of the ROC curve, respectively. Different points are formed progressively by continually increasing the classification threshold, and these points are eventually joined to form a ROC curve. The vertical axis TPR in ROC represents the proportion where the outcome is positive and the prediction is also positive. Therefore, the higher the model prediction performance, the closer the ROC curve is to the upper left corner.<sup>[</sup>\n##REF##34211533##\n44\n##\n<sup>]</sup> If the ROC curves of the two models cross each other, it is difficult to conclude intuitively, then AUC is calculated to compare the models. When the AUC value is 1, it means that the model gets a perfect prediction no matter what threshold is set. When the AUC value is in the range of 0.5–1, it means that the model is superior to a random guess, and it has a predictive value if the threshold is set properly. When the AUC value is 0.5, it means that the model has no predictive value like a random guess.</p>", "<p>In bioelectrocatalysis, PPV, TPR, and F1 score are often used to evaluate classification models. Ganguly et al.<sup>[</sup>\n##UREF##23##\n45\n##\n<sup>]</sup> used multiplexed point of care (POC) biosensors to classify disease states based on severity, in which an RF model was used for digital classification. In the “infectious, systemic” state, PPV, TPR, and F1 score exhibited their highest values. This is desirable because this state corresponds to the peak of disease and entails the widespread dissemination of disease‐causing microorganisms throughout the body, as evidenced by elevated levels of all targeted inflammatory biomarkers in urine.</p>", "<title>Summary of Machine Learning Modeling</title>", "<p>ML modeling mainly includes four steps: data collection, feature extraction, algorithm design, model training, and model evaluation. Data collection is the foundation of model building, and both the quantity and quality of data sets are critical. Feature extraction transforms raw data into algorithms, including descriptor generation and descriptor selection. The selected descriptor should involve the least computational effort. Algorithm design and model training are the main parts of ML modeling, and selecting the right algorithm is the key step. Model evaluation is the evaluation of the ML modeling effect. There are different parameters to evaluate regression and classification models.</p>", "<title>Applications of Machine Learning in Bioelectrocatalysis</title>", "<p>The applications of bioelectrocatalysis mainly include biosensors, biofuel cells, and bioelectrosynthesis, and in red font, the areas where ML is widely applied are electrochemical (EC) biosensors and MFCs (<bold>Figure</bold> ##FIG##3##\n4a##). To the best of our knowledge, ML was first applied to bioelectrocatalysis in 2006, and the specific application is an EC biosensor.<sup>[</sup>\n##UREF##24##\n46\n##\n<sup>]</sup> In 2013, ML was applied to MFCs,<sup>[</sup>\n##UREF##12##\n19\n##\n<sup>]</sup> and microbial electrosynthesis<sup>[</sup>\n##REF##31918296##\n47\n##\n<sup>]</sup> in 2020. By searching the papers published till December 31, 2022, on Web of Science (WOS) using “Machine Learning” and one additional keyword like “Electrochemical Biosensors”, “Microbial Fuel Cells”, “Enzymatic Fuel Cells”, “Microbial Electrosynthesis”, “Biosolar Cells”, or “Enzymatic Electrosynthesis”, the number of publications found after manual screening and supplementation is shown in <bold>Table</bold> ##TAB##2##\n3\n## and Figure ##FIG##3##4b##. The number of publications and citations by topic terms “Machine Learning” and “Electrochemical Biosensors” on WOS is shown in Figure ##FIG##3##4c##, while the information for “Machine Learning” and “Microbial Fuel Cells” is in Figure ##FIG##3##4d##. It is clear that the attention to these topics increased rapidly after 2019, and more were paid to the use of ML in EC biosensors. Moreover, it is found the top three ML algorithms applied in bioelectrocatalysis are ANN (40 times), PCA (33 times), and SVM (14 times). The following sections discuss the applications of different ML algorithms in EC biosensors, MFCs, and microbial electrosynthesis.</p>", "<title>Applications of Machine Learning in Electrochemical Biosensors</title>", "<p>Analytical devices that provide information about biological processes through sensors are called biosensors.<sup>[</sup>\n##REF##34562926##\n48\n##\n<sup>]</sup> More specifically, EC biosensors are a type of biosensors that combine a recognition element and an electronic transducer to detect analytes in body fluids with high sensitivity.<sup>[</sup>\n##UREF##25##\n49\n##\n<sup>]</sup> The performance of biosensors is usually impacted by impurities, and ML assists in removing the signal acquired from pollutants to gain high sensitivity.<sup>[</sup>\n##REF##34562926##\n48\n##\n<sup>]</sup> By incorporating ML into biosensing systems, data interpretation also becomes simpler and more effective.<sup>[</sup>\n##REF##33901823##\n37\n##, ##REF##31907460##\n50\n##\n<sup>]</sup> ML was reported to efficiently manage vast amounts of sensing data with complicated matrices or samples and directly, automatically, precisely, and swiftly help biosensors read out findings, which may then be utilized to create better biosensors.<sup>[</sup>\n##REF##33185417##\n11\n##\n<sup>]</sup>\n<bold>Table</bold> ##TAB##3##\n4\n## shows the applications of different ML algorithms in EC biosensors from 2018 to 2022 (in descending order of publication date) from 16 research papers.</p>", "<p>As seen from Table ##TAB##3##4##, the purpose of ML in EC biosensors is mainly to classify, predict, and discriminate the influencing factors, which are discussed in the following sections.</p>", "<title>Classification</title>", "<p>ML algorithms automatically learn complex feature relationships from raw signals generated by EC biosensors, thus avoiding the subjective bias and workload associated with manual feature selection. In addition, ML algorithms deal with the issues related to nonlinear decision boundaries, and thus provide more accurate classification for EC biosensors. Therefore, ML algorithms assist EC biosensors in classifying substances in a fast and accurate way.</p>", "<p>Sugar is an additive in beverage products and excessive consumption of sugar leads to an increase in various diseases. Therefore, it is necessary to classify and detect the sugar in drinks. Umar et al.<sup>[</sup>\n##REF##36618051##\n51\n##\n<sup>]</sup> used a whole‐cell immobilized amperometric biosensor to determine the sugar content in bottled beverages. PCA was used to calculate the proportion of errors by comparing the reported concentration values indicated on the sample package composition with the concentration data discovered by measurements. <bold>Figure</bold> ##FIG##4##\n5a,b## highlight the difference between natural sugars and artificial sweeteners. The narrower clustering pattern of natural sugars indicates that the detection process of natural sugars is stable, and PCA distinguishes their type and concentration. In contrast, the data generated by each sweetener concentration has a high degree of overlap, and thus it was difficult to classify both sweeteners and their concentrations measured by the sensor. Therefore, PCA was used to reduce the irrelevant data generated in measurements, so that the data is classified and clustered.</p>", "<p>In addition, ML algorithms are used to classify bacteria. Classification of bacteria is important in many practical applications, such as the food industry. Ali et al.<sup>[</sup>\n##REF##29651022##\n61\n##\n<sup>]</sup> proposed a new impedance‐based biosensor that easily and quickly detects three different types of bacteria, including <italic toggle=\"yes\">Salmonella typhimurium</italic>, and the <italic toggle=\"yes\">Escherichia coli</italic> strains JM109 and DH5‐α. The biosensor's capability was evaluated using three kinds of algorithms, including MLE, LDA, and BPNN, and accuracy was used as the evaluation parameter. As shown in Figure ##FIG##4##5c##, the MLE classifier's overall accuracy is 100%. In the case of LDA, except for a few samples of these bacterial groups at the edges of the linear discriminant plane, all test samples clustered well along the two hyperplanes (Figure ##FIG##4##5d##). The overall accuracy of LDA reaches 100%, indicating an accurate distinction of bacterial types. Moreover, nonlinear BPNN was also applied to a given dataset classification problem. A total of 120 data vectors were employed, of which 84 were used for training and 36 were equally split between the test and validation datasets (Figure ##FIG##4##5e–g##). In training, testing, and cross‐validation, the BPNN achieved 100% accuracy, accurately classifying every bacterial sample (Figure ##FIG##4##5h##). The accuracy of MLE, LDA, and BPNN for bacterial classification reached 100%, demonstrating that these ML algorithms achieved good results in classifying different bacterial classes and the scheme is simple, fast, accurate, and economical.</p>", "<p>The ML algorithms used in the above studies include PCA, MLE, LDA, and BPNN. PCA helps remove redundant information and noise and find the main features in the data. MLE finds the most likely classification result according to the probability distribution of data, providing a more flexible classification method. LDA finds the optimal projection direction, maximizes the distance between different categories, and minimizes the variance within the same category, thus improving the accuracy of classification. BPNN is a powerful nonlinear model with strong fitting ability. It learns complex feature relationships through multi‐layer neural networks and automatically adjusts network weights so that the model adapts to different complex classification tasks. These algorithms assist EC biosensors in classification tasks.</p>", "<title>Prediction</title>", "<p>There are multiple influencing factors involved in EC biosensors, and ML algorithms automatically synthesize multiple features for prediction and capture the comprehensive influence of multiple factors. Thus, ML makes it possible to forecast the concentration of compounds detected by EC biosensors more quickly and accurately. The algorithms used for prediction possess the advantages of linear or nonlinear signal stimulation, real‐time operation, and rapid calculations.</p>", "<p>To overcome the overlapping of glucose and lactate oxidation peaks and enhance the selectivity of non‐enzymatic electrochemical detection, Zhou et al.<sup>[</sup>\n##REF##36397204##\n38b\n##\n<sup>]</sup> introduced BPNN into non‐enzymatic electrochemical biosensing (<bold>Figure</bold> ##FIG##5##\n6a##). By analyzing the chronoamperometry results of multiple EC biosensors, the non‐enzymatic sensors using BPNN could achieve high sensitivity and wide‐range detection of glucose and lactate, with an R<sup>2</sup> value of 0.9997 and a relative standard deviation of less than 6.5%. The results show that BPNN could help identify and predict glucose and lactate concentrations. It can be seen that BPNN has been used to perform both classification and prediction tasks. The reason is that its multi‐layered structure and backpropagation algorithms allow it to learn complex features from input data and make classifications or predictions based on those features. For classification tasks, BPNN judges the category of a new sample by learning the relationship between input data and the corresponding labels. For prediction tasks, it predicts continuous values by learning the relationship between input data and actual output values.</p>", "<p>Additionally, ML techniques have been applied to enhance the precision of bacterial concentration determination. Xu et al.<sup>[</sup>\n##UREF##28##\n58\n##\n<sup>]</sup> employed an ML‐based electrochemical impedance spectroscopy (EIS) biosensor to detect <italic toggle=\"yes\">E. coli</italic> (Figure ##FIG##5##6b##). The goal was to use EIS data to automatically synthesize numerous impedance parameters into a recognition machine that determines bacterial concentrations. To automatically create quantitative correlations between multiple impedimetric parameters and bacterial concentrations, PCA was used to extract impedance parameters from EIS data recorded at various bacterial concentrations. Subsequently, the first four main components (p1, p2, p3, p4) were kept and fed into the SVR, with the concentration of <italic toggle=\"yes\">E. coli</italic> serving as the model output. The average prediction error (<italic toggle=\"yes\">n</italic> = 10) reached 1.52 ± 0.136%, revealing that the ML model accurately determines <italic toggle=\"yes\">E. coli</italic> concentrations and has advantages in adaptability, automation, and accuracy. ML‐based EIS biosensors exhibit a self‐learning capability and hence are more adaptable to a variety of sensor designs for molecular and cellular detection. Furthermore, if more dimensions of EIS data are studied, the detection accuracy may be further enhanced.</p>", "<p>The ML algorithms used in the above studies include BPNN, PCA, and SVR. BPNN automatically learns complex nonlinear relationships and is suitable for processing nonlinear EC biosensor data. PCA be used to reduce the dimensionality of data, remove redundant information and noise in data, and improve the efficiency and generalization ability of prediction models. SVR learns complex nonlinear patterns through kernel function techniques to provide high prediction accuracy. These algorithms improve the prediction ability of EC biosensors.</p>", "<title>Discriminating Influencing Factors</title>", "<p>ML algorithms automatically learn the correlation between multiple influencing factors, find complex causal relationships, and assist factor discrimination. To determine what and how certain influencing elements impact EC biosensors, ML algorithms have been employed in reports. For instance, Emaminejad et al.<sup>[</sup>\n##UREF##26##\n55\n##\n<sup>]</sup> have used sophisticated data analysis and microbiological approaches to measure the sensitivity of a bio‐electrochemical sensor (BES) deployed in the major effluent channel of a water resource recovery facility (<bold>Figure</bold> ##FIG##6##\n7\n##). PCA was used as a dimensionality reduction approach to expose the pattern and direction of the highest variance in data and to demonstrate the effect of BES signal variance on observed environmental factors. However, PCA is built on linear assumptions, which is inapplicable to biological wastewater treatment systems with inherently nonlinear features. Therefore, kernel PCA (KPCA) was used to interpret the data's nonlinearity. In addition, singular spectrum analysis (SSA) was conducted to recognize the system structure in biosensor signal responses and compare it to a dissolved oxygen probe mounted in an active sludge tank near the BES probe.</p>", "<p>Results show that PCA revealed substantial differences in sensor response signal behavior between warm and cold months, and no significant linear effects of any of the examined factors on total signal variance were discovered during the cold weather runs. KPCA confirmed the nonlinearity of the cold weather data. The signal was impacted by seasonal and monthly cycle patterns, which may be attributable to the influence of rainfall events and seasonal temperature fluctuations, according to SSA. These algorithms possess the capability to rapidly and distinctly explicate the long‐term carbon monitoring potential of BESs under diverse environmental circumstances. Therefore, ML methods are used to investigate the linear or nonlinear interaction between environmental conditions and biosensor signals to improve the sensing capability of biosensors.</p>", "<p>ML algorithms such as PCA, KPCA, and SSA were used to discriminate influencing factors. PCA is suitable for reducing and removing data noise, KPCA is suitable for dealing with nonlinear relations, and SSA is suitable for dealing with time series data. These algorithms help to identify the key influencing factors and improve the accuracy and efficiency of identifying influencing factors.</p>", "<title>Applications of Machine Learning in Microbial Fuel Cells</title>", "<p>With the help of immobilized cell populations, MFCs employ bacteria as catalysts to oxidize both organic and inorganic materials, dramatically lowering the barrier to electron transfer in biofilms and solid electrodes to achieve the necessary power production capacity.<sup>[</sup>\n##UREF##16##\n27\n##\n<sup>]</sup>\n</p>", "<p>Due to the sensitivity of MFCs to environmental factors, the mathematical modeling of MFC models is difficult.<sup>[</sup>\n##UREF##30##\n63\n##\n<sup>]</sup> MFCs are a complex nonlinear process that requires a strategy nonlinearly controlled to obtain the most favorable results. ML helps reduce computational and modeling costs, saves time, and is more efficient than manual methods previously used.<sup>[</sup>\n##UREF##30##\n63\n##\n<sup>]</sup>\n<bold>Table</bold> ##TAB##4##\n5\n## shows the applications of different ML algorithms in MFCs from 2018 to 2022 (in descending order of publication date) from 25 research papers.</p>", "<p>As seen from Table ##TAB##4##5##, the purpose of ML in MFCs is mainly to classify, predict, and discriminate the influencing factors, which are discussed in the following sections.</p>", "<title>Classification</title>", "<p>MFCs involve the relationship between multiple complex factors, and ML algorithms automatically learn and capture these complex relationships to improve the accuracy of classification tasks.</p>", "<p>By exposing terrestrial soil‐based microbial fuel cells (tMFCs) to gasoline, petroleum, 2,4‐dinitrotoluene, fertilizer, and urea, Barbato et al.<sup>[</sup>\n##REF##34937056##\n66\n##\n<sup>]</sup> created a sensor technique for molecules suggestive of anthropological compounds. RBF and KNN were trained to detect chemicals based on voltage patterns. KNN is one of the simplest ML algorithms,<sup>[</sup>\n##UREF##41##\n81\n##\n<sup>]</sup> and RBF improves on it by using the distance between the input and the training data set to evaluate confidence and provide “unknown” confidence.<sup>[</sup>\n##UREF##42##\n82\n##\n<sup>]</sup> For KNN, the classification of the test input is defined by its K nearest neighbors in the training input, with the majority of the K nearest neighbors having the same classification as the test input. Because the KNN approach fires all neurons, it cannot produce an “unknown” confidence level. The RBF approach is identical to KNN, except that the neuron only fires if its internal weight is within one unit of the input parameter. Compared with KNN, RBF classifies anthropological compounds more effectively. Specifically, RBF was able to categorize gasoline, urea, and fertilizer with 100%, 88%, and 94.5% accuracy, demonstrating that tMFCs could be utilized as biosensors for environmental monitoring.</p>", "<p>The advantage of ML algorithms in MFC classification tasks is high accuracy and effectiveness. Compared with a simple KNN algorithm, RBF classifies samples containing man‐made compounds more effectively, thus providing a reliable classification solution for the application of MFC in environmental monitoring and other fields.</p>", "<title>Prediction</title>", "<p>The performance of MFCs is affected by a variety of factors, including temperature, pH, substrate type, etc., and ML algorithms consider multiple factors at the same time and build complex predictive models. For example, bioelectrochemical reaction rates in MFCs were reported to be improved by introducing self‐calibrating and automatically optimizing ML tools such as ANN. ANN algorithms allow easier model creation, which do not require predefined knowledge to create a new model but have the disadvantage of not providing additional outputs in addition to those being trained.<sup>[</sup>\n##UREF##30##\n63\n##\n<sup>]</sup>\n<bold>Figure</bold> ##FIG##7##\n8\n## illustrates the various inputs and outputs of an MFC coupled with ANNs (nodes, layers, and networks). These ANNs were used to predict performance more accurately by simulating the weights of important parameters for forward and backward propagation through the layers.<sup>[</sup>\n##REF##34893375##\n83\n##\n<sup>]</sup> With the help of neural networks, it is also possible to filter key performance indicators and determine their sensitivity.<sup>[</sup>\n##REF##34893375##\n83\n##\n<sup>]</sup>\n</p>", "<p>The following is an example of the specific application of ANN in MFCs. In order to predict the voltage output of MFCs in polarization tests, Tsompanas et al.<sup>[</sup>\n##UREF##37##\n76\n##\n<sup>]</sup> developed an ANN with a 4‐10‐1 topology. The reason for using ANN is that ANN is ideal for studying complex MFC systems because it is not necessary to know the detailed rules of the control system. After one training, the network displayed a high correlation coefficient (R) of 0.99662 for the complete dataset (<bold>Figure</bold> ##FIG##8##\n9a##), indicating its exceptional proficiency in accurately and promptly predicting the voltage output of MFCs. In future research, a time component is encouraged to be introduced to ANN to predict MFC output as a time series.</p>", "<p>In addition to ANN, other ML algorithms have also been used for prediction. Shabani et al. proposed an energy‐autonomous water quality monitoring device with a single MFC as its sensory input and the only power source for computing chemical oxygen demand (COD).<sup>[</sup>\n##UREF##11##\n18\n##\n<sup>]</sup> To strike a good balance between high accuracy and low execution time, an SVR with an RBF core was selected to find the relationship between MFC output voltage and COD. The geometric properties of MFC voltage distribution were sent into the SVR as input. A low‐power microcontroller that records the MFC voltage and powers the SVR was driven by the power produced by MFCs. The device was capable of precisely detecting COD in water samples from natural ponds, with R<sup>2</sup> = 0.94 (Figure ##FIG##8##9b##). In the experiments, a large range of COD (70–900 mg L<sup>−1</sup>) was considered. Training the algorithm in a smaller range results in higher accuracy in that range.</p>", "<p>In reports, the ML algorithm predicts not only COD but also feed substrate. To test whether it was possible to identify feed substrates from the ensuing microbial communities, Cai et al.<sup>[</sup>\n##REF##30909014##\n20\n##\n<sup>]</sup> gathered 69 samples of three distinct substrate types (acetate, glucose, and wastewater) from various laboratory conditions. The capacity of neural network (NNET), scalable tree boosting system (XGBOOST), logistic regression multiclass (GLMNET), RF, KNN, and SVM to predict feed substrates from genomic datasets were trained and assessed. The identification of suitable data inputs and the selection of appropriate ML algorithms provide a direct link between substrate groupings and genomic data without the need for additional information such as operating conditions and currents, making this approach more broadly applicable to systems with mixed microbial communities. The model built by the NNET algorithm showed the highest accuracy. The accuracy and <italic toggle=\"yes\">kappa</italic> values of NNET trained on the dataset with phyla classification were 93 ± 6% and 0.87 ± 0.10, respectively (Figure ##FIG##8##9c##). The accuracy and <italic toggle=\"yes\">kappa</italic> values of NNET trained on the dataset with family classification were 92 ± 5% and 0.86 ± 0.09, respectively (Figure ##FIG##8##9d##). These findings reveal a novel use of ML approaches with significant practical implications in the field of biotechnology for feed substrate prediction and MFC‐based biosensor signal specificity enhancement.</p>", "<p>Through the above research, it can be concluded that the advantages of ML algorithms in MFC prediction tasks mainly include: high precision and fast execution, suitable for complex systems, and prediction of a variety of parameters. ANN could accurately and quickly predict the voltage output of MFC, SVR found a good balance between high accuracy and low execution time to predict COD, and NNET excelled at predicting substrates. The applications of ML algorithms in MFC have important practical values and bring significant advantages for substrate prediction and MFC‐based biosensor signal enhancement.</p>", "<title>Discriminating Influencing Factors</title>", "<p>PCA can be used not only for classification but also to identify influencing factors. In classification, PCA is used to reduce dimension. By selecting the appropriate number of principal components, the accuracy, and efficiency of classification are improved by retaining high data information while reducing the number of features. For the identification of influencing factors, the relevant variables are transformed into a set of unrelated principal components by PCA. These principal components reflect the different influencing factors in data and are ordered by the magnitude of their explanatory variance. Therefore, by analyzing the load of principal components (i.e., the relationship between principal components and original variables), it is possible to determine which variable contributes the most to the principal component.</p>", "<p>The following is a study in which PCA was used to identify influencing factors. Du et al.<sup>[</sup>\n##UREF##32##\n65\n##\n<sup>]</sup> introduced the synergistic effect of potato solid waste (SPW) and waste‐activated sludge (WAS) to improve the waste conversion capacity of MFCs. PCA was used to successfully examine the influence of the mixing ratio on the hydrolytic breakdown and energy recovery of SPW. The higher loadings of peaks 1–6 and UV260 in the same direction as PC1 in <bold>Figure</bold> ##FIG##9##\n10a## indicate that SPW and WAS were effectively hydrolyzed. SUVA and DOC loadings as PC2 in the opposite direction are rather high. This might be due to the varying rates of the humic compound and other dissolved organic matter breakdown in MFC anode dissolution solutions. For PC1 in Figure ##FIG##9##10b##, except for the fractions with mixing ratios of 2:1 and 10:1, the scores of all fractions increased positively and then reversed, demonstrating a rise in the reduction in tryptophan‐ and tyrosine‐like amino acids, aromatic proteins, and humic compounds with time. Except for PC2 with mixing ratios of 2:1 and 10:1, which increased positively with time, the rest of PC2 increased positively and then reversed to positive, and PC2 with the mixing ratio of 0:1 scored the highest. Dissolved organic matter in WAS was more easily degraded, and the relative content of humus‐like substances in dissolved organic matter was higher. The results show that the mixture ratio of SPW and WAS had a significant effect on the composition of dissolved organic matter. Therefore, PCA helps better understand the association between total chemical oxygen demand, soluble chemical oxygen demand, dissolved organic carbon, ultraviolet absorbance at the wavelength of 260 nm, specific ultraviolet absorbance, and primary fluorescence peak intensity of each sample during MFC operation. PCA is further used to analyze the factors that affect MFCs and provide a reference for improving MFC performance.</p>", "<title>Switching Models</title>", "<p>ML has been reported to switch MFC models from algorithms including RBA, WkNN, GMA, etc. For instance, Yewale et al.<sup>[</sup>\n##UREF##21##\n39\n##\n<sup>]</sup> proposed an MMB controller strategy to solve the nonlinearity problem in CMFC and implemented it on the developed MIMO system. For MMB controllers, the model‐switching approach needs to work precisely on the overlap of multiple subspaces created by decomposing operational regimes into local regimes. Therefore, weighted methods, including recursive Bayesian methods (RBA), WkNN, GMA, MWA, and HT<sup>2</sup>S, were used for MMB controller integration to combine many controllers into a single global controller.<sup>[</sup>\n##UREF##43##\n84\n##\n<sup>]</sup> Besides, the gap metric technique was used to break the nonlinear portion of CMFC into numerous linear regions. As shown in <bold>Figure</bold> ##FIG##10##\n11\n##, WkNN outperformed other approaches. The average stabilization time of the MMB controller using WkNN was lowered by roughly 65% when compared to the single linear model controller, and thus the nonlinear problem of CMFC was solved successfully. In short, ML algorithms such as WkNN demonstrate an outstanding ability to deal with complex nonlinear problems of MFCs in switching models more efficiently, accurately, and flexibly, affording strong support for the development of MFC control strategies.</p>", "<title>Applications of Machine Learning in Microbial Electrosynthesis</title>", "<p>Only several works applied ML to microbial electrosynthesis and mainly concentrated on experimental data analysis. Currently, an unsupervised learning algorithm, hierarchical clustering, has been introduced to microbial electrosynthesis. The principle of hierarchical clustering is that given a set of data points, the output is a binary tree (tree graph). Its leaves are data points, its internal nodes represent nested clusters of varying sizes, and the tree organizes these clusters in a hierarchy that hopefully aligns with the intuitive organization of real‐world data.<sup>[</sup>\n##UREF##44##\n85\n##\n<sup>]</sup> Here is an example.</p>", "<p>To improve the methane production rate of anaerobic digestion microbial electrosynthesis, Flores‐Rodriguez and Min<sup>[</sup>\n##REF##31918296##\n47\n##\n<sup>]</sup> examined the dispersion of microbial populations at varied voltages (0.5, 1.0, and 1.5 V) to find the optimal voltage for the enrichment of specific microbial communities. It was found that methane generation is more advantageous at 1.0 V. Then, all samples were submitted to hierarchical clustering based on the Braye Curtis index, principal component vertical coordinate (PCO), and non‐metric multidimensional scaling (nMDS) (<bold>Figure</bold> ##FIG##11##\n12\n##). Significant variations between samples were visible in the nMDS and PCO plots (Anosim, <italic toggle=\"yes\">P</italic> = 0.009, <italic toggle=\"yes\">R</italic> = 0.377) (Figure ##FIG##11##12a,b##). The findings of the nMDS and PCO plots are supported by the hierarchical clustering plot (Figure ##FIG##11##12c##). The C1.0 biofilm aggregated independently of other biofilms, indicating the distinct enrichment of microbial biofilms generated by the applied voltage. In this work, hierarchical clustering assists in undertaking a non‐quantitative multidimensional analysis to discover systematic differences between samples.</p>", "<p>Hierarchical clustering in microbial electrosynthesis helps to analyze the similarities and differences of microbial communities, reveal systematic changes, infer biological reactions, and optimize reaction conditions. The application of hierarchical clustering in microbial electrosynthesis provides an effective analytical tool for researchers to understand the complex community structure and influencing factors in microbial electrosynthesis.</p>", "<title>Summary and Outlook</title>", "<p>Bioelectrocatalysis is a multi‐factors involved complicated system that is challenging to study simply through artificial experiments. The ability to cope with nonlinear issues, classification, prediction, identification of influencing factors, optimization of operating conditions, and other operations, reflects the originality and advantage of ML applications in bioelectrocatalysis. Despite these achievements in ML‐assisted bioelectrocatalysis research, there are still many challenges, problems, and unexplored potential research fields.\n<list list-type=\"order\" id=\"advs6660-list-0001\"><list-item><p>There are a few relevant databases, which should be established in the future to facilitate access to large amounts of bioelectrocatalysis data. Moreover, the data used are mainly collected manually from experiments or literature. ML could also assist in the data collection process, especially through popular large language models. In addition, existing data could be utilized for more efficient algorithmic tuning, such as employing data augmentation techniques to expand the size of datasets. Data scarcity can also be mitigated through domain knowledge sharing and collaboration, which avoids redundant data collection, thereby reducing costs and resource wastage.</p></list-item><list-item><p>Specifically for EC biosensors, although many applications such as food evaluation and medical diagnostic analysis have benefitted from ML, the hurdles of stability, sensitivity, dependability, and simplicity for practical use and commercialization require the involvement of ML more broadly and deeply.</p></list-item><list-item><p>MFCs can be used for wastewater treatment, desalination, water quality testing, green power supply, etc. Its performance is heavily influenced by complex factors including substrates in the anode chamber, anode and cathode materials, electrolytes, operating temperature, and the situation of microorganisms.<sup>[</sup>\n##UREF##30##\n63\n##\n<sup>]</sup> These multi‐dimensional data could provide a great opportunity for training and developing bioelectrocatalysis‐fitted ML algorithms, which may potentially solve the low electrical power generation efficiency issue that has long restricted the use of MFCs.</p></list-item><list-item><p>ANN is one of the most used ML methods in research of bioelectrocatalysis, but there are still many problems, such as long training time, the requirement of large amounts of training data, lack of incremental learning ability, not quite suitable for high‐precision computing, etc. The study on ANN is thus still crucial with emphasis on some practical issues, including the creation of a universal neural network processor or implementation of a huge number of dynamic neural‐free linkages.</p></list-item><list-item><p>The applications of ML in bioelectrocatalysis are limited to EC biosensors and MFCs. Its exploration in bioelectrosynthesis and other fields deserves more attention and effort.</p></list-item></list>\n</p>", "<p>ML has great potential to be useful in bioelectrocatalysis for clean energy production and organic waste/environmental pollutant treatment. It optimizes reaction conditions and increases bioelectrocatalysis efficiency. Besides, it is employed in data/signal processing and classification. Deeper rules and patterns may be mined using ML, which can help to speed the development of bioelectrocatalysis technology. Such an interdisciplinary research direction is showing great potential to change the rules of the traditional research paradigm of bioelectrocatalysis.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>" ]
[ "<title>Acknowledgements</title>", "<p>J.H. and Y.G. contributed equally to this work. The authors thank the financial support from the National Key R&amp;D Program of China (2022YFF0712200, 2021YFA1202802), the Young Elite Scientists Sponsorship Program by BAST (BYESS2023410), and the CAS Pioneer Hundred Talents Program.</p>", "<p>\n<bold>Jiamin Huang</bold> received the B.E. degree in environmental science from University of Science and Technology Beijing (USTB) in 2022. She is currently pursuing the M.E. degree in environmental science and technology from USTB. She is now an experimenter at the National Center for Nanoscience and Technology (NCNST), China. Her research interests mainly focus on microbial fuel cells and machine learning.</p>", "<p>\n<bold>Yang Gao</bold> received his Ph.D. in electrochemistry from Tianjin University in 2020. He is now a postdoctoral research fellow at the National Center for Nanoscience and Technology (NCNST), China. His research interests mainly focus on the design and fabrication of functional materials for energy storage and conversion applications.</p>", "<p>\n<bold>Yanhong Chang</bold> is an associate professor at University of Science and Technology Beijing. She received her Ph.D. degree from Institute of Coal Chemistry Chinese Academy of Sciences in 2001. Her research mainly focuses on assembling structure‐controllable and functional nanomaterial to provide desirable properties and preparing biocatalysts for environmental protection.</p>", "<p>\n<bold>Bin Wang</bold> is a Professor in the National Center for Nanoscience and Technology (NCNST). His research interests include nanomaterials synthesis (particularly CVD graphene and other 2D materials) and the related mechanical and electrochemical studies, such as the reinforcement of composites and the intrinsic battery and catalytic properties.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0001\"><label>Figure 1</label><caption><p>Workflow of building a traditional ML model. MSE: mean square error. RMSE: root‐mean‐square error. MAE: mean average error. ACC: accuracy. PPV: positive predictive value. TPR: true positive rate. TNR: true negative rate. FPR: false positive rate. FNR: false negative rate. ROC: receiver's operating characteristic. AUC: area under the receiver's operating characteristic.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0002\"><label>Figure 2</label><caption><p>ML algorithms used in bioelectrocatalysis research. Unsupervised learning algorithms include k‐means and PCA, while supervised learning algorithms include decision tree (DT), support vector machine (SVM), relevance vector machine (RVM), naive Bayes (NB), k‐nearest neighbor (KNN), random forest (RF), maximum likelihood estimation (MLE), partial least squares (PLS) and artificial neural network (ANN). Algorithms should be selected according to research purposes. Some supervised learning algorithms are applied to both regression and classification.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0003\"><label>Figure 3</label><caption><p>Confusion matrix metrics and classification model evaluation methods.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0004\"><label>Figure 4</label><caption><p>a) Classification of bioelectrocatalytic applications. b) Percentage of ML applications in bioelectrocatalysis. c) The number of publications and citations by year on WOS for the topic terms “Machine Learning” and “Electrochemical Biosensors”. d) The number of publications and citations by year on WOS for the topic terms “Machine Learning” and “Microbial Fuel Cells”.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0005\"><label>Figure 5</label><caption><p>Based on a) the type of sugar and b) the content of several common beverages, sugar was categorized. Reproduced with permission.<sup>[</sup>\n##REF##36618051##\n51\n##\n<sup>]</sup> Copyright 2022, Springer. c) Prediction of three bacterial samples (<italic toggle=\"yes\">E. coli</italic> DH5‐α, JM 109, and Salmonella are depicted in red, blue, and green, respectively) using the MLE model and d) LDA clustering analysis of three bacteria. Reproduced with permission.<sup>[</sup>\n##REF##29651022##\n61\n##\n<sup>]</sup> Copyright 2018, Springer. Classification of bacteria with BPNN: e) 70% training, f) 15% validation, g) 15% test data, h) 40 samples of each kind of bacteria correctly classified. Reproduced with permission.<sup>[</sup>\n##REF##29651022##\n61\n##\n<sup>]</sup> Copyright 2018, Springer.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0006\"><label>Figure 6</label><caption><p>a) Illustration of highly specific non‐enzymatic electrochemical sensing with BPNN. Reproduced with permission.<sup>[</sup>\n##REF##36397204##\n38b\n##\n<sup>]</sup> Copyright 2022, ACS. b) A schematic representation of an EIS biosensor system based on ML for <italic toggle=\"yes\">E. coli</italic> detection. Reproduced with permission.<sup>[</sup>\n##UREF##28##\n58\n##\n<sup>]</sup> Copyright 2020, IOP.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0007\"><label>Figure 7</label><caption><p>Overview of the BES case study for field applications. a) From June 20, 2019, to February 22, 2020, BES response signals (also known as MET, or microbiological electron transfer) were recorded, and within the same time frame, field measurements were taken to compare them to the BES signals. b) After being transmitted over an Internet connection via the HTTP or MQTT network protocol, data were stored on a cloud‐based data server and, for redundancy, added to a local SD card at the controller. c) To assess the BES signals in reaction to environmental conditions, PCA, KPCA, and SSA were applied. Reproduced with permission.<sup>[</sup>\n##UREF##26##\n55\n##\n<sup>]</sup> Copyright 2022, the Royal Society of Chemistry.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0008\"><label>Figure 8</label><caption><p>ML‐driven MFC system. Reproduced with permission.<sup>[</sup>\n##REF##34893375##\n83\n##\n<sup>]</sup> Copyright 2022, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0009\"><label>Figure 9</label><caption><p>a) Regression plot comparing network results to the objectives of the entire dataset. Reproduced with permission.<sup>[</sup>\n##UREF##37##\n76\n##\n<sup>]</sup> Copyright 2019, Elsevier. b) The connection between the observed and estimated COD concentrations is shown by the integrated system's sensing data (R<sup>2</sup> = 0.94). Reproduced with permission.<sup>[</sup>\n##UREF##11##\n18\n##\n<sup>]</sup> Copyright 2021, IEEE. Phyla dataset c) and family dataset d) combined with accuracy and kappa metrics of several algorithms. Reproduced with permission.<sup>[</sup>\n##REF##30909014##\n20\n##\n<sup>]</sup> Copyright 2019, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0010\"><label>Figure 10</label><caption><p>PCA was performed on data from TCOD, SCOD, DOC, UV260, SUVA, and 5 EEM peak intensity changes of MFCs with various SPW and WAS mixing ratios. a) The component loading plots. b) The component score plots. Reproduced with permission.<sup>[</sup>\n##UREF##32##\n65\n##\n<sup>]</sup> Copyright 2022, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0011\"><label>Figure 11</label><caption><p>Average performance criteria for MMB controller's multiple switching mechanisms (ST: stability time; ISE: integral square of error; ICE: integral control command; CE: control command). Reproduced with permission.<sup>[</sup>\n##UREF##21##\n39\n##\n<sup>]</sup> Copyright 2020, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6660-fig-0012\"><label>Figure 12</label><caption><p>Anode‐A, cathode‐C, and suspension‐S biofilm communities from each MES‐AD (0.5, 1.0, and 1.5 V) and control biofilms were used as the basis for a systematic cluster analysis of nMDS, PCO, and BrayeCurtis indices. a) The nMDS plot. b) The PCO plot. c) The hierarchical cluster plot. Reproduced with permission.<sup>[</sup>\n##REF##31918296##\n47\n##\n<sup>]</sup> Copyright 2016, BMC.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6660-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Evaluation parameters of the regression model.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Parameter</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Definition</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Characteristic</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Formula<sup>[</sup>\n##REF##35862246##\n13\n##, ##UREF##22##\n43\n##\n<sup>]</sup>\n</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">R<sup>2</sup>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Reflect the proportion of dependent variable changes that can be explained by independent variables using a regression relationship.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The normal range is [0,1], and the closer the model is to 1, the better it matches the data.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:mrow><mml:mspace width=\"0.33em\"/><mml:msup><mml:mi>R</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mo>=</mml:mo><mml:mspace width=\"0.33em\"/><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mspace width=\"0.33em\"/><mml:mfrac><mml:mrow><mml:msubsup><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mspace width=\"0.33em\"/><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:msubsup><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>−</mml:mo><mml:mover accent=\"true\"><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>^</mml:mo></mml:mover></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:msubsup><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mspace width=\"0.33em\"/><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:msubsup><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>−</mml:mo><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>¯</mml:mo></mml:mover></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mfrac><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:msubsup><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:msubsup><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mover accent=\"true\"><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>^</mml:mo></mml:mover><mml:mo>−</mml:mo><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>¯</mml:mo></mml:mover></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:msubsup><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:msubsup><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>−</mml:mo><mml:mover accent=\"true\"><mml:mi>y</mml:mi><mml:mo>¯</mml:mo></mml:mover></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">MSE</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">It is often used to detect the difference between the model‘s predicted and actual values.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The degree of data change may be calculated, and the lower the number, the more accurate the prediction model is at representing the experimental data.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>M</mml:mi><mml:mi>S</mml:mi><mml:mi>E</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mi>n</mml:mi></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mspace width=\"0.33em\"/><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:munderover><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>−</mml:mo><mml:mover accent=\"true\"><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>^</mml:mo></mml:mover></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mrow></mml:math>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">RMSE</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The square root is used to calculate the difference between the predicted and actual values based on MSE.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">It is an order of magnitude with data, and it is easier to perceive data, but it is susceptible to outliers.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-5\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>R</mml:mi><mml:mi>M</mml:mi><mml:mi>S</mml:mi><mml:mi>E</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:msqrt><mml:mfrac><mml:mrow><mml:msubsup><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:msubsup><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mover accent=\"true\"><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>^</mml:mo></mml:mover><mml:mo>−</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:mi>n</mml:mi></mml:mfrac></mml:msqrt><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">MAE</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The mean difference between the predicted and actual values.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">It reflects the actual situation of prediction error.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-6\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>M</mml:mi><mml:mi>A</mml:mi><mml:mi>E</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mi>n</mml:mi></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mspace width=\"0.33em\"/><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:munderover><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mrow><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>−</mml:mo><mml:mover accent=\"true\"><mml:msub><mml:mi>y</mml:mi><mml:mi>i</mml:mi></mml:msub><mml:mo>^</mml:mo></mml:mover></mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>\n</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6660-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Correlation evaluation parameters of the confusion matrix.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Parameter</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Definition</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Formula<sup>[</sup>\n##REF##32128792##\n36\n##, ##REF##31898477##\n40\n##\n<sup>]</sup>\n</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ACC</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The proportion of all instances predicted correctly.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-7\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>A</mml:mi><mml:mi>C</mml:mi><mml:mi>C</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>T</mml:mi><mml:mi>P</mml:mi><mml:mo>+</mml:mo><mml:mi>T</mml:mi><mml:mi>N</mml:mi></mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:mi>P</mml:mi><mml:mo>+</mml:mo><mml:mi>T</mml:mi><mml:mi>N</mml:mi><mml:mo>+</mml:mo><mml:mi>F</mml:mi><mml:mi>P</mml:mi><mml:mo>+</mml:mo><mml:mi>F</mml:mi><mml:mi>N</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PPV</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The proportion of instances that are predicted to be positive and turned out to be positive.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-8\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>P</mml:mi><mml:mi>P</mml:mi><mml:mi>V</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>T</mml:mi><mml:mi>P</mml:mi></mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:mi>P</mml:mi><mml:mo>+</mml:mo><mml:mi>F</mml:mi><mml:mi>P</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">TPR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The proportion of instances predicted to be positive and actually positive to all positive instances.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-9\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:mi>P</mml:mi><mml:mi>R</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>T</mml:mi><mml:mi>P</mml:mi></mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:mi>P</mml:mi><mml:mo>+</mml:mo><mml:mi>F</mml:mi><mml:mi>N</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">TNR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The proportion of instances that were predicted to be negative and were actually negative to all negative instances.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-10\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:mi>N</mml:mi><mml:mi>R</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>T</mml:mi><mml:mi>N</mml:mi></mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:mi>N</mml:mi><mml:mo>+</mml:mo><mml:mi>F</mml:mi><mml:mi>P</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FPR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The proportion of instances that are predicted to be positive and actually negative to all negative instances.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-11\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>F</mml:mi><mml:mi>P</mml:mi><mml:mi>R</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>F</mml:mi><mml:mi>P</mml:mi></mml:mrow><mml:mrow><mml:mi>F</mml:mi><mml:mi>P</mml:mi><mml:mo>+</mml:mo><mml:mi>T</mml:mi><mml:mi>N</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FNR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The proportion of instances that are predicted to be negative and actually positive to all positive instances.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-12\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>F</mml:mi><mml:mi>N</mml:mi><mml:mi>R</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>F</mml:mi><mml:mi>N</mml:mi></mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:mi>N</mml:mi><mml:mo>+</mml:mo><mml:mi>F</mml:mi><mml:mi>N</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">F1 score</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Harmonic average of recall and accuracy.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<mml:math id=\"jats-math-13\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>F</mml:mi><mml:mn>1</mml:mn><mml:mspace width=\"0.33em\"/><mml:mi>s</mml:mi><mml:mi>c</mml:mi><mml:mi>o</mml:mi><mml:mi>r</mml:mi><mml:mi>e</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mn>2</mml:mn><mml:mo>·</mml:mo><mml:mi>T</mml:mi><mml:mi>P</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn><mml:mo>·</mml:mo><mml:mi>T</mml:mi><mml:mi>P</mml:mi><mml:mo>+</mml:mo><mml:mi>F</mml:mi><mml:mi>P</mml:mi><mml:mo>+</mml:mo><mml:mi>F</mml:mi><mml:mi>N</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mspace width=\"0.33em\"/><mml:mn>2</mml:mn><mml:mo>·</mml:mo><mml:mfrac><mml:mrow><mml:mi>P</mml:mi><mml:mi>P</mml:mi><mml:mi>V</mml:mi><mml:mo>·</mml:mo><mml:mi>T</mml:mi><mml:mi>P</mml:mi><mml:mi>R</mml:mi></mml:mrow><mml:mrow><mml:mi>P</mml:mi><mml:mi>P</mml:mi><mml:mi>V</mml:mi><mml:mo>+</mml:mo><mml:mi>T</mml:mi><mml:mi>P</mml:mi><mml:mi>R</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6660-tbl-0003\" content-type=\"Table\"><label>Table 3</label><caption><p>The number of publications on ML for bioelectrocatalytic applications.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"center\" colspan=\"2\" style=\"border-bottom:solid 1px #000000\" rowspan=\"1\">Topic words</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Number of publications on WOS</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Number of publications on WOS (after manual screening)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Number of manual additions to the literature</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Total number of literature</th></tr></thead><tbody><tr><td rowspan=\"6\" align=\"left\" colspan=\"1\">Machine Learning+</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Electrochemical Biosensors</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">58</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">55</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Microbial Fuel Cells</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">26</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">37</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Enzymatic Fuel Cells</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Microbial Electrosynthesis</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Biosolar Cells</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Enzymatic Electrosynthesis</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6660-tbl-0004\" content-type=\"Table\"><label>Table 4</label><caption><p>Applications of ML in EC biosensors.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">#</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Algorithms</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Application Scenarios</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Advantages</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Disadvantages</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Results</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ref.</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cluster and classify the sugar content from the amperometric microbial biosensor.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No additional sample processing is required. Fast measurement.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Data variance percentages of 92.80% and 89.40% for the two main components.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##36618051##51##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">BPNN<xref rid=\"advs6660-tbl4-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Identify and predict glucose and lactate concentrations from the nonenzymatic EC biosensor.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">High selectivity, high sensitivity, and wide range of detection.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The data collection process is time‐consuming and expensive.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">R<xref rid=\"advs6660-tbl4-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>: 0.9997, RSD<xref rid=\"advs6660-tbl4-note-0003\" ref-type=\"table-fn\">\n<sup>c)</sup>\n</xref>: less than 6.5%.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##36397204##38b##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">RF</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Multiplexed point of care biosensor to implement severity‐based disease state stratification.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Solve the problem of bias and high variance of DT. Adding new data will not be affected much.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The accuracy is not high.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The accuracy was 70.88%.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##23##45##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cluster and classify the type and concentration of pesticides from the clay/AuNPs/AChE<xref rid=\"advs6660-tbl4-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref> biosensor.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Effective determination of pesticide types and their corresponding concentrations.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Expensive and complex in some issues.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The total concentration of the pesticide mixture in the actual sample was 0.5 ng mL<sup>−1</sup> for a particularly low identification.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##36385833##52##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">RF</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Apply to ultrasensitive combinatorial EC urine biosensor to implement severity‐based disease state stratification.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Solved the problem of bias and high variance of DT. Adding new data will not be affected much.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Only the 3 most important features were studied.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The accuracy was 98.437%.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##36298107##53##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA, PLS‐DA<xref rid=\"advs6660-tbl4-note-0005\" ref-type=\"table-fn\">\n<sup>e)</sup>\n</xref>, SISSO<xref rid=\"advs6660-tbl4-note-0006\" ref-type=\"table-fn\">\n<sup>f)</sup>\n</xref>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Apply to modular label‐free EC biosensor to make the COVID‐19 screening into healthy and infected groups.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Compared to PLS‐DA, the SISSO‐based learning task provides simpler descriptors.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Lack of further analysis of large samples.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The accuracy was 100%.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##35969505##54##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Determine the main contributors of variation in the BES<xref rid=\"advs6660-tbl4-note-0007\" ref-type=\"table-fn\">\n<sup>g)</sup>\n</xref> signals.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Simple and effective.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Not applicable to nonlinear cases.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The key contributors are pH, VFA<xref rid=\"advs6660-tbl4-note-0008\" ref-type=\"table-fn\">\n<sup>h)</sup>\n</xref> concentration, and temperature.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##26##55##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVD<xref rid=\"advs6660-tbl4-note-0009\" ref-type=\"table-fn\">\n<sup>i)</sup>\n</xref>, PCR<xref rid=\"advs6660-tbl4-note-0010\" ref-type=\"table-fn\">\n<sup>j)</sup>\n</xref>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVD: analyze the MTX<xref rid=\"advs6660-tbl4-note-0011\" ref-type=\"table-fn\">\n<sup>k)</sup>\n</xref> concentration from EIS<xref rid=\"advs6660-tbl4-note-0012\" ref-type=\"table-fn\">\n<sup>l)</sup>\n</xref>, PCR: analyze the correlation between theoretical and measured concentrations of MTX.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVD enables easier analysis of capacitance changes.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The R<sup>2</sup> values of two capacitive biosensors measuring MTX concentration were obtained by PCR as 0.99.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##27##56##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVR, ANN</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Establish the Ca<sup>2+</sup> concentration processing model.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVR: Obtain the global optimal solution. High reliability of prediction.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN: lack of learning, overfitting, and trouble figuring out the network‘s structure.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The EC biosensor could measure Ca<sup>2+</sup> content in the range of 7.5–1000 <sc>m</sc> with a detection limit of 5.48 µ<sc>m</sc> for the optimum algorithm of SVR.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##33465700##57##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA, SVR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Establish relationships between multiple barrier parameters and bacterial concentrations.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Accurately predict <italic toggle=\"yes\">E. coli</italic> concentrations.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVR: solely demonstrates the reliability of detecting <italic toggle=\"yes\">E. coli</italic> concentrations at specified discrete levels.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The average training error and the average prediction error of SVR (<italic toggle=\"yes\">n</italic> = 10) were 1.44 ± 0.052% and 1.52 ± 0.136%, respectively.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##28##58##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Analyze carbendazim residues in tea and rice.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Wide range of applications. No need to study the relationship between processing parameters.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Subjective choices may lead to overfitting or underfitting.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN has a larger R<sup>2</sup> and smaller RMSE and has better performance than all traditional regression models.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##29##59##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">12</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA, SOM<xref rid=\"advs6660-tbl4-note-0013\" ref-type=\"table-fn\">\n<sup>m)</sup>\n</xref>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Classify 31 wine samples from amperometric biosensors.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The SOM treatment provides a nice resolution.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The resolution of PCA is low.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The visualization of the output data based on nonlinear SOM is mostly consistent with linear PCA, enabling the differentiation of wines.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##30744861##60##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">13</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVM</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The decline in enzyme activity over time was used to predict nitrate levels.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Simple and gives the user a better knowledge of the system's behavior.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The kernel function's performance is affected by the type of sample dispersion in the feature space.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The R<sup>2</sup> and MSE were 0.93 and 0.0016, respectively.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##33901823##37g##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">14</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">LDA<xref rid=\"advs6660-tbl4-note-0014\" ref-type=\"table-fn\">\n<sup>n)</sup>\n</xref>, MLE, BPNN</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Classify pathogens from disposable all‐printed electronic biosensors.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Simple, fast, accurate, and economical.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">MLE: computationally expensive, a waste of time. BPNN: when dealing with ambiguity, the user cannot comprehend the link between input and outcome.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The accuracy of LDA, MLE, and BPNN was 100%.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##29651022##61##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">15</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVD, PCA, SVM</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVD and PCA: decompose 152 features into two principal components. SVM: analyze the obstacle data from the impedimetric biosensor.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Gaussian RBF kernel with high correctness.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The dataset for the default kernel settings is not linearly divisible. RBF<xref rid=\"advs6660-tbl4-note-0015\" ref-type=\"table-fn\">\n<sup>o)</sup>\n</xref> kernel suffers from an overfitting problem.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVM achieved an accuracy of 95±4% in cross‐validation and test sample prediction.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##29629449##62##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">16</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">DT, RF, NB, ANN, SVM, LSSVM</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Learn the features of the training samples to predict the concentration of nitrate in liquid samples with a wide pH range (3.5–8.5).</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">It is possible to improve the accuracy and reliability of the response.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVM outperformed other ML methods. SVM predicted the nitrate concentration of plant‐ and bacterial‐based enzymes with R<sup>2</sup> = 0.97 and 0.96.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##REF##33901823##37h##]</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6660-tbl-0005\" content-type=\"Table\"><label>Table 5</label><caption><p>Applications of ML in MFCs.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">#</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Algorithms</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Application Scenarios</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Advantages</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Disadvantages</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Results</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ref.</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">CNN, JSCNN, LR<xref rid=\"advs6660-tbl5-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref>, ANN, SVR, CART<xref rid=\"advs6660-tbl5-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>, KNN</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Predict power generation from PMFCs.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The computation of the hybrid JSCNN model is fast.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The accuracy of LR, ANN, SVR, CART, and KNN is low.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The MAPE<xref rid=\"advs6660-tbl5-note-0003\" ref-type=\"table-fn\">\n<sup>c)</sup>\n</xref> was 11.00% for PMFC data containing wolfsbane and 11.88% for PMFC data containing narrow‐leaved balsam.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##31##64##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Examine how the mixing ratio affects the hydrolytic breakdown and energy recovery of SPW<xref rid=\"advs6660-tbl5-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref>.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Accurate and simple.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Throughout the procedure, the composition of dissolved organic matter was significantly impacted by various SPW mixing ratios.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##32##65##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">KNN, RBF</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Identify compounds based on voltage patterns.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">RBF's improvement on KNN may better determine the confidence level.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">KNN cannot output unknown confidence levels.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">RBF, and consistent interpreters classified gasoline, urea, and fertilizer with 100%, 88%, and 94.5% accuracy.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##34937056##66##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Compare the electroactive capacity of microbial communities.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Select the optimal combination of parameters.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Blue and green lakes with the lowest power output of concentrated cultures.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##33##67##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Record the MFC voltage and run the SVR.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The high correlation between input (characteristics) and output (COD values).</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ignore individual COD values to produce voltage distributions with different peak heights.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The device accurately measured COD in natural pond water samples (R<sup>2</sup> = 0.94).</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##11##18##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Augmented K‐means clustering</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Determine the number of cycles for the stable CV curve. Predict the duration of the stable power output.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Overcome the disadvantages of k‐means clustering.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The parameters are set with a bound on the associated minimum and maximum input values.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">An excellent estimate of the CV cycles required to obtain a stable voltage‐current curve was obtained.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##16##27##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Obtain the best model for predicting the MFC power output.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The power output of MFCs is swiftly and precisely predicted by ANN.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN cannot provide additional outputs.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The R<sup>2</sup> values for SCG<xref rid=\"advs6660-tbl5-note-0005\" ref-type=\"table-fn\">\n<sup>e)</sup>\n</xref> and time series were 0.98802 and 0.99115, respectively.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##33901823##37d##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Evaluate the relationship between different samples.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The relationship between different populations was successfully evaluated.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The microbial structure of UMFCs<xref rid=\"advs6660-tbl5-note-0006\" ref-type=\"table-fn\">\n<sup>f)</sup>\n</xref> was similar to that of the methane bioreactor.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##33848821##68##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">NARX<xref rid=\"advs6660-tbl5-note-0007\" ref-type=\"table-fn\">\n<sup>g)</sup>\n</xref>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Predict the electrical output of MFCs.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Easy to implement, with the ability to switch modes.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Performance is vulnerable to initial values.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">R: 0.99978 (training), 0.99988 (validation), 0.99994 (test), and 0.9998 (whole data set).</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##36397204##38a##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Determine the factors that affect MFC voltage and power density.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA accurately determines the factors.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">These factors include volume, hydraulic retention period, COD loading rate, COD removal, and internal resistance.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##34##69##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Investigate the effect of external electrical impedance.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA shows how external resistance affects the microbial population in the anode chamber.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The external resistance induced changes in substrate removal and power generation, which in turn affected the microbial community.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##33442823##70##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">12</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Simulate the impact of flow rate on the output power of a ceramic MFC made from human urine.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">QN<xref rid=\"advs6660-tbl5-note-0008\" ref-type=\"table-fn\">\n<sup>h)</sup>\n</xref>, LM<xref rid=\"advs6660-tbl5-note-0009\" ref-type=\"table-fn\">\n<sup>i)</sup>\n</xref>, and CG<xref rid=\"advs6660-tbl5-note-0010\" ref-type=\"table-fn\">\n<sup>j)</sup>\n</xref> accurately simulate power prediction.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">It is impossible to predict in advance the ideal number of neurons for the buried layer.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The LM algorithm had the highest accuracy (R = 95%) and the shortest convergence time (7.8s).</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##33335352##12##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">13</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Investigate the effects of Zn addition and circuit patterns on different factors.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The interaction between different factors is successfully analyzed.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Significant accumulation of antibiotics and zinc and circuit patterns significantly influenced the distribution characteristics of ARGs<xref rid=\"advs6660-tbl5-note-0011\" ref-type=\"table-fn\">\n<sup>k)</sup>\n</xref> and bacterial communities.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##32806463##71##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">14</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">RBA<xref rid=\"advs6660-tbl5-note-0012\" ref-type=\"table-fn\">\n<sup>l)</sup>\n</xref>, WkNN<xref rid=\"advs6660-tbl5-note-0013\" ref-type=\"table-fn\">\n<sup>m)</sup>\n</xref>, GMA<xref rid=\"advs6660-tbl5-note-0014\" ref-type=\"table-fn\">\n<sup>n)</sup>\n</xref>, MWA<xref rid=\"advs6660-tbl5-note-0015\" ref-type=\"table-fn\">\n<sup>o)</sup>\n</xref>, HT<sup>2</sup>S<xref rid=\"advs6660-tbl5-note-0016\" ref-type=\"table-fn\">\n<sup>p)</sup>\n</xref>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Control integration in the MMB<xref rid=\"advs6660-tbl5-note-0017\" ref-type=\"table-fn\">\n<sup>q)</sup>\n</xref> control strategy.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">WkNN is able to solve nonlinear problems.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No other multivariate dynamic models are available.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Using WkNN as the model switching method for MMB reduces the average setup time by about 65% compared to the single linear model controller.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##21##39##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">15</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Evaluate the formation of biofilms on the anode surface of MFCs operated.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Successfully analyze significant differences in anode biofilm maturation in different MFCs.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The MFC performance is significantly higher for dynamic adjustment of external resistance, but the operational stability is relatively low.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##32289659##72##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">16</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Adjust the optimal conditions for the proper operation of MFCs.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Provide adaptive solutions and re‐estimation of model parameters in a relatively simple form.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The dataset must contain at least 100 input/output patterns.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The internal resistance of the system was reduced to 1.63 × 10<sup>3</sup> Ω cm<sup>2</sup>. This resulted in a high power density of 8314 mW m<sup>−2</sup>.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##35##73##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">17</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Describe how the microbial community of MFCs is affected by the S: N ratio.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Effective and simple.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The first and second principal components were responsible for 59.59% and 33.04% of the total variance, respectively.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##36##74##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">18</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PLS, KNN, RF, NNET<xref rid=\"advs6660-tbl5-note-0018\" ref-type=\"table-fn\">\n<sup>r)</sup>\n</xref>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Predict resistance and resilience.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">NNET: fully approximate complex nonlinear relationships. RF and KNN: no need to select a feature.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The inadequate sample size for model development and evaluation.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The classification accuracy of the resistance and elasticity classes corresponding to the risk of deactivation was 70.47 ± 15.88% and 65.33 ± 19.71%.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##31790212##22##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">19</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Examine how toxins and microorganisms that produce electricity are related.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Accurate and simple.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The microbial community shifted from left to right with increasing concentrations of Cu (II) and 2,4‐dichlorophenol.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##31759717##75##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">20</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Estimate the voltage of each MFC.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN is developed very quickly and easily.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Time‐consuming and does not provide additional output.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">R</italic> = 0.99662.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##37##76##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">21</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Recursive Bayesian, KNN, Hotelling's T<sup>2</sup>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The suggested control scheme's efficacy is validated, and switching approaches are contrasted.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">KNN is simple and easy to implement.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The stabilization time of the MMB control strategy is reduced by ≈47.3% compared to the single‐model linear proportional‐integral controller.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##38##77##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">22</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Investigate the effects of different temperatures. Analyze the microbial community structure of the anode biofilm.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA successfully visualizes the structure of the anode biofilm community of MFCs.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">A clear separation between the inoculum pretreated at 4 °C and 10 °C, and the inoculum pretreated at low temperatures forms the bacterial community structure.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##31118927##78##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">23</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">GLMNET<xref rid=\"advs6660-tbl5-note-0019\" ref-type=\"table-fn\">\n<sup>s)</sup>\n</xref>, RF, XGBOOST<xref rid=\"advs6660-tbl5-note-0020\" ref-type=\"table-fn\">\n<sup>t)</sup>\n</xref>, NNET, KNN, SVM</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Train input variables and evaluate their ability to predict feed substrates from genomic datasets.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Feed substrates are successfully predicted. The specificity of the MFC‐based biosensor signal is improved.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">More samples and input features need to be considered.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The model developed by the NNET algorithm had the highest accuracy (93 ± 6%), corresponding to a kappa value of 0.87 ± 0.10.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##REF##30909014##20##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">24</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN, RVM, ELM<xref rid=\"advs6660-tbl5-note-0021\" ref-type=\"table-fn\">\n<sup>u)</sup>\n</xref>, GPR<xref rid=\"advs6660-tbl5-note-0022\" ref-type=\"table-fn\">\n<sup>v)</sup>\n</xref>, SVM</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVM is used for classification and other algorithms are used for regression.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">SVM works faster and better in high‐dimensional space. RVM: strong sparsity and generalization ability, short testing time, suitable for online detection.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">ANN: slow convergence and local miniaturization.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">R<sup>2</sup> for offline performance model evaluation: ELM (0.9998)&gt;ANN (0.9983)&gt;RVM (0.9951)&gt;GPR (0.9664)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##39##79##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">25</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Use dairy feed water with different characteristics and analyze using PCA.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">PCA determines the possible reduction in the number of data dimensions generated when manipulating MFCs.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">—</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">The eigenvalue of PC1 was 2.84 with a variance of 35.54%, the eigenvalue of PC2 was 2.04 with a variance of 25.46%, and the eigenvalue of PC3 was 1.56 with a variance of 19.51%.</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[##UREF##40##80##]</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
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[ "<table-wrap-foot><fn id=\"advs6660-tbl4-note-0001\"><label>\n<sup>a)</sup>\n</label><p>BPNN: back propagation neural network</p></fn><fn id=\"advs6660-tbl4-note-0002\"><label>\n<sup>b)</sup>\n</label><p>R: coefficient of correlation</p></fn><fn id=\"advs6660-tbl4-note-0003\"><label>\n<sup>c)</sup>\n</label><p>RSD: relative standard deviation</p></fn><fn id=\"advs6660-tbl4-note-0004\"><label>\n<sup>d)</sup>\n</label><p>Clay/AuNPs/AChE: clay mineral/gold nanoparticles/acetylcholinesterase</p></fn><fn id=\"advs6660-tbl4-note-0005\"><label>\n<sup>e)</sup>\n</label><p>PLS‐DA: partial least squares discriminant analysis</p></fn><fn id=\"advs6660-tbl4-note-0006\"><label>\n<sup>f)</sup>\n</label><p>SISSO: sure independence screening and sparsifying operator</p></fn><fn id=\"advs6660-tbl4-note-0007\"><label>\n<sup>g)</sup>\n</label><p>BES: bio‐electrochemical sensor</p></fn><fn id=\"advs6660-tbl4-note-0008\"><label>\n<sup>h)</sup>\n</label><p>VFA: volatile fatty acid</p></fn><fn id=\"advs6660-tbl4-note-0009\"><label>\n<sup>i)</sup>\n</label><p>SVD: singular value decomposition</p></fn><fn id=\"advs6660-tbl4-note-0010\"><label>\n<sup>j)</sup>\n</label><p>PCR: principal component regression</p></fn><fn id=\"advs6660-tbl4-note-0011\"><label>\n<sup>k)</sup>\n</label><p>MTX: methotrexate</p></fn><fn id=\"advs6660-tbl4-note-0012\"><label>\n<sup>l)</sup>\n</label><p>EIS: electrochemical impedance spectroscopy</p></fn><fn id=\"advs6660-tbl4-note-0013\"><label>\n<sup>m)</sup>\n</label><p>SOM: self‐organized maps</p></fn><fn id=\"advs6660-tbl4-note-0014\"><label>\n<sup>n)</sup>\n</label><p>LDA: a linear discriminant analysis</p></fn><fn id=\"advs6660-tbl4-note-0015\"><label>\n<sup>o)</sup>\n</label><p>RBF: radial basis function</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"advs6660-tbl5-note-0001\"><label>\n<sup>a)</sup>\n</label><p>LR: linear regression</p></fn><fn id=\"advs6660-tbl5-note-0002\"><label>\n<sup>b)</sup>\n</label><p>CART: classification and regression tree</p></fn><fn id=\"advs6660-tbl5-note-0003\"><label>\n<sup>c)</sup>\n</label><p>MAPE: mean absolute percentage error</p></fn><fn id=\"advs6660-tbl5-note-0004\"><label>\n<sup>d)</sup>\n</label><p>SPW: solid potato waste</p></fn><fn id=\"advs6660-tbl5-note-0005\"><label>\n<sup>e)</sup>\n</label><p>SCG: scaled conjugate gradient</p></fn><fn id=\"advs6660-tbl5-note-0006\"><label>\n<sup>f)</sup>\n</label><p>UMFCs: up‐flow air‐cathode chamber microbial fuel cells</p></fn><fn id=\"advs6660-tbl5-note-0007\"><label>\n<sup>g)</sup>\n</label><p>NARX: nonlinear autoregressive networks with exogenous inputs</p></fn><fn id=\"advs6660-tbl5-note-0008\"><label>\n<sup>h)</sup>\n</label><p>QN: Quasi‐Newton</p></fn><fn id=\"advs6660-tbl5-note-0009\"><label>\n<sup>i)</sup>\n</label><p>LM: Levenberg‐Marquardt</p></fn><fn id=\"advs6660-tbl5-note-0010\"><label>\n<sup>j)</sup>\n</label><p>CG: Conjugate Gradient</p></fn><fn id=\"advs6660-tbl5-note-0011\"><label>\n<sup>k)</sup>\n</label><p>ARGs: antibiotic resistance genes</p></fn><fn id=\"advs6660-tbl5-note-0012\"><label>\n<sup>l)</sup>\n</label><p>RBA: recursive Bayesian approach</p></fn><fn id=\"advs6660-tbl5-note-0013\"><label>\n<sup>m)</sup>\n</label><p>WkNN: weighted k‐nearest neighbor</p></fn><fn id=\"advs6660-tbl5-note-0014\"><label>\n<sup>n)</sup>\n</label><p>GMA: gap metric approach</p></fn><fn id=\"advs6660-tbl5-note-0015\"><label>\n<sup>o)</sup>\n</label><p>MWA: multi‐model weighting algorithm</p></fn><fn id=\"advs6660-tbl5-note-0016\"><label>\n<sup>p)</sup>\n</label><p>HT<sup>2</sup>S: Hotelling T‐squared strategy</p></fn><fn id=\"advs6660-tbl5-note-0017\"><label>\n<sup>q)</sup>\n</label><p>MMB: multiple model‐based control</p></fn><fn id=\"advs6660-tbl5-note-0018\"><label>\n<sup>r)</sup>\n</label><p>NNET: neural network</p></fn><fn id=\"advs6660-tbl5-note-0019\"><label>\n<sup>s)</sup>\n</label><p>GLMNET: logistic regression multiclass</p></fn><fn id=\"advs6660-tbl5-note-0020\"><label>\n<sup>t)</sup>\n</label><p>XGBOOST: scalable tree boosting system</p></fn><fn id=\"advs6660-tbl5-note-0021\"><label>\n<sup>u)</sup>\n</label><p>ELM: extreme learning machine</p></fn><fn id=\"advs6660-tbl5-note-0022\"><label>\n<sup>v)</sup>\n</label><p>GPR: Gaussian process regression</p></fn></table-wrap-foot>" ]
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{ "acronym": [], "definition": [] }
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2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 9; 11(2):2306583
oa_package/e5/30/PMC10787072.tar.gz
PMC10787073
37985651
[ "<title>Introduction</title>", "<p>The biological system has embedded sophisticated organisms that hold finely tuned and versatile regulatory processes, allowing them to effectively navigate and respond to changes in their surroundings. For instance, the auto‐capture of prey by Venus flytraps, the automatic closing of the human iris when being exposed to different lighting conditions, and the circadian rhythm of sunflower plants are examples of such complex systems.<sup>[</sup>\n##REF##25209884##\n1\n##\n<sup>]</sup> This rich source of inspiration provides designers and engineers the opportunity to create intelligent robots that possess similar precise and autonomous perception feedback and behavior regulation.</p>", "<p>Different and enormous bioinspired smart materials and actuators, with synergistic environmental responses, have been designed previously to decrease the gap between machinery and the natural world. Such provoked mechanical components can generate active force and motions in response to applied stimuli such as light,<sup>[</sup>\n##REF##33356119##\n2\n##\n<sup>]</sup> temperature,<sup>[</sup>\n##REF##28967260##\n3\n##\n<sup>]</sup> humidity,<sup>[</sup>\n##REF##34643083##\n4\n##\n<sup>]</sup> magnetic fields,<sup>[</sup>\n##UREF##0##\n5\n##\n<sup>]</sup> electric,<sup>[</sup>\n##REF##35648519##\n6\n##\n<sup>]</sup> and pH level<sup>[</sup>\n##REF##35575373##\n7\n##\n<sup>]</sup>), and make a big difference in the fields like soft robotics, artificial muscles, and biomimetic devices.<sup>[</sup>\n##REF##25209884##\n1c\n##\n<sup>]</sup> Besides, the emerging functional materials, like liquid crystal elastomers,<sup>[</sup>\n##REF##34275290##\n8\n##\n<sup>]</sup> stimuli‐responsive hydrogels,<sup>[</sup>\n##REF##28181798##\n9\n##\n<sup>]</sup> thermal‐responsive polymers,<sup>[</sup>\n##UREF##1##\n10\n##\n<sup>]</sup> conducting polymers,<sup>[</sup>\n##REF##27744680##\n11\n##\n<sup>]</sup> dielectric elastomers<sup>[</sup>\n##REF##27008455##\n12\n##\n<sup>]</sup> and magnetic composite materials<sup>[</sup>\n##REF##27671658##\n13\n##\n<sup>]</sup> have significantly boosted the effectiveness of soft actuators in recent years. The exceptional properties of these materials donate the soft actuators' ability to considerably improve the deformation amplitude, generate large force, accelerate the response time, and execute sequential motion output, making them an ideal choice for widespread application in soft robotics and medical devices.<sup>[</sup>\n##REF##34958196##\n14\n##\n<sup>]</sup> However, despite the significant progress in this field, realizing intelligent soft actuators with self‐sensing, real‐time motion feedback, and self‐controlled capabilities remains a huge challenge. Specifically, the most advanced driving strategies currently developed, such as the asymmetric expansion,<sup>[</sup>\n##REF##27636903##\n15\n##\n<sup>]</sup> the pneumatic expansion,<sup>[</sup>\n##UREF##2##\n16\n##\n<sup>]</sup> and the hydraulic drive,<sup>[</sup>\n##REF##28145412##\n17\n##\n<sup>]</sup> typically rely on materials with purely structural functions that cannot be stimulated by trigger signals. As a result, these approaches cannot sense their own movements, which may yield to hampering their overall functionality.</p>", "<p>A traditional strategy for action‐sensing consists of using external cameras and image processing systems to capture the actuation behavior of the soft muscles.<sup>[</sup>\n##UREF##3##\n18\n##\n<sup>]</sup> However, this approach is complex and often immobile. Inspired by biological sensing systems, some researches have showcased soft actuators that incorporate mechanical‐sensing features. Therefore, various sensing devices, based on optical loss,<sup>[</sup>\n##UREF##4##\n19\n##\n<sup>]</sup> capacitance,<sup>[</sup>\n##REF##26941316##\n20\n##\n<sup>]</sup> electroluminescence,<sup>[</sup>\n##REF##26941316##\n20\n##\n<sup>]</sup> triboelectricity,<sup>[</sup>\n##UREF##5##\n21\n##\n<sup>]</sup> and piezoresistivity,<sup>[</sup>\n##UREF##6##\n22\n##\n<sup>]</sup> were physically laminated or embedded with soft actuators to perform the self‐sensing function. For instance, Metin et al.<sup>[</sup>\n##REF##27636903##\n15a\n##\n<sup>]</sup> successfully incorporated flexible microcrack‐based strain sensors onto the pneumatically actuated soft gripper fingers. As a result, the soft gripper fingers were able to accurately discern their touch status, contact force, and bending position. A single elastomer fiber artificial muscle<sup>[</sup>\n##UREF##7##\n23\n##\n<sup>]</sup> was also designed to achieve sensing, signaling, tensile, and torsional actuation by implementing a bi‐sheath buckled carbon nanotube (CNT) skin on an elastomer fiber core. This inventive design enabled the artificial muscle to be actuate and sense using just a single electrical stimulus. In addition, these sensing approaches, when being used in the artificial muscles, involve the application of electric signals, which enables to capture the information relative to the bending and the contractile deformation during actuation. Despite their substantial merits, one potential issue lies in the possibility of damaging the device or separating the interface due to the modulus mismatch between the two components.<sup>[</sup>\n##UREF##8##\n24\n##\n<sup>]</sup> Additionally, few of them could realize closed‐loop control functions to achieve real‐time posture self‐regulation.</p>", "<p>Herein, we proposed a LBL assembling strategy to prevents nanointerfacial detachment or slipping associated with moduli mismatch between the sensing layer and the actuating layer, resulting in stable real‐time sensory feedback and self‐regulation capabilities. We employed a bilayer structure and the classical microcrack‐based structure could facilitate their high sensing performance. The thermally responsive liquid crystal elastomer (LCE), with large and reversible deformation, is selected as the action layer; moreover, the MXene with excellent photothermal conversion and a high Young's modulus (≈330 GPa),<sup>[</sup>\n##REF##29922719##\n25\n##\n<sup>]</sup> is chosen to realize the photothermal driving and enhance the driving force. In addition, MXene possesses high conductivity and can generate radial cracks and axial micro ridges during action when being combined with the contracted LCE, allowing it to simultaneously serve as a sensing layer for the self‐sensing attitude. Besides, the linear cationic polymer PDDA is selected as a mediator and stabilizer to assemble the MXene with the LCE, weakening their modulus mismatch, and enhancing the interface interaction to achieve stable driving and sensing. Furthermore, the PM‐LCE can perform grasping, traction, and crawling movements by controlling the Near‐Infrared (NIR) laser. It could even achieve wing actuation and closed‐loop controlled motion, demonstrating its potential in the fields of bionic robotics, artificial muscles and the intelligence of soft actuators.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Preparation Process of the Actuation Sensing Integrated PM‐LCE</title>", "<p>\n<bold>Figure</bold> ##FIG##0##\n1\n## depicts the preparation process of the PM‐LCE. Firstly, the LCE layer is prepared using Finkelmann's two‐step cross‐linking process. Specifically, the configured LCE monomer solution is prepared, degassed, and injected into a customized poly‐tetra‐fluoro‐ethylene (PTFE) mold to be pre‐crosslinked for ten hours, where 1,4‐bis‐[4‐(6‐acryloyloxyhexyloxy)benzoyl‐oxy]−2‐methylbenzene (RM82) is selected as the liquid crystal monomer, penta‐erythritol tetra (3‐mercapto propionate) (PETMP) as the crosslinker, 1,10‐decane‐di‐thiol (1,10‐DT) as the spacer, 2,2‐di‐methoxy‐2‐phenyl‐acetophenone (DMPA) as the photoinitiator, and di‐propyl‐amine (DPA) as the Michael addition catalyst. Subsequently, the pre‐crosslinked LCE is removed from the mold and cut into the desired shape, then programmed for orientation through mechanical stretching.<sup>[</sup>\n##REF##27418031##\n26\n##\n<sup>]</sup> After that, the second crosslinked, under UV irradiation at 365 nm, is conducted to fix the spatial arrangement of liquid crystal primitives to obtain the monodomain elastomers (optimized thickness is 1 mm). Moreover, the delaminated MXene nanosheets are prepared by selectively etching bulk Ti<sub>3</sub>AlC<sub>2</sub>, followed by subsequent exfoliation in distilled water.<sup>[</sup>\n##UREF##9##\n27\n##\n<sup>]</sup> The obtained Ti<sub>3</sub>C<sub>2</sub>T<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> nanosheets are predominantly ultrathin nanoflakes with a thickness of ≈1.5 nm and lateral length of 2–3 µm ((Figure ##SUPPL##0##S1a,b##, Supporting Information). Therefore, these nanosheets confirm that the Ti<sub>3</sub>AlC<sub>2</sub> MAX is successfully exfoliated into monolayers MXene.<sup>[</sup>\n##UREF##10##\n28\n##\n<sup>]</sup>\n</p>", "<p>Moreover, the colloidal suspension of MXene is stable due to its hydrophilicity and electrostatic repulsion<sup>[</sup>\n##REF##29536044##\n29\n##\n<sup>]</sup> between neighboring nanospheres, and the Tyndall phenomenon can be observed (as shown in Figure ##SUPPL##0##S1c##, Supporting Information). A linear cationic polymer PDDA is selected as a mediator and a stabilizer to ensure that the combined PM‐LCE can be actuated without shedding the PM functional layer. Typically, the Ti<sub>3</sub>C<sub>2</sub>T<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> MXene nanoflakes are negatively charged whereas the linear cationic polymer PDDA is positively charged (−26.7 mV and +19.9 mV by zeta potential respectively). Impacted by the electrostatic interactions, the Ti<sub>3</sub>C<sub>2</sub>T<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> MXene and the PDDA could be assembled layer‐by‐layer (LBL) as a functional layer (denoted as PM layer) on LCE. Specifically, the surface of LCE is treated with oxygen plasma to get a hydrophilic layer (Figure ##SUPPL##0##S2##, Supporting Information). Then the positively charged PDDA is first adsorbed and soaked in DI water to remove the residual weaker PDDA. Subsequently, the PDDA‐LCE layer is immersed in an aqueous dispersion of monolayer MXene to absorb another layer of negatively charged MXene (step iv). Finally, the above two processes (step iv and v) are repeated until the required layers were achieved.</p>", "<p>Besides, to compare the adhesion effects of several assembly processes on the surface of the bilayer membranes, samples are also prepared by applying MXene onto LCE through the methods of spraying and screen printing. All samples prepared by spraying and screen printing exhibit unstable interface adhesion and detachment of the sensing layer. However, the sensing layer and the actuator layer of the PM‐LCE, prepared by the LBL method, are tightly bonded without detachment (Figure ##SUPPL##0##S3##, Supporting Information). This in situ adsorption assembly strategy allows tight adhesion between the PM functional layer and the LCE layer. In addition, the incorporation of long chains of PDDA moduli alleviates the mismatch between the sensing and the actuating layers and contributes to its flexibility.</p>", "<title>Structure and Characterization of PM‐LCE</title>", "<p>The structure and morphology of the multilayer coating are further examined. The Fourier Transform Infrared (FTIR) spectroscopy spectrum is characterized to elucidate the synthesis process of LCE. As shown in <bold>Figure</bold> ##FIG##1##\n2a## and Figure ##SUPPL##0##S4## (Supporting Information), the ─SH stretching vibration peak of PETMP and 1,10‐DT at 2567 cm<sup>−1</sup> and the C═C stretching vibration peak in the liquid crystal monomers at 1630 cm<sup>−1</sup> almost disappear after photopolymerization, demonstrating that the monomers achieve high levels of cross‐linking. The X‐ray diffraction (XRD) pattern (Figure ##SUPPL##0##S5##, Supporting Information) confirms the successful exfoliation of MAX into MXene.<sup>[</sup>\n##UREF##11##\n30\n##\n<sup>]</sup> In addition, the (002) peaks of the PM showed a significant shift downward from 6.9° to 5.6°, indicating an increase in the spacing between MXene layers upon the inclusion of PDDA. With the adsorption of MXene and PDDA alternately, the samples become successively darker with the number of layer pairs increases from 0 to 30 (Figure ##FIG##1##2b##). The SEM cross‐sectional images of PM<sub>20</sub>‐LCE showed a distinct bilayer structure. Added to that, there is a direct positive correlation between the number of assembled layers and the thickness of the PM functional layer, and each pair of layers is about 8 nm (as shown in Figure ##FIG##1##2c## and Figure ##SUPPL##0##S6##, Supporting Information). Furthermore, clear distribution boundaries of Ti elements in MXene and S elements in LCE could be clearly observed in the EDS images (Figure ##SUPPL##0##S7##, Supporting Information), further echoing its bilayer structure.</p>", "<p>Subsequently, polarized optical microscopy (POM), thermal gravity analysis (TGA), and 2D wide‐angle X‐ray diffraction (2D‐WAXD) are deployed to verify the mesomorphic properties of the above LCE samples. As depicted in Figure ##SUPPL##0##S8## (Supporting Information), the pre‐crosslinked LCE exhibits a nematic schlieren texture at 25 °C, and completely turned black at 120 °C, indicating its transition from anisotropy to isotropy while the temperature gets above the clearing point temperature <italic toggle=\"yes\">T</italic>\n<sub>NI</sub>.<sup>[</sup>\n##REF##35040453##\n31\n##\n<sup>]</sup> Moreover, the POM images (Figure ##FIG##1##2d,e##) of the PM‐LCE show the characteristic changes from dark‐field to bright‐field when being observed between crossed or parallel polarizers, confirming that the LCE in the bilayer PM‐LCE displays uniaxial orientation and exhibits monodomain state.<sup>[</sup>\n##REF##34275290##\n8d\n##\n<sup>]</sup> In addition, Figure ##SUPPL##0##S9## (Supporting Information) presents the TGA curves of the monodomain samples, and the decomposition temperature (<italic toggle=\"yes\">T</italic>\n<sub>d</sub>) of LCE and PM‐LCE is approximately 300 °C, indicating that both have good stability. In addition, compared to the pre‐crosslinked and the secondary cross‐linked LCEs, the PM‐LCE exhibits better thermal stability. The phase transition temperature of the samples is then analyzed using the differential scanning calorimetry (DSC) (Figure ##FIG##1##2f##), the glass transition temperature (<italic toggle=\"yes\">T</italic>\n<sub>g</sub>) and the clearing point temperature (<italic toggle=\"yes\">T</italic>\n<sub>NI</sub>) of PM‐LCE appeared at 1 °C and 100 °C respectively, which was consistent with the pure LCE. The 2D wide‐angle X‐ray diffraction (2D‐WAXD) images of LCE film (Figure ##FIG##1##2g##) further confirm that all the above polymeric materials form a nematic phase. The narrow equatorial diffraction arcs, under room temperature, illustrate the uniaxial orientation of the nematic mesogens in LCE along the mechanical stretch direction.<sup>[</sup>\n##UREF##12##\n32\n##\n<sup>]</sup> When the sample warm up to 150 °C, the 2D‐WAXD pattern shows a uniform ring, indicating its transformation into the isotropic phase under this temperature. Based on the fitting of the azimuthal angle plots, the orientation degree of the sample is calculated using the following equation<sup>[</sup>\n##UREF##13##\n33\n##\n<sup>]</sup>:\n\n</p>", "<p>In this equation, Π represents the degree of orientation and <italic toggle=\"yes\">H</italic> corresponds to the half‐maximum width of the azimuthal distribution curve observed in the equatorial reflection. The Π value of PM‐LCE is calculated at about 0.65 under room temperature (Figure ##FIG##1##2h##), indicating a high‐quality uniaxial orientation of the mesogenic directors inside the LCE samples. Furthermore, a high Π value is beneficial for large deformation under temperature stimulation.</p>", "<p>The driving performance of LCEs is greatly influenced by their mechanical properties, so the mechanical measurements of the LCE‐based samples are conducted. As shown in Figure ##FIG##1##2i## and Figure ##SUPPL##0##S10## (Supporting Information), the conventional elastomeric response along with the director (||), are observed in the stress‐strain curves of all monodomain LCE‐based samples. This is in line with the reported elastomeric behavior of the monodomain nematic main‐chain LCEs.<sup>[</sup>\n##REF##29974115##\n34\n##\n<sup>]</sup> Moreover, the PM‐LCE exhibits, in both the parallel and perpendicular orientations, a significantly greater tensile strength compared to LCE, which is mainly due to the MXene that has a very high Young's modulus (a single‐layer modulus of around 330 GPa),<sup>[</sup>\n##REF##29922719##\n25\n##\n<sup>]</sup> and to the adhesion of the PM layer is very strong.</p>", "<title>Mechanical, Photothermal, and Actuating Properties of PM‐LCE</title>", "<p>LCE is a thermal‐responsive shape memory polymer that deforms with temperature changes.<sup>[</sup>\n##UREF##14##\n35\n##\n<sup>]</sup> As illustrated in <bold>Figure</bold> ##FIG##2##\n3a##, during the cycle process between cooling and heating, both PM‐LCE films and pure LCEs will undergo reversible lengthening and shortening as they experience extension and contraction due to the transition from the liquid crystalline phase to the isotropic phase. Meanwhile, the macroscopic motion of the LCE, such as shrinkage, bending, and rotation, could be programmed by editing the microscopic arrangement of the liquid crystal monomers.<sup>[</sup>\n##UREF##15##\n36\n##\n<sup>]</sup> A soft actuator, having a ZZU shape at room temperature, is tailored by customizing a locally oriented PM‐LCE (Figure ##SUPPL##0##S11##, Supporting Information). In this process, we folded the prepolymer to induce orientation of the LCE around the folding angle. Further, we performed secondary polymerization by using UV light (365 nm UV lamp for 30 s) to permanently fix this orientation. As depicted in Figure ##FIG##2##3a##, Figure ##SUPPL##0##S11## (Supporting Information), and Video ##SUPPL##1##S1## (Supporting Information), the ZZU model is deformed when heated up by a heat air gun and reverted to its original shape when the heat source is removed. During the heating process, the oriented liquid crystal monomers transformed from the liquid crystal phase to the isotropic phase, causing the actuators to flatten into the programmed shape, thereby achieving large‐angle deformation of the actuators. Once colling down, the isotropic phase recovered to the nematic state, resulting in reversible shape change.</p>", "<p>To study the thermo‐mechanical properties of LCE and PM‐LCE, a dynamic mechanical analyzer (DMA Q800) is used to investigate the relationship between the sample temperature and the actuation strain. Moreover, DMA's program is utilized to create a temperature‐time curve for the furnace. The initial heating and cooling cycle are implemented to alleviate any internal stress in PM‐LCE material. Therefore, the following heating and cooling cycle data is used to generate a relationship curve connecting temperature and actuation strain (Figure ##SUPPL##0##S12##, Supporting Information). The strain changes of LCE and PM‐LCE are similar (Figure ##FIG##2##3b##), indicating that the PM layer did not affect the thermo‐mechanical properties of LCE. When the temperature increases, the PM‐LCE starts to produce actuation strain, and the sample gradually contracts and shortens. The initial strain change rate is relatively low. However, as the heating temperature rapidly increases, the change rate becomes higher and the highest rate occurs in the temperature range of 80–110 °C. Moreover, as the temperature continues to increase and reaches the range of 110–150 °C, the actuation strain gradually increases, but the change rate slowly decreases. The maximum value of 35% is reached at a temperature of 150 °C. Furthermore, Figure ##FIG##2##3c## and Figure ##SUPPL##0##S13## (Supporting Information) showed the changes of length in the long axis parallel to the orientation direction and the short axis perpendicular to the orientation direction. It is clear that, PM‐LCE can still recover the initial shape after undergoing 100 heating–cooling thermal‐mechanical cycles, demonstrating its excellent shape memory stability.</p>", "<p>The PM functional layer also provides PM‐LCE with excellent photothermal performance. As shown in the UV‐Vis‐NIR absorption spectrum in Figure ##FIG##2##3d##, pure LCE presents a negligible absorption in the visible and infrared regions; however, after absorbing the PM layer, the sample exhibited a wide absorption in the 200–1200 nm region with an absorption peak at 808 nm. Furthermore, the maximum absorption increases with the thickness of the PM layers. To assess the photothermal actuation capabilities of the LCE‐based samples, sophisticated tools, including a thermal imager (Testo 869) and specific light sources, such as an 808 nm NIR laser, are deployed. As indicated in Figure ##FIG##2##3e##, under NIR irradiation, the surface temperature of the pure LCE increases slightly; however, PM<sub>5</sub>‐LCE, PM<sub>10</sub>‐LCE, PM<sub>20</sub>‐LCE and PM<sub>30</sub>‐LCE exhibit significant temperature increases, reaching peaks of 28, 119, 134, 158 and 182°C, respectively. The surface temperature of PM<sub>30</sub>‐LCE reaches a maximum value within 26 seconds. Therefore, Figure ##FIG##2##3f## shows the temperature curves of PM‐LCE at different optical power densities of NIR irradiation. Referring to this figure, the heating rate is positively correlated with the optical power density and the PM layers. Moreover, the actuation stress, generated by the PM‐LCE, is found to be directly proportional to the PM layers and the optical power density (Figure ##FIG##2##3g## and Figures ##SUPPL##0##S14## and ##SUPPL##0##S15##, Supporting Information). In more detail, Figure ##FIG##2##3g## presents the variation of the actuating stress of PM<sub>30</sub>‐LCE with 0.21, 0.45, and 1.05 W cm<sup>−2</sup> of NIR laser where the maximum actuating stresses can reach 0.38, 0.72, and 1.56 MPa respectively. However, pure LCE exhibited almost no infrared driving ability (Figure ##SUPPL##0##S14##, Supporting Information). The actuating stress of PM‐LCE far exceeds human muscles (≈0.35 MPa), making it possible for many biomimetic applications. To visually demonstrate the photothermal actuation performance of the PM‐LCE, a light‐driven lifting experiment is carried out. Referring to Figure ##SUPPL##0##S16## (Supporting Information), the PM‐LCE film (≈53 mg) could easily lift counterpoises with a hook weight of 52, 102, and 202 g, irradiated by the NIR laser. Finally, the maximum lifting weight is more than 4000 times its own weight (200 g of hook weight and 2 g of metal clips).</p>", "<title>Self‐Sensing and Closed‐Loop Control</title>", "<p>The high metallic conductivity (up to 6500 S cm<sup>−1[</sup>\n##UREF##16##\n37\n##\n<sup>]</sup>) of MXene endows the prepared PM‐LCE with good conductivity. As displayed in <bold>Figure</bold> ##FIG##3##\n4a##, the sheet resistance of the PM‐LCE film decreases when the PM layers increase. Moreover, PM<sub>30</sub>‐LCE has a sheet resistance of 180 KΩ sq<sup>−1</sup>, which is consistent with the previous reports.<sup>[</sup>\n##REF##29536044##\n29b\n##\n<sup>]</sup> Meanwhile, to eliminate the influence of the temperature on the sensor signal, its conductivity is tested at different temperatures. Therefore, Figure ##FIG##3##4b## shows that the resistance of the MXene can remain relatively stable within 0– 200 °C, allowing it to be used as a sensor under variable temperature conditions. Upon being stimulated by the IR light, the photothermal effect causes a change in the local temperature of the PM‐LCE, leading to shorten (or enlarge) the sample in the orientation direction and deformation in the direction perpendicular to the orientation. Figure ##FIG##3##4c## exhibited the resistance change as a function of the applied strain for the optimized PM‐LCE sensor where a characteristic linear response in 0–22% regions is observed. This is a novel strain sensing that differs from the traditional microcracks‐based strain sensing, which reduces the conductive path and increases the resistance under strain. The calculated sensitivity values of the Gauge factors (GF) for these regions are 4.7. The linear response of the PM‐LCE sensing film represents the result of uniform formation of the recoverable radial cracks and axial micro ridges across the whole film, which can be restored to a relatively flat state after the removal of light stimulation (Figure ##FIG##3##4e–g##). Finally, the relative resistance changes of the proposed strain sensor, under cyclic strain, are recorded as shown in Figure ##SUPPL##0##S17## (Supporting Information), and the stable response curve shows its good sensing stability. Compared with embedded structure<sup>[</sup>\n##REF##33356119##\n2c\n##\n<sup>]</sup> or device that involving complex components,<sup>[</sup>\n##REF##35648519##\n6c\n##\n<sup>]</sup> this bilayer‐structured self‐sensing actuator, employed classical microcrack sensing theory to monitor motion, is more simplified and could facilitate higher sensing performance.</p>", "<p>The principle of suppressed interface mismatch and stable response is illustrated in Figure ##FIG##3##4d##. Taking the orientation direction of the liquid crystalline motif as the axis, when the PM‐LCE performs shrink actuation, the PM layer forms recoverable radial cracks and axial micro ridges as shown in Figure ##FIG##3##4d,f##. This leads to the increase in the charge transport pathways and to the decrease in the resistance. During the deformation process, MXene nanosheets tightly adhere to the LCE layer due to the electrostatic interaction with PDDA. Thus, the radial cracks and the axial micro ridges can recover to their initial state. However, for samples prepared using printing or spraying methods, there is only a weak van der Waals force between MXene and LCE, resulting in detachment due to the interface mismatch after multiple movements (Figure ##SUPPL##0##S4##, Supporting Information). By using the LBL assembly strategy and the electrostatic interaction, the potential issues, caused by the difference in the moduli between the sensing and actuating layers in smart sensors can be effectively addressed. These strategies work together to prevent the unstable combination and response of the sensors, ensuring therefore an accurate and reliable readings.</p>", "<p>Furthermore, the self‐sensing function with closed‐loop control is indispensable in the development of intelligent soft actuators. Inspired by the spontaneous response of human muscles and the octopus tentacles, the PM‐LCE‐based closed‐loop control system is analyzed (<bold>Figure</bold> ##FIG##4##\n5a##). After being irradiated by the NIR light, the PM‐LCE will contract and actuate, and the resistance will change accordingly. The microcontroller unit receives the signal of the resistance change, identify it, and issues a command to modulate the NIR laser irradiation to realize the closed‐loop control of the PM‐LCE actuation (Figure ##FIG##4##5b##). The light‐driven dragonflies are assembled to explore the self‐sensing and closed‐loop control functions. When stimulated by a NIR laser, the PM‐LCE is heated to drive the dragonfly's wings (Figure ##FIG##4##5c##). After several preactivated deformations, the PM layer can reach a stable stage without significant detachment to form stable microcracks. By connecting wires at both ends, the resistance signal of the PM‐LCE motion can be monitored in real‐time. Meanwhile, the PM‐LCE can adapt to feedback changes in the state of motion through resistance signals. The correspondence between the bending angle and the resistance during PM‐LCE bending are shown in Figure ##FIG##4##5d##. Once a fixed angle command is inserted, the closed‐loop control system identifies the existing position through resistance and achieves specific position adjustments by adjusting the light source (Figure ##FIG##4##5e## and Video ##SUPPL##2##S2##, Supporting Information). The establishment of this closed‐loop control system can offer valuable insight for precise control and equipment intelligence in the future.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Preparation Process of the Actuation Sensing Integrated PM‐LCE</title>", "<p>\n<bold>Figure</bold> ##FIG##0##\n1\n## depicts the preparation process of the PM‐LCE. Firstly, the LCE layer is prepared using Finkelmann's two‐step cross‐linking process. Specifically, the configured LCE monomer solution is prepared, degassed, and injected into a customized poly‐tetra‐fluoro‐ethylene (PTFE) mold to be pre‐crosslinked for ten hours, where 1,4‐bis‐[4‐(6‐acryloyloxyhexyloxy)benzoyl‐oxy]−2‐methylbenzene (RM82) is selected as the liquid crystal monomer, penta‐erythritol tetra (3‐mercapto propionate) (PETMP) as the crosslinker, 1,10‐decane‐di‐thiol (1,10‐DT) as the spacer, 2,2‐di‐methoxy‐2‐phenyl‐acetophenone (DMPA) as the photoinitiator, and di‐propyl‐amine (DPA) as the Michael addition catalyst. Subsequently, the pre‐crosslinked LCE is removed from the mold and cut into the desired shape, then programmed for orientation through mechanical stretching.<sup>[</sup>\n##REF##27418031##\n26\n##\n<sup>]</sup> After that, the second crosslinked, under UV irradiation at 365 nm, is conducted to fix the spatial arrangement of liquid crystal primitives to obtain the monodomain elastomers (optimized thickness is 1 mm). Moreover, the delaminated MXene nanosheets are prepared by selectively etching bulk Ti<sub>3</sub>AlC<sub>2</sub>, followed by subsequent exfoliation in distilled water.<sup>[</sup>\n##UREF##9##\n27\n##\n<sup>]</sup> The obtained Ti<sub>3</sub>C<sub>2</sub>T<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> nanosheets are predominantly ultrathin nanoflakes with a thickness of ≈1.5 nm and lateral length of 2–3 µm ((Figure ##SUPPL##0##S1a,b##, Supporting Information). Therefore, these nanosheets confirm that the Ti<sub>3</sub>AlC<sub>2</sub> MAX is successfully exfoliated into monolayers MXene.<sup>[</sup>\n##UREF##10##\n28\n##\n<sup>]</sup>\n</p>", "<p>Moreover, the colloidal suspension of MXene is stable due to its hydrophilicity and electrostatic repulsion<sup>[</sup>\n##REF##29536044##\n29\n##\n<sup>]</sup> between neighboring nanospheres, and the Tyndall phenomenon can be observed (as shown in Figure ##SUPPL##0##S1c##, Supporting Information). A linear cationic polymer PDDA is selected as a mediator and a stabilizer to ensure that the combined PM‐LCE can be actuated without shedding the PM functional layer. Typically, the Ti<sub>3</sub>C<sub>2</sub>T<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> MXene nanoflakes are negatively charged whereas the linear cationic polymer PDDA is positively charged (−26.7 mV and +19.9 mV by zeta potential respectively). Impacted by the electrostatic interactions, the Ti<sub>3</sub>C<sub>2</sub>T<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> MXene and the PDDA could be assembled layer‐by‐layer (LBL) as a functional layer (denoted as PM layer) on LCE. Specifically, the surface of LCE is treated with oxygen plasma to get a hydrophilic layer (Figure ##SUPPL##0##S2##, Supporting Information). Then the positively charged PDDA is first adsorbed and soaked in DI water to remove the residual weaker PDDA. Subsequently, the PDDA‐LCE layer is immersed in an aqueous dispersion of monolayer MXene to absorb another layer of negatively charged MXene (step iv). Finally, the above two processes (step iv and v) are repeated until the required layers were achieved.</p>", "<p>Besides, to compare the adhesion effects of several assembly processes on the surface of the bilayer membranes, samples are also prepared by applying MXene onto LCE through the methods of spraying and screen printing. All samples prepared by spraying and screen printing exhibit unstable interface adhesion and detachment of the sensing layer. However, the sensing layer and the actuator layer of the PM‐LCE, prepared by the LBL method, are tightly bonded without detachment (Figure ##SUPPL##0##S3##, Supporting Information). This in situ adsorption assembly strategy allows tight adhesion between the PM functional layer and the LCE layer. In addition, the incorporation of long chains of PDDA moduli alleviates the mismatch between the sensing and the actuating layers and contributes to its flexibility.</p>", "<title>Structure and Characterization of PM‐LCE</title>", "<p>The structure and morphology of the multilayer coating are further examined. The Fourier Transform Infrared (FTIR) spectroscopy spectrum is characterized to elucidate the synthesis process of LCE. As shown in <bold>Figure</bold> ##FIG##1##\n2a## and Figure ##SUPPL##0##S4## (Supporting Information), the ─SH stretching vibration peak of PETMP and 1,10‐DT at 2567 cm<sup>−1</sup> and the C═C stretching vibration peak in the liquid crystal monomers at 1630 cm<sup>−1</sup> almost disappear after photopolymerization, demonstrating that the monomers achieve high levels of cross‐linking. The X‐ray diffraction (XRD) pattern (Figure ##SUPPL##0##S5##, Supporting Information) confirms the successful exfoliation of MAX into MXene.<sup>[</sup>\n##UREF##11##\n30\n##\n<sup>]</sup> In addition, the (002) peaks of the PM showed a significant shift downward from 6.9° to 5.6°, indicating an increase in the spacing between MXene layers upon the inclusion of PDDA. With the adsorption of MXene and PDDA alternately, the samples become successively darker with the number of layer pairs increases from 0 to 30 (Figure ##FIG##1##2b##). The SEM cross‐sectional images of PM<sub>20</sub>‐LCE showed a distinct bilayer structure. Added to that, there is a direct positive correlation between the number of assembled layers and the thickness of the PM functional layer, and each pair of layers is about 8 nm (as shown in Figure ##FIG##1##2c## and Figure ##SUPPL##0##S6##, Supporting Information). Furthermore, clear distribution boundaries of Ti elements in MXene and S elements in LCE could be clearly observed in the EDS images (Figure ##SUPPL##0##S7##, Supporting Information), further echoing its bilayer structure.</p>", "<p>Subsequently, polarized optical microscopy (POM), thermal gravity analysis (TGA), and 2D wide‐angle X‐ray diffraction (2D‐WAXD) are deployed to verify the mesomorphic properties of the above LCE samples. As depicted in Figure ##SUPPL##0##S8## (Supporting Information), the pre‐crosslinked LCE exhibits a nematic schlieren texture at 25 °C, and completely turned black at 120 °C, indicating its transition from anisotropy to isotropy while the temperature gets above the clearing point temperature <italic toggle=\"yes\">T</italic>\n<sub>NI</sub>.<sup>[</sup>\n##REF##35040453##\n31\n##\n<sup>]</sup> Moreover, the POM images (Figure ##FIG##1##2d,e##) of the PM‐LCE show the characteristic changes from dark‐field to bright‐field when being observed between crossed or parallel polarizers, confirming that the LCE in the bilayer PM‐LCE displays uniaxial orientation and exhibits monodomain state.<sup>[</sup>\n##REF##34275290##\n8d\n##\n<sup>]</sup> In addition, Figure ##SUPPL##0##S9## (Supporting Information) presents the TGA curves of the monodomain samples, and the decomposition temperature (<italic toggle=\"yes\">T</italic>\n<sub>d</sub>) of LCE and PM‐LCE is approximately 300 °C, indicating that both have good stability. In addition, compared to the pre‐crosslinked and the secondary cross‐linked LCEs, the PM‐LCE exhibits better thermal stability. The phase transition temperature of the samples is then analyzed using the differential scanning calorimetry (DSC) (Figure ##FIG##1##2f##), the glass transition temperature (<italic toggle=\"yes\">T</italic>\n<sub>g</sub>) and the clearing point temperature (<italic toggle=\"yes\">T</italic>\n<sub>NI</sub>) of PM‐LCE appeared at 1 °C and 100 °C respectively, which was consistent with the pure LCE. The 2D wide‐angle X‐ray diffraction (2D‐WAXD) images of LCE film (Figure ##FIG##1##2g##) further confirm that all the above polymeric materials form a nematic phase. The narrow equatorial diffraction arcs, under room temperature, illustrate the uniaxial orientation of the nematic mesogens in LCE along the mechanical stretch direction.<sup>[</sup>\n##UREF##12##\n32\n##\n<sup>]</sup> When the sample warm up to 150 °C, the 2D‐WAXD pattern shows a uniform ring, indicating its transformation into the isotropic phase under this temperature. Based on the fitting of the azimuthal angle plots, the orientation degree of the sample is calculated using the following equation<sup>[</sup>\n##UREF##13##\n33\n##\n<sup>]</sup>:\n\n</p>", "<p>In this equation, Π represents the degree of orientation and <italic toggle=\"yes\">H</italic> corresponds to the half‐maximum width of the azimuthal distribution curve observed in the equatorial reflection. The Π value of PM‐LCE is calculated at about 0.65 under room temperature (Figure ##FIG##1##2h##), indicating a high‐quality uniaxial orientation of the mesogenic directors inside the LCE samples. Furthermore, a high Π value is beneficial for large deformation under temperature stimulation.</p>", "<p>The driving performance of LCEs is greatly influenced by their mechanical properties, so the mechanical measurements of the LCE‐based samples are conducted. As shown in Figure ##FIG##1##2i## and Figure ##SUPPL##0##S10## (Supporting Information), the conventional elastomeric response along with the director (||), are observed in the stress‐strain curves of all monodomain LCE‐based samples. This is in line with the reported elastomeric behavior of the monodomain nematic main‐chain LCEs.<sup>[</sup>\n##REF##29974115##\n34\n##\n<sup>]</sup> Moreover, the PM‐LCE exhibits, in both the parallel and perpendicular orientations, a significantly greater tensile strength compared to LCE, which is mainly due to the MXene that has a very high Young's modulus (a single‐layer modulus of around 330 GPa),<sup>[</sup>\n##REF##29922719##\n25\n##\n<sup>]</sup> and to the adhesion of the PM layer is very strong.</p>", "<title>Mechanical, Photothermal, and Actuating Properties of PM‐LCE</title>", "<p>LCE is a thermal‐responsive shape memory polymer that deforms with temperature changes.<sup>[</sup>\n##UREF##14##\n35\n##\n<sup>]</sup> As illustrated in <bold>Figure</bold> ##FIG##2##\n3a##, during the cycle process between cooling and heating, both PM‐LCE films and pure LCEs will undergo reversible lengthening and shortening as they experience extension and contraction due to the transition from the liquid crystalline phase to the isotropic phase. Meanwhile, the macroscopic motion of the LCE, such as shrinkage, bending, and rotation, could be programmed by editing the microscopic arrangement of the liquid crystal monomers.<sup>[</sup>\n##UREF##15##\n36\n##\n<sup>]</sup> A soft actuator, having a ZZU shape at room temperature, is tailored by customizing a locally oriented PM‐LCE (Figure ##SUPPL##0##S11##, Supporting Information). In this process, we folded the prepolymer to induce orientation of the LCE around the folding angle. Further, we performed secondary polymerization by using UV light (365 nm UV lamp for 30 s) to permanently fix this orientation. As depicted in Figure ##FIG##2##3a##, Figure ##SUPPL##0##S11## (Supporting Information), and Video ##SUPPL##1##S1## (Supporting Information), the ZZU model is deformed when heated up by a heat air gun and reverted to its original shape when the heat source is removed. During the heating process, the oriented liquid crystal monomers transformed from the liquid crystal phase to the isotropic phase, causing the actuators to flatten into the programmed shape, thereby achieving large‐angle deformation of the actuators. Once colling down, the isotropic phase recovered to the nematic state, resulting in reversible shape change.</p>", "<p>To study the thermo‐mechanical properties of LCE and PM‐LCE, a dynamic mechanical analyzer (DMA Q800) is used to investigate the relationship between the sample temperature and the actuation strain. Moreover, DMA's program is utilized to create a temperature‐time curve for the furnace. The initial heating and cooling cycle are implemented to alleviate any internal stress in PM‐LCE material. Therefore, the following heating and cooling cycle data is used to generate a relationship curve connecting temperature and actuation strain (Figure ##SUPPL##0##S12##, Supporting Information). The strain changes of LCE and PM‐LCE are similar (Figure ##FIG##2##3b##), indicating that the PM layer did not affect the thermo‐mechanical properties of LCE. When the temperature increases, the PM‐LCE starts to produce actuation strain, and the sample gradually contracts and shortens. The initial strain change rate is relatively low. However, as the heating temperature rapidly increases, the change rate becomes higher and the highest rate occurs in the temperature range of 80–110 °C. Moreover, as the temperature continues to increase and reaches the range of 110–150 °C, the actuation strain gradually increases, but the change rate slowly decreases. The maximum value of 35% is reached at a temperature of 150 °C. Furthermore, Figure ##FIG##2##3c## and Figure ##SUPPL##0##S13## (Supporting Information) showed the changes of length in the long axis parallel to the orientation direction and the short axis perpendicular to the orientation direction. It is clear that, PM‐LCE can still recover the initial shape after undergoing 100 heating–cooling thermal‐mechanical cycles, demonstrating its excellent shape memory stability.</p>", "<p>The PM functional layer also provides PM‐LCE with excellent photothermal performance. As shown in the UV‐Vis‐NIR absorption spectrum in Figure ##FIG##2##3d##, pure LCE presents a negligible absorption in the visible and infrared regions; however, after absorbing the PM layer, the sample exhibited a wide absorption in the 200–1200 nm region with an absorption peak at 808 nm. Furthermore, the maximum absorption increases with the thickness of the PM layers. To assess the photothermal actuation capabilities of the LCE‐based samples, sophisticated tools, including a thermal imager (Testo 869) and specific light sources, such as an 808 nm NIR laser, are deployed. As indicated in Figure ##FIG##2##3e##, under NIR irradiation, the surface temperature of the pure LCE increases slightly; however, PM<sub>5</sub>‐LCE, PM<sub>10</sub>‐LCE, PM<sub>20</sub>‐LCE and PM<sub>30</sub>‐LCE exhibit significant temperature increases, reaching peaks of 28, 119, 134, 158 and 182°C, respectively. The surface temperature of PM<sub>30</sub>‐LCE reaches a maximum value within 26 seconds. Therefore, Figure ##FIG##2##3f## shows the temperature curves of PM‐LCE at different optical power densities of NIR irradiation. Referring to this figure, the heating rate is positively correlated with the optical power density and the PM layers. Moreover, the actuation stress, generated by the PM‐LCE, is found to be directly proportional to the PM layers and the optical power density (Figure ##FIG##2##3g## and Figures ##SUPPL##0##S14## and ##SUPPL##0##S15##, Supporting Information). In more detail, Figure ##FIG##2##3g## presents the variation of the actuating stress of PM<sub>30</sub>‐LCE with 0.21, 0.45, and 1.05 W cm<sup>−2</sup> of NIR laser where the maximum actuating stresses can reach 0.38, 0.72, and 1.56 MPa respectively. However, pure LCE exhibited almost no infrared driving ability (Figure ##SUPPL##0##S14##, Supporting Information). The actuating stress of PM‐LCE far exceeds human muscles (≈0.35 MPa), making it possible for many biomimetic applications. To visually demonstrate the photothermal actuation performance of the PM‐LCE, a light‐driven lifting experiment is carried out. Referring to Figure ##SUPPL##0##S16## (Supporting Information), the PM‐LCE film (≈53 mg) could easily lift counterpoises with a hook weight of 52, 102, and 202 g, irradiated by the NIR laser. Finally, the maximum lifting weight is more than 4000 times its own weight (200 g of hook weight and 2 g of metal clips).</p>", "<title>Self‐Sensing and Closed‐Loop Control</title>", "<p>The high metallic conductivity (up to 6500 S cm<sup>−1[</sup>\n##UREF##16##\n37\n##\n<sup>]</sup>) of MXene endows the prepared PM‐LCE with good conductivity. As displayed in <bold>Figure</bold> ##FIG##3##\n4a##, the sheet resistance of the PM‐LCE film decreases when the PM layers increase. Moreover, PM<sub>30</sub>‐LCE has a sheet resistance of 180 KΩ sq<sup>−1</sup>, which is consistent with the previous reports.<sup>[</sup>\n##REF##29536044##\n29b\n##\n<sup>]</sup> Meanwhile, to eliminate the influence of the temperature on the sensor signal, its conductivity is tested at different temperatures. Therefore, Figure ##FIG##3##4b## shows that the resistance of the MXene can remain relatively stable within 0– 200 °C, allowing it to be used as a sensor under variable temperature conditions. Upon being stimulated by the IR light, the photothermal effect causes a change in the local temperature of the PM‐LCE, leading to shorten (or enlarge) the sample in the orientation direction and deformation in the direction perpendicular to the orientation. Figure ##FIG##3##4c## exhibited the resistance change as a function of the applied strain for the optimized PM‐LCE sensor where a characteristic linear response in 0–22% regions is observed. This is a novel strain sensing that differs from the traditional microcracks‐based strain sensing, which reduces the conductive path and increases the resistance under strain. The calculated sensitivity values of the Gauge factors (GF) for these regions are 4.7. The linear response of the PM‐LCE sensing film represents the result of uniform formation of the recoverable radial cracks and axial micro ridges across the whole film, which can be restored to a relatively flat state after the removal of light stimulation (Figure ##FIG##3##4e–g##). Finally, the relative resistance changes of the proposed strain sensor, under cyclic strain, are recorded as shown in Figure ##SUPPL##0##S17## (Supporting Information), and the stable response curve shows its good sensing stability. Compared with embedded structure<sup>[</sup>\n##REF##33356119##\n2c\n##\n<sup>]</sup> or device that involving complex components,<sup>[</sup>\n##REF##35648519##\n6c\n##\n<sup>]</sup> this bilayer‐structured self‐sensing actuator, employed classical microcrack sensing theory to monitor motion, is more simplified and could facilitate higher sensing performance.</p>", "<p>The principle of suppressed interface mismatch and stable response is illustrated in Figure ##FIG##3##4d##. Taking the orientation direction of the liquid crystalline motif as the axis, when the PM‐LCE performs shrink actuation, the PM layer forms recoverable radial cracks and axial micro ridges as shown in Figure ##FIG##3##4d,f##. This leads to the increase in the charge transport pathways and to the decrease in the resistance. During the deformation process, MXene nanosheets tightly adhere to the LCE layer due to the electrostatic interaction with PDDA. Thus, the radial cracks and the axial micro ridges can recover to their initial state. However, for samples prepared using printing or spraying methods, there is only a weak van der Waals force between MXene and LCE, resulting in detachment due to the interface mismatch after multiple movements (Figure ##SUPPL##0##S4##, Supporting Information). By using the LBL assembly strategy and the electrostatic interaction, the potential issues, caused by the difference in the moduli between the sensing and actuating layers in smart sensors can be effectively addressed. These strategies work together to prevent the unstable combination and response of the sensors, ensuring therefore an accurate and reliable readings.</p>", "<p>Furthermore, the self‐sensing function with closed‐loop control is indispensable in the development of intelligent soft actuators. Inspired by the spontaneous response of human muscles and the octopus tentacles, the PM‐LCE‐based closed‐loop control system is analyzed (<bold>Figure</bold> ##FIG##4##\n5a##). After being irradiated by the NIR light, the PM‐LCE will contract and actuate, and the resistance will change accordingly. The microcontroller unit receives the signal of the resistance change, identify it, and issues a command to modulate the NIR laser irradiation to realize the closed‐loop control of the PM‐LCE actuation (Figure ##FIG##4##5b##). The light‐driven dragonflies are assembled to explore the self‐sensing and closed‐loop control functions. When stimulated by a NIR laser, the PM‐LCE is heated to drive the dragonfly's wings (Figure ##FIG##4##5c##). After several preactivated deformations, the PM layer can reach a stable stage without significant detachment to form stable microcracks. By connecting wires at both ends, the resistance signal of the PM‐LCE motion can be monitored in real‐time. Meanwhile, the PM‐LCE can adapt to feedback changes in the state of motion through resistance signals. The correspondence between the bending angle and the resistance during PM‐LCE bending are shown in Figure ##FIG##4##5d##. Once a fixed angle command is inserted, the closed‐loop control system identifies the existing position through resistance and achieves specific position adjustments by adjusting the light source (Figure ##FIG##4##5e## and Video ##SUPPL##2##S2##, Supporting Information). The establishment of this closed‐loop control system can offer valuable insight for precise control and equipment intelligence in the future.</p>" ]
[ "<title>Conclusion</title>", "<p>In this paper, an integrated strategy to prepare NIR‐driven and self‐sensing intelligent bilayer soft actuator PM‐LCE was presented. The high‐precision, self‐sensing and feedback loop control functions actuator were realized by combining the actuation and sensing materials into a bilayer membrane through the LBL self‐assembly process. This assembly process prevents potential detachment associated with the moduli mismatch between the sensing layer and the actuating layer interface and exhibits stable interface adhesion and with tightly bonded. Due to the photothermal effects and the high conductivity, the prepared PM‐LCE could simultaneously respond to the light and sense its own motion state. The grasping, traction and crawling movements could be performed with the control of the NIR laser. Finally, the PM‐LCE‐based closed‐loop control system was also developed and demonstrated, which was beneficial for precise control and equipment intelligence in the future. To sum up, the current research provides a new strategy for developing soft actuators integrated with self‐sensing and actuation functions and demonstrates its potential in the fields of bionic robotics, artificial muscles and the intelligence of soft actuators.</p>" ]
[ "<title>Abstract</title>", "<p>More recently, soft actuators have evoked great interest in the next generation of soft robots. Despite significant progress, the majority of current soft actuators suffer from the lack of real‐time sensory feedback and self‐control functions, prohibiting their effective sensing and multitasking functions. Therefore, in this work, a near‐infrared‐driven bimorph membrane, with self‐sensing and feedback loop control functions, is produced by layer by layer (LBL) assembling MXene/PDDA (PM) onto liquid crystal elastomer (LCE) film. The versatile integration strategy successfully prevents the separation issues that arise from moduli mismatch between the sensing and the actuating layers, ultimately resulting in a stable and tightly bonded interface adhesion. As a result, the resultant membrane exhibited excellent mechanical toughness (tensile strengths equal to 16.3 MPa (||)), strong actuation properties (actuation stress equal to 1.56 MPa), and stable self‐sensing (gauge factor equal to 4.72) capabilities. When applying the near‐infrared (NIR) laser control, the system can perform grasping, traction, and crawling movements. Furthermore, the wing actuation and the closed‐loop controlled motion are demonstrated in combination with the insect microcontroller unit (MCU) models. The remote precision control and the self‐sensing capabilities of the soft actuator pave a way for complex and precise task modulation in the future.</p>", "<p>A light‐driven and self‐sensing intelligent bilayer soft actuator, the PM‐liquid crystal elastomer (LCE), built with LCE, MXene, and Poly(dimethyldiallylammonium chloride) (PDDA) is prepared through the layer‐by‐layer self‐assembly strategy; moreover, the high‐precision, self‐sensing and feedback loop control functions are realized. Furthermore, a PM‐LCE‐based closed‐loop control system is also demonstrated.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6886-cit-0073\">\n<string-name>\n<given-names>Y.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Meng</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Gao</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Hao</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Niu</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Liu</surname>\n</string-name>, <article-title>Near‐Infrared Light‐Driven MXene/Liquid Crystal Elastomer Bimorph Membranes for Closed‐Loop Controlled Self‐Sensing Bionic Robots</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2307862</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202307862</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>Y.Y., L.M., and J.Z. contributed equally to this work. The work reported here was supported by National Natural Science Foundation of China (52003253, 52203245), the China Postdoctoral Innovative Talent Support Program (BX 20220274) and Henan Science and Technology Department (222301420004).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6886-fig-0001\"><label>Figure 1</label><caption><p>Schematic diagram of the preparation process of PM‐LCE.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6886-fig-0002\"><label>Figure 2</label><caption><p>a) FTIR spectra of raw materials and different crosslinking states of LCE. b) Photographs of LCE and PM‐LCE with different thicknesses of PM layers. c) Cross‐sectional SEM images of liquid nitrogen embrittlement of PM<sub>20</sub>‐LCE. POM image of LCE membrane d) before and e) after 45° rotation. f) DSC profiles of LCE and PM‐LCE. g) 2D‐WAXD patterns of PM‐LCE. h) Correlation of orientation and temperature of LCE and PM‐LCE. i) Stress–strain curves of samples perpendicular to the orientation of the LCE and the PM‐LCE.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6886-fig-0003\"><label>Figure 3</label><caption><p>Performance characterization and demonstration of soft actuators based on LCE. a) ZZU model with shape memory based on PM‐LCE. b) Shape memory curves of PM‐LCE. c) Schematic diagram of the variation of film deformation (<italic toggle=\"yes\">L</italic>‐<italic toggle=\"yes\">L</italic>\n<sub>0</sub>)/<italic toggle=\"yes\">L</italic>\n<sub>0</sub> with temperature during the warming and cooling of liquid crystal elastomer film. d) UV–vis spectra of neat LCE and PM‐LCE with 5, 10, 20, and 30 PM layer pairs. e) Heat‐up curves under NIR irradiation of neat LCE and PM‐LCE with 5, 10, 20, and 30 PM layer pairs. f) Temperature of PM‐LCE under NIR light irradiation with different optical power densities. g) Actuating stress of PM‐LCE under laser irradiation with different optical power densities.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6886-fig-0004\"><label>Figure 4</label><caption><p>Demonstration of the electrical signal of the PM‐LCE. a) Sheet resistance of PM‐LCE for different thicknesses of PM layers, inset shows the results of PM‐LCE resistance measurements using a multimeter. b) The resistance of MXene as a function of temperature. c) The resistance of the PM‐LCE varies under various strains, GF values can be obtained by linear fitting. d) Schematic representation of the structure of the samples prepared by different processes after deformation. e–g) SEM images of the surface of the PM layer before and after actuation.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6886-fig-0005\"><label>Figure 5</label><caption><p>Demonstration of the application of PM‐LCE for self‐sensing. a) Schematic diagram of closed‐loop control. b) Principle of closed‐loop control of PM‐LCE is realized by MCU. c) Relative resistance of PM‐LCE and the angle of dragonfly's wings as a function of time. d) Application demonstration of the light‐driven dragonfly constructed by PM‐LCE. e) Optical images of dragonfly in a stable attitude during closed‐loop control.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6886-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6886-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 1</p></caption></supplementary-material>", "<supplementary-material id=\"advs6886-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 2</p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"advs6886-note-0001\"><p>Poly dimethyl diallyl ammonium chloride</p></fn></fn-group>" ]
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[ "<media xlink:href=\"ADVS-11-2307862-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2307862-s002.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2307862-s003.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
37
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2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 20; 11(2):2307862
oa_package/db/09/PMC10787073.tar.gz
PMC10787074
38037848
[ "<title>Introduction</title>", "<p>In many industries, for example, seawater desalination, mining, petrochemical, and textile dyeing, high‐salinity wastewater is produced every day.<sup>[</sup>\n##REF##23885720##\n1\n##, ##UREF##0##\n2\n##, ##UREF##1##\n3\n##, ##UREF##2##\n4\n##, ##REF##24769559##\n5\n##, ##REF##24355856##\n6\n##\n<sup>]</sup> The daily discharge of high‐salinity wastewater from a plant may range from 0.1–10 000 m<sup>3</sup>, depending on the industrial process.<sup>[</sup>\n##UREF##3##\n7\n##, ##UREF##4##\n8\n##, ##UREF##5##\n9\n##\n<sup>]</sup> Due to the cost and treatment difficulty, these brines are often discharged into aquatic environments without proper treatment, which causes a fatal impact on the aquatic ecosystems.<sup>[</sup>\n##UREF##6##\n10\n##, ##UREF##7##\n11\n##, ##UREF##8##\n12\n##, ##UREF##9##\n13\n##\n<sup>]</sup> To address this issue, zero liquid discharge (ZLD) technology aimed at eliminating all waste liquid and producing solid salts as the only by‐product, is considered a promising strategy for maximizing resource recycling and minimizing wastewater discharge.<sup>[</sup>\n##REF##31125930##\n14\n##, ##REF##27275867##\n15\n##\n<sup>]</sup> Traditional ZLD systems are composed of a concentration sub‐system and a crystallization sub‐system.<sup>[</sup>\n##REF##35042172##\n16\n##\n<sup>]</sup> The former concentrates the high‐salinity brine to near the saturation brine through reverse osmosis, electrodialysis, membrane distillation, and/or mechanical vapor compression concentrator.<sup>[</sup>\n##UREF##10##\n17\n##\n<sup>]</sup> The latter then extract solid salts from the saturation brine using brine crystallizers or evaporation ponds.<sup>[</sup>\n##UREF##11##\n18\n##\n<sup>]</sup> The crystallization process generally consumes huge amounts of electricity or fossil fuel with high capital costs.<sup>[</sup>\n##UREF##12##\n19\n##\n<sup>]</sup> Therefore, it is crucial to develop a low‐cost, green and high‐performance brine crystallization process.</p>", "<p>Interfacial solar brine crystallizers, which crystallize salts from the near‐saturation brines through local heating by solar‐thermal conversion near the liquid‐air interface, bring a new dimension to ZLD for their potential in efficiency and cost‐effectiveness.<sup>[</sup>\n##UREF##13##\n20\n##, ##REF##34858615##\n21\n##, ##UREF##14##\n22\n##, ##UREF##15##\n23\n##, ##REF##34691905##\n24\n##, ##UREF##16##\n25\n##\n<sup>]</sup> Over the past few years, many efforts have been directed to advance the performance and stability of solar crystallizers for ZLD.<sup>[</sup>\n##REF##34982541##\n26\n##, ##REF##33432803##\n27\n##, ##UREF##17##\n28\n##, ##UREF##18##\n29\n##, ##UREF##19##\n30\n##\n<sup>]</sup> In 2017, Finnerty et al.<sup>[</sup>\n##REF##28892371##\n31\n##\n<sup>]</sup> reported the possibility of achieving ZLD through salt accumulation by evaporation on “artificial leaves”. However, it was found, when treating 15 wt.% NaCl brine, the white salt layer formed on the surface could drastically decrease the evaporation rate to 0.5 kg m<sup>−2</sup> h<sup>−1</sup>. To improve the evaporation performance, various solar brine crystallizers, such as the bio‐mimetic conical evaporator,<sup>[</sup>\n##REF##31988314##\n32\n##\n<sup>]</sup> 3D‐printed polylactic acid/carbon composites synthetic tree crystallizer,<sup>[</sup>\n##REF##37050270##\n33\n##\n<sup>]</sup> volcano‐like solar evaporator,<sup>[</sup>\n##REF##36323206##\n34\n##\n<sup>]</sup> and solar evaporators with localized salt crystallization<sup>[</sup>\n##UREF##20##\n35\n##\n<sup>]</sup> were developed. Nevertheless, in most of these studies, NaCl solution was used as the surrogate for seawater, which however behave very differently from the real brine.<sup>[</sup>\n##REF##33895587##\n36\n##, ##UREF##21##\n37\n##, ##UREF##22##\n38\n##, ##UREF##23##\n39\n##\n<sup>]</sup> In 2021, Zhang et al.<sup>[</sup>\n##REF##33579914##\n40\n##\n<sup>]</sup> presented a novel design with the spatial isolation of salt crystallization from water evaporation and obtained a stable and high evaporation performance (1.61 kg m<sup>−2</sup> h<sup>−1</sup> for 24 h continuous evaporation) in 24 wt.% NaCl brine. However, their solar crystallizer lost its water evaporation capability after 20 h when treating real seawater brine. This is because loose NaCl crystals have less impact on the evaporation surface and brine‐wicking channels, but the multivalent ions in the real brine, especially Mg<sup>2+</sup> and Ca<sup>2+</sup>, would generate the scales to block the pores of the wicking channels to restrain further evaporation.<sup>[</sup>\n##REF##30221518##\n41\n##, ##UREF##24##\n42\n##\n<sup>]</sup> The use of the crystallization inhibitor, nitrilotriacetic acid (NTA), could alleviate this salt‐clogged problem during the real brine evaporation process,<sup>[</sup>\n##UREF##18##\n29\n##\n<sup>]</sup> but it would increase operating costs and bring secondary pollution to the ZLD system. Therefore, the development of solar crystallizers with stable and efficient real brine evaporation and salt accumulation is a remaining challenge and much needed for advanced ZLD technology.</p>", "<p>In this work, we present a rationally designed artificial tree solar crystallizer (ATSC) for the real brine treatment with the ZLD goal. This ATSC is composed of multiple unit cells based on body‐centered cubic (BCC) with an added frame cellular microarchitecture, which could be fabricated by 3D printing. After coating with carbon black (CB) nanoparticles, the ATSC has high solar absorption and superhydrophilicity. Consequently, the cellular microarchitecture of ATSC could facilitate rapid wicking of brine through the multi‐branched and interconnected wicking channels from the “roots” to the “trunk” and then to the “leaves” of this structure. Besides, the 3D porous structure of ATSC hugely increased the available surface area for evaporation. The synergistic effect of ATSC make it an excellent water evaporator under solar radiation. We demonstrated that ATSC had an exceptionally high evaporation rate (2.30 kg m<sup>−2</sup> h<sup>−1</sup> over 2 h exposure) in concentrated real seawater under one sun radiation (1000 W m<sup>−2</sup>) with ultra‐high solar‐thermal conversion efficiency (128%). It was shown that the novel design of ATSC promoted salt crystallization on the outer frame of the unit cell, preventing the blocking of wicking channels for continuous brine evaporation. Additionally, the unit cell structure enhances the inhomogeneity of salt accumulation, resulting in the formed salt crust layer being irregular and highly porous, which ensured stable brine transport and light absorption even after prolonged salt accumulation in concentrated real seawater. As a result, ATSC maintained an exceptionally high and stable brine evaporation performance (average evaporation rate of 1.94 kg m<sup>−2</sup> h<sup>−1</sup>) over 80 h in concentrated real seawater under one sun radiation without manual salt removal. The robust high performance and relatively low operating cost of ATSC is a major step forward toward the sustainable ZLD real brine treatment.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Design and Structure of the Tree‐Inspired Solar Crystallizer</title>", "<p>In nature, trees have the intrinsic ability to use solar energy and groundwater to sustain themselves via the continuous transport of water and nutrients<sup>[</sup>\n##UREF##25##\n43\n##, ##REF##26160930##\n44\n##\n<sup>]</sup> from the bottom roots up to the trunk and top leaves through the vertically aligned channels (<bold>Figure</bold> ##FIG##0##\n1a##), which inspired us to develop an ATSC and study its performance in the high‐salinity brine. Figure ##FIG##0##1b## presents a schematic diagram of the ATSC, which is assembled by roots, trunk, and leaves based on multiple unit cells, thus increasing the available evaporation surface by at least 3.4 times. This cellular microarchitecture of ATSC is scalable with multi‐branches and linked channels, thus enabling ATSC to have good water transmission and vapor escape properties, offering a novel approach toward ZLD brine treatment.</p>", "<p>As illustrated in Figure ##FIG##0##1c##, to treat high‐salinity brine, we constructed an ATSC by one‐step 3D printing and dip coating in a carbon black (CB) solution. The raw material used for 3D printing is a resin consisting of acrylated monomer(s), photoinitiator(s), and urethane dimethacrylate. CB are widely used as solar‐absorbing material because of their excellent light absorption performance and low cost. The adhesion between CB nanoparticles and ATSC mainly involved van der Waals forces. The bonding between CB and ATSC was found to be sufficient during the photothermal process, as no additional CB shedding was found in the subsequent experimental process after the CB‐coated ATSC was rinsed with water immediately after coating. Figure ##SUPPL##0##S1## (Supporting Information) shows the ATSC shaking for five minutes in concentrated seawater. Clearly, there were no visible black particles in the concentrated seawater after shaking, indicating the CB was tightly bound to the solar crystallizer surface. The solar crystallizer was directly placed on top of a polystyrene (PS) foam with a low thermal conductivity (0.034–0.040 W m<sup>−1</sup> K<sup>−1</sup>)<sup>[</sup>\n##UREF##26##\n45\n##\n<sup>]</sup> to minimize the heat loss to the bulk brine. In addition to thermal insulation and light reflection, the PS foam provided buoyancy which enabled the ATSC to float on the brine while the root length of ATSC below the water was ≈2.80 mm (Figure ##SUPPL##0##S2##, Supporting Information). The source brine was transported from the reservoir to the solar crystallizer by the root of the ATSC via capillary action. The evaporated water could be quickly compensated by continuous wicking of water through multi‐branched structures and interconnected channels. Furthermore, the design of ATSC allowed the brine to spread over the entire structure for evaporation. Over time, the salt accumulated on the crystallizer as water flew up the lattice and evaporated through.</p>", "<p>The ATSC consisted of the unit cell of BCC with an added cubic frame (Figure ##FIG##0##1d##), including four body‐diagonals as inter rods and a cubic frame as the outer frame. Generally, the liquid capillary flow in simple tubes can be described by the Young–Laplace equation (ΔP  = 2γcos θ/<italic toggle=\"yes\">R</italic> ) and Jurin's law.<sup>[</sup>\n##UREF##27##\n46\n##\n<sup>]</sup> While it is complex in cellular open‐cell structures and is relevant to the liquid‐solid contact perimeter, surface tension, and contact angle.<sup>[</sup>\n##REF##34194019##\n47\n##\n<sup>]</sup> In our cells, this liquid‐solid boundary in a periodic manner with the liquid position in the cellular structure with local minima at the central node of the cell varied as a function of the struct diameter (D). Increasing the D reduces the effective pore size, the smaller capillary pores are necessary for a larger capillary rise. During the liquid‐wicking process within the cellular structure, the high capillary force and low flow resistance of the unit cell result in a higher overall liquid height. Furthermore, this type of unit cell has good mechanical strength and resistance to deformation,<sup>[</sup>\n##UREF##28##\n48\n##\n<sup>]</sup> which is critical for collecting salts and reusing the crystallizer. This unit cell is a cubic structure with a unit size of 2.5 mm and a D varying from 0.4 to 0.6 mm. As D increases, the effective pore size decreases, leading to the rise in both capillary force and flow resistance of water transport. This cellular structure has numerous tetragonal pyramid cavities formed by the diagonal structs exposed to air, and air has extremely low thermal conductivity (≈0.023 W m<sup>−1</sup> K<sup>−1</sup>)<sup>[</sup>\n##REF##33528238##\n49\n##\n<sup>]</sup> to minimize heat loss, thus enhancing localized heating. Figure ##FIG##0##1e## is the side and top views of ATSC, which shows the height and width of this structure were 41 and 20 mm, respectively.</p>", "<title>Water Transport Performance</title>", "<p>For efficient water evaporation, water transportation, light absorption, and thermal management properties of the solar brine crystallizers are the three key factors. To provide insight into the water transport performance of the ATSC composed of BCC (with added frame) unit cells, the wettability transition, cavity size change of the unit cell after coating with CB, and water‐wicking performance were investigated. To reveal the relationship between the water‐wicking performance and D of the unit cell, a series of columnar structures were prepared with increasing D of 0.40, 0.45, 0.50, 0.55, and 0.60 mm.</p>", "<p>As shown by X‐ray photoelectron spectroscopy (XPS) results, coated with CB increased the amounts of oxygen‐containing groups from 6.9% of O‐C = O to 7.3% of C‐OH (Figure ##SUPPL##0##S3a–c##, Supporting Information). The water contact angles of ATSC changed from 101.6° to 6.9° after coating with CB (<bold>Figure</bold> ##FIG##1##\n2a##), indicating that the surface of the CB‐coated ATSC was superhydrophilic. The scanning electron microscopy (SEM) images show that the surface of the ATSC changed to rather rough after coating with CB (Figure ##SUPPL##0##S3d,e##, Supporting Information). Besides, Figure ##SUPPL##0##S3f## (Supporting Information) indicates the size of CB nanoparticles is ≈30–50 nm. The color of the ATSC became black after coating with CB (Figure ##FIG##1##2c##), demonstrating that CB is successfully loading to the ATSC. As we can see from Figure ##FIG##1##2b and c##, the area marked with red dashed lines has been shrunk when every unit cell has been covered with CB. Figure ##SUPPL##0##S4## (Supporting Information) is the microscopy image of a CB‐coated unit cell, which shows every unit cell has six tetragonal pyramid cavities formed by the diagonal structs.</p>", "<p>It was found that water can flow and wick quickly through the cellular columnar structure after coating with CB and that further increasing D resulted in a narrower effective pore size, which led to the wicking height first increasing and then decreasing (Figure ##FIG##1##2d##). When D was equal to 0.55 mm, the columnar structure reached the maximum wicking height of 42.7 mm in only 180 s (Figure ##FIG##1##2e##), showing the fast water upward transporting capability of the cellular columnar structure. Additionally, Figure ##FIG##1##2f## demonstrates that the wicking velocity increased as D increased first and then started to decrease when the D was larger than 0.55 mm, which was a similar trend to the wicking height. Although a higher capillary height can be obtained by increasing D due to the decreasing the effective pore size, the smaller pores also lead to a greater flow resistance which presents an insufficient permeability, resulting in a lower wicking velocity.<sup>[</sup>\n##UREF##29##\n50\n##\n<sup>]</sup> Considering trade‐offs between capillary action and flow resistance, we choose 0.55 mm as the optimal D to compose the ATSC with continuous and rapid water transport capability and conduct subsequent evaporation experiments.</p>", "<title>Light Absorption and Thermal Management Performance of ATSC</title>", "<p>High‐efficiency light absorption is the primary requirement for maximizing evaporation performance for solar brine crystallizers. Therefore, the sunlight absorption property of the ATSC was evaluated. <bold>Figure</bold> ##FIG##2##\n3a## shows the ATSC absorbed ≈94% of the incident light over the entire wavelength range of the solar spectrum due to the synergistic effects of the inherent black property of the CB and the light‐trapping property of the cellular structure.</p>", "<p>In addition to water transport and sunlight absorption, the thermal localization and photothermal conversion capabilities of the crystallizer are also critical. Therefore, we tested the temperature increase of the ATSC in a dry state on a hot plate (60 °C) for 10 min (Figure ##FIG##2##3b##), and we found that the average temperature of the trunk only increased from 26.2 to 30.8 °C. Figure ##FIG##2##3c## shows that the surface temperature of the wetted ATSC, especially the leaf and trunk portions, almost no increase after heating for 10 min and even lower than environmental temperature, indicating the good heat‐trapping and thermal management ability of ATSC. The above results benefit from the low thermal conductivity of CB‐coated ATSC, thus ensuring that a large amount of heat is localized at the evaporation interface rather than dissipating to the underlying bulk water, thereby enhancing the evaporation performance.</p>", "<p>Here we used the 3D ATSC and a 2D counterpart evaporator as two different solar crystallizers to measure their temperature distribution in pure water under one sun radiation by thermocouples. In the case of the ATSC, the temperature was not uniformly distributed across the entire structure and the temperature of the leaf portion was higher than the trunk portion (Figure ##FIG##2##3d##). As illustrated in Figure ##FIG##2##3e##, the temperature of the leaf portion (position b) was increased from ≈18 to ≈31 °C after 1 h of operation due to the continuous heat input. However, the bulk water (position e) temperature only increased from ≈19 to ≈21 °C, thus confirming the suppression of heat dissipation into the bulk water because of little contact area with water. Temperature evolution of the leaf portion (position a) shows the fast response of the absorber (steady‐state value of 24 °C in 7 min), which is attributed to the good photothermal conversion capability. Besides, the huge temperature difference between the evaporation layer and the bulk water shows an interfacial heating model. Although the temperature of the ATSC's side surface rose with increased radiation time, the temperature of the majority of the side surface remains lower than the surrounding environment temperature (25 °C) due to water transportation and evaporation from the side surface. Additionally, the temperature of ATSC in pure water under dark conditions was also much lower than the ambient temperature (Figure ##SUPPL##0##S5##, Supporting Information). Under the above conditions, the temperature of the side surface of ATSC was lower than the environmental temperature due to evaporative cooling, thus it is possible for ATSC to absorb heat from the air via heat convection, conduction, and radiation, further enhancing evaporation performance.<sup>[</sup>\n##UREF##30##\n51\n##\n<sup>]</sup>\n</p>", "<p>Figure ##FIG##2##3f## shows the temperature distribution of the 2D root evaporator in pure water under one sun radiation. The corresponding temperature variation from 0 to 60 min, including the top photothermal surface and the bottom bulk water, were presented in Figure ##FIG##2##3g##. The top surface of the 2D root evaporator was heated up to ≈33 °C within 7 min and finally reached a steady–state temperature of 34 °C. It was over 11 °C higher than that of bulk water, suggesting it can localize heat at the air/water evaporative interface. Compared with the 2D root evaporator, the 3D tree structure used by ATSC has a greater actual evaporation area and the temperature of its side surface is lower than ambient temperature, thus it may absorb extra energy from the environment. In conclusion, this ATSC has excellent solar absorption efficiency, good heat localization, and outstanding photothermal conversion capability.</p>", "<title>Solar‐Driven Water Evaporation Performance of ATSC in the Different Source Water</title>", "<p>A lab‐made setup with one sun radiation was used to assess the performance of solar‐driven water evaporation (<bold>Figure</bold> ##FIG##3##\n4a##). We prepared three ATSC with a distinct D of 0.45, 0.50, and 0.55 mm, respectively. Figure ##SUPPL##0##S6## (Supporting Information) reveals that the ATSC constituted of 0.55 mm struct has the highest evaporation rate (ER) in pure water, thus we use 0.55 mm as D to construct the 3D tree‐inspired ATSC and 2D root evaporator and compare their evaporation performance in the various source water (Figure ##FIG##3##4b##). The ER of our evaporators is described by the equation <mml:math id=\"jats-math-1\" display=\"inline\"><mml:mrow><mml:mrow><mml:mover accent=\"true\"><mml:mi>m</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>d</mml:mi><mml:mi mathvariant=\"normal\">m</mml:mi></mml:mrow><mml:mrow><mml:mi>A</mml:mi><mml:mo>×</mml:mo><mml:mi>d</mml:mi><mml:mi>t</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>, where <italic toggle=\"yes\">m</italic> is the mass of evaporated water, <italic toggle=\"yes\">t</italic> is time and <italic toggle=\"yes\">A</italic> is the projected ground area.<sup>[</sup>\n##REF##34739209##\n52\n##\n<sup>]</sup> Furthermore, we designed and fabricated a heterogeneous artificial tree solar crystallizer (H‐ATSC) with different D. The root, trunk and leaf portions were composed of unit cells with D of 0.45, 0.50 and 0.55 mm, respectively (Figure ##SUPPL##0##S7a,b##, Supporting Information). The water ER of H‐ATSC was found to be similar to that of the homogeneous cellular structure (viz. ATSC) (Figure ##SUPPL##0##S7c,d##, Supporting Information) since they have similar performance in terms of water transportation, photothermal conversion and thermal management. Consequently, we used the homogeneous cellular structure (viz. ATSC) owing to its structural simplicity as the solar crystallizer for the subsequent wastewater treatment experiments. As Figure ##FIG##3##4c## shows, in the darkness, the ER of pure water is 0.15 kg m<sup>−2</sup> h<sup>−1</sup>, and it became more pronounced with the incorporation of evaporators to 0.42 kg m<sup>−2</sup> h<sup>−1</sup> for the 2D root crystallizer and 1.07 kg m<sup>−2</sup> h<sup>−1</sup> for ATSC, due to the highly increased total surface area available for evaporation by the trunk and leaf portions of the ATSC for at least 3.4 times larger than the projected area of 2D root crystallizer. Similarly, under one sun radiation, the steam generation rate increases from 0.51 kg m<sup>−2</sup> h<sup>−1</sup> for pure water to 1.82 kg m<sup>−2</sup> h<sup>−1</sup> for the 2D root crystallizer in pure water and 3.64 kg m<sup>−2</sup> h<sup>−1</sup> for ATSC under the same conditions. Currently, many interfacial solar crystallizers use NaCl solution to simulate seawater, while treating real seawater, the capacity to evaporate water was almost lost due to the crystallization of high‐valent cations hindering the water‐wicking channels. To investigate the feasibility of ATSC in actual high‐salinity wastewater, 24 wt.% NaCl aqueous solution and concentrated seawater from natural seawater after concentration were chosen for evaporation experiments. Besides sodium and chlorine, the other primary ions in real seawater include magnesium, calcium, and potassium. The concentration of Na<sup>+</sup> increased from 8.8 g L<sup>−1</sup> in natural seawater to 54.0 g L<sup>−1</sup> after concentration. Meantime, the concentrations of Mg<sup>2+</sup>, Ca<sup>2+</sup>, and K<sup>+</sup> were 5.3, 1.3, and 4.0 g L<sup>−1</sup>, respectively in concentrated seawater (Table ##SUPPL##0##S1##, Supporting Information). The ER of ATSC under one sun radiation in the 24 wt.% NaCl solution (2.96 kg m<sup>−2</sup> h<sup>−1</sup>) and the concentrated seawater (2.30 kg m<sup>−2</sup> h<sup>−1</sup>) is lower than in pure water (3.64 kg m<sup>−2</sup> h<sup>−1</sup>), which can be ascribed to the lower water vapor pressure at the evaporative interface of the saline water, thus lowering the driving force for evaporation and decreasing the solar steam generation rate.</p>", "<p>The net ER is the difference between the solar steam generation rate under one sun radiation and the water evaporation rate in darkness. The energy efficiency of the solar crystallizer was calculated as the percentage of the energy that is utilized by net ER compared with the total energy of the incident sunlight to evaluate the photothermal conversion performance (calculation details in Supporting Information Section <xref rid=\"advs6793-sec-0030\" ref-type=\"sec\">2.1</xref>). The ATSC presents ultra‐high energy efficiency when treating various source water (128% of concentrated seawater, 150% of 24 wt.% NaCl, 175% of pure water) compared with the 2D root crystallizer (96% of pure water) (Figure ##FIG##3##4d##), which can be attributed to the environmental energy‐enhanced effect and the vast effective evaporation area. The corresponding heat loss analysis of the evaporation process of ATSC in pure water under radiation can be found in the Supporting Information (Section <xref rid=\"advs6793-sec-0040\" ref-type=\"sec\">2.2</xref>). To investigate the evaporation contribution of the leaf and trunk portions to the overall ATSC, we used some plastic wrap to cover the trunk portion of ATSC, which is denoted as ATSC‐NT, to avoid vapor escape from trunk portion and then we measured its evaporation performance (Figure ##SUPPL##0##S8a,b##, Supporting Information). The weight change of the ATSC‐NT and ATSC in pure water was recorded in real‐time (Figure ##SUPPL##0##S8c##, Supporting Information). After analyzing, we found the ER of ATSC‐NT was lower than that of ATSC due to the reduced evaporation area of ATSC‐NT. Specifically, the solar steam generation rate under one solar radiation for the ATSC‐NT and ATSC was 2.66 and 3.64 kg m<sup>−2</sup> h<sup>−1</sup>, respectively (Figure ##SUPPL##0##S8d##, Supporting Information), which means the trunk contributed 26.9% ER of the whole ATSC. In conclusion, the ATSC with advanced designs in structures and materials can enable effective suppression of heat loss through conduction and energy gain from the environment. Hence, the overall evaporation performance was significantly improved.</p>", "<title>Solar Crystallization of ATSC in Real Seawater Brine</title>", "<p>To further investigate the long‐term operational stability, the different solar crystallizers in various high‐salinity brine were continuously radiated by the simulated sunlight for 80 h in lab conditions. There was no manual salt removal from the solar crystallizer during the whole evaporation process. For comparison, a typical interfacial evaporation system was built with CB‐coated commercial filter paper (diameter of 90 mm) as a photothermal layer and a hydrophilic cotton rod to deliver water (Figure ##SUPPL##0##S9##, Supporting Information). <bold>Figure</bold> ##FIG##4##\n5a## shows the ER of the conventional solar crystallizer quickly decreased by 48% in 0.5 h and plummeted to near zero water evaporation by the end of 9 h. The reason for the rapid decline of the evaporation performance of the conventional solar crystallizer is that the densely packed salt formed in the cotton rod during evaporation hinders water transportation for continuous evaporation (Figure ##SUPPL##0##S10##, Supporting Information). During the whole testing period, the performance of the 2D root crystallizer in concentrated seawater, ATSC in concentrated seawater and 24 wt.% NaCl brine was largely stable, and the average ER of 1.26, 1.94, and 2.42 kg m<sup>−2</sup> h<sup>−1</sup> were achieved, respectively. As mentioned above, the effective evaporation area of the 2D root crystallizer is smaller than those of the ATSC, resulting in lower ER. Furthermore, the vapor pressure of concentrated seawater is lower than that of 24 wt.% NaCl brine, thus decreasing the ER. During 80 h of operation in high‐salinity brine, the ATSC and 2D root crystallizer were gradually covered with a salt layer (Figure ##SUPPL##0##S11##, Supporting Information). Since the brine is not saturated, including 24 wt.% NaCl and concentrated seawater, the salt crystal formed in the early stage may re‐dissolve or collapse when the water wicks to that area again (Figure ##SUPPL##0##S12##, Supporting Information). This phenomenon coupled with environmental disturbances can explain some fluctuation in the ER during the long‐time operation. Compared to treating the concentrated seawater, the salt deposited on the ATSC was faster when treating 24 wt.% NaCl brine, resulting in a more drastic ER curve.</p>", "<p>It is interesting to note that with much salt accumulation on these solar crystallizers during 80 h of operation, the ER was almost constant<sup>[</sup>\n##UREF##31##\n53\n##\n<sup>]</sup> and retained a high ER over 1.0 kg m<sup>−2</sup> h<sup>−1</sup> (except the filter paper) in various high‐salinity brine, thus maintaining a durable water evaporation performance. Compared with the reported 3D evaporators and solar crystallizers, the comprehensive performance (salinity, evaporation rate and duration) of ATSC is optimal (Table ##SUPPL##0##S2##, Supporting Information). For each BCC (with added frame) unit cell, since the evaporation of water only occurs on the outer surface composed of the outer framework, the salt concentration on the outer surface gradually concentrates until it reaches saturation and eventually crystallizes. Therefore, the salt preferentially accumulated on the outer frame of the unit cell instead of the inter rods thus achieving the separation of the crystallization interface and the water transportation pathways. Such a phenomenon is proven by Figure ##FIG##4##5b## and Figure ##SUPPL##0##S13## (Supporting Information). Inside one unit cell, salt crystals first nucleate on the structs, and then with continuous exposure to the light, the salt crystals gradually grow to block the micrometer‐sized cavities formed between the crossed structs (Figure ##SUPPL##0##S14a##, Supporting Information), and finally, the salt blocks the millimeter‐sized cavities on the end face of the unit cell (Figure ##SUPPL##0##S14b##, Supporting Information). Additionally, for the overall tree structure of ATSC, as the leaf portion is closer to the light source and therefore has a higher surface temperature than the trunk portion (Figure ##FIG##2##3e##), the salt preferentially crystallizes on the leaf portion, while the trunk portion has very little salt crystallization (Figure ##FIG##4##5c##), finally ensuring sufficient water supply for the whole tree structure. Specifically, there was a small amount of salt formation on the trunk portion of ATSC after 24 h while salt accumulation on the leaf portion was substantial. 72 h later, a large amount of salt particles formed on the leaf portion due to the crystallization of salt, while a thin salt crust layer formed on the trunk portion of ATSC, covering its external surface (Figure ##SUPPL##0##S14c##, Supporting Information). Meanwhile, the trunk portion also provides a certain evaporation surface, which contributes 26.9% ER of the whole ATSC (Figure ##SUPPL##0##S8##, Supporting Information). During the longtime radiation, the ER of ATSC in concentrated seawater decreased from 2.55 to 1.65 kg m<sup>−2</sup> h<sup>−1</sup>. In contrast to salt‐resistant evaporators, although the water evaporation performance of solar crystallizers can degrade after prolonged salt accumulation, it has the advantage of simultaneously harvesting clean water and solid salts, resulting in ZLD that eliminates liquid waste and maximizes water usage efficiency. Compared to ATSC without salt formation (2.55 kg m<sup>−2</sup> h<sup>−1</sup>), the ER with salt accumulation after stabilization (1.65 kg m<sup>−2</sup> h<sup>−1</sup>) only decreased by 35%, indicating the leaf portion with much salt accumulated was still evaporating. The above results prove that the strategy based on separating the crystallization interface and water‐wicking channel as well as the salt formation sequence from the outer frame to the inter rods and from top to bottom are the main reasons for the stable and ultra‐efficient crystallization of ATSC in concentrated real seawater.</p>", "<p>The structure of the salt crystal collected from the ATSC when treating concentrated seawater was investigated using SEM observation with energy‐dispersive X‐ray spectroscopy (EDS) elemental mapping analysis. Figure ##SUPPL##0##S15## (Supporting Information) shows that the salt crust layer contained sodium, potassium, chlorine, magnesium, calcium, sulfur, and oxygen elements. Figure ##SUPPL##0##S16## (Supporting Information) shows that the salt crystals were piled up in a mixed mode and some micron‐scale pores were still present, which indicates that the formed salt crust layer was not very dense. Then we used optical microscopy to observe the morphology of salts on different parts of the ATSC. Figure ##SUPPL##0##S17## (Supporting Information) shows the salt accumulated on the leaf portion is thicker and whiter due to more salt accumulated than on the trunk portion. Moreover, the formed salt crust layer no matter on the leaf or trunk portion of ATSC exhibits a rough surface and loose porosity. The Kelvin equation<sup>[</sup>\n##UREF##32##\n54\n##\n<sup>]</sup> predicted that evaporation would occur more quickly on the convex/planar salt crystals formed over the ASTC surface than on the concave water surface formed within the pores,<sup>[</sup>\n##UREF##33##\n55\n##\n<sup>]</sup> leading to open pore formation in the crystallization front as salt crystals continued to grow on the convex salt extrudes. Similar preferential sites for salt accumulation are also observed in the process of water evaporation from porous media.<sup>[</sup>\n##UREF##34##\n56\n##, ##REF##34723007##\n57\n##\n<sup>]</sup> Figure ##SUPPL##0##S18## (Supporting Information) shows the salt crystals formed after various durations of light exposure. As can be seen, all salt crystals have rough surfaces and multiple layers of interconnected pores. Water can transport through these pores in salt crystals, giving the salt crystals their transparent color. As Figure ##SUPPL##0##S19a,b## (Supporting Information) show, magnesium sulfate tended to grow in the voids between sodium chloride crystals, and the surface morphology of the two crystals was very different. The former had a rough, uneven, multilayered surface with multiple cracks on the scale of a few hundred nanometers to a few micrometers (Figure ##SUPPL##0##S19c##, Supporting Information), whereas the latter had a smooth and flat surface. Figure ##SUPPL##0##S19d## (Supporting Information) further indicates that magnesium sulfate and sodium chloride crystals mixed in a porous structure. It is believed that nano‐/micro‐pores of salt crystals were formed by the following mechanisms: 1) as Kelvin equation predicts, salt crystal nucleation and growth on previously precipitated crystal surfaces, leading to open pore formation in the crystallization front; 2) the presence of rough and often cracking magnesium sulfate at the interstitial spaces between the sodium chloride crystals promoted the formation of nano‐/micro‐pores. In contrast to most solar crystallizers that allow salt to grow on flat surfaces, our ATSC had open pores along with the cellular structure, which enabled the salt crystals to develop in 3D space<sup>[</sup>\n##REF##34576344##\n58\n##, ##UREF##35##\n59\n##\n<sup>]</sup> and have 10–100 µm pores for the transport of water (Figure ##FIG##4##5d##). This also provides additional evaporation area, thus compensating for the reduced ER due to salt coverage of the original evaporation surface, and maintaining a stable ER for a long time even with a large amount of salt accumulation. In summary, when treating concentrated seawater, the salt crystallized on the ATSC was highly porous, independent of the location of the salt crystallization (inside the unit cell or along the external cellular structure, leaf portion or trunk portion) and the duration of light exposure.</p>", "<p>After 80 h of radiation in concentrated seawater, we used filter paper to contact ATSC. Figure ##FIG##4##5e## demonstrates that the salt layer that was produced on the upper surface of the leaf portion was wet. Moreover, the salt on the trunk portion was also wet (Figure ##SUPPL##0##S20##, Supporting Information), indicating the salt layer does not affect the water transport capability of ATSC. Furthermore, it has been documented that when the water delivery channel in the crystallizer is nanoscale, Mg<sup>2+</sup> and Ca<sup>2+</sup> will block the channel during the evaporation of high‐salinity brine.<sup>[</sup>\n##REF##32305700##\n60\n##\n<sup>]</sup> In contrast, the water channels in ATSC are all in the micron size and the salt layer contains 10–100 µm pores, so the water transportation capability is hardly affected by ion plugging and salt crystallization. Thermal images show that the surface temperature of the ATSC during the solar evaporation experiment using concentrated seawater (right of Figure ##FIG##4##5f##, 36–50 °C) was higher than that using pure water (left of Figure ##FIG##4##5f##, &lt; 35 °C), indicating that a large portion of light was still able to transmit through the salt crystals accumulated on the ATSC for absorption by CB. The solar absorption spectra of the salt crystals collected from ATSC show pure salt crystals possess a high reflectance (&gt; 80%) in the short wavelength range (&lt; 1300 nm) and a slightly lower reflectance (40%–90%) in the long wavelength range, which demonstrates poor solar absorption and energy utilization due to its inherent white color and the poor light‐trapping property (Figure ##SUPPL##0##S21##, Supporting Information). This further suggests that the salt crystals on the surface of the ATSC are almost incapable of absorbing light, while light can reach the surface of the open‐cell cellular structure through the diffuse reflection and scattering and finally be converted into heat, leading to a minimal effect of the accumulated salt on the light absorption efficiency of the ATSC. Moreover, we also studied the solar absorption spectra of the ATSC with salts. Figure ##SUPPL##0##S22## (Supporting Information) indicates that the ATSC with salt has a similar light absorption efficiency with ATSC, especially in the UV–vis region. In other words, the formation of a salt crust layer did not significantly decrease the light absorption efficiency of the ATSC. These results demonstrate that the ATSC has the potential for continuously stable crystallization toward high‐salinity real brine for the ZLD goal.</p>", "<title>Feasibility Under Practical Conditions</title>", "<p>To verify the solar crystallization capability of ATSC in practical applications, we performed outdoor evaporation experiments with an easy‐to‐implement scale‐up solution and use concentrated real seawater as the source brine. <bold>Figure</bold> ##FIG##5##\n6a## shows nine ATSC were assembled to form an array (with inter‐device space of 21 mm uniformly), which was tested on the campus rooftop on December 27, 2022, from 8:00 to 18:00. Moreover, the real‐time temperature, relative humidity, and natural wind velocity variation of the field test were also recorded in Figure ##SUPPL##0##S23## (Supporting Information). The cumulative weight change of the concentrated seawater during the 10 h test period was 17.5 kg m<sup>−2</sup> (Figure ##FIG##5##6b##), indicating its potential for high efficiency and sustainable brine treatment in the future.</p>", "<p>Figure ##FIG##5##6c## shows that the natural solar intensity increased to the highest 0.77 kW m<sup>−2</sup> at noon. It is worth noting that the sun ≈10:00 was blocked by nearby buildings, thus there was a paradoxical drop in solar intensity and therefore ER, which was consistent with the results for temperature and relative humidity in Figure ##SUPPL##0##S23## (Supporting Information). Additionally, the arrayed ATSC delivered an ultra‐high ER of 2.47 kg m<sup>−2</sup> h<sup>−1</sup> in concentrated seawater. Under field conditions, the solar incident angle, environment temperature, relative humidity, and natural wind all affect the evaporation performance of the solar crystallizer. The continuous air convection across the arrayed solar crystallizer improved ER, which explained why the ER of ATSC in outdoor experiments was higher than that in a laboratory under the same solar intensity, indicating the versatility of the environmental‐enhanced solar crystallizer. After 10 h of outdoor testing, all nine ATSC had apparent salt accumulation, especially on the leaf portion (Figure ##FIG##5##6d##), demonstrating that the array of ATSC has great potential for large‐scale salt production under natural sunlight.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Design and Structure of the Tree‐Inspired Solar Crystallizer</title>", "<p>In nature, trees have the intrinsic ability to use solar energy and groundwater to sustain themselves via the continuous transport of water and nutrients<sup>[</sup>\n##UREF##25##\n43\n##, ##REF##26160930##\n44\n##\n<sup>]</sup> from the bottom roots up to the trunk and top leaves through the vertically aligned channels (<bold>Figure</bold> ##FIG##0##\n1a##), which inspired us to develop an ATSC and study its performance in the high‐salinity brine. Figure ##FIG##0##1b## presents a schematic diagram of the ATSC, which is assembled by roots, trunk, and leaves based on multiple unit cells, thus increasing the available evaporation surface by at least 3.4 times. This cellular microarchitecture of ATSC is scalable with multi‐branches and linked channels, thus enabling ATSC to have good water transmission and vapor escape properties, offering a novel approach toward ZLD brine treatment.</p>", "<p>As illustrated in Figure ##FIG##0##1c##, to treat high‐salinity brine, we constructed an ATSC by one‐step 3D printing and dip coating in a carbon black (CB) solution. The raw material used for 3D printing is a resin consisting of acrylated monomer(s), photoinitiator(s), and urethane dimethacrylate. CB are widely used as solar‐absorbing material because of their excellent light absorption performance and low cost. The adhesion between CB nanoparticles and ATSC mainly involved van der Waals forces. The bonding between CB and ATSC was found to be sufficient during the photothermal process, as no additional CB shedding was found in the subsequent experimental process after the CB‐coated ATSC was rinsed with water immediately after coating. Figure ##SUPPL##0##S1## (Supporting Information) shows the ATSC shaking for five minutes in concentrated seawater. Clearly, there were no visible black particles in the concentrated seawater after shaking, indicating the CB was tightly bound to the solar crystallizer surface. The solar crystallizer was directly placed on top of a polystyrene (PS) foam with a low thermal conductivity (0.034–0.040 W m<sup>−1</sup> K<sup>−1</sup>)<sup>[</sup>\n##UREF##26##\n45\n##\n<sup>]</sup> to minimize the heat loss to the bulk brine. In addition to thermal insulation and light reflection, the PS foam provided buoyancy which enabled the ATSC to float on the brine while the root length of ATSC below the water was ≈2.80 mm (Figure ##SUPPL##0##S2##, Supporting Information). The source brine was transported from the reservoir to the solar crystallizer by the root of the ATSC via capillary action. The evaporated water could be quickly compensated by continuous wicking of water through multi‐branched structures and interconnected channels. Furthermore, the design of ATSC allowed the brine to spread over the entire structure for evaporation. Over time, the salt accumulated on the crystallizer as water flew up the lattice and evaporated through.</p>", "<p>The ATSC consisted of the unit cell of BCC with an added cubic frame (Figure ##FIG##0##1d##), including four body‐diagonals as inter rods and a cubic frame as the outer frame. Generally, the liquid capillary flow in simple tubes can be described by the Young–Laplace equation (ΔP  = 2γcos θ/<italic toggle=\"yes\">R</italic> ) and Jurin's law.<sup>[</sup>\n##UREF##27##\n46\n##\n<sup>]</sup> While it is complex in cellular open‐cell structures and is relevant to the liquid‐solid contact perimeter, surface tension, and contact angle.<sup>[</sup>\n##REF##34194019##\n47\n##\n<sup>]</sup> In our cells, this liquid‐solid boundary in a periodic manner with the liquid position in the cellular structure with local minima at the central node of the cell varied as a function of the struct diameter (D). Increasing the D reduces the effective pore size, the smaller capillary pores are necessary for a larger capillary rise. During the liquid‐wicking process within the cellular structure, the high capillary force and low flow resistance of the unit cell result in a higher overall liquid height. Furthermore, this type of unit cell has good mechanical strength and resistance to deformation,<sup>[</sup>\n##UREF##28##\n48\n##\n<sup>]</sup> which is critical for collecting salts and reusing the crystallizer. This unit cell is a cubic structure with a unit size of 2.5 mm and a D varying from 0.4 to 0.6 mm. As D increases, the effective pore size decreases, leading to the rise in both capillary force and flow resistance of water transport. This cellular structure has numerous tetragonal pyramid cavities formed by the diagonal structs exposed to air, and air has extremely low thermal conductivity (≈0.023 W m<sup>−1</sup> K<sup>−1</sup>)<sup>[</sup>\n##REF##33528238##\n49\n##\n<sup>]</sup> to minimize heat loss, thus enhancing localized heating. Figure ##FIG##0##1e## is the side and top views of ATSC, which shows the height and width of this structure were 41 and 20 mm, respectively.</p>", "<title>Water Transport Performance</title>", "<p>For efficient water evaporation, water transportation, light absorption, and thermal management properties of the solar brine crystallizers are the three key factors. To provide insight into the water transport performance of the ATSC composed of BCC (with added frame) unit cells, the wettability transition, cavity size change of the unit cell after coating with CB, and water‐wicking performance were investigated. To reveal the relationship between the water‐wicking performance and D of the unit cell, a series of columnar structures were prepared with increasing D of 0.40, 0.45, 0.50, 0.55, and 0.60 mm.</p>", "<p>As shown by X‐ray photoelectron spectroscopy (XPS) results, coated with CB increased the amounts of oxygen‐containing groups from 6.9% of O‐C = O to 7.3% of C‐OH (Figure ##SUPPL##0##S3a–c##, Supporting Information). The water contact angles of ATSC changed from 101.6° to 6.9° after coating with CB (<bold>Figure</bold> ##FIG##1##\n2a##), indicating that the surface of the CB‐coated ATSC was superhydrophilic. The scanning electron microscopy (SEM) images show that the surface of the ATSC changed to rather rough after coating with CB (Figure ##SUPPL##0##S3d,e##, Supporting Information). Besides, Figure ##SUPPL##0##S3f## (Supporting Information) indicates the size of CB nanoparticles is ≈30–50 nm. The color of the ATSC became black after coating with CB (Figure ##FIG##1##2c##), demonstrating that CB is successfully loading to the ATSC. As we can see from Figure ##FIG##1##2b and c##, the area marked with red dashed lines has been shrunk when every unit cell has been covered with CB. Figure ##SUPPL##0##S4## (Supporting Information) is the microscopy image of a CB‐coated unit cell, which shows every unit cell has six tetragonal pyramid cavities formed by the diagonal structs.</p>", "<p>It was found that water can flow and wick quickly through the cellular columnar structure after coating with CB and that further increasing D resulted in a narrower effective pore size, which led to the wicking height first increasing and then decreasing (Figure ##FIG##1##2d##). When D was equal to 0.55 mm, the columnar structure reached the maximum wicking height of 42.7 mm in only 180 s (Figure ##FIG##1##2e##), showing the fast water upward transporting capability of the cellular columnar structure. Additionally, Figure ##FIG##1##2f## demonstrates that the wicking velocity increased as D increased first and then started to decrease when the D was larger than 0.55 mm, which was a similar trend to the wicking height. Although a higher capillary height can be obtained by increasing D due to the decreasing the effective pore size, the smaller pores also lead to a greater flow resistance which presents an insufficient permeability, resulting in a lower wicking velocity.<sup>[</sup>\n##UREF##29##\n50\n##\n<sup>]</sup> Considering trade‐offs between capillary action and flow resistance, we choose 0.55 mm as the optimal D to compose the ATSC with continuous and rapid water transport capability and conduct subsequent evaporation experiments.</p>", "<title>Light Absorption and Thermal Management Performance of ATSC</title>", "<p>High‐efficiency light absorption is the primary requirement for maximizing evaporation performance for solar brine crystallizers. Therefore, the sunlight absorption property of the ATSC was evaluated. <bold>Figure</bold> ##FIG##2##\n3a## shows the ATSC absorbed ≈94% of the incident light over the entire wavelength range of the solar spectrum due to the synergistic effects of the inherent black property of the CB and the light‐trapping property of the cellular structure.</p>", "<p>In addition to water transport and sunlight absorption, the thermal localization and photothermal conversion capabilities of the crystallizer are also critical. Therefore, we tested the temperature increase of the ATSC in a dry state on a hot plate (60 °C) for 10 min (Figure ##FIG##2##3b##), and we found that the average temperature of the trunk only increased from 26.2 to 30.8 °C. Figure ##FIG##2##3c## shows that the surface temperature of the wetted ATSC, especially the leaf and trunk portions, almost no increase after heating for 10 min and even lower than environmental temperature, indicating the good heat‐trapping and thermal management ability of ATSC. The above results benefit from the low thermal conductivity of CB‐coated ATSC, thus ensuring that a large amount of heat is localized at the evaporation interface rather than dissipating to the underlying bulk water, thereby enhancing the evaporation performance.</p>", "<p>Here we used the 3D ATSC and a 2D counterpart evaporator as two different solar crystallizers to measure their temperature distribution in pure water under one sun radiation by thermocouples. In the case of the ATSC, the temperature was not uniformly distributed across the entire structure and the temperature of the leaf portion was higher than the trunk portion (Figure ##FIG##2##3d##). As illustrated in Figure ##FIG##2##3e##, the temperature of the leaf portion (position b) was increased from ≈18 to ≈31 °C after 1 h of operation due to the continuous heat input. However, the bulk water (position e) temperature only increased from ≈19 to ≈21 °C, thus confirming the suppression of heat dissipation into the bulk water because of little contact area with water. Temperature evolution of the leaf portion (position a) shows the fast response of the absorber (steady‐state value of 24 °C in 7 min), which is attributed to the good photothermal conversion capability. Besides, the huge temperature difference between the evaporation layer and the bulk water shows an interfacial heating model. Although the temperature of the ATSC's side surface rose with increased radiation time, the temperature of the majority of the side surface remains lower than the surrounding environment temperature (25 °C) due to water transportation and evaporation from the side surface. Additionally, the temperature of ATSC in pure water under dark conditions was also much lower than the ambient temperature (Figure ##SUPPL##0##S5##, Supporting Information). Under the above conditions, the temperature of the side surface of ATSC was lower than the environmental temperature due to evaporative cooling, thus it is possible for ATSC to absorb heat from the air via heat convection, conduction, and radiation, further enhancing evaporation performance.<sup>[</sup>\n##UREF##30##\n51\n##\n<sup>]</sup>\n</p>", "<p>Figure ##FIG##2##3f## shows the temperature distribution of the 2D root evaporator in pure water under one sun radiation. The corresponding temperature variation from 0 to 60 min, including the top photothermal surface and the bottom bulk water, were presented in Figure ##FIG##2##3g##. The top surface of the 2D root evaporator was heated up to ≈33 °C within 7 min and finally reached a steady–state temperature of 34 °C. It was over 11 °C higher than that of bulk water, suggesting it can localize heat at the air/water evaporative interface. Compared with the 2D root evaporator, the 3D tree structure used by ATSC has a greater actual evaporation area and the temperature of its side surface is lower than ambient temperature, thus it may absorb extra energy from the environment. In conclusion, this ATSC has excellent solar absorption efficiency, good heat localization, and outstanding photothermal conversion capability.</p>", "<title>Solar‐Driven Water Evaporation Performance of ATSC in the Different Source Water</title>", "<p>A lab‐made setup with one sun radiation was used to assess the performance of solar‐driven water evaporation (<bold>Figure</bold> ##FIG##3##\n4a##). We prepared three ATSC with a distinct D of 0.45, 0.50, and 0.55 mm, respectively. Figure ##SUPPL##0##S6## (Supporting Information) reveals that the ATSC constituted of 0.55 mm struct has the highest evaporation rate (ER) in pure water, thus we use 0.55 mm as D to construct the 3D tree‐inspired ATSC and 2D root evaporator and compare their evaporation performance in the various source water (Figure ##FIG##3##4b##). The ER of our evaporators is described by the equation <mml:math id=\"jats-math-1\" display=\"inline\"><mml:mrow><mml:mrow><mml:mover accent=\"true\"><mml:mi>m</mml:mi><mml:mo>˙</mml:mo></mml:mover><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>d</mml:mi><mml:mi mathvariant=\"normal\">m</mml:mi></mml:mrow><mml:mrow><mml:mi>A</mml:mi><mml:mo>×</mml:mo><mml:mi>d</mml:mi><mml:mi>t</mml:mi></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>, where <italic toggle=\"yes\">m</italic> is the mass of evaporated water, <italic toggle=\"yes\">t</italic> is time and <italic toggle=\"yes\">A</italic> is the projected ground area.<sup>[</sup>\n##REF##34739209##\n52\n##\n<sup>]</sup> Furthermore, we designed and fabricated a heterogeneous artificial tree solar crystallizer (H‐ATSC) with different D. The root, trunk and leaf portions were composed of unit cells with D of 0.45, 0.50 and 0.55 mm, respectively (Figure ##SUPPL##0##S7a,b##, Supporting Information). The water ER of H‐ATSC was found to be similar to that of the homogeneous cellular structure (viz. ATSC) (Figure ##SUPPL##0##S7c,d##, Supporting Information) since they have similar performance in terms of water transportation, photothermal conversion and thermal management. Consequently, we used the homogeneous cellular structure (viz. ATSC) owing to its structural simplicity as the solar crystallizer for the subsequent wastewater treatment experiments. As Figure ##FIG##3##4c## shows, in the darkness, the ER of pure water is 0.15 kg m<sup>−2</sup> h<sup>−1</sup>, and it became more pronounced with the incorporation of evaporators to 0.42 kg m<sup>−2</sup> h<sup>−1</sup> for the 2D root crystallizer and 1.07 kg m<sup>−2</sup> h<sup>−1</sup> for ATSC, due to the highly increased total surface area available for evaporation by the trunk and leaf portions of the ATSC for at least 3.4 times larger than the projected area of 2D root crystallizer. Similarly, under one sun radiation, the steam generation rate increases from 0.51 kg m<sup>−2</sup> h<sup>−1</sup> for pure water to 1.82 kg m<sup>−2</sup> h<sup>−1</sup> for the 2D root crystallizer in pure water and 3.64 kg m<sup>−2</sup> h<sup>−1</sup> for ATSC under the same conditions. Currently, many interfacial solar crystallizers use NaCl solution to simulate seawater, while treating real seawater, the capacity to evaporate water was almost lost due to the crystallization of high‐valent cations hindering the water‐wicking channels. To investigate the feasibility of ATSC in actual high‐salinity wastewater, 24 wt.% NaCl aqueous solution and concentrated seawater from natural seawater after concentration were chosen for evaporation experiments. Besides sodium and chlorine, the other primary ions in real seawater include magnesium, calcium, and potassium. The concentration of Na<sup>+</sup> increased from 8.8 g L<sup>−1</sup> in natural seawater to 54.0 g L<sup>−1</sup> after concentration. Meantime, the concentrations of Mg<sup>2+</sup>, Ca<sup>2+</sup>, and K<sup>+</sup> were 5.3, 1.3, and 4.0 g L<sup>−1</sup>, respectively in concentrated seawater (Table ##SUPPL##0##S1##, Supporting Information). The ER of ATSC under one sun radiation in the 24 wt.% NaCl solution (2.96 kg m<sup>−2</sup> h<sup>−1</sup>) and the concentrated seawater (2.30 kg m<sup>−2</sup> h<sup>−1</sup>) is lower than in pure water (3.64 kg m<sup>−2</sup> h<sup>−1</sup>), which can be ascribed to the lower water vapor pressure at the evaporative interface of the saline water, thus lowering the driving force for evaporation and decreasing the solar steam generation rate.</p>", "<p>The net ER is the difference between the solar steam generation rate under one sun radiation and the water evaporation rate in darkness. The energy efficiency of the solar crystallizer was calculated as the percentage of the energy that is utilized by net ER compared with the total energy of the incident sunlight to evaluate the photothermal conversion performance (calculation details in Supporting Information Section <xref rid=\"advs6793-sec-0030\" ref-type=\"sec\">2.1</xref>). The ATSC presents ultra‐high energy efficiency when treating various source water (128% of concentrated seawater, 150% of 24 wt.% NaCl, 175% of pure water) compared with the 2D root crystallizer (96% of pure water) (Figure ##FIG##3##4d##), which can be attributed to the environmental energy‐enhanced effect and the vast effective evaporation area. The corresponding heat loss analysis of the evaporation process of ATSC in pure water under radiation can be found in the Supporting Information (Section <xref rid=\"advs6793-sec-0040\" ref-type=\"sec\">2.2</xref>). To investigate the evaporation contribution of the leaf and trunk portions to the overall ATSC, we used some plastic wrap to cover the trunk portion of ATSC, which is denoted as ATSC‐NT, to avoid vapor escape from trunk portion and then we measured its evaporation performance (Figure ##SUPPL##0##S8a,b##, Supporting Information). The weight change of the ATSC‐NT and ATSC in pure water was recorded in real‐time (Figure ##SUPPL##0##S8c##, Supporting Information). After analyzing, we found the ER of ATSC‐NT was lower than that of ATSC due to the reduced evaporation area of ATSC‐NT. Specifically, the solar steam generation rate under one solar radiation for the ATSC‐NT and ATSC was 2.66 and 3.64 kg m<sup>−2</sup> h<sup>−1</sup>, respectively (Figure ##SUPPL##0##S8d##, Supporting Information), which means the trunk contributed 26.9% ER of the whole ATSC. In conclusion, the ATSC with advanced designs in structures and materials can enable effective suppression of heat loss through conduction and energy gain from the environment. Hence, the overall evaporation performance was significantly improved.</p>", "<title>Solar Crystallization of ATSC in Real Seawater Brine</title>", "<p>To further investigate the long‐term operational stability, the different solar crystallizers in various high‐salinity brine were continuously radiated by the simulated sunlight for 80 h in lab conditions. There was no manual salt removal from the solar crystallizer during the whole evaporation process. For comparison, a typical interfacial evaporation system was built with CB‐coated commercial filter paper (diameter of 90 mm) as a photothermal layer and a hydrophilic cotton rod to deliver water (Figure ##SUPPL##0##S9##, Supporting Information). <bold>Figure</bold> ##FIG##4##\n5a## shows the ER of the conventional solar crystallizer quickly decreased by 48% in 0.5 h and plummeted to near zero water evaporation by the end of 9 h. The reason for the rapid decline of the evaporation performance of the conventional solar crystallizer is that the densely packed salt formed in the cotton rod during evaporation hinders water transportation for continuous evaporation (Figure ##SUPPL##0##S10##, Supporting Information). During the whole testing period, the performance of the 2D root crystallizer in concentrated seawater, ATSC in concentrated seawater and 24 wt.% NaCl brine was largely stable, and the average ER of 1.26, 1.94, and 2.42 kg m<sup>−2</sup> h<sup>−1</sup> were achieved, respectively. As mentioned above, the effective evaporation area of the 2D root crystallizer is smaller than those of the ATSC, resulting in lower ER. Furthermore, the vapor pressure of concentrated seawater is lower than that of 24 wt.% NaCl brine, thus decreasing the ER. During 80 h of operation in high‐salinity brine, the ATSC and 2D root crystallizer were gradually covered with a salt layer (Figure ##SUPPL##0##S11##, Supporting Information). Since the brine is not saturated, including 24 wt.% NaCl and concentrated seawater, the salt crystal formed in the early stage may re‐dissolve or collapse when the water wicks to that area again (Figure ##SUPPL##0##S12##, Supporting Information). This phenomenon coupled with environmental disturbances can explain some fluctuation in the ER during the long‐time operation. Compared to treating the concentrated seawater, the salt deposited on the ATSC was faster when treating 24 wt.% NaCl brine, resulting in a more drastic ER curve.</p>", "<p>It is interesting to note that with much salt accumulation on these solar crystallizers during 80 h of operation, the ER was almost constant<sup>[</sup>\n##UREF##31##\n53\n##\n<sup>]</sup> and retained a high ER over 1.0 kg m<sup>−2</sup> h<sup>−1</sup> (except the filter paper) in various high‐salinity brine, thus maintaining a durable water evaporation performance. Compared with the reported 3D evaporators and solar crystallizers, the comprehensive performance (salinity, evaporation rate and duration) of ATSC is optimal (Table ##SUPPL##0##S2##, Supporting Information). For each BCC (with added frame) unit cell, since the evaporation of water only occurs on the outer surface composed of the outer framework, the salt concentration on the outer surface gradually concentrates until it reaches saturation and eventually crystallizes. Therefore, the salt preferentially accumulated on the outer frame of the unit cell instead of the inter rods thus achieving the separation of the crystallization interface and the water transportation pathways. Such a phenomenon is proven by Figure ##FIG##4##5b## and Figure ##SUPPL##0##S13## (Supporting Information). Inside one unit cell, salt crystals first nucleate on the structs, and then with continuous exposure to the light, the salt crystals gradually grow to block the micrometer‐sized cavities formed between the crossed structs (Figure ##SUPPL##0##S14a##, Supporting Information), and finally, the salt blocks the millimeter‐sized cavities on the end face of the unit cell (Figure ##SUPPL##0##S14b##, Supporting Information). Additionally, for the overall tree structure of ATSC, as the leaf portion is closer to the light source and therefore has a higher surface temperature than the trunk portion (Figure ##FIG##2##3e##), the salt preferentially crystallizes on the leaf portion, while the trunk portion has very little salt crystallization (Figure ##FIG##4##5c##), finally ensuring sufficient water supply for the whole tree structure. Specifically, there was a small amount of salt formation on the trunk portion of ATSC after 24 h while salt accumulation on the leaf portion was substantial. 72 h later, a large amount of salt particles formed on the leaf portion due to the crystallization of salt, while a thin salt crust layer formed on the trunk portion of ATSC, covering its external surface (Figure ##SUPPL##0##S14c##, Supporting Information). Meanwhile, the trunk portion also provides a certain evaporation surface, which contributes 26.9% ER of the whole ATSC (Figure ##SUPPL##0##S8##, Supporting Information). During the longtime radiation, the ER of ATSC in concentrated seawater decreased from 2.55 to 1.65 kg m<sup>−2</sup> h<sup>−1</sup>. In contrast to salt‐resistant evaporators, although the water evaporation performance of solar crystallizers can degrade after prolonged salt accumulation, it has the advantage of simultaneously harvesting clean water and solid salts, resulting in ZLD that eliminates liquid waste and maximizes water usage efficiency. Compared to ATSC without salt formation (2.55 kg m<sup>−2</sup> h<sup>−1</sup>), the ER with salt accumulation after stabilization (1.65 kg m<sup>−2</sup> h<sup>−1</sup>) only decreased by 35%, indicating the leaf portion with much salt accumulated was still evaporating. The above results prove that the strategy based on separating the crystallization interface and water‐wicking channel as well as the salt formation sequence from the outer frame to the inter rods and from top to bottom are the main reasons for the stable and ultra‐efficient crystallization of ATSC in concentrated real seawater.</p>", "<p>The structure of the salt crystal collected from the ATSC when treating concentrated seawater was investigated using SEM observation with energy‐dispersive X‐ray spectroscopy (EDS) elemental mapping analysis. Figure ##SUPPL##0##S15## (Supporting Information) shows that the salt crust layer contained sodium, potassium, chlorine, magnesium, calcium, sulfur, and oxygen elements. Figure ##SUPPL##0##S16## (Supporting Information) shows that the salt crystals were piled up in a mixed mode and some micron‐scale pores were still present, which indicates that the formed salt crust layer was not very dense. Then we used optical microscopy to observe the morphology of salts on different parts of the ATSC. Figure ##SUPPL##0##S17## (Supporting Information) shows the salt accumulated on the leaf portion is thicker and whiter due to more salt accumulated than on the trunk portion. Moreover, the formed salt crust layer no matter on the leaf or trunk portion of ATSC exhibits a rough surface and loose porosity. The Kelvin equation<sup>[</sup>\n##UREF##32##\n54\n##\n<sup>]</sup> predicted that evaporation would occur more quickly on the convex/planar salt crystals formed over the ASTC surface than on the concave water surface formed within the pores,<sup>[</sup>\n##UREF##33##\n55\n##\n<sup>]</sup> leading to open pore formation in the crystallization front as salt crystals continued to grow on the convex salt extrudes. Similar preferential sites for salt accumulation are also observed in the process of water evaporation from porous media.<sup>[</sup>\n##UREF##34##\n56\n##, ##REF##34723007##\n57\n##\n<sup>]</sup> Figure ##SUPPL##0##S18## (Supporting Information) shows the salt crystals formed after various durations of light exposure. As can be seen, all salt crystals have rough surfaces and multiple layers of interconnected pores. Water can transport through these pores in salt crystals, giving the salt crystals their transparent color. As Figure ##SUPPL##0##S19a,b## (Supporting Information) show, magnesium sulfate tended to grow in the voids between sodium chloride crystals, and the surface morphology of the two crystals was very different. The former had a rough, uneven, multilayered surface with multiple cracks on the scale of a few hundred nanometers to a few micrometers (Figure ##SUPPL##0##S19c##, Supporting Information), whereas the latter had a smooth and flat surface. Figure ##SUPPL##0##S19d## (Supporting Information) further indicates that magnesium sulfate and sodium chloride crystals mixed in a porous structure. It is believed that nano‐/micro‐pores of salt crystals were formed by the following mechanisms: 1) as Kelvin equation predicts, salt crystal nucleation and growth on previously precipitated crystal surfaces, leading to open pore formation in the crystallization front; 2) the presence of rough and often cracking magnesium sulfate at the interstitial spaces between the sodium chloride crystals promoted the formation of nano‐/micro‐pores. In contrast to most solar crystallizers that allow salt to grow on flat surfaces, our ATSC had open pores along with the cellular structure, which enabled the salt crystals to develop in 3D space<sup>[</sup>\n##REF##34576344##\n58\n##, ##UREF##35##\n59\n##\n<sup>]</sup> and have 10–100 µm pores for the transport of water (Figure ##FIG##4##5d##). This also provides additional evaporation area, thus compensating for the reduced ER due to salt coverage of the original evaporation surface, and maintaining a stable ER for a long time even with a large amount of salt accumulation. In summary, when treating concentrated seawater, the salt crystallized on the ATSC was highly porous, independent of the location of the salt crystallization (inside the unit cell or along the external cellular structure, leaf portion or trunk portion) and the duration of light exposure.</p>", "<p>After 80 h of radiation in concentrated seawater, we used filter paper to contact ATSC. Figure ##FIG##4##5e## demonstrates that the salt layer that was produced on the upper surface of the leaf portion was wet. Moreover, the salt on the trunk portion was also wet (Figure ##SUPPL##0##S20##, Supporting Information), indicating the salt layer does not affect the water transport capability of ATSC. Furthermore, it has been documented that when the water delivery channel in the crystallizer is nanoscale, Mg<sup>2+</sup> and Ca<sup>2+</sup> will block the channel during the evaporation of high‐salinity brine.<sup>[</sup>\n##REF##32305700##\n60\n##\n<sup>]</sup> In contrast, the water channels in ATSC are all in the micron size and the salt layer contains 10–100 µm pores, so the water transportation capability is hardly affected by ion plugging and salt crystallization. Thermal images show that the surface temperature of the ATSC during the solar evaporation experiment using concentrated seawater (right of Figure ##FIG##4##5f##, 36–50 °C) was higher than that using pure water (left of Figure ##FIG##4##5f##, &lt; 35 °C), indicating that a large portion of light was still able to transmit through the salt crystals accumulated on the ATSC for absorption by CB. The solar absorption spectra of the salt crystals collected from ATSC show pure salt crystals possess a high reflectance (&gt; 80%) in the short wavelength range (&lt; 1300 nm) and a slightly lower reflectance (40%–90%) in the long wavelength range, which demonstrates poor solar absorption and energy utilization due to its inherent white color and the poor light‐trapping property (Figure ##SUPPL##0##S21##, Supporting Information). This further suggests that the salt crystals on the surface of the ATSC are almost incapable of absorbing light, while light can reach the surface of the open‐cell cellular structure through the diffuse reflection and scattering and finally be converted into heat, leading to a minimal effect of the accumulated salt on the light absorption efficiency of the ATSC. Moreover, we also studied the solar absorption spectra of the ATSC with salts. Figure ##SUPPL##0##S22## (Supporting Information) indicates that the ATSC with salt has a similar light absorption efficiency with ATSC, especially in the UV–vis region. In other words, the formation of a salt crust layer did not significantly decrease the light absorption efficiency of the ATSC. These results demonstrate that the ATSC has the potential for continuously stable crystallization toward high‐salinity real brine for the ZLD goal.</p>", "<title>Feasibility Under Practical Conditions</title>", "<p>To verify the solar crystallization capability of ATSC in practical applications, we performed outdoor evaporation experiments with an easy‐to‐implement scale‐up solution and use concentrated real seawater as the source brine. <bold>Figure</bold> ##FIG##5##\n6a## shows nine ATSC were assembled to form an array (with inter‐device space of 21 mm uniformly), which was tested on the campus rooftop on December 27, 2022, from 8:00 to 18:00. Moreover, the real‐time temperature, relative humidity, and natural wind velocity variation of the field test were also recorded in Figure ##SUPPL##0##S23## (Supporting Information). The cumulative weight change of the concentrated seawater during the 10 h test period was 17.5 kg m<sup>−2</sup> (Figure ##FIG##5##6b##), indicating its potential for high efficiency and sustainable brine treatment in the future.</p>", "<p>Figure ##FIG##5##6c## shows that the natural solar intensity increased to the highest 0.77 kW m<sup>−2</sup> at noon. It is worth noting that the sun ≈10:00 was blocked by nearby buildings, thus there was a paradoxical drop in solar intensity and therefore ER, which was consistent with the results for temperature and relative humidity in Figure ##SUPPL##0##S23## (Supporting Information). Additionally, the arrayed ATSC delivered an ultra‐high ER of 2.47 kg m<sup>−2</sup> h<sup>−1</sup> in concentrated seawater. Under field conditions, the solar incident angle, environment temperature, relative humidity, and natural wind all affect the evaporation performance of the solar crystallizer. The continuous air convection across the arrayed solar crystallizer improved ER, which explained why the ER of ATSC in outdoor experiments was higher than that in a laboratory under the same solar intensity, indicating the versatility of the environmental‐enhanced solar crystallizer. After 10 h of outdoor testing, all nine ATSC had apparent salt accumulation, especially on the leaf portion (Figure ##FIG##5##6d##), demonstrating that the array of ATSC has great potential for large‐scale salt production under natural sunlight.</p>" ]
[ "<title>Conclusion</title>", "<p>Herein, we presented a rationally designed ATSC based on the cellular architecture composed of multiple unit cells of BCC (with added frame). CB‐coated ATSC demonstrated excellent evaporation performance owing to its vast surface area, fast water transport ability, enhanced light absorption efficiency and outstanding thermal management property, which make it possible to achieve long‐term stable ZLD treatment of real seawater brines. With the novel design of ATSC, the salt was preferentially crystallized on the outer frame rather than in the inner voids, ensuring the water‐wicking channels remain open after prolonged salt crystallization. In addition, when salt covered the leaf portion of ATSC in large amounts, the trunk portion was less salt crystallized and continued to have enough surface area for evaporation. Besides, the accumulated salt was irregular and highly porous, making ATSC sustain a stable and ultra‐high evaporation rate of 1.94 kg m<sup>−2</sup> h<sup>−1</sup> on average over 80 h in the real brine from concentrated seawater under one sun radiation. The designed structure presented in this paper represents a significant advancement toward ZLD treatment of high‐salinity brine in many industry processes, such as salt recovery from waste brines and salt mineral extraction from salt lakes.</p>" ]
[ "<title>Abstract</title>", "<p>Recent developed interfacial solar brine crystallizers, which employ solar‐driven water evaporation for salts crystallization from the near‐saturation brine to achieve zero liquid discharge (ZLD) brine treatment, are promising due to their excellent energy efficiency and sustainability. However, most existing interfacial solar crystallizers are only tested using NaCl solution and failed to maintain high evaporation capability when treating real seawater due to the scaling problem caused by the crystallization of high‐valent cations. Herein, an artificial tree solar crystallizer (ATSC) with a multi‐branched and interconnected open‐cell cellular structure that significantly increased evaporation surface is rationally designed, achieving an ultra‐high evaporation rate (2.30 kg m<sup>−2</sup> h<sup>−1</sup> during 2 h exposure) and high energy efficiency (128%) in concentrated real seawater. The unit cell design of ATSC promoted salt crystallization on the outer frame rather than the inner voids, ensuring that salt crystallization does not affect the continuous transport of brine through the pores inside the unit cell, thus ATSC can maintain a stable evaporation rate of 1.94 kg m<sup>−2</sup> h<sup>−1</sup> on average in concentrated seawater for 80 h continuous exposure. The design concept of ATSC represents a major step forward toward ZLD treatment of high‐salinity brine in many industrial processes is believed.</p>", "<p>A rationally designed artificial tree solar crystallizer with multi‐branched and interconnected open‐cell cellular structures, which can maintain an ultra‐high and stable brine evaporation performance over a prolonged exposure (1.94 kg m<sup>−2</sup> h<sup>−1</sup> on average in concentrated real seawater for 80 h exposure), due to salt crystallization on the outer frame rather than the inner voids, ensuring continuous transport of brine.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6793-cit-0061\">\n<string-name>\n<given-names>C.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Kang</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Fan</surname>\n</string-name>, <article-title>3D Cellular Solar Crystallizer for Stable and Ultra‐Efficient High‐Salinity Wastewater Treatment</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305313</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305313</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Design and Fabrication of the Solar Brine Crystallizer</title>", "<p>The model of the crystallizer was designed using SOLIDWORKS 2019 software. The tree‐shaped solar crystallizer consisted of three parts: the root, the trunk, and the leaf. The detailed crystallizer design is presented in Figure ##FIG##0##1b##. The root and the leaf had the same structure. The height of the root, trunk, and leaf was designed as 10.30, 20.05, and 10.30 mm, respectively, thus the total height is 40.65 mm. All parts with fine features were printed using High Temp Resin by a Form 3 printer (Formlabs) with 25 µm layers and post‐cured for 120 min at 80 °C while exposed to 405 nm light (Form Cure, Formlabs). The 3D‐printed structure was immersed in CB nanoparticles (2 g) dissolved in ethanol (100 mL) and taken out to allow it to dry in an oven (80 °C). This process was repeated 3 times and the CB loading amount was ≈90 mg per crystallizer.</p>", "<title>Preparation of Concentrated Real Seawater</title>", "<p>The seawater (collected from Victoria Harbor, Hong Kong in December 2022) was concentrated in a blast oven at 85 °C and then filtrated by 0.45 µm cellulose acetate membrane. The detailed water quality of real seawater samples was shown in Table ##SUPPL##0##S1## (Supporting Information). During the concentration process of natural seawater, there were some white precipitates formed, which were removed by filtration. The XRD pattern of the precipitates (Figure ##SUPPL##0##S24##, Supporting Information) indicates that their main compositions were calcium sulfate hydrate (CaSO<sub>4</sub>·2H<sub>2</sub>O) and calcium sulfate (CaSO<sub>4</sub>), which have poor solubility in water.</p>", "<title>Solar Evaporation and Crystallization Experiments</title>", "<p>A lab‐scale setup was built to evaluate the solar evaporation and crystallization performance of the solar crystallizer. A solar simulator (Newport Oriel Solar Simulator, 94021A and power supply 69 907) equipped with AM 1.5G filter was used to provide solar radiation with a constant intensity of 1000 W m<sup>−2</sup>. The intensity of the solar radiation was measured by a solar power meter (Solar‐100, AMPROBE). The beam size (5 cm × 5 cm) was slightly larger than the photothermal material and exactly perpendicular to the solar crystallizer. An electronic analytical balance (ME204E, Mettler Toledo) with an accuracy of 0.1 mg was used to record the mass change of brine in real‐time which was then used to calculate the water evaporation rate. The temperature distribution was monitored by an IR camera (A600‐series, FLIR). The real‐time temperature distributions were measured using thermocouples (K type, KAIPUSEN) and recorded by a data logger (AT4208). During the water evaporation test, the crystallizer was embedded in the polystyrene (PS) foam to isolate the natural evaporation of bulk water. The evaporation rates of the solar crystallizer when treating various source water were measured in the dark for 1 h and under one sun radiation for 2 h. When treating concentrated seawater and 24 wt.% NaCl solution, there was no manual salt removal from the solar crystallizer unless otherwise specified. All lab measurements were conducted at an ambient temperature of 22–25 °C with a relative humidity of 55 ± 5% as monitored using a temperature and humidity meter (AZ88162). The outdoor field test was conducted on the rooftop of a housing unit inside The Hong Kong Polytechnic University campus on December 27, 2022.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>Work in 3D printing was supported by the University Research Facility in 3D Printing (U3DP). This research was also supported by the Hong Kong Polytechnic University (AoEC project number: ZE1H) and the PolyU postdoc matching fund scheme (1‐W21H).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available in the supplementary material of this article.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6793-fig-0001\"><label>Figure 1</label><caption><p>The design concept of the tree‐inspired cellular structure. a) and b) Natural tree and tree‐inspired cellular design for solar brine crystallizer, respectively. They share several key features: the bottom roots for absorbing water, the middle trunk for transporting water, and the upper leaves for absorbing sunlight and water evaporation. The cellular structure of ATSC can be designed and assembled by multiple unit cells. c) Schematic illustration of the ATSC under sunlight for salt crystallization from high‐salinity brine. d) Diagram of one unit cell in ATSC, which is body‐centered cubic (with frame). e) The side and top view of the ATSC.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6793-fig-0002\"><label>Figure 2</label><caption><p>Water transport performance of the columnar structures with different D. a) The water contact angles of the ATSC before and after coating with CB. The optical images of the ATSC before b) and after c) coating with CB, demonstrate every void within the unit cell of ATSC reduced in size after coated. Anti‐gravity transport of water along the CB‐coated columnar structures composed with different D. d) The infrared (IR) images of the wicking height of five columnar structures. The corresponding wicking height e) and wicking velocity f) over time indicate that when D is equal to 0.55 mm, the columnar structure has the best capillary property.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6793-fig-0003\"><label>Figure 3</label><caption><p>Light absorption and thermal management property of ATSC. a) The solar absorption spectra (250–2500 nm) of the ATSC before and after coating with CB, and standard AM 1.5G solar spectrum. The high solar absorption is contributed to both CB with high light absorbability and multiple light reflections of the cellular microarchitecture. Surface IR images of ATSC on a hot plate for 10 minutes in dry b) and wet c) states, demonstrating ATSC has good heat localization capability. White dashed lines indicate ATSC and hot plate. The thermal management performance of the ATSC under one sun radiation, taking a 2D root evaporator as control: d) The IR image of the ATSC under simulated sunlight in pure water, showing the temperature was not uniformly distributed across the entire structure and the temperature of the leaf portion was higher than the trunk portion. e) The temperature evolution profiles of different positions in ATSC from 0 to 3600 s, show an interfacial heating model. f) The IR image of a 2D root evaporator under one sun radiation in pure water. g) Temperature change profiles of the 2D root evaporator (top surface) and the underlying bulk water in 1 h. The insets in e) and g) are optical images of the actual device tested which uses thermocouples to measure temperature.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6793-fig-0004\"><label>Figure 4</label><caption><p>The water evaporation performance of ATSC and 2D root crystallizer in various source water. a) The scheme of the lab‐made setup for solar evaporation performance measurement, including solar simulator, solar crystallizer, electrical balance, and computer. b) The vapor generation performance in the different source water was calculated by monitoring the mass loss of source water for 3 h, with pure water as control, in which 1 h of the dark experiment and 2 h of the light experiment. c) The corresponding water evaporation rate (ER) under dark conditions and one sun radiation of ATSC and 2D root crystallizer in the different source water. The error bars in the ER resulted from environmental disturbance. Each error bar represents the standard deviation of at least five data points. d) The net ER, which subtracts the water ER in darkness from the solar steam generation rate under one sun radiation, and corresponding energy efficiencies. The error bars in the energy efficiency values resulted from errors in the measurement of the interface temperature, solar illumination power and the ER. Each error bar represents the standard deviation of at least five data points.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6793-fig-0005\"><label>Figure 5</label><caption><p>Long‐term evaporation performance and crystallization behavior of ATSC in high‐salinity brine. a) Water evaporation endurance test of different solar crystallizers in various high‐salinity brine under one sun radiation for 80 h (each point on the curve was the average ER of 1 h). b) The salt formation process of the ATSC under light radiation in concentrated seawater for 12 h, indicating the salt crystallization was from the outer frame to the inter rods and from top to bottom. c) The corresponding digital photo of the ATSC after 80 h of exposure using concentrated seawater. The red dashed lines mark the evaporation area, and the green and blue boxes are the leaf and trunk portions of the ATSC, respectively. d) An optical microscope image of salt accumulated on ATSC after operating with concentrated seawater for 80 h, indicating the salt is rough and highly porous. e) When a piece of filter paper was brought into contact with the salt layer, water can be absorbed from the salt, indicating the salt layer deposited on the ATSC is wet, thus the salt crust layer does not affect the water transport ability. f) The temperature distribution of ATSC in pure water (left) and in concentrated seawater (right) after radiation for 80 h, indicates partial areas in the leaf portion are still available for photothermal conversion.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6793-fig-0006\"><label>Figure 6</label><caption><p>Outdoor experiments with the arrayed ATSC under natural sunlight. a) Digital image of the outdoor evaporation experiments module setup, including arrayed ATSC, electronic balance, temperature and relative humidity sensors, solar power meter, wind speed sensor, and a laptop computer. b) The cumulative mass change of concentrated seawater during 8:00–18:00. c) The solar intensity of outdoor environments during 10 h of operation and the corresponding ER of the arrayed ATSC. d) Photograph of the arrayed ATSC after the one‐day operation, many salts formed over the arrayed ATSC, indicating this device has good salt crystallization performance.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6793-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2305313-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
60
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Dec 1; 11(2):2305313
oa_package/5a/d7/PMC10787074.tar.gz
PMC10787075
37985793
[ "<title>Introduction</title>", "<p>The development of sustainable energy conversion and storage technologies is crucial for mitigating environmental pollution and addressing energy shortages.<sup>[</sup>\n##UREF##0##\n1\n##, ##UREF##1##\n2\n##, ##UREF##2##\n3\n##, ##REF##36813780##\n4\n##\n<sup>]</sup> HER and OER are important half‐reactions in the electrochemical water‐splitting process. The OER reaction is a four‐electron transfer process, and its kinetics are slow, which severely hampers the performance of electrochemical hydrogen production.<sup>[</sup>\n##UREF##3##\n5\n##\n<sup>]</sup> Materials based on Pt, Ir, and Ru are currently promising catalysts for HER and OER. However, their high cost and scarcity hinder their widespread application.<sup>[</sup>\n##UREF##4##\n6\n##, ##UREF##5##\n7\n##, ##UREF##6##\n8\n##\n<sup>]</sup> Therefore, it is of paramount significance to seek efficient, low‐cost metal catalysts as alternatives to precious metal catalysts for water electrolysis.<sup>[</sup>\n##UREF##7##\n9\n##, ##UREF##8##\n10\n##, ##REF##37920333##\n11\n##\n<sup>]</sup>\n</p>", "<p>Metal–Organic Frameworks (MOFs) are a class of versatile porous materials constructed from the coordination of metal ions and organic ligands.<sup>[</sup>\n##UREF##9##\n12\n##\n<sup>]</sup> MOFs possess an extremely high specific surface area, unique pore channel structures, and abundantly accessible metal centers, making them ideal candidate materials for electrocatalysts.<sup>[</sup>\n##UREF##10##\n13\n##, ##UREF##11##\n14\n##\n<sup>]</sup> However, the application of MOFs in the field of electrochemistry is limited due to their poor chemical/mechanical stability and conductivity. Researches indicate that materials derived from MOFs can enhance their conductivity and stability while preserving the structural diversity and porous characteristics of MOFs.<sup>[</sup>\n##UREF##12##\n15\n##, ##UREF##13##\n16\n##\n<sup>]</sup> Additionally, incorporating MOFs into certain composite materials can improve their electrical conductivity.<sup>[</sup>\n##UREF##11##\n14\n##\n<sup>]</sup> For example, Rinawati et al. utilized the synergistic effects between transition metal sites to design a straightforward transformation from bimetallic NiFe‐MOF 74 to NiFe‐LDH. This retained the framework structure of MOF, enabling more effective substrate diffusion. The NiFe‐LDH electrocatalyst derived from MOF‐74 exhibited a low overpotential (<italic toggle=\"yes\">η</italic>) of 299 mV at 10 mA cm<sup>−2</sup>.<sup>[</sup>\n##UREF##14##\n17\n##\n<sup>]</sup> Zhang et al.<sup>[</sup>\n##UREF##15##\n18\n##\n<sup>]</sup> introduced selenium to modulate the morphology of MOF‐74. The coupling of selenide with MOF‐74 resulted in Fe<sub>x</sub>Co<sub>y</sub>NizSe–MOF, which exhibited only a 260 mV overpotential at a current density (CD) of 10 mA cm<sup>−2</sup> in a 1 mol L<sup>−1</sup> KOH electrolyte. However, these materials suffer from issues such as poor long‐term stability and insufficient electrocatalytic activity, which limit their large‐scale industrial applications. Transition metal phosphides (TMPs) have emerged as a hot topic in electrocatalysis due to their impressive activity, stability, and conductivity.<sup>[</sup>\n##UREF##16##\n19\n##, ##UREF##17##\n20\n##\n<sup>]</sup> Due to their differential adsorption capabilities for various reaction intermediates, most TMPs exhibit excellent HER or OER performance.<sup>[</sup>\n##REF##31613082##\n21\n##\n<sup>]</sup> Phosphorus possesses a strong electronegativity, attracting electrons from metal atoms, thus becoming a negatively charged center that attracts positively charged protons to enhance HER activity.<sup>[</sup>\n##UREF##18##\n22\n##, ##UREF##19##\n23\n##\n<sup>]</sup> Additionally, the presence of oxygen‐containing functional groups can enhance the hydrophilicity of electrocatalysts, thereby favorably contributing to the improvement of electrocatalytic performance.<sup>[</sup>\n##UREF##20##\n24\n##\n<sup>]</sup> MOF‐74 is an MOF formed by the coordination of divalent transition metals with 2,5‐dihydroxyterephthalic acid (H<sub>4</sub>DOT). Its distinctive features include the wide range of choices and tunability in the composition of divalent metals, as well as varying bond strengths between divalent transition metals and the H<sub>4</sub>DOT ligand. These characteristics make MOF‐74 an ideal precursor for catalysts with extensive tunability.<sup>[</sup>\n##UREF##21##\n25\n##, ##UREF##22##\n26\n##\n<sup>]</sup>\n</p>", "<p>Besides the chemical components, a material's performance is closely related to its construction. Surface engineering design strategies are commonly used to enhance the electrocatalytic performance of catalysts.<sup>[</sup>\n##REF##37596263##\n27\n##, ##UREF##23##\n28\n##, ##UREF##24##\n29\n##\n<sup>]</sup> Among them, the creation of hollow structures has attracted increasing attention, and the hollow nanostructured materials have emerged as promising candidates with extensive applications in catalytic nitrogen fixation,<sup>[</sup>\n##UREF##25##\n30\n##\n<sup>]</sup> NOx storage,<sup>[</sup>\n##UREF##26##\n31\n##\n<sup>]</sup> photocatalytic degradation,<sup>[</sup>\n##UREF##27##\n32\n##\n<sup>]</sup> energy storage and conversion<sup>[</sup>\n##UREF##28##\n33\n##, ##UREF##29##\n34\n##, ##UREF##30##\n35\n##\n<sup>]</sup> and more. This is due to their enriched surface area, significantly increased exposed active sites, shortened electron diffusion pathways, low density, rapid mass diffusion rates, and high atomic utilization. Furthermore, the construction of hollow structures can mitigate volume effects, thus enhancing the cyclic stability of the structure.<sup>[</sup>\n##UREF##31##\n36\n##, ##REF##35312311##\n37\n##\n<sup>]</sup>\n</p>", "<p>In this study, the FeCo–MOF‐74 precursor was synthesized using a simple hydrothermal method, followed by a phosphorization process through calcination to produce a hollow spherical FeCo‐P catalyst composed of nanosheets. The resulting hollow structure possesses a larger specific surface area and plenty of accessible active sites.<sup>[</sup>\n##UREF##32##\n38\n##, ##REF##25798849##\n39\n##\n<sup>]</sup> Furthermore, the hollow structure can enhance the chemical adsorption between the catalyst and active intermediates, further improving catalytic efficiency.<sup>[</sup>\n##UREF##33##\n40\n##\n<sup>]</sup> FeCo‐P exhibits excellent HER/OER and OWS performance. FeCo‐P only requires overpotentials (<italic toggle=\"yes\">η</italic>) of 131/240 mV for HER/OER, with Tafel slopes of 89.90/38.24 mV dec<sup>−1</sup> @ 10 mA cm<sup>−2</sup> in 1 mol L<sup>−1</sup> KOH, respectively. Moreover, it retains its original structural morphology and exhibits excellent stability even after prolonged reactions. When assembling FeCo‐P as the cathode and anode in an electrolysis cell, it achieves current densities of 10, 100, and 300 mA cm<sup>−2</sup> with only 1.49, 1.55, and 1.57 V in 1 mol L<sup>−1</sup> KOH, respectively. This catalyst exhibits wonderful industrial potential thanks to its good performance at high current densities. Density Functional Theory (DFT) calculations, XPS (X‐ray Photoelectron Spectroscopy), and electrochemical analyses indicate that the heterostructure formed by FeP and Co<sub>2</sub>P in the hollow spherical FeCo‐P catalyst effectively tunes the local electronic structure. This increases the contact area between the catalyst and the electrolyte while reducing the mass/charge transport length. It establishes a strong and integrated heterogeneous interface, addressing issues related to insufficient electrocatalytic activity, interface contact effects, and poor stability during the catalytic process. The incorporation of externally formed nanosheet hollow spheres promotes the efficient progression of HER and OER reactions, thus facilitating high‐efficiency OWS. This provides insights for the rational design of highly efficient catalysts for OWS.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Characterization of Electrocatalyst</title>", "<p>As shown in <bold>Scheme</bold> ##FIG##0##\n1\n##, we employed a one‐pot hydrothermal method to initially synthesize the precursor FeCo–MOF‐74, followed by phosphorization to obtain FeCo‐P. To further investigate the surface morphology of the prepared samples, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) characterization tests were performed on the electrocatalysts. <bold>Figure</bold> ##FIG##1##\n1a–c## represent the morphology of Fe─P, Co─P, and FeCo─P, respectively. As shown in the figures, Fe─P is a shuttle like structure with a diameter of ≈200 nm, Co─P is a rod‐shaped structure with a diameter of ≈250 nm, and FeCo‐P is a hollow spherical structure composed of nanosheets with a diameter of ≈1 µm. Its hollow structure not only exposes more active sites, but also increases the contact area between the catalyst and electrolyte, which shortens the mass/charge transfer distance. The hollow structure is hence more conducive to the progress of HER and OER reactions. Further analysis of the structural characteristics and chemical composition of FeCo‐P was conducted using TEM. Figure ##FIG##1##1d## shows a local HR–TEM analysis of the outer nanosheets of the hollow sphere, clearly revealing the morphological structure of the external nanosheets, with small particles formed inside after phosphorization. Figure ##FIG##1##1e## displays lattice spacings of 0.193 and 0.253 nm corresponding to the (220) and (120) planes of FeP, as well as lattice spacings of 0.271 and 0.205 nm corresponding to the (111) and (130) planes of Co<sub>2</sub>P.<sup>[</sup>\n##UREF##15##\n18\n##\n<sup>]</sup> Moreover, the diffraction rings in Figure ##FIG##1##1f## clearly reveal the presence of the (130) plane of Co<sub>2</sub>P and the (031) plane of FeP. From the lattice fringe images, it can also be observed that Co<sub>2</sub>P and FeP particles have formed a heterojunction within the nanosheets.<sup>[</sup>\n##UREF##16##\n19\n##\n<sup>]</sup> As shown in Figure ##FIG##1##1g–j##, EDS analysis of FeCo‐P confirms the uniform distribution of Fe, Co, and P elements within the hollow sphere composed of nanosheets, further substantiating the successful preparation of the FeCo‐P material. The results of the energy dispersion spectrum of FeCo‐P are shown in Figure ##SUPPL##0##S9## (Supporting Information), which indicate that the atomic fraction (%) of Co, Fe, and P is 17.27:25.38:57.35 (or 1:1.47:3.32).</p>", "<p>The crystal structures of Fe─P, Co─P, and FeCo─P were studied through XRD analysis. As shown in Figure ##SUPPL##0##S1## (Supporting Information), the XRD spectrum of Fe‐P exhibits distinct diffraction peaks at 2<italic toggle=\"yes\">θ</italic> = 32.7°, 37.1°, 47.0°, 48.3°, and 56.1°, corresponding to the (011), (111), (220), (211), and (031) planes of FeP (PDF#39‐0809), respectively, consistent with previous reports.<sup>[</sup>\n##UREF##34##\n41\n##\n<sup>]</sup> The XRD spectrum of Co‐P shows distinct diffraction peaks appear at 2<italic toggle=\"yes\">θ</italic> = 32.9°, 37.1°, 48.7°, and 56.2°, which correspond to the (111), (210), (031), and (320) planes of Co<sub>2</sub>P (PDF#32‐0306), respectively, confirming the successful synthesis of Co‐P.<sup>[</sup>\n##REF##29633825##\n42\n##\n<sup>]</sup> The XRD spectrum of FeCo‐P exhibits distinct diffraction peaks at 2<italic toggle=\"yes\">θ</italic> = 32.9°, 40.9°, 48.7°, 44.1°, and 52°, corresponding to the (111), (201), (031), (130), and (002) planes of Co<sub>2</sub>P (PDF#32‐0306), respectively. Additionally, at 2<italic toggle=\"yes\">θ</italic> = 32.7°, 35.5°, 37.2°, 47°, 48.3°, and 56.1°, there are evident diffraction peaks, which correspond to the (011), (120), (111), (220), (211), and (031) planes of FeP (PDF#39‐0809), This is consistent with the results from TEM, confirming the successful synthesis of FeCo‐P.<sup>[</sup>\n##UREF##35##\n43\n##\n<sup>]</sup>\n</p>", "<p>The chemical composition and oxidation states of the catalyst were characterized using XPS. As shown in <bold>Figure</bold> ##FIG##2##\n2a## and Figure ##SUPPL##0##S2## (Supporting Information), the Fe<sub>2</sub>p<sub>3/2</sub> spectrum in FeCo‐P can be deconvoluted into three main peaks at 707.4, 710.4, and 712.1 eV, which are attributed to the Fe─P bond, Fe<sup>2+</sup>, and Fe<sup>3+</sup>, respectively.<sup>[</sup>\n##UREF##36##\n44\n##\n<sup>]</sup> The Fe<sub>2</sub>p<sub>1/2</sub> spectrum in FeCo‐P can be deconvoluted into three main peaks at 720.4, 724.5, and 728.9 eV, respectively, which are attributed to the satellite peak, Fe<sup>2+</sup>, and Fe.<sup>3+[</sup>\n##UREF##37##\n45\n##\n<sup>]</sup> Compared to the monometallic phosphide Fe‐P, the Fe 2p<sub>3/2</sub> peak in the bimetallic phosphide FeCo‐P shifts by 0.5 eV toward a lower binding energy region, and the Fe<sub>2</sub>p<sub>1/2</sub> peak shifts by 2.2 eV toward a higher binding energy region. This indicates a significant electron transfer occurring between the heterojunction of bimetallic phosphides Co<sub>2</sub>P and FeP.</p>", "<p>From Figure ##FIG##2##2b##, it is evident that the Co<sub>2</sub>p spectrum exhibits four distinct peaks at 778.9, 783.2, 794.1, and 802.8 eV, corresponding to Co─P, Co─PO<sub>x</sub>, Co─P, and Co─PO<sub>x</sub>, respectively.<sup>[</sup>\n##UREF##34##\n41\n##, ##UREF##38##\n46\n##\n<sup>]</sup> Compared to the monometallic phosphide Co─P, the Co<sub>2</sub>p<sub>3/2</sub> and the Co<sub>2</sub>p<sub>1/2</sub> peaks in FeCo‐P have shifted by 3.0 and 4.0 eV toward a lower binding energy region, respectively. Taking into account the changes in binding energies for both Fe<sub>2</sub>p and Co<sub>2</sub>p, it can be observed that electrons are transferred from Fe to Co in FeCo‐P, indicating a synergistic effect between Fe and Co bimetallic interaction that further tunes the electronic structure.</p>", "<p>As shown in Figure ##FIG##2##2c##, the P<sub>2</sub>p spectrum can be deconvoluted into three distinct peaks at 129.6, 130.4, and 133.7 eV, respectively, corresponding to P<sub>2</sub>p<sub>3/2</sub>, P<sub>2</sub>p<sub>1/2</sub>, and P─O bonds.<sup>[</sup>\n##UREF##36##\n44\n##\n<sup>]</sup> Figure ##FIG##2##2d## displays multiple oxygen spectra for O 1 s, with peaks at 531.6 and 533.3 eV, which are attributed to the metal‐oxygen bonds and oxygen from adsorbed water, respectively.<sup>[</sup>\n##UREF##39##\n47\n##\n<sup>]</sup> These XPS experimental results further confirm the successful synthesis of the phosphide. The binding energies of Fe<sub>2</sub>p in FeCo‐P shift toward higher values, while those of Co<sub>2</sub>p shift toward lower values due to the interaction between P and the metal elements. Phosphorous possesses a strong electronegativity, enabling it to attract electrons from the metal atoms and become a negatively charged center, while Fe and Co in FeCo‐P become positively charged centers, promoting the binding of more OH‐ ions. This is favorable for the progression of OER and accelerates HER to produce more H<sub>2</sub>.<sup>[</sup>\n##UREF##20##\n24\n##, ##UREF##40##\n48\n##\n<sup>]</sup>\n</p>", "<title>Electrocatalytic Properties</title>", "<title>HER Performance</title>", "<p>The HER performance of the sample was measured in a typical three‐electrode system in a 1 mol L<sup>−1</sup> KOH solution saturated with N<sub>2</sub>. Based on the LSV (Linear Sweep Voltammetry) in <bold>Figure</bold> ##FIG##3##\n3a## and <italic toggle=\"yes\">η</italic> in Figure ##FIG##3##3b##, it can be observed that the hollow spherical nanosheets of FeCo‐P exhibit higher HER activity compared to monometallic Fe‐P and Co‐P. FeCo‐P requires an <italic toggle=\"yes\">η</italic> of 131 mV to achieve a CD of 10 mA cm<sup>−2</sup>, which is higher than Pt/C (75 mV) but lower than Fe‐P (159 mV) and Co‐P (167 mV). The above results indicate that bimetallic phosphides are more effective in enhancing electrocatalysts compared to monometallic ones, and the synergistic effect of bimetallic interaction facilitates rapid mass transfer.<sup>[</sup>\n##UREF##41##\n49\n##\n<sup>]</sup> It is worth noting that at current densities greater than 50 mA cm<sup>−2</sup>, the activity of FeCo‐P surpasses that of Pt/C. Furthermore, the kinetic characteristics of the reaction were studied by examining the Tafel slopes. As shown in Figure ##FIG##3##3c##, the Tafel slopes for FeCo─P, Fe─P, Co─P, and Pt/C are 89.90, 111.54, 123.24, and 100.02 mV dec<sup>−1</sup>, respectively. The Tafel slope for FeCo‐P is lower than those of Pt/C and other samples, indicating its excellent HER kinetic performance.</p>", "<p>The electronic transport rate of electrode materials is related to the conductivity of material. Generally, higher conductive electrode materials exhibit faster electronic transport rates. To further understand the material's conductivity, EIS was analyzed. Figure ##FIG##3##3d## indicates that, through circuit fitting analysis, the impedance plot of FeCo‐P exhibits a characteristic semicircle with the smallest diameter, representing the lowest charge transfer resistance.<sup>[</sup>\n##UREF##42##\n50\n##\n<sup>]</sup> The charge transfer rate of FeCo‐P hollow nanospheres is the fastest, which is attributed to the synergistic effect of bimetallic interaction and the hollow structure that promotes the generation of more active sites while reducing the charge transfer distance,<sup>[</sup>\n##UREF##43##\n51\n##\n<sup>]</sup> thus enhancing the conductivity. The sloping lines in the low‐frequency region reflect Warburg impedance caused by ionic diffusion, with the characteristic that a steep slope favors the migration of ions within the material, while a gradual slope indicates a more pronounced hindrance.<sup>[</sup>\n##REF##34027659##\n52\n##\n<sup>]</sup> As observed in the inset of Figure ##FIG##3##3d##, FeCo‐P exhibits the steepest slope, indicating the highest diffusion migration rate. The impedance results are consistent with the electrocatalytic performance results.</p>", "<p>The catalyst's specific surface area and pore size were analyzed using N<sub>2</sub> adsorption‐desorption isotherms. As shown in Figure ##SUPPL##0##S3## and Table ##SUPPL##0##S1## (Supporting Information), the specific surface area of Fe─P, Co─P, and FeCo─P are 10.2, 13.6, and 14.3 m<sup>2</sup> g<sup>−1</sup>, respectively, indicating that they all possess mesoporous structures, and FeCo‐P has the largest specific surface area among them, owing to its unique hollow structure, which increases the catalyst's interface area and is more favorable for both of HER and OER.</p>", "<p>In addition, the Turnover Frequency (TOF) value is also an evaluation criterion for catalytic activity.<sup>[</sup>\n##REF##29959325##\n53\n##\n<sup>]</sup> TOF values were further calculated at a <italic toggle=\"yes\">η</italic> of 100 mV to assess the intrinsic HER activity of the catalysts. From Table ##SUPPL##0##S2## (Supporting Information), it can be observed that the TOF value of FeCo‐P is 0.134 s<sup>−1</sup>, nearly 11 times that of Fe–P (0.012 s<sup>−1</sup>) and 5 times that of Co‐P (0.026 s<sup>−1</sup>) at the same <italic toggle=\"yes\">η</italic>. This further underscores that FeCo‐P exhibits excellent intrinsic HER activity, attributed to the synergistic effect of bimetallic phosphides and the hollow structure of FeCo‐P. In addition to high activity, good stability is also an important parameter for evaluating electrocatalysts. As shown in Figure ##FIG##3##3e##, the stability of the catalyst was analyzed using chronoamperometry and LSV curves initial and after 2000 cycles. The chronoamperometry curve for FeCo‐P shows no decay in CD at 10 mA cm<sup>−2</sup> within 24 h, and there is negligible change in the LSV curve initial and after 2000 cycles, indicating that the catalyst exhibits excellent long‐term stability. Furthermore, postreaction SEM analysis revealed that FeCo‐P retained its initial morphological structure, providing additional evidence of its excellent HER stability (see Figure ##SUPPL##0##S4##, Supporting Information). FeCo‐P's outstanding HER activity surpasses that of some recently reported nonprecious metal HER catalysts, as shown in Figure ##FIG##3##3f## and Table ##SUPPL##0##S3## (Supporting Information).</p>", "<title>OER Performance</title>", "<p>The OER performance of the samples was tested in a N<sub>2</sub>‐saturated 1 mol L<sup>−1</sup> KOH solution. As shown in <bold>Figure</bold> ##FIG##4##\n4a,b##, the overpotentials for achieving 10 mA cm<sup>−2</sup> are 240, 267, 307, and 287 mV for FeCo─P, Fe─P, Co─P, and IrO<sub>2</sub>, respectively. FeCo─P demonstrates a significant advantage at high current densities, with an overpotential of only 306 mV at 300 mA cm<sup>−2</sup>. These results indicate that the hollow nanospheres of FeCo─P exhibit higher OER activity compared to monometallic Fe─P and Co─P, and even outperform the precious metal IrO<sub>2</sub>. From Figure ##FIG##4##4c##, it can be observed that the Tafel slopes for FeCo─P, Fe─P, Co─P, and IrO<sub>2</sub> are 38.24, 45.29, 88.37 and 72.79 mV dec<sup>−1</sup>, respectively. FeCo‐P hollow nanospheres exhibit the smallest Tafel slope, indicating their excellent OER kinetics.<sup>[</sup>\n##UREF##43##\n51\n##\n<sup>]</sup> For the catalyst's application, long‐term stability is also a crucial factor.<sup>[</sup>\n##UREF##44##\n54\n##\n<sup>]</sup> The OER stability of the samples was evaluated in a N<sub>2</sub>‐saturated 1 mol L<sup>−1</sup> KOH solution. As shown in Figure ##FIG##4##4d##, there is negligible change in the LSV curves before and after 2000 cycles. Chronoamperometry curves indicate that the catalyst maintains excellent catalytic activity even after 24 h. Additionally, post‐OER long‐term stability testing SEM analysis (as shown in Figure ##SUPPL##0##S5##, Supporting Information) reveals no significant changes in morphological structure. FeCo‐P exhibits superior OER activity compared to some recently reported non‐precious metal OER catalysts, as shown in Figure ##FIG##4##4e## and Table ##SUPPL##0##S4## (Supporting Information).</p>", "<p>The electrochemical double‐layer capacitance (<italic toggle=\"yes\">C</italic>\n<sub>dl</sub>) is an important factor in estimating the activity of electrocatalysts. The number of active sites is directly proportional to the electrochemical surface area evaluated by <italic toggle=\"yes\">C</italic>\n<sub>dl</sub>.<sup>[</sup>\n##REF##29341596##\n55\n##\n<sup>]</sup>\n<italic toggle=\"yes\">C</italic>\n<sub>dl</sub> values were calculated by obtaining Cyclic Voltammetry (CV) curves at different scan rates within the non‐Faradaic voltage range (see Figure ##SUPPL##0##S6##, Supporting Information). From Figure ##FIG##4##4f##, it can be observed that the <italic toggle=\"yes\">C</italic>\n<sub>dl</sub> value for FeCo‐P (1.48 mF cm<sup>−2</sup>) is greater than that of Fe─P (1.26 mF cm<sup>−2</sup>) and Co─P (0.97 mF cm<sup>−2</sup>). This indicates that the bimetallic phosphide FeCo increases the number of active sites more effectively compared to monometallic phosphides, thereby improving HER and OER activities, which consistent with the results of Tafel slopes and impedance.</p>", "<title>OWS Performance</title>", "<p>To demonstrate the practical application of the FeCo‐P catalyst in an alkaline medium, a bifunctional water splitting device was assembled using FeCo‐P as both the cathode and anode, and tested in a 1 mol L<sup>−1</sup> KOH solution. Commercially Pt/C was used as the HER electrocatalyst, and IrO<sub>2</sub> was used as the OER electrocatalyst for comparison. As shown in <bold>Figure</bold> ##FIG##5##\n5a##, the cell voltage for FeCo‐P || FeCo‐P is only 1.49 V@10 mA cm<sup>−2</sup>, significantly outperforming the performance of the precious metal Pt/C || IrO<sub>2</sub> (1.58 V) for overall water splitting. Furthermore, at 100 and 300 mA cm<sup>−2</sup>, the cell voltages for FeCo‐P || FeCo‐P are 1.55 and 1.57 V, respectively. It can be observed from the data that the FeCo‐P catalyst has a distinct advantage at high current densities, making it highly promising for practical applications. The catalytic performance of FeCo‐P in OWS surpasses that of most reported powder TMP electrocatalysts and some in situ grown phosphide electrocatalysts, as shown in Table ##SUPPL##0##S5## (Supporting Information). Stability is another critical criterion for evaluating electrocatalysts. Therefore, the overall water stability of the FeCo‐P electrode was further tested. As shown in Figure ##FIG##5##5b,c##, the LSV curves after 2000 cycles of CV are essentially identical to the initial LSV curve, indicating excellent durability during the cyclic scanning process. In the long‐term stability test of 24 h at a CD of 10 mA cm<sup>−2</sup>, chronoamperometry curves demonstrate that there is no significant decrease in CD after 24 h, highlighting its excellent stability. Furthermore, SEM characterization of the material after long‐term stability testing in overall water splitting, as shown in Figure ##SUPPL##0##S7## (Supporting Information), reveals that the sample still retains its original hollow structure, indicating good structural stability. As depicted in Figure ##FIG##5##5d,e##, a significant number of bubbles appear on the surfaces of both the cathode and anode during the electrolysis of water. Collection and measurement of these bubbles were performed using a water displacement method. The measured ratio of H<sub>2</sub> to O<sub>2</sub> closely approximates the theoretical value of 2:1, and the Faradaic efficiency is close to 100%. A comparison of the OWS performance of FeCo‐P || FeCo‐P with other reported materials is shown in Figure ##FIG##5##5f##, illustrating the outstanding performance of FeCo‐P || FeCo‐P. These results collectively indicate that the FeCo‐P catalyst exhibits excellent OWS activity and stability, with an voltage of only 1.57 V at a CD of 300 mA cm<sup>−2</sup>, demonstrating its potential for industrial applications.</p>", "<title>Density Functional Theory (DFT) Theoretical Calculations</title>", "<p>To better elucidate the mechanisms behind the HER and OER activities of the FeCo‐P catalyst, a series of DFT calculations were conducted. As shown in Figure ##SUPPL##0##S8## (Supporting Information), theoretical models for FeP, Co<sub>2</sub>P, and FeCo‐P were constructed. For the alkaline HER process, the activity site with a Δ<italic toggle=\"yes\">G</italic>\n<sub>H</sub>* (hydrogen adsorption free energy) of 0 attains the best HER activity. In other words, the closer Δ<italic toggle=\"yes\">G</italic>\n<sub>H</sub>* to 0, the better the catalyst's HER activity.<sup>[</sup>\n##UREF##45##\n56\n##, ##REF##32309830##\n57\n##\n<sup>]</sup> Calculations yielded Δ<italic toggle=\"yes\">G</italic>\n<sub>H</sub>* values for FeP, Co<sub>2</sub>P, and FeCo‐P of 0.124, −0.277, and 0.119 eV, respectively (as shown in <bold>Figure</bold> ##FIG##6##\n6a##). This indicates that the Δ<italic toggle=\"yes\">G</italic>\n<sub>H</sub>* value of heterostructure FeCo‐P is the closest one to 0, facilitating H* adsorption and thus enhancing HER activity. For the OER process in an alkaline electrolyte solution, the computed free energies, as shown in Figure ##FIG##6##6b##, indicate that the formation of the *OOH intermediate in all the three samples is the slowest step, typically considered as the rate‐determining step, as stabilizing *OOH requires high energy.<sup>[</sup>\n##UREF##38##\n46\n##\n<sup>]</sup> The change in free energy for FeCo‐P is 2.39 eV, which is lower than that for FeP (2.64 eV) and Co<sub>2</sub>P (3.47 eV). The lower energy barrier for the heterostructure compared to the monomers suggests that FeCo‐P exhibits better OER activity. All of the above findings demonstrate that the FeP/Co<sub>2</sub>P heterostructure effectively tunes and optimizes the adsorption abilities of different intermediates in the HER and OER processes, thus enhancing its bifunctional activity. In an alkaline solution, OER involves four proton‐coupled reaction steps, including the adsorption of *OH, *O, and *OOH intermediates. The OER mechanism is illustrated in Figure ##FIG##6##6c##, where it begins with the adsorption of *OH at the active sites of FeCo‐P, forming HO‐FeCo‐P (Step 1). Subsequently, through deprotonation, oxygen binds into the structure, generating O‐FeCo‐P (Step 2). The exposed oxygen undergoes nucleophilic attack by accepting ‐OH, leading to the formation of *OOH (Step 3). *OOH is further attacked by ‐OH, resulting in the release of O<sub>2</sub> (Step 4).</p>" ]
[ "<title>Results and Discussion</title>", "<title>Characterization of Electrocatalyst</title>", "<p>As shown in <bold>Scheme</bold> ##FIG##0##\n1\n##, we employed a one‐pot hydrothermal method to initially synthesize the precursor FeCo–MOF‐74, followed by phosphorization to obtain FeCo‐P. To further investigate the surface morphology of the prepared samples, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) characterization tests were performed on the electrocatalysts. <bold>Figure</bold> ##FIG##1##\n1a–c## represent the morphology of Fe─P, Co─P, and FeCo─P, respectively. As shown in the figures, Fe─P is a shuttle like structure with a diameter of ≈200 nm, Co─P is a rod‐shaped structure with a diameter of ≈250 nm, and FeCo‐P is a hollow spherical structure composed of nanosheets with a diameter of ≈1 µm. Its hollow structure not only exposes more active sites, but also increases the contact area between the catalyst and electrolyte, which shortens the mass/charge transfer distance. The hollow structure is hence more conducive to the progress of HER and OER reactions. Further analysis of the structural characteristics and chemical composition of FeCo‐P was conducted using TEM. Figure ##FIG##1##1d## shows a local HR–TEM analysis of the outer nanosheets of the hollow sphere, clearly revealing the morphological structure of the external nanosheets, with small particles formed inside after phosphorization. Figure ##FIG##1##1e## displays lattice spacings of 0.193 and 0.253 nm corresponding to the (220) and (120) planes of FeP, as well as lattice spacings of 0.271 and 0.205 nm corresponding to the (111) and (130) planes of Co<sub>2</sub>P.<sup>[</sup>\n##UREF##15##\n18\n##\n<sup>]</sup> Moreover, the diffraction rings in Figure ##FIG##1##1f## clearly reveal the presence of the (130) plane of Co<sub>2</sub>P and the (031) plane of FeP. From the lattice fringe images, it can also be observed that Co<sub>2</sub>P and FeP particles have formed a heterojunction within the nanosheets.<sup>[</sup>\n##UREF##16##\n19\n##\n<sup>]</sup> As shown in Figure ##FIG##1##1g–j##, EDS analysis of FeCo‐P confirms the uniform distribution of Fe, Co, and P elements within the hollow sphere composed of nanosheets, further substantiating the successful preparation of the FeCo‐P material. The results of the energy dispersion spectrum of FeCo‐P are shown in Figure ##SUPPL##0##S9## (Supporting Information), which indicate that the atomic fraction (%) of Co, Fe, and P is 17.27:25.38:57.35 (or 1:1.47:3.32).</p>", "<p>The crystal structures of Fe─P, Co─P, and FeCo─P were studied through XRD analysis. As shown in Figure ##SUPPL##0##S1## (Supporting Information), the XRD spectrum of Fe‐P exhibits distinct diffraction peaks at 2<italic toggle=\"yes\">θ</italic> = 32.7°, 37.1°, 47.0°, 48.3°, and 56.1°, corresponding to the (011), (111), (220), (211), and (031) planes of FeP (PDF#39‐0809), respectively, consistent with previous reports.<sup>[</sup>\n##UREF##34##\n41\n##\n<sup>]</sup> The XRD spectrum of Co‐P shows distinct diffraction peaks appear at 2<italic toggle=\"yes\">θ</italic> = 32.9°, 37.1°, 48.7°, and 56.2°, which correspond to the (111), (210), (031), and (320) planes of Co<sub>2</sub>P (PDF#32‐0306), respectively, confirming the successful synthesis of Co‐P.<sup>[</sup>\n##REF##29633825##\n42\n##\n<sup>]</sup> The XRD spectrum of FeCo‐P exhibits distinct diffraction peaks at 2<italic toggle=\"yes\">θ</italic> = 32.9°, 40.9°, 48.7°, 44.1°, and 52°, corresponding to the (111), (201), (031), (130), and (002) planes of Co<sub>2</sub>P (PDF#32‐0306), respectively. Additionally, at 2<italic toggle=\"yes\">θ</italic> = 32.7°, 35.5°, 37.2°, 47°, 48.3°, and 56.1°, there are evident diffraction peaks, which correspond to the (011), (120), (111), (220), (211), and (031) planes of FeP (PDF#39‐0809), This is consistent with the results from TEM, confirming the successful synthesis of FeCo‐P.<sup>[</sup>\n##UREF##35##\n43\n##\n<sup>]</sup>\n</p>", "<p>The chemical composition and oxidation states of the catalyst were characterized using XPS. As shown in <bold>Figure</bold> ##FIG##2##\n2a## and Figure ##SUPPL##0##S2## (Supporting Information), the Fe<sub>2</sub>p<sub>3/2</sub> spectrum in FeCo‐P can be deconvoluted into three main peaks at 707.4, 710.4, and 712.1 eV, which are attributed to the Fe─P bond, Fe<sup>2+</sup>, and Fe<sup>3+</sup>, respectively.<sup>[</sup>\n##UREF##36##\n44\n##\n<sup>]</sup> The Fe<sub>2</sub>p<sub>1/2</sub> spectrum in FeCo‐P can be deconvoluted into three main peaks at 720.4, 724.5, and 728.9 eV, respectively, which are attributed to the satellite peak, Fe<sup>2+</sup>, and Fe.<sup>3+[</sup>\n##UREF##37##\n45\n##\n<sup>]</sup> Compared to the monometallic phosphide Fe‐P, the Fe 2p<sub>3/2</sub> peak in the bimetallic phosphide FeCo‐P shifts by 0.5 eV toward a lower binding energy region, and the Fe<sub>2</sub>p<sub>1/2</sub> peak shifts by 2.2 eV toward a higher binding energy region. This indicates a significant electron transfer occurring between the heterojunction of bimetallic phosphides Co<sub>2</sub>P and FeP.</p>", "<p>From Figure ##FIG##2##2b##, it is evident that the Co<sub>2</sub>p spectrum exhibits four distinct peaks at 778.9, 783.2, 794.1, and 802.8 eV, corresponding to Co─P, Co─PO<sub>x</sub>, Co─P, and Co─PO<sub>x</sub>, respectively.<sup>[</sup>\n##UREF##34##\n41\n##, ##UREF##38##\n46\n##\n<sup>]</sup> Compared to the monometallic phosphide Co─P, the Co<sub>2</sub>p<sub>3/2</sub> and the Co<sub>2</sub>p<sub>1/2</sub> peaks in FeCo‐P have shifted by 3.0 and 4.0 eV toward a lower binding energy region, respectively. Taking into account the changes in binding energies for both Fe<sub>2</sub>p and Co<sub>2</sub>p, it can be observed that electrons are transferred from Fe to Co in FeCo‐P, indicating a synergistic effect between Fe and Co bimetallic interaction that further tunes the electronic structure.</p>", "<p>As shown in Figure ##FIG##2##2c##, the P<sub>2</sub>p spectrum can be deconvoluted into three distinct peaks at 129.6, 130.4, and 133.7 eV, respectively, corresponding to P<sub>2</sub>p<sub>3/2</sub>, P<sub>2</sub>p<sub>1/2</sub>, and P─O bonds.<sup>[</sup>\n##UREF##36##\n44\n##\n<sup>]</sup> Figure ##FIG##2##2d## displays multiple oxygen spectra for O 1 s, with peaks at 531.6 and 533.3 eV, which are attributed to the metal‐oxygen bonds and oxygen from adsorbed water, respectively.<sup>[</sup>\n##UREF##39##\n47\n##\n<sup>]</sup> These XPS experimental results further confirm the successful synthesis of the phosphide. The binding energies of Fe<sub>2</sub>p in FeCo‐P shift toward higher values, while those of Co<sub>2</sub>p shift toward lower values due to the interaction between P and the metal elements. Phosphorous possesses a strong electronegativity, enabling it to attract electrons from the metal atoms and become a negatively charged center, while Fe and Co in FeCo‐P become positively charged centers, promoting the binding of more OH‐ ions. This is favorable for the progression of OER and accelerates HER to produce more H<sub>2</sub>.<sup>[</sup>\n##UREF##20##\n24\n##, ##UREF##40##\n48\n##\n<sup>]</sup>\n</p>", "<title>Electrocatalytic Properties</title>", "<title>HER Performance</title>", "<p>The HER performance of the sample was measured in a typical three‐electrode system in a 1 mol L<sup>−1</sup> KOH solution saturated with N<sub>2</sub>. Based on the LSV (Linear Sweep Voltammetry) in <bold>Figure</bold> ##FIG##3##\n3a## and <italic toggle=\"yes\">η</italic> in Figure ##FIG##3##3b##, it can be observed that the hollow spherical nanosheets of FeCo‐P exhibit higher HER activity compared to monometallic Fe‐P and Co‐P. FeCo‐P requires an <italic toggle=\"yes\">η</italic> of 131 mV to achieve a CD of 10 mA cm<sup>−2</sup>, which is higher than Pt/C (75 mV) but lower than Fe‐P (159 mV) and Co‐P (167 mV). The above results indicate that bimetallic phosphides are more effective in enhancing electrocatalysts compared to monometallic ones, and the synergistic effect of bimetallic interaction facilitates rapid mass transfer.<sup>[</sup>\n##UREF##41##\n49\n##\n<sup>]</sup> It is worth noting that at current densities greater than 50 mA cm<sup>−2</sup>, the activity of FeCo‐P surpasses that of Pt/C. Furthermore, the kinetic characteristics of the reaction were studied by examining the Tafel slopes. As shown in Figure ##FIG##3##3c##, the Tafel slopes for FeCo─P, Fe─P, Co─P, and Pt/C are 89.90, 111.54, 123.24, and 100.02 mV dec<sup>−1</sup>, respectively. The Tafel slope for FeCo‐P is lower than those of Pt/C and other samples, indicating its excellent HER kinetic performance.</p>", "<p>The electronic transport rate of electrode materials is related to the conductivity of material. Generally, higher conductive electrode materials exhibit faster electronic transport rates. To further understand the material's conductivity, EIS was analyzed. Figure ##FIG##3##3d## indicates that, through circuit fitting analysis, the impedance plot of FeCo‐P exhibits a characteristic semicircle with the smallest diameter, representing the lowest charge transfer resistance.<sup>[</sup>\n##UREF##42##\n50\n##\n<sup>]</sup> The charge transfer rate of FeCo‐P hollow nanospheres is the fastest, which is attributed to the synergistic effect of bimetallic interaction and the hollow structure that promotes the generation of more active sites while reducing the charge transfer distance,<sup>[</sup>\n##UREF##43##\n51\n##\n<sup>]</sup> thus enhancing the conductivity. The sloping lines in the low‐frequency region reflect Warburg impedance caused by ionic diffusion, with the characteristic that a steep slope favors the migration of ions within the material, while a gradual slope indicates a more pronounced hindrance.<sup>[</sup>\n##REF##34027659##\n52\n##\n<sup>]</sup> As observed in the inset of Figure ##FIG##3##3d##, FeCo‐P exhibits the steepest slope, indicating the highest diffusion migration rate. The impedance results are consistent with the electrocatalytic performance results.</p>", "<p>The catalyst's specific surface area and pore size were analyzed using N<sub>2</sub> adsorption‐desorption isotherms. As shown in Figure ##SUPPL##0##S3## and Table ##SUPPL##0##S1## (Supporting Information), the specific surface area of Fe─P, Co─P, and FeCo─P are 10.2, 13.6, and 14.3 m<sup>2</sup> g<sup>−1</sup>, respectively, indicating that they all possess mesoporous structures, and FeCo‐P has the largest specific surface area among them, owing to its unique hollow structure, which increases the catalyst's interface area and is more favorable for both of HER and OER.</p>", "<p>In addition, the Turnover Frequency (TOF) value is also an evaluation criterion for catalytic activity.<sup>[</sup>\n##REF##29959325##\n53\n##\n<sup>]</sup> TOF values were further calculated at a <italic toggle=\"yes\">η</italic> of 100 mV to assess the intrinsic HER activity of the catalysts. From Table ##SUPPL##0##S2## (Supporting Information), it can be observed that the TOF value of FeCo‐P is 0.134 s<sup>−1</sup>, nearly 11 times that of Fe–P (0.012 s<sup>−1</sup>) and 5 times that of Co‐P (0.026 s<sup>−1</sup>) at the same <italic toggle=\"yes\">η</italic>. This further underscores that FeCo‐P exhibits excellent intrinsic HER activity, attributed to the synergistic effect of bimetallic phosphides and the hollow structure of FeCo‐P. In addition to high activity, good stability is also an important parameter for evaluating electrocatalysts. As shown in Figure ##FIG##3##3e##, the stability of the catalyst was analyzed using chronoamperometry and LSV curves initial and after 2000 cycles. The chronoamperometry curve for FeCo‐P shows no decay in CD at 10 mA cm<sup>−2</sup> within 24 h, and there is negligible change in the LSV curve initial and after 2000 cycles, indicating that the catalyst exhibits excellent long‐term stability. Furthermore, postreaction SEM analysis revealed that FeCo‐P retained its initial morphological structure, providing additional evidence of its excellent HER stability (see Figure ##SUPPL##0##S4##, Supporting Information). FeCo‐P's outstanding HER activity surpasses that of some recently reported nonprecious metal HER catalysts, as shown in Figure ##FIG##3##3f## and Table ##SUPPL##0##S3## (Supporting Information).</p>", "<title>OER Performance</title>", "<p>The OER performance of the samples was tested in a N<sub>2</sub>‐saturated 1 mol L<sup>−1</sup> KOH solution. As shown in <bold>Figure</bold> ##FIG##4##\n4a,b##, the overpotentials for achieving 10 mA cm<sup>−2</sup> are 240, 267, 307, and 287 mV for FeCo─P, Fe─P, Co─P, and IrO<sub>2</sub>, respectively. FeCo─P demonstrates a significant advantage at high current densities, with an overpotential of only 306 mV at 300 mA cm<sup>−2</sup>. These results indicate that the hollow nanospheres of FeCo─P exhibit higher OER activity compared to monometallic Fe─P and Co─P, and even outperform the precious metal IrO<sub>2</sub>. From Figure ##FIG##4##4c##, it can be observed that the Tafel slopes for FeCo─P, Fe─P, Co─P, and IrO<sub>2</sub> are 38.24, 45.29, 88.37 and 72.79 mV dec<sup>−1</sup>, respectively. FeCo‐P hollow nanospheres exhibit the smallest Tafel slope, indicating their excellent OER kinetics.<sup>[</sup>\n##UREF##43##\n51\n##\n<sup>]</sup> For the catalyst's application, long‐term stability is also a crucial factor.<sup>[</sup>\n##UREF##44##\n54\n##\n<sup>]</sup> The OER stability of the samples was evaluated in a N<sub>2</sub>‐saturated 1 mol L<sup>−1</sup> KOH solution. As shown in Figure ##FIG##4##4d##, there is negligible change in the LSV curves before and after 2000 cycles. Chronoamperometry curves indicate that the catalyst maintains excellent catalytic activity even after 24 h. Additionally, post‐OER long‐term stability testing SEM analysis (as shown in Figure ##SUPPL##0##S5##, Supporting Information) reveals no significant changes in morphological structure. FeCo‐P exhibits superior OER activity compared to some recently reported non‐precious metal OER catalysts, as shown in Figure ##FIG##4##4e## and Table ##SUPPL##0##S4## (Supporting Information).</p>", "<p>The electrochemical double‐layer capacitance (<italic toggle=\"yes\">C</italic>\n<sub>dl</sub>) is an important factor in estimating the activity of electrocatalysts. The number of active sites is directly proportional to the electrochemical surface area evaluated by <italic toggle=\"yes\">C</italic>\n<sub>dl</sub>.<sup>[</sup>\n##REF##29341596##\n55\n##\n<sup>]</sup>\n<italic toggle=\"yes\">C</italic>\n<sub>dl</sub> values were calculated by obtaining Cyclic Voltammetry (CV) curves at different scan rates within the non‐Faradaic voltage range (see Figure ##SUPPL##0##S6##, Supporting Information). From Figure ##FIG##4##4f##, it can be observed that the <italic toggle=\"yes\">C</italic>\n<sub>dl</sub> value for FeCo‐P (1.48 mF cm<sup>−2</sup>) is greater than that of Fe─P (1.26 mF cm<sup>−2</sup>) and Co─P (0.97 mF cm<sup>−2</sup>). This indicates that the bimetallic phosphide FeCo increases the number of active sites more effectively compared to monometallic phosphides, thereby improving HER and OER activities, which consistent with the results of Tafel slopes and impedance.</p>", "<title>OWS Performance</title>", "<p>To demonstrate the practical application of the FeCo‐P catalyst in an alkaline medium, a bifunctional water splitting device was assembled using FeCo‐P as both the cathode and anode, and tested in a 1 mol L<sup>−1</sup> KOH solution. Commercially Pt/C was used as the HER electrocatalyst, and IrO<sub>2</sub> was used as the OER electrocatalyst for comparison. As shown in <bold>Figure</bold> ##FIG##5##\n5a##, the cell voltage for FeCo‐P || FeCo‐P is only 1.49 V@10 mA cm<sup>−2</sup>, significantly outperforming the performance of the precious metal Pt/C || IrO<sub>2</sub> (1.58 V) for overall water splitting. Furthermore, at 100 and 300 mA cm<sup>−2</sup>, the cell voltages for FeCo‐P || FeCo‐P are 1.55 and 1.57 V, respectively. It can be observed from the data that the FeCo‐P catalyst has a distinct advantage at high current densities, making it highly promising for practical applications. The catalytic performance of FeCo‐P in OWS surpasses that of most reported powder TMP electrocatalysts and some in situ grown phosphide electrocatalysts, as shown in Table ##SUPPL##0##S5## (Supporting Information). Stability is another critical criterion for evaluating electrocatalysts. Therefore, the overall water stability of the FeCo‐P electrode was further tested. As shown in Figure ##FIG##5##5b,c##, the LSV curves after 2000 cycles of CV are essentially identical to the initial LSV curve, indicating excellent durability during the cyclic scanning process. In the long‐term stability test of 24 h at a CD of 10 mA cm<sup>−2</sup>, chronoamperometry curves demonstrate that there is no significant decrease in CD after 24 h, highlighting its excellent stability. Furthermore, SEM characterization of the material after long‐term stability testing in overall water splitting, as shown in Figure ##SUPPL##0##S7## (Supporting Information), reveals that the sample still retains its original hollow structure, indicating good structural stability. As depicted in Figure ##FIG##5##5d,e##, a significant number of bubbles appear on the surfaces of both the cathode and anode during the electrolysis of water. Collection and measurement of these bubbles were performed using a water displacement method. The measured ratio of H<sub>2</sub> to O<sub>2</sub> closely approximates the theoretical value of 2:1, and the Faradaic efficiency is close to 100%. A comparison of the OWS performance of FeCo‐P || FeCo‐P with other reported materials is shown in Figure ##FIG##5##5f##, illustrating the outstanding performance of FeCo‐P || FeCo‐P. These results collectively indicate that the FeCo‐P catalyst exhibits excellent OWS activity and stability, with an voltage of only 1.57 V at a CD of 300 mA cm<sup>−2</sup>, demonstrating its potential for industrial applications.</p>", "<title>Density Functional Theory (DFT) Theoretical Calculations</title>", "<p>To better elucidate the mechanisms behind the HER and OER activities of the FeCo‐P catalyst, a series of DFT calculations were conducted. As shown in Figure ##SUPPL##0##S8## (Supporting Information), theoretical models for FeP, Co<sub>2</sub>P, and FeCo‐P were constructed. For the alkaline HER process, the activity site with a Δ<italic toggle=\"yes\">G</italic>\n<sub>H</sub>* (hydrogen adsorption free energy) of 0 attains the best HER activity. In other words, the closer Δ<italic toggle=\"yes\">G</italic>\n<sub>H</sub>* to 0, the better the catalyst's HER activity.<sup>[</sup>\n##UREF##45##\n56\n##, ##REF##32309830##\n57\n##\n<sup>]</sup> Calculations yielded Δ<italic toggle=\"yes\">G</italic>\n<sub>H</sub>* values for FeP, Co<sub>2</sub>P, and FeCo‐P of 0.124, −0.277, and 0.119 eV, respectively (as shown in <bold>Figure</bold> ##FIG##6##\n6a##). This indicates that the Δ<italic toggle=\"yes\">G</italic>\n<sub>H</sub>* value of heterostructure FeCo‐P is the closest one to 0, facilitating H* adsorption and thus enhancing HER activity. For the OER process in an alkaline electrolyte solution, the computed free energies, as shown in Figure ##FIG##6##6b##, indicate that the formation of the *OOH intermediate in all the three samples is the slowest step, typically considered as the rate‐determining step, as stabilizing *OOH requires high energy.<sup>[</sup>\n##UREF##38##\n46\n##\n<sup>]</sup> The change in free energy for FeCo‐P is 2.39 eV, which is lower than that for FeP (2.64 eV) and Co<sub>2</sub>P (3.47 eV). The lower energy barrier for the heterostructure compared to the monomers suggests that FeCo‐P exhibits better OER activity. All of the above findings demonstrate that the FeP/Co<sub>2</sub>P heterostructure effectively tunes and optimizes the adsorption abilities of different intermediates in the HER and OER processes, thus enhancing its bifunctional activity. In an alkaline solution, OER involves four proton‐coupled reaction steps, including the adsorption of *OH, *O, and *OOH intermediates. The OER mechanism is illustrated in Figure ##FIG##6##6c##, where it begins with the adsorption of *OH at the active sites of FeCo‐P, forming HO‐FeCo‐P (Step 1). Subsequently, through deprotonation, oxygen binds into the structure, generating O‐FeCo‐P (Step 2). The exposed oxygen undergoes nucleophilic attack by accepting ‐OH, leading to the formation of *OOH (Step 3). *OOH is further attacked by ‐OH, resulting in the release of O<sub>2</sub> (Step 4).</p>" ]
[ "<title>Conclusion</title>", "<p>In summary, we prepared a hollow spherical FeCo‐P catalyst composed of nanosheets via a hydrothermal and annealing process and investigated its performance in the HER, OER, and OWS. The hollow structure of FeCo‐P provides abundant active sites, increasing the contact area between the catalyst and the electrolyte, and reducing mass/charge transport distances. Combined with its nanosheet spherical configuration, this structure is highly conducive to the progress of both HER and OER, enabling efficient OWS. The results demonstrate that in 1 mol L<sup>−1</sup> KOH, FeCo‐P achieves current densities of 10 mA cm<sup>−2</sup> with overpotentials of only 131 mV for HER and 240 mV for OER, with Tafel slopes of 89.90 and 38.24 mV dec<sup>−1</sup>, respectively. Furthermore, it retains its original structural morphology after long‐term reactions, demonstrating excellent stability. FeCo‐P, when used as both of cathode and anode, achieves low cell voltages of only 1.49 and 1.55 V to reach current densities of 10 and 100 mA cm<sup>−2</sup>, respectively. Additionally, the overall water voltage at a CD of 300 mA cm<sup>−2</sup> is only 1.57 V, highlighting the industrial potential of this catalyst. This work employs an economical and straightforward approach, providing valuable strategies for the preparation of highly efficient electrocatalysts for energy‐related applications.</p>" ]
[ "<title>Abstract</title>", "<p>The design of catalysts with tunable active sites in heterogeneous interface structures is crucial for addressing challenges in the water‐splitting process. Herein, a hollow spherical heterostructure FeCo‐P is successfully prepared by hydrothermal and phosphorization methods. This hollow structure, along with the heterogeneous interface between Co<sub>2</sub>P and FeP, not only facilitates the exposure of more active sites, but also increases the contact area between the catalyst and the electrolyte, as well as shortens the distance for mass/electron transfer. This enhancement promotes electron transfer to facilitate water decomposition. FeCo‐P exhibits excellent hydrogen evolution (HER) and oxygen evolution (OER) performance when reaching @ 10 mA cm<sup>−2</sup> in 1 mol L<sup>−1</sup> KOH, with overpotentials of 131/240 mV for HER/OER. Furthermore, when FeCo‐P is used as both the cathode and anode for overall water splitting (OWS), it only requires low voltages of 1.49, 1.55, and 1.57 V to achieve CDs of 10, 100, and 300 mA cm<sup>−2</sup>, respectively. Density functional theory calculations indicate that constructing a Co<sub>2</sub>P and FeP heterogeneous interface with good lattice matching can facilitate electron redistribution, thereby enhancing the electrocatalytic performance of OWS. This work opens up new possibilities for the rational design of efficient water electrolysis catalysts derived from MOFs.</p>", "<p>The synthesis of FeCo‐P with a hollow spherical heterostructure is achieved through hydrothermal and phosphorization methods. The catalyst exhibits high HER/OER activity in alkaline solutions, with an over potential of 131/240 mV. The heterostructure enhances the catalytic reaction rate. FeCo‐P exhibits an ultra‐low OWS potential of 1.49 V at 10 mA cm<sup>−2</sup>.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6831-cit-0058\">\n<string-name>\n<given-names>H.</given-names>\n<surname>Jiang</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Zhao</surname>\n</string-name>, <string-name>\n<given-names>G.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>P.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Tu</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Hu</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Shen</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Wu</surname>\n</string-name>, <article-title>Hollow Spherical Heterostructured FeCo‐P Catalysts Derived from MOF‐74 for Efficient Overall Water Splitting</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2306919</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202306919</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Materials</title>", "<p>Co(NO<sub>3</sub>)<sub>2</sub>· 6H<sub>2</sub>O and Pt/C (Pt 20%) were obtained from Macklin. FeCl<sub>2</sub>·4H<sub>2</sub>O and anhydrous ethanol were bought from Xilong Chemical Co., Ltd. RuO<sub>2</sub> and 2,5‐dihydroxyterephthalic acid (H<sub>4</sub>DOT) were sourced from Aladdin. Nafion (5 wt.%) was got from Alfa Aesar. N, N‐dimethylformamide (DMF) was acquired from Tianjin Damao Chemical Reagent Factory. All reagents were used directly. Deionized (DI) water was used throughout the entire experimental process. The nickel foam (NF) substrates were sonicated in 3 mol L<sup>−1</sup> HCl and DI water for 15 min before use.</p>", "<title>Preparation of FeCo–MOF‐74</title>", "<p>H<sub>4</sub>DOT (0.9 mmol), Co(NO<sub>3</sub>)<sub>2</sub>·6H<sub>2</sub>O (0.18 mmol), and FeCl<sub>2</sub>·4H<sub>2</sub>O (0.9 mmol) were added in a mixture of 30 mL DMF and 30 mL ethanol under magnetic stirring until uniform. The resulting mixture was then transferred to a stainless steel high‐pressure autoclave lined with Teflon and maintained at 170 °C for 24 h. After natural cooling, the product was washed with DMF and ethanol and centrifuged, then the final product was obtained through freeze‐drying.</p>", "<p>The synthesis of Fe‐MOF‐74 and Co‐MOF‐74 was similar to the method used for FeCo‐MOF‐74, with an equal amount of iron source/cobalt source added in a mixture of 30 mL DMF and 30 mL ethanol. Subsequently, the homogeneous mixture was transferred to a stainless steel high‐pressure autoclave lined with Teflon, and maintained at 170 °C for 24 h. After natural cooling, the product was obtained through washing with DMF and ethanol, centrifugation, and freeze‐drying.</p>", "<title>Preparation of FeCo‐P</title>", "<p>A 50 mg of FeCo–MOF‐74 precursor and 1 g of NaH<sub>2</sub>PO<sub>2</sub>•H<sub>2</sub>O were placed separately in ceramic boats. FeCo–MOF‐74 was positioned downstream in the furnace and heated to 350 °C under a nitrogen atmosphere, with a heating rate of 2 °C min<sup>−1</sup>. The mixture was annealed and held at this temperature for 2 h. After cooling to room temperature, FeCo─P was collected. Fe─P and Co─P were synthesized using the same method for comparison.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank the National Natural Science Foundation of China (52362012, 42077162, and 51978323), the Jiangxi Natural Science Foundation Project (2022ACB203014), the Jiangxi Major Discipline Academic and Technical Leaders Training Program (20232BCJ22048, 20213BCJ22018), the Natural Science Project of the Educational Department in Jiangxi Province (GJJ2201121), the Natural Science Foundation of Nanchang Hangkong University (EA202202256), Educational Reform Project of Jiangxi Province (JXYJG‐2022‐135), and the Nanchang Hangkong University Educational Reform Project (sz2214, sz2213, JY22017, and KCPY1806).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6831-fig-0007\"><label>Scheme 1</label><caption><p>Schematic illustration of synthetic process of FeCo‐P.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6831-fig-0001\"><label>Figure 1</label><caption><p>a) SEM images of Fe‐P. b) SEM images of Co‐P. c,d) SEM and TEM images of FeCo‐P. e,f) HRTEM images of FeCo‐P, and g‐j) STEM‐EDS elemental mapping images of the FeCo‐P.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6831-fig-0002\"><label>Figure 2</label><caption><p>XPS spectrum of Fe─P, Co─P, and FeCo─P: a) Fe 2p spectra, b) Co 2p spectra, c) P 2p spectra, d) O 1s spectra.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6831-fig-0003\"><label>Figure 3</label><caption><p>a) HER polarization curves, b) <italic toggle=\"yes\">η</italic> and c) Tafel slope of the as‐prepared electrocatalysts. d) Electrochemical impedance spectroscopy (EIS) of CoP, FeP and FeCo‐P. e) The long‐term stability test of FeCo‐P. f) Comparison of the <italic toggle=\"yes\">η</italic> at a CD of 10 mA cm<sup>−2</sup> and Tafel slope for FeCo‐P with other state‐of‐art HER catalysts.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6831-fig-0004\"><label>Figure 4</label><caption><p>a) OER polarization curves, b) <italic toggle=\"yes\">η</italic> and c) Tafel slope of the as‐prepared electrocatalysts. d) The long‐term stability test of FeCo‐P. e) Comparison of the <italic toggle=\"yes\">η</italic> at a CD of 10 mA cm<sup>−2</sup> and Tafel slope for FeCo‐P with other state‐of‐art OER catalysts. f) <italic toggle=\"yes\">C</italic>\n<sub>dl</sub> of CoP, FeP, and FeCo‐P.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6831-fig-0005\"><label>Figure 5</label><caption><p>a) Polarization curves of FeCo‐P||FeCo‐P and Pt/C||RuO2 toward overall water splitting. b) Chrono‐potentiometric curves of FeCo‐P||FeCo‐P at ≈10 mA cm<sup>−2</sup> for 24 h. c) LSV curves of FeCo‐P||FeCo‐P before and after 2000 cycles. d) Gas collection of H<sub>2</sub> and O<sub>2</sub>. e) FeCo‐P||FeCo‐P Plot of gas production as a function of time during the electrolysis of water. f) Comparison of the required cell voltage @ 10 mA cm<sup>−2</sup> for FeCo‐P with other state‐of‐the‐art bifunctional electrocatalysts.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6831-fig-0006\"><label>Figure 6</label><caption><p>a) Calculated free energy illustration of HER intermediated species. b) Calculated free energy diagram of OER intermediates (U = 1.23 V). c) The OER reaction pathway on FeCo‐P interface.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6831-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting information</p></caption></supplementary-material>" ]
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{ "acronym": [], "definition": [] }
57
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 20; 11(2):2306919
oa_package/fe/1d/PMC10787075.tar.gz
PMC10787076
37984880
[ "<title>Introduction</title>", "<p>Congenital heart defects (CHDs) refer to the general structural abnormality of the heart or thoracic great vessels at birth, which is the commonest congenital disease with an incidence of 4–50 per 1000 live births.<sup>[</sup>\n##REF##12084585##\n1\n##\n<sup>]</sup> Over the past decades, the therapeutic paradigm for CHDs has shifted from open‐chest surgery to minimally invasive transcatheter procedure.<sup>[</sup>\n##REF##33964482##\n2\n##\n<sup>]</sup> Currently, four main types of CHDs can be cured by transcatheter closure, including atrial septal defect (ASD), patent foramen ovale (PFO), patent ductus arteriosus (PDA), and ventricular septal defect (VSD).<sup>[</sup>\n##REF##12084585##\n1\n##, ##REF##33964482##\n2\n##, ##REF##33007088##\n3\n##\n<sup>]</sup> Biodegradable biomaterials aimed at inducing native tissue regeneration offer a promising alternative to cardiovascular implants compared to the formation of severe complications caused by metal‐based implant occlusion, such as cardiac perforation, erosion, rupture, arrhythmia and thrombosis.<sup>[</sup>\n##REF##24560920##\n4\n##\n<sup>]</sup> Recently, biodegradable occluders made of polydioxanone (PDO) and poly (l‐lactic acid) (PLLA) have been testified in clinical trials, suggesting the feasibility and safety of polymer‐based implants to occlude the defect.<sup>[</sup>\n##REF##36401954##\n5\n##\n<sup>]</sup>\n</p>", "<p>Most degradable polymer materials used in occluders including polylactic acid and PDO, have a relatively fast degradation rate in comparison with nitinol, and the degradation of biomaterials leads to a loss of mechanical strength, which therefore requires rapid tissue regeneration to withstand load transfer. However, such polymers have high crystallinity and high hydrophobicity,<sup>[</sup>\n##REF##24090987##\n6\n##\n<sup>]</sup> which are not advantageous to cell adhesion and migration. Degradable polymers are generally relatively plastic,<sup>[</sup>\n##UREF##0##\n7\n##\n<sup>]</sup> and if the biophysical properties of the biomaterial do not match those of the local tissue, it can lead to loss of regenerated tissue and loosening of the polymeric implants. Occasional complications related to the material design have been reported in previous studies. Residual shunts developed in 3 of the 5 patients with degradable occluder implantation, which was increased during the 3 year follow‐up.<sup>[</sup>\n##UREF##1##\n8\n##\n<sup>]</sup> Meanwhile, device malformation with disc expansion was observed in one case, which could be attributed to incomplete endothelialization after degradation initiation.<sup>[</sup>\n##UREF##1##\n8\n##\n<sup>]</sup> Sievert et al. reported that moderate or large shunt occurred in 3 of 15 patients with poly(lactic‐co‐glycolic) acid (PLGA) occluders after implantation for 2 years.<sup>[</sup>\n##REF##34726601##\n9\n##\n<sup>]</sup> Therefore, the degradation rate of biomaterials should match the rate of in situ tissue regeneration for optimal nascent tissue growth and material–tissue integration, yet the balance between these two relationships remains clinically elusive based on previous cases. Additionally, the inflammatory response raised by polymer is still a risk for tissue erosion and rhythm disturbance. Our pre‐clinical studies also suggested that PDO occluder still induced transient arrhythmia and the frequencies decreased with device degradation and the relief of inflammatory response in a canine VSD model.<sup>[</sup>\n##REF##36401954##\n5d\n##\n<sup>]</sup> Moreover, 3 of 54 patients implanted with PDO occluder developed persistent right bundle branch block in a randomized controlled study during 2 year follow‐up.<sup>[</sup>\n##REF##36401954##\n5b\n##\n<sup>]</sup> Surface coating on degradable implant was used to improve material biocompatibility, such as hydrogel coatings.<sup>[</sup>\n##REF##22007787##\n10\n##\n<sup>]</sup> However, hydrogel coatings are not suitable for percutaneous catheter interventional delivery of occluders implanted in cardiac defects, due to the uncontrolled coating thickness that leads to the loss of hydrogel body structure during interventional therapy and the decrease of elasticity of the occluder itself.</p>", "<p>Biomaterials interact with cells through their biophysical and biochemical properties, which can regulate the local tissue microenvironment by recruiting endogenous cells including immune cells, and endothelial cells, to guide the process of in situ tissue regeneration.<sup>[</sup>\n##UREF##2##\n11\n##\n<sup>]</sup> As for the surface properties of biomaterials, the improvement of hydrophilicity ensures the promotion of albumin adsorption, leading to the local macrophages to produce anti‐inflammatory cytokines, which promotes the regenerative repair of damaged tissues.<sup>[</sup>\n##REF##32563944##\n12\n##\n<sup>]</sup> Optionally, biocompatible natural macromolecules are modified on the surface of scaffold materials to regulate cell‐biomaterial interactions and enhance cell spreading.<sup>[</sup>\n##UREF##3##\n13\n##\n<sup>]</sup> Engineered biomaterials that guide the rapid recruitment, adhesion, migration, and infiltration of endogenous cells through biochemical pathways are critical for promoting in situ tissue regeneration.<sup>[</sup>\n##REF##28221776##\n14\n##\n<sup>]</sup> Biomaterials decorated with cell adhesion proteins presenting in the native extracellular matrix (ECM) enable biochemical signaling with cells through the recognition of these ECM proteins by cell surface receptors, including integrins.<sup>[</sup>\n##REF##34890973##\n15\n##\n<sup>]</sup> Therefore, we hypothesize the designed bioactive polymers to be decorated on the surface of implant materials, serving as biophysical and biochemical cues, would dictate cell adhesion and proliferation, and ECM remodeling on the polymer scaffolds, to induce endogenous tissue regeneration.</p>", "<p>Herein, to address the unmet need of matching the degradation rate of implants to the rate of endogenous tissue regeneration, a bioactive molecular dressing was decorated on the surface of degradable PDO occluders, which consist of a PDO frame and PLLA barrier film. The PDO occluder decorated with bioactive molecules is identified as PGAG occluder (<bold>Figure</bold> ##FIG##0##\n1A##). The polymer consists of gelatin covalently bonded with the laminin‐derived A5G81 peptide via Michael addition reaction. This peptide sequence (AGQWHRVSVRWG) is the cell adhesion domain in laminin that specifically interacts with integrins α3β1 and α6β1.<sup>[</sup>\n##REF##29891655##\n16\n##\n<sup>]</sup> Gelatin provides a biocompatible matrix for cell spreading, which is conducive to cell proliferation and growth,<sup>[</sup>\n##UREF##4##\n17\n##\n<sup>]</sup> while A5G81 peptide is introduced to enhance the structural accuracy of the interaction with cells. The bioactive structure results in sustained activation of cell–material interface by providing more integrin adhesion sites. Moreover, the active dressing induced an anti‐inflammatory phenotypic differentiation of immune cells, inhibited inflammatory responses, and produced lower foreign body responses in vivo. The treatment with newly prepared occluder, without drug or cytokine, significantly induced heart tissue regeneration in ASD models (Figure ##FIG##0##1B##). This bioactive modification on the surface of biodegradable materials exhibited optimized cell‐biomaterial interactions while retaining the mechanical properties and dimensions of the implant, providing a broad design platform for next‐generation biodegradable medical devices that powerfully induce endogenous tissue regeneration and material–tissue fusion.</p>" ]
[]
[ "<title>Results</title>", "<title>Preparation and Characterization of PGAG</title>", "<p>PGAG occluder is manufactured through the surface modification of PDO occluder decorated with bioactive polymers, including the flow blocking membrane, and the frame. The synthesis of bioactive polymers involved the coupling of gelatin with Maleimide‐terminated A5G81 (Mal‐A5G81) peptide covalently via amino‐maleimide click chemistry reaction (Figure ##SUPPL##0##S1##, Supporting Information). A5G81 (AGQWHRVSVRWG) is a 12‐amino acid sequence screened from the soluble peptides from the laminin α5 chain G domain sequences, which is a cell adhesion domain of laminin.<sup>[</sup>\n##REF##29891655##\n16\n##, ##REF##22391228##\n18\n##\n<sup>]</sup> The molecular weights of gelatin‐A5G81 and gelatin were determined by gel permeation chromatography (GPC). The Mp (molecular weight of the highest peak) of gelatin‐A5G81 and gelatin were 9913 and 9106 g mol<sup>−1</sup>, respectively, indicating that 0.52 mol of A5G81 peptide were bonded to 1 mol of gelatin (Figure ##SUPPL##0##S2##, Supporting Information). To further confirm the amino‐maleimide click reaction, the amino acid concentration of gelatin and gelatin‐A5G81 was determined by ninhydrin reaction. The concentration of amino acid in 1 mg mL<sup>−1</sup> gelatin was 3.03 µg mL<sup>−1</sup>, while the concentration of amino acid in gelatin‐A5G81 was 1.77 µg mL<sup>−1</sup>, which suggested that the concentration of amino groups in gelatin‐A5G81 decreased after Mal‐A5G81 was bonded. Furthermore, the ultraviolet–visible (UV–vis) spectrum showed that the Mal‐A5G81 possessed an absorbance peak at 300 nm, which corresponds to the absorption peak of the maleimide group,<sup>[</sup>\n##REF##33535669##\n19\n##\n<sup>]</sup> while gelatin‐A5G81 did not, which indicated that the maleimide group was fully reacted (Figure ##SUPPL##0##S3##, Supporting Information).</p>", "<p>PDO occluder was processed through oxygen surface plasma treatment and modified with a silane coupling agent containing an epoxy group. The silane pre‐treatment has been an innovative modification of cardiovascular implants, which degrade into single molecule of Si(OH)<sub>4</sub> and would be removed by the urinary system without adverse reactions.<sup>[</sup>\n##REF##37382394##\n20\n##\n<sup>]</sup> Subsequently, gelatin‐A5G81 polymer was covalently grafted onto the occluder material surface through the ring‐opening reaction of amino and epoxy groups. Therefore, PGAG was synthesized by PDO grafting with Gelatin‐A5G81 (Figure ##FIG##0##1A##). The surface morphology of PGAG monofilaments was observed. Scanning electron microscopy (SEM) images of PGAG monofilaments showed a uniform diameter size and relatively obvious longitudinal grooves (<bold>Figure</bold> ##FIG##1##\n2A##). Surface optical profile analysis revealed the existence of longitudinal grooves with a depth of 5–15 µm and groove width of 2–8 µm, uniformly distributed on the surface of PGAG frame (Figure ##FIG##1##2B,C##).</p>", "<p>Furthermore, the presence of bioactive polymers on the surface of the PDO monofilament was characterized by various analytical methods. Bioactive polymers were visualized on the monofilament surface by molecularly labeling gelatin and A5G81 with Cy5 and FITC fluorescent dye, respectively, and further analyzed by fluorescence microscopy (Figure ##FIG##1##2D##). Results showed that strong red and green fluorescence on the surface of PGAG monofilaments were observed, clearly reflecting the continuous and stable bonding of bioactive molecules on the surface of the monofilaments. In addition, the surface chemical element of a representative PGAG characterized by X‐ray photoelectron spectroscopy (XPS) indicated the appearance of N peaks due to the bonding of gelatin and peptide, with the strongest characteristic peak attributed to nitrogen in N─C bonds, and the weaker peak corresponding to nitrogen in N─H bonds (Figure ##FIG##1##2E##). The GPC traces showed that the Mp of PGAG and PDO were 119460 and 108130 g mol<sup>−1</sup>, respectively (Figure ##SUPPL##0##S4##, Supporting Information), indicating that 1.14 mol of gelatin‐A5G81 were bonded to 1 mol of PDO molecule and therefore, 0.59 mol of A5G81 peptide were bonded to 1 mol of PDO molecule. Fourier transform infrared spectroscopy (FTIR) spectrum also showed the characteristic stretching vibration absorption peaks at 3345 cm<sup>−1</sup> and 3413 cm<sup>−1</sup> assigned to O─H and N─H bonds in gelatin and A5G81, respectively (Figure ##FIG##1##2F##). These data suggested the successful preparation of peptide‐gelatin conjugated PDO occluder.</p>", "<p>The mechanical properties of cardiovascular occluders grafted with bioactive polymers were further investigated. As shown in Figure ##FIG##1##2G##, the prepared PGAG occluder had good elasticity and deformability, which facilitated the transcatheter delivery of the occluder. PGAG monofilaments showed the same tensile strength and elongation at break as PDO monofilaments without significant differences (Figure ##FIG##1##2H##), indicating a favorable adaptability and reliability of this continuous modification process for fabricating degradable implants. Modification of the surface of implants with bioactive polymers affects their surface physical properties. PGAG material demonstrated a water contact angle of 20.7° (Figure ##SUPPL##0##S5##, Supporting Information), which is significantly lower than that of native PDO material (87.1°). The improved hydrophilicity may facilitate the binding of extracellular matrix molecules to the material surface and enhance cell adhesion. Furthermore, the modification of gelatin and peptides slightly increased the glass transition temperature of PDO from −11.3 °C to −10.3 °C (Figure ##SUPPL##0##S6##, Supporting Information), which may be attributed to the facile hydrogen bonding interactions between gelatin and polyester molecules, thus confining the mobility and molecular state of the polyester chains. Wide‐angle X‐ray diffraction (XRD) analysis demonstrated that the modification of the bioactive polymer did not affect the crystalline nature of the polyester (Figure ##SUPPL##0##S7##, Supporting Information). These results indicate surface modification of PDO fibers has no effect on the mechanical property of occluder, while significantly promotes the hydrophilicity.</p>", "<title>Promotion of Adhesion and Proliferation of Endothelial Cells on PGAG</title>", "<p>The biological cues of endothelial cells on biomaterials, including activation of survival, adhesion, migration, and proliferation, are closely associated with the process of endothelialization.<sup>[</sup>\n##REF##32927304##\n21\n##\n<sup>]</sup> PDO is highly hydrophobic, which is not advantageous to cell adhesion and infiltration. The ECM‐mimic structure of gelatin interface was expected to provide 3D porous microenvironment for cell adhesion and proliferation.<sup>[</sup>\n##UREF##4##\n17\n##, ##REF##30680322##\n22\n##\n<sup>]</sup> Moreover, the laminin‐derived A5G81 peptide is a potent tethered cell adhesion‐, proliferation‐, and endothelium‐inducing ligand that interacts specifically with the integrin receptors to promote endogenous tissue regeneration.<sup>[</sup>\n##REF##29891655##\n16\n##\n<sup>]</sup> To investigate the cytocompatibility, adhesion and pro‐endothelialization, human umbilical vein endothelial cells (HUVECs) were seeded on PDO, PDGA (gelatin modified PDO), PDAG (A5G81 modified PDO), or PGAG membranes. As shown in <bold>Figure</bold> ##FIG##2##\n3A##, the distribution of HUVECs was sparse and the amount did not obviously increase on the PDO surface from 24 h to 48 h, while the adhesion and proliferation of HUVECs was significantly improved after surface modification, with the maximum count on the PGAG membrane (Figure ##SUPPL##0##S8##, Supporting Information). The endothelium completely covered the surface of PGAG within 48 h in vitro (Figure ##FIG##2##3A##). Moreover, the cellular morphology of HUVECs on PDGA and PGAG exhibited elongated and pseudopod‐like structures, while those on PDO and PDAG were significantly smaller and rounder (Figure ##FIG##2##3A##). The axis ratio of HUVECs on PDGA and PGAG, which indicated the cell morphology of adhesion and extension status, was significantly greater than that on PDO (Figure ##SUPPL##0##S9##, Supporting Information), indicating the ECM‐mimic structure of gelatin could activate the adhesion and migration of HUVECs. The same phenomenon was also observed in L929 (a rat fibroblast line) implanted on PGAG (Figure ##SUPPL##0##S10##, Supporting Information), demonstrating that PGAG had the potential to recruit and facilitate proliferation of various cell types in vivo.</p>", "<p>To further visualize the adhesion and migration status, cell morphology was inspected by SEM. Figure ##FIG##2##3B## shows that endotheliocytes on PDO possessed a sphere shape. However, cells tightly sticked and fully extended with multiple pseudopods on the PGAG surface. The coverage area of single cell on PGAG was significantly larger than that of PDO and PDAG (Figure ##SUPPL##0##S11##, Supporting Information). Collectively, the surface gelatin‐peptide structure on PDO could induce tight adhesion of cells, which was expected to promote the process of endothelium in vivo.</p>", "<title>Activation of Integrin‐FAK Related PI3K/AKT and ERK/MAPK Pathways</title>", "<p>The molecular mechanism of adhesion and proliferation was further investigated by immunofluorescence staining and western blot. The integrin α3β1 complex is a key regulator for cell migration and re‐epithelialization, and interacts specifically with laminin.<sup>[</sup>\n##REF##34890973##\n15\n##, ##REF##29891655##\n16\n##\n<sup>]</sup> PGAG possess abundant laminin‐derived peptide and ECM similar structure. Therefore, we hypothesized that the cell–material interface would activate the integrin complex to facilitate endotheliocyte bioactivities. As shown in Figure ##FIG##2##3C##, the integrin α3 was remarkedly activated on PDAG and PGAG membranes compared with PDO, due to the high affinity of A5G81 peptide (Figure ##SUPPL##0##S12A##, Supporting Information). Focal adhesion kinase (FAK), a cytoplasmic protein tyrosine kinase that distinctly co‐localizes with integrins,<sup>[</sup>\n##REF##10806474##\n23\n##\n<sup>]</sup> was also significantly augmented by PDAG and PGAG as a consequence of activation of integrin complex (Figure ##FIG##2##3C## and Figure ##SUPPL##0##S12B##, Supporting Information). We further investigated the downstream of FAK, including the pathways of phosphoinositide 3‐kinase/protein Kinase B (PI3K/AKT) and phosphorylated extracellular signal‐regulated kinase/mitogen‑activated protein kinase (Erk/MAPK), which are important in regulating the cell survival, adhesion and proliferation.<sup>[</sup>\n##REF##35163418##\n24\n##\n<sup>]</sup> Western blot demonstrated that PI3K/AKT and MAPK pathways were significantly upregulated by stimulus of PDAG and PGAG, consistent with the activation of FAK (Figure ##FIG##2##3D–G## and Figure ##SUPPL##0##S13##, Supporting Information). The signaling intensity was greater on A5G81 modified membrane, indicating that the specific affinity of the peptide could additionally activate the survival and proliferation pathway, which was consistent with results of 48 h proliferation assay (Figure ##FIG##2##3A##). Collectively, these data indicated that endothelial cells could substantially proliferate on PGAG by activation of FAK/PI3K/AKT and Erk/MAPK signaling pathway, due to interactions between integrin receptor and protein–peptide unit (Figure ##FIG##2##3H##).</p>", "<title>Modulation of Inflammation by Decreasing M1 Macrophages and Promoting Proreparative Cytokine Release</title>", "<p>Inflammation caused by implanted devices plays a central role in innate tissue regeneration. Immune cells recruited or induced by biomaterials are broadly divided into two categories: pro‐inflammatory (including M1 macrophages) and anti‐inflammatory (such as M2 macrophages).<sup>[</sup>\n##REF##32234529##\n25\n##\n<sup>]</sup> Previous studies suggested that the hydrophilia and surface morphology of biomaterials were related to the immune response.<sup>[</sup>\n##UREF##5##\n26\n##\n<sup>]</sup> Gelatin could improve biocompatibility and trigger anti‐inflammation response.<sup>[</sup>\n##REF##30680322##\n22\n##\n<sup>]</sup> Thus, we hypothesized that the modification of hydrophilia and biochemical cues from gelatin and peptide could improve biocompatibility by polarizing immune cell toward a pro‐reparative diagram. Bone marrow‐derived macrophages (BMDMs) from C57BL/6 mice were seeded on materials and incubated for 48 h. The morphology was determined by immunofluorescence staining, with F4/80 to label the macrophages and CD86 to identify M1 type. As shown in <bold>Figure</bold> ##FIG##3##\n4A## and Figure ##SUPPL##0##S14## (Supporting Information), the number of BMDMs per view did not differ among the four groups, indicating that the interface strategy would not provoke immune cell adhesion and recruitment. However, compared with PDO, the percentage of M1‐type macrophages (F4/80<sup>+</sup> and CD86<sup>+</sup>) within BMDMs (F4/80<sup>+</sup>) significantly decreased in PDGA, PDAG and PGAG groups (Figure ##FIG##3##4A,B##), which demonstrated that gelatin and peptide improved the biocompatibility and mitigated the macrophage M1 polarization‐associated inflammatory response.</p>", "<p>The expression of representative pro‐reparative cytokines, including transforming growth factor‐β (TGF‐β), vascular endothelial growth factors (VEGF), interleukin‐4 (IL‐4) and interleukin‐10 (IL‐10), and pro‐inflammatory cytokines, such as tumor necrosis factor‐α (TNF‐α) and interferon‐γ (IFN‐γ) were further determined by enzyme‐linked immunosorbent assay (ELISA). Figure ##FIG##2##3B–H## shows that the concentration of TGF‐β, VEGF, IL‐4 and IL‐10 were substantially up‐regulated by PGAG treatment compared with PDO, while TNF‐α was remarkedly reduced. IFN‐γ was secreted in a relatively low concentration in all groups (mean concentration &lt; 3 pg mL<sup>−1</sup>). The matrix metallopeptidase 9 (MMP9), a key gelatinase linked with inflammation, extracellular matrix degradation and adverse cardiac remodeling,<sup>[</sup>\n##REF##23562601##\n27\n##\n<sup>]</sup> was also significantly alleviated by surface modification, which could prevent the constant enzymolysis of the interface and newly formed ECM, consistent with the decreased proportion of pro‐inflammatory macrophages by PGAG treatment. Altogether, these results suggested that PGAG alleviated the inflammatory response and provoked a pro‐reparative process by decreasing M1 macrophages and regulating innate cytokines.</p>", "<title>Safety and Efficacy of PGAG Occluder in a Porcine ASD Model</title>", "<p>Next, the effectiveness of PGAG occluder in cardiac tissue regeneration was verified in a porcine ASD model with PDO occluder as a control. ASD was created by perforating the atrial septum and subsequent balloon dilatation (Figure ##SUPPL##0##S15##, Supporting Information). The diameter of created ASD was 8 mm. Therefore, percutaneous transcatheter implantation of PDO and PGAG occluders with a waist diameter of 8 mm and a disc diameter of 16 mm was performed under the transthoracic echocardiography (TTE) and X‐ray guidance. All of the PDO and PGAG occluders were successfully released from the delivery system and occluded the defects at the first attempt. All animals survived in good physical condition after the procedures. No evidence of hematoma, pericardial effusion, valve damage, limb ischemia, dyspnea, or infection occurred during the procedures.</p>", "<p>At 1, 3, 6 months, pigs were sacrificed to evaluate the efficacy of occlusion. As shown in <bold>Figure</bold> ##FIG##4##\n5A##, all the occluders were well positioned and no displacement happened. The discs of PGAG occluder tightly adhered to the atrial septum and formed a cohesive plane at 1 month, with endothelial coverage over 60% (Figure ##FIG##4##5B##). However, the discs of PDO occluder were visibly separable from the atrial septum, with 40% overlay by an endothelial layer (Figure ##FIG##4##5A,B##). At 3 months, the PGAG occluder seamlessly integrated with the surrounding cardiac tissue devoid of any protrusion. While the endothelium covered over 70% of PDO occluder's surface, a discernable cavity persisted between PDO occluder and tissue, and the disc residual area was significantly larger in PDO occluder (Figure ##FIG##4##5A,B##). At 6 months, the endothelium covered over 95% in both groups (Figure ##FIG##4##5B##). In PGAG group, the surface of neo‐regenerated tissue appeared smooth, and the PGAG occluder became nearly imperceptible, leaving only a circular boundary. In contrast, the PDO occluder exhibited an uneven surface with a transparent fibrous capsule with significantly more disc residual area (Figure ##FIG##4##5A,B##). No obvious erosion or destruction of surrounding cardiac tissue and valves occurred in both groups. These anatomic examinations demonstrated that PGAG with bioactive interface could accelerate the process of endothelial coverage, and orchestrate a proper endogenous tissue regeneration.</p>", "<p>Multiple imaging methods were utilized during the follow‐up for in vivo functional evaluation. At 3 months, cardiac magnetic resonance imaging (MRI) demonstrated that the neo‐tissue grew into the PGAG occluder and formed an integral septum at 3 months, while the interspace in the PDO occluder was still obvious and a round and protruding fibrous capsule was formed (Figure ##FIG##4##5D##). TTE showed that the occluder was in the correct position and degraded gradually with time prolonged (Figure ##FIG##4##5E##). No residual shunt was observed surrounding the occluder in both groups (Figure ##FIG##4##5E##). However, the occluder and neo‐tissue thickness was significantly higher in PDO group than these in PGAG group, with an obvious disc protrusion at 1 and 3 months (Figure ##FIG##4##5F##). Cardiac function was in the normal range during the follow‐up (Figure ##SUPPL##0##S16##, Supporting Information). No valvular stenosis or regurgitation was found.</p>", "<p>Arrhythmia is a common but severe complication caused by percutaneous occluder, which is associated with foreign body response and persistent inflammation.<sup>[</sup>\n##UREF##6##\n28\n##\n<sup>]</sup> To assess the safety of biodegradable occluder, arrhythmias were observed by Holter (a dynamic 24 h ECG) during the follow‐up. Figure ##FIG##4##5G## showed that the frequency declined in accordance with the degradation of occluders in both groups. The occurrence of frequencies was all accidental and transient. The arrhythmia was mainly atrial and ventricular premature beats and no fatal arrhythmia was observed in both groups. The arrhythmia frequency was less in PGAG group at 1 month, but no significant difference was observed between two groups, which could be attributed to the relatively small sample number and short examination period in the animal study. Additionally, the artificial ASD was created relatively far away from the conduction system (for animal safety) compared with natural ASD and VSD, resulting in less disturbance caused by occluders.</p>", "<p>No abnormalities were found in both blood tests and hepatic examinations, indicating that PGAG occluder was not toxic during long‐term follow‐up (Figure ##FIG##4##5H##). No thrombus, infarction or PDO residuals were observed in other organs (liver, spleen, lung, and kidney) in gross and microscopic examination (Figure ##SUPPL##0##S17##, Supporting Information).</p>", "<title>Mitigation of Fibrosis and Inflammation by PGAG Occluder</title>", "<p>Masson's trichrome and H&amp;E staining were performed to analyze the pathological changes. Masson's trichrome staining shows that the newly formed collagen was distributed disorderly in the PDO group, while the fiber arrangement was ordered and tight in the PGAG group (<bold>Figure</bold> ##FIG##5##\n6A##). Furthermore, excessive collagen disposition formed a fibrous capsule besieging the PDO fibers at 1, 3, and 6 months, while it was unobservable surrounding the PGAG fibers (Figure ##FIG##5##6A##). H&amp;E staining showed that the area of fibrous capsule accompanied with moderate inflammatory response indicated by immune cell infiltration at 1 month, while mild inflammation was observed by PGAG treatment (Figure ##FIG##5##6B##). Notably, the infiltration of inflammatory cell was also found in the atrial septum tissue by the PDO treatment at 1 month, which might cause tissue destruction and affect the conduction system (Figure ##FIG##5##6B##). The inflammation score of cardiac tissue was significantly higher in PDO group and reached a moderate inflammation degree at 1 month, while it was mild degree in PGAG group (Figure ##FIG##5##6D##). At 3 months, the inflammation score decreased to slight degree in both groups (Figure ##FIG##5##6D##). At 6 months, the inflammation in PGAG group was completely degraded and constructed a compact and ordered collagen barrier between the cardiac tissue, while the collagen was organized in a loosened and irregular array by PDO treatment, owing to the moderate and repetitive inflammatory response induced by PDO from 1 to 3 months (Figure ##FIG##5##6A,B##).</p>", "<p>To further evaluate the degree of fibrosis, the expression of COLA1, a collagen formed in the scar tissue, was determined by immunohistochemistry. In accordance with Masson staining, the arrangement of COLA1 was more compact and regularly ordered surrounding PGAG fibers, compared with PDO (Figure ##FIG##5##6C##). The fiber disorder score was significantly higher in PDO group and increased from 1 to 6 months (Figure ##FIG##5##6E##), while the score decreased to mild degree at 6 months in PGAG group. Figure ##FIG##5##6F## shows that the diameter of PDO and PGAG fibers decreased evenly from 1 to 6 months, suggesting the steady degradation process. No significant difference was observed between the two groups at 1 and 3 months, indicating that the interface did not affect the degradation of PDO fibers. At 6 months, most polymers in both groups degraded (Figure ##FIG##5##6A,B##). The diameter of remaining polymers was slightly higher in PDO group (29.4 ± 13.3 µm in PGAG vs 61.5 ± 38.0 µm in PDO, p = 0.0025), which could be attributed to the influence of fibrous encapsulation (Figure ##FIG##4##5A##). Representative images of SEM showed that a fibrillar layer similar to natural cardiac ECM formed on the surface of PGAG at 1 month and multiple cells with pseudopodium tightly adhered (Figure ##FIG##5##6G##). However, cells with round morphography and small size sparsely distributed on the bare PDO (Figure ##FIG##5##6G##). All these results indicated that the PGAG occluder treatment orchestrated a well‐organized endogenous regeneration without excessive inflammation and fibrosis formation.</p>", "<title>Promotion of Endothelialization and Regulation of Immune Response by PGAG Occluder</title>", "<p>Endothelium process was further evaluated by immunofluorescence staining of CD31, a marker of endotheliocytes. As shown in <bold>Figure</bold> ##FIG##6##\n7A##, the number of endotheliocytes surrounding the PGAG fiber was significantly higher than the PDO fiber at 1 month (Figure ##FIG##6##7A,C##). What is more, the integrin α3, which related to the interaction with the peptide interface, was remarkedly up‐regulated by PGAG treatment (Figure ##FIG##6##7A,D##), indicating the activation of cell survival, adhesion, and proliferation. Both PDO and PGAG triggered endothelial cell encapsulation at 3 months, while PGAG still induced more integrin protein expression (Figure ##FIG##6##7C,D##). At 6 months, the endotheliocyte and integrin receptor remained at a significantly higher intensity in PGAG group than PDO group after the fiber degraded, which indicated that the activation of endogenous regeneration process was persistent and the repair process was dominated by endothelium (Figure ##FIG##6##7A,C,D##). The macrophages, indicated by CD68 positive staining, were obviously recruited around PDO and PGAG fibers at 1 months. However, the percentage of pro‐inflammatory type of macrophages was significantly lower in PGAG group (Figure ##FIG##6##7B,E,F##). Meanwhile, the number of surrounding macrophages decreased significantly in both groups from 1 to 3 months, and the pro‐inflammatory type was almost invisible in PGAG group at 3 months (Figure ##FIG##6##7B,F##). Collectively, the process of endothelialization was activated and accelerated, and the inflammation response was down‐regulated by PAGA occluder during ASD therapy.</p>", "<title>Immunomodulation and Proendothelialization in Endogenous Tissue Regeneration Revealed by Multiomics</title>", "<p>Finally, we performed multi‐omics of neo‐formed tissue at 3 months to comprehensively investigate the mechanisms of PGAG induced tissue regeneration. Transcriptomics revealed that a total of 324 differentially expressed genes (DEGs) including 130 genes upregulated and 194 genes downregulated were identified in transcriptomics (<bold>Figure</bold> ##FIG##7##\n8A##). The DEGs were visualized by the cluster heatmap (Figure ##FIG##7##8B##). The top significantly enriched terms in KEGG pathway enrichment comprised ECM–receptor interaction, PI3K‐AKT signaling pathway, focal adhesion, and MAPK signaling pathway (Figure ##FIG##7##8C##), which was consistent with the cellular signaling investigation. GO pathway‐enrichment analyses including biological process (BP), cellular component (CC), and molecular function (MF) were conducted to demonstrate the main biological processes regulated by PGAG (Figure ##FIG##7##8D##). MF analysis included signaling receptor binding, collagen binding, actin filament binding and ECM binding. CC analysis mainly referred to extracellular region, cell–cell junction, adherens junction, indicating the interaction between cell and ECM–mimic interface. MF analysis revealed that immune response, cell population proliferation, cell activation, regulation of cell migration, regulation of cell adhesion, response to wounding, ECM organization and regulation of MAPK cascade were significantly modulated by PGAG treatment. To further testified these findings of transcriptomics, proteomics was also performed. A total of 2,299 proteins were identified, including 132 up‐regulated and 61 down‐regulated differentially expressed proteins (DEPs) (Figure ##SUPPL##0##S18##, Supporting Information). GO analysis demonstrated that ECM organization, cell adhesion, collagen fibril organization, cell‐matrix adhesion, cell differentiation, regulation of immune response, collagen biding, and ECM binding pathways were significantly enhanced by PGAG treatment (Figure ##FIG##7##8E##). Both the transcriptomics and the proteomics corroborated each other and coincided with the in vitro investigation, further confirming that PGAG occluder could program multiple cell survival, adhesion, and migration, as well as immunoregulation pathways for endogenous tissue regeneration.</p>" ]
[ "<title>Summary and Discussion</title>", "<p>In summary, we have demonstrated the efficacy of a biophysically and biochemically optimized biodegradable cardiac implant for promoting in situ tissue regeneration in a porcine ASD model. A bioactive polymer with a structure composed of gelatin and laminin‐derived A5G81 peptide through covalent bonds formed by Michael addition reaction was modified on the surface of the implant material. The bioactive cell‐material interface can significantly promote endotheliocyte adhesion and proliferation by activation of integrin receptor and FAK complex. Moreover, the interface improved the biocompatibility of the implantation by polarizing immune cells into anti‐inflammatory phenotypes and augmenting the release of reparative cytokines. In vivo implantation of the PGAG occluder in pigs showed activation of endothelialization and suppression of inflammatory responses and excessive fibrosis in ASDs. In situ tissue regeneration was mainly attributed to significant enhancement of ECM remodeling, endogenous cell adhesion, cell proliferation, immune response regulation, and activation of ECM binding pathways by PGAG treatment.</p>", "<p>Enhancing the rapid endothelialization and facilitating tissue regenerative processes are pivotal considerations in the design of biodegradable occluders, crucial for the success of occlusion, prevention of displacement, and inhibition of thrombosis. Various surface modifications, utilizing ECM derived or ECM mimic polymers such as chitosan, collagen, elastin, gelatin, laminin, and decellularized ECM tissue, have been extensively explored to enhance the physiochemical and biological characteristics of cardiovascular implants.<sup>[</sup>\n##REF##31454565##\n29\n##\n<sup>]</sup> Gelatin, an ECM derivative from collagen, stands out for its ability to mimic native vascular architecture, thereby improving biocompatibility and enhancing implant hydrophilicity, which, in turn, facilitates cell adhesion and proliferation while inhibiting thrombosis.<sup>[</sup>\n##REF##32261529##\n30\n##\n<sup>]</sup> However, gelatin modification alone lacks the specificity needed for recruiting and proliferating endothelial cells, making it less effective in promoting endothelialization compared to coatings with specific antibodies like CD34 or CD133.<sup>[</sup>\n##UREF##7##\n31\n##\n<sup>]</sup> Nevertheless, specific antibody or drug coatings often have a short in vivo lifespan and are impractical for clinical storage. As an alternative, endotheliocyte‐selective peptides, such as A5G81, present a promising avenue for specifically amplifying endothelial cell recruitment.<sup>[</sup>\n##REF##20349926##\n32\n##\n<sup>]</sup> Yet, peptides have limitations in terms of spatial architecture and stability, rendering them less suitable for the migration, spread, and proliferation of various cell types in vivo. This study introduces a grafting modification strategy to augment cell‐material interactions and promote endogenous tissue regeneration for cardiac implants. The gelatin‐peptide modification serves a dual purpose by providing ECM‐derived bioactive cues and serving as a rough, hydrophilic substrate for cell adhesion and proliferation. Simultaneously, the endotheliocyte‐selective peptide (A5G81) is incorporated to activate proliferative signaling pathway and enhance endothelialization. This innovative approach holds promise for advancing the field of biodegradable cardiovascular implant design, addressing limitations associated with present biodegradable cardiac occluder. The simple and economical manufacture process and storage condition would facilitate the clinical translation.</p>", "<p>Our study still remained some limitations for future work. First, although porcine ASD models are standardized animal models for investigations of CHDs and occluder implantation, the location and size of artificial ASDs cannot adequately reflect the conditions of the ASD patients, which may underestimate the complications such as arrhythmia, residual shunt or cardiac erosion. Second, this surface modification strategy may also benefit interactions with other cell populations participating in endogenous tissue repair such as platelets, T cells and fibroblasts, which calls for further investigations to comprehensively unveil the proregenerative mechanisms. Third, multiple time points of multi‐omics analysis, e.g., &lt;1 month, would allow for a horizontal and longitudinal contrast, and offer a comprehensive understanding of immune response, population dynamics, and the impact of mitigating inflammation during the early stages of endogenous tissue regeneration on the bioactive material. Finally, the storage condition and the effective time of the interface should be further evaluated for clinical use. Collectively, the PGAG occluder offers a simple and economical manufacture process to facilitate cardiac defect repair, which we envision could provide clinical opportunity to improve the prognosis for CHD patients.</p>" ]
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[ "<title>Abstract</title>", "<p>Transcatheter intervention has been the preferred treatment for congenital structural heart diseases by implanting occluders into the heart defect site through minimally invasive access. Biodegradable polymers provide a promising alternative for cardiovascular implants by conferring therapeutic function and eliminating long‐term complications, but inducing in situ cardiac tissue regeneration remains a substantial clinical challenge. PGAG (polydioxanone/poly (<sc>l</sc>‐lactic acid)–gelatin–A5G81) occluders are prepared by covalently conjugating biomolecules composed of gelatin and layer adhesive protein‐derived peptides (A5G81) to the surface of polydioxanone and poly (<sc>l</sc>‐lactic acid) fibers. The polymer microfiber–biomacromolecule–peptide frame with biophysical and biochemical cues could orchestrate the biomaterial–host cell interactions, by recruiting endogenous endothelial cells, promoting their adhesion and proliferation, and polarizing immune cells into anti‐inflammatory phenotypes and augmenting the release of reparative cytokines. In a porcine atrial septal defect (ASD) model, PGAG occluders promote in situ tissue regeneration by accelerating surface endothelialization and regulating immune response, which mitigate inflammation and fibrosis formation, and facilitate the fusion of occluder with surrounding heart tissue. Collectively, this work highlights the modulation of cell–biomaterial interactions for tissue regeneration in cardiac defect models, ensuring endothelialization and extracellular matrix remodeling on polymeric scaffolds. Bioinspired cell–material interface offers a highly efficient and generalized approach for constructing bioactive coatings on medical devices.</p>", "<p>In this study, the surface of the biodegradable cardiac occluder is modified by covalently conjugating biomolecules composed of gelatin and layer adhesive protein‐derived peptides, which promotes in situ tissue regeneration by accelerating surface endothelialization and regulating immune response in a porcine atrial septal defect model.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6827-cit-0060\">\n<string-name>\n<given-names>P.</given-names>\n<surname>Kong</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>R.</given-names>\n<surname>Gao</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Feng</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>F.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Feng</surname>\n</string-name>, <string-name>\n<given-names>P.</given-names>\n<surname>Huang</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Zhuang</surname>\n</string-name>, <string-name>\n<given-names>W.</given-names>\n<surname>Ouyang</surname>\n</string-name>, <string-name>\n<given-names>W.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Pan</surname>\n</string-name>, <article-title>Biodegradable Cardiac Occluder with Surface Modification by Gelatin–Peptide Conjugate to Promote Endogenous Tissue Regeneration</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305967</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305967</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Chemical Reagents</title>", "<p>(3‐Glycidoxypropyl) trimethoxy silane (GOPS) and gelatin were purchased from Sigma‐Aldrich. Mal‐A5G81 (Mal‐AGQWHRVSVRWGC) was provided by Bankpeptide Biological Technology Co., LTD (Hefei, China). PDO occluders were provided by Shanghai Shape Memory Alloy Co. Ltd.</p>", "<title>Synthesis of Gelatin‐A5G81</title>", "<p>Gelatin‐A5G81 was synthesized by mixing gelatin and Mal‐A5G81 (1:2 in molar ratio) in aqueous solution for 3 h at room temperature, and further dialyzed against water and lyophilized. Mal‐A5G81 peptide was bonded to gelatin molecule through the amino‐maleimide click reaction.</p>", "<title>Preparation of PGAG Occluder</title>", "<p>PDO occluder is prepared through three steps. First, PDO occluder was placed in the plasma surface treatment machine, and pure O<sub>2</sub> was fed in, and the excitation frequency of the plasma surface treatment machine was set to 13.56 MHz, and the working time was 120 s. Subsequently, PDO occluder (≈170 mg) treated with oxygen plasma was immediately immersed in 50 mL of 1% GOPS aqueous solution, and reacted at room temperature for 120 min, so that reactive epoxy groups were bonded to the surface of PDO occluder. Finally, the PDO occluder treated in the second step was immersed in 50 mL of 0.5% gelatin‐A5G81 aqueous solution, and continued to react at room temperature for 12 h, and finally gelatin‐A5G81 was bonded on the surface of the occluder material. The amino groups on the gelatin react with the epoxy groups on the surface of the PDO occluder to achieve gelatin‐A5G81 bonding. PDGA and PDAG was prepared by surface plasma treatment of PDO and modified with silane coupling agent, and further covalently grafted with gelatin and A5G81, respectively.</p>", "<title>Evaluation of Cytocompatibility, Adhesion, and Proliferation of HUVECs</title>", "<p>To evaluate the cytocompatibility, adhesion and proliferation, PDO, PDGA, PDAG, PGAG membranes with thickness of 40 µm were prepared. Then, the membranes were plated in 6‐well plates. A total of 1.5 × 10<sup>5</sup> HUVECs were seeded on each membrane, and were cultured in endothelial cell medium supplied with 10% FBS. After incubation for 24 h and 48 h, the membranes were washed with PBS for 3 times, stained with crystal violet solution (0.5%) for 30 min and the cells on membranes were counted.</p>", "<p>For immunofluorescent staining, after incubation for 24 h, the cells seeded on membranes were incubated with Integrin α3 (Proteintech, 66070‐1) and FAK (Abcam, ab40794) overnight, and were stained with 488 conjugate (Cell Signaling, #4408), 594 conjugate (Cell Signaling, #8889) and DAPI (Solarbio, C0065) according to the manufacture's guidelines and were observed by confocal laser scanning microscopy (TCS SP5II, Leica, Ernst‐Leitz‐Strasse, Germany).</p>", "<p>The interior morphology of HUVECs on PDO, PDGA, PDAG, and PGAG membranes was investigated by SEM (S‐4800, Hitachi, Japan). Samples were fixed in 2.5% glutaraldehyde, dehydrated by CO2 critical point drying (K850X, Emitech), quick‐frozen in liquid nitrogen, lyophilized, and then coated with gold particles.</p>", "<title>Western Blot Assays</title>", "<p>Cell lysates were lysed by RIPA lysis buffer (Beyotime, P0013B) containing 1 × 10<sup>−3</sup> <sc>m</sc> PMSF (Beyotime, ST506). After incubation for 30 min on ice, the supernatant was collected after centrifugation. Then protein was denatured at 95 °C for 10 min. After mixing with loading buffer containing bromophenol blue, protein samples were separated by a 10% sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) and transferred onto poly (vinylidene difluoride) (PVDF) membranes (0.45 µm). The membranes were blocked by bovine albumin and then incubated with antibody overnight at 4 °C. After washing with TBST, the membranes were incubated with horseradish peroxidase‐conjugated secondary antibodies for 1 h at room temperature. The proteins on the membranes were visualized by Chemiluminescence Imaging system (ChemiScope 6000 Pro, China). The intensity of immunoreactive bands was quantified by ImageJ software. The primary antibody included FAK (1:1000, Abcam, ab40794), phospho‐MEK1/2 (Ser217/221) (1:1000, Cell Signaling, #9154), p44/42 MAPK (Erk1/2) (1:1000, Cell Signaling, # 4695), PI3 Kinase p110a (C73F8) (1:1000, Cell Signaling, #4249), and Phospho‐Akt (Ser473) (1:1000, Cell Signaling, #4060) and β‐actin (1:2000, Abcam, ab8226). The secondary antibody included HRP‐labeled goat anti‐mouse IgG (1:2000, Beyotime, A0216) and HRP‐labeled goat anti‐rabbit IgG (1:2000, Beyotime, A0208).</p>", "<title>Macrophage Polarization</title>", "<p>BMDMs were isolated from C57BL/6 mice (6 weeks old, Vital River Laboratory, China). After lysing red blood cells, the collected cells were seeded in six‐well plates and cultured with RPMI 1640 medium supplemented with 10% heat‐inactivated fetal bovine serum and 20 ng mL<sup>−1</sup> M‐CSF (MCE, HY‐P7085). After incubation for 6 d, adhered cells were BMDMs. After that, BMDMs were seeded on PDO, PDGA, PDAG, PGAG membranes, cocultured for 48 h, washed with PBS for 3 times, and stained with FITC‐labeled anti‐CD86 antibodies (Biolegend, 105006), PE‐labeled F4/80 antibodies (Biolegend, 123110) and DAPI (Solarbio, C0065) according to the manufacture's guidelines and were observed by confocal laser scanning microscopy (TCS SP5II, Leica, Ernst‐Leitz‐Strasse, Germany).</p>", "<title>ELISA</title>", "<p>The supernatant of BMDMs was analyzed by Mouse TGF‐β1 Precoated ELISA kit (DAKEWE, 1217102), Mouse IL‐4 Precoated ELISA kit (DAKEWE, 1210402), Mouse IFN‐γ Precoated ELISA kit (DAKEWE, 1210002), Mouse TNF‐α ELISA KIT (CUSABIO, CSB‐E04741m), Mouse VEGF ELISA Kit (CUSABIO, CSB‐E04756m), Mouse IL‐10 ELISA KIT (SenBeiJia Biological Technology Co., Ltd., SBJ‐M0073) according to the manufacturer's instructions.</p>", "<title>Transcatheter ASD Closure of Porcine Model</title>", "<p>All animal experiments were approved by the Institutional Animal Care and Use Committee, Fuwai Hospital, Chinese Academy of Medical Sciences (0101‐1‐18‐ZX(X)2). A total of 18 Bama mini‐pigs (male, 30–40 kg) were implanted with the PDO and PGAG occluder through transcatheter access (<italic toggle=\"yes\">n</italic> = 9 each group). Specifically, after general anesthesia and tracheal intubation, all pigs were fixed on the operating table in a supine position. ECG, heart rate, blood pressure, and blood oxygen saturation were monitored during the operation. The right femoral vein was punctured. The guide wire was inserted into the right atrium under the guidance of the fluoroscopy. Then, a septal puncture needle was used to puncture the fossa ovalis. An 8 mm diameter balloon catheter was used to create an ASD model. After that, transcatheter ASD occlusion was implanted under the TTE and fluoroscopy guidance. Ampicillin (1 g) was administered intravenously after implantation and all pigs received aspirin (5 mg/kg/d) postoperatively for 3 d.</p>", "<p>Animals were followed up at 1, 3, and 6 months (<italic toggle=\"yes\">n</italic> = 3 each group at each time point). TTE, 24 h‐ dynamic electrocardiogram (Holter monitor) and hematological tests were performed at each point. The diameters of the left and right discs of the occluder were measured at each time point. General anatomical examination, H&amp;E staining, Masson staining, and SEM were performed for analysis. Inflammation was blindly graded by a pathologist using an inflammatory score (0‐4+ scale), with 4+ representing maximal inflammation.<sup>[</sup>\n##REF##17284483##\n33\n##\n<sup>]</sup>\n</p>", "<title>Immunofluorescence and Immunohistochemistry for Porcine Tissue</title>", "<p>The neo‐formed cardiac tissue surrounding occluders were harvested and fixed with 4% paraformaldehyde, embedded in paraffin, and sliced into 4 µm thick sections. For macrophage polarization investigation, the slices were incubated with mouse CD68 monoclonal antibody (1:200, Proteintech, 66231‐2‐Ig) and rabbit CD86 monoclonal antibody (1:200, Cell Signaling, #76755). For endothelialization analysis, the slices were incubated with mouse Integrin α3 (Proteintech, 66070‐1) and rabbit CD31 Polyclonal antibody (1:200, Proteintech, 11265‐1‐AP). After incubation overnight, slices were incubated with Alexa Flour 488 anti‐mouse IgG (1:200, Thermo Fisher Scientific), Alexa Flour 594 anti‐rabbit IgG (1:200, Thermo Fisher Scientific), or anti‐rat Alexa Fluor 488 Conjugate (Cell Signaling, #4416) and anti‐mouse Alexa Fluor 594 Conjugate (Cell Signaling, #8890) corresponding to the primary antibody. Images were observed by CLSM and quantitatively analyzed by ImageJ software.</p>", "<p>For immunohistochemistry assay, the slices were incubated with COL1A1 (1:200, Cell Signaling, #72026) overnight and enhanced enzyme labeled goat anti‐mouse/rabbit IgG polymer (ZSGB‐BIO, PV‐6000) at room temperature for 20 min. Fiber disorder score, judged by Masson staining and immunohistochemistry of COL1A1, was blindly graded by a pathologist using a 0–4+ scale, with 4+ representing maximal disorder (Figure ##SUPPL##0##S19##, Supporting Information).</p>", "<title>Transcriptomics and Proteomics Analysis</title>", "<p>At 3 months, cardiac neo‐tissue from PDO and PGAG treatment was collected (4 samples for each group). For transcriptome, total RNA in cardiac tissue was extracted and the concentration and purity were measured by NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Bremen, Germany). Illumina platform was used to construct a sequencing library and perform PE150 sequencing. Similarly, for proteomics, Nanoflow LC MS/MS analysis of tryptic peptides was conducted on a quadrupole Orbitrap mass spectrometer (Q Exactive HF X, Thermo Fisher Scientific, Bremen, Germany) coupled to an EASY nLC 1200 ultra high‐pressure system (Thermo Fisher Scientific) via a nanoelectrospray ion source. All RAW files were analyzed using the Proteome Discoverer suite (version 2.4, Thermo Fisher Scientific). The functional analysis of RNA and proteins was further analyzed by the Gene Ontology (GO) database and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Experiment details are provided in supporting materials.</p>", "<title>Statistical Analysis</title>", "<p>Statistical analysis was performed using GraphPad Prism 8 (GraphPad Software). Data were expressed as mean ± SD. Comparisons between two groups were performed with unpaired Student's t‐test. For multiple group comparison, one‐way ANOVA was used with Bonferroni post correction. Statistical significance is denoted by *<italic toggle=\"yes\">p</italic> &lt; 0.05, **<italic toggle=\"yes\">p</italic> &lt; 0.01, ***<italic toggle=\"yes\">p</italic> &lt; 0.001 and ****<italic toggle=\"yes\">p</italic> &lt; 0.0001.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>P.K., X.L., and Z.L. contributed equally to this work. Conceptualization: P.K., X.L., W.W., X.P.; Methodology: P.K., X.L., Z.L., R.G., J.W., Z.F., P.H., S.W., F.Z., W.O., W.W., and X.P.; Investigation: P.K., X.L., Z.L., J.W., S.F., R.G., S.W., F.Z., D.Z.; Visualization: P.K., X.L., R.G., J.W.; Funding acquisition: W.W., X.P., W.O.; Project administration: P.K., X.L, Z.L.,W.W., X.P., W.O.; Supervision: W.W., X.P., P.H., Z.F.; Writing—original draft: P.K., X.L.; Writing—review &amp; editing: All authors.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The work was supported by CAMS Innovation Fund for Medical Sciences (2021‐I2M‐1‐065, 2021‐I2M‐1‐058); National Natural Science Foundation of China (81970444, 82272162); The Fundamental Research Funds for the Central Universities (2019PT350005); Beijing Municipal Science and Technology Project (Z201100005420030); the National Key Research and Development Program of China (2022YFC2503400); National high level talents special support plan (2020‐RSW02); Sanming Project of Medicine in Shenzhen (SZSM202011013); Natural Science Fund for Distinguished Young Scholars of Tianjin (21JCJQJC00020).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6827-fig-0001\"><label>Figure 1</label><caption><p>Schematic illustration for the preparation and application of PGAG occluder. A) PGAG occluder is composed of a PGAG frame and a PGAG flow‐blocking membrane. The gelatin‐peptide structure interacts with integrin receptor, promotes endothelial cell (EC) adhesion and proliferation, and mitigates pro‐inflammatory macrophage activation and fibrosis. B) Follow‐up of a porcine ASD model demonstrates cardiac repair induced by implantation of a PGAG occluder.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6827-fig-0002\"><label>Figure 2</label><caption><p>Characterization of surface structure and mechanical properties of PGAG. A) Cross‐sectional and lateral SEM micrographs of PGAG monofilaments. B,C) Surface optical profile images of PGAG monofilaments with longitudinal grooves. D) Fluorescent images of GA and A5GB1 of PGAG labeled with Cy5 and FITC, respectively. E) XPS survey scan, C 1s and N 1s spectra of PGAG. F) FTIR spectra of PGAG. G) Morphology of the PGAG occluder under compression and tension. H) The maximum stress, fracture strain for PGAG and PDO (<italic toggle=\"yes\">n</italic> = 3). Data are presented as mean ± SD. <italic toggle=\"yes\">p</italic>‐values are calculated using unpaired t‐test. N.S. means no significant.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6827-fig-0003\"><label>Figure 3</label><caption><p>PGAG promoted survival, adhesion, and proliferation of endothelial cells. A) HUVECs cocultured on PDO, PDGA, PDAG and PGAG membranes for 24 and 48 h. B) Representative SEM images of HUVECs adhering on membranes. C) Representative immunofluorescence images of HUVECs cocultured on PDO, PDGA, PDAG and PGAG membranes (blue: nuclear; green: integrin α3; red: FAK). D) Western blot analysis of FAK, PI3K, AKT, Erk1/2, MEK1/2 protein expression by treated HUVECs. E) Quantitative expression of FAK, F) PI3K, and G) Erk1/2 (<italic toggle=\"yes\">n</italic> = 4 for each test). H) Schematic diagram of PGAG promoting survival, adhesion, and proliferation of endothelial cells. Data are presented as mean ± SD. <italic toggle=\"yes\">p</italic>‐values are calculated using one‐way ANOVA with Bonferroni correction. ns = no significance, *<italic toggle=\"yes\">p</italic> &lt; 0.05, **<italic toggle=\"yes\">p</italic> &lt; 0.01, and ***<italic toggle=\"yes\">p</italic> &lt; 0.001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6827-fig-0004\"><label>Figure 4</label><caption><p>PGAG mitigated inflammation and promoted release of reparative cytokines. A) Representative images of BMDMs treated on PDO, PDGA, PDAG, and PGAG membranes (blue: nuclear; red: F4/80<sup>+</sup>; green: CD86<sup>+</sup>). B) Quantification of percentage of CD86<sup>+</sup> expression within F4/80<sup>+</sup> BMDMs (<italic toggle=\"yes\">n</italic> = 3). The box plot indicates the range from min to max. Relative protein expression of C) TGF‐β, D) VEGF, E) IL‐4, F) IL‐10, G) TNF‐α and H) IFN‐γ in supernate of BMDMs determined by ELISA (<italic toggle=\"yes\">n</italic> = 4 for each test). I) Relative protein expression of MMP9 in BMDMs determined by western blotting (<italic toggle=\"yes\">n</italic> = 3). Data are presented as mean ± SD. <italic toggle=\"yes\">p</italic>‐values are calculated using one‐way ANOVA with Bonferroni correction. ns = no significance, *<italic toggle=\"yes\">p</italic> &lt; 0.05, **<italic toggle=\"yes\">p</italic> &lt; 0.01, and ***<italic toggle=\"yes\">p</italic> &lt; 0.001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6827-fig-0005\"><label>Figure 5</label><caption><p>PGAG occluder was safe and effective in a porcine ASD model. A) Macroscopic views of implanted PDO and PGAG occluders in an ASD model at 1, 3, 6 months. B) Quantification of endothelium coverage area of discs (<italic toggle=\"yes\">n</italic> = 3 pigs at each time point, left and right discs for each pig). C) Quantification of disc residual area (<italic toggle=\"yes\">n</italic> = 3 pigs at each time point). D) Cardiac MRI for occluders at 3 months. (E) TTE images of occluders at 1, 3, and 6 months. F) Occluder thickness determined by TTE (<italic toggle=\"yes\">n</italic> = 9 at 1 month, <italic toggle=\"yes\">n</italic> = 6 at 3 month and <italic toggle=\"yes\">n</italic> = 3 at 6 month). G) Frequency of arrhythmia (<italic toggle=\"yes\">n</italic> = 9 at 1 month, <italic toggle=\"yes\">n</italic> = 6 at 3 month and <italic toggle=\"yes\">n</italic> = 3 at 6 month). H) Quantification of blood examination at 6 months. The square indicates the mean value (<italic toggle=\"yes\">n</italic> = 3). WBC: white blood cell; HGB: hemoglobin; PLT: platelet; CREA: creatinine; ALT: albumin; ALT: alanine transaminase; AST: aspartate transaminase. Data are presented as mean ± SD. <italic toggle=\"yes\">p</italic>‐values are calculated using unpaired t test. ns = no significance, *<italic toggle=\"yes\">p</italic> &lt; 0.05, **<italic toggle=\"yes\">p</italic> &lt; 0.01, ***<italic toggle=\"yes\">p</italic> &lt; 0.001, ****<italic toggle=\"yes\">p</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6827-fig-0006\"><label>Figure 6</label><caption><p>PGAG occluder alleviated inflammation and fibrosis during the regeneration process. A,B) Masson and H&amp;E staining of cardiac tissue surrounding occluders. C) Immunohistochemical staining of COLA1. D,E) Inflammation score and fiber disorder score of surrounding fibers, with score 0 = normal, 1 = slight, 2 = mild, 3 = moderate, 4 = severe (<italic toggle=\"yes\">n</italic> = 20 at each time point). F) Diameter of monofilament (<italic toggle=\"yes\">n</italic> = 20 at each time point). <bold>G</bold>) Representative SEM image of monofilament at 1 month. Data are presented as mean ± SD. <italic toggle=\"yes\">p</italic>‐values are calculated using unpaired t test. ns = no significance, *<italic toggle=\"yes\">p</italic> &lt; 0.05, **<italic toggle=\"yes\">p</italic> &lt; 0.01, ***<italic toggle=\"yes\">p</italic> &lt; 0.001, ****<italic toggle=\"yes\">p</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6827-fig-0007\"><label>Figure 7</label><caption><p>PGAG occluder promoted endothelialization and mitigated polarization of pro‐inflammatory macrophages. A) Immunofluorescence staining of CD31 (green) and integrin α3 (red). The white line indicates 100 µm. B) Immunofluorescence staining of CD68 (green) and CD86 (red). The white line indicates 200 µm. Statistical data of average fluorescence intensity of C) CD31, D) integrin α3, E) CD68, and F) CD86 (<italic toggle=\"yes\">n</italic> = 5 for each test). Data are presented as mean ± SD. <italic toggle=\"yes\">p</italic>‐values are calculated using unpaired t test. ns = no significance, *<italic toggle=\"yes\">p</italic> &lt; 0.05, **<italic toggle=\"yes\">p</italic> &lt; 0.01, ***<italic toggle=\"yes\">p</italic> &lt; 0.001, ****<italic toggle=\"yes\">p</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6827-fig-0008\"><label>Figure 8</label><caption><p>Immunomodulation and proendothelialization revealed by multiomics. A) Cluster heatmap of significantly upregulated and downregulated DEGs by transcriptomics. B) Volcano plots. The red dots indicate the proteins selected based on adjusted <italic toggle=\"yes\">P</italic> value &lt; 0.05 and log<sub>2</sub>FC &gt; 2. C) KEGG pathway‐enrichment analysis of DEGs. D) GO pathway‐enrichment analysis of DEGs. E) GO pathway‐enrichment analysis of DEPs by proteomics. BP: biological process; CC: cellular component; MF: molecular function.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6827-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2305967-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
[{"label": ["7"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n"], "given-names": ["M.", "I.", "C.", "U. S."], "surname": ["Dirauf", "Muljajew", "Weber", "Schubert"], "source": ["Prog. Polym. Sci."], "year": ["2022"], "volume": ["129"], "elocation-id": ["101547"]}, {"label": ["8"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["Y.", "Y.", "B.", "Z.", "J.", "S.", "Z."], "surname": ["Li", "Xie", "Li", "Xie", "Shen", "Wang", "Zhang"], "source": ["J. Interventional Cardiol."], "year": ["2021"], "volume": ["2021"], "elocation-id": ["6369493"]}, {"label": ["11"], "mixed-citation": ["a) ", "b) ", "c) ", "d) ", "e) "], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["A. K.", "I.", "A.", "E. R.", "C. A.", "X.", "Z.", "L.", "D.", "J.", "J.", "X.", "X.", "Y.", "J."], "surname": ["Gaharwar", "Singh", "Khademhosseini", "Ruskowitz", "DeForest", "Wan", "Liu", "Li", "Cao", "Ding", "Gao", "Yu", "Wang", "He", "Ding"], "source": ["Nat. Rev. Mater.", "Nat. Rev. Mater.", "Adv. Funct. Mater.", "Regener. Biomater.", "Engineering"], "year": ["2020", "2018", "2021", "2022", "2022"], "volume": ["5", "3", "31", "9", "13"], "fpage": ["686", "31"], "elocation-id": ["17087", "2010626", "rbac098"]}, {"label": ["13"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n"], "given-names": ["M. A.", "B.", "Y."], "surname": ["Tasdelen", "Kiskan", "Yagci"], "source": ["Prog. Polym. Sci."], "year": ["2016"], "volume": ["52"], "fpage": ["19"]}, {"label": ["17"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n"], "given-names": ["A. B.", "D.", "D.", "H.", "S.\u2010H."], "surname": ["Bello", "Kim", "Kim", "Park", "Lee"], "source": ["Tissue Eng., Part B"], "year": ["2020"], "volume": ["26"], "fpage": ["164"]}, {"label": ["26"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n"], "given-names": ["B.", "Y.", "J.", "Y.", "D."], "surname": ["Zhang", "Su", "Zhou", "Zheng", "Zhu"], "source": ["Adv. Sci."], "year": ["2021"], "volume": ["8"], "elocation-id": ["2100446"]}, {"label": ["28"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n"], "given-names": ["W. C.", "F.", "Z. M."], "surname": ["Yip", "Zimmerman", "Hijazi"], "source": ["Catheterization Cardiovasc. Interventions"], "year": ["2005"], "volume": ["66"], "fpage": ["436"]}, {"label": ["31"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["X.", "T.", "J.", "C.", "J.", "Y.", "X.", "X.", "Y.", "D."], "surname": ["Wu", "Yin", "Tian", "Tang", "Huang", "Zhao", "Zhang", "Deng", "Fan", "Yu"], "source": ["Regener. Biomater."], "year": ["2015"], "volume": ["2"], "fpage": ["87"]}]
{ "acronym": [], "definition": [] }
33
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 20; 11(2):2305967
oa_package/0d/95/PMC10787076.tar.gz
PMC10787077
37984872
[ "<title>Introduction</title>", "<p>Mechanism research on mammalian pre‐implantation development enhances our understanding of the origin and progression of our life. Emerging evidence indicates that long non‐coding RNAs (lncRNA) perform essential functions in gene regulation and epigenetic processes in mammalian pre‐implantation development. <italic toggle=\"yes\">XIST</italic>‐mediated X chromosome inactivation,<sup>[</sup>\n##REF##34178980##\n1\n##\n<sup>]</sup>\n<italic toggle=\"yes\">Air</italic> and <italic toggle=\"yes\">Kcnq1ot1</italic>‐mediated gene imprinting,<sup>[</sup>\n##REF##23239737##\n2\n##\n<sup>]</sup>\n<italic toggle=\"yes\">pancIL17d</italic>‐mediated DNA demethylation,<sup>[</sup>\n##REF##25633350##\n3\n##\n<sup>]</sup> and long intergenic non‐coding RNA <italic toggle=\"yes\">LincGET</italic>‐mediated first cell fate bias<sup>[</sup>\n##REF##30550787##\n4\n##\n<sup>]</sup> are all essential for pre‐implantation development.</p>", "<p>Transposable elements (TEs) are genetic elements in the genome that have the ability to move or transpose from one location to another. There are two main types of TEs: retrotransposons, which include short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), and endogenous retroviruses (ERVs); and DNA transposons. They account for a substantial proportion of mammalian genomes (40% in mice and 44% in humans).<sup>[</sup>\n##REF##12188048##\n5\n##\n<sup>]</sup> TEs regulate gene transcription, chromatin structure and function, and cell differentiation.<sup>[</sup>\n##REF##34178980##\n1\n##, ##REF##30454069##\n6\n##\n<sup>]</sup> TEs are major components of genomes, serving as main drivers of genome evolution while also being highly activated and transcribed during mammalian early embryonic development.<sup>[</sup>\n##REF##21251689##\n7\n##\n<sup>]</sup> In mammals, ≈80% of lncRNAs contain TEs, and these TEs‐associated lncRNAs play crucial roles in regulating embryonic development.<sup>[</sup>\n##REF##23181609##\n8\n##\n<sup>]</sup> The ERV‐associated lncRNA, <italic toggle=\"yes\">LincGET</italic>, is essential for mouse embryonic development, and it plays an indispensable role in the determination of cell fate.<sup>[</sup>\n##REF##30550787##\n4\n##, ##REF##27496889##\n9\n##\n<sup>]</sup> The SINE‐associated lncRNA, <italic toggle=\"yes\">Lx8‐SINE B2</italic>, driven by Oct4 and Sox2, acts as a novel marker lncRNA by working with Eno1 in mouse ESCs.<sup>[</sup>\n##UREF##0##\n10\n##\n<sup>]</sup> The activation of <italic toggle=\"yes\">LINE‐1</italic> increases the global chromatin accessibility in early mouse embryos.<sup>[</sup>\n##REF##28846101##\n11\n##\n<sup>]</sup> The collective evidence indicates that TEs‐associated lncRNAs exert regulatory functions during the early stages of embryonic development.</p>", "<p>The potential regulatory mechanisms with TEs‐associated lncRNA remain unclear. Interestingly, the totipotency pioneer factor, Nr5a2 activates ZGA by binding to the <italic toggle=\"yes\">SINE B1/Alu</italic> transposable element in the <italic toggle=\"yes\">cis</italic>‐regulatory element of the ZGA gene.<sup>[</sup>\n##REF##36423263##\n12\n##\n<sup>]</sup> Therefore, SINE‐mediated <italic toggle=\"yes\">cis</italic>‐regulatory elements could have an important regulatory role in early embryonic development and merit further investigation. In addition, <italic toggle=\"yes\">cis</italic>‐regulatory elements could mediate regulatory effects by transcribing lncRNAs. Some lncRNAs, such as <italic toggle=\"yes\">ncRNA‐a7</italic> and <italic toggle=\"yes\">DXPas34</italic>, serve as enhancer‐related lncRNAs,<sup>[</sup>\n##REF##21831473##\n13\n##\n<sup>]</sup> while the others, such as <italic toggle=\"yes\">ncRNA‐CCND1</italic> and <italic toggle=\"yes\">iab‐7</italic>,<sup>[</sup>\n##REF##18509338##\n14\n##\n<sup>]</sup> act as promoter‐related lncRNAs; some of them, such as <italic toggle=\"yes\">LINoCR</italic> and <italic toggle=\"yes\">H19</italic>, act as insulators.<sup>[</sup>\n##REF##18851839##\n15\n##\n<sup>]</sup> In addition, there are lncRNAs that could <italic toggle=\"yes\">trans</italic>‐regulate gene transcription by binding <italic toggle=\"yes\">cis</italic>‐regulatory elements containing repetitive sequences. <italic toggle=\"yes\">LincGET</italic> achieves transcriptional regulation in <italic toggle=\"yes\">trans</italic> by mediating the activity of the <italic toggle=\"yes\">cis</italic>‐regulatory elements of GLK‐LTR.<sup>[</sup>\n##REF##27496889##\n9\n##\n<sup>]</sup>\n<italic toggle=\"yes\">HOTAIR</italic> inhibits the expression of the Hox D gene cluster, which contains major regulatory genes involved in fore‐posterior axis formation, in <italic toggle=\"yes\">trans</italic> by interacting with the PRC2 complex (catalyzes H3K27me3 establishment) and LSD1‐CoREST‐REST (catalyzes H3K4me2/3 erases).<sup>[</sup>\n##REF##36110328##\n16\n##\n<sup>]</sup> Therefore, SINE‐associated lncRNAs might regulate transcription both in <italic toggle=\"yes\">cis</italic> and trans. This sheds new light on the mechanism underlying early embryonic development.</p>", "<p>Research on SINE‐associated lncRNAs in early embryonic development has been relatively limited, and it remains unconfirmed whether these lncRNAs play a regulatory role in the early development of mammals. Here, we identified <italic toggle=\"yes\">SAWPA</italic> (SINE‐associated and WDR26 promoter‐associated lncRNA) as a novel nuclear lncRNA. It is 8‐cell porcine embryo‐specific and is associated with SINEs. It is regulated by the partner mRNA, <italic toggle=\"yes\">WDR26</italic>. <italic toggle=\"yes\">SAWPA</italic> depletion leads to the developmental arrest at the 8‐cell stage and regulates porcine ZGA. It also decreases chromatin accessibility. <italic toggle=\"yes\">SAWPA</italic> acts as a transcription factor via forming an RNA‐protein complex with HNRNPA1 and MED8; this mediates the <italic toggle=\"yes\">cis</italic>‐regulatory activity of SINE and enhances the transcription of <italic toggle=\"yes\">JNK</italic>. The inhibition of JNK phosphorylation or si_<italic toggle=\"yes\">JNK</italic> injection decreased the pre‐implantation development and led to embryo arrest at the 8‐cell stage. To the best of our knowledge, this is the first study to demonstrate the essential role of SINE‐associated lncRNA in porcine ZGA processes. Additionally, we found that <italic toggle=\"yes\">SAWPA</italic> promotes the cleavage of 8‐cell embryos by regulating the transcription of <italic toggle=\"yes\">JNK</italic> through SINE elements. The discovery provides a novel regulatory mechanism for SINE‐associated lncRNAs that are involved in early embryonic development, shedding light on how lncRNAs are activated in ZGA during early embryonic development.</p>" ]
[]
[ "<title>Result</title>", "<title>SINE‐Associated LncRNAs Have High Expression During the ZGA Period in Pigs</title>", "<p>TEs‐associated lncRNAs play an active role in development.<sup>[</sup>\n##REF##30550787##\n4\n##, ##REF##36087098##\n17\n##\n<sup>]</sup> To investigate the function of TEs‐associated lncRNAs in porcine pre‐implantation embryos, we analyzed early embryonic RNA‐seq data (Poly(A) selecting, rRNA depleting) to identify TEs‐associated lncRNAs. We classified TEs‐associated lncRNAs into SINE‐, LINE‐, ERV‐, and other repeat‐associated lncRNAs. These lncRNAs are crucial for the early development of mammalian embryos and are involved in processes such as ZGA, blastocyst formation rate, cell apoptosis, and pluripotency.<sup>[</sup>\n##REF##23358118##\n18\n##\n<sup>]</sup> Subsequently, We determine the type of lncRNA by identifying overlapping sequences between the exons of lncRNA and TEs. Considering the possible presence of more than one of TEs within a lncRNA. We conducted a statistical analysis for each type of TEs contained within the lncRNA, following the methods reported in published papers.<sup>[</sup>\n##REF##36012216##\n19\n##\n<sup>]</sup> By analyzing the RNA‐Seq data of pigs (GSE163620) and comparing the expression levels at various stages of pre‐implantation development, we observed that TEs‐associated lncRNAs exhibit higher expression levels during the 4–8‐cell stage (<bold>Figure</bold> ##FIG##0##\n1A,B##), which is a critical period for ZGA in porcine.<sup>[</sup>\n##REF##1493177##\n20\n##\n<sup>]</sup> To validate this finding, we performed the same analysis on porcine RNA‐Seq data (CRA004237) once again and obtained consistent results (Figure ##SUPPL##0##S1A##, Supporting Information). This implies that TEs‐associated lncRNAs may play a crucial role in ZGA in porcine.</p>", "<p>To explore the function of TEs‐associated lncRNAs, we conducted an analysis of RNA‐Seq data from mice (GSE138760) and humans (GSE36552). We found that TEs‐associated lncRNAs also exhibit higher expression levels during the 2–4‐cell stage in mice and the 4–8‐cell stage in humans (representing the respective ZGA timepoints in mouse and human embryos<sup>[</sup>\n##REF##3352746##\n21\n##\n<sup>]</sup>), indicating the conservation of TEs‐associated lncRNA function in ZGA across species (Figure ##SUPPL##0##S1A##, Supporting Information). Furthermore, we performed a quantitative analysis of lncRNAs belonging to different TE types in the porcine RNA‐Seq data (GSE163620, CRA004237) at the 8‐cell stage. We found that SINE‐associated lncRNAs are mostly abundant during the 8‐cell stage (Figure ##FIG##0##1C##; Figure ##SUPPL##0##S1B##, Supporting Information). Subsequently, we screened mRNA and lncRNA during ZGA in pigs. Based on previous research, we conducted differential gene analysis using DESeq2, where genes with a |log<sub>2</sub> fold change| ≥ 1 at 8C/MII and a p adjust &lt; 0.01 were identified as ZGA genes.<sup>[</sup>\n##REF##27626382##\n22\n##\n<sup>]</sup> When analyzing the number of different TE types in mRNA and lncRNA during the ZGA period, we found that SINE‐associated mRNA and lncRNA also exhibited the highest numbers (Figure ##FIG##0##1C##; Figure ##SUPPL##0##S1B##, Supporting Information). Moreover, in the expression patterns of mice and humans, SINE‐associated lncRNA showed the highest expression levels during the ZGA period (Figure ##FIG##0##1D##), implying the significance of SINE‐associated lncRNAs during the ZGA period.</p>", "<title>\n<italic toggle=\"yes\">SAWPA</italic> Is a SINE‐Associated, Highly Expressed in 8‐Cell Stage, and Nuclear‐Localized LncRNA</title>", "<p>In order to investigate the role of SINE‐associated lncRNA in ZGA, we specifically selected newly discovered transcripts that were upregulated during the 4–8‐cell stage and maintained high levels of expression. By sorting these transcripts based on their differential expression levels between the 4‐cell and 8‐cell stages, we systematically selected lncRNAs with significant expression changes for interference experiments. Subsequently, we closely monitored the embryonic development process. Through this methodical process, we ultimately identified <italic toggle=\"yes\">SAWPA</italic>, named based on its functional attributes and positional characteristics. Using the UCSC blat tool (<ext-link xlink:href=\"http://genome.ucsc.edu/cgi-bin/hgBlat\" ext-link-type=\"uri\">http://genome.ucsc.edu/cgi‐bin/hgBlat</ext-link>), we found <italic toggle=\"yes\">SAWPA</italic> is located on chromosome 10 in the opposite direction of transcription of the <italic toggle=\"yes\">WDR26</italic> gene. It is a transcript of an intron located in the <italic toggle=\"yes\">CNIH3</italic> gene (<bold>Figure</bold> ##FIG##1##\n2A##). Due to the sequencing data analyzed lacking complete information for the full length, we performed 3′ RACE and 5′ RACE to obtain the full‐length <italic toggle=\"yes\">SAWPA</italic>. There were no other variants of <italic toggle=\"yes\">SAWPA</italic>; it was a 1380 bp transcript consisting of 5 exons (Distinguished by the AT‐GC regio). Exon 2 contains the SINE element, Pre0‐SS; exon 4 contains 4 SINE elements, <italic toggle=\"yes\">PRE1g</italic>, <italic toggle=\"yes\">Pre0‐SS</italic>, <italic toggle=\"yes\">PRE1h</italic>, and <italic toggle=\"yes\">PRE1</italic>; and exon 5 contains the Line element, <italic toggle=\"yes\">L1MB7</italic> (Figure ##FIG##1##2A,B##; Figure ##SUPPL##0##S2A##, Supporting Information).</p>", "<p>We assessed whether <italic toggle=\"yes\">SAWPA</italic> are lncRNAs. Initially, we used NCBI ORF Finder (<ext-link xlink:href=\"http://www.ncbi.nlm.nih.gov/projects/gorf/\" ext-link-type=\"uri\">http://www.ncbi.nlm.nih.gov/projects/gorf/</ext-link>) to analyze the open‐reading frames (ORFs) of <italic toggle=\"yes\">SAWPA</italic> and assess its coding potential. The results revealed several short ORFs. A subsequent comparison of these regions using the NCBI BLAST tool (NCBI/BLAST/blastp suite) failed to identify any conserved protein domains or kozak sequences. Therefore, <italic toggle=\"yes\">SAWPA</italic> likely does not have coding potential (Figure ##SUPPL##0##S2B,C##, Supporting Information). To further confirm this, we analyzed the subcellular localization of <italic toggle=\"yes\">SAWPA</italic> using RNA extraction and SYBR Green real‐time quantitative PCR (qPCR) assay. We divided 8‐cell stage porcine embryos into two fractions: cytoplasmic (Cyt) and nuclear‐soluble (Nuc), and examined the expression of <italic toggle=\"yes\">SAWPA</italic> in each fraction; GAPDH and U6 were used as controls. <italic toggle=\"yes\">SAWPA</italic> was predominantly localized in the nucleus, further supporting its non‐coding status as lncRNA (Figure ##FIG##1##2C##).</p>", "<p>We performed qPCR analysis of <italic toggle=\"yes\">SAWPA</italic> expression at various embryonic development stages. The expression of <italic toggle=\"yes\">SAWPA</italic> was relatively constant and below the detectable range during the GV stage oocyte to 4‐cell stage embryo. However, it dramatically increased and peaked at the 8‐cell stage; it then decreased to below the detectable range level in blastocysts (Figure ##FIG##1##2D##). We analyzed <italic toggle=\"yes\">SAWPA</italic> expression in ESCs and various tissues; the expression was the highest in the 8‐cell stage (Figure ##SUPPL##0##S2D##, Supporting Information). RNA‐FISH revealed high <italic toggle=\"yes\">SAWPA</italic> levels in the nuclei of the 8‐cell and morula stages (Figure ##FIG##1##2E##). The fluorescence intensity test also proved that <italic toggle=\"yes\">SAWPA</italic> expression was the highest at the 8‐cell stage (Figure ##FIG##1##2F##). Therefore, <italic toggle=\"yes\">SAWPA</italic> is an 8‐cell stage embryo‐specific SINE‐associated nuclear lncRNA during preimplantation.</p>", "<title>Interference with <italic toggle=\"yes\">SAWPA</italic> Results in Embryo Arrest at 8‐Cell Stage and Affects the Activation of the Zygote Genome</title>", "<p>To explore the function of <italic toggle=\"yes\">SAWPA</italic> in porcine embryonic development, an RNA interference assay (RNAi) was performed. Embryos were microinjected with negative control siRNA (si_NC) or siRNA targeting <italic toggle=\"yes\">SAWPA</italic> (si_<italic toggle=\"yes\">SAWPA</italic>) at the pronuclear stage (<bold>Figure</bold> ##FIG##2##\n3A##). We screened four interference fragments and found that si_<italic toggle=\"yes\">SAWPA</italic>‐1 and si_<italic toggle=\"yes\">SAWPA</italic>‐3 achieved nearly 80% interference efficiency (Figure ##FIG##2##3B##). We then evaluated embryonic development and observed that depletion of <italic toggle=\"yes\">SAWPA</italic> (si_<italic toggle=\"yes\">SAWPA</italic>‐1) led to developmental arrest at the 8‐cell stage in porcine embryos (Figure ##FIG##2##3C##). We assessed the embryonic development following the injection of the relevant RNA fragments (Figure ##FIG##2##3D##). Our findings revealed a clear arrest in development at the 8‐cell stage for embryos injected with si_<italic toggle=\"yes\">SAWPA</italic>‐1 and si_<italic toggle=\"yes\">SAWPA</italic>‐3, with si_<italic toggle=\"yes\">SAWPA</italic>‐1 exhibiting the most pronounced inhibitory effect. Consequently, we selected si_<italic toggle=\"yes\">SAWPA</italic>‐1 as the interference fragment for subsequent studies. In addition, si_<italic toggle=\"yes\">SAWPA</italic>‐2 and si_<italic toggle=\"yes\">SAWP</italic>‐4 did not cause an obvious interference with the expression of <italic toggle=\"yes\">SAWPA</italic> (but they did reduce the expression level of <italic toggle=\"yes\">SAWPA</italic> by ≈30%); however, embryonic development was still arrested at the 8‐cell stage. At the same time, we found that overexpression of <italic toggle=\"yes\">SAWPA</italic> did not affect embryonic development. This indicated that <italic toggle=\"yes\">SAWPA</italic> could play an important role in the development of zygotic genome activation (ZGA) in porcine embryos. ZGA occurs in porcine between the 4‐cell and 8‐cell stages.<sup>[</sup>\n##REF##1493177##\n20\n##\n<sup>]</sup> The expression of <italic toggle=\"yes\">SAWPA</italic> during the early, middle, and late 4‐cell embryonic stages was below the detection limit; therefore, we focused our follow‐up experiments on the 8‐cell stage arrest.</p>", "<p>To investigate the impact of <italic toggle=\"yes\">SAWPA</italic> interference on ZGA, we performed immunofluorescence staining (IF) for BrdU (added at post‐PA 56 h) and visualized DNA replication. <italic toggle=\"yes\">SAWPA</italic>‐depleted 8‐cell embryos (si_<italic toggle=\"yes\">SAWPA</italic>‐1 8‐cell) exhibited an interphase chromatin status and strong BrdU staining (Figure ##SUPPL##0##S3A##, Supporting Information). To assess the initiation of major ZGA in <italic toggle=\"yes\">SAWPA</italic>‐depleted 8‐cell embryos, we used 5′‐ethynyluridine (EU) staining (added at post‐PA 64 h) to detect total <italic toggle=\"yes\">de novo</italic> transcripts (test at 72 h). si_NC and si_<italic toggle=\"yes\">SAWPA</italic>‐1 were injected at the 1‐cell stage. The 8‐cell stage embryo of si_NC and si_<italic toggle=\"yes\">SAWPA</italic>‐1 showed significant differences in EU signals, with the fluorescence intensity of si_<italic toggle=\"yes\">SAWPA</italic>‐1 8‐cell being lower than si_NC (Figure ##FIG##2##3E##). These findings suggest that transcription was affected by <italic toggle=\"yes\">SAWPA</italic> interference in the 8‐cell stage embryos.</p>", "<p>ZGA is a crucial process in the maternal‐to‐embryonic transition and the establishment of the totipotent state.<sup>[</sup>\n##REF##19700615##\n23\n##\n<sup>]</sup> Various genes such as <italic toggle=\"yes\">ACLY</italic>, <italic toggle=\"yes\">ACSS1</italic>, <italic toggle=\"yes\">ASH2L</italic>, <italic toggle=\"yes\">EIF1A</italic>, <italic toggle=\"yes\">EIF3A</italic>, <italic toggle=\"yes\">HSP70</italic>, <italic toggle=\"yes\">NID2</italic>, <italic toggle=\"yes\">PDHA1</italic>, <italic toggle=\"yes\">ZSCAN4</italic>, <italic toggle=\"yes\">SMYD3</italic>, <italic toggle=\"yes\">SQLE</italic>, and <italic toggle=\"yes\">TFIIA</italic> are actively transcribed during ZGA.<sup>[</sup>\n##REF##31935425##\n24\n##\n<sup>]</sup> To investigate the effect of <italic toggle=\"yes\">SAWPA</italic> interference on ZGA, we analyzed the expression levels of ZGA initiation genes using qPCR. Compared with si_NC, the expression of ZGA‐associated genes <italic toggle=\"yes\">ACLY</italic>, <italic toggle=\"yes\">ACSS1</italic>, <italic toggle=\"yes\">ASH2L</italic>, <italic toggle=\"yes\">EIF1A</italic>, <italic toggle=\"yes\">EIF3A</italic>, <italic toggle=\"yes\">PDHA1</italic>, <italic toggle=\"yes\">SMYD3</italic>, <italic toggle=\"yes\">SQLE</italic>, and <italic toggle=\"yes\">ZSCAN4</italic> was decreased in si_<italic toggle=\"yes\">SAWPA</italic>‐1 (Figure ##FIG##2##3F##). We evaluated the expression of genes associated with pluripotency, such as <italic toggle=\"yes\">OCT4</italic>, <italic toggle=\"yes\">SOX2</italic>, <italic toggle=\"yes\">NANOG</italic>, and <italic toggle=\"yes\">KLF4</italic>, which are transcription factors that regulate ZGA. However, there was no significant difference between si_<italic toggle=\"yes\">SAWPA</italic>‐1 and si_NC (Figure ##FIG##2##3G##). Thus, <italic toggle=\"yes\">SAWPA</italic> depletion has a significant effect on the initiation of ZGA by specifically influencing gene expression.</p>", "<p>Global chromatin accessibility is an important factor that influences ZGA.<sup>[</sup>\n##REF##27259149##\n25\n##\n<sup>]</sup> To investigate whether si_<italic toggle=\"yes\">SAWPA</italic>‐1 affects the activation of ZGA by influencing chromatin openness, we performed an <italic toggle=\"yes\">in</italic>\n<italic toggle=\"yes\">vivo</italic> DNase I‐TUNEL assay to detect chromatin openness. si_<italic toggle=\"yes\">SAWPA</italic>‐1 led to significantly lower levels of TUNEL staining compared to that in the si_NC control blastomeres (Figure ##FIG##2##3H##; Figure ##SUPPL##0##S3B,C##, Supporting Information). We compared nuclear volumes, which is another parameter for chromatin openness.<sup>[</sup>\n##REF##28846101##\n11\n##\n<sup>]</sup> There was a significant decrease in nuclear volume after si_<italic toggle=\"yes\">SAWPA</italic>‐1 compared to that in the si_NC control blastomeres (Figure ##FIG##2##3H##; Figure ##SUPPL##0##S3C##, Supporting Information). This indicates that si_<italic toggle=\"yes\">SAWPA</italic>‐1 in 8‐cell embryos affects global chromatin accessibility.</p>", "<title>\n<italic toggle=\"yes\">SAWPA</italic> Depletion Does Not Affect the Expression of the Neighbor Gene</title>", "<p>To determine whether there is a regulatory relationship between <italic toggle=\"yes\">SAWPA</italic> and the mRNAs of its neighboring genes, we analyzed the expression patterns of <italic toggle=\"yes\">SAWPA</italic>, <italic toggle=\"yes\">WDR26</italic>, and <italic toggle=\"yes\">CNIH3</italic> at different stages of porcine preimplantation embryos using qPCR. <italic toggle=\"yes\">WDR26</italic> had an expression pattern similar to that of <italic toggle=\"yes\">SAWPA</italic>, with higher expression in the 8‐cell stage. <italic toggle=\"yes\">CNIH3</italic> was detected only in the 2‐cell stage (Figure ##FIG##1##2D##). We performed RNA interference of <italic toggle=\"yes\">SAWPA</italic>, <italic toggle=\"yes\">WDR26</italic>, and <italic toggle=\"yes\">CNIH3</italic> on 1‐cell stage embryos; qPCR analysis showed that RNAi of <italic toggle=\"yes\">SAWPA</italic> and CNIH3 did not affect the expression of <italic toggle=\"yes\">WDR26</italic>. However, RNAi of <italic toggle=\"yes\">WDR26</italic> significantly decreased the expression of <italic toggle=\"yes\">SAWPA</italic> (<bold>Figure</bold> ##FIG##3##\n4A##). These results increased the possibility of <italic toggle=\"yes\">WDR26</italic> regulating <italic toggle=\"yes\">SAWPA</italic> expression.</p>", "<p>We conducted a developmental analysis of embryos following RNAi of WDR26 and CNIH3. RNAi of WDR26 influenced embryonic development, with some embryos arrested in the 8‐cell stage. Interference with <italic toggle=\"yes\">CNIH3</italic> blocked embryonic development at the 2‐cell stage (Figure ##FIG##2##3D##). Therefore, <italic toggle=\"yes\">SAWPA</italic> could have a regulatory relationship with <italic toggle=\"yes\">WDR26</italic> but not with <italic toggle=\"yes\">CNIH3</italic>. We further investigated this by co‐injecting full‐length <italic toggle=\"yes\">SAWPA</italic> with <italic toggle=\"yes\">si_WDR26‐</italic>3; this partially rescued embryonic development to the 8‐cell stage. However, co‐injecting full‐length <italic toggle=\"yes\">WDR26</italic> with si_<italic toggle=\"yes\">SAWPA</italic>‐1 had no effect on rescuing embryonic development (Figure ##FIG##2##3D##; Figure ##SUPPL##0##S4A,B##, Supporting Information). To explore the relationship between <italic toggle=\"yes\">SAWPA</italic> and <italic toggle=\"yes\">WDR26</italic>, we performed a double luciferase reporter system experiment; <italic toggle=\"yes\">WDR26</italic> mRNA can enhance the fluorescence of <italic toggle=\"yes\">SAWPA</italic> promoter‐pGL3‐luciferase vectors after interfering with endogenous <italic toggle=\"yes\">WDR26</italic> (Figure ##SUPPL##0##S4C##, Supporting Information). In summary, we confirmed that <italic toggle=\"yes\">WDR26</italic> is indeed an upstream regulatory factor of <italic toggle=\"yes\">SAWPA</italic>.</p>", "<title>\n<italic toggle=\"yes\">SAWPA</italic> Depletion Leads to JNK Signaling Pathway Inhibition</title>", "<p>To investigate the mechanism of porcine embryonic development arrest at the 8‐cell stage after interfering with <italic toggle=\"yes\">SAWPA</italic>, we collected 1600 8‐cell stage embryos injected with si_NC and si_<italic toggle=\"yes\">SAWPA</italic>‐1 at 1‐cell stage, respectively, and subjected them to low sample volume RNA‐Seq. Compared to si_NC, si_<italic toggle=\"yes\">SAWPA</italic>‐1 resulted in the deregulation of 875 genes, including 539 upregulated and 336 downregulated genes, referred to as differentially expressed genes (DEGs) (<italic toggle=\"yes\">P</italic> ≤  0.05, FPKM ≥ 1, and |log<sub>2</sub>foldchange| ≥ 1) (Figure ##FIG##3##4B##). KEGG pathway analysis of DEGs suggested that <italic toggle=\"yes\">SAWPA</italic> depletion disrupted the MAPK signaling pathway by inhibiting key factors in the JNK‐MAPK signaling pathways (Figure ##FIG##3##4C##; Figure ##SUPPL##0##S5A##, Supporting Information). In addition, <italic toggle=\"yes\">SAWPA</italic> depletion affected the PI3K‐AKT signaling pathway but did not affect the key factors in the pathway. We verified the key factors responsible for changes in expression in the MAPK and PI3K‐AKT signaling pathways using qPCR. The expression of <italic toggle=\"yes\">JNK</italic> in <italic toggle=\"yes\">SAWPA</italic>‐depleted embryos decreased by approximately four times (Figure ##FIG##3##4D##), and western blotting indicated a decrease in JNK phosphorylation levels and a decrease in total <italic toggle=\"yes\">JNK</italic> protein levels in <italic toggle=\"yes\">SAWPA</italic>‐depleted embryos (Figure ##FIG##3##4E##). The results indicate that the JNK signaling pathway plays a vital role in early embryonic development in porcine.</p>", "<p>To verify whether the JNK signaling pathway is a key signaling pathway for ZGA in porcine, we analyzed the expression level of <italic toggle=\"yes\">JNK</italic> in various stages of embryonic development using qPCR. The expression of <italic toggle=\"yes\">JNK</italic> was high during the embryonic development from the 4‐cell to 8‐cell stage, suggesting that <italic toggle=\"yes\">JNK</italic> played an important role in the ZGA during the early embryonic development in pigs (Figure ##SUPPL##0##S5B##, Supporting Information). We injected si_<italic toggle=\"yes\">JNK</italic> and si_<italic toggle=\"yes\">SAWPA</italic>‐1 at the 1‐cell stage and detected the expression levels of <italic toggle=\"yes\">JNK</italic> and <italic toggle=\"yes\">SAWPA</italic> using qPCR. <italic toggle=\"yes\">SAWPA</italic> depletion affected the expression level of <italic toggle=\"yes\">JNK</italic>, while <italic toggle=\"yes\">JNK</italic> depletion did not affect the expression level of <italic toggle=\"yes\">SAWPA</italic>, implying that there is a regulatory relationship between <italic toggle=\"yes\">SAWPA</italic> and <italic toggle=\"yes\">JNK</italic> (Figure ##FIG##3##4D##; Figure ##SUPPL##0##S5C##, Supporting Information). The embryos injected with si_<italic toggle=\"yes\">JNK</italic> were affected by blastocyst rate, and embryos arrest and 8‐cell stage. We then co‐injected si_<italic toggle=\"yes\">SAWPA</italic>‐1 embryos with overexpression of <italic toggle=\"yes\">JNK</italic> mRNA; overexpressed <italic toggle=\"yes\">JNK</italic> rescued embryonic development arrest compared to the si_<italic toggle=\"yes\">SAWPA</italic>‐1 group (Figure ##FIG##3##4F##).</p>", "<p>To evaluate whether <italic toggle=\"yes\">SAWPA</italic> depletion at the 8‐cell stage affects development by influencing JNK protein phosphorylation levels, we analyzed the expression level of pJNK in various stages of embryonic development through western blotting. The expression of pJNK was high during embryonic development from the 4‐cell to 8‐cell stage (Figure ##SUPPL##0##S5D##, Supporting Information). We then statistically analyzed embryonic development by interfering with JNK and treatment with pJNK inhibitors (TCS JNK 6o). Interference with JNK‐MAPK led to a significant decrease in the embryonic development blastocyst rate (<bold>Table</bold> ##TAB##0##\n1\n##). Some embryos were arrested in the 8‐cell stage. When different concentrations of the JNK inhibitor, TCS <italic toggle=\"yes\">JNK</italic> 6o, were added, the 1 and 5 µ<sc>m</sc> treatments had little effect on development. However, the blastocyst rate of embryos in the 10, 20, 25, 50, and 100 µ<sc>m</sc> groups decreased significantly, thereby impeding embryonic development (Table ##TAB##0##1##). Western blotting for pJNK in embryos treated with inhibitors revealed that the low concentrations of 1 and 5 µ<sc>m</sc> could not inhibit the phosphorylation of <italic toggle=\"yes\">JNK</italic> in the 8‐cell stage (Figure ##SUPPL##0##S5E##, Supporting Information). In order to make the results more accurate, we conducted gray value analysis on the western blotting results and found that pJNK had a high expression level at the 8‐cell stage, and JNK phosphorylation screen breakage was successfully inhibited by the inhibitor, which verified the previous results This finding further confirms the significance of JNK phosphorylation during the ZGA period (Figure ##SUPPL##0##S5F,G##, Supporting Information). In conclusion, the depletion of <italic toggle=\"yes\">SAWPA</italic> led to the arrest of embryonic development at the 8‐cell stage by influencing the JNK signaling pathway.</p>", "<title>\n<italic toggle=\"yes\">SAWPA</italic> Binds to HHNRNPA1 and MED8</title>", "<p>To investigate the mechanism that <italic toggle=\"yes\">SAWPA</italic> functions, we performed RNA pull‐down‐mass spectrometry with biotin‐labeled <italic toggle=\"yes\">SAWPA</italic> to elucidate the proteins that interact with <italic toggle=\"yes\">SAWPA</italic> using 2000 8‐cell embryos. Two specific bands in the <italic toggle=\"yes\">SAWPA</italic> group were identified as HNRNPA1 and MED8, compared to the <italic toggle=\"yes\">SAWPA</italic>‐rev control (<bold>Figure</bold> ##FIG##4##\n5A##). To verify this result, western blotting analysis was carried out (Figure ##FIG##4##5B##). The results of IF and qPCR indicated that HNRNPA1 and MED8 exhibited higher expression levels at the 8‐cell stage (Figure ##FIG##4##5C–E##), consistent with the high expression level of <italic toggle=\"yes\">SAWPA</italic> at the 8‐cell stage (Figure ##FIG##1##2D##). Furthermore, to confirm the <italic toggle=\"yes\">SAWPA</italic> protein complex, a co‐immunoprecipitation (co‐IP) assay was conducted using 8‐cell embryos overexpressing HA‐tagged MS2 protein and MS2‐tagged <italic toggle=\"yes\">SAWPA</italic>. The co‐IP results using an anti‐HA antibody (with IgG as a control) demonstrated that <italic toggle=\"yes\">SAWPA</italic> indeed interacts with HNRNPA1 and MED8 to form an RNA‐protein complex (Figure ##FIG##4##5F##). MED8 is an essential component of the mediator complex, which acts as a coactivator to regulate the transcription of almost all RNA polymerase II‐dependent genes.<sup>[</sup>\n##REF##10838567##\n26\n##\n<sup>]</sup> As part of this complex, MED8 interacts with RNA polymerase II and gene‐specific transcription factors to facilitate transcriptional activation.<sup>[</sup>\n##REF##10838567##\n26\n##, ##REF##15896740##\n27\n##\n<sup>]</sup> HNRNPA1 is a typical RNA‐binding protein that plays a significant role in transcription and alternative splicing. HNRNPA1 can interact with various non‐coding RNAs to exert its functions, participating in neurodegenerative diseases and cancer‐related conditions.<sup>[</sup>\n##REF##23247072##\n28\n##\n<sup>]</sup> These findings also suggest that <italic toggle=\"yes\">SAWPA</italic> interacts with HNRNPA1 and MED8 to execute its function.</p>", "<title>SINE Is the Key Sequence for the Functioning of <italic toggle=\"yes\">SAWPA</italic>\n</title>", "<p>SINE acts as a regulator, regulating gene expression through epigenetic mechanisms or directly as a binding site for distal enhancers, promoters, and transcription factors.<sup>[</sup>\n##REF##21976282##\n29\n##\n<sup>]</sup> In order to investigate if <italic toggle=\"yes\">SAWPA</italic> regulates downstream genes through SINE elements, we initially defined SINE‐associated genes as those harboring a SINE sequence within 2 kb upstream and 1 kb downstream of the transcription start site (TSS). We then observed that out of 875 DEGs, 714 were SINE‐associated genes. To determine the statistical significance of this number, we performed a Wilcoxon rank‐sum test by comparing the observed number of SINE‐associated genes in DEGs to 875 genes randomly selected from the entire genome in 10 000 trials. The rank of DEGs was significantly higher than the distribution of 10 000 random controls (5% = 697, <italic toggle=\"yes\">p</italic> &lt; 1.12e‐3), indicating that interference with <italic toggle=\"yes\">SAWPA</italic> was more likely to affect SINE‐associated genes (<bold>Figure</bold> ##FIG##5##\n6A##).</p>", "<p>To investigate the key sequences involved in the regulatory mechanism of <italic toggle=\"yes\">SAWPA</italic>, we generated five <italic toggle=\"yes\">SAWPA</italic> truncated mutations (from Δ1 to Δ5). To avoid the influence of the si_<italic toggle=\"yes\">SAWPA</italic>‐1 site on the <italic toggle=\"yes\">SAWPA</italic> sequence, we mutated the si_<italic toggle=\"yes\">SAWPA</italic>‐1 sites in each truncated mutation, and mutated si_<italic toggle=\"yes\">SAWPA</italic>‐1 sites in <italic toggle=\"yes\">SAWPA</italic> as the Mut control group (Figure ##FIG##5##6B##). Next, we divided the embryos into six groups and overexpressed six RNA fragments upon <italic toggle=\"yes\">SAWPA</italic> depletion (si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ1 OE, si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ2 OE, si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ3 OE, si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ4 OE, si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ5 OE, and si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Mut OE). The development data revealed that injection of Δ1, Δ2, Δ4, Δ5, and Mut, but not Δ3, can rescue the development arrest upon <italic toggle=\"yes\">SAWPA</italic> depletion, (Figure ##FIG##5##6C,D## and <bold>Table</bold> ##TAB##1##\n2\n##). This suggests that 3 (540–810 bp of <italic toggle=\"yes\">SAWPA</italic>) is the critical domain for the regulatory function of <italic toggle=\"yes\">SAWPA</italic>. As 3 contains the SINE sequence Pre0‐SS (the exon2 of <italic toggle=\"yes\">SAWPA</italic>), we hypothesized that <italic toggle=\"yes\">SAWPA</italic> exerts its regulatory function through the SINE element. To validate this hypothesis, we conducted an experiment on PK15 cells. We overexpressed the five truncated mations tagged with MS2 and HA‐tagged MS2 protein and performed co‐IP assays using HA antibodies. The results showed that Δ1, Δ2, Δ4, and Δ5 could bind to HNRNPA1 and MED8 through the 3 sequence, whereas Δ3, which lacks the SINE element, could not bind to HNRNPA1 and MED8 (Figure ##FIG##5##6E##). Next, we overexpressed <italic toggle=\"yes\">SAWPA</italic>‐MS2 and HA‐MS2P at the 1‐cell stage of embryo and PK15, then performed co‐IP followed by RT‐PCR (test <italic toggle=\"yes\">SAWPA</italic>) and PCR (test SINE (3): DNA sequence of 3) assays at the 8‐cell stage (Figure ##FIG##4##5F##) and PK15 (Figure ##FIG##5##6E##), we successfully detected the presence of <italic toggle=\"yes\">SAWPA</italic> and SINE (3) element. This indicates that <italic toggle=\"yes\">SAWPA</italic> exerts its regulatory function by binding to HNRNPA1 and MED8 through the SINE element. Therefore, our results demonstrate that <italic toggle=\"yes\">SAWPA</italic> can interact with MED8 and HNRNPA1 to form RNA‐protein complexes through the SINE sequence, playing a crucial role in the early embryonic development and ZGA process in pigs.</p>", "<title>\n<italic toggle=\"yes\">SAWPA</italic> Regulates JNK Transcription Through SINE Sequences</title>", "<p>To investigate the mechanism by which <italic toggle=\"yes\">SAWPA</italic> regulates <italic toggle=\"yes\">JNK</italic>, we analyzed the sequences of <italic toggle=\"yes\">SAWPA</italic> and <italic toggle=\"yes\">JNK</italic>. The SINE‐associated element sequences of <italic toggle=\"yes\">SAWPA</italic> highly coincided with the SINE sequences of <italic toggle=\"yes\">JNK</italic>, particularly those located near the transcription start site (TSS), which had an overlapping region of ≈200 bp (Figure ##FIG##5##6F##; Figure ##SUPPL##0##S6##, Supporting Information). This suggested that <italic toggle=\"yes\">SAWPA</italic> regulates the transcription of <italic toggle=\"yes\">JNK</italic>. For ease of reference, we named the SINE sequences upstream and downstream of the <italic toggle=\"yes\">JNK</italic> TSS site as SINE1‐7, in their sequential order. SINE4 (#4) showed a high degree of overlap with exon 2 of <italic toggle=\"yes\">SAWPA</italic> (Figure ##FIG##5##6F##).</p>", "<p>TEs play an important role in transcription by regulating the transcription of related genes in both <italic toggle=\"yes\">cis</italic>‐ and <italic toggle=\"yes\">trans‐</italic>acting forms.<sup>[</sup>\n##REF##27496889##\n9\n##, ##REF##36423263##\n12\n##, ##REF##36110328##\n16\n##\n<sup>]</sup> Long non‐coding RNA can act as a scaffold and play a critical role in transcription. TEs‐associated lincRNAs act as enhancers in transcription.<sup>[</sup>\n##REF##31331261##\n30\n##\n<sup>]</sup> Therefore, we hypothesis that <italic toggle=\"yes\">SAWPA</italic> may bind to related SINE elements and mediate its <italic toggle=\"yes\">cis</italic>‐regulatory activity in <italic toggle=\"yes\">trans</italic>. We confirmed this hypothesis through a double luciferase experiment to detect whether <italic toggle=\"yes\">SAWPA</italic> increased the SV40 promoter activity in PK15 cells by a specific JNK SINE sequence. First, we found that 7SINE (SINE1∼7) of JNK can increase fluorescence intensity, suggesting that 7SINE of JNK has an enhancer effect, but the specific mechanism remains unclear (Figure ##FIG##5##6G##). Next, the result shows that overexpression of <italic toggle=\"yes\">SAWPA</italic> increased the SV40 promoter activity by <italic toggle=\"yes\">JNK</italic> 7SINE, regardless of whether the sense and antisense 7SINE of JNK were inserted upstream or downstream of the pGL3‐luciferase vectors (Figure ##FIG##5##6G##). Overexpression of <italic toggle=\"yes\">SAWPA</italic> and <italic toggle=\"yes\">JNK</italic> SINE4 resulted in fluorescence intensity of the pGL3‐luciferase vector that was similar to that of <italic toggle=\"yes\">JNK</italic> 7SINE. This indicated that SINE4 was the key sequence of <italic toggle=\"yes\">SAWPA</italic> binds to JNK. In addition, Overexpression of 7x <italic toggle=\"yes\">JNK</italic> SINE4 and <italic toggle=\"yes\">SAWPA</italic> led to further increases in the fluorescence intensity of the pGL3‐luciferase vector, while 7x <italic toggle=\"yes\">JNK</italic> SINE7 and 7x EGFP (same length as 7x <italic toggle=\"yes\">JNK</italic> SINE4) and <italic toggle=\"yes\">SAWPA</italic> did not achieve the same fluorescence intensity (Figure ##FIG##5##6G##). Therefore, <italic toggle=\"yes\">SAWPA</italic> may act as a transcription factor by binding to SINE and enhancing <italic toggle=\"yes\">cis</italic> adjustment activity of SINE in the <italic toggle=\"yes\">JNK</italic> promoter region by binding to SINE4.</p>", "<p>To further confirm that the RNA‐protein complex is associated with JNK by SINE sequence, we performed co‐IP followed by PCR assay with HA‐tagged MS2‐labeled <italic toggle=\"yes\">SAWPA</italic> overexpression in PK15 cells. The co‐IP followed by PCR assay (The SINE – <italic toggle=\"yes\">JNK</italic> primers consist of a SINE sequence (#4) and a <italic toggle=\"yes\">JNK</italic> promoter region) results using anti‐MED8 and anti‐HA antibodies showed that <italic toggle=\"yes\">SAWPA</italic> can bind to JNK promoter sequences (Figure ##FIG##5##6H##). In summary, <italic toggle=\"yes\">SAWPA</italic> can act as a transcription factor to <italic toggle=\"yes\">tran</italic>s‐activate target genes through its reverse action on <italic toggle=\"yes\">cis</italic>‐regulatory elements. <italic toggle=\"yes\">SAWPA</italic> activates target gene expression by binding to SINE elements in the <italic toggle=\"yes\">JNK</italic> promoter region and transactivating <italic toggle=\"yes\">JNK</italic> transcription through interaction with HNRNPA1 and MED8 in <italic toggle=\"yes\">trans</italic> (<bold>Figure</bold> ##FIG##6##\n7\n##).</p>" ]
[ "<title>Discussion</title>", "<p>In this study, we identified a SINE‐associated lncRNA in porcine preimplantation embryos and named it <italic toggle=\"yes\">SAWPA</italic>. <italic toggle=\"yes\">SAWPA</italic> is 8‐cell‐specific and localizes to the nucleus. Interference of <italic toggle=\"yes\">SAWPA</italic> leads to embryonic developmental arrest at the 8‐cell stage; in addition, it restricts the opening of chromatin and the activation of ZGA. Mechanistically, <italic toggle=\"yes\">SAWPA</italic> forms a complex with HNRNPA1 and MED8 and binds SINE elements in the promoter of <italic toggle=\"yes\">JNK</italic> to activate its transcription, regulating the development through JNK‐MAPK signaling pathway. For the first time, we found that TEs‐associated lncRNA functions in pig early embryonic development, providing a new perspective for mechanism research on porcine‐specific early embryonic development.</p>", "<p>The activity of TEs gradually increases during early mammalian embryonic development; it plays an important regulatory role in early embryonic development.<sup>[</sup>\n##REF##15469847##\n31\n##\n<sup>]</sup> MERVL is highly activated in mouse 2‐cell embryos, resulting in large amounts of ERV‐associated chimeric transcripts.<sup>[</sup>\n##REF##15469847##\n31\n##, ##REF##15237213##\n32\n##\n<sup>]</sup> Based on those 2‐cell‐specific chimeric transcripts, 2C‐like embryonic stem cells were identified,<sup>[</sup>\n##REF##22722858##\n33\n##\n<sup>]</sup> indicating that the activation of ERVs is correlated with the acquisition of pluripotency both in early embryos and in stem cells. In humans, the activation of ERVK is associated with blastocyst pluripotency; HERVK is a marker for naïve‐like human ES cells.<sup>[</sup>\n##REF##22722858##\n33\n##, ##REF##25896322##\n34\n##\n<sup>]</sup> Despite the appearance of a large number of TE element transcripts during early embryonic development, their regulatory mechanisms remain unclear. However, SINE can affect gene transcription.<sup>[</sup>\n##REF##23358118##\n18\n##, ##REF##19307572##\n35\n##\n<sup>]</sup> During transcription, SINEs are spread throughout the genome, and their copies can be inserted into gene regions, where they can bind to nuclear proteins or become part of the gene regulatory system through modification, regulating gene transcription. SINE sequences provide multiple protein‐binding sites that mediate the transcription of RNA polymerase II. SINE B1 and SINE B2 were found in mice under heat shock reaction conditions. After heat shock, polymerase III specifically enhances the transcription of SINE B2 and Alu, which then binds to polymerase II, and inhibits the transcription of specific genes, such as actin and histone H1 genes, in a trans‐manner.<sup>[</sup>\n##REF##15300240##\n36\n##\n<sup>]</sup> Besides, the degradation of SINE B2 is also involved in upregulating stress genes in heat shock stress response, where EZH2 is recruited to trigger the cleavage of SINE B2.<sup>[</sup>\n##REF##27984727##\n37\n##\n<sup>]</sup> Here, we determined that the SINE‐associated <italic toggle=\"yes\">SAWPA</italic> can bind to MED8, a component of Mediator, and then activate the transcription of target genes including <italic toggle=\"yes\">JNK</italic>, These findings have expanded our understanding of the mechanisms regulating transcription of SINE‐associated sequences.</p>", "<p>SINE‐associated lncRNA could be involved in transcriptional regulation.<sup>[</sup>\n##REF##8419337##\n38\n##\n<sup>]</sup> TEs can regulate transcription by binding lncRNAs; the ERV‐associated lncRNA, <italic toggle=\"yes\">LincGET</italic> regulates transcription by mediating the <italic toggle=\"yes\">cis</italic>‐regulatory activity of GLKLTRs and ZGA‐related genes.<sup>[</sup>\n##REF##27496889##\n9\n##, ##REF##31331261##\n30\n##\n<sup>]</sup> The expression of LINE1 elements increases chromatin accessibility.<sup>[</sup>\n##REF##28846101##\n11\n##\n<sup>]</sup>\n<italic toggle=\"yes\">SAWPA</italic> can mediate the regulatory activity of SINE elements to regulate the expression of target genes by binding HNRNPA1 and MED8, providing a <italic toggle=\"yes\">trans</italic>‐regulatory model for SINE elements. SINE elements are widely distributed throughout the genome; therefore, SINE‐associated lncRNA is likely that their target genes are also widely distributed. Therefore, cut&amp;tag could be used to detect whether <italic toggle=\"yes\">SAWPA</italic> target genes play a key role in porcine‐specific early embryonic development on a genome‐wide scale.</p>", "<p>Heterogeneous nuclear RNA‐protein complex (hnRNP) is well‐known to mediate the function of lncRNAs. For example, in mice, hnRNPU can interact with <italic toggle=\"yes\">LincGET</italic> to produce regulatory effects in early embryonic development<sup>[</sup>\n##REF##27496889##\n9\n##\n<sup>]</sup>; hnRNPK can bind to <italic toggle=\"yes\">Neat1</italic> to mediate paraspeckles formation<sup>[</sup>\n##REF##22960638##\n39\n##\n<sup>]</sup>; hnRNPK interacts with <italic toggle=\"yes\">Xist</italic> to regulate chromatin diffusion, gene silencing, and expression<sup>[</sup>\n##REF##22960638##\n39\n##, ##REF##30428357##\n40\n##\n<sup>]</sup>; hnRNPK interacts with lncRNAs containing SINE derived nuclear RNA localization (SIRLOIN) and mediates nuclear enrichment nuclear cell function.<sup>[</sup>\n##REF##31279651##\n41\n##\n<sup>]</sup> In this study, we found that HNRNPA1 can bind to SINE‐associated lncRNA <italic toggle=\"yes\">SAWPA</italic> to regulate the transcription of JNK, reflecting a conserved mechanism of SINE elements in transcription regulation between mice and pigs.</p>", "<p>John et al. used chromatin immunoprecipitation‐sequencing (ChIP‐seq) to show that lncRNAs are generally located at the junction between active and inactive chromatin during the early stages of embryonic development.<sup>[</sup>\n##REF##17604720##\n42\n##\n<sup>]</sup> Several lncRNAs can recruit epigenetic factors upon binding to target genes to regulate chromatin structure. The human lncRNA, HOTAIR interacts with PRC2 and LSD1‐CoREST‐REST complexes, inhibiting the expression of HoxD gene clusters by erasing H3K4me2/3 and establishing H3K27me3.<sup>[</sup>\n##REF##17604720##\n42\n##, ##REF##20616235##\n43\n##\n<sup>]</sup> Similarly, human HOTTIP recruits MLL through WDR5 into the 5′ region of the HoxA gene cluster, catalyzing the establishment of H3K4me3 and <italic toggle=\"yes\">cis</italic>‐activating the expression of genes such as Hoxa11 and Hoxa13. <italic toggle=\"yes\">LincGET</italic> promotes the target gene methylation of histone H3 arginine 26 (H3R26me) by recruiting CARM1, which increases chromatin openness.<sup>[</sup>\n##REF##21423168##\n44\n##\n<sup>]</sup> The recruitment of epigenetic factors by lncRNAs provides a novel perspective. Therefore, we speculate that <italic toggle=\"yes\">SAWPA</italic> may be involved in the recruitment of epigenetic factors that promote chromatin opening. Our future research will focus on detecting the epigenetic factors recruited by <italic toggle=\"yes\">SAWPA</italic>, through IP mass spectrometry, to explore the specific mechanism of <italic toggle=\"yes\">SAWPA</italic> regulation in early embryonic development.</p>", "<p>This study identified that the JNK‐MAPK signaling pathway is crucial for early embryonic development in pigs. We observed that inhibiting <italic toggle=\"yes\">JNK</italic> expression and phosphorylation hindered embryonic development, primarily at the 8‐cell stage. This finding aligns with the regulatory role of the MAPK signaling pathway in other species and cell types. In mice, the ERK‐MAPK signaling pathways affect ZGA, with inhibitors arresting embryos at the G2 stage of the 2‐cell stage.<sup>[</sup>\n##REF##17611221##\n45\n##\n<sup>]</sup> Inhibition of the p38‐MAPK pathway led to developmental arrest at the 8–16‐cell stage and inhibited blastocyst expansion and incubation.<sup>[</sup>\n##REF##15031106##\n46\n##\n<sup>]</sup> In pig embryo research, the MAPK signaling pathway is vital in the formation of the inner cell mass and the induction of ectodermal stem cells (EpiSCs).<sup>[</sup>\n##REF##25172095##\n47\n##\n<sup>]</sup> Therefore, the MAPK signaling pathway plays a crucial regulatory role in early pig embryos, reflecting the regulatory mechanisms involved in early pig embryo development. Although the specific mechanisms underlying the effects of the JNK signaling pathway are not yet clear, we will also focus our attention on the target genes affected by JNK in the future, in order to further investigate the root causes of blockages that occur.</p>", "<p>In summary, our study revealed the crucial involvement of SINE‐associated lncRNAs during the ZGA of embryonic development, highlighting the indispensability of SINE, an endogenous retrovirus, in this process. However, the precise regulatory mechanisms behind this phenomenon are yet to be fully understood. Given the significant presence of SINE in animal genomes, investigating the connection between SINE‐associated lncRNAs and pluripotency or reprogramming in the future would be a valuable endeavor.</p>" ]
[]
[ "<title>Abstract</title>", "<p>In mice, retrotransposon‐associated long noncoding RNAs (lncRNA) play important regulatory roles in pre‐implantation development; however, it is largely unknown whether they function in the pre‐implantation development in pigs. The current study aims to screen for retrotransposon‐associated lncRNA in porcine early embryos and identifies a porcine 8‐cell embryo‐specific SINE‐associated nuclear long noncoding RNA named <italic toggle=\"yes\">SAWPA</italic>. <italic toggle=\"yes\">SAWPA</italic> is essential for porcine embryonic development as depletion of <italic toggle=\"yes\">SAWPA</italic> results in a developmental arrest at the 8‐cell stage, accompanied by the inhibition of the JNK‐MAPK signaling pathway. Mechanistically, <italic toggle=\"yes\">SAWPA</italic> works in <italic toggle=\"yes\">trans</italic> as a transcription factor for <italic toggle=\"yes\">JNK</italic> through the formation of an RNA‐protein complex with HNRNPA1 and MED8 binding the SINE elements upstream of <italic toggle=\"yes\">JNK</italic>. Therefore, as the first functional SINE‐associated long noncoding RNAs in pigs, <italic toggle=\"yes\">SAWPA</italic> provides novel insights for the mechanism research on retrotransposons in mammalian pre‐implantation development.</p>", "<p>During the early embryonic development of pigs, the SINE‐associated long non‐coding RNA <italic toggle=\"yes\">SAWPA</italic> binds to MED8 and HNRNPA1 to regulate the transcription of <italic toggle=\"yes\">JNK</italic> through SINE sequences, affecting the activation of the zygotic genome. Depletion of <italic toggle=\"yes\">SAWPA</italic> leads to an impact on the JNK‐MAPK signaling pathway, causing embryonic development to become arrested at the 8‐cell stage.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6924-cit-0086\">\n<string-name>\n<given-names>T.</given-names>\n<surname>He</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Peng</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Gao</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Zhu</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Chai</surname>\n</string-name>, <string-name>\n<given-names>B. C.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>R.</given-names>\n<surname>Wei</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>J.‐X.</given-names>\n<surname>Jin</surname>\n</string-name>, <article-title>SINE‐Associated LncRNA <italic toggle=\"yes\">SAWPA</italic> Regulates Porcine Zygotic Genome Activation</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2307505</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202307505</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Primer and Probe Design</title>", "<p>The primers were designed using PrimerPremier5 (Table ##SUPPL##0##S1##, Supporting Information), and primers and FISH probes were synthesized by Beijing Genomics Institute (Beijing, China).</p>", "<title>Antibodies</title>", "<p>The following antibodies were used for BrdU, western blot, and co‐IP assay: anti‐BrdU (#ab1893; Abcam), anti‐β‐actin (#sc47778; Santacruz), anti‐JNK1 + JNK2 + JNK3 (phospho‐T183 + T183 + T221) (#ab124956; Abcam), anti‐JNK1 + JNK2 + JNK3 (#ab179461; Abcam), anti‐MED8 (#PA5‐118854; Thermo), anti‐HBRNPA1 (#11176‐1‐AP; proteintech) and anti‐HA (#ab1424; Abcam).</p>", "<title>Embryo culture and collection</title>", "<p>Pig ovaries were collected from the slaughterhouse and transported in 37 °C saline solution. Upon arrival, they were thoroughly rinsed with a physiological saline solution containing penicillin (S9137; Sigma) and streptomycin (P3032; Sigma) at a temperature of 37 °C. To obtain the cumulus‐oocyte complex (COCs) from follicles measuring 3–6 mm in diameter, a 10 mL syringe fitted with an 18‐gauge needle was used for aspiration. The COCs were then washed three times with a HEPES (H3784‐1KG; Sigma) buffer solution. High‐quality COCs were selected for in vitro mature. Fifty COCs were transferred to 500 µL of TCM‐199 culture medium (3100‐027; Invitrogen) supplemented with 0.14% PVA (P8136; Sigma), 10 ng mL−1 epidermal growth factor (E4127; Sigma), 0.57 mm cysteine (C7602; Sigma), 0.5 IU mL−1 pregnant mare serum gonadotropin (PMSG, hor272; PROSPEC), and 0.5 IU mL−1 human chorionic gonadotropin (hCG, hor250; PROSPEC). After being collected, the COCs were cultured at 39 °C until they matured, which took ≈42–44 h. Once mature, they were transferred to an Eppendorf tube (MCT‐150‐C; AXYGEN) containing 0.1% hyaluronidase, and the surrounding cumulus cells were manually removed using a pipette. COCs with visible polar bodies were then selected for parthenogenetic activation (PA). The parthenogenetically activated embryos were cultured in PZM3 medium, which was 500 µL PZM‐3 containing 0.15% BSA (A8022; Sigma), 200 µL BME (B6766; Merck) Amino Acids Solution, and 100 µL MEM (M7145; Merck) with no essential amino acid solution.</p>", "<p>Post parthenogenetic activation (pPA), embryos were collected at different time points: 1‐cell stage (pPA 12 h), 2‐cell stage (pPA 24 h), early 4‐cell stage (pPA 40 h), middle 4‐cell stage (pPA 48 h), late 4‐cell stage (pPA 56 h), 8‐cell stage (pPA 72 h), morula stage (pPA 108 h), early blastocyst stage (pPA 120 h), middle blastocyst stage (pPA 144 h), and late blastocyst stage (pPA 168 h).</p>", "<title>RNA‐Seq and Analysis</title>", "<p>Embryos at the 8‐cell stage were collected from the si_<italic toggle=\"yes\">SAWPA</italic>‐1 and si_NC groups using TRIZOL. Each experiment involved 400 embryos and was repeated twice. The collected embryos were washed with PBSA at least three times and PBSA was removed as thoroughly as possible. The Beijing Genomics Institute performed the RNA extraction, quality control, library construction, and sequencing of the embryo samples using the DNBSEQ Low Input Smart‐Seq Eukaryotic mRNA library, following the manufacturer's instructions.</p>", "<title>Analysis of TEs‐Associated LncRNA</title>", "<p>In data quality control, first, RNA‐seq data were downloaded from public databases with the following data identifiers: GSE163620, CRA004237, GSE138760, and GSE36552. Trim_galore(v0.6.7) was used to remove adapters and low‐quality sequences from the downloaded raw data, using default parameters. The resulting clean data were used for subsequent analysis.</p>", "<title>Prediction of LncRNA Transcripts</title>", "<p>First, STAR (v2.7.10b) was used to align the clean data to the genome (using parameters: –outSAMstrandField intronMotif –outFilterIntronMotifs RemoveNoncanonical –outFilterMismatchNmax 2 –outFilterMultimapNmax 20 –outFilterMatchNmin 16 –alignEndsType EndToEnd –runThreadN 20 –outSAMtype BAM SortedByCoordinate –outBAMsortingThreadN 10). Then transcript assembly was performed using stringtie(v2.1.7) with default parameters. The assembled transcripts were compared to the genome annotation file using gffcompare (v0.12.6) (using default parameters). Transcripts with tags “u,” “x,” “i,” “j,” or “o,” a sequence length greater than or equal to 200, and containing at least 2 exons were selected as candidate transcripts for new lncRNAs. Subsequently, CPC2 (v0.1) (with default parameters), CNCI(v2) (with parameter ‐m ve), and PLEK (v1.2) (with default parameters) were used to predict the coding potential of the new transcripts. Transcripts, for which all three software tools predicted “nocoding”, were extracted. Finally, cufflinks (v2.2.1) were used for expression quantification of the predicted new lncRNA transcripts (using the parameter –library‐type fr‐unstranded). The quantified results were used for further analysis.</p>", "<title>Analysis of LncRNA‐Repeat Associations</title>", "<p>Repeat element annotation files were downloaded from UCSC (pig: <ext-link xlink:href=\"https://hgdownload.soe.ucsc.edu/goldenPath/susScr3/database/rmsk.txt.gz\" ext-link-type=\"uri\">https://hgdownload.soe.ucsc.edu/goldenPath/susScr3/database/rmsk.txt.gz</ext-link>. mouse: <ext-link xlink:href=\"https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/rmsk.txt.gz\" ext-link-type=\"uri\">https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/rmsk.txt.gz</ext-link>. human: <ext-link xlink:href=\"https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz\" ext-link-type=\"uri\">https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz</ext-link>) and lncRNAs were classified into four types based on the types of repetitive elements found within their exons: SINE‐, LINE‐, ERVL‐, and other repeat‐ associated elements. Then the expression patterns of these different types of lncRNAs during embryonic development were analyzed.</p>", "<title>Analysis of ZGA‐Associated LncRNAs</title>", "<p>The functions of significantly upregulated ZGA‐associated lncRNA and mRNA transcripts during the ZGA period were explored. Differential gene analysis was performed using DESeq2 (R3.5) for the 8C/MII stage, with a selection criterion of padjust&lt;0.01 and |log2FoldChange|&gt;1 for lncRNAs and mRNAs as ZGA‐associated candidates. These candidates were used for subsequent ZGA‐lncRNA analysis, including the counting of different TE types.</p>", "<title>Quantitative Real‐Time PCR</title>", "<p>Real‐time quantitative PCR was performed to detect the expression of genes using TB Green Premix Ex Taq (RR420A; Takara). Total RNA was extracted from 100 embryos using TRIZOL reagent (15 596 018; Ambion) and quality check analysis was performed. Reverse transcription was performed using RevertAid (M1631; Thermo) under the following conditions: 60 min at 42 °C, followed by 5 s at 85 °C. The cDNA was stored at −20 °C until use. For qPCR, the following conditions were used: 30 s at 95 °C, 40 cycles of 5 s at 95 °C, and 34 s at 60 °C, followed by a dissociation stage comprising 15 s at 95 °C and 1 min at 60 °C. The cycle threshold (Ct) value for each sample was obtained from three experimental replicates. The target sequence was normalized to the reference sequence using the 2^−ΔΔCt method.</p>", "<title>RNA‐FISH</title>", "<p>The RNA fluorescence in situ hybridization (RNA‐FISH) was carried out following a previously established protocol.<sup>[</sup>\n##REF##30550787##\n4\n##\n<sup>]</sup> The probes were labeled through in vitro transcription using the MEGAshortscript Kit (AM1354; Ambion), and 75% of the uracil was labeled with Alexa Fluor 488 (C11403; Invitrogen) in a 4:1 ratio of Alexa Fluor 488‐5‐UTP to UTP. The vitelline membrane was removed with acidic treatment (10 µL HCl, 1 mL MAN) and the pig embryos were incubated in PBS containing 6 mg mL<sup>−1</sup> BSA for 3 min. Subsequently, the embryos were transferred onto Superfrost/Plus microscope slides (12‐550‐15; Fisher) and dried immediately. The embryos were fixed and permeabilized with 4% paraformaldehyde (PFA). The D‐T‐G lncRNA in situ hybridization kit (D‐074; FOCO) was employed to detect the localization of <italic toggle=\"yes\">SAWPA</italic> embryos, and imaging was performed using a confocal microscope (TCS SP8; Leica, Wetzlar, Germany).</p>", "<title>Microinjection</title>", "<p>For lncRNA and mRNA downregulation/or overexpression, the RNA (si_RNA, 20 µ<sc>m</sc>; mRNA, 150 ng µL<sup>−1</sup>) was injected into the cytoplasm of mature oocytes using a FemtoJet microinjector (Eppendorf; Hamburg, Germany), the same amount was injected into each embryo, and the injection conditions were 150 hPa injection pressure, 50 hPa compensation pressure, and 0.7 s injection time. The injection amount per embryo was ≈10 pL. The RNA was delivered into the porcine mature oocyte at 6 h after PA. The operation was performed on a heated stage of an inverted microscope (Nikon Corporation; Tokyo, Japan), and microinjection was carried out in MAN buffer medium.</p>", "<title>BrdU Staining</title>", "<p>The embryos injected with si_RNA or si_NC were cultured in PZM‐3 after PA 6 h. After PA 66 h, BrdU was added at a final concentration of 20 µg mL<sup>−1</sup> and aphidicolin at 0.5 µg mL<sup>−1</sup>. The embryos were cultured in PZM‐3 for 24 h, fixed for 90 h, and subjected to IF. Zona pellucida was removed at 90 h after PA, and the embryos were transferred into the acid operating solution (10 µL HCL in 1 mL MAN). The 8‐cell stage embryos were immediately cleaned in MAN thrice. The embryo was placed in a 4% PFA fixation solution and fixed at room temperature for 30 min. After three washes for 5 min each in PBSA (0.2 g BSA in 100 mL PBS), the embryos were incubated at room temperature for 30 min in 1.5 <sc>m</sc> HCl (concentrated hydrochloric acid:H2O = 1:7). The embryos were washed three times with PBSA, then they were subjected to permeabilization in a normal permeation solution, which involved dissolving 0.75 mL of TritonX‐100 (T9284‐100ML; Sigma) in 50 mL of PBS (P2272; Sigma). The embryos were transferred to 500 µL membrane permeable solution and permeated overnight at 4 °C for 8−12 h (0.75 mL TritonX‐100 in 50 mL PBS). The embryos were washed with PBSA twice (5 min/time). After incubating at room temperature for 1 h, the primary antibody was incubated overnight at 4 °C with a blocking solution (0.1 g BSA in 10 mL PBS) diluted. Following three washes in PBSA, the embryos were incubated with the secondary antibody diluted with blocking solution and incubated at room temperature and away from light for 2 h. Once the embryos were washed three times with the cleaning solution, they were stained with Hoechst33342 (10 ng µL<sup>−1</sup> in 1× PBS, H3570, Invitrogen) for 8 min. Then, after washing three times with PBSA, the embryos were mounted on a glass slide, sealed, and visualized.</p>", "<title>EU Staining</title>", "<p>At 56 h after PA, the pig embryos injected in si_NC or si_<italic toggle=\"yes\">SAWPA</italic>‐1 groups were supplemented with EU to achieve a final concentration of 10 m<sc>m</sc>. The embryos were then cultured for an additional 16 h. The cumulus cells were removed using acidic Tyrode's solution, and the resulting 8‐cell stage embryos were washed twice. Next, the embryos were fixed with 4% PFA, washed three times with PBSA, and permeabilized with a permeabilization buffer. Subsequently, experiments were carried out using the click‐iT RNA Alexa Fluor 488 Imaging Kit (C10329; Invitrogen) to detect the levels of newly synthesized EU.</p>", "<title>In Vivo DNase I‐TUNEL Assay</title>", "<p>The DNase I‐TUNEL assay in vivo was conducted as per a previously published article.<sup>[</sup>\n##REF##30550787##\n4\n##\n<sup>]</sup> si_<italic toggle=\"yes\">SAWPA</italic>‐1 and si_NC were injected during the 1‐cell stage, and samples were collected at the 8‐cell stage of embryonic development. The embryos were washed twice with PBSA and then subjected to in vivo permeabilization on ice for 5 min using extraction buffer (50 m<sc>m</sc> NaCl, 3 m<sc>m</sc> MgCl2, 0.5% Triton X‐100, and 300 m<sc>m</sc> sucrose, 25 m<sc>m</sc> HEPES, pH 7.4). Afterward, the embryos were washed twice with extraction buffer without Triton X‐100 and incubated with 1 U mL<sup>−1</sup> of DNase I (AM2222; Ambion) in the same buffer at 37 °C for 5 min. Following fixation, the TUNEL BrightRed Cell Apoptosis Detection Kit (A113‐01; Vazyme) was utilized to detect TUNEL cell apoptosis. TUNEL staining solution containing FITC‐conjugated staining solution and terminal deoxynucleotidyl transferase was prepared in accordance with the instructions. The embryos were washed three times with PBSA and treated with 1% Triton X‐100 in PBSA for 1 h. Subsequently, the embryos were incubated with a TUNEL staining solution at 38 °C for 1.5 h. After washing thrice with PBS, the samples were transferred to PBSA containing 10 ng µL<sup>−1</sup> Hoechst33342 for 10 min, mounted on slides with an anti‐fading solution, and examined using a fluorescence inverted microscope (ECLIPSE Ti‐S; Nikon, Japan). The experiment was repeated three times.</p>", "<title>Western Blot Analysis</title>", "<p>Each group consisted of 200 embryos at a corresponding developmental stage. The embryos were lysed for 2 h in 60 µL of lysis buffer containing 20 m<sc>m</sc> HEPES, 1 m<sc>m</sc> EDTA, 20 m<sc>m</sc> glycerol phosphate, 150 m<sc>m</sc> NaCl, 2 m<sc>m</sc> EGTA, 10% glycerol supplemented, and 1% Triton X‐100 with 0.6 µL PMSF (100 m<sc>m</sc>, ST506; Beyotime). The lysates were then boiled at 100 °C for 5 min. The resulting proteins were separated using a 12% ExpressPlus PAGE gel (TM0645; GenScript), transferred to nitrocellulose membranes (3 010 040 001; Millipore), and detected by immunoblotting. The membranes were blocked with 5% BSA in TBST at room temperature for 2 h and then incubated overnight at 4 °C with primary antibodies against JNK, pJNK, or β‐actin. The antibody dilution ratio was 1:1000. After washing with TBST, they were incubated with HRP‐conjugated secondary antibodies. The antibody dilution ratio was 1:2000. SuperSignal West Pico PLUS (34 577; Thermo) was used for chemiluminescent detection in Western blot analysis according to the manufacturer's instructions, and images were captured using MiniChemi (MiniChemi580; SAGECREATION, Beijing, China).</p>", "<title>Double Luciferase Assay</title>", "<p>Porcine kidney epithelial cells, PK15, were cultured; the interference fragment and control group were transfected into PK15 cells and cultured for 24 h. The plasmid TK was co‐transfected with <italic toggle=\"yes\">SAWPA</italic> promoter‐pGL3‐luciferase, CMV‐, <italic toggle=\"yes\">JNK</italic> SINE‐associated pGL3‐luciferase, CMV‐, and cultured for 48 h, to ensure that the cell density did not exceed 95%. The culture medium was removed, and PBS was added and washed twice by gently shaking the plate. The fluorescence intensity was measured using the Dual‐Luciferase Reporter Assay System (E1910; Promega).</p>", "<title>RNA Pull‐Down assay</title>", "<p>RNAs were in vitro‐transcribed with mMESSAGEmMACHINE T7 ULTRA Kit (AMB1345‐5; Ambion) and biotinylated with Pierce RNA 3″‐End Desthiobiotinylation Kit (20 163; Pierce) following the manufacturer's manual. A slot blot was performed to demonstrate that RNAs were efficiently biotinylated. Biotinylated RNAs (50 pmol) were heated at 85 °C for 2 min, immediately put on ice for at least 2 min, and an equal volume of RNA structure buffer (10 m<sc>m</sc> Tris pH 7.0, 0.1 <sc>m</sc> KCl, 10 m<sc>m</sc> MgCl<sub>2</sub>) was added. The samples were then shifted to RT for at least 20 min to allow proper secondary structure formation. Eight‐cell stage embryos (for pull‐down mass spectrum, 2000 embryos were used, and for pulldown Western blot, ≈500 embryos were used for each time) were digested with Pierce IP Lysis Buffer (87 787; Pierce) supplied with protease inhibitor cocktail (78 441; Pierce) according to the manufacturer's protocol. RNA pull‐down was performed by Pierce Magnetic RNA‐Protein Pull‐Down Kit (20 164; Pierce) according to the manufacturer's protocol. The retrieved protein was detected by mass spectrometry (24 600; Thermo) according to the manufacturer's protocol or Western blot test.</p>", "<title>Co‐Immunoprecipitation</title>", "<p>First, HA‐MS2P and <italic toggle=\"yes\">SAWPA</italic>‐24×MS2 vectors were transfected into PK15 cells by Lipofectamine LTX &amp; PLUS Reagent (15 338 100; Thermo). In the co‐IP experiment, Pierce Crosslink Magnetic IP/co‐IP Kit (88 805; Thermo), which had HA antibodies crosslinked to the Pierce Protein A/G Magnetic Beads, was used. First, cells were collected and washed thoroughly with PBS before dissolving 10<sup>6</sup> PK15 cells in 100 µL of IP lysis buffer. Next, 10 µL of the resulting lysate was used as input. The remaining lysate was then incubated overnight at 4 °C with Protein A/G beads that were conjugated with anti‐HA antibodies. The beads were washed twice using IP lysis buffer for 5 min each time, and subsequently, the beads were resuspended in 500 µL of ultrapure water while gently agitating. Hundred microliters of elution buffer was added to collect the supernatant containing the target antigen, which was then mixed with 15 µL of western blot sample buffer and incubated at boiling water for 5 min. Finally, MED8 and HNRNPA1 were detected through Western blot analysis.</p>", "<title>Statistical Analyses</title>", "<p>The experimental data were subjected to statistical analysis using EXCEL and GraphPad Prism 5.0 software and presented as means ± S.E.M. Between‐group comparisons were conducted using <italic toggle=\"yes\">t</italic>‐tests or Wilcoxon rank sum tests, and the significance level was indicated by <italic toggle=\"yes\">p</italic>‐values.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>T.H., J.W., Z.L., and J.‐X.J. conceived and designed the study. T.H. and D.L. performed porcine embryo collection. T.H. performed porcine embryo experiments with contributions from J.P., S.Y., D.L., S.G., Y.Z., and Z.C. T.H. performed molecule associated experiments with contributions from S.G. and Z.C. T.H. performed cell associated experiments with contributions from Y.Z. and R.W. T.H. and Y.Z. analyzed the data with contributions from J.W. J.‐X.J. and B.C.L. supervised the project. T.H. and J.W. wrote the manuscript.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank all members of the Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province for their help. Thanks to Dr. Yiwei Zhang from Northeast Agricultural University for his contribution to the analysis of experimental data, and to Dr. Chaoqian Jiang from Northeast Agricultural University for providing the experimental luciferase related vector. This work was supported by the National Natural Science Foundation of China (31970588, 32372884 and 32002179), the Natural Science Foundation of Heilongjiang Province (YQ2020C003 and YQ2020C007), and the National Key R&amp;D Program of China (2021YFA0805902).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6924-fig-0001\"><label>Figure 1</label><caption><p>SINE‐associated lncRNA demonstrates elevated expression levels during the ZGA stage in pigs. A) The box plot for the expression levels analysis of TEs‐associated lncRNA during early embryonic development in porcine (GSE163620). GV, germinal vesicle oocyst; MII, metaphase of second meiosis; 2C, 2‐cell stage; 4C, 4‐cell stage; 8C, 8‐cell stage; MO, morula; BL, 7 days blastocyst. Significant difference analyses and <italic toggle=\"yes\">p</italic>‐values can be found in Table ##SUPPL##0##S2## (Supporting Information). B) Screening of RNA seq datasets. C) The distribution of different types of TEs during the ZGA stage in porcine (GSE163620). D) Analysis of the expression levels of SINE‐associated lncRNA during early embryonic development in mice and humans (GSE138760, GSE36552). GV, germinal vesicle oocyst; MII, metaphase of second meiosis; 2C, 2‐cell stage; 4C, 4‐cell stage; 8C, 8‐cell stage; MO, morula; BL, 7 days blastocyst. Significant difference analyses and <italic toggle=\"yes\">p</italic>‐values can be found in Table ##SUPPL##0##S2## (Supporting Information).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6924-fig-0002\"><label>Figure 2</label><caption><p>\n<italic toggle=\"yes\">SAWPA</italic> is a SINE‐associated and nuclear‐located lncRNA. A) Gene locus of <italic toggle=\"yes\">SAWPA</italic>. <italic toggle=\"yes\">SAWPA</italic> is located upstream of <italic toggle=\"yes\">WDR26</italic> and in the intron region of <italic toggle=\"yes\">CNIH3</italic>. There are five SINE sequences and one LINE fragment of <italic toggle=\"yes\">L1MB7</italic>. AATAAA is the polyadenylated signal site. B) 3′ RACE and 5′ RACE results for <italic toggle=\"yes\">SAWPA</italic>. Gene‐specific primers (F3, F4, R3, and R2) are shown in Figure ##SUPPL##0##S1A## (Supporting Information). *Indicates the bands corresponding to the correct band of 3′ RACE and 5′ RACE for <italic toggle=\"yes\">SAWPA</italic>. Approximately 200 early 8‐cell embryos were used for each RACE experiment, and three experimental replicates were used. C) Subcellular localization of <italic toggle=\"yes\">SAWPA</italic> using RNA fractionation and qPCR analysis. <italic toggle=\"yes\">SAWPA</italic> is localized in the nucleus. The error bars represent S.E.M. Nuc, nucleoplasm; Cyt, cytoplasm. <italic toggle=\"yes\">GAPDH</italic> and <italic toggle=\"yes\">U6</italic> act as Cyt and Nuc control, respectively. About 200 early 8‐cell embryos were used for each experiment, and three experimental replicates were used. D) Expression pattern of <italic toggle=\"yes\">SAWPA</italic>, <italic toggle=\"yes\">WDR26</italic>, and <italic toggle=\"yes\">CNIH3</italic> at different stages of preimplantation porcine embryos analyzed using qPCR. GV, germinal vesicle oocyst; 1C, 1‐cell stage; 2C, 2‐cell stage; E4C, early 4‐cell stage; M4C, middle 4‐cell stage; L4C, late 4‐cell stage; 8C, 8‐cell stage; MO, morula; 5D, 5 days blastocyst. 6D, 6 days blastocyst; 7D, 7 days blastocyst. The error bars represent S.E.M. Approximately 50 embryos of each stage were used, and three experimental replicates were used. E) RNA‐FISH in the oocyte to blastocyst embryos for <italic toggle=\"yes\">SAWPA</italic>. <italic toggle=\"yes\">SAWPA</italic> is present in the nucleus of 8‐ to morula‐cell embryos. GV, germinal vesicle oocyst; 1C, 1‐cell stage (<italic toggle=\"yes\">n</italic> = 10 for each probe); 2C, 2‐cell stage (<italic toggle=\"yes\">n</italic> = 8 for each probe); 4C, 4‐cell stage (<italic toggle=\"yes\">n</italic> = 9 for each probe); 8C, 8‐cell stage (<italic toggle=\"yes\">n</italic> = 11 for each probe); MO, morula (<italic toggle=\"yes\">n</italic> = 10 for each probe); BL, blastocyst (<italic toggle=\"yes\">n</italic> = 10 for each probe). Scale bar, 50 µm. Three experimental replicates were used. F) Fluorescence intensity analysis showed that <italic toggle=\"yes\">SAWPA</italic> was expressed specifically in the 8‐cell and morula stages. Three experimental replicates were performed, and ≈20 embryos were used in each group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6924-fig-0003\"><label>Figure 3</label><caption><p>\n<italic toggle=\"yes\">SAWPA</italic> depletion results in developmental arrest at the 8‐cell stage with effects on ZGA initiation. A) Experimental scheme to analyze the effects of <italic toggle=\"yes\">SAWPA</italic> depletion on embryonic development. pPA, post‐parthenogenetic activation; IF, immunofluorescence. For BrdU staining, BrdU was added at pPA 56 h. For EU staining, EU was added at pPA 64 h. IF, including detection of BrdU and EU, was performed at pPA 72 h. B) RNAi efficiently mediated <italic toggle=\"yes\">SAWPA</italic> knockdown. si_<italic toggle=\"yes\">SAWPA</italic>‐1 was injected at pPA 6 h, and embryos were collected at pPA 72 h at the 8‐cell stage for qPCR analysis. The error bars represent S.E.M. Approximately 50 embryos of each stage were used, and three experimental replicates were used. <italic toggle=\"yes\">18S</italic> is an internal reference gene. C) si_<italic toggle=\"yes\">SAWPA</italic>‐1 embryos arrest at 8‐cell stage. The photographs were taken at pPA 168 h at the blastocyst stage. Embryos injected with si_NC can develop to the blastocyst stage, while si_<italic toggle=\"yes\">SAWPA</italic>‐1 embryos are arrested at the 8‐cell stage. Scale bar, 100 µm. At least three experimental replicates were performed for each RNAi injection. D) Embryonic development after microinjection. 8C, 8‐cell stage; 4–8C, 4‐ to 8‐cell stage; BL, blastocyst stage; si_, siRNA; OE, overexpression. Differences of data [mean ± standard error of the mean (s.e.m.)] were analyzed by using a two‐tailed Student's <italic toggle=\"yes\">t</italic>‐test. Specific <italic toggle=\"yes\">p</italic>‐values can be found in Table ##SUPPL##0##S3## (Supporting Information). E) EU staining indicates the abnormal major ZGA process following si_<italic toggle=\"yes\">SAWPA</italic>‐1 injected at the 1‐cell stage. EU was added to the culture medium at pPA 64 h, and EU signals were detected at pPA 72 h. The si_NC fluorescence intensity was significantly higher than that of si_<italic toggle=\"yes\">SAWPA</italic>‐1. Scale bar, 50 µm. Three experimental replicates were used. The error bars represent S.E.M. F) Expression of genes related to major ZGA initiation, such as <italic toggle=\"yes\">ACLY</italic>, <italic toggle=\"yes\">ACSS1</italic>, <italic toggle=\"yes\">ASH2L</italic>, <italic toggle=\"yes\">EIF1A</italic>, <italic toggle=\"yes\">EIF3A</italic>, <italic toggle=\"yes\">HSP70</italic>, <italic toggle=\"yes\">NID2</italic>, <italic toggle=\"yes\">PDHA1</italic>, <italic toggle=\"yes\">ZSCAN4</italic>, <italic toggle=\"yes\">SMYD3</italic>, <italic toggle=\"yes\">SQLE</italic>, and <italic toggle=\"yes\">TFIIA</italic> in comparison between si_<italic toggle=\"yes\">SAWPA</italic>‐1 and si_NC embryos. Embryos injected with RNAi were collected at pPA 72 h at the 8‐cell stage for qPCR analysis. The error bars represent S.E.M. Approximately 100 embryos were used for each group, and three experimental replicates were used. n.s., <italic toggle=\"yes\">p</italic> &gt; 0.05. <italic toggle=\"yes\">18S</italic> is an internal reference gene. G) Expression of genes related to pluripotency, such as <italic toggle=\"yes\">OCT4</italic>, <italic toggle=\"yes\">SOX2</italic>, <italic toggle=\"yes\">NANOG</italic>, and <italic toggle=\"yes\">KLF4</italic>, are expressed normally in si_<italic toggle=\"yes\">SAWPA</italic>‐1 embryos compared to that in si_NC embryos. Embryos injected with RNAi were collected at pPA 72 h at the 8‐cell stage for qPCR analysis. The error bars represent S.E.M. Approximately 100 embryos were used for each group, and three experimental replicates were used. n.s., P &gt;0.05. H) <italic toggle=\"yes\">SAWPA</italic> depletion decreased the fluorescence intensity of the TUNEL assay and nuclear volume in the 8‐cell stage. Two‐tailed Student's <italic toggle=\"yes\">t</italic>‐tests were used for statistical analysis. The number of si_NC and si_<italic toggle=\"yes\">SAWPA</italic>‐1 were 19 and 27. Three experimental replicates were used.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6924-fig-0004\"><label>Figure 4</label><caption><p>\n<italic toggle=\"yes\">SAWPA</italic> depletion results in the inhibition of the MAPK signaling pathway and downregulates the expression of the SINE‐associated gene <italic toggle=\"yes\">JNK</italic>. A) <italic toggle=\"yes\">SAWPA</italic>, <italic toggle=\"yes\">WDR26</italic>, and <italic toggle=\"yes\">CNIH3</italic> expression analysis relative to the control group after RNAi with si_NC and negative control siRNA; si_<italic toggle=\"yes\">SAWPA</italic>‐1, RNAi of <italic toggle=\"yes\">SAWPA</italic>; <italic toggle=\"yes\">si_WDR26‐3</italic>, RNAi of <italic toggle=\"yes\">WDR26</italic>; si_<italic toggle=\"yes\">CNIH3</italic>, RNAi of <italic toggle=\"yes\">CNIH3</italic>; The error bars represent S.E.M. About 50 embryos of each stage were used, and three experimental replicates were used. 18S is an internal reference gene. B) DEGs analysis based on RNA‐seq data. Compared to that in the si_NC 8‐cells, 539 genes were upregulated and 226 genes were downregulated in si_<italic toggle=\"yes\">SAWPA</italic>‐1 embryos. Approximately 400 embryos were used for each group, and two experimental replicates were used. C) KEGG pathway analysis of DEGs showed that the MAPK and PI3K‐Akt signaling pathways are mainly affected by <italic toggle=\"yes\">SAWPA</italic> depletion. D) The expression of genes related to the JNK‐MAPK or PI3K‐Akt signaling pathways was significantly affected by <italic toggle=\"yes\">SAWPA</italic> depletion. Embryos injected with si_<italic toggle=\"yes\">SAWPA</italic>‐1 were collected at pPA 72 h at the 8‐cell stage for qPCR analysis. The error bars represent S.E.M. Approximately 80 embryos were used for each group, and three experimental replicates were used. Two‐tailed Student's <italic toggle=\"yes\">t</italic>‐test was used for statistical analysis. E) Western blot and grayscale analysis indicate that the protein and phosphorylation levels of JNK and pJNK, key kinases in the MAPK signaling pathway, decreased in <italic toggle=\"yes\">SAWPA</italic>‐depleted 8‐cell. Embryos injected with si_<italic toggle=\"yes\">SAWPA</italic>‐1 and si_NC were collected at pPA 72 h at the 8‐cell stage for western blot analysis, and ≈200 embryos were used for each lane. The error bars represent S.E.M. Three experimental replicates were used. F) Embryonic development after si_<italic toggle=\"yes\">SAWPA</italic>‐1 and si_<italic toggle=\"yes\">JNK</italic> microinjection. 8C, 8‐cell stage; 4–8C, 4‐ to 8‐cell stage; BL, blastocyst stage; si_, siRNA. Differences of data [mean ± standard error of the mean (s.e.m.)] were analyzed by using a two‐tailed Student's <italic toggle=\"yes\">t</italic>‐test. Specific <italic toggle=\"yes\">p</italic>‐values can be found in Table ##SUPPL##0##S4## (Supporting Information).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6924-fig-0005\"><label>Figure 5</label><caption><p>\n<italic toggle=\"yes\">SAWPA</italic> binds to HNRNPA1 and MED8. A) <italic toggle=\"yes\">SAWPA</italic> interacts with HNRNPA1 and MED8 <italic toggle=\"yes\">in</italic>\n<italic toggle=\"yes\">vitro</italic>. The samples of RNA pull‐down experiment were subjected to SDS‐PAGE gel electrophoresis, and then the binding protein of <italic toggle=\"yes\">SAWPA</italic> and <italic toggle=\"yes\">SAWPA</italic>‐rev was analyzed by silver staining and MS. Only one pull‐down assay for mass spectrometry analysis was performed with 2000 early 8‐cell stage embryos. Two specific bands in the right lane (arrow) were analyzed through mass spectrometry and confirmed as HNRNPA1 and MED8. B) Mass spectrometry results of HNRNPA1 and MED8 were confirmed by Western blot following RNA pull‐down assay (pull‐down WB); <italic toggle=\"yes\">SAWPA</italic>‐rev, reverse sequence of <italic toggle=\"yes\">SAWPA</italic>. α‐, anti‐. For each pull‐down WB assay, ≈500 eight‐cell stage embryos were used and three experimental replicates were performed. C) Expression pattern of HNRNPA1 and MED8 at different stages of preimplantation porcine embryos analyzed using qPCR. GV, germinal vesicle oocyst; 1C, 1‐cell stage; 2C, 2‐cell stage; 4C, 4‐cell stage; 8C, 8‐cell stage; MO, morula; BL, 7 days blastocyst. The error bars represent S.E.M. Approximately 50 embryos of each stage were used, and three experimental replicates were used. D) IF assay in the oocyte to blastocyst embryos for HNRNPA1 and MED8. HNRNPA1 is present in the nucleus of 4‐cell to blastocyst‐cell embryos. MED8 is present in the nucleus of 4‐ cell to 8‐cell embryos GV, germinal vesicle oocyst (<italic toggle=\"yes\">n</italic> = 19, 13); 1C, 1‐cell stage (<italic toggle=\"yes\">n</italic> = 17, 14); 2C, 2‐cell stage (<italic toggle=\"yes\">n</italic> = 22, 21); 4C, 4‐cell stage (<italic toggle=\"yes\">n</italic> = 33, 17); 8C, 8‐cell stage (<italic toggle=\"yes\">n</italic> = 42, 23); MO, morula (<italic toggle=\"yes\">n</italic> = 48, 34); BL, blastocyst (<italic toggle=\"yes\">n</italic> = 37, 29). Scale bar, 100 µm. Three experimental replicates were used. E) Fluorescence intensity analysis showed that HNRNPA1 and MED8 were highest expressed at 8‐cell stage embryos. Three experimental replicates were performed. F) Co‐IP results in eight‐cell stage embryos (<italic toggle=\"yes\">SAWPA‐</italic>MS2 was injected at the 1‐cell stage) using anti‐HA (for HA‐labeled MS2 coat protein). The results show that <italic toggle=\"yes\">SAWPA</italic> forms an RNA‐protein complex with HNRNPA1 and MED8. <italic toggle=\"yes\">SAWPA</italic>‐rev, antisense sequence of <italic toggle=\"yes\">SAWPA</italic> overexpression; <italic toggle=\"yes\">SAWPA</italic>, <italic toggle=\"yes\">SAWPA</italic> overexpression; The primer of RT‐PCR <italic toggle=\"yes\">SAWPA</italic>‐1 were used to test <italic toggle=\"yes\">SAWPA</italic>; SINE(3), DNA sequence of 3 (SINE element of <italic toggle=\"yes\">SAWPA</italic>); For each co‐IP assay, ≈500 eight‐cell embryos were used, and three experimental replicates were performed.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6924-fig-0006\"><label>Figure 6</label><caption><p>\n<italic toggle=\"yes\">SAWPA</italic> regulates <italic toggle=\"yes\">JNK</italic> transcription by binding to MED8 and HNRNPA1 through SINE sequences. A) The SINE‐associated genes of DEGs (red arrow) and the number of SINE‐associated random genes (black) (<italic toggle=\"yes\">P</italic> &lt; 1.12e‐3) measured using the Wilcoxon rank single test. SINE‐associated genes are gene loci that contain SINE elements. The interference with <italic toggle=\"yes\">SAWPA</italic> was more likely to affect SINE‐associated genes. B) Experimental scheme to analyze the truncated sequence of <italic toggle=\"yes\">SAWPA</italic>. Mut, <italic toggle=\"yes\">SAWPA</italic> with mutation of si_<italic toggle=\"yes\">SAWPA</italic>‐1 site. WT, wild type; RT‐PCR <italic toggle=\"yes\">SAWPA</italic>; The RT‐PCR primer of <italic toggle=\"yes\">SAWPA</italic> C) Blastocyst rate of the overexpressed six RNA fragments upon <italic toggle=\"yes\">SAWPA</italic> depletion. si_<italic toggle=\"yes\">SAWPA</italic>‐1 <italic toggle=\"yes\">and</italic> si_<italic toggle=\"yes\">SAWPA</italic>‐1 <italic toggle=\"yes\">+</italic> Δ3 OE significantly decreased blastocyst rate. Three experimental replicates were used. Two‐tailed Student's <italic toggle=\"yes\">t</italic>‐test was used for statistical analysis, and the error bars represent S.E.M. D) Photographs of the overexpressed six RNA fragments upon <italic toggle=\"yes\">SAWPA</italic> depletion. The photographs were taken at pPA 168 h at the blastocyst stage. Embryos injected with si_<italic toggle=\"yes\">SAWPA</italic>‐1 <italic toggle=\"yes\">+</italic> Δ1 OE, si_<italic toggle=\"yes\">SAWPA</italic>‐1 <italic toggle=\"yes\">+</italic> Δ2 OE, OE, si_<italic toggle=\"yes\">SAWPA</italic>‐1 <italic toggle=\"yes\">+</italic> Δ4 OE, si_<italic toggle=\"yes\">SAWPA</italic>‐1 <italic toggle=\"yes\">+</italic> Δ5 OE, and si_<italic toggle=\"yes\">SAWPA</italic>‐1 <italic toggle=\"yes\">+</italic> Mut OE can develop to the blastocyst stage, while si_<italic toggle=\"yes\">SAWPA</italic>‐1 <italic toggle=\"yes\">and</italic> si_<italic toggle=\"yes\">SAWPA</italic>‐1 <italic toggle=\"yes\">+</italic> Δ3 OE embryos are arrested at the 8‐cell stage. Scale bar, 100 µm. At least three experimental replicates were used for each RNAi injection E) Co‐IP results in porcine PK15 using anti‐HA (for HA‐labeled MS2 coat protein). <italic toggle=\"yes\">SAWPA</italic> forms an RNA–protein complex with HNRNPA1 and MED8. <italic toggle=\"yes\">SAWPA</italic>‐rev, antisense sequence of <italic toggle=\"yes\">SAWPA</italic> overexpression; <italic toggle=\"yes\">SAWPA</italic>, <italic toggle=\"yes\">SAWPA</italic> overexpression; The primer of RT‐PCR <italic toggle=\"yes\">SAWPA</italic>‐1 were used to test <italic toggle=\"yes\">SAWPA</italic> except Δ2 (RT‐PCR <italic toggle=\"yes\">SAWPA</italic>‐2 were used); SINE(3), The SINE element of <italic toggle=\"yes\">SAWPA</italic>; α‐, anti. For each co‐IP assay, ≈1 × 10<sup>6</sup> porcine PK15s were used, and three experimental replicates were performed. F) Correlation between the <italic toggle=\"yes\">SAWPA</italic> sequence and the <italic toggle=\"yes\">JNK</italic> sequence. Complementary information of the sequence of exon 2 of <italic toggle=\"yes\">SAWPA</italic> and the SINE sequence of the <italic toggle=\"yes\">JNK</italic> promoter region. The SINE element located upstream and downstream of the TSS site in the <italic toggle=\"yes\">JNK</italic> promoter region is named #1‐7. Different colors represent the degree of base matching; E1, exon1. G) <italic toggle=\"yes\">SAWPA</italic> dual‐luciferase reporter system shows that <italic toggle=\"yes\">SAWPA</italic> increased the enhancer activity of SINE in PK15 cells in a special sequence. The enhancer activity of SINE is increased by overexpression of <italic toggle=\"yes\">SAWPA</italic>. The <italic toggle=\"yes\">y</italic>‐axis shows the construction of luciferase reporter plasmids and overexpressed genes. Three experimental replicates were used. Two‐tailed Student's <italic toggle=\"yes\">t</italic>‐test was used for the statistical analysis. Different letters indicate a significant difference (<italic toggle=\"yes\">p</italic> &lt; 0.01). H) Co‐IP followed by PCR assays results in porcine PK15 using anti‐MED8 and anti‐HA (for HA‐labeled MS2 coat protein). <italic toggle=\"yes\">SAWPA</italic>, <italic toggle=\"yes\">SAWPA</italic> overexpression; <italic toggle=\"yes\">SAWPA</italic>‐rev, antisense sequence of <italic toggle=\"yes\">SAWPA</italic> overexpression; SINE‐JNK, The PCR products were composed of SINE sequence (#4) and JNK; SINE(3), DNA sequence of 3 (SINE element of <italic toggle=\"yes\">SAWPA</italic>); JNK E1, exon1 of JNK. Three experimental replicates were used.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6924-fig-0007\"><label>Figure 7</label><caption><p>Model showing that <italic toggle=\"yes\">SAWPA</italic> regulates <italic toggle=\"yes\">JNK</italic> by binding to MED8 and HNRNPA1 through the SINE sequence.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6924-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Embryonic development after microinjection or inhibition treatment.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\"/><th align=\"center\" rowspan=\"1\" colspan=\"1\">Experiments [n]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Embryos [n]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">BL [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">2C arrest [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">8C arrest [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">4–8C arrest [%]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">DMSO</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">221</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">43.6 ± 5.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.9 ± 3.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">19.1 ± 4.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24.5 ± 6.9</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1 µ<sc>m</sc> TCS JNK 6o</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">308</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">44.1 ± 4.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.3 ± 2.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20.8 ± 5.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30.3 ± 7.4</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5 µ<sc>m</sc> TCS JNK 6o</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">329</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">41.4 ± 7.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.9 ± 4.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22.2 ± 7.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30.4 ± 9.3</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">10 µ<sc>m</sc> TCS JNK 6o</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">306</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27.2 ± 7.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.3 ± 1.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">39.4 ± 9.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">46.0 ± 10.5</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">20 µ<sc>m</sc> TCS JNK 6o</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">329</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">25.9 ± 8.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.2 ± 4.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">39.3 ± 6.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">46.8 ± 8.3</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">25 µ<sc>m</sc> TCS JNK 6o</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">106</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22.7 ± 3.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6.5 ± 3.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">39.4 ± 5.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">48.9 ± 5.4</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">50 µ<sc>m</sc> TCS JNK 6o</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">85</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15.4 ± 2.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12.6 ± 8.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">38.7 ± 3.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">46.8 ± 8.5</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">100 µ<sc>m</sc> TCS JNK 6o</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">95</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10.3 ± 8.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.9 ± 6.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">58.9 ± 0.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">66.3 ± 1.5</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6924-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Embryonic development about <italic toggle=\"yes\">SAWPA</italic> depletion with different lengths of <italic toggle=\"yes\">SAWPA</italic> overexpression.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\"/><th align=\"center\" rowspan=\"1\" colspan=\"1\">Experiments [n]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Embryos [n]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">BL [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">2C arrest [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">8C arrest [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">4–8C arrest [%]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">si_<italic toggle=\"yes\">SAWPA</italic>‐1‐1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">209</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.5 ± 1.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.7 ± 4.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">62.0 ± 2.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">80.5 ± 6.0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">163</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">37.7 ± 4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">7.7 ± 2.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22.0 ± 4.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">33.8 ± 6.5</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">182</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">38.3 ± 8.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.1 ± 3.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22.9 ± 3.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">33.3 ± 6.5</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">164</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.0 ± 1.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">12.4 ± 2.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">48.9 ± 1.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">60.5 ± 3.3</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">169</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">32.7 ± 1.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">9.1 ± 4.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">23.0 ± 5.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40.5 ± 6.5</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Δ5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">250</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">39.4 ± 5.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.8 ± 2.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">21.5 ± 2.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">36.8 ± 4.3</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">si_<italic toggle=\"yes\">SAWPA</italic>‐1 + Mut</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">119</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">34.7 ± 6.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10.9 ± 2.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">26.0 ± 3.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">39.4 ± 1.0</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
[]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
[]
[]
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[ "<supplementary-material id=\"advs6924-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6924-tbl1-note-0001\"><p>8C, 8‐cell stage; 4–8C, 4‐ to 8‐cell stage; BL, blastocyst stag. Differences of data [mean ± standard error of the mean (s.e.m.)] were analyzed by using a two‐tailed Student's <italic toggle=\"yes\">t</italic>‐test. Specific <italic toggle=\"yes\">p</italic>‐values can be found in Table ##SUPPL##0##S5## (Supporting Information).</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"advs6924-tbl2-note-0001\"><p>8C, 8‐cell stage; 4–8C, 4‐ to 8‐cell stage; BL, blastocyst stage; si_, siRNA. Differences of data [mean ± standard error of the mean (s.e.m.)] were analyzed by using a two‐tailed Student's <italic toggle=\"yes\">t</italic>‐test. Specific <italic toggle=\"yes\">p</italic>‐values can be found in Table ##SUPPL##0##S6## (Supporting Information).</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2307505-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
[{"label": ["10"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["F.", "M.", "X.", "X.", "H.", "X."], "surname": ["Chen", "Zhang", "Feng", "Li", "Sun", "Lu"], "source": ["Stem Cells Int"], "year": ["2021"], "volume": ["1"], "elocation-id": ["6657597"]}]
{ "acronym": [], "definition": [] }
47
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 20; 11(2):2307505
oa_package/dc/a1/PMC10787077.tar.gz
PMC10787078
37997189
[ "<title>Introduction</title>", "<p>Directed self‐assembly of materials into patterned structures is very important for many diverse areas of nanotechnology, such as, optoelectronics and sensing devices.<sup>[</sup>\n##REF##11923529##\n1\n##, ##UREF##0##\n2\n##, ##REF##12879065##\n3\n##, ##REF##27152335##\n4\n##\n<sup>]</sup> This has stimulated mass researches on the self‐assembly of block copolymers (BCPs). It is now well known that BCPs can be organized into a variety of morphologies depending on volume fraction and sequence length of the blocks, the compatibility between the components, film thickness, nature of the substrate, and preparation condition, etc.<sup>[</sup>\n##REF##22776960##\n5\n##, ##REF##12144400##\n6\n##, ##UREF##1##\n7\n##, ##REF##27152327##\n8\n##\n<sup>]</sup> A key challenge in this field is to create well‐controlled unique structures of the self‐assembled entities. Therefore, various methods have been developed to control the uniformity and directionality through molecular interactions and/or external fields.<sup>[</sup>\n##REF##27152335##\n4\n##, ##REF##25401922##\n9\n##, ##REF##25362475##\n10\n##, ##REF##24599020##\n11\n##, ##REF##18703735##\n12\n##, ##REF##18703736##\n13\n##\n<sup>]</sup> Among them, the combination of bottom‐up self‐assembly with “top‐down” patterned templates, that is, directed self‐assembly (DSA), is confirmed to offer great opportunity for a source of innovation in nanofabrication.<sup>[</sup>\n##UREF##2##\n14\n##\n<sup>]</sup> The orientation and placement of BCP domains are directed by topographically or chemically patterned templates. The specific organization of the molecules is realized though either graphoepitaxy or colloidal particles depending on the commensurability between the sphere diameter and length scale of the template.</p>", "<p>An advantage of the DSA method is the arbitrary geometrical design and the superior nanometer‐level precision of the templates. The lack of specific crystallography registration of deposited polymers to the templates makes, however, difficult to purposefully control the crystal modification of polymorphic polymers. In contrast to DSA method, epitaxy based on crystallographic matching of depositing crystalline polymers with the underlying crystalline substrates exhibits specific crystallography registration between every small molecule or chain segment of polymers in crystalline state and the substrate.<sup>[</sup>\n##UREF##3##\n15\n##, ##REF##12487579##\n16\n##\n<sup>]</sup> It can, therefore, control the orientation and position of atoms, molecules, or chain segments of polymers in the depositing layer precisely through crystallographic interactions. Taking this into account, the epitaxy‐directed crystal growth possesses the following advantages in the structure control of polymeric materials. i) The substrate can be any kind of crystalline materials, such as inorganic and organic single crystals as well as highly oriented polymer thin films,<sup>[</sup>\n##UREF##4##\n17\n##, ##UREF##5##\n18\n##, ##UREF##6##\n19\n##\n<sup>]</sup> which makes an easy fabrication and diversity selection of the templates. The substrate and the overgrowth layer can even crystallize synchronously during a single process as long as the substrate crystals form prior to the nucleation of the over layer.<sup>[</sup>\n##UREF##7##\n20\n##\n<sup>]</sup> ii) It can lead to a polymorphic polymer crystallizes in a desired crystal modification but with different molecular chain and crystal orientation.<sup>[</sup>\n##UREF##8##\n21\n##, ##UREF##9##\n22\n##, ##UREF##10##\n23\n##, ##UREF##11##\n24\n##, ##UREF##12##\n25\n##\n<sup>]</sup> Occasionally, a combination of heteroepitaxy induced by used foreign substrate and homoepitaxy triggered by early formed epitaxial crystals can even create more complicated pattern structures.<sup>[</sup>\n##UREF##13##\n26\n##\n<sup>]</sup> iii) The epitaxy‐directed crystal growth can be achieved from different initial states including vapor, amorphous glassy, and melt phases as well as by solution crystallization,<sup>[</sup>\n##UREF##8##\n21\n##, ##UREF##9##\n22\n##, ##UREF##10##\n23\n##, ##UREF##11##\n24\n##, ##UREF##12##\n25\n##, ##UREF##13##\n26\n##, ##UREF##14##\n27\n##\n<sup>]</sup> which endows the self‐repairing capability of the oriented structures simply through melt‐recrystallization.<sup>[</sup>\n##UREF##15##\n28\n##\n<sup>]</sup> This benefits for different processes and is of great significance to extend their lifetime and reduce maintenance costs. iv) The epitaxy‐directed crystal growth can even be realized during in situ polymerization,<sup>[</sup>\n##UREF##16##\n29\n##\n<sup>]</sup> which can simplify the fabrication process and avoid the processing‐caused structural damage or foreign impurities.</p>", "<p>In spite of the aforementioned advantages, there is relatively little research on epitaxy directed crystallization of copolymers. De Rosa et al.<sup>[</sup>\n##UREF##17##\n30\n##, ##REF##10839533##\n31\n##\n<sup>]</sup> have first studied the self‐organization of BCPs containing crystallizable polyethylene (PE) blocks. Based on the directional solidification from eutectic solution of crystallizable organic solvent for the strongly segregated semicrystalline BCPs, large area 2D periodic thin films with uniformly aligned cylindrical domains have been fabricated. They have further conducted the epitaxy‐template‐crystallization of a crystalline–crystalline BCP containing PE and syndiotactic polypropylene (sPP) blocks, that is, PE‐<italic toggle=\"yes\">b</italic>‐sPP copolymer on <italic toggle=\"yes\">p</italic>‐terphenyl single crystal surface.<sup>[</sup>\n##UREF##18##\n32\n##\n<sup>]</sup> It has been demonstrated that oriented lamellar structure of both PE and sPP blocks can be produced. The orientation of both blocks depends on the crystallization sequence. When sPP crystallized first, parallel‐aligned lamellar structure of both sPP and PE was observed. On the other hand, cross‐hatched lamellar structure was obtained if PE block crystallizes before sPP. This is related to the intrinsic different epitaxial orientation of sPP and PE on the <italic toggle=\"yes\">p</italic>‐terphenyl crystals in the way that the epitaxially crystallized block determines the orientation of the other block via confined crystallization of it. Here, we demonstrate the capability of epitaxy to direct the alignment of not only crystalline–crystalline BCPs but also polymer blends. Considering the wide applications of polymer blends, such as the donor and acceptor in photovoltaic devices, the self‐assembly of polymer blends into patterned structures is of even great importance. To this end, poly(ε‐carolactone)‐<italic toggle=\"yes\">b</italic>‐methoxy‐poly(ethylene glycol) (PCL‐<italic toggle=\"yes\">b</italic>‐PEG) diblock and poly(ε‐carolactone)‐<italic toggle=\"yes\">b</italic>‐poly(butylene adipate)‐<italic toggle=\"yes\">b</italic>‐poly(ε‐carolactone) (PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL) triblock copolymers with different block lengths were synthesized. For direct comparison, the capability of oriented alignment of PCL/PBA blend through epitaxial crystallization was also checked.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Epitaxy‐Directed Self‐Assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL on Oriented PE Films</title>", "<title>Morphologies of PCL and PBA Grown on Oriented PE Thin Films</title>", "<p>The epitaxial crystallization of PCL and PBA homopolymers on oriented PE has been reported previously.<sup>[</sup>\n##UREF##8##\n21\n##, ##UREF##19##\n33\n##, ##UREF##20##\n34\n##\n<sup>]</sup> For the completeness and legibility of this article, <bold>Figure</bold>\n##FIG##0##\n1\n## presents the representative AFM phase images showing the morphologies of PCL (Figure ##FIG##0##1a##) and PBA (Figure ##FIG##0##1b##) crystallized on oriented PE thin films. It is clear that the oriented PE substrate can induce epitaxial crystallization of both PCL and PBA, which results in a parallel alignment of PCL and PBA edge‐on lamellae perpendicular to the PE molecular chain direction, i.e., a parallel chain arrangement of both PCL and PBA along the PE chain direction, which has been supported by the corresponding electron diffraction via the same orientation of (00l) reflections for PCL, PBA, and PE.<sup>[</sup>\n##UREF##8##\n21\n##, ##UREF##19##\n33\n##\n<sup>]</sup> Therefore, highly oriented edge‐on lamellar structure is expected also for the PCL and PBA blocks in the PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL triblock copolymers.</p>", "<title>Morphologies of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL Crystallized on Oriented PE Thin Films</title>", "<p>\n<bold>Figure</bold>\n##FIG##1##\n2\n## shows the AFM height and phase images of a PCL(13.5k)‐<italic toggle=\"yes\">b</italic>‐PBA(11k)‐<italic toggle=\"yes\">b</italic>‐PCL(13.5k) triblock copolymer grown isothermally on highly oriented PE substrate at 37.5 °C, respectively. Parallel aligned edge‐on lamellar structure can be clearly seen in both the height (Figure ##FIG##1##2a##) and phase (Figure ##FIG##1##2b##) images, indicating the occurrence of epitaxial crystallization of both PCL and PBA blocks on PE substrate, resulting in the directed self‐assembly of the copolymer. The corresponding electron diffraction pattern shown in Figure ##FIG##1##2c## displays the well‐defined reflection spots of both PCL and PBA blocks as well as the highly oriented PE substrate, confirming the high orientation of both PCL and PBA blocks in the copolymer on the oriented PE film. Moreover, the alignment of (00l) diffraction spots for PCL and PBA crystals in the same direction of PE (002) diffraction demonstrates the same crystallographic <italic toggle=\"yes\">c</italic>‐axis orientation of PCL and PBA crystals with PE ones, i.e., the parallel chain alignment of PCL and PBA blocks in the copolymer along the PE chain like each homopolymer. From the AFM height profile shown in Figure ##FIG##1##2d##, it can be seen that the parallel aligned PCL and PBA lamellae exhibit nice periodicity in nanometer scale. The corresponding full width at half‐maximum (FWHM) distribution obtained from Figure ##FIG##1##2d## is presented in Figure ##FIG##1##2e##.</p>", "<p>It should be noted that the PE substrate caused self‐assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL BCPs is not block length dependent, as shown in Figure ##SUPPL##0##S1## (Supporting Information). Also the polymorphic behavior PBA blocks in the copolymers has been controlled, i.e., the growth of β‐PBA crystals regardless of crystallization temperature, like the PBA homopolymer grown epitaxially on oriented PE substrate.<sup>[</sup>\n##UREF##8##\n21\n##\n<sup>]</sup> Moreover, the patterned thin film exhibits a quite smooth surface with an ultralow surface roughness of only ≈1.4 nm (see <bold>Table</bold>\n##TAB##0##\n1\n##), which is reported to be crucial for many systems, such as Low Voltage Non‐Volatile Polymer Memory.<sup>[</sup>\n##UREF##21##\n35\n##\n<sup>]</sup> Most importantly, the long period and surface roughness of the unique oriented structure can be simply regulated by controlling the crystallization temperature. As summarized in Table ##TAB##0##1##, with decreasing crystallization temperature, the long period decreases from 22 nm (grown at 37.5 °C) to 19.8 nm (grown at 32.5 °C), while the roughness declines from 1.43 to 1.30 nm. The decrease of long period with decreasing crystallization temperature rests on the dependence of lamellar thickness on crystallization temperature according to the L−H model,<sup>[</sup>\n##UREF##22##\n36\n##\n<sup>]</sup> i.e., Equation (##FORMU##0##1##):\nwhere <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>T</mml:mi><mml:mi mathvariant=\"normal\">m</mml:mi><mml:mn>0</mml:mn></mml:msubsup></mml:mrow></mml:math> is the equilibrium melting temperature, σ<sub>e</sub> is the folding surface free energy, Δ<italic toggle=\"yes\">H</italic>\n<sub>m</sub> is the heat of fusion, <italic toggle=\"yes\">c</italic> is a constant, and <italic toggle=\"yes\">l</italic>\n<sub>c</sub> is the lamellar thickness obtained at crystallization temperature <italic toggle=\"yes\">T</italic>\n<sub>c</sub>.</p>", "<title>Directed Self‐Assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PEG Copolymer on Oriented PE Film</title>", "<p>The self‐assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL copolymer on oriented PE film is based on the epitaxial capability of both PCL and PBA blocks on highly oriented PE substrate with exactly the same crystallographic orientation feature. One may argue that both blocks of a copolymer exhibiting exactly the same mutual chain orientation relationship with one substrate is seldom satisfied, and thus the method can be applied only to very limited systems. This is actually not the case. We have confirmed that it is also effective for copolymers with only one block can grow epitaxially. Here, the PCL‐<italic toggle=\"yes\">b</italic>‐PEG diblock copolymer has been taken as an example. It is confirmed that the PE substrate cannot induce the epitaxial crystallization of PEG. As presented in Figure ##SUPPL##0##S3## (Supporting Information), the PEG grown on PE substrate shows the same spherulitic morphology as on glass slide surface, indicating the incapability of PE for inducing PEG epitaxial crystallization. However, as presented in <bold>Figure</bold>\n##FIG##2##\n3a,b##, the PCL(50k)‐<italic toggle=\"yes\">b</italic>‐PEG(1.9k) diblock copolymer crystallized on oriented PE substrate creates also a parallel aligned edge‐on lamellar structure similar to that of the PCL–PBA triblock copolymer. The corresponding wide angle X‐ray diffraction (WAXD) pattern shown in Figure ##FIG##2##3c## confirms the orientation of both blocks in copolymer unambiguously. In the WAXD pattern, the inner most diffraction arc is contributed by (120) lattice planes of PEG block, which disappears at 54 °C (Figure ##SUPPL##0##S4##, Supporting Information) since it has a lower molecular weight of only 1.9k and thus a relatively lower melting point. The appearance of (120)<sub>PEG</sub>, (110)<sub>PCL</sub>, and (200)<sub>PCL</sub> in the same direction perpendicular to the PE chain direction demonstrates a parallel chain alignment of both PCL and PEG blocks along PE chain direction. The inset of Figure ##FIG##2##3b## shows an enlarged part marked by a yellow rectangle in upper‐right corner. It is measured that the length corresponding to 43 parallel aligned lamellae is ≈695 nm. This means that the periodicity of the parallel arranged lamellae is ≈16.2 nm.</p>", "<p>To figure out the specific distribution of PCL and PEG blocks in the film grown on the PE substrate, small angle X‐ray scattering (SAXS) experiments were conducted. <bold>Figure</bold>\n##FIG##3##\n4\n## presents the 2D SAXS patterns of the PCL(50k)‐b‐PEG(1.9k) diblock copolymer grown on PE but after removing the PE substrate taken at different temperatures. The appearance of second‐order scattering in the SAXS pattern indicates a high degree of crystal orientation for both PCL and PEG blocks. To get quantitative information about the periodic structure, the 2D‐SAXS patterns shown in Figure ##FIG##3##4## have been converted into 1D‐SAXS profiles as presented in Figure ##SUPPL##0##S5## (Supporting Information). According to the second peak of the 1D‐SAXS profile taken at room temperature shown in Figure ##SUPPL##0##S5a## (Supporting Information) a long period of 16.5 nm has been obtained. It corresponds clearly to the periodicity of the parallel arranged alternative PCL and PEG lamellae shown in Figure ##FIG##2##3b##. The second peak disappears at 55 °C due to the melting of PEG crystals while the first peak remains essentially unchanged. The long period obtained from the first peak is approximately 31 nm, which is about two times of that acquired from the second peak. This refers unambiguously an alternatively arranged PCL and PEG lamellar structure. This illustrates the capability of epitaxy‐directed self‐assembly for fabricating perpendicularly and alternatively arranged lamellar phase separation structure of copolymers with even only one component exhibiting epitaxial crystallization ability. It should be noticed that the oriented self‐assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PEG diblock copolymers on PE substrate is also independent of PCL and PEG sequence length (Figure ##SUPPL##0##S6##, Supporting Information) and the phase size (i.e., lamellar thickness or long period) is directly related to the crystallization temperature as well.</p>", "<title>Directed Self‐Assembly of PCL/PBA Blend on Oriented PE Film</title>", "<p>It should be mentioned that the synergistic control of phase separation behavior and intrinsic structures of each component for blend systems is also very important in many cases. For example, Shah and Ganesan reported that the most desirable morphology for a photovoltaic device based on semiconductive polymers is the perpendicularly oriented and alternatively distributed donor and acceptor lamellar phases with optimal domain size of 10–25 nm.<sup>[</sup>\n##UREF##23##\n37\n##\n<sup>]</sup> This has been confirmed to be successfully realized by epitaxy‐directed self‐assembly. Taken the PCL/PBA blend on oriented PE substrate as an example, <bold>Figure</bold>\n##FIG##4##\n5a,b## shows the AFM height and phase images of a PBA/PCL (50/50 wt.%) blend crystallized isothermally on oriented PE substrate at 20 °C. Periodically aligned edge‐on lamellar structure of PBA/PCL blend on PE substrate can be clearly observed with lamellae oriented perpendicular to the molecular chain direction of PE. The corresponding electron diffraction pattern (Figure ##FIG##4##5c##) shows the well‐defined reflection spots of PBA, PCL, and PE, demonstrating the high degree of orientation of both PBA and PCL components in the blend on ordered PE substrate. The appearance of (003)<sub>PBA</sub>, (004)<sub>PCL</sub>, and (002)<sub>PE</sub> diffractions in the same direction confirms a parallel alignment of both PBA and PCL molecular chains along the PE chain direction. This is further confirmed by the polarized infrared spectra shown in Figure ##FIG##4##5d##. Furthermore, according to Figure ##FIG##4##5d##, an orientation function can be obtained by Equation (##FORMU##1##2##).<sup>[</sup>\n##UREF##10##\n23\n##, ##UREF##24##\n38\n##\n<sup>]</sup>\nwhere <italic toggle=\"yes\">I</italic>\n<sub>//</sub> and <italic toggle=\"yes\">I</italic>\n<sub>⊥</sub> are the intensities of the interested band measured with electron vectors parallel (0°) and perpendicular (90°) to the reference direction (here the molecular chain direction of PE substrate), while <italic toggle=\"yes\">α</italic> is the angle between the transition moment vector of the used band and the molecular chain axis, which is 90° for both the 1245 cm<sup>−1</sup> band of PCL and 1263 cm<sup>−1</sup> band of PBA. The obtained orientation functions of PCL and PBA are 0.87 and 0.86, respectively, reflecting a high degree of orientation for both of PCL and PBA.</p>", "<p>The above AFM and polarized FTIR results demonstrate the epitaxial crystallization of both components in PCL/PBA blend on oriented PE substrate, which result in the ordered edge‐on lamellar structure. They can, however, not provide the information about the phase distribution of PCL and PBA. To find out this, small angle X‐ray scattering (SAXS) and AFM experiments during selective melting of PBA were conducted. As presented in <bold>Figure</bold>\n##FIG##5##\n6\n##, the AFM phase image taken at room temperature (Figure ##FIG##5##6a##) shows tightly stacked edge‐on lamellae. The corresponding phase profiles along the white lines in the phase image demonstrate a long period of the sample crystallized at 25 °C to be ≈18.4 nm, which becomes ≈36 nm after selective melting of the PBA crystals at 54 °C (Figure ##FIG##5##6b##. An approximately doubled long period after melting of PBA indicates an alternative distribution of the PCL and PBA lamellae as schematically displayed in the right panel below the phase profiles, i.e., the formation of an alternatively arranged PCL and PBA lamellar structure. This has further been confirmed by the SAXS conducted at room temperature and 54 °C (Figure ##FIG##5##6c,d##). Even though the calculated long periods from SAXS of 18.7 and 36.5 nm, respectively, are slightly larger than those obtained from AFM results, the multiplied long period after melting of PBA supports the alternative arrangement of the PCL and PBA lamellae.</p>", "<p>The perpendicular and alternative arrangement of the PCL and PBA lamellae has the following advantages. First, as summarized in <bold>Table</bold>\n##TAB##1##\n2\n##, the long period of the lamellar pattern, i.e., the domain size of PCL and PBA, can be simply regulated by control the crystallization temperature. This rests on the crystallization‐temperature‐dependent PCL and PBA lamellar thicknesses, namely the higher the temperature, the thicker the lamellar thickness. Second, it is well documented that the PBA is a polymorphic polymer exhibiting α and β phases grown at high (&gt;40 °C) and low (&lt;28 °C) temperatures during melt crystallization, respectively. By crystallizing the PBA/PCL blend on oriented PE substrate, except for the same parallel chain alignment of PCL and PBA along PE chain direction, the PBA crystallizes always in its β phase regardless of temperature.</p>", "<title>Directed Self‐Assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PEG Copolymer on Oriented iPP</title>", "<p>All of the examples shown above illustrate the ability of epitaxy‐directed self‐assembly of copolymers and polymer blends for generating parallel‐aligned lamellar structure with tunable domain size of alternatively and perpendicularly separated phases, as well as the crystal modification and parallel chain alignment of each component. The epitaxy‐directed self‐assembly has also another advantage. As emphasized in the introduction part, it can realize different molecular chain and crystal orientation of deposit polymer depending on the specific crystallographic interaction of it with the substrate crystals.<sup>[</sup>\n##UREF##8##\n21\n##, ##UREF##9##\n22\n##, ##UREF##10##\n23\n##, ##UREF##11##\n24\n##, ##UREF##12##\n25\n##\n<sup>]</sup> We have taken the PCL‐<italic toggle=\"yes\">b</italic>‐PEG copolymer as an example again and checked the crystalline morphology of it grown on an oriented iPP substrate. It is well documented that epitaxial crystallization of PCL on oriented iPP substrate results in the formation of a cross‐hatched lamellar pattern with the PCL lamellae ± 40° apart from the molecular chain direction of iPP as illustrated in Figure ##SUPPL##0##S8## (Supporting Information).<sup>[</sup>\n##UREF##20##\n34\n##, ##UREF##25##\n39\n##\n<sup>]</sup> In other words, the PCL and iPP chains are inclined to an angle of ± 50°. On the other hand, it has been confirmed that the PEG does not exhibit epitaxial ability on iPP substrate as well. <bold>Figure</bold>\n##FIG##6##\n7\n## presents AFM phase images of a PCL(10k)‐<italic toggle=\"yes\">b</italic>‐PEG(10k) copolymer crystallized from its 0.5 wt.% chloroform solution spin‐coated on the surface of an oriented iPP substrate. Like the PCL grown on the iPP substrate (Figure ##SUPPL##0##S8##, Supporting Information), similar cross‐hatched lamellar structure of PCL‐<italic toggle=\"yes\">b</italic>‐PEG copolymer is observed on the oriented iPP substrate (Figure ##FIG##6##7a##). To reveal the exact phase structure of the copolymer, the obvious lamellar thickening of PEG, which not evident for PCL (cf. Figure ##SUPPL##0##S9##, Supporting Information), during heating was utilized. As presented in Figure ##FIG##6##7b##, when heating the sample shown in Figure ##FIG##6##7a## from room temperature up to 56 °C, the AFM phase image becomes more clearly due to the structure reorganization or secondary crystallization. Moreover, owing to the lamellar thickening of PEG block, the phase structure can now be clearly identified (see the enlarged inset of Figure ##FIG##6##7b##). It is evident that the epitaxial crystallization of PCL on iPP substrate promotes a similar organization of the PEG blocks even though without epitaxy ability on iPP, which is more clearly seen after the melting of crystals corresponding to PCL blocks at 58 °C (Figure ##FIG##6##7c##). It should be emphasized that similar cross‐hatched lamellar assembly can be reconstructed after melting of both components and recrystallization during cooling, indicating its independence of crystallization pathway.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Epitaxy‐Directed Self‐Assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL on Oriented PE Films</title>", "<title>Morphologies of PCL and PBA Grown on Oriented PE Thin Films</title>", "<p>The epitaxial crystallization of PCL and PBA homopolymers on oriented PE has been reported previously.<sup>[</sup>\n##UREF##8##\n21\n##, ##UREF##19##\n33\n##, ##UREF##20##\n34\n##\n<sup>]</sup> For the completeness and legibility of this article, <bold>Figure</bold>\n##FIG##0##\n1\n## presents the representative AFM phase images showing the morphologies of PCL (Figure ##FIG##0##1a##) and PBA (Figure ##FIG##0##1b##) crystallized on oriented PE thin films. It is clear that the oriented PE substrate can induce epitaxial crystallization of both PCL and PBA, which results in a parallel alignment of PCL and PBA edge‐on lamellae perpendicular to the PE molecular chain direction, i.e., a parallel chain arrangement of both PCL and PBA along the PE chain direction, which has been supported by the corresponding electron diffraction via the same orientation of (00l) reflections for PCL, PBA, and PE.<sup>[</sup>\n##UREF##8##\n21\n##, ##UREF##19##\n33\n##\n<sup>]</sup> Therefore, highly oriented edge‐on lamellar structure is expected also for the PCL and PBA blocks in the PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL triblock copolymers.</p>", "<title>Morphologies of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL Crystallized on Oriented PE Thin Films</title>", "<p>\n<bold>Figure</bold>\n##FIG##1##\n2\n## shows the AFM height and phase images of a PCL(13.5k)‐<italic toggle=\"yes\">b</italic>‐PBA(11k)‐<italic toggle=\"yes\">b</italic>‐PCL(13.5k) triblock copolymer grown isothermally on highly oriented PE substrate at 37.5 °C, respectively. Parallel aligned edge‐on lamellar structure can be clearly seen in both the height (Figure ##FIG##1##2a##) and phase (Figure ##FIG##1##2b##) images, indicating the occurrence of epitaxial crystallization of both PCL and PBA blocks on PE substrate, resulting in the directed self‐assembly of the copolymer. The corresponding electron diffraction pattern shown in Figure ##FIG##1##2c## displays the well‐defined reflection spots of both PCL and PBA blocks as well as the highly oriented PE substrate, confirming the high orientation of both PCL and PBA blocks in the copolymer on the oriented PE film. Moreover, the alignment of (00l) diffraction spots for PCL and PBA crystals in the same direction of PE (002) diffraction demonstrates the same crystallographic <italic toggle=\"yes\">c</italic>‐axis orientation of PCL and PBA crystals with PE ones, i.e., the parallel chain alignment of PCL and PBA blocks in the copolymer along the PE chain like each homopolymer. From the AFM height profile shown in Figure ##FIG##1##2d##, it can be seen that the parallel aligned PCL and PBA lamellae exhibit nice periodicity in nanometer scale. The corresponding full width at half‐maximum (FWHM) distribution obtained from Figure ##FIG##1##2d## is presented in Figure ##FIG##1##2e##.</p>", "<p>It should be noted that the PE substrate caused self‐assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL BCPs is not block length dependent, as shown in Figure ##SUPPL##0##S1## (Supporting Information). Also the polymorphic behavior PBA blocks in the copolymers has been controlled, i.e., the growth of β‐PBA crystals regardless of crystallization temperature, like the PBA homopolymer grown epitaxially on oriented PE substrate.<sup>[</sup>\n##UREF##8##\n21\n##\n<sup>]</sup> Moreover, the patterned thin film exhibits a quite smooth surface with an ultralow surface roughness of only ≈1.4 nm (see <bold>Table</bold>\n##TAB##0##\n1\n##), which is reported to be crucial for many systems, such as Low Voltage Non‐Volatile Polymer Memory.<sup>[</sup>\n##UREF##21##\n35\n##\n<sup>]</sup> Most importantly, the long period and surface roughness of the unique oriented structure can be simply regulated by controlling the crystallization temperature. As summarized in Table ##TAB##0##1##, with decreasing crystallization temperature, the long period decreases from 22 nm (grown at 37.5 °C) to 19.8 nm (grown at 32.5 °C), while the roughness declines from 1.43 to 1.30 nm. The decrease of long period with decreasing crystallization temperature rests on the dependence of lamellar thickness on crystallization temperature according to the L−H model,<sup>[</sup>\n##UREF##22##\n36\n##\n<sup>]</sup> i.e., Equation (##FORMU##0##1##):\nwhere <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>T</mml:mi><mml:mi mathvariant=\"normal\">m</mml:mi><mml:mn>0</mml:mn></mml:msubsup></mml:mrow></mml:math> is the equilibrium melting temperature, σ<sub>e</sub> is the folding surface free energy, Δ<italic toggle=\"yes\">H</italic>\n<sub>m</sub> is the heat of fusion, <italic toggle=\"yes\">c</italic> is a constant, and <italic toggle=\"yes\">l</italic>\n<sub>c</sub> is the lamellar thickness obtained at crystallization temperature <italic toggle=\"yes\">T</italic>\n<sub>c</sub>.</p>", "<title>Directed Self‐Assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PEG Copolymer on Oriented PE Film</title>", "<p>The self‐assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL copolymer on oriented PE film is based on the epitaxial capability of both PCL and PBA blocks on highly oriented PE substrate with exactly the same crystallographic orientation feature. One may argue that both blocks of a copolymer exhibiting exactly the same mutual chain orientation relationship with one substrate is seldom satisfied, and thus the method can be applied only to very limited systems. This is actually not the case. We have confirmed that it is also effective for copolymers with only one block can grow epitaxially. Here, the PCL‐<italic toggle=\"yes\">b</italic>‐PEG diblock copolymer has been taken as an example. It is confirmed that the PE substrate cannot induce the epitaxial crystallization of PEG. As presented in Figure ##SUPPL##0##S3## (Supporting Information), the PEG grown on PE substrate shows the same spherulitic morphology as on glass slide surface, indicating the incapability of PE for inducing PEG epitaxial crystallization. However, as presented in <bold>Figure</bold>\n##FIG##2##\n3a,b##, the PCL(50k)‐<italic toggle=\"yes\">b</italic>‐PEG(1.9k) diblock copolymer crystallized on oriented PE substrate creates also a parallel aligned edge‐on lamellar structure similar to that of the PCL–PBA triblock copolymer. The corresponding wide angle X‐ray diffraction (WAXD) pattern shown in Figure ##FIG##2##3c## confirms the orientation of both blocks in copolymer unambiguously. In the WAXD pattern, the inner most diffraction arc is contributed by (120) lattice planes of PEG block, which disappears at 54 °C (Figure ##SUPPL##0##S4##, Supporting Information) since it has a lower molecular weight of only 1.9k and thus a relatively lower melting point. The appearance of (120)<sub>PEG</sub>, (110)<sub>PCL</sub>, and (200)<sub>PCL</sub> in the same direction perpendicular to the PE chain direction demonstrates a parallel chain alignment of both PCL and PEG blocks along PE chain direction. The inset of Figure ##FIG##2##3b## shows an enlarged part marked by a yellow rectangle in upper‐right corner. It is measured that the length corresponding to 43 parallel aligned lamellae is ≈695 nm. This means that the periodicity of the parallel arranged lamellae is ≈16.2 nm.</p>", "<p>To figure out the specific distribution of PCL and PEG blocks in the film grown on the PE substrate, small angle X‐ray scattering (SAXS) experiments were conducted. <bold>Figure</bold>\n##FIG##3##\n4\n## presents the 2D SAXS patterns of the PCL(50k)‐b‐PEG(1.9k) diblock copolymer grown on PE but after removing the PE substrate taken at different temperatures. The appearance of second‐order scattering in the SAXS pattern indicates a high degree of crystal orientation for both PCL and PEG blocks. To get quantitative information about the periodic structure, the 2D‐SAXS patterns shown in Figure ##FIG##3##4## have been converted into 1D‐SAXS profiles as presented in Figure ##SUPPL##0##S5## (Supporting Information). According to the second peak of the 1D‐SAXS profile taken at room temperature shown in Figure ##SUPPL##0##S5a## (Supporting Information) a long period of 16.5 nm has been obtained. It corresponds clearly to the periodicity of the parallel arranged alternative PCL and PEG lamellae shown in Figure ##FIG##2##3b##. The second peak disappears at 55 °C due to the melting of PEG crystals while the first peak remains essentially unchanged. The long period obtained from the first peak is approximately 31 nm, which is about two times of that acquired from the second peak. This refers unambiguously an alternatively arranged PCL and PEG lamellar structure. This illustrates the capability of epitaxy‐directed self‐assembly for fabricating perpendicularly and alternatively arranged lamellar phase separation structure of copolymers with even only one component exhibiting epitaxial crystallization ability. It should be noticed that the oriented self‐assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PEG diblock copolymers on PE substrate is also independent of PCL and PEG sequence length (Figure ##SUPPL##0##S6##, Supporting Information) and the phase size (i.e., lamellar thickness or long period) is directly related to the crystallization temperature as well.</p>", "<title>Directed Self‐Assembly of PCL/PBA Blend on Oriented PE Film</title>", "<p>It should be mentioned that the synergistic control of phase separation behavior and intrinsic structures of each component for blend systems is also very important in many cases. For example, Shah and Ganesan reported that the most desirable morphology for a photovoltaic device based on semiconductive polymers is the perpendicularly oriented and alternatively distributed donor and acceptor lamellar phases with optimal domain size of 10–25 nm.<sup>[</sup>\n##UREF##23##\n37\n##\n<sup>]</sup> This has been confirmed to be successfully realized by epitaxy‐directed self‐assembly. Taken the PCL/PBA blend on oriented PE substrate as an example, <bold>Figure</bold>\n##FIG##4##\n5a,b## shows the AFM height and phase images of a PBA/PCL (50/50 wt.%) blend crystallized isothermally on oriented PE substrate at 20 °C. Periodically aligned edge‐on lamellar structure of PBA/PCL blend on PE substrate can be clearly observed with lamellae oriented perpendicular to the molecular chain direction of PE. The corresponding electron diffraction pattern (Figure ##FIG##4##5c##) shows the well‐defined reflection spots of PBA, PCL, and PE, demonstrating the high degree of orientation of both PBA and PCL components in the blend on ordered PE substrate. The appearance of (003)<sub>PBA</sub>, (004)<sub>PCL</sub>, and (002)<sub>PE</sub> diffractions in the same direction confirms a parallel alignment of both PBA and PCL molecular chains along the PE chain direction. This is further confirmed by the polarized infrared spectra shown in Figure ##FIG##4##5d##. Furthermore, according to Figure ##FIG##4##5d##, an orientation function can be obtained by Equation (##FORMU##1##2##).<sup>[</sup>\n##UREF##10##\n23\n##, ##UREF##24##\n38\n##\n<sup>]</sup>\nwhere <italic toggle=\"yes\">I</italic>\n<sub>//</sub> and <italic toggle=\"yes\">I</italic>\n<sub>⊥</sub> are the intensities of the interested band measured with electron vectors parallel (0°) and perpendicular (90°) to the reference direction (here the molecular chain direction of PE substrate), while <italic toggle=\"yes\">α</italic> is the angle between the transition moment vector of the used band and the molecular chain axis, which is 90° for both the 1245 cm<sup>−1</sup> band of PCL and 1263 cm<sup>−1</sup> band of PBA. The obtained orientation functions of PCL and PBA are 0.87 and 0.86, respectively, reflecting a high degree of orientation for both of PCL and PBA.</p>", "<p>The above AFM and polarized FTIR results demonstrate the epitaxial crystallization of both components in PCL/PBA blend on oriented PE substrate, which result in the ordered edge‐on lamellar structure. They can, however, not provide the information about the phase distribution of PCL and PBA. To find out this, small angle X‐ray scattering (SAXS) and AFM experiments during selective melting of PBA were conducted. As presented in <bold>Figure</bold>\n##FIG##5##\n6\n##, the AFM phase image taken at room temperature (Figure ##FIG##5##6a##) shows tightly stacked edge‐on lamellae. The corresponding phase profiles along the white lines in the phase image demonstrate a long period of the sample crystallized at 25 °C to be ≈18.4 nm, which becomes ≈36 nm after selective melting of the PBA crystals at 54 °C (Figure ##FIG##5##6b##. An approximately doubled long period after melting of PBA indicates an alternative distribution of the PCL and PBA lamellae as schematically displayed in the right panel below the phase profiles, i.e., the formation of an alternatively arranged PCL and PBA lamellar structure. This has further been confirmed by the SAXS conducted at room temperature and 54 °C (Figure ##FIG##5##6c,d##). Even though the calculated long periods from SAXS of 18.7 and 36.5 nm, respectively, are slightly larger than those obtained from AFM results, the multiplied long period after melting of PBA supports the alternative arrangement of the PCL and PBA lamellae.</p>", "<p>The perpendicular and alternative arrangement of the PCL and PBA lamellae has the following advantages. First, as summarized in <bold>Table</bold>\n##TAB##1##\n2\n##, the long period of the lamellar pattern, i.e., the domain size of PCL and PBA, can be simply regulated by control the crystallization temperature. This rests on the crystallization‐temperature‐dependent PCL and PBA lamellar thicknesses, namely the higher the temperature, the thicker the lamellar thickness. Second, it is well documented that the PBA is a polymorphic polymer exhibiting α and β phases grown at high (&gt;40 °C) and low (&lt;28 °C) temperatures during melt crystallization, respectively. By crystallizing the PBA/PCL blend on oriented PE substrate, except for the same parallel chain alignment of PCL and PBA along PE chain direction, the PBA crystallizes always in its β phase regardless of temperature.</p>", "<title>Directed Self‐Assembly of PCL‐<italic toggle=\"yes\">b</italic>‐PEG Copolymer on Oriented iPP</title>", "<p>All of the examples shown above illustrate the ability of epitaxy‐directed self‐assembly of copolymers and polymer blends for generating parallel‐aligned lamellar structure with tunable domain size of alternatively and perpendicularly separated phases, as well as the crystal modification and parallel chain alignment of each component. The epitaxy‐directed self‐assembly has also another advantage. As emphasized in the introduction part, it can realize different molecular chain and crystal orientation of deposit polymer depending on the specific crystallographic interaction of it with the substrate crystals.<sup>[</sup>\n##UREF##8##\n21\n##, ##UREF##9##\n22\n##, ##UREF##10##\n23\n##, ##UREF##11##\n24\n##, ##UREF##12##\n25\n##\n<sup>]</sup> We have taken the PCL‐<italic toggle=\"yes\">b</italic>‐PEG copolymer as an example again and checked the crystalline morphology of it grown on an oriented iPP substrate. It is well documented that epitaxial crystallization of PCL on oriented iPP substrate results in the formation of a cross‐hatched lamellar pattern with the PCL lamellae ± 40° apart from the molecular chain direction of iPP as illustrated in Figure ##SUPPL##0##S8## (Supporting Information).<sup>[</sup>\n##UREF##20##\n34\n##, ##UREF##25##\n39\n##\n<sup>]</sup> In other words, the PCL and iPP chains are inclined to an angle of ± 50°. On the other hand, it has been confirmed that the PEG does not exhibit epitaxial ability on iPP substrate as well. <bold>Figure</bold>\n##FIG##6##\n7\n## presents AFM phase images of a PCL(10k)‐<italic toggle=\"yes\">b</italic>‐PEG(10k) copolymer crystallized from its 0.5 wt.% chloroform solution spin‐coated on the surface of an oriented iPP substrate. Like the PCL grown on the iPP substrate (Figure ##SUPPL##0##S8##, Supporting Information), similar cross‐hatched lamellar structure of PCL‐<italic toggle=\"yes\">b</italic>‐PEG copolymer is observed on the oriented iPP substrate (Figure ##FIG##6##7a##). To reveal the exact phase structure of the copolymer, the obvious lamellar thickening of PEG, which not evident for PCL (cf. Figure ##SUPPL##0##S9##, Supporting Information), during heating was utilized. As presented in Figure ##FIG##6##7b##, when heating the sample shown in Figure ##FIG##6##7a## from room temperature up to 56 °C, the AFM phase image becomes more clearly due to the structure reorganization or secondary crystallization. Moreover, owing to the lamellar thickening of PEG block, the phase structure can now be clearly identified (see the enlarged inset of Figure ##FIG##6##7b##). It is evident that the epitaxial crystallization of PCL on iPP substrate promotes a similar organization of the PEG blocks even though without epitaxy ability on iPP, which is more clearly seen after the melting of crystals corresponding to PCL blocks at 58 °C (Figure ##FIG##6##7c##). It should be emphasized that similar cross‐hatched lamellar assembly can be reconstructed after melting of both components and recrystallization during cooling, indicating its independence of crystallization pathway.</p>" ]
[ "<title>Conclusion</title>", "<p>In summary, crystallization of PCL‐<italic toggle=\"yes\">b</italic>‐PEG diblock and PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL triblock copolymers as well as PCL/PBA blends on highly oriented PE and/or iPP substrates has been studied. It was found that the crystallization of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL triblock copolymers and PCL/PBA blends on highly oriented PE substrate results in the self‐assembly of both components into patterned structures with parallel oriented lamellae owing to the capability of epitaxy for both PCL and PBA with PE. The oriented lamellae of PCL and PBA are confirmed to be alternatively arranged with molecular chains or chain segments aligned in the same direction of oriented PE chains, which is ideal for the donor and acceptor phases of photovoltaic device based on semiconductive polymers. Most importantly, the separated domain size of PCL and PBA can be easily regulated by controlled crystallization temperature. Even though both oriented PE and iPP substrates lack the epitaxial capacity toward the PEG block in the PCL‐<italic toggle=\"yes\">b</italic>‐PEG diblock copolymers, similar perpendicularly separated and alternatively distributed PCL and PEG lamellae with temperature‐dependent thicknesses aligned normal to the PE chain direction are produced when crystallizing on oriented PE substrate. Moreover, the change of substrate from PE to iPP leads to the molecular chains of both PCL and PEG in the perpendicularly separated lamellar domains ± 50° apart from the chain direction of iPP substrate. All these manifest the possibility of epitaxy‐directed self‐assembly strategy for regulating the patterned structures including both phase structure with controlled size at nanometer scale as well as crystal modification and orientation of each component of copolymers and polymer blends.</p>" ]
[ "<title>Abstract</title>", "<p>Directed self‐assembly of materials into patterned structures is of great importance since the performance of them depends remarkably on their multiscale hierarchical structures. Therefore, purposeful structural regulation at different length scales through crystallization engineering provides an opportunity to modify the properties of polymeric materials. Here, an epitaxy‐directed self‐assembly strategy for regulating the pattern structures including phase structure as well as crystal modification and orientation of each component for both copolymers and polymer blends is reported. Owing to the specific crystallography registration between the depositing crystalline polymers and the underlying crystalline substrate, not only order phase structure with controlled size at nanometer scale but also the crystal structure and chain orientation of each component within the separated phases for both copolymers and polymer blend systems can be precisely regulated.</p>", "<p>The epitaxy‐directed autonomous self‐assembly of alternatively arranged and alternatively distributed PCL and PEG edge‐on lamellar structures with temperature‐controlled domain size in ultrathin films of PCL‐<italic toggle=\"yes\">b</italic>‐PEG diblock copolymers on highly oriented PE and iPP substrates, respectively, is reported. The arrows show the molecular chain directions of melt‐drawn oriented PE and iPP substrate films.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6853-cit-0041\">\n<string-name>\n<given-names>C.</given-names>\n<surname>Hou</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>P.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Cui</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>R.</given-names>\n<surname>Xin</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Sun</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Ren</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Yan</surname>\n</string-name>, <article-title>Epitaxy‐Directed Self‐Assembly of Copolymers and Polymer Blends</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2207707</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202207707</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Materials</title>", "<p>High‐density PE was obtained from Lanzhou Petrochemical, China. IPP was produced by Yanshan Petroleum and Chemical Company, China. PBA (weight‐average molecular weight of ≈4 × 10<sup>4</sup> g mol<sup>−1</sup> and polydispersity of 1.7) and PCL (weight‐average molecular weight of ≈6.5 × 10<sup>4</sup> g mol<sup>−1</sup> and polydispersity of 1.5) used for studying the epitaxy of homopolymers on oriented substrate were produced by BASF AG Ludwigshafen, Germany. The xylene, toluene, and chloroform solvents were purchased from Beijing Chemical Reagent Co., Ltd. and used without further purification.</p>", "<title>Synthesis of PCL‐b‐PEG Diblock Copolymer</title>", "<p>To obtain the block copolymers of PEG‐<italic toggle=\"yes\">b</italic>‐PCL, the stannous octoate was adopted as catalyst (0.1 mol% of the amount of ε‐caprolactone) and methoxypolyethylene glycols with different molecular weights, for example, 1900, 10 000, and 20 000, were used to serve as initiators to achieve the ring opening polymerization of ε‐caprolactone. The length of PCL segment has been regulated by controlling the feed ratio of ε‐caprolactone monomer. The mixture of reagents was dissolved into anhydrous toluene (20 mL) under Ar atmosphere and stirred at 130 °C for 24 h. After that, the reaction system was cooled to room temperature, and extra toluene solvent was removed by vacuum rotatory evaporator. The resultant crude product was then re‐dissolved by chloroform solvent, and subsequently dropped into cold diethyl ether/<italic toggle=\"yes\">n</italic>‐hexane (1/1) to gain precipitation. After suction filtration and re‐dissolution for three times, the final precipitation was further purified by Soxhlet using <italic toggle=\"yes\">n</italic>‐hexane as extractor and thoroughly dried in vacuum oven at 40 °C for 24 h to gain the product of PEG‐<italic toggle=\"yes\">b</italic>‐PCL. Five kinds of block polymers, i.e., PEG(1.9k)–PCL(5k); PEG(1.9k)–PCL(10k), PEG(1.9k)–PCL(20k), PEG(10k)–PCL(10k), and PEG(20k)–PCL(20k), were obtained by changing feed ratio. The corresponding <sup>1</sup>H NMR spectra (400 MHz, CDCl<sub>3</sub>) <italic toggle=\"yes\">δ</italic> 4.08 (br), 3.66 (s), 3.40 (s), 2.33 (br), 1.67 (br), 1.41 (br) are presented in Figure ##SUPPL##0##S10## (Supporting Information).</p>", "<title>Synthesis of Poly(butylene adipate) Diol (PBA)</title>", "<p>To prepare PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL triblock copolymers, hydroxyl capped PBA block was first synthesized in the following way. A suitable amount of mixture of adipic acid and 1, 4‐butanediol at a molar ratio of 1:1.05 was added into reaction flask, followed by dropping tetrabutyl titanate (0.02 mL) catalyst into the reaction system under stirring. The manifold instrument and condenser pipe were connected with reaction flask in sequence. After stirring at 180 °C for 12 h under Ar atmosphere, the manifold instrument and condenser pipe were removed, and the mixture was further stirred at 180 °C for another 4 h under low pressure condition. When the reaction systems were cooled down to room temperature, a suitable amount of chloroform was added into reaction system to dissolve the product, and then dropped into cold <italic toggle=\"yes\">n</italic>‐hexane to gain precipitation. After suction filtration and re‐dissolution for three times, the final precipitation was further purified by Soxhlet using <italic toggle=\"yes\">n</italic>‐hexane as extractor and thoroughly dried in vacuum oven for 24 h to gain the PBA product for further use. The corresponding <sup>1</sup>H NMR spectrum (400 MHz, CDCl<sub>3</sub>) <italic toggle=\"yes\">δ</italic> 1.62‐1.73 (br), 2.30‐2.35 (br), 4.06 (br), 6.8–8.0 (─OH, br) is shown in Figure ##SUPPL##0##S11## (Supporting Information). The number average molecular weight determined by end group to be <italic toggle=\"yes\">M</italic>\n<sub>n</sub> = 10 956.</p>", "<title>Synthesis of PCL‐b‐PBA‐b‐PCL Triblock Copolymers</title>", "<p>The synthesis of PCL‐<italic toggle=\"yes\">b</italic>‐PBA‐<italic toggle=\"yes\">b</italic>‐PCL block copolymers was performed in a similar process as that of PEG‐<italic toggle=\"yes\">b</italic>‐PCL, except for using the hydroxyl capped PBA as initiator for ring opening polymerization of ε‐caprolactone. The stannous octoate (0.02 mL) was also adopted as catalyst. Four copolymers, i.e., PCL(54.5k)–PBA(11k)–PCL(54.5k), PCL(22k)–PBA(11k)–PCL(22k), PCL(13.5k)–PBA(11k)–PCL(13.5k), and PCL(3.5k)–PBA(11k)–PCL(3.5k), were obtained by changing feed ratio. The related <sup>1</sup>H NMR spectra (400 MHz, CDCl<sub>3</sub>) <italic toggle=\"yes\">δ</italic> 1.33–1.43(br), 1.60–1.73(br), 2.25–2.45(br), 4.06–4.20(br) can be found in Figure ##SUPPL##0##S12## (Supporting Information).</p>", "<title>Sample Preparation</title>", "<p>The highly oriented PE and iPP ultrathin films were prepared by a melt‐draw technique introduced by Petermann and Gohil.<sup>[</sup>\n##UREF##26##\n40\n##\n<sup>]</sup> According to this method, a small amount of 0.5 wt.% solution in xylene of PE or iPP was poured and uniformly spread on a preheated glass slide at around 130 °C. After the evaporation of xylene, a thin molten layer of the related polymer was then picked up by the motor‐driven cylinder with a drawing speed of 4–20 cm s<sup>−1</sup> and highly oriented ultrathin polymer films of 30–60 nm in thickness and square centimeters in area were collected by glass slides. Samples used for studying the epitaxial crystallization of the homopolymers, copolymers, and blends were prepared by spin‐coating the 0.5 wt.% chloroform solution of them onto surface of the highly oriented PE or iPP substrate films. The double‐layered thin films were used either directly after spin‐coating or heat‐treated at 80 °C for 10 min to erase their previous thermal history and then cooled down to desired temperature for a complete isothermal crystallization.</p>", "<title>1H NMR Characterization</title>", "<p>\n<sup>1</sup>H NMR spectra were recorded on a Bruker AV400 (400 MHz) spectrometer. Chemical shifts (<italic toggle=\"yes\">δ</italic>) were given in parts per million (ppm) relative to tetramethylsilane (TMS; <italic toggle=\"yes\">δ</italic> = 0) as the internal reference. <sup>1</sup>H NMR spectra data were reported as chemical shift, relative integral, multiplicity (s = singlet, d = doublet, m = multiplet), coupling constant (J in Hz), and assignment.</p>", "<title>AFM Characterization</title>", "<p>AFM images were collected on the Fastscan A instrument (Bruker) and analyzed by the Nanoscope software. For in situ study during heating process, a heating rate of 1 °C min<sup>−1</sup> from room temperature to the desired temperature was used, and each AFM image was obtained after the sample had been held ≈7 min at the corresponding temperature. The scanning density was 512 lines per frame.</p>", "<title>TEM Characterization</title>", "<p>For transmission electron microscopy (TEM) study, a JEOL JEM‐2100 with an accelerating voltage of 200 kV was used in this study. To minimize radiation damage by the electron beam, focusing was carried out on an area; then the specimen film was translated to an adjacent undamaged area for recording the images immediately.</p>", "<title>XRD Characterization</title>", "<p>The 2D X‐ray diffraction (XRD) data were obtained on the beamline 1W2A of Beijing Synchrotron Radiation Facility (BSRF), Beijing, China. The wavelength of X‐ray was 0.154 nm. The measurement of 2D‐small angle X‐ray scattering (SAXS) data was performed at a Xenocs Xeuss 2.0 instrument equipped with a Linkmam THMS600 hot stage in a transmissive mode. The X‐ray exposure time was 100 s for every measurement and the heating rate of 1°C min<sup>−1</sup>.</p>", "<title>FTIR Characterization</title>", "<p>The FTIR analysis was carried out by a Spectrum 100 FTIR spectrometer (PerkinElmer). Polarized FTIR was used to calculate the orientation function of oriented films. FTIR spectra in the wavenumber range from 3000 to 800 cm<sup>−1</sup> were obtained by averaging 32 scans at 4 cm<sup>−1</sup> resolution.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>C.H. and J.W. contributed equally to this work. The financial support of the National Natural Science Foundation of China (nos. 52027804 and 22022501) is gratefully acknowledged.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6853-fig-0001\"><label>Figure 1</label><caption><p>AFM phase images of PCL (a) and PBA (b) homopolymers crystallized isothermally on oriented PE thin films at 30 °C for 24 h after melting at 80 °C for 10 min. The white arrows indicate the molecular chain direction of oriented PE films.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6853-fig-0002\"><label>Figure 2</label><caption><p>a,b) AFM height and phase images of the PCL(13.5k)‐<italic toggle=\"yes\">b</italic>‐PBA(11k)‐<italic toggle=\"yes\">b</italic>‐PCL(13.5k) triblock copolymer grown epitaxially on highly oriented PE substrate at 37.5 °C after melting at 80 °C for 10 min. The white arrows in the AFM images indicate the molecular chain direction of the PE substrate. c) A corresponding electron diffraction pattern of the sample. d) The height profile corresponding to the white line shown in part (b). e) The FWHM distribution obtained from part (d).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6853-fig-0003\"><label>Figure 3</label><caption><p>a,b) AFM height and phase images of a PCL(50k)‐<italic toggle=\"yes\">b</italic>‐PEG(1.9k) diblock copolymer grown epitaxially on highly oriented PE substrate at 40 °C after melting at 80 °C for 10 min. c) A corresponding WAXD pattern of the sample after removing the PE substrate taken at room temperature. The white arrows indicate the molecular chain direction of the PE substrate.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6853-fig-0004\"><label>Figure 4</label><caption><p>2D SAXS patterns of PCL(50k)‐<italic toggle=\"yes\">b</italic>‐PEG(1.9k) diblock copolymer grown epitaxially on highly oriented PE substrate at 40 °C taken at room temperature (a), and during heating at 50 °C (b), and 55 °C (c), respectively.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6853-fig-0005\"><label>Figure 5</label><caption><p>a,b) AFM height and phase images of a PCL/PBA (50/50 wt.%) blend film crystallized isothermally on oriented PE substrate at 20 °C. The white arrows indicate the molecular chain direction of PE. c) A corresponding electron diffraction pattern and d) polarized FTIR spectra measured with the electron vectors parallel (0°) and perpendicular (90°) to the PE chain direction, respectively.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6853-fig-0006\"><label>Figure 6</label><caption><p>AFM phase images of a PCL/PBA (50/50 wt.%) blend crystallized on the oriented PE substrate isothermally at 25 °C recorded at room temperature (a) and at 54 °C after selective melting of PBA (b). The white arrows indicate the PE molecular chain. The corresponding phase profles along the white lines in the phase images and sketches illustrating the structures with long periods of 18.4 and 36 nm before and after melting of PBA crystals (right panels of parts (a) and (b)). The molten PBA crystals are indicated by the red rectangles. 2D SAXS patterns taken at room temperature (c) and at 54 °C (d), respectively.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6853-fig-0007\"><label>Figure 7</label><caption><p>AFM images of PCL(10k)‐<italic toggle=\"yes\">b</italic>‐PEG(10k) scanned at a) room temperature, b) 56 °C, c) and 58 °C, respectively. The inset in (b) is an enlarged image of the part marked by the yellow rectangle. The white arrow indicates the molecular chain direction of the used iPP substrate.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6853-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Temperature‐dependent long period and roughness of PCL–PBA triblock copolymer grown on oriented PE substrate.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Temperature [°C]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Long period [nm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Roughness [nm]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">37.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">22.0<xref rid=\"advs6853-tbl1-note-0001\" ref-type=\"table-fn\">\n<sup>a</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.43<xref rid=\"advs6853-tbl1-note-0001\" ref-type=\"table-fn\">\n<sup>a</sup>\n</xref>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">32.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">19.8<xref rid=\"advs6853-tbl1-note-0002\" ref-type=\"table-fn\">\n<sup>b</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.30<xref rid=\"advs6853-tbl1-note-0002\" ref-type=\"table-fn\">\n<sup>b</sup>\n</xref>\n</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6853-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Temperature‐dependent long period of PCL/PBA blend grown on PE.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Temperature [°C]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Long period [nm]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">20<xref rid=\"advs6853-tbl2-note-0001\" ref-type=\"table-fn\">\n<sup>a</sup>\n</xref>\n<sup>)</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">14.3</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">25<xref rid=\"advs6853-tbl2-note-0002\" ref-type=\"table-fn\">\n<sup>b</sup>\n</xref>\n<sup>)</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18.7</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">30<xref rid=\"advs6853-tbl2-note-0003\" ref-type=\"table-fn\">\n<sup>c</sup>\n</xref>\n<sup>)</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20.5</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">40<xref rid=\"advs6853-tbl2-note-0004\" ref-type=\"table-fn\">\n<sup>d</sup>\n</xref>\n<sup>)</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">23.8</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
[ "<disp-formula id=\"advs6853-disp-0001\">\n<label>(1)</label>\n<mml:math id=\"jats-math-1\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>l</mml:mi><mml:mi>c</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mn>2</mml:mn><mml:msub><mml:mi>σ</mml:mi><mml:mi>e</mml:mi></mml:msub><mml:msubsup><mml:mi>T</mml:mi><mml:mi>m</mml:mi><mml:mn>0</mml:mn></mml:msubsup><mml:mo>/</mml:mo><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msubsup><mml:mi>T</mml:mi><mml:mi>m</mml:mi><mml:mn>0</mml:mn></mml:msubsup><mml:mo>−</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi>c</mml:mi></mml:msub></mml:mrow></mml:mfenced><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>H</mml:mi><mml:mi>m</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:mi>c</mml:mi></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6853-disp-0002\">\n<label>(2)</label>\n<mml:math id=\"jats-math-3\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>f</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mo>/</mml:mo><mml:mo>/</mml:mo></mml:mrow></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mi>⊥</mml:mi></mml:msub><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mrow><mml:msub><mml:mi>I</mml:mi><mml:mrow><mml:mo>/</mml:mo><mml:mo>/</mml:mo></mml:mrow></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>I</mml:mi><mml:mi>⊥</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/><mml:mo linebreak=\"goodbreak\">×</mml:mo><mml:mfrac><mml:mn>2</mml:mn><mml:mrow><mml:mn>3</mml:mn><mml:msup><mml:mi>cos</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mi>a</mml:mi><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:mfrac><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>\n</disp-formula>" ]
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[ "<supplementary-material id=\"advs6853-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6853-tbl1-note-0001\"><label>\n<sup>a)</sup>\n</label><p>Obtained according to Figure ##FIG##1##2##\n</p></fn><fn id=\"advs6853-tbl1-note-0002\"><label>\n<sup>b)</sup>\n</label><p>Obtained according to Figure ##SUPPL##0##S2## (Supporting Information).</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"advs6853-tbl2-note-0001\"><label>\n<sup>a)</sup>\n</label><p>See Figure ##FIG##3##4##\n</p></fn><fn id=\"advs6853-tbl2-note-0002\"><label>\n<sup>b)</sup>\n</label><p>See Figure ##FIG##4##5##\n</p></fn><fn id=\"advs6853-tbl2-note-0003\"><label>\n<sup>c)</sup>\n</label><p>See Figure ##SUPPL##0##S7a## (Supporting Information)</p></fn><fn id=\"advs6853-tbl2-note-0004\"><label>\n<sup>d)</sup>\n</label><p>See Figure ##SUPPL##0##S7b## (Supporting Information).</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2207707-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
40
CC BY
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2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 23; 11(2):2207707
oa_package/20/fb/PMC10787078.tar.gz
PMC10787080
0
[ "<title>Introduction and background</title>", "<p>Peanut allergy is one the most common and severe forms of food allergy. The prevalence of peanut allergy has also been increasing over the past few decades and is more common in younger populations [##REF##29157945##1##]. Only 20% of the patients will outgrow their allergy to peanuts, so for many, it remains a lifelong burden [##UREF##0##2##]. With the recent uptick in peanut allergy and the most common lifelong course of the disease, finding therapies for this population is paramount. Palforzia is the first oral immunotherapy (OIT) of its kind to help desensitize patients aged 4-17 years to peanut allergens.</p>", "<p>Through a stepwise fashion of gradually introducing more antigens to the immune system of someone who is allergic, Palforzia slowly reduces the immune system's robust anaphylactic response, allowing for greater tolerance to peanuts. While avoidance of peanuts remains the best form of prophylaxis, Palforzia can be valuable in dampening anaphylaxis in accidental exposure. Some of the downsides to Palforzia therapy are that it is a daily medication and anaphylaxis remains a risk factor upon ingestion. For these reasons, studies are also looking into the benefits of other routes of administrating immunotherapy to patients with peanut allergy through sublingual therapy, subcutaneous injections, epicutaneous patches, and recombinant anti-immunoglobulin E (IgE) antibodies. Understanding the body’s immune system allows for using approaches that cause anergy to the body’s response to allergens. Classically, avoidance and post-exposure epinephrine to combat anaphylaxis have been the mainstays for peanut-allergic patients, but with the introduction of Palforzia and continued research into other pathways of subverting the immune system, patients with peanut allergies may soon have a treatment that can build tolerance and possibly cure their allergy.</p>" ]
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[ "<title>Conclusions</title>", "<p>Peanut allergy poses a significant burden on individuals, particularly children, with limited options for long-term management. Palforzia, the first OIT approved by the FDA, offers a promising approach to desensitize patients to peanut allergens. By gradually introducing increasing doses of peanut protein, Palforzia aims to reduce the immune system's hypersensitivity and enhance tolerance to peanuts. However, it is important to note that Palforzia is not without limitations, as it requires daily medication and carries the risk of anaphylaxis. To address these challenges, research is underway to explore alternative routes of immunotherapy, including sublingual therapy, subcutaneous injections, epicutaneous patches, and recombinant anti-IgE antibodies. These approaches aim to modulate the immune response and improve patient outcomes. Diagnostic methods for peanut allergy have also evolved, with serological tests gaining popularity for their accuracy and convenience. While Palforzia has shown efficacy in clinical trials, further investigations are necessary to compare its effectiveness with other administration routes. Moreover, ongoing studies are examining the clinical potential of more specialized immunotherapy based on targeting subsets of patients who may be more receptive to OIT. Ultimately, the development of safe and effective treatments for peanut allergy holds the promise of significantly improving the quality of life for affected individuals, reducing anxiety, and potentially even offering a cure for this lifelong condition.</p>" ]
[ "<p>With Palforzia appearing as the first oral immunotherapy for patients with peanut allergy, the present investigation aims to summarize recent clinical trials, the mechanism of dosing, and the real-world usage of this novel therapy. Palforzia offers a new avenue for treating the human allergic response in previous immune modulation refractory patients or patients who have undergone immune environment sensitivity testing, which allows for more specialized treatment. Current studies are focusing on certain age groups that have been shown to be more receptive to treatment. Further, studies are tailoring oral immunotherapy treatment alongside other immune modulators to elicit greater targeted immune tolerance. With an increasing prevalence of patient allergies, many questions remain surrounding the optimization of therapies in reaching therapeutic goals. Overall, Palforzia offers a hopeful treatment for peanut-allergic patients to attenuate their immune response while furthering research in related therapies.</p>" ]
[ "<title>Review</title>", "<p>Peanut allergy: Mechanism of disease</p>", "<p>Understanding the body’s immune system aids in creating effective interventions. The basic physiological response after ingesting any new substance involves the body processing possible pathogenic components and displaying them to the immune system for review. This process begins at the mucosal surface of the gastrointestinal tract, where the food components are taken up by specialized microfold cells (M cells) [##REF##18456104##3##]. Most of the compounds involved in eliciting an immune response are proteins, which allow for the conservation of their original structure as they traverse the digestion tract [##REF##15985358##4##]. After the M cells sample the components of digestion, they transfer the food proteins to dendritic cells for further processing and lymphocyte presentation through surface major histocompatibility complex class II (MHC II) receptors. These dendritic cells migrate to nearby lymph nodes, where they induce cellular changes in naïve T-cells through antigen presentation. In allergic patients, these naïve T-cells are activated into T-helper 2 (Th2) cells, which, through interleukin-4 and interleukin-13 production, begin the cascade of an immune environment that primes B-cells to produce immunoglobulin E (IgE), which are highly sensitive to the antigen. These IgE attach to mast cells and mount an immune response [##REF##16048551##5##].</p>", "<p>Upon immune activation, the process of IgE-mediated anaphylaxis begins rapidly. Crosslinking of IgE on mast cells and basophils causes degranulation and subsequent immune mediator production alongside the recruitment of other inflammatory cells. Immediate inflammatory effects include smooth muscle spasms, vasodilation, increased vascular permeability, hypovolemia, myocardial depression, and edema. Anaphylaxis is acutely treated with epinephrine, removal of the allergen, postural changes, and bronchodilator administration [##REF##28800865##6##].</p>", "<p>In the past, diagnosing a suspected peanut allergy has classically been done through a double-blind oral food challenge. Recently, however, diagnostic tests have transitioned to a more serological approach. Commonly used modalities include skin prick testing, measuring serum whole peanut IgE levels, measuring serum IgE levels to peanut components, basophil or mast cell activation tests, and histamine release assays. These serological tests have the added benefit of testing patients before an anaphylactic incident or monitoring serum levels as they change in response to immune therapy [##REF##30581130##7##].</p>", "<p>Palforzia pharmacodynamics: OIT</p>", "<p>Palforzia is a member of the OIT class of drugs. It is the only drug in this class approved for use in the United States [##REF##33417257##8##]. OIT drugs have demonstrated benefits in the treatment of many food-related allergies, such as peanuts, eggs, milk, etc. Treatment with OIT requires daily exposure to the allergen at increasing dosages [##UREF##1##9##]. The mechanism of action of OIT lies in its constant activation of the immune system. This repetitive activation causes systemic anergy through the desensitization of IgE-mediated mast cells and basophils. While oral immunotherapies are rising in popularity, a competing treatment option is epicutaneous immunotherapy (EPIT). EPIT involves a dosed patch that is placed on the skin of allergic patients. The patients are exposed to increasing levels of allergen, but the benefit of the epicutaneous administration route avoids any systemic reaction that may be caused by other forms of immunotherapy, including OIT [##REF##32758254##10##]. </p>", "<p>Palforzia uses peanut proteins that mimic peanut-induced similar immune responses. In phase 3 trials, patients were exposed to increasing doses starting at 0.5 mg and maximizing at 100 mg [##REF##30449234##11##], a process referred to as crescendo dosing. In the initial meeting with the patient, they are introduced to increasing doses of the allergen until they find the highest dose that does not cause an allergic reaction. The patient then takes the highest established dosage, termed the maintenance dose. The maintenance phase dosage is the top of the crescendo, where the patient’s dosage remains for an extended period, sometimes even lasting years. Clinical trials have indicated that Palforzia had great indications for children but less for adults. Thus, it is indicated by the U.S. Food and Drug Administration (FDA) for children aged 4-17 years. Based on survey responses from prescribing physicians, it is particularly important to closely monitor the conditions in which patients are taking their dosages. Some of these recommendations include the dose after a full meal and avoiding things that may cause reactions, such as nonsteroidal anti-inflammatory drugs [##REF##33526464##12##,##REF##35534909##13##]. The most concerning adverse effect of any therapy that introduces a patient to an allergen is anaphylaxis. In the case of Palforzia, there has been an established association with anaphylaxis as well as moderate gastrointestinal distress [##REF##32314071##14##]. The seriousness of these side effects is an important consideration for physicians when administering this therapy.</p>", "<p>Clinical efficacy of Palforzia</p>", "<p>With Palforzia being the only drug approved by the FDA for mitigating the immune system's response to peanut allergens, it has been shown that the oral route of immune therapy may be the most effective option. Research is still being done into other routes of administration to see if other pathways may rival the efficacy of OIT. The other routes of administration that are being investigated are subcutaneous immunotherapy (SCIT), sublingual immunotherapy (SLIT), EPIT, and serological approaches through recombinant immunoglobin vaccines that are anti-peanut IgE [##REF##25276342##15##]. The efficacy of Palforzia monotherapy has been explored in two-phase three clinical trials named ARTEMIS (AR101 Treatment Evaluation in Children and Adults - A Randomized, Double-Blind, Placebo-Controlled Study) and PALISADE (Peanut Allergy Oral Immunotherapy Study of AR101 for Desensitization). The ARTEMIS study found that 58.3% of patients tolerated 1,000 mg (three to four peanut kernels) of peanut protein after treatment, with 18.2% of patients experiencing moderate symptoms and another 4.5% of patients experiencing severe symptoms. In the PALISADE study, 50.3% of participants could tolerate the 1,000 mg peanut protein challenge, with moderate symptoms in 25.3% of patients and severe symptoms in 5.1% [##UREF##2##16##]. Reaching this tolerance threshold to the peanut allergen may increase the patient’s quality of life by lowering anxiety surrounding accidental ingestion when traveling or dining out [##UREF##3##17##].</p>", "<p>Regarding the other pathways of immunotherapy, currently, an EPIT known as Viaskin is undergoing phase three clinical trials with the FDA to find the clinical efficacy of the immunotherapy. Results from the VITESSE study are expected in 2025 [##UREF##4##18##]. Phase two trials of the Viaskin EPIT patch concluded that after 52 weeks of therapy, patients had modest gains in tolerance to peanut allergens. Younger patients had a greater immunological tolerance response, the majority of the patients had minor patch site reactions, and the immunologic changes noticed in the patients were similar to other routes of immune therapy [##REF##28091362##19##]. An open-label study investigating SLIT found that only 4 mg of peanut protein resulted in clinically significant desensitization that persisted for multiple months following discontinuation of the therapy. The rate of side effects in the SLIT study was low, mostly consisting of a mouth itch. In a preclinical mouse model looking into the efficacy of SCIT, they found that modifying peanut extract and introducing it subcutaneously led to a modification of the animal allergic response, leading to reduced allergenicity to peanut antigens [##REF##36828080##20##,##REF##30506686##21##]. Given the age restrictions and dosing limitations of Palforzia, there is still a large void in the therapeutic options offered to patients with peanut allergy (Table ##TAB##0##1##) [##UREF##5##22##].</p>" ]
[ "<p>The authors would like to thank the Paolo Procacci Foundation for its generous support in the publication process.</p>" ]
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[ "<table-wrap position=\"float\" id=\"TAB1\"><label>Table 1</label><caption><title>Clinical trials relating to peanut oral immunotherapy (OIT) efficacy and safety.</title></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Author (year)</td><td rowspan=\"1\" colspan=\"1\">Population and intervention</td><td rowspan=\"1\" colspan=\"1\">Results and findings</td><td rowspan=\"1\" colspan=\"1\">Conclusions</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Vickery et al. [##REF##30449234##11##]</td><td rowspan=\"1\" colspan=\"1\">Phase 3, randomized, double-blind, placebo-controlled food challenge; 496 participants aged 4 to 17 years</td><td rowspan=\"1\" colspan=\"1\">67.2% of patients receiving treatment were able to tolerate 600 mg of peanut, whereas only 4% of patients taking placebo were able to tolerate the same dose.</td><td rowspan=\"1\" colspan=\"1\">Treatment resulted in higher doses of peanuts that could be tolerated in highly allergic participants and lower symptom severity.</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Chinthrajah et al. [##REF##31522849##23##]</td><td rowspan=\"1\" colspan=\"1\">Phase 2, randomized, double-blind, placebo-controlled trial; 152 patients aged 7 to 55 years with peanut allergy</td><td rowspan=\"1\" colspan=\"1\">35% of treated patients were able to tolerate 4,000 mg of peanut at 104 and 117 weeks, while just one placebo participant (4%) was able to do the same.</td><td rowspan=\"1\" colspan=\"1\">Treatment with daily 300 mg of oral peanut allergen could desensitize patients up to 4,000 mg of peanut, but discontinuation or reduction of therapy increases the likelihood of becoming clinically reactive to peanut allergen once again.</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Monian et al. [##UREF##6##24##]</td><td rowspan=\"1\" colspan=\"1\">Phase 1/2, double-blind, placebo-controlled peanut allergen intervention to elicit and obtain data regarding T-cell function during OIT therapy</td><td rowspan=\"1\" colspan=\"1\">Participants were built up to a dose of 4,000 mg of peanut, maintained treatment for 12 weeks and then discontinued treatment and underwent an avoidance phase for 12 weeks to find out the changes in immune system function.</td><td rowspan=\"1\" colspan=\"1\">OIT did not reduce the number of reactive Th2 cells but rather led to specific clonal suppression, which may explain why sustained tolerance is difficult to achieve. Some participants who failed to respond to OIT had high baseline Th17 and other T-helper cells, which may be useful in further studies as a predictor for OIT therapy success.</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Loke et al. [##REF##35123664##25##]</td><td rowspan=\"1\" colspan=\"1\">Multicenter, randomized, phase 2b trial in children aged 1-10 years with known peanut allergy to look into whether probiotics aid in OIT therapy</td><td rowspan=\"1\" colspan=\"1\">46% of probiotic plus OIT and 51% of OIT monotherapy patients achieved sustained unresponsiveness to peanut.</td><td rowspan=\"1\" colspan=\"1\">Adding a probiotic to the OIT regimen did not improve the efficacy of OIT but may aid in reducing some negative side effects of OIT therapy.</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Jones et al. [##REF##35065784##26##]</td><td rowspan=\"1\" colspan=\"1\">Randomized, placebo-controlled, double-blind study in children aged 1-3</td><td rowspan=\"1\" colspan=\"1\">71% of treated participants vs. 2% of placebo participants reached the targeted end goal, with 21% of treated patients meeting remission requirements. Remission requirements were defined by 26 weeks of no allergen exposure. Then, sensitivity was measured again.</td><td rowspan=\"1\" colspan=\"1\">Initiation of OIT therapy in children aged 1-3 years can be associated with higher rates of desensitization and remission from peanut allergy.</td></tr></tbody></table></table-wrap>" ]
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[ "<fn-group content-type=\"other\"><title>Author Contributions</title><fn fn-type=\"other\"><p><bold>Concept and design:</bold>  Sahar Shekoohi, Shahab Ahmadzadeh, Rucha A. Kelkar, Alexandra Nolen, Connor J. Plaisance, Maxwell J. Wagner, Charles P. Daniel, Grant E. Borne, Giustino Varrassi, Alan D. Kaye</p><p><bold>Acquisition, analysis, or interpretation of data:</bold>  Sahar Shekoohi, Shahab Ahmadzadeh, Rucha A. Kelkar, Alexandra Nolen, Connor J. Plaisance, Maxwell J. Wagner, Charles P. Daniel, Grant E. Borne, Giustino Varrassi, Alan D. Kaye, Dariusz Myrcik</p><p><bold>Drafting of the manuscript:</bold>  Sahar Shekoohi, Shahab Ahmadzadeh, Rucha A. Kelkar, Alexandra Nolen, Connor J. Plaisance, Maxwell J. Wagner, Charles P. Daniel, Grant E. Borne, Giustino Varrassi, Alan D. Kaye, Dariusz Myrcik</p><p><bold>Critical review of the manuscript for important intellectual content:</bold>  Sahar Shekoohi, Shahab Ahmadzadeh, Rucha A. Kelkar, Alexandra Nolen, Connor J. Plaisance, Maxwell J. Wagner, Charles P. Daniel, Grant E. Borne, Giustino Varrassi, Alan D. Kaye, Dariusz Myrcik</p><p><bold>Supervision:</bold>  Sahar Shekoohi, Alan D. Kaye</p></fn></fn-group>", "<fn-group content-type=\"competing-interests\"><fn fn-type=\"COI-statement\"><p>The authors have declared that no competing interests exist.</p></fn></fn-group>" ]
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[{"label": ["2"], "article-title": ["First oral Immunotherapy for peanut allergy"], "source": ["Am J Nurs"], "person-group": ["\n"], "surname": ["Aschenbrenner"], "given-names": ["DS"], "fpage": ["22"], "volume": ["120"], "year": ["2020"]}, {"label": ["9"], "article-title": ["Oral immunotherapy (OIT): a personalized medicine"], "source": ["Medicina (Kaunas)"], "person-group": ["\n"], "surname": ["Mori", "Barni", "Liccioli", "Novembre"], "given-names": ["F", "S", "G", "E"], "volume": ["55"], "year": ["2019"]}, {"label": ["16"], "article-title": ["Palforzia for desensitisation of peanut allergy in children"], "source": ["Prescriber"], "person-group": ["\n"], "surname": ["Chaplin"], "given-names": ["S"], "fpage": ["4"], "lpage": ["34"], "volume": ["32"], "year": ["2021"]}, {"label": ["17"], "article-title": ["Understanding Caregiver Goals, Benefits, and Acceptable Risks of Peanut Allergy Therapies - ClinicalKey"], "date-in-citation": ["\n"], "month": ["3"], "year": ["2023", "2023"], "uri": [" https://www.clinicalkey.com/#!/content/playContent/1-s2.0-S1081120618305106?returnurl=null&referrer=null"]}, {"label": ["18"], "article-title": ["FDA Removes Hold Allowing DBV\u2019s Pivotal Phase 3 Peanut Patch Trial to Commence"], "date-in-citation": ["\n"], "month": ["5"], "year": ["2023", "2022"], "uri": ["http://snacksafely.com/2022/12/fda-removes-hold-allowing-dbvs-pivotal-phase-3-peanut-patch-trial-to-commence/"]}, {"label": ["22"], "article-title": ["Real world adoption of FDA-approved peanut oral immunotherapy with Palforzia"], "source": ["J Allergy Clin Immunol"], "person-group": ["\n"], "surname": ["Mustafa", "Patrawala"], "given-names": ["SS", "S"], "fpage": ["108"], "volume": ["147"], "year": ["2021"]}, {"label": ["24"], "article-title": ["Peanut oral immunotherapy differentially suppresses clonally distinct subsets of T helper cells"], "source": ["J Clin Invest"], "person-group": ["\n"], "surname": ["Monian", "Tu", "Ruiter"], "given-names": ["B", "AA", "B"], "volume": ["132"], "year": ["2022"]}]
{ "acronym": [], "definition": [] }
26
CC BY
no
2024-01-14 23:41:56
Cureus.; 15(12):e50485
oa_package/4d/09/PMC10787080.tar.gz
PMC10787081
37946699
[ "<title>Introduction</title>", "<p>As the global population continues to grow and modern technology advances, the demand for renewable energy and energy storage technologies increases. The growth of both portable electronics and electronic vehicle markets necessitates the development of energy storage with longer cycling life, more reliable safety, and higher energy density than today's technologies.<sup>[</sup>\n##REF##22096188##\n1\n##\n<sup>]</sup> Moreover, the development of environmentally friendly renewable energy technologies calls for reliable electrochemical storage devices.<sup>[</sup>\n##REF##18256660##\n2\n##\n<sup>]</sup> In this regard, lithium‐ion batteries (LIBs) have seen a meteoric rise in popularity due to their high theoretical energy densities. Despite considerable efforts invested in this field, state‐of‐the‐art battery systems are approaching the threshold of their performance limits.<sup>[</sup>\n##UREF##0##\n3\n##\n<sup>]</sup> To overcome these challenges, lithium–metal batteries (LMBs) demonstrate even higher capacities and have recently been referred to as the “holy grail” for next‐generation energy systems.<sup>[</sup>\n##UREF##1##\n4\n##, ##UREF##2##\n5\n##, ##REF##35878245##\n6\n##, ##REF##37695100##\n7\n##\n<sup>]</sup>\n</p>", "<p>Currently, both LIBs and LMBs continue to face countless restrictions to their electrochemical performances, notably, due to their capacity fading during repeated electrochemical cycling.<sup>[</sup>\n##UREF##3##\n8\n##\n<sup>]</sup> A major factor of this loss is due to corrosive hydrogen fluoride (HF) that is generated through the hydrolysis of electrolytes.<sup>[</sup>\n##UREF##4##\n9\n##, ##UREF##5##\n10\n##\n<sup>]</sup> Furthermore, these effects are exacerbated in complex operating environments due to exposure to high voltages<sup>[</sup>\n##UREF##6##\n11\n##\n<sup>]</sup> and elevated temperatures.<sup>[</sup>\n##UREF##7##\n12\n##, ##UREF##8##\n13\n##\n<sup>]</sup> Lithium dendrite growth also remains a recurring problem for lithium‐based batteries, leading to safety hazards and short lifespans.<sup>[</sup>\n##UREF##9##\n14\n##\n<sup>]</sup> Although a significant amount of research exists in this field, many of these challenges persist. Drawbacks in these current systems drive investigation into the development of new materials for energy storage devices.</p>", "<p>Metal–organic frameworks (MOFs) are a class of porous crystalline materials comprised of metal‐based nodes coordinated to organic ligands that have attracted wide research interests in recent years.<sup>[</sup>\n##REF##23990564##\n15\n##, ##UREF##10##\n16\n##, ##REF##34280313##\n17\n##\n<sup>]</sup> Due to their modular nature, the combinations of possible metallic elements and organic linkers are boundless, leading to the experimental synthesis of over 90 000 MOFs thus far.<sup>[</sup>\n##REF##32792486##\n18\n##\n<sup>]</sup> Before their introduction into the battery field, MOFs have experienced great success in various applications, such as gas adsorbents,<sup>[</sup>\n##REF##12750515##\n19\n##\n<sup>]</sup> sensors,<sup>[</sup>\n##REF##18841964##\n20\n##\n<sup>]</sup> drug carriers,<sup>[</sup>\n##REF##18454528##\n21\n##\n<sup>]</sup> and catalysts,<sup>[</sup>\n##REF##34692015##\n22\n##\n<sup>]</sup> owing to their extensive chemical functionality and topological control. Recent efforts have pushed MOFs into the field of energy materials due to their inherent porosity, well‐ordered networks, and chemical stability, which allow for ion compatibility and electrochemical robustness.<sup>[</sup>\n##UREF##11##\n23\n##\n<sup>]</sup> Consequently, electrode materials<sup>[</sup>\n##REF##35479575##\n24\n##\n<sup>]</sup> and separator components<sup>[</sup>\n##UREF##12##\n25\n##\n<sup>]</sup> have benefited from the properties of MOFs. Furthermore, MOF‐based electrolytes have achieved ionic conductivities of up to 10<sup>−3</sup> S cm<sup>−1</sup>, demonstrating promising results for next‐generation battery applications.<sup>[</sup>\n##UREF##13##\n26\n##, ##UREF##14##\n27\n##, ##UREF##15##\n28\n##\n<sup>]</sup> The recognized mechanism of these MOF‐based electrolytes, electrodes, and separators relies on well‐defined pore architectures of MOFs that can facilitate fast ion transport, host active materials, and selectively screen ions, respectively. While this exploits one defining trait of MOFs, they exhibit countless other important properties for battery applications, such as large hygroscopic adsorption capacities, high thermal stabilities, excellent electrochemical stabilities, and high mechanical robustness. These properties have recently been used to rectify the aforementioned challenges in current battery materials.<sup>[</sup>\n##UREF##16##\n29\n##\n<sup>]</sup>\n</p>", "<p>In this mini review, we detail these emerging MOF applications in batteries used to 1) scavenge impurities to improve cycling stability, 2) widen the operating temperature range of electrolytes, 3) widen the operating voltage range of electrolytes, 4) and operate as artificial solid‐electrolyte interphases (SEIs) to prevent lithium‐dendrite formation (<bold>Figure</bold> ##FIG##0##\n1\n##). The unique advantages of each MOF material are comprehensively discussed and current challenges are summarized. Lastly, the prospective solutions for the future fabrication of MOF‐based batteries are presented.</p>" ]
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[ "<title>Conclusions and Outlook</title>", "<p>In recent times, increasing attention has been on MOF‐based materials for battery applications. Beyond their well‐defined porosity, MOF‐based materials also exhibit large hygroscopic adsorption capacities, high thermal stabilities, excellent electrochemical stabilities, and mechanical robustness, which offer solutions to the current challenges in both LIBs and LMBs, including the hydrolysis of electrolytes, mediocre thermal and electrochemical stabilities, and poor compatibility of common electrolytes with electrodes. As detailed in this mini‐review, the properties of MOF‐based materials were in remarkable alignment for each of these challenges. Nevertheless, the exploration of novel applications using MOF‐based materials remains in its nascent stages and several challenges and issues need to be addressed. Some of the key problems facing this field are as follows:\n<list list-type=\"order\" id=\"advs6652-list-0001\"><list-item><p>Despite the extraordinary impurity scavenging abilities of the MOF‐based separators and additives, there exists a finite adsorption capacity to the MOF materials. For this reason, using similar functionalization strategies to install scavenging moieties on other MOF‐based battery components, such as electrolytes, is important to broaden the capabilities of this field.</p></list-item><list-item><p>Although the effects of nanoconfinement on liquid/gas electrolytes toward their melting/boiling points are well‐known, the fine‐tuning of pore size in comparison to confined molecules has not been thoroughly studied. In order to attain the threshold temperature range for MOF‐based electrolytes, a fundamental investigation should be done to give us insight into optimal electrolyte/MOF combinations.</p></list-item><list-item><p>As the limiting factor of electrochemical stability is often the solvent molecules, much of the focus is toward solvent depletion to improve oxidative stability. In this context, fully solid‐state MOF‐based electrolytes have the advantage since they are only comprised of highly electrochemically stable MOFs and lithium salts. While these systems typically lack adequately high ionic conductivities, this represents another important area for research. Increased focus on developing solvent‐free MOF‐based electrolytes will be crucial for reaching the limit of electrochemical stability.</p></list-item><list-item><p>While examples of the MOF‐based SEI films demonstrate effective Li dendrite suppression, there is a lack of focus on the mechanical strength of these layers. In order to draw reliable structure‐property relationships between certain MOF materials and inhibition of dendrite growth, mechanical properties (bulk modulus, shear modulus, etc.) are expected to be investigated further.</p></list-item><list-item><p>Preparation of these MOF‐based batteries requires costly materials, such as zirconium and ionic liquids. Moreover, the synthesis and processing of MOFs are made even more complex with the introduction of grafted scavengers and polymers. Utilization of these MOF materials requires significant effort and resources, which is a major obstacle in the commercialization of these batteries. Thus, the selected MOFs should maintain a balance between their synthetic cost and desirable properties and maintain an emphasis on using inexpensive starting materials as well as fewer synthetic steps.</p></list-item><list-item><p>MOFs possess many more unexplored characteristics that could prove valuable for battery materials. For example, while the majority of MOFs are insulating materials, recent strategies have been employed to develop electrically conductive MOFs,<sup>[</sup>\n##REF##32275412##\n49\n##\n<sup>]</sup> further permitting their use for cathode materials in energy storage devices.<sup>[</sup>\n##UREF##29##\n50\n##, ##REF##31940192##\n51\n##, ##UREF##30##\n52\n##\n<sup>]</sup> Moreover, the properties of MOFs discussed in this review have not been considered for other types of batteries, such as in other metal‐based batteries (Zn, Na, Al, etc.), and will most likely provide the same benefits as they have shown toward Li‐based batteries.</p></list-item></list>\n</p>", "<p>The development and research of MOF‐based battery materials based on their less widely utilized attributes is still in its infancy but has proven to be important in the future development of LIBs and LMBs. The underlying mechanisms for enhancing the performance of these materials remain uncertain, necessitating further research to achieve a comprehensive understanding. Significant progress is needed before these materials can be effectively employed in real‐world batteries. As greater attention is directed toward exploring these advantages of MOFs, the challenges presented in this mini‐review will be addressed with more systematic studies, leading to the realization of the potential of MOFs in battery applications.</p>" ]
[ "<title>Abstract</title>", "<p>Metal–organic frameworks (MOFs) have played a crucial role in recent advancements in developing lithium‐based battery electrolytes, electrodes, and separators. Although many MOF‐based battery components rely on their well‐defined porosity and controllable functionality, they also boast a myriad of other significant properties relevant to battery applications. In this mini‐review, the distinct advantages of MOFs in battery applications are discussed, including using MOFs to 1) scavenge impurities to increase cycling stability, 2) widen the operation temperature range of conventional electrolytes, 3) widen the operation voltage range of common electrolytes, and 4) employ as artificial solid‐electrolyte interphases to prevent lithium dendrite growth. Furthermore, subsisting challenges of developing these emerging MOF‐based battery technologies are discussed and guidance for shaping the future of this field is given.</p>", "<p>MOFs possess distinct advantages in scavenging impurities to increase cycling stability, increasing operation temperatures and voltages of common electrolytes, and can be used as artificial solid‐electrolyte interphases to prevent lithium dendrite growth. In this mini‐review, the emerging battery applications of metal–organic frameworks (MOFs) are outlined, and a perspective of future MOF‐based battery technologies is proposed.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6652-cit-0053\">\n<string-name>\n<given-names>A. U.</given-names>\n<surname>Mu</surname>\n</string-name>, <string-name>\n<given-names>G.</given-names>\n<surname>Cai</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Chen</surname>\n</string-name>, <article-title>Metal–Organic Frameworks for the Enhancement of Lithium‐Based Batteries: A Mini Review on Emerging Functional Designs</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305280</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305280</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>MOFs Used as Scavengers to Improve Cycling Stability</title>", "<p>Transition metal dissolution and electrode erosion are the well‐known origins of capacity decay and the limited stability of LIBs during repeated cycling.<sup>[</sup>\n##UREF##17##\n30\n##\n<sup>]</sup> Conventional lithium salts, such as LiPF<sub>6</sub>, readily undergo hydrolysis reactions with trace water, potentially leading to the generation of highly corrosive HF (<bold>Figure</bold> ##FIG##1##\n2\n##), which acts as a main factor in the aforementioned detrimental phenomena. Furthermore, gaseous product formation through hydrogen (or hydrocarbon molecules) and oxygen evolution reactions also leads to cell swelling and other safety concerns. These destructive processes are intensified at higher operating temperatures, preventing the development of safer and longer lifespan LIBs and LMBs. Although attempts to ameliorate these effects largely rely on coating the cathode to protect against erosion,<sup>[</sup>\n##UREF##18##\n31\n##\n<sup>]</sup> the other adverse effects of HF generation fail to be addressed by this method. In this regard, various additives with high affinities for water and HF have been reported to scavenge these harmful impurities.<sup>[</sup>\n##REF##33945248##\n32\n##\n<sup>]</sup>\n</p>", "<p>MOF materials comprised of abundant absorption sites and porous crystalline structures demonstrate promising abilities to scavenge impurities, facilitating HF, water, and gas capture. For example, the tenacious water‐scavenging properties of a copper‐based MOF (HKUST‐1) were employed in fabricating a battery separator for LIBs.<sup>[</sup>\n##UREF##19##\n33\n##\n<sup>]</sup> As a result, the removal of moisture has led to a decrease in the hydrolysis of electrolytes, granting an increased capacity retention of 72% after 400 cycles in Li||LiNi<sub>0.8</sub>Co<sub>0.1</sub>Mn<sub>0.1</sub>O<sub>2</sub> cells, even in the presence of an additional 200 ppm of water in the electrolyte (<bold>Figure</bold> ##FIG##2##\n3a,b##). Even after increasing the electrolyte water content to 800 ppm, acceptable performance was sustained. The advantages of MOF materials are not limited to their inherent impurity scavenging properties, as they also possess ease of functionalization, providing more options to install additional scavenging moieties.</p>", "<p>By equipping an amine‐functionalized zirconium‐based MOF (UiO‐66‐NH<sub>2</sub>) backbone with (3‐glycidyloxypropyl) trimethoxy‐silane (GPTMS) as an HF scavenger to form GPTMS‐functionalized UiO‐66‐NH<sub>2</sub>, scavenging abilities were extended beyond water to include HF.<sup>[</sup>\n##UREF##20##\n34\n##\n<sup>]</sup> The resulting all‐impurity scavenging separator was constructed from the combination of functionalized MOFs and polyacrylonitrile binders, which demonstrated the effective removal of harmful HF. In addition, the CO and CO<sub>2</sub> confinement capabilities of UiO‐66‐NH<sub>2</sub> were important in lessening the gaseous volume expansion leading to cell swelling due to gas generation, thereby the deterioration of battery components was decreased (Figure ##FIG##2##3c,d##). The scavenging of these major impurities led to an improved capacity retention of 75% after 200 cycles, performing even at higher temperatures (55 °C) and demonstrated stability even with an additional 500 ppm of water in the electrolyte.</p>", "<p>The effective moisture, HF, and gas adsorbing abilities of the presented MOFs demonstrate a promising method for the enhancement of LIB cycling performances. Considering that these impurities are major factors in transition metal dissolution and electrode erosion, the introduction of the aforementioned MOF separators led to an enhanced capacity retention of LIBs, even with a significant amount of water in the electrolyte during cell assembly. The current investigations showcase the possibilities of utilizing MOF separators to mitigate the deleterious effects of common electrolyte impurities.</p>", "<title>MOFs Used to Widen the Operation Temperature Range of Electrolytes</title>", "<p>Generally, solid‐state electrolytes possess many inherent advantages to their liquid counterparts in terms of thermal stability and eliminating the use of flammable organic solvents. Despite their improved safety, solid‐state electrolytes tend to exhibit inferior ionic conductivity and poor mechanical properties. To circumvent the drawback of both liquid and solid‐state electrolytes, quasi‐solid electrolytes can be expected to enhance ionic conductivities while reducing the amounts of dangerous organic solvents. As quasi‐solid electrolytes are prepared by hosting a minuscule amount of liquid or gas electrolyte inside a porous matrix, physical and chemical properties can be tuned to enable a much wider range of safe operating temperatures, enabling both high and low‐temperature applications (<bold>Figure</bold> ##FIG##3##\n4\n##).</p>", "<p>Nanoconfinement and sub‐nanoconfinement of liquids have been shown to substantially change their physicochemical properties, such as boiling points, melting points, ion transport abilities, etc. Using these effects, CuBTC MOF was functionalized with poly(sodium 4‐styrenesulfonate) and employed as a host material to confine the liquid electrolyte, bis(trifluoromethanesulfonyl)imide (LiTFSI) in propylene carbonate (PC).<sup>[</sup>\n##REF##35314688##\n35\n##\n<sup>]</sup> Although the conventional electrolyte suffered from low decomposition temperatures at ≈100 °C, an increase in decomposition temperature of up to 200 °C was observed after fabrication of the quasi‐solid electrolyte. The resulting LMB pouch cells containing this MOF‐based quasi‐solid electrolyte demonstrated 89% capacity retention after 200 cycles at high working temperatures of 90 °C, even functioning after being bent and cut (<bold>Figure</bold> ##FIG##4##\n5a##). Similarly, further enhancement of LMB operating temperatures was achieved through the MOF‐facilitated (HKUST‐1) confinement of a Li salt‐containing ionic liquid ([EMIM][TFSI]).<sup>[</sup>\n##REF##33804099##\n38\n##\n<sup>]</sup> The high thermal stability of ionic liquids in contrast to conventional electrolyte solvents was exploited through the immobilization in MOF nanopores. Consequently, the resulting quasi‐solid electrolyte was employed in LiFePO<sub>4</sub>||Li batteries, achieving a 92% capacity retention after 100 cycles at 0.5 C.</p>", "<p>In addition to manipulating the boiling points of confined solvents within sub‐nanoscale environments, MOFs themselves have also been manipulated to widen the operating temperatures of these electrolytes. For instance, to further increase the high‐temperature stability of a MOF‐based solid‐state electrolyte in LMBs, an aluminum‐based MOF (MIL‐96) was selected due to the high binding energy of Al─O bonds and exposed Al<sup>3+</sup> coordination sites upon activation, which guaranteed excellent stability of microporous ion channels at high temperatures and enhanced Li<sup>+</sup> conductivity (Figure ##FIG##4##5b##).<sup>[</sup>\n##UREF##21##\n36\n##\n<sup>]</sup> A hybrid solid‐state electrolyte was prepared with the aluminum‐based MOF and polyvinylidene fluoride (PVDF), leading to exceptional stability compared to its liquid electrolyte counterparts. After 200 cycles at 120 °C, the LiFePO<sub>4</sub>||Li batteries exhibited 93% capacity retention and maintained 99% Coulombic efficiency. Furthermore, these results were in direct contrast of the copper‐containing MOF (Cu‐MOF), which could not cycle at such high temperatures due to its poor stability.</p>", "<p>While improving the operating temperature range of batteries is crucial for long‐term stability, batteries that can function in low temperatures are equally necessary for applications in extremely cold conditions, such as in outer space or deep ocean exploration.<sup>[</sup>\n##REF##35787034##\n40\n##\n<sup>]</sup> In this context, Cai et al. utilized MOF‐confinement effects of gaseous molecules (fluoromethane) in sub‐nanometer MOF pores to exploit the capillary condensation effect (<bold>Figure</bold> ##FIG##5##\n6\n##).<sup>[</sup>\n##REF##34099643##\n39\n##\n<sup>]</sup> The fluoromethane‐loaded MOF‐polymer membranes formed a liquefied gas electrolyte that was able to operate below its vapor pressure. Furthermore, the resulting Li||CF<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> cells demonstrated significantly higher capacities (≈500 mAh g<sup>−1</sup>) at −40 °C than those with conventional Celgard membranes (&lt;0.03 mAh g<sup>−1</sup>). To reduce the strong friction between the nanopore walls and confined electrolyte molecules without sacrificing the strong confinement effect, the same research group systematically adjusted the microenvironments of nanopore chemistry by modifying the linker group chemistry of the UiO‐66 series.<sup>[</sup>\n##REF##37522917##\n37\n##\n<sup>]</sup> These functionalized MOFs were shown to have enhanced trapping capabilities for volatile low‐temperature electrolyte solvents (Figure ##FIG##4##5c##). This improvement not only addresses safety concerns but also allows a wider range of working temperatures. The study also revealed aggregated solvation structures, modulated solvent molecular configurations, and tunable transport mechanisms from quasi‐solid to quasi‐liquid in functionalized MOFs, which deviated from the bulk counterparts.</p>", "<p>These quasi‐solid electrolytes prepared by hosting liquid and gas electrolytes in porous MOF matrices circumvent many of the shortcomings of both liquid electrolytes and solid‐state electrolytes. The capillary condensation and confinement effects of liquid and gas electrolytes not only alter their physicochemical properties, but also maintain their ionic conductivities, highlighting the potential of these quasi‐solid electrolytes in various extreme temperature battery applications. While the examples demonstrate that high operating temperatures were achieved through the confinement of conventional liquid and ionic liquid electrolytes and further enhancing the thermal stability of the MOF itself, low operating temperatures were also achieved by confining gaseous electrolyte molecules. The results underscore the high potential of MOF‐confined electrolytes as a novel approach for the development of next‐generation batteries.</p>", "<title>MOFs Used to Widen the Operation Voltage Range of Electrolytes</title>", "<p>Pairing lithium metal with various high‐voltage cathode materials holds great promise in the pursuit of high‐energy‐density batteries. However, this approach poses demanding requirements for electrolytes, necessitating both excellent oxidative stability and high reversibility toward lithium metal. At high voltages, the oxidation of solvent molecules restricts the electrochemical stability window of the electrolytes. Adding more salts into typical diluent electrolytes to form high‐concentration electrolytes can eliminate free solvents. It also leads to a shift in solvation structure from the solvent‐separated ion pair‐dominated configuration to the contact‐ion pair‐dominated configuration, resulting in denser SEI enriched with anion‐derived inorganic species (<bold>Figure</bold> ##FIG##6##\n7\n##). Consequently, high‐concentration electrolytes exhibit aggregated solvation structures with reduced free solvent content, thereby simultaneously enhancing Li metal compatibility and oxidative stability.</p>", "<p>Despite the promising benefits, the practical implementation of this approach is hindered by the high cost and viscosity of the salts, making them unsuitable for real‐world battery cells. An alternative strategy involves introducing a diluent solvent to create locally high‐concentration electrolytes, reducing viscosity without noticeably compromising the solvation structures. Nonetheless, this dilution process results in mediocre ionic conductivity, leading to inferior rate performances and even causing short circuit events in high‐loading cells. Furthermore, even concentrated electrolytes are not completely immune to solvent‐related decomposition issues, because free solvent molecules can still form during the desolvation of Li<sup>+</sup> ions on the electrolyte surface. While solid‐state electrolytes offer a solution to these problems by entirely avoiding solvent decomposition, their low ionic conductivity still remains as a challenge to satisfy the demand for practical batteries. Consequently, liquid electrolytes remain the most widely used option for lithium‐ion batteries.</p>", "<p>Desolvated Li<sup>+</sup> ions in MOF (ZIF‐7) pores were discovered in ether‐based electrolytes, where the ether solvents exhibited a “frozen” behavior within the MOF pores (<bold>Figure</bold> ##FIG##7##\n8a,b##).<sup>[</sup>\n##UREF##22##\n41\n##\n<sup>]</sup> This “frozen‐like” solvent, combined with the crystal‐like salt solute in MOFs, enabled the ether‐based electrolytes to operate stably at over 4.5 V. Based on the aforementioned mechanism, MOFs (ZIF‐71) with narrow pore sizes (4.2 Å) were used as a unique electrolyte solvation sheath filter to isolate free or weakly‐coordinated solvents from electrode contact. As a result, these special electrolytes composed of only strongly coordinated solvent molecules were achieved. This MOF‐filtered electrolyte, containing LiTFSI in PC, exhibited remarkably widened electrochemical stability windows of up to 5.2 V. Similarly, to further deplete solvents contained in electrolytes, which is considered an effective method for improving the electrochemical performances of high‐energy‐density LMBs, a more aggregative electrolyte configuration than a saturated liquid electrolyte was constructed in MOFs (HKUST‐1).<sup>[</sup>\n##UREF##23##\n42\n##\n<sup>]</sup> The solvated Li<sup>+</sup> ions in an ester‐based solvent encounter a partial desolvation process for the adaptation of narrow pore spaces. This unique electrolyte configuration allowed for significant expansion of the electrochemical oxidation stability window for MOF‐confined LiTFSI salt in the PC solvent system, increasing it from the original 4.5 to 5.4 V, while also exhibiting superior Li metal compatibility (Figure ##FIG##7##8c,d##). In addition, the suppression of lithium reactivity with electrolytes was also achieved through a MOF‐based nanoporous separator.<sup>[</sup>\n##REF##35013293##\n43\n##\n<sup>]</sup> The small nanopores of the separator partially desolvated Li<sup>+</sup> ions and created a confined environment that deactivated solvents for electrochemical reduction before Li metal deposition.</p>", "<p>In summary, the quasi‐solid electrolyte formed by the MOF‐confined lean liquid electrolytes offers a promising combination of the advantages found in both conventional liquid electrolytes and solid‐state electrolytes. The MOFs act as a solid shell, preventing direct contact between the solvent and electrodes, while also deactivating the free solvent, depleting solvated Li<sup>+</sup> ion, and even promoting electrolyte aggregation (Figure ##FIG##6##7##). Differing from solid electrolytes, confined liquids in MOF pores allow for high Li<sup>+</sup> conductivity. A quasi‐liquid transport mechanism was found in UiO‐66‐NH<sub>2</sub> confined nanoporous spaces, which proved useful for addressing stability concerns associated with volatile organic electrolytes while simultaneously endowing ultrafast transport of solvates (<bold>Figure</bold> ##FIG##8##\n9\n##).<sup>[</sup>\n##REF##37522917##\n37\n##\n<sup>]</sup> Similarly, a liquid‐electrolyte‐like transport mechanism was reported in the MOF‐confined LiPF<sub>6</sub> in PC‐contained open metal sites that effectively trapped PF<sub>6</sub>\n<sup>−</sup> anions, thus hindering their mobility.<sup>[</sup>\n##UREF##24##\n44\n##\n<sup>]</sup> Furthermore, the fixed counter‐ions on the MOF channels generate a negatively charged field, facilitating the transport of Li<sup>+</sup> ions and increasing the effective Li<sup>+</sup> ion transfer number compared to standard liquid electrolytes. These findings highlight the potential of MOF‐confined electrolytes as an innovative approach to enhance the performance of advanced battery systems.</p>", "<title>MOFs Used as Artificial Solid‐Electrolyte Interphases</title>", "<p>The in situ formation of SEI interfacial films on the Li metal surface, utilizing electrolyte additives and other methods, has proven to be an effective strategy for passivating the Li metal and preventing parasitic electrolyte decomposition. However, the unsatisfactory mechanical robustness of the vulnerable SEI struggles to effectively mitigate volume expansion. Furthermore, the low modulus of the as‐formed SEI layers commonly cannot withstand the mechanical deformation induced by dendrite growth. As for artificial SEI layers, integrating inorganic Li<sup>+</sup> conductors pose difficulties due to their brittle nature. In contrast, polymeric Li<sup>+</sup> conductors can form conformal coatings on Li metal with better integrity. Nevertheless, artificial SEI layers composed of polymers typically encounter poor conductivity issues, impacting the rate performance of lithium metal batteries.</p>", "<p>MOF materials hold great promise as efficient artificial SEI layers, offering both mechanical strength and ionic conductivity. The chemical environment of MOF pores can be engineered to manipulate the Li<sup>+</sup> ion transport behavior. The high mechanical strength of MOF particles poses a high potential for MOF films as artificial SEI layers to avoid Li dendrite puncturing (<bold>Figure</bold> ##FIG##9##\n10\n##), although films assembled from isotropically grown bulk MOF nanoparticles are mechanically brittle. In this context, 2D MOF nanosheets with flexible skeletons offer remarkable advantages compared to bulk MOF grains. An open‐architecture MOF film constructed by vertically growing 2D MOF nanosheets presents stereoscopic lithiophilic sites.<sup>[</sup>\n##UREF##25##\n45\n##\n<sup>]</sup> This unique configuration serves as a dynamic solid‐electrolyte interphase (SEI), exhibiting elastic expansion and contraction of the volume of stereoscopic lithiophilic sites. The self‐adjustment distribution of lithiophilic sites of the vertical growth of MOF nanosheets enables the homogenization of Li<sup>+</sup> ion flux, smart control of Li mass transport, and compact Li deposition, which leads to improved cycling performance (<bold>Figure</bold> ##FIG##10##\n11a,b##). These findings demonstrate the significant potential of 2D MOF nanosheets in advancing lithium‐ion battery technology through the efficient manipulation of lithiophilic sites and the formation of dynamic SEI.</p>", "<p>Incorporating polymer binders as a “glue” to cement rigid MOFs has also been proven as an alternative strategy to address the inherent brittleness of bulk MOF assemblies. For instance, a MOF/polymer composite SEI layer was formed by in situ growth of a Zn‐MOF on Cu foil and spin‐coating polyvinyl alcohol solution to enhance flexibility.<sup>[</sup>\n##UREF##26##\n46\n##\n<sup>]</sup> In addition, the polar O─H and Zn─N bonds in MOFs contributed to excellent electrolyte wettability and high Li<sup>+</sup> ion flux, reducing surface concentration gradients. Nanoporous expanses within MOFs effectively screen ions and hinder anion migration, leading to enhanced Li<sup>+</sup> ion migration with uniform Li<sup>+</sup> ion flux and inhibition of Li dendrite formation. The artificial MOF‐polymer composite SEI film efficiently adapts to the changes in volume during the cycle and also exhibits a decent ionic conductivity, thereby significantly extending battery cycle life (Figure ##FIG##10##11c##). Furthermore, a polymer with abundant lithiophilic sites was introduced into MOFs to mitigate the impedance between MOF grain boundaries.<sup>[</sup>\n##UREF##27##\n47\n##\n<sup>]</sup> The polymer then acts as a “chain” that interlinks Li “blocks” stored within the MOF pores. The MOF pores effectively compartmentalize bulk Li deposition, creating a 3D matrix for Li storage, which results in low‐barrier and dendrite‐free Li plating/stripping with exceptional Coulombic efficiency (Figure ##FIG##10##11d##). Additionally, the N‐rich polypyrrole component guides rapid Li<sup>+</sup> infiltration/extrusion and serves as the nucleation site for isotropic Li growth.</p>", "<p>The functions of MOF‐based artificial films are not limited to condensed and robust SEI films. In fact, they can also serve as electrolyte modulators and ion‐transport rectifiers on electrodes.<sup>[</sup>\n##UREF##24##\n44\n##, ##UREF##28##\n48\n##\n<sup>]</sup> By dispersing them in the electrolyte or by drop‐casting on the electrodes, the MOF layer undergoes a transformation into an ion‐conducting interphase, facilitating preferential Li<sup>+</sup> ion transport when the liquid electrolyte is introduced during battery assembly. The confined electrolyte within the MOF pore channels induces partial desolvation of Li<sup>+</sup> ions, effectively lowering the activation energy for charge transfer during Li deposition. Furthermore, the strong binding of anions to the MOFs results in increased lithium transport numbers and effectively suppresses the formation of ion‐concentration gradients in full cells. These insights into the behavior of MOF‐coated electrodes shed light on the potential for designing effective SEI layers and improving the performance and safety of lithium‐ion batteries. Further investigation into the intricate interactions between MOFs and Li<sup>+</sup> ions will advance the understanding of battery interfaces and guide the development of next‐generation energy storage technologies.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>" ]
[ "<title>Acknowledgements</title>", "<p>This work was supported by NSF through the UC San Diego Materials Research Science and Engineering Center (UCSD MRSEC), DMR‐2011924.</p>", "<p>\n<bold>Anthony U. Mu</bold> received his B.S. and Ph.D. degrees in Chemistry from Texas A&amp;M University in 2016 and 2022, respectively. During this time, he worked under the supervision of Professor Lei Fang. He is now working as a postdoctoral researcher in Professor Zheng Chen's group at UC San Diego. His current research focuses on the development of metal–organic framework‐based materials for battery applications.</p>", "<p>\n<bold>Guorui Cai</bold> received his Ph.D. in Inorganic Chemistry at the University of Science and Technology of China (USTC) in 2019 under the supervision of Prof. Hai‐Long Jiang. He subsequently worked as a postdoctoral researcher in Prof. Zheng Chen's group at UC San Diego until 2022. He is currently a postdoctoral researcher in Prof. Chunsheng Wang's group at University of Maryland. His research focused on the design of hierarchically porous MOF‐based materials for heterogeneous catalysis, electrolyte chemistry, and functional separators for rechargeable batteries at extreme temperatures.</p>", "<p>\n<bold>Zheng Chen</bold> is an Associate Professor in the Department of NanoEngineering, Programs of Chemical Engineering, and Materials Science and Engineering at UC San Diego. He received his B.S. from Tianjin University (2007) and Ph.D. from University of California Los Angeles (2012), both in Chemical Engineering. Then he served as postdoctoral researcher at Stanford before joining UC San Diego in 2016. His research focuses on understanding the fundamental properties of electrochemical interfaces and structures as well as designing materials and processes for more efficient and sustainable electrochemical energy storage and conversion.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0001\"><label>Figure 1</label><caption><p>Schematic showing the emerging battery applications of MOFs.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0002\"><label>Figure 2</label><caption><p>Proposed reaction pathways for the formation of common impurities in lithium batteries and relative scavenging processes by MOFs.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0003\"><label>Figure 3</label><caption><p>a) Schematic showing a HKUST‐1 MOF‐based membrane as a water scavenger. b) Cycling performances of Celgard separator and MOF‐based in‐built water scavenger in Li||Ni<sub>0.5</sub>Mn<sub>1.5</sub>O<sub>4</sub> cells at 25 °C (1 C current rate). c) Illustration of scavenging moiety functionalized MOFs and related membrane fabrication process for scavenging HF leading to d) improved cycling stability even with 500 ppm water at 55 °C. (a,b) Reproduced with permission.<sup>[</sup>\n##UREF##19##\n33\n##\n<sup>]</sup> Copyright 2020, Royal Society of Chemistry. (c,d) Reproduced with permission.<sup>[</sup>\n##UREF##20##\n34\n##\n<sup>]</sup> Copyright 2023, Wiley‐VCH.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0004\"><label>Figure 4</label><caption><p>Schematic showing the MOF‐based electrolytes for batteries operating under extreme temperatures.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0005\"><label>Figure 5</label><caption><p>a) Cycling performance of LMB pouch cell assembled with MOF‐based quasi‐solid electrolyte at 90 °C and after sustaining damage. b) Cycling performance of hybrid solid‐state electrolyte with activated Al‐based MOFs in comparison with previously reported liquid electrolytes. c) Wide‐temperature testing of Li||Cu with UiO‐66‐NH<sub>2</sub> mixed‐matrix membrane‐trapped electrolyte systems. (a) Reproduced with permission.<sup>[</sup>\n##REF##35314688##\n35\n##\n<sup>]</sup> Copyright 2023, Springer Nature. (b) Reproduced with permission.<sup>[</sup>\n##UREF##21##\n36\n##\n<sup>]</sup> Copyright 2023, Royal Society of Chemistry. (c) Reproduced with permission.<sup>[</sup>\n##REF##37522917##\n37\n##\n<sup>]</sup> Copyright 2022, American Chemical Society.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0006\"><label>Figure 6</label><caption><p>Schematic showing the mechanism of nano‐confinement effects for lowering the equilibrium pressure of liquefied gas and the implementation of MPM‐based liquefied gas electrolytes (LGE) for Li batteries. Reproduced with permission.<sup>[</sup>\n##REF##34099643##\n39\n##\n<sup>]</sup> Copyright 2021, Springer Nature.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0007\"><label>Figure 7</label><caption><p>Schematic showing the MOF‐based electrolytes used to increase the operating voltage range of batteries.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0008\"><label>Figure 8</label><caption><p>a) Improved oxidative stability of the MOF‐based Li<sup>+</sup> desolvated electrolyte and the b) discharge capacity against cycle number collected from NCM‐811||Li‐metal full‐cells using this electrolyte. The inset shows the corresponding galvanostatic discharge curves versus the gravimetric energy density. c) Linear sweep voltammetry curves of typical electrolyte and the prepared solvent‐depleted electrolyte in MOFs. The inset schematically illustrates the cell configuration for the measurement. d) Cycling performance of the NCM‐811||Li half‐cell using the MOF‐based electrolyte. (a,b) Reproduced with permission.<sup>[</sup>\n##UREF##22##\n41\n##\n<sup>]</sup> Copyright 2020, Elsevier. (c,d) Reproduced with permission.<sup>[</sup>\n##UREF##23##\n42\n##\n<sup>]</sup> Copyright 2020, Royal Society of Chemistry.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0009\"><label>Figure 9</label><caption><p>Schematic showing the ultrafast Li<sup>+</sup> ion migration and tunable transport mechanism inside MOFs. Reproduced with permission.<sup>[</sup>\n##REF##37522917##\n37\n##\n<sup>]</sup> Copyright 2022, American Chemical Society.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0010\"><label>Figure 10</label><caption><p>Illustration of comparison between dendrite formation on the bare electrode and dendrite suppression with MOF‐based artificial SEI layer.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6652-fig-0011\"><label>Figure 11</label><caption><p>a) Evaluation of Coulombic efficiency plots of Li||Cu cells based on pristine Cu and the OA‐MOF/Cu at 3 mA cm<sup>−2</sup> with a constant lithiation capacity of 1 mAh cm<sup>−2</sup>. Inset: corresponding galvanostatic Li plating/stripping curves at the 100th cycle. b) Average Coulombic efficiency and corresponding standard deviation for Li||Cu cells based on pristine Cu and OA‐MOF/Cu at 3, 5, and 15 mA cm<sup>−2</sup>. c) Cycle performance of Li||LiFePO<sub>4</sub> full cells made with the artificial SEI protected Cu foil at 1 C. d) Long‐term cycling stability of the PHK@Cu versus bare‐Cu cells tested at 1 C. (a,b) Reproduced with permission.<sup>[</sup>\n##UREF##25##\n45\n##\n<sup>]</sup> Copyright 2021, Wiley‐VCH. (c) Reproduced with permission.<sup>[</sup>\n##UREF##26##\n46\n##\n<sup>]</sup> Copyright 2019, Royal Society of Chemistry. (d) Reproduced with permission.<sup>[</sup>\n##UREF##27##\n47\n##\n<sup>]</sup> Copyright 2022, Wiley‐VCH.</p></caption></fig>" ]
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{ "acronym": [], "definition": [] }
52
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 9; 11(2):2305280
oa_package/0d/51/PMC10787081.tar.gz
PMC10787082
0
[ "<title>Introduction</title>", "<p>Pheochromocytoma (PHEO) and paraganglioma (PGL) are rare neuroendocrine tumors that arise from chromaffin cells. PHEOs arise from the adrenal medulla, whereas PGLs arise from the neural crest localized outside the adrenal gland [##REF##35158861##1##]. Since the two tumor types cannot be differentiated on the basis of histologic findings, anatomical location is used to distinguish between them, and the overall incidence is approximately 0.6 cases per 100,000 person-years [##UREF##0##2##]. Although most pheochromocytoma and paraganglioma (PPGL) are benign, approximately 10% have metastatic potential. Approximately 40% of PPGL cases carry germline mutations [##REF##35158861##1##,##REF##33820394##3##]. More than 20 genes are known to cause inherited PPGL [##REF##35158861##1##], and approximately 20% of these are caused by pathogenic germline variants in succinate dehydrogenase complex (<italic>SDHx</italic>), <italic>TMEM127,</italic> or <italic>MAX</italic> genes [##REF##30536464##4##]. Less frequently, mutations in the genes responsible for Von Hippel Lindau disease (VHL), multiple endocrine neoplasia type 2 (MEN2) and neurofibromatosis type 1 (NF1) are also found in patients with hereditary PPGL [##REF##21358191##5##]. Most patients with metastatic PPGL are sporadic, whereas in patients with inherited PPGL, metastatic tumors caused by <italic>SDHB </italic>mutations account for up to 43% of cases, followed by <italic>VHL</italic>, <italic>SDHD</italic>, and <italic>NF1</italic> mutations [##UREF##0##2##].</p>", "<p>VHL (OMIM #193300) is an autosomal dominant multisystemic tumor predisposition syndrome characterized by benign and malignant tumors, including PPGL, central nervous system and retinal hemangioblastomas, clear cell renal cell carcinoma (RCC), pancreatic neuroendocrine tumors, endolymphatic sac tumors, and epididymal and broad ligament cystadenomas, as well as renal and pancreatic cysts [##UREF##1##6##]. The incidence of VHL is estimated to be one in 36,000. The lifetime penetrance is close to 100% by the age of 75 years [##UREF##1##6##]. Clinically, VHL is divided into two major types: type 1, which does not involve the PPGL, and type 2, which does involve the PPGL. Type 2 is further subdivided into type 2a, which is associated with central nervous system and retinal hemangioblastoma (CNB/RB) but not RCC, type 2b, which is associated with both CNB/RB and RCC, and type 2c, which is associated with neither [##REF##12814730##7##]. Although little is known about the proportion of each type, the lifetime risk of developing PPLG in VHL patients is estimated to be 10-25%, which is consistent with the frequency of type 2 [##UREF##1##6##]. According to the results of a nationwide survey in Japan, 62 (15%) of 409 registered VHL patients developed PPGL, of which 31 were type 2A, 20 were type 2B, and 11 were type 2C [##REF##22876661##8##]. The frequency of type 2C is equivalent to 2.7% of all VHL patients, which is an indication that it is a very rare phenotype. Accordingly, PPGL itself is a rare tumor, and VHL is rarely found in patients with PPGL alone, making diagnosis extremely difficult. Here we report a patient with VHL who developed PGL at the age of five years and relapsed four years later without any symptoms other than PGL. There will be a discussion of the importance of genetic diagnosis and appropriate follow-up.</p>" ]
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[ "<title>Discussion</title>", "<p>Our patient was diagnosed with VHL type 2c. The only symptom was PGL, which is considered a rare case of VHL. The type of VHL pathogenic variant has been shown to account for differences in PPGL risk. There is a strong genotype-phenotype correlation, and protein-truncating variants have been identified in individuals with type 1, whereas missense variants have been associated with type 2 [##UREF##1##6##]. The risk of CNB/RB and RCC in affected individuals may reflect the ability of the variant protein to regulate the hypoxia-inducible factor (HIF) pathway. Higher levels of HIF expression appear to be associated with a lower risk of CNB/RB and RCC [##REF##25533676##14##]. The two most common type 2C-associated <italic>VHL</italic> missense mutations are the amino acid substitutions Val84Leu and Leu188Val [##UREF##1##6##]. There are also reports of Gly93Ser with PHEO [##REF##17922902##15##], and Leu163Phe with PGL [##UREF##4##16##]. The <italic>VHL</italic> missense variant Arg161Gln (R161Q) detected in our patient has been previously reported in another family. Qi et al. reported a family with VHL R161Q variant and all three patients in the family had no symptoms other than PHEO consistent with type 2c [##REF##23842656##17##]. Santarpia et al. reported a patient with type 2c VHL, who had bilateral PHEOs, multiple PGLs, and an extra-axial supratentorial frontal meningioma [##REF##17102087##18##]. Iida et al. reported a variety of phenotypes in a family with the R161Q variant. The proband has VHL type 2A with PHEO and retinal hemangioblastoma (RB) [##REF##14767570##19##]. Another family member also developed a large PHEO and RB. In addition, another patient developed neuroendocrine tumors of the pancreas without a PHEO. These cases show that the symptoms associated with R161Q are diverse and not necessarily limited to type 2c. In our patient in the current case, it was not confirmed whether the variant was inherited or a de novo mutation because the parents were reluctant to undergo genetic testing; and the relationship with the paternal grandfather's renal cancer cannot be denied. Follow-up is required to monitor not only for PGL recurrence but also for other VHL lesions to develop.</p>", "<p>Deciding when and to what extent to perform genetic testing for PPGL is difficult. Sixty percent of PPGL is not hereditary, and hereditary PPGL genes are diverse. In the current case, the SDHx genes were tested in the PGL at the time of onset to assess the risk of tumor metastasis, but no mutation was found, so germline genetic testing was not performed. At the time of the relapse, the patient had germline genetic testing and the diagnosis was VHL. According to an Endocrine Society clinical practice guideline, all patients with PPGLs should be engaged in shared decision-making for genetic testing [##REF##24893135##20##]. This guideline also provides an algorithm for determining which genes to test. When the patient is non-syndromic, has no metastases, and has a noradrenergic tumor in the extra-adrenal gland,<italic> SDHB</italic>, <italic>SDHD</italic>, <italic>SDHC</italic>, <italic>VHL</italic>, and <italic>MAX</italic> are tested. In the present case, there were no symptoms other than PGL, so we could not initially diagnose it as syndromic (VHL), but according to the algorithm above, <italic>VHL</italic> is also a first-line target gene. In addition, according to another guideline for genetic testing for inherited PPGL by Muth et al., <italic>FH</italic>, <italic>NF1</italic>, <italic>RET</italic>, <italic>SDHB</italic>, <italic>SDHD</italic>, and <italic>VHL</italic> should be tested as a minimum, and the addition of MEN1, SDHA, SDHAF2, SDHC, TMEM127, and MAX is recommended [##REF##30536464##4##]. Again, <italic>VHL</italic> is listed as one of the genes that should be tested. RB and PHEO are also the lesions that occur in the youngest patients with VHL, as the minimum/average age of 0/25 and 2/27, respectively, makes <italic>VHL</italic> genetic testing particularly important in pediatric patients with PPGLs.</p>" ]
[ "<title>Conclusions</title>", "<p>Although rare, it is necessary to consider VHL in the differential diagnosis of isolated PGL. PGL may be the only symptom of VHL. Genetic diagnosis is important for proper diagnosis and medical intervention, especially in pediatric patients. If germline genetic testing for PLG is performed, it must include VHL. In the present case, a definitive diagnosis was delayed because the initial genetic testing was performed for somatic mutations of the SDHx genes in the tumor. The development of PGL tends to correlate with VHL missense mutations, but other VHL lesions may be highly variable among patients. A variety of phenotypes have been reported for R161Q, and it is necessary to follow up on this patient, keeping in mind the occurrence of VHL lesions other than PGL.</p>" ]
[ "<p>Pheochromocytoma and paraganglioma (PPGL) are rare neuroendocrine tumors. Catecholamine production by the tumors leads to high blood pressure. Although most PPGLs are benign, some have metastatic potential. Almost half of PPGLs are caused by germline mutations, and the causative genes are diverse. Von Hippel-Lindau disease (VHL) is an autosomal dominant multisystem tumor predisposition syndrome characterized by central nervous system and retinal hemangioblastomas, clear cell renal cell carcinoma, pancreatic neuroendocrine tumors, and PPGLs. Sometimes VHL presents only as paraganglioma (PGL), making its diagnosis difficult. A male child aged five years and one month was found to have isolated catecholamine-producing PGL in the right renal hilum during evaluation for hypertension. The patient was completely cured by tumor resection, and somatic mutation testing of the tumor revealed no abnormalities. At the age of nine years and 11 months, the patient had a recurrence of PGL in the left border of the abdominal aorta. Comprehensive germline genetic testing was performed and revealed a pathologic missense variant NM_000551.4:c.482G&gt;A p.(Arg161Gln) in the<italic> VHL</italic> gene. This variant showed loss of heterozygosity in both primary and recurrent tumors by Sanger sequencing, and DNA microarray analysis revealed a monosomy of the entire chromosome 3 where <italic>VHL</italic> is located. Arg161Gln has been previously reported in several other VHL families, and the symptoms were diverse beyond PPGLs. This case demonstrates the importance of genetic diagnosis with VHL in mind. It was also recognized that this patient needed to be followed for symptoms of VHL other than PGL.</p>" ]
[ "<title>Case presentation</title>", "<p>A male child, aged five years and one month, was admitted to our hospital for evaluation of hypertension. His height, weight, and blood pressure were 106 cm (-0.2 SD), 15.5 kg (-0.9 SD), and 154/114 mmHg, respectively. Headaches and excessive sweating were reported. Although there was no family history of PPGL, his paternal grandfather had renal cancer. Urinalysis, complete blood count, and blood biochemistry showed no abnormalities. Endocrinologic tests showed normal thyroid function and elevated catecholamines as plasma norepinephrine 1529 pg/ml, urinary norepinephrine 323.9 μg/day, urinary normetanephrine 1.61 μg/mg·Cr (Table ##TAB##0##1##).</p>", "<p>Abdominal MRI showed a 1.4 cm tumor with speckled high signal intensity on T2-weighted images near the right renal hilum (Figure ##FIG##0##1a##). 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) showed localized accumulation near the right renal hilum with a maximum standardized uptake value (SUVmax) of 8.2 (cut-off &gt; 3.0), but no other uptake consistent with distant metastases was observed (Figure ##FIG##0##1b##). There was no accumulation at the lesion on 123I-metaiodobenzylguanidine (MIBG) scintigraphy. The preoperative diagnosis was a noradrenaline-producing retroperitoneal PGL. Hypertension was treated with oral doxazosin and enalapril maleate, and tumor resection was performed at the age of five years and four months. Antihypertensive therapy was discontinued immediately after surgery, the postoperative course was uneventful, and the patient recovered without complications.</p>", "<p>The removed tumor was 1.5 cm in size with a hard capsule and no capsule rupture was observed (Figure ##FIG##1##2a##). Tumor growth exhibited the so-called zellballen pattern, consisting of well-developed short spindle-shaped to polygonal tumor cells showing nested growth with an intervening stromal component of fibrovascular tissue and peripheral sustentacular cells (Figure ##FIG##1##2b##) [##UREF##0##2##]. Immunohistochemically, the tumor cells were diffusely stained by chromogranin A (Figure ##FIG##1##2c##), and the tumor was confirmed as PGL. The Ki-67 positive cell rate was 4%. The grading of adrenal PPGL (GAPP) score was 4 points, which predicts metastatic potential based on histopathologic evaluation and the type of catecholamine produced, 0-2 low risk, 3-6 intermediate risk, and 7-10 high risk [##UREF##2##9##]. Tumor tissue DNA was tested for succinate dehydrogenase (SDH) genes (<italic>SDHB</italic>, <italic>SDHAF2</italic>, <italic>SDHB</italic>, <italic>SDHC</italic>, and <italic>SDHD</italic>) by targeted DNA sequencing, but no pathogenic variants were detected. Antihypertensive medication was discontinued immediately after surgery and no hypertension was observed. Endocrinological tests on postoperative day 14 showed a decrease in urinary noradrenaline to 34.6 μg/day and urinary normetanephrine to 0.08 mg/day. Thereafter, we periodically evaluated blood and urine catecholamines and performed follow-up observations using 18F-FDG PET and abdominal MRI.</p>", "<p>At four years and seven months after surgery (when the patient was nine years and 11 months), there were no subjective symptoms such as headache or excessive sweating as observed at the time of initial onset, and blood pressure was normal at 111/83 mmHg, but Abdominal MRI showed a 1.2 cm tumor with high signal intensity on T2-weighted images at the same site (Figure ##FIG##2##3a##), and urinary normetanephrine level was elevated to 1.11 μg/mg·Cr (Table ##TAB##0##1##). 18F-FDG-PET showed an accumulation of SUVmax 19.5 localized to the left border of the abdominal aorta (Figure ##FIG##2##3b##) and there was an accumulation on 123I- MIBG scintigraphy (Figure ##FIG##2##3c##). It was diagnosed as a recurrence of PGL.</p>", "<p>The tumor was resected at the age of 10 years zero months after the same antihypertensive therapy as at the time of initial PGL. The size of the resected tumor was 15 mm. In contrast to the first surgery, some rupture of the capsule was observed (Figure ##FIG##3##4a##). Polygonal tumor cells were observed growing in a zellballen pattern, similar to the initial tumor (Figure ##FIG##3##4b##). The tumor cells were chromogranin A positive (Figure ##FIG##3##4c##), confirming the recurrence of the PGL. The Ki-67 positive cell rate was 5% and the GAPP score was 5 points. Two months after surgery, urinary normetanephrine decreased to 0.25 μg/mg·Cre, and no accumulation was observed on 18F-FDG-PET. The patient was subsequently followed with catecholamines and imaging studies and is currently 11 years and one month old and in remission.</p>", "<p>Considering the possibility of hereditary PPGL syndrome, we provided genetic counseling to the patient and parents, obtained their consent, and performed genetic testing using the TruSight One Expanded panel (Illumina, Inc., San Diego, California, United States). Shortly, DNA was extracted from peripheral blood using a standard method. The library was prepared from 50 ng of DNA according to the manufacturer's recommended protocol, and a 12.5 pM library was sequenced on an Illumina MiSeq system (2 × 250 cycles) following the standard Illumina protocol. Data analysis was conducted as previously reported [##REF##34449562##10##]. In short, haplotype variant calling was performed using HaplotypeCaller version 4.0.6.0 (GATK (Genome Analysis Toolkit); Broad Institute, Cambridge, Massachusetts, United States) [##UREF##3##11##], and functional classification of variants was performed using SnpEff (version 4.3t) [##REF##22728672##12##]. The Integrative Genomic Viewer (IGV version 2.4.13) was used for visualization [##REF##22517427##13##]. The previously reported pathogenic missense variant was detected in <italic>VHL</italic>, NM_000551.4:c.482G&gt;A p.(Arg161Gln) (Figure ##FIG##4##5a##). The variant was confirmed by Sanger sequencing using the VHL exon 3 specific primer set (VHL_Ex3-F: 5'-TACAGGTAGTTGTTGGCAAAGC-3' and VHL_Ex3-R: 5'-GAAACTAAGGAAGGAACCAGTCC-3', product size 360 bp) and BigDye Terminator v3.1 cycle sequencing kit on the ABI PRISM 3100xl genetic analyzer (Thermo Fisher Scientific Inc., Waltham, Massachusetts, United States). It turned out that this patient had von Hippel-Lindau disease, and the PGL was a symptom of that disease. In PGLs, the peak of the wild-type allele decreased in both tumors, suggesting that loss of heterozygosity of the <italic>VHL</italic> gene occurred within the tumors (Figure ##FIG##4##5b##). Structural chromosomal aberration analysis was performed by DNA microarray (OncoScan™ CNV Assay, Thermo Fisher Scientific Inc.), and both tumors showed monosomy for the entire chromosome 3 (Figure ##FIG##4##5c##). In the PGL at the time of recurrence, partial monosomies were observed on chromosomes 1, 5, and 13, which were not observed in the PGL at the time of initial onset. On the other hand, monosomy of chromosomes 3 and 11 was common to both tumors, suggesting that the original tumor had recurred with additional chromosomal abnormalities.</p>", "<p>After the diagnosis of VHL, a systemic screening was performed to evaluate for other lesions of VHL. However, no abnormalities were found on brain MRI or fundus examination, and no lesions other than the PGL were found in the patient.</p>" ]
[ "<p>We sincerely thank the patient and the parents for their participation.</p>" ]
[ "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG1\"><label>Figure 1</label><caption><title>Imaging studies of the patient at initial onset</title><p>Axial abdominal MRI T2-weighted images (a) and 18F-FDG-PET (b). Tumors are indicated by yellow arrows.</p><p>FDG: F-18 fluorodeoxyglucose; PET: positron emission tomography</p></caption></fig>", "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG2\"><label>Figure 2</label><caption><title>Pathological findings of initial PGL</title><p>Hematoxylin and eosin staining (a, b);  Immunohistochemical staining of chromogranin A (c).</p><p>PGL: paraganglioma</p></caption></fig>", "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG3\"><label>Figure 3</label><caption><title>Imaging studies of the patient at recurrence</title><p>Axial abdominal MRI T2-weighted images (a), 18F-FDG-PET (b), and coronal 123I-MIBG scintigraphy (c). Tumors are indicated by yellow arrows.</p><p>FDG: F-18 fluorodeoxyglucose; PET: positron emission tomography; MIBG: meta-iodobenzylguanidine</p></caption></fig>", "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG4\"><label>Figure 4</label><caption><title>Pathological findings of recurrent PGL</title><p>Hematoxylin and eosin staining (a, b). Rupture of the capsule was observed in recurrent PGL (yellow arrow in a). Immunohistochemical staining of chromogranin A (c).</p><p>PGL: paraganglioma</p></caption></fig>", "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG5\"><label>Figure 5</label><caption><title>Genetic analysis.</title><p>A missense variant in <italic>VHL</italic>, NM_000551.4:c.482G&gt;A p.(Arg161Gln), was detected by next-generation sequencing (a), and Sanger sequencing revealed loss of heterozygosity in both PGLs (b). DNA microarray showed complete monosomy of chromosome 3 in both PGLs, and the recurrent PGL showed a pattern of chromosomal abnormalities derived from the initial PGL.</p><p>PGL: paraganglioma</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"TAB1\"><label>Table 1</label><caption><title>Catecholamine levels in blood and urine</title></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Catecholamines</td><td rowspan=\"1\" colspan=\"1\">Reference values</td><td rowspan=\"1\" colspan=\"1\">Initial onset</td><td rowspan=\"1\" colspan=\"1\">Recurrence</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Plasma</td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\"> </td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Dopamine</td><td rowspan=\"1\" colspan=\"1\">&lt; 30 pg/ml</td><td rowspan=\"1\" colspan=\"1\">10</td><td rowspan=\"1\" colspan=\"1\">≤ 5</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Adrenaline</td><td rowspan=\"1\" colspan=\"1\">≤ 100 pg/ml</td><td rowspan=\"1\" colspan=\"1\">67</td><td rowspan=\"1\" colspan=\"1\">80</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Noradrenaline</td><td rowspan=\"1\" colspan=\"1\">100-450 pg/ml</td><td rowspan=\"1\" colspan=\"1\">1529</td><td rowspan=\"1\" colspan=\"1\">488</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Urine</td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\"> </td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Adrenaline</td><td rowspan=\"1\" colspan=\"1\">3.4-26.9 μg/day</td><td rowspan=\"1\" colspan=\"1\">11.5</td><td rowspan=\"1\" colspan=\"1\">8.0</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Noradrenaline</td><td rowspan=\"1\" colspan=\"1\">48.6-168 μg/day</td><td rowspan=\"1\" colspan=\"1\">323.9</td><td rowspan=\"1\" colspan=\"1\">222.4</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Metanephrine</td><td rowspan=\"1\" colspan=\"1\">0.04-0.19 mg/day</td><td rowspan=\"1\" colspan=\"1\">0.08</td><td rowspan=\"1\" colspan=\"1\">0.12</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Normetanephrine</td><td rowspan=\"1\" colspan=\"1\">0.09-0.33 mg/day</td><td rowspan=\"1\" colspan=\"1\">0.76</td><td rowspan=\"1\" colspan=\"1\">0.63</td></tr></tbody></table></table-wrap>" ]
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[ "<fn-group content-type=\"other\"><title>Author Contributions</title><fn fn-type=\"other\"><p><bold>Concept and design:</bold>  Yo Niida</p><p><bold>Drafting of the manuscript:</bold>  Yo Niida</p><p><bold>Supervision:</bold>  Yo Niida</p><p><bold>Acquisition, analysis, or interpretation of data:</bold>  Naoki Okada, Akihiro Shioya, Sumihito Togi, Hiroki Ura</p><p><bold>Critical review of the manuscript for important intellectual content:</bold>  Naoki Okada, Akihiro Shioya, Sumihito Togi, Hiroki Ura</p></fn></fn-group>", "<fn-group content-type=\"other\"><title>Human Ethics</title><fn fn-type=\"other\"><p>Consent was obtained or waived by all participants in this study. Institutional Review Board of Kanazawa Medical University issued approval G161 dated August 29, 2022. This study was conducted by the Declaration of Helsinki</p></fn></fn-group>", "<fn-group content-type=\"competing-interests\"><fn fn-type=\"COI-statement\"><p>The authors have declared that no competing interests exist.</p></fn></fn-group>" ]
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[{"label": ["2"], "article-title": ["Pheochromocytoma and paraganglioma [Letters to the Editor]"], "source": ["N Engl J Med"], "person-group": ["\n"], "surname": ["Neumann", "Young WF", "Eng"], "given-names": ["HP", "Jr", "C"], "fpage": ["1883"], "volume": ["381"], "year": ["2019"]}, {"label": ["6"], "article-title": ["Von Hippel-Lindau and hereditary pheochromocytoma/paraganglioma syndromes: clinical features, genetics, and surveillance recommendations in childhood"], "source": ["Clin Cancer Res"], "person-group": ["\n"], "surname": ["Rednam", "Erez", "Druker"], "given-names": ["SP", "A", "H"], "fpage": ["0"], "lpage": ["75"], "volume": ["23"], "year": ["2017"]}, {"label": ["9"], "article-title": ["Validation of pathological grading systems for predicting metastatic potential in pheochromocytoma and paraganglioma"], "source": ["PLoS One"], "person-group": ["\n"], "surname": ["Koh", "Ahn", "Kim"], "given-names": ["JM", "SH", "H"], "fpage": ["0"], "volume": ["12"], "year": ["2017"]}, {"label": ["11"], "article-title": ["From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline"], "source": ["Curr Protoc Bioinformatics"], "person-group": ["\n"], "surname": ["Van der Auwera", "Carneiro", "Hartl"], "given-names": ["GA", "MO", "C"], "fpage": ["11"], "volume": ["43"], "year": ["2013"]}, {"label": ["16"], "article-title": ["Isolated paraganglioma in a patient with VHL P.L163F mutation"], "source": ["AACE Clin Case Rep"], "person-group": ["\n"], "surname": ["Goldstein", "Neril", "Rothberger"], "given-names": ["M", "RE", "GD"], "fpage": ["0"], "lpage": ["6"], "volume": ["6"], "year": ["2020"]}]
{ "acronym": [], "definition": [] }
20
CC BY
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2024-01-14 23:41:56
Cureus.; 15(12):e50484
oa_package/38/ee/PMC10787082.tar.gz
PMC10787083
37974381
[ "<title>Introduction</title>", "<p>Monolayer 1H‐phase transition metal dichalcogenides (TMDs) such as WS<sub>2</sub> are direct band gap semiconductors that consist of an atomic layer of tungsten sandwiched between a top and a bottom layer of sulfur atoms that are arranged in their respective hexagonal lattice structure.<sup>[</sup>\n##REF##21230799##\n1\n##, ##REF##20229981##\n2\n##\n<sup>]</sup> The band structures of monolayer TMDs<sup>[</sup>\n##REF##23464873##\n3\n##, ##REF##24660756##\n4\n##, ##REF##24328329##\n5\n##, ##UREF##0##\n6\n##, ##REF##23132225##\n7\n##\n<sup>]</sup> consist of two inequivalent K (−K) valleys in the hexagonal Brillouin zone. The strong spin‐orbit coupling and broken inversion symmetry in monolayer TMDs result in a large energy splitting between the top spin‐up (spin‐down) valence band and the bottom spin‐down (spin‐up) valence band in the K (−K) valley via the preservation of time reversal symmetry.<sup>[</sup>\n##REF##22706701##\n8\n##, ##REF##22706698##\n9\n##, ##REF##22673914##\n10\n##, ##REF##23003071##\n11\n##, ##UREF##1##\n12\n##, ##REF##31442375##\n13\n##\n<sup>]</sup> Given that both of the Berry curvature and orbital magnetic moment are odd under the time‐reversal symmetry operation, one can selectively populate excitons in different valleys (K or −K) by means of circularly polarized light (CPL), where CPL with positive helicity (σ<sup>+</sup>) couples to the K valley and that of the negative helicity (σ<sup>−</sup>) couples to the −K valley according to valley‐dependent optical selection rules.<sup>[</sup>\n##REF##18233399##\n14\n##, ##UREF##2##\n15\n##, ##REF##23403575##\n16\n##\n<sup>]</sup> However, the degree of valley polarized emission in monolayer TMDs under CPL depends strongly on the intervalley scatterring time and exciton lifetimes. Therefore, understanding the processes that govern the exciton lifetimes and the associated degree of valley polarization is essential for assessing the emergent applications of valley‐polarized excitons in devices.<sup>[</sup>\n##UREF##3##\n17\n##\n<sup>]</sup> Various strategies aiming at enhancing the valley polarization by further breaking the spatial‐inversion symmetry have been proposed, including applying magnetic fields, chemical doping of magnetic elements, and employing magnetic proximity effects.<sup>[</sup>\n##UREF##3##\n17\n##, ##UREF##4##\n18\n##, ##REF##32806059##\n19\n##, ##UREF##5##\n20\n##, ##REF##34259493##\n21\n##, ##UREF##6##\n22\n##\n<sup>]</sup> However, with respect to these methods for enhancing the valley polarization, the efficiency of applying an external magnetic field is extremely low for valley polarization (≈0.3 meV per Tesla); magnetic doping suffers from the formation of inhomogeneously distributed dopant clusters; and magnetic proximity effects are easily diminished by the valley submergence. Alternative approaches by electrical and optical control of the valley polarization in TMDs at room temperature and under off‐resonance conditions would be more practical and desirable.<sup>[</sup>\n##REF##31442375##\n13\n##, ##UREF##3##\n17\n##\n<sup>]</sup> Towards this goal, carrier doping, including chemical and physical approaches, appears to be an efficient way to manipulate the valley polarization, because excess carriers introduced in the TMDs not only tailor the exciton species but also modify the valley polarization dynamics considerably. Chemical doping is known to be an effective and convenient method to modify the carrier concentrations and electronic bandstructures in monolayer TMD materials, which can induce shifts in the Fermi level as well as modifications to the electronic, optical, and valley polarization properties. Physcial doping, via either electrostatic carrier doping by gating or light excitation by creating electron‐hole pairs, can also induce valley polarization enhancement through stronger screening of the Coulomb interaction by excess carriers, which helps suppress the intervalley scattering.<sup>[</sup>\n##UREF##3##\n17\n##\n<sup>]</sup>\n</p>", "<p>For effective manipulation of the valley degrees of freedom in semiconducting monolayer TMDs by electrostatic doping, it is essential to address the interfacial issues of Fermi level pinning and Schottky barrier heights when making electrical contacts to the TMDs. To date, several approaches to circumvent these issues in TMD‐based field effect transistors (FETs) have been reported, including the use of a low work function (WF) metal for the electrical contact,<sup>[</sup>\n##REF##23240655##\n23\n##, ##REF##25514512##\n24\n##\n<sup>]</sup> the use of a Fermi‐level de‐pinning layer,<sup>[</sup>\n##UREF##7##\n25\n##, ##UREF##8##\n26\n##\n<sup>]</sup> and various techniques of molecule/chemical doping of TMDs.<sup>[</sup>\n##REF##23570647##\n27\n##, ##UREF##9##\n28\n##, ##REF##25310177##\n29\n##, ##REF##27299957##\n30\n##, ##UREF##10##\n31\n##, ##REF##26434774##\n32\n##\n<sup>]</sup> Developing heterostructures that consist of a two‐dimensional (2D) van der Waals (vdW) metal as the top contact material on a 2D semiconductor is another approach to lower the Schottky barrier height (SBH).<sup>[</sup>\n##UREF##11##\n33\n##, ##REF##28749686##\n34\n##, ##REF##30235414##\n35\n##, ##REF##29400979##\n36\n##\n<sup>]</sup> For this purpose, a natural material for consideration is graphene.<sup>[</sup>\n##UREF##12##\n37\n##\n<sup>]</sup> However, deposition of another metallic layer on graphene is required for electrical characterizations, and the carrier injection efficiency generally varies, depending on the metal deposited. Alternatively, the metallic 1T′‐phase WTe<sub>2</sub> with a low WF<sup>[</sup>\n##REF##27152360##\n38\n##\n<sup>]</sup> and a vdW clean surface<sup>[</sup>\n##UREF##13##\n39\n##\n<sup>]</sup> may be considered as an efficient electron‐type (<italic toggle=\"yes\">n</italic>‐type) contact material for 2D semiconductors. However, there have not been extensive studies to date on using the 1T′‐phase WTe<sub>2</sub> as the metal contact to lower the contact resistance of TMD‐based devices due to the challenges of material preparation and material stability.<sup>[</sup>\n##UREF##14##\n40\n##, ##REF##31314531##\n41\n##, ##REF##29255139##\n42\n##, ##UREF##15##\n43\n##\n<sup>]</sup>\n</p>", "<p>In this study, ternary WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1) alloys were synthesized via chemical vapor deposition in a one‐step synthesis process to produce high‐quality 2D semiconductors of tunable bandgaps for high‐performance eletronic devices. By alloying Te into tungsten disulfide WS<sub>2</sub>, the WF of the ternary WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1) alloy could be tuned to match that of the 2D contacts as the source (S) / drain (D) electrodes in the FET structure to reduce the SBH. These monolayer ternary WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1) alloys evolved from the semiconducting 1H phase to the metallic 1T′ phase, depending on the Te concentration (<italic toggle=\"yes\">x</italic>). X‐ray photoelectron spectroscopic (XPS) characterizations confirmed the existence of W, S, and Te with controlled ratios. The optical bandgap of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy could be tuned from 2 to 1.65 eV in the 1H semiconducting phase and then dropped down to 0 in the 1T′ metallic phase. The FET devices based on monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys revealed characteristics that confirmed the 1H phase being n‐type semiconductors and the 1T′ phase being a metal. Moreover, the use of WTe<sub>2</sub> metallic contacts with a WF close to the band edge of the WTe<sub>0.12</sub>S<sub>1.88</sub> alloy resulted in WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub>‐based FETs with excellent electronic characteristics, including a high electron carrier mobility up to 50 cm<sup>2</sup>V<sup>−1</sup>S<sup>−1</sup> and an on/off current ratio up to 10<sup>6</sup>. Furthermore, it has been reported that valley polarization can be tuned by doping,<sup>[</sup>\n##UREF##16##\n44\n##\n<sup>]</sup> defects,<sup>[</sup>\n##REF##31442375##\n13\n##, ##UREF##17##\n45\n##\n<sup>]</sup> and alloying engineering.<sup>[</sup>\n##REF##26657930##\n46\n##\n<sup>]</sup> In particular, alloying with heavier elements can modify the valley polarization by enhancing the spin‐orbit coupling (SOC). Therefore, it is worth investigating how the valley polarized emission from WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys under CPL evolves with the concentration of Te. We note that the degree of valley polarization (DVP) for as‐grown monolayer WS<sub>2</sub> is typically very low (&lt;5%) at RT due to significant phonon‐ and defect‐induced inter‐valley scattering (<bold>Figure</bold>\n##FIG##0##\n1a##), where the DVP value (<italic toggle=\"yes\">P</italic>\n<sub>DVP</sub>) is defined by the following expression:with <italic toggle=\"yes\">I</italic> (<italic toggle=\"yes\">σ</italic>\n<sup>+</sup>) and <italic toggle=\"yes\">I</italic> (<italic toggle=\"yes\">σ</italic>\n<sup>−</sup>) denoting the right‐handed (RH) and left‐handed (LH) circular polarization‐resolved photoluminescence (PL) intensity, respectively. In contrast, the <italic toggle=\"yes\">P</italic>\n<sub>DVP</sub> values in monolayer ternary alloys WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> with <italic toggle=\"yes\">x</italic> &gt; 0 were found to be tunable and were enhanced up to 40% under the excitation of right‐handed circularly polarized (RCP) light. The underlying mechanism for tailoring the valley‐polarized PL of monolayer 1H‐ternary WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys may be attributed to the enhanced SOC strength and broken mirror symmetry by mixing the Te‐S species, as schematically shown in Figure ##FIG##0##1b##. The stronger SOC of the Te atoms than that of the S atoms can increase the spin‐orbit energy splitting (Δ<sub>SO</sub>) so that Δ<sub>SO</sub> (WTe<sub>2</sub>) = 484 meV and Δ<sub>SO</sub> (WS<sub>2</sub>) = 412 meV.<sup>[</sup>\n##REF##29255139##\n42\n##\n<sup>]</sup> Additionally, by applying a back‐gated voltage <italic toggle=\"yes\">V</italic>\n<sub>G</sub> to WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub>‐based FETs with 1T′‐WTe<sub>2</sub> as the contact electrodes, the resulting DVP values were found to be further enhanced from 40% for <italic toggle=\"yes\">V</italic>\n<sub>G</sub> = 0 up to ≈75% for <italic toggle=\"yes\">V</italic>\n<sub>G</sub> = −20 V. This finding suggests that modulating the carrier doping level can enhance the valley polarization by screening the long‐range electron‐hole exchange interactions, thus reducing the momentum‐dependent intervalley scattering, as shown in Figure ##FIG##0##1c##. Overall, we have demonstrated successfully tuning and drastically enhancing the DVP values in semiconducting monolayer 1H‐TMDs at RT by combined strategies of chemically alloying and electrically gating the monolayer TMD‐based FETs with electrodes of reduced SBH and weakened Fermi level pinning. Our approach thus offers new opportunities toward developing realistic valley‐dependent optoelectronic devices for energy‐efficient information processing at room temperature.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<p>The experimental setup for the growth of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1) alloys is schematically depicted in Supporting Information Figure S1a (see details of the synthesis process in the Experimental Section). By tuning the ratios of the chalcogen precursors and that of the Ar/H<sub>2</sub> gas flow, we were able to synthesize both 1H and 1T′ phases of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1). <bold>Figure</bold>\n##FIG##1##\n2a–d## show typical optical microscopy (OM) images of the 1H and 1T′ WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> monolayers. When the chalcogen ratio (Te/S) increased from 1 to 7 and the Ar/H<sub>2</sub> ratio increased from 80/40 to 80/50, monolayer 1T′ WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> was obtained. The reactivity of the Te with WO<sub>3</sub> was far lower than that of S with WO<sub>3</sub>, so the usage of a large amount of Te precursors and higher H<sub>2</sub> gas flow was necessary to ensure that Te could be incorporated into the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> matrix to form the 1T′ phase.</p>", "<p>X‐ray photoelectron spectroscopic (XPS) was used to investigate the chemical composition of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1) alloys synthesized by atmosphere‐pressure chemical vapor deposition (APCVD) and to evaluate the electron doping concentration as a function of the Te doping concentration. The core level spectra were calibrated via fitting adventitious carbon at 284.8 eV. The high‐resolution spectra of W 4f, S 2p, and Te 3d peaks are shown in Figure ##FIG##1##2e–g##. For 1H‐phase WS<sub>2</sub>, the corresponding binding energies of the W 4f <italic toggle=\"yes\">\n<sub>7/2</sub>\n</italic> and W 4f <italic toggle=\"yes\">\n<sub>5/2</sub>\n</italic> peaks were located at 33.2 and 35.3 eV, respectively, and the binding energies for the S 2p<italic toggle=\"yes\">\n<sub>3/2</sub>\n</italic> and S 2p<italic toggle=\"yes\">\n<sub>1/2</sub>\n</italic> peaks were located at 162.9 and 164.2 eV, respectively, which were all consistent with the values reported previously.<sup>[</sup>\n##REF##26758908##\n47\n##\n<sup>]</sup> By tuning the mass ratios of Te and S powder from 1 to 100 with specific H<sub>2</sub> flow rates from 40 to 60 sccm during the synthesis process, W‐Te bonds at 573.8 eV (Te 3d<sub>5/2</sub>) and 584.1 eV (Te 3d<sub>3/2</sub>) appeared in the spectra, which provided direct evidence for Te doping into the original WS<sub>2</sub> crystal lattice. The binding energy of W 4f and S 2p peaks displayed a downshift ≈0.4 eV in the alloy with <italic toggle=\"yes\">x</italic> = 13%, indicating that Te doping resulted in reduced electronegativity. When a structural phase transition occurred at a higher stoichiometric ratio (<italic toggle=\"yes\">x</italic> &gt; 0.5), the binding energies of W 4f, S 2p, and Te 3d all shifted to lower energy states concurrently. For 1T′‐phase WTe<sub>2</sub>, the main W 4f peaks at 31.28 eV (4f<sub>7/2</sub>) and 33.44 eV(4f<sub>5/2</sub>) and the Te 3d peaks located at 572.6 (3d<sub>5/2</sub>) and 583 eV (3d<sub>3/2</sub>) were assigned to the W–Te bond. The chemical stoichiometry information mentioned above directly indicated that the mole fraction of Te and the structural evolution between the 1H and 1T′ phases could be tuned by changing the mass ratio of Te and S powder together with specific H<sub>2</sub> concentrations during the APCVD growth. Furthermore, the distinct binding energy redshifts of W 4f, Te 3d, and S 2p with increasing Te concentration up to <italic toggle=\"yes\">x</italic> = 35% indicate that the Fermi level moved downward closer to the valence band and hence the p‐type doping of Te into the WS<sub>2</sub> lattice, which was further corroborated by measurements of the increasing work function of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> with <italic toggle=\"yes\">x</italic> for 0 &lt; <italic toggle=\"yes\">x</italic> ≤ 0.35 by ultraviolet photoelectron spectroscopy (UPS, to be further elaborated below), as shown in the inset of <bold>Figure</bold> ##FIG##2##\n3c##. Both of the XPS and UPS showed that Te as the p‐type dopant doped in the n‐type semiconductor.</p>", "<p>To quantitatively evaluate the changes in the electron carrier concentration with Te doping, which plays a critical role in determining the DVP of 1H‐ternary WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (0 &lt; <italic toggle=\"yes\">x</italic> ≤ 0.35), we need to evaluate the (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) values of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub>, where <italic toggle=\"yes\">E</italic>\n<sub>c</sub> and <italic toggle=\"yes\">E</italic>\n<sub>F</sub> denote the conduction band edge energy and the Fermi level, respectively. We employed the UPS studies to extract the (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) values and the PL measurements to obtain the optical bandgap <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> values for WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 &lt; <italic toggle=\"yes\">x</italic> ≤ 0.35), where <italic toggle=\"yes\">E</italic>\n<sub>v</sub> denotes the valance band edge energy, and the bandgap between the conduction and valence band edges is given by <italic toggle=\"yes\">E</italic>\n<sub>g</sub> ≡ (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) = <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> + <italic toggle=\"yes\">E</italic>\n<sub>binding</sub>, where <italic toggle=\"yes\">E</italic>\n<sub>binding</sub> represents the binding energy of A‐excitons. As shown in Figure ##FIG##1##2h##, linear extraction of the valence band edge tail was used to determine the (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) values. We found that the (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) value first increased from 1.8 eV for <italic toggle=\"yes\">x</italic> = 0 to 1.9 eV for <italic toggle=\"yes\">x</italic> = 6%, and then steadily decreased with increasing <italic toggle=\"yes\">x</italic> down to 1.57 eV for <italic toggle=\"yes\">x</italic> = 35%, as shown in Figure ##FIG##1##2h,i##.</p>", "<p>Next, using the optical bandgap <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> of the 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> obtained from the PL measurements (Figure ##FIG##2##3b##), and noting that <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> = (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) − <italic toggle=\"yes\">E</italic>\n<sub>binding</sub> = (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) + (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) − <italic toggle=\"yes\">E</italic>\n<sub>binding</sub> where (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) were given by the UPS studies as mentioned above, we derived the (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) values for the 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> by using <italic toggle=\"yes\">E</italic>\n<sub>binding</sub> = Ry (<italic toggle=\"yes\">µ</italic>/<italic toggle=\"yes\">m</italic>\n<sub>e</sub>) (<italic toggle=\"yes\">ε</italic>\n<sub>0</sub>/<italic toggle=\"yes\">ε</italic>\n<sub>s</sub>)<sup>2</sup> ∼ 0.1 eV, with Ry being the Rydberg energy 13.6 eV, <italic toggle=\"yes\">µ</italic> ∼ 0.178 <italic toggle=\"yes\">m</italic>\n<sub>e</sub> the reduced mass of A‐excitons, <italic toggle=\"yes\">m</italic>\n<sub>e</sub> the free electron mass, and (<italic toggle=\"yes\">ε</italic>\n<sub>s</sub>/<italic toggle=\"yes\">ε</italic>\n<sub>0</sub>) ∼ 5 the dielectric constant of the substrate. After the (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) values were determined as a function of the Te doping, the electron doping concerntrations (<italic toggle=\"yes\">N</italic>\n<sub>D</sub>) may be calculated by using the effective density of state (<italic toggle=\"yes\">N</italic>\n<sub>C</sub>) near the bottom of the conduction band for two‐dimensional electrons\nwhere <italic toggle=\"yes\">h</italic> is the Planck constant. Thus, we obtained <italic toggle=\"yes\">N</italic>\n<sub>D</sub> from the following expression\nwhere <italic toggle=\"yes\">T</italic> is the temperature and <italic toggle=\"yes\">k</italic>\n<sub>B</sub> is the Boltzmann constant. The results of the <italic toggle=\"yes\">N</italic>\n<sub>D</sub> analysis are presented in Figure ##FIG##1##2j##, showing that <italic toggle=\"yes\">N</italic>\n<sub>D</sub> decreases from (3 × 10<sup>10</sup>) cm<sup>−2</sup> to (1 × 10<sup>7</sup>) cm<sup>−2</sup> when varies the Te concentration from 6% to 35%, and that the Fermi level for all samples with <italic toggle=\"yes\">x</italic> ≤ 35% was below <italic toggle=\"yes\">E</italic>\n<sub>c</sub> at room temperature. This analysis suggests that the carrier densities in the semiconducting 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys may be controlled by tuning the Te doping level.</p>", "<p>The optical properties of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys were investigated by Raman and PL spectra, and the <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> values derived from the PL spectra were applied to estimating the (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) values and the electron doping concentrations using Equations (##FORMU##1##2##) and (##FORMU##2##3##) as stated above. In Figure ##FIG##2##3a##, Raman spectra of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with various Te concentrations were collected to examine the composition‐dependent lattice vibrational modes. For monolayer 1H‐phase WS<sub>2</sub>, the two characteristic peaks <mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>E</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi>g</mml:mi></mml:mrow><mml:mn>1</mml:mn></mml:msubsup></mml:mrow></mml:math>and <italic toggle=\"yes\">A</italic>\n<sub>1</sub>\n<italic toggle=\"yes\">\n<sub>g</sub>\n</italic> were located at 351 cm<sup>−1</sup> and 419 cm<sup>−1</sup>, respectively, in agreement with previous reports.<sup>[</sup>\n##REF##31442375##\n13\n##\n<sup>]</sup> In the 1H‐phase alloys, it was evident that the Raman footprints changed with increasing Te concentration relative to those of the pure WS<sub>2</sub>, where the 1H‐phase characteristic peaks weakened and additional peaks associated with the 1T′‐phase appeared around 163 cm<sup>−1</sup> and 213 cm<sup>−1</sup>. The positions of the two WS<sub>2</sub> vibrational modes were softened and redshifted with the increase of Te concentration, which may be attributed to the effect of heavier Te atoms on decreasing the vibrational frequencies. In comparison with pure 1T′‐WTe<sub>2</sub> with main <italic toggle=\"yes\">A</italic>\n<sub>1</sub> modes<sup>[</sup>\n##REF##26797573##\n48\n##\n<sup>]</sup> at 120, 132, 162, and 213 cm<sup>−1</sup>, the observed new peaks around 195, 225, 290, and 400 cm<sup>−1</sup> in Figure ##FIG##2##3a## were similar to the 1H‐phase and 1T′‐phase WS<sub>2</sub>‐like peaks reported previously.<sup>[</sup>\n##REF##28112926##\n49\n##, ##REF##30323336##\n50\n##, ##UREF##18##\n51\n##, ##UREF##19##\n52\n##, ##REF##30525432##\n53\n##\n<sup>]</sup>\n</p>", "<p>In addition to the Raman spectra, PL measurements were performed on the alloys to investigate the composition‐dependent optical bandgap (<italic toggle=\"yes\">E</italic>\n<sub>emission</sub>) evolution and phase transition in Figure ##FIG##2##3b##. We found that the optical bandgap of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys could be tuned from 2 eV (for pure 1H‐WS<sub>2</sub>) to zero (for pure 1T′‐WTe<sub>2</sub>) as the concentration of Te increased, and 1H to 1T′ phase transition existed at an intermediate Te concentration (<italic toggle=\"yes\">x</italic> &gt; 0.35) in the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys. For 1T′ ternary tellurides, no PL signal could be detected because of their metallic nature. Notably, within the 1H phase, the correlation between the optical bandgap and the Te concentration was approximately linear to each other, and the 1H‐phase optical bandgap ranged between 2 eV (pure WS<sub>2</sub>, <italic toggle=\"yes\">x</italic> = 0) and 1.75 eV (WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy, <italic toggle=\"yes\">x</italic> = 0.35), as presented in the inset of Figure ##FIG##2##3b##. Additionally, the composition‐dependent PL peak position of the as‐grown alloys was found to be in good agreement with the quadratic rule of the bandgap (<italic toggle=\"yes\">E</italic>\n<sub>g</sub>) estimation reported by Kang et al:<sup>[</sup>\n##UREF##20##\n54\n##\n<sup>]</sup>\nwhere the parameter <italic toggle=\"yes\">b</italic> for WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1−</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy equals 0.08,<sup>[</sup>\n##UREF##20##\n54\n##\n<sup>]</sup> and the bandgap of the 1H‐phase WTe<sub>2</sub> is 1.03 eV from literature.<sup>[</sup>\n##REF##23132225##\n7\n##, ##REF##26479493##\n55\n##, ##UREF##21##\n56\n##\n<sup>]</sup>\n</p>", "<p>The validation of the correlation between the <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> value and the Te doping level in Equation (##FORMU##3##4##) thus provides a fast and efficient way to determine the chemical composition of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy. The neutral A‐exciton PL peak of different WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys, which resulted from direct‐gap A‐exciton recombination at the K/K′ points in the Brillouin zone, exhibited an approximately 250 meV redshift when doped with ≈ 35% Te. We also fitted the PL spectra of pure WS<sub>2</sub> and the 1H‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> &lt; 0.5) to deconvolve (Supporting Information, Figure S2) the A‐exciton and trion contributions, and found that the optimal lineshape for the spectral contributions was a mixed Gaussian–Lorentzian function. As shown in Figure ##FIG##2##3c##, the A‐exciton and trion peaks of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> &lt; 0.5) were both redshifted relative to those of pure WS<sub>2</sub>, which was consistent with the decreasing optical bandgap with increasing Te doping.</p>", "<p>Figure ##FIG##2##3d–i## show the polarization‐dependent PL spectra of 1H phase monolayer WS<sub>2</sub> and WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys on SiO<sub>2</sub>/Si substrate under <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> circularly polarized excitation. The valley polarization of WS<sub>2</sub> at room temperature (RT) rarely exceeded 5%, but the DVP in monolayer ternary WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (<italic toggle=\"yes\">x</italic> &lt; 0.5) alloys were found to vary from 3% (for <italic toggle=\"yes\">x</italic> = 35%) to 40% (for <italic toggle=\"yes\">x</italic> = 6%). The significant enhancement in the valley‐polarization at RT from WS<sub>2</sub> to WTe<sub>0.12</sub>S<sub>1.88</sub> may be attributed to the enhanced spin‐orbit coupling by introducing Te atoms in WS<sub>2</sub> lattice. On the other hand, the substitutions of S atoms by Te atoms also markedly affect the carrier density. The estimated 2D carrier density versus Te‐concentration is shown in Figure ##FIG##1##2j##, showing an initial rapid increase from <italic toggle=\"yes\">x</italic> = 0 to <italic toggle=\"yes\">x</italic> = 6% followed by a monotonic decreasing trend with a further increase in the Te‐concentration. The Te‐doping dependence of the 2D carrier density is similar to that of the DVP shown in Figure ##FIG##2##3i##, where the highest enhancement in the valley polarization (≈ 40%) at RT was found when the carrier density reached the highest value (≈3 × 10<sup>10</sup>) cm<sup>−2</sup> in the WTe<sub>0.12</sub>S<sub>1.88</sub> (<italic toggle=\"yes\">x</italic> = 6%) alloy. Similar behavior of the DVP dependence on Te doping for WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys is also found under <italic toggle=\"yes\">σ <sup>−</sup>\n</italic> circularly polarized excitation, as shown in Figure S3 (Supporting Information). This correlation between the carrier density and the DVP may be understood in terms of increasing exciton screening effects with increasing carrier densities, which resulted in reduced long‐range electron‐hole exchanging interactions and hence suppressed the momentum‐dependent intervalley scattering and improved the DVP.</p>", "<p>Noting the benefits of carrier doping and increased spin‐orbit coupling on enhancing the DVP in WTe<sub>0.12</sub>S<sub>1.88</sub>, we conjectured that further enhancement of the DVP may be achieved by controlling the carrier densities via electrostatic doping, which would require the development of high‐quality electrical contacts with reduced SBH and weakened Fermi level pinning to the 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys. To this end, we fabricated back‐gated FETs based on WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys on (P++)Si/SiO<sub>2</sub> substrates and used specially designed electrical contacts to evaluate the performance of these devices, which provided critical information about the quality of our electrical contacts on the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys.</p>", "<p>To fabricate 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> based FETs, monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> flakes were first transferred to heavily p‐doped Si substrates with a SiO<sub>2</sub> top layer of 285 nm thickness, which served as a bottom gate and a gate dielectric, respectively. The metallic contact electrodes were fabricated by E‐beam lithography, and 200 nm Au contact electrodes were deposited on silanol functionalized SiO<sub>2</sub>/Si substrate using E‐beam evaporation. The channel length (<italic toggle=\"yes\">L</italic>) and width (<italic toggle=\"yes\">W</italic>) of the fabricated devices were 0.5 µm and 1 µm (<bold>Figure</bold>\n##FIG##3##\n4a##), respectively. The metallic contact electrodes were transferred and aligned on top of the WTe<sub>2x</sub>S<sub>2(1‐x)</sub> monolayer flake by means of a metal transferred method, to be elaborated in the experimental section. Using cross‐sectional analysis by transmission electron microscopy (TEM), we examined the interface between the transferred Au and the monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> as shown in Figure ##FIG##3##4b##, and found that in contrast to the direct Au deposition onto monolayer TMD via electron‐beam evaporation, our process of transferring Au contacts to WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> did not incur any damages to the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> layer, as evidenced by the perfect rows of atoms clearly visible in the TEM image (Figure ##FIG##3##4b##). The electrical performance of the CVD‐grown WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with metal‐transferred Au contact electrodes was investigated by studying the backgated FETs made of monolayer WTe<sub>2x</sub>S<sub>2(1‐x)</sub> alloys. The transfer characteristic curves of the monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> devices are presented in Figure ##FIG##3##4## and Figure S4, Supporting Information. In Figure ##FIG##3##4c–e##, all semiconducting 1H‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> = 0, 0.06, 0.13, 0.26, and 0.35) devices showed typical n‐type transport behavior with high on/off (&gt; 10<sup>5</sup>) current ratios. Additionally, the field‐effect mobility (μ<sub>FE</sub>) may be evaluated by the following relation:<sup>[</sup>\n##REF##29896954##\n57\n##, ##REF##25961515##\n58\n##\n<sup>]</sup>\nwhere <italic toggle=\"yes\">I</italic>\n<sub>ds</sub> is the source‐drain current, <italic toggle=\"yes\">V</italic>\n<sub>gs</sub> the gate‐source voltage; <italic toggle=\"yes\">V</italic>\n<sub>ds</sub> the source‐drain voltage, and <italic toggle=\"yes\">C</italic>\n<sub>g</sub> the gate capacitance. Using Equation (##FORMU##4##5##) and the transfer characteristic curves in Figure ##FIG##3##4c–e##, we obtained mobility values of 0.58 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup>, 35 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup>, 10.5 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup>, 2.8 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup>, and 1.8 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup> for the 1H‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with <italic toggle=\"yes\">x</italic> = 0, 0.06, 0.13, 0.26, and 0.35, respectively. The ON current (<italic toggle=\"yes\">I</italic>\n<sub>on</sub>) for the WTe<sub>0.12</sub>S<sub>1.88</sub> alloy‐based devices was improved by 2 orders of magnitude relative to the control devices (WS<sub>2</sub>‐FET devices). In contrast, for the 1T′‐phase alloys, the drain current was found to increase by ≈50 times in magnitude from the 1T′‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> = 0.52) to pure WTe<sub>2</sub>, which implied that the metallic behavior of tellurides could be modified by controlling the concentration of the alloying S atoms. Furthermore, the source‐drain current (<italic toggle=\"yes\">I</italic>\n<sub>ds</sub>) was completely independent of the backgated voltage (<italic toggle=\"yes\">V</italic>\n<sub>gs</sub>) in all three semimetallic 1T′‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> = 0.52, 0.64 and 1), as shown in Figure ##FIG##3##4f–h##, and the resistivity of the WTe<sub>2</sub> devices was reduced by 2 orders of magnitude as compared to that of the 1T′‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (<italic toggle=\"yes\">x</italic> = 0.52) devices.</p>", "<p>The improvement in the electrical performance of the FETs based on the 1H‐phase semiconducting WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with Au electrode can be attributed to several effects. At the metal‐semiconductor interface, electrons can be injected from the metal to the semiconductor either by thermionic emission over the Schottky barrier or via tunneling through the Schottky barrier. The width of the Schottky barrier is equal to the width of the depletion region (<italic toggle=\"yes\">W</italic>\n<sub>dep</sub>), which depends on the doping concentration (<italic toggle=\"yes\">N</italic>\n<sub>D</sub>) of the semiconductor and is proportional to (<italic toggle=\"yes\">N<sub>D</sub>\n</italic>)<sup>−1/2</sup>according to the following relation: <mml:math id=\"jats-math-7\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi>dep</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msqrt><mml:mrow><mml:mn>2</mml:mn><mml:msub><mml:mi>ε</mml:mi><mml:mi mathvariant=\"normal\">s</mml:mi></mml:msub><mml:msub><mml:mi>V</mml:mi><mml:mi>bi</mml:mi></mml:msub><mml:msub><mml:mi>d</mml:mi><mml:mi>TMD</mml:mi></mml:msub><mml:mo>/</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mi>e</mml:mi><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant=\"normal\">D</mml:mi></mml:msub></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:msqrt><mml:mo>,</mml:mo></mml:mrow></mml:mrow></mml:math> where <italic toggle=\"yes\">d</italic>\n<sub>TMD</sub> ∼ 0.6 nm is the monolayer thickness of the TMD sample, <italic toggle=\"yes\">ε<sub>s</sub>\n</italic> (≈5) is the dielectric constant of semiconductors, <italic toggle=\"yes\">V</italic>\n<sub>bi</sub> = (<italic toggle=\"yes\">ϕ</italic>\n<sub>M</sub> − <italic toggle=\"yes\">ϕ</italic>\n<sub>s</sub>)/<italic toggle=\"yes\">e</italic> is the built‐in potential between the metallic contact and the TMD semiconductor, and <italic toggle=\"yes\">e</italic> is the elementary charge. Therefore, <italic toggle=\"yes\">W</italic>\n<sub>dep</sub> decreased with increasing <italic toggle=\"yes\">N</italic>\n<sub>D,</sub> and the probability of electron injection into the semiconductor via tunneling through the Schottky barrier increased. Indeed, we found the largest <italic toggle=\"yes\">I</italic>\n<sub>on</sub> and highest <italic toggle=\"yes\">µ</italic>\n<sub>FE</sub> in the lightly Te‐doped FET devices (WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> with <italic toggle=\"yes\">x</italic> = 6%) because of the maximum <italic toggle=\"yes\">N</italic>\n<sub>D</sub> value ∼(3 × 10<sup>10</sup>) cm<sup>−2</sup> that induced the minimum depletion width <italic toggle=\"yes\">W</italic>\n<sub>dep</sub>, which enhanced the electron tunneling through the Schottky barrier. Additionally, we note that the quality of the electrical contact between the metallic electrode and the semiconducting channel directly affects the carrier injection and therefore the performance of the devices. In the case of TMD‐based devices, at the metal electrode/TMD interface, the large bandgap of TMDs leads to a Schottky barrier (SB) and a van der Waal (vdW) gap without chemical bonds, which gives rise to a high contact resistance for the as‐fabricated devices. Thus, it is imperative to eliminate the interfacial vdW gap and to depin the Fermi level of the metallic electrode to facilitate efficient charge transport across the contact interface for optimized FET device performances as well as efficient control of electrostatic doping.</p>", "<p>To overcome the Fermi level pinning effect and to lower the Schottky barrier height (SBH) at the interface, we developed a new process to transfer surface‐functionalized, water‐assisted wafer Au electrodes onto monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> to form WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub>‐based FETs with Au contacts, as schematically illustrated in Figure S5. Besides using the Au contacts, there are two known methods to date for eliminating the Fermi‐level pinning effects of electrical contacts to TMDs. One is to strengthen the hybridization by doping the underlying TMDs. The other is to weaken the hybridization between the contact electrode and the TMDs by inserting graphene to greatly reduce the contact resistance and SBH. The use of heterostructures that consist of a 2D van der Waals (vdW) semi‐metal, such as graphene, as the top contact material on a 2D semiconductor, is a common approach to lower the SBH and contact resistance. However, deposition of another metallic layer on graphene is required for electrical characterizations, and the carrier injection efficiency generally varies, depending on the metal deposited on graphene. Alternatively, the metallic 1T′‐phase WTe<sub>2</sub> with a low work function and a vdW clean surface may be an efficient electron‐type (<italic toggle=\"yes\">n</italic>‐type) contact material for 2D semiconductors. However, there have not been extensive studies to date on using the 1T′‐phase WTe<sub>2</sub> as the metal contact to lower the contact resistance of TMD‐based devices because of the challenges in materials preparation and stability. Noting that Te‐based monolayers are known to be unstable in ambient conditions, we chose multilayer WTe<sub>2</sub> as the electrodes alternative to Au contacts for the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy‐based FET devices. The stability test of multilayer WTe<sub>2</sub> is illustrated in Figure S6 (Supporting Information), which demonstrates that multilayer WTe<sub>2</sub> could be stable in air beyond 15 days.</p>", "<p>Next, we investigated the characteristics of the 1H‐WTe<sub>2x</sub>S<sub>2(1‐x)</sub>‐based FETs with two types of transferred source(S)/drain(D) electrodes: Au (work function ≈ 5.2 eV), and 1T′‐WTe<sub>2</sub> (work function ≈ 4.6 eV), as shown in <bold>Figure</bold>\n##FIG##4##\n5\n##. Given that 1T′‐WTe<sub>2</sub> has the closest electron affinity to the work function of 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub>, we expected the use of 1T′‐WTe<sub>2</sub> electrodes to induce the lowest Schottky barrier height. The work function of each electrode was measured by ultraviolet photoelectron spectroscopy (UPS) and the results are shown in Figure S7, Supporting Information. Figure ##FIG##4##5a,b## illustrate the band diagrams of the Au/1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> and 1T′‐WTe<sub>2</sub>/1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> interfaces in the equilibrium condition after both of the contacts were made. The charge injection in the 2D WTe<sub>0.12</sub>S<sub>1.88</sub> channel was determined by the SBH and Schottky barrier width (SBW), both largely dependent on the extent of the semiconductor band‐bending at the metal (Au or 1T′ WTe<sub>2</sub>) and 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> Schottky contact region. While the SBH governed the extent of thermionic emission of carriers over the barrier, the SBW determined the extent of the thermionic field emission and quantum tunneling of charge carriers. Hence, both the SBH and SBW must be minimized to achieve efficient injection of charge carriers from the contact into the semiconducting WTe<sub>0.12</sub>S<sub>1.88</sub> channel as shown in Figure ##FIG##4##5b##.</p>", "<p>The field‐effect mobility and the on/off current ratios of 1H‐phase WTe<sub>0.12</sub>S<sub>1.88</sub> crystal for Au and WTe<sub>2</sub> electrodes were found to be <italic toggle=\"yes\">µ</italic>\n<sub>FE</sub> = 35 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup> and (<italic toggle=\"yes\">I</italic>\n<sub>on</sub>/<italic toggle=\"yes\">I</italic>\n<sub>off</sub>) = 5 × 10<sup>5</sup>, and <italic toggle=\"yes\">µ</italic>\n<sub>FE</sub> = 50 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup> and (<italic toggle=\"yes\">I</italic>\n<sub>on</sub>/<italic toggle=\"yes\">I</italic>\n<sub>off</sub>) = 1.1 × 10<sup>6</sup>, respectively. In particular, we found substantially more efficient gate tunability in the FET with 1T′‐WTe<sub>2</sub> contacts. That is a smaller threshold voltage <italic toggle=\"yes\">V</italic>\n<sub>g,th</sub> of 18 V (compared with <italic toggle=\"yes\">V</italic>\n<sub>g,th</sub> = 50 V for Au contacts) and a higher on‐current of ≈50 µA µm<sup>−1</sup> (compared with ≈30 µA µm<sup>−1</sup> for Au contacts). These findings implied that the types of electrical contacts could substantially modify the FET characteristics.</p>", "<p>To quantitatively investigate the SBH, the FET output characteristics were measured at different temperatures (200–300 K) and presented in Figure S8. The SBH <italic toggle=\"yes\">ϕ</italic>\n<sub>B</sub> can be extracted from the data by using the following thermionic emission model:<sup>[</sup>\n##REF##36080075##\n59\n##, ##UREF##22##\n60\n##, ##REF##28088846##\n61\n##, ##UREF##23##\n62\n##\n<sup>]</sup>\nwhere <italic toggle=\"yes\">A</italic> is the junction area, <italic toggle=\"yes\">A<sup>*</sup>\n</italic> is the effective Richardson‐Boltzmann constant given by<mml:math id=\"jats-math-9\" display=\"inline\"><mml:mrow><mml:mrow><mml:msup><mml:mi>A</mml:mi><mml:mo>∗</mml:mo></mml:msup><mml:mo>=</mml:mo><mml:mn>4</mml:mn><mml:mi>π</mml:mi><mml:mi>e</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi mathvariant=\"normal\">n</mml:mi></mml:msub><mml:msubsup><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>/</mml:mo><mml:msup><mml:mi>h</mml:mi><mml:mn>3</mml:mn></mml:msup></mml:mrow></mml:mrow></mml:math>, <italic toggle=\"yes\">m</italic>\n<sub>n</sub> is the electronic effective mass of WTe<sub>2x</sub>S<sub>2(1‐x)</sub>, and the effective “emission current” <italic toggle=\"yes\">I</italic>\n<sub>0</sub> is obtained from the <italic toggle=\"yes\">I</italic>\n<sub>ds</sub>‐versus‐<italic toggle=\"yes\">V</italic>\n<sub>ds</sub> curves measured at different temperatures and gate voltages. Thus, we obtained ϕ<sub>\n<italic toggle=\"yes\">B</italic>\n</sub> at the two contacts/ WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (<italic toggle=\"yes\">x</italic> &lt; 0.5) interfaces from the slop of the linear fit to ln (<italic toggle=\"yes\">I</italic>\n<sub>0</sub>/<italic toggle=\"yes\">T</italic>\n<sup>3/2</sup>) as a function of 1/(<italic toggle=\"yes\">k</italic>\n<sub>B</sub>\n<italic toggle=\"yes\">T</italic>) (Figure ##FIG##4##5c,d## and Figure S7, Supporting Information). In Figure ##FIG##4##5e##, the effective SBH were extracted under the flat band gate voltage (<italic toggle=\"yes\">V</italic>\n<sub>g</sub>) condition, which corresponded to the start of deviation of the ϕ<sub>\n<italic toggle=\"yes\">B</italic>\n</sub> versus <italic toggle=\"yes\">V</italic>\n<sub>g</sub> curve from the linear slope. Figure ##FIG##4##5f## summarizes the relation between the SBH (at the <italic toggle=\"yes\">V</italic>\n<sub>FB</sub>) of the metal‐semiconductor junction (MSJ) and the work functions of the Au and WTe<sub>2</sub> in contact with monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys. The SBH between the Au electrode and WTe<sub>0.12</sub>S<sub>1.88</sub> alloy was ≈150 meV, which confirmed the existence of Fermi‐level pinning compared to the ideal Schottky‐Mott rule theoretically calculated SBH (≈620 meV). In contrast, in the case of WTe<sub>2</sub> electrodes, the value of the SBH (≈80 meV) between 1T′‐WTe<sub>2</sub> and WTe<sub>0.12</sub>S<sub>1.88</sub> alloy was much closer to the ideal Schottky‐Mott rule theoretically calculated SBH (≈20 meV) for monolayer WTe<sub>0.12</sub>S<sub>1.88</sub>‐based FETs with 1T′‐WTe<sub>2</sub> contacts. This finding revealed that WTe<sub>2</sub> electrical contacts weakened the Fermi level pinning and thus improved the electron charge injection to the WTe<sub>0.12</sub>S<sub>1.88</sub> alloy substantially. Additionally, the SBW for the 1T′‐WTe<sub>2</sub> contact can be estimated by using the built‐in potential <italic toggle=\"yes\">V</italic>\n<sub>bi</sub> = (<italic toggle=\"yes\">ϕ</italic>\n<sub>M</sub> − <italic toggle=\"yes\">ϕ</italic>\n<sub>s</sub>)/<italic toggle=\"yes\">e</italic> = 0.02 and <italic toggle=\"yes\">N</italic>\n<sub>D</sub> ≈ (1.3 × 10<sup>11</sup>) cm<sup>−2</sup> for the WTe<sub>0.12</sub>S<sub>1.88</sub> alloy, which yields a small SBW ≈2.2 nm for 1T′‐WTe<sub>2</sub> on WTe<sub>0.12</sub>S<sub>1.88</sub>.</p>", "<p>\n<bold>Figure</bold>\n##FIG##5##\n6a## shows a schematic of a back‐gated FET device based on monolayer WTe<sub>0.12</sub>S<sub>1.88</sub> alloy with WTe<sub>2</sub> electrode. For a given gate voltage, there were two well‐defined PL spectral components associated with the emission bands of the neutral excitons (X) and the negatively charged trions (X<sup>−</sup>). We found that the emission near 650 nm (≈1.91 eV) from neutral excitons (X) was dominant around the charge neutrality point at <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0. The PL spectral evolution of these two emission bands with gate voltage is illustrated in Figure ##FIG##5##6b,c## for the 1T′‐WTe<sub>2</sub>/1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> device. We note that the trion‐to‐exciton intensity ratios of monolayer 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> exhibited dependence on the gate voltage, as shown in Figure ##FIG##5##6c##. The gate voltage‐dependent DVP became significantly different in the case of 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> device with 1T′‐WTe<sub>2</sub> electrodes. Figure ##FIG##5##6b,c## shows the PL spectral evolution of X and X<sup>−</sup> emissions with gate voltage from the 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> device with WTe<sub>2</sub> electrodes. Additionally, polarization‐resolved PL spectra of the 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> device with WTe<sub>2</sub> electrodes under σ<sup>+</sup>excitations are shown in Figure ##FIG##5##6d–g## for <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0, −5 V, −10 V and −20 V, respectively. For <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0, which corresponded to the valley‐polarized state in pristine 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> alloy, excitons at the K valley were more populated under σ<sup>+</sup> excitations with the DVP ≈40% as expected. By increasing the electron density via decreasing the gate voltage from 0 to −5 V, −10 V and −20 V, the difference between the σ<sup>+</sup> and σ<sup>−</sup> components of the PL spectra became increasingly more significant, implying enhanced valley polarization of the neutral excitons. Specifically, we found that the values of DVP for <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0, −5 V, −10 V, and −20 V were ≈40%, 45%, 50%, and 70%, respectively, suggesting significantly enhanced valley polarization as the applied bias moved away from the charge neutral point. Neutral excitons are the natural low‐energy excitations of a charge‐neutral semiconductor, whereas trions are only formed in the presence of excess charge. Therefore, the intensity of trion emissions is generally dependent on the amount of excess charge in the semiconductor. For this reason, trion emissions were usually not found in the PL spectra of our CVD‐grown monolayer WS<sub>2</sub> samples unless a back gate voltage was applied. For the gated samples, the PL spectra typically exhibited additional emissions at 30–60 meV below the neutral excitonic line, which may be attributed to the emission from negatively charged trions (X<sup>−</sup>). Thus, by simply varying the applied back gate voltage, we were able to control the ratio between neutral exciton and charged trion emissions.</p>", "<p>To gain further insights into this behavior, we performed gate‐dependent transport measurements, using a scheme where a positive bias induced hole‐doping and a negative bias introduced electron‐doping. We observed typical <italic toggle=\"yes\">n</italic>‐type transport behavior with on/off current ratios greater than 10<sup>6</sup> at room temperature, as shown in Figure S9. The doped carrier density <italic toggle=\"yes\">n</italic> = [(εε<sub>0</sub>/<italic toggle=\"yes\">t</italic>\n<sub>ox</sub>)(<italic toggle=\"yes\">V</italic>\n<sub>g</sub> − <italic toggle=\"yes\">V</italic>\n<sub>CNP</sub>)/<italic toggle=\"yes\">e</italic>] under gate voltage <italic toggle=\"yes\">V</italic>\n<sub>g</sub> was estimated, where <italic toggle=\"yes\">ε</italic> = 3.9 is the dielectric constant of SiO<sub>2</sub>, <italic toggle=\"yes\">t</italic>\n<sub>ox</sub> is the thickness of SiO<sub>2</sub>, and <italic toggle=\"yes\">ε</italic>\n<sub>0</sub> is the vacuum permittivity. As shown in Figure S9, the charge neutral point (CNP) was observed to be at 20 V so that the <italic toggle=\"yes\">n</italic>‐type carrier concentration could be estimated, which yielded 1.5 × 10<sup>12</sup> cm<sup>−2</sup>, 1.89 × 10<sup>12</sup> cm<sup>−2</sup>, 2.27 × 10<sup>12</sup> cm<sup>−2</sup>, and 3.03 × 10<sup>12</sup> cm<sup>−2</sup> for 0 V, −5 V, −10 V, and −20 V, respectively. These values confirmed the notion that the enhancement of valley polarization by electrostatic doping in the WTe<sub>0.12</sub>S<sub>1.88</sub> alloy may be attributed to carrier doping‐induced suppression on the inter‐valley relaxation process, because the inter‐valley relaxation process of bright excitons is dominated by the long‐range electron‐hole (e‐h) exchange interaction, and the long‐range e‐h exchange interactions may be efficiently screened by increasing the 2D carriers in the monolayer TMD with electrostatic doping. Here the screen length is determined by the inverse of the Thomas‐Fermi wave vector<sup>[</sup>\n##UREF##24##\n63\n##\n<sup>]</sup>\n<mml:math id=\"jats-math-10\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>TF</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mi>T</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">F</mml:mi></mml:msub></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mrow><mml:mi>TF</mml:mi><mml:mn>0</mml:mn></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi>exp</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mo>−</mml:mo><mml:mfrac><mml:msub><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">F</mml:mi></mml:msub><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, where <italic toggle=\"yes\">k</italic>\n<sub>TF0</sub> = <italic toggle=\"yes\">g</italic>\n<sub>s</sub>\n<italic toggle=\"yes\">g</italic>\n<sub>v</sub>\n<italic toggle=\"yes\">m</italic>*<italic toggle=\"yes\">e</italic>\n<sup>2</sup>/(4πεℏ<sup>2</sup>) is the zero temperature Thomas‐Fermi wave vector, <italic toggle=\"yes\">g</italic>\n<sub>s</sub> (<italic toggle=\"yes\">g</italic>\n<sub>v</sub>) is the degeneracy for spins (valleys), <italic toggle=\"yes\">m</italic>* is the effective electron or hole mass, and <italic toggle=\"yes\">ε</italic> is the dielectric constant. The Fermi energy <italic toggle=\"yes\">E</italic>\n<sub>F</sub> measured from the bottom of the conduction band (to the top of the valance band) is defined by <italic toggle=\"yes\">E</italic>\n<sub>F</sub> = 2π<italic toggle=\"yes\">n</italic>ℏ<sup>2</sup>/(<italic toggle=\"yes\">g</italic>\n<sub>s</sub>\n<italic toggle=\"yes\">g</italic>\n<sub>v</sub>\n<italic toggle=\"yes\">m</italic>*), where <italic toggle=\"yes\">n</italic> is the doped 2D electron (hole) density. Therefore, <italic toggle=\"yes\">k</italic>\n<sub>TF</sub> increases rapidly with increasing <italic toggle=\"yes\">n</italic>. In the strong scattering limit, the inter‐valley scattering rate (τ<sub>v</sub>)<sup>−1</sup> due to e‐h exchange interaction may be approximated by the relation (τ<sub>v</sub>)<sup>−1</sup>∝(<italic toggle=\"yes\">k</italic>\n<sub>TF</sub>)<sup>−2</sup>. Therefore, the inter‐valley scattering rate (τ<sub>v</sub>)<sup>−1</sup>is strongly suppressed by increasing carrier doping.<sup>[</sup>\n##UREF##24##\n63\n##\n<sup>]</sup> In contrast, the intra‐valley relaxation time τ<sub>0</sub> is much less affected by carrier doping, as supported by the stable linewidths and integrated intensities upon doping. Noting that the valley polarization <italic toggle=\"yes\">P</italic>\n<sub>DVP</sub>\n<sup>[</sup>\n##REF##24215567##\n64\n##, ##UREF##25##\n65\n##\n<sup>]</sup> is given by\nwith <italic toggle=\"yes\">P</italic>\n<sub>0</sub> being the ideal valley polarization, we find that the suppression of (τ<sub>v</sub>)<sup>−1</sup>by electrostatic doping leads to enhanced <italic toggle=\"yes\">P</italic>\n<sub>DVP</sub>, which agrees well with our experimental observations.</p>" ]
[ "<title>Results and Discussion</title>", "<p>The experimental setup for the growth of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1) alloys is schematically depicted in Supporting Information Figure S1a (see details of the synthesis process in the Experimental Section). By tuning the ratios of the chalcogen precursors and that of the Ar/H<sub>2</sub> gas flow, we were able to synthesize both 1H and 1T′ phases of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1). <bold>Figure</bold>\n##FIG##1##\n2a–d## show typical optical microscopy (OM) images of the 1H and 1T′ WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> monolayers. When the chalcogen ratio (Te/S) increased from 1 to 7 and the Ar/H<sub>2</sub> ratio increased from 80/40 to 80/50, monolayer 1T′ WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> was obtained. The reactivity of the Te with WO<sub>3</sub> was far lower than that of S with WO<sub>3</sub>, so the usage of a large amount of Te precursors and higher H<sub>2</sub> gas flow was necessary to ensure that Te could be incorporated into the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> matrix to form the 1T′ phase.</p>", "<p>X‐ray photoelectron spectroscopic (XPS) was used to investigate the chemical composition of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1) alloys synthesized by atmosphere‐pressure chemical vapor deposition (APCVD) and to evaluate the electron doping concentration as a function of the Te doping concentration. The core level spectra were calibrated via fitting adventitious carbon at 284.8 eV. The high‐resolution spectra of W 4f, S 2p, and Te 3d peaks are shown in Figure ##FIG##1##2e–g##. For 1H‐phase WS<sub>2</sub>, the corresponding binding energies of the W 4f <italic toggle=\"yes\">\n<sub>7/2</sub>\n</italic> and W 4f <italic toggle=\"yes\">\n<sub>5/2</sub>\n</italic> peaks were located at 33.2 and 35.3 eV, respectively, and the binding energies for the S 2p<italic toggle=\"yes\">\n<sub>3/2</sub>\n</italic> and S 2p<italic toggle=\"yes\">\n<sub>1/2</sub>\n</italic> peaks were located at 162.9 and 164.2 eV, respectively, which were all consistent with the values reported previously.<sup>[</sup>\n##REF##26758908##\n47\n##\n<sup>]</sup> By tuning the mass ratios of Te and S powder from 1 to 100 with specific H<sub>2</sub> flow rates from 40 to 60 sccm during the synthesis process, W‐Te bonds at 573.8 eV (Te 3d<sub>5/2</sub>) and 584.1 eV (Te 3d<sub>3/2</sub>) appeared in the spectra, which provided direct evidence for Te doping into the original WS<sub>2</sub> crystal lattice. The binding energy of W 4f and S 2p peaks displayed a downshift ≈0.4 eV in the alloy with <italic toggle=\"yes\">x</italic> = 13%, indicating that Te doping resulted in reduced electronegativity. When a structural phase transition occurred at a higher stoichiometric ratio (<italic toggle=\"yes\">x</italic> &gt; 0.5), the binding energies of W 4f, S 2p, and Te 3d all shifted to lower energy states concurrently. For 1T′‐phase WTe<sub>2</sub>, the main W 4f peaks at 31.28 eV (4f<sub>7/2</sub>) and 33.44 eV(4f<sub>5/2</sub>) and the Te 3d peaks located at 572.6 (3d<sub>5/2</sub>) and 583 eV (3d<sub>3/2</sub>) were assigned to the W–Te bond. The chemical stoichiometry information mentioned above directly indicated that the mole fraction of Te and the structural evolution between the 1H and 1T′ phases could be tuned by changing the mass ratio of Te and S powder together with specific H<sub>2</sub> concentrations during the APCVD growth. Furthermore, the distinct binding energy redshifts of W 4f, Te 3d, and S 2p with increasing Te concentration up to <italic toggle=\"yes\">x</italic> = 35% indicate that the Fermi level moved downward closer to the valence band and hence the p‐type doping of Te into the WS<sub>2</sub> lattice, which was further corroborated by measurements of the increasing work function of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> with <italic toggle=\"yes\">x</italic> for 0 &lt; <italic toggle=\"yes\">x</italic> ≤ 0.35 by ultraviolet photoelectron spectroscopy (UPS, to be further elaborated below), as shown in the inset of <bold>Figure</bold> ##FIG##2##\n3c##. Both of the XPS and UPS showed that Te as the p‐type dopant doped in the n‐type semiconductor.</p>", "<p>To quantitatively evaluate the changes in the electron carrier concentration with Te doping, which plays a critical role in determining the DVP of 1H‐ternary WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (0 &lt; <italic toggle=\"yes\">x</italic> ≤ 0.35), we need to evaluate the (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) values of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub>, where <italic toggle=\"yes\">E</italic>\n<sub>c</sub> and <italic toggle=\"yes\">E</italic>\n<sub>F</sub> denote the conduction band edge energy and the Fermi level, respectively. We employed the UPS studies to extract the (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) values and the PL measurements to obtain the optical bandgap <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> values for WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (0 &lt; <italic toggle=\"yes\">x</italic> ≤ 0.35), where <italic toggle=\"yes\">E</italic>\n<sub>v</sub> denotes the valance band edge energy, and the bandgap between the conduction and valence band edges is given by <italic toggle=\"yes\">E</italic>\n<sub>g</sub> ≡ (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) = <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> + <italic toggle=\"yes\">E</italic>\n<sub>binding</sub>, where <italic toggle=\"yes\">E</italic>\n<sub>binding</sub> represents the binding energy of A‐excitons. As shown in Figure ##FIG##1##2h##, linear extraction of the valence band edge tail was used to determine the (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) values. We found that the (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) value first increased from 1.8 eV for <italic toggle=\"yes\">x</italic> = 0 to 1.9 eV for <italic toggle=\"yes\">x</italic> = 6%, and then steadily decreased with increasing <italic toggle=\"yes\">x</italic> down to 1.57 eV for <italic toggle=\"yes\">x</italic> = 35%, as shown in Figure ##FIG##1##2h,i##.</p>", "<p>Next, using the optical bandgap <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> of the 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> obtained from the PL measurements (Figure ##FIG##2##3b##), and noting that <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> = (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) − <italic toggle=\"yes\">E</italic>\n<sub>binding</sub> = (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) + (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) − <italic toggle=\"yes\">E</italic>\n<sub>binding</sub> where (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>v</sub>) were given by the UPS studies as mentioned above, we derived the (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) values for the 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> by using <italic toggle=\"yes\">E</italic>\n<sub>binding</sub> = Ry (<italic toggle=\"yes\">µ</italic>/<italic toggle=\"yes\">m</italic>\n<sub>e</sub>) (<italic toggle=\"yes\">ε</italic>\n<sub>0</sub>/<italic toggle=\"yes\">ε</italic>\n<sub>s</sub>)<sup>2</sup> ∼ 0.1 eV, with Ry being the Rydberg energy 13.6 eV, <italic toggle=\"yes\">µ</italic> ∼ 0.178 <italic toggle=\"yes\">m</italic>\n<sub>e</sub> the reduced mass of A‐excitons, <italic toggle=\"yes\">m</italic>\n<sub>e</sub> the free electron mass, and (<italic toggle=\"yes\">ε</italic>\n<sub>s</sub>/<italic toggle=\"yes\">ε</italic>\n<sub>0</sub>) ∼ 5 the dielectric constant of the substrate. After the (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) values were determined as a function of the Te doping, the electron doping concerntrations (<italic toggle=\"yes\">N</italic>\n<sub>D</sub>) may be calculated by using the effective density of state (<italic toggle=\"yes\">N</italic>\n<sub>C</sub>) near the bottom of the conduction band for two‐dimensional electrons\nwhere <italic toggle=\"yes\">h</italic> is the Planck constant. Thus, we obtained <italic toggle=\"yes\">N</italic>\n<sub>D</sub> from the following expression\nwhere <italic toggle=\"yes\">T</italic> is the temperature and <italic toggle=\"yes\">k</italic>\n<sub>B</sub> is the Boltzmann constant. The results of the <italic toggle=\"yes\">N</italic>\n<sub>D</sub> analysis are presented in Figure ##FIG##1##2j##, showing that <italic toggle=\"yes\">N</italic>\n<sub>D</sub> decreases from (3 × 10<sup>10</sup>) cm<sup>−2</sup> to (1 × 10<sup>7</sup>) cm<sup>−2</sup> when varies the Te concentration from 6% to 35%, and that the Fermi level for all samples with <italic toggle=\"yes\">x</italic> ≤ 35% was below <italic toggle=\"yes\">E</italic>\n<sub>c</sub> at room temperature. This analysis suggests that the carrier densities in the semiconducting 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys may be controlled by tuning the Te doping level.</p>", "<p>The optical properties of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys were investigated by Raman and PL spectra, and the <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> values derived from the PL spectra were applied to estimating the (<italic toggle=\"yes\">E</italic>\n<sub>c</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) values and the electron doping concentrations using Equations (##FORMU##1##2##) and (##FORMU##2##3##) as stated above. In Figure ##FIG##2##3a##, Raman spectra of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with various Te concentrations were collected to examine the composition‐dependent lattice vibrational modes. For monolayer 1H‐phase WS<sub>2</sub>, the two characteristic peaks <mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>E</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi>g</mml:mi></mml:mrow><mml:mn>1</mml:mn></mml:msubsup></mml:mrow></mml:math>and <italic toggle=\"yes\">A</italic>\n<sub>1</sub>\n<italic toggle=\"yes\">\n<sub>g</sub>\n</italic> were located at 351 cm<sup>−1</sup> and 419 cm<sup>−1</sup>, respectively, in agreement with previous reports.<sup>[</sup>\n##REF##31442375##\n13\n##\n<sup>]</sup> In the 1H‐phase alloys, it was evident that the Raman footprints changed with increasing Te concentration relative to those of the pure WS<sub>2</sub>, where the 1H‐phase characteristic peaks weakened and additional peaks associated with the 1T′‐phase appeared around 163 cm<sup>−1</sup> and 213 cm<sup>−1</sup>. The positions of the two WS<sub>2</sub> vibrational modes were softened and redshifted with the increase of Te concentration, which may be attributed to the effect of heavier Te atoms on decreasing the vibrational frequencies. In comparison with pure 1T′‐WTe<sub>2</sub> with main <italic toggle=\"yes\">A</italic>\n<sub>1</sub> modes<sup>[</sup>\n##REF##26797573##\n48\n##\n<sup>]</sup> at 120, 132, 162, and 213 cm<sup>−1</sup>, the observed new peaks around 195, 225, 290, and 400 cm<sup>−1</sup> in Figure ##FIG##2##3a## were similar to the 1H‐phase and 1T′‐phase WS<sub>2</sub>‐like peaks reported previously.<sup>[</sup>\n##REF##28112926##\n49\n##, ##REF##30323336##\n50\n##, ##UREF##18##\n51\n##, ##UREF##19##\n52\n##, ##REF##30525432##\n53\n##\n<sup>]</sup>\n</p>", "<p>In addition to the Raman spectra, PL measurements were performed on the alloys to investigate the composition‐dependent optical bandgap (<italic toggle=\"yes\">E</italic>\n<sub>emission</sub>) evolution and phase transition in Figure ##FIG##2##3b##. We found that the optical bandgap of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys could be tuned from 2 eV (for pure 1H‐WS<sub>2</sub>) to zero (for pure 1T′‐WTe<sub>2</sub>) as the concentration of Te increased, and 1H to 1T′ phase transition existed at an intermediate Te concentration (<italic toggle=\"yes\">x</italic> &gt; 0.35) in the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys. For 1T′ ternary tellurides, no PL signal could be detected because of their metallic nature. Notably, within the 1H phase, the correlation between the optical bandgap and the Te concentration was approximately linear to each other, and the 1H‐phase optical bandgap ranged between 2 eV (pure WS<sub>2</sub>, <italic toggle=\"yes\">x</italic> = 0) and 1.75 eV (WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy, <italic toggle=\"yes\">x</italic> = 0.35), as presented in the inset of Figure ##FIG##2##3b##. Additionally, the composition‐dependent PL peak position of the as‐grown alloys was found to be in good agreement with the quadratic rule of the bandgap (<italic toggle=\"yes\">E</italic>\n<sub>g</sub>) estimation reported by Kang et al:<sup>[</sup>\n##UREF##20##\n54\n##\n<sup>]</sup>\nwhere the parameter <italic toggle=\"yes\">b</italic> for WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1−</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy equals 0.08,<sup>[</sup>\n##UREF##20##\n54\n##\n<sup>]</sup> and the bandgap of the 1H‐phase WTe<sub>2</sub> is 1.03 eV from literature.<sup>[</sup>\n##REF##23132225##\n7\n##, ##REF##26479493##\n55\n##, ##UREF##21##\n56\n##\n<sup>]</sup>\n</p>", "<p>The validation of the correlation between the <italic toggle=\"yes\">E</italic>\n<sub>emission</sub> value and the Te doping level in Equation (##FORMU##3##4##) thus provides a fast and efficient way to determine the chemical composition of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy. The neutral A‐exciton PL peak of different WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys, which resulted from direct‐gap A‐exciton recombination at the K/K′ points in the Brillouin zone, exhibited an approximately 250 meV redshift when doped with ≈ 35% Te. We also fitted the PL spectra of pure WS<sub>2</sub> and the 1H‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> &lt; 0.5) to deconvolve (Supporting Information, Figure S2) the A‐exciton and trion contributions, and found that the optimal lineshape for the spectral contributions was a mixed Gaussian–Lorentzian function. As shown in Figure ##FIG##2##3c##, the A‐exciton and trion peaks of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> &lt; 0.5) were both redshifted relative to those of pure WS<sub>2</sub>, which was consistent with the decreasing optical bandgap with increasing Te doping.</p>", "<p>Figure ##FIG##2##3d–i## show the polarization‐dependent PL spectra of 1H phase monolayer WS<sub>2</sub> and WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys on SiO<sub>2</sub>/Si substrate under <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> circularly polarized excitation. The valley polarization of WS<sub>2</sub> at room temperature (RT) rarely exceeded 5%, but the DVP in monolayer ternary WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (<italic toggle=\"yes\">x</italic> &lt; 0.5) alloys were found to vary from 3% (for <italic toggle=\"yes\">x</italic> = 35%) to 40% (for <italic toggle=\"yes\">x</italic> = 6%). The significant enhancement in the valley‐polarization at RT from WS<sub>2</sub> to WTe<sub>0.12</sub>S<sub>1.88</sub> may be attributed to the enhanced spin‐orbit coupling by introducing Te atoms in WS<sub>2</sub> lattice. On the other hand, the substitutions of S atoms by Te atoms also markedly affect the carrier density. The estimated 2D carrier density versus Te‐concentration is shown in Figure ##FIG##1##2j##, showing an initial rapid increase from <italic toggle=\"yes\">x</italic> = 0 to <italic toggle=\"yes\">x</italic> = 6% followed by a monotonic decreasing trend with a further increase in the Te‐concentration. The Te‐doping dependence of the 2D carrier density is similar to that of the DVP shown in Figure ##FIG##2##3i##, where the highest enhancement in the valley polarization (≈ 40%) at RT was found when the carrier density reached the highest value (≈3 × 10<sup>10</sup>) cm<sup>−2</sup> in the WTe<sub>0.12</sub>S<sub>1.88</sub> (<italic toggle=\"yes\">x</italic> = 6%) alloy. Similar behavior of the DVP dependence on Te doping for WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys is also found under <italic toggle=\"yes\">σ <sup>−</sup>\n</italic> circularly polarized excitation, as shown in Figure S3 (Supporting Information). This correlation between the carrier density and the DVP may be understood in terms of increasing exciton screening effects with increasing carrier densities, which resulted in reduced long‐range electron‐hole exchanging interactions and hence suppressed the momentum‐dependent intervalley scattering and improved the DVP.</p>", "<p>Noting the benefits of carrier doping and increased spin‐orbit coupling on enhancing the DVP in WTe<sub>0.12</sub>S<sub>1.88</sub>, we conjectured that further enhancement of the DVP may be achieved by controlling the carrier densities via electrostatic doping, which would require the development of high‐quality electrical contacts with reduced SBH and weakened Fermi level pinning to the 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys. To this end, we fabricated back‐gated FETs based on WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys on (P++)Si/SiO<sub>2</sub> substrates and used specially designed electrical contacts to evaluate the performance of these devices, which provided critical information about the quality of our electrical contacts on the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys.</p>", "<p>To fabricate 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> based FETs, monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> flakes were first transferred to heavily p‐doped Si substrates with a SiO<sub>2</sub> top layer of 285 nm thickness, which served as a bottom gate and a gate dielectric, respectively. The metallic contact electrodes were fabricated by E‐beam lithography, and 200 nm Au contact electrodes were deposited on silanol functionalized SiO<sub>2</sub>/Si substrate using E‐beam evaporation. The channel length (<italic toggle=\"yes\">L</italic>) and width (<italic toggle=\"yes\">W</italic>) of the fabricated devices were 0.5 µm and 1 µm (<bold>Figure</bold>\n##FIG##3##\n4a##), respectively. The metallic contact electrodes were transferred and aligned on top of the WTe<sub>2x</sub>S<sub>2(1‐x)</sub> monolayer flake by means of a metal transferred method, to be elaborated in the experimental section. Using cross‐sectional analysis by transmission electron microscopy (TEM), we examined the interface between the transferred Au and the monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> as shown in Figure ##FIG##3##4b##, and found that in contrast to the direct Au deposition onto monolayer TMD via electron‐beam evaporation, our process of transferring Au contacts to WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> did not incur any damages to the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> layer, as evidenced by the perfect rows of atoms clearly visible in the TEM image (Figure ##FIG##3##4b##). The electrical performance of the CVD‐grown WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with metal‐transferred Au contact electrodes was investigated by studying the backgated FETs made of monolayer WTe<sub>2x</sub>S<sub>2(1‐x)</sub> alloys. The transfer characteristic curves of the monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> devices are presented in Figure ##FIG##3##4## and Figure S4, Supporting Information. In Figure ##FIG##3##4c–e##, all semiconducting 1H‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> = 0, 0.06, 0.13, 0.26, and 0.35) devices showed typical n‐type transport behavior with high on/off (&gt; 10<sup>5</sup>) current ratios. Additionally, the field‐effect mobility (μ<sub>FE</sub>) may be evaluated by the following relation:<sup>[</sup>\n##REF##29896954##\n57\n##, ##REF##25961515##\n58\n##\n<sup>]</sup>\nwhere <italic toggle=\"yes\">I</italic>\n<sub>ds</sub> is the source‐drain current, <italic toggle=\"yes\">V</italic>\n<sub>gs</sub> the gate‐source voltage; <italic toggle=\"yes\">V</italic>\n<sub>ds</sub> the source‐drain voltage, and <italic toggle=\"yes\">C</italic>\n<sub>g</sub> the gate capacitance. Using Equation (##FORMU##4##5##) and the transfer characteristic curves in Figure ##FIG##3##4c–e##, we obtained mobility values of 0.58 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup>, 35 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup>, 10.5 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup>, 2.8 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup>, and 1.8 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup> for the 1H‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with <italic toggle=\"yes\">x</italic> = 0, 0.06, 0.13, 0.26, and 0.35, respectively. The ON current (<italic toggle=\"yes\">I</italic>\n<sub>on</sub>) for the WTe<sub>0.12</sub>S<sub>1.88</sub> alloy‐based devices was improved by 2 orders of magnitude relative to the control devices (WS<sub>2</sub>‐FET devices). In contrast, for the 1T′‐phase alloys, the drain current was found to increase by ≈50 times in magnitude from the 1T′‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> = 0.52) to pure WTe<sub>2</sub>, which implied that the metallic behavior of tellurides could be modified by controlling the concentration of the alloying S atoms. Furthermore, the source‐drain current (<italic toggle=\"yes\">I</italic>\n<sub>ds</sub>) was completely independent of the backgated voltage (<italic toggle=\"yes\">V</italic>\n<sub>gs</sub>) in all three semimetallic 1T′‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (<italic toggle=\"yes\">x</italic> = 0.52, 0.64 and 1), as shown in Figure ##FIG##3##4f–h##, and the resistivity of the WTe<sub>2</sub> devices was reduced by 2 orders of magnitude as compared to that of the 1T′‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (<italic toggle=\"yes\">x</italic> = 0.52) devices.</p>", "<p>The improvement in the electrical performance of the FETs based on the 1H‐phase semiconducting WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with Au electrode can be attributed to several effects. At the metal‐semiconductor interface, electrons can be injected from the metal to the semiconductor either by thermionic emission over the Schottky barrier or via tunneling through the Schottky barrier. The width of the Schottky barrier is equal to the width of the depletion region (<italic toggle=\"yes\">W</italic>\n<sub>dep</sub>), which depends on the doping concentration (<italic toggle=\"yes\">N</italic>\n<sub>D</sub>) of the semiconductor and is proportional to (<italic toggle=\"yes\">N<sub>D</sub>\n</italic>)<sup>−1/2</sup>according to the following relation: <mml:math id=\"jats-math-7\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi>dep</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:msqrt><mml:mrow><mml:mn>2</mml:mn><mml:msub><mml:mi>ε</mml:mi><mml:mi mathvariant=\"normal\">s</mml:mi></mml:msub><mml:msub><mml:mi>V</mml:mi><mml:mi>bi</mml:mi></mml:msub><mml:msub><mml:mi>d</mml:mi><mml:mi>TMD</mml:mi></mml:msub><mml:mo>/</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mi>e</mml:mi><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant=\"normal\">D</mml:mi></mml:msub></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:msqrt><mml:mo>,</mml:mo></mml:mrow></mml:mrow></mml:math> where <italic toggle=\"yes\">d</italic>\n<sub>TMD</sub> ∼ 0.6 nm is the monolayer thickness of the TMD sample, <italic toggle=\"yes\">ε<sub>s</sub>\n</italic> (≈5) is the dielectric constant of semiconductors, <italic toggle=\"yes\">V</italic>\n<sub>bi</sub> = (<italic toggle=\"yes\">ϕ</italic>\n<sub>M</sub> − <italic toggle=\"yes\">ϕ</italic>\n<sub>s</sub>)/<italic toggle=\"yes\">e</italic> is the built‐in potential between the metallic contact and the TMD semiconductor, and <italic toggle=\"yes\">e</italic> is the elementary charge. Therefore, <italic toggle=\"yes\">W</italic>\n<sub>dep</sub> decreased with increasing <italic toggle=\"yes\">N</italic>\n<sub>D,</sub> and the probability of electron injection into the semiconductor via tunneling through the Schottky barrier increased. Indeed, we found the largest <italic toggle=\"yes\">I</italic>\n<sub>on</sub> and highest <italic toggle=\"yes\">µ</italic>\n<sub>FE</sub> in the lightly Te‐doped FET devices (WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> with <italic toggle=\"yes\">x</italic> = 6%) because of the maximum <italic toggle=\"yes\">N</italic>\n<sub>D</sub> value ∼(3 × 10<sup>10</sup>) cm<sup>−2</sup> that induced the minimum depletion width <italic toggle=\"yes\">W</italic>\n<sub>dep</sub>, which enhanced the electron tunneling through the Schottky barrier. Additionally, we note that the quality of the electrical contact between the metallic electrode and the semiconducting channel directly affects the carrier injection and therefore the performance of the devices. In the case of TMD‐based devices, at the metal electrode/TMD interface, the large bandgap of TMDs leads to a Schottky barrier (SB) and a van der Waal (vdW) gap without chemical bonds, which gives rise to a high contact resistance for the as‐fabricated devices. Thus, it is imperative to eliminate the interfacial vdW gap and to depin the Fermi level of the metallic electrode to facilitate efficient charge transport across the contact interface for optimized FET device performances as well as efficient control of electrostatic doping.</p>", "<p>To overcome the Fermi level pinning effect and to lower the Schottky barrier height (SBH) at the interface, we developed a new process to transfer surface‐functionalized, water‐assisted wafer Au electrodes onto monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> to form WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub>‐based FETs with Au contacts, as schematically illustrated in Figure S5. Besides using the Au contacts, there are two known methods to date for eliminating the Fermi‐level pinning effects of electrical contacts to TMDs. One is to strengthen the hybridization by doping the underlying TMDs. The other is to weaken the hybridization between the contact electrode and the TMDs by inserting graphene to greatly reduce the contact resistance and SBH. The use of heterostructures that consist of a 2D van der Waals (vdW) semi‐metal, such as graphene, as the top contact material on a 2D semiconductor, is a common approach to lower the SBH and contact resistance. However, deposition of another metallic layer on graphene is required for electrical characterizations, and the carrier injection efficiency generally varies, depending on the metal deposited on graphene. Alternatively, the metallic 1T′‐phase WTe<sub>2</sub> with a low work function and a vdW clean surface may be an efficient electron‐type (<italic toggle=\"yes\">n</italic>‐type) contact material for 2D semiconductors. However, there have not been extensive studies to date on using the 1T′‐phase WTe<sub>2</sub> as the metal contact to lower the contact resistance of TMD‐based devices because of the challenges in materials preparation and stability. Noting that Te‐based monolayers are known to be unstable in ambient conditions, we chose multilayer WTe<sub>2</sub> as the electrodes alternative to Au contacts for the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy‐based FET devices. The stability test of multilayer WTe<sub>2</sub> is illustrated in Figure S6 (Supporting Information), which demonstrates that multilayer WTe<sub>2</sub> could be stable in air beyond 15 days.</p>", "<p>Next, we investigated the characteristics of the 1H‐WTe<sub>2x</sub>S<sub>2(1‐x)</sub>‐based FETs with two types of transferred source(S)/drain(D) electrodes: Au (work function ≈ 5.2 eV), and 1T′‐WTe<sub>2</sub> (work function ≈ 4.6 eV), as shown in <bold>Figure</bold>\n##FIG##4##\n5\n##. Given that 1T′‐WTe<sub>2</sub> has the closest electron affinity to the work function of 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub>, we expected the use of 1T′‐WTe<sub>2</sub> electrodes to induce the lowest Schottky barrier height. The work function of each electrode was measured by ultraviolet photoelectron spectroscopy (UPS) and the results are shown in Figure S7, Supporting Information. Figure ##FIG##4##5a,b## illustrate the band diagrams of the Au/1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> and 1T′‐WTe<sub>2</sub>/1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> interfaces in the equilibrium condition after both of the contacts were made. The charge injection in the 2D WTe<sub>0.12</sub>S<sub>1.88</sub> channel was determined by the SBH and Schottky barrier width (SBW), both largely dependent on the extent of the semiconductor band‐bending at the metal (Au or 1T′ WTe<sub>2</sub>) and 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> Schottky contact region. While the SBH governed the extent of thermionic emission of carriers over the barrier, the SBW determined the extent of the thermionic field emission and quantum tunneling of charge carriers. Hence, both the SBH and SBW must be minimized to achieve efficient injection of charge carriers from the contact into the semiconducting WTe<sub>0.12</sub>S<sub>1.88</sub> channel as shown in Figure ##FIG##4##5b##.</p>", "<p>The field‐effect mobility and the on/off current ratios of 1H‐phase WTe<sub>0.12</sub>S<sub>1.88</sub> crystal for Au and WTe<sub>2</sub> electrodes were found to be <italic toggle=\"yes\">µ</italic>\n<sub>FE</sub> = 35 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup> and (<italic toggle=\"yes\">I</italic>\n<sub>on</sub>/<italic toggle=\"yes\">I</italic>\n<sub>off</sub>) = 5 × 10<sup>5</sup>, and <italic toggle=\"yes\">µ</italic>\n<sub>FE</sub> = 50 cm<sup>2</sup> V<sup>−1</sup> s<sup>−1</sup> and (<italic toggle=\"yes\">I</italic>\n<sub>on</sub>/<italic toggle=\"yes\">I</italic>\n<sub>off</sub>) = 1.1 × 10<sup>6</sup>, respectively. In particular, we found substantially more efficient gate tunability in the FET with 1T′‐WTe<sub>2</sub> contacts. That is a smaller threshold voltage <italic toggle=\"yes\">V</italic>\n<sub>g,th</sub> of 18 V (compared with <italic toggle=\"yes\">V</italic>\n<sub>g,th</sub> = 50 V for Au contacts) and a higher on‐current of ≈50 µA µm<sup>−1</sup> (compared with ≈30 µA µm<sup>−1</sup> for Au contacts). These findings implied that the types of electrical contacts could substantially modify the FET characteristics.</p>", "<p>To quantitatively investigate the SBH, the FET output characteristics were measured at different temperatures (200–300 K) and presented in Figure S8. The SBH <italic toggle=\"yes\">ϕ</italic>\n<sub>B</sub> can be extracted from the data by using the following thermionic emission model:<sup>[</sup>\n##REF##36080075##\n59\n##, ##UREF##22##\n60\n##, ##REF##28088846##\n61\n##, ##UREF##23##\n62\n##\n<sup>]</sup>\nwhere <italic toggle=\"yes\">A</italic> is the junction area, <italic toggle=\"yes\">A<sup>*</sup>\n</italic> is the effective Richardson‐Boltzmann constant given by<mml:math id=\"jats-math-9\" display=\"inline\"><mml:mrow><mml:mrow><mml:msup><mml:mi>A</mml:mi><mml:mo>∗</mml:mo></mml:msup><mml:mo>=</mml:mo><mml:mn>4</mml:mn><mml:mi>π</mml:mi><mml:mi>e</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi mathvariant=\"normal\">n</mml:mi></mml:msub><mml:msubsup><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>/</mml:mo><mml:msup><mml:mi>h</mml:mi><mml:mn>3</mml:mn></mml:msup></mml:mrow></mml:mrow></mml:math>, <italic toggle=\"yes\">m</italic>\n<sub>n</sub> is the electronic effective mass of WTe<sub>2x</sub>S<sub>2(1‐x)</sub>, and the effective “emission current” <italic toggle=\"yes\">I</italic>\n<sub>0</sub> is obtained from the <italic toggle=\"yes\">I</italic>\n<sub>ds</sub>‐versus‐<italic toggle=\"yes\">V</italic>\n<sub>ds</sub> curves measured at different temperatures and gate voltages. Thus, we obtained ϕ<sub>\n<italic toggle=\"yes\">B</italic>\n</sub> at the two contacts/ WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> (<italic toggle=\"yes\">x</italic> &lt; 0.5) interfaces from the slop of the linear fit to ln (<italic toggle=\"yes\">I</italic>\n<sub>0</sub>/<italic toggle=\"yes\">T</italic>\n<sup>3/2</sup>) as a function of 1/(<italic toggle=\"yes\">k</italic>\n<sub>B</sub>\n<italic toggle=\"yes\">T</italic>) (Figure ##FIG##4##5c,d## and Figure S7, Supporting Information). In Figure ##FIG##4##5e##, the effective SBH were extracted under the flat band gate voltage (<italic toggle=\"yes\">V</italic>\n<sub>g</sub>) condition, which corresponded to the start of deviation of the ϕ<sub>\n<italic toggle=\"yes\">B</italic>\n</sub> versus <italic toggle=\"yes\">V</italic>\n<sub>g</sub> curve from the linear slope. Figure ##FIG##4##5f## summarizes the relation between the SBH (at the <italic toggle=\"yes\">V</italic>\n<sub>FB</sub>) of the metal‐semiconductor junction (MSJ) and the work functions of the Au and WTe<sub>2</sub> in contact with monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys. The SBH between the Au electrode and WTe<sub>0.12</sub>S<sub>1.88</sub> alloy was ≈150 meV, which confirmed the existence of Fermi‐level pinning compared to the ideal Schottky‐Mott rule theoretically calculated SBH (≈620 meV). In contrast, in the case of WTe<sub>2</sub> electrodes, the value of the SBH (≈80 meV) between 1T′‐WTe<sub>2</sub> and WTe<sub>0.12</sub>S<sub>1.88</sub> alloy was much closer to the ideal Schottky‐Mott rule theoretically calculated SBH (≈20 meV) for monolayer WTe<sub>0.12</sub>S<sub>1.88</sub>‐based FETs with 1T′‐WTe<sub>2</sub> contacts. This finding revealed that WTe<sub>2</sub> electrical contacts weakened the Fermi level pinning and thus improved the electron charge injection to the WTe<sub>0.12</sub>S<sub>1.88</sub> alloy substantially. Additionally, the SBW for the 1T′‐WTe<sub>2</sub> contact can be estimated by using the built‐in potential <italic toggle=\"yes\">V</italic>\n<sub>bi</sub> = (<italic toggle=\"yes\">ϕ</italic>\n<sub>M</sub> − <italic toggle=\"yes\">ϕ</italic>\n<sub>s</sub>)/<italic toggle=\"yes\">e</italic> = 0.02 and <italic toggle=\"yes\">N</italic>\n<sub>D</sub> ≈ (1.3 × 10<sup>11</sup>) cm<sup>−2</sup> for the WTe<sub>0.12</sub>S<sub>1.88</sub> alloy, which yields a small SBW ≈2.2 nm for 1T′‐WTe<sub>2</sub> on WTe<sub>0.12</sub>S<sub>1.88</sub>.</p>", "<p>\n<bold>Figure</bold>\n##FIG##5##\n6a## shows a schematic of a back‐gated FET device based on monolayer WTe<sub>0.12</sub>S<sub>1.88</sub> alloy with WTe<sub>2</sub> electrode. For a given gate voltage, there were two well‐defined PL spectral components associated with the emission bands of the neutral excitons (X) and the negatively charged trions (X<sup>−</sup>). We found that the emission near 650 nm (≈1.91 eV) from neutral excitons (X) was dominant around the charge neutrality point at <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0. The PL spectral evolution of these two emission bands with gate voltage is illustrated in Figure ##FIG##5##6b,c## for the 1T′‐WTe<sub>2</sub>/1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> device. We note that the trion‐to‐exciton intensity ratios of monolayer 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> exhibited dependence on the gate voltage, as shown in Figure ##FIG##5##6c##. The gate voltage‐dependent DVP became significantly different in the case of 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> device with 1T′‐WTe<sub>2</sub> electrodes. Figure ##FIG##5##6b,c## shows the PL spectral evolution of X and X<sup>−</sup> emissions with gate voltage from the 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> device with WTe<sub>2</sub> electrodes. Additionally, polarization‐resolved PL spectra of the 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> device with WTe<sub>2</sub> electrodes under σ<sup>+</sup>excitations are shown in Figure ##FIG##5##6d–g## for <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0, −5 V, −10 V and −20 V, respectively. For <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0, which corresponded to the valley‐polarized state in pristine 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub> alloy, excitons at the K valley were more populated under σ<sup>+</sup> excitations with the DVP ≈40% as expected. By increasing the electron density via decreasing the gate voltage from 0 to −5 V, −10 V and −20 V, the difference between the σ<sup>+</sup> and σ<sup>−</sup> components of the PL spectra became increasingly more significant, implying enhanced valley polarization of the neutral excitons. Specifically, we found that the values of DVP for <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0, −5 V, −10 V, and −20 V were ≈40%, 45%, 50%, and 70%, respectively, suggesting significantly enhanced valley polarization as the applied bias moved away from the charge neutral point. Neutral excitons are the natural low‐energy excitations of a charge‐neutral semiconductor, whereas trions are only formed in the presence of excess charge. Therefore, the intensity of trion emissions is generally dependent on the amount of excess charge in the semiconductor. For this reason, trion emissions were usually not found in the PL spectra of our CVD‐grown monolayer WS<sub>2</sub> samples unless a back gate voltage was applied. For the gated samples, the PL spectra typically exhibited additional emissions at 30–60 meV below the neutral excitonic line, which may be attributed to the emission from negatively charged trions (X<sup>−</sup>). Thus, by simply varying the applied back gate voltage, we were able to control the ratio between neutral exciton and charged trion emissions.</p>", "<p>To gain further insights into this behavior, we performed gate‐dependent transport measurements, using a scheme where a positive bias induced hole‐doping and a negative bias introduced electron‐doping. We observed typical <italic toggle=\"yes\">n</italic>‐type transport behavior with on/off current ratios greater than 10<sup>6</sup> at room temperature, as shown in Figure S9. The doped carrier density <italic toggle=\"yes\">n</italic> = [(εε<sub>0</sub>/<italic toggle=\"yes\">t</italic>\n<sub>ox</sub>)(<italic toggle=\"yes\">V</italic>\n<sub>g</sub> − <italic toggle=\"yes\">V</italic>\n<sub>CNP</sub>)/<italic toggle=\"yes\">e</italic>] under gate voltage <italic toggle=\"yes\">V</italic>\n<sub>g</sub> was estimated, where <italic toggle=\"yes\">ε</italic> = 3.9 is the dielectric constant of SiO<sub>2</sub>, <italic toggle=\"yes\">t</italic>\n<sub>ox</sub> is the thickness of SiO<sub>2</sub>, and <italic toggle=\"yes\">ε</italic>\n<sub>0</sub> is the vacuum permittivity. As shown in Figure S9, the charge neutral point (CNP) was observed to be at 20 V so that the <italic toggle=\"yes\">n</italic>‐type carrier concentration could be estimated, which yielded 1.5 × 10<sup>12</sup> cm<sup>−2</sup>, 1.89 × 10<sup>12</sup> cm<sup>−2</sup>, 2.27 × 10<sup>12</sup> cm<sup>−2</sup>, and 3.03 × 10<sup>12</sup> cm<sup>−2</sup> for 0 V, −5 V, −10 V, and −20 V, respectively. These values confirmed the notion that the enhancement of valley polarization by electrostatic doping in the WTe<sub>0.12</sub>S<sub>1.88</sub> alloy may be attributed to carrier doping‐induced suppression on the inter‐valley relaxation process, because the inter‐valley relaxation process of bright excitons is dominated by the long‐range electron‐hole (e‐h) exchange interaction, and the long‐range e‐h exchange interactions may be efficiently screened by increasing the 2D carriers in the monolayer TMD with electrostatic doping. Here the screen length is determined by the inverse of the Thomas‐Fermi wave vector<sup>[</sup>\n##UREF##24##\n63\n##\n<sup>]</sup>\n<mml:math id=\"jats-math-10\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>TF</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mi>T</mml:mi><mml:mo>,</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">F</mml:mi></mml:msub></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mrow><mml:mi>TF</mml:mi><mml:mn>0</mml:mn></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">[</mml:mo><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi>exp</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mrow><mml:mo>−</mml:mo><mml:mfrac><mml:msub><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">F</mml:mi></mml:msub><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo stretchy=\"false\">]</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, where <italic toggle=\"yes\">k</italic>\n<sub>TF0</sub> = <italic toggle=\"yes\">g</italic>\n<sub>s</sub>\n<italic toggle=\"yes\">g</italic>\n<sub>v</sub>\n<italic toggle=\"yes\">m</italic>*<italic toggle=\"yes\">e</italic>\n<sup>2</sup>/(4πεℏ<sup>2</sup>) is the zero temperature Thomas‐Fermi wave vector, <italic toggle=\"yes\">g</italic>\n<sub>s</sub> (<italic toggle=\"yes\">g</italic>\n<sub>v</sub>) is the degeneracy for spins (valleys), <italic toggle=\"yes\">m</italic>* is the effective electron or hole mass, and <italic toggle=\"yes\">ε</italic> is the dielectric constant. The Fermi energy <italic toggle=\"yes\">E</italic>\n<sub>F</sub> measured from the bottom of the conduction band (to the top of the valance band) is defined by <italic toggle=\"yes\">E</italic>\n<sub>F</sub> = 2π<italic toggle=\"yes\">n</italic>ℏ<sup>2</sup>/(<italic toggle=\"yes\">g</italic>\n<sub>s</sub>\n<italic toggle=\"yes\">g</italic>\n<sub>v</sub>\n<italic toggle=\"yes\">m</italic>*), where <italic toggle=\"yes\">n</italic> is the doped 2D electron (hole) density. Therefore, <italic toggle=\"yes\">k</italic>\n<sub>TF</sub> increases rapidly with increasing <italic toggle=\"yes\">n</italic>. In the strong scattering limit, the inter‐valley scattering rate (τ<sub>v</sub>)<sup>−1</sup> due to e‐h exchange interaction may be approximated by the relation (τ<sub>v</sub>)<sup>−1</sup>∝(<italic toggle=\"yes\">k</italic>\n<sub>TF</sub>)<sup>−2</sup>. Therefore, the inter‐valley scattering rate (τ<sub>v</sub>)<sup>−1</sup>is strongly suppressed by increasing carrier doping.<sup>[</sup>\n##UREF##24##\n63\n##\n<sup>]</sup> In contrast, the intra‐valley relaxation time τ<sub>0</sub> is much less affected by carrier doping, as supported by the stable linewidths and integrated intensities upon doping. Noting that the valley polarization <italic toggle=\"yes\">P</italic>\n<sub>DVP</sub>\n<sup>[</sup>\n##REF##24215567##\n64\n##, ##UREF##25##\n65\n##\n<sup>]</sup> is given by\nwith <italic toggle=\"yes\">P</italic>\n<sub>0</sub> being the ideal valley polarization, we find that the suppression of (τ<sub>v</sub>)<sup>−1</sup>by electrostatic doping leads to enhanced <italic toggle=\"yes\">P</italic>\n<sub>DVP</sub>, which agrees well with our experimental observations.</p>" ]
[ "<title>Conclusion</title>", "<p>In this work, we presented new strategies to efficiently tailor the valley‐polarized PL from semiconducting monolayer 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> at RT through chemical and electrostatic doping. We synthesized different compositions of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys (0 ≤ <italic toggle=\"yes\">x</italic> ≤ 1) by alloying Te into tungsten disulfide WS<sub>2</sub> with a single‐step APCVD method, and demonstrated a structural phase transition from the 1H semiconducting phase for <italic toggle=\"yes\">x</italic> &lt; 0.5 to the 1T′ metallic phase for <italic toggle=\"yes\">x</italic> &gt; 0.5. The compositions of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys were identified by using XPS and Raman spectroscopic studies. The PL spectra revealed that the optical bandgap of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy could be tuned from 2 to 1.75 eV in the 1H‐semiconducting phase and then drop to 0 in the 1T′‐metallic phase for <italic toggle=\"yes\">x</italic> &gt; 0.5. Additionally, studies of the FET devices based on monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys confirmed that the 1H‐phase alloys were <italic toggle=\"yes\">n</italic>‐type semiconductors and the 1T′‐phase alloys were metals. We observed drastic enhancement of the DVP at RT from ∼ 5% in WS<sub>2</sub> to ∼ 40% in WTe<sub>0.12</sub>S<sub>1.88</sub> alloy, and found that the DVP values in 1H‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> correlated with the 2D carrier densities in the alloys. These findings may be attributed to (<italic toggle=\"yes\">i</italic>) enhanced spin‐orbit coupling due to Te‐doping, and (<italic toggle=\"yes\">ii</italic>) enhanced screening of the electron‐hole exchanging interactions by increasing the carrier densities that resulted in reduced inter‐valley scattering of excitons. By further applying a back‐gate bias voltage (<italic toggle=\"yes\">V</italic>\n<sub>g</sub>) to monolayer 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub>‐based FETs with 1T′‐WTe<sub>2</sub> electrodes that exhibited the lowest Schottky barrier height, we were able to further enhance the DVP value from ≈40% for <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0 to ≈70% for <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = −20 V, which corroborated with the notion that excess carriers provided efficient screening of the momentum‐dependent long‐range electron‐hole exchange interaction and led to reduced intervalley scattering. The methodology described in this work thus provides a promising platform to tailor the valley degree of freedom in 1H‐TMD alloys efficiently at RT, paving ways for investigating various fundamental physical properties in 2D‐TMD materials (e.g., new types of TMD‐based Wyle semimetals, spin Hall effects, opto‐valleytronic and opto‐spintronic characteristics) and for future applications of valley‐dependent optoelectronic devices in energy‐efficient information processing.</p>" ]
[ "<title>Abstract</title>", "<p>Monolayer ternary tellurides based on alloying different transition metal dichalcogenides (TMDs) can result in new two‐dimensional (2D) materials ranging from semiconductors to metals and superconductors with tunable optical and electrical properties. Semiconducting WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> monolayer possesses two inequivalent valleys in the Brillouin zone, each valley coupling selectively with circularly polarized light (CPL). The degree of valley polarization (DVP) under the excitation of CPL represents the purity of valley polarized photoluminescence (PL), a critical parameter for opto‐valleytronic applications. Here, new strategies to efficiently tailor the valley‐polarized PL from semiconducting monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> at room temperature (RT) through alloying and back‐gating are presented. The DVP at RT is found to increase drastically from &lt; 5% in WS<sub>2</sub> to 40% in WTe<sub>0.12</sub>S<sub>1.88</sub> by Te‐alloying to enhance the spin‐orbit coupling. Further enhancement and control of the DVP from 40% up to 75% is demonstrated by electrostatically doping the monolayer WTe<sub>0.12</sub>S<sub>1.88</sub> via metallic 1T′‐WTe<sub>2</sub> electrodes, where the use of 1T′‐WTe<sub>2</sub> substantially lowers the Schottky barrier height (SBH) and weakens the Fermi‐level pinning of the electrical contacts. The demonstration of drastically enhanced DVP and electrical tunability in the valley‐polarized emission from 1T′‐WTe<sub>2</sub>/WTe<sub>0.12</sub>S<sub>1.88</sub> heterostructures paves new pathways towards harnessing valley excitons in ultrathin valleytronic devices for RT applications.</p>", "<p>The degree of valley polarization at room temperature is found to increase drastically from &lt;5% in monolayer WS<sub>2</sub> to 40% in monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> due to enhanced spin‐orbit coupling, and is further enhanced to 75% by electrostatically gating the 1T′‐WTe<sub>2</sub>/WTe<sub>0.12</sub>S<sub>1.88</sub> heterostructures, where the use of 1T′‐WTe<sub>2</sub> substantially lowers the Schottky barrier height and weakens the Fermi‐level pinning.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6719-cit-0066\">\n<string-name>\n<given-names>W.‐H.</given-names>\n<surname>Lin</surname>\n</string-name>, <string-name>\n<given-names>C.‐S.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Wu</surname>\n</string-name>, <string-name>\n<given-names>G. R.</given-names>\n<surname>Rossman</surname>\n</string-name>, <string-name>\n<given-names>H. A.</given-names>\n<surname>Atwater</surname>\n</string-name>, <string-name>\n<given-names>N.‐C.</given-names>\n<surname>Yeh</surname>\n</string-name>, <article-title>Dramatically Enhanced Valley‐Polarized Emission by Alloying and Electrical Tuning of Monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> Alloys at Room Temperature with 1T′‐WTe<sub>2</sub>‐Contact</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304890</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304890</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Synthesis of WTe<sub>2x</sub>S<sub>2(1‐x)</sub>\n</title>", "<p>WTe<sub>2x</sub>S<sub>2(1‐x)</sub> was grown by atmosphere‐pressure chemical vapor deposition (APCVD). Sulfur (S) and tellurium (Te) powders were placed into two quartz boats. The amount of sulfur was fixed at 10 mg, while the amount of Te was adjusted according to the weight ratio from 1 to 10. 95 mg of WO<sub>3</sub> precursor mixed with 5 mg of KI was placed in a quartz boat containing the SiO<sub>2</sub>/Si substrates set face‐down directly above the W source precursor, and the quartz boat was then positioned upstream at 8 cm away from the Te source. A sulfur boat was placed upstream at 18 cm away from the center of the furnace and a tellurium boat was placed downstream at 5 cm away from the S source. Next, the system was pumped down to 3 × 10<sup>−2</sup> torr to eliminate air and moisture. After the system reached the base pressure, the Ar/H<sub>2</sub> (80/40 sccm) carrier gas was introduced until atmospheric pressure was achieved. The furnace was then heated up with a ramp rate of 35 °C min<sup>−1</sup> to the growth temperatures (750 to 850 °C). The S component melted at 150 °C and the Te component melted at 450 °C were sent into the furnace at the growth temperature to grow WTe<sub>2x</sub>S<sub>2(1‐x)</sub>. The sample growth procedure proceeded for 10 minutes, after which the furnace was directly opened to room temperature to stop the reaction immediately.</p>", "<title>Synthesis of WS<sub>2</sub>\n</title>", "<p>Monolayer WS<sub>2</sub> was grown using APCVD as previously reported. 95 mg of WO<sub>3</sub> precursor mixed with 5 mg of KI was placed in a quartz boat containing the SiO<sub>2</sub>/Si substrates set face‐down directly above the W source precursor, and the quartz boat was then positioned at the center of the furnace. A second boat containing 100 mg S was placed upstream at 18 cm away from the W source. Next, the system was pumped down to 3 × 10<sup>−2</sup> torr to eliminate air and moisture. After the system reached the base pressure, the Ar/H<sub>2</sub> (80/40 sccm) carrier gas was introduced until atmospheric pressure was achieved. The furnace was then heated up with a ramp rate of 35 °C min<sup>−1</sup> to the growth temperatures (750 to 850 °C). The S component melted at 150 °C was sent into the furnace at the growth temperature to grow WS<sub>2</sub>. The sample growth procedure proceeded for 10 minutes, after which the furnace was directly opened to room temperature to stop the reaction immediately.</p>", "<title>Synthesis of WTe<sub>2</sub>\n</title>", "<p>Multilayer WTe<sub>2</sub> was grown using APCVD. 120 mg of WO<sub>3</sub> precursor mixed with 15 mg of KI was placed in a quartz boat containing the SiO<sub>2</sub>/Si substrates set face‐down directly above the W source precursor, and the quartz boat was then positioned at the center of the furnace. A second boat containing 500 mg Te was placed upstream at 10 cm away from the W source. Next, the system was pumped down to 3 × 10<sup>−2</sup> torr to eliminate air and moisture. After the system reached the base pressure, the Ar/H<sub>2</sub> (80/40 sccm) carrier gas was introduced until atmospheric pressure was achieved. The furnace was then heated up with a ramp rate of 35 °C min<sup>−1</sup> to the growth temperatures (775 to 800 °C). The Te component melted at 450 °C was sent into the furnace at the growth temperature to grow WTe<sub>2</sub>. The sample growth procedure proceeded for 25 minutes, after which the furnace was directly opened to room temperature to stop the reaction immediately.</p>", "<title>Metal Transfer Process</title>", "<p>A 4‐inch SiO<sub>2</sub>/Si wafer with a 300 nm‐thick oxide layer was first functionalized with an OH group by the following squence: The SiO<sub>2</sub>/Si wafers were dipped into 80°C piranha solution (H<sub>2</sub>SO<sub>4</sub> : H<sub>2</sub>O<sub>2</sub> = 3:1) for 2 h to render the surface of the substrates hydrophilic, which were subsequently washed with deionized water and dried with nitrogen gas. Next, the SiO<sub>2</sub>/Si wafers were cleaned with O<sub>2</sub> plasma (300 mTorr, 10 sccm, and 100 W) for 10 min. Finally, the wafers were soaked in 60°C H<sub>2</sub>O<sub>2</sub> solution for 60 min to become superhydrophilic on the surface. The functionalized surface of SiO<sub>2</sub>/Si, as schematically shown in Figure S5, Supporting Information, was used for the growth of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys and for the deposition of metal electrodes. The gold deposited on the functionalized surface of SiO<sub>2</sub>/Si was patterned into electrodes by conventional e‐beam lithography (Figure S5c, Supporting Information). The patterned gold electrodes on the SiO<sub>2</sub>/Si wafer was then spin‐coated with a polystyrene (PS) or poly(methhyl methacrylate) (PMMA) layer (Figure S5d) followed by slow immersion into deionized (DI) water for the transfer (Figure S5e). Water instantly penetrated through the PS/Au or PMMA/Au stack. The growth substrate with a higher surface energy compared to the polymer/Au stack led to easy delamination and suspension of the polymer/Au stack on the surface of water. Thus, polymer‐supported wafer‐scale Au electrodes were achieved in the form of a stack, which was subsequently transferred onto the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloy (Figure S5e–g, Supporting Information) for the fabrication of FETs.</p>", "<title>XPS and UPS Measurements</title>", "<p>XPS and UPS studies were performed under ultra‐high vacuum (residual gas pressure 5 × 10<sup>−9</sup> torr) with a Kratos AXIS Ultra DLD and a magnetic immersion lens that consisted of a spherical mirror and concentric hemispherical analyzers with a delay‐line detector (DLD). An Al Kα (1.486 KeV) monochromatic source and He 1 (21.2 eV) source were used as excitation sources for the XPS and UPS measurements, respectively. Ejected electrons were collected at a 90° angle from the horizontal.</p>", "<title>Raman and PL Characterizations</title>", "<p>The Raman and PL spectra were taken with a Renishaw InVia Raman spectrometer system using a 514.3 nm laser (2.41 eV) as the excitation source. A 50× objective lens with a numerical aperture of 0.75 and a 2400 lines mm<sup>−1</sup> and 1800 lines mm<sup>−1</sup> grating were chosen during the measurement to achieve a better signal‐to‐noise ratio.</p>", "<title>STEM Characterization</title>", "<p>The cross‐sectional sample for the TEM experiments was prepared using a dual beam‐focused ion beam (FIB)/SEM system (SMI3050SE, SEIKO). HR‐TEM and SAED were performed using a field emission transmission electron microscope (JEM‐2100F, Joel) with an acceleration voltage of 100 kV.</p>", "<title>Device Fabrication and Measurements</title>", "<p>WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> field‐effect transistors (FETs) were fabricated using standard electron‐beam (E‐beam) lithography techniques. First, the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> monolayer flakes were transferred on a heavily p‐doped Si substrate with 300 nm thick SiO<sub>2</sub> layer, which served as a bottom gate and a gate dielectric, respectively. The metallic contact electrodes were fabricated by E‐beam lithography, and 200 nm Au contact electrodes were deposited on silanol functionalized SiO<sub>2</sub>/Si substrate using E‐beam evaporation. The channel length (<italic toggle=\"yes\">L</italic>) and width (<italic toggle=\"yes\">W</italic>) of the fabricated devices were 0.5 µm and 1 µm. The metallic contact electrodes were transferred and aligned on top of the WTe<sub>2x</sub>S<sub>2(1‐x)</sub> monolayer flake using our metal transferred method described earlier under the paragraph of metal transfer process. To transfer WTe<sub>2</sub> contacts onto the WTe<sub>2x</sub>S<sub>2(1‐x)</sub> monolayer flakes, the synthesized WTe<sub>2</sub> films were first transferred onto the silanol functionalized SiO<sub>2</sub>/Si substrates by the PMMA‐assisted wet‐transferred method. Next, the WTe<sub>2</sub> electrodes were patterned using E‐beam lithography and oxygen plasma treatment (10 sccm O<sub>2</sub> gas, 20 mtorr, and 80 W) that selectively etched away the exposed WTe<sub>2</sub> regions. The WTe<sub>2</sub> patterns (<italic toggle=\"yes\">L</italic> = 0.5 µm and <italic toggle=\"yes\">L</italic> = 1 µm) were subsequently transferred onto the WTe<sub>2x</sub>S<sub>2(1‐x)</sub> monolayer flake on a Si/SiO<sub>2</sub> substrate using the transferred method. The electrical properties of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐x)</sub> FETs were studied using a Keithley 2636 sourcemeter as a DC voltage source in vacuum at 200 −300 K.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>W.‐H.L. and N.‐C.Y. conceived the research ideas. W.‐H.L. and C.‐S.L. contributed equally to this work. W.‐H.L. constructed the CVD system for WS<sub>2</sub>, WTe<sub>2,</sub> and WTe<sub>2x</sub>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> growth and participated in all the measurements and data analysis. W.‐H.L. and H.A.A. contributed to the XPS measurement. W.‐H.L., C.‐S.L., and G.R.R. contributed to the Raman and PL mapping measurements. W.‐H.L., C.‐S.L., and C.I.W. contributed to the FET device measurements. W.‐H.L. and N.‐C.Y. wrote the manuscript, and N.‐C.Y. supervised and coordinated the project.</p>" ]
[ "<title>Acknowledgements</title>", "<p>This work was jointly supported by the Army Research Office under the Multi‐University Research Initiative (MURI) program (award #W911NF‐16‐1‐0472) and the National Science Foundation under the Physics Frontier Center program for Institute for Quantum Information and Matter (IQIM) at the California Institute of Technology (award #1733907). The authors also acknowledged support from the Beckman Institute at the California Institute of Technology for access to facilities at the Molecular Materials Research Center. W.‐H. Lin thanks Ruohan Wang for great discussion and support and acknowledged a graduate fellowship from the J. Yang Family Foundation. C.‐S. Li acknowledges the support from the Ministry of Science and Technology in Taiwan (award #108‐2911‐I‐002‐524 and 109‐2622‐8‐002‐003) for his visit and research at Caltech.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6719-fig-0001\"><label>Figure 1</label><caption><p>Proposed mechanism for tailoring the valley polarized PL of gated WTe<sub>2</sub>/6%‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> heterostructure: a) Schematics of the energy bands of monolayer WS<sub>2</sub> under right‐handed CPL with significant intervalley scattering and therefore comparable decay rates for both <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> and <italic toggle=\"yes\">σ</italic>\n<sup>−</sup> excitons. b) Schematics of the energy bands of monolayer 6%‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> under right‐handed CPL, showing a significantly increased decay rate for <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> excitons. c) Schematics of the energy bands of a gated 6%‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub>/WTe<sub>2</sub> heterostructure, showing both an increased decay rate of <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> excitons and suppressed intervalley scattering due to carrier doping‐induced screening of the long‐range electron‐hole interaction.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6719-fig-0002\"><label>Figure 2</label><caption><p>Optical microscopic images, chemical compositions and carrier doping of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys for a) 1H‐WS<sub>2</sub>, b) 1H‐WTe<sub>0.12</sub>S<sub>1.88</sub>, c) 1T′‐ WTe<sub>1.28</sub>S<sub>0.72</sub>, d) 1T′‐ WTe<sub>2</sub>. XPS spectra of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with <italic toggle=\"yes\">x</italic> = 0, 0.06, 0.13, 0.52, 0.64, and 1, respectively: e) XPS W 4f spectra, f) XPS S 2p spectra, and g) XPS Te 3d spectra. h) Valence band spectra with increasing Te doping concentration in WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys. i) (<italic toggle=\"yes\">E</italic>\n<sub>F</sub> − <italic toggle=\"yes\">E</italic>\n<sub>V</sub>) values extracted from the UPS spectra in h) for WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with different <italic toggle=\"yes\">x</italic>‐values. j) Electron doping concentration versus Te doping concentration in WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys by using the (<italic toggle=\"yes\">E</italic>\n<sub>C</sub> − <italic toggle=\"yes\">E</italic>\n<sub>F</sub>) values extracted from ultraviolet photoelectron spectroscopy (UPS) and PL spectra as explained in the main text.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6719-fig-0003\"><label>Figure 3</label><caption><p>Raman, PL and valley‐polarized PL spectra of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys: a) Raman spectra of the alloys with <italic toggle=\"yes\">x</italic> = 0, 0.06, 0.13, 0.52, 0.64 and 1. b) PL spectra of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with <italic toggle=\"yes\">x</italic> = 0, 0.03, 0.06, 0.13, 0.26, and 0.35, respectively. The inset shows the corresponding composition‐dependent (<italic toggle=\"yes\">x</italic>) bandgap of the WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys, as determined by PL. c) The peak positions of A‐excitons and trions, and the corresponding work function of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with <italic toggle=\"yes\">x</italic> = 0, 0.06, 0.13, 0.26, and 0.35, respectively. Circularly polarized PL spectra of monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys under the excitation of <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> light (514 nm) at RT: d) WS<sub>2</sub>, e) WTe<sub>0.12</sub>S<sub>1.88</sub>, f) WTe<sub>0.26</sub>S<sub>1.74</sub>, g) WTe<sub>0.52</sub>S<sub>1.48</sub>, and h) WTe<sub>0.7</sub>S<sub>1.3</sub>. (i) DVP versus increasing Te doping concentration on WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys extracted from (d) to (h), showing much enhanced DVP in WTe<sub>0.12</sub>S<sub>1.88</sub>, WTe<sub>0.26</sub>S<sub>1.74</sub> and WTe<sub>0.52</sub>S<sub>1.48</sub> relative to that in WS<sub>2</sub>.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6719-fig-0004\"><label>Figure 4</label><caption><p>Transport characterizations of back‐gated FET devices based on 1H‐phase and 1T′‐phase WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys: a) Schematic illustration of a fabricated FET device. b) Cross‐sectional image of the metal‐semiconductor interface captured by transmission electron microscopy (TEM). Current‐voltage (<italic toggle=\"yes\">I</italic>\n<sub>ds</sub> vs. <italic toggle=\"yes\">V</italic>\n<sub>ds</sub>) characteristics with different bottom gate voltage (<italic toggle=\"yes\">V</italic>\n<sub>g</sub>) and gating response (<italic toggle=\"yes\">I</italic>\n<sub>ds</sub> vs. <italic toggle=\"yes\">V</italic>\n<sub>gs</sub>) with different source‐drain voltages (<italic toggle=\"yes\">V</italic>\n<sub>ds</sub>) from 0.5 V to 2 V for c) 1H‐WS<sub>2</sub>, and d) 1H‐WTe<sub>0.26</sub>S<sub>1.74</sub>. e) Room‐temperature µ<sub>FE</sub> and <italic toggle=\"yes\">I</italic>\n<sub>on</sub> of monolayer semiconducting WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with <italic toggle=\"yes\">x</italic> = 0, 0.06, 0.13, 0.26, and 0.35. Current‐voltage (<italic toggle=\"yes\">I</italic>\n<sub>ds</sub> vs. <italic toggle=\"yes\">V</italic>\n<sub>ds</sub>) characteristics with different bottom gate voltage (<italic toggle=\"yes\">V</italic>\n<sub>g</sub>) and gating response (<italic toggle=\"yes\">I</italic>\n<sub>ds</sub> vs. <italic toggle=\"yes\">V</italic>\n<sub>gs</sub>) with different source‐drain voltages (<italic toggle=\"yes\">V</italic>\n<sub>ds</sub>) from 0.5 V to 2 V for f) 1T′‐WTe<sub>1.04</sub>S<sub>0.96</sub> and g) 1T′‐WTe<sub>2</sub>. h) Room‐temperature resistivity of monolayer metallic WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with <italic toggle=\"yes\">x</italic> = 0.52, 0.64, and 1.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6719-fig-0005\"><label>Figure 5</label><caption><p>Schottky barrier height between metal electrodes (Au, WTe<sub>2</sub>) and WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys: a) Schematic band diagram of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> FET interface with Au electrode obtained from UPS measurements. b) Schematic band diagram of WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> FET interface with 1T′‐WTe<sub>2</sub> electrode obtained from UPS measurements. Temperature‐dependent two‐terminal current <italic toggle=\"yes\">I</italic>\n<sub>ds</sub> as a function of <italic toggle=\"yes\">V</italic>\n<sub>gs</sub> at <italic toggle=\"yes\">V</italic>\n<sub>ds</sub> = 2 V for the FET devices with c‐left) Au, and d‐left) WTe<sub>2</sub> electrical contacts. Gate‐voltage‐dependent ln (<italic toggle=\"yes\">I</italic>\n<sub>0</sub>/<italic toggle=\"yes\">T</italic>\n<sup>3/2</sup>) versus (<italic toggle=\"yes\">1</italic>/<italic toggle=\"yes\">kT</italic>) plot with two different contacts: c‐right) Au, and d‐right) WTe<sub>2</sub>. From the slopes of the curves shown in Figure c), d) and Figure S7, the gate‐voltage‐dependent SBH (<italic toggle=\"yes\">ϕ</italic>\n<sub>B</sub>) of the FETs are extracted in e). f) Comparisons of the extracted SBH at <italic toggle=\"yes\">V</italic>\n<sub>FB</sub> of the monolayer 6%‐WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with WTe<sub>2</sub> electrode and the monolayer WTe<sub>2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>S<sub>2(1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>)</sub> alloys with <italic toggle=\"yes\">x</italic> = 0.06, 0.26, and 0.35 and Au electrode.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6719-fig-0006\"><label>Figure 6</label><caption><p>Electrically tunable valley polarization of WTe<sub>0.12</sub>S<sub>1.88</sub> /1T′‐ WTe<sub>2</sub> with lowest SBH. a) Schematic illustration of a WTe<sub>2</sub>/WTe<sub>0.12</sub>S<sub>1.88</sub> heterostructure. b) PL spectra at RT for <italic toggle=\"yes\">V</italic>\n<sub>g</sub> values ranging from −20 V to 20 V, with an increment of 5 V. c) Gate voltage dependence of the PL peak position for neutral excitons (blue) and trions (red) under <italic toggle=\"yes\">V</italic>\n<sub>g</sub> from −20 V to 20 V. The intensity ratio of trions and excitons (green) is also shown as a function of <italic toggle=\"yes\">V</italic>\n<sub>g</sub> from −20 V to 20 V. The <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> (blue) and <italic toggle=\"yes\">σ</italic>\n<sup>−</sup> (black) PL intensity were taken at RT under d) <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = 0, The <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> (green) and <italic toggle=\"yes\">σ</italic>\n<sup>−</sup> (black) PL intensity were taken at RT under e) <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = −5 V. The <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> (yellow) and <italic toggle=\"yes\">σ</italic>\n<sup>−</sup> (black) PL intensity taken at RT under f) <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = −10 V. The <italic toggle=\"yes\">σ</italic>\n<sup>+</sup> (red) and <italic toggle=\"yes\">σ</italic>\n<sup>−</sup> (black) PL intensity taken at RT under g) <italic toggle=\"yes\">V</italic>\n<sub>g</sub> = −20 V.</p></caption></fig>" ]
[]
[ "<disp-formula id=\"advs6719-disp-0001\">\n<label>(1)</label>\n<mml:math id=\"jats-math-1\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mi>DVP</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:mi>I</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:msup><mml:mi>σ</mml:mi><mml:mo>+</mml:mo></mml:msup></mml:mfenced><mml:mo>−</mml:mo><mml:mi>I</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:msup><mml:mi>σ</mml:mi><mml:mo>−</mml:mo></mml:msup></mml:mfenced></mml:mrow><mml:mrow><mml:mi>I</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:msup><mml:mi>σ</mml:mi><mml:mo>+</mml:mo></mml:msup></mml:mfenced><mml:mo>+</mml:mo><mml:mi>I</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:msup><mml:mi>σ</mml:mi><mml:mo>−</mml:mo></mml:msup></mml:mfenced></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6719-disp-0002\">\n<label>(2)</label>\n<mml:math id=\"jats-math-2\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant=\"normal\">C</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mn>4</mml:mn><mml:mi>π</mml:mi><mml:msubsup><mml:mi>m</mml:mi><mml:mi>e</mml:mi><mml:mo>∗</mml:mo></mml:msubsup><mml:mo>/</mml:mo><mml:msup><mml:mi>h</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6719-disp-0003\">\n<label>(3)</label>\n<mml:math id=\"jats-math-3\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant=\"normal\">D</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>N</mml:mi><mml:mi mathvariant=\"normal\">C</mml:mi></mml:msub><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msub><mml:mi>T</mml:mi><mml:mi>ln</mml:mi><mml:mfenced separators=\"\" open=\"[\" close=\"]\"><mml:mrow><mml:mn>1</mml:mn><mml:mo>+</mml:mo><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mo linebreak=\"badbreak\">−</mml:mo><mml:mfrac><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mi>c</mml:mi></mml:msub><mml:mo>−</mml:mo><mml:msub><mml:mi>E</mml:mi><mml:mi>F</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mfenced></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6719-disp-0004\">\n<label>(4)</label>\n<mml:math id=\"jats-math-5\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>WTe</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi>x</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mi mathvariant=\"normal\">S</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi>x</mml:mi><mml:msub><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>WTe</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>1</mml:mn><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>WS</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mi>b</mml:mi><mml:mi>x</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>1</mml:mn><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6719-disp-0005\">\n<label>(5)</label>\n<mml:math id=\"jats-math-6\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>FE</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mi>L</mml:mi><mml:mrow><mml:mi>W</mml:mi><mml:msub><mml:mi>V</mml:mi><mml:mi>ds</mml:mi></mml:msub><mml:msub><mml:mi>C</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi></mml:msub></mml:mrow></mml:mfrac><mml:mfrac><mml:mrow><mml:mi>d</mml:mi><mml:msub><mml:mi>I</mml:mi><mml:mi>ds</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:mi>d</mml:mi><mml:msub><mml:mi>V</mml:mi><mml:mi>gs</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6719-disp-0006\">\n<label>(6)</label>\n<mml:math id=\"jats-math-8\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>ln</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:msub><mml:mi>I</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:msup><mml:mi>T</mml:mi><mml:mrow><mml:mn>3</mml:mn><mml:mo>/</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mfrac></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi>ln</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:mi>A</mml:mi><mml:msup><mml:mi>A</mml:mi><mml:mo>∗</mml:mo></mml:msup></mml:mrow></mml:mfenced><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mfrac><mml:mrow><mml:mi>e</mml:mi><mml:msub><mml:mi>ϕ</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6719-disp-0007\">\n<label>(7)</label>\n<mml:math id=\"jats-math-11\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mi>DVP</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:msub><mml:mi>P</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mrow><mml:mn>1</mml:mn><mml:mo>+</mml:mo><mml:mn>2</mml:mn><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mrow><mml:msub><mml:mi>τ</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>τ</mml:mi><mml:mi>v</mml:mi></mml:msub></mml:mrow></mml:mfenced></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>" ]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
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2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 16; 11(2):2304890
oa_package/be/77/PMC10787083.tar.gz
PMC10787084
37870206
[ "<title>Introduction</title>", "<p>Immunotherapy is one of the most revolutionary therapeutic methods for cancer, which leverages the natural immune system to defeat tumor cells and protect healthy cells.<sup>[</sup>\n##REF##25742450##\n1\n##\n<sup>]</sup> The enhancement of immunotherapy has become an emerging direction to develop highly effective and practical cancer therapeutic methods. Generally, the efficacy of immunotherapy is determined by three key aspects, the weakened resistance of tumor cells, the enhanced activation of immune cells, and the promotion of immune‐killing.<sup>[</sup>\n##REF##27551071##\n2\n##\n<sup>]</sup> Many crafty tumor cells have evolved various ways to resist the immune system for survival, which mainly utilize the overexpression of the inhibitory receptor‐binding ligands to block the recognition between immune cells and tumor cells.<sup>[</sup>\n##REF##24325346##\n3\n##\n<sup>]</sup> The glycosylation of these ligands, especially the sialylation, often plays critical functions in many tumor cell progressions,<sup>[</sup>\n##REF##20956342##\n4\n##\n<sup>]</sup> including decreased immunogenicity and increased tumor immune evasion.<sup>[</sup>\n##REF##27551071##\n2\n##, ##REF##24292068##\n5\n##\n<sup>]</sup> On the other hand, the activation of immune cells can be enhanced by many signal response pathways, including the blockade of immune checkpoint<sup>[</sup>\n##REF##33750922##\n6\n##\n<sup>]</sup> and the binding between cells‐activating receptors and ligands.<sup>[</sup>\n##REF##27551071##\n2\n##, ##REF##20956342##\n4\n##, ##REF##14523385##\n7\n##\n<sup>]</sup> Among these immune cells, natural killer (NK) cells are a type of lymphocyte and play critical roles in the innate immunity against tumors.<sup>[</sup>\n##REF##24292068##\n5\n##, ##REF##26635792##\n8\n##\n<sup>]</sup> Especially, the activation of NK cells can be enhanced by specific glycans,<sup>[</sup>\n##REF##17226049##\n9\n##\n<sup>]</sup> which are widely present on mammalian cell surfaces. In addition, the immune‐killing can be initiated by releasing the cytotoxic granules including pore‐forming perforin proteins and serine proteases‐granzymes (especially granzyme B, GrB) to lyse tumor cells.<sup>[</sup>\n##REF##33407739##\n10\n##\n<sup>]</sup> The perforation is a decisive and membrane‐disruptive step to form pores on tumor cells<sup>[</sup>\n##REF##21037563##\n11\n##\n<sup>]</sup> and assist GrB for inducing cell death.<sup>[</sup>\n##REF##33407739##\n10\n##, ##REF##12766758##\n12\n##\n<sup>]</sup>\n</p>", "<p>At present, the enhancement of immunotherapy by separately blocking the immune inhibition or activating immune cells is steadily popular. The blockage between the sialic acid (SA) on tumor cells and the sialic acid‐binding immunoglobulin‐like lectins (Siglecs) on immune cells is the most common method, which can transmit immunosuppressive signals to relieve immune inhibition and promote immune enhancement.<sup>[</sup>\n##REF##27551071##\n2\n##, ##REF##24292068##\n5\n##\n<sup>]</sup> This blockage can be achieved by the inhibition of intracellular sialyltransferase,<sup>[</sup>\n##REF##29703719##\n13\n##\n<sup>]</sup> or direct cleavage by the sialidase anchored on the tumor cell surface.<sup>[</sup>\n##REF##27551071##\n2\n##, ##REF##32807964##\n14\n##\n<sup>]</sup> The activation of immune cells is usually applied to promote the targeting and the secretion of cytokines from NK cells by increasing the NK‐activating glycan on tumor cells.<sup>[</sup>\n##REF##33407739##\n10\n##, ##REF##29398707##\n15\n##\n<sup>]</sup> In particular, the galactose (Gal) or fructose‐terminated glycoconjugates have been reported to have strong activating abilities for NK cells.<sup>[</sup>\n##REF##17226049##\n9\n##, ##REF##29398707##\n15\n##\n<sup>]</sup> Despite of the certain success accomplished by these methods, the efficiency of single enhancement is always limited. Besides, the enhancement of the perforating process in the immune‐killing has not yet received attention.</p>", "<p>To break through the limited immunotherapeutic efficacy, this work ingeniously integrates the weakening of immune cell inhibition and the boosting of immune cell activation with extra perforation assistance to achieve for the first time triple enhancement of the immunotherapy. The endogenous perforin is difficult to be utilized in immunotherapy due to its susceptibility to environment or modification.<sup>[</sup>\n##REF##12766758##\n12a\n##\n<sup>]</sup> To introduce the perforation assistance, streptolysin O (SLO), a bacterium exogenously‐secreted pore‐forming toxin, is used to construct the triply enhanced immunotherapy drug (TEID). SLO possesses excellent perforating activity and stability after different modifications.<sup>[</sup>\n##REF##28186501##\n16\n##\n<sup>]</sup> Upon decoration with dibenzocyclooctyne‐sulfo‐N‐hydroxysuccinimidyl (DBCO‐sulfo‐NHS) ester, the formed SLO‐DBCO can be conveniently connected with azide functionalized galactose (Gal‐N<sub>3</sub>) or α2‐3,6,8 neuraminidase A (NEU‐N<sub>3</sub>) through copper‐free click chemistry<sup>[</sup>\n##UREF##0##\n17\n##\n<sup>]</sup> to obtain SLO‐Gal and SLO‐NEU (<bold>Figure</bold>\n##FIG##0##\n1\n##). After co‐encapsulating SLO‐Gal and SLO‐NEU in hyaluronic acid (HA) cross‐linked shell, the constructed TEID can be specifically recognized by a cluster of differentiation 44 (CD44) on the tumor cell surface to achieve targeted delivery and HAase‐mediated degradation in the tumor microenvironment,<sup>[</sup>\n##REF##24618921##\n18\n##\n<sup>]</sup> which releases SLO‐Gal and SLO‐NEU to anchor the NEU and Gal on cell membrane via perforation. The anchored NEU can cleave the original cell surface SA to weaken immune cell inhibition, while the anchored Gal increases the amount of cell surface Gal and thus boosts NK cell activation. Furthermore, the perforation promotes the delivery of secreted GrB to greatly accelerate the immune‐killing process. As a proof of concept, 4T1 tumor‐bearing mice are used as models to demonstrate the triple immunotherapeutic enhancements of the designed TEID. The integration of in situ dual glycan reforming with perforation provides a powerful strategy to improve the clinical immunotherapeutic efficacy of cancer.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Characterization of SLO‐Gal and SLO‐NEU</title>", "<p>Gal‐N<sub>3</sub> obtained by deacetylation of 4AC‐Gal‐N<sub>3</sub>\n<sup>[</sup>\n##REF##26280598##\n19\n##\n<sup>]</sup> showed an <italic toggle=\"yes\">m/z</italic> value of 360, obviously lower than 528 of 4AC‐Gal‐N<sub>3</sub> (Figure ##SUPPL##0##S1a,b##, Supporting Information). The mass spectra of SLO and SLO‐DBCO exhibited obvious variation of their m/z values from 60 206 to 61 394 (Figure ##SUPPL##0##S1c##, Supporting Information), indicating the successful conjugation of two DBCO to a single SLO. Upon copper‐free click linkage<sup>[</sup>\n##UREF##0##\n17\n##\n<sup>]</sup> of SLO‐DBCO with Gal‐N<sub>3</sub>, the obtained SLO‐Gal exhibited an <italic toggle=\"yes\">m/z</italic> value of 62 087, indicating that two Gal were conjugated to SLO due to the presence of two DBCO.</p>", "<p>The <italic toggle=\"yes\">m/z</italic> values of NEU and NEU‐N<sub>3</sub> were 73 482 and 74 621, respectively (Figure ##SUPPL##0##S1d##, Supporting Information), indicating the presence of two N<sub>3</sub> on a single NEU. The conjugation of SLO‐DBCO with NEU‐N<sub>3</sub> was characterized by the cleaving performance of NEU and SLO‐NEU with 2′‐(4‐methylumbelliferyl)‐α‐D‐N‐acetylneuraminic acid (MuNeuNAc) as the substrate. After incubating MuNeuNAc with NEU or SLO‐NEU, both mixtures showed the fluorescence of methylumbelliferone. At an incubation time of 70 min, the fluorescence intensity of SLO‐NEU incubated MuNeuNAc was 80% of NEU incubated MuNeuNAc (Figure ##SUPPL##0##S2##, Supporting Information), demonstrating the good maintenance of the enzymatic activity of SLO‐NEU.</p>", "<title>Functions of SLO‐Gal and SLO‐NEU on Tumor Cells</title>", "<p>The functions of SLO‐Gal and SLO‐NEU on tumor cells were first investigated by incubating mouse breast cancer 4T1 cells or human breast cancer MCF‐7 cells with SLO, SLO‐Gal, NEU, or SLO‐NEU, and then staining them with propidium iodide (PI) or Cy3 labeled Sambucus Nigra lectin (Cy3‐SNA), which can specifically recognize SA on the cell surface.<sup>[</sup>\n##REF##3805045##\n20\n##\n<sup>]</sup> All the SLO‐NEU, SLO‐Gal, or SLO treated and then PI stained 4T1 (<bold>Figure</bold>\n##FIG##1##\n2a##) and MCF‐7 cells (Figure ##SUPPL##0##S3a##, Supporting Information) showed obvious PI fluorescence, indicating that the SLO‐Gal and SLO‐NEU maintained similar perforating function of SLO on the tumor cell membrane. The CLSM images of SLO and SLO‐Gal treated and then Cy3‐SNA stained 4T1 and MCF‐7 cells exhibited Cy3 fluorescence similar to the Control on cell surface, while the Cy3 fluorescence disappeared on SLO‐NEU or NEU treated cells (Figure ##FIG##1##2b##; Figure ##SUPPL##0##S3b##, Supporting Information), demonstrating the SA‐cleaving function of SLO‐NEU on cell membrane.</p>", "<p>After NK cells were treated with SLO‐NEU, SLO‐Gal or SLO, and stained with PI, they did not exhibit any PI fluorescence (Figure ##SUPPL##0##S4##, Supporting Information), indicating that SLO could not perforate on NK cells, consistent to previous reports on the immune‐killing,<sup>[</sup>\n##REF##23885110##\n21\n##\n<sup>]</sup> which was beneficial to maintain the viability of NK cells during immunotherapy.</p>", "<p>To examine the Gal‐introducing function of SLO‐Gal, the original Gal on the cell membrane was firstl cleaved by incubating the cells with β‐galactosidase (GD). The GD‐treated cells were then incubated with SLO, SLO‐Gal, or SLO‐NEU, and stained with fluorescein labeled Jacalin (F‐Jac), which can specifically recognize Gal on the cell surface.<sup>[</sup>\n##REF##31896587##\n22\n##\n<sup>]</sup> Only the GD‐treated 4T1 and MCF‐7 cells incubated with SLO‐Gal showed obvious fluorescence of fluorescein, as the Control cells (Figure ##FIG##1##2c##; Figure ##SUPPL##0##S3c##, Supporting Information), indicating a Gal‐introducing process.</p>", "<p>The flow cytometric analysis also showed the increasing fluorescence of PI and F‐Jac and the decreasing fluorescence of Cy3‐SNA on 4T1 and MCF‐7 cells upon the similar treatments, further demonstrating the perforating, Gal‐introducing, and SA‐cleaving functions of SLO‐Gal and SLO‐NEU on tumor cells, respectively (Figure ##SUPPL##0##S5##, Supporting Information). Thus, the SLO‐Gal and SLO‐NEU could successfully perform triple functions on the membranes of different tumor cells.</p>", "<title>SLO‐Gal and SLO‐NEU Enhanced in Vitro Immune‐Killing</title>", "<p>The in vitro immune‐killing was investigated by incubating 4T1 and MCF‐7 cells with Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or the mixture of SLO‐Gal and SLO‐NEU (SLO‐Gal&amp;SLO‐NEU), and then with NK cells at a ratio of 1:1 for different times to perform CCK8 assay. With the increasing incubation time, the viability of these incubated 4T1 and MCF‐7 cells obviously decreased (Figure ##SUPPL##0##S6##, Supporting Information), which indicated the universal immune‐killing ability of NK cells. In addition, the cell viability of the untreated or Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or SLO‐Gal&amp;SLO‐NEU treated tumor cells exhibited the in‐turn decrease, which demonstrated the enhancing immune‐killing ability, and that SLO‐Gal&amp;SLO‐NEU led to the significantly stronger immune‐killing ability of NK cells than Gal, NEU, SLO, SLO‐Gal, or SLO‐NEU. Thus, the integration of Gal‐introduction, SA‐cleavage, and perforation could exactly triply enhance the immune‐killing of NK cells.</p>", "<p>The enhancement of SLO‐Gal&amp;SLO‐NEU on the immune‐killing ability of different effectors (E) was examined with CCK8 assay after incubating SLO‐Gal&amp;SLO‐NEU treated MCF‐7 or 4T1 cells with T cells, peripheral blood mononuclear cells (PBMCs) and NK cells, which demonstrated that SLO‐Gal&amp;SLO‐NEU possessed significantly stronger enhancement on NK cells than on both T cells and PBMCs. Therefore, SLO‐Gal&amp;SLO‐NEU mainly activated NK cells to enhance NK‐induced immune‐killing (Figure ##SUPPL##0##S7##, Supporting Information).</p>", "<p>The ratio of NK cells to tumor cells in the in vitro immune‐killing was optimized by incubating SLO‐Gal&amp;SLO‐NEU treated MCF‐7 or 4T1 cells with NK cells at 10:1, 1:1, 1:10, 1:50, and 1:100 to perform CCK8 assay. Using untreated tumor cells as the control, the enhancing efficiency of immune‐killing was calculated with (ViabilityNK–ViabilitySLO‐Gal&amp;SLO‐NEU+NK)/ViabilityNK. The largest enhancing efficiency was both at the ratio of 1:10 for both 4T1 and MCF‐7 cells (Figure ##SUPPL##0##S8##, Supporting Information).</p>", "<p>The apoptosis or necrosis of tumor cells resulted from immune‐killing was further investigated with flow cytometric analysis by bicolor staining with Annexin V‐FITC and propidine iodide.<sup>[</sup>\n##REF##31438862##\n23\n##\n<sup>]</sup> In the absence of NK cells, all of the PBS, Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or SLO‐Gal&amp;SLO‐NEU treated 4T1 cells maintained &gt;90% in the viable region (Figure ##SUPPL##0##S9##, Supporting Information), indicating that these treatments could not bring obvious apoptosis of tumor cells. However, after these treated 4T1 cells were further incubated with NK cells at the optimal ratio of 1:10 for 24 h, the cells in the viable region obviously decreased, and the lowest maintaining occurred in SLO‐Gal&amp;SLO‐NEU treatment (<bold>Figure</bold>\n##FIG##2##\n3a##), indicating the maximum apoptosis and necrosis of tumor cells due to the immune‐killing, which was consistent to the CCK8 assay.</p>", "<p>In NK cell‐based immunotherapy, the immune‐killing could be attributed to the secretion of cytokines from NK cells.<sup>[</sup>\n##REF##33407739##\n10\n##\n<sup>]</sup> The cytokines, including IFN‐γ, TNF‐α, IL‐2, perforin, and GrB, secreted from NK cells during the triply enhanced immune‐killing (Figure ##FIG##2##3b##) were analyzed by ELISA. All these cytokines exhibited an obvious in‐turn increase after NK cells were incubated with Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or SLO‐Gal&amp;SLO‐NEU treated 4T1 cells (Figure ##FIG##2##3c–g##, non‐shaded columns), which indicated that the integration of Gal‐introduction, SA‐cleavage, and perforation exhibited the maximum enhancement in the in vitro immune‐killing.</p>", "<title>Performance of TEID</title>", "<p>The encapsulation of SLO‐Gal&amp;SLO‐NEU in an HA cross‐linked shell could avoid the denaturation of SLO‐Gal and SLO‐NEU in plasma and achieve tumor targeting through the specific recognition of HA to CD44 receptor on the tumor cell surface.<sup>[</sup>\n##REF##24618921##\n18\n##, ##REF##15229478##\n24\n##\n<sup>]</sup> The synthesized TEID displayed a uniform spheroid structure with a diameter of ≈105 nm and a hydrodynamic size distribution narrower than those of previously reported HA structures<sup>[</sup>\n##REF##24618921##\n18\n##, ##REF##15229478##\n24\n##\n<sup>]</sup>(<bold>Figure</bold>\n##FIG##3##\n4a##). To verify the degradation of HA shell by HAase in the tumor microenvironment,<sup>[</sup>\n##REF##24618921##\n18\n##\n<sup>]</sup> the TEID was incubated with HAase at different pHs for different times and subjected to Zeta potential analysis. The mixtures incubated at pH 5.0 and 6.5 showed the change of Zeta potential from negative to positive value after incubation for 1 and 2 h (Figure ##FIG##3##4b##), respectively, while the Zeta potentials of TEID at these pHs did not change (Figure ##SUPPL##0##S10##, Supporting Information), indicating the degradation of TEID to release positively charged SLO‐Gal and SLO‐NEU at low pHs. As the in vivo tumor microenvironment was weakly acidic (≈pH 6.5),<sup>[</sup>\n##REF##15229478##\n24a\n##\n<sup>]</sup> the HA shell of TEID could be quickly degraded by HAase to release SLO‐Gal and SLO‐NEU.</p>", "<p>The function maintenance of the SLO‐Gal and SLO‐NEU released from TEID was investigated by treating the tumor cells with TEID, HA degraded TEID (Figure ##FIG##3##4c##), or the mixture of SLO‐Gal and SLO‐NEU, and then staining them with PI, Cy3‐SNA, or F‐Jac. In the absence of HA degradation, the TEID treated cells showed the same images as control cells (Figure ##FIG##3##4d–f##; Figure ##SUPPL##0##S11##, Supporting Information), indicating the efficient isolation of SLO‐Gal and SLO‐NEU by HA shell. By contrary, the degradation of HA led to obvious fluorescence of PI, fluorescein, and Cy3, as those treated directly with the mixture of SLO‐Gal and SLO‐NEU, demonstrating the efficient performance of perforating, SA‐cleaving, and Gal‐introducing functions of the released SLO‐Gal and SLO‐NEU from TEID. The function maintenance was also demonstrated by the changes of PI, Cy3‐SNA, and F‐Jac fluorescence signals in flow cytometric analysis (Figure ##SUPPL##0##S12##, Supporting Information).</p>", "<p>The secretion of cytokines from NK cells was further examined with ELISA analysis after incubating 4T1 cells with PBS, TEID, or HAase degraded TEID, and then NK cells. Both PBS and TEID and then NK cells treated 4T1 cells showed the same low levels of cytokines (Figure ##SUPPL##0##S13##, Supporting Information), indicating the excellent protective capacity of the HA shell to TEID, which limited the functions of encapsulated SLO‐Gal and SLO‐NEU. After the TEID was degraded by HAase, the released SLO‐Gal and SLO‐NEU could be anchored on 4T1 cells to perform the three functions, which led to the secretion of cytokines from NK cells, and thus significantly increased the levels of the cytokines. Moreover, the increases were significantly greater than those treated with the degraded products of HAase and HA encapsulated PBS, Gal, NEU, SLO, SLO‐Gal, or SLO‐NEU (Figure ##FIG##2##3c–g##, shaded columns), demonstrating the triply enhanced secretion of cytokines, demonstrating the triply enhanced secretion of cytokines, which promised the application of TEID in the in vivo immunotherapy.</p>", "<title>In Vivo Immunotherapy by TEID</title>", "<p>To demonstrate the triply enhanced in vivo immunotherapy by TEID, seven groups of the 4T1 tumor xenograft mice with tumor volume of ≈80 mm<sup>3</sup> received intravenous injections of saline, HA encapsulated Gal (Gal@HA), NEU (NEU@HA), SLO (SLO@HA), SLO‐Gal (SLO‐Gal@HA), SLO‐NEU (SLO‐NEU@HA), and TEID every other day for 22 days, respectively (<bold>Figure</bold>\n##FIG##4##\n5a##). The body weight of all mice did not exhibit discernible difference during the treatment (Figure ##FIG##4##5b##), and their heart, liver, spleen, lung, and kidney did not also show abnormalities in the pathological observation (Figure ##SUPPL##0##S14##, Supporting Information), indicating the negligible side effects under these treatments. The tumor volumes of the mice treated with Gal@HA, NEU@HA, and SLO@HA exhibited tiny variations comparing to these treated with saline (Figure ##FIG##4##5c,d##). In contrast, the mice treated with SLO‐Gal@HA or SLO‐NEU@HA exhibited a certain degree of inhibition to tumor volume, which could be attributed to the anchoring of SLO‐Gal or SLO‐NEU on tumor cells in tumor microenvironment to improve the NK cell‐based immune‐killing through the perforating and Gal‐introducing or SA‐cleaving functions, respectively. The mice treated with TEID exhibited the minimum volume, indicating the enhanced in vivo immunotherapy due to the integration of in situ dual glycan reforming with perforation. The pathological states of tumor tissues dissected from each treated group were assessed by hematoxylin and eosin (H&amp;E) and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. The sectioned tissue from TEID treated mouse exhibited the largest necrotic area compared to those from SLO‐Gal@HA or SLO‐NEU@HA treated mouse (Figure ##FIG##4##5e##), which was consistent to the changes of tumor volumes. Thus, the TEID exactly exhibited the maximum enhancement in in vivo immunotherapy.</p>", "<p>To further validate the enhancing mechanisms of TEID in in vivo immunotherapy, the tumor tissues sectioned from seven treated mouse groups were respectively stained with Cy3‐SNA and F‐Jac (<bold>Figure</bold>\n##FIG##5##\n6a##). The tissue slices from the mice treated with Gal@HA, NEU@HA, and SLO@HA exhibited similar fluorescence of Cy3‐SNA and F‐Jac compared to those treated with saline (Figure ##FIG##5##6b–d##). In contrast, the tissue slices from SLO‐Gal@HA or SLO‐NEU@HA treated mice exhibited a significant increase of F‐Jac fluorescence or a decrease of Cy3‐SNA fluorescence (Figure ##FIG##5##6b–d##). Besides, the tissue slice from the TEID treated mouse exhibited a simultaneous decrease of Cy3‐SNA and an increase of F‐Jac fluorescence (Figure ##FIG##5##6b–d##). These results indicated that the perforation of SLO and the introduction of Gal and NEU to tumor tissue for performing dual glycan reforming played critical roles in in vivo immunotherapy.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Characterization of SLO‐Gal and SLO‐NEU</title>", "<p>Gal‐N<sub>3</sub> obtained by deacetylation of 4AC‐Gal‐N<sub>3</sub>\n<sup>[</sup>\n##REF##26280598##\n19\n##\n<sup>]</sup> showed an <italic toggle=\"yes\">m/z</italic> value of 360, obviously lower than 528 of 4AC‐Gal‐N<sub>3</sub> (Figure ##SUPPL##0##S1a,b##, Supporting Information). The mass spectra of SLO and SLO‐DBCO exhibited obvious variation of their m/z values from 60 206 to 61 394 (Figure ##SUPPL##0##S1c##, Supporting Information), indicating the successful conjugation of two DBCO to a single SLO. Upon copper‐free click linkage<sup>[</sup>\n##UREF##0##\n17\n##\n<sup>]</sup> of SLO‐DBCO with Gal‐N<sub>3</sub>, the obtained SLO‐Gal exhibited an <italic toggle=\"yes\">m/z</italic> value of 62 087, indicating that two Gal were conjugated to SLO due to the presence of two DBCO.</p>", "<p>The <italic toggle=\"yes\">m/z</italic> values of NEU and NEU‐N<sub>3</sub> were 73 482 and 74 621, respectively (Figure ##SUPPL##0##S1d##, Supporting Information), indicating the presence of two N<sub>3</sub> on a single NEU. The conjugation of SLO‐DBCO with NEU‐N<sub>3</sub> was characterized by the cleaving performance of NEU and SLO‐NEU with 2′‐(4‐methylumbelliferyl)‐α‐D‐N‐acetylneuraminic acid (MuNeuNAc) as the substrate. After incubating MuNeuNAc with NEU or SLO‐NEU, both mixtures showed the fluorescence of methylumbelliferone. At an incubation time of 70 min, the fluorescence intensity of SLO‐NEU incubated MuNeuNAc was 80% of NEU incubated MuNeuNAc (Figure ##SUPPL##0##S2##, Supporting Information), demonstrating the good maintenance of the enzymatic activity of SLO‐NEU.</p>", "<title>Functions of SLO‐Gal and SLO‐NEU on Tumor Cells</title>", "<p>The functions of SLO‐Gal and SLO‐NEU on tumor cells were first investigated by incubating mouse breast cancer 4T1 cells or human breast cancer MCF‐7 cells with SLO, SLO‐Gal, NEU, or SLO‐NEU, and then staining them with propidium iodide (PI) or Cy3 labeled Sambucus Nigra lectin (Cy3‐SNA), which can specifically recognize SA on the cell surface.<sup>[</sup>\n##REF##3805045##\n20\n##\n<sup>]</sup> All the SLO‐NEU, SLO‐Gal, or SLO treated and then PI stained 4T1 (<bold>Figure</bold>\n##FIG##1##\n2a##) and MCF‐7 cells (Figure ##SUPPL##0##S3a##, Supporting Information) showed obvious PI fluorescence, indicating that the SLO‐Gal and SLO‐NEU maintained similar perforating function of SLO on the tumor cell membrane. The CLSM images of SLO and SLO‐Gal treated and then Cy3‐SNA stained 4T1 and MCF‐7 cells exhibited Cy3 fluorescence similar to the Control on cell surface, while the Cy3 fluorescence disappeared on SLO‐NEU or NEU treated cells (Figure ##FIG##1##2b##; Figure ##SUPPL##0##S3b##, Supporting Information), demonstrating the SA‐cleaving function of SLO‐NEU on cell membrane.</p>", "<p>After NK cells were treated with SLO‐NEU, SLO‐Gal or SLO, and stained with PI, they did not exhibit any PI fluorescence (Figure ##SUPPL##0##S4##, Supporting Information), indicating that SLO could not perforate on NK cells, consistent to previous reports on the immune‐killing,<sup>[</sup>\n##REF##23885110##\n21\n##\n<sup>]</sup> which was beneficial to maintain the viability of NK cells during immunotherapy.</p>", "<p>To examine the Gal‐introducing function of SLO‐Gal, the original Gal on the cell membrane was firstl cleaved by incubating the cells with β‐galactosidase (GD). The GD‐treated cells were then incubated with SLO, SLO‐Gal, or SLO‐NEU, and stained with fluorescein labeled Jacalin (F‐Jac), which can specifically recognize Gal on the cell surface.<sup>[</sup>\n##REF##31896587##\n22\n##\n<sup>]</sup> Only the GD‐treated 4T1 and MCF‐7 cells incubated with SLO‐Gal showed obvious fluorescence of fluorescein, as the Control cells (Figure ##FIG##1##2c##; Figure ##SUPPL##0##S3c##, Supporting Information), indicating a Gal‐introducing process.</p>", "<p>The flow cytometric analysis also showed the increasing fluorescence of PI and F‐Jac and the decreasing fluorescence of Cy3‐SNA on 4T1 and MCF‐7 cells upon the similar treatments, further demonstrating the perforating, Gal‐introducing, and SA‐cleaving functions of SLO‐Gal and SLO‐NEU on tumor cells, respectively (Figure ##SUPPL##0##S5##, Supporting Information). Thus, the SLO‐Gal and SLO‐NEU could successfully perform triple functions on the membranes of different tumor cells.</p>", "<title>SLO‐Gal and SLO‐NEU Enhanced in Vitro Immune‐Killing</title>", "<p>The in vitro immune‐killing was investigated by incubating 4T1 and MCF‐7 cells with Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or the mixture of SLO‐Gal and SLO‐NEU (SLO‐Gal&amp;SLO‐NEU), and then with NK cells at a ratio of 1:1 for different times to perform CCK8 assay. With the increasing incubation time, the viability of these incubated 4T1 and MCF‐7 cells obviously decreased (Figure ##SUPPL##0##S6##, Supporting Information), which indicated the universal immune‐killing ability of NK cells. In addition, the cell viability of the untreated or Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or SLO‐Gal&amp;SLO‐NEU treated tumor cells exhibited the in‐turn decrease, which demonstrated the enhancing immune‐killing ability, and that SLO‐Gal&amp;SLO‐NEU led to the significantly stronger immune‐killing ability of NK cells than Gal, NEU, SLO, SLO‐Gal, or SLO‐NEU. Thus, the integration of Gal‐introduction, SA‐cleavage, and perforation could exactly triply enhance the immune‐killing of NK cells.</p>", "<p>The enhancement of SLO‐Gal&amp;SLO‐NEU on the immune‐killing ability of different effectors (E) was examined with CCK8 assay after incubating SLO‐Gal&amp;SLO‐NEU treated MCF‐7 or 4T1 cells with T cells, peripheral blood mononuclear cells (PBMCs) and NK cells, which demonstrated that SLO‐Gal&amp;SLO‐NEU possessed significantly stronger enhancement on NK cells than on both T cells and PBMCs. Therefore, SLO‐Gal&amp;SLO‐NEU mainly activated NK cells to enhance NK‐induced immune‐killing (Figure ##SUPPL##0##S7##, Supporting Information).</p>", "<p>The ratio of NK cells to tumor cells in the in vitro immune‐killing was optimized by incubating SLO‐Gal&amp;SLO‐NEU treated MCF‐7 or 4T1 cells with NK cells at 10:1, 1:1, 1:10, 1:50, and 1:100 to perform CCK8 assay. Using untreated tumor cells as the control, the enhancing efficiency of immune‐killing was calculated with (ViabilityNK–ViabilitySLO‐Gal&amp;SLO‐NEU+NK)/ViabilityNK. The largest enhancing efficiency was both at the ratio of 1:10 for both 4T1 and MCF‐7 cells (Figure ##SUPPL##0##S8##, Supporting Information).</p>", "<p>The apoptosis or necrosis of tumor cells resulted from immune‐killing was further investigated with flow cytometric analysis by bicolor staining with Annexin V‐FITC and propidine iodide.<sup>[</sup>\n##REF##31438862##\n23\n##\n<sup>]</sup> In the absence of NK cells, all of the PBS, Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or SLO‐Gal&amp;SLO‐NEU treated 4T1 cells maintained &gt;90% in the viable region (Figure ##SUPPL##0##S9##, Supporting Information), indicating that these treatments could not bring obvious apoptosis of tumor cells. However, after these treated 4T1 cells were further incubated with NK cells at the optimal ratio of 1:10 for 24 h, the cells in the viable region obviously decreased, and the lowest maintaining occurred in SLO‐Gal&amp;SLO‐NEU treatment (<bold>Figure</bold>\n##FIG##2##\n3a##), indicating the maximum apoptosis and necrosis of tumor cells due to the immune‐killing, which was consistent to the CCK8 assay.</p>", "<p>In NK cell‐based immunotherapy, the immune‐killing could be attributed to the secretion of cytokines from NK cells.<sup>[</sup>\n##REF##33407739##\n10\n##\n<sup>]</sup> The cytokines, including IFN‐γ, TNF‐α, IL‐2, perforin, and GrB, secreted from NK cells during the triply enhanced immune‐killing (Figure ##FIG##2##3b##) were analyzed by ELISA. All these cytokines exhibited an obvious in‐turn increase after NK cells were incubated with Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or SLO‐Gal&amp;SLO‐NEU treated 4T1 cells (Figure ##FIG##2##3c–g##, non‐shaded columns), which indicated that the integration of Gal‐introduction, SA‐cleavage, and perforation exhibited the maximum enhancement in the in vitro immune‐killing.</p>", "<title>Performance of TEID</title>", "<p>The encapsulation of SLO‐Gal&amp;SLO‐NEU in an HA cross‐linked shell could avoid the denaturation of SLO‐Gal and SLO‐NEU in plasma and achieve tumor targeting through the specific recognition of HA to CD44 receptor on the tumor cell surface.<sup>[</sup>\n##REF##24618921##\n18\n##, ##REF##15229478##\n24\n##\n<sup>]</sup> The synthesized TEID displayed a uniform spheroid structure with a diameter of ≈105 nm and a hydrodynamic size distribution narrower than those of previously reported HA structures<sup>[</sup>\n##REF##24618921##\n18\n##, ##REF##15229478##\n24\n##\n<sup>]</sup>(<bold>Figure</bold>\n##FIG##3##\n4a##). To verify the degradation of HA shell by HAase in the tumor microenvironment,<sup>[</sup>\n##REF##24618921##\n18\n##\n<sup>]</sup> the TEID was incubated with HAase at different pHs for different times and subjected to Zeta potential analysis. The mixtures incubated at pH 5.0 and 6.5 showed the change of Zeta potential from negative to positive value after incubation for 1 and 2 h (Figure ##FIG##3##4b##), respectively, while the Zeta potentials of TEID at these pHs did not change (Figure ##SUPPL##0##S10##, Supporting Information), indicating the degradation of TEID to release positively charged SLO‐Gal and SLO‐NEU at low pHs. As the in vivo tumor microenvironment was weakly acidic (≈pH 6.5),<sup>[</sup>\n##REF##15229478##\n24a\n##\n<sup>]</sup> the HA shell of TEID could be quickly degraded by HAase to release SLO‐Gal and SLO‐NEU.</p>", "<p>The function maintenance of the SLO‐Gal and SLO‐NEU released from TEID was investigated by treating the tumor cells with TEID, HA degraded TEID (Figure ##FIG##3##4c##), or the mixture of SLO‐Gal and SLO‐NEU, and then staining them with PI, Cy3‐SNA, or F‐Jac. In the absence of HA degradation, the TEID treated cells showed the same images as control cells (Figure ##FIG##3##4d–f##; Figure ##SUPPL##0##S11##, Supporting Information), indicating the efficient isolation of SLO‐Gal and SLO‐NEU by HA shell. By contrary, the degradation of HA led to obvious fluorescence of PI, fluorescein, and Cy3, as those treated directly with the mixture of SLO‐Gal and SLO‐NEU, demonstrating the efficient performance of perforating, SA‐cleaving, and Gal‐introducing functions of the released SLO‐Gal and SLO‐NEU from TEID. The function maintenance was also demonstrated by the changes of PI, Cy3‐SNA, and F‐Jac fluorescence signals in flow cytometric analysis (Figure ##SUPPL##0##S12##, Supporting Information).</p>", "<p>The secretion of cytokines from NK cells was further examined with ELISA analysis after incubating 4T1 cells with PBS, TEID, or HAase degraded TEID, and then NK cells. Both PBS and TEID and then NK cells treated 4T1 cells showed the same low levels of cytokines (Figure ##SUPPL##0##S13##, Supporting Information), indicating the excellent protective capacity of the HA shell to TEID, which limited the functions of encapsulated SLO‐Gal and SLO‐NEU. After the TEID was degraded by HAase, the released SLO‐Gal and SLO‐NEU could be anchored on 4T1 cells to perform the three functions, which led to the secretion of cytokines from NK cells, and thus significantly increased the levels of the cytokines. Moreover, the increases were significantly greater than those treated with the degraded products of HAase and HA encapsulated PBS, Gal, NEU, SLO, SLO‐Gal, or SLO‐NEU (Figure ##FIG##2##3c–g##, shaded columns), demonstrating the triply enhanced secretion of cytokines, demonstrating the triply enhanced secretion of cytokines, which promised the application of TEID in the in vivo immunotherapy.</p>", "<title>In Vivo Immunotherapy by TEID</title>", "<p>To demonstrate the triply enhanced in vivo immunotherapy by TEID, seven groups of the 4T1 tumor xenograft mice with tumor volume of ≈80 mm<sup>3</sup> received intravenous injections of saline, HA encapsulated Gal (Gal@HA), NEU (NEU@HA), SLO (SLO@HA), SLO‐Gal (SLO‐Gal@HA), SLO‐NEU (SLO‐NEU@HA), and TEID every other day for 22 days, respectively (<bold>Figure</bold>\n##FIG##4##\n5a##). The body weight of all mice did not exhibit discernible difference during the treatment (Figure ##FIG##4##5b##), and their heart, liver, spleen, lung, and kidney did not also show abnormalities in the pathological observation (Figure ##SUPPL##0##S14##, Supporting Information), indicating the negligible side effects under these treatments. The tumor volumes of the mice treated with Gal@HA, NEU@HA, and SLO@HA exhibited tiny variations comparing to these treated with saline (Figure ##FIG##4##5c,d##). In contrast, the mice treated with SLO‐Gal@HA or SLO‐NEU@HA exhibited a certain degree of inhibition to tumor volume, which could be attributed to the anchoring of SLO‐Gal or SLO‐NEU on tumor cells in tumor microenvironment to improve the NK cell‐based immune‐killing through the perforating and Gal‐introducing or SA‐cleaving functions, respectively. The mice treated with TEID exhibited the minimum volume, indicating the enhanced in vivo immunotherapy due to the integration of in situ dual glycan reforming with perforation. The pathological states of tumor tissues dissected from each treated group were assessed by hematoxylin and eosin (H&amp;E) and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. The sectioned tissue from TEID treated mouse exhibited the largest necrotic area compared to those from SLO‐Gal@HA or SLO‐NEU@HA treated mouse (Figure ##FIG##4##5e##), which was consistent to the changes of tumor volumes. Thus, the TEID exactly exhibited the maximum enhancement in in vivo immunotherapy.</p>", "<p>To further validate the enhancing mechanisms of TEID in in vivo immunotherapy, the tumor tissues sectioned from seven treated mouse groups were respectively stained with Cy3‐SNA and F‐Jac (<bold>Figure</bold>\n##FIG##5##\n6a##). The tissue slices from the mice treated with Gal@HA, NEU@HA, and SLO@HA exhibited similar fluorescence of Cy3‐SNA and F‐Jac compared to those treated with saline (Figure ##FIG##5##6b–d##). In contrast, the tissue slices from SLO‐Gal@HA or SLO‐NEU@HA treated mice exhibited a significant increase of F‐Jac fluorescence or a decrease of Cy3‐SNA fluorescence (Figure ##FIG##5##6b–d##). Besides, the tissue slice from the TEID treated mouse exhibited a simultaneous decrease of Cy3‐SNA and an increase of F‐Jac fluorescence (Figure ##FIG##5##6b–d##). These results indicated that the perforation of SLO and the introduction of Gal and NEU to tumor tissue for performing dual glycan reforming played critical roles in in vivo immunotherapy.</p>" ]
[ "<title>Conclusion</title>", "<p>In summary, a triply enhanced immunotherapy strategy is proposed with a designed TEID to integrate in situ dual glycan reforming with perforation of exogenous perforating molecule on cell surface. The TEID can be conveniently prepared by encapsulating SLO‐Gal&amp;SLO‐NEU in HA shell to achieve targeted delivery, HAase‐induced degradation in tumor microenvironment, and easily anchoring of SLO‐Gal and SLO‐NEU on tumor cells to perform the Gal‐introduction, SA‐cleavage and perforation in vivo, which exhibits the significant enhancement of immunotherapeutic efficacy of the tumors through simultaneously boosting NK cell activation, weakening immune cell inhibition and promoting the delivery of NK cell‐secreted cytokines. The proposed strategy provides a significant and promising route for clinical immunotherapy of tumors.</p>" ]
[ "<title>Abstract</title>", "<p>The enhancement of immunotherapy is an emerging direction to develop highly effective and practical cancer therapeutic methods. Here a triply enhanced immunotherapy drug (TEID) is designed for ingeniously integrating in situ dual glycan reforming with perforation on cell membrane. The TEID is composed of galactose and neuraminidase conjugated streptolysin O (SLO‐Gal and SLO‐NEU), which are encapsulated in a hyaluronic acid (HA) shell for targeted recognition to tumor tissue via cell surface CD44. After targeted delivery and HAase‐mediated degradation in the tumor region, the TEID releases SLO‐Gal and SLO‐NEU, which can easily anchor Gal and NEU on the tumor cell membrane via the perforation of SLO to perform dual glycan reforming for the introduction of Gal and the cleavage of sialic acid. The former can activate immune cells to secret cytokines for immune‐killing, and the latter can weaken the immune inhibition to improve the immunotherapeutic efficacy. Meanwhile, the perforation of SLO can promote the delivery of cytokines into the tumor cells to further enhance the efficacy. The designed triply enhanced immunotherapy strategy opens a significant and promising route to promote clinical immunotherapy of cancer.</p>", "<p>A triply enhanced immunotherapy strategy is achieved by integrating the introduction of galactose and the cleavage of sialic acid with perforation on the tumor cell membrane, which simultaneously promotes immune activation, weakens immune inhibition, and stimulates cytokines secretion for effective immunotherapy of cancer.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6705-cit-0045\">\n<string-name>\n<given-names>Y.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Chao</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Fang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Ding</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Ju</surname>\n</string-name>, <article-title>Triply Enhanced Immunotherapy via Dual Glycan Reforming Integrated with Perforation</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304971</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304971</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was supported by the National Natural Science Foundation of China (21974063, 21827812 and 21890741) and the program B for Outstanding Ph.D. candidate of Nanjing University.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6705-fig-0001\"><label>Figure 1</label><caption><p>Schematic illustration of triply enhanced immunotherapy via integrating dual glycan reforming and perforation. SLO‐Gal and SLO‐NEU prepared by conjugating Gal and NEU with SLO‐DBCO are encapsulated in HA to obtain TEID for injection into tumor‐bearing mice. After delivered to tumor region by targeting cell surface CD44, TEID is degraded by HAase in the tumor microenvironment to release SLO‐Gal and SLO‐NEU for performing perforation, Gal‐introducing, and SA‐cleaving functions, which triply enhances NK cell‐based immunotherapy.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6705-fig-0002\"><label>Figure 2</label><caption><p>Verification of triple functions of SLO‐Gal and SLO‐NEU on 4T1 cells. a,b) CLSM images of 4T1 cells after incubated with PBS (Control), SLO, SLO‐Gal, or SLO‐NEU and then stained with PI to verify perforating function (a), and with PBS (Control), SLO, SLO‐Gal, NEU or SLO‐NEU and then stained with Cy3‐SNA to verify the SA‐cleaving function (b). c) CLSM images of 4T1 cells and GD per‐treated 4T1 cells after incubated with PBS (Control and GD), SLO, SLO‐Gal, or SLO‐NEU and then stained with F‐Jac to verify Gal‐introducing function.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6705-fig-0003\"><label>Figure 3</label><caption><p>Cytotoxicity and enhanced release of immune‐cytokines. a) Flow cytometric analysis of 4T1 cells after incubated with PBS, Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or SLO‐Gal&amp;SLO‐NEU and then NK cells, and stained with Annexin V‐FITC and PI. b) Schematic illustration of cytokines (IFN‐γ, TNF‐α, IL‐2, perforin, and GrB) secreted from NK cells in triply enhanced immune‐killing. c–g) ELISA analysis of the secreted cytokines from NK cells after incubation with PBS, Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or SLO‐Gal&amp;SLO‐NEU pre‐treated 4T1 cells for 24 h (non‐shaded columns), and with 4T1 cells that were pre‐treated with the products of HAase and HA encapsulated PBS, Gal, NEU, SLO, SLO‐Gal, SLO‐NEU, or SLO‐Gal&amp;SLO‐NEU for 24 h (shaded columns). Statistical analysis was performed by unpaired two‐tailed <italic toggle=\"yes\">t</italic>‐tests (<sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.001), n = 3.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6705-fig-0004\"><label>Figure 4</label><caption><p>Characterization, degradation and triple functions of TEID. a) Dynamic light scattering (DLS) measurement of hydrodynamic size of TEID. Inset: TEM image of TEID. b) Zeta potentials of TEID after incubated with HAase at pH 5.0, 6.5, and 7.4 for different times. c) Schematic illustration of SLO‐Gal and SLO‐NEU release from TEID by HAase degradation to perform triple functions. d,e) CLSM images of 4T1 cells incubated with PBS (Control), TEID, HA degraded TEID, and SLO‐Gal&amp;SLO‐NEU, and then stained with PI to verify perforating function (d) and Cy3‐SNA to verify SA‐cleaving function (e). f) CLSM images of GD pre‐treated 4T1 cells incubated with PBS (Control), TEID, HA degraded TEID, and SLO‐Gal&amp;SLO‐NEU, and then stained with F‐Jac to verify Gal‐introducing function.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6705-fig-0005\"><label>Figure 5</label><caption><p>Triply enhanced immunotherapy with TEID on tumor‐bearing mice. a) Schematic illustration for implantation and treatment of 4T1 tumor‐bearing mice. b) Photo of tumor tissues dissected from 4T1 tumor‐bearing mice after injecting saline, Gal@HA, NEU@HA, SLO@HA, SLO‐Gal@HA, SLO‐NEU@HA, and TEID every other day for 12 times. c,d) Variation of body weight (c) and tumor volume (d) of 4T1 tumor‐bearing mice during injection. e) Histology and CLSM images of sectioned tumor tissues after H&amp;E and TUNEL staining.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6705-fig-0006\"><label>Figure 6</label><caption><p>Verification of triple functions on tumor tissue for immunotherapy with TEID. a) Schematic illustration of sectioned tumor tissues after treated with saline, Gal@HA, NEU@HA, SLO@HA, SLO‐Gal@HA, SLO‐NEU@HA, or TEID. b) CLSM images of DAPI, Cy3‐SNA, and F‐Jac stained tumor tissue slices from tumor‐bearing mice after therapy with saline, Gal@HA, NEU@HA, SLO@HA, SLO‐Gal@HA, SLO‐NEU@HA, or TEID. c,d) Fluorescence intensities (FI) of Cy3‐SNA (c) and F‐Jac (d) from (b). Statistical analysis was performed by unpaired two‐tailed <italic toggle=\"yes\">t</italic>‐tests (<sup>**</sup>\n<italic toggle=\"yes\">p</italic> &lt;0.01; <sup>***</sup>\n<italic toggle=\"yes\">p</italic> &lt;0.001; NS, not significant), n = 3.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6705-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2304971-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
[{"label": ["17"], "mixed-citation": ["\n"], "string-name": ["\n", "\n"], "given-names": ["E. M.", "C. R."], "surname": ["Sletten", "Bertozzi"], "source": ["Angew. Chem., Int. Ed."], "year": ["2009"], "volume": ["48"], "fpage": ["6974"]}]
{ "acronym": [], "definition": [] }
24
CC BY
no
2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Oct 23; 11(2):2304971
oa_package/07/f6/PMC10787084.tar.gz
PMC10787085
37984864
[ "<title>Introduction</title>", "<p>Artificial photosynthesis, converting solar energy into chemical energy, presents a promising avenue for sustainable fuel production.<sup>[</sup>\n##REF##17043226##\n1\n##\n<sup>]</sup> The seminal work by Fujishima and Honda demonstrated water splitting on a TiO<sub>2</sub> photoanode, heralding the exploration of photoelectrochemical (PEC) devices based on light‐absorbing metal oxide semiconductors.<sup>[</sup>\n##REF##12635268##\n2\n##\n<sup>]</sup> Within a PEC system, the photoanode holds paramount significance as the site governing the oxygen evolution reaction (OER), which entails intricate proton‐coupled electron transfer steps.<sup>[</sup>\n##UREF##0##\n3\n##\n<sup>]</sup> To emulate the roles of the P680 chromophore and the oxygen‐evolving Mn<sub>4</sub>CaO<sub>5</sub> cluster in natural Photosystem II (PSII), an adeptly designed photoanode typically integrates a light‐harvesting semiconductor antenna and a water oxidation catalyst (WOC) for surface catalytic OER.<sup>[</sup>\n##REF##33404560##\n4\n##\n<sup>]</sup> Nevertheless, the prevailing approach involves combining metal oxide cocatalysts with semiconductors to form solid‐state materials, inadvertently constraining contact areas between cocatalyst and reactants, as well as the availability of active catalytic sites.<sup>[</sup>\n##UREF##1##\n5\n##\n<sup>]</sup> In particular, the solid‐solid interface between nanoparticle cocatalysts and semiconductors exacerbates the transport distance of photogenerated charges, leading to pronounced photogenerated charge recombination.</p>", "<p>In contrast to inorganic solid cocatalysts, molecular cocatalysts offer the advantage of facile modulation through substitution. Transition metal complexes, particularly cobalt cubane molecules (Co<sub>4</sub>O<sub>4</sub>), sharing structural similarities with the oxygen‐evolving complex Mn<sub>4</sub>CaO<sub>5</sub> in PSII of green plants, were initially reported by Christou and colleagues.<sup>[</sup>\n##REF##21739983##\n6\n##\n<sup>]</sup> Co<sub>4</sub>O<sub>4</sub> molecules have emerged as highly efficient water oxidation cocatalysts in homogeneous solutions. However, their performance tends to be unsatisfactory when integrated onto semiconductor surfaces, primarily due to poor interfacial charge transfer and inadequate surface anchoring.<sup>[</sup>\n##UREF##2##\n7\n##\n<sup>]</sup> In natural PSII, numerous amino acids and coenzymes, in addition to the chromophore and OER center, regulate the direction of charge separation and transfer.<sup>[</sup>\n##REF##19908828##\n8\n##\n<sup>]</sup> Drawing inspiration from this, charge transfer mediators, such as graphene, have demonstrated the ability to facilitate hole transfer from semiconductors to cocatalysts.<sup>[</sup>\n##REF##29338218##\n9\n##\n<sup>]</sup> Nevertheless, the transfer of photogenerated charges between layers remains suboptimal due to the lack of a specific transfer channel that establishes a robust bond between the semiconductor and cocatalysts. Thus, the development of a charge transfer mediator is imperative, one that can not only govern the charge transfer pathway of semiconductors but also effectively bind with cocatalysts to promote charge transfer.</p>", "<p>In this study, we present an artificial photoanode comprising a BiVO<sub>4</sub> semiconductor as the light absorber, Co<sub>4</sub>O<sub>4</sub> molecules as the cocatalyst, and Au nanoparticles (NPs) as the binding bridge. The integration of Au NPs serves to accumulate photogenerated holes, effectively operating as “hole transfer channels” at the BiVO<sub>4</sub> surface. The terminal catalytic site, represented by Co<sub>4</sub>O<sub>4</sub> molecular cocatalysts, is meticulously affixed to the Au surface via cyano anchoring groups. This rational arrangement establishes an ordered pathway for charge transfer between BiVO<sub>4</sub> and Co<sub>4</sub>O<sub>4</sub> molecules. Diverging from conventional “molecular cocatalyst/semiconductor” binary photoanodes, the systematically assembled photoanode, characterized by the “Au@Co<sub>4</sub>O<sub>4</sub>” structure, facilitates directional hole transfer along the Au channels, considerably mitigating surface charge recombination. As a result, the Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanode showcases remarkable performance in PEC water splitting. It attains an impressive photocurrent density of 5.06 mA cm<sup>−2</sup> (3.4 times that of pristine BiVO<sub>4</sub>) at 1.23 V versus the reversible hydrogen electrode (RHE), accompanied by an ultrahigh surface charge transfer efficiency exceeding 95%.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<p>Despite being proposed as efficient WOC for BiVO<sub>4</sub> photoanode, Co<sub>4</sub>O<sub>4</sub> molecules often face performance limitations due to inadequate interfacial charge transfer and surface anchoring when integrated onto BiVO<sub>4</sub> surface. Au NPs, previously investigated extensively as charge transfer mediators through interfacing with semiconductors or cocatalysts, offer potential solutions in this context.<sup>[</sup>\n##REF##27380539##\n10\n##\n<sup>]</sup> In this study, we leverage Au NPs as charge transfer channels, specifically aiming to achieve selective assembly of Co<sub>4</sub>O<sub>4</sub> molecules on their surfaces. This selective assembly is a critical stride toward enabling efficient photogenerated hole transfer from BiVO<sub>4</sub> to Co<sub>4</sub>O<sub>4</sub> molecules, thereby enhancing the overall performance of the PEC water oxidation process.</p>", "<title>Interaction of Au NPs and Co<sub>4</sub>O<sub>4</sub> Molecules</title>", "<p>In this study, cyano‐functionalized Co<sub>4</sub>O<sub>4</sub> molecules were selected for their ability to establish robust coordination bonds with heavy metals like Au, owing to the cyano groups they bear.<sup>[</sup>\n##UREF##3##\n11\n##\n<sup>]</sup> Consequently, Co<sub>4</sub>O<sub>4</sub> molecules readily adsorb onto the Au surface, creating an organic–inorganic hybrid nanostructure termed Au@Co<sub>4</sub>O<sub>4</sub> (<bold>Figure</bold> ##FIG##0##\n1a##). The presence of characteristic Raman vibrations within the range of 1000–2300 cm<sup>−1</sup>, attributed to the pyridine ring and cyano group, validates the successful synthesis of cyano‐functionalized Co<sub>4</sub>O<sub>4</sub> molecules (Figure ##SUPPL##0##S1##, Supporting Information). Leveraging steric and geometric attributes, individual Co<sub>4</sub>O<sub>4</sub> molecule serves as bridges, linking two Au NPs together to form Au@Co<sub>4</sub>O<sub>4</sub> aggregate. A biphasic adsorption experiment corroborates this aggregation phenomenon.<sup>[</sup>\n##REF##35905473##\n12\n##\n<sup>]</sup> As depicted in Figure ##FIG##0##1b##, citrate‐encapsulated Au NPs disperse in the upper water phase, while the lower dichloromethane layer contains Co<sub>4</sub>O<sub>4</sub> molecules. Over time, stirring prompts the gradual gathering of Au NPs at the interface, resulting in the upper layer becoming colorless and transparent. Furthermore, introducing Co<sub>4</sub>O<sub>4</sub> molecules into an Au colloid solution leads to noticeable agglomeration of Au NPs (Figure ##FIG##0##1c##; Figure ##SUPPL##0##S2##, Supporting Information). Spectral confirmation of this aggregation is provided by the UV–vis spectrum, which exhibits a substantial red shift of 24 nm upon Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs co‐mingling (Figure ##FIG##0##1d##). These collective outcomes denote a closely packed interfacial arrangement between Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs, thereby offering ample potential for subsequent integration.</p>", "<title>Fabrication and Characterization of BiVO<sub>4</sub>‐Based Photoanodes</title>", "<p>Two strategies were employed for the photoanode assembly, as illustrated in <bold>Figure</bold> ##FIG##1##\n2a##. In Route 1, Au NPs were initially deposited onto the BiVO<sub>4</sub> surface, followed by the introduction of Co<sub>4</sub>O<sub>4</sub> molecules onto the Au/BiVO<sub>4</sub> photoanode to yield Au@Co<sub>4</sub>O<sub>4</sub> NPs (designated as Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub>). Alternatively, Route 2 involved blending Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs to create Au@Co<sub>4</sub>O<sub>4</sub> aggregates, which were subsequently directly integrated onto the BiVO<sub>4</sub> film (designated as Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub>). The porous nature of the BiVO<sub>4</sub> films provided ample loading sites for the catalysts (Figure ##FIG##1##2b##). Loading Co<sub>4</sub>O<sub>4</sub> molecules onto the Au/BiVO<sub>4</sub> photoanode had minimal impact on the morphology of the Au NPs, owing to their monolayer deposition (Figure ##FIG##1##2c##; Figure ##SUPPL##0##S3##, Supporting Information). In contrast, the Scanning electron microscope (SEM) image of Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> distinctly revealed the presence of Au@Co<sub>4</sub>O<sub>4</sub> aggregates on the photoanode surface (Figure ##FIG##1##2d##).</p>", "<p>To validate the distribution of the Co element on Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, high‐angle annular dark field scanning transmission electron microscopy (HAADF‐STEM) and energy‐dispersive X‐ray spectroscopy (EDS) elemental mapping were performed (Figure ##FIG##1##2e,f##). The results indicated that the majority of Co elements were situated around the Au NPs in both the Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, suggesting preferential anchoring of Co<sub>4</sub>O<sub>4</sub> molecules to the Au surface. The electronic coupling interaction within the Au@Co<sub>4</sub>O<sub>4</sub> NPs and aggregates was verified using X‐ray photoelectron spectroscopy (XPS). The Co 2p binding energies for Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> exhibited noticeable positive shifts compared to Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> (Figure ##FIG##1##2g##), indicating enhanced electron transfer from Co<sub>4</sub>O<sub>4</sub> molecules to BiVO<sub>4</sub> facilitated by the presence of Au NPs. Apart from the typical peak of BiVO<sub>4</sub> at 826 cm<sup>−1</sup>, the characteristic vibrations of pyridine ring in Co<sub>4</sub>O<sub>4</sub> molecules between 1000 and 1800 cm<sup>−1</sup> were found in the Raman spectra of Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub>. In particular, a characteristic peak at 2237 cm<sup>−1</sup> corresponds to the vibration of cyano group in Co<sub>4</sub>O<sub>4</sub> molecules, appears in the Raman spectra of Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> (Figure ##SUPPL##0##S1##, Supporting Information). Furthermore, UV–vis absorption spectra of the photoanodes incorporating Au NPs exhibited a distinct absorption peak ≈540 nm, attributed to plasmonic light absorption induced by Au NPs. Notably, the introduction of Co<sub>4</sub>O<sub>4</sub> molecules had negligible impact on the light absorption characteristics of the photoanodes (Figure ##SUPPL##0##S4##, Supporting Information).</p>", "<title>Photoelectrochemical (PEC) Water Oxidation Over BiVO<sub>4</sub>‐Based Photoanodes</title>", "<p>The PEC performance of the fabricated photoanodes was assessed within a typical three‐electrode cell under AM 1.5G illumination in a neutral phosphate buffer solution. As depicted in <bold>Figure</bold> ##FIG##2##\n3a##, the unmodified BiVO<sub>4</sub> photoanode displayed a modest photocurrent density of 1.51 mA cm<sup>−2</sup> at 1.23 V versus RHE. Upon incorporation of Co<sub>4</sub>O<sub>4</sub> molecules, a promising enhancement in photocurrent density was evident for the Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> configuration. Particularly noteworthy, both Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> exhibited further augmented photocurrent density when Co<sub>4</sub>O<sub>4</sub> molecules were anchored onto the BiVO<sub>4</sub> surface via Au mediators, yielding photocurrent density of 4.65 mA cm<sup>−2</sup> and 5.06 mA cm<sup>−2</sup> at 1.23 V versus RHE, respectively, surpassing those reported in previous studies (Table ##SUPPL##0##S2##, Supporting Information). Furthermore, the onset potential for both Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub>, corresponding to a photocurrent density of 0.5 mA cm<sup>−2</sup>, was cathodically shifted by ≈550 mV compared to pristine BiVO<sub>4</sub>. While Au NPs and Co<sub>4</sub>O<sub>4</sub> molecules serve as cocatalysts that collaborate in catalyzing the water oxidation reaction, it's crucial to emphasize that the modest increase in photocurrent density observed in Au/BiVO<sub>4</sub> compared to BiVO<sub>4</sub> can be primarily attributed to the effective function of Au NPs as “hole transfer channels” (Figures ##SUPPL##0##S5–S7##, Supporting Information).</p>", "<p>To enhance the vertical integration of the Au@Co<sub>4</sub>O<sub>4</sub> hybrid nanostructure, cobalt cubane molecules (1‐Co<sub>4</sub>O<sub>4</sub>) without functional groups were also introduced onto the Au/BiVO<sub>4</sub> surface for comparative analysis (Figures ##SUPPL##0##S8## and ##SUPPL##0##S9##, Supporting Information). Notably, both 1‐Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> and Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> configurations exhibited nearly identical photocurrent density. However, a distinct trend emerged in the photocurrent behavior of Au‐incorporated photoanodes (Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> &gt; Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> &gt; 1‐Co<sub>4</sub>O<sub>4</sub>/Au/BiVO<sub>4</sub>) in accordance with the interaction affinity between the Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs (Figure ##FIG##2##3b##). This observation underscores the critical influence of their binding mode on interfacial charge transfer. Evaluation of linear sweep voltammograms facilitated the calculation of applied bias photon‐to‐current efficiency (ABPE) values for the integrated photoanodes, as depicted in Figure ##FIG##2##3c##. The highest ABPE values were attained by the Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, reaching 1.64% at 0.65 V and 1.88% at 0.66 V, respectively.</p>", "<title>The Surface Charge Transfer and Recombination of BiVO<sub>4</sub>‐Based Photoanodes</title>", "<p>To evaluate the charge transfer efficiencies of the BiVO<sub>4</sub>‐based photoanodes, the hole scavenger Na<sub>2</sub>SO<sub>3</sub> was employed to alleviate surface charge recombination.<sup>[</sup>\n##REF##21942320##\n13\n##\n<sup>]</sup> As illustrated in Figure ##FIG##2##3d##, all photoanodes incorporating Au NPs displayed comparable photocurrent levels, surpassing those of pristine BiVO<sub>4</sub> in Na<sub>2</sub>SO<sub>3</sub> solution, which suggest an indication of enhanced hole generation upon Au NPs integration. Surface charge transfer efficiencies (<italic toggle=\"yes\">η</italic>\n<sub>trans</sub>) of the BiVO<sub>4</sub>‐based photoanodes were calculated using the formula <italic toggle=\"yes\">η</italic>\n<sub>trans</sub> = <italic toggle=\"yes\">J</italic>\n<sub>H2O</sub>/<italic toggle=\"yes\">J</italic>\n<sub>Na2SO3</sub>, with <italic toggle=\"yes\">J</italic>\n<sub>H2O</sub> and <italic toggle=\"yes\">J</italic>\n<sub>Na2SO3</sub> denoting photocurrent density measured with and without Na<sub>2</sub>SO<sub>3</sub>, respectively. The data in Figure ##FIG##2##3e## reveals that Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> exhibited higher <italic toggle=\"yes\">η</italic>\n<sub>trans</sub> than BiVO<sub>4</sub>. Nevertheless, the values remained below 60% across the voltage range, underscoring the constrained charge transfer at the Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> photoanode interface. Remarkably, immobilizing Co<sub>4</sub>O<sub>4</sub> molecules onto the BiVO<sub>4</sub> photoanode surface via an Au mediator led to a successive increase in <italic toggle=\"yes\">η</italic>\n<sub>trans</sub> for the resultant Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, aligning with the photocurrent density order depicted in Figure ##FIG##2##3a##. Notably, Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> exhibited an exceptional <italic toggle=\"yes\">η</italic>\n<sub>trans</sub>, reaching a maximum value of 95.2% at 1.23 V versus RHE. Electrochemical impedance spectroscopy (EIS) measurements of the prepared photoanodes were consistent with the charge transfer efficiency results (Figure ##FIG##2##3f##). The semidiameters of the semicircles in the Nyquist plots for BiVO<sub>4</sub>, Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub>, Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub>, and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> followed a sequence of increasing to decreasing order. This sequence signifies a corresponding acceleration in interfacial charge transfer.</p>", "<p>To more accurately assess the charge transfer and charge recombination kinetics, we conducted intensity‐modulated photocurrent spectroscopy (IMPS) utilizing monochromatic light at 460 nm.<sup>[</sup>\n##UREF##4##\n14\n##\n<sup>]</sup>\n<bold>Figure</bold> ##FIG##3##\n4a## presents typical IMPS responses of BiVO<sub>4</sub>‐based photoanodes at 0.8 V versus RHE, which unveil insights into charge transfer and recombination kinetics. By analyzing the semicircles in the IMPS plots (Figure ##SUPPL##0##S10##, Supporting Information), the charge transfer rate constant (<italic toggle=\"yes\">k</italic>\n<sub>trans</sub>) and charge recombination rate constant (<italic toggle=\"yes\">k</italic>\n<sub>rec</sub>) were derived at various applied potentials. Figure ##FIG##3##4b,c## illustrate that both Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes exhibit lower <italic toggle=\"yes\">k</italic>\n<sub>rec</sub> but elevated <italic toggle=\"yes\">k</italic>\n<sub>trans</sub> values across the entire voltage spectrum compared to Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> photoanodes. These findings underscore that the introduction of Au NPs between BiVO<sub>4</sub> and Co<sub>4</sub>O<sub>4</sub> molecules can effectively curtail interfacial charge recombination while accelerating charge transfer. Determination of the steady‐state charge transfer efficiency (TE) for each photoanode involved calculating <italic toggle=\"yes\">k</italic>\n<sub>trans</sub>/(<italic toggle=\"yes\">k</italic>\n<sub>trans</sub> + <italic toggle=\"yes\">k</italic>\n<sub>rec</sub>). Particularly noteworthy, IMPS analysis revealed that the highest TE value for Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> was 97.2% at 1.0 V (Figure ##FIG##3##4d##), consistent with the computed outcome in Figure ##FIG##2##3e##. This nearly perfect efficiency underscores the pivotal role played by Au NPs in enhancing interfacial charge transfer.</p>", "<title>Identification of Au NPs as Hole Transfer Channels</title>", "<p>To establish the crucial function of Au NPs as hole transfer channels on the BiVO<sub>4</sub> surface, we undertook targeted control experiments and characterizations. Initially, in situ photochemical deposition was employed to examine the sites of oxidation reactions on the Au/BiVO<sub>4</sub> photoanode.<sup>[</sup>\n##REF##23385577##\n15\n##\n<sup>]</sup> We observed that the hole‐mediated oxidative deposition of PbO<sub>2</sub> from Pb<sup>2+</sup> was notably concentrated around the Au NPs, indicative of photogenerated hole accumulation near Au NPs (<bold>Figure</bold> ##FIG##4##\n5a##). This observation supports the notion that the Au NPs can serve as hole trappers, effectively capturing photogenerated holes from BiVO<sub>4</sub>. Additionally, we conducted an experiment involving treatment of the Au/BiVO<sub>4</sub> photoanode with 1,2‐benzenedithiol (BDT). This treatment selectively forms Au─S covalent bonds to coat the surface of Au NPs. Notably, this treatment hindered water molecules from interacting with the Au NPs, while the PEC activity of BiVO<sub>4</sub> remained unaffected (Figure ##SUPPL##0##S11##, Supporting Information). As depicted in Figure ##FIG##4##5b##, following the BDT treatment, the Au channels became obstructed, resulting in a substantial decrease in the photocurrent density of Au/BiVO<sub>4</sub>, approaching that of pristine BiVO<sub>4</sub>. This outcome conclusively validates the pivotal role of Au NPs as effective hole transfer channels.</p>", "<p>To delve deeper into the significance of charge transfer between Au NPs and Co<sub>4</sub>O<sub>4</sub> molecules, an Al<sub>2</sub>O<sub>3</sub> film was introduced onto the surface of the Au/BiVO<sub>4</sub> photoanode.<sup>[</sup>\n##UREF##5##\n16\n##\n<sup>]</sup> The Al<sub>2</sub>O<sub>3</sub> film, with a thickness of ≈3.5 nm, provided complete coverage of the Au/BiVO<sub>4</sub> surface (Figure ##SUPPL##0##S12##, Supporting Information). Serving as an interlayer, this film effectively separated the Co<sub>4</sub>O<sub>4</sub> molecules from the Au NPs, preventing Co<sub>4</sub>O<sub>4</sub> molecules attachment to the Au surface and the formation of the Au@Co<sub>4</sub>O<sub>4</sub> hybrids structure (Figure ##FIG##4##5c##). Notably, the photocurrent density of Al<sub>2</sub>O<sub>3</sub>/Au/BiVO<sub>4</sub> remained comparable to that of Au/BiVO<sub>4</sub>, indicating that the presence of the Al<sub>2</sub>O<sub>3</sub> film did not disrupt charge transfer at the Au/BiVO<sub>4</sub> surface. However, upon the introduction of Co<sub>4</sub>O<sub>4</sub> molecules, the resulting Co<sub>4</sub>O<sub>4</sub>/Al<sub>2</sub>O<sub>3</sub>/Au/BiVO<sub>4</sub> photoanode exhibited a marked reduction in activity compared to Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> (Figure ##FIG##4##5d##). This observation underscores the essential role of charge transfer between Au NPs and Co<sub>4</sub>O<sub>4</sub> molecules in ensuring the efficient PEC performance of the photoanode.</p>", "<p>To reinforce this hypothesis, we introduced 1‐Co<sub>4</sub>O<sub>4</sub> molecules lacking cyano groups for comparative analysis. Notably, these 1‐Co<sub>4</sub>O<sub>4</sub> molecules were unable to assemble on the surface of Au NPs, as evidenced in Figure ##SUPPL##0##S13## (Supporting Information). Direct introduction of 1‐Co<sub>4</sub>O<sub>4</sub> molecules onto the Au/BiVO<sub>4</sub> surface resulted in only a marginal increase in photocurrent density, indicative of the absence of an effective charge transfer channel between BiVO<sub>4</sub> and 1‐Co<sub>4</sub>O<sub>4</sub> molecules. Furthermore, the introduction of an Al<sub>2</sub>O<sub>3</sub> film onto the Au/BiVO<sub>4</sub> photoanode had no discernible impact on the photocurrent density of 1‐Co<sub>4</sub>O<sub>4</sub>/Al<sub>2</sub>O<sub>3</sub>/Au/BiVO<sub>4</sub> and 1‐Co<sub>4</sub>O<sub>4</sub>/Au/BiVO<sub>4</sub> at 1.23 V versus RHE (Figure ##SUPPL##0##S14##, Supporting Information). Based on the aforementioned findings, we posit that the enhanced charge transfer between Co<sub>4</sub>O<sub>4</sub> molecules and BiVO<sub>4</sub> facilitated by the Au bridge significantly contributes to the augmentation of PEC water oxidation.</p>", "<p>Of significance is the observation that the photocurrent density of Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub>, where Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs form Au@Co<sub>4</sub>O<sub>4</sub> aggregates, surpasses that of Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub>, where Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs form Au@Co<sub>4</sub>O<sub>4</sub> NPs. To eliminate the possibility that the improved PEC performance observed in Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> was solely due to an increased loading of Au NPs, we prepared a series of photoanodes with varying amounts of Au NPs by adjusting the immersion time. As the loading of Au NPs increases, the resulting photoanodes exhibit a characteristic volcano‐shaped curve with respect to photocurrent density, where excessive Au NPs loading leads to a decline in PEC activity (<bold>Figure</bold> ##FIG##5##\n6a##; Figure ##SUPPL##0##S15##, Supporting Information). Numerical simulations utilizing finite‐difference time‐domain (FDTD) for plasmon‐induced electric field intensity reveal that Au NPs aggregations generate enhanced regions within the nanogap, outperforming isolated Au NPs (Figure ##SUPPL##0##S16##, Supporting Information).<sup>[</sup>\n##UREF##6##\n17\n##\n<sup>]</sup> In the Au@Co<sub>4</sub>O<sub>4</sub> aggregates, Co<sub>4</sub>O<sub>4</sub> molecules are strategically positioned at the nanogap of Au NPs, acting as linkers. This arrangement maximizes the localized near‐field enhancement, fostering hole accumulation, and consequently leading to improved OER catalysis.</p>", "<p>To gain deeper insights into the impact of multicomponent photoanodes on interface modulation, we assessed the photovoltage and surface recombination rate by conducting open circuit voltage decay measurements on the photoanodes.<sup>[</sup>\n##UREF##7##\n18\n##\n<sup>]</sup> The sequence of photovoltages and recovery constants “b” for the photoanodes aligns as Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> &gt; Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> &gt; Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> &gt; BiVO<sub>4</sub>, as anticipated. This corresponds to a progressive reduction in the driving force and a subsequent increase in charge recombination (Figure ##SUPPL##0##S17##, Supporting Information). We also employed time‐resolved photoluminescence (TRPL) to determine the carrier lifetime (Figure ##FIG##5##6b##).<sup>[</sup>\n##UREF##8##\n19\n##\n<sup>]</sup> The PL decay curves were fitted using a biexponential function, enabling the capture of the initial rapid decay (<italic toggle=\"yes\">τ</italic>\n<sub>1</sub>) and the subsequent slower decay (<italic toggle=\"yes\">τ</italic>\n<sub>2</sub>), where <italic toggle=\"yes\">τ</italic>\n<sub>1</sub> signifies the fall of photogenerated electrons near the conduction band, and <italic toggle=\"yes\">τ</italic>\n<sub>2</sub> indicates the recombination of electron‐hole pairs. The average carrier lifetimes of Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> (6.8 ns), Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> (4.0 ns), Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> (2.3 ns), and BiVO<sub>4</sub> (1.8 ns) were determined using the formula <italic toggle=\"yes\">τ</italic>\n<sub>ave</sub> = <italic toggle=\"yes\">P</italic>\n<sub>1</sub>\n<italic toggle=\"yes\">τ</italic>\n<sub>1</sub> + <italic toggle=\"yes\">P</italic>\n<sub>2</sub>\n<italic toggle=\"yes\">τ</italic>\n<sub>2</sub> (Table ##SUPPL##0##S1##, Supporting Information). These results unequivocally affirm the pivotal role played by Au NPs in facilitating efficient hole transfer from BiVO<sub>4</sub> to Co<sub>4</sub>O<sub>4</sub> molecules.</p>", "<p>Figure ##FIG##5##6c## illustrates the incident photon‐to‐current conversion efficiencies (IPCEs) of the sample photoanodes. Notably, the IPCE values of Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> exhibit substantial enhancements compared to those of Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> and BiVO<sub>4</sub> across the entire wavelength range. A discrete rise in IPCE ≈540 nm for Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> can be attributed to plasmon‐induced water oxidation. The integrated IPCE curves over the AM 1.5G solar spectrum yield photocurrent densities of 4.51 mA cm<sup>−2</sup> and 5.01 mA cm<sup>−2</sup> at 1.23 V for Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, respectively (Figure ##SUPPL##0##S18##, Supporting Information), aligning closely with the experimentally measured photocurrent densities.</p>", "<p>Stability is a pivotal concern for PEC devices, including the photoanode. Au‐decorated semiconductor photoanodes, as a rule, exhibit unsatisfactory stability.<sup>[</sup>\n##REF##32157799##\n20\n##\n<sup>]</sup> Similarly, while Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> demonstrates remarkably high PEC activity, a discernible decline in photocurrent density during constant‐potential electrolysis is evident. Addressing this challenge, we introduced an Al<sub>2</sub>O<sub>3</sub> protective layer to the outer surface of the Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanode through atomic layer deposition (ALD).<sup>[</sup>\n##UREF##9##\n21\n##\n<sup>]</sup> With the protective Al<sub>2</sub>O<sub>3</sub> layer, the resulting Al<sub>2</sub>O<sub>3</sub>/Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanode maintains a photocurrent density comparable to Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> while exhibiting significantly enhanced stability (Figure ##SUPPL##0##S19##, Supporting Information). Remarkably, over 95% of the initial photocurrent density is retained after 120 min of photoelectrolysis (Figure ##FIG##5##6d##). The faradaic efficiency of the Al<sub>2</sub>O<sub>3</sub>/Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanode for water oxidation is ≈88.9%, strongly indicating that the photocurrent originates from the water oxidation reaction (Figure ##SUPPL##0##S20##, Supporting Information). Further investigations into achieving more stable photoanodes through adjustments in protective layer type and thickness are currently underway in our laboratory.</p>" ]
[ "<title>Results and Discussion</title>", "<p>Despite being proposed as efficient WOC for BiVO<sub>4</sub> photoanode, Co<sub>4</sub>O<sub>4</sub> molecules often face performance limitations due to inadequate interfacial charge transfer and surface anchoring when integrated onto BiVO<sub>4</sub> surface. Au NPs, previously investigated extensively as charge transfer mediators through interfacing with semiconductors or cocatalysts, offer potential solutions in this context.<sup>[</sup>\n##REF##27380539##\n10\n##\n<sup>]</sup> In this study, we leverage Au NPs as charge transfer channels, specifically aiming to achieve selective assembly of Co<sub>4</sub>O<sub>4</sub> molecules on their surfaces. This selective assembly is a critical stride toward enabling efficient photogenerated hole transfer from BiVO<sub>4</sub> to Co<sub>4</sub>O<sub>4</sub> molecules, thereby enhancing the overall performance of the PEC water oxidation process.</p>", "<title>Interaction of Au NPs and Co<sub>4</sub>O<sub>4</sub> Molecules</title>", "<p>In this study, cyano‐functionalized Co<sub>4</sub>O<sub>4</sub> molecules were selected for their ability to establish robust coordination bonds with heavy metals like Au, owing to the cyano groups they bear.<sup>[</sup>\n##UREF##3##\n11\n##\n<sup>]</sup> Consequently, Co<sub>4</sub>O<sub>4</sub> molecules readily adsorb onto the Au surface, creating an organic–inorganic hybrid nanostructure termed Au@Co<sub>4</sub>O<sub>4</sub> (<bold>Figure</bold> ##FIG##0##\n1a##). The presence of characteristic Raman vibrations within the range of 1000–2300 cm<sup>−1</sup>, attributed to the pyridine ring and cyano group, validates the successful synthesis of cyano‐functionalized Co<sub>4</sub>O<sub>4</sub> molecules (Figure ##SUPPL##0##S1##, Supporting Information). Leveraging steric and geometric attributes, individual Co<sub>4</sub>O<sub>4</sub> molecule serves as bridges, linking two Au NPs together to form Au@Co<sub>4</sub>O<sub>4</sub> aggregate. A biphasic adsorption experiment corroborates this aggregation phenomenon.<sup>[</sup>\n##REF##35905473##\n12\n##\n<sup>]</sup> As depicted in Figure ##FIG##0##1b##, citrate‐encapsulated Au NPs disperse in the upper water phase, while the lower dichloromethane layer contains Co<sub>4</sub>O<sub>4</sub> molecules. Over time, stirring prompts the gradual gathering of Au NPs at the interface, resulting in the upper layer becoming colorless and transparent. Furthermore, introducing Co<sub>4</sub>O<sub>4</sub> molecules into an Au colloid solution leads to noticeable agglomeration of Au NPs (Figure ##FIG##0##1c##; Figure ##SUPPL##0##S2##, Supporting Information). Spectral confirmation of this aggregation is provided by the UV–vis spectrum, which exhibits a substantial red shift of 24 nm upon Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs co‐mingling (Figure ##FIG##0##1d##). These collective outcomes denote a closely packed interfacial arrangement between Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs, thereby offering ample potential for subsequent integration.</p>", "<title>Fabrication and Characterization of BiVO<sub>4</sub>‐Based Photoanodes</title>", "<p>Two strategies were employed for the photoanode assembly, as illustrated in <bold>Figure</bold> ##FIG##1##\n2a##. In Route 1, Au NPs were initially deposited onto the BiVO<sub>4</sub> surface, followed by the introduction of Co<sub>4</sub>O<sub>4</sub> molecules onto the Au/BiVO<sub>4</sub> photoanode to yield Au@Co<sub>4</sub>O<sub>4</sub> NPs (designated as Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub>). Alternatively, Route 2 involved blending Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs to create Au@Co<sub>4</sub>O<sub>4</sub> aggregates, which were subsequently directly integrated onto the BiVO<sub>4</sub> film (designated as Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub>). The porous nature of the BiVO<sub>4</sub> films provided ample loading sites for the catalysts (Figure ##FIG##1##2b##). Loading Co<sub>4</sub>O<sub>4</sub> molecules onto the Au/BiVO<sub>4</sub> photoanode had minimal impact on the morphology of the Au NPs, owing to their monolayer deposition (Figure ##FIG##1##2c##; Figure ##SUPPL##0##S3##, Supporting Information). In contrast, the Scanning electron microscope (SEM) image of Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> distinctly revealed the presence of Au@Co<sub>4</sub>O<sub>4</sub> aggregates on the photoanode surface (Figure ##FIG##1##2d##).</p>", "<p>To validate the distribution of the Co element on Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, high‐angle annular dark field scanning transmission electron microscopy (HAADF‐STEM) and energy‐dispersive X‐ray spectroscopy (EDS) elemental mapping were performed (Figure ##FIG##1##2e,f##). The results indicated that the majority of Co elements were situated around the Au NPs in both the Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, suggesting preferential anchoring of Co<sub>4</sub>O<sub>4</sub> molecules to the Au surface. The electronic coupling interaction within the Au@Co<sub>4</sub>O<sub>4</sub> NPs and aggregates was verified using X‐ray photoelectron spectroscopy (XPS). The Co 2p binding energies for Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> exhibited noticeable positive shifts compared to Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> (Figure ##FIG##1##2g##), indicating enhanced electron transfer from Co<sub>4</sub>O<sub>4</sub> molecules to BiVO<sub>4</sub> facilitated by the presence of Au NPs. Apart from the typical peak of BiVO<sub>4</sub> at 826 cm<sup>−1</sup>, the characteristic vibrations of pyridine ring in Co<sub>4</sub>O<sub>4</sub> molecules between 1000 and 1800 cm<sup>−1</sup> were found in the Raman spectra of Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub>. In particular, a characteristic peak at 2237 cm<sup>−1</sup> corresponds to the vibration of cyano group in Co<sub>4</sub>O<sub>4</sub> molecules, appears in the Raman spectra of Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> (Figure ##SUPPL##0##S1##, Supporting Information). Furthermore, UV–vis absorption spectra of the photoanodes incorporating Au NPs exhibited a distinct absorption peak ≈540 nm, attributed to plasmonic light absorption induced by Au NPs. Notably, the introduction of Co<sub>4</sub>O<sub>4</sub> molecules had negligible impact on the light absorption characteristics of the photoanodes (Figure ##SUPPL##0##S4##, Supporting Information).</p>", "<title>Photoelectrochemical (PEC) Water Oxidation Over BiVO<sub>4</sub>‐Based Photoanodes</title>", "<p>The PEC performance of the fabricated photoanodes was assessed within a typical three‐electrode cell under AM 1.5G illumination in a neutral phosphate buffer solution. As depicted in <bold>Figure</bold> ##FIG##2##\n3a##, the unmodified BiVO<sub>4</sub> photoanode displayed a modest photocurrent density of 1.51 mA cm<sup>−2</sup> at 1.23 V versus RHE. Upon incorporation of Co<sub>4</sub>O<sub>4</sub> molecules, a promising enhancement in photocurrent density was evident for the Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> configuration. Particularly noteworthy, both Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> exhibited further augmented photocurrent density when Co<sub>4</sub>O<sub>4</sub> molecules were anchored onto the BiVO<sub>4</sub> surface via Au mediators, yielding photocurrent density of 4.65 mA cm<sup>−2</sup> and 5.06 mA cm<sup>−2</sup> at 1.23 V versus RHE, respectively, surpassing those reported in previous studies (Table ##SUPPL##0##S2##, Supporting Information). Furthermore, the onset potential for both Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub>, corresponding to a photocurrent density of 0.5 mA cm<sup>−2</sup>, was cathodically shifted by ≈550 mV compared to pristine BiVO<sub>4</sub>. While Au NPs and Co<sub>4</sub>O<sub>4</sub> molecules serve as cocatalysts that collaborate in catalyzing the water oxidation reaction, it's crucial to emphasize that the modest increase in photocurrent density observed in Au/BiVO<sub>4</sub> compared to BiVO<sub>4</sub> can be primarily attributed to the effective function of Au NPs as “hole transfer channels” (Figures ##SUPPL##0##S5–S7##, Supporting Information).</p>", "<p>To enhance the vertical integration of the Au@Co<sub>4</sub>O<sub>4</sub> hybrid nanostructure, cobalt cubane molecules (1‐Co<sub>4</sub>O<sub>4</sub>) without functional groups were also introduced onto the Au/BiVO<sub>4</sub> surface for comparative analysis (Figures ##SUPPL##0##S8## and ##SUPPL##0##S9##, Supporting Information). Notably, both 1‐Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> and Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> configurations exhibited nearly identical photocurrent density. However, a distinct trend emerged in the photocurrent behavior of Au‐incorporated photoanodes (Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> &gt; Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> &gt; 1‐Co<sub>4</sub>O<sub>4</sub>/Au/BiVO<sub>4</sub>) in accordance with the interaction affinity between the Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs (Figure ##FIG##2##3b##). This observation underscores the critical influence of their binding mode on interfacial charge transfer. Evaluation of linear sweep voltammograms facilitated the calculation of applied bias photon‐to‐current efficiency (ABPE) values for the integrated photoanodes, as depicted in Figure ##FIG##2##3c##. The highest ABPE values were attained by the Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, reaching 1.64% at 0.65 V and 1.88% at 0.66 V, respectively.</p>", "<title>The Surface Charge Transfer and Recombination of BiVO<sub>4</sub>‐Based Photoanodes</title>", "<p>To evaluate the charge transfer efficiencies of the BiVO<sub>4</sub>‐based photoanodes, the hole scavenger Na<sub>2</sub>SO<sub>3</sub> was employed to alleviate surface charge recombination.<sup>[</sup>\n##REF##21942320##\n13\n##\n<sup>]</sup> As illustrated in Figure ##FIG##2##3d##, all photoanodes incorporating Au NPs displayed comparable photocurrent levels, surpassing those of pristine BiVO<sub>4</sub> in Na<sub>2</sub>SO<sub>3</sub> solution, which suggest an indication of enhanced hole generation upon Au NPs integration. Surface charge transfer efficiencies (<italic toggle=\"yes\">η</italic>\n<sub>trans</sub>) of the BiVO<sub>4</sub>‐based photoanodes were calculated using the formula <italic toggle=\"yes\">η</italic>\n<sub>trans</sub> = <italic toggle=\"yes\">J</italic>\n<sub>H2O</sub>/<italic toggle=\"yes\">J</italic>\n<sub>Na2SO3</sub>, with <italic toggle=\"yes\">J</italic>\n<sub>H2O</sub> and <italic toggle=\"yes\">J</italic>\n<sub>Na2SO3</sub> denoting photocurrent density measured with and without Na<sub>2</sub>SO<sub>3</sub>, respectively. The data in Figure ##FIG##2##3e## reveals that Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> exhibited higher <italic toggle=\"yes\">η</italic>\n<sub>trans</sub> than BiVO<sub>4</sub>. Nevertheless, the values remained below 60% across the voltage range, underscoring the constrained charge transfer at the Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> photoanode interface. Remarkably, immobilizing Co<sub>4</sub>O<sub>4</sub> molecules onto the BiVO<sub>4</sub> photoanode surface via an Au mediator led to a successive increase in <italic toggle=\"yes\">η</italic>\n<sub>trans</sub> for the resultant Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, aligning with the photocurrent density order depicted in Figure ##FIG##2##3a##. Notably, Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> exhibited an exceptional <italic toggle=\"yes\">η</italic>\n<sub>trans</sub>, reaching a maximum value of 95.2% at 1.23 V versus RHE. Electrochemical impedance spectroscopy (EIS) measurements of the prepared photoanodes were consistent with the charge transfer efficiency results (Figure ##FIG##2##3f##). The semidiameters of the semicircles in the Nyquist plots for BiVO<sub>4</sub>, Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub>, Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub>, and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> followed a sequence of increasing to decreasing order. This sequence signifies a corresponding acceleration in interfacial charge transfer.</p>", "<p>To more accurately assess the charge transfer and charge recombination kinetics, we conducted intensity‐modulated photocurrent spectroscopy (IMPS) utilizing monochromatic light at 460 nm.<sup>[</sup>\n##UREF##4##\n14\n##\n<sup>]</sup>\n<bold>Figure</bold> ##FIG##3##\n4a## presents typical IMPS responses of BiVO<sub>4</sub>‐based photoanodes at 0.8 V versus RHE, which unveil insights into charge transfer and recombination kinetics. By analyzing the semicircles in the IMPS plots (Figure ##SUPPL##0##S10##, Supporting Information), the charge transfer rate constant (<italic toggle=\"yes\">k</italic>\n<sub>trans</sub>) and charge recombination rate constant (<italic toggle=\"yes\">k</italic>\n<sub>rec</sub>) were derived at various applied potentials. Figure ##FIG##3##4b,c## illustrate that both Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes exhibit lower <italic toggle=\"yes\">k</italic>\n<sub>rec</sub> but elevated <italic toggle=\"yes\">k</italic>\n<sub>trans</sub> values across the entire voltage spectrum compared to Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> photoanodes. These findings underscore that the introduction of Au NPs between BiVO<sub>4</sub> and Co<sub>4</sub>O<sub>4</sub> molecules can effectively curtail interfacial charge recombination while accelerating charge transfer. Determination of the steady‐state charge transfer efficiency (TE) for each photoanode involved calculating <italic toggle=\"yes\">k</italic>\n<sub>trans</sub>/(<italic toggle=\"yes\">k</italic>\n<sub>trans</sub> + <italic toggle=\"yes\">k</italic>\n<sub>rec</sub>). Particularly noteworthy, IMPS analysis revealed that the highest TE value for Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> was 97.2% at 1.0 V (Figure ##FIG##3##4d##), consistent with the computed outcome in Figure ##FIG##2##3e##. This nearly perfect efficiency underscores the pivotal role played by Au NPs in enhancing interfacial charge transfer.</p>", "<title>Identification of Au NPs as Hole Transfer Channels</title>", "<p>To establish the crucial function of Au NPs as hole transfer channels on the BiVO<sub>4</sub> surface, we undertook targeted control experiments and characterizations. Initially, in situ photochemical deposition was employed to examine the sites of oxidation reactions on the Au/BiVO<sub>4</sub> photoanode.<sup>[</sup>\n##REF##23385577##\n15\n##\n<sup>]</sup> We observed that the hole‐mediated oxidative deposition of PbO<sub>2</sub> from Pb<sup>2+</sup> was notably concentrated around the Au NPs, indicative of photogenerated hole accumulation near Au NPs (<bold>Figure</bold> ##FIG##4##\n5a##). This observation supports the notion that the Au NPs can serve as hole trappers, effectively capturing photogenerated holes from BiVO<sub>4</sub>. Additionally, we conducted an experiment involving treatment of the Au/BiVO<sub>4</sub> photoanode with 1,2‐benzenedithiol (BDT). This treatment selectively forms Au─S covalent bonds to coat the surface of Au NPs. Notably, this treatment hindered water molecules from interacting with the Au NPs, while the PEC activity of BiVO<sub>4</sub> remained unaffected (Figure ##SUPPL##0##S11##, Supporting Information). As depicted in Figure ##FIG##4##5b##, following the BDT treatment, the Au channels became obstructed, resulting in a substantial decrease in the photocurrent density of Au/BiVO<sub>4</sub>, approaching that of pristine BiVO<sub>4</sub>. This outcome conclusively validates the pivotal role of Au NPs as effective hole transfer channels.</p>", "<p>To delve deeper into the significance of charge transfer between Au NPs and Co<sub>4</sub>O<sub>4</sub> molecules, an Al<sub>2</sub>O<sub>3</sub> film was introduced onto the surface of the Au/BiVO<sub>4</sub> photoanode.<sup>[</sup>\n##UREF##5##\n16\n##\n<sup>]</sup> The Al<sub>2</sub>O<sub>3</sub> film, with a thickness of ≈3.5 nm, provided complete coverage of the Au/BiVO<sub>4</sub> surface (Figure ##SUPPL##0##S12##, Supporting Information). Serving as an interlayer, this film effectively separated the Co<sub>4</sub>O<sub>4</sub> molecules from the Au NPs, preventing Co<sub>4</sub>O<sub>4</sub> molecules attachment to the Au surface and the formation of the Au@Co<sub>4</sub>O<sub>4</sub> hybrids structure (Figure ##FIG##4##5c##). Notably, the photocurrent density of Al<sub>2</sub>O<sub>3</sub>/Au/BiVO<sub>4</sub> remained comparable to that of Au/BiVO<sub>4</sub>, indicating that the presence of the Al<sub>2</sub>O<sub>3</sub> film did not disrupt charge transfer at the Au/BiVO<sub>4</sub> surface. However, upon the introduction of Co<sub>4</sub>O<sub>4</sub> molecules, the resulting Co<sub>4</sub>O<sub>4</sub>/Al<sub>2</sub>O<sub>3</sub>/Au/BiVO<sub>4</sub> photoanode exhibited a marked reduction in activity compared to Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> (Figure ##FIG##4##5d##). This observation underscores the essential role of charge transfer between Au NPs and Co<sub>4</sub>O<sub>4</sub> molecules in ensuring the efficient PEC performance of the photoanode.</p>", "<p>To reinforce this hypothesis, we introduced 1‐Co<sub>4</sub>O<sub>4</sub> molecules lacking cyano groups for comparative analysis. Notably, these 1‐Co<sub>4</sub>O<sub>4</sub> molecules were unable to assemble on the surface of Au NPs, as evidenced in Figure ##SUPPL##0##S13## (Supporting Information). Direct introduction of 1‐Co<sub>4</sub>O<sub>4</sub> molecules onto the Au/BiVO<sub>4</sub> surface resulted in only a marginal increase in photocurrent density, indicative of the absence of an effective charge transfer channel between BiVO<sub>4</sub> and 1‐Co<sub>4</sub>O<sub>4</sub> molecules. Furthermore, the introduction of an Al<sub>2</sub>O<sub>3</sub> film onto the Au/BiVO<sub>4</sub> photoanode had no discernible impact on the photocurrent density of 1‐Co<sub>4</sub>O<sub>4</sub>/Al<sub>2</sub>O<sub>3</sub>/Au/BiVO<sub>4</sub> and 1‐Co<sub>4</sub>O<sub>4</sub>/Au/BiVO<sub>4</sub> at 1.23 V versus RHE (Figure ##SUPPL##0##S14##, Supporting Information). Based on the aforementioned findings, we posit that the enhanced charge transfer between Co<sub>4</sub>O<sub>4</sub> molecules and BiVO<sub>4</sub> facilitated by the Au bridge significantly contributes to the augmentation of PEC water oxidation.</p>", "<p>Of significance is the observation that the photocurrent density of Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub>, where Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs form Au@Co<sub>4</sub>O<sub>4</sub> aggregates, surpasses that of Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub>, where Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs form Au@Co<sub>4</sub>O<sub>4</sub> NPs. To eliminate the possibility that the improved PEC performance observed in Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> was solely due to an increased loading of Au NPs, we prepared a series of photoanodes with varying amounts of Au NPs by adjusting the immersion time. As the loading of Au NPs increases, the resulting photoanodes exhibit a characteristic volcano‐shaped curve with respect to photocurrent density, where excessive Au NPs loading leads to a decline in PEC activity (<bold>Figure</bold> ##FIG##5##\n6a##; Figure ##SUPPL##0##S15##, Supporting Information). Numerical simulations utilizing finite‐difference time‐domain (FDTD) for plasmon‐induced electric field intensity reveal that Au NPs aggregations generate enhanced regions within the nanogap, outperforming isolated Au NPs (Figure ##SUPPL##0##S16##, Supporting Information).<sup>[</sup>\n##UREF##6##\n17\n##\n<sup>]</sup> In the Au@Co<sub>4</sub>O<sub>4</sub> aggregates, Co<sub>4</sub>O<sub>4</sub> molecules are strategically positioned at the nanogap of Au NPs, acting as linkers. This arrangement maximizes the localized near‐field enhancement, fostering hole accumulation, and consequently leading to improved OER catalysis.</p>", "<p>To gain deeper insights into the impact of multicomponent photoanodes on interface modulation, we assessed the photovoltage and surface recombination rate by conducting open circuit voltage decay measurements on the photoanodes.<sup>[</sup>\n##UREF##7##\n18\n##\n<sup>]</sup> The sequence of photovoltages and recovery constants “b” for the photoanodes aligns as Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> &gt; Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> &gt; Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> &gt; BiVO<sub>4</sub>, as anticipated. This corresponds to a progressive reduction in the driving force and a subsequent increase in charge recombination (Figure ##SUPPL##0##S17##, Supporting Information). We also employed time‐resolved photoluminescence (TRPL) to determine the carrier lifetime (Figure ##FIG##5##6b##).<sup>[</sup>\n##UREF##8##\n19\n##\n<sup>]</sup> The PL decay curves were fitted using a biexponential function, enabling the capture of the initial rapid decay (<italic toggle=\"yes\">τ</italic>\n<sub>1</sub>) and the subsequent slower decay (<italic toggle=\"yes\">τ</italic>\n<sub>2</sub>), where <italic toggle=\"yes\">τ</italic>\n<sub>1</sub> signifies the fall of photogenerated electrons near the conduction band, and <italic toggle=\"yes\">τ</italic>\n<sub>2</sub> indicates the recombination of electron‐hole pairs. The average carrier lifetimes of Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> (6.8 ns), Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> (4.0 ns), Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> (2.3 ns), and BiVO<sub>4</sub> (1.8 ns) were determined using the formula <italic toggle=\"yes\">τ</italic>\n<sub>ave</sub> = <italic toggle=\"yes\">P</italic>\n<sub>1</sub>\n<italic toggle=\"yes\">τ</italic>\n<sub>1</sub> + <italic toggle=\"yes\">P</italic>\n<sub>2</sub>\n<italic toggle=\"yes\">τ</italic>\n<sub>2</sub> (Table ##SUPPL##0##S1##, Supporting Information). These results unequivocally affirm the pivotal role played by Au NPs in facilitating efficient hole transfer from BiVO<sub>4</sub> to Co<sub>4</sub>O<sub>4</sub> molecules.</p>", "<p>Figure ##FIG##5##6c## illustrates the incident photon‐to‐current conversion efficiencies (IPCEs) of the sample photoanodes. Notably, the IPCE values of Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> exhibit substantial enhancements compared to those of Co<sub>4</sub>O<sub>4</sub>/BiVO<sub>4</sub> and BiVO<sub>4</sub> across the entire wavelength range. A discrete rise in IPCE ≈540 nm for Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> can be attributed to plasmon‐induced water oxidation. The integrated IPCE curves over the AM 1.5G solar spectrum yield photocurrent densities of 4.51 mA cm<sup>−2</sup> and 5.01 mA cm<sup>−2</sup> at 1.23 V for Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes, respectively (Figure ##SUPPL##0##S18##, Supporting Information), aligning closely with the experimentally measured photocurrent densities.</p>", "<p>Stability is a pivotal concern for PEC devices, including the photoanode. Au‐decorated semiconductor photoanodes, as a rule, exhibit unsatisfactory stability.<sup>[</sup>\n##REF##32157799##\n20\n##\n<sup>]</sup> Similarly, while Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> demonstrates remarkably high PEC activity, a discernible decline in photocurrent density during constant‐potential electrolysis is evident. Addressing this challenge, we introduced an Al<sub>2</sub>O<sub>3</sub> protective layer to the outer surface of the Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanode through atomic layer deposition (ALD).<sup>[</sup>\n##UREF##9##\n21\n##\n<sup>]</sup> With the protective Al<sub>2</sub>O<sub>3</sub> layer, the resulting Al<sub>2</sub>O<sub>3</sub>/Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanode maintains a photocurrent density comparable to Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> while exhibiting significantly enhanced stability (Figure ##SUPPL##0##S19##, Supporting Information). Remarkably, over 95% of the initial photocurrent density is retained after 120 min of photoelectrolysis (Figure ##FIG##5##6d##). The faradaic efficiency of the Al<sub>2</sub>O<sub>3</sub>/Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanode for water oxidation is ≈88.9%, strongly indicating that the photocurrent originates from the water oxidation reaction (Figure ##SUPPL##0##S20##, Supporting Information). Further investigations into achieving more stable photoanodes through adjustments in protective layer type and thickness are currently underway in our laboratory.</p>" ]
[ "<title>Conclusion</title>", "<p>In summary, our study presents a novel multicomponent photoanode designed to modulate interfacial charge transfer behavior. We introduce Au NPs as efficient hole transfer channels, facilitating the transfer of photogenerated charges between the BiVO<sub>4</sub> light absorber and Co<sub>4</sub>O<sub>4</sub> molecular cocatalysts. Notably, Co<sub>4</sub>O<sub>4</sub> molecules and Au NPs are meticulously assembled onto the photoanode surface through cyano groups, resulting in the formation of unique Au@Co<sub>4</sub>O<sub>4</sub> nanoparticles and aggregates. This distinctive structural arrangement effectively suppresses surface charge recombination and significantly accelerates water oxidation kinetics. Among the designed photoanodes, the Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> configuration demonstrates the highest activity, yielding a substantial photocurrent density of 5.06 mA cm<sup>−2</sup> at 1.23 V. Furthermore, an impressive near‐unit charge transfer efficiency and an enhanced ABPE value of 1.88% at 0.66 V (9.7 times that of BiVO<sub>4</sub>) are achieved. Supported by control experiments and an analysis of carrier transfer kinetics, these enhancements in PEC performance are primarily attributed to the hole channel effect of Au NPs and the facilitated interfacial charge transfer. These findings underscore the critical significance of precisely regulating hole transfer between semiconductors and molecular cocatalysts, providing a viable strategy for developing efficient hybrid photoanodes for PEC solar conversion.</p>" ]
[ "<title>Abstract</title>", "<p>Regulating the interfacial charge transfer behavior between cocatalysts and semiconductors remains a critical challenge for attaining efficient photoelectrochemical water oxidation reactions. Herein, using bismuth vanadate (BiVO<sub>4</sub>) photoanode as a model, it introduces an Au binding bridge as holes transfer channels onto the surfaces of BiVO<sub>4</sub>, and the cyano‐functionalized cobalt cubane (Co<sub>4</sub>O<sub>4</sub>) molecules are preferentially immobilized on the Au bridge due to the strong adsorption of cyano groups with Au nanoparticles. This orchestrated arrangement facilitates the seamless transfer of photogenerated holes from BiVO<sub>4</sub> to Co<sub>4</sub>O<sub>4</sub> molecules, forming an orderly charge transfer pathway connecting the light‐absorbing layer to reactive sites. An exciting photocurrent density of 5.06 mA cm<sup>−2</sup> at 1.23 V versus the reversible hydrogen electrode (3.4 times that of BiVO<sub>4</sub>) is obtained by the Co<sub>4</sub>O<sub>4</sub>@Au(A)/BiVO<sub>4</sub> photoanode, where the surface charge recombination is almost completely suppressed accompanied by a surface charge transfer efficiency over 95%. This work represents a promising strategy for accelerating interfacial charge transfer and achieving efficient photoelectrochemical water oxidation reaction.</p>", "<p>The BiVO<sub>4</sub> photoanode's surface is adorned with assemblies of Au@Co<sub>4</sub>O<sub>4</sub> aggregates, which consist of cyano‐functionalized Co<sub>4</sub>O<sub>4</sub> molecules and Au nanoparticles. This distinctive arrangement results in the remarkable performance of the Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanode, which attains an impressive photocurrent density of 5.06 mA cm<sup>−2</sup> and near‐unit charge‐transfer efficiency at 1.23 V vs. RHE.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6815-cit-0049\">\n<string-name>\n<given-names>W.</given-names>\n<surname>Jiang</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>Q.</given-names>\n<surname>Sui</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Gao</surname>\n</string-name>, <string-name>\n<given-names>F.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Xia</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Jiang</surname>\n</string-name>, <article-title>A Facile Design for Water‐Oxidation Molecular Catalysts Precise Assembling on Photoanodes</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305919</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305919</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was financially supported by the National Natural Science Foundation of China (NSFC) (22179056, 22172018), the Liaoning Revitalization Talents Program (XLYC2002097, XLYC1807210).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.;</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6815-fig-0001\"><label>Figure 1</label><caption><p>a) Schematic illustration of the structure of Au@Co<sub>4</sub>O<sub>4</sub>. b) The biphasic adsorption experiment of Au sol and Co<sub>4</sub>O<sub>4</sub> molecules. c) Transmission electron microscope (TEM image of Au@Co<sub>4</sub>O<sub>4</sub> aggregates. d) UV–vis spectra of Au NPs, Co<sub>4</sub>O<sub>4</sub> molecules and Au@Co<sub>4</sub>O<sub>4</sub>. aggregates.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6815-fig-0002\"><label>Figure 2</label><caption><p>a) The preparation routes of Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes. SEM images of b) BiVO<sub>4</sub>, c) Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and d) Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes. HAADF‐STEM and EDS elemental mapping images of e) Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> and f) Au@Co<sub>4</sub>O<sub>4</sub>(A)/BiVO<sub>4</sub> photoanodes. g) High‐resolution XPS of Co 2p spectra for BiVO<sub>4</sub>‐based photoanodes.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6815-fig-0003\"><label>Figure 3</label><caption><p>The LSV curves a) and the photocurrent density value at 1.23 V b) of BiVO<sub>4</sub>‐based photoanodes. c) The ABPE values, d) LSV curves in Na<sub>2</sub>SO<sub>3</sub> solution, e) surface charge transfer efficiencies, and f) EIS data of BiVO<sub>4</sub>‐based photoanodes. (The illuminated area of photoanodes is 1 cm<sup>2</sup>).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6815-fig-0004\"><label>Figure 4</label><caption><p>a) IMPS responses at 0.8 V versus RHE of BiVO<sub>4</sub>‐based photoanodes under 460 nm. b) The charge recombination rate constants (<italic toggle=\"yes\">k</italic>\n<sub>trans</sub>), c) charge transfer rate constants (<italic toggle=\"yes\">k</italic>\n<sub>rec</sub>), and d) charge transfer efficiencies of BiVO<sub>4</sub>‐based photoanodes obtained from IMPS analysis.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6815-fig-0005\"><label>Figure 5</label><caption><p>a) SEM image of Au/BiVO<sub>4</sub> photoanode after hole‐involved oxidative photo‐deposition of PbO<sub>2</sub> from Pb<sup>2+</sup> ion. b) The photocurrent density values comparison of Au/BiVO<sub>4</sub> with or without the treatment of BDT at 1.23 V. c) Schematic illustration of the water oxidation mechanism comparison with or without the introduction of Al<sub>2</sub>O<sub>3</sub> interlayer. d) LSV curves of BiVO<sub>4</sub>‐based photoanodes.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6815-fig-0006\"><label>Figure 6</label><caption><p>a) Photocurrent densities of Au/BiVO<sub>4</sub> and Au@Co<sub>4</sub>O<sub>4</sub>(N)/BiVO<sub>4</sub> photoanodes with different Au NPs loading at 1.23 V. b) PL decay profiles at 490 nm detection of BiVO<sub>4</sub>‐based photoanodes under 460 nm excitation. c) IPCE values of BiVO<sub>4</sub>‐based photoanodes at 1.23 V. d) I–t curves of BiVO<sub>4</sub>‐based photoanodes under 0.7 V.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6815-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2305919-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
21
CC BY
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2024-01-14 23:41:56
Adv Sci (Weinh). 2023 Nov 20; 11(2):2305919
oa_package/74/26/PMC10787085.tar.gz
PMC10787086
38010981
[ "<title>Introduction</title>", "<p>Conversion reaction mechanism for electrodes in rechargeable energy storage devices implies the provision of high theoretical specific capacity and flat voltage plateau compared to ion intercalation and surface redox mechanisms, ensuring an appealing stable energy supply.<sup>[</sup>\n##UREF##0##\n1\n##, ##UREF##1##\n2\n##, ##UREF##2##\n3\n##, ##UREF##3##\n4\n##, ##UREF##4##\n5\n##, ##REF##37772918##\n6\n##\n<sup>]</sup> Driven by the potential high‐performance perspective, intensive efforts have been aimed at developing conversion‐type material electrodes for conventional lithium‐ion batteries and emerging aqueous batteries, including sulfur,<sup>[</sup>\n##UREF##5##\n7\n##, ##UREF##6##\n8\n##\n<sup>]</sup> selenium,<sup>[</sup>\n##UREF##7##\n9\n##, ##UREF##8##\n10\n##\n<sup>]</sup> tellurium,<sup>[</sup>\n##UREF##3##\n4\n##, ##UREF##9##\n11\n##\n<sup>]</sup> and transition metal chalcogenides.<sup>[</sup>\n##UREF##10##\n12\n##, ##REF##35136082##\n13\n##, ##REF##36975102##\n14\n##, ##REF##34824249##\n15\n##\n<sup>]</sup> Nevertheless, the exploration of advanced conversion electrodes has been hindered by its major scientific challenges, especially in aqueous batteries with multivalent carriers; these challenges involve a significant capacity fading with undesirable operating life triggered by structural degradation at the microstructural and chemical bonding levels.<sup>[</sup>\n##REF##26847657##\n16\n##, ##REF##31895532##\n17\n##, ##UREF##11##\n18\n##\n<sup>]</sup> At the microstructural level, excessive embedding of large‐scale multivalent ions with destructive Coulomb potential fields expedites the collapse of pristine well‐defined ion diffusion channels and the crushing of anisotropic structures.<sup>[</sup>\n##REF##31721411##\n19\n##, ##UREF##12##\n20\n##, ##UREF##13##\n21\n##\n<sup>]</sup> At the chemical bonding level, deep conversion reactions initiate the complete breakage and reorganization of bonding structures with low reversibility, fundamentally contributing to phase segregation and deterioration of the structural integrity.<sup>[</sup>\n##UREF##14##\n22\n##\n<sup>]</sup> Thus, it is crucial to develop precise strategies to address microstructural disintegration and irreversible evolution of chemical bonds for the development of stable conversion‐type materials with high capacities for aqueous batteries.</p>", "<p>For microstructures, tremendous efforts have been dedicated to inhibiting structure degradation by designing functional cladding,<sup>[</sup>\n##UREF##15##\n23\n##\n<sup>]</sup> constructing heterojunctions<sup>[</sup>\n##UREF##16##\n24\n##, ##REF##36604413##\n25\n##\n<sup>]</sup> and other advanced strategies,<sup>[</sup>\n##REF##36131017##\n26\n##, ##UREF##17##\n27\n##\n<sup>]</sup> but the collapse of anisotropic ion channels in pristine crystals after long‐term cycling is still inevitable. In this regard, amorphous materials with sustainable isotropic open channels promoting solid‐state ion diffusion offer some additional opportunities.<sup>[</sup>\n##UREF##13##\n21\n##, ##REF##32841453##\n28\n##\n<sup>]</sup> Amorphous microstructures with both short‐range order and long‐range disorder have been well demonstrated to effectively break the diffusion confinement of topological ordering;<sup>[</sup>\n##UREF##18##\n29\n##\n<sup>]</sup> in addition, these microstructures provide a buffering effect in adapting to lattice strain caused by multivalent ion embedding. However, at the chemical bonding level, bond breakage, side reactions, and irreversible processes caused by repeated conversion reactions (especially overload ion insertion and low‐quality deep alloying upon over‐discharge) fundamentally limit the performance of the conversion‐type cathode, which lacks a sufficient level of stable capacity retention.<sup>[</sup>\n##UREF##19##\n30\n##, ##REF##36150378##\n31\n##\n<sup>]</sup> For example, destructive deep conversion reactions induce deconstruction of the bismuth sulfide (Bi<sub>2</sub>S<sub>3</sub>) structure either to crystalline nanosheets or amorphous hollow spheres, which only retained 40–53% of capacity after 500 cycles.<sup>[</sup>\n##UREF##20##\n32\n##, ##UREF##21##\n33\n##\n<sup>]</sup> Obviously, the design of a synergistic strategy to manipulate both the microstructure and chemical bonding evolution based on novel amorphous materials with controlled moderate conversion mechanisms is essential to meet the future demand for high‐performance conversion‐type electrodes; however, this goal remains elusive.</p>", "<p>Herein, we report that Bi<sub>2</sub>S<sub>3</sub> can be transformed in situ into highly amorphous structures by an electrochemical Cu<sup>2+</sup> embedding process. The reversible storage capability of Cu<sup>2+</sup> in aqueous batteries was explored based on transformed amorphous Bi<sub>2</sub>S<sub>3</sub> (a‐BS), demonstrating an attractive specific capacity of 326.7 mAh g<sup>−1</sup> at 1 A g<sup>−1</sup> and outstanding rate performance of 194.5 mAh g<sup>−1</sup> at 10 A g<sup>−1</sup>. Operando synchrotron X‐ray diffraction (SXRD) and composite ex situ characterizations reveal unprecedented self‐controlled moderate conversion operating in a‐BS. The reserved Bi─S bonds in the reaction and the simultaneous generation of dispersed conductive bismuth monomers in amorphous materials synergistically facilitate fast electron transfer and local chemical electron compensation. Furthermore, the amorphous structure formed in situ and the unprecedented moderate conversion jointly addressed the structural degradation and irreversible bonding evolution faced by the conversion‐type electrode and initiated an excellent cycling stability with a decent capacity decay rate of only 0.02 ‰ per cycle over 8000 cycles at 10 A g<sup>−1</sup>, the highest value in all Bi<sub>2</sub>S<sub>3</sub>‐based batteries. The established a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery delivers durable ion capacity storage performance and a high energy supply of 238.6 Wh kg<sup>−1</sup> at a power density of 9760 W kg<sup>−1</sup>. The synergistic optimization strategies at the microstructure and bonding levels based on amorphous electrodes with intrinsically high‐stable conversion mechanisms reported here provide insights for the design of conversion‐type electrodes.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<p>The crystallized Bi<sub>2</sub>S<sub>3</sub> (c‐BS) precursors were synthesized by an eco‐friendly one‐step synthesis (Figure ##SUPPL##0##S1##, Supporting Information). The corresponding X‐ray diffraction (XRD) peaks are well indexed to orthorhombic Bi<sub>2</sub>S<sub>3</sub> (JCPDS No.89‐8963) in <bold>Figure</bold> ##FIG##0##\n1a##. Scanning electron microscopy (SEM) was used to investigate the morphology of c‐BS, as shown in Figure ##FIG##0##1b##, which displays a uniform hierarchical nanostructure with a particle size of ≈500 nm (Figure ##SUPPL##0##S2##, Supporting Information). Energy dispersive X‐ray spectroscopy (EDS) mapping (Figure ##SUPPL##0##S3##, Supporting Information) was employed to verify the morphology and uniform distribution of Bi and S in c‐BS, and the atomic ratio was close to 2/3 for Bi and S (Figure ##SUPPL##0##S4##, Supporting Information). The high‐resolution transmission electron microscopy (HRTEM) images of c‐BS in Figure ##FIG##0##1c## and Figure ##SUPPL##0##S5## (Supporting Information) show a lattice distance of ≈0.35 nm, which conforms to the (310) crystal plane. The a‐BS with a large number of defects was further constructed by the electrochemical activation process developed in situ to deform a metastable state containing a large rearrangement of the Bi─S bond during the insertion and extraction process of Cu<sup>2+</sup> (Figure ##FIG##0##1d##; Figure ##SUPPL##0##S6##, Supporting Information). A schematic diagram of the evolution of the crystal structure model is shown in Figure ##FIG##0##1e##. The selective area electron diffraction (SAED) pattern visually confirms the complete transformation of crystallinity (Figure ##SUPPL##0##S7##, Supporting Information). The SAED pattern of c‐BS shows two distinct diffraction rings belonging to the (310) and (431) planes with lattice spacings of 3.52 and 1.95 Å, respectively, as displayed in Figure ##FIG##0##1f##, confirming the high crystallinity of c‐BS and its orthorhombic Pbnm space group. In contrast, the SAED image of a‐BS does not contain any visible diffraction spot features, demonstrating an amorphous configuration. X‐ray photoelectron spectroscopy (XPS) was performed to determine the electronic structure and chemical components of c‐BS and a‐BS. The XPS survey scan image in Figure ##SUPPL##0##S8## (Supporting Information) confirms that c‐BS is mainly composed of S and Bi elements, which is consistent with the result of EDS mapping. The high‐resolution XPS spectrum of Bi 4f is shown in Figure ##FIG##0##1g##. Two strong peaks located at 158.7 and 164 eV can be attributed to Bi 4f<sub>7/2</sub> and Bi 4f<sub>5/2</sub>, respectively, and split into two shoulders at 159.7 and 165 eV.<sup>[</sup>\n##REF##36631254##\n34\n##\n<sup>]</sup> Moreover, the two peaks have a typical 5.3 eV energy difference for the spin‐orbit splitting of the Bi 4f core level, illustrating that the valence state of Bi is +3.<sup>[</sup>\n##UREF##22##\n35\n##\n<sup>]</sup> The weaker peaks at 161.3 and 162.6 eV correspond to S 2p<sub>3/2</sub> and S 2p<sub>1/2</sub> as‐signed. Noticeably, c‐BS and a‐BS exhibit the same identical Bi 4f and S 2p core‐level peaks, and only the shoulder peak area ratio is varied, which is ascribed to the disorder rearrangement of the Bi─S bonds in the amorphous structure.<sup>[</sup>\n##UREF##23##\n36\n##\n<sup>]</sup> Trace amounts of Cu─S bonds reveal the induction of amorphous structure formation by Cu<sup>2+</sup>. The bonding structure of c‐BS and a‐BS was further confirmed by Raman analysis, as shown in Figure ##FIG##0##1h##. The c‐BS was characterized by five distinct vibration peaks at 70, 99, 180, 234, and 256 cm<sup>−1</sup>,<sup>[</sup>\n##UREF##24##\n37\n##\n<sup>]</sup> and a‐BS is essentially the same as c‐BS with the peak positions exhibiting good consistency. Thus, the unique a‐BS was successfully obtained based on an in situ electrochemical activation process that was certified by multiple characterization methods.</p>", "<p>The unique aqueous Cu<sup>2+</sup>‐driven amorphous transformation of Bi<sub>2</sub>S<sub>3</sub> further prompted the investigation of its performance for reversible storage of Cu<sup>2+</sup>. <bold>Figure</bold>\n##FIG##1##\n2a## shows the cyclic voltammetry (CV) curves of a‐BS with a scan rate of 0.4 mV s<sup>−1</sup> over the voltage range of 0.34–0.84 V versus standard hydrogen electrode (SHE). The first four cycles of the CV curves almost overlap, indicating that the electrochemical reaction in a‐BS is highly reversible. Two pairs of redox peaks positioned at 0.454/0.506 and 0.517/0.547 V can be observed, corresponding to the reversible electrochemical accommodation of Cu<sup>2+</sup> into a‐BS. The galvanostatic charge/discharge (GCD) profiles (Figure ##FIG##1##2b##) demonstrate that a‐BS delivers an initial discharge capacity of ≈414.7 mAh g<sup>−1</sup> at a current density of 1 A g<sup>−1</sup>. Moreover, the GCD curves display two quasi‐discharge plateaus at 0.51 and 0.45 V, which is consistent with the location of reduction peak in the CV curves. In addition, the polarization voltage is ≈0.14 V, much lower than that of other Bi<sub>2</sub>S<sub>3</sub>‐metal ion systems (Li,<sup>[</sup>\n##REF##30801168##\n38\n##\n<sup>]</sup> Na,<sup>[</sup>\n##UREF##25##\n39\n##\n<sup>]</sup> K,<sup>[</sup>\n##UREF##26##\n40\n##\n<sup>]</sup> Zn<sup>[</sup>\n##REF##31184851##\n41\n##\n<sup>]</sup>//Bi<sub>2</sub>S<sub>3</sub>, at a current density of 1 A g−1) (Figure ##SUPPL##0##S9##, Supporting Information); these results suggest that amorphous Bi2S3 contributes to high ion solid‐phase diffusion kinetics and good interfacial ion/electron transport capability. The GCD curves and corresponding rate performance are shown in Figure ##FIG##1##2c,d##. The GCD curves at different current densities depict excellent recoverability in Figure ##FIG##1##2c##. The specific capacities of the a‐BS cathodes at current densities of 1, 2, 4, 6, 8, and 10 A g<sup>−1</sup> are 326.7, 308.9, 285.5, 265.1, 237.9, and 194.5 mAh g<sup>−1</sup>, respectively. When the current density returned to 1 A g<sup>−1</sup>, the capacity gradually returned to 289.2 mAh g<sup>−1</sup>, demonstrating high reversibility and fast charge storage kinetics. Notably, the rate performance of a‐BS surpasses that of other well‐designed Bi<sub>2</sub>S<sub>3</sub> electrodes in typical ion battery systems,<sup>[</sup>\n##UREF##26##\n40\n##, ##REF##31184851##\n41\n##, ##UREF##27##\n42\n##, ##REF##35132814##\n43\n##, ##REF##34138045##\n44\n##\n<sup>]</sup> as shown in Figure ##FIG##1##2e##, which can be attributed to the high ionic conductivity of the aqueous electrolyte and the remarkable Cu<sup>2+</sup> accommodation capability of a‐BS. The long‐term cyclic stability was evaluated at a current density of 1 A g<sup>−1</sup>, as shown in Figure ##FIG##1##2f##. The a‐BS can deliver a high capacity of 234.3 mAh g<sup>−1</sup> after 450 cycles. Even at an ultrahigh current density of 10 A g<sup>−1</sup> (Figure ##FIG##1##2g##), a‐BS maintains a discharge capacity of 191.7 mAh g<sup>−1</sup> after 8000 cycles with a Coulombic efficiency (CE) of almost 100%, which far exceeds that of all reported Bi<sub>2</sub>S<sub>3</sub>‐based secondary ion batteries (Table ##SUPPL##0##S1##, Supporting Information). When conditions are relaxed to mild aqueous batteries with reliable safety, the a‐BS electrode established here also maintains significant superiority in long‐term cycle lifespan performance and capacity retention (Figure ##FIG##1##2h##).<sup>[</sup>\n##REF##34138045##\n44\n##, ##UREF##28##\n45\n##, ##UREF##29##\n46\n##, ##UREF##30##\n47\n##, ##UREF##31##\n48\n##, ##REF##31553172##\n49\n##, ##UREF##32##\n50\n##, ##UREF##33##\n51\n##, ##UREF##34##\n52\n##, ##UREF##35##\n53\n##, ##REF##35912958##\n54\n##, ##REF##34714615##\n55\n##\n<sup>]</sup> More efforts to evaluate the electrochemical properties of a‐BS electrodes with limit electrolyte quantity (from 200 to 10 µL per cell) or high mass loadings were dedicated, which all demonstrate decent performance (Figures ##SUPPL##0##S10## and ##SUPPL##0##S11##, Supporting Information).</p>", "<p>The kinetics properties of the a‐BS cathode and Cu<sup>2+</sup> storage mechanism were subsequently investigated by consecutive CV measurements at diverse scan rates from 0.1 to 1 mV s<sup>−1</sup> (<bold>Figure</bold>\n##FIG##2##\n3a##). The CV curves of Bi<sub>2</sub>S<sub>3</sub> display a high overlapping shape with different sweep rates, indicating fast kinetics and a small polarization voltage. The peak current (i) and sweep rate (<italic toggle=\"yes\">v</italic>) are subject to the following relationship:\n\n</p>", "<p>In this equation, <italic toggle=\"yes\">a</italic> and <italic toggle=\"yes\">b</italic> are constants, in which the value of <italic toggle=\"yes\">b</italic> is correlated with surface‐controlled processes (capacitive behavior) and diffusion‐limited processes (battery behavior). <italic toggle=\"yes\">b</italic> can be derived by fitting the log (i) versus log (<italic toggle=\"yes\">v</italic>) curve with a value between 0.5 and 1. A <italic toggle=\"yes\">b</italic>‐value of 1 indicates capacitive behavior, whereas a value of 0.5 suggests battery behavior. In this work, the fitted <italic toggle=\"yes\">b</italic>‐values are 0.62, 0.71, 0.84, and 0.96 for peaks 1, 2, 3, and 4, respectively (Figure ##FIG##2##3b##), indicating the coexistence of a synergistic charge storage process. To quantify the capacitance contribution, the following equations:\nor\nare utilized to evaluate the contributions of capacitance (<italic toggle=\"yes\">k</italic>\n<sub>1</sub>\n<italic toggle=\"yes\">v</italic>) and diffusion (<italic toggle=\"yes\">k</italic>\n<sub>2</sub>\n<italic toggle=\"yes\">v</italic>\n<sup>1/2</sup>) at a particular scan rate. As shown in Figure ##FIG##2##3c##, the shaded area of the CV curve fitted at a sweep rate of 1 mV s<sup>−1</sup> indicates that the capacitance contribution is ≈92.4%. The capacitive contribution gradually rises from 56.7% to 92.4% along with the increase in sweep rate from 0.1 to 1 mV s<sup>−1</sup>, indicating that the capacitive behavior dominates in Figure ##FIG##2##3d##. Reaction kinetics were probed by the galvanostatic intermittent titration technique (GITT) (Figure ##FIG##2##3e##). A slight fluctuation in the ion diffusion coefficient (<italic toggle=\"yes\">D</italic>\n<sub>ion</sub>\n<sup>2+</sup>) can be observed ranging from 6.76  × 10<sup>−11</sup> to 7.84 × 10<sup>−9</sup> and 2.67  × 10<sup>−10</sup> to 2.28  × 10<sup>−8</sup> cm<sup>2</sup> s<sup>−1</sup> over the entire Cu<sup>2+</sup> insertion/extraction process, respectively. The high ion diffusion coefficient suggests that a‐BS exhibits a fast ion diffusion capability. This superb kinetics performed in the a‐BS cathode is further confirmed by the low resistances of both charge transfer and Warburg diffusion, as shown in Figure ##SUPPL##0##S12## (Supporting Information).</p>", "<p>To explore the Cu<sup>2+</sup> storage mechanism of a‐BS, the structural changes of a‐BS were investigated by operando SXRD (<italic toggle=\"yes\">λ</italic> = 0.6887 Å) during the discharge–charge process. The results are shown in <bold>Figure</bold>\n##FIG##3##\n4a## and Figure ##SUPPL##0##S13## (Supporting Information), including the 2D contour map of the SXRD patterns and the corresponding discharge–charge curve. During the discharge process, three sets of characterized peaks located at 5.9°, 11.2°, and 9.9° emerged, which are indexed to the (140) and (340) crystal planes of Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> and the (003) crystal planes of Bi, respectively. The charge process is the reverse of the discharge process. It can be clearly observed from the 2D contour map of the SXRD patterns that the discharge products Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> and Bi disappeared and then returned to the a‐BS phase, namely, a highly reversible moderate conversion reaction occurred between a‐BS and Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> as well as Bi. Ex situ XPS analyses of a‐BS electrodes at different states were employed to further elucidate the transformation process and investigate the valence state change of a‐BS electrodes, as shown in Figure ##FIG##3##4b##. At the two consecutively fully discharged states (D 0 V), there are two obvious peaks corresponding to Bi 4f<sub>5/2</sub> and Bi 4f<sub>7/2</sub> at 164.7 and 159.5 eV in a‐BS and remain highly consistent, which are attributed to Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub>.<sup>[</sup>\n##UREF##36##\n56\n##\n<sup>]</sup> Notably, the Bi 4f valence band is noticeably redshifted compared with the original states, which is caused by the blending of the Bi‐metal phase with Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> upon the discharge process. After being fully charged to 0.5 V, the Bi 4f double peaks return to high binding energy and represent the a‐BS phase, confirming that the conversion between Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> and Bi to a‐BS upon the charge process is highly reversible. Interestingly, total destruction of the Bi─S bond during the entire discharge–charge process was not observed; instead, a trend opposite to the change in intensity of the Cu─S bond formed occurred, which demonstrates a moderate conversion reaction with reserved Bi─S bond. Different from the traditional deep conversion reaction in alkali metal batteries and aqueous batteries, a‐BS undergoes a self‐controlled moderate conversion reaction without an alloy reaction between Bi and Cu upon the discharge process, ensuring high electrical conductivity and cathode activity (a Bi‐loaded CuS composite cathode with a deep conversion as a control group as shown in Figure ##SUPPL##0##S14##, Supporting Information). In addition, the Cu 2p XPS spectra of a‐BS electrodes at various discharge–charge states are displayed in Figure ##SUPPL##0##S15## (Supporting Information). The intensity of Cu 2p regularly increases and decreases during the discharge–charge process with the embedding and release of Cu<sup>2+</sup>, in agreement with the evolution of the Cu─S bond in Figure ##FIG##3##4b##. Additionally, the binding energy of Cu 2p without shifting indicates that the valence state of Cu ions remains +2 upon the overall discharge–charge process.</p>", "<p>HRTEM of the a‐BS electrode in the fully discharged state was carried out to better corroborate the above conversion process. The EDS pattern reveals that Cu, S, and Bi are uniformly distributed on the surface during the discharge process (Figure ##FIG##3##4c##), suggesting the effective storage of Cu<sup>2+</sup>. Moreover, the HRTEM images reveal the presence of two phases of orthorhombic Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> with a lattice spacing of 0.56 nm and rhombohedral Bi with a lattice spacing of 0.32 nm. The SAED pattern of the discharge products shows a defined diffraction spot array with the [00‐1] zone axis, indicating the generated Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> with high crystallinity (Figure ##FIG##3##4e##). After 50 cycles, the HRTEM images display the same discharge species, suggesting the robust self‐controlled conversion process (Figure ##SUPPL##0##S16##, Supporting Information). Notably, the HRTEM and SAED associated with the fully charged products were observed without any crystalline features, as shown in Figures ##SUPPL##0##S17## and ##SUPPL##0##S18## (Supporting Information). Based on the above analysis, we proposed that the electrochemical reactions of the a‐BS electrode with Cu<sup>2+</sup> storage can be identified as a reversible self‐controlled moderate conversion reaction and formulated as Bi<sub>2</sub>S<sub>3</sub> + Cu<sup>2+</sup> ⇌ Bi + Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> (Figure ##FIG##3##4f##). Note that the moderate conversion reaction process revealed on amorphous electrodes essentially differs from conventional crystalline cathode intercalation and deep conversion reactions, as shown in Figure ##FIG##3##4g##. During this self‐controlled moderate conversion process, the total destruction of the Bi─S bond and unsustainable low‐quality deep alloying are fully restrained, while bismuth monomers with high conductivity are generated to synergistically facilitate rapid electron transfer and highly reversible bond evolution.<sup>[</sup>\n##UREF##37##\n57\n##, ##REF##34463011##\n58\n##\n<sup>]</sup>\n</p>", "<p>Encouraged by the highly reversible reaction of a‐BS with Cu<sup>2+</sup> and the lower electrode potential of the zinc electrode, a high energy density hybrid ion battery was subtly constructed. We employ an anion‐exchange membrane (AEM) to separate the cell into the following compartments: one for the aqueous a‐BS cathode and one for the Zn metal anode. The working mechanism of the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery is illustrated in Figure ##SUPPL##0##S19## (Supporting Information). During the discharge process, Zn<sup>2+</sup> is stripped from the Zn metal anode, and Cu<sup>2+</sup> is inserted into a‐BS to form Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub>. The reverse reaction then occurs during the subsequent charging process. To balance the charge neutrality, SO<sub>4</sub>\n<sup>2−</sup> anions common in both compartments act as the commuting shuttles between the CuSO<sub>4</sub> and ZnSO<sub>4</sub> electrolytes. The reactions during cathode and anode discharge are suggested by the following equation:\n\n\n</p>", "<p>Benefiting from the unique amorphous structure and self‐controlled moderate conversion, the assembled hybrid ion battery exhibited distinguished ionic transportation kinetics, resulting in decent rate performance. <bold>Figure</bold>\n##FIG##4##\n5a## shows that the reversible capacities of the a‐BS cathode were 266.7, 234.5, 220.1, 210.1, and 195.6 mA h g<sup>−1</sup> at 1, 2, 4, 6, and 8 A g<sup>−1</sup>, respectively, and the Coulombic efficiency was almost 100%. When the current returns to 1 A g<sup>−1</sup>, the a‐BS cathode could quickly recover a reversible capacity of 227.6 mA h g<sup>−1</sup> and remain stable. Galvanostatic charge–discharge voltage profiles at various current densities shown in Figure ##FIG##4##5b##. Profit from the low redox potential of Zn (−0.76 V vs SHE), the aqueous a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery delivers a stable discharging voltage of ≈1.22 V at 1 A g<sup>−1</sup>, while the polarization voltage is maintained at ≈140 mV. Because of the enhanced output voltage, the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery can achieve a high energy density of 238.6 Wh kg<sup>−1</sup> at a power density of 9760 W kg<sup>−1</sup>. In addition, the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery can be easily cycled for more than 1000 cycles at a high current density of 8 A g<sup>−1</sup> and maintains a specific capacity of 171.1 mAh g<sup>−1</sup>, as shown in Figure ##FIG##4##5c##. Obviously, the excellent electrochemical performance of the aqueous a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery outperforms the typical cathodes in aqueous zinc ion batteries,<sup>[</sup>\n##UREF##29##\n46\n##, ##UREF##35##\n53\n##, ##REF##34714615##\n55\n##, ##UREF##38##\n59\n##, ##REF##33090646##\n60\n##, ##UREF##39##\n61\n##, ##REF##34432437##\n62\n##\n<sup>]</sup> as shown in Figure ##FIG##4##5d##. It delivers desired energy densities at admire power densities (Figure ##FIG##4##5e##).<sup>[</sup>\n##UREF##29##\n46\n##, ##UREF##35##\n53\n##, ##REF##34714615##\n55\n##, ##UREF##38##\n59\n##, ##REF##33090646##\n60\n##, ##UREF##39##\n61\n##, ##REF##34432437##\n62\n##\n<sup>]</sup> The decent performance of the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery demonstrates its preponderance in amorphous structures along with self‐controlled moderate conversion.</p>" ]
[ "<title>Results and Discussion</title>", "<p>The crystallized Bi<sub>2</sub>S<sub>3</sub> (c‐BS) precursors were synthesized by an eco‐friendly one‐step synthesis (Figure ##SUPPL##0##S1##, Supporting Information). The corresponding X‐ray diffraction (XRD) peaks are well indexed to orthorhombic Bi<sub>2</sub>S<sub>3</sub> (JCPDS No.89‐8963) in <bold>Figure</bold> ##FIG##0##\n1a##. Scanning electron microscopy (SEM) was used to investigate the morphology of c‐BS, as shown in Figure ##FIG##0##1b##, which displays a uniform hierarchical nanostructure with a particle size of ≈500 nm (Figure ##SUPPL##0##S2##, Supporting Information). Energy dispersive X‐ray spectroscopy (EDS) mapping (Figure ##SUPPL##0##S3##, Supporting Information) was employed to verify the morphology and uniform distribution of Bi and S in c‐BS, and the atomic ratio was close to 2/3 for Bi and S (Figure ##SUPPL##0##S4##, Supporting Information). The high‐resolution transmission electron microscopy (HRTEM) images of c‐BS in Figure ##FIG##0##1c## and Figure ##SUPPL##0##S5## (Supporting Information) show a lattice distance of ≈0.35 nm, which conforms to the (310) crystal plane. The a‐BS with a large number of defects was further constructed by the electrochemical activation process developed in situ to deform a metastable state containing a large rearrangement of the Bi─S bond during the insertion and extraction process of Cu<sup>2+</sup> (Figure ##FIG##0##1d##; Figure ##SUPPL##0##S6##, Supporting Information). A schematic diagram of the evolution of the crystal structure model is shown in Figure ##FIG##0##1e##. The selective area electron diffraction (SAED) pattern visually confirms the complete transformation of crystallinity (Figure ##SUPPL##0##S7##, Supporting Information). The SAED pattern of c‐BS shows two distinct diffraction rings belonging to the (310) and (431) planes with lattice spacings of 3.52 and 1.95 Å, respectively, as displayed in Figure ##FIG##0##1f##, confirming the high crystallinity of c‐BS and its orthorhombic Pbnm space group. In contrast, the SAED image of a‐BS does not contain any visible diffraction spot features, demonstrating an amorphous configuration. X‐ray photoelectron spectroscopy (XPS) was performed to determine the electronic structure and chemical components of c‐BS and a‐BS. The XPS survey scan image in Figure ##SUPPL##0##S8## (Supporting Information) confirms that c‐BS is mainly composed of S and Bi elements, which is consistent with the result of EDS mapping. The high‐resolution XPS spectrum of Bi 4f is shown in Figure ##FIG##0##1g##. Two strong peaks located at 158.7 and 164 eV can be attributed to Bi 4f<sub>7/2</sub> and Bi 4f<sub>5/2</sub>, respectively, and split into two shoulders at 159.7 and 165 eV.<sup>[</sup>\n##REF##36631254##\n34\n##\n<sup>]</sup> Moreover, the two peaks have a typical 5.3 eV energy difference for the spin‐orbit splitting of the Bi 4f core level, illustrating that the valence state of Bi is +3.<sup>[</sup>\n##UREF##22##\n35\n##\n<sup>]</sup> The weaker peaks at 161.3 and 162.6 eV correspond to S 2p<sub>3/2</sub> and S 2p<sub>1/2</sub> as‐signed. Noticeably, c‐BS and a‐BS exhibit the same identical Bi 4f and S 2p core‐level peaks, and only the shoulder peak area ratio is varied, which is ascribed to the disorder rearrangement of the Bi─S bonds in the amorphous structure.<sup>[</sup>\n##UREF##23##\n36\n##\n<sup>]</sup> Trace amounts of Cu─S bonds reveal the induction of amorphous structure formation by Cu<sup>2+</sup>. The bonding structure of c‐BS and a‐BS was further confirmed by Raman analysis, as shown in Figure ##FIG##0##1h##. The c‐BS was characterized by five distinct vibration peaks at 70, 99, 180, 234, and 256 cm<sup>−1</sup>,<sup>[</sup>\n##UREF##24##\n37\n##\n<sup>]</sup> and a‐BS is essentially the same as c‐BS with the peak positions exhibiting good consistency. Thus, the unique a‐BS was successfully obtained based on an in situ electrochemical activation process that was certified by multiple characterization methods.</p>", "<p>The unique aqueous Cu<sup>2+</sup>‐driven amorphous transformation of Bi<sub>2</sub>S<sub>3</sub> further prompted the investigation of its performance for reversible storage of Cu<sup>2+</sup>. <bold>Figure</bold>\n##FIG##1##\n2a## shows the cyclic voltammetry (CV) curves of a‐BS with a scan rate of 0.4 mV s<sup>−1</sup> over the voltage range of 0.34–0.84 V versus standard hydrogen electrode (SHE). The first four cycles of the CV curves almost overlap, indicating that the electrochemical reaction in a‐BS is highly reversible. Two pairs of redox peaks positioned at 0.454/0.506 and 0.517/0.547 V can be observed, corresponding to the reversible electrochemical accommodation of Cu<sup>2+</sup> into a‐BS. The galvanostatic charge/discharge (GCD) profiles (Figure ##FIG##1##2b##) demonstrate that a‐BS delivers an initial discharge capacity of ≈414.7 mAh g<sup>−1</sup> at a current density of 1 A g<sup>−1</sup>. Moreover, the GCD curves display two quasi‐discharge plateaus at 0.51 and 0.45 V, which is consistent with the location of reduction peak in the CV curves. In addition, the polarization voltage is ≈0.14 V, much lower than that of other Bi<sub>2</sub>S<sub>3</sub>‐metal ion systems (Li,<sup>[</sup>\n##REF##30801168##\n38\n##\n<sup>]</sup> Na,<sup>[</sup>\n##UREF##25##\n39\n##\n<sup>]</sup> K,<sup>[</sup>\n##UREF##26##\n40\n##\n<sup>]</sup> Zn<sup>[</sup>\n##REF##31184851##\n41\n##\n<sup>]</sup>//Bi<sub>2</sub>S<sub>3</sub>, at a current density of 1 A g−1) (Figure ##SUPPL##0##S9##, Supporting Information); these results suggest that amorphous Bi2S3 contributes to high ion solid‐phase diffusion kinetics and good interfacial ion/electron transport capability. The GCD curves and corresponding rate performance are shown in Figure ##FIG##1##2c,d##. The GCD curves at different current densities depict excellent recoverability in Figure ##FIG##1##2c##. The specific capacities of the a‐BS cathodes at current densities of 1, 2, 4, 6, 8, and 10 A g<sup>−1</sup> are 326.7, 308.9, 285.5, 265.1, 237.9, and 194.5 mAh g<sup>−1</sup>, respectively. When the current density returned to 1 A g<sup>−1</sup>, the capacity gradually returned to 289.2 mAh g<sup>−1</sup>, demonstrating high reversibility and fast charge storage kinetics. Notably, the rate performance of a‐BS surpasses that of other well‐designed Bi<sub>2</sub>S<sub>3</sub> electrodes in typical ion battery systems,<sup>[</sup>\n##UREF##26##\n40\n##, ##REF##31184851##\n41\n##, ##UREF##27##\n42\n##, ##REF##35132814##\n43\n##, ##REF##34138045##\n44\n##\n<sup>]</sup> as shown in Figure ##FIG##1##2e##, which can be attributed to the high ionic conductivity of the aqueous electrolyte and the remarkable Cu<sup>2+</sup> accommodation capability of a‐BS. The long‐term cyclic stability was evaluated at a current density of 1 A g<sup>−1</sup>, as shown in Figure ##FIG##1##2f##. The a‐BS can deliver a high capacity of 234.3 mAh g<sup>−1</sup> after 450 cycles. Even at an ultrahigh current density of 10 A g<sup>−1</sup> (Figure ##FIG##1##2g##), a‐BS maintains a discharge capacity of 191.7 mAh g<sup>−1</sup> after 8000 cycles with a Coulombic efficiency (CE) of almost 100%, which far exceeds that of all reported Bi<sub>2</sub>S<sub>3</sub>‐based secondary ion batteries (Table ##SUPPL##0##S1##, Supporting Information). When conditions are relaxed to mild aqueous batteries with reliable safety, the a‐BS electrode established here also maintains significant superiority in long‐term cycle lifespan performance and capacity retention (Figure ##FIG##1##2h##).<sup>[</sup>\n##REF##34138045##\n44\n##, ##UREF##28##\n45\n##, ##UREF##29##\n46\n##, ##UREF##30##\n47\n##, ##UREF##31##\n48\n##, ##REF##31553172##\n49\n##, ##UREF##32##\n50\n##, ##UREF##33##\n51\n##, ##UREF##34##\n52\n##, ##UREF##35##\n53\n##, ##REF##35912958##\n54\n##, ##REF##34714615##\n55\n##\n<sup>]</sup> More efforts to evaluate the electrochemical properties of a‐BS electrodes with limit electrolyte quantity (from 200 to 10 µL per cell) or high mass loadings were dedicated, which all demonstrate decent performance (Figures ##SUPPL##0##S10## and ##SUPPL##0##S11##, Supporting Information).</p>", "<p>The kinetics properties of the a‐BS cathode and Cu<sup>2+</sup> storage mechanism were subsequently investigated by consecutive CV measurements at diverse scan rates from 0.1 to 1 mV s<sup>−1</sup> (<bold>Figure</bold>\n##FIG##2##\n3a##). The CV curves of Bi<sub>2</sub>S<sub>3</sub> display a high overlapping shape with different sweep rates, indicating fast kinetics and a small polarization voltage. The peak current (i) and sweep rate (<italic toggle=\"yes\">v</italic>) are subject to the following relationship:\n\n</p>", "<p>In this equation, <italic toggle=\"yes\">a</italic> and <italic toggle=\"yes\">b</italic> are constants, in which the value of <italic toggle=\"yes\">b</italic> is correlated with surface‐controlled processes (capacitive behavior) and diffusion‐limited processes (battery behavior). <italic toggle=\"yes\">b</italic> can be derived by fitting the log (i) versus log (<italic toggle=\"yes\">v</italic>) curve with a value between 0.5 and 1. A <italic toggle=\"yes\">b</italic>‐value of 1 indicates capacitive behavior, whereas a value of 0.5 suggests battery behavior. In this work, the fitted <italic toggle=\"yes\">b</italic>‐values are 0.62, 0.71, 0.84, and 0.96 for peaks 1, 2, 3, and 4, respectively (Figure ##FIG##2##3b##), indicating the coexistence of a synergistic charge storage process. To quantify the capacitance contribution, the following equations:\nor\nare utilized to evaluate the contributions of capacitance (<italic toggle=\"yes\">k</italic>\n<sub>1</sub>\n<italic toggle=\"yes\">v</italic>) and diffusion (<italic toggle=\"yes\">k</italic>\n<sub>2</sub>\n<italic toggle=\"yes\">v</italic>\n<sup>1/2</sup>) at a particular scan rate. As shown in Figure ##FIG##2##3c##, the shaded area of the CV curve fitted at a sweep rate of 1 mV s<sup>−1</sup> indicates that the capacitance contribution is ≈92.4%. The capacitive contribution gradually rises from 56.7% to 92.4% along with the increase in sweep rate from 0.1 to 1 mV s<sup>−1</sup>, indicating that the capacitive behavior dominates in Figure ##FIG##2##3d##. Reaction kinetics were probed by the galvanostatic intermittent titration technique (GITT) (Figure ##FIG##2##3e##). A slight fluctuation in the ion diffusion coefficient (<italic toggle=\"yes\">D</italic>\n<sub>ion</sub>\n<sup>2+</sup>) can be observed ranging from 6.76  × 10<sup>−11</sup> to 7.84 × 10<sup>−9</sup> and 2.67  × 10<sup>−10</sup> to 2.28  × 10<sup>−8</sup> cm<sup>2</sup> s<sup>−1</sup> over the entire Cu<sup>2+</sup> insertion/extraction process, respectively. The high ion diffusion coefficient suggests that a‐BS exhibits a fast ion diffusion capability. This superb kinetics performed in the a‐BS cathode is further confirmed by the low resistances of both charge transfer and Warburg diffusion, as shown in Figure ##SUPPL##0##S12## (Supporting Information).</p>", "<p>To explore the Cu<sup>2+</sup> storage mechanism of a‐BS, the structural changes of a‐BS were investigated by operando SXRD (<italic toggle=\"yes\">λ</italic> = 0.6887 Å) during the discharge–charge process. The results are shown in <bold>Figure</bold>\n##FIG##3##\n4a## and Figure ##SUPPL##0##S13## (Supporting Information), including the 2D contour map of the SXRD patterns and the corresponding discharge–charge curve. During the discharge process, three sets of characterized peaks located at 5.9°, 11.2°, and 9.9° emerged, which are indexed to the (140) and (340) crystal planes of Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> and the (003) crystal planes of Bi, respectively. The charge process is the reverse of the discharge process. It can be clearly observed from the 2D contour map of the SXRD patterns that the discharge products Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> and Bi disappeared and then returned to the a‐BS phase, namely, a highly reversible moderate conversion reaction occurred between a‐BS and Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> as well as Bi. Ex situ XPS analyses of a‐BS electrodes at different states were employed to further elucidate the transformation process and investigate the valence state change of a‐BS electrodes, as shown in Figure ##FIG##3##4b##. At the two consecutively fully discharged states (D 0 V), there are two obvious peaks corresponding to Bi 4f<sub>5/2</sub> and Bi 4f<sub>7/2</sub> at 164.7 and 159.5 eV in a‐BS and remain highly consistent, which are attributed to Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub>.<sup>[</sup>\n##UREF##36##\n56\n##\n<sup>]</sup> Notably, the Bi 4f valence band is noticeably redshifted compared with the original states, which is caused by the blending of the Bi‐metal phase with Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> upon the discharge process. After being fully charged to 0.5 V, the Bi 4f double peaks return to high binding energy and represent the a‐BS phase, confirming that the conversion between Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> and Bi to a‐BS upon the charge process is highly reversible. Interestingly, total destruction of the Bi─S bond during the entire discharge–charge process was not observed; instead, a trend opposite to the change in intensity of the Cu─S bond formed occurred, which demonstrates a moderate conversion reaction with reserved Bi─S bond. Different from the traditional deep conversion reaction in alkali metal batteries and aqueous batteries, a‐BS undergoes a self‐controlled moderate conversion reaction without an alloy reaction between Bi and Cu upon the discharge process, ensuring high electrical conductivity and cathode activity (a Bi‐loaded CuS composite cathode with a deep conversion as a control group as shown in Figure ##SUPPL##0##S14##, Supporting Information). In addition, the Cu 2p XPS spectra of a‐BS electrodes at various discharge–charge states are displayed in Figure ##SUPPL##0##S15## (Supporting Information). The intensity of Cu 2p regularly increases and decreases during the discharge–charge process with the embedding and release of Cu<sup>2+</sup>, in agreement with the evolution of the Cu─S bond in Figure ##FIG##3##4b##. Additionally, the binding energy of Cu 2p without shifting indicates that the valence state of Cu ions remains +2 upon the overall discharge–charge process.</p>", "<p>HRTEM of the a‐BS electrode in the fully discharged state was carried out to better corroborate the above conversion process. The EDS pattern reveals that Cu, S, and Bi are uniformly distributed on the surface during the discharge process (Figure ##FIG##3##4c##), suggesting the effective storage of Cu<sup>2+</sup>. Moreover, the HRTEM images reveal the presence of two phases of orthorhombic Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> with a lattice spacing of 0.56 nm and rhombohedral Bi with a lattice spacing of 0.32 nm. The SAED pattern of the discharge products shows a defined diffraction spot array with the [00‐1] zone axis, indicating the generated Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> with high crystallinity (Figure ##FIG##3##4e##). After 50 cycles, the HRTEM images display the same discharge species, suggesting the robust self‐controlled conversion process (Figure ##SUPPL##0##S16##, Supporting Information). Notably, the HRTEM and SAED associated with the fully charged products were observed without any crystalline features, as shown in Figures ##SUPPL##0##S17## and ##SUPPL##0##S18## (Supporting Information). Based on the above analysis, we proposed that the electrochemical reactions of the a‐BS electrode with Cu<sup>2+</sup> storage can be identified as a reversible self‐controlled moderate conversion reaction and formulated as Bi<sub>2</sub>S<sub>3</sub> + Cu<sup>2+</sup> ⇌ Bi + Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub> (Figure ##FIG##3##4f##). Note that the moderate conversion reaction process revealed on amorphous electrodes essentially differs from conventional crystalline cathode intercalation and deep conversion reactions, as shown in Figure ##FIG##3##4g##. During this self‐controlled moderate conversion process, the total destruction of the Bi─S bond and unsustainable low‐quality deep alloying are fully restrained, while bismuth monomers with high conductivity are generated to synergistically facilitate rapid electron transfer and highly reversible bond evolution.<sup>[</sup>\n##UREF##37##\n57\n##, ##REF##34463011##\n58\n##\n<sup>]</sup>\n</p>", "<p>Encouraged by the highly reversible reaction of a‐BS with Cu<sup>2+</sup> and the lower electrode potential of the zinc electrode, a high energy density hybrid ion battery was subtly constructed. We employ an anion‐exchange membrane (AEM) to separate the cell into the following compartments: one for the aqueous a‐BS cathode and one for the Zn metal anode. The working mechanism of the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery is illustrated in Figure ##SUPPL##0##S19## (Supporting Information). During the discharge process, Zn<sup>2+</sup> is stripped from the Zn metal anode, and Cu<sup>2+</sup> is inserted into a‐BS to form Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub>. The reverse reaction then occurs during the subsequent charging process. To balance the charge neutrality, SO<sub>4</sub>\n<sup>2−</sup> anions common in both compartments act as the commuting shuttles between the CuSO<sub>4</sub> and ZnSO<sub>4</sub> electrolytes. The reactions during cathode and anode discharge are suggested by the following equation:\n\n\n</p>", "<p>Benefiting from the unique amorphous structure and self‐controlled moderate conversion, the assembled hybrid ion battery exhibited distinguished ionic transportation kinetics, resulting in decent rate performance. <bold>Figure</bold>\n##FIG##4##\n5a## shows that the reversible capacities of the a‐BS cathode were 266.7, 234.5, 220.1, 210.1, and 195.6 mA h g<sup>−1</sup> at 1, 2, 4, 6, and 8 A g<sup>−1</sup>, respectively, and the Coulombic efficiency was almost 100%. When the current returns to 1 A g<sup>−1</sup>, the a‐BS cathode could quickly recover a reversible capacity of 227.6 mA h g<sup>−1</sup> and remain stable. Galvanostatic charge–discharge voltage profiles at various current densities shown in Figure ##FIG##4##5b##. Profit from the low redox potential of Zn (−0.76 V vs SHE), the aqueous a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery delivers a stable discharging voltage of ≈1.22 V at 1 A g<sup>−1</sup>, while the polarization voltage is maintained at ≈140 mV. Because of the enhanced output voltage, the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery can achieve a high energy density of 238.6 Wh kg<sup>−1</sup> at a power density of 9760 W kg<sup>−1</sup>. In addition, the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery can be easily cycled for more than 1000 cycles at a high current density of 8 A g<sup>−1</sup> and maintains a specific capacity of 171.1 mAh g<sup>−1</sup>, as shown in Figure ##FIG##4##5c##. Obviously, the excellent electrochemical performance of the aqueous a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery outperforms the typical cathodes in aqueous zinc ion batteries,<sup>[</sup>\n##UREF##29##\n46\n##, ##UREF##35##\n53\n##, ##REF##34714615##\n55\n##, ##UREF##38##\n59\n##, ##REF##33090646##\n60\n##, ##UREF##39##\n61\n##, ##REF##34432437##\n62\n##\n<sup>]</sup> as shown in Figure ##FIG##4##5d##. It delivers desired energy densities at admire power densities (Figure ##FIG##4##5e##).<sup>[</sup>\n##UREF##29##\n46\n##, ##UREF##35##\n53\n##, ##REF##34714615##\n55\n##, ##UREF##38##\n59\n##, ##REF##33090646##\n60\n##, ##UREF##39##\n61\n##, ##REF##34432437##\n62\n##\n<sup>]</sup> The decent performance of the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery demonstrates its preponderance in amorphous structures along with self‐controlled moderate conversion.</p>" ]
[ "<title>Conclusion</title>", "<p>In this study, we obtained a‐BS with sustainable isotropic open channels by elaborate in situ amorphization of c‐BS. The constructed a‐BS cathode exhibits an unprecedented self‐controlled moderate conversion Cu<sup>2+</sup> storage capacity, which effectively surmounts the collapse of anisotropic ion diffusion channels in the pristine crystal and irreversible bond fracture during repeated conversion. Operando SXRD and substantial ex situ characterization reveal that the reserved Bi‐S bond during the electrochemical reaction and the dispersed conducting bismuth monomer produced in the cathode material synergistically promote electron transfer and local charge compensation. Consequently, a‐BS delivers a remarkable reversible capacity of 191.7 mA g<sup>−1</sup> after 8000 cycles at 10 A g<sup>−1</sup> and a decay rate of only 0.02‰ per cycle. Moreover, the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery can supply a stable energy density of 238.6 Wh kg<sup>−1</sup> at 9760 W kg<sup>−1</sup>. This work presents synergistic optimization strategies at the microstructure and bonding levels based on amorphous electrodes with intrinsically high‐stability conversion mechanisms and provides insights for the design of conversion‐type electrodes.</p>" ]
[ "<title>Abstract</title>", "<p>Conversion‐type electrodes offer a promising multielectron transfer alternative to intercalation hosts with potentially high‐capacity release in batteries. However, the poor cycle stability severely hinders their application, especially in aqueous multivalence‐ion systems, which can fundamentally impute to anisotropic ion diffusion channel collapse in pristine crystals and irreversible bond fracture during repeated conversion. Here, an amorphous bismuth sulfide (a‐BS) formed in situ with unprecedentedly self‐controlled moderate conversion Cu<sup>2+</sup> storage is proposed to comprehensively regulate the isotropic ion diffusion channels and highly reversible bond evolution. Operando synchrotron X‐ray diffraction and substantive verification tests reveal that the total destruction of the Bi─S bond and unsustainable deep alloying are fully restrained. The amorphous structure with robust ion diffusion channels, unique self‐controlled moderate conversion, and high electrical conductivity discharge products synergistically boosts the capacity (326.7 mAh g<sup>−1</sup> at 1 A g<sup>−1</sup>), rate performance (194.5 mAh g<sup>−1</sup> at 10 A g<sup>−1</sup>), and long‐lifespan stability (over 8000 cycles with a decay rate of only 0.02 ‰ per cycle). Moreover, the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery can well supply a stable energy density of 238.6 Wh kg<sup>−1</sup> at 9760 W kg<sup>−1</sup>. The intrinsically high‐stability conversion mechanism explored on amorphous electrodes provides a new opportunity for advanced aqueous storage.</p>", "<p>An amorphous bismuth sulfide formed in situ demonstrates an unprecedentedly self‐controlled moderate conversion Cu<sup>2+</sup> storage mechanism for aqueous battery. The amorphous structure with robust ion diffusion channels, unique self‐controlled moderate conversion, and high electrical conductivity discharge products synergistically boosts the capacity, rate performance, and long‐lifespan stability (up to 8000 cycles).\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6823-cit-0063\">\n<string-name>\n<given-names>W.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Sun</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Ren</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Zhao</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Yao</surname>\n</string-name>, <string-name>\n<given-names>Q.</given-names>\n<surname>Lei</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Si</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Ren</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>A.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>W.</given-names>\n<surname>Wen</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Zhu</surname>\n</string-name>, <article-title>In Situ Formed Amorphous Bismuth Sulfide Cathodes with a Self‐Controlled Conversion Storage Mechanism for High Performance Hybrid Ion Batteries</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304146</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304146</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>W.Z., Y.S., and Z.R. contributed equally to this work. This work was financially supported by the Photon Science Research Center for Carbon Dioxide, the National Key Research and Development Program of China (No. 2022YFA1605400), the National Natural Science Foundation of China (No. 12275342, 12005286, U2032204), the Natural Science Foundation of Shanghai (No. 20ZR1464200), and the Youth Innovation Promotion Association of the Chinese Academy of Sciences (2022293). The authors thank the staff from Shanghai Synchrotron Radiation Facility (SSRF) at BL02U2, BL11B, D‐Line, and User Experiment Assist System. The authors thank Dr. Chen Hou for her assistance in TEM and SEM analysis.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6823-fig-0001\"><label>Figure 1</label><caption><p>Characterization of c‐BS and a‐BS. a) XRD pattern of c‐BS. b) SEM image of c‐BS at low magnitude. c) HRTEM image of c‐BS. d) The synthesis process of a‐BS by in situ electrochemical activation. e) Schematic diagram of the conversion of c‐BS to a‐BS. f) SAED image of c‐BS and a‐BS. g) XPS spectra of c‐BS and a‐BS. h) Raman spectra of c‐BS and a‐BS.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6823-fig-0002\"><label>Figure 2</label><caption><p>a) CV curves of the a‐BS cathode at a scan rate of 0.4 mV s<sup>−1</sup>. b) Galvanostatic charge‒discharge voltage profiles at 1 A g<sup>−1</sup> (the first four cycles). c) Galvanostatic charge‒discharge profiles at various current densities: 1–10 A g<sup>−1</sup>. d) Rate performance of the a‐BS‖Cu battery at the indicated current density. e) Comparison of the specific capacity at various current densities between this work and previously reported Bi<sub>2</sub>S<sub>3</sub> electrodes. f) Cycling performance of the a‐BS cathode at 1 A g<sup>−1</sup>. g) Cycling performance of the a‐BS cathode at 10 A g<sup>−1</sup>. h) Performance comparison of long‐term cycling and capacity retention between this work and previously reported aqueous batteries.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6823-fig-0003\"><label>Figure 3</label><caption><p>a) CV curves at various sweep rates from 0.1 to 1 mV s<sup>−1</sup>. b) Log (peak current) versus log (sweep rate) plots of the a‐BS‖Cu battery at Peaks 1, 2, 3, and 4. c) CV profile at 1.0 mV s<sup>−1</sup> indicating the capacitive contribution (green region) to the total current. d) The contribution ratios of the ion diffusion and surface capacitive contribution. e) GITT curves of the a‐BS cathode. f) Cu<sup>2+</sup> diffusion coefficients (<italic toggle=\"yes\">D</italic>\n<sub>ions</sub>) of the a‐BS electrode.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6823-fig-0004\"><label>Figure 4</label><caption><p>a) Galvanostatic discharge‐charge curve and corresponding 2D contour map of SXRD. b) Ex situ XPS spectrum of Bi 4f and S 2p of a‐BS cathodes at the various discharging–charging states. c) HAADF image and corresponding EDS mappings of a‐BS cathodes in the fully discharged state. d) HRTEM image of a‐BS cathodes in the fully discharged state, square i1 for Cu<sub>4</sub>Bi<sub>4</sub>S<sub>9</sub>, square i2 for Bi. e) SAED image of a‐BS cathodes in the fully discharged state. f) Schematic illustration of the Cu<sup>2+</sup> storage mechanism of a‐BS. g) Conceptual diagram of the soft landing of self‐controlled moderate conversion versus electrode breaking of uncontrolled deep conversion during discharge</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6823-fig-0005\"><label>Figure 5</label><caption><p>a) Galvanostatic discharging‐charging curves of the a‐BS Cu<sup>2+</sup>‖Zn<sup>2+</sup> hybrid ion battery at various current densities. b) Galvanostatic charge‐discharge voltage profiles at various current densities: 1–8 A g<sup>−1</sup>. c) Cycling performance of the a‐BS cathode at 8 A g<sup>−1</sup>. d,e) Comparison of the specific capacity and Ragone plot at various current densities between this work and previously reported representative aqueous zinc ion batteries.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6823-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2304146-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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Energy"], "year": ["2016"], "volume": ["1"], "elocation-id": ["16039"]}, {"label": ["3"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["Z.", "J.", "Z.", "X.", "Y.", "Y.", "J.", "Q.", "W.", "Z.", "Y.", "J.", "W.", "D.", "X.", "R."], "surname": ["Yao", "Yang", "Ren", "Ren", "Sun", "Zhao", "Si", "Lei", "Zhang", "Li", "Yin", "Chen", "Wen", "Zhu", "Li", "Tai"], "source": ["Adv. Energy Mater."], "year": ["2023"], "volume": ["13"], "elocation-id": ["2300236"]}, {"label": ["4"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["Y.", "Y.", "Q.", "W.", "Z.", "W.", "J.", "Z.", "J.", "Y.", "W.", "R.", "X.", "D."], "surname": ["Sun", "Zhao", "Lei", "Du", "Yao", "Zhang", "Si", "Ren", "Chen", "Gao", "Wen", "Tai", "Li", "Zhu"], "source": ["Adv. 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{ "acronym": [], "definition": [] }
62
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 27; 11(2):2304146
oa_package/7a/63/PMC10787086.tar.gz
PMC10787087
37949674
[ "<title>Introduction</title>", "<p>Intelligent electronic devices such as wearable electronics, intelligent displays and electronic skins have been widely spread and used in modern society.<sup>[</sup>\n##REF##24151185##\n1\n##, ##UREF##0##\n2\n##, ##UREF##1##\n3\n##, ##UREF##2##\n4\n##, ##UREF##3##\n5\n##\n<sup>]</sup> Recently, it is in great demand for achieving smart electronic devices by functionally adjusting the chemical or physical properties and the process optimization including the single element or the complex hybrid systems.<sup>[</sup>\n##REF##26300307##\n6\n##, ##UREF##4##\n7\n##, ##REF##36975324##\n8\n##\n<sup>]</sup> The battery as a power supply for integrated electronic devices is a very promising electrochemical energy storage system, it also puts forward more advanced intelligent requirements for battery systems in the future development of intelligent equipment.<sup>[</sup>\n##UREF##5##\n9\n##, ##UREF##6##\n10\n##\n<sup>]</sup> Under the background of carbon neutralization, concerns about the unsustainability of fossil fuels and greenhouse gas emissions necessitate the development of new self‐charging rechargeable batteries that harvest clean energy.<sup>[</sup>\n##UREF##7##\n11\n##, ##UREF##8##\n12\n##, ##UREF##9##\n13\n##\n<sup>]</sup> From the perspective of battery safety, it is necessary to consider the safety accidents caused by short circuit, heating, damage and other factors.<sup>[</sup>\n##UREF##10##\n14\n##, ##UREF##11##\n15\n##, ##UREF##12##\n16\n##\n<sup>]</sup> In addition, battery failure at high or low temperatures is also an obstacle to the realization of advanced smart batteries.<sup>[</sup>\n##REF##35319992##\n17\n##, ##UREF##13##\n18\n##\n<sup>]</sup> This forced the development of an adaptive and self‐protective battery system to avoid battery failure.</p>", "<p>Currently, a wide variety of lithium‐ion batteries with stimulus‐response have been developed to accommodate the external environment changes.<sup>[</sup>\n##UREF##14##\n19\n##, ##UREF##15##\n20\n##\n<sup>]</sup> However, the limited application scenarios and the high‐cost of lithium sources as well as the high flammability of organic electrolytes still retards their applications.<sup>[</sup>\n##UREF##16##\n21\n##, ##UREF##17##\n22\n##, ##UREF##18##\n23\n##\n<sup>]</sup> Consequently, according to the availability of the aforementioned responsive lithium battery, it is desirable to explore the novel and safe energy storage system. Various alkali metal ion batteries (Na<sup>+</sup>, K<sup>+</sup>) and multivalent ion batteries (Zn<sup>2+</sup>, Mg<sup>2+</sup>, Ca<sup>2+</sup>, Al<sup>3+</sup>,etc.) have been extensively developed. Zinc ion battery (ZIB) as one of the promising candidates in next‐generation battery systems has attracted much attention due to its high theoretical capacity (820 mAh g<sup>−1</sup> and 5854 mAh cm<sup>−3</sup>), low redox potential (−0.763 V vs. a standard hydrogen electrode (SHE)), high safety, and abundant zinc resources.<sup>[</sup>\n##REF##34081440##\n24\n##, ##REF##32478772##\n25\n##\n<sup>]</sup> In particular, the aqueous electrolyte of ZIB has low toxicity to the human body and favorable compatibility to the environment, which is suitable to be used as advanced energy in intelligent electronic devices.<sup>[</sup>\n##UREF##19##\n26\n##, ##UREF##20##\n27\n##\n<sup>]</sup> However, there are still many challenges in ZIBs, such as the formation of zinc dendrites and the dissolution of cathode materials owing to their complexity and compatibility.<sup>[</sup>\n##UREF##21##\n28\n##, ##UREF##22##\n29\n##, ##UREF##23##\n30\n##\n<sup>]</sup> Apart from the traditional design of electrodes, the design of smart materials has also utilized in ZIBs. The ingenious design of intelligent ZIBs utilizes functional electrodes or functional electrolytes to integrate functions such as energy harvesting and self‐protection into zinc batteries. For example, the novel charging patterns such as the self‐charging system utilizing air/photo are also reported in ZIBs, realizing clean energy harvesting and application in the independent grid charging system.<sup>[</sup>\n##REF##32366904##\n31\n##\n<sup>]</sup> In addition, the functional hydrogel electrolytes are fabricated to replace the traditional aqueous electrolytes for achieving smart properties of ZIBs including the self‐healing and thermal stimulus‐responsive characteristics (<bold>Table</bold> ##TAB##0##\n1\n##).<sup>[</sup>\n##UREF##24##\n32\n##, ##UREF##25##\n33\n##\n<sup>]</sup>\n</p>", "<p>In spite of wide investigations focusing on the design and integration of the smart battery, there is still no systematic and comprehensive review to correlate the sensitive structures with the energy storage performance. Herein, this review first summarizes the preparation methods and principles of realizing smart ZIBs and then focuses on the development of the smart ZIBs, including the design of the functional cathode materials and the intelligent hydrogel electrolytes. In addition, the corresponding reaction mechanism and the design strategies of the various intelligent materials in smart battery systems are also highlighted. Besides, the development route of the smart ZIBs and their application fields was proposed and summarized in <bold>Figure</bold> ##FIG##0##\n1\n## for clearly exhibiting the landmark events. Finally, we present the challenges and future development of smart materials and their application in the ZIBs system, thereby providing new insights for smart devices.</p>" ]
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[ "<title>Conclusion and Perspectives</title>", "<p>The development of the smart ZIBs as a new type of intelligent energy storage device has attracted great attention on the road to the high‐security and low‐cost as well as the self‐adapting battery system. In this review, the design of the cathode and anode materials and the development of the corresponding hydrogel electrolytes in the aqueous ZIB are summarized in detail. To further extend the practical application of the integrated functional aqueous battery and avoid the challenges in fabricating the active electrodes and the smart interface among the electrode interfaces and battery system, the potential strategies and the corresponding perspectives are in the following:</p>", "<title>The Development of Smart Active Electrode Materials</title>", "<p>The design of the active cathode and anode electrodes plays an important role in charging/discharging process for the development of the smart ZIBs. For example, when the smart materials serve as active electrodes for achieving the self‐charging or electrochromic device, the capacity degradation of the electrode derived from the leakage and evaporation of the electrolytes in an open battery system and the color shift caused by the degradation of the active cathodes would accelerate the degradation of the electrode modules during the long‐term operation and leads to the functional failure of the smart devices based on the ZIBs. In addition, the relatively low specific capacity and the operation voltage of the smart electrode still limit the energy storage capability and cycling stability for realizing the practical application. There are several strategies to fabricate the stable and high‐performance electrodes in the intelligentization process of ZIBs.</p>", "<p>For cathode materials, a) the doping of metal ions or heteroatoms (N, P, S, O atoms) of cathode materials could improve the energy density and rate performance of the ZIBs by enhancing the stability and conductivity of the cathode crystalline structure. b) The rational design of the interlayer spacing and morphology of the cathode materials. It cannot only accelerate the kinetic redox reaction, but also provide the external active sites for anchoring much more zinc ion or anion by introducing the vacancy defects, which contributes to improving the electrochemical performance. c) The chemical activity and reversibility of the cathode with a high working voltage. It is also necessary for achieving the high‐energy density, such as the dual‐ions intercalation and de‐intercalation redox mechanism or other multi‐ions insertion reaction (ion capacitor combined with the battery) in the cathode materials.</p>", "<p>For smart zinc anode materials, a) the adjustment of the chemical composition (such as zinc alloying) and structure of the zinc anode is beneficial in providing nucleation sites for zinc ions and achieving uniform charge distribution, thereby suppressing the formation of zinc dendrites. b) The functional surface coating on the zinc anode effectively physically isolates the electrolyte from the surface of the zinc and forms the uniform interfacial protective layer, thereby mitigating the occurrence of hydrogen evolution side reactions and the dendrite growth for realizing the good cycling stability and high energy density. Furthermore, the corresponding smart package of the battery is also desirable for prolonging the cycling stability. Therefore, the development of smart active electrode materials is dependent on the rational regulation of the surface properties, the chemical reversibility, the electronic structure, the micro‐morphology, and the assembled strategy of cathodes and anodes as well as the smart package are necessary for achieving the high energy storage capability and cycling stability.</p>", "<title>The Development of the Smart Response Hydrogel Electrolytes</title>", "<p>Hydrogel electrolytes as an important component integrate the dual functions of separator and electrolyte because of their relatively high ionic conductivity and excellent electrode compatibility in ZIBs. In addition, the excellent flexibility of hydrogel electrolytes also provides an important way to realize wearable electronic devices in the age of intelligence. In this review, for the design of the smart hydrogel electrolytes, the working principle and the research progress of self‐healing, self‐protection and wide working temperature range hydrogels are discussed in detail. The ZIBs based on the smart hydrogel electrolyte could timely self‐regulate under the changes of the external environment. However, the efficiency and stability of the self‐healing and self‐protection functions of current hydrogel electrolytes are insufficient, which cannot provide the applicability in practical application. In addition, most of the smart functions of hydrogels are synergistic, which also limits the targeted response requirement in a working battery. As a result, to extend the utilization of the smart hydrogel electrolyte, the development of hydrogel electrolytes with multiple smart functions and the chemical reversibility is the significant factor in guaranteeing the stability of ZIBs and the corresponding adaptability under the complex working environments. a) The relatively high ionic conductivity. Electrolyte as the charge diffusion carrier determinates the electrochemical performance. The rapid charge transfer in the charge/discharge process is desirable, especially at the fast‐charging field. b) The appropriate flexibility. The design of the flexible hydrogel electrolyte could effectively avoid the leakage of the electrolyte and the induced short circuit and the environmental problem in the traditional aqueous working battery. Moreover, the wearable electronic devices are usually in direct contact with the human skin, and the development of flexible hydrogels for wearable electronic devices should be harmless to the human body and other substrate material. From the perspective of the ecological environment, the degradable and biocompatible hydrogel electrolytes also have great potential for alleviating the environmental pollution. c) The targeted specificity. The reversible ability to recover the functional hydrogel is also desirable for extending the application under the extreme conditions (such as the anti‐fatigue ability, the high elasticity, and the ultra‐low temperature).</p>", "<title>The Development of the Integrated Smart Device</title>", "<p>Smart electronic devices are desirable in the development of the miniaturization and multi‐function to meet the needs of the portable and diversified applications. Therefore, the smart ZIB with the integrated systems could provide energy storage and energy conversion, but also possess the super functional units such as the self‐charging, and self‐healing property. The integrated system also plays an important role in delivering the energy supplying even under the condition of tolerating a variety of complex environmental changes. The superior performance is ascribed to the integrated high compatibility and durability requirements among functional integration units in integrated electronic devices. The temperature adaptability also requires the wide temperature range of the aqueous electrolyte in the smart integrated ZIB. For the wearable electronic devices, the electrochemical stability under the bending states and the cycling performance determinate the application scenarios of the wearable electronic devices. The wearable electronic devices based on the smart ZIB are suitable for diverse application scenarios such as wearable electronic devices, electronic skins and flexible textiles in comparison with the traditional rigid substrates. Importantly, the non‐toxic and low harmless characteristics are necessary for achieving the comfort and safety in the utilization of the electronic devices. The smart ZIBs could eliminate concerns about device compatibility and durability by simplifying the complex integrated device configurations. Aqueous ZIB as a green and sustainable energy supply via the reversible chemical redox reaction can not only promote the optimization of energy structure, but also contribute to the low carbon transition. Therefore, the new‐type integrated system is also in great need for improving the energy storage and conversion, such as the construction of the aqueous battery mixed with the sensors, the energy storage derived from the solar battery, as well as the integration with the traditional devices. There are also some challenges in the integration process between the different types of devices. a) The interface compatibility of the electrode materials in all‐in‐one devices. b) The reversible stability during the electrochemical process. c) The lifespan of the integrated smart devices. All the above‐mentioned issues should be taken into consideration, especially in a complex working process. Therefore, the application of the computer simulation (such as the artificial intelligence technology or the ChatGPT) will provide effective strategies for smart devices.</p>", "<p>As the component of the smart response devices, the selection and design of the active electrode will also induce the unsatisfactory electrochemical performance of a working zinc battery due to the sacrifice the ionic conductivity and the working voltage window in the electrochemical process. As a result, the reported ZIBs with smart responses only stay at the concept stage and cannot achieve the widespread application. It is noted that a satisfactory balance should be achieved between the inherent electrochemical performance sacrifice and the introduction of smart functions in an integrated device. In addition, the smart properties lifespan of the smart ZIBs is far shorter than the lifespan of the traditional ZIBs. It is also desirable for developing the reversible and stable active materials for prolonging the lifespan. Consequently, the successful and initial achievement of the smart ZIBs device in the laboratory stage will provide the commercialization of large‐scale industrial production in future.</p>" ]
[ "<title>Abstract</title>", "<p>The zinc ion battery (ZIB) as a promising energy storage device has attracted great attention due to its high safety, low cost, high capacity, and the integrated smart functions. Herein, the working principles of smart responses, smart self‐charging, smart electrochromic as well as smart integration of the battery are summarized. Thus, this review enables to inspire researchers to design the novel functional battery devices for extending their application prospects. In addition, the critical factors associated with the performance of the smart ZIBs are comprehensively collected and discussed from the viewpoint of the intellectualized design. A profound understanding for correlating the design philosophy in cathode materials and electrolytes with the electrode interface is provided. To address the current challenging issues and the development of smart ZIB systems, a wide variety of emerging strategies regarding the integrated battery system is finally prospected.</p>", "<p>This review discusses the design of smart zinc ion batteries (ZIBs) in self‐charging, electrochromic, self‐healing, self‐protection, wide operating temperature range and their applications in different fields. The critical factors and design philosophy determining the function and performance of smart ZIBs are comprehensively analyzed from the intellectualized design, the main challenges and the development of smart zinc battery systems are discussed and prospected.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6727-cit-0207\">\n<string-name>\n<given-names>X.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Jia</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Liu</surname>\n</string-name>, <article-title>Smart Aqueous Zinc Ion Battery: Operation Principles and Design Strategy</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305201</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305201</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>The Smart Response Principles of ZIBs</title>", "<title>Energy Harvesting and Utilization</title>", "<p>The development of clean renewable energy is desirable to solve the unsustainability of fossil fuels and discontinuity of the wind energy and solar energy, as well as other negative impacts on the environment in modern society. Renewable energy sources such as power grids play an important role in commercial batteries in global energy supply.<sup>[</sup>\n##UREF##33##\n41\n##, ##UREF##34##\n42\n##, ##UREF##35##\n43\n##\n<sup>]</sup> However, the electrical grid is not available in harsh environments or special areas (ocean and space) and is also difficult to provide a reliable energy supply. In addition, integrated energy harvesting devices and energy storage devices also increase costs and device complexity. Therefore, it is significant to construct self‐charging power systems to simplify the device configuration and provide the continuous energy supply at a certain solution. Inspired by the solar charging system, the self‐charging electrical device could be achieved through the natural environment. The chemical redox reaction as a type of traditional energy conversion is the available energy source and could be utilized to achieve self‐charging behavior. Moreover, the chemical redox based on the oxygen in the air also widely served as the active material in the metal‐air battery. As a consequence, the self‐charging property is also desirable for the energy storage supply in the smart device. The self‐charging batteries through air or sunlight effectively overcome the above problems, which provide a feasible way for off‐grid power demand such as wearable electronic devices or the energy supply for remote rural areas (<bold>Figure</bold> ##FIG##1##\n2\n##). In consideration of safety, the aqueous ZIB with the self‐charging behavior also plays an important role in achieving the new‐type energy storage device and integrated smart battery system.</p>", "<title>Stimulus Response</title>", "<p>Materials with the “intelligent” behavior, that is, when the external environment such as the temperature, voltage, magnetism, force, light, or pH changes will make the corresponding transformation by changing the molecular structure or the chain skeleton distortion to adapt the external environmental changes (<bold>Figure</bold> ##FIG##2##\n3\n##). However, materials are generally considered to be isolated and static, which can only achieve some low‐level functions without the ability to respond intelligently. To solve these issues, various kinds of stimuli‐responsive materials with different functional properties are integrated into hydrogels, nanomaterials, carbon nanotubes, and polymers and have been utilized in different fields such as drug delivery, tissue engineering, smart energy storage, soft robotics, optoelectronics, food science, etc.<sup>[</sup>\n##UREF##39##\n47\n##, ##REF##27134415##\n48\n##, ##UREF##40##\n49\n##, ##REF##35040453##\n50\n##\n<sup>]</sup> For example, smart responsive hydrogel materials are used as drug delivery systems, wound dressings, biosensors and tissue substitutes in the field of biomedicine. The responsive nano‐protein particles are utilized to produce food and drugs, and the responsive liquid crystal polymers are used in the fields of soft robots, photonics and optoelectronics. Besides, the smart hydrogel materials serve as charge transfer carriers in the functional electrolytes of the intelligent energy storage. The preparation of the smart materials is necessary for achieving the self‐adapting property in the smart response fields and their further application in the smart responsive devices. The smart responsive materials were widely distributed in the pH, heat, and voltage in the ZIB system.<sup>[</sup>\n##UREF##41##\n51\n##\n<sup>]</sup> They could effectively and intuitively monitor and avoid safety problems such as overcharging or overheating at a working battery system. In addition, the introduction of electrochromic smart materials is can also be very convenient to detect the change of the state of the ZIB system. The application fields of smart electrochromic devices are briefly distributed in the smart window, energy storage monitoring, sensor, and electrochromic display, etc. (<bold>Figure</bold> ##FIG##3##\n4\n##).<sup>[</sup>\n##REF##23955225##\n52\n##, ##UREF##42##\n53\n##, ##REF##35684910##\n54\n##, ##REF##35980039##\n55\n##\n<sup>]</sup> The design of the smart response materials also plays an important role in achieving the smart devices with different external stimuli, and further are integrated into the energy storage and conversion system for sustainable development.</p>", "<title>Self‐Healing</title>", "<p>For the ZIB as an energy supply device, a certain degree of fatigue damage will inevitably occur during the practical application of the materials, which could shorten their service lifespan or lead to safety hazards to some extent, especially under special working conditions. It is desirable for constructing the new‐type materials to withstand the destruction derived from the external factors and avoid secondary disasters such as the short circuit of the working battery, especially with the flammable organic electrolyte. Inspired by the concept of the smart response, the self‐healing materials with the self‐repair management have been widely developed recently. To prolong the lifespan of the devices, abundant efforts have been devoted to developing smart materials with the self‐healing property. Self‐healing materials can be divided into active self‐healing materials and non‐active self‐healing materials. The active self‐healing materials can realize the self‐healing process without the triggering of external stimuli (similar to the wound healing). The non‐active self‐healing materials could realize the healing construction based on external stimuli, such as light, heat, pH, etc. As illustrated in <bold>Figure</bold> ##FIG##4##\n5\n##, there are several strategies to achieve the self‐healing property in aqueous ZIBs, including dynamic covalent bonding, metal‐ligand coordination, hydrogen bonding, electrostatic interaction, host‐guest interaction and ion‐dipole interaction.<sup>[</sup>\n##REF##23864042##\n58\n##, ##REF##36577085##\n59\n##, ##UREF##43##\n60\n##, ##REF##25339592##\n61\n##, ##REF##26422642##\n62\n##, ##UREF##44##\n63\n##\n<sup>]</sup> The design of the heal‐healing materials is utilized to achieve the normal working under different working conditions by self‐repairing the internal structure of the material through external stimulation or response. It is desirable for achieving self‐healing ZIB and provides an uninterrupted energy supply. Therefore, self‐healing materials have been widely used in electronic devices such as the smart energy storage devices, electronic skin, artificial muscles, and sensors.<sup>[</sup>\n##UREF##45##\n64\n##, ##REF##27219708##\n65\n##, ##UREF##46##\n66\n##\n<sup>]</sup>\n</p>", "<title>Smart Integrated Device</title>", "<p>Modern electronic devices have been upgraded from single‐function isolated devices to smart integrated interactive devices, which greatly improves the user experience. Meanwhile, it also promotes the development of modern electronic devices, such as integration with flexible textiles, electronic skin and wearable electronics for achieving faster, more convenient and direct information acceptance and processing.<sup>[</sup>\n##REF##36662335##\n67\n##, ##REF##37070933##\n68\n##\n<sup>]</sup> Multifunctional electronic devices can be integrated by multiple single‐function electronic devices, such as sensors integrated with energy harvesting devices to power the sensor.<sup>[</sup>\n##REF##36839014##\n69\n##, ##UREF##47##\n70\n##\n<sup>]</sup> However, poor compatibility and high cost of such multifunctional integrated devices is not an optimal choice in consideration of the complex configurations. To solve these issues, the design of the smart material with both energy storage and sensing functions would greatly simplify the device configuration, decrease the cost, and eliminate the compatibility concerns during the integrated process.<sup>[</sup>\n##UREF##48##\n71\n##\n<sup>]</sup> For example, an all‐in‐one ZIB‐based pressure sensor is integrated with the functionality of a working battery and a common pressure sensor. The resistance of the device is changed by external pressure to convert mechanical signals into electrical signals for output, and at the same time, it can also be charged and discharged repeatedly as an energy supply device. This ZIB‐type sensor greatly solves the shortcomings of complex device integration, high cost, and large volume. As a result, the smart integration of a single device with multifunctional materials solves the above issues, which is also a promising direction for smart electronic devices.</p>", "<title>The Multifunctional Design of Cathode Materials in Smart ZIBs</title>", "<p>Cathode material as the important component in aqueous ZIBs determinates the working voltage, specific capacity, and cycling stability by the insertion/extraction of zinc ions during the charge/discharge process. In general, the requirements of cathode materials in the aqueous ZIBs with high performance are summarized as follows: 1) Structural stability for long‐term cycling life. 2) Abundant active sites for Zn<sup>2+</sup> intercalation/de‐intercalation with fast kinetic reaction. 3) Appropriate operating voltage. 4) Low cost and environmental suitability. 5) High energy density and power density.</p>", "<p>Currently, there are various electrode materials utilized in ZIBs, including vanadium‐based materials, manganese‐based materials, Prussian blue analogs, organic materials and other composites.<sup>[</sup>\n##UREF##49##\n72\n##, ##UREF##50##\n73\n##\n<sup>]</sup> As a classic electrode material for zinc ion storage, manganese oxides are the first mentioned cathode materials and studied in ZIBs. There are several different reaction mechanisms of the manganese oxides (α‐MnO<sub>2</sub>, β‐MnO<sub>2</sub>, γ‐MnO<sub>2</sub> and other manganese oxides).<sup>[</sup>\n##REF##34081440##\n24\n##, ##UREF##51##\n74\n##\n<sup>]</sup> Among which, the reversible zinc ion insertion/de‐insertion mechanism is widely accepted and developed, which involves a reversible phase transition between α‐MnO<sub>2</sub> and spinel ZnMnO<sub>4</sub>.<sup>[</sup>\n##UREF##52##\n75\n##, ##UREF##53##\n76\n##\n<sup>]</sup> However, the capacity decay derived from the irreversible Jahn‐Teller effect in electrochemical performance still limits its further application despite the high voltage platform.<sup>[</sup>\n##REF##35156981##\n77\n##, ##UREF##54##\n78\n##\n<sup>]</sup> For vanadium‐based materials, the diverse oxidation states and chemical properties endow the ZIB with high capacity and good rate performance.<sup>[</sup>\n##UREF##55##\n79\n##\n<sup>]</sup> As a typical intercalation oxide cathode electrode, the reversible insertion and de‐insertion of Zn<sup>2+</sup> is accompanied a certain amount of H<sup>+</sup> and H<sub>2</sub>O in charging/discharging process.<sup>[</sup>\n##UREF##56##\n80\n##\n<sup>]</sup> The layered vanadium‐based materials with large inter‐lamellar spacing are beneficial for achieving the high rate performance in comparison with manganese oxides materials. However, the dissolution of the vanadium in aqueous electrolyte is urgent to resolve. For Prussian blue analogs cathode, its large interstitial sites and special tunnels allow the reversible insertion/extraction of active diverse ions including Zn ions.<sup>[</sup>\n##UREF##57##\n81\n##\n<sup>]</sup> The relatively low specific capacity and optional variety of Prussian blue analogs still limit its application. Different from the common inorganic compound electrode, the energy storage capability of organic cathodes such as conductive polymer (polyaniline) and quinone‐based material is dependent on the ion coordination effect between negatively charged atoms on the polymer chain or the functional groups.<sup>[</sup>\n##UREF##58##\n82\n##, ##UREF##59##\n83\n##\n<sup>]</sup> The complex preparation process of organic materials is also not beneficial for the practical application. The layered structure with large spacing and a variety of chemical valence states as the important components promise the reversible intercalation/de‐intercalation of zinc ions to obtain the high specific capacity in an electrochemical process. To solve the aforementioned issues, a series of strategies were developed to improve the structure stability of active electrode materials by pre‐intercalating cation, structural water, and active defect.<sup>[</sup>\n##UREF##60##\n84\n##\n<sup>]</sup>\n</p>", "<p>On the basis of considering the chemical reversibility and stability, the functional design of electrode material also plays an important role in achieving the smart battery system. And this issue would determine the application of smart energy storage devices in wearable electronic devices or other intelligent fields in future. A kind of cathode materials with special chemical or physical properties are explored and utilized in aqueous batteries, which provide potential possibilities for intelligent devices. In this section, we will summarize the smart cathode materials and their application in aqueous ZIBs and provide the potential design strategies for the smart electrode materials.</p>", "<title>Cathode Materials with Energy Harvesting Function</title>", "<p>As the reversible secondary battery system, it has been widely utilized in electronic devices such as mobile phones and electric vehicles because of its convenience and portability. However, the vast majority of electronic devices are recharged by the power grids at special charging stations, which is not available for the power supplement without grids. As a consequence, electronic devices without power supplies are unable to continuously work and affect our normal life to some extent, especially in the harsh environment or remote areas. Although abundant efforts have devoted to collecting external energy patterns (such as solar energy, mechanical energy, or thermal energy) to supply the electronic devices, the complex integration and conversion of these energy devices and their continuous property at all‐weather condition states still retard their widespread application in the present situation. Therefore, it is desirable to explore novel and simple charging patterns such as self‐charging mode to simplify this energy supply mode for achieving long‐term cycling properties in the smart battery system.<sup>[</sup>\n##REF##24845707##\n85\n##, ##REF##28393912##\n86\n##, ##UREF##61##\n87\n##\n<sup>]</sup>\n</p>", "<title>Air‐Charging Cathode Materials</title>", "<p>Oxygen as an extremely abundant substance in the air apart from could release energy through the chemical redox reaction, such as burning and metabolism. Oxygen as the chemically stored energy is an available energy source and could be converted into electronic energy through a redox reaction. Inspired by this, the development of self‐charging aqueous ZIBs system would effectively resolve the above‐mentioned continuous energy supply and universality in all‐working conditions. For example, vanadium oxides as the common cathodes are easily oxidized by oxygen in the ZIB open air atmosphere when the vanadium element is in the reduced state (low chemical valence).<sup>[</sup>\n##UREF##62##\n88\n##\n<sup>]</sup> The vanadium oxides were reduced with the insertion of Zn<sup>2+</sup> during the discharging process, corresponding to the valence change of vanadium from V<sup>5+</sup> to V<sup>4+</sup> and V<sup>3+</sup>, respectively. The voltage of the vanadate composite at discharged state is much lower than the oxygen in the open air in the three‐electrode test system. It would result in the potential difference in comparison with the standard electrode potential of oxygen. Therefore, according to the relationship between thermodynamic function and battery voltage, the vanadate with low chemical valence could be oxidized in theory. During this oxidization process, oxygen was stored into the cathode materials in the aqueous ZIBs. The chemical oxidization of vanadium with the assistance of oxygen is similar to the traditional charging process, contributing to the smart charging mode without the external power supply. This novel phenomenon is defined as smart self‐charging behavior. It provides a new strategy for collecting energy through the timely charging mode.</p>", "<p>For example, Niu et al. has first reported the self‐charging battery with the CaV<sub>3</sub>O<sub>8</sub> cathode in aqueous Zn(CF<sub>3</sub>SO<sub>3</sub>)<sub>2</sub> electrolyte.<sup>[</sup>\n##REF##32366904##\n31\n##\n<sup>]</sup> Owing to the difference in redox potential between oxygen and the discharged product of CaZn<sub>3.6</sub>VO at discharging state, there is a spontaneous electron transfer between oxygen and CaZn<sub>3.6</sub>VO accompanied with the redox reactions (<bold>Figure</bold> ##FIG##5##\n6a##). The oxidation of vanadium could be realized, and the self‐charging process would take place with the extraction of Zn<sup>2+</sup> from the layered structure to balance the charge without any external power supply at the same time. It is a similar power charging behavior with a reversible process. In addition, based on the oxidation of vanadium element in an open air environment, another self‐charging all‐solid‐state ZIB (SS‐ZIB) was successfully fabricated using vanadium dioxide (VO<sub>2</sub>) as the cathode and polyacrylamide (PAM)‐chitin nanofiber (ChNF) hydrogel as the electrolyte (Figure ##FIG##5##6b##).<sup>[</sup>\n##UREF##63##\n89\n##\n<sup>]</sup> Based on these redox action of vanadate oxides (Figure ##FIG##5##6c##), some freestanding fiber cathodes or the multi‐dimensional structure electrodes were also prepared in the self‐charging ZIB system.</p>", "<p>Apart from the inorganic materials as cathodes in ZIBs, organic materials with diverse and designable structures are also utilized in aqueous zinc battery. During the charge/discharge process, the rearrangement of chemical bonds in organic materials is susceptible to redox reactions and accompanied by special self‐charging behavior. Wan et al. constructed a zinc‐organic battery with the self‐charging property.<sup>[</sup>\n##REF##34491047##\n90\n##\n<sup>]</sup> The poly (1,5‐naphthalenediamine) was the cathode electrode in 6 M KOH/0.2 M Zn(CH<sub>3</sub>COO)<sub>2</sub> electrolyte. Based on the conversion of the C═N/C─N bond, the reversible zinc storage achieved a high capacity of 188.9 mAh g<sup>−1</sup>. When the battery was discharged to a low voltage, the fully discharged product poly(1,5‐NAPD) (K<sup>+</sup>)n with weak binding energy was easily oxidized by the oxygen (Figure ##FIG##5##6d##). The design of such organic cathode materials broadens the application of ZIBs and would be beneficial for achieving a fast self‐charging process. However, the relatively low working voltage and capacity are still a challenge for assembling the high‐energy battery system. Moreover, the self‐charging behavior will proceed in an irreversible direction during the repeated self‐charging process. With the continuous self‐charging process, the formation of by‐product alkaline zinc salt massively accumulates on the surface of the active electrode, which seriously affects the intercalation of Zn<sup>2+</sup> into the electrode during the power charging process. Therefore, the rational regulation of the oxidization time and the condition of electrolytes in the charging/discharging process plays an important role in realizing the reversible electrochemical performance in ZIBs with self‐charging functions. The flexible and environmentally friendly solid‐state ZIBs system is very suitable for wearable electronic devices, and its self‐charging function is easily charged in any scenario.</p>", "<p>To extend the self‐charging working process, the ZIB with multiple modes was also carried out to avoid the drawbacks of a single battery system. Inspired by this phenomenon, a multi‐mode switching smart zinc battery system via “All‐in‐One” polymer cathodes was successfully fabricated. The active cathode (PANINA/CC@WBL@ABL) in the battery was composed of PANINA grown on carbon cloth (CC), a waterproof and breathable layer (WBL), and a transparent air barrier layer (ABL) to achieve three different working modes.<sup>[</sup>\n##UREF##38##\n46\n##\n<sup>]</sup> Among which, the PANINA was used as the redox‐active species and oxygen reduction electrocatalysts with a photothermal‐responsive (Figure ##FIG##5##6e##). 1) It is a typical ZIBs mode with a capacity of 430 mAh g<sup>−1</sup>, in which ABL is turned off; 2) The ABL was turned on after the battery was fully discharged. The reduced PANINA reacted with oxygen in the air, which was equivalent to the charging process of the battery; 3) The ABL was opened, and the battery was switched to Zn‐air battery in the fully discharged state. The photo‐thermal effect of PANINA significantly improved the electrochemical performance and self‐charging efficiency in the presence of light.</p>", "<title>Photo‐Charging Cathode Materials</title>", "<p>In addition to oxygen, sunlight is also considered to be an inexhaustible renewable clean energy. The harvest and utilization of clean energy is an important way to solve the pressing need of energy saving and emission reduction. The integrated system of solar cells and rechargeable batteries with complex configurations increases energy loss.<sup>[</sup>\n##REF##29425044##\n91\n##\n<sup>]</sup> The design of bi‐functional photo‐active materials with energy harvesting and storage solved these problems. Vanadium pentoxide (V<sub>2</sub>O<sub>5</sub>) nanofibers mixed with poly(3‐hexylthiophene‐2,5‐diyl) (P3HT) were used as photo‐recharging active materials, which both realized the bi‐functions of solar energy harvesting and charge storage.<sup>[</sup>\n##UREF##31##\n39\n##\n<sup>]</sup> The energy levels of P3HT and rGO allowed the transport of photo‐excited electrons from V<sub>2</sub>O<sub>5</sub> nanofibers to the current collector, and the unpaired photo‐induced holes were blocked by P2HT and accumulated in the photo‐active material. The capacity of ZIB with the photo‐active material as the cathode increases from 190 to 370 mAh g<sup>−1</sup> in illuminated condition with ≈1.2% photo‐conversion efficiencies. The 100 cm<sup>2</sup> large‐scale pouch ZIBs also achieve a long‐term cycle of photo‐charging/constant‐current discharging process, demonstrating its potential off‐grid charging applications. To reduce the cost of the integrated devices, the reduced graphene oxide with the photoelectric conversion function was introduced into the energy storage and conversion system.<sup>[</sup>\n##UREF##64##\n92\n##\n<sup>]</sup> The photoactive positive electrode prepared by mixing vanadium dioxide and rGO offers the necessary charge separation and storage for photo‐charging (Figure ##FIG##5##6f##).</p>", "<p>Apart from the vanadium oxides, MoS<sub>2</sub> is also used as a photo‐active material in photo‐rechargeable ZIBs by generating photo‐excited electron‐hole pairs and acting as a carrier for storing zinc ions.<sup>[</sup>\n##REF##34609134##\n93\n##\n<sup>]</sup> In the integrated smart device, the capacity increases from 245 to 340 mAh g<sup>−1</sup> at a light power of 12 mW cm<sup>−2</sup> at 455 nm. The design of the binder‐free photo‐cathode material could further increase the photo‐electric conversion efficiency, which could effectively promote energy storage and conversion in integrated smart devices, especially for the response‐based battery system. The sufficient capacity and light utilization efficiency are the significant parameters for realizing the expected photo‐charging ZIB. However, the low specific surface area of the flat electrode reduces its light utilization efficiency, and the flat ZIB cannot be effectively illuminated after being packaged and wrapped. Therefore, a new class of 3D light‐trapping structures (LTSs) was proposed for the practical photo‐charging ZIBs.<sup>[</sup>\n##UREF##37##\n45\n##\n<sup>]</sup> The large specific surface area exhibited a 400% photo response current density in comparison with the reported flat electrode and delivered 0.19 mWh cm<sup>−2</sup> at 0.51 mW cm<sup>−2</sup>, which is attributed to the enhanced multiple internal reflections and the large surface area (Figure ##FIG##5##6g##). The simulated integration of photo‐charging ZIB into the roof for power supply based on the rigid SiCuOC possessed a high enough strength (over 9 Mpa) for guaranteeing its potential application. The photo‐charging smart ZIB could provide the continuous powered supply, which is a living example for simulating the actual environment of a dark environment.</p>", "<p>As a consequence, self‐charging ZIBs easily charge using air or photo without external power grids. It greatly meets the application requirements of electronic equipment in special scenarios, especially in the next‐generation energy storage devices. The current challenges and corresponding design strategies of the self‐charging ZIBs are as follows:\n<list list-type=\"order\" id=\"advs6727-list-0001\"><list-item><p>The exposed environment for realizing the self‐charging process would lead to the irreversible electrolyte leakage or evaporation, causing the capacity decay and the poor cycling stability or safety hazards. The corresponding solution is to develop the new encapsulation materials and battery structure. For example, the selectively permeable packaging materials with inner hydrophobicity only allow air permeability and effectively prevent the loss of the liquid electrolyte.</p></list-item><list-item><p>The short self‐charging time is necessary for the practical application. The self‐charging time is mainly determined by the redox reaction process in the cathode electrode during the oxygen charging or the photo charging process. The corresponding solution is mainly the rapid charge transfer on the cathode electrode. a) The construction of the hierarchical porous structure of the electrode provides the large contact surface area, which contributes to the abundant physical space and active sites for the redox reaction. b) The content adjustment of external influencing factors is also desirable for improving the redox reaction process, such as the oxygen contents in the electrolytes, the duration time at exposure atmosphere, or the control of the photo power for the photo‐charging process.</p></list-item><list-item><p>The high energy density and availability of self‐charging ZIBs. High theoretical capacity and open circuit voltage determinate the energy density of the battery. To extend its practical application, the dual‐ion insertion or the organic/inorganic hybridized cathode materials will be the possible alternatives in future for the high energy density self‐charging battery.<sup>[</sup>\n##UREF##65##\n94\n##, ##UREF##66##\n95\n##\n<sup>]</sup>\n</p></list-item><list-item><p>The reaction mechanism of self‐charging ZIBs is not well understood. During the self‐charging process, the oxidization of the cathode is also accompanied with other side reactions, such as the solid electrolyte interlayer on the cathode. It would affect the cycling stability and the reproducibility of the self‐charging behavior. Therefore, the in‐situ or the real‐time detection of the cathode and electrolyte is also desirable, including the structural analysis and chemical environment analysis. In addition, the booming theoretical simulation calculations could also provide the essential insights into the self‐charging reaction mechanism.</p></list-item><list-item><p>The integration of the self‐charging ZIBs in wearable electronic devices or the micro‐integrated electronic textiles. The traditional coin‐type battery is not suitable for the wearable devices. Therefore, the variously selectable shape of ZIB is desirable for promising the energy supplying and the self‐charging process.</p></list-item></list>\n</p>", "<title>Cathode Materials with Electrochromic Function</title>", "<p>Intelligence transforms the life experience. With the development of the intelligence system, the corresponding devices with the visual control in the human‐machine interface. Currently, the electronic devices operate at the visible region is desirable for detecting the real‐time working variation in the devices, especially in the fields of the smart electronic devices.<sup>[</sup>\n##UREF##67##\n96\n##\n<sup>]</sup> The electrochromic energy storage devices have attracted great interest recently, especially in the fields of smart windows, electrochromic displays, and electronic skins.<sup>[</sup>\n##UREF##68##\n97\n##, ##UREF##69##\n98\n##, ##REF##26300307##\n99\n##\n<sup>]</sup> Furthermore, the optical properties such as the reflectance, transmittance, and absorptivity of the electrochromic materials would undergo a stable and reversible color change under the application of the electric field or the change of the external voltage, which is called electrochromism.<sup>[</sup>\n##UREF##27##\n35\n##, ##UREF##67##\n96\n##\n<sup>]</sup> These color changes in the devices would reflect the important information of these devices and play an important role in warning or remaindering functions. Consequently, these electrochromic materials and energy storage devices can be integrated by utilizing the voltage change of the battery during the charging and discharging processes to achieve the diversified display or even the early warning function.<sup>[</sup>\n##UREF##70##\n100\n##\n<sup>]</sup>\n</p>", "<p>The battery as the energy storage and conversion device possesses an electrochromic function that can easily monitor residual capacity of the electronic devices through the variation of battery color. The electrochromic batteries can maintain only one constant color when the voltage is constant without the continuous energy consumption, which will be the optimal choice under the extreme conditions. The current collectors of the electrochromic material are usually transparent to observe the changes of color. There are two different electrochromic materials including inorganic and organic materials. The mechanism of inorganic electrochromic materials is the d‐level splitting of transition metal atoms through ion external insertion/extraction process.<sup>[</sup>\n##REF##36239257##\n101\n##\n<sup>]</sup> For example, WO<sub>3</sub> as the first electrochromic material could realize the color change by injecting the electrons and the inserting metal ions (H, Li or Na). During the process, the corresponding valence state of tungsten in WO<sub>3</sub> is reduced from hexavalent to pentavalent, and the color of WO<sub>3</sub> changes from transparent to dark blue.<sup>[</sup>\n##UREF##71##\n102\n##\n<sup>]</sup> Besides, MoO<sub>3</sub>, TiO<sub>2</sub>, NiO, V<sub>2</sub>O<sub>5</sub> and other transition metal oxides with variable chemical valence are also utilized in the electrochromic fields due to their variable chemical valences in electrochemical process.<sup>[</sup>\n##UREF##72##\n103\n##, ##REF##33707439##\n104\n##, ##UREF##73##\n105\n##\n<sup>]</sup> For organic electrochromic materials, the reaction mechanism mainly includes small organic molecules (viologen and its derivatives) and the conductive polymers (such as polyaniline, polypyrrole, polythiophene).<sup>[</sup>\n##REF##33078186##\n106\n##\n<sup>]</sup> Their discoloration mechanism is mainly dependent on the direct electron transfer on the polymer chain or the functional groups on the branched chain with the ion doping or ion adsorption.<sup>[</sup>\n##REF##22581710##\n107\n##\n<sup>]</sup> For example, the electrochromic properties of polyaniline are determined by the dynamic ion doping/de‐doping process. The corresponding optical properties are controlled by the delocalization of p electrons in the polymer structure. These electrochromic materials also provide potential application in smart energy storage devices due to the color changes at an external voltage. The tungsten molybdenum oxide as the cathode material is utilized in the rechargeable aqueous zinc ion electrochromic battery (ZIEB).<sup>[</sup>\n##UREF##74##\n108\n##\n<sup>]</sup> The cation vacancies could greatly improve the electrochemical performance of ZIEB by increasing the electrochemical activity of Zn‐ions. The smart color response occurs accompanied with the process of embedding Zn‐ions into the cathode, which is caused by the MTWO (self‐coloring) (<bold>Figure</bold> ##FIG##6##\n7a##). The MTWO cathode displayed a strong optical contrast of ≈76% at 632.8 nm (Figure ##FIG##6##7b##) and a maximum optical contrast of 90% within only 14 s of self‐coloring time. During the self‐coloring process, the ZIEB could also deliver a high area specific capacity with 69% optical contrast. The integrated electrochromic performance and electrochemical performance based on the reconstruction of the electron structure could provide a new idea for the design of electrochromic batteries.</p>", "<p>An electrochromic ZIB with manganese oxide as the cathode electrode exhibited the multiple distinct colors when operating at different potentials.<sup>[</sup>\n##UREF##75##\n109\n##\n<sup>]</sup> Different from the conventional Mn<sub>2</sub>O<sub>3</sub> electrode, the bilayer structures of Ti and Mn<sub>2</sub>O<sub>3</sub> layers with modulated thicknesses possess a rich color gamut. The as‐assembled battery could present up to seven diverse colors by modulating the thickness of the manganese oxide layer in comparison with the only brown color of the conventional Mn<sub>2</sub>O<sub>3</sub> (Figure ##FIG##6##7c##). At different voltages, the electrode could deliver violet at 2.0 V, crimson at 1.8 V, orange at 0.6 V, and coral at 0.3 V, respectively. As a consequence, the fabricated ZIB could present a series of colors at different voltage plateaus, which is beneficial for achieving the real‐time detection of the residual capacity. In addition, polyaniline with different oxidation or reduction states could also exhibit the different colors.<sup>[</sup>\n##UREF##76##\n110\n##\n<sup>]</sup> During the storage of the cations in the electrochemical process, there are three oxidation states of polyaniline cathode: the full reduction state, the half‐oxidization state and the full oxidation state accompanied by the color switching from green to yellow (Figure ##FIG##6##7d##). As a result, the corresponding color of the battery with the modified polyaniline will also gradually change from light yellow to dark‐green at different voltages, which could demonstrate the intelligent feature of the energy storage state in a working battery (switching from a 100% full‐charged battery to low battery state). When the battery was re‐charged to a full charge state, the color of the battery could also recover to its initial state, which also reveals the reversible variable coloration feature in the battery system.</p>", "<p>The visible color change in a working battery is realized under the operation of the external electronic field, which could unavoidably consume energy such as the electric energy. If there is a green method to trigger the color change without much energy consumption, it would be exciting. Therefore, it is desirable that the energy consumed in the electrochromic battery could be supplied during the discharging process or the other forms of energy could be converted into the driving force of the color change in a working battery through an energy recovery function. Li et al. have successfully synthesized the V<sub>3</sub>O<sub>7</sub> colloidal particle with electrochromic function as ZIB cathode electrode for electrochromic display.<sup>[</sup>\n##UREF##77##\n111\n##\n<sup>]</sup> When zinc ions were inserted or extracted, V<sub>3</sub>O<sub>7</sub> accordingly switched between gray‐blue (coloring process) and yellow (bleaching process) with the response time of 10.4 and 28.6 s (the coloring efficiency was 20.6 cm<sup>2</sup> C<sup>−1</sup>). During the electrochemical process, the electrochromic display with energy retrieval function switches between fully yellow, fully grayish‐blue, and half yellow‐half grayish‐blue (Figure ##FIG##6##7e##). The recovered energy could also power the LED for lighting 28 min, which further confirms that the electrochromic display in the coloring process achieved zero energy consumption, and recovered a moiety of energy to compensate for fading process energy consumption. Apart from the design of the single cathode materials, the integration of the battery system including the anode, the separator, the electrolyte or the external packing should also be taken into consideration.<sup>[</sup>\n##UREF##78##\n112\n##\n<sup>]</sup> As a result, the design of these devices with the energy recovery function displays the novel working pattern in the visual smart energy storage devices.</p>", "<title>The Multifunctional Design of Hydrogel Electrolyte in Smart ZIBs</title>", "<p>Large‐scale, high‐safety and low‐cost energy storage equipment is regarded as the next‐generation substitute for meeting the great demand for new‐type electronic devices in comparison with the current commercial battery system. The leakage of liquid organic electrolytes and the induced flammable issues of the traditional lithium ion battery is still a challenge in wearable and implantable devices in the human body although the ionic conductivity is high.<sup>[</sup>\n##UREF##79##\n113\n##\n<sup>]</sup> Therefore, the solid electrolyte has attracted abundant interest recently due to their high safety and ability to effectively prevent pollution or corrosion caused by electrolyte leakage.<sup>[</sup>\n##UREF##80##\n114\n##, ##UREF##81##\n115\n##\n<sup>]</sup> Moreover, the strong mechanical properties of the all‐solid or quasi‐solid electrolyte could withstand the extreme pressure and external deformation, contributing to the cycling stability of the battery.<sup>[</sup>\n##UREF##82##\n116\n##, ##UREF##83##\n117\n##\n<sup>]</sup> In addition, the solid electrolyte with the less free water can greatly avoid the occurrence of side reactions and the formation of zinc dendrites. Therefore, the solid electrolyte is a promising candidate for realizing the flexible wearable electronic devices. However, the corresponding slow migration of zinc ions in all‐solid electrolytes still leads to the low ionic conductivity of all‐solid flexible devices.<sup>[</sup>\n##UREF##84##\n118\n##, ##UREF##85##\n119\n##\n<sup>]</sup> The lack of sufficient electrolyte wetting at the electrode/electrolyte interface causes the poor contact and the increased charge transfer resistance at the electrode interface, which hinders the kinetic reaction and the utilization of the active electrode and limits the further development of high‐performance all‐solid‐state ZIBs.<sup>[</sup>\n##UREF##86##\n120\n##, ##UREF##87##\n121\n##\n<sup>]</sup> In consideration of the excellent electrochemical kinetic and environmental friendliness in a working battery system, the quasi‐state or all‐solid hydrogel electrolyte composed with the polymer skeleton and abundant functional groups is gradually explored. In addition, the diverse hydrophilic groups in the hydrogel polymer molecular chains lock a large number of water molecules into the voids inside the hydrogel network, contributing to the flexible and moist property in assembled devices. The cross‐linked 2D or 3D network would increase the strength of the hydrogel and change its elasticity and display the good mechanical property, which extend their application in flexible devices. Therefore, the content of free water, electrolyte salt, the external additive of solvents could effectively promote the electrochemical activity and reversibility and realize the high performance and good mechanical property in a flexible device based on the hydrogel electrolyte, quasi‐solid electrolyte, or the all‐solid electrolyte.</p>", "<p>Traditional hydrogel materials are usually divided into natural polymer hydrogels and synthetic polymer hydrogels. Natural polymers (sodium alginate, collagen, fibrin, agarose, gelatin) possess many hydrophilic groups on the molecular chains (‐NH<sub>2</sub>, ‐OH, ‐COOH), which could serve as the physical crosslinking points for forming the gel electrolyte.<sup>[</sup>\n##UREF##88##\n122\n##, ##REF##31808668##\n123\n##, ##REF##26991248##\n124\n##, ##REF##28360862##\n125\n##\n<sup>]</sup> In addition, there are also synthetic polymer hydrogels based on the different polymer skeletons such as polyethylene glycol (PEG), polyacrylamide (PAM), or polyvinylalcohol (PVA), polyacrylicacid (PAA), sodium polyacrylate (PANa).<sup>[</sup>\n##UREF##89##\n126\n##, ##UREF##90##\n127\n##, ##UREF##91##\n128\n##, ##UREF##92##\n129\n##\n<sup>]</sup> For example, the polyacrylamide as hydrogel skeleton was first utilized to engineer the high‐performance, waterproof, tailorable, and stretchable ZIBs. Then, the polyvinyl alcohol‐based hydrogel electrolyte with Zn(CF<sub>3</sub>SO<sub>3</sub>)<sub>2</sub> as electrolyte salt was widely utilized in aqueous zinc battery due to its hydrophilic and film‐forming property. The assembled quasi‐solid‐state ZIB delivers the excellent electrochemical performance, high flexibility and high temperature stability. Besides, the water‐in‐salt hydrogel electrolytes were also developed to decrease the corrosion reaction between the free water and the zinc metal, such as the water‐in‐salt polyacrylamide electrolyte with 1 M Zn (TFSI)<sub>2</sub> and 21 M LiTFSI.</p>", "<p>In comparison with traditional polymers, functional hydrogels with smart features could be obtained by introducing additional functional groups or chemically changing the interface/surface properties.<sup>[</sup>\n##UREF##93##\n130\n##\n<sup>]</sup> For example, the chemical and physical cross‐linked interaction or the weak interaction between molecular of the polymers could endow the hydrogel with self‐healing, self‐recovery, thermo‐responsive, pH‐responsive, and adaptability over a wide temperature range.<sup>[</sup>\n##UREF##78##\n112\n##, ##UREF##94##\n131\n##\n<sup>]</sup> Besides, the hydrogel with the electrolyte salt could also provide the high ionic conductivity and good compatibility with the electrode, contributing to achieving the high‐performance flexible ZIB. Herein, we will discuss the design, preparation, functionalization, and the editability of the smart hydrogel in ZIBs (<bold>Table</bold> ##TAB##1##\n2\n##).</p>", "<title>Self‐Healing Hydrogel Electrolytes</title>", "<p>The design of self‐healing materials plays an important role in the stability, the performance, and the safety of working battery devices operated under extreme working conditions. When the flexible battery experiences damage or fatigue under an external force, the self‐healing mechanism would overcome the cracks or failure of the devices and prolong the lifetime and promise the strength. Therefore, the design of self‐healing features in the flexible devices is beneficial for achieving the smart intelligence in the practical applications.</p>", "<p>Self‐healing hydrogels are defined as hydrogels capable of spontaneously bonding to their original shape and recovering mechanical properties after physical damage.<sup>[</sup>\n##REF##27488822##\n139\n##\n<sup>]</sup> Generally, there are two ways for hydrogel self‐healing: chemical cross‐linking and physical crosslinking. Physical cross‐linked self‐healing hydrogels realize spontaneous healing through covalent bonding, metal‐ligand coordination, hydrogen bonding, electrostatic interaction, host‐guest interaction and ion‐dipole interaction without external stimuli factors.<sup>[</sup>\n##UREF##102##\n140\n##, ##REF##35607147##\n141\n##, ##REF##23423947##\n142\n##, ##UREF##103##\n143\n##\n<sup>]</sup> Chemical cross‐linked self‐healing hydrogels require external stimuli to realize the healing process, such as pH, and UV light or other chemical reactions.<sup>[</sup>\n##UREF##104##\n144\n##, ##UREF##105##\n145\n##\n<sup>]</sup> To achieve the self‐healing effects in various situations, mixed chemical and physical interactions are induced into the battery system. The inevitable crush and deformation of the secondary batteries lead to battery damage in the long‐term cycle processes, which increases the probability of safety accidents. Self‐healing materials used in secondary batteries can avoid serious consequences caused by damage accumulation of batteries.</p>", "<p>The self‐healing property of electrode or electrolyte or current carriers is the key factor to achieve the self‐healing battery devices. The electrostatic interaction of molecules is the key parameter to achieve the self‐healing property in the hydrogel electrolyte.<sup>[</sup>\n##UREF##95##\n132\n##\n<sup>]</sup> The high water retention capacity and ion transport channels with abundant branches endow the electrolyte with the high ionic conductivity, which is beneficial for the rapid electrochemical process. In addition, the electrochemical interaction between charged groups and the hydrogen bonding between SO<sub>3</sub>\n<sup>−</sup> groups and water molecules could facilitate the reconnection within the broken two‐part gel. Its reconstruction of the electrolyte interface could also maintain its original mechanical strength after standing for 24 h and sustaining the 200 g of mass (<bold>Figure</bold> ##FIG##7##\n8a##). The excellent self‐healing performance of the hydrogel electrolyte is widely utilized in flexible aqueous battery systems. The supramolecular interaction also contributes to achieving self‐healing of hydrogel electrolytes in the high‐performance wearable ZIBs. Shu et al. designed a self‐healing chitosan chain/polyacrylamide hydrogel (Zn<sup>2+</sup>‐CS/PAAM) for high‐performance wearable ZIBs.<sup>[</sup>\n##UREF##96##\n133\n##\n<sup>]</sup> Among which, the reversible coordination interaction between zinc ions and amino groups and the strong internal hydrogen bonds in aqueous electrolyte simultaneously promote the self‐healing behavior and overcome the possible physical damage in the wearable electronic devices. Furthermore, the abundant hydroxyl groups endow the hydrogel electrolyte with the excellent self‐healing properties and good mechanical properties with high elasticity and tensile strength. An all‐round hydrogel electrolyte was prepared by using cellulose‐containing cotton as hydrogel skeleton, tetraethyl orthosilicate, and glycerol as a cross linker and anti‐freezing agent, respectively.<sup>[</sup>\n##UREF##97##\n134\n##\n<sup>]</sup> The addition of the glycerol could decrease the freezing point by retarding the evaporation of solvent water through the hydrogen bonds between the hydroxyl groups and water molecules, contributing to its application in low‐temperature environment. Without any external interaction, the repaired hydrogel electrolyte was reconnected without obvious cracks and could maintain a high self‐healing efficiency of 82.6%. It is ascribed to the reversible reform interaction of abundant hydrogen bonds within the hydrogel skeleton and Si─O─Si bonds.</p>", "<p>The good hydrogen bond interaction between the polar functional groups of the hydrogel polymer skeletons plays a significant role in achieving the self‐healing property, especially for extending the practical application of aqueous zinc battery in smart wearable devices in future. Consequentially, the polymer with a large amount of hydrophilic functional groups is desirable for fabricating the self‐healing hydrogel electrolyte due to the formation of hydrogen bond interaction between the branches of the polymer skeleton. For example, the hydroxyl side groups on chain segments of the poly (vinyl alcohol)‐based (PVA) hydrogel could also achieve the self‐healing property once cut by an external force because of the spontaneous hydrogen bonding interaction when the repaired hydrogels connect together. A PVA‐based hydrogel (PVA/Zn(CF<sub>3</sub>SO<sub>3</sub>)<sub>2</sub>) was fabricated via a facile freeze/thaw approach.<sup>[</sup>\n##UREF##28##\n36\n##\n<sup>]</sup> A large amount of PVA crystalline micro‐regions at low temperatures could serve as the cross‐linking agent during the formation PVA gel hydrogel and guarantee the 3D network with porous structure, providing the good ionic conductivity. When the PVA‐based electrolyte was damaged, the exposed uncrystallized PVA segments on the fracture surface could interact and form the hydrogen bonding and finally complete the self‐healing process (Figure ##FIG##7##8b##). Two parts of the damaged ZIB based on the hydrogel electrolyte could also normally only through the simple direct contact after being cut off and display the similar electrochemical performance. Besides, the good adhesion of the gel electrolyte with good flexibility is also beneficial for tailoring the shapes and patterns of the battery, demonstrating its wide application in stretchable and printable electronics.</p>", "<p>Apart from hydrogel electrolyte with a single self‐healing function, the integrated electrode with the electrolyte is desirable for the full flexibility of the wearable devices, especially at the extreme condition. Therefore, the all‐in‐one type electrode with reversible self‐healing property is explored. With the flexible collector substrate, the active dense VS<sub>2</sub> nanosheets were in‐situ deposited on the carbon cloth (as the cathode) and the Zn nanowires anode was obtained by electrodepositing on the surface of the carbon cloth by a three‐electrode system. Then, the integrated all‐in‐one flexible electrode in a battery was obtained for assembling the all‐in‐one wearable battery system.<sup>[</sup>\n##UREF##98##\n135\n##\n<sup>]</sup> With the assistance of the PVA‐based hydrogel electrolyte, the flexible Zn//VS<sub>2</sub> battery delivers the reversible self‐healing property. When the PVA‐based hydrogel was cut to a diameter of 5 cm and then connected for 30 min, two hydrogel pieces could tightly adhere and achieve a high loading of 500 g and keep well without obvious breaking. It could be ascribed to the good self‐healing property derived from the large amount of hydroxyl groups in the PVA skeleton. The self‐healing performance could also be improved by modulating the groups on the PVA polymer and the thickness of the hydrogel. Besides, the micro‐structure such as the pore diameter and the porous structure of the hydrogel also determinates the mechanical property and the self‐healing property, extending the practical application in portable and wearable electronic devices. Even after several seal‐healing processes by cutting vertically or horizontally, the battery could also light up the LED. As a result, the design of the all‐in‐one electrode or battery with the self‐healing property is desirable in the smart electronic devices of the future energy‐storage systems.</p>", "<title>Self‐Protection Hydrogel Electrolytes</title>", "<p>Safety is one of the most critical issues in the electrochemical energy storage devices. Dendrites are inevitably generated and growing during the repeated cycling process, which will finally lead to the internal short circuits and uncontrollable overcharging of batteries.<sup>[</sup>\n##UREF##106##\n146\n##, ##UREF##107##\n147\n##, ##UREF##108##\n148\n##\n<sup>]</sup> In recent years, there are many reported explosions, fires, and other dangerous accidents of the electric vehicles due to these hazard factors.<sup>[</sup>\n##UREF##109##\n149\n##, ##UREF##110##\n150\n##\n<sup>]</sup> In addition, a large amount of Joule heat during the cycling processes of the energy storage devices will be also the potential security risk. The kinetics reaction at high temperature and the limited heat‐removal system would also comprise the capacity or even is not working properly of the battery. The excessive heat accumulation in the narrow and small space of a working battery module would likely cause an explosion.<sup>[</sup>\n##UREF##111##\n151\n##\n<sup>]</sup> Developing the battery with self‐protection functions is a promising approach to eliminating these safety hazards. To achieve the self‐protection function in working, the responsive materials should be introduced into the battery system. For example, functional hydrogels with various responsive abilities have been utilized the different scenarios to adapt the environmental change or the dangerous signals, including the biomedical field (the blood sugar monitoring) and the food packaging field (the moisture detection) in a timely manner. According to the above‐mentioned responsiveness characteristic, a series of hydrogels are fabricated and used in the aqueous to achieve the responsive property, such as the pH response and the temperature dependent hydrogel.<sup>[</sup>\n##UREF##30##\n38\n##, ##UREF##112##\n152\n##\n<sup>]</sup> Herein, the recent advancement of the self‐protected ZIBs will be summarized and discussed in detail (<bold>Table</bold> ##TAB##2##\n3\n##).</p>", "<title>Overcharge Self‐Protection Hydrogel Electrolytes</title>", "<p>The deep charging and deep discharging process of the battery will be inevitably at the cost of the decreased electrochemical performance such as the rated capacity and the cycling stability in the repeated charge/discharge process. In the traditional “rocking chair” lithium ion battery, the over‐discharged behavior would result in the external redox reaction of the copper ion derived from the conductive collector and finally diffuse into the liquid electrolyte. In contrast, the over‐charging process maybe cause the collapse of the positive cathode materials in the lithium ion de‐intercalation process. All of these results are not beneficial for achieving the long‐term cycling stability. In a working aqueous zinc battery, the external reaction in over‐charging or over‐discharging process will contribute to the decomposition reaction of water in aqueous electrolyte accompanied with the H<sub>2</sub> and O<sub>2</sub> evolution. It would increase the pressure of inside the working battery and induce the explosion to some extent in the limited space of the coin‐type battery or pouch battery. Therefore, it is desirable to detect the over‐charging behavior and effectively avoid the irreversible reaction. For example, Feng et al. have demonstrated a smart zinc‐iodine aqueous battery with an overcharge protection function.<sup>[</sup>\n##UREF##30##\n38\n##\n<sup>]</sup> The primary smart material is the poly (2‐vinylpyridine) in the battery, which can complete the transition from the hydrophilic soluble state to the hydrophobic gel state within 30 s and then prevent the battery away from overcharging (Figure ##FIG##7##8c##). Herein, the pH of the electrolyte as the stimulus‐responsive inducement could effectively reflect the working situation of the working ZIB. When the zinc‐iodine battery was over‐charged, the internal resistance increases by four orders of magnitude because of the fast transformation of poly (2‐vinylpyridine) derived from the de‐protonation effect. The battery cannot normally work and rapidly switched off with the almost no capacity contribution. When the pH increases from 4 to 6, the resistance sharply increases from 10 to 220 ohms. It could effectively avoid the short circuit or even the fire in a working device system. Importantly, the self‐protected battery could also switch to the initial state accompanied with the recovery of the pH value in the battery system. As a result, the pH of the electrolyte was readjusted to the normal level by adding dilute sulfuric acid and the battery also restored to its normal capacity. The repeated overcharge/recovery cycle and the normal working capacity with almost no loss indicate that the smart self‐protection reversibility in a ZIB. This work opens a novel way for the development of overcharge‐protected ZIBs.</p>", "<title>Thermal Self‐Protection Hydrogel Electrolytes</title>", "<p>Thermal self‐protection is an attractive strategy to achieve the operation safety of the battery especially at high temperature states and avoid the thermal runaway. The deionized water as the electrolyte solvent endows the diffusion of the positive and negative charges in the electrochemical process. The resistance variation in the electrolyte plays an important role in affecting the electrochemical performance of the Zinc battery. The resistance increases accompanied with the evaporation of water at high temperature and decreases the charge transfer (or ion diffusion), resulting in the sluggish reaction kinetic process or the poor operation of a working battery even shut down. When the temperature was recovered to the normal situation, the battery could also be normally charged and discharged for the energy conversion and storage. As the important component of the battery, the design of the hydrogel electrolyte with the thermal responsive ability is beneficial for achieving the thermal‐protection battery devices. For example, a smart hygroscopic hydrogel was fabricated for thermally self‐protected ZIBs based on the polyacrylamide (PAAm) hydrogel electrolyte.<sup>[</sup>\n##UREF##113##\n153\n##\n<sup>]</sup> Herein, the ZnCl<sub>2</sub> was chosen as the electrolyte salt because its saturated vapor pressure could be easily regulated by the concentration in the hydrogel electrolyte, which is an important factor in determining the thermal protection. When the battery was working at high temperature, the Zn‐PAAm with appropriate saturated vapor pressure evaporated water rapidly (Figure ##FIG##7##8d##). It causes the blocked zinc ion migration with an order of magnitude from 3.8 × 10<sup>−10</sup> to 3.4 × 10<sup>−11</sup> cm<sup>2</sup> s<sup>−1</sup> due to the evaporation of water and then the working battery was cut off. When the temperature recovered to room temperature again, Zn‐PAAm could absorb the water vapor in the air and resume normal work. When the battery was heated at 50.5 °C, the zinc ions could hardly migrate, and the capacity decreased rapidly because of the water evaporation and thermal resistance increase in aqueous ZIBs. When the temperature was re‐covered to the initial working state (normally the room temperature), the battery also delivers the matched capacity with almost no decay. This thermal reversibility also confirms the thermal self‐protection function based on the water content.</p>", "<p>Although the porous structure is beneficial for the ion diffusion in the electrochemical process, they are not desirable at any temperature, especially at the high temperature. Niu et al. constructed the thermal self‐protection ZIBs employing thermal‐responsive porous poly(N‐isopropylacrylamide) (PNIPAM) hydrogel electrolytes.<sup>[</sup>\n##UREF##112##\n152\n##\n<sup>]</sup> The PNIPAM formed intermolecular hydrogen bonds after exceeding its volume phase transition temperature (VPTT) and the PNIPAM molecular chain shrank and changed from hydrophilicity to hydrophobicity. To increase the VPTT from 33 to 45 °C, acrylamide incorporated with hydrophilic molecules was introduced into the PNIPAM hydrogel and obtained the PNIPAM/AM‐5 with the thermal self‐protection. When the temperature exceeded the VPTT, the exposed hydrophobic isopropyl of PNIPAM/AM‐5 changed from hydrophilicity to hydrophobicity accompanied with the disappearance of the porous structure and the ionic conductivity of the hydrogel electrolyte also decreased by about one order of magnitude. As a result, the PNIPAM/AM‐5 based ZIB displays the strong thermal response at high temperature and these changes were reversible when the temperature dropped to room temperature (Figure ##FIG##7##8e##). Even after several rapid temperature increases/decreases, the thermal self‐protection performance is not affected, and the battery could also achieve the good electrochemical performance.</p>", "<p>It was worth noting that the smart thermal self‐protection function was not unique to PAAm or PAM hydrogels. The hydrogels with the sol‐gel transition point or the hydrophilic and hydrophobic functional groups play an important role in achieving the self‐protection property in the battery. For example, the PVA hydrogels are also utilized in battery to achieve the similar thermal self‐protection functions. When the temperature exceeded the sol‐gel transition point of the hydrogel, the polymer sol was transformed into the solid hydrogel, resulting in the poor ion migration in the electrochemical process. The strong temperature dependence of the hydrogel with the resistance change contributes to assembling the smart self‐protection ZIB. For example, a proton‐incorporated poly(N‐isopropylacrylamide‐co‐acrylic acid) (PNA) sol‐gel transition electrolyte was fabricated for the thermal self‐protection ZIBs.<sup>[</sup>\n##UREF##26##\n34\n##\n<sup>]</sup> At the transition temperature, the hydrogen bonding force formed by PNA was stronger than that of the hydrophobic part because of the good water solubility of acrylic acid and PNA exists as the form of the transparent flowing sol. When the temperature increased to the phase transition point 50 °C, the hydrogen bond in the PNA sol was destroyed and the hydrophobic block structure mainly dominated the large part of the PNA chain (Figure ##FIG##7##8f##). It would affect the ion diffusion in the electrochemical process by decreasing the wettability of the electrolyte. The low transition time of 10 and 15 s exhibits the good reversibility. Even after multiple heating/cooling cycles, the battery still possesses the thermal self‐protection function, and the electrochemical performance had no obvious attenuation. The feasibility of the electrochemical performance based on the thermal self‐protection property provides the novel design of the hydrogel electrolyte, such as the molecular structure of the chain skeleton, the functional groups, and the hydrophobic and hydrophilic property for addressing the thermal runaway in the practical application in smart electronic devices.</p>", "<title>Wide Operational Temperature Hydrogel Electrolytes</title>", "<p>Aerospace, high altitude, deep sea and other special environments put forward higher requirements for the working temperature range within the battery.<sup>[</sup>\n##REF##35319992##\n17\n##\n<sup>]</sup> At the low‐temperature, the increase of electrolytes viscosity and the sluggish ion diffusion would decrease the ionic conductivity. At the same time, the low‐temperature environment could lead to the water icing and the separation of the electrode/electrolyte interface, which greatly hinders the ion migration on the electrode interface in a working battery. The electrochemical performance of battery is sharply reduced or even completely cut off at a low‐temperature. In contrast, when the battery was operated at high‐temperature conditions, the electrochemical capacity of the battery could increase at the initial state due to the accelerated ion diffusion. However, the moisture molecule in the electrolyte rapidly evaporates and the electrolyte salts accordingly precipitate with the increasing temperature, which greatly affects the long‐term cycling stability of the battery. In addition, the high temperature also affects the stability between the electrode and electrolyte such as the thermal instability of the electrode structure, which further deteriorate the electrochemical performance of battery.<sup>[</sup>\n##UREF##114##\n154\n##\n<sup>]</sup> Therefore, the design of the battery that could operate at a wide temperature window is desirable for extending their practical application especially at extreme working fields.</p>", "<title>Decrease the Hydrogen Bond in the Aqueous Electrolytes</title>", "<p>The abundant amount of water in the aqueous electrolyte would freeze and not normally work under the sub‐zero temperature situation, causing the poor ionic conductivity and large interface resistance according to the law of thermodynamics. These results decrease the electrochemical performance of the ZIB or even at the out‐of‐work state. To solve the frozen aqueous electrolyte at the low temperature, it is a significant factor to break the hydrogen bonds in the original aqueous electrolyte with abundant water molecules. A series of strategies have been developed to decrease the hydrogen bonds between the water molecules, such as the water‐soluble organic molecule additives in electrolyte, the antifreeze solvent, the high‐concentration electrolyte or hydrogel electrolyte. In addition, the aqueous electrolyte with only a little free water molecule is also desirable for achieving the weak hydrogen bonds and the good ionic conductivity and rational electrochemical performance. For example, an aqueous‐salt hydrates deep eutectic solvent of 3.5 M Mg(ClO<sub>4</sub>)<sub>2</sub> and 1 M Zn(ClO<sub>4</sub>)<sub>2</sub> was fabricated in ZIBs.<sup>[</sup>\n##REF##34625857##\n155\n##\n<sup>]</sup> The synergistic effect of anion and cation in the electrolyte destroyed the hydrogen bond among water molecules by altering the coordination environment of H atom and O atom, displaying an ultra‐low freezing point of −121 °C. Its good ionic conductivity and low viscosity are also ascribed to the pure water solvent, contributing to the rapid ion diffusion and low interface resistance in the charge/discharge process. Apart from the deep eutectic solvent, the modulation of the electrolyte structure by the ZnCl<sub>2</sub> could also reduce the solid‐liquid transition point from 0 to −114 °C, and successfully realized the wide working temperature window from −90 to 60 °C.<sup>[</sup>\n##REF##32901045##\n156\n##\n<sup>]</sup> The solvation configurations of charge carrier (such as Zn<sup>2+</sup>) with the water molecules in the aqueous electrolyte plays an important role in maintaining the stability of the aqueous electrolyte and suppressing them to dissociate into free water. It is desirable for achieving the stable electrolyte at wide working temperature windows and the superior electrochemical performance in an aqueous battery system, especially extending their practical application in various electronic devices in future.</p>", "<title>The Organic Electrolyte or the Mixed Organic/Water Electrolyte</title>", "<p>In addition to changing the electrolyte solute, the non‐aqueous organic solvent instead of the solvent water also achieved a wide operating temperature in ZIBs. A zinc trifluoromethanesulfonate electrolyte dissolved in N, N‐dimethylformamide was successfully developed and it could normally work at a wide temperature range from −70 to 150 °C. The large operation temperature range provides its potential application in extreme scenarios without the consideration of the low energy density in Zn‐organic battery.<sup>[</sup>\n##UREF##115##\n157\n##\n<sup>]</sup> Although the regulation of the concentration of electrolyte salt and the organic electrolyte could broaden the working temperature of the zinc battery and provide the application at the low or high temperature states, the high cost of electrolytes with the water‐in‐salt type and the safety problem of organic problem still limit their wide application, which is a similar problem within the commercial lithium ion battery. It is noted that the weakened hydrogen bonds in aqueous electrolytes are desirable for achieving the wide operation temperature windows without the addition of the organic solvent or the high‐concentration electrolytes in the aqueous zinc battery. As a result, it is significant to decrease the amount of the active water content and increase the coordination interaction with the charge carrier (Zn<sup>2+</sup>) or the salt in the electrolyte, contributing to the higher or lower temperature operation and achieving the smart battery.</p>", "<title>The Development of the Quasi‐Solid Electrolytes</title>", "<p>Low free water content in the quasi‐solid electrolyte also decreases the freezing point, commonly lower than the ice point. The rational design of the hydrogel electrolytes could also broaden the operation temperature window of the ZIBs. A large number of hydrophilic residues of the cross‐linked hydrogel polymer could connect the water molecules (bound water) in the network and decrease the content of the free water in the hydrogel. In general, free water is easy to form regular ice crystals and has a common freezing point (≈0 °C). Bound water could destroy the hydrogen bond among the free water and decrease the freezing point.<sup>[</sup>\n##UREF##94##\n131\n##\n<sup>]</sup> Therefore, the lower free water content in the hydrogel leads to realize a lower ice point and contributes to the ion diffusion under 0 °C, which endows the normal electrochemical process of the battery. In addition, the hydrophobic residues in the polymer chain expand in contact with water and maintain the good mechanical property, which is also desirable for constructing the flexible smart devices at low‐temperature environment. Therefore, the hydrogel electrolytes with the limited existence of free water molecules provide a promising approach to realize wide operating temperature, especially at the low‐temperature operation situation of ZIBs.<sup>[</sup>\n##UREF##116##\n158\n##\n<sup>]</sup> A borax‐crosslinked polyvinyl alcohol/glycerol gel electrolyte (PVA‐B‐G) with good flexibility has been developed to work at −35 °C (<bold>Figure</bold> ##FIG##8##\n9a##).<sup>[</sup>\n##UREF##99##\n136\n##\n<sup>]</sup> Glycerol as the water‐soluble solvent can not only destroy the strong hydrogen bond among free water molecules, but also react with the PVA chain and restrict the formation of the ice crystal in the hydrogel network, leading to a sharp decrease to −60 °C. In addition, with the synergistic effect of the Borax mediated the cross‐linking effect, the co‐crosslinking of glycerol and PVA greatly reduced the interaction among PVA chains and eliminated the formation of crystallization microdomains, which is also conducive to the charge transport. When the test temperature decreased from 25 to −35 °C, the charge transfer resistance only increased from 238 to 453 ohms (Figure ##FIG##8##9b##), which is much better than the increasing 62 times of the pristine state. Therefore, the design of the binary co‐solvent hydrogel could achieve a low freezing point, providing a low‐cost anti‐freezing gel electrolyte for flexible smart power supply.</p>", "<title>The Additives of the External Solutes in the Electrolytes</title>", "<p>Without the additive of the external solvent, electrolyte solutes with a highly hydrated synergistic cationic are efficient for decreasing the content of free water and achieving the anti‐freezing hydrogel electrolyte. For example, the sodium chloride salts could keep the road from freezing on rainy or snowy days under subzero temperatures. The anti‐freezing tolerance of the salts is derived from the ion hydration of concentrated solutions with many ionic compounds, which can decrease the temperature of the ice crystallization in water. Based on the above‐mentioned results, the inorganic salts with small ionic radii and weak coordination of metal ions such as alkali metal salt could weaken the intermolecular hydrogen bonds and extend the working temperature range. For example, apart from the strong hydration ions SO<sub>4</sub>\n<sup>2−</sup> and Zn<sup>2+</sup>, the high hydration number of Li<sup>+</sup> could also significantly weaken the intermolecular hydrogen bonding.<sup>[</sup>\n##UREF##100##\n137\n##\n<sup>]</sup> When the temperature is below 0 °C, the ionic conductivity of polyacrylamide hydrogel with LiCl salt decreased slightly due to the auxiliary hydration of Li<sup>+</sup> (Figure ##FIG##8##9c##). Typical discharge curves were also observed after resting at −20 °C for 24 h. The development of the cooperative hydrated cations is a promising approach to obtain the anti‐freezing hydrogel with good flexible property in achieving the high‐performance zinc battery over a wide working temperature range. The hydrogel electrolyte with its low cost and high safety is desirable for assembling the flexible smart devices in extreme conditions.</p>", "<title>The Multifunctional Electrolytes for the Integrated Devices</title>", "<p>Modulating the structure of electrolyte solvents such as the mixed solvent of the electrolytes is also an important way to realize wide operating temperature ZIBs. The regular formation of ice crystals in water solution is ascribed to the strong hydrogen bonds among free water molecules. When the external soluble organic solvent was added to the aqueous solution, the initial hydrogel bond would be destroyed, and the corresponding ice crystal cannot generate. As a result, the freezing point would decrease to some extent according to the formula of freezing point reduction in the colligative properties of dilute solutions. For example, a binary ethylene glycol (EG)/H<sub>2</sub>O solvent hydrogel electrolyte with ZnCl<sub>2</sub>/NH<sub>4</sub>Cl salts was utilized to realize the ZIB operating from −30 to 80 °C.<sup>[</sup>\n##UREF##32##\n40\n##\n<sup>]</sup> When the hydrogel electrolyte was operated at a high temperature above 40 °C, its high ionic conductivity is attributed to the high evaporation of water in the binary EG/H<sub>2</sub>O solvent, which is much higher than only H<sub>2</sub>O solvent. The good ionic conductivity also affects the electrochemical performance with a wide operating temperature range (worked for more than 60 days at −20 °C) (Figure ##FIG##8##9d##). Even the temperature is 80 °C, the battery could also normally operate for more than 1000 times. Apart from the good ionic conductivity at low temperature, the normal charge/discharge process at high temperature also determinates its wide application. In addition, soluble organic solvents with hydrophilic groups such as ‐OH, ‐COOH, ‐NH<sub>2</sub> could serve as the active sites for adsorbing the water molecule, which weakens the strong interaction among water molecules. It could be beneficial for decreasing the content of free water in an aqueous solution and extending the operating temperature range. As proof of the concept, an anti‐freezing/thermally stable hydrogel electrolyte (ZS/GL/AN) composed of polyacrylamide (PAM), glycerin (EG), acetonitrile (AN), and zinc sulfate was developed.<sup>[</sup>\n##UREF##101##\n138\n##\n<sup>]</sup> The high electron density of oxygen and ammonium in PAM and GL could regulate the Zn<sup>2+</sup> shell structure and destroy the hydrogen bonds among water molecules. Water molecules that form hydrogen bonds with PAM or GL were considered as bound water, which was locked in the hydrogel 3D interpenetrating network. The existence of bound water would destroy the lattice of water molecules and reduce the activity of water by weakening the internal hydrogen bond, which endows the hydrogel electrolyte with wide temperature range stability and successfully realizes the normal operation of ZIBs from −20–60 °C. The integrated hydrogel electrolyte possesses the lower polarization and longer cycle performance (more than 500 h) at low‐temperature or high‐temperature in comparison with ≈50 h in traditional liquid electrolytes. Benefiting from the strong affinity between water and electron‐rich oxygen groups and the large amount of moisture holding in the 3D hydrogel networks, the formation of ice crystals at low temperature and the evaporation of water molecules at high temperature is effectively limited (Figure ##FIG##8##9e,f##). It provides a novel strategy for realizing the normal operation of ZIBs at a wide temperature window and extends its application in the deep space and deep sea. Apart the above‐mentioned strategies to achieve the wide operation temperature, the hydrogel based on the ionic liquid is also the promising candidate for fabricating the smart device at a high working situation due to its high ionic conductivity, non‐evaporation, and thermal stability.<sup>[</sup>\n##REF##34699172##\n159\n##\n<sup>]</sup>\n</p>", "<p>In the development of ZIB with a wide working temperature range, the water content in hydrogels is always inevitably discussed. The lattice structure of water molecules is arranged neatly, which leads to their easy freezing at low‐temperature, complete closure of ion migration channels, and decline or even complete loss the batteries performance. The addition of some electron cloud‐dense groups such as ‐OH, ‐COOH, ‐NH<sub>2</sub> can destroy hydrogen bonds among water molecules and reduce the freezing point of water molecules. For high‐temperature, due to the high saturated vapor pressure of water, the rapid evaporation of water molecules in the hydrogel leads to a sharp increase in salt concentration and even salt precipitation, which seriously hinders the normal migration of Zn<sup>2+</sup>. It is very effective to adjust the saturated vapor pressure of electrolytes by adding some different salts. Tightly locking the water molecules into hydrogels is the primary problem for the realization of wide operating temperature ZIBs.</p>", "<title>The Smart ZIB and the Integrated Application Fields</title>", "<title>The Design Principles for Smart ZIBs Components</title>", "<p>For the active zinc anode, the adaptability and stability of the zinc anode is necessary for achieving the high performance and prolonging the cycling life.<sup>[</sup>\n##UREF##117##\n160\n##\n<sup>]</sup> The inherent ductility and flexibility of the metal zinc, zinc foil, zinc fiber, zinc rod are widely common and utilized in the smart ZIB configuration. The contents of active zinc sites for the reversible deposition and precipitation and the corresponding ductility is a significant role in the assembly of the smart devices. The alloying mixed zinc metal is beneficial for uniform deposition of active zinc ion on the mixed zinc surface by providing abundant zinc nucleation sites for zinc deposition in charge/discharge process. For example, the zincophilic noble metals such as Ag or Au are introduced into the zinc metal and serve as the nucleation sites for inducing the uniform distribution of the metal zinc ion. In addition, the conductive substrate as the zinc host possesses the large surface area and the interworking conductive network structure is also beneficial for the flexible battery, such as the fabrication of the porous zinc, zinc sponge, zinc layer (<bold>Figure</bold> ##FIG##9##\n10a##).<sup>[</sup>\n##UREF##118##\n161\n##, ##UREF##119##\n162\n##\n<sup>]</sup> The large specific surface area enables the uniform charge distribution and contributes to the oriented deposition on the conductive framework such as the Cu substrate, graphene, porous activated carbon. The formation of the compact zinc particle layer could further effectively suppress the formation of zinc dendrites. Besides, the mixed zinc anode could increase the nucleation barrier and limit the 2D diffusion of Zn<sup>2+</sup> and promote the uniform deposition of Zn<sup>2+</sup>. The mixed zinc anode could avoid the direct contact with the aqueous electrolyte, which greatly decreases the hydrogen gas production during the electrochemical process, and reduces the side effects on the bare zinc metal anode. The mixed zinc anode can not only endow the battery with the reversible redox reaction process, but also decrease the side reaction on the metal zinc surface in the electrochemical process.</p>", "<p>For the cathode materials, the additional functionality of cathode materials is considered to simplify the configuration in the smart integrated battery devices apart from the normal zinc ion storage.<sup>[</sup>\n##UREF##120##\n163\n##\n<sup>]</sup> It requires the development of the cathode composites through the various physical recombination or chemical synthesis. For example, the selection of cathode materials with the functional integration of the air‐charging, the photo‐sensitive, or the self‐charging property is also taken into consideration apart from the zinc ion storage. The content of the inactive material in the cathode is reduced as much as possible on the basis of meeting these intelligences integrations.<sup>[</sup>\n##UREF##121##\n164\n##\n<sup>]</sup> In addition, the corresponding electrochemical performance of the cathode materials and the energy density of the smart devices cannot be at the cost of the functional integration in the devices because of the cathode as the energy carrier. Therefore, the balance of the capacity, cycling life, and the energy density of the smart battery is the cardinal principle.</p>", "<p>For the electrolytes in smart integrated devices, the quasi‐solid or solid state electrolytes with the low free‐water content play a key role in improving the mechanical performance of intelligent integrated devices, especially in the flexible devices at special working condition or some extreme situation (self‐protection, self‐healing, and environmental compatibility).<sup>[</sup>\n##UREF##122##\n165\n##\n<sup>]</sup> For the integrated battery, the selection of the polymer chain, functional groups, and the hydrophilic property as well as the water contents can interact with Zn<sup>2+</sup> through the electrostatic interaction to regulate Zn<sup>2+</sup> deposition. Moreover, the hierarchical porous frameworks of hydrogels also provide the uniform, stable, and rapid transfer pathway for electrolyte ions. The outstanding mechanical properties and adhesive effects of hydrogel materials could effectively restrict growth of the zinc dendrites on the interface of the metal zinc anode, but also contribute to the realization of flexible and integrated devices in the intelligentization process of ZIBs. The external additives in the electrolytes are also desirable for achieving the stimulus‐responsive hydrogel electrolytes of the smart battery devices. Besides, the oxygen content, the moisture content, as well as the air atmosphere in the electrolytes are also the critically influencing factors in affecting electrochemical performance and the cycling life in repeated charge/discharge process of the smart ZIB as well as their utilization fields.</p>", "<p>For the assembly structure of the smart integrated devices, the simple assembly method, stable energy output and collection, and the high integration of various functional units are the three important designing principles in the smart ZIBs.<sup>[</sup>\n##REF##30395434##\n166\n##\n<sup>]</sup> Planar‐type battery and the flexible battery are the common energy supplying in the smart device structure and they are applicable to the various application scenarios according to the different requirements (Figure ##FIG##9##10b##). 1) As the representative of the planar device, the sandwich‐type battery is a simple preparation approach through the layer‐by‐layer stacking model.<sup>[</sup>\n##UREF##123##\n167\n##\n<sup>]</sup> Among which, the interfacial contact is the main challenge for realizing the fast charge transfer and the ion diffusion in the electrochemical process. The good interfacial contact contributes to the reversibly chemical redox reaction and promotes the utilization of the active materials for the high performance and good cycling stability. In addition, the interdigital electrode structure of the battery is desirable to promise the integration of the micro‐battery in the portable devices or the small‐area chip and realize the large‐area functional integration in the smart zinc battery. 2) For the flexible electronic devices, the development of the fibrous and the soft pack batteries is necessary due to its good mechanical stability and compatibility under the external forces such as the different bending or folding states (Figure ##FIG##9##10c##).<sup>[</sup>\n##UREF##124##\n168\n##\n<sup>]</sup> Moreover, their large volumetric density, good stretchability, and wearability are beneficial for the wearable electronics with the display function, pressure sensing, or the energy harvesting property.</p>", "<title>The Self‐Powered Battery with the Energy Harvesting</title>", "<p>The green and sustainable energy supply in electronic devices is a prerequisite to ensure the charging/discharging process at the normal state and special state of the equipment.<sup>[</sup>\n##UREF##125##\n169\n##, ##UREF##126##\n170\n##, ##UREF##127##\n171\n##\n<sup>]</sup> Self‐charging via the air or the solar is the common strategy to achieve the self‐powered devices.<sup>[</sup>\n##UREF##128##\n172\n##, ##UREF##129##\n173\n##, ##UREF##130##\n174\n##, ##UREF##131##\n175\n##, ##REF##37000876##\n176\n##, ##UREF##132##\n177\n##\n<sup>]</sup> For the efficient utilization of a single self‐charging device type in consideration of the energy saving field, the property of self‐charging in active electrode is attractive in aqueous ZIB, which also determinates the electrochemical performance of the working battery. Therefore, based on the afore‐mentioned self‐charging mechanism, the rational design of the active electrodes is conducive to the energy harvesting for promoting the self‐powered battery system. 1) It is desirable for improving the electrochemical performance by optimizing the micro‐morphology and the electronic structure of the cathode materials. As shown in Figure ##FIG##9##10d##, the design of the controlled defects in the vanadium oxides could contribute to the reversible utilization in the charge/discharge process, especially at a low current density.<sup>[</sup>\n##UREF##133##\n178\n##, ##REF##32392033##\n179\n##, ##UREF##134##\n180\n##\n<sup>]</sup> The optimization of the active cathode materials plays an important role in achieving the self‐charging battery system and maintaining the good performance in the long‐term cycle process. 2) To decrease the manufacturing cost and the external energy consumption, the multifunctional cathode materials will also play an important role in the complex energy supply system. For example, the energy storage device is integrated with the smart electrochromic characteristic via a simple approach, extending the application of the energy supply field.<sup>[[</sup>\n##UREF##135##\n181\n##, ##REF##25247385##\n182\n##\n<sup>]</sup> The response of the color change at different voltage plateaus could serve as a detector for the real‐time capacity display, which delivers the good response to the external environment changes. It is also a significant response parameter to detect the energy harvesting and supply in a working electronic device.<sup>[</sup>\n##UREF##67##\n96\n##, ##REF##29399689##\n183\n##\n<sup>]</sup> To obtain the smart ZIB with the sustainable energy harvesting property is also attractive in practical applications and the corresponding design of the active electrodes or the smart packages also promotes the production landing in future.</p>", "<title>The Environmental Self‐Adaptation Battery with the Flexibility</title>", "<p>The environmental self‐adaptions refer to the ability of the battery to achieve all the intended performance and function without being destroyed under the effect of the comprehensive environmental factors at a working state (such as at the state of the energy supply in the discharging process).<sup>[</sup>\n##UREF##136##\n184\n##, ##REF##28112894##\n185\n##, ##UREF##137##\n186\n##\n<sup>]</sup> With the development of the wearable electronic devices such as the smart electronic skin, the wearable electronic display clothing, or the flexible electronic equipment terminal, the corresponding self‐adaption energy supply (battery system) is also derived.<sup>[</sup>\n##REF##26691661##\n187\n##, ##REF##25842997##\n188\n##, ##UREF##138##\n189\n##, ##UREF##139##\n190\n##\n<sup>]</sup> The external changes including the temperature, force, or the light would determinates the electrochemical performance. The concrete embodiment of the battery's ability is to adapt to the environment.</p>", "<p>The flexible and wearable battery with high security and stability could extend their practical application. 1) The design of the smart electrodes is based on the environmental response. The timely self‐regulation under the changes of the external environment is in great demand of the smart battery. For example, the high temperature working situation usually appears in summer or some special area. Based on the thermal response requirement, the smart ZIB with the functional electrolyte has been fabricated.<sup>[</sup>\n##UREF##140##\n191\n##\n<sup>]</sup> Within the rational temperature working window, the battery could provide the theoretical capacity. When the external surrounding exceeds the temperature window, the capacity of battery decreases, or the battery is not working with the failure (Figure ##FIG##9##10e##). The concept is also widely utilized in the design of the battery module. However, the separate detector and the battery could not achieve the fast response at the critical situation, which would result in a lot of financial damage. Therefore, the smart battery with the response ability is desirable in future. 2) The assembly of the wearable battery for adapting the external force change. The bulk and rigid coin‐type battery in mobile phones or battery modules in the electric car is common in our daylily life.<sup>[</sup>\n##UREF##141##\n192\n##\n<sup>]</sup> However, the poor mechanical deformation is not suitable for the wearable electronic or smart clothes. The hydrogel electrolyte as the flexible carrier with low water content, relative ionic conductivity, and the reversibly chemical interface between electrode and electrolyte has attracted increasing attention, especially for the wearable devices with good flexibility (Figure ##FIG##9##10f##). Based on the hydrogel electrolyte, the assembled battery could normally work under the suitable mechanical strength such as the bending, twisting, or even folded states. In addition, the certain adhesion of the hydrogel electrolyte with flexibility also contributes to promoting the integrating degree, avoiding the active electrode separation or battery failure derived from the external force. Therefore, to extend the practical application in the wearable electronics with the environmental self‐adaptation, the smart battery based on the functional hydrogel electrolyte is the key factor. The self‐adaptation property of the hydrogel should possess the good ionic conductivity, crush resistance, anti‐high and low temperature as well as the high water conservation.</p>", "<title>The Integrated System Based on Smart Zinc Battery</title>", "<p>As the energy supply system, the next generation of the intelligent electronic devices plays a significant role in energy storage and conversion, which also presents demands for the convenient energy supply methods and highly integrated device structures. The widely reported integration systems include the energy supplying and energy harvesting fields in the smart ZIB. However, the traditional device integration is on the basis of the indirect connection with the external power supply.<sup>[</sup>\n##UREF##93##\n130\n##, ##UREF##121##\n164\n##\n<sup>]</sup> The discontinuous external power grid supply is an inconvenient and complicated process for realizing the stability of the integrated intelligent battery system.<sup>[</sup>\n##UREF##142##\n193\n##\n<sup>]</sup> This phenomenon will be exacerbated in the emerging micro‐integrated systems and the wearable devices. The simple assembly method, the stable energy output and collection, and the high integration of various functional units are the three important designing principles in the smart ZIB. Based on the above‐mentioned designing principles, the assembled smart battery will contribute to achieving the convenience, compatibility, and efficiency during the energy supplying process and further improving the user experience.\n<list list-type=\"order\" id=\"advs6727-list-0002\"><list-item><p>As the energy supplying system, the integration of the smart ZIBs with various sensor parts effectively solve the discontinuous supply of external power.<sup>[</sup>\n##REF##36047718##\n194\n##, ##UREF##143##\n195\n##\n<sup>]</sup> More importantly, the integrated self‐power sensors could also avoid the short comings of the multi‐device integration, such as the multi‐step process, compatibility and interface stability. The high‐efficiency energy supplying is also desirable for the multi‐functional electronic devices.<sup>[</sup>\n##REF##30507152##\n196\n##\n<sup>]</sup> The integration of the ZIB and sensor unit within a single device possesses both sensing and energy storage and supplying is a new strategy for realizing next‐generation miniature integrated devices with superior miniaturization, flexibility and durability (Figure ##FIG##9##10g##). To achieve the miniaturization and high integration of electronic devices, the following challenges and solutions of the integrated smart ZIB should be also taken into consideration.<sup>[</sup>\n##UREF##144##\n197\n##\n<sup>]</sup> a) The electrochemical stability and compatibility as well as the cost of the micro‐battery are necessary for the long‐term cycling life. b) The Young's modulus is an important parameter to evaluate the commercialization of the flexible ZIBs. c) The toxicity, degradability and renewable value of the integrated devices (sensor) are also considered.</p></list-item><list-item><p>As the energy harvesting system, the integration of the smart ZIB with the photo‐rechargeable system (solar battery) or the friction power generation system (triboelectric nanogenerator) could realize the reversible energy storage and conversion.<sup>[</sup>\n##UREF##145##\n198\n##, ##UREF##146##\n199\n##\n<sup>]</sup> The effective integration could significantly reduce the inner volume space and the weight of the wearable electronics, which is also beneficial for the utilization and portability.<sup>[</sup>\n##UREF##144##\n197\n##\n<sup>]</sup> It is also the direct strategy to achieve the collection of discontinuous resources, and provide the continuous energy supplying in the integrated system for electronic devices in future. The connection between the ZIB and the solar cells is activated by the simple push‐button switch within the integrated system. The collected luminous energy is utilized to charge the ZIB and obtain the passive self‐charging device (Figure ##FIG##9##10h##). In addition, the electrostatic energy generated by the friction could also be converted into the electric energy, which provides a green and sustainable power supply. The combination of micro‐battery and the mechanical energy (such as the triboelectric nanogenerator) serves as the main body of the energy supply and promises the normal working of the microelectronic device. However, there are several issues to be solved in the integrated energy harvesting systems in the practical application. a) The matching of voltage and current of integrated devices determines the energy density and service life in energy harvesting systems. b) The recycling and secondary utilization of the smart ZIB and the mechanical devices in the integrated system are also taken into consideration, especially for the large‐scale application of the wearable electronic devices. c) The new packaging technology such as the 3D printing approach also plays an important role in solving the interfacial contact and the fabrication and design of the microstructure electrode.</p></list-item><list-item><p>The intelligent management based on the smart battery. The release of heat from battery module maybe result in the failure of the battery supply. Moreover, the large heat release in a short lead to the explosion in a limited space. Therefore, the good sensitivity of the smart battery with thermal response could avoid or decrease the insecurity derived from the thermal runaway.<sup>[</sup>\n##UREF##147##\n200\n##\n<sup>]</sup> Apart from the thermal response, the force response or the photo response of the smart battery is also desirable in the detection system of intelligent devices in future.</p></list-item></list>\n</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>" ]
[ "<title>Acknowledgements</title>", "<p>This work was financially supported by the National Natural Science Foundation of China (52202118, 52373315), the Henan Science and Technology Department (222301420004), the Nature Science Foundation of Henan Province (222300420286), the China Postdoctoral Science Foundation (XJ2022024, 2020TQ0275), and Youth top program and Postdoctoral science foundation of Zhengzhou University.</p>", "<p>\n<bold>Xiaosheng Zhang</bold> is currently a graduate student at the School of Materials Science and Engineering, Zhengzhou Key Laboratory of Flexible Electronic Materials and Thin‐Film Technologies, Zhengzhou University. His main research interest focus on the design and synthesis of new aqueous electrolyte and their applications in energy storage devices.</p>", "<p>\n<bold>Linlin Zhang</bold> is an Associate Professor at Zhengzhou University. She received her Ph.D. degree from Nankai University (the Key Laboratory of Advanced Energy Material Chemistry) in 2019, then continue her study at HongKong University of Science and Technology through the “Hong Kong Scholar”. Her research interest focus on high‐performance energy storage devices including the nano‐materials chemistry, wearable electronics, and novel battery system.</p>", "<p>\n<bold>Xuying Liu</bold> is currently working as a Full Professor at the Zhengzhou University. In 2014, he obtained his Ph.D. at the Tokyo lnstitute of Technology, then moved to be an ICYS Researcher at the National Institute for Materials Science to continue his study on flexible printed electronics. His research interests include printed flexible organic thin‐film transistors, printed flexible sensors and actuators.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0001\"><label>Figure 1</label><caption><p>The brief development of the smart ZIBs. From left to right: Reproduced with permission.<sup>[</sup>\n##UREF##26##\n34\n##\n<sup>]</sup> Copyright 2018, Elsevier. Reproduced with permission.<sup>[</sup>\n##UREF##27##\n35\n##\n<sup>]</sup> Copyright 2018, Royal Society of Chemistry. Reproduced with permission.<sup>[</sup>\n##UREF##28##\n36\n##\n<sup>]</sup> Copyright 2019, Wiley‐VCH. Reproduced with permission.<sup>[</sup>\n##UREF##29##\n37\n##\n<sup>]</sup> Copyright 2019, Royal Society of Chemistry. Reproduced with permission.<sup>[</sup>\n##REF##32366904##\n31\n##\n<sup>]</sup> Copyright 2020, Springer Nature. Reproduced with permission.<sup>[</sup>\n##UREF##30##\n38\n##\n<sup>]</sup> Copyright 2020, Wiley‐VCH. Reproduced with permission.<sup>[</sup>\n##UREF##31##\n39\n##\n<sup>]</sup> Copyright 2020, Royal Society of Chemistry. Reproduced with permission.<sup>[</sup>\n##UREF##32##\n40\n##\n<sup>]</sup> Copyright 2021, American Chemical Society.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0002\"><label>Figure 2</label><caption><p>Application scenarios of self‐charging ZIBs. Reproduced with permission.<sup>[</sup>\n##UREF##31##\n39\n##\n<sup>]</sup> Copyright 2020, Royal Society of Chemistry. Reproduced with permission.<sup>[</sup>\n##UREF##36##\n44\n##\n<sup>]</sup> Copyright 2021, Royal Society of Chemistry. Reproduced with permission.<sup>[</sup>\n##UREF##37##\n45\n##\n<sup>]</sup> Reproduced with permission.<sup>[</sup>\n##UREF##38##\n46\n##\n<sup>]</sup> Copyright 2021, Wiley‐VCH.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0003\"><label>Figure 3</label><caption><p>The stimulus‐responsive materials correspond to the external experimental changes including the voltage, force, light, temperature, pH, and magnetism.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0004\"><label>Figure 4</label><caption><p>Principle and applications of the electrochromic materials such as the smart window, energy storage device, biosensor, and electrochromic display. From left to right: Boeing aircraft produced by SmartTintW. Reproduced with permission.<sup>[</sup>\n##REF##27404116##\n56\n##\n<sup>]</sup> Copyright 2016, American Chemical Society. Reproduced with permission.<sup>[</sup>\n##REF##33492928##\n57\n##\n<sup>]</sup> Copyright 2021, American Chemical Society. Reproduced with permission.<sup>[</sup>\n##REF##35980039##\n55\n##\n<sup>]</sup> Copyright 2022, American Chemical Society.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0005\"><label>Figure 5</label><caption><p>Self‐healing materials based on the physical/chemical reaction mechanisms, including the covalent bonding, hydrogen bonding, metal‐ligand coordination, electrostatic interaction, host‐guest interaction, and ion‐dipole interaction.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0006\"><label>Figure 6</label><caption><p>Self‐charging ZIBs. a) Working mechanism of chemically self‐charging ZIBs during a chemical charging process. Reproduced with permission.<sup>[</sup>\n##REF##32366904##\n31\n##\n<sup>]</sup> Copyright 2020, Springer Nature. b) Galvanostatic discharging profiles of the ssZIBs at 0.2 A g<sup>−1</sup> after the oxidation of the VO<sub>2</sub> cathode for different times. Reproduced with permission.<sup>[</sup>\n##UREF##63##\n89\n##\n<sup>]</sup> Copyright 2021, Wiley‐VCH. c) Schematic to the VCF/Zn battery fiber during an air‐recharging process. Reproduced with permission.<sup>[</sup>\n##UREF##36##\n44\n##\n<sup>]</sup> Copyright 2021, Royal Society of Chemistry. d) Self‐charging schematic diagram of poly(1,5‐NAPD)//Zn cell. Reproduced with permission.<sup>[</sup>\n##REF##34491047##\n90\n##\n<sup>]</sup> Copyright 2021, American Chemical Society. e) Proposed redox process at the cathode for different charging modes. Reproduced with permission.<sup>[</sup>\n##UREF##38##\n46\n##\n<sup>]</sup> Copyright 2021, Wiley‐VCH. f) Schematic illustration of the proposed photocharging mechanism of VO<sub>2</sub>‐rGO photo‐ZIBs. Reproduced with permission.<sup>[</sup>\n##UREF##64##\n92\n##\n<sup>]</sup> Copyright 2021, Wiley‐VCH. g) Schematic illustration of the LTSs preparation process. Reproduced with permission.<sup>[</sup>\n##UREF##37##\n45\n##\n<sup>]</sup> Copyright 2023, Wiley‐VCH.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0007\"><label>Figure 7</label><caption><p>The electrochromic materials in ZIBs. a) Photographs of a 5 × 5 cm<sup>2</sup> MTWO cathode before and after self‐coloring. b) In situ self‐coloring (discharge) process of the MTWO cathode. a and b) Reproduced with permission.<sup>[[</sup>\n##UREF##74##\n108\n##\n<sup>]</sup> Copyright 2019, Wiley‐VCH. c) Optical images of i) conventional and ii) colorful electrochromic electrodes at different voltages (vs. Zn<sup>2+</sup>/Zn). Reproduced with permission.<sup>[</sup>\n##UREF##75##\n109\n##\n<sup>]</sup> Copyright 2021, Wiley‐VCH. d) Molecular structure and electrochromic effect of self‐doped polyaniline in different oxidation states. Reproduced with permission.<sup>[</sup>\n##UREF##76##\n110\n##\n<sup>]</sup> Copyright 2020, Royal Society of Chemistry. e) The functionalities of the electrochromic battery display were demonstrated with digital photographs. Reproduced with permission.<sup>[</sup>\n##UREF##77##\n111\n##\n<sup>]</sup> Copyright 2019, Wiley‐VCH.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0008\"><label>Figure 8</label><caption><p>The smart hydrogel electrolytes in ZIBs. a) Self‐healing hydrogel electrolyte. Reproduced with permission.<sup>[</sup>\n##UREF##95##\n132\n##\n<sup>]</sup> Copyright 2020, Wiley‐VCH. b) Self‐healing integrated all‐in‐one ZIBs. Reproduced with permission.<sup>[</sup>\n##UREF##28##\n36\n##\n<sup>]</sup> Copyright 2019, Wiley‐VCH. c) Illustration of the self‐protection ZIABs. Reproduced with permission.<sup>[</sup>\n##UREF##30##\n38\n##\n<sup>]</sup> Copyright 2020, Wiley‐VCH d) Working principle of the thermal self‐protective ZIBs based on hygroscopic hydrogel electrolyte. Reproduced with permission.<sup>[</sup>\n##UREF##113##\n153\n##\n<sup>]</sup> Copyright 2020, Wiley‐VCH. e) The thermal‐responsive reversibility of the aqueous ZIBs. Reproduced with permission.<sup>[</sup>\n##UREF##112##\n152\n##\n<sup>]</sup> Copyright 2020, Wiley‐VCH. f) Mechanism of the reversible sol‐gel transition of PNA copolymer. Reproduced with permission. Copyright 2018, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0009\"><label>Figure 9</label><caption><p>Wide operational temperature hydrogels in ZIBs. a) Photographs of PVA/G and PVA‐B‐G at 25 °C and ‐35 °C under twisting, bending, and folding states. b) Nyquist plots of PVA‐B‐G battery. a and b) Reproduced with permission.<sup>[</sup>\n##UREF##99##\n136\n##\n<sup>]</sup> Copyright 2020, Royal Society of Chemistry. c) Variation in conductivity with and without LiCl. Reproduced with permission.<sup>[</sup>\n##UREF##100##\n137\n##\n<sup>]</sup> Copyright 2019, Wiley‐VCH. d) Optical and infrared thermal imaging photos of the timer driven by the OHE‐based battery at ≈80 and −30 °C. Reproduced with permission.<sup>[</sup>\n##UREF##32##\n40\n##\n<sup>]</sup> Copyright 2021, American Chemical Society. e) Photos of hydrogels at different temperatures. f) The weight retention of hydrogels at 60 °C. e and f) Reproduced with permission.<sup>[</sup>\n##UREF##101##\n138\n##\n<sup>]</sup> Copyright 2022, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6727-fig-0010\"><label>Figure 10</label><caption><p>The design principles of smart ZIBs and their integrated application fields. a) 3D volume‐rendered X‐ray tomogram of zinc sponges of different densities. Reproduced with permission.<sup>[</sup>\n##UREF##148##\n201\n##\n<sup>]</sup> Copyright 2019, American Chemical Society. b) Flexible smart wristband integrated from two ZIB modules and a flexible pressure sensor. Reproduced with permission.<sup>[</sup>\n##REF##30507152##\n196\n##\n<sup>]</sup> Copyright 2018, American Chemical Society. c) Demonstration of the preparation process of the multifunctional battery fiber. Reproduced with permission.<sup>[</sup>\n##REF##36047718##\n194\n##\n<sup>]</sup> Copyright 2022, American Chemical Society. d) Schematic images of the defective crystal with efficient ion transports. Reproduced with permission.<sup>[</sup>\n##UREF##149##\n202\n##\n<sup>]</sup> Copyright 2020, Elsevier. e) Schematic illustration of smart ZIBs with thermal‐gated PNIPAM/AM electrolytes. Reproduced with permission.<sup>[</sup>\n##UREF##112##\n152\n##\n<sup>]</sup> Copyright 2020, Wiley‐VCH. f) Schematic of the aqueous ZIB fiber with air‐recharging capability integrated into multifunctional wearable systems. Reproduced with permission.<sup>[</sup>\n##UREF##36##\n44\n##\n<sup>]</sup> Copyright 2021, Royal Society of Chemistry. g) Device design and principle of the integrated multifunctional devices strategy.<sup>[</sup>\n##UREF##144##\n197\n##\n<sup>]</sup> Reproduced with permission. Copyright 2022, Wiley‐VCH. h) Schematics of the device configuration of the integrated flexible photo‐rechargeable system. Reproduced with permission.<sup>[</sup>\n##UREF##150##\n203\n##\n<sup>]</sup> Copyright 2022, Elsevier.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6727-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Comparison of properties of different alkali metals and multivalent metal ion batteries.<sup>[</sup>\n##UREF##151##\n204\n##, ##UREF##152##\n205\n##, ##UREF##153##\n206\n##\n<sup>]</sup>\n</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>Metal‐ion</p>\n<p>Battery</p>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ionicradius[Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cost of metal anode [USD kg<sup>−1</sup>]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Charge density [C mm<sup>−3</sup>]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>Theoretical volume specific capacity</p>\n<p>[mAh cm<sup>−3</sup>]</p>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>Electrolyte</p>\n<p>Type</p>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>Ionic conductivity</p>\n<p>[S cm<sup>−1</sup>]</p>\n</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Zn</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">112</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5854</td><td rowspan=\"3\" align=\"center\" colspan=\"1\">\n<p>aqueous</p>\n<p>electrolytes</p>\n</td><td rowspan=\"3\" align=\"center\" colspan=\"1\">≈1‐10</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mg</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.72</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">120</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3834</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Al</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.53</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">364</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8046</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Li</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.76</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">19.2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">52</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2061</td><td rowspan=\"3\" align=\"center\" colspan=\"1\">organic electrolytes</td><td rowspan=\"3\" align=\"center\" colspan=\"1\">≈10<sup>−3</sup>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Na</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.02</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1129</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">K</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.38</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">13.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">610</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6727-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Summary of strategies and the electrochemical performance of ZIBs based on the hydrogel electrolytes with self‐healing function and temperature window.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Hydrogel electrolyte</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cathode</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>Capacity</p>\n<p>(mAh g<sup>−1</sup>)</p>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Capacity retention</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Self‐healing principle</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Healing time</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Working window</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ref.</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PSBMA/ZnSO<sub>4</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>MnO<sub>2</sub>@</p>\n<p>CNT</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>≈225.0</p>\n<p>(1.5 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>600 cycles</p>\n<p>(1.5 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">electrostatic interaction</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24 h</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−20–25 <sup>o</sup>C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##95##132##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>Zn(CF<sub>3</sub>SO<sub>3</sub>)<sub>2</sub>/</p>\n<p>chitosan</p>\n<p>/PAAM</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">PANI</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>≈210.0</p>\n<p>(1.0 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">94.6% after 2000 cycles (3 A g<sup>−1</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">reversible coordination and hydrogen bond</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##96##133##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>Cellulose/TEOS/</p>\n<p>glycerol/ZnSO<sub>4</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">MnO<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>277.3</p>\n<p>(0.2 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">99.2% after 2000 cycles (3 A g<sup>−1</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">hydrogen bond and Si─O─Si bond</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2 h</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−40–60 <sup>o</sup>C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##97##134##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PVA/Zn(CF<sub>3</sub>SO<sub>3</sub>)<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">PANI@ SWCNT</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>123.0</p>\n<p>(0.1 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">97.1% after 1000 cycles (1 A g<sup>−1</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">hydrogen bond</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.5 h</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##28##36##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>PVA/Zn(CH<sub>3</sub>COO)<sub>2</sub>/</p>\n<p>Mn(CH<sub>3</sub>COO)<sub>2</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">VS<sub>2</sub>/CC</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>175.0</p>\n<p>(0.2 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">70.3% after 40 cycles (0.2 A g<sup>−1</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">hydrogen bond</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.5 h</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##98##135##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>PVA/borax/glycerol/</p>\n<p>ZnSO<sub>4</sub>/MnSO<sub>4</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>rGO/</p>\n<p>MnO<sub>2</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>242.5</p>\n<p>(0.5 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">93.7% after 2000 cycles (1 A g<sup>−1</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−35–25 °C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##99##136##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PAAM/ZnSO<sub>4</sub>/LiCl</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiFePO<sub>4</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>106.0</p>\n<p>(0.1 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100.0% after 500 cycles (0.5 A g<sup>−1</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−20–25 °C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##100##137##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>PAMPS/PAAm/</p>\n<p>ZnCl<sub>2</sub>/NH<sub>4</sub>Cl/EG</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">PANI</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>207.7</p>\n<p>(0.2 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">81.5% after 4000 cycles (5 A g<sup>−1</sup>)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−30–80 °C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##32##40##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>PAM/glycerol/AN/</p>\n<p>ZnSO<sub>4</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">V<sub>2</sub>O<sub>5</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>185.0</p>\n<p>(5 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>88.0% after 10000 cycles</p>\n<p>(5 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−20–60 °C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##101##138##]</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6727-tbl-0003\" content-type=\"Table\"><label>Table 3</label><caption><p>Summary of the strategies and electrochemical performance of ZIBs based on the hydrogel electrolytes with self‐protection function.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Hydrogel electrolyte</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cathode</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Capacity [mAh g<sup>−1</sup>]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Capacity retention</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Self‐protection principle</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Switch off time</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ref.</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>poly(2‐vinylpyridine)</p>\n<p>/ZnSO<sub>4</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>iodine/</p>\n<p>Ndoped‐carbon</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>193.0</p>\n<p>(0.14 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">85.0% after 250 cycles at 0.3 A g<sup>−1</sup>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>pH‐responsive electrolyte based on de‐protonation</p>\n<p>of quaternary pyridinic groups</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30 s</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##30##38##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>PNIPAM/AM/</p>\n<p>Zn(CF<sub>3</sub>SO<sub>3</sub>)<sub>2</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">PANI</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>168.7</p>\n<p>(0.1 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">thermal‐responsive hydrogel based on pore structure evolution</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">/</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##112##152##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PAAm/ZnCl<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">MnO<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>≈370.0</p>\n<p>(2 mA cm<sup>−2</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈100.0% after 500 cycles at 10 mA cm<sup>−2</sup>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">zinc chloride‐enriched hygroscopic hydrogel electrolyte</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈1 h</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##113##153##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<p>PNA/ZnSO<sub>4</sub>/</p>\n<p>MnSO<sub>4</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>MnO<sub>2</sub>/</p>\n<p>CNT</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>145.0</p>\n<p>(0.1 A g<sup>−1</sup>)</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈100.0% after 500 cycles at 0.5 A g<sup>−1</sup>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Thermo‐responsive polymer based on sol‐gel transition</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;15 s</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##26##34##]</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
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{ "acronym": [], "definition": [] }
206
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 10; 11(2):2305201
oa_package/2f/a0/PMC10787087.tar.gz
PMC10787088
37987032
[ "<title>Introduction</title>", "<p>Ribosomally synthesized and post‐translationally modified peptides (RiPPs) are a rapidly expanding class of natural products.<sup>[</sup>\n##REF##23165928##\n1\n##\n<sup>]</sup> RiPPs exhibit a unique biosynthetic pathway that involves genetically encoded precursor peptides and enzymes, with the latter installing diverse post‐translational modifications (PTMs) on the precursor peptides. The precursor peptides typically have two modules: the leader and core regions, which are recognized and modified by PTM enzymes, respectively. This biosynthetic simplicity and modularity, and thereby high evolvability, underlies not only the structural and functional diversity of RiPPs but also the high potential for engineering novel functional biomolecules.</p>", "<p>The hallmark of RiPP diversity is the distinct PTMs and associated biosynthetic pathways, which individually define the subclasses of RiPPs. The number of RiPP subclasses has increased from 23 in 2013<sup>[</sup>\n##REF##23165928##\n1a\n##\n<sup>]</sup> to 41 in 2021,<sup>[</sup>\n##REF##23165928##\n1b\n##\n<sup>]</sup> highlighting the recent expansion of the RiPP diversity, which is likely to continue in the near future. Discovery of new RiPP subclasses has traditionally relied on fortuitous isolation by activity‐based screening.<sup>[</sup>\n##REF##23165928##\n1a\n##\n<sup>]</sup> While the explosion of genome sequence data and development of genome mining tools have allowed the identification of a large number of putative biosynthetic gene clusters (BGCs) for RiPPs,<sup>[</sup>\n##REF##32637669##\n2\n##\n<sup>]</sup> these methods are generally inefficient at uncovering novel RiPP subclasses; unlike nonribosomal peptide synthetases (NRPSs), RiPP biosynthetic enzymes lack common features across all RiPP subclasses, and therefore, the typical genome mining approach based on homology of biosynthetic enzymes is mostly limited to the expansion of known or closely related RiPP subclasses.</p>", "<p>Dissecting phylogenetically distinct orphan BGCs has proven effective for revealing novel PTMs and RiPP‐associated pathways, exemplified by recent discoveries of spliceotides,<sup>[</sup>\n##REF##29449488##\n3\n##\n<sup>]</sup> ranthipeptides,<sup>[</sup>\n##REF##31059252##\n4\n##\n<sup>]</sup> streptides,<sup>[</sup>\n##REF##30398325##\n5\n##\n<sup>]</sup> pearlins,<sup>[</sup>\n##REF##31320540##\n6\n##\n<sup>]</sup> and triceptides.<sup>[</sup>\n##REF##32807886##\n7\n##\n<sup>]</sup> However, this approach depends on the functional divergence of enzymes known for other class‐defining PTMs and has particularly been successful with an enzyme family with versatile activities, radical <italic toggle=\"yes\">S</italic>‐adenosylmethionine (rSAM) enzymes.<sup>[</sup>\n##REF##28895719##\n8\n##\n<sup>]</sup> Furthermore, it is often challenging to find candidate BGCs that significantly diverge from those responsible for known PTMs. To bypass the requirement for homologous biosynthetic enzymes, a marker‐independent strategy called decRiPPter has recently emerged.<sup>[</sup>\n##REF##33351797##\n9\n##\n<sup>]</sup> This method uncovered a new subfamily of lanthipeptides, but it may be biased on the characteristics of known RiPP precursors and requires further exploration to unveil novel PTMs. Overall, new strategies are needed to systematically uncover the unexplored chemical and biosynthetic space associated with RiPPs.</p>", "<p>Here, using homologs of protein L‐(iso)aspartyl <italic toggle=\"yes\">O</italic>‐methyltransferases (PIMTs), we demonstrate that the genome mining of a secondary modification enzyme can promote the identification of a novel RiPP subclass. PIMTs, also known as L‐isoaspartyl protein carboxyl methyltransferases (PCMs), were originally discovered as repair enzymes for damaged proteins. They catalyze the conversion of isoaspartate (isoAsp), which is spontaneously formed from an Asp or Asn residue, to Asp (<bold>Figure</bold>\n##FIG##0##\n1a##).<sup>[</sup>\n##REF##3472227##\n10\n##\n<sup>]</sup> Recently, PIMT homologs were found in BGCs of several RiPP subclasses, including lanthipeptides, lasso peptides, and graspetides, where they install secondary modifications on conserved Asp residues.<sup>[</sup>\n##REF##31568727##\n11\n##\n<sup>]</sup> This results in the formation of an aspartimide or isoAsp, the former of which can be spontaneously hydrolyzed to the latter or Asp (Figure ##FIG##0##1##).</p>", "<p>We have expanded the structural diversity of the graspetide family of RiPPs, also known as omega‐ester‐containing peptides (OEPs).<sup>[</sup>\n##REF##28841794##\n12\n##\n<sup>]</sup> Graspetides and their biosynthesis have been also studied by bioinformatic,<sup>[</sup>\n##REF##34766760##\n13\n##\n<sup>]</sup> biochemical,<sup>[</sup>\n##REF##33360751##\n14\n##\n<sup>]</sup> and structural analyses.<sup>[</sup>\n##REF##27669417##\n15\n##\n<sup>]</sup> Using heterologous co‐expression, in vitro reconstitution of enzyme reactions, and structural analyses of the product peptides with mass spectrometry and nulear magnetic resonance (NMR), we discovered that SsfM, a PIMT homolog associated with graspetide biosynthesis, has the same activity as other PIMT homologs in RiPP biosynthesis. Genome mining of PIMT homologs revealed not only homologous enzymes playing a secondary role for known RiPP subclasses but also those mediating the same conversion of Asp as the primary modification, leading to a new RiPP subclass. This result highlights the potential of leveraging the evolutionary dissemination of tailoring enzymes across diverse RiPP BGCs to identify a novel biosynthetic pathway of RiPPs.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>\n<italic toggle=\"yes\">O</italic>‐methyltransferase‐Associated Gene Cluster Produces an Isoaspartate‐Containing Pentacyclic Graspetide</title>", "<p>Previous genome mining studies of graspetides have revealed the high co‐occurrence of PIMT homologs in graspetide BGCs (group 13 graspetides).<sup>[</sup>\n##REF##34766760##\n13\n##, ##REF##20023723##\n16\n##\n<sup>]</sup> Heterologous expression of genes in two BGCs yielded aspartimidylated graspetides.<sup>[</sup>\n##REF##31568727##\n11c,d\n##\n<sup>]</sup> Here, we tested another graspetide BGC from <italic toggle=\"yes\">Streptomyces</italic> sp. F‐3, encoding a precursor peptide (SsfA), an ATP‐grasp enzyme (SsfB), and a PIMT homolog (SsfM; <bold>Figure</bold>\n##FIG##1##\n2a##). Heterologous co‐expression of SsfA and SsfB in <italic toggle=\"yes\">Escherichia coli</italic> (<italic toggle=\"yes\">E. coli</italic>) produced the SsfB‐modified SsfA, named SsfA(B), which was 90 Da lighter than SsfA (Figure ##FIG##1##2b##). Incubation of the GluC‐digested SsfA(B), SsfA(B)<sub>63–97</sub>, with methoxide resulted in up to five‐fold methanolysis, suggesting that SsfA(B)<sub>63–97</sub> has five ester linkages (Figure ##SUPPL##0##S1a##, Supporting Information). The tandem mass (MS/MS) analysis of the fivefold methanolized SsfA(B)<sub>63–97</sub> suggested that the five ring‐forming carboxylates reside within the C‐terminal 12 residues, which have only four Asp residues and no Glu (Figure ##SUPPL##0##S1b##, Supporting Information). This result suggests the involvement of the C‐terminal carboxylate in ester formation, generating a side‐to‐end linkage not previously observed in graspetides. Various efforts to determine the ring connectivity using the previously established tandem mass (MS/MS) analysis of reaction intermediates or partially hydrolyzed products were unsuccessful.<sup>[</sup>\n##REF##28841794##\n12\n##\n<sup>]</sup> Collectively, these data suggest that the PIMT homolog‐containing BGC produces a graspetide.</p>", "<p>Biochemical analyses suggest that SsfM shares the same enzymatic activity as other RiPP‐associated PIMT homologs. First, we co‐expressed SsfM with SsfA and SsfB, and found that the resulting modified SsfA, named SsfA(BM), and its GluC‐digested fragment, SsfA(BM)<sub>63–97</sub>, had the same molecular weight (MW) as SsfA(B) and SsfA(B)<sub>63–97</sub>, respectively (Figure ##FIG##1##2b##; Figure ##SUPPL##0##S2a##, Supporting Information). Unlike other PIMT homolog‐modified RiPPs,<sup>[</sup>\n##REF##31568727##\n11\n##\n<sup>]</sup> we could not separate SsfA(BM)<sub>63–97</sub> and SsfA(B)<sub>63–97</sub>, using HPLC (Figure ##SUPPL##0##S2b##, Supporting Information). Second, we reconstituted the reaction in vitro with the purified SsfM, the leaderless SsfA(B)<sub>63–97</sub>, and <italic toggle=\"yes\">S</italic>‐adenosylmethionine (SAM). MALDI‐TOF‐MS analyses at multiple time points revealed an initial gain of 14 Da, followed by a loss of 32 Da and a gain of 18 Da, which are consistent with the previously reported reaction pathway including methylation, aspartimidylation, and hydrolysis (Figures ##FIG##0##1a## and ##FIG##1##2c##). Third, the isolated intermediates enriched in the aspartyl‐<italic toggle=\"yes\">O</italic>‐methyl ester or aspartimide intermediate (+14 Da or −18 Da from the SsfA(B)<sub>63–97</sub> MW, respectively) underwent the same MW changes in the absence of SsfM, suggesting that the last two steps, aspartimidylation and hydrolysis, do not require SsfM (Figure ##SUPPL##0##S2c##, Supporting Information). Fourth, MS and MS/MS analyses of the hydrazine‐added aspartimide intermediate resulted in a 32 Da increase in Asp81, providing another evidence for the presence of the aspartimide intermediate (Figure ##SUPPL##0##S3##, Supporting Information).<sup>[</sup>\n##REF##25043726##\n17\n##\n<sup>]</sup> Finally, SsfM did not efficiently modify partially cyclized SsfA<sub>63–97</sub> variants containing 0–4 ester linkages or the full‐length unmodified SsfA, indicating that SsfM requires the fully cyclized (fivefold) peptide (Figure ##SUPPL##0##S4##, Supporting Information). These results are consistent with previous reports,<sup>[</sup>\n##REF##31568727##\n11\n##\n<sup>]</sup> suggesting that the RiPP‐associated PIMT homologs generally recognize the cyclized peptide as their substrate.</p>", "<p>The multidimensional NMR analyses indicate that SsfM converts Asp81 to a mixture of isoAsp81 and Asp81. We used SsfA(B)<sub>66–97</sub> and SsfA(BM)<sub>66–97</sub> enriched with <sup>13</sup>C and <sup>15</sup>N to perform 2D <sup>1</sup>H‐<sup>15</sup>N HSQC, 3D HNCACB,<sup>[</sup>\n##UREF##0##\n18\n##\n<sup>]</sup> 3D HNcoCACB,<sup>[</sup>\n##UREF##1##\n19\n##\n<sup>]</sup> 3D HNCO,<sup>[</sup>\n##UREF##2##\n20\n##\n<sup>]</sup> 3D HNcaCO,<sup>[</sup>\n##UREF##3##\n21\n##\n<sup>]</sup> and 3D hNcocancaNH<sup>[</sup>\n##REF##29489342##\n22\n##\n<sup>]</sup> experiments. We assigned the chemical shifts of backbone amide proton (H<sup>N</sup>), nitrogen (N), CO, C<sup>α</sup>, and C<sup>β</sup> nuclei for all non‐proline residues. We identified seven independent peptide fragments (chains A‐G for SsfA(B)<sub>66–97</sub>; chains A’‐G’ for SsfA(BM)<sub>66–97</sub>), in which chains B, C, and E comprise a single long chain and chains A and D constitute another one (Figure ##SUPPL##0##S5## and Supporting Dataset S1, Supporting Information). <sup>1</sup>H‐<sup>15</sup>N HSQC resonances from a smaller region of chain D’ (Gly77–Thr78) and chain F’ (Asp81–Ser89) were uniquely observed with SsfA(BM)<sub>66–97</sub>, while the others were observed in both molecules (Figure ##SUPPL##0##S5##, Supporting Information). Close inspections of spectra clearly indicate the presence of isoAsp at the position of Asp81 in the chain F’ of SsfA(BM)<sub>66–97</sub>. First, the phases of C<sup>α</sup> and C<sup>β</sup> cross‐peaks were inverted both in the strips taken from the <sup>1</sup>H<sup>N</sup>─<sup>13</sup>C planes at the nitrogen chemical shifts of Gly82 of HNcoCACB and HNCACB spectra (Figure ##FIG##1##2d##). Several studies have previously reported these signals as indicative of the isopeptide linkage.<sup>[</sup>\n##REF##12188667##\n23\n##\n<sup>]</sup> Second, the HNCO signal of Gly82 was not connected to the HNcaCO signal of Asp81, which indicates that C<sup>β</sup> is between backbone C<sup>α</sup> and CO, suggesting that isoAsp has been formed (Figure ##SUPPL##0##S6##, Supporting Information). We also observed isoAsp at the Asn83 position in chain G of SsfA(B)<sub>66–97</sub> and in chain G’ of SsfA(BM)<sub>66–97</sub>, suggesting that Asn83 underwent spontaneous aspartimidylation and hydrolysis (Figure ##SUPPL##0##S7##, Supporting Information).<sup>[</sup>\n##REF##1939272##\n24\n##\n<sup>]</sup>\n</p>", "<title>RiPP‐Associated PIMT Homologs Share a Conserved C‐Terminal Domain</title>", "<p>The common enzymatic activity of PIMT homologs associated with several RiPP subclasses suggests that these enzymes have a close evolutionary relationship. To investigate this further, we used a bioinformatic approach (Figure ##SUPPL##0##S8##, Supporting Information). Initially, we used SsfM as a single query for the PSI‐BLAST<sup>[</sup>\n##REF##9254694##\n25\n##\n<sup>]</sup> to retrieve 73855 PIMTs or their homologs. To simplify the analysis, we reduced the number of proteins to 23490 using a cutoff of 70% sequence identity. We generated a maximum likelihood tree and analyzed their domain architecture as well as gene neighbors. We identified putative BGCs for lanthipeptides, lasso peptides, and graspetides, as well as over 1750 <italic toggle=\"yes\">surE</italic>‐<italic toggle=\"yes\">pcm</italic> clusters in which <italic toggle=\"yes\">pcm</italic> encodes a PIMT homolog not associated with RiPP biosynthesis. This PIMT mediates the isoAsp‐to‐Asp conversion in abnormal proteins in which isoAsp spontaneously arises from Asp and Asn residues, and enhances <italic toggle=\"yes\">E. coli</italic> survival under stress conditions in the late stationary phase.<sup>[</sup>\n##REF##9785447##\n26\n##\n<sup>]</sup>\n</p>", "<p>Notably, we observed that the majority of putative RiPP BGCs were contained in a single clade of 4003 enzymes, while the <italic toggle=\"yes\">surE</italic>‐<italic toggle=\"yes\">pcm</italic> clusters were predominantly located outside of this clade (Figure ##SUPPL##0##S8##, Supporting Information). Additionally, in this clade, 3200 PIMT homologs (80%) possessed a C‐terminal extension of over 100 amino acids (Figure ##SUPPL##0##S8##, Supporting Information). This C‐terminal domain was also identified in PIMT homologs for lanthipeptides, lasso peptides, and graspetides (OlvS, TceM, and AmdM, respectively).<sup>[</sup>\n##REF##31568727##\n11a,b,d\n##\n<sup>]</sup> A PIMT enzyme from <italic toggle=\"yes\">Thermotoga maritima</italic> (<italic toggle=\"yes\">Tm</italic>PIMT) is, to our knowledge, the only enzyme in this clade with an experimentally determined 3D structure (PDB 1DL5).<sup>[</sup>\n##REF##11080641##\n27\n##\n<sup>]</sup> By comparing this structure and several predicted structures, we found that the C‐terminal domains in this clade are highly homologous. First, we obtained the predicted structures of full‐length SsfM, OlvS, and TceM using AlphaFold<sup>[</sup>\n##REF##34265844##\n28\n##\n<sup>]</sup> (Figure ##SUPPL##0##S9a##, Supporting Information). To avoid the potential bias from using the structure of <italic toggle=\"yes\">Tm</italic>PIMT as the template, we also obtained the predicted structures of their C‐terminal domains using ColabFold<sup>[</sup>\n##REF##35637307##\n29\n##\n<sup>]</sup> (Figure ##SUPPL##0##S9b##, Supporting Information) and those of full‐length enzymes using a template‐independent ESMFold<sup>[</sup>\n##REF##36927031##\n30\n##\n<sup>]</sup> (Figure ##SUPPL##0##S9c##, Supporting Information). For each enzyme, the structures of the C‐terminal domain in the latter two models were highly homologous to the one in the full‐length AlphaFold model (R.M.S.D. ≤1 Å). All structures have the same arrangement of secondary structures, βαββββα, as that in <italic toggle=\"yes\">Tm</italic>PIMT (Figures ##SUPPL##0##S9a–c##, Supporting Information). The pairwise structural alignments of the domains in the AlphaFold structure on the Dali server<sup>[</sup>\n##REF##20457744##\n31\n##\n<sup>]</sup> revealed, albeit weak due to shifts of secondary structures, similarity between these regions with a <italic toggle=\"yes\">Z</italic>‐score of 3.4–7.3 (Figure ##SUPPL##0##S9d##, Supporting Information). These findings suggest that this domain is conserved among RiPP‐associated PIMT homologs and may have a potential role in RiPP biosynthesis. The latter has been recently proposed in a biochemical analysis of AmdM involved in the maturation of a graspetide, amycolimiditide.<sup>[</sup>\n##REF##31568727##\n11d\n##\n<sup>]</sup> We suggest renaming these RiPP‐associated PIMT homologs as peptide/protein L‐aspartyl <italic toggle=\"yes\">O</italic>‐methyltransferases or PAMTs, given that they primarily modify L‐aspartate as a natural substrate while they may also accept isoaspartate as well.</p>", "<title>Genome Mining of PAMTs Reveals a Novel RiPP Subclass</title>", "<p>High sequence homology, the conserved C‐terminal domain, and the common enzymatic reaction suggest that PAMTs have evolved from a common ancestor. Furthermore, their frequent association with RiPP biosynthesis implies that this ancestral PAMT has spread to multiple unrelated RiPP subclasses. Therefore, we hypothesized that further exploration of this clade could uncover novel RiPP subclasses that utilize PAMTs as either primary or secondary modification enzymes. To test this idea, we compiled the expanded list of PAMTs in this clade without the cutoff of 70% sequence identity and eliminated proteins that are either shorter than 300 amino acids or devoid of genomic information for neighboring genes, resulting in 9408 enzymes (<bold>Figure</bold>\n##FIG##2##\n3a##). Analysis of gene neighbors for known RiPP biosynthetic enzymes or precursor peptides revealed additional BGCs for linear azol(in)e‐containing peptides (LAPs; 2 BGCs) as well as lanthipeptides (1305 BGCs), lasso peptides (67 BGCs), and graspetides (1432 BGCs), of which the numbers of BGCs for the latter three increased 5–50% from previous reports (lanthipeptides, 837; lasso peptides, 48; graspetides, 1326; Figure ##FIG##2##3a,b##; Supporting Dataset S1, Supporting Information).<sup>[</sup>\n##REF##31568727##\n11\n##, ##REF##34766760##\n13\n##, ##REF##32493223##\n32\n##\n<sup>]</sup> Consistent with recent comprehensive genome mining of lanthipeptides,<sup>[</sup>\n##REF##32493223##\n32\n##\n<sup>]</sup> PAMTs in lanthipeptide BGCs are associated with class I lanthipeptides and most precursor peptides adopt the TxDGC core motif (Figure ##SUPPL##0##S10a##, Supporting Information). Precursors for lasso peptides can be classified into two groups based on core motifs; one group contains the DTAD motif in the lasso ring as previously reported,<sup>[</sup>\n##REF##31568727##\n11b\n##\n<sup>]</sup> while the other group shares a highly conserved Asp residue in the putative lasso loop (Figure ##SUPPL##0##S10b##, Supporting Information). Precursors encoded in two LAP BGCs have an Asp residue within the C/S/T/G‐rich core motif (Figure ##FIG##2##3c##; Figure ##SUPPL##0##S10c##, Supporting Information).<sup>[</sup>\n##REF##23165928##\n1\n##, ##REF##28256131##\n33\n##\n<sup>]</sup> In total, we assigned 2806 of 9408 PAMTs into four known subclasses of RiPPs.</p>", "<p>Nonetheless, most enzymes (70.2%) did not show any obvious association with known RiPP BGCs. We hypothesized that some of these enzymes could be involved in the biosynthesis of new RiPP subclasses. Indeed, we found a large number of two‐gene clusters encoding a putative precursor peptide and a PAMT (1183 non‐redundant putative precursors associated with 1539 non‐redundant PAMTs), but no primary modification enzymes for known RiPPs. Analysis of putative precursor peptides revealed two major types with distinct sequence features. Type I precursors have ≈45 amino acids and are rich in Gly (17.3%), Pro (16.8%), and Asp (10.2%; Figure ##FIG##2##3d##; Figure ##SUPPL##0##S11a##, Supporting Information). They present several different conservation patterns of the sequences but commonly have at least one highly conserved Asp residue nearby conserved prolines or glycines. By contrast, type II precursors contain a highly conserved zinc ribbon motif commonly found in DnaJ (PF00684) with a conserved Asp at the center (CxxCxGxG_D_CxxCxGxG; Figure ##FIG##2##3e##; Figure ##SUPPL##0##S11b##, Supporting Information).<sup>[</sup>\n##REF##10891270##\n34\n##\n<sup>]</sup> Four conserved cysteines in the zinc ribbon motif coordinate a zinc ion and the intervening residues form two anti‐parallel β‐strands (Figure ##SUPPL##0##S12##, Supporting Information). The predicted structure of a type II precursor by AlphaFold and a metal ion‐binding site prediction server (MIB) also showed the typical zinc ribbon, in which the conserved Asp residue is located in the hairpin (Figure ##FIG##2##3e##).<sup>[</sup>\n##REF##34265844##\n28\n##, ##REF##27976886##\n35\n##\n<sup>]</sup> The two‐gene architecture with a highly homologous PAMT enzyme and the presence of a conserved Asp residue in putative precursors suggest that these PAMTs serve as a primary modification enzyme for the Asp derivatization in the putative precursor, defining a novel subclass of RiPPs. We propose the name “pamtides” for those produced by these distinct BGCs.</p>", "<p>We also identified 1410 PAMTs associated with the conserved gene clusters that typically contain ten genes as well as ABC transporter genes (Figure ##SUPPL##0##S13a##, Supporting Information). In particular, the PAMT gene is located next to a gene encoding forkhead‐associated (FHA) domain‐containing protein. This protein contains a long N‐terminal Pro/Gly‐rich region with a few Asp residues, similar to the putative precursors for type I pamtides, suggesting that PAMT in this gene cluster may modify the FHA domain‐containing protein.</p>", "<p>We also observed an additional 249 distinct gene clusters consisting of two genes encoding a radical <italic toggle=\"yes\">S</italic>‐adenosylmethionine (rSAM) enzyme and a PAMT. However, we could not find any neighboring genes encoding putative precursors or substrate proteins for modification (Figure ##SUPPL##0##S13b##, Supporting Information). Although we could not obtain any clues that the remaining 3653 enzymes are associated with RiPP biosynthesis or protein PTM, we cannot exclude the possibility that these enzymes are also involved in the same type of modification reactions.</p>", "<title>A PAMT Enzyme in Type II Pamtide Biosynthesis Mediate the Asp‐to‐isoAsp Conversion</title>", "<p>To test whether PAMTs in the pamtide BGCs convert Asp to aspartimide or/and isoaspartate in the precursor peptides, we initially selected one BGC for type II pamtide from <italic toggle=\"yes\">Frankia cauarinae</italic> BR AAY23_1099 (Figures ##FIG##2##3e## and ##FIG##3##\n4a##). Heterologous co‐expression of the precursor (FcaA) and PAMT (FcaM) in <italic toggle=\"yes\">E. coli</italic> showed that the product, FcaA(M), had the same MW as the unmodified FcaA (Figure ##FIG##3##4b##). We purified FcaA(M) and digested it with trypsin to obtain FcaA(M)<sub>19–26</sub> (<bold>3</bold>; Figure ##FIG##3##4c##) containing the conserved Asp residue. We also chemically synthesized the FcaA<sub>19–26</sub> equivalent (ITVTSDGK, <bold>1</bold>) and its isoAsp variant (ITVTS(isoD)GK, <bold>2</bold>). The comparison of HPLC chromatograms of individual peptides or their combinations revealed that the major component of FcaA(M)<sub>19–26</sub> is equivalent to the isoAsp variant and clearly different from FcaA<sub>19–26</sub> (Figure ##FIG##3##4c##).</p>", "<p>We also obtained the <sup>1</sup>H, <sup>1</sup>H‐<sup>1</sup>H COSY, <sup>1</sup>H‐<sup>1</sup>H TOCSY, and <sup>1</sup>H‐<sup>1</sup>H NOESY spectra for the three peptides and assigned the chemical shifts of protons. In the NOESY spectrum of FcaA(M)<sub>19‐26</sub>, we observed a NOE signal between G25 H<sup>N</sup> and D24 H<sup>β</sup>, but not between G25 H<sup>N</sup> and D24 H<sup>α</sup> (Figure ##FIG##3##4d##; Figure ##SUPPL##0##S14## and Supporting Dataset S1, Supporting Information), which is consistent with the previous observation for OlvA(BCS<sub>A</sub>)<sup>GluC</sup>, an isoAsp‐containing lanthipeptide.<sup>[</sup>\n##REF##31568727##\n11a\n##\n<sup>]</sup> The chemically synthesized ITVTS(isoD)GK (<bold>2</bold>) also showed this correlation, but the unmodified peptide ITVTSDGK (<bold>1</bold>) presented the reverse correlation (Figure ##SUPPL##0##S15##, Supporting Information). These analyses consistently support that FcaM mediates the Asp‐to‐isoAsp conversion in FcaA.</p>", "<p>To characterize the FcaM‐mediated reaction in detail, we reconstituted the reaction in vitro under various conditions (Figure ##FIG##3##4e##). To prevent the formation of disulfide bonds, we provided 1,4‐dithiothreitol (DTT) in the reaction solutions. In the presence of Zn<sup>2+</sup>, FcaA displayed the same MW changes as those of SsfA(B)<sub>63‐97</sub> and other cyclized intermediates of RiPPs associated with PAMT enzymes: an initial gain of 14 Da, followed by a loss of 32 Da and a gain of 18 Da (Figure ##FIG##3##4e##). The isolated intermediates also showed spontaneous conversions to the species with the original MW and hydrazine trapping of the putative aspartimide species (−18 Da) resulted in the hydrazine‐added species (+14 Da; Figure ##FIG##3##4f,g##). However, no MW changes were observed when Zn<sup>2+</sup> was absent or cysteines in FcaA were blocked by iodoacetamide (IAA), indicating that coordination of cysteines in FcaA to Zn<sup>2+</sup> is essential for the modification. Additionally, the complex of Zn<sup>2+</sup> and 4‐(2‐pyridylazo)resorcinol (PAR),<sup>[</sup>\n##REF##10964414##\n36\n##\n<sup>]</sup> a metal‐sensitive colorimetric reagent, was completely dissociated by adding equal amount of FcaA or FcaA(M), but not by FcaM or IAA‐labeled FcaA, suggesting that Zn<sup>2+</sup> binds to FcaA or FcaA(M) in a 1:1 ratio (Figure ##FIG##3##4h##). Although we are not entirely confident that the endogenous metal ion would be Zn<sup>2+</sup>, our bioinformatic analysis and in vitro reconstitution strongly suggest that, in line with other PAMT‐associated RiPPs, the type II pamtides require the “cyclic” or “hairpin‐like” architecture for the Asp‐to‐isoAsp conversion and metal–ligand interactions can be a strategy for the formation of cyclic architecture.</p>", "<title>A PAMT Enzyme in Type I Pamtide Biosynthesis Catalyzes the Similar Conversion in the Precursor Peptide</title>", "<p>We also tested a model precursor (SpaA) and a PAMT (SpaM) for type I pamtides from <italic toggle=\"yes\">Streptomyces sparsogenes</italic> DSM 40 356 (Figure ##FIG##2##3d##). Co‐expression of SpaM and SpaA yielded the species without MW change from intact SpaA as a major product, while those with −18 and +14 Da MW change were also observed (<bold>Figure</bold>\n##FIG##4##\n5a##). We additionally found that the SpaM‐mediated reaction displayed almost the same features as those of PAMTs in RiPP biosynthesis: the same pattern of MW changes at the conserved aspartate in the in vitro reaction, the spontaneous conversions of the reaction intermediates, and the hydrazine trapping of the aspartimide intermediate (Figure ##FIG##4##5b–d##; Figure ##SUPPL##0##S16##, Supporting Information). Although we could not directly confirm the Asp‐to‐isoAsp conversion with SpaM, the same reaction features and the evolutionary relationship of SpaM with other PAMT enzymes suggest that SpaM most likely mediates the same modification reaction.</p>", "<p>Notably, BGCs for type I pamtides do not encode a conserved cyclase and precursors do not present known intrinsically cyclic or hairpin‐like motifs. Additionally, AlphaFold‐predicted structures of SpaA and SpaA‐SpaM complex do not present the cyclic architecture within SpaA (Figure ##SUPPL##0##S17a##, Supporting Information). Most precursors contain highly conserved acidic/basic residues at their N‐/C‐termini (Figure ##SUPPL##0##S11a##, Supporting Information), and the substitution of the conserved C‐terminal region to alanines was deleterious for the SpaM activity (Figure ##SUPPL##0##S17b##, Supporting Information). We suggest that these conserved C‐terminal residues might play a critical role in either recognition of PAMT or formation of a cyclic/hairpin structure. Collectively, these data suggest that PAMTs in the pamtide BGCs serve as a primary modification enzyme by mediating the same chemical conversion as other RiPP‐associated PAMT enzymes.</p>" ]
[ "<title>Results and Discussion</title>", "<title>\n<italic toggle=\"yes\">O</italic>‐methyltransferase‐Associated Gene Cluster Produces an Isoaspartate‐Containing Pentacyclic Graspetide</title>", "<p>Previous genome mining studies of graspetides have revealed the high co‐occurrence of PIMT homologs in graspetide BGCs (group 13 graspetides).<sup>[</sup>\n##REF##34766760##\n13\n##, ##REF##20023723##\n16\n##\n<sup>]</sup> Heterologous expression of genes in two BGCs yielded aspartimidylated graspetides.<sup>[</sup>\n##REF##31568727##\n11c,d\n##\n<sup>]</sup> Here, we tested another graspetide BGC from <italic toggle=\"yes\">Streptomyces</italic> sp. F‐3, encoding a precursor peptide (SsfA), an ATP‐grasp enzyme (SsfB), and a PIMT homolog (SsfM; <bold>Figure</bold>\n##FIG##1##\n2a##). Heterologous co‐expression of SsfA and SsfB in <italic toggle=\"yes\">Escherichia coli</italic> (<italic toggle=\"yes\">E. coli</italic>) produced the SsfB‐modified SsfA, named SsfA(B), which was 90 Da lighter than SsfA (Figure ##FIG##1##2b##). Incubation of the GluC‐digested SsfA(B), SsfA(B)<sub>63–97</sub>, with methoxide resulted in up to five‐fold methanolysis, suggesting that SsfA(B)<sub>63–97</sub> has five ester linkages (Figure ##SUPPL##0##S1a##, Supporting Information). The tandem mass (MS/MS) analysis of the fivefold methanolized SsfA(B)<sub>63–97</sub> suggested that the five ring‐forming carboxylates reside within the C‐terminal 12 residues, which have only four Asp residues and no Glu (Figure ##SUPPL##0##S1b##, Supporting Information). This result suggests the involvement of the C‐terminal carboxylate in ester formation, generating a side‐to‐end linkage not previously observed in graspetides. Various efforts to determine the ring connectivity using the previously established tandem mass (MS/MS) analysis of reaction intermediates or partially hydrolyzed products were unsuccessful.<sup>[</sup>\n##REF##28841794##\n12\n##\n<sup>]</sup> Collectively, these data suggest that the PIMT homolog‐containing BGC produces a graspetide.</p>", "<p>Biochemical analyses suggest that SsfM shares the same enzymatic activity as other RiPP‐associated PIMT homologs. First, we co‐expressed SsfM with SsfA and SsfB, and found that the resulting modified SsfA, named SsfA(BM), and its GluC‐digested fragment, SsfA(BM)<sub>63–97</sub>, had the same molecular weight (MW) as SsfA(B) and SsfA(B)<sub>63–97</sub>, respectively (Figure ##FIG##1##2b##; Figure ##SUPPL##0##S2a##, Supporting Information). Unlike other PIMT homolog‐modified RiPPs,<sup>[</sup>\n##REF##31568727##\n11\n##\n<sup>]</sup> we could not separate SsfA(BM)<sub>63–97</sub> and SsfA(B)<sub>63–97</sub>, using HPLC (Figure ##SUPPL##0##S2b##, Supporting Information). Second, we reconstituted the reaction in vitro with the purified SsfM, the leaderless SsfA(B)<sub>63–97</sub>, and <italic toggle=\"yes\">S</italic>‐adenosylmethionine (SAM). MALDI‐TOF‐MS analyses at multiple time points revealed an initial gain of 14 Da, followed by a loss of 32 Da and a gain of 18 Da, which are consistent with the previously reported reaction pathway including methylation, aspartimidylation, and hydrolysis (Figures ##FIG##0##1a## and ##FIG##1##2c##). Third, the isolated intermediates enriched in the aspartyl‐<italic toggle=\"yes\">O</italic>‐methyl ester or aspartimide intermediate (+14 Da or −18 Da from the SsfA(B)<sub>63–97</sub> MW, respectively) underwent the same MW changes in the absence of SsfM, suggesting that the last two steps, aspartimidylation and hydrolysis, do not require SsfM (Figure ##SUPPL##0##S2c##, Supporting Information). Fourth, MS and MS/MS analyses of the hydrazine‐added aspartimide intermediate resulted in a 32 Da increase in Asp81, providing another evidence for the presence of the aspartimide intermediate (Figure ##SUPPL##0##S3##, Supporting Information).<sup>[</sup>\n##REF##25043726##\n17\n##\n<sup>]</sup> Finally, SsfM did not efficiently modify partially cyclized SsfA<sub>63–97</sub> variants containing 0–4 ester linkages or the full‐length unmodified SsfA, indicating that SsfM requires the fully cyclized (fivefold) peptide (Figure ##SUPPL##0##S4##, Supporting Information). These results are consistent with previous reports,<sup>[</sup>\n##REF##31568727##\n11\n##\n<sup>]</sup> suggesting that the RiPP‐associated PIMT homologs generally recognize the cyclized peptide as their substrate.</p>", "<p>The multidimensional NMR analyses indicate that SsfM converts Asp81 to a mixture of isoAsp81 and Asp81. We used SsfA(B)<sub>66–97</sub> and SsfA(BM)<sub>66–97</sub> enriched with <sup>13</sup>C and <sup>15</sup>N to perform 2D <sup>1</sup>H‐<sup>15</sup>N HSQC, 3D HNCACB,<sup>[</sup>\n##UREF##0##\n18\n##\n<sup>]</sup> 3D HNcoCACB,<sup>[</sup>\n##UREF##1##\n19\n##\n<sup>]</sup> 3D HNCO,<sup>[</sup>\n##UREF##2##\n20\n##\n<sup>]</sup> 3D HNcaCO,<sup>[</sup>\n##UREF##3##\n21\n##\n<sup>]</sup> and 3D hNcocancaNH<sup>[</sup>\n##REF##29489342##\n22\n##\n<sup>]</sup> experiments. We assigned the chemical shifts of backbone amide proton (H<sup>N</sup>), nitrogen (N), CO, C<sup>α</sup>, and C<sup>β</sup> nuclei for all non‐proline residues. We identified seven independent peptide fragments (chains A‐G for SsfA(B)<sub>66–97</sub>; chains A’‐G’ for SsfA(BM)<sub>66–97</sub>), in which chains B, C, and E comprise a single long chain and chains A and D constitute another one (Figure ##SUPPL##0##S5## and Supporting Dataset S1, Supporting Information). <sup>1</sup>H‐<sup>15</sup>N HSQC resonances from a smaller region of chain D’ (Gly77–Thr78) and chain F’ (Asp81–Ser89) were uniquely observed with SsfA(BM)<sub>66–97</sub>, while the others were observed in both molecules (Figure ##SUPPL##0##S5##, Supporting Information). Close inspections of spectra clearly indicate the presence of isoAsp at the position of Asp81 in the chain F’ of SsfA(BM)<sub>66–97</sub>. First, the phases of C<sup>α</sup> and C<sup>β</sup> cross‐peaks were inverted both in the strips taken from the <sup>1</sup>H<sup>N</sup>─<sup>13</sup>C planes at the nitrogen chemical shifts of Gly82 of HNcoCACB and HNCACB spectra (Figure ##FIG##1##2d##). Several studies have previously reported these signals as indicative of the isopeptide linkage.<sup>[</sup>\n##REF##12188667##\n23\n##\n<sup>]</sup> Second, the HNCO signal of Gly82 was not connected to the HNcaCO signal of Asp81, which indicates that C<sup>β</sup> is between backbone C<sup>α</sup> and CO, suggesting that isoAsp has been formed (Figure ##SUPPL##0##S6##, Supporting Information). We also observed isoAsp at the Asn83 position in chain G of SsfA(B)<sub>66–97</sub> and in chain G’ of SsfA(BM)<sub>66–97</sub>, suggesting that Asn83 underwent spontaneous aspartimidylation and hydrolysis (Figure ##SUPPL##0##S7##, Supporting Information).<sup>[</sup>\n##REF##1939272##\n24\n##\n<sup>]</sup>\n</p>", "<title>RiPP‐Associated PIMT Homologs Share a Conserved C‐Terminal Domain</title>", "<p>The common enzymatic activity of PIMT homologs associated with several RiPP subclasses suggests that these enzymes have a close evolutionary relationship. To investigate this further, we used a bioinformatic approach (Figure ##SUPPL##0##S8##, Supporting Information). Initially, we used SsfM as a single query for the PSI‐BLAST<sup>[</sup>\n##REF##9254694##\n25\n##\n<sup>]</sup> to retrieve 73855 PIMTs or their homologs. To simplify the analysis, we reduced the number of proteins to 23490 using a cutoff of 70% sequence identity. We generated a maximum likelihood tree and analyzed their domain architecture as well as gene neighbors. We identified putative BGCs for lanthipeptides, lasso peptides, and graspetides, as well as over 1750 <italic toggle=\"yes\">surE</italic>‐<italic toggle=\"yes\">pcm</italic> clusters in which <italic toggle=\"yes\">pcm</italic> encodes a PIMT homolog not associated with RiPP biosynthesis. This PIMT mediates the isoAsp‐to‐Asp conversion in abnormal proteins in which isoAsp spontaneously arises from Asp and Asn residues, and enhances <italic toggle=\"yes\">E. coli</italic> survival under stress conditions in the late stationary phase.<sup>[</sup>\n##REF##9785447##\n26\n##\n<sup>]</sup>\n</p>", "<p>Notably, we observed that the majority of putative RiPP BGCs were contained in a single clade of 4003 enzymes, while the <italic toggle=\"yes\">surE</italic>‐<italic toggle=\"yes\">pcm</italic> clusters were predominantly located outside of this clade (Figure ##SUPPL##0##S8##, Supporting Information). Additionally, in this clade, 3200 PIMT homologs (80%) possessed a C‐terminal extension of over 100 amino acids (Figure ##SUPPL##0##S8##, Supporting Information). This C‐terminal domain was also identified in PIMT homologs for lanthipeptides, lasso peptides, and graspetides (OlvS, TceM, and AmdM, respectively).<sup>[</sup>\n##REF##31568727##\n11a,b,d\n##\n<sup>]</sup> A PIMT enzyme from <italic toggle=\"yes\">Thermotoga maritima</italic> (<italic toggle=\"yes\">Tm</italic>PIMT) is, to our knowledge, the only enzyme in this clade with an experimentally determined 3D structure (PDB 1DL5).<sup>[</sup>\n##REF##11080641##\n27\n##\n<sup>]</sup> By comparing this structure and several predicted structures, we found that the C‐terminal domains in this clade are highly homologous. First, we obtained the predicted structures of full‐length SsfM, OlvS, and TceM using AlphaFold<sup>[</sup>\n##REF##34265844##\n28\n##\n<sup>]</sup> (Figure ##SUPPL##0##S9a##, Supporting Information). To avoid the potential bias from using the structure of <italic toggle=\"yes\">Tm</italic>PIMT as the template, we also obtained the predicted structures of their C‐terminal domains using ColabFold<sup>[</sup>\n##REF##35637307##\n29\n##\n<sup>]</sup> (Figure ##SUPPL##0##S9b##, Supporting Information) and those of full‐length enzymes using a template‐independent ESMFold<sup>[</sup>\n##REF##36927031##\n30\n##\n<sup>]</sup> (Figure ##SUPPL##0##S9c##, Supporting Information). For each enzyme, the structures of the C‐terminal domain in the latter two models were highly homologous to the one in the full‐length AlphaFold model (R.M.S.D. ≤1 Å). All structures have the same arrangement of secondary structures, βαββββα, as that in <italic toggle=\"yes\">Tm</italic>PIMT (Figures ##SUPPL##0##S9a–c##, Supporting Information). The pairwise structural alignments of the domains in the AlphaFold structure on the Dali server<sup>[</sup>\n##REF##20457744##\n31\n##\n<sup>]</sup> revealed, albeit weak due to shifts of secondary structures, similarity between these regions with a <italic toggle=\"yes\">Z</italic>‐score of 3.4–7.3 (Figure ##SUPPL##0##S9d##, Supporting Information). These findings suggest that this domain is conserved among RiPP‐associated PIMT homologs and may have a potential role in RiPP biosynthesis. The latter has been recently proposed in a biochemical analysis of AmdM involved in the maturation of a graspetide, amycolimiditide.<sup>[</sup>\n##REF##31568727##\n11d\n##\n<sup>]</sup> We suggest renaming these RiPP‐associated PIMT homologs as peptide/protein L‐aspartyl <italic toggle=\"yes\">O</italic>‐methyltransferases or PAMTs, given that they primarily modify L‐aspartate as a natural substrate while they may also accept isoaspartate as well.</p>", "<title>Genome Mining of PAMTs Reveals a Novel RiPP Subclass</title>", "<p>High sequence homology, the conserved C‐terminal domain, and the common enzymatic reaction suggest that PAMTs have evolved from a common ancestor. Furthermore, their frequent association with RiPP biosynthesis implies that this ancestral PAMT has spread to multiple unrelated RiPP subclasses. Therefore, we hypothesized that further exploration of this clade could uncover novel RiPP subclasses that utilize PAMTs as either primary or secondary modification enzymes. To test this idea, we compiled the expanded list of PAMTs in this clade without the cutoff of 70% sequence identity and eliminated proteins that are either shorter than 300 amino acids or devoid of genomic information for neighboring genes, resulting in 9408 enzymes (<bold>Figure</bold>\n##FIG##2##\n3a##). Analysis of gene neighbors for known RiPP biosynthetic enzymes or precursor peptides revealed additional BGCs for linear azol(in)e‐containing peptides (LAPs; 2 BGCs) as well as lanthipeptides (1305 BGCs), lasso peptides (67 BGCs), and graspetides (1432 BGCs), of which the numbers of BGCs for the latter three increased 5–50% from previous reports (lanthipeptides, 837; lasso peptides, 48; graspetides, 1326; Figure ##FIG##2##3a,b##; Supporting Dataset S1, Supporting Information).<sup>[</sup>\n##REF##31568727##\n11\n##, ##REF##34766760##\n13\n##, ##REF##32493223##\n32\n##\n<sup>]</sup> Consistent with recent comprehensive genome mining of lanthipeptides,<sup>[</sup>\n##REF##32493223##\n32\n##\n<sup>]</sup> PAMTs in lanthipeptide BGCs are associated with class I lanthipeptides and most precursor peptides adopt the TxDGC core motif (Figure ##SUPPL##0##S10a##, Supporting Information). Precursors for lasso peptides can be classified into two groups based on core motifs; one group contains the DTAD motif in the lasso ring as previously reported,<sup>[</sup>\n##REF##31568727##\n11b\n##\n<sup>]</sup> while the other group shares a highly conserved Asp residue in the putative lasso loop (Figure ##SUPPL##0##S10b##, Supporting Information). Precursors encoded in two LAP BGCs have an Asp residue within the C/S/T/G‐rich core motif (Figure ##FIG##2##3c##; Figure ##SUPPL##0##S10c##, Supporting Information).<sup>[</sup>\n##REF##23165928##\n1\n##, ##REF##28256131##\n33\n##\n<sup>]</sup> In total, we assigned 2806 of 9408 PAMTs into four known subclasses of RiPPs.</p>", "<p>Nonetheless, most enzymes (70.2%) did not show any obvious association with known RiPP BGCs. We hypothesized that some of these enzymes could be involved in the biosynthesis of new RiPP subclasses. Indeed, we found a large number of two‐gene clusters encoding a putative precursor peptide and a PAMT (1183 non‐redundant putative precursors associated with 1539 non‐redundant PAMTs), but no primary modification enzymes for known RiPPs. Analysis of putative precursor peptides revealed two major types with distinct sequence features. Type I precursors have ≈45 amino acids and are rich in Gly (17.3%), Pro (16.8%), and Asp (10.2%; Figure ##FIG##2##3d##; Figure ##SUPPL##0##S11a##, Supporting Information). They present several different conservation patterns of the sequences but commonly have at least one highly conserved Asp residue nearby conserved prolines or glycines. By contrast, type II precursors contain a highly conserved zinc ribbon motif commonly found in DnaJ (PF00684) with a conserved Asp at the center (CxxCxGxG_D_CxxCxGxG; Figure ##FIG##2##3e##; Figure ##SUPPL##0##S11b##, Supporting Information).<sup>[</sup>\n##REF##10891270##\n34\n##\n<sup>]</sup> Four conserved cysteines in the zinc ribbon motif coordinate a zinc ion and the intervening residues form two anti‐parallel β‐strands (Figure ##SUPPL##0##S12##, Supporting Information). The predicted structure of a type II precursor by AlphaFold and a metal ion‐binding site prediction server (MIB) also showed the typical zinc ribbon, in which the conserved Asp residue is located in the hairpin (Figure ##FIG##2##3e##).<sup>[</sup>\n##REF##34265844##\n28\n##, ##REF##27976886##\n35\n##\n<sup>]</sup> The two‐gene architecture with a highly homologous PAMT enzyme and the presence of a conserved Asp residue in putative precursors suggest that these PAMTs serve as a primary modification enzyme for the Asp derivatization in the putative precursor, defining a novel subclass of RiPPs. We propose the name “pamtides” for those produced by these distinct BGCs.</p>", "<p>We also identified 1410 PAMTs associated with the conserved gene clusters that typically contain ten genes as well as ABC transporter genes (Figure ##SUPPL##0##S13a##, Supporting Information). In particular, the PAMT gene is located next to a gene encoding forkhead‐associated (FHA) domain‐containing protein. This protein contains a long N‐terminal Pro/Gly‐rich region with a few Asp residues, similar to the putative precursors for type I pamtides, suggesting that PAMT in this gene cluster may modify the FHA domain‐containing protein.</p>", "<p>We also observed an additional 249 distinct gene clusters consisting of two genes encoding a radical <italic toggle=\"yes\">S</italic>‐adenosylmethionine (rSAM) enzyme and a PAMT. However, we could not find any neighboring genes encoding putative precursors or substrate proteins for modification (Figure ##SUPPL##0##S13b##, Supporting Information). Although we could not obtain any clues that the remaining 3653 enzymes are associated with RiPP biosynthesis or protein PTM, we cannot exclude the possibility that these enzymes are also involved in the same type of modification reactions.</p>", "<title>A PAMT Enzyme in Type II Pamtide Biosynthesis Mediate the Asp‐to‐isoAsp Conversion</title>", "<p>To test whether PAMTs in the pamtide BGCs convert Asp to aspartimide or/and isoaspartate in the precursor peptides, we initially selected one BGC for type II pamtide from <italic toggle=\"yes\">Frankia cauarinae</italic> BR AAY23_1099 (Figures ##FIG##2##3e## and ##FIG##3##\n4a##). Heterologous co‐expression of the precursor (FcaA) and PAMT (FcaM) in <italic toggle=\"yes\">E. coli</italic> showed that the product, FcaA(M), had the same MW as the unmodified FcaA (Figure ##FIG##3##4b##). We purified FcaA(M) and digested it with trypsin to obtain FcaA(M)<sub>19–26</sub> (<bold>3</bold>; Figure ##FIG##3##4c##) containing the conserved Asp residue. We also chemically synthesized the FcaA<sub>19–26</sub> equivalent (ITVTSDGK, <bold>1</bold>) and its isoAsp variant (ITVTS(isoD)GK, <bold>2</bold>). The comparison of HPLC chromatograms of individual peptides or their combinations revealed that the major component of FcaA(M)<sub>19–26</sub> is equivalent to the isoAsp variant and clearly different from FcaA<sub>19–26</sub> (Figure ##FIG##3##4c##).</p>", "<p>We also obtained the <sup>1</sup>H, <sup>1</sup>H‐<sup>1</sup>H COSY, <sup>1</sup>H‐<sup>1</sup>H TOCSY, and <sup>1</sup>H‐<sup>1</sup>H NOESY spectra for the three peptides and assigned the chemical shifts of protons. In the NOESY spectrum of FcaA(M)<sub>19‐26</sub>, we observed a NOE signal between G25 H<sup>N</sup> and D24 H<sup>β</sup>, but not between G25 H<sup>N</sup> and D24 H<sup>α</sup> (Figure ##FIG##3##4d##; Figure ##SUPPL##0##S14## and Supporting Dataset S1, Supporting Information), which is consistent with the previous observation for OlvA(BCS<sub>A</sub>)<sup>GluC</sup>, an isoAsp‐containing lanthipeptide.<sup>[</sup>\n##REF##31568727##\n11a\n##\n<sup>]</sup> The chemically synthesized ITVTS(isoD)GK (<bold>2</bold>) also showed this correlation, but the unmodified peptide ITVTSDGK (<bold>1</bold>) presented the reverse correlation (Figure ##SUPPL##0##S15##, Supporting Information). These analyses consistently support that FcaM mediates the Asp‐to‐isoAsp conversion in FcaA.</p>", "<p>To characterize the FcaM‐mediated reaction in detail, we reconstituted the reaction in vitro under various conditions (Figure ##FIG##3##4e##). To prevent the formation of disulfide bonds, we provided 1,4‐dithiothreitol (DTT) in the reaction solutions. In the presence of Zn<sup>2+</sup>, FcaA displayed the same MW changes as those of SsfA(B)<sub>63‐97</sub> and other cyclized intermediates of RiPPs associated with PAMT enzymes: an initial gain of 14 Da, followed by a loss of 32 Da and a gain of 18 Da (Figure ##FIG##3##4e##). The isolated intermediates also showed spontaneous conversions to the species with the original MW and hydrazine trapping of the putative aspartimide species (−18 Da) resulted in the hydrazine‐added species (+14 Da; Figure ##FIG##3##4f,g##). However, no MW changes were observed when Zn<sup>2+</sup> was absent or cysteines in FcaA were blocked by iodoacetamide (IAA), indicating that coordination of cysteines in FcaA to Zn<sup>2+</sup> is essential for the modification. Additionally, the complex of Zn<sup>2+</sup> and 4‐(2‐pyridylazo)resorcinol (PAR),<sup>[</sup>\n##REF##10964414##\n36\n##\n<sup>]</sup> a metal‐sensitive colorimetric reagent, was completely dissociated by adding equal amount of FcaA or FcaA(M), but not by FcaM or IAA‐labeled FcaA, suggesting that Zn<sup>2+</sup> binds to FcaA or FcaA(M) in a 1:1 ratio (Figure ##FIG##3##4h##). Although we are not entirely confident that the endogenous metal ion would be Zn<sup>2+</sup>, our bioinformatic analysis and in vitro reconstitution strongly suggest that, in line with other PAMT‐associated RiPPs, the type II pamtides require the “cyclic” or “hairpin‐like” architecture for the Asp‐to‐isoAsp conversion and metal–ligand interactions can be a strategy for the formation of cyclic architecture.</p>", "<title>A PAMT Enzyme in Type I Pamtide Biosynthesis Catalyzes the Similar Conversion in the Precursor Peptide</title>", "<p>We also tested a model precursor (SpaA) and a PAMT (SpaM) for type I pamtides from <italic toggle=\"yes\">Streptomyces sparsogenes</italic> DSM 40 356 (Figure ##FIG##2##3d##). Co‐expression of SpaM and SpaA yielded the species without MW change from intact SpaA as a major product, while those with −18 and +14 Da MW change were also observed (<bold>Figure</bold>\n##FIG##4##\n5a##). We additionally found that the SpaM‐mediated reaction displayed almost the same features as those of PAMTs in RiPP biosynthesis: the same pattern of MW changes at the conserved aspartate in the in vitro reaction, the spontaneous conversions of the reaction intermediates, and the hydrazine trapping of the aspartimide intermediate (Figure ##FIG##4##5b–d##; Figure ##SUPPL##0##S16##, Supporting Information). Although we could not directly confirm the Asp‐to‐isoAsp conversion with SpaM, the same reaction features and the evolutionary relationship of SpaM with other PAMT enzymes suggest that SpaM most likely mediates the same modification reaction.</p>", "<p>Notably, BGCs for type I pamtides do not encode a conserved cyclase and precursors do not present known intrinsically cyclic or hairpin‐like motifs. Additionally, AlphaFold‐predicted structures of SpaA and SpaA‐SpaM complex do not present the cyclic architecture within SpaA (Figure ##SUPPL##0##S17a##, Supporting Information). Most precursors contain highly conserved acidic/basic residues at their N‐/C‐termini (Figure ##SUPPL##0##S11a##, Supporting Information), and the substitution of the conserved C‐terminal region to alanines was deleterious for the SpaM activity (Figure ##SUPPL##0##S17b##, Supporting Information). We suggest that these conserved C‐terminal residues might play a critical role in either recognition of PAMT or formation of a cyclic/hairpin structure. Collectively, these data suggest that PAMTs in the pamtide BGCs serve as a primary modification enzyme by mediating the same chemical conversion as other RiPP‐associated PAMT enzymes.</p>" ]
[ "<title>Conclusion</title>", "<p>Overall, we report that highly homologous PAMTs have evolutionarily spread across multiple RiPP subclasses and mediate the same modification reaction that converts between Asp and isoAsp via aspartyl‐<italic toggle=\"yes\">O</italic>‐methyl ester and aspartimide intermediates. More importantly, we show that this evolutionary feature could guide the identification of a novel RiPP subclass, pamtides, in which the PAMT‐mediated Asp‐to‐isoAsp conversion is the primary modification reaction. Using various biochemical characterizations including heterologous co‐expression, in vitro reconstitution, time‐course experiment, and hydrazine trapping as well as mass spectrometry and NMR analyses, we confirmed the conserved PAMT‐mediated Asp‐to‐isoAsp conversion for a group 13 graspetide and a type II pamtide. We also showed the similar reaction features in a type I pamtide. We identified more than 4300 putative RiPP BGCs encoding a PAMT enzyme by mining bacterial genomes. Currently, PAMT‐associated subclasses of RiPPs include pamtides, graspetides, lanthipeptides, lasso peptides, and LAPs. Among them, pamtides are the only subclass in which PAMT functions as a class‐defining modification enzyme.</p>", "<p>The functional role of the Asp‐to‐isoAsp conversion is largely unknown. One possibility is that the conversion to isoAsp generates a β‐amino acid that has one additional hydrocarbon in the peptide backbone, thus releasing the ring strain in the macrocyclic structures. Indeed, the majority of the characterized PAMTs modify an Asp residue located in the macrocyclic (e.g., graspetides, lanthipeptides, and lasso peptides) or hairpin‐like (type II pamtides) region of precursor peptides, requiring fully cyclized peptides as substrates.<sup>[</sup>\n##REF##31568727##\n11\n##\n<sup>]</sup> Another non‐exclusive possibility is that this conversion simply changes the structure in the loop or hairpin region, thus diversifying the physical or functional properties of RiPPs.<sup>[</sup>\n##REF##31568727##\n11a\n##\n<sup>]</sup> Alternatively, as previously suggested, the electrophilic aspartimide intermediate might be the functional product.<sup>[</sup>\n##REF##31568727##\n11\n##\n<sup>]</sup> The microcin C7 biosynthetic pathway was previously reported to involve the formation of an aspartimide intermediate, which is subsequently linked to adenosine monophosphate (AMP) through a P‐N bond and hydrolyzed to produce the Asp‐NH‐AMP moiety within microcin C7.<sup>[</sup>\n##REF##18290647##\n37\n##\n<sup>]</sup>\n</p>", "<p>The widespread distribution of an accessory protein in multiple RiPP subclasses was also illustrated by the RiPP precursor peptide recognition element (RRE) domain,<sup>[</sup>\n##REF##26167873##\n38\n##\n<sup>]</sup> which has not been found in PAMTs. The recent RRE‐guided bioinformatic analysis revealed a novel RiPP class termed daptides.<sup>[</sup>\n##REF##36959188##\n39\n##\n<sup>]</sup> It is highly probable that many other proteins with secondary roles in RiPP biosynthesis are also evolutionarily disseminated to unrelated RiPP subclasses. Tailoring enzymes are often shared by distinct classes of natural products,<sup>[</sup>\n##REF##34880494##\n40\n##\n<sup>]</sup> and genome mining of a tailoring enzyme was recently applied to discover unprecedented fungal arginine‐containing cyclodipeptides.<sup>[</sup>\n##REF##36702957##\n41\n##\n<sup>]</sup> Given that the genome mining focused on a class‐defining modification enzyme typically expands the members of the same RiPP subclass, we believe that genome mining of accessory proteins is a powerful approach to identify novel RiPP subclasses and unprecedented PTMs.</p>" ]
[ "<title>Abstract</title>", "<p>Ribosomally synthesized and post‐translationally modified peptides (RiPPs) are a structurally diverse class of natural products with a distinct biosynthetic logic, the enzymatic modification of genetically encoded precursor peptides. Although their structural and biosynthetic diversity remains largely underexplored, the identification of novel subclasses with unique structural motifs and biosynthetic pathways is challenging. Here, it is reported that peptide/protein L‐aspartyl <italic toggle=\"yes\">O</italic>‐methyltransferases (PAMTs) present in several RiPP subclasses are highly homologous. Importantly, it is discovered that the apparent evolutionary transmission of the PAMT gene to unrelated RiPP subclasses can serve as a basis to identify a novel RiPP subclass. Biochemical and structural analyses suggest that homologous PAMTs convert aspartate to isoaspartate via aspartyl‐<italic toggle=\"yes\">O</italic>‐methyl ester and aspartimide intermediates, and often require cyclic or hairpin‐like structures for modification. By conducting homology‐based bioinformatic analysis of PAMTs, over 2,800 biosynthetic gene clusters (BGCs) are identified for known RiPP subclasses in which PAMTs install a secondary modification, and over 1,500 BGCs where PAMTs function as a primary modification enzyme, thereby defining a new RiPP subclass, named pamtides. The results suggest that the genome mining of proteins with secondary biosynthetic roles can be an effective strategy for discovering novel biosynthetic pathways of RiPPs through the principle of “guilt by association”.</p>", "<p>Comprehensive bioinformatic analysis demonstrates the close evolutionary relationship of peptide/protein L‐aspartyl <italic toggle=\"yes\">O</italic>‐methyltransferases (PAMTs) found in biosynthetic gene clusters for ribosomally synthesized and post‐translationally modified peptides (RiPPs). Genome mining, heterologous expression, mass analysis, and multidimensional nuclear magnetic resonance analyses uncover pamtides, a unique subclass of RiPPs containing isoaspartyl moiety.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6855-cit-0061\">\n<string-name>\n<given-names>H.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>S. H.</given-names>\n<surname>Park</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Kim</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>M. S.</given-names>\n<surname>Koh</surname>\n</string-name>, <string-name>\n<given-names>J. H.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Kim</surname>\n</string-name>, <article-title>Evolutionary Spread of Distinct <italic toggle=\"yes\">O</italic>‐methyltransferases Guides the Discovery of Unique Isoaspartate‐Containing Peptides, Pamtides</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305946</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305946</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank Sihyeong Yi, Yoon Soo Hwang, Jesang Lee for technical support with the NMR analysis. The authors also appreciate Jae‐seung Yu, Woo Jae Jeong, Se‐Min Jung, Inseok Song, Hyunjin Cho, Hyunsung Nam, Seungyeon Woo, Kijeong Yang, Younghyun Kim, and Hye Won Kim for their helpful discussions. The authors also acknowledge the NMR support from the Analysis Center of the Advanced Institute of Convergence Technology, Suwon, Korea. This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) and funded by the Ministry of Education (2021R1A2C1008730 to S.K.; 2022R1A6A3A01086883 to H.L.).</p>", "<p>While this manuscript was under review, another study reported similar biosynthetic gene clusters and enzymatic characterization of an aspartimidylated product (akin to an intermediate on the route to type I pamtide), proposing the name “imiditide” for this peptide class (L. Cao, T. Do, A. Zhu, J. Duan, N. Alam, A. J. Link, J. Am. Chem. Soc. 2023, 145, 18834).</p>", "<p>[Correction added on 18 December 2023 after online publication: Acknowledgment section is updated in this version.]</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available in the supplementary material of this article.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6855-fig-0001\"><label>Figure 1</label><caption><p>Overview of PIMT homolog‐associated peptide maturation. a) Molecular mechanism of reactions by PIMTs and homologs. Isoaspartates (bottom left) are methylated by PIMTs or their homologs to yield isoaspartyl‐<italic toggle=\"yes\">O</italic>‐methylesters (bottom right). Aspartates are similarly transformed to aspartyl‐<italic toggle=\"yes\">O</italic>‐methylesters by the homologs. Nitrogen in the backbone amide of the methylesters attacks the carbonyl group to yield aspartimides (middle), and these can be hydrolyzed either to aspartates or isoaspartates. Accompanying molecular weight changes in these conversions are written below; atoms that added or removed in each step are colored in blue (methyl group from SAM) or red (water molecule or hydroxyl group in methanol). b) Structure of PIMT homolog‐modified lanthipeptide (OlvA(BCS<sub>A</sub>)<sup>GluC</sup>, top left), lasso peptide (lihuanodin, bottom left), and graspetide (fuscimiditide, right). Isoaspartate and aspartimides are highlighted in purple and red, respectively. D‐Aminobutyric acids in the lanthipeptide are denoted as “X” and colored in green. Class‐defining modifications are colored in brown.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6855-fig-0002\"><label>Figure 2</label><caption><p>A PIMT homolog in the model BGC generates isoaspartate in a graspetide. a) Selected model BGC (top) and precursor peptide sequence (bottom). Arrows are color‐coded based on the predicted domains in the proteins. Cleavage sites by either GluC or trypsin are designated by arrows under the precursor sequence. Residues with hydroxyl or acidic side chains are highlighted in red. b) MALDI‐TOF‐MS spectra of purified SsfA, SsfA(B), and SsfA(BM). c) MALDI‐TOF‐MS spectra of the SsfM‐mediated modification of SsfA(B)<sub>63–97</sub> in vitro. Substrates (20 µ<sc>m</sc>) were mixed with SsfM (5 µ<sc>m</sc>) in the presence of SAM (1 m<sc>m</sc>), DTT (1 m<sc>m</sc>), and Tris‐HCl pH 8.0 (50 m<sc>m</sc>) at 25 °C. Reactions were quenched at designated time points and monitored by a mass analyzer. Relative mass values to SsfA(B)<sub>63–97</sub> are indicated above peaks. d) Strip plots of HNCACB and HNcoCACB spectra showing the presence of isoaspartate in SsfA(BM). Magnetization transfer in Asp‐Gly and isoAsp‐Gly for HNCACB and HNcoCACB experiments are illustrated above. Positive and negative contours are colored in black and red, respectively. Chemical shift values, observed, and calculated mass values can be found in Supporting Dataset S1 (Supporting Information).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6855-fig-0003\"><label>Figure 3</label><caption><p>PAMTs are involved in the biosynthesis of various RiPPs. a) A schematic workflow of the genome mining of PAMTs containing C‐terminal domains. b) A maximum likelihood tree of 9408 enzymes is generated, and biochemically characterized PAMTs are annotated. PAMTs encoded in either known RiPP BGCs (graspetides, blue; lanthipeptides, brown; lasso peptides, green; LAPs, purple), newly identified RiPP BGCs (pamtides, red), or conserved gene clusters (FHA‐VWA, dark green; rSAM, dark blue) are labeled with color strips. c–e) Model BGCs for LAPs (c), type I pamtides (d; SpaA, precursor; SpaM, PAMT) and type II pamtides (e; FcaA, precursor; FcaM, PAMT). Sequences of precursors (SpaA and FcaA) are shown below each gene cluster. The structure of FcaA was predicted by Alphafold and zinc ion was modeled by MIB. Conserved residues in FcaA are highlighted by colors (cysteine, blue; glycine, purple; aspartate, red).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6855-fig-0004\"><label>Figure 4</label><caption><p>FcaM mediates isoaspartate installation in a type II pamtide. a) Trypsin cleavage sites in FcaA. b) MALDI‐TOF‐MS spectra of the purified recombinant FcaA and FcaA(M). c) HPLC analysis of FcaA(M)<sub>19–26</sub> (<bold>3</bold>) with synthetic peptides <bold>1</bold> (ITVTSDGK) and <bold>2</bold> (ITVTSisoDGK). d) NMR analysis of FcaA(M)<sub>19–26</sub>. The NOE signal indicates that Asp24 is converted to isoaspartate. e) MALDI‐TOF‐MS spectra of FcaM‐mediated modification of FcaA or its variant in vitro. FcaA or iodoacetamide‐labeled FcaA (FcaA+4IAA, 50 µ<sc>m</sc>) was mixed with FcaM (10 µ<sc>m</sc>) in the presence of DTT (1 m<sc>m</sc>), Tris‐HCl pH 8.0 (20 m<sc>m</sc>), and ZnCl<sub>2</sub> (0 or 100 µ<sc>m</sc>) at 25 °C. Reactions were monitored at designated time points by mass analyzer. f) MALDI‐TOF‐MS spectra showing spontaneous chemical transformation of methylester‐ (left) or aspartimide‐containing intermediates (right). Peptides (20‐100 µM) were dissolved in a buffer containing Tris‐HCl (20 m<sc>m</sc>, pH 8.0), DTT (1 m<sc>m</sc>), and ZnCl<sub>2</sub> (100 µ<sc>m</sc>). The mixture was incubated at 25 °C for designated time points. g) MALDI‐TOF‐MS spectrum of the hydrazide‐containing peptide. The reaction condition for Figure ##SUPPL##0##S3a## (Supporting Information) was adopted to trap the aspartimide by hydrazine. h) Competition assay of 4‐(2‐pyridylazo)resorcinol (PAR) and various substrates toward Zn<sup>2+</sup>. ZnCl<sub>2</sub> (10 µ<sc>m</sc>) was mixed with PAR (100 µ<sc>m</sc>) in a buffer containing Tris‐HCl (20 m<sc>m</sc>, pH 8.0) and NaCl (100 m<sc>m</sc>). 0–15  µ<sc>m</sc> substrates were added to the mixture and absorbance at 500 nm was monitored in each mixture. Each data point is colored based on the substrate. Chemical shift values, observed, and calculated mass values can be found in Supporting Dataset S1 (Supporting Information).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6855-fig-0005\"><label>Figure 5</label><caption><p>SpaM for a type I pamtide catalyzes the homologous reaction to the linear peptide, SpaA. a) MALDI‐TOF‐MS spectra of the purified recombinant SpaA (top) or SpaA(M) (bottom). Brown asterisks denote the laser‐induced deamination of 0 Da species in the mass analyzer. b) MALDI‐TOF‐MS spectra of SpaM‐mediated SpaA modification in vitro. SpaA (20 µ<sc>m</sc>) was mixed with SpaM (5 µ<sc>m</sc>) in presence of DTT (1 m<sc>m</sc>), SAM (1 m<sc>m</sc>), and Tris‐HCl pH 8.0 (50 m<sc>m</sc>) at 25 °C. Reaction was monitored at designated time points by mass analyzer. Relative mass value changes to the intact SpaA are given above peaks. c) MALDI‐TOF‐MS spectra of spontaneous rearrangement of methylester‐ (left) or aspartimide‐containing intermediates (right). Reaction conditions for Figure ##SUPPL##0##S2c## (Supporting Information) were adopted to observe the spontaneous rearrangement of the intermediates. d) MALDI‐TOF‐MS spectrum of hydrazide‐containing peptide. Same reaction condition as Figure ##SUPPL##0##S3a## (Supporting Information) was applied to the aspartimide‐containing intermediate to generate hydrazide. The relative mass value to the intact SpaA is given above the peak. Calculated and observed mass values can be found in Supporting Dataset S1 (Supporting Information).</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6855-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6855-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2305946-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305946-s002.xlsx\"><caption><p>Click here for additional data file.</p></caption></media>" ]
[{"label": ["18"], "mixed-citation": ["\n"], "string-name": ["\n", "\n"], "given-names": ["S.", "A."], "surname": ["Grzesiek", "Bax"], "source": ["J. Magn. Reson."], "year": ["1992"], "volume": ["99"], "fpage": ["201"]}, {"label": ["19"], "mixed-citation": ["\n"], "string-name": ["\n", "\n"], "given-names": ["S.", "A."], "surname": ["Grzesiek", "Bax"], "source": ["J. Am. Chem. Soc."], "year": ["1992"], "volume": ["114"], "fpage": ["6291"]}, {"label": ["20"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n"], "given-names": ["L. E.", "M.", "R.", "A."], "surname": ["Kay", "Ikura", "Tschudin", "Bax"], "source": ["J. Magn. Reson."], "year": ["1990"], "volume": ["89"], "fpage": ["496"]}, {"label": ["21"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n"], "given-names": ["R. T.", "V.", "G."], "surname": ["Clubb", "Thanabal", "Wagner"], "source": ["J. Magn. Reson."], "year": ["1992"], "volume": ["97"], "fpage": ["213"]}]
{ "acronym": [], "definition": [] }
41
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 20; 11(2):2305946
oa_package/9b/b3/PMC10787088.tar.gz
PMC10787089
37997197
[ "<title>Introduction</title>", "<p>Manipulation of light‐matter interactions relies on the electrodynamic properties of the media, and leads to the exploration of new material platforms with unique optical properties in which the refractive index and/or the permittivity is near zero at a given spectral range.<sup>[</sup>\n##REF##29269463##\n1\n##, ##UREF##0##\n2\n##\n<sup>]</sup> Recently, thermal emission in epsilon‐near‐zero (ENZ) and the intimately related near‐zero‐index (NZI) media in the form of thin films and metamaterials has received particular attention because of its capability to engineer the directionality and emissivity of thermal emission with the excitation of the ENZ mode.<sup>[</sup>\n##REF##33888638##\n3\n##, ##UREF##1##\n4\n##, ##REF##12443413##\n5\n##, ##REF##23188363##\n6\n##, ##REF##23389280##\n7\n##, ##UREF##2##\n8\n##\n<sup>]</sup> Among various homogeneous ENZ material platforms satisfying the low optical‐loss condition for realizing NZI property,<sup>[</sup>\n##UREF##3##\n9\n##\n<sup>]</sup> phononic materials are widely utilized in radiative cooling systems that require thermal emissions within the atmospheric transparency window of wavelengths between 8 and 13 µm because ENZ wavelengths of these materials are located beyond 6 µm.</p>", "<p>To realize the concepts of controlling thermal radiations with NZI materials in the mid‐infrared (MIR) range into energy harvesting systems operating at high temperatures of at least 800 °C, where the near‐infrared (NIR) thermal radiations are dominant, metal oxides are considered as potential candidates. However, the optical properties of metal oxides such as indium tin oxide (ITO)<sup>[</sup>\n##REF##27636495##\n10\n##, ##UREF##4##\n11\n##\n<sup>]</sup> and doped zinc oxide (ZnO),<sup>[</sup>\n##UREF##5##\n12\n##\n<sup>]</sup> are very sensitive to high temperatures because thermal treatment of such metal oxides can influence their optical properties due to changes in carrier density and mobility.<sup>[</sup>\n##UREF##6##\n13\n##\n<sup>]</sup> Therefore, there is currently no suitable NZI material operational at high temperatures in the NIR spectral range. Although metal nitrides, such as titanium nitride (TiN) and zirconium nitride (ZrN), have been proposed as refractory ENZ materials covering the spectral range from the visible to NIR,<sup>[</sup>\n##REF##25327161##\n14\n##, ##REF##24744364##\n15\n##, ##REF##28820932##\n16\n##, ##UREF##7##\n17\n##, ##UREF##8##\n18\n##, ##UREF##9##\n19\n##, ##REF##30114830##\n20\n##\n<sup>]</sup> their high optical losses prevent the realization of NZI characteristics. Moreover, most refractory metals are only able to operate in vacuum due to oxidation in air. Thus, discovering new refractory low‐loss ENZ materials that are chemically stable at high temperatures in air while preserving their optical properties is essential. This is particularly important for realizing conceptual advances in NZI performance for practical application in high‐temperature energy harvesting systems such as thermophotovoltaics (TPV) and solar thermoelectric generators.<sup>[</sup>\n##REF##23389280##\n7\n##, ##REF##29041299##\n21\n##, ##REF##36138203##\n22\n##, ##REF##35416207##\n23\n##\n<sup>]</sup>\n</p>", "<p>In this paper, we will present experimental results illustrating perovskite lanthanum doped barium stannate (La:BaSnO<sub>3</sub> [LBSO]) as one of the first candidate for refractory NZI materials operating in the NIR spectral range. Owing to its high electron mobility,<sup>[</sup>\n##UREF##10##\n24\n##, ##UREF##11##\n25\n##\n<sup>]</sup> outstanding thermal stability,<sup>[</sup>\n##UREF##12##\n26\n##\n<sup>]</sup> and tunable electrical properties with controlled doping, LBSO has been highlighted as a promising material for transparent electrodes in perovskite solar cells and optoelectronic devices.<sup>[</sup>\n##UREF##13##\n27\n##\n<sup>]</sup> Extensive research has been conducted on utilizing its superior physical properties in the form of thin films,<sup>[</sup>\n##UREF##14##\n28\n##, ##UREF##15##\n29\n##, ##UREF##16##\n30\n##\n<sup>]</sup> and thus much progress has been made in the synthesis of doped BaSnO<sub>3</sub> (BSO) films for electronic components. Nevertheless, the optical properties of LBSO films compatible with NZI optical media has been overlooked. In our experiments, we focused on optimizing the optical properties of the LBSO films for low‐loss ENZ, which can serve as NZI components, and uncovering the limitation of the physical properties of the doped BSO as refractory materials. In stark contrast to other refractory materials, crystalline LBSO films possess superior thermal stability up to temperatures of 1000 °C in air without any passivation. Furthermore, the NZI property of LBSO films can be maintained remarkably well under high‐intensity UV‐pulsed laser illumination below average power of 1.8 W cm<sup>−2</sup>. Along with the characterization on high‐temperature stability and intense irradiation durability of LBSO films, we employed LBSO films as refractory metallic component in a metal‐insulator‐metal (MIM) configuration to realize a Fabry–Pérot nanocavity which served as a selective narrow‐band thermal emitter operating in the NIR regime. For the dielectric spacer in MIM nanocavity, a perovskite barium stannate (BaTiO<sub>3</sub> [BTO]) film was selected due to its small lattice mismatch with LBSO (lattice constant of LBSO: 4.1 Å and BTO: 4.0 Å). From the analysis of lattice strain, we observed that the fully relaxed lattice strain in the MIM structure helps to retain the excellent refractory properties of LBSO materials, resulting in LBSO‐based thermal emitters that can survive under extreme environmental conditions. Our findings reveal the potential of LBSO as refractory NZI materials that can withstand thermal and optical stress for practical applications in thermal management.</p>" ]
[ "<title>Simulation Methods</title>", "<p>Numerical simulations of the LBSO‐BTO‐LBSO MIM structure was carried out in the frequency domain by using COMSOL Multiphysics simulation software. The absorption spectra were calculated via BTO layer thickness and bottom LBSO layer thickness to determine the optimized thickness of each layer as shown in Figure ##SUPPL##0##S6## (Supporting Information). The measured dielectric properties of LBSO and BTO were used in the simulations.</p>" ]
[ "<title>Results and Discussion</title>", "<p>Highly conductive La‐doped BSO films were deposited on a magnesium oxide (MgO) substrate by pulsed laser deposition (PLD) with a KrF‐excimer laser (<italic toggle=\"yes\">λ</italic> = 248 nm) for source material ablation as shown in <bold>Figure</bold> ##FIG##0##\n1a##. A careful consideration of deposition parameters is required to achieve a low‐loss ENZ property and smooth surface morphology, because certain combinations of deposition temperatures and oxygen partial pressures may induce surface defects such as cracks and voids (see Figure ##SUPPL##0##S3##, Supporting Information). The doping ratio of lanthanum (La) was varied from 3 to 7 wt.% and all LBSO films were deposited at a substrate temperature of 750 °C and an oxygen partial pressure of 100 mTorr, which are the optimal conditions to achieve the lowest optical loss. We achieved precise stoichiometry for the dopant (<italic toggle=\"yes\">L</italic>a) using commercial targets with 3, 5, and 7 wt.% La. This was subsequently confirmed through Energy‐dispersive X‐ray spectroscopy (see Figure ##SUPPL##0##S1##, Supporting Information).</p>", "<p>For characteristic comparison, an AZO film deposited on MgO substrate via PLD and commercial ITO film on glass substrate (MTI Corp.) were prepared, and the thicknesses of the three materials (ITO, AZO, and LBSO) were kept constant at 170 ± 10 nm. The dielectric functions of all the films were measured with ellipsometry by fitting a lossy Drude oscillator model:\nwhere, ε<sub>∞</sub> is the high‐frequency limit of the permittivity, ω<sub>p</sub> is the plasma frequency (proportional to the carrier density), and Γ<sub>p</sub> is the damping factor (inversely proportional to the carrier mobility). As shown in the dielectric functions (Figure ##FIG##0##1b,c##), all three material systems exhibit ENZ conditions within the NIR range; 1.21, 1.34, and 1.44 µm for ITO, AZO, and 7 wt.% La‐doped BSO film, respectively, with the imaginary part of the permittivity (<italic toggle=\"yes\">Im</italic>(ε)) at ENZ points of 0.41 (ITO), 0.47 (AZO), and 0.45 (LBSO). The results indicate that the optical properties of the LBSO are suitable to be considered as an alternative NZI material in the NIR range as they satisfy the permittivity condition defined as <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>I</mml:mi><mml:mi>m</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ε</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:msqrt><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi>R</mml:mi><mml:mi>e</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ε</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msqrt></mml:mrow></mml:mrow></mml:math>, where <italic toggle=\"yes\">Re</italic>(ε) and <italic toggle=\"yes\">Im</italic>(ε) are the real and imaginary part of the permittivity, respectively. The ENZ wavelength can be broadly tuned from 1.44 to 2.1 µm by controlling the doping ratio (<italic toggle=\"yes\">x</italic>) of La while maintaining the low‐loss characteristics. The optical properties (ω<sub>p</sub> and Γ<sub>p</sub>) and the electrical properties including electron mobility (µ<sub>e</sub>) and carrier concentration (<italic toggle=\"yes\">n</italic>\n<sub>e</sub>) of all materials examined in this experiment is provided in <bold>Table</bold> ##TAB##0##\n1\n##. We note that the high mobility of LBSO films helps to compensate for its large µ<sub>∞</sub>, which in‐turn satisfies the NZI condition by decreasing the imaginary part of the permittivity at the ENZ wavelength.</p>", "<p>The refractory properties of LBSO films were characterized by monitoring the change of optical properties upon a cycle of heating and cooling in ambient air. For heating, the samples were maintained at designated temperatures (200–1100 °C) for 1 h and for cooling, the samples were cooled down to room temperature at a rate of 5 °C min<sup>−1</sup> to prevent cracking. The ITO and AZO films were treated in the same way to compare the thermal stability of all conducting oxides examined in this study. The <italic toggle=\"yes\">p</italic>‐polarized transmittances with an incident angle of 60° clearly display the variation of the ENZ wavelength and optical loss from the spectral location and intensity of the absorption dip induced by the ENZ mode (see Figure ##SUPPL##0##S2##, Supporting Information). To accurately compare the impact of exposure to high temperature, the optical properties (ω<sub>p</sub> and Γ<sub>p</sub>) of all materials are plotted in <bold>Figure</bold> ##FIG##1##\n2a,b##. Both ITO and AZO maintain their optical properties up to temperatures of 300 °C, while considerable changes in ω<sub>p</sub> are observed as the temperature approaches 350 °C. In particular, Γ<sub>p</sub> of the AZO is less stable than that of the ITO even at lower temperatures. It indicates that oxygen defects within the films initially generated to achieve high carrier density actually plays a significant role in degrading the thermal stability in air. On the other hand, ω<sub>p</sub> and Γ<sub>p</sub> of the LBSO films remain consistent up to a temperature of 350 °C, with only a marginal change of ≈5% before a noticeable change is observed at 1100 °C. The maximum operating temperature of the LBSO as a refractory material is comparable to that of the existing plasmonic refractory materials such as TiN,<sup>[</sup>\n##UREF##8##\n18\n##, ##UREF##9##\n19\n##, ##UREF##17##\n31\n##\n<sup>]</sup> molybdenum (Mo),<sup>[</sup>\n##UREF##18##\n32\n##, ##UREF##19##\n33\n##\n<sup>]</sup> iridium (Ir),<sup>[</sup>\n##UREF##20##\n34\n##\n<sup>]</sup> and tungsten (W),<sup>[</sup>\n##REF##27263653##\n35\n##, ##REF##30395478##\n36\n##, ##UREF##21##\n37\n##, ##REF##31076610##\n38\n##, ##UREF##22##\n39\n##\n<sup>]</sup> which have been reported to be stable up to temperatures of 900, 1000, 1000, and 1200 °C, respectively (see <bold>Table</bold> ##TAB##1##\n2\n##). The results highlight the fact that optical properties of LBSO films are preserved in air without the aid of a passivating layer (e.g., Al<sub>2</sub>O<sub>3</sub> or HfO<sub>2</sub>) to prevent oxidation in ambient air, which clearly reveals that the LBSO system is well‐suited for applications with demanding stability requirements, especially the ones designed for high temperature operation in air atmosphere.</p>", "<p>The scanning electron microscope (SEM) in Figure ##FIG##1##2c## shows the changes in surface morphology after exposure to high temperatures. There is no significant change on the surface when the temperature is increased to 700 °C; however, small particles with radii varying from 10 to 20 nm are generated on the surface that increase in size with increasing temperature of up to 900 °C. At 1100 °C, the formation of randomly distributed rectangular features of a few hundred nanometers was observed on the surface. From the total reflectance at an incident angle of 8° and a diffuse (scattered) reflectance at normal incidence (Figure ##SUPPL##0##S5##, Supporting Information), we notice that rectangular features formed on the surface at 1100 °C may have an impact on the optical performance, whereas there is no discernible scattering of incident light from the LBSO films exposed to temperatures below 1000 °C.</p>", "<p>The out‐of‐plane X‐ray diffraction (XRD) patterns (Figure ##FIG##1##2d##) display the crystal structure of the LBSO after heating at various temperatures. The as‐grown LBSO film has diffraction peaks only at (00α), referring to a highly crystalline <italic toggle=\"yes\">c</italic>‐axis oriented perovskite crystal structure. Interestingly, we observe a negligible shift of LBSO peak (Δθ<sub>(002)</sub> ≈0.03°) despite heating at a temperature of 1100 °C in air. Strain characterization of the as‐deposited LBSO film with the reciprocal space map (RSM) in Figure ##FIG##1##2e## provides a possible explanation for the remarkable thermal stability from the crystal structure of the LBSO film. The diffraction peak position of the as‐grown LBSO film is located on a relaxation line, implying that there is no lattice strain and stress in the LBSO film in the as‐deposited state. In general, notable XRD peak shifts in crystalline films by thermal‐annealing are observed when the crystal lattices of the films are strongly strained in the presence of defects and dislocations.<sup>[</sup>\n##REF##35354865##\n40\n##\n<sup>]</sup> Therefore, we expect that the thermal stability of the LBSO film to be a result of the unstrained (fully relaxed) lattice in the as‐deposited state.</p>", "<p>As a next step to verify the applicability of refractory LBSO films to practical thermal processing as well as for TPV systems, we designed a selective narrow‐band thermal emitter in the NIR regime based on an MIM Fabry–Pérot nano‐cavity.<sup>[</sup>\n##REF##30114830##\n20\n##, ##UREF##17##\n31\n##, ##UREF##20##\n34\n##, ##REF##27263653##\n35\n##, ##UREF##23##\n41\n##\n<sup>]</sup> The schematic of the MIM thermal emitter is shown in <bold>Figure</bold> ##FIG##2##\n3a##. Perovskite BTO film was chosen as the dielectric spacer considering the lattice parameter of each layer (lattice constant of LBSO: 4.1 Å and BTO: 4.0 Å) for crystal growth on MgO substrate with minimal lattice strain. In general, nanopatterning of practical refractory metal is required to achieve narrow‐band spectral absorption due to its high optical loss and large magnitude of real permittivity. On the other hand, the low optical loss in optimized LBSO thin films enables a narrow‐band thermal emission with simple MIM geometry without nanopatterning as depicted in the simulated absorption spectrum of MIM thermal emitter by changing Γ<sub>p</sub> of LBSO film (Figure ##FIG##2##3b##). We designed the thermal emitter to achieve a near‐unity absorption at a wavelength of 2.2 µm which corresponds to the peak of black body radiation at 1000 °C. The thickness of bottom LBSO layer (<italic toggle=\"yes\">t</italic>\n<sub>1</sub>), BTO layer (<italic toggle=\"yes\">t</italic>\n<sub>2</sub>), and top LBSO layer (<italic toggle=\"yes\">t</italic>\n<sub>3</sub>) was set to 400, 200, and 100 nm, respectively. The details on the design and optimization of MIM thermal emitter are described in Figure ##SUPPL##0##S6## (Supporting Information).</p>", "<p>Figure ##FIG##2##3c## shows the measured absorption spectrum of MIM thermal emitter, obtained by UV–vis spectroscopy between 1.0 and 2.7 µm. The measured absorption spectrum of the as‐fabricated thermal emitter is in good agreement with the simulated absorption spectrum based on the optical properties of as‐deposited LBSO film. To examine the long‐term stability of MIM thermal emitters, repeated heating cycles were performed by maintaining the sample at high temperatures in air for 8 h. Similar to changes in the optical properties of LBSO films under high temperature, the narrow band absorption peak of the thermal emitter exhibits a slight shift with increasing temperature of up to 1000 °C, while a notable shift is observed at 1100 °C. After the initial modification of characteristics upon first heating cycle, absorption spectra of thermal emitters were preserved with repeated heating cycles. Figure ##FIG##2##3d## shows the simulated absorption spectra of the thermal emitter with the optical properties of the LBSO thin film modified after heating at temperatures of 900, 1000, and 1100 °C, respectively, which are well‐matched with the experimental data. Based on the cross‐sectional SEM image and RSM data, we confirm that exposure to high temperatures of up to 1000 °C does not significantly affect to the design and the crystal structure of the LBSO‐based MIM thermal emitter. Therefore, it is feasible to design a thermal emitter tailored to desired operating temperatures by estimating the performance with modified optical properties of the LBSO film upon heating. Lastly, we performed the heating process at 900 °C for 24 h to confirm the long‐term stability, as shown in Figure ##SUPPL##0##S7## (Supporting Information). We clearly observed that absorption spectra of thermal emitters were preserved regardless of heating duration.</p>", "<p>In addition to investigating the stability of LBSO film at high temperatures using thermal sources, we evaluated the durability of the NZI property upon laser irradiation because intense optical excitation such as sunlight is one of the main heating sources for emission systems operating at high temperatures in practical applications. For this experiment, we prepared ITO, AZO, and LBSO films with dielectric functions as depicted in Figure ##FIG##0##1b##. Under UV excimer pulsed laser illumination with an average power of 1.0 W cm<sup>−2</sup> (peak power of 5 MW cm<sup>−2</sup>) for 30 min, the LBSO film retained its optical properties as shown in <bold>Figure</bold> ##FIG##3##\n4a##. In contrast, the ENZ wavelengths of the AZO and ITO films are significantly red‐shifted with their peaks broadened owing to the increased optical loss. When the average power is increased to 1.8 W cm<sup>−2</sup> (peak power of 9 MW cm<sup>−2</sup>), AZO and ITO films were significantly damaged, and we are no longer able to analyze these films. Strikingly, the ENZ wavelength of the LBSO is approximately constant despite etching of the films down to 90 nm (see Figure ##SUPPL##0##S9##, Supporting Information), even though the optical loss is increased due to surface cracks at grain boundaries and thickness reduction. We further performed the same experiment on the MIM thermal emitter. It can be seen that the absorption of LBSO‐based MIM thermal emitter is maintained under the laser excitation with an average power of 1.0 W cm<sup>−2</sup>, but the absorption was slightly decreased when an average power of 1.8 W cm<sup>−2</sup> was used as shown in Figure ##FIG##3##4b##. Considering that the laser powers used in this experimental set up is similar to the conditions of excimer laser annealing (ELA), our results suggest that the optical properties of the LBSO materials can be retained under exposure to UV excitation with an intensity that is high enough to induce strong interband absorption causing melting and ablation of the films associated with localized heating.</p>" ]
[ "<title>Results and Discussion</title>", "<p>Highly conductive La‐doped BSO films were deposited on a magnesium oxide (MgO) substrate by pulsed laser deposition (PLD) with a KrF‐excimer laser (<italic toggle=\"yes\">λ</italic> = 248 nm) for source material ablation as shown in <bold>Figure</bold> ##FIG##0##\n1a##. A careful consideration of deposition parameters is required to achieve a low‐loss ENZ property and smooth surface morphology, because certain combinations of deposition temperatures and oxygen partial pressures may induce surface defects such as cracks and voids (see Figure ##SUPPL##0##S3##, Supporting Information). The doping ratio of lanthanum (La) was varied from 3 to 7 wt.% and all LBSO films were deposited at a substrate temperature of 750 °C and an oxygen partial pressure of 100 mTorr, which are the optimal conditions to achieve the lowest optical loss. We achieved precise stoichiometry for the dopant (<italic toggle=\"yes\">L</italic>a) using commercial targets with 3, 5, and 7 wt.% La. This was subsequently confirmed through Energy‐dispersive X‐ray spectroscopy (see Figure ##SUPPL##0##S1##, Supporting Information).</p>", "<p>For characteristic comparison, an AZO film deposited on MgO substrate via PLD and commercial ITO film on glass substrate (MTI Corp.) were prepared, and the thicknesses of the three materials (ITO, AZO, and LBSO) were kept constant at 170 ± 10 nm. The dielectric functions of all the films were measured with ellipsometry by fitting a lossy Drude oscillator model:\nwhere, ε<sub>∞</sub> is the high‐frequency limit of the permittivity, ω<sub>p</sub> is the plasma frequency (proportional to the carrier density), and Γ<sub>p</sub> is the damping factor (inversely proportional to the carrier mobility). As shown in the dielectric functions (Figure ##FIG##0##1b,c##), all three material systems exhibit ENZ conditions within the NIR range; 1.21, 1.34, and 1.44 µm for ITO, AZO, and 7 wt.% La‐doped BSO film, respectively, with the imaginary part of the permittivity (<italic toggle=\"yes\">Im</italic>(ε)) at ENZ points of 0.41 (ITO), 0.47 (AZO), and 0.45 (LBSO). The results indicate that the optical properties of the LBSO are suitable to be considered as an alternative NZI material in the NIR range as they satisfy the permittivity condition defined as <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>I</mml:mi><mml:mi>m</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ε</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>&lt;</mml:mo><mml:msqrt><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi>R</mml:mi><mml:mi>e</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>ε</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:msqrt></mml:mrow></mml:mrow></mml:math>, where <italic toggle=\"yes\">Re</italic>(ε) and <italic toggle=\"yes\">Im</italic>(ε) are the real and imaginary part of the permittivity, respectively. The ENZ wavelength can be broadly tuned from 1.44 to 2.1 µm by controlling the doping ratio (<italic toggle=\"yes\">x</italic>) of La while maintaining the low‐loss characteristics. The optical properties (ω<sub>p</sub> and Γ<sub>p</sub>) and the electrical properties including electron mobility (µ<sub>e</sub>) and carrier concentration (<italic toggle=\"yes\">n</italic>\n<sub>e</sub>) of all materials examined in this experiment is provided in <bold>Table</bold> ##TAB##0##\n1\n##. We note that the high mobility of LBSO films helps to compensate for its large µ<sub>∞</sub>, which in‐turn satisfies the NZI condition by decreasing the imaginary part of the permittivity at the ENZ wavelength.</p>", "<p>The refractory properties of LBSO films were characterized by monitoring the change of optical properties upon a cycle of heating and cooling in ambient air. For heating, the samples were maintained at designated temperatures (200–1100 °C) for 1 h and for cooling, the samples were cooled down to room temperature at a rate of 5 °C min<sup>−1</sup> to prevent cracking. The ITO and AZO films were treated in the same way to compare the thermal stability of all conducting oxides examined in this study. The <italic toggle=\"yes\">p</italic>‐polarized transmittances with an incident angle of 60° clearly display the variation of the ENZ wavelength and optical loss from the spectral location and intensity of the absorption dip induced by the ENZ mode (see Figure ##SUPPL##0##S2##, Supporting Information). To accurately compare the impact of exposure to high temperature, the optical properties (ω<sub>p</sub> and Γ<sub>p</sub>) of all materials are plotted in <bold>Figure</bold> ##FIG##1##\n2a,b##. Both ITO and AZO maintain their optical properties up to temperatures of 300 °C, while considerable changes in ω<sub>p</sub> are observed as the temperature approaches 350 °C. In particular, Γ<sub>p</sub> of the AZO is less stable than that of the ITO even at lower temperatures. It indicates that oxygen defects within the films initially generated to achieve high carrier density actually plays a significant role in degrading the thermal stability in air. On the other hand, ω<sub>p</sub> and Γ<sub>p</sub> of the LBSO films remain consistent up to a temperature of 350 °C, with only a marginal change of ≈5% before a noticeable change is observed at 1100 °C. The maximum operating temperature of the LBSO as a refractory material is comparable to that of the existing plasmonic refractory materials such as TiN,<sup>[</sup>\n##UREF##8##\n18\n##, ##UREF##9##\n19\n##, ##UREF##17##\n31\n##\n<sup>]</sup> molybdenum (Mo),<sup>[</sup>\n##UREF##18##\n32\n##, ##UREF##19##\n33\n##\n<sup>]</sup> iridium (Ir),<sup>[</sup>\n##UREF##20##\n34\n##\n<sup>]</sup> and tungsten (W),<sup>[</sup>\n##REF##27263653##\n35\n##, ##REF##30395478##\n36\n##, ##UREF##21##\n37\n##, ##REF##31076610##\n38\n##, ##UREF##22##\n39\n##\n<sup>]</sup> which have been reported to be stable up to temperatures of 900, 1000, 1000, and 1200 °C, respectively (see <bold>Table</bold> ##TAB##1##\n2\n##). The results highlight the fact that optical properties of LBSO films are preserved in air without the aid of a passivating layer (e.g., Al<sub>2</sub>O<sub>3</sub> or HfO<sub>2</sub>) to prevent oxidation in ambient air, which clearly reveals that the LBSO system is well‐suited for applications with demanding stability requirements, especially the ones designed for high temperature operation in air atmosphere.</p>", "<p>The scanning electron microscope (SEM) in Figure ##FIG##1##2c## shows the changes in surface morphology after exposure to high temperatures. There is no significant change on the surface when the temperature is increased to 700 °C; however, small particles with radii varying from 10 to 20 nm are generated on the surface that increase in size with increasing temperature of up to 900 °C. At 1100 °C, the formation of randomly distributed rectangular features of a few hundred nanometers was observed on the surface. From the total reflectance at an incident angle of 8° and a diffuse (scattered) reflectance at normal incidence (Figure ##SUPPL##0##S5##, Supporting Information), we notice that rectangular features formed on the surface at 1100 °C may have an impact on the optical performance, whereas there is no discernible scattering of incident light from the LBSO films exposed to temperatures below 1000 °C.</p>", "<p>The out‐of‐plane X‐ray diffraction (XRD) patterns (Figure ##FIG##1##2d##) display the crystal structure of the LBSO after heating at various temperatures. The as‐grown LBSO film has diffraction peaks only at (00α), referring to a highly crystalline <italic toggle=\"yes\">c</italic>‐axis oriented perovskite crystal structure. Interestingly, we observe a negligible shift of LBSO peak (Δθ<sub>(002)</sub> ≈0.03°) despite heating at a temperature of 1100 °C in air. Strain characterization of the as‐deposited LBSO film with the reciprocal space map (RSM) in Figure ##FIG##1##2e## provides a possible explanation for the remarkable thermal stability from the crystal structure of the LBSO film. The diffraction peak position of the as‐grown LBSO film is located on a relaxation line, implying that there is no lattice strain and stress in the LBSO film in the as‐deposited state. In general, notable XRD peak shifts in crystalline films by thermal‐annealing are observed when the crystal lattices of the films are strongly strained in the presence of defects and dislocations.<sup>[</sup>\n##REF##35354865##\n40\n##\n<sup>]</sup> Therefore, we expect that the thermal stability of the LBSO film to be a result of the unstrained (fully relaxed) lattice in the as‐deposited state.</p>", "<p>As a next step to verify the applicability of refractory LBSO films to practical thermal processing as well as for TPV systems, we designed a selective narrow‐band thermal emitter in the NIR regime based on an MIM Fabry–Pérot nano‐cavity.<sup>[</sup>\n##REF##30114830##\n20\n##, ##UREF##17##\n31\n##, ##UREF##20##\n34\n##, ##REF##27263653##\n35\n##, ##UREF##23##\n41\n##\n<sup>]</sup> The schematic of the MIM thermal emitter is shown in <bold>Figure</bold> ##FIG##2##\n3a##. Perovskite BTO film was chosen as the dielectric spacer considering the lattice parameter of each layer (lattice constant of LBSO: 4.1 Å and BTO: 4.0 Å) for crystal growth on MgO substrate with minimal lattice strain. In general, nanopatterning of practical refractory metal is required to achieve narrow‐band spectral absorption due to its high optical loss and large magnitude of real permittivity. On the other hand, the low optical loss in optimized LBSO thin films enables a narrow‐band thermal emission with simple MIM geometry without nanopatterning as depicted in the simulated absorption spectrum of MIM thermal emitter by changing Γ<sub>p</sub> of LBSO film (Figure ##FIG##2##3b##). We designed the thermal emitter to achieve a near‐unity absorption at a wavelength of 2.2 µm which corresponds to the peak of black body radiation at 1000 °C. The thickness of bottom LBSO layer (<italic toggle=\"yes\">t</italic>\n<sub>1</sub>), BTO layer (<italic toggle=\"yes\">t</italic>\n<sub>2</sub>), and top LBSO layer (<italic toggle=\"yes\">t</italic>\n<sub>3</sub>) was set to 400, 200, and 100 nm, respectively. The details on the design and optimization of MIM thermal emitter are described in Figure ##SUPPL##0##S6## (Supporting Information).</p>", "<p>Figure ##FIG##2##3c## shows the measured absorption spectrum of MIM thermal emitter, obtained by UV–vis spectroscopy between 1.0 and 2.7 µm. The measured absorption spectrum of the as‐fabricated thermal emitter is in good agreement with the simulated absorption spectrum based on the optical properties of as‐deposited LBSO film. To examine the long‐term stability of MIM thermal emitters, repeated heating cycles were performed by maintaining the sample at high temperatures in air for 8 h. Similar to changes in the optical properties of LBSO films under high temperature, the narrow band absorption peak of the thermal emitter exhibits a slight shift with increasing temperature of up to 1000 °C, while a notable shift is observed at 1100 °C. After the initial modification of characteristics upon first heating cycle, absorption spectra of thermal emitters were preserved with repeated heating cycles. Figure ##FIG##2##3d## shows the simulated absorption spectra of the thermal emitter with the optical properties of the LBSO thin film modified after heating at temperatures of 900, 1000, and 1100 °C, respectively, which are well‐matched with the experimental data. Based on the cross‐sectional SEM image and RSM data, we confirm that exposure to high temperatures of up to 1000 °C does not significantly affect to the design and the crystal structure of the LBSO‐based MIM thermal emitter. Therefore, it is feasible to design a thermal emitter tailored to desired operating temperatures by estimating the performance with modified optical properties of the LBSO film upon heating. Lastly, we performed the heating process at 900 °C for 24 h to confirm the long‐term stability, as shown in Figure ##SUPPL##0##S7## (Supporting Information). We clearly observed that absorption spectra of thermal emitters were preserved regardless of heating duration.</p>", "<p>In addition to investigating the stability of LBSO film at high temperatures using thermal sources, we evaluated the durability of the NZI property upon laser irradiation because intense optical excitation such as sunlight is one of the main heating sources for emission systems operating at high temperatures in practical applications. For this experiment, we prepared ITO, AZO, and LBSO films with dielectric functions as depicted in Figure ##FIG##0##1b##. Under UV excimer pulsed laser illumination with an average power of 1.0 W cm<sup>−2</sup> (peak power of 5 MW cm<sup>−2</sup>) for 30 min, the LBSO film retained its optical properties as shown in <bold>Figure</bold> ##FIG##3##\n4a##. In contrast, the ENZ wavelengths of the AZO and ITO films are significantly red‐shifted with their peaks broadened owing to the increased optical loss. When the average power is increased to 1.8 W cm<sup>−2</sup> (peak power of 9 MW cm<sup>−2</sup>), AZO and ITO films were significantly damaged, and we are no longer able to analyze these films. Strikingly, the ENZ wavelength of the LBSO is approximately constant despite etching of the films down to 90 nm (see Figure ##SUPPL##0##S9##, Supporting Information), even though the optical loss is increased due to surface cracks at grain boundaries and thickness reduction. We further performed the same experiment on the MIM thermal emitter. It can be seen that the absorption of LBSO‐based MIM thermal emitter is maintained under the laser excitation with an average power of 1.0 W cm<sup>−2</sup>, but the absorption was slightly decreased when an average power of 1.8 W cm<sup>−2</sup> was used as shown in Figure ##FIG##3##4b##. Considering that the laser powers used in this experimental set up is similar to the conditions of excimer laser annealing (ELA), our results suggest that the optical properties of the LBSO materials can be retained under exposure to UV excitation with an intensity that is high enough to induce strong interband absorption causing melting and ablation of the films associated with localized heating.</p>" ]
[ "<title>Conclusion</title>", "<p>In this study, crystalline LBSO thin film exhibits NZI property in the NIR regime similar to conventional metal oxides, and the unstrained lattice structure of LBSO helps to achieve superior stability under thermal heating and intense laser irradiation. Compared to the existing refractory materials summarized in Table ##TAB##1##2##, it is clear that the LBSO system has the potential as a refractory material for practical applications operating in various gaseous (e.g., oxygen and nitrogen) environments due to its thermal stability in air. For efficient control of thermal emission with NZI materials, it is essential to choose a material with their ENZ bandwidths closer to the desired thermal emission spectrum. Therefore, the tunable optical properties of LBSO through doping can provide the flexibility in designing thermal emitters with tailored operating spectrum. Moreover, with a combination of strong nonlinear efficiency in ENZ property and superior durability against intense laser irradiation, the LBSO system is a great material platform for nonlinear optics including carrier dynamics, harmonic generations, and saturable absorptions. Thus, we expect that the introduction of this new refractory NZI material into the realm of nanophotonics will expand the application domain and enhance the performance of various devices in energy harvesting, high‐temperature material processing, aerospace technologies and other high temperature optical systems.</p>" ]
[ "<title>Abstract</title>", "<p>The recent interests in bridging intriguing optical phenomena and thermal energy management has led to the demonstration of controlling thermal radiation with epsilon‐near‐zero (ENZ) and the related near‐zero‐index (NZI) optical media. In particular, the manipulation of thermal emission using phononic ENZ and NZI materials has shown promise in mid‐infrared radiative cooling systems operating under low‐temperature environments (below 100 °C). However, the absence of NZI materials capable of withstanding high temperatures has limited the spectral extension of these advanced technologies to the near‐infrared (NIR) regime. Herein, a perovskite conducting oxide, lanthanum‐doped barium stannate (La:BaSnO<sub>3</sub> [LBSO]), as a refractory NZI material well suited for engineering NIR thermal emission is proposed. This work focuses on the experimental demonstration of superior high‐temperature stability (of at least 1000 °C) of LBSO films in air and its durability under intense UV‐pulsed laser irradiation below peak power of 9 MW cm<sup>−2</sup>. Based on the low optical‐loss in LBSO, a selective narrow‐band thermal emission utilizing a metal‐insulator‐metal (MIM) Fabry–Pérot nanocavity consisting of LBSO films as metallic component is demonstrated. This study shows that LBSO is an ideal candidate as a refractory NZI component for thermal energy conversion operating at high temperatures in air and under strong light irradiations.</p>", "<p>Recent research has explored optical phenomena for thermal energy management using near‐zero‐index (NZI) materials. A perovskite oxide, La:BaSnO<sub>3</sub> (LBSO), as a high‐temperature NZI material for near‐infrared thermal emission is introduced. LBSO exhibits stability at 1000 °C and resistance to intense UV laser. Using LBSO in a metal‐insulator‐metal nanocavity, selective narrow‐band thermal emission, promising for high‐temperature energy conversion, is achieved.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6848-cit-0050\">\n<string-name>\n<given-names>H.</given-names>\n<surname>Kim</surname>\n</string-name>, <string-name>\n<given-names>G.</given-names>\n<surname>Kim</surname>\n</string-name>, <string-name>\n<given-names>Y.‐U.</given-names>\n<surname>Jeon</surname>\n</string-name>, <string-name>\n<given-names>W.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>B.‐H.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>I. S.</given-names>\n<surname>Kim</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Lee</surname>\n</string-name>, <string-name>\n<given-names>S. J.</given-names>\n<surname>Kim</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Kim</surname>\n</string-name>, <article-title>Perovskite Lanthanum‐Doped Barium Stannate: A Refractory Near‐Zero‐Index Material for High‐Temperature Energy Harvesting Systems</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2302410</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202302410</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Sample Preparation</title>", "<p>The LBSO films were deposited on MgO substrates with (100) orientation by the PLD using a KrF excimer laser (Coherent, wavelength of 248 nm, energy density of 1.4 J cm<sup>−2</sup>, and repetition rate of 1 Hz). The LBSO target was purchased from Toshima Co, Ltd., and the doping concentration of La was 3, 5, and 7 wt.%. The AZO films were deposited on soda‐lime glass substrates by the same PLD maintaining the deposition temperature at 200 °C with an energy of 1.4 J cm<sup>−2</sup> in the absence of oxygen.</p>", "<title>Thermal Emitter Fabrication</title>", "<p>A BTO layer sandwiched between two LBSO layers was deposited on a MgO substrate to form a LBSO‐BTO‐LBSO MIM structure by PLD. Top LBSO layer (100 nm) and bottom LBSO layer (400 nm) were deposited at 750 °C, with oxygen pressure of 100 mTorr and energy density of 1.4 J cm<sup>−2</sup>, which are the optimized conditions in this work. The BTO layer was deposited at the same temperature and energy density, but with an oxygen pressure of 10 mTorr. The deposition of the entire structure was performed in situ within the PLD chamber.</p>", "<title>High‐Temperature Thermal Treatments</title>", "<p>All the films were thermally treated using an electric furnace (CWF 1200, Carbolite) at various temperatures ranging from 200 to 1100 °C. Specifically, AZO and ITO films were exposed to temperatures of up to 500 °C, while the LBSO film was exposed to the full temperature range. The samples were maintained at the peak temperature for 8 h and the furnace was slowly heated and cooled at a rate of 5 °C min<sup>−1</sup> to minimize film damage.</p>", "<title>Laser Irradiation</title>", "<p>For UV laser irradiation, the same KrF excimer laser used for film deposition was employed. The laser frequency was set to 10 Hz and the laser pulse duration was 20 ns. The duration for the laser illumination was 30 min for an average power of 1.0 W cm<sup>−2</sup>, but the laser with an average power of 1.8 W cm<sup>−2</sup> was illuminated for a relatively short duration (10 min) owing to the etching of the film. During the laser irradiation, the real‐time temperatures of the samples were measured and imaged using a thermal camera (FLIR E8).</p>", "<title>Optical Measurement</title>", "<p>The optical properties of all the films before and after heating were characterized by spectroscopic ellipsometry (SE MG‐1000). The dielectric function of the films was retrieved by fitting the Drude model to ellipsometry data. To confirm the extracted dielectric functions, a simulation on transmittance spectra using COMSOL Multiphysics was performed. The linear optical properties of the films were characterized by a UV–vis spectrophotometer (UV‐3600 Plus, Shimadzu, Japan) analysis, with wavelengths ranging from 700 to 2200 nm. The incident beam was polarized by rotating a linear polarizer to measure the <italic toggle=\"yes\">p‐</italic>polarized and <italic toggle=\"yes\">s‐</italic>polarized transmittance.</p>", "<title>XRD and RSM Characterization</title>", "<p>Structural analyses of the samples were conducted by using a high resolution X‐ray diffraction (HRXRD, Rigaku ATX‐G) with CuKα. A symmetric Ge[220] monochromator was used on the primary beam with a scan width and scan speed of 0.01° and 0.4° min<sup>−1</sup>, respectively. Reciprocal space mapping (RSM) was performed around the (224) diffraction spots to estimate the extent of relaxation of the deposited thin films.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was partially supported by the Institute of Information &amp; Communications Technology Planning &amp; Evaluation (IITP) grant funded by the Korean government (MSIT) (No. RS‐2023‐00223082, Development of Quantum Technology for High‐Precision Gravity Sensing) and by the R&amp;D Program (2E32541) funded by the Korea Institute of Science and Technology (KIST).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6848-fig-0001\"><label>Figure 1</label><caption><p>Epsilon‐near‐zero (ENZ) characteristics of LBSO films. a) Cross‐sectional scanning electron microscope (SEM) image and schematic of the crystal structure of LBSO thin film on MgO substrate. b) Real and c) imaginary parts of the dielectric functions of ITO, AZO, and LBSO films. The La doping rate of LBSO film is varied from 3 to 7 wt.%. The ENZ wavelengths of the three materials are at 1.21, 1.34, and 1.44 µm for ITO, AZO, and 7 wt.% La‐doped BSO, respectively.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6848-fig-0002\"><label>Figure 2</label><caption><p>Refractory property of LBSO thin film under air atmosphere. a) Plasma‐frequency (ω<sub>p</sub>) and b) damping coefficient (Γ<sub>p</sub>) of ITO, AZO, and LBSO films with three different La doping rate as a function of the heating temperature. c) SEM images of the surface morphology and d) X‐ray diffraction (XRD) patterns of the LBSO films before and after heating at high temperatures of 700, 900, and 1100 °C. e) The reciprocal space mapping (RSM) of the (224) diffraction of the as‐grown LBSO film deposited on the MgO substrate. Gray dashed line corresponds to the condition of strain relaxation. The diffraction peak position of the LBSO film located on the relaxation line shows that the LBSO film is fully relaxed at the grown stage.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6848-fig-0003\"><label>Figure 3</label><caption><p>Long‐term thermal stability of refractory LBSO‐based MIM thermal emitter in air atmosphere. a) Schematic image of the refractory thermal emitter design and crystal structure of nanocavity based on LBSO/BTO/LBSO multilayers. b) Simulated absorption spectrum of the thermal emitter as a function of damping coefficient of LBSO thin film (<mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mrow><mml:mi mathvariant=\"normal\">p</mml:mi><mml:mo>_</mml:mo><mml:mi>LBSO</mml:mi></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and wavelength. <mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mrow><mml:mi mathvariant=\"normal\">p</mml:mi><mml:mo>_</mml:mo><mml:mi>LBSO</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math> of 7 wt.% La‐doped BSO film optimized in this work corresponds to the data represented by the white dashed line. c) Measured and d) simulated absorption spectra of the MIM structure at room temperature and after heating cycles at various high temperatures. A normalized blackbody radiation spectrum obtained at 1000 °C is also shown in the background for comparison. e) SEM cross‐sectional view and f) Reciprocal space mapping (RSM) of the (224) diffraction of MIM thermal emitter before heating and after 1000 °C heating cycle. Gray‐dashed line corresponds to the condition of strain relaxation.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6848-fig-0004\"><label>Figure 4</label><caption><p>Durability of LBSO film and LBSO‐based MIM thermal emitter to intense laser irradiation. a) The ratio of transmittance for <italic toggle=\"yes\">p</italic>‐polarized (<italic toggle=\"yes\">T</italic>\n<sub>TM</sub>) and <italic toggle=\"yes\">s</italic>‐polarized (<italic toggle=\"yes\">T</italic>\n<sub>TE</sub>) with an angle of incidence at 60° under dark and laser illumination with average power of 1.0 and 1.8 W cm<sup>−2</sup>. Inset: Thermal images of LBSO films obtained by IR camera. b) Optical absorption spectra of the MIM emitter under dark and laser illumination with 1.0 and 1.8 W cm<sup>−2</sup>.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6848-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Drude model parameters and electrical properties.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\"/><th align=\"center\" rowspan=\"1\" colspan=\"1\">ε<sub>∞</sub>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">ω<sub>\n<bold>p</bold>\n</sub> [<italic toggle=\"yes\">eV</italic>]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Γ<sub>\n<bold>p</bold>\n</sub> [<italic toggle=\"yes\">eV</italic>]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">n</italic>\n<sub>\n<bold>e</bold>\n</sub> [<italic toggle=\"yes\">cm</italic>\n<sup>−3</sup>]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">µ<sub>\n<bold>e</bold>\n</sub> [<italic toggle=\"yes\">cm</italic>\n<sup>2</sup>\n<italic toggle=\"yes\">V</italic>\n<sup>−1</sup>\n<italic toggle=\"yes\">s</italic>\n<sup>−1</sup>]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">ITO</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.00</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.05</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.105</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.04E21</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">23.19</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">AZO</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.68</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.135</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8.53E20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">20.93</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">La<sub>0.07</sub>Ba<sub>0.93</sub>SnO<sub>3</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.35</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.81</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.089</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5.28E20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">85.92</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">La<sub>0.05</sub>Ba<sub>0.95</sub>SnO<sub>3</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.35</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.55</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.095</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3.75E20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">84.63</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">La<sub>0.03</sub>Ba<sub>0.97</sub>SnO<sub>3</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4.35</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.19</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.09</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.31E20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">82.66</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6848-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Refractory materials.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"left\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Material</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Heating Temperature [°C]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Time Duration [h]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Atmosphere</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Passivation</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Comment</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">W<sup>[</sup>\n##REF##27263653##\n35\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1000</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Metamaterial (Selective Emitter)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">W<sup>[</sup>\n##REF##30395478##\n36\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1200</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HfO<sub>2</sub>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Metasurface (Absorber/Emitter)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">W<sup>[</sup>\n##UREF##21##\n37\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">800/600</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4/4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum/Air</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Al<sub>2</sub>O<sub>3</sub>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Multilayer (Absorber)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">W<sup>[</sup>\n##REF##31076610##\n38\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1400</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HfO<sub>2</sub>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Metamaterial (Emitter)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">W<sup>[</sup>\n##UREF##22##\n39\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1000</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ar</td><td align=\"center\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">Nanodisc (Thermal Emitter)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">TiN<sup>[</sup>\n##REF##25327161##\n14\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">800</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Metamaterial (Absorber)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">TiN<sup>[</sup>\n##UREF##8##\n18\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1400</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Thin film</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">TiN<sup>[</sup>\n##REF##34567729##\n42\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">600</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Metasurface (Absorber)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">TiN<sup>[</sup>\n##REF##36598796##\n43\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">800</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Metasurface (Absorber)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">TiN<sup>[</sup>\n##UREF##17##\n31\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">800</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Nitrogen</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Si<sub>3</sub>N<sub>4</sub>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Thin film (Thermal Emitter)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">TiN<sup>[</sup>\n##UREF##24##\n44\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">100</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Air</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Nanodisc</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ta<sup>[</sup>\n##REF##23670005##\n45\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1000/900</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1/144</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Argon/Argon</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HfO<sub>2</sub>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Photonic Crystal (Thermal Emitter)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ta<sup>[</sup>\n##UREF##25##\n46\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">700</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Air</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Multilayer (Solar Absorber)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ta<sup>[</sup>\n##UREF##26##\n47\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">500</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Multilayer (Thermal Absorber)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo<sup>[</sup>\n##UREF##18##\n32\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1000</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Metamaterial (Thermal Emitter)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mo<sup>[</sup>\n##UREF##19##\n33\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1200</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">24</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Ar</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Nanopillar (Selective Emitter)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Nb<sup>[</sup>\n##UREF##27##\n48\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1000</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Al<sub>2</sub>O<sub>3</sub>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Nanoantenna</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Au<sup>[</sup>\n##REF##28853899##\n49\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">800</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Air</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Al<sub>2</sub>O<sub>3</sub>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Nanostructure</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ir<sup>[</sup>\n##UREF##20##\n34\n##\n<sup>]</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1000</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Vacuum</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">HfO<sub>2</sub>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Multilayer (Selective Emitter)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LBSO (This work)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1000</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Air</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">MIM cavity (Thermal Emitter)</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
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[ "<supplementary-material id=\"advs6848-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6848-tbl1-note-0001\"><p>The fitting parameters of conducting oxide films with a lossy Drude model consisting of infinite dielectric constant (ε<sub>∞</sub>), plasma frequency (ω<sub>p</sub>), and damping coefficient (Γ<sub>p</sub>).</p></fn><fn id=\"advs6848-tbl1-note-0002\"><p>The electrical properties (carrier density (<italic toggle=\"yes\">n</italic>\n<sub>e</sub>) and mobility (µ<sub>e</sub>)) obtained by hall measurement.</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2302410-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
49
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 23; 11(2):2302410
oa_package/21/20/PMC10787089.tar.gz
PMC10787091
38009788
[ "<title>Introduction</title>", "<p>Thin film solar cells with a CuIn<sub>x</sub>Ga<sub>(1‐x)</sub>Se<sub>2</sub> (CIGS) chalcopyrite absorber offer a promising and commercially viable alternative to Si‐wafer‐based solar cells with potential for cost‐effective single‐junction and tandem solar cells.<sup>[</sup>\n##UREF##0##\n1\n##, ##REF##27081076##\n2\n##, ##UREF##1##\n3\n##, ##REF##30166487##\n4\n##\n<sup>]</sup> The progress of this technology, achieving efficiency &gt;23%,<sup>[</sup>\n##UREF##2##\n5\n##\n<sup>]</sup> was made possible by two main breakthroughs: a proper Ga–In grading profile and a heavy‐Alkali postdeposition treatment.<sup>[</sup>\n##UREF##3##\n6\n##\n<sup>]</sup> At Empa, such steps were implemented in a multi‐stage process<sup>[</sup>\n##UREF##4##\n7\n##\n<sup>]</sup> that, however, introduced voids in the top region of the absorber layer, close to the CdS buffer layer. In fact, the formation of voids and pinholes is a relatively common shortcoming, reported for various polycrystalline thin‐film absorbers.<sup>[</sup>\n##REF##32804480##\n8\n##, ##UREF##5##\n9\n##, ##UREF##6##\n10\n##, ##UREF##7##\n11\n##, ##REF##33958474##\n12\n##\n<sup>]</sup>\n</p>", "<p>To increase the cost‐efficiency of the cells and bridge the efficiency gap between cells and modules, recombination losses must be reduced. Besides undermining the structural integrity of the device, voids reduce contact area and are suspected to host recombination centers.<sup>[</sup>\n##UREF##8##\n13\n##\n<sup>]</sup> With respect to performance, Avancini et al. assessed their effect as detrimental through simulations.<sup>[</sup>\n##REF##30479675##\n14\n##\n<sup>]</sup> In their investigation and the others, single voids were imaged in lateral cross sections by transmission electron microscopy and energy dispersive spectroscopy, and a top view of the absorber was obtained by uncovering the upper layers through focus ion beam (FIB) milling. However, the drawbacks of FIB milling are to inevitably enlarge the voids of interest and to prevent further analysis by destroying the sample.</p>", "<p>In this paper, we build upon these previous investigations by applying synchrotron X‐ray imaging to elucidate the nature of these structural defects. Exploiting multimodal scanning X‐ray microscopy, we have demonstrated the ability to map areas of up to several hundred square microns, measuring electrical performance through X‐ray beam‐induced current and voltage (XBIC<sup>[</sup>\n##UREF##9##\n15\n##\n<sup>]</sup> and XBIV<sup>[</sup>\n##UREF##10##\n16\n##\n<sup>]</sup>), optical performance via X‐ray excited optical luminescence (XEOL<sup>[</sup>\n##REF##33466442##\n17\n##\n<sup>]</sup>), elemental composition through X‐ray fluorescence (XRF), and electron area‐density via ptychography.<sup>[</sup>\n##REF##18635796##\n18\n##\n<sup>]</sup> This approach is established for top view<sup>[</sup>\n##REF##33466442##\n17\n##\n<sup>]</sup> and cross sections<sup>[</sup>\n##REF##35822496##\n19\n##\n<sup>]</sup> of a layer stack, but still only in 2D. However, voids are known to extend along a certain depth of the absorber and it is desirable to visualize them along all dimensions. Ptychographic X‐ray computed tomography (PXCT)<sup>[</sup>\n##REF##20864997##\n20\n##, ##UREF##11##\n21\n##\n<sup>]</sup> appears well suited for this purpose, based on previous results on other thin‐film solar cells,<sup>[</sup>\n##UREF##12##\n22\n##\n<sup>]</sup> enabling nondestructive quantitative 3D imaging. State‐of‐the‐art beamlines can currently measure a tomogram of a volume in the order of 10 µm<sup>3</sup> at 20 nm resolution in a matter of hours.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Multimodal 2D X‐ray Imaging</title>", "<p>Some of the maps obtained through different modalities are reported in <bold>Figure</bold>\n##FIG##1##\n2A##. Voids are identified both through fluorescence and ptychography. Among all fluorescence signals, the most reliable and statistically relevant for this purpose is arguably the Se Kα, because of the stoichiometry of CIGS including at least twice as many atoms as the other elements and because possible secondary phases are all likely to contain Se. Nonetheless, the presence of voids can also be well noted in the Cu and Ga Kα maps (Figure ##SUPPL##0##S1##, Supporting Information). Unlike fluorescence, ptychography does not have elemental sensitivity but provides quantitative maps of the electron density. Moreover, ptychography can have a resolution that is not limited by the beam size and achieves in our case the higher resolution (30 nm estimated via Fourier ring correlation,<sup>[</sup>\n##REF##16125414##\n27\n##\n<sup>]</sup> Figure ##SUPPL##0##S2##, Supporting Information) that resolves crevices between CIGS grains. Due to these features, fluorescence and ptychography provide pictures of voids in the absorber layer, respectively, before and after the deposition of the top layers. However, these are known from previous investigations to be strongly correlated,<sup>[</sup>\n##REF##33466442##\n17\n##\n<sup>]</sup> to the extent that ultimately the ptychography map and the Se map describe essentially the same features, i.e., local material deficits and the morphology of the grains in the absorber layer. The latter is responsible for a larger length scale variation that makes it more appropriate to analyze single voids with respect to their own surroundings, i.e., the sets of nearest neighboring pixels. The average size of the segmented voids is estimated with fitting ellipses or Feret diameters as ≈300 nm but exhibits considerable variation (Figure ##FIG##1##2B##). In Figure ##FIG##1##2D## we report statistics extracted from the 26 largest voids segmented from the Se map. For each void labeled in Figure ##FIG##1##2C##, Figure ##FIG##1##2D## shows the ratio of the measurements averaged over pixels within a void and the measurements averaged over its surroundings. The XRF values fall below one by definition and the deviation from one relates to the material deficit of a void or the porosity of the filling. The ptychography values are strongly correlated to XRF values, and for this reason, statistics extracted from the segmentation of voids in XRF and ptychography do not differ substantially (cf. Figure ##SUPPL##0##S3##, Supporting Information). In fact, scanning electron microscopy (SEM) cross‐sections from previous investigations have shown that the layers deposited on the absorber mostly follow the morphology of the absorber, which leads to assuming that a top‐view image of the stack essentially depicts the absorber. Later in this work, we use tomography to validate this assumption.</p>", "<p>More importantly, both the relative XBIC and XEOL measurements appear almost exclusively below one, indicating and quantifying a local performance impairment. These techniques image competing processes, i.e., they count, respectively, generated electron‐hole pairs that diffuse to the electrodes without recombining, and photons with an energy corresponding to the bandgap emitted upon radiative recombination. XBIC appears less impaired by voids than XEOL. The larger error bars from XEOL are due to the nature of the tracked process, i.e., XEOL is intrinsically a photon‐hungry technique. Performance is locally impaired up to 8% for XBIC and 60% for XEOL. On average, the effect of voids can be quantified by the meta‐analysis (see Supporting Information for details) in a 4% loss for XBIC and 20% for XEOL (Figure ##FIG##1##2E##). XEOL, in particular, degrades more than expected from the missing absorber, which might be an indication that voids and crevices are detrimental to cell voltage. This impairment can be attributed to the amount of missing material or an enhanced recombination velocity at interfaces with voids.<sup>[</sup>\n##UREF##15##\n28\n##, ##UREF##16##\n29\n##\n<sup>]</sup> However, it is not trivial to decouple these effects, as the performance maps are effectively blurred by the diffusion length of the carriers and by the electron shower produced by the beam (see Supporting Information). Such blurring leads to an underestimation of the XBIC dips, which explains why on most voids the relative reduction of XRF exceeds its XBIC counterpart. Despite the underestimation, the measured impairment is consistent and significant, and given the high overall performance of the device, suggests that charge transport in the functioning device is mostly sustained by alternative current paths than those below the worst performing areas. The optical and electrical performance losses correlate positively with the amount of missing material (Figure ##FIG##1##2F##) (correlation coefficients ≈0.7), whereas they do not correlate, if not weakly, with the projected area of the voids.</p>", "<p>The local performance impairment observed through measurements of current and luminescence cannot be as clearly observed when induced by a laser beam or an electron beam. In the case of lasers, the fundamentally limited resolution does not allow us to investigate the topic, as even the largest voids are smaller than the diffraction limit of photoluminescence measurements.<sup>[</sup>\n##UREF##17##\n30\n##\n<sup>]</sup> In the case of electrons, the investigation of the effect of voids is hampered by internal scattering effects. Our complementary measurements of EBIC and CL show high‐signal spikes in the proximity of voids (see Figures ##SUPPL##0##S12## and ##SUPPL##0##S13##, Supporting Information). These spikes are not an indication of enhanced electrical or optical performance due to specific material properties, but rather a measurement artifact due to secondary electrons being reabsorbed (see Supporting Information). Whereas these scattering phenomena are negligible for X‐rays, voids can have positive effects under AM1.5G illumination due to light trapping.<sup>[</sup>\n##UREF##18##\n31\n##\n<sup>]</sup> A minor performance impairment at voids is predicted by 3D numerical simulations of simple exemplary cases, although without accounting for optical effects.<sup>[</sup>\n##REF##30479675##\n14\n##\n<sup>]</sup>\n</p>", "<title>Ptychographic Nanotomography</title>", "<p>Whereas the 2D top‐view of the sample highlights lateral differences in the operational device, it cannot provide depth information about the disclosed features. Effectively, they can be vertical projections of multiple features, in the same or different layers. In fact, it is of interest to locate their depth, as due to the Ga–In grading<sup>[</sup>\n##UREF##19##\n32\n##\n<sup>]</sup> and the vertical inhomogeneity of the CdS layer, voids can have a different impact depending on their depth in the stack. Ptychographic tomography can elucidate such features. The technique uses a set of coherent diffractive scanning projections from different angles and phase‐retrieval algorithms to map in 3D the complex refractive index of the interaction volume, whose real part δ is proportional to the electron density and whose imaginary part β is proportional to the mass absorption coefficient (see Supporting Information for details). The technique is today renowned for its astounding resolution and quantitativeness.<sup>[</sup>\n##UREF##20##\n33\n##\n<sup>]</sup> Some exemplary cuts and a volume rendering of the device under investigation are shown in <bold>Figure</bold>\n##FIG##2##\n3\n##. The δ‐tomogram shows clearly the layer stack and the voids. Spatial resolution for the δ‐tomogram was assessed in the 30–40 nm range (see Figure ##SUPPL##0##S4##, Supporting Information), with the standard deviation of measured electron densities being below 2% of the average measurement (see Figure ##SUPPL##0##S6##, Supporting Information). The edge profile across voids and interfaces (Figure ##SUPPL##0##S4##, Supporting Information) decays roughly within the same distance for δ‐ and β‐tomograms, whereas uncertainty is larger in β‐tomograms and artifacts are more severe. Quantitative values of electron density extracted from δ reveal the profile distribution of Figure ##FIG##2##3E##, which locates the voids in the upper part of the absorber, ≈500 nm below the buffer‐absorber interface. The electron‐density distribution is more uniform in the lower part of the cell, except for a slight rise in the direction of the top electrode, which is due to the Ga grading<sup>[</sup>\n##UREF##21##\n34\n##\n<sup>]</sup> and is better visible in the β‐tomogram (Figure ##SUPPL##0##S5##, Supporting Information). Moreover, very small voids are visible at the bottom of the absorber (Figure ##FIG##2##3E##, slices g‐i), which are not expected to be detrimental<sup>[</sup>\n##UREF##18##\n31\n##\n<sup>]</sup> and likely correspond to the nucleation sites of CIGS grains. Finally, lower electron‐density traits can be noticed at mid‐height (Figure ##FIG##2##3E##, slices k,l), which we may identify as grain boundaries, based on the expected grain size. It is not possible to ascertain whether the contrast for these traits is provided by a gap between grains, or by Na or Rb selenides, among which RbInSe<sub>2</sub> is likely.<sup>[</sup>\n##UREF##22##\n35\n##, ##UREF##23##\n36\n##\n<sup>]</sup> Other secondary phases, such as Cu‐or Mo‐selenides, which would be discernible by electron‐density contrast, are not present in the device.</p>", "<p>The voids were segmented in an inner 2 µm‐diameter cylinder unaffected by sample preparation artifacts with a threshold‐and‐watershed algorithm as 45 labeled regions with a spatially confined material deficit (<bold>Figure</bold>\n##FIG##3##\n4A##). The segmentation parameters were set to exclude any nonporous components of the CIGS‐CdS interface region. In particular, the threshold value was set below the expected electron density of the lightest element material (CdS), taking measurement uncertainty into account. Moreover, this segmentation excludes very small voids that are within the lower part of the CIGS and voids that are below resolution (3‐voxel size) but includes sets of voxels that are partly void and partly filled by CdS, as in spots of imperfect adherence. The voids were then fit by ellipsoids to analyze their size and orientation (Figures ##SUPPL##0##S7–S9##, Supporting Information). This analysis shows that there is no evident correlation between height and volume of the voids. Figure ##FIG##3##4B## illustrates the electron‐density distribution within the void regions, which possibly relates to the CdS filling for the largest voids, but is affected also by partially filled voxels and blurred edges in the smallest material‐deficit regions. Orthogonal views and renderings of the single voids are reported in Figure ##SUPPL##0##S10## (Supporting Information). Notable examples are voids nine and 13 which are likely occluded from the top and are not reached by the CdS chemical bath deposition (cf. Figure ##FIG##3##4B##; Figure ##SUPPL##0##S10a,b##, Supporting Information). No particular shape is detected except for a few almost spherical voids (e.g., 9,19). The general picture supported by the statistics of Figure ##SUPPL##0##S7## (Supporting Information) is that of voids with sizes between 100 and 400 nm, mostly elongated in the vertical direction, and generally with low convexity.</p>", "<p>Besides the voids, we segmented every single layer of the device stack (see Supporting Information for details), which resulted in the exploded view displayed in Figure ##FIG##0##1##. This allows us to verify and quantify the assumption that a 2D map of the cell is mostly representative of the absorber. The top view projection of the full stack and groups of layers is depicted in <bold>Figure</bold>\n##FIG##4##\n5A–D##. There, we note that the other layers (including highly scattering Mo) show their own structure and features and that the dispersion in the absorber (Figure ##FIG##4##5E##) is higher than in the other layers altogether (σ<sub>CIGS</sub> = 8 mrad vs σ<sub>rest</sub> = 3 mrad). Consequently, the stack projection predominantly follows variations of the absorber, with the correlation coefficient between the CIGS projection and the full stack projection being R = 0.95, and the correlation coefficient between the CIGS projection and that of the stack of layers above CIGS being the second largest R = −0.67. Such a large negative value can be attributed to an overall effective filling of voids within the chemical bath deposition of CdS. Besides, the absorptance of each layer above CIGS is negligible compared to that of CIGS (Figure ##SUPPL##0##S14##, Supporting Information). Within this comparison of 2D and 3D data, we also note that regardless of a certain degree of arbitrariness involved in the choice of segmentation parameters, the void segmentation for 2D and 3D data contains notable differences. Whether segmented using the Se or the ptychography map, the voids cover an area of ≈6% of the multimodal maps vs ≈25% of the 2D projection extrapolated from the tomogram (Figure ##FIG##4##5F##). A similar disproportion is observed for the density of single voids. The reasons can be ascribed to a better intrinsic sensitivity to the void edges provided by 3D data, the inaccurate grouping of distinct overlapping voids as single, and the inability to discriminate between regions of CdS and topographical variation. The improved clarity of features obtainable in 3D is also illustrated by a minimum intensity projection (Figure ##FIG##4##5G##), which is a multiplanar image of the lowest‐density features along the projection axis. Moreover, this type of projection (cf. Figure ##SUPPL##0##S11##, Supporting Information) emphasizes the numerosity of the voids, whose area density appears significantly higher than previously reported.<sup>[</sup>\n##REF##30479675##\n14\n##\n<sup>]</sup>\n</p>", "<p>Along with better sensitivity to edges, the tomogram slices show the crevices between grain boundaries in the top part of the absorber (Figure ##FIG##4##5I##), which are likely filled by CdS. These features are partly visible in 2D (Figure ##SUPPL##0##S2##, Supporting Information) and in 3D show that they form a network of voids in which most but not all are connected (Figure ##FIG##4##5H##). Whereas all voids originate from the crevices of the polycrystal, the ones that form at a lower depth are more likely to be enclosed and not be reached by the CdS. Numerical simulations show that for the same surface recombination velocity, a buried void is slightly less detrimental than an interface void.<sup>[</sup>\n##REF##30479675##\n14\n##\n<sup>]</sup> As Rb tends to segregate at grain boundaries,<sup>[</sup>\n##UREF##22##\n35\n##, ##REF##33306357##\n37\n##, ##REF##30383349##\n38\n##\n<sup>]</sup> whether CdS locally forms a p‐n junction or not, determines whether downward or upward band‐bending occurs, hence causing a detrimental or beneficial effect for charge carrier transport.<sup>[</sup>\n##REF##31484943##\n39\n##\n<sup>]</sup> In our case, only a minor downward bending and a moderate recombination velocity at the interface are expected, based on more recent measurements of PL and charge carrier lifetimes from cells of the same process flow with similar performance<sup>[</sup>\n##UREF##17##\n30\n##\n<sup>]</sup> (see Figure ##SUPPL##0##S16##, Supporting Information).</p>", "<p>The network of voids is of critical importance for performance as it contains pathways for the diffusion of impurities, possibly leading to interface recombination. Recent developments for high‐energy X‐ray focusing,<sup>[</sup>\n##UREF##13##\n23\n##\n<sup>]</sup> resonant ptychographic tomography, and correlative 3D microscopy<sup>[</sup>\n##UREF##24##\n40\n##, ##REF##30406204##\n41\n##\n<sup>]</sup> can further reveal the extent to which this network is filled by CdS and impurities, and will enable the unambiguous distinction between Cd and In to determine whether p–n junctions are locally formed. Whether only the large void regions or the whole network with deep small voids are considered within the absorber, the two scenarios of the distance map in Figure ##FIG##4##5J## can be drawn (see Figure ##SUPPL##0##S6C##, Supporting Information). These maps yield an average free path well below the diffusion length,<sup>[</sup>\n##UREF##21##\n34\n##\n<sup>]</sup> 0.6 versus 3 µm in the worst case, which, along with the good cell performance, suggests that most of the voids are effectively passivated and supports the model of preferential current paths within CIGS grain.<sup>[</sup>\n##UREF##25##\n42\n##\n<sup>]</sup>\n</p>" ]
[ "<title>Results and Discussion</title>", "<title>Multimodal 2D X‐ray Imaging</title>", "<p>Some of the maps obtained through different modalities are reported in <bold>Figure</bold>\n##FIG##1##\n2A##. Voids are identified both through fluorescence and ptychography. Among all fluorescence signals, the most reliable and statistically relevant for this purpose is arguably the Se Kα, because of the stoichiometry of CIGS including at least twice as many atoms as the other elements and because possible secondary phases are all likely to contain Se. Nonetheless, the presence of voids can also be well noted in the Cu and Ga Kα maps (Figure ##SUPPL##0##S1##, Supporting Information). Unlike fluorescence, ptychography does not have elemental sensitivity but provides quantitative maps of the electron density. Moreover, ptychography can have a resolution that is not limited by the beam size and achieves in our case the higher resolution (30 nm estimated via Fourier ring correlation,<sup>[</sup>\n##REF##16125414##\n27\n##\n<sup>]</sup> Figure ##SUPPL##0##S2##, Supporting Information) that resolves crevices between CIGS grains. Due to these features, fluorescence and ptychography provide pictures of voids in the absorber layer, respectively, before and after the deposition of the top layers. However, these are known from previous investigations to be strongly correlated,<sup>[</sup>\n##REF##33466442##\n17\n##\n<sup>]</sup> to the extent that ultimately the ptychography map and the Se map describe essentially the same features, i.e., local material deficits and the morphology of the grains in the absorber layer. The latter is responsible for a larger length scale variation that makes it more appropriate to analyze single voids with respect to their own surroundings, i.e., the sets of nearest neighboring pixels. The average size of the segmented voids is estimated with fitting ellipses or Feret diameters as ≈300 nm but exhibits considerable variation (Figure ##FIG##1##2B##). In Figure ##FIG##1##2D## we report statistics extracted from the 26 largest voids segmented from the Se map. For each void labeled in Figure ##FIG##1##2C##, Figure ##FIG##1##2D## shows the ratio of the measurements averaged over pixels within a void and the measurements averaged over its surroundings. The XRF values fall below one by definition and the deviation from one relates to the material deficit of a void or the porosity of the filling. The ptychography values are strongly correlated to XRF values, and for this reason, statistics extracted from the segmentation of voids in XRF and ptychography do not differ substantially (cf. Figure ##SUPPL##0##S3##, Supporting Information). In fact, scanning electron microscopy (SEM) cross‐sections from previous investigations have shown that the layers deposited on the absorber mostly follow the morphology of the absorber, which leads to assuming that a top‐view image of the stack essentially depicts the absorber. Later in this work, we use tomography to validate this assumption.</p>", "<p>More importantly, both the relative XBIC and XEOL measurements appear almost exclusively below one, indicating and quantifying a local performance impairment. These techniques image competing processes, i.e., they count, respectively, generated electron‐hole pairs that diffuse to the electrodes without recombining, and photons with an energy corresponding to the bandgap emitted upon radiative recombination. XBIC appears less impaired by voids than XEOL. The larger error bars from XEOL are due to the nature of the tracked process, i.e., XEOL is intrinsically a photon‐hungry technique. Performance is locally impaired up to 8% for XBIC and 60% for XEOL. On average, the effect of voids can be quantified by the meta‐analysis (see Supporting Information for details) in a 4% loss for XBIC and 20% for XEOL (Figure ##FIG##1##2E##). XEOL, in particular, degrades more than expected from the missing absorber, which might be an indication that voids and crevices are detrimental to cell voltage. This impairment can be attributed to the amount of missing material or an enhanced recombination velocity at interfaces with voids.<sup>[</sup>\n##UREF##15##\n28\n##, ##UREF##16##\n29\n##\n<sup>]</sup> However, it is not trivial to decouple these effects, as the performance maps are effectively blurred by the diffusion length of the carriers and by the electron shower produced by the beam (see Supporting Information). Such blurring leads to an underestimation of the XBIC dips, which explains why on most voids the relative reduction of XRF exceeds its XBIC counterpart. Despite the underestimation, the measured impairment is consistent and significant, and given the high overall performance of the device, suggests that charge transport in the functioning device is mostly sustained by alternative current paths than those below the worst performing areas. The optical and electrical performance losses correlate positively with the amount of missing material (Figure ##FIG##1##2F##) (correlation coefficients ≈0.7), whereas they do not correlate, if not weakly, with the projected area of the voids.</p>", "<p>The local performance impairment observed through measurements of current and luminescence cannot be as clearly observed when induced by a laser beam or an electron beam. In the case of lasers, the fundamentally limited resolution does not allow us to investigate the topic, as even the largest voids are smaller than the diffraction limit of photoluminescence measurements.<sup>[</sup>\n##UREF##17##\n30\n##\n<sup>]</sup> In the case of electrons, the investigation of the effect of voids is hampered by internal scattering effects. Our complementary measurements of EBIC and CL show high‐signal spikes in the proximity of voids (see Figures ##SUPPL##0##S12## and ##SUPPL##0##S13##, Supporting Information). These spikes are not an indication of enhanced electrical or optical performance due to specific material properties, but rather a measurement artifact due to secondary electrons being reabsorbed (see Supporting Information). Whereas these scattering phenomena are negligible for X‐rays, voids can have positive effects under AM1.5G illumination due to light trapping.<sup>[</sup>\n##UREF##18##\n31\n##\n<sup>]</sup> A minor performance impairment at voids is predicted by 3D numerical simulations of simple exemplary cases, although without accounting for optical effects.<sup>[</sup>\n##REF##30479675##\n14\n##\n<sup>]</sup>\n</p>", "<title>Ptychographic Nanotomography</title>", "<p>Whereas the 2D top‐view of the sample highlights lateral differences in the operational device, it cannot provide depth information about the disclosed features. Effectively, they can be vertical projections of multiple features, in the same or different layers. In fact, it is of interest to locate their depth, as due to the Ga–In grading<sup>[</sup>\n##UREF##19##\n32\n##\n<sup>]</sup> and the vertical inhomogeneity of the CdS layer, voids can have a different impact depending on their depth in the stack. Ptychographic tomography can elucidate such features. The technique uses a set of coherent diffractive scanning projections from different angles and phase‐retrieval algorithms to map in 3D the complex refractive index of the interaction volume, whose real part δ is proportional to the electron density and whose imaginary part β is proportional to the mass absorption coefficient (see Supporting Information for details). The technique is today renowned for its astounding resolution and quantitativeness.<sup>[</sup>\n##UREF##20##\n33\n##\n<sup>]</sup> Some exemplary cuts and a volume rendering of the device under investigation are shown in <bold>Figure</bold>\n##FIG##2##\n3\n##. The δ‐tomogram shows clearly the layer stack and the voids. Spatial resolution for the δ‐tomogram was assessed in the 30–40 nm range (see Figure ##SUPPL##0##S4##, Supporting Information), with the standard deviation of measured electron densities being below 2% of the average measurement (see Figure ##SUPPL##0##S6##, Supporting Information). The edge profile across voids and interfaces (Figure ##SUPPL##0##S4##, Supporting Information) decays roughly within the same distance for δ‐ and β‐tomograms, whereas uncertainty is larger in β‐tomograms and artifacts are more severe. Quantitative values of electron density extracted from δ reveal the profile distribution of Figure ##FIG##2##3E##, which locates the voids in the upper part of the absorber, ≈500 nm below the buffer‐absorber interface. The electron‐density distribution is more uniform in the lower part of the cell, except for a slight rise in the direction of the top electrode, which is due to the Ga grading<sup>[</sup>\n##UREF##21##\n34\n##\n<sup>]</sup> and is better visible in the β‐tomogram (Figure ##SUPPL##0##S5##, Supporting Information). Moreover, very small voids are visible at the bottom of the absorber (Figure ##FIG##2##3E##, slices g‐i), which are not expected to be detrimental<sup>[</sup>\n##UREF##18##\n31\n##\n<sup>]</sup> and likely correspond to the nucleation sites of CIGS grains. Finally, lower electron‐density traits can be noticed at mid‐height (Figure ##FIG##2##3E##, slices k,l), which we may identify as grain boundaries, based on the expected grain size. It is not possible to ascertain whether the contrast for these traits is provided by a gap between grains, or by Na or Rb selenides, among which RbInSe<sub>2</sub> is likely.<sup>[</sup>\n##UREF##22##\n35\n##, ##UREF##23##\n36\n##\n<sup>]</sup> Other secondary phases, such as Cu‐or Mo‐selenides, which would be discernible by electron‐density contrast, are not present in the device.</p>", "<p>The voids were segmented in an inner 2 µm‐diameter cylinder unaffected by sample preparation artifacts with a threshold‐and‐watershed algorithm as 45 labeled regions with a spatially confined material deficit (<bold>Figure</bold>\n##FIG##3##\n4A##). The segmentation parameters were set to exclude any nonporous components of the CIGS‐CdS interface region. In particular, the threshold value was set below the expected electron density of the lightest element material (CdS), taking measurement uncertainty into account. Moreover, this segmentation excludes very small voids that are within the lower part of the CIGS and voids that are below resolution (3‐voxel size) but includes sets of voxels that are partly void and partly filled by CdS, as in spots of imperfect adherence. The voids were then fit by ellipsoids to analyze their size and orientation (Figures ##SUPPL##0##S7–S9##, Supporting Information). This analysis shows that there is no evident correlation between height and volume of the voids. Figure ##FIG##3##4B## illustrates the electron‐density distribution within the void regions, which possibly relates to the CdS filling for the largest voids, but is affected also by partially filled voxels and blurred edges in the smallest material‐deficit regions. Orthogonal views and renderings of the single voids are reported in Figure ##SUPPL##0##S10## (Supporting Information). Notable examples are voids nine and 13 which are likely occluded from the top and are not reached by the CdS chemical bath deposition (cf. Figure ##FIG##3##4B##; Figure ##SUPPL##0##S10a,b##, Supporting Information). No particular shape is detected except for a few almost spherical voids (e.g., 9,19). The general picture supported by the statistics of Figure ##SUPPL##0##S7## (Supporting Information) is that of voids with sizes between 100 and 400 nm, mostly elongated in the vertical direction, and generally with low convexity.</p>", "<p>Besides the voids, we segmented every single layer of the device stack (see Supporting Information for details), which resulted in the exploded view displayed in Figure ##FIG##0##1##. This allows us to verify and quantify the assumption that a 2D map of the cell is mostly representative of the absorber. The top view projection of the full stack and groups of layers is depicted in <bold>Figure</bold>\n##FIG##4##\n5A–D##. There, we note that the other layers (including highly scattering Mo) show their own structure and features and that the dispersion in the absorber (Figure ##FIG##4##5E##) is higher than in the other layers altogether (σ<sub>CIGS</sub> = 8 mrad vs σ<sub>rest</sub> = 3 mrad). Consequently, the stack projection predominantly follows variations of the absorber, with the correlation coefficient between the CIGS projection and the full stack projection being R = 0.95, and the correlation coefficient between the CIGS projection and that of the stack of layers above CIGS being the second largest R = −0.67. Such a large negative value can be attributed to an overall effective filling of voids within the chemical bath deposition of CdS. Besides, the absorptance of each layer above CIGS is negligible compared to that of CIGS (Figure ##SUPPL##0##S14##, Supporting Information). Within this comparison of 2D and 3D data, we also note that regardless of a certain degree of arbitrariness involved in the choice of segmentation parameters, the void segmentation for 2D and 3D data contains notable differences. Whether segmented using the Se or the ptychography map, the voids cover an area of ≈6% of the multimodal maps vs ≈25% of the 2D projection extrapolated from the tomogram (Figure ##FIG##4##5F##). A similar disproportion is observed for the density of single voids. The reasons can be ascribed to a better intrinsic sensitivity to the void edges provided by 3D data, the inaccurate grouping of distinct overlapping voids as single, and the inability to discriminate between regions of CdS and topographical variation. The improved clarity of features obtainable in 3D is also illustrated by a minimum intensity projection (Figure ##FIG##4##5G##), which is a multiplanar image of the lowest‐density features along the projection axis. Moreover, this type of projection (cf. Figure ##SUPPL##0##S11##, Supporting Information) emphasizes the numerosity of the voids, whose area density appears significantly higher than previously reported.<sup>[</sup>\n##REF##30479675##\n14\n##\n<sup>]</sup>\n</p>", "<p>Along with better sensitivity to edges, the tomogram slices show the crevices between grain boundaries in the top part of the absorber (Figure ##FIG##4##5I##), which are likely filled by CdS. These features are partly visible in 2D (Figure ##SUPPL##0##S2##, Supporting Information) and in 3D show that they form a network of voids in which most but not all are connected (Figure ##FIG##4##5H##). Whereas all voids originate from the crevices of the polycrystal, the ones that form at a lower depth are more likely to be enclosed and not be reached by the CdS. Numerical simulations show that for the same surface recombination velocity, a buried void is slightly less detrimental than an interface void.<sup>[</sup>\n##REF##30479675##\n14\n##\n<sup>]</sup> As Rb tends to segregate at grain boundaries,<sup>[</sup>\n##UREF##22##\n35\n##, ##REF##33306357##\n37\n##, ##REF##30383349##\n38\n##\n<sup>]</sup> whether CdS locally forms a p‐n junction or not, determines whether downward or upward band‐bending occurs, hence causing a detrimental or beneficial effect for charge carrier transport.<sup>[</sup>\n##REF##31484943##\n39\n##\n<sup>]</sup> In our case, only a minor downward bending and a moderate recombination velocity at the interface are expected, based on more recent measurements of PL and charge carrier lifetimes from cells of the same process flow with similar performance<sup>[</sup>\n##UREF##17##\n30\n##\n<sup>]</sup> (see Figure ##SUPPL##0##S16##, Supporting Information).</p>", "<p>The network of voids is of critical importance for performance as it contains pathways for the diffusion of impurities, possibly leading to interface recombination. Recent developments for high‐energy X‐ray focusing,<sup>[</sup>\n##UREF##13##\n23\n##\n<sup>]</sup> resonant ptychographic tomography, and correlative 3D microscopy<sup>[</sup>\n##UREF##24##\n40\n##, ##REF##30406204##\n41\n##\n<sup>]</sup> can further reveal the extent to which this network is filled by CdS and impurities, and will enable the unambiguous distinction between Cd and In to determine whether p–n junctions are locally formed. Whether only the large void regions or the whole network with deep small voids are considered within the absorber, the two scenarios of the distance map in Figure ##FIG##4##5J## can be drawn (see Figure ##SUPPL##0##S6C##, Supporting Information). These maps yield an average free path well below the diffusion length,<sup>[</sup>\n##UREF##21##\n34\n##\n<sup>]</sup> 0.6 versus 3 µm in the worst case, which, along with the good cell performance, suggests that most of the voids are effectively passivated and supports the model of preferential current paths within CIGS grain.<sup>[</sup>\n##UREF##25##\n42\n##\n<sup>]</sup>\n</p>" ]
[ "<title>Conclusion and Outlook</title>", "<p>Altogether, we have shown in this study the 3D nature of structural defects in thin‐film CIGS solar cells and we identified local performance deficits attributable to voids. Although possibly detrimental at a local level, the high density of voids highlighted by tomography suggests that their effect cannot be dramatic at the device level, given the high efficiency of the cell. We point out that such a complex system is not easily modeled and available finite element simulation results are not directly comparable with our measurements.<sup>[</sup>\n##REF##30479675##\n14\n##\n<sup>]</sup> Our measurements with absolute electron densities quantified at the nanoscale enable the development of adequate models simulating structural and electronic defects.<sup>[</sup>\n##REF##35822496##\n19\n##\n<sup>]</sup> This investigation does not alter the void size or shape as FIB‐SEM might do, however, it does require a state‐of‐the‐art X‐ray microscopy beamline and involves a delicate sample preparation. Future experiments should aim to avoid it, probe larger areas, and explore the sample in a multi‐scale approach. Such goals may be achieved with a laminography setup.<sup>[</sup>\n##UREF##26##\n43\n##\n<sup>]</sup> Regarding the availability of beamtime, accepting a loss of resolution, similar studies can be extended to the best lab‐CT instruments. Other thin film solar cells, perovskites before all, in single‐junction or tandem configuration, demand studies of this kind to elucidate fabrication defects and improve cost‐efficiency.</p>", "<p>In general, our study highlights the sensitivity at the nanoscale to a multitude of physical, chemical, and electrical properties, enabled by synchrotron imaging. These results are particularly timely in view of novel scanning X‐ray microscopes that are under development and will become operational in the coming years, in which the full set of techniques of the multimodal toolset may be performed at the same time and in 3D. The possibility of such simultaneous measurements can in turn foster future in situ and operando studies of growth, performance, and degradation,<sup>[</sup>\n##UREF##27##\n44\n##, ##REF##31911652##\n45\n##\n<sup>]</sup> which can help bridge the gap between cell and module efficiency. The enhanced brilliance of fourth‐generation sources<sup>[</sup>\n##REF##25177976##\n46\n##\n<sup>]</sup> will overcome limitations of sample size and scan duration for the 3D case.</p>" ]
[ "<title>Abstract</title>", "<p>Small voids in the absorber layer of thin‐film solar cells are generally suspected to impair photovoltaic performance. They have been studied on Cu(In,Ga)Se<sub>2</sub> cells with conventional laboratory techniques, albeit limited to surface characterization and often affected by sample‐preparation artifacts. Here, synchrotron imaging is performed on a fully operational as‐deposited solar cell containing a few tens of voids. By measuring operando current and X‐ray excited optical luminescence, the local electrical and optical performance in the proximity of the voids are estimated, and via ptychographic tomography, the depth in the absorber of the voids is quantified. Besides, the complex network of material‐deficit structures between the absorber and the top electrode is highlighted. Despite certain local impairments, the massive presence of voids in the absorber suggests they only have a limited detrimental impact on performance.</p>", "<p>3D X‐ray microscopy quantifies the distribution of voids in thin‐film solar cells and associated electrical performance deficits.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6754-cit-0047\">\n<string-name>\n<given-names>G.</given-names>\n<surname>Fevola</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Ossig</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Verezhak</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Garrevoet</surname>\n</string-name>, <string-name>\n<given-names>H. L.</given-names>\n<surname>Guthrey</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Seyrich</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Brückner</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Hagemann</surname>\n</string-name>, <string-name>\n<given-names>F.</given-names>\n<surname>Seiboth</surname>\n</string-name>, <string-name>\n<given-names>A.</given-names>\n<surname>Schropp</surname>\n</string-name>, <string-name>\n<given-names>G.</given-names>\n<surname>Falkenberg</surname>\n</string-name>, <string-name>\n<given-names>P. S.</given-names>\n<surname>Jørgensen</surname>\n</string-name>, <string-name>\n<given-names>A.</given-names>\n<surname>Slyamov</surname>\n</string-name>, <string-name>\n<given-names>Z. I.</given-names>\n<surname>Balogh</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Strelow</surname>\n</string-name>, <string-name>\n<given-names>T.</given-names>\n<surname>Kipp</surname>\n</string-name>, <string-name>\n<given-names>A.</given-names>\n<surname>Mews</surname>\n</string-name>, <string-name>\n<given-names>C. G.</given-names>\n<surname>Schroer</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Nishiwaki</surname>\n</string-name>, <string-name>\n<given-names>R.</given-names>\n<surname>Carron</surname>\n</string-name>, <string-name>\n<given-names>J. W.</given-names>\n<surname>Andreasen</surname>\n</string-name>, <string-name>\n<given-names>M. E.</given-names>\n<surname>Stuckelberger</surname>\n</string-name>, <article-title>3D and Multimodal X‐Ray Microscopy Reveals the Impact of Voids in CIGS Solar Cells</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2301873</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202301873</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<p>To investigate the effect of nano‐voids on performance, samples for two different synchrotron experiments were prepared. The experimental concept and setup are illustrated in <bold>Figure</bold>\n##FIG##0##\n1\n##. The layer stack of the samples under investigation comprises from top to bottom: a MgF<sub>2</sub> antireflective coating (105 nm); Al:ZnO top contact layer (65 nm); ZnO window layer (120 nm); CdS buffer layer (20–50 nm); CIGS absorber (≈3 µm); Mo rear contact layers (500 nm); and a polyimide substrate. The samples were taken from a cell whose fabrication process resulted in a 20.2% efficiency for its best cell.<sup>[</sup>\n##UREF##4##\n7\n##\n<sup>]</sup> Details about the cell are available in the Supporting Information. In the first multimodal measurement, an area sized ca. 5 × 5 µm<sup>2</sup> was raster‐scanned at the microprobe of PETRA‐III beamline P06 (DESY)<sup>[</sup>\n##UREF##13##\n23\n##\n<sup>]</sup> at an energy of 15.25 keV, slightly above the absorption edge of Rb. Compound refractive lenses were used with a phase plate to focus the coherent beam to a 105 nm spot size.<sup>[</sup>\n##REF##29271759##\n24\n##\n<sup>]</sup> The different techniques were performed in three successive scans and scan parameters were differently optimized for ptychography and XEOL, respectively, and registered for the analysis. For the second experiment, a pillar of 5 µm diameter covering the entire layer stack was isolated through FIB, and a PXCT scan was performed at the SLS beamline cSAXS (PSI)<sup>[</sup>\n##REF##22852697##\n25\n##\n<sup>]</sup> at an energy of 6.2 keV on the flOMNI setup.<sup>[</sup>\n##UREF##14##\n26\n##\n<sup>]</sup> Whereas the multimodal scans provide a single top view of the sample, tomography provides the full 3D image that can be represented by vertical or horizontal slices and can be further processed to independently analyze the single layers. Both for 2D and 3D images, the ultimate goal was to label pixels and voxels that present evidence of material deficit, and therefore refer to voids, i.e., volumes of thin films characterized by absence of material.<sup>[</sup>\n##REF##30479675##\n14\n##\n<sup>]</sup>\n</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>M.E.S.: Conceptualization; G.Fe, C.O., M.V.: Data Curation; M.E.S., G.Fe.: Methodology; R.C., S.N., M.V., H.L.G., J.G., G.Fa., A.Sc., F.S., C.G.S., C.S., T.K., A.M., Z.I.B., J.W.A, M.E.S.: Resources; G.Fe., C.O., M.V., H.G., M.S., A.Sc., M.E.S.: Visualization; A.M., G.Fa., C.G.S., J.W.A., M.E.S.: Funding acquisition; G.Fe., C.O., H.L.G., A.Sl., P.S.J., M.V., C.S., D.B., J.H., A.Sc., F.S., T.K., J.W.A., M.E.S.: Investigation; G.Fe., C.O., M.V., M.E.S. : Formal Analysis; M.E.S.: Project administration; M.S.: Software; A.M., C.G.S., T.K., J.W.A., M.E.S.: Supervision; G.Fe., C.O., M.V., H.L.G., J.H., G.Fa., R.C., J.W.A., M.E.S.: Validation; G.Fe., M.E.S.: Writing—original draft; G.Fe, C.O., M.V., J.H., G.Fa., R.C., J.W.A., M.E.S.: Writing—review and editing.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors acknowledge DESY, a member of the Helmholtz Association, and Paul Scherrer Institute for granting beamtime at beamlines P06 (PETRA III) and cSAXS (SLS); European Union's Horizon 2020 research and innovation program under the Marie Skłodowska‐Curie Grant Agreements No. 701647 (M.V.) and No. 765604 (MUMMERING) (J.W.A.); Swiss Federal Office of Energy SFOE (R.C., S.N.) under the ImproCIS project (Contract no.: SI/501614‐01) (R.C., S.N.); H2020 European Research Council through the SEEWHI Consolidator grant, ERC‐2015‐CoG‐681881 (J.W.A.); U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Solar Energy Technology (H.L.G.). This work was authored in part by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE‐AC36‐08GO28308. This research was partly supported by the Maxwell computational resources operated at DESY. Beamtime at DESY (ID: 11005475) was allocated for proposal I‐20180471. The authors acknowledge Enrico Avancini and Ayodhya Tiwari (Empa) for their contribution to the fabrication of the solar cells and Andreas Kolditz, Jan Flügge, Jan Siebels (Universität Hamburg), as well as Kathryn Spiers and the FS‐PETRA Engineering team (DESY) for experiment support.</p>", "<p>Open access funding enabled and organized by Projekt DEAL.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available at the open‐access repository <ext-link xlink:href=\"https://doi.org/10.5281/zenodo.10018968\" ext-link-type=\"uri\" specific-use=\"dataset is-supplemented-by\">https://doi.org/10.5281/zenodo.10018968</ext-link>. Raw data are available from the corresponding authors upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6754-fig-0001\"><label>Figure 1</label><caption><p>Experimental concept. Two samples of the same layer stack are prepared for two different experiments. In the first experiment, a sample is mounted on a printed circuit board and electrically contacted so that maps of the induced current can be measured. In the second experiment, the sample is carved out and mounted on a pin, where it is molded to a cylindrical shape. Projections from different angles are acquired to yield a 3D reconstruction that can be processed and decomposed into individual layers.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6754-fig-0002\"><label>Figure 2</label><caption><p>Multimodal 2D X‐ray imaging of CIGS solar cell. A) Stack of top‐view multimodal maps. Ptychography and fluorescence maps (top), locating voids in the absorber; XEOL and XBIC (bottom) mapping their optical and electrical performance. B) Extent of voids estimated from ellipse‐fitting or Feret diameters. Fitting dashed lines relate to the eccentricity of the voids. C) Labels of voids and surroundings segmented from the XRF map and represented in overlay transparency on the ptychography map. D) Relative measurements of XBIC, XEOL, XRF, and ptychography within labeled voids. Expressed as the ratio between average intensity within void and outside void. E) Average loss and extent of voids resulting from a meta‐analysis of measurement in (D). F) Scatter plot of XBIC and XEOL versus Se fluorescence counts. Dashed lines indicate a linear trend of increasing performance per increasing XRF counts. The size of markers in (B) and (F) is proportional to the void area.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6754-fig-0003\"><label>Figure 3</label><caption><p>Depth information from PXCT of CIGS solar cell. A) Volume rendering of cylindrical sub‐volume with electron density in greyscale. The diameter is 2 µm. B–D) Sagittal, coronal, and axial slices. Segmented voids are highlighted by colored contours E) Depth profile of electron density across the layer stack. Blue and red lines indicate the 5–95 and the 25–75 percentile variations. Most variation occurs within 500 nm below the CdS layer. Axial slices a–f) from the upper region of the CIGS layer are reported above. Slices g–l) from the lower part of the absorber, represented with truncated greyscale to enhance contrast. Scale bars are 1 µm.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6754-fig-0004\"><label>Figure 4</label><caption><p>3D segmentation and analysis of voids. A) Volume rendering of the PXCT data with segmented voids. The left inset depicts a spherical deep void, right inset depicts a group of vertically elongated voids B) Electron density within the single voids. Blue and red lines indicate the 5–95 percentile and the 25–75 percentile variations.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6754-fig-0005\"><label>Figure 5</label><caption><p>Comparison of 2D versus 3D ptychography. A–D) Vertical projections as computed from tomography of the CIGS layer, CdS‐ZnO‐MgF<sub>2</sub>, layer stack, and Mo‐polyimide (PI). E) Dispersion of values within layers illustrated in A, B, D. F) Map of overlapping voids at different heights. Areas in yellow and purple cross one and two voids respectively. G) Minimum intensity projection of the absorber. H) Volume rendering of voids as isolated (green) and connected to the buffer layer (red). I) The network of crevices connecting the voids (color highlight, slice view). J) Two hypothetical scenarios of free path distance for charge carriers across the absorber, based on measured electron density values. Void surfaces lie mostly at the large voids (left) or they lie across the whole stack (right), i.e., across unpassivated grain boundaries and minor voids.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6754-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6754-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 1</p></caption></supplementary-material>", "<supplementary-material id=\"advs6754-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 2</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2301873-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2301873-s003.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2301873-s002.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>" ]
[{"label": ["1"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["M.", "S.", "D.", "R.", "F.", "P.", "W.", "T. M."], "surname": ["Powalla", "Paetel", "Hariskos", "Wuerz", "Kessler", "Lechner", "Wischmann", "Friedlmeier"], "source": ["Engineering"], "year": ["2017"], "volume": ["3"], "fpage": ["445"]}, {"label": ["3"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n"], "given-names": ["M.", "L.", "L.", "S."], "surname": ["Jost", "Kegelmann", "Korte", "Albrecht"], "source": ["Adv. Energy Mater."], "year": ["2020"], "volume": ["10"], "elocation-id": ["1904102"]}, {"label": ["5"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["M. A.", "E. D.", "J.", "M.", "N.", "K.", "D.", "M.", "X."], "surname": ["Green", "Dunlop", "Hohl\u2010Ebinger", "Yoshita", "Kopidakis", "Bothe", "Hinken", "Rauer", "Hao"], "source": ["Prog. Photovoltaics Res. Appl."], "year": ["2022"], "volume": ["30"], "fpage": ["687"]}, {"label": ["6"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n"], "given-names": ["D.", "K.", "M.", "H.\u2010P.", "M. J."], "surname": ["Colombara", "Conley", "Malitckaya", "Komsa", "Puska"], "source": ["J. Mater. Chem. A"], "year": ["2020"], "volume": ["8"], "fpage": ["6471"]}, {"label": ["7"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["R.", "S.", "T.", "R.", "E.", "J.", "S.\u2010C. C.", "S.", "A. N."], "surname": ["Carron", "Nishiwaki", "Feurer", "Hertwig", "Avancini", "L\u00f6ckinger", "Yang", "Buecheler", "Tiwari"], "source": ["Adv. Energy Mater"], "year": ["2019"], "volume": ["9"], "elocation-id": ["1900408"]}, {"label": ["9"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["T.", "K.", "O.", "R.", "S.", "Y. S.", "J. 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{ "acronym": [], "definition": [] }
46
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2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 27; 11(2):2301873
oa_package/ca/c5/PMC10787091.tar.gz
PMC10787092
37990757
[ "<title>Introduction</title>", "<p>The coordination chemistry of 2‐aza‐21‐carbaporphyrin, a.k.a. N‐confused porphyrin (<bold>NCP</bold>, <bold>Figure</bold> ##FIG##0##\n1\n##) started simultaneously with the discovery of this porphyrinoid.<sup>[</sup>\n##UREF##0##\n1\n##, ##UREF##1##\n2\n##\n<sup>]</sup> For almost three decades this macrocycle has attracted the attention of the researchers involved in the coordination chemistry of macrocycles due to its unusual NNNC coordination core, several distinct coordination modes that can be adopted by this porphyrinoid, as well as stabilization of the uncommon oxidation states.<sup>[</sup>\n##UREF##2##\n3\n##, ##UREF##3##\n4\n##, ##UREF##4##\n5\n##, ##UREF##5##\n6\n##, ##UREF##6##\n7\n##, ##REF##12010019##\n8\n##, ##REF##12688742##\n9\n##, ##REF##14989654##\n10\n##, ##UREF##7##\n11\n##, ##REF##16676941##\n12\n##, ##REF##17173392##\n13\n##, ##UREF##8##\n14\n##, ##REF##18954046##\n15\n##, ##UREF##9##\n16\n##, ##REF##35230807##\n17\n##, ##REF##36852929##\n18\n##\n<sup>]</sup> The unique feature of <bold>NCP</bold> is the presence of a built‐in extra‐annular nitrogen donor that can be treated as an additional ligation site, naturally enriching the coordination chemistry of this macrocycle when compared with its isomer, i.e., regular porphyrin or various core‐modified analogues, including carbaporphyrins.<sup>[</sup>\n##REF##27657332##\n19\n##, ##REF##36771158##\n20\n##\n<sup>]</sup> Thus, for the group 12 metals, manganese(II), or iron(II) complexes, the external nitrogen  N2 is coordinated to the metal center bound within the core of the adjacent <bold>NCP</bold> subunit forming a bridgeless homodimer or homotrimer.<sup>[</sup>\n##REF##12010019##\n8\n##, ##REF##14989654##\n10\n##, ##UREF##10##\n21\n##, ##UREF##11##\n22\n##, ##UREF##12##\n23\n##\n<sup>]</sup> In a quite complicated structure of mixed‐valence tetrarhodium bis(<bold>NCP</bold>) tetracarbonyl complex, two external nitrogens are coordinated to a bridging dicarbonylrhodium(0) unit.<sup>[</sup>\n##REF##17173392##\n13\n##\n<sup>]</sup> Meanwhile, in a monomeric dirhodium(I) system, one dicarbonylrhodium(I) center occupies two internal nitrogen sites and the external nitrogen is coordinated to the chlorodicarbonylrhodium(I) unit.<sup>[</sup>\n##UREF##6##\n7\n##\n<sup>]</sup> Upon coordination of two dicarbonyliridium(I) moieties, the <bold>NCP</bold> ligand undergoes inversion which results in the ligation of all four nitrogens inside the distorted macrocycle.<sup>[</sup>\n##REF##16676941##\n12\n##\n<sup>]</sup> Owing to the close location of the meso‐aryl at C20, the metal binding N2 can be a part of a six‐membered metallacycle involving C1, C20, C<italic toggle=\"yes\">\n<sub>ipso</sub>\n</italic>, and C<italic toggle=\"yes\">\n<sub>ortho</sub>\n</italic> (Figure ##FIG##0##1##). Such an <italic toggle=\"yes\">ortho</italic>‐metallation has been relatively rarely observed and structurally characterized for <bold>NCP</bold> derivatives. In palladium(II) and platinum(II) dimers, the <bold>NCP</bold> subunits are bridged by the metal ions,<sup>[</sup>\n##REF##11154554##\n24\n##, ##UREF##13##\n25\n##, ##REF##15018507##\n26\n##\n<sup>]</sup> while doubly‐<italic toggle=\"yes\">ortho</italic>‐metallation of Pt<sup>II</sup> or Pt<sup>IV</sup> has been found to occur in [Pt(3,3′‐(<bold>NCP</bold>)<sub>2</sub>)] or [Pt{3,3′‐(<bold>NCP</bold>)}L<sup>1</sup>L<sup>2</sup>] comprising two directly linked <bold>NCP</bold> subunits.<sup>[</sup>\n##UREF##14##\n27\n##, ##UREF##15##\n28\n##\n<sup>]</sup> In some of these complexes, the macrocyclic core is not involved in coordination, and in all of them, the confused pyrrole is tipped from the mean plane of the regular pyrroles which may be a prerequisite for the <italic toggle=\"yes\">ortho</italic>‐metallation.</p>", "<p>In this paper, we report the synthesis and characterization of several late transition metal complexes comprising <bold>NCP</bold> or its derivatives with the <italic toggle=\"yes\">ortho</italic>‐C20–N2 chelating motif. We focus on the structural features of the <bold>NCP</bold> complexes that can be useful for transferring chirality onto the exposed “external” metal center M<sup>1</sup> or potential catalytic activity.</p>" ]
[ "<title>General Methods and Instrumentation</title>", "<p>Commercial reagents were used without further purification. Solvents were freshly distilled from the appropriate drying agents or purified under nitrogen with the mBraun MBSPS‐800 before use. Column chromatography was performed by using silica gel 60 (200–300 mesh ASTM). The NMR spectra were recorded on a Bruker Avance III spectrometer, operating at 500 MHz for <sup>1</sup>H and 125 MHz for <sup>13</sup>C, or a Bruker Avance III spectrometer operating at 600 MHz for <sup>1</sup>H and 150 MHz for <sup>13</sup>C. TMS was used as an internal reference for <sup>1</sup>H and <sup>13</sup>C chemical shifts and CDCl<sub>3</sub> was used as solvent. Standard pulse programs from the Bruker library were used for homo‐ and heteronuclear 2D experiments. ESR spectra (X‐band) were recorded on a Bruker ELEXSYS E500 spectrometer. Mass spectrometry measurements were conducted by using the electrospray ionization technique on a Bruker Daltonics microTOF‐Q or using the MALDI method on a Bruker ultrafleXtreme spectrometer. Absorption UV/Vis/NIR spectra were recorded by using a Varian Cary 60 and Jasco V‐770 spectrophotometers. Circular dichroic spectra were recorded by means of Jasco 1500 spectropolarimeter equipped with a flow cell attached to the Hitachi‐Merck LaChrom HPLC system allowing detection of the chiral fraction and CD spectra measurement in a stopped‐flow technique. Enantiomer resolutions were performed using either Chirex 3010 or Chirex 3014 column (25 × 0.46 cm). The product of the catalytic reactions was analyzed utilizing an Agilent 8890 gas chromatograph equipped with an Agilent 122–5532 column (30 m × 250 µm × 0.25 µm with DB‐5 ms stationary phase) and with mass spectrometer detector Agilent 5977B. Quantitative analyses were performed on the same chromatograph with Agilent 19091S‐433UI column and FID detector. Electrochemical measurements were performed by means of Autolab (Metrohm) potentiostat/galvanostat system for dichloromethane solutions with a glassy carbon, a platinum wire, and Ag/Ag<sup>+</sup> as the working, auxiliary, and pseudoreference electrodes, respectively. Tetrabutylammonium hexafluorophosphate was used as a supporting electrolyte. The potentials were referenced with the ferrocene/ferrocenium couple used as an internal standard.</p>", "<p>The X‐ray diffraction was measured using either XtaLAB Synergy R or Xcalibur, Onyx diffractometers using a copper source of radiation (λ = 1.54184 Å), and collected with CCD camera. The standard temperature of the measurement was 100 K. The structures were solved using direct methods with SHELXT<sup>[</sup>\n##UREF##26##\n52\n##\n<sup>]</sup> and refined by the full‐matrix least‐squares method on all <italic toggle=\"yes\">F</italic>\n<sup>2</sup> data by using the SHELXL<sup>[</sup>\n##UREF##27##\n53\n##\n<sup>]</sup> incorporated in the OLEX2 program.<sup>[</sup>\n##UREF##28##\n54\n##\n<sup>]</sup> All hydrogen atoms, including those located in the difference density map, were placed in calculated positions and refined as the riding model. Crystallographic details are collected in Tables ##SUPPL##0##S2–S6## (Supporting Information). CCDC 2 284 427, 2 284 430, 2 284 431, 2 284 433, and 2 284 434 contain supplementary crystallographic data for this paper. These data can be obtained free of charge from The Cambridge Crystallographic Data Centre via <ext-link xlink:href=\"http://www.ccdc.cam.ac.uk/data_request/cif\" ext-link-type=\"uri\">www.ccdc.cam.ac.uk/data_request/cif</ext-link>.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Syntheses and Characterizations</title>", "<p>As starting materials for our syntheses of bis‐metallic systems, we chose two previously reported compounds bearing a substituent at the C21 position coordinated to either nickel(II)<sup>[</sup>\n##UREF##16##\n29\n##, ##REF##11151364##\n30\n##, ##UREF##17##\n31\n##, ##REF##12467409##\n32\n##, ##REF##12950206##\n33\n##\n<sup>]</sup> or ruthenium(II).<sup>[</sup>\n##UREF##18##\n34\n##, ##REF##31944014##\n35\n##\n<sup>]</sup> The common features of these, otherwise different complexes are chirality, significant deviation from planarity of the porphyrin ring in the region of confused pyrrole, and unoccupied/non‐protonated N2. These systems were subjected to reaction with organometallic dimeric complexes of ruthenium(II), rhodium(III), or iridium(III) with two chlorides and either neutral η<sup>6</sup>‐<italic toggle=\"yes\">para‐</italic>cymene (Cym) or η<sup>5</sup>‐pentamethylcyclopentadienyl anion (Cp*). Under mild conditions (reflux of DCM solution in the presence of sodium acetate as a proton scavenger) the reaction resulted in the substitution of one chloride by carbanionic <italic toggle=\"yes\">ortho‐</italic>C20 and coordination of N2 atoms (<bold>Scheme</bold> ##FIG##1##\n1\n##). The <italic toggle=\"yes\">ortho</italic>‐metallation efficacy varied depending on the metal ion from 35–40% reaction yield for Rh<sup>III</sup>, 54–60% for Ru<sup>II</sup>, and up to 85–93% for Ir<sup>III</sup>. Slightly better results were obtained for <bold>NiMeP</bold> compared with those for <bold>RuSPy</bold>. We showed also that under the analogous condition, the reaction of [IrCl<sub>2</sub>Cp*]<sub>2</sub> with <bold>ClNCP</bold> free base yielded <italic toggle=\"yes\">ortho</italic>‐metallated derivative <bold>ClNCP</bold>IrCp* (Scheme ##FIG##1##1##) with a good outcome (83% yield).</p>", "<p>The new complexes were characterized by high‐resolution mass spectrometry, <sup>1</sup>H and <sup>13</sup>C NMR, including homo‐ and heteronuclear 2D correlation experiments, UV–vis–NIR spectroscopy, and single crystal XRD analyses. The ESI+ HRMS indicated the presence of the incoming metal ion as well as Cym or Cp* moieties in each case, though all cations were stripped of chloride. The <sup>1</sup>H NMR spectra revealed the preservation of most of the spectral features typical of <bold>NiMeP</bold>, <bold>RuSPy</bold>, or <bold>ClNCP</bold> in the complexes formed and the appearance of new signals related to the presence of Cp* or Cym (<bold>Figure</bold> ##FIG##2##\n2\n##). Thus, the spectra of the systems with Cp* comprise a very strong (15H) signal at about <italic toggle=\"yes\">δ</italic> 0.8 ppm due to methyl protons, indicating fast rotation around the M–Cp* direction. On the other hand, the differentiation of aryl and isopropyl resonances of the RuCym moiety is in line with the slow motions of the Cym ligand at the <sup>1</sup>H NMR time scale. Moreover, an upfield shift of all the Cym protons with respect to those observed for starting [RuCl<sub>2</sub>Cym]<sub>2</sub>, indicates the position of this moiety over the aromatic frame of the macrocyclic ligands. Significantly, this aromatic ring shielding effect is strongest for the cymene methyl Me<italic toggle=\"yes\">\n<sub>c</sub>\n</italic> (Δ<italic toggle=\"yes\">δ</italic> 0.7–1.4 ppm) suggesting the orientation of the ligand with the isopropyl group situated rather outside, while Me<italic toggle=\"yes\">\n<sub>c</sub>\n</italic> is above the macrocycle. The number of meso‐aryl distinct signals in the spectra of <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RuCym recorded at room temperature, reflects diastereotopic inequivalence of the macrocyclic faces and slow, at the NMR timescale, rotation of these substituents around C<sub>ipso</sub>─C<sub>meso</sub> bonds, resulting in differentiation of <italic toggle=\"yes\">ortho‐</italic> and <italic toggle=\"yes\">meta‐</italic>H resonances of phenyls at C5, C10, and C15. Conversely, these meso‐phenyl protons in <bold>NiMeP</bold>IrCp* and <bold>NiMeP</bold>RuCym give rise to severely broadened signals indicating intermediate rotation rate of the substituents and diastereotopicity of the complex faces. The only sharp meso‐aryl signals are those of phenyl at the C20 position due to the complete freezing of its rotation by <italic toggle=\"yes\">ortho</italic>‐metallation. The chemical shifts and coupling patterns are similar in all these <italic toggle=\"yes\">ortho</italic>‐metallated complexes comprising a doublet for 20‐<italic toggle=\"yes\">m</italic> at about 8.3 ppm, a doublet for 20‐<italic toggle=\"yes\">o</italic>′ at about 7.7 ppm, and two triplets for 20‐<italic toggle=\"yes\">m</italic>′ and 20‐<italic toggle=\"yes\">p</italic> at ≈7.3 and 7.2 ppm, respectively (Figure ##FIG##2##2##). For the <italic toggle=\"yes\">ortho</italic>‐metallated rhodium(III) complexes, <bold>NiMeP</bold>RhCp* and <bold>RuSPy</bold>RhCp*, a close resemblance of</p>", "<p>\n<sup>1</sup>H NMR spectral patterns to those of the respective Ir<sup>III</sup> systems were observed. The major difference is an additional splitting of all multiplets of the 20‐phenyl protons due to <sup>1</sup>H‐<sup>103</sup>Rh spin–spin coupling (<italic toggle=\"yes\">J<sub>RhH</sub>\n</italic> = 1.3–1.5 Hz). Significantly, the <italic toggle=\"yes\">ortho</italic>‐carbon of the C20 phenyl substituent, identified on the basis of <sup>1</sup>H,<sup>13</sup>C HSQC and <sup>1</sup>H,<sup>13</sup>C HMBC experiments (Figure ##SUPPL##0##S7B## and ##SUPPL##0##S13B##, Supporting Information), gives rise to a doublet at <italic toggle=\"yes\">δ<sub>C</sub>\n</italic> 169.8 ppm with <sup>1</sup>\n<italic toggle=\"yes\">J<sub>RhC</sub>\n</italic> = 31.1 Hz for <bold>NiMeP</bold>RhCp* and at <italic toggle=\"yes\">δ<sub>C</sub>\n</italic> 169.9 ppm with <sup>1</sup>\n<italic toggle=\"yes\">J<sub>RhC</sub>\n</italic> = 30.9 Hz for <bold>RuSPy</bold>RhCp* unequivocally proving coordination of the carbanion. The <sup>13</sup>C–<sup>103</sup>Rh coupling could be observed also for cyclopentadiene carbon atoms in <sup>13</sup>C NMR of both complexes giving rise to doublets at about <italic toggle=\"yes\">δ<sub>C</sub>\n</italic> 96 ppm with <sup>1</sup>\n<italic toggle=\"yes\">J<sub>RhC</sub>\n</italic> = 6.1 Hz. The <sup>1</sup>H NMR characteristics of <bold>Cl</bold>\n<bold>NCP</bold>IrCp* differ from the nickel(II) and ruthenium(II) complexes with 21‐CH and 22,24‐NH resonances arising in the upfield region of the spectrum (<italic toggle=\"yes\">δ</italic> −4.69 and broad signals at <italic toggle=\"yes\">δ</italic> −1.05, −1.10 ppm, respectively) reflecting a free‐base character of the macrocyclic core. Interestingly, for all pentamethylcyclopentadienyl‐comprising systems, correlations of the coordinated <italic toggle=\"yes\">ortho</italic>‐C with methyl protons of the η<sup>5</sup>‐Cp* ligand were observed in the <sup>1</sup>H,<sup>13</sup>C HMBC maps (Figures ##SUPPL##0##S3B##, ##SUPPL##0##S7B##, ##SUPPL##0##S9B##, ##SUPPL##0##S13B##, and ##SUPPL##0##S15B##, Supporting Information), regardless of the metal ion. Such correlations appeared despite the fact that the coupled nuclei were separated by four bonds. The correlations may be accounted for by the anionic character of the Cp* ligand resulting in a relatively high electron density available that enhanced <sup>1</sup>H‐<sup>13</sup>C coupling. Significantly, for the neutral η<sup>6</sup>‐Cym ligand in <bold>NiMeP</bold>RuCym or <bold>RuSPy</bold>RuCym, there was no such a correlation observed, in spite of only three bonds separating aryl protons of this ligand and the Ru<sup>II</sup>‐coordinating <italic toggle=\"yes\">ortho</italic>‐C at 20‐Ph.</p>", "<p>The electronic spectrum of <bold>ClNCP</bold>IrCp* resembles that of the starting porphyrin <bold>ClNCP</bold> with ≈65 nm and 15 nm bathochromic shifts of the lowest‐energy Q band and the Soret band, respectively observed for the complex (Figure ##SUPPL##0##S1##, Supporting Information). For the <bold>NiMeP</bold> and <bold>RuSPy,</bold> the spectral changes due to external coordination are much more profound, though similar to each other, regardless of the <italic toggle=\"yes\">ortho</italic>‐metallated cation (<bold>Figure</bold> ##FIG##3##\n3\n##). These alterations involve a decrease in the relative intensity of the spectra in the Soret region near 430 nm and an increase of the absorbance in the Q band region, i.e., above 500 nm.</p>", "<title>Crystal Structures</title>", "<p>Solid state structures of the selected <italic toggle=\"yes\">ortho</italic>‐metallated systems were elucidated using the single crystal X‐ray diffraction analyses (<bold>Figure</bold> ##FIG##4##\n4\n## Figures ##SUPPL##0##S39–S44##, Supporting Information). The structures determined based on diffraction data clearly showed the coordination mode of iridium(III), ruthenium(II), and rhodium(III) ions to <bold>ClNCP</bold> or metalloligands <bold>NiMeP</bold> and <bold>RuSPy</bold>. Metalloligands bind iridium(III), ruthenium(II), and rhodium(III) ions through the N2 donor atom and the <italic toggle=\"yes\">ortho</italic>‐carbon of the aryl ring from the C20 meso‐position. The coordination sphere of metal ions located at the periphery of the macrocycle is supplemented by chloride and pentamethylcyclopentadienyl ligands (in <bold>ClNCP</bold>IrCp*, <bold>NiMeP</bold>IrCp<sup>*</sup>, <bold>RuSPy</bold>IrCp*, and <bold>RuSPy</bold>RhCp*) or chloride and <italic toggle=\"yes\">p‐</italic>cymene ligands (in <bold>NiMeP</bold>RuCym). Coordinating metal ions at the edges of metalloligands retain a structural motif referred to as a “piano stool” or a half‐sandwich complex.<sup>[</sup>\n##UREF##19##\n36\n##\n<sup>]</sup> Data on bond lengths around iridium(III), ruthenium(II), and rhodium(III) ions are summarized in <bold>Table</bold> ##TAB##0##\n1\n## along with selected bond lengths for the dimeric metal sources. The average M–L distances (where L = Cp* or Cym) are significantly longer than in starting half‐sandwich organometallic chlorides, while M–Cl bond lengths are close to those observed for terminally bound chlorides in the respective dimeric precursors or only slightly longer.<sup>[</sup>\n##UREF##20##\n37\n##, ##UREF##21##\n38\n##, ##REF##30942794##\n39\n##\n<sup>]</sup> Interestingly, <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RhCp* are isostructural when crystallized from benzene/hexane, both forming tris(benzene) solvates.</p>", "<p>The steric hindrance introduced by Cp* or Cym ligands forces them to be specifically positioned relative to methyl or mercaptopyridyl substituents at the C21 atom of metalloligand. As a consequence, they are located on opposite sides of the macrocyclic plane, and, in the case of compounds <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RhCp*, on the same side as the CO ligand. The specific setting of the <italic toggle=\"yes\">p</italic>‐cymene relative to the macrocyclic system was established for <bold>NiMeP</bold>RuCym with the isopropyl group above the metalloligand plane. Such an orientation of the Cym ligand is somewhat unexpected considering solution <sup>1</sup>H NMR results suggesting methyl rather than the isopropyl group directed toward the macrocycle interior (vide supra). It may be accounted for by packing forces for which the ligand orientation in the crystal with a smaller substituent situated beyond the perimeter of the macrocycle is more favorable. The deviation of the porphyrin ring from planarity due to sp<sup>3</sup> hybridization of C21, characteristic for the starting metalloligand <bold>NiMeP</bold> and <bold>RuSPy</bold>, is retained upon coordinating the metal ion to the periphery of the macrocycle. However, the external <italic toggle=\"yes\">ortho</italic>‐metallation does not significantly change the bond distance between the metal ion [nickel(II) or ruthenium(II)] located in the cavity of the macrocycle and the C21 carbon atom. The Ni─C21 bond length is 2.004(4) Å<sup>[</sup>\n##UREF##16##\n29\n##\n<sup>]</sup> in <bold>NiMeP</bold>, while in <bold>NiMeP</bold>IrCp* and <bold>NiMeP</bold>RuCym it is 2.022(1) Å and 2.015(2) Å, respectively. For <bold>RuSPy</bold>‐containing systems, this bond length alteration is even less pronounced: from 2.118(3) Å in the metalloligand to 2.110(2) and 2.116(1) Å in <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RhCp*, respectively. Analyses of the out‐of‐plane porphyrin ring distortions were carried out using the <italic toggle=\"yes\">PorphStruct</italic> tool<sup>[</sup>\n##REF##34061410##\n40\n##\n<sup>]</sup> which was based on the normal‐coordinate structure decomposition (NSD) approach<sup>[</sup>\n##UREF##22##\n41\n##, ##REF##9533688##\n42\n##\n<sup>]</sup> (<bold>Table</bold> ##TAB##1##\n2\n## and <bold>Figure</bold> ##FIG##5##\n5\n##). The comparative NSD analyses applied for starting systems, i.e., <bold>ClNCP</bold>, <bold>NiMeP</bold>, and <bold>RuSPy</bold>, indicated a moderate effect of the <italic toggle=\"yes\">ortho</italic>‐metallation on the total out‐of‐plane distortion of the porphyrin (<italic toggle=\"yes\">D<sub>oop</sub>\n</italic>). In fact, in some instances (<bold>Cl</bold>\n<bold>NCP</bold>IrCp*, <bold>RuSPy</bold>IrCp*, <bold>RuSPy</bold>RhCp*, Table ##TAB##1##2##, entries 2, 7, and 8, respectively) the chelation at the <bold>NCP</bold> perimeter led to a less pronounced displacement than that observed in the starting ligand (<bold>NCP</bold>, entry 1; <bold>RuSPy</bold>, entry 6). The most significant deviation increase due to <italic toggle=\"yes\">ortho</italic>‐metallation was observed for the <bold>NiMeP</bold> metalloligand (Table ##TAB##1##2##, entry 3) upon chelation of RuCymCl moiety (entry 5). All systems indicated a significant saddling distortion which, again, increased only in <bold>NiMeP</bold>RuCym. The increasing doming, ruffling, and waving distortions were observed for almost all systems upon external chelation, although these components gave rather minor contributions to <italic toggle=\"yes\">D<sub>oop</sub>\n</italic> which is dominated by the saddling. Displacement of metal ions from the mean plane of the porphyrin in a metalloligand (<italic toggle=\"yes\">d<sub>M‐mpln</sub>\n</italic>) slightly increased after an external metal ion was introduced, though an opposite effect was observed for the displacement from an MCNNN mean plane (<italic toggle=\"yes\">d<sub>M‐ccpln</sub>\n</italic>). A common structural feature for the complexes under study as well as for <bold>NCP</bold> free base, is a pronounced deviation of the confused pyrrole plane from that of the porphyrin ring. Such a deviation can be parametrized by a dihedral angle (<italic toggle=\"yes\">DH</italic>, Table ##TAB##1##2##) between the confused pyrrole mean plane and the mean plane defined by all non‐hydrogen atoms of the macrocycle, except N2, C3, and C21. Apparently, a significant increase of this angle upon external chelation was observed only for the <bold>NiMeP‐</bold>containing complexes (Table ##TAB##1##2##, entries 4 and 5). The individual atom displacements from the mean plane are typical for the saddle‐distorted porphyrins with alternate directions of the pyrrole deviation (Figure ##FIG##5##5##). Significantly, in the bimetallic systems <bold>NiMeP</bold>IrCp* and <bold>NiMeP</bold>RuCym, the displacement of the meso‐carbons is significantly more pronounced than in the starting <bold>NiMeP</bold>, where those atoms are located almost in the mean plane. It is particularly evident for C20 and is related to the coordination of N2 and the aryl at C20. The external chelation slightly increases the displacement of N2 and C3 in these two systems with respect to the metalloligand, in line with the increasing <italic toggle=\"yes\">DH</italic>. Generally, the atoms are more displaced in <bold>NiMeP</bold> and its <italic toggle=\"yes\">ortho</italic>‐metallated derivatives than in <bold>RuSPy</bold> and its complexes.</p>", "<p>All <italic toggle=\"yes\">ortho</italic>‐metallated complexes are chiral, as are their precursors in the solid state. However, these systems crystallized in centrosymmetric space groups as racemates and in Figure ##FIG##4##4## only one enantiomer for each of the complexes has been shown.</p>", "<title>Chirality</title>", "<p>Our attempt to separate enantiomers of the externally metallated <bold>NCP</bold> derivatives involved HPLC methods with a chiral stationary phase. The enantiomers of several of these systems are presented in <bold>Figure</bold> ##FIG##6##\n6\n## as they appear in the solid‐state structures, along with definitions of their absolute configurations. For these definitions, we took an external metallacycle which is common to all these <italic toggle=\"yes\">ortho</italic>‐metallated systems, i.e., M─N2─C1─C20─C<italic toggle=\"yes\">\n<sub>ipso</sub>\n</italic>─C<italic toggle=\"yes\">\n<sub>ortho</sub>\n</italic> as a chirality plane.</p>", "<p>Although metalloligands <bold>NiMeP</bold> and <bold>RuSPy</bold> are intrinsically chiral due to the presence of a chirality center at the coordinated C21,<sup>[</sup>\n##REF##21226119##\n43\n##\n<sup>]</sup> the <italic toggle=\"yes\">ortho</italic>‐metallation introduces its own chirality related to a differentiation of the porphyrin faces. Apparently, these two chirality sources are not independent, that is, upon external chelation of the racemic mixture of <bold>NiMeP</bold> or <bold>RuSPy</bold> only a pair of enantiomers is formed and no other NMR‐distinguishable stereoisomers can be observed. Hence, the external metallation is stereoselective although two diastereomers can be potentially formed, differing in orientation of chloride and the organometallic ligands (Cp* or Cym) at the externally chelated metal with respect to the macrocycle. The crystal structures reveal roughly the same orientation of the chloride ligand at the external metal center and the substituent at C21. Thus, the chirality of the bimetallic monomers in the solid state and solution is predefined by the starting metalloligands<sup>[</sup>\n##REF##21226119##\n43\n##, ##UREF##23##\n44\n##\n<sup>]</sup> with absolute configurations <italic toggle=\"yes\">S</italic> or <italic toggle=\"yes\">R</italic> at C21 in the metalloligands invariantly giving rise to the configurations <italic toggle=\"yes\">P</italic> or <italic toggle=\"yes\">M</italic>, respectively in the <italic toggle=\"yes\">ortho</italic>‐metallated complexes. The separation of the bimetallic enantiomers by the HPLC method was expected to be effective through two approaches (<bold>Scheme</bold> ##FIG##7##\n2\n##). The first method involved a separation of enantiomers prior to the external chelation (<bold>Figure</bold> ##FIG##8##\n7A,B,C,E##), while in the second approach, separation proceeded <italic toggle=\"yes\">ortho</italic>‐metallation (Figure ##FIG##8##7D,F##; Figures ##SUPPL##0##S29## and ##SUPPL##0##S30##, Supporting Information). The first method allows high enantiopurity of the bimetallic systems and, in principle, can be applied for many other metal ions resulting in chirality transfer from the metalloligand toward the external metal center which may be a site of catalytic reaction. Importantly, the absolute configurations of such complexes can be deduced directly from the absolute configuration of the metalloligand. The second method is more useful for the systems for which the external chelation is less effective, such as <bold>NiMeP</bold>RhCp* or <bold>RuSPy</bold>RhCp*.</p>", "<p>The asymmetry of these configurationally stable systems arises from the presence of the chiral center at the C21 atom. Conversely, the <bold>NCP</bold> free base is chiral in the solid state owing to its non‐planarity but in solution, the molecule is configurationally unstable and no enantiomer separation is possible. This is due to a flipping of the confused pyrrole allowing fast interconversion of the enantiomers, unlike in several 21‐substituted <bold>NCP</bold> derivatives.<sup>[</sup>\n##REF##22924766##\n45\n##, ##REF##24601636##\n46\n##\n<sup>]</sup> Thus, chelation of metal ion by N2 and the <italic toggle=\"yes\">ortho</italic> carbon atom of the adjacent meso‐aryl such as in <bold>ClNCP</bold>IrCp* or <bold>NCP</bold>PtPPh<sub>3</sub>\n<sup>[</sup>\n##UREF##13##\n25\n##\n<sup>]</sup> as well as double chelation in directly bound 3,3′‐(<bold>NCP</bold>)<sub>2</sub>Pt<sup>[</sup>\n##UREF##15##\n28\n##\n<sup>]</sup> is sufficient to stabilize the configuration. The external <italic toggle=\"yes\">ortho</italic>‐metallation provides a lock preventing fast interconversion of enantiomers and participates in the differentiation of the macrocycle faces. Thus, for <bold>ClNCP</bold>IrCp*, we were able to separate enantiomers and record their circular dichroic spectra (Figures ##SUPPL##0##S27## and ##SUPPL##0##S28##, Supporting Information) indicating the chirality of this system and its configurational stability. The absolute configurations of the separated enantiomers were assigned based on TD–DFT simulations of the CD spectra (Figures ##SUPPL##0##S23–S27##, Tables ##SUPPL##0##S7##–##SUPPL##0##S12##, Supporting Information).</p>", "<title>Redox Properties</title>", "<p>The electrochemical properties of the <italic toggle=\"yes\">ortho</italic>‐metallated complexes were studied by means of cyclic and differential pulse voltammetry (<bold>Figure</bold> ##FIG##9##\n8\n##; Figure ##SUPPL##0##S35##, Supporting Information). The electrode potentials were collected in <bold>Table</bold> ##TAB##2##\n3\n##. For all but one complex system the first oxidations were reversible, and for a majority, the second oxidations appeared to be reversible as well. Conversely, for almost all complexes there was no reversible reduction. Oxidation potentials were relatively low and the external coordination did not significantly affect the first oxidation potentials compared to the metalloligands <bold>NiMeP</bold> and <bold>RuSPy</bold> (Table ##TAB##2##3##, entries 8, 9) or ligand <bold>ClNCP</bold> (Table ##TAB##2##3##, entry 10). It was not the case for <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RuCym (Table ##TAB##2##3##, entries 5 and 7) for which 90 and 190 mV cathodic shifts were observed, respectively.</p>", "<p>The redox properties of the <italic toggle=\"yes\">ortho</italic>‐metallated species and their precursors can be analyzed theoretically through comparison of the frontier orbitals energies (<bold>Figure</bold> ##FIG##10##\n9\n##). Apparently, the calculated HOMO energies are very similar for all these systems with only a small rise of potential on going from <bold>RuSPy</bold> to the <italic toggle=\"yes\">ortho</italic>‐metallated derivatives which can also be noticed experimentally as an increase of oxidation potentials. The DFT‐calculated HOMO energies are in good agreement with those estimated based on the first oxidation potentials [calculated as −e(<italic toggle=\"yes\">E</italic>\n<sub>Ox1</sub> + 4.8 V)], but LUMO energies are systematically higher than those derived from the first reduction potentials <italic toggle=\"yes\">E</italic>\n<sub>Red1</sub> [calculated as −e(<italic toggle=\"yes\">E</italic>\n<sub>Red1</sub> + 4.8 V)]. Consequently, the electrochemical HOMO–LUMO gaps [calculated as e(<italic toggle=\"yes\">E</italic>\n<sub>Ox1</sub> − <italic toggle=\"yes\">E</italic>\n<sub>Red1</sub>)] are considerably smaller (by 0.4–0.6 eV) in comparison with those based on DFT calculations (cHLG in Table ##TAB##2##3##). On the other hand, the optical HOMO–LUMO energy gaps (oHLG in Table ##TAB##2##3##.), obtained from the experimental UV–vis spectra are even lower (by 0.1–0.2 eV) than the values derived from the electrochemical potentials.</p>", "<p>Spectrophotometric titration of both <bold>NiMeP</bold> and <bold>RuSPy</bold>\n<italic toggle=\"yes\">ortho</italic>‐metallated derivatives with tris(4‐bromophenyl)ammoniumyl hexachloroantimonate (BAHA, Magic blue), a one‐electron oxidant of reduction potential 0.70 V<sup>[</sup>\n##REF##11848774##\n47\n##\n<sup>]</sup> allowed monitoring of the spectral changes upon oxidation (<bold>Figure</bold> ##FIG##11##\n10\n##). According to our electrochemical data, this oxidant was sufficiently strong for the first and the second oxidation to be achieved for all systems, except <bold>RuSPy</bold> for which <italic toggle=\"yes\">E</italic>\n<sub>Ox2</sub> is too high (Table ##TAB##2##3##, entry 9). The observed changes in the spectral region between 400 and 800 nm upon the addition of one equivalent of BAHA, suggested metal‐centered oxidation in all the bimetallic systems (Figure ##FIG##11##10A,D##; Figure ##SUPPL##0##S31##–##SUPPL##0##S34##, Supporting Information). For the <bold>RuSPy</bold>MCp* complexes (M = Ir<sup>III</sup>, Rh<sup>III</sup>), the first oxidation resulted in an increase of the Soret‐like band intensity with a small (Δ<italic toggle=\"yes\">λ</italic> = 15 nm) bathochromic shift and a decrease of the Q‐type band (Figure ##FIG##11##10A##; Figure ##SUPPL##0##S34##, Supporting Information). Such changes suggest that the conjugation of the π‐electrons of the aromatic macrocycle remains intact after one electron is removed. Further addition of BAHA resulted in a gradual increase of the absorbance in the NIR region at ≈1500 nm which is indicative of a radical species, thus suggesting a ligand‐centered second oxidation process. These spectral changes are in sharp contrast to those observed for the <bold>RuSPy</bold> metalloligand for which a pronounced decrease of the Soret‐like and an increase of the Q‐like bands were observed and no further spectral alteration occurred after passing 1 equiv of BAHA (Figure ##FIG##11##10B##). Such a pattern of spectral changes may suggest a porphyrin‐centered oxidation to the cation metalloradical rather than Ru‐centered oxidation. On the other hand, titration of <bold>ClNCP</bold>IrCp* with BAHA indicated an initial decrease of the Soret‐like band at 448 nm and its bathochromic shift up to 463 nm upon the addition of 1 equiv of the oxidant. The changes were followed by an increase in intensity of this band with a further redshift to 469 nm which was accompanied by the absorbance increase at 816 nm and the formation of the broadband at 1500 nm when approaching 2 equiv of BAHA (Figure ##SUPPL##0##S31##, Supporting Information). Thus, apparently despite oxidation of the “empty” macrocycle in <bold>ClNCP</bold>IrCp* the aromaticity of the system is retained and typical spectral features of the porphyrinoids, i.e., the strong Soret‐like band and weaker Q‐type bands are observed even for the two‐electron oxidized species. The first oxidations of the systems comprising <bold>NiMeP</bold> are nickel‐centered. The highly anisotropic orthorhombic frozen dichloromethane ESR spectra obtained by the BAHA addition (Figure ##FIG##10##9C##) closely resemble those of various 21‐alkylated nickel(III) <bold>NCP</bold> species.<sup>[</sup>\n##REF##12467409##\n32\n##, ##REF##12950206##\n33\n##, ##UREF##24##\n48\n##, ##REF##17269762##\n49\n##\n<sup>]</sup> For <bold>NiMeP</bold>IrCp*, the addition of more than 1.5 equiv of BAHA resulted in a gradual decrease of the nickel(III) signal intensity, moderate changes of the Zeeman tensor components, and in the appearance of a radical signal at <italic toggle=\"yes\">g</italic> = 2.0029. Also, spectrophotometric titration with BAHA revealed fine changes in the Soret and Q regions up to 1.2 equiv, followed by a gradual increase of the band at 435 nm and the final appearance of the NIR band upon the addition of more than 2 equiv of the oxidant (Figure ##FIG##10##9D##).<sup>[</sup>\n##UREF##25##\n50\n##\n<sup>]</sup> Interestingly, for the very similar complex, i.e., <bold>NiMeP</bold>RhCp*, the changes of the ESR spectra upon the addition of 1.5 or more equivalents of BAHA are different, involving slight alteration of <italic toggle=\"yes\">g</italic>\n<sub>2</sub> and <italic toggle=\"yes\">g</italic>\n<sub>3</sub> components, not the appearance of the radical signal (Figure ##SUPPL##0##S35##, Supporting Information). Similarly, the addition of BAHA to the solution of <bold>NiMeP</bold>RuCym gave rise to an orthorhombic spectrum in frozen DCM (Figure ##SUPPL##0##S36##, Supporting Information) but no strong radical signal was observed upon the addition of more than 2 equiv of BAHA. For reference purposes, we performed also the ESR‐monitored oxidation for the starting metalloligand <bold>NiMeP</bold> indicating a decrease of the Zeeman tensor anisotropy upon the addition of an excess of BAHA with changes of <italic toggle=\"yes\">g</italic>\n<sub>1</sub> from 2.382 to 2.285, <italic toggle=\"yes\">g</italic>\n<sub>2</sub> from 2.168 to 2.2019, and <italic toggle=\"yes\">g</italic>\n<sub>3</sub> from 2.086 to 2.111 for the spectra recorded in the presence of 1.2 and 3 equiv, respectively (Figure ##SUPPL##0##S37##, Supporting Information). Again, no accompanying radical formation was observed. The differences among the systems comprising <bold>NiMeP</bold> in the second oxidation potentials and ESR behavior are surely related to the external coordination, although no clear tendencies can be derived from such a limited data set. It can be also rationally expected that for both groups of the <italic toggle=\"yes\">ortho</italic>‐metallated complexes, oxidation of the metalloligand strongly affects electron density in the environment of the externally coordinated metal ion.</p>", "<title>Catalysis</title>", "<p>For preliminary studies of the catalytic function of the externally <italic toggle=\"yes\">ortho</italic>‐metallated systems, we chose <italic toggle=\"yes\">N</italic>‐heterocyclization reaction of benzylamine with 1,6‐hexanediol which has been shown to be effectively catalyzed by iridium(III) complex [IrCl<sub>2</sub>Cp*]<sub>2</sub> in toluene under basic conditions (<bold>Table</bold> ##TAB##3##\n4\n##).<sup>[</sup>\n##REF##15387539##\n51\n##\n<sup>]</sup> Small‐scale reactions (0.5 mmol) were carried out in the presence of all <italic toggle=\"yes\">ortho</italic>‐metallated iridium(III) complexes described in this paper as well as for the original catalyst [IrCl<sub>2</sub>Cp*]<sub>2</sub>, <bold>ClNCP</bold> ligand, and both metalloligands, for the reference. The samples were prepared in the inert and dry atmosphere of a glove box to avoid any interference of oxygen and moisture with the reagents, and the reactions were carried out in sealed vials. The reaction results were analyzed qualitatively using GC/MS and quantitatively using the GC/FID technique, and for the selected systems, <sup>1</sup>H NMR quantitative analysis was applied with 2,4,6‐collidine as the internal standard. As expected, only iridium(III)‐comprising systems appeared to be catalytically active in the heterocyclizaction reaction, while neither of the ligands supported the 7‐membered ring formation. The best catalyst, i.e., <bold>ClNCP</bold>IrCp* (Table ##TAB##3##4##, entry 6) gave rise to the yield exceeding that of the original catalyst [IrCl<sub>2</sub>Cp*]<sub>2</sub> with higher glycol conversion and better chemoselectivity. Also <bold>NiMeP</bold>IrCp* seemed to be a more selective catalyst than [IrCl<sub>2</sub>Cp*]<sub>2</sub> with a similar yield of the main reaction product (Table ##TAB##3##4##, entries 2 and 1). Surprisingly, no heterocyclization was observed for <bold>RuSPy</bold>IrCp* used as a catalyst, despite several attempts. It may be due to a less labile character of the Ir─Cl bond in this complex than in other systems. According to the proposed reaction mechanism,<sup>[</sup>\n##REF##15387539##\n51\n##\n<sup>]</sup> in the early stage of the catalytic process, coordination of the glycolic anion to the iridium center is required which implies chloride substitution (originally present in the <italic toggle=\"yes\">ortho</italic>‐metallated systems). A significantly longer C─Ir bond in <bold>RuSPy</bold>IrCp* (2.083(5) Å) than those in <bold>NiMeP</bold>IrCp* (2.041(3) Å) or <bold>ClNCP</bold>IrCp* (2.051(6) Å) may be responsible for a weaker <italic toggle=\"yes\">trans</italic> effect of the meso‐aryl carbanion coordinated to the iridium(III) center on the opposite side to the chloride, making its exchange less effective. Of course, some other structural features, such as the presence and type of the metal ion within the macrocyclic cavity, flexibility of the molecular skeleton and its deformations, etc., may be decisive for the catalytic activity of the iridium complexes. Although at the present stage, we cannot offer any more conclusive accounting for the observed differences, it is clear that distinctions in the reaction yields among the systems used in this study indicate an influence of the porphyrin‐chelating ligand on the catalytic activity of the externally coordinated metal center.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Syntheses and Characterizations</title>", "<p>As starting materials for our syntheses of bis‐metallic systems, we chose two previously reported compounds bearing a substituent at the C21 position coordinated to either nickel(II)<sup>[</sup>\n##UREF##16##\n29\n##, ##REF##11151364##\n30\n##, ##UREF##17##\n31\n##, ##REF##12467409##\n32\n##, ##REF##12950206##\n33\n##\n<sup>]</sup> or ruthenium(II).<sup>[</sup>\n##UREF##18##\n34\n##, ##REF##31944014##\n35\n##\n<sup>]</sup> The common features of these, otherwise different complexes are chirality, significant deviation from planarity of the porphyrin ring in the region of confused pyrrole, and unoccupied/non‐protonated N2. These systems were subjected to reaction with organometallic dimeric complexes of ruthenium(II), rhodium(III), or iridium(III) with two chlorides and either neutral η<sup>6</sup>‐<italic toggle=\"yes\">para‐</italic>cymene (Cym) or η<sup>5</sup>‐pentamethylcyclopentadienyl anion (Cp*). Under mild conditions (reflux of DCM solution in the presence of sodium acetate as a proton scavenger) the reaction resulted in the substitution of one chloride by carbanionic <italic toggle=\"yes\">ortho‐</italic>C20 and coordination of N2 atoms (<bold>Scheme</bold> ##FIG##1##\n1\n##). The <italic toggle=\"yes\">ortho</italic>‐metallation efficacy varied depending on the metal ion from 35–40% reaction yield for Rh<sup>III</sup>, 54–60% for Ru<sup>II</sup>, and up to 85–93% for Ir<sup>III</sup>. Slightly better results were obtained for <bold>NiMeP</bold> compared with those for <bold>RuSPy</bold>. We showed also that under the analogous condition, the reaction of [IrCl<sub>2</sub>Cp*]<sub>2</sub> with <bold>ClNCP</bold> free base yielded <italic toggle=\"yes\">ortho</italic>‐metallated derivative <bold>ClNCP</bold>IrCp* (Scheme ##FIG##1##1##) with a good outcome (83% yield).</p>", "<p>The new complexes were characterized by high‐resolution mass spectrometry, <sup>1</sup>H and <sup>13</sup>C NMR, including homo‐ and heteronuclear 2D correlation experiments, UV–vis–NIR spectroscopy, and single crystal XRD analyses. The ESI+ HRMS indicated the presence of the incoming metal ion as well as Cym or Cp* moieties in each case, though all cations were stripped of chloride. The <sup>1</sup>H NMR spectra revealed the preservation of most of the spectral features typical of <bold>NiMeP</bold>, <bold>RuSPy</bold>, or <bold>ClNCP</bold> in the complexes formed and the appearance of new signals related to the presence of Cp* or Cym (<bold>Figure</bold> ##FIG##2##\n2\n##). Thus, the spectra of the systems with Cp* comprise a very strong (15H) signal at about <italic toggle=\"yes\">δ</italic> 0.8 ppm due to methyl protons, indicating fast rotation around the M–Cp* direction. On the other hand, the differentiation of aryl and isopropyl resonances of the RuCym moiety is in line with the slow motions of the Cym ligand at the <sup>1</sup>H NMR time scale. Moreover, an upfield shift of all the Cym protons with respect to those observed for starting [RuCl<sub>2</sub>Cym]<sub>2</sub>, indicates the position of this moiety over the aromatic frame of the macrocyclic ligands. Significantly, this aromatic ring shielding effect is strongest for the cymene methyl Me<italic toggle=\"yes\">\n<sub>c</sub>\n</italic> (Δ<italic toggle=\"yes\">δ</italic> 0.7–1.4 ppm) suggesting the orientation of the ligand with the isopropyl group situated rather outside, while Me<italic toggle=\"yes\">\n<sub>c</sub>\n</italic> is above the macrocycle. The number of meso‐aryl distinct signals in the spectra of <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RuCym recorded at room temperature, reflects diastereotopic inequivalence of the macrocyclic faces and slow, at the NMR timescale, rotation of these substituents around C<sub>ipso</sub>─C<sub>meso</sub> bonds, resulting in differentiation of <italic toggle=\"yes\">ortho‐</italic> and <italic toggle=\"yes\">meta‐</italic>H resonances of phenyls at C5, C10, and C15. Conversely, these meso‐phenyl protons in <bold>NiMeP</bold>IrCp* and <bold>NiMeP</bold>RuCym give rise to severely broadened signals indicating intermediate rotation rate of the substituents and diastereotopicity of the complex faces. The only sharp meso‐aryl signals are those of phenyl at the C20 position due to the complete freezing of its rotation by <italic toggle=\"yes\">ortho</italic>‐metallation. The chemical shifts and coupling patterns are similar in all these <italic toggle=\"yes\">ortho</italic>‐metallated complexes comprising a doublet for 20‐<italic toggle=\"yes\">m</italic> at about 8.3 ppm, a doublet for 20‐<italic toggle=\"yes\">o</italic>′ at about 7.7 ppm, and two triplets for 20‐<italic toggle=\"yes\">m</italic>′ and 20‐<italic toggle=\"yes\">p</italic> at ≈7.3 and 7.2 ppm, respectively (Figure ##FIG##2##2##). For the <italic toggle=\"yes\">ortho</italic>‐metallated rhodium(III) complexes, <bold>NiMeP</bold>RhCp* and <bold>RuSPy</bold>RhCp*, a close resemblance of</p>", "<p>\n<sup>1</sup>H NMR spectral patterns to those of the respective Ir<sup>III</sup> systems were observed. The major difference is an additional splitting of all multiplets of the 20‐phenyl protons due to <sup>1</sup>H‐<sup>103</sup>Rh spin–spin coupling (<italic toggle=\"yes\">J<sub>RhH</sub>\n</italic> = 1.3–1.5 Hz). Significantly, the <italic toggle=\"yes\">ortho</italic>‐carbon of the C20 phenyl substituent, identified on the basis of <sup>1</sup>H,<sup>13</sup>C HSQC and <sup>1</sup>H,<sup>13</sup>C HMBC experiments (Figure ##SUPPL##0##S7B## and ##SUPPL##0##S13B##, Supporting Information), gives rise to a doublet at <italic toggle=\"yes\">δ<sub>C</sub>\n</italic> 169.8 ppm with <sup>1</sup>\n<italic toggle=\"yes\">J<sub>RhC</sub>\n</italic> = 31.1 Hz for <bold>NiMeP</bold>RhCp* and at <italic toggle=\"yes\">δ<sub>C</sub>\n</italic> 169.9 ppm with <sup>1</sup>\n<italic toggle=\"yes\">J<sub>RhC</sub>\n</italic> = 30.9 Hz for <bold>RuSPy</bold>RhCp* unequivocally proving coordination of the carbanion. The <sup>13</sup>C–<sup>103</sup>Rh coupling could be observed also for cyclopentadiene carbon atoms in <sup>13</sup>C NMR of both complexes giving rise to doublets at about <italic toggle=\"yes\">δ<sub>C</sub>\n</italic> 96 ppm with <sup>1</sup>\n<italic toggle=\"yes\">J<sub>RhC</sub>\n</italic> = 6.1 Hz. The <sup>1</sup>H NMR characteristics of <bold>Cl</bold>\n<bold>NCP</bold>IrCp* differ from the nickel(II) and ruthenium(II) complexes with 21‐CH and 22,24‐NH resonances arising in the upfield region of the spectrum (<italic toggle=\"yes\">δ</italic> −4.69 and broad signals at <italic toggle=\"yes\">δ</italic> −1.05, −1.10 ppm, respectively) reflecting a free‐base character of the macrocyclic core. Interestingly, for all pentamethylcyclopentadienyl‐comprising systems, correlations of the coordinated <italic toggle=\"yes\">ortho</italic>‐C with methyl protons of the η<sup>5</sup>‐Cp* ligand were observed in the <sup>1</sup>H,<sup>13</sup>C HMBC maps (Figures ##SUPPL##0##S3B##, ##SUPPL##0##S7B##, ##SUPPL##0##S9B##, ##SUPPL##0##S13B##, and ##SUPPL##0##S15B##, Supporting Information), regardless of the metal ion. Such correlations appeared despite the fact that the coupled nuclei were separated by four bonds. The correlations may be accounted for by the anionic character of the Cp* ligand resulting in a relatively high electron density available that enhanced <sup>1</sup>H‐<sup>13</sup>C coupling. Significantly, for the neutral η<sup>6</sup>‐Cym ligand in <bold>NiMeP</bold>RuCym or <bold>RuSPy</bold>RuCym, there was no such a correlation observed, in spite of only three bonds separating aryl protons of this ligand and the Ru<sup>II</sup>‐coordinating <italic toggle=\"yes\">ortho</italic>‐C at 20‐Ph.</p>", "<p>The electronic spectrum of <bold>ClNCP</bold>IrCp* resembles that of the starting porphyrin <bold>ClNCP</bold> with ≈65 nm and 15 nm bathochromic shifts of the lowest‐energy Q band and the Soret band, respectively observed for the complex (Figure ##SUPPL##0##S1##, Supporting Information). For the <bold>NiMeP</bold> and <bold>RuSPy,</bold> the spectral changes due to external coordination are much more profound, though similar to each other, regardless of the <italic toggle=\"yes\">ortho</italic>‐metallated cation (<bold>Figure</bold> ##FIG##3##\n3\n##). These alterations involve a decrease in the relative intensity of the spectra in the Soret region near 430 nm and an increase of the absorbance in the Q band region, i.e., above 500 nm.</p>", "<title>Crystal Structures</title>", "<p>Solid state structures of the selected <italic toggle=\"yes\">ortho</italic>‐metallated systems were elucidated using the single crystal X‐ray diffraction analyses (<bold>Figure</bold> ##FIG##4##\n4\n## Figures ##SUPPL##0##S39–S44##, Supporting Information). The structures determined based on diffraction data clearly showed the coordination mode of iridium(III), ruthenium(II), and rhodium(III) ions to <bold>ClNCP</bold> or metalloligands <bold>NiMeP</bold> and <bold>RuSPy</bold>. Metalloligands bind iridium(III), ruthenium(II), and rhodium(III) ions through the N2 donor atom and the <italic toggle=\"yes\">ortho</italic>‐carbon of the aryl ring from the C20 meso‐position. The coordination sphere of metal ions located at the periphery of the macrocycle is supplemented by chloride and pentamethylcyclopentadienyl ligands (in <bold>ClNCP</bold>IrCp*, <bold>NiMeP</bold>IrCp<sup>*</sup>, <bold>RuSPy</bold>IrCp*, and <bold>RuSPy</bold>RhCp*) or chloride and <italic toggle=\"yes\">p‐</italic>cymene ligands (in <bold>NiMeP</bold>RuCym). Coordinating metal ions at the edges of metalloligands retain a structural motif referred to as a “piano stool” or a half‐sandwich complex.<sup>[</sup>\n##UREF##19##\n36\n##\n<sup>]</sup> Data on bond lengths around iridium(III), ruthenium(II), and rhodium(III) ions are summarized in <bold>Table</bold> ##TAB##0##\n1\n## along with selected bond lengths for the dimeric metal sources. The average M–L distances (where L = Cp* or Cym) are significantly longer than in starting half‐sandwich organometallic chlorides, while M–Cl bond lengths are close to those observed for terminally bound chlorides in the respective dimeric precursors or only slightly longer.<sup>[</sup>\n##UREF##20##\n37\n##, ##UREF##21##\n38\n##, ##REF##30942794##\n39\n##\n<sup>]</sup> Interestingly, <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RhCp* are isostructural when crystallized from benzene/hexane, both forming tris(benzene) solvates.</p>", "<p>The steric hindrance introduced by Cp* or Cym ligands forces them to be specifically positioned relative to methyl or mercaptopyridyl substituents at the C21 atom of metalloligand. As a consequence, they are located on opposite sides of the macrocyclic plane, and, in the case of compounds <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RhCp*, on the same side as the CO ligand. The specific setting of the <italic toggle=\"yes\">p</italic>‐cymene relative to the macrocyclic system was established for <bold>NiMeP</bold>RuCym with the isopropyl group above the metalloligand plane. Such an orientation of the Cym ligand is somewhat unexpected considering solution <sup>1</sup>H NMR results suggesting methyl rather than the isopropyl group directed toward the macrocycle interior (vide supra). It may be accounted for by packing forces for which the ligand orientation in the crystal with a smaller substituent situated beyond the perimeter of the macrocycle is more favorable. The deviation of the porphyrin ring from planarity due to sp<sup>3</sup> hybridization of C21, characteristic for the starting metalloligand <bold>NiMeP</bold> and <bold>RuSPy</bold>, is retained upon coordinating the metal ion to the periphery of the macrocycle. However, the external <italic toggle=\"yes\">ortho</italic>‐metallation does not significantly change the bond distance between the metal ion [nickel(II) or ruthenium(II)] located in the cavity of the macrocycle and the C21 carbon atom. The Ni─C21 bond length is 2.004(4) Å<sup>[</sup>\n##UREF##16##\n29\n##\n<sup>]</sup> in <bold>NiMeP</bold>, while in <bold>NiMeP</bold>IrCp* and <bold>NiMeP</bold>RuCym it is 2.022(1) Å and 2.015(2) Å, respectively. For <bold>RuSPy</bold>‐containing systems, this bond length alteration is even less pronounced: from 2.118(3) Å in the metalloligand to 2.110(2) and 2.116(1) Å in <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RhCp*, respectively. Analyses of the out‐of‐plane porphyrin ring distortions were carried out using the <italic toggle=\"yes\">PorphStruct</italic> tool<sup>[</sup>\n##REF##34061410##\n40\n##\n<sup>]</sup> which was based on the normal‐coordinate structure decomposition (NSD) approach<sup>[</sup>\n##UREF##22##\n41\n##, ##REF##9533688##\n42\n##\n<sup>]</sup> (<bold>Table</bold> ##TAB##1##\n2\n## and <bold>Figure</bold> ##FIG##5##\n5\n##). The comparative NSD analyses applied for starting systems, i.e., <bold>ClNCP</bold>, <bold>NiMeP</bold>, and <bold>RuSPy</bold>, indicated a moderate effect of the <italic toggle=\"yes\">ortho</italic>‐metallation on the total out‐of‐plane distortion of the porphyrin (<italic toggle=\"yes\">D<sub>oop</sub>\n</italic>). In fact, in some instances (<bold>Cl</bold>\n<bold>NCP</bold>IrCp*, <bold>RuSPy</bold>IrCp*, <bold>RuSPy</bold>RhCp*, Table ##TAB##1##2##, entries 2, 7, and 8, respectively) the chelation at the <bold>NCP</bold> perimeter led to a less pronounced displacement than that observed in the starting ligand (<bold>NCP</bold>, entry 1; <bold>RuSPy</bold>, entry 6). The most significant deviation increase due to <italic toggle=\"yes\">ortho</italic>‐metallation was observed for the <bold>NiMeP</bold> metalloligand (Table ##TAB##1##2##, entry 3) upon chelation of RuCymCl moiety (entry 5). All systems indicated a significant saddling distortion which, again, increased only in <bold>NiMeP</bold>RuCym. The increasing doming, ruffling, and waving distortions were observed for almost all systems upon external chelation, although these components gave rather minor contributions to <italic toggle=\"yes\">D<sub>oop</sub>\n</italic> which is dominated by the saddling. Displacement of metal ions from the mean plane of the porphyrin in a metalloligand (<italic toggle=\"yes\">d<sub>M‐mpln</sub>\n</italic>) slightly increased after an external metal ion was introduced, though an opposite effect was observed for the displacement from an MCNNN mean plane (<italic toggle=\"yes\">d<sub>M‐ccpln</sub>\n</italic>). A common structural feature for the complexes under study as well as for <bold>NCP</bold> free base, is a pronounced deviation of the confused pyrrole plane from that of the porphyrin ring. Such a deviation can be parametrized by a dihedral angle (<italic toggle=\"yes\">DH</italic>, Table ##TAB##1##2##) between the confused pyrrole mean plane and the mean plane defined by all non‐hydrogen atoms of the macrocycle, except N2, C3, and C21. Apparently, a significant increase of this angle upon external chelation was observed only for the <bold>NiMeP‐</bold>containing complexes (Table ##TAB##1##2##, entries 4 and 5). The individual atom displacements from the mean plane are typical for the saddle‐distorted porphyrins with alternate directions of the pyrrole deviation (Figure ##FIG##5##5##). Significantly, in the bimetallic systems <bold>NiMeP</bold>IrCp* and <bold>NiMeP</bold>RuCym, the displacement of the meso‐carbons is significantly more pronounced than in the starting <bold>NiMeP</bold>, where those atoms are located almost in the mean plane. It is particularly evident for C20 and is related to the coordination of N2 and the aryl at C20. The external chelation slightly increases the displacement of N2 and C3 in these two systems with respect to the metalloligand, in line with the increasing <italic toggle=\"yes\">DH</italic>. Generally, the atoms are more displaced in <bold>NiMeP</bold> and its <italic toggle=\"yes\">ortho</italic>‐metallated derivatives than in <bold>RuSPy</bold> and its complexes.</p>", "<p>All <italic toggle=\"yes\">ortho</italic>‐metallated complexes are chiral, as are their precursors in the solid state. However, these systems crystallized in centrosymmetric space groups as racemates and in Figure ##FIG##4##4## only one enantiomer for each of the complexes has been shown.</p>", "<title>Chirality</title>", "<p>Our attempt to separate enantiomers of the externally metallated <bold>NCP</bold> derivatives involved HPLC methods with a chiral stationary phase. The enantiomers of several of these systems are presented in <bold>Figure</bold> ##FIG##6##\n6\n## as they appear in the solid‐state structures, along with definitions of their absolute configurations. For these definitions, we took an external metallacycle which is common to all these <italic toggle=\"yes\">ortho</italic>‐metallated systems, i.e., M─N2─C1─C20─C<italic toggle=\"yes\">\n<sub>ipso</sub>\n</italic>─C<italic toggle=\"yes\">\n<sub>ortho</sub>\n</italic> as a chirality plane.</p>", "<p>Although metalloligands <bold>NiMeP</bold> and <bold>RuSPy</bold> are intrinsically chiral due to the presence of a chirality center at the coordinated C21,<sup>[</sup>\n##REF##21226119##\n43\n##\n<sup>]</sup> the <italic toggle=\"yes\">ortho</italic>‐metallation introduces its own chirality related to a differentiation of the porphyrin faces. Apparently, these two chirality sources are not independent, that is, upon external chelation of the racemic mixture of <bold>NiMeP</bold> or <bold>RuSPy</bold> only a pair of enantiomers is formed and no other NMR‐distinguishable stereoisomers can be observed. Hence, the external metallation is stereoselective although two diastereomers can be potentially formed, differing in orientation of chloride and the organometallic ligands (Cp* or Cym) at the externally chelated metal with respect to the macrocycle. The crystal structures reveal roughly the same orientation of the chloride ligand at the external metal center and the substituent at C21. Thus, the chirality of the bimetallic monomers in the solid state and solution is predefined by the starting metalloligands<sup>[</sup>\n##REF##21226119##\n43\n##, ##UREF##23##\n44\n##\n<sup>]</sup> with absolute configurations <italic toggle=\"yes\">S</italic> or <italic toggle=\"yes\">R</italic> at C21 in the metalloligands invariantly giving rise to the configurations <italic toggle=\"yes\">P</italic> or <italic toggle=\"yes\">M</italic>, respectively in the <italic toggle=\"yes\">ortho</italic>‐metallated complexes. The separation of the bimetallic enantiomers by the HPLC method was expected to be effective through two approaches (<bold>Scheme</bold> ##FIG##7##\n2\n##). The first method involved a separation of enantiomers prior to the external chelation (<bold>Figure</bold> ##FIG##8##\n7A,B,C,E##), while in the second approach, separation proceeded <italic toggle=\"yes\">ortho</italic>‐metallation (Figure ##FIG##8##7D,F##; Figures ##SUPPL##0##S29## and ##SUPPL##0##S30##, Supporting Information). The first method allows high enantiopurity of the bimetallic systems and, in principle, can be applied for many other metal ions resulting in chirality transfer from the metalloligand toward the external metal center which may be a site of catalytic reaction. Importantly, the absolute configurations of such complexes can be deduced directly from the absolute configuration of the metalloligand. The second method is more useful for the systems for which the external chelation is less effective, such as <bold>NiMeP</bold>RhCp* or <bold>RuSPy</bold>RhCp*.</p>", "<p>The asymmetry of these configurationally stable systems arises from the presence of the chiral center at the C21 atom. Conversely, the <bold>NCP</bold> free base is chiral in the solid state owing to its non‐planarity but in solution, the molecule is configurationally unstable and no enantiomer separation is possible. This is due to a flipping of the confused pyrrole allowing fast interconversion of the enantiomers, unlike in several 21‐substituted <bold>NCP</bold> derivatives.<sup>[</sup>\n##REF##22924766##\n45\n##, ##REF##24601636##\n46\n##\n<sup>]</sup> Thus, chelation of metal ion by N2 and the <italic toggle=\"yes\">ortho</italic> carbon atom of the adjacent meso‐aryl such as in <bold>ClNCP</bold>IrCp* or <bold>NCP</bold>PtPPh<sub>3</sub>\n<sup>[</sup>\n##UREF##13##\n25\n##\n<sup>]</sup> as well as double chelation in directly bound 3,3′‐(<bold>NCP</bold>)<sub>2</sub>Pt<sup>[</sup>\n##UREF##15##\n28\n##\n<sup>]</sup> is sufficient to stabilize the configuration. The external <italic toggle=\"yes\">ortho</italic>‐metallation provides a lock preventing fast interconversion of enantiomers and participates in the differentiation of the macrocycle faces. Thus, for <bold>ClNCP</bold>IrCp*, we were able to separate enantiomers and record their circular dichroic spectra (Figures ##SUPPL##0##S27## and ##SUPPL##0##S28##, Supporting Information) indicating the chirality of this system and its configurational stability. The absolute configurations of the separated enantiomers were assigned based on TD–DFT simulations of the CD spectra (Figures ##SUPPL##0##S23–S27##, Tables ##SUPPL##0##S7##–##SUPPL##0##S12##, Supporting Information).</p>", "<title>Redox Properties</title>", "<p>The electrochemical properties of the <italic toggle=\"yes\">ortho</italic>‐metallated complexes were studied by means of cyclic and differential pulse voltammetry (<bold>Figure</bold> ##FIG##9##\n8\n##; Figure ##SUPPL##0##S35##, Supporting Information). The electrode potentials were collected in <bold>Table</bold> ##TAB##2##\n3\n##. For all but one complex system the first oxidations were reversible, and for a majority, the second oxidations appeared to be reversible as well. Conversely, for almost all complexes there was no reversible reduction. Oxidation potentials were relatively low and the external coordination did not significantly affect the first oxidation potentials compared to the metalloligands <bold>NiMeP</bold> and <bold>RuSPy</bold> (Table ##TAB##2##3##, entries 8, 9) or ligand <bold>ClNCP</bold> (Table ##TAB##2##3##, entry 10). It was not the case for <bold>RuSPy</bold>IrCp* and <bold>RuSPy</bold>RuCym (Table ##TAB##2##3##, entries 5 and 7) for which 90 and 190 mV cathodic shifts were observed, respectively.</p>", "<p>The redox properties of the <italic toggle=\"yes\">ortho</italic>‐metallated species and their precursors can be analyzed theoretically through comparison of the frontier orbitals energies (<bold>Figure</bold> ##FIG##10##\n9\n##). Apparently, the calculated HOMO energies are very similar for all these systems with only a small rise of potential on going from <bold>RuSPy</bold> to the <italic toggle=\"yes\">ortho</italic>‐metallated derivatives which can also be noticed experimentally as an increase of oxidation potentials. The DFT‐calculated HOMO energies are in good agreement with those estimated based on the first oxidation potentials [calculated as −e(<italic toggle=\"yes\">E</italic>\n<sub>Ox1</sub> + 4.8 V)], but LUMO energies are systematically higher than those derived from the first reduction potentials <italic toggle=\"yes\">E</italic>\n<sub>Red1</sub> [calculated as −e(<italic toggle=\"yes\">E</italic>\n<sub>Red1</sub> + 4.8 V)]. Consequently, the electrochemical HOMO–LUMO gaps [calculated as e(<italic toggle=\"yes\">E</italic>\n<sub>Ox1</sub> − <italic toggle=\"yes\">E</italic>\n<sub>Red1</sub>)] are considerably smaller (by 0.4–0.6 eV) in comparison with those based on DFT calculations (cHLG in Table ##TAB##2##3##). On the other hand, the optical HOMO–LUMO energy gaps (oHLG in Table ##TAB##2##3##.), obtained from the experimental UV–vis spectra are even lower (by 0.1–0.2 eV) than the values derived from the electrochemical potentials.</p>", "<p>Spectrophotometric titration of both <bold>NiMeP</bold> and <bold>RuSPy</bold>\n<italic toggle=\"yes\">ortho</italic>‐metallated derivatives with tris(4‐bromophenyl)ammoniumyl hexachloroantimonate (BAHA, Magic blue), a one‐electron oxidant of reduction potential 0.70 V<sup>[</sup>\n##REF##11848774##\n47\n##\n<sup>]</sup> allowed monitoring of the spectral changes upon oxidation (<bold>Figure</bold> ##FIG##11##\n10\n##). According to our electrochemical data, this oxidant was sufficiently strong for the first and the second oxidation to be achieved for all systems, except <bold>RuSPy</bold> for which <italic toggle=\"yes\">E</italic>\n<sub>Ox2</sub> is too high (Table ##TAB##2##3##, entry 9). The observed changes in the spectral region between 400 and 800 nm upon the addition of one equivalent of BAHA, suggested metal‐centered oxidation in all the bimetallic systems (Figure ##FIG##11##10A,D##; Figure ##SUPPL##0##S31##–##SUPPL##0##S34##, Supporting Information). For the <bold>RuSPy</bold>MCp* complexes (M = Ir<sup>III</sup>, Rh<sup>III</sup>), the first oxidation resulted in an increase of the Soret‐like band intensity with a small (Δ<italic toggle=\"yes\">λ</italic> = 15 nm) bathochromic shift and a decrease of the Q‐type band (Figure ##FIG##11##10A##; Figure ##SUPPL##0##S34##, Supporting Information). Such changes suggest that the conjugation of the π‐electrons of the aromatic macrocycle remains intact after one electron is removed. Further addition of BAHA resulted in a gradual increase of the absorbance in the NIR region at ≈1500 nm which is indicative of a radical species, thus suggesting a ligand‐centered second oxidation process. These spectral changes are in sharp contrast to those observed for the <bold>RuSPy</bold> metalloligand for which a pronounced decrease of the Soret‐like and an increase of the Q‐like bands were observed and no further spectral alteration occurred after passing 1 equiv of BAHA (Figure ##FIG##11##10B##). Such a pattern of spectral changes may suggest a porphyrin‐centered oxidation to the cation metalloradical rather than Ru‐centered oxidation. On the other hand, titration of <bold>ClNCP</bold>IrCp* with BAHA indicated an initial decrease of the Soret‐like band at 448 nm and its bathochromic shift up to 463 nm upon the addition of 1 equiv of the oxidant. The changes were followed by an increase in intensity of this band with a further redshift to 469 nm which was accompanied by the absorbance increase at 816 nm and the formation of the broadband at 1500 nm when approaching 2 equiv of BAHA (Figure ##SUPPL##0##S31##, Supporting Information). Thus, apparently despite oxidation of the “empty” macrocycle in <bold>ClNCP</bold>IrCp* the aromaticity of the system is retained and typical spectral features of the porphyrinoids, i.e., the strong Soret‐like band and weaker Q‐type bands are observed even for the two‐electron oxidized species. The first oxidations of the systems comprising <bold>NiMeP</bold> are nickel‐centered. The highly anisotropic orthorhombic frozen dichloromethane ESR spectra obtained by the BAHA addition (Figure ##FIG##10##9C##) closely resemble those of various 21‐alkylated nickel(III) <bold>NCP</bold> species.<sup>[</sup>\n##REF##12467409##\n32\n##, ##REF##12950206##\n33\n##, ##UREF##24##\n48\n##, ##REF##17269762##\n49\n##\n<sup>]</sup> For <bold>NiMeP</bold>IrCp*, the addition of more than 1.5 equiv of BAHA resulted in a gradual decrease of the nickel(III) signal intensity, moderate changes of the Zeeman tensor components, and in the appearance of a radical signal at <italic toggle=\"yes\">g</italic> = 2.0029. Also, spectrophotometric titration with BAHA revealed fine changes in the Soret and Q regions up to 1.2 equiv, followed by a gradual increase of the band at 435 nm and the final appearance of the NIR band upon the addition of more than 2 equiv of the oxidant (Figure ##FIG##10##9D##).<sup>[</sup>\n##UREF##25##\n50\n##\n<sup>]</sup> Interestingly, for the very similar complex, i.e., <bold>NiMeP</bold>RhCp*, the changes of the ESR spectra upon the addition of 1.5 or more equivalents of BAHA are different, involving slight alteration of <italic toggle=\"yes\">g</italic>\n<sub>2</sub> and <italic toggle=\"yes\">g</italic>\n<sub>3</sub> components, not the appearance of the radical signal (Figure ##SUPPL##0##S35##, Supporting Information). Similarly, the addition of BAHA to the solution of <bold>NiMeP</bold>RuCym gave rise to an orthorhombic spectrum in frozen DCM (Figure ##SUPPL##0##S36##, Supporting Information) but no strong radical signal was observed upon the addition of more than 2 equiv of BAHA. For reference purposes, we performed also the ESR‐monitored oxidation for the starting metalloligand <bold>NiMeP</bold> indicating a decrease of the Zeeman tensor anisotropy upon the addition of an excess of BAHA with changes of <italic toggle=\"yes\">g</italic>\n<sub>1</sub> from 2.382 to 2.285, <italic toggle=\"yes\">g</italic>\n<sub>2</sub> from 2.168 to 2.2019, and <italic toggle=\"yes\">g</italic>\n<sub>3</sub> from 2.086 to 2.111 for the spectra recorded in the presence of 1.2 and 3 equiv, respectively (Figure ##SUPPL##0##S37##, Supporting Information). Again, no accompanying radical formation was observed. The differences among the systems comprising <bold>NiMeP</bold> in the second oxidation potentials and ESR behavior are surely related to the external coordination, although no clear tendencies can be derived from such a limited data set. It can be also rationally expected that for both groups of the <italic toggle=\"yes\">ortho</italic>‐metallated complexes, oxidation of the metalloligand strongly affects electron density in the environment of the externally coordinated metal ion.</p>", "<title>Catalysis</title>", "<p>For preliminary studies of the catalytic function of the externally <italic toggle=\"yes\">ortho</italic>‐metallated systems, we chose <italic toggle=\"yes\">N</italic>‐heterocyclization reaction of benzylamine with 1,6‐hexanediol which has been shown to be effectively catalyzed by iridium(III) complex [IrCl<sub>2</sub>Cp*]<sub>2</sub> in toluene under basic conditions (<bold>Table</bold> ##TAB##3##\n4\n##).<sup>[</sup>\n##REF##15387539##\n51\n##\n<sup>]</sup> Small‐scale reactions (0.5 mmol) were carried out in the presence of all <italic toggle=\"yes\">ortho</italic>‐metallated iridium(III) complexes described in this paper as well as for the original catalyst [IrCl<sub>2</sub>Cp*]<sub>2</sub>, <bold>ClNCP</bold> ligand, and both metalloligands, for the reference. The samples were prepared in the inert and dry atmosphere of a glove box to avoid any interference of oxygen and moisture with the reagents, and the reactions were carried out in sealed vials. The reaction results were analyzed qualitatively using GC/MS and quantitatively using the GC/FID technique, and for the selected systems, <sup>1</sup>H NMR quantitative analysis was applied with 2,4,6‐collidine as the internal standard. As expected, only iridium(III)‐comprising systems appeared to be catalytically active in the heterocyclizaction reaction, while neither of the ligands supported the 7‐membered ring formation. The best catalyst, i.e., <bold>ClNCP</bold>IrCp* (Table ##TAB##3##4##, entry 6) gave rise to the yield exceeding that of the original catalyst [IrCl<sub>2</sub>Cp*]<sub>2</sub> with higher glycol conversion and better chemoselectivity. Also <bold>NiMeP</bold>IrCp* seemed to be a more selective catalyst than [IrCl<sub>2</sub>Cp*]<sub>2</sub> with a similar yield of the main reaction product (Table ##TAB##3##4##, entries 2 and 1). Surprisingly, no heterocyclization was observed for <bold>RuSPy</bold>IrCp* used as a catalyst, despite several attempts. It may be due to a less labile character of the Ir─Cl bond in this complex than in other systems. According to the proposed reaction mechanism,<sup>[</sup>\n##REF##15387539##\n51\n##\n<sup>]</sup> in the early stage of the catalytic process, coordination of the glycolic anion to the iridium center is required which implies chloride substitution (originally present in the <italic toggle=\"yes\">ortho</italic>‐metallated systems). A significantly longer C─Ir bond in <bold>RuSPy</bold>IrCp* (2.083(5) Å) than those in <bold>NiMeP</bold>IrCp* (2.041(3) Å) or <bold>ClNCP</bold>IrCp* (2.051(6) Å) may be responsible for a weaker <italic toggle=\"yes\">trans</italic> effect of the meso‐aryl carbanion coordinated to the iridium(III) center on the opposite side to the chloride, making its exchange less effective. Of course, some other structural features, such as the presence and type of the metal ion within the macrocyclic cavity, flexibility of the molecular skeleton and its deformations, etc., may be decisive for the catalytic activity of the iridium complexes. Although at the present stage, we cannot offer any more conclusive accounting for the observed differences, it is clear that distinctions in the reaction yields among the systems used in this study indicate an influence of the porphyrin‐chelating ligand on the catalytic activity of the externally coordinated metal center.</p>" ]
[ "<title>Conclusion</title>", "<p>We have shown here that the <italic toggle=\"yes\">ortho</italic>‐metallation of the <bold>NCP</bold> by representative late metals of the second and third rows of transition metals appears to be facilitated by a deviation of the confused pyrrole from the macrocycle mean plane. Such a deviation can be easily achieved when the macrocyclic crevice is empty, and thus, when the ligand is sufficiently flexible to conform the external donor set, i.e., the external N2 atom and a C<italic toggle=\"yes\">\n<sub>ortho</sub>\n</italic> atom of the aryl at the meso‐C20 position to afford chelation. This strong out‐of‐plane deflection also allows the coordination of other ligands supplementing the coordination sphere of the metal. Importantly, in the already known <italic toggle=\"yes\">ortho</italic>‐metallated <bold>NCP</bold> complexes, the metals (Pd<sup>2+</sup>, Pt<sup>2+</sup>) coordinated to the ligand exterior adopt invariantly a square‐planar geometry. In the present report, we show that a piano‐stool environment is also a suitable geometry for this type of complex, despite the presence of relatively voluminous ligands (Cym or Cp*). Although not as flexible as a free base, the C21‐substituted <bold>NCP</bold> derivatives coordinating in the macrocyclic interior to Ni<sup>2+</sup> in the square planar or Ru<sup>2+</sup> in the octahedral environments, comprise the confused pyrrole unit that is permanently deviated from the mean plane of the porphyrinoid. This arrangement makes complexes such as <bold>NiMeP</bold> or <bold>RuSPy</bold> effective metalloligands suitable for <italic toggle=\"yes\">ortho</italic>‐metallation. The <italic toggle=\"yes\">ortho</italic>‐metallated systems are chiral and can be obtained in a non‐racemic form by either separation of the final bimetallic complexes or by the external metalation of the separated enantiomers of metalloligands, as no racemization is possible upon N2–C<italic toggle=\"yes\">\n<sub>ortho</sub>\n</italic> chelation. Favorably, the external chelation occurs stereoselectively with only one arrangement of the metal environment and the macrocycle. Thus, the chiral information can be transferred from the metalloligand to the externally situated metal center of the asymmetric environment. The redox properties of the bimetallic complexes are not profoundly altered in comparison to those of the appropriate metalloligands as has been shown here by electrochemical studies as well as by spectrophotometric and ESR‐monitored oxidation. Preliminary recognition of an influence of the <italic toggle=\"yes\">ortho</italic>‐metallated ligand on the catalytic activity of the externally coordinated iridium(III) centers indicated that the heterocyclization reaction is totally absent for the system comprising <bold>RuSPy</bold> metalloligand (i.e., <bold>RuSPy</bold>IrCp*), despite the same donor set as in <bold>NiMeP</bold>IrCp* or <bold>ClNCP</bold>IrCp* that effectively catalyzed this reaction. The study on these and other analogous systems directed toward recognition of their catalytic potential and redox properties will be continued in our laboratory.</p>" ]
[ "<title>Abstract</title>", "<p>A family of transition metal complexes of meso‐aryl‐2‐aza‐21‐carbaporphyrin (N‐confused porphyrin, <bold>NCP</bold>) derivatives acting as <italic toggle=\"yes\">ortho</italic>‐metallating ligands for ruthenium(II), rhodium(III), and iridium(III) is synthesized and characterized by XRD, spectroscopic, and electrochemical methods. The chirality of these systems is shown by the separation of the enantiomers and analyzed by circular dichroism and DFT. A preliminary catalytic study indicates the activity of the iridium(III) <italic toggle=\"yes\">ortho</italic>‐metallated complexes in the N‐heterocyclization of primary amines with diols.</p>", "<p>N‐confused porphyrin and its 21‐substituted nickel(II) and ruthenium(II) complexes are used as chelating ligands for a series of late transition metals by exploiting external nitrogen of the confused pyrrole and an <italic toggle=\"yes\">ortho</italic>‐carbon of the adjacent meso‐aryl. A new chirality center appears on the externally coordinated metal. Two higher oxidation states are available for the <italic toggle=\"yes\">ortho</italic>‐metallated systems.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6762-cit-0056\">\n<string-name>\n<given-names>S.</given-names>\n<surname>Koniarz</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Szydełko</surname>\n</string-name>, <string-name>\n<given-names>M. J.</given-names>\n<surname>Białek</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Hurej</surname>\n</string-name>, <string-name>\n<given-names>P. J.</given-names>\n<surname>Chmielewski</surname>\n</string-name>, <article-title>Complexes of N‐Confused Porphyrin Derivatives as <italic toggle=\"yes\">Ortho</italic>‐Metallating Ligands. Synthesis, Structure, Redox Properties, and Chirality</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2306696</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202306696</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Syntheses of Precursors</title>", "<p>\n<bold>NCP</bold> ligands<sup>[</sup>\n##REF##10825994##\n55\n##\n<sup>]</sup> and metalloligands <bold>NiMeP</bold>\n<sup>[</sup>\n##UREF##16##\n29\n##, ##REF##11151364##\n30\n##, ##REF##12950206##\n33\n##\n<sup>]</sup> and <bold>RuSPy</bold>\n<sup>[</sup>\n##UREF##18##\n34\n##\n<sup>]</sup> were obtained by the literature methods.</p>", "<title>Synthesis of ClNCPIrCp*</title>", "<p>A sample of 0.040 g (0.054 mmol) <bold>ClNCP</bold>, 0.044 g (0.054 mmol) dichloro(pentamethylcyclopentadienyl)iridium(III) dimer, 0.044 g (0.540 mmol) anhydrous sodium acetate and 20 mL dichloromethane were placed in a two‐necked flask. The reaction mixture was purged for 20 min with N<sub>2</sub> and then refluxed for 12 h. After this time, the reaction mixture was filtered, and the solution was concentrated and separated on a silica‐gel column. The compound was eluted using 0.5% MeOH in dichloromethane. The collected fraction was evaporated to dryness and recrystallized from the dichloromethane/<italic toggle=\"yes\">n</italic>‐hexane system. Yield 0.049 g (83%).</p>", "<title>Selected Data for <bold>ClNCP</bold>IrCp*</title>", "<p>\n<sup>1</sup>H NMR (500 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ</italic>): 9.36 (d, <italic toggle=\"yes\">J</italic> = 4.8 Hz, 1H, pyrrH), 8.56 (d, <italic toggle=\"yes\">J</italic> = 4.7 Hz, 1H, pyrrH), 8.48 (d, <italic toggle=\"yes\">J</italic> = 5.0 Hz, 1H, pyrrH), 8.31 (AB, <italic toggle=\"yes\">J</italic> = 4.8 Hz, 1H, pyrrH), 8.30 (AB, <italic toggle=\"yes\">J</italic> = 4.8 Hz, 1H, pyrrH), 8.28 (s, 1H, pyrrH), 8.26 (d, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 2.3 Hz, 1H, ArH), 8.21 (d, <italic toggle=\"yes\">J</italic> = 4.8 Hz, 1H, pyrrH), 8.07 (td, <italic toggle=\"yes\">J</italic> = 8.4 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 2.0 Hz, 2H, ArH), 8.04 (d, <italic toggle=\"yes\">J</italic> = 8.4 Hz, 2H, ArH), 7.79 (td, <italic toggle=\"yes\">J</italic> = 8.4 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 2.3 Hz, 3H, ArH), 7.75 (dd, <italic toggle=\"yes\">J</italic> = 8.2 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 2.2 Hz, 2H, ArH), 7.71 (dd, <italic toggle=\"yes\">J</italic> = 8.1 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 2.2 Hz, 1H, ArH), 7.62–7.66 (overlapping multiplets, 3H, ArH), 7.27 (dd, <italic toggle=\"yes\">J</italic> = 8.1 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 2.3 Hz, 1H, ArH), 0,85 (s, 15H, Cp*H), –1.08(br, 2H, NH), –4.69 (s, 1H, ‐CH). <sup>13</sup>C NMR (150 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ<sub>C</sub>\n</italic>): 159.1, 157.6, 155.4, 149.5, 141.8, 141.6, 140.7, 139.4, 139.3, 138.2, 138.1, 136.9, 136.6, 136.55, 136.49, 136.0, 135.6, 135.5, 135.4, 135.1, 134.9, 134.8, 134.7, 134.5, 134.4, 134.0, 131.2, 129.8, 128.9, 127.72, 127.65, 127.6, 127.5, 127.4, 127.2, 125.4, 124.4, 117.7, 115.3, 88.0, 85.1 (<italic toggle=\"yes\">C</italic>21), 8.3. HRMS (ESI) <italic toggle=\"yes\">m/z</italic>: [M─Cl]<sup>+</sup> calcd for C<sub>54</sub>H<sub>40</sub>N<sub>4</sub>Cl<sub>4</sub>Ir, 1079.1631; found, 1079,1638. UV–vis (CH<sub>2</sub>Cl<sub>2</sub>) <italic toggle=\"yes\">λ</italic>\n<sub>max</sub>, (ε/10<sup>4</sup> [M<sup>−1</sup> cm<sup>−1</sup>]) = 299 (3.12), 335 (sh), 391 (4.01), 402 (sh), 455 (12.57), 550(sh), 564 (1.79), 606 (1.31), 642(sh), 794 (1.41).</p>", "<title>Synthesis of NiMePIrCp*</title>", "<p>A sample of 0.025 g (0.036 mmol) of <bold>NiMeP</bold>, along with 0.016 g (0.020 mmol) of dichloro(pentamethylcyclopentadienyl)iridium(III) dimer, 0.016 g (0.2 mmol) anhydrous sodium acetate and 10 mL of dichloromethane were placed in a two‐neck round bottom flask. The mixture was purged for 20 min with N<sub>2</sub> and then refluxed for 18 h. In the next stage, The reaction mixture was then filtered, concentrated, and passed down a silica gel column. The compound was eluted with 30% ethyl acetate in <italic toggle=\"yes\">n</italic>‐hexane. The collected fraction was evaporated to dryness and recrystallized from the dichloromethane/<italic toggle=\"yes\">n</italic>‐hexane. Yield 0.035 g (93%).</p>", "<title>Selected Data for NiMePIrCp*</title>", "<p>\n<sup>1</sup>H NMR (500 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ</italic>): 9.25 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 1H, pyrrH), 8.98 (s, 1H, pyrrH), 8.45 (AB, <italic toggle=\"yes\">J</italic> = 5.0 Hz, 1H, pyrrH), 8.30 (AB, <italic toggle=\"yes\">J</italic> = 5,0 Hz, 1H, pyrrH), 8.29 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 2H, pyrrH), 8.28 (AB, <italic toggle=\"yes\">J</italic> = 5.0 Hz, 1H, pyrrH), 8.20 (dd, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.5 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.4 Hz, 1H, ArH), 8.15 (br, 4H, ArH), 7.64–7.75 (overlapping multiplets, 10H, ArH), 7.61 (br, 3H, ArH), 7.28 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.4 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.5 Hz, 1H, ArH), 7.24 (m, 1H, ArH), 0.7 (s, 15H, ─CH<sub>3</sub>(Cp*H)), –2.23 (s, 3H, ─CH<sub>3</sub>). <sup>13</sup>C NMR (150 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ<sub>C</sub>\n</italic>): 170.5, 154.2, 151.9, 151.8, 151.7, 151.5, 150.1, 148.8, 147.5, 145.9, 141.2, 140.7, 140.6, 139.5, 136.0, 135.2, 134.9, 133.6, 133.5, 133.4, 133.3, 132.9, 129.2, 128.7, 128.6, 128.1, 127.9, 127.3, 127.1, 124.7, 120.3, 119.8, 87.8, 28.2, 8.1. HRMS (ESI) <italic toggle=\"yes\">m/z</italic>: [M─Cl]<sup>+</sup> calcd for: C<sub>55</sub>H<sub>44</sub>N<sub>4</sub>NiIr, 1011,2543; found, 1011,2540. UV–vis (CH<sub>2</sub>Cl<sub>2</sub>) <italic toggle=\"yes\">λ</italic>\n<sub>max</sub>, (ε/10<sup>4</sup> [M<sup>−1</sup> cm<sup>−1</sup>]) = 294(3.57), 341(3.20), 392(sh), 439(4.29), 486(sh), 568(sh), 676 (0.7), 743(sh).</p>", "<title>Synthesis of NiMePRuCym</title>", "<p>A sample of 0.020 g (0.030 mmol) of <bold>NiMeP</bold>, 0.009 g (0.015 mmol) dichloro(<italic toggle=\"yes\">p</italic>‐cymene)ruthenium(II) dimer, 0.012 g (0.150 mmol) anhydrous sodium acetate were placed in a two‐neck flask and 10 mL of dichloromethane were added. The mixture was purged for 20 min. with N<sub>2</sub>, and then refluxed for 48 h. After that, the mixture was filtered, concentrated, and subjected to silica‐gel column chromatography. The compound was eluted with 30% ethyl acetate in <italic toggle=\"yes\">n</italic>‐hexane. The collected fraction was evaporated to dryness and recrystallized from the dichloromethane/<italic toggle=\"yes\">n</italic>‐hexane. Yield 0.017 g (60%).</p>", "<title>Selected Data for NiMePRuCym</title>", "<p>\n<sup>1</sup>H NMR (500 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ</italic>): 9.47 (s, 1H, pyrrH), 9.30 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 1H, pyrrH), 8.49 (AB, <italic toggle=\"yes\">J</italic> = 4.9 Hz, 1H, pyrrH), 8.36 (dd, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.6 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.0 Hz, 1H, ArH), 8.33 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 1H, pyrrH), 8.32 (AB, <italic toggle=\"yes\">J</italic> = 4.8 Hz, 1H, pyrrH), 8.30 (AB, <italic toggle=\"yes\">J</italic> = 4.9 Hz, 1H, pyrrH), 8.28 (AB, <italic toggle=\"yes\">J</italic> = 4.9 Hz, 1H, pyrrH), 8.13 (br, 3H, ArH), 7.50–7.79 (overlapping multiplets + br, 13H, ArH), 7.30 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.3 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.1 Hz, 1H, ArH), 7.23 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.2 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.4 Hz, 1H, ArH), 4.97 (d, <italic toggle=\"yes\">J</italic> = 5.8 Hz, 1H, ArH(<italic toggle=\"yes\">p</italic>Cym)), 4.77 (AB, <italic toggle=\"yes\">J</italic> = 5.8 Hz, 1H, ArH(<italic toggle=\"yes\">p</italic>Cym)), 4.58 (AB, <italic toggle=\"yes\">J</italic> = 5.8 Hz, 1H, ArH(<italic toggle=\"yes\">p</italic>Cym)), 4.08 (d, <italic toggle=\"yes\">J</italic> = 5.8 Hz, 1H, ArH(<italic toggle=\"yes\">p</italic>Cym)), 1.84 (sep, <italic toggle=\"yes\">J</italic> = 6.9 Hz, 1H, ─CH─(<italic toggle=\"yes\">p</italic>Cym)), 0.82 (s, 3H, ─CH<sub>3</sub>(<italic toggle=\"yes\">p</italic>Cym)), 0.69 (d, <italic toggle=\"yes\">J</italic> = 6.9 Hz, 3H, ─CH<sub>3</sub>(<italic toggle=\"yes\">p</italic>Cym)), 0.38 (d, <italic toggle=\"yes\">J</italic> = 6.9 Hz, 3H, ─CH<sub>3</sub>(<italic toggle=\"yes\">p</italic>Cym)), –2.39 (s, 3H, ─CH<sub>3</sub>). <sup>13</sup>C NMR (150 MHz, CDCl<sub>3</sub>\n<italic toggle=\"yes\">δ<sub>C</sub>\n</italic>): 174.0, 170.7, 152.0, 151.8, 151.2, 151.0, 149.9, 149.3, 148.7, 147.5, 144.1, 140.69, 140.66, 139.6, 136.8, 135.8, 135.5, 134.9, 134.7, 134.1, 133.6, 133.54, 133.46, 132.8, 129.1, 128.6, 128.2, 128.1, 127.9, 127.1, 125.3, 124.4, 120,.9, 119.9, 104.7, 96.3, 88.7, 86.8, 84.73, 84.71, 29.9, 22.0, 21.9, 17.9, 15.6. HRMS (ESI) <italic toggle=\"yes\">m/z</italic>: [M–Cl]<sup>+</sup> calcd for C<sub>55</sub>H<sub>43</sub>N<sub>4</sub>NiRu, 919.1879; found, 919.1871. UV–vis (CH<sub>2</sub>Cl<sub>2</sub>) <italic toggle=\"yes\">λ</italic>\n<sub>max</sub>, (ε/10<sup>4</sup> [M<sup>−1</sup> cm<sup>−1</sup>]) = 295(2.76), 343(2.58), 392(sh), 439(4.10), 525(sh), 655(sh) 738(sh).</p>", "<title>Synthesis of NiMePRhCp*</title>", "<p>The compound was synthesized and purified in the same way as <bold>NiMeP</bold>RuCym, except that dichloro(p‐cymene)ruthenium(II) was replaced by dichloro(pentamethylcyclopentadienyl)rhodium(III) dimer (0.009 g, (0.015 mmol)). Yield 0.011 g (40%).</p>", "<title>Selected Data for NiMePRhCp*</title>", "<p>\n<sup>1</sup>H NMR (500 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ</italic>): 9.29 (AB, <italic toggle=\"yes\">J</italic> = 5.2 Hz, 1H, pyrrH), 9.19 (s, 1H, pyrrH), 8,.47 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 1H, pyrrH), 8.35 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 1H, pyrrH), 8.33 (AB, <italic toggle=\"yes\">J</italic> = 5.0 Hz, 1H, pyrrH), 8.32 (AB, <italic toggle=\"yes\">J</italic> = 4.9 Hz, 1H, pyrrH) 8.30 (AB, <italic toggle=\"yes\">J</italic> = 4.7 Hz, 1H, pyrrH) 8.25 (dd, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.8 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.1 Hz, 1H, ArH), 8.16 (br, 3H, ArH), 7.65–7.74 (overlapping multiplets, 9H, ArH), 7.62 (br, 4H, ArH), 7.32 (td, <italic toggle=\"yes\">J</italic> = 7.2, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.4, 1H, ArH), 7.27 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.4 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.5 Hz, 1H, ArH), 0.69 (s, 15H, Cp*H), –2.36 (s, 3H, ─CH<sub>3</sub>). <sup>13</sup>C NMR (150 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ<sub>C</sub>\n</italic>): 171.5, 169.9, 169.6, 152.44, 152.37, 152.0, 151.1, 150.0, 148.9, 147.3, 146.1, 140.8, 140.64, 140.58, 139.5, 136.3, 135.9, 135.30, 135.25, 134.3, 133.8, 133.6, 133.50, 133.47, 132.9, 129.2, 128.6, 128.1, 128.0, 127.5, 127.1, 126.6, 124.6, 121.0, 120.0, 95.40, 95.36, 15.2, 8.3. HRMS (ESI) <italic toggle=\"yes\">m/z</italic>: [M–Cl]<sup>+</sup> calcd for C<sub>55</sub>H<sub>44</sub>N<sub>4</sub>NiRh, 921.1969; found, 921,1963. UV–vis (CH<sub>2</sub>Cl<sub>2</sub>) <italic toggle=\"yes\">λ</italic>\n<sub>max</sub>, (ε/10<sup>4</sup> [M<sup>−1</sup> cm<sup>−1</sup>]) = 293 (3.03), 336 (2.78), 392(sh), 442 (3.73), 606(sh) 656(sh), 734(sh).</p>", "<title>Synthesis of RuSPyIrCp*</title>", "<p>The compound was synthesized and purified in the same way as <bold>NiMeP</bold>IrCp*. A sample of 0.020 g (0.024 mmol) of compound <bold>RuSPy</bold>, 0.010 g (0.012 mmol) dichloro(pentamethylcyclopentadienyl)iridium(III) dimer and 0.010 g (0.120 mmol) anhydrous sodium acetate were used. Yield 0.025 g (85%).</p>", "<title>Selected Data for RuSPyIrCp*</title>", "<p>\n<sup>1</sup>H NMR (500 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ</italic>): 8.86 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 1H, pyrrH), 8,34 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 1H, pyrrH), 8.31 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 1H, pyrrH), 8.30 (AB, <italic toggle=\"yes\">J</italic> = 5.2 Hz, 1H, pyrrH), 8.20 (dd, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.5 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.4 Hz, 1H, ArH), 8.15 (br, 2H, ArH), 8.14 (s, 1H, pyrrH), 8.13 (AB, <italic toggle=\"yes\">J</italic> = 5.2 Hz, 1H, pyrrH), 8.08–8.10 (m, 1H, ArH), 8.02–8.04 (m, 1H, ArH), 8.01 (AB, <italic toggle=\"yes\">J</italic> = 5.2 Hz, 1H, pyrrH), 7.79–7.80 (overlapping multiplets, 1H, ArH), 7.64–7.75 (overlapping multiplets, 8H, ArH), 7.54–7.62 (overlapping multiplets, 3H, ArH), 7.23 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.4 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.7 Hz, 1H, ArH), 7.19 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.4 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.7 Hz, 1H, ArH), 6.21 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.7 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.6 Hz, 1H, pyH), 5.61 (d, <italic toggle=\"yes\">J</italic> = 8.1 Hz, 1H, pyH), 5.44 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 6.7 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.3 Hz, 1H, pyH), 3.00 (dq, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 6.0 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 0.8 Hz, 1H, pyH), 0.97 (s, 15H, Cp*H). <sup>13</sup>C NMR (150 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ<sub>C</sub>\n</italic>): 195.5, 170.3, 167.5, 154.6, 154.1, 152.2, 151.9, 151.3, 150.7, 145.7, 144.5, 142.9, 141.4, 141.3, 141.2, 140.5, 138.5, 137.9, 137.1, 135.9, 135.3, 135.1, 134.9, 134.1, 133.94, 133.92, 133.8, 133.7, 133.6, 133.5, 133.2, 132.2, 128.9, 128.3, 127.7, 127.6, 127.03, 126.99, 126.92, 126.85, 126.7, 124.5, 121.6, 120.6, 117.0, 116.5, 88.2, 8.4. HRMS (ESI) <italic toggle=\"yes\">m/z</italic>: [M─Cl]<sup>+</sup> calcd for C<sub>60</sub>H<sub>45</sub>N<sub>5</sub>OSRuIr, 1178.2012; found, 1178.2014. UV–vis (CH<sub>2</sub>Cl<sub>2</sub>) <italic toggle=\"yes\">λ</italic>\n<sub>max</sub>, (ε/10<sup>4</sup> [M<sup>−1</sup> cm<sup>−1</sup>]) = 302 (3.28), 367(sh), 433 (3.26), 498 (sh), 510 (2.51), 604(sh), 728 (1.41).</p>", "<title>Synthesis of RuSPyRuCym</title>", "<p>The compound was synthesized and purified in the same way as <bold>NiMeP</bold>RuCym. A sample of 0.020 g (0.024 mmol) of compound <bold>RuSPy</bold>, 0.007 g (0.012 mmol) dichloro(<italic toggle=\"yes\">p</italic>‐cymene) ruthenium(II) dimer and 0.010 g (0.120 mmol) of anhydrous sodium acetate were used. Yield 0.014 g (54%).</p>", "<title>Selected Data for RuSPyRuCym</title>", "<p>\n<sup>1</sup>H NMR (500 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ</italic>): 8,91 (AB, <italic toggle=\"yes\">J</italic> = 5.2 Hz, 1H, pyrrH), 8.52 (s, 1H, pyrrH), 8.38 (AB, <italic toggle=\"yes\">J</italic> = 5.0 Hz, 1H, pyrrH), 8,37 (dd, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.5 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.3 Hz, 1H, ArH), 8.34 (AB, <italic toggle=\"yes\">J</italic> = 5.0 Hz, 2H, pyrrH), 8.15–8.17 (overlapping multiplets, 2H, ArH), 8.15 (AB, <italic toggle=\"yes\">J</italic> = 5.1 Hz, 1H, pyrrH), 8.06–8.09 (m, 1H, ArH), 8.03 (AB, <italic toggle=\"yes\">J</italic> = 5.2 Hz, 1H, pyrrH), 7.95–7.97 (m, 1H, ArH), 7.78 (m, 1H, ArH), 7.56–7.75 (overlapping multiplets, 12H, ArH), 7.31 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.3 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.3 Hz, 1H, ArH), 7.22 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.4 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.4 Hz, 1H, ArH), 6.20 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.7 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.7 Hz, 1H, pyH), 5.60 (d, <italic toggle=\"yes\">J</italic> = 8,.1 Hz, 1H, pyH), 5,.43 (td, <italic toggle=\"yes\">J</italic> = 6.7 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.0 Hz, 1H, pyH), 4.87 (d, <italic toggle=\"yes\">J</italic> = 5.9 Hz, 1H, ArH(<italic toggle=\"yes\">p</italic>Cym)), 4.48 (d, <italic toggle=\"yes\">J</italic> = 6.0 Hz, 2H, ArH(<italic toggle=\"yes\">p</italic>Cym)), 3.05 (d, <italic toggle=\"yes\">J</italic> = 5.8 Hz, 1H, ArH(<italic toggle=\"yes\">p</italic>Cym)), 2.92 (d, <italic toggle=\"yes\">J</italic> = 6.0 Hz, 1H, pyH), 2.47 (sep, <italic toggle=\"yes\">J</italic> = 7.0 Hz, 1H, ─CH─(<italic toggle=\"yes\">p</italic>Cym)), 1.53 (s, 3H, ─CH<sub>3</sub>(<italic toggle=\"yes\">p</italic>Cym)), 0.81 (d, <italic toggle=\"yes\">J</italic> = 6.8 Hz, 3H, ─CH<sub>3</sub>(<italic toggle=\"yes\">p</italic>Cym)), 0.73 (d, <italic toggle=\"yes\">J</italic> = 7.1 Hz, 3H, ─CH<sub>3</sub>(<italic toggle=\"yes\">p</italic>Cym)). <sup>13</sup>C NMR (125 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ<sub>C</sub>\n</italic>): 195.8, 175.2, 172.6, 167.7, 154.9, 151.8, 151.5, 151.2, 150.5, 145.5, 144.5, 144.0, 142.7, 141.4, 141.3, 140.4, 140.3, 138.5, 138.0, 136.0, 135.3, 135.2, 134.5, 134.02, 133.96, 133.94, 133.8, 133.6, 133.54, 133.49, 133.0, 132.2, 128.9, 128.2, 127.7, 127.6, 126.98, 126.95, 126.8, 126.7, 125.2, 124.2, 121.9, 117.0, 116.5, 110.8, 97.8, 88.3, 86.8, 84.5, 30.2, 23.4, 20.9, 18.6. HRMS (ESI) <italic toggle=\"yes\">m/z</italic>: [M─Cl]<sup>+</sup> calcd for C<sub>60</sub>H<sub>44</sub>N<sub>5</sub>OSRu<sub>2</sub>, 1086.1348; found, 1086.1343; [M + Na]<sup>+</sup> calcd for C<sub>60</sub>H<sub>44</sub>N<sub>5</sub>OSClRu<sub>2</sub>Na, 1144,0934; found, 1144,0936. UV–vis (CH<sub>2</sub>Cl<sub>2</sub>) <italic toggle=\"yes\">λ</italic>\n<sub>max</sub>, (ε/10<sup>4</sup> [M<sup>−1</sup> cm<sup>−1</sup>]) = 300 (3.41), 366(sh), 424 (3.38), 459(sh), 538 (1.70), 625(sh), 723 (1.40).</p>", "<title>Synthesis of RuSPyRhCp*</title>", "<p>A sample of 0.020 g (0.024 mmol) of compound <bold>RuSPy</bold>, 0.007 g (0.012 mmol) dichloro(pentamethylcyclopentadienyl)rhodium(III) dimer, 0.010 g (0.120 mmol) of anhydrous sodium acetate and 10 mL of chloroform was placed in a two‐neck round‐bottom flask. The mixture was purged with N<sub>2</sub> gas for 20 min and then refluxed for 24 h. After this time, another portion of 0.007 g (0.012 mmol) of dichloro(cyclopentadienyl) rhodium(III) dimer and 0.010 g (0.120 mmol) of anhydrous sodium acetate was added and heated for another 24 h under reflux. In the next stage, the mixture was filtered, concentrated and separated by a silica gel chromatographic column. The compound was eluted with 30–35% ethyl acetate in <italic toggle=\"yes\">n</italic>‐hexane. The collected fraction was evaporated to dryness and recrystallized from the dichloromethane/<italic toggle=\"yes\">n</italic>‐hexane. Yield 0.009 g (35%).</p>", "<title>Selected Data for RuSPyRhCp*</title>", "<p>\n<sup>1</sup>H NMR (500 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ</italic>): 8.90 (AB, <italic toggle=\"yes\">J</italic> = 5.2 Hz, 1H, pyrrH), 8.35 (AB, <italic toggle=\"yes\">J</italic> = 5.2 Hz, 1H, pyrrH), 8.33 (AB, <italic toggle=\"yes\">J</italic> = 5.0 Hz, 1H, pyrrH), 8.32 (AB, <italic toggle=\"yes\">J</italic> = 5.0 Hz, 1H, pyrrH), 8.30 (s, 1H, pyrrH), 8.24 (dd, <italic toggle=\"yes\">J</italic> = 7.8 Hz, 1H, ArH), 8.16 (AB, <italic toggle=\"yes\">J</italic> = 5.2 Hz, 1H, pyrrH), 8.14–8.17 (overlapping multiplets, 2H, ArH), 8.09–8.11 (m, 1H, ArH), 8.03–8.05 (overlapping multiplets, 1H, ArH), 8.03 (AB, <italic toggle=\"yes\">J</italic> = 4.9 Hz, 1H, pyrrH), 7.79–7.80 (m, 1H, ArH), 7.64–7.76 (overlapping multiplets, 8H, ArH), 7.54–7.62 (overlapping multiplets, 3H, ArH), 7.28 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.4 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.2 Hz, 1H, ArH), 7.23 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.4 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.4 Hz, 1H, ArH), 6.20 (td, <sup>3</sup>\n<italic toggle=\"yes\">J</italic> = 7.8 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.7 Hz, 1H, pyH), 5.60 (d, <italic toggle=\"yes\">J</italic> = 8.0 Hz, 1H, pyH), 5.43 (td, <italic toggle=\"yes\">J</italic> = 6.6 Hz, <sup>4</sup>\n<italic toggle=\"yes\">J</italic> = 1.2 Hz, 1H, pyH), 2.96 (d, <italic toggle=\"yes\">J</italic> = 6.0 Hz, 1H, pyH), 0.9 (s, 15H, Cp*). <sup>13</sup>C NMR (150 MHz, CDCl<sub>3</sub>, <italic toggle=\"yes\">δ<sub>C</sub>\n</italic>): 195.3, 172.1, 170.0, 169.8, 167.5, 155.0, 152.6, 152.0, 151.0, 150.7, 145.7, 144.3, 142.8, 141.3, 141.2, 140.7, 140.4, 139.0, 138.7, 136.6, 136.4, 135.9, 135.5, 134.8, 134.2, 134.0, 133.9, 133.7, 133.6, 133.5, 133.2, 131.0, 128.9, 128.3, 127.74, 127.66, 127.0, 126.9, 126.8, 126.7, 126.4, 124.4, 122.2, 120.6, 117.0, 116.5, 95.83, 95.79, 8.6. HRMS (ESI) <italic toggle=\"yes\">m/z</italic>: [M─Cl]<sup>+</sup> calcd for C<sub>60</sub>H<sub>45</sub>N<sub>5</sub>OSRuRh, 1088,1438; found, 1088,1432. UV–vis (CH<sub>2</sub>Cl<sub>2</sub>) <italic toggle=\"yes\">λ</italic>\n<sub>max</sub>, (ε/10<sup>4</sup> [M<sup>−1</sup> cm<sup>−1</sup>]) = 303 (3.04), 369(sh), 439(3.43), 492(sh), 506(2.67), 598(sh), 719(1.30).</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was supported by the Polish National Science Center (2022/45/B/ST4/01229). DFT calculations were carried out using resources provided by the Wrocław Center for Networking and Supercomputing, grant 329.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available in the supplementary material of this article.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0001\"><label>Figure 1</label><caption><p>Schematic structures of NCP and its <italic toggle=\"yes\">ortho</italic>‐metallated complexes.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6762-fig-0011\"><label>Scheme 1</label><caption><p>Syntheses of the <italic toggle=\"yes\">ortho</italic>‐metallated <bold>NCP</bold> complexes.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0002\"><label>Figure 2</label><caption><p>A) Selected regions of <sup>1</sup>H NMR spectra (500 MHz, CDCl<sub>3</sub>, 300 K) of <bold>NiMeP</bold>IrCp* (top) and <bold>NiMeP</bold>RuCym (bottom) along with a partial signal assignment. B) Selected regions of <sup>1</sup>H NMR spectra (500 MHz, CDCl<sub>3</sub>, 300 K) of <bold>RuSPy</bold>IrCp* (top) and <bold>RuSPy</bold>RuCym (bottom) along with a partial signal assignment. s, residual CHCl<sub>3</sub> signal; w, dissolved water signal. The signal of impurities is marked with asterisks.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0003\"><label>Figure 3</label><caption><p>Optical spectra (DCM, 298 K): A) <bold>NiMeP</bold> and its <italic toggle=\"yes\">ortho</italic>‐metallated derivatives and B) <bold>RuSPy</bold> and its <italic toggle=\"yes\">ortho</italic>‐metallated derivatives.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0004\"><label>Figure 4</label><caption><p>Perspective views (50% displacement ellipsoid plots and stick diagrams) of molecular structures of A) <bold>ClNCP</bold>IrCp*, B) <bold>NiMeP</bold>RuCym, C) <bold>NiMeP</bold>IrCp*, and D) <bold>RuSPy</bold>IrCp*. All solvent molecules are omitted. In the stick representations of the side views, all hydrogens and all but ortho‐metallated aryl substituents are removed for clarity.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0005\"><label>Figure 5</label><caption><p>Atom displacements from the porphyrin mean plane calculated from SCXRD data of <bold>NiMeP</bold>RuCym (black dots), <bold>NiMeP</bold>IrCp* (red dots), <bold>RuSPy</bold>IrCp* (green dots), and <bold>NiMeP</bold> (violet circles).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0006\"><label>Figure 6</label><caption><p>Definition of absolute configuration at metalacyclic part of the systems A) and enantiomers along with chirality definitions for the selected <italic toggle=\"yes\">ortho</italic>‐metallated <bold>NCP</bold> complexes, B) <bold>ClNCP</bold>IrCp*, C) <bold>NiMeP</bold>RuCym, and D) <bold>RuSPy</bold>RhCp*.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6762-fig-0012\"><label>Scheme 2</label><caption><p>Two approaches applicable for the separation of enantiomers of the <italic toggle=\"yes\">ortho</italic>‐metallated complexes.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0007\"><label>Figure 7</label><caption><p>A) HPLC profiles for <bold>RuSPy</bold> on chiral stationary phase column (Chirex 3010, 1% MeOH in CH<sub>2</sub>Cl<sub>2</sub>, 2 mL min<sup>−1</sup>); top, CD and bottom, absorbance detection at 363 nm. B) CD (top) and absorbance (bottom) spectra of the HPLC‐separated fractions of <bold>RuSPy</bold>. C) superimposed CD spectra (CH<sub>2</sub>Cl<sub>2</sub>, 298 K) of <italic toggle=\"yes\">S‐</italic>\n<bold>NiMeP</bold> (orange trace) and <italic toggle=\"yes\">P</italic>‐<bold>NiMeP</bold>IrCP* (purple trace) obtained by metalation of the former with [IrCl<sub>2</sub>Cp*]<sub>2</sub>. D) CD spectra of enantiomers of <bold>NiMeP</bold>RuCym separated by the chiral stationary phase HPLC. E) superimposed CD spectra (CH<sub>2</sub>Cl<sub>2</sub>, 298 K) of <italic toggle=\"yes\">S‐</italic>\n<bold>RuSPy</bold> (blue trace) and <italic toggle=\"yes\">P</italic>‐<bold>RuSPy</bold>IrCP* (red trace) obtained by metallation of the former with [IrCl<sub>2</sub>Cp*]<sub>2</sub>. F) CD spectra of enantiomers of <bold>RuSPy</bold>RuCym separated by the chiral stationary phase HPLC. The absolute configurations were assigned to the enantiomers on the basis of TD‐DFT simulations of the CD spectra (Figures ##SUPPL##0##S23–S26##, Supporting Information).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0008\"><label>Figure 8</label><caption><p>Cyclic (CV, black traces) and differential pulse (DP, purple traces) voltammograms of A) <bold>NiMeP</bold>IrCp*, B) <bold>RuSPy</bold>IrCp*, C) <bold>ClNCP</bold>IrCp*, D) <bold>NiMe</bold>RuCym, E) <bold>RuSPy</bold>RuCym, and F) <bold>RuSPy</bold>RhCp*. The experiments were carried out in a dichloromethane solution of [Bu<sub>4</sub>N]PF<sub>6</sub> (0.1 <sc>m</sc>) using a glassy carbon working electrode, a platinum wire as an auxiliary electrode, and Ag/AgCl as a pseudoreference electrode. The green numbers associated with DP peaks are electrode potentials in volts. The partial CV scans are given to indicate the reversibility of some of the processes.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0009\"><label>Figure 9</label><caption><p>DFT‐calculated frontier orbitals energies of specified systems with the experimentally estimated energies of the HOMO and LUMO derived from the electrochemical data (green sticks).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6762-fig-0010\"><label>Figure 10</label><caption><p>Spectrophotometric titration of dichloromethane solutions of A) <bold>RuSPy</bold>IrCp*, B) <bold>RuSPy</bold>, and D) <bold>NiMeP</bold>IrCp* with tris(4‐bromophenyl)ammoniumyl hexachloroantimonate (BAHA) and selected ESR spectra recorded in frozen dichloromethane solutions (120 K) upon addition of specified amounts of BAHA (C). The black arrows in (A) and (B) indicate the direction of the absorbance changes before, while the red arrows—after the addition of 1 equiv of BAHA.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6762-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Bond lengths <italic toggle=\"yes\">d</italic> for the externally chelated metal ions.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Compound</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">d</italic> M–N [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">d</italic> M–C [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">d</italic> M–Cl [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">d</italic> M–(<italic toggle=\"yes\">η<sup>n</sup>─</italic>L)<xref rid=\"advs6762-tbl1-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref> [Å]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>ClNCP</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.066(5)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.051(6)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.406(2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.187(6)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.065(2)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.041(3)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.407(1)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.193(2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>RuCym</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.069(3)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.047(3)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.408(1)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.215(3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.060(4)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.083(5)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.420(1)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.198(3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>RhCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.072(4)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.030(4)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.402(1)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.201(4)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">[RuCl<sub>2</sub>Cym]<sub>2</sub>\n<xref rid=\"advs6762-tbl1-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>2.444(4)<xref rid=\"advs6762-tbl1-note-0005\" ref-type=\"table-fn\">\n<sup>#</sup>\n</xref>\n</p>\n<p>2.392(4)<xref rid=\"advs6762-tbl1-note-0006\" ref-type=\"table-fn\">\n<sup>&amp;</sup>\n</xref>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.158</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">[RhCl<sub>2</sub>Cp*]<sub>2</sub>\n<xref rid=\"advs6762-tbl1-note-0003\" ref-type=\"table-fn\">\n<sup>c)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>2.458(9)<xref rid=\"advs6762-tbl1-note-0005\" ref-type=\"table-fn\">\n<sup>#</sup>\n</xref>\n</p>\n<p>2.397(1)<xref rid=\"advs6762-tbl1-note-0006\" ref-type=\"table-fn\">\n<sup>&amp;</sup>\n</xref>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.126</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">[IrCl<sub>2</sub>Cp*]<sub>2</sub>\n<xref rid=\"advs6762-tbl1-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>2.453(5)<xref rid=\"advs6762-tbl1-note-0005\" ref-type=\"table-fn\">\n<sup>#</sup>\n</xref>\n</p>\n<p>2.387(4)<xref rid=\"advs6762-tbl1-note-0006\" ref-type=\"table-fn\">\n<sup>&amp;</sup>\n</xref>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.132</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6762-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>Analyses of the out‐of‐plane displacements for the macrocyclic ring of <bold>NCP</bold> calculated by means of PorphyStruct.<sup>[</sup>\n##REF##34061410##\n40\n##\n<sup>]</sup> on the basis of SCXRD structures.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Entry</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Compound</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">doming</italic> [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">saddling</italic> [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">ruffling</italic> [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">wavingX</italic> [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">wavingY</italic> [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">propellering</italic> [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">d<sub>M‐mpln</sub>\n</italic>\n<xref rid=\"advs6762-tbl2-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref> [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">d<sub>M‐ccpln</sub>\n</italic>\n<xref rid=\"advs6762-tbl2-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref> [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">D<sub>oop</sub>\n</italic>\n<xref rid=\"advs6762-tbl2-note-0003\" ref-type=\"table-fn\">\n<sup>c)</sup>\n</xref> [Å]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">DH</italic>\n<xref rid=\"advs6762-tbl2-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref> [deg]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NCP</bold>\n<xref rid=\"advs6762-tbl2-note-0005\" ref-type=\"table-fn\">\n<sup>e)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.196</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.360</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.070</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.259</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.055</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.040</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.465</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">27.0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>ClNCP</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.341</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.165</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.047</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.108</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.354</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.026</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.325</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">28.0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>\n<xref rid=\"advs6762-tbl2-note-0006\" ref-type=\"table-fn\">\n<sup>f)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.271</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−2.069</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.092</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.011</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.353</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.003</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.022</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.077</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.181</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">38.2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.428</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.020</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.729</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.515</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.180</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.027</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.088</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.061</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.290</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">43.7</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>RuCym</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.437</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−2.233</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.580</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.499</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.090</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.028</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.083</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.067</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.445</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">45.5</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>\n<xref rid=\"advs6762-tbl2-note-0007\" ref-type=\"table-fn\">\n<sup>g)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.415</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.804</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.282</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.058</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.326</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.003</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.046</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.108</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.990</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">40.2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.559</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.343</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.312</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.607</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.246</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.018</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.086</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.098</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.689</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">41.3</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>RhCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.554</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.315</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.291</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.590</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.258</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.018</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.088</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.096</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.657</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">41.2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NCP</bold>PtPPh<sub>3</sub>\n<xref rid=\"advs6762-tbl2-note-0008\" ref-type=\"table-fn\">\n<sup>h)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.278</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.290</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−0.320</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.107</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.437</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.008</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.501</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">31.5</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6762-tbl-0003\" content-type=\"Table\"><label>Table 3</label><caption><p>Electrode potentials of the orthometallated complexes and metalloligands.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Entry</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Compound</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">E</italic>\n<sub>Red3</sub> [V]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">E</italic>\n<sub>Red2</sub> [V]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">E</italic>\n<sub>Red1</sub> [V]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">E</italic>\n<sub>Ox1</sub> [V]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">E</italic>\n<sub>Ox2</sub> [V]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">E</italic>\n<sub>Ox3</sub> [V]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Δ<italic toggle=\"yes\">E</italic>\n<xref rid=\"advs6762-tbl3-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref> [V]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">oHLG<xref rid=\"advs6762-tbl3-note-0005\" ref-type=\"table-fn\">\n<sup>e)</sup>\n</xref> [eV]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">cHLG<xref rid=\"advs6762-tbl3-note-0006\" ref-type=\"table-fn\">\n<sup>f)</sup>\n</xref> [eV]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>ClNCP</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−2.03<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.72<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.61<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.87<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.68</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.53</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.02</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−2.31<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.99<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.48<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.23</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.42</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.92<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.71</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.60</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.29</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>RhCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−2.18<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.96<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.46</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.29<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.52</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.91<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.75</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.56</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">N.A.</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>RuCym</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.46<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.21</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.04<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.67</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.27</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.47<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.63</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.06<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.72</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.61</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.15</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>RhCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−2.08<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.46<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.71<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.80</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.63</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.19</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>RuCym</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−2.28<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.94<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.58</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.57</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.00<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.73</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.60</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">N.A.</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>\n<xref rid=\"advs6762-tbl3-note-0003\" ref-type=\"table-fn\">\n<sup>c)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.37</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.22</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.50<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.59</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.46</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">N.A.</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>\n<xref rid=\"advs6762-tbl3-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.39<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.34</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.79</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.73</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.65</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.39</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>ClNCP</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−2.09<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">−1.42<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.36<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.63<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.84<xref rid=\"advs6762-tbl3-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.78</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.61</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">N.A.</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6762-tbl-0004\" content-type=\"Table\"><label>Table 4</label><caption><p>Reaction conditions and yields for benzylamine (A) reacting with 1,6‐hexanediol (B) in the presence of various catalysts.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th colspan=\"8\" align=\"left\" rowspan=\"1\">\n\n</th></tr><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Entry<xref rid=\"advs6762-tbl4-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Catalyst</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">%mol<xref rid=\"advs6762-tbl4-note-0002\" ref-type=\"table-fn\">\n<sup>b)</sup>\n</xref>\n</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">µmol of Ir</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Conversion of B [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Yield C [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Yield D [%]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Yield E [%]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">[IrCl<sub>2</sub>Cp*]<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">90</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">66<xref rid=\"advs6762-tbl4-note-0003\" ref-type=\"table-fn\">\n<sup>c)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">43</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">96</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">67</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt;1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>NiMeP</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt; 5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n.d.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n.d.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15<xref rid=\"advs6762-tbl4-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt; 5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n.d.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n.d.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">11<xref rid=\"advs6762-tbl4-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>RuSPy</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt; 5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n.d.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n.d.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">18<xref rid=\"advs6762-tbl4-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>ClNCP</bold>IrCp*</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.1</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">99</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">86</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">19</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>ClNCP</bold>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">1.0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">&lt; 5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n.d.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n.d.</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2<xref rid=\"advs6762-tbl4-note-0004\" ref-type=\"table-fn\">\n<sup>d)</sup>\n</xref>\n</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
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[ "<supplementary-material id=\"advs6762-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6762-tbl1-note-0001\"><label>\n<sup>a)</sup>\n</label><p>Mean values of the M–C distances for <italic toggle=\"yes\">η</italic>\n<sup>5</sup>‐Cp*–M or <italic toggle=\"yes\">η</italic>\n<sup>6</sup>‐Cym–Ru;</p></fn><fn id=\"advs6762-tbl1-note-0002\"><label>\n<sup>b)</sup>\n</label><p>Data from ref. [##REF##30942794##39##];</p></fn><fn id=\"advs6762-tbl1-note-0003\"><label>\n<sup>c)</sup>\n</label><p>Data from ref. [##UREF##21##38##];</p></fn><fn id=\"advs6762-tbl1-note-0004\"><label>\n<sup>d)</sup>\n</label><p>Data from ref. [##UREF##20##37##];</p></fn><fn id=\"advs6762-tbl1-note-0005\"><label>\n<sup>#</sup>\n</label><p>Bridging chloride;</p></fn><fn id=\"advs6762-tbl1-note-0006\"><label>\n<sup>&amp;</sup>\n</label><p>Terminal chloride.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"advs6762-tbl2-note-0001\"><label>\n<sup>a)</sup>\n</label><p>The metal ion (Ni<sup>II</sup> or Ru<sup>II</sup>) displacement out of the porphyrin mean plane;</p></fn><fn id=\"advs6762-tbl2-note-0002\"><label>\n<sup>b)</sup>\n</label><p>The metal ion (Ni<sup>II</sup> or Ru<sup>II</sup>) displacement out of the mean plane of the coordination core (<italic toggle=\"yes\">M</italic>CNNN);</p></fn><fn id=\"advs6762-tbl2-note-0003\"><label>\n<sup>c)</sup>\n</label><p>total out‐of‐plane distortion;</p></fn><fn id=\"advs6762-tbl2-note-0004\"><label>\n<sup>d)</sup>\n</label><p>dihedral angle between the mean plane defined by all non‐hydrogen atoms of the macrocyclic ring except C21, N2, and C3 but including core‐coordinated metal, and the mean plane of the confused pyrrole;</p></fn><fn id=\"advs6762-tbl2-note-0005\"><label>\n<sup>e)</sup>\n</label><p>X‐ray data taken from ref. [##UREF##1##2##];</p></fn><fn id=\"advs6762-tbl2-note-0006\"><label>\n<sup>f)</sup>\n</label><p>X‐ray data taken from ref. [##UREF##16##29##];</p></fn><fn id=\"advs6762-tbl2-note-0007\"><label>\n<sup>g)</sup>\n</label><p>X‐ray data taken from ref. [##UREF##18##34##];</p></fn><fn id=\"advs6762-tbl2-note-0008\"><label>\n<sup>h)</sup>\n</label><p>X‐ray data taken from ref. [##UREF##13##25##];</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"advs6762-tbl3-note-0001\"><label>\n<sup>a)</sup>\n</label><p>Electrochemical HOMO–LUMO gaps Δ<italic toggle=\"yes\">E</italic> = <italic toggle=\"yes\">E</italic>\n<sub>Ox1</sub> ─ <italic toggle=\"yes\">E</italic>\n<sub>Red1</sub>;</p></fn><fn id=\"advs6762-tbl3-note-0002\"><label>\n<sup>b)</sup>\n</label><p>Irreversible process;</p></fn><fn id=\"advs6762-tbl3-note-0003\"><label>\n<sup>c)</sup>\n</label><p>Data from ref. [##REF##12950206##33##];</p></fn><fn id=\"advs6762-tbl3-note-0004\"><label>\n<sup>d)</sup>\n</label><p>Data from ref. [##UREF##18##34##];</p></fn><fn id=\"advs6762-tbl3-note-0005\"><label>\n<sup>e)</sup>\n</label><p>Optical HOMO–LUMO energy gaps derived from onsets of the lowest‐energy bands in the electronic spectra;</p></fn><fn id=\"advs6762-tbl3-note-0006\"><label>\n<sup>f)</sup>\n</label><p>HOMO–LUMO energy gaps derived from DFT calculations.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"advs6762-tbl4-note-0001\"><label>\n<sup>a)</sup>\n</label><p>Reactions were carried out for 0.5 mmol (59 mg) of 1,6‐hexanediol <bold>B</bold> and 0.75 mmol (80 mg) of benzylamine <bold>A</bold> in the presence of 1 mg of NaHCO<sub>3</sub>. The yields were estimated employing quantitative <sup>1</sup>H NMR of the reaction mixtures with 2,4,6‐collidine as an internal reference unless stated otherwise;</p></fn><fn id=\"advs6762-tbl4-note-0002\"><label>\n<sup>b)</sup>\n</label><p>With respect to 1,6‐hexanediol;</p></fn><fn id=\"advs6762-tbl4-note-0003\"><label>\n<sup>c)</sup>\n</label><p>The reported yield was 74%<sup>[</sup>\n##REF##15387539##\n51\n##\n<sup>]</sup>;</p></fn><fn id=\"advs6762-tbl4-note-0004\"><label>\n<sup>d)</sup>\n</label><p>Results from GC–MS/FID analysis only.</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2306696-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
55
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 21; 11(2):2306696
oa_package/ca/ee/PMC10787092.tar.gz
PMC10787093
37953442
[ "<title>Introduction</title>", "<p>Gastric cancer (GC) is one of the most prevalent malignant tumors globally. Owing to its indistinct early‐stage symptoms, most patients have already progressed into advanced stages at the time of initial diagnosis, resulting in poor overall prognosis.<sup>[</sup>\n##REF##33538338##\n1\n##\n<sup>]</sup> Chemotherapy is still the mainstream workforce for advanced GC.<sup>[</sup>\n##REF##29488121##\n2\n##\n<sup>]</sup> Paclitaxel (PTX), one of chemotherapeutic drugs in the first‐line regimen for advanced GC, is a cell cycle‐specific antitumor drug that inhibits mitosis and proliferation of tumor cells.<sup>[</sup>\n##REF##25240821##\n3\n##\n<sup>]</sup> Despite its excellent antitumor effect against GC, PTX shares the similar issues as other chemotherapeutic agents, such as poor water solubility, lack of targeting specificity, a short retention time, and severe toxic side effects, which have hampered its widespread use in clinical practice.<sup>[</sup>\n##REF##37655323##\n4\n##\n<sup>]</sup>\n</p>", "<p>The combination of chemotherapy and molecular targeted therapy could synergistically exert antitumor effects, holding an immense prospect of its application in treating GC.<sup>[</sup>\n##REF##33592120##\n5\n##\n<sup>]</sup> Currently, the majority of targeted drugs for GC are anti‐human epidermal growth factor receptor 2 or anti‐epidermal growth factor receptor gene therapy drugs, and immunotherapy drugs.<sup>[</sup>\n##REF##24626858##\n6\n##\n<sup>]</sup> However, positive response rates of these targeted agents for GC are relatively low, and only a very few patients can benefit from targeted therapy. Significant efforts have been dedicated to the identification of novel targeted drug candidates. The phosphatidylinositol‐3‐kinase (PI3K)/Protein kinase B (AKT) signaling pathway has a crucial regulatory function in cellular processes including cell growth, proliferation, differentiation, apoptosis and glucose transport.<sup>[</sup>\n##REF##12094235##\n7\n##\n<sup>]</sup> Activation of this signaling pathway is commonly observed in different types of solid tumors and its activation may be associated with poor prognosis.<sup>[</sup>\n##REF##25037117##\n8\n##\n<sup>]</sup> A retrospective study revealed that positive expression of AKT was detected in 81.54% of GC tissues, notably higher than that in 20.8% of normal tissues.<sup>[</sup>\n##REF##29143985##\n9\n##\n<sup>]</sup> Abnormal activation of the PI3K/AKT signaling pathway enhances the proliferation, metastasis, and drug resistance of GC cells, while suppressing their apoptosis. PI3K and AKT inhibitors have been demonstrated with promising antitumor effects for GC, thus they have great potential as therapeutic targeted agents.<sup>[</sup>\n##REF##18841391##\n10\n##\n<sup>]</sup>\n</p>", "<p>It was reported that the combination of AKT inhibitors and chemotherapeutic drugs could synergistically triggers apoptosis and impedes tumor growth.<sup>[</sup>\n##REF##22294718##\n11\n##\n<sup>]</sup> Capivasertib (CAP), a highly potent pan‐AKT kinase inhibitor, demonstrates a comparable inhibitory efficacy against three different subtypes of AKT. CAP inhibits the phosphorylation of AKT substrates, thereby blocking the PI3K/AKT signaling pathway. As a result, the growth of cells is inhibited, and apoptosis is promoted.<sup>[</sup>\n##REF##23394218##\n12\n##\n<sup>]</sup> Nonetheless, several limitations, such as poor water solubility and low bioavailability, have restricted its widespread application. Encouragingly, combined treatment with PTX and CAP has been shown with an enhancement in the level of PTX‐induced tumor cell apoptosis,<sup>[</sup>\n##REF##24088382##\n13\n##\n<sup>]</sup> suggesting that their combination could provide a promising new approach for the treatment of GC. It has been reported that patients could tolerate the combination of AKT inhibitors and chemotherapeutic agents, however, they suffer from serious toxic side effects such as diarrhea, infection, neutropenia, rash, and fatigue, which might be attributed to their suboptimal pharmacokinetics and poor biodistribution in the body.<sup>[</sup>\n##REF##33326257##\n14\n##\n<sup>]</sup> Hence, effective means of delivering both AKT inhibitors and chemotherapeutic agents to achieve potent combinatorial therapeutic effects and reduce their side effects have been pursued.</p>", "<p>One of the most effective means for potent and low‐toxicity combine therapy is achieved via a nano‐scale drug delivery system by incorporating chemotherapeutic and targeted drugs through physical encapsulation or covalent bonding.<sup>[</sup>\n##REF##33393582##\n15\n##\n<sup>]</sup> The nano‐scale delivery system offers active or passive targeting of tumors and enables controlled release of drugs from the system within a tumor microenvironment (TME). Therefore, they can enhance drug distribution and reduce their toxic effects. Polymer‐based nano‐drug delivery systems have been showcased as the most promising one, and some of them have already progressed to clinical trials or clinical practice.<sup>[</sup>\n##UREF##0##\n16\n##\n<sup>]</sup> Sugar‐derived polymers stand out from other polymers due to their hydrophilicity, cellular affinity, and degradability. In addition, multiple hydroxyl and aldehyde/ketone groups in sugar‐based polymers could form intermolecular hydrogen bonds, contributing to stable nano‐structures.<sup>[</sup>\n##UREF##1##\n17\n##\n<sup>]</sup>\n</p>", "<p>The efficacy of drugs in the polymer‐based drug delivery system largely depends on the molecular structure, composition, and molecular weight of the polymer carrier.<sup>[</sup>\n##REF##36875053##\n18\n##\n<sup>]</sup> Advances in controlled polymerization and click chemistry have expanded the portfolio of polymer carriers, paving the way for novel sugar‐based carriers with specific chemical compositions and molecular structures.<sup>[</sup>\n##UREF##2##\n19\n##\n<sup>]</sup> Our preliminary study suggests that polymers with branched structures offer better modifiability for both structure and function than linear polymers, thus they are promising templates for nano‐delivery systems.<sup>[</sup>\n##UREF##1##\n17\n##, ##REF##37908735##\n20\n##\n<sup>]</sup> Additionally, leveraging unique characteristic factors in the TME, including overexpressed enzymes, a low pH, and redox conditions, intelligent drug delivery systems, can achieve controlled drug release at tumor sites.<sup>[</sup>\n##REF##33426371##\n21\n##\n<sup>]</sup> Enzymes have advantages of their substrate specificity and mild reaction conditions. Response of nano‐delivery systems to overexpressed enzymes in the TME could minimize drug leakage and degradation during in vivo circulation, thus improving the drug delivery efficiency into tumor sites.</p>", "<p>In this study, an innovative approach was proposed by utilizing 2‐lactobionamidoethylmethacrylamide (LAEMA) as a key building unit for branched glycopolymers to design and prepare an enzyme‐responsive nano‐drug delivery system for PTX and CAP. This system was engineered for precise targeting of tumor cells and controlled release of PTX and CAP. As illustrated in the <bold>Scheme</bold> ##FIG##0##\n1\n##, LAEMA‐based branched polymer frameworks as a PTX prodrug were prepared through RAFT polymerization and thiol‐ene click reaction. These frameworks displayed self‐assembly characteristics, and they were used to encapsulate CAP during the self‐assembly process. Upon encountering tumor cells, the nano‐drug system underwent rapid disintegration due to the presence of overexpressed cathepsin B in the lysosomes to release PTX and CAP. This dual‐agent strategy exhibited notable synergy for GC: PTX hindered tumor cell proliferation by inhibiting mitosis and inducing apoptosis, and CAP restrained tumor cell growth and promoted apoptosis by suppressing the PI3K/AKT pathway. The encouraging therapeutic enhancement achieved through the nano‐delivery system underlines the potential of this dual‐drug co‐delivery approach as a promising therapeutic avenue for advancing GC treatment by combining chemotherapy and AKT inhibition.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Expression of AKT in GC Tissues and its Clinical Significance</title>", "<p>Previous studies have validated abnormal activation of the PI3K/AKT signaling pathway in different types of tumors including GC could lead to unfavorable prognoses.<sup>[</sup>\n##REF##32333246##\n22\n##\n<sup>]</sup> The amplification of AKT mutations is believed to contribute to the activation of the PI3K/AKT signaling pathway, serving as one of the important factors responsible for this process.<sup>[</sup>\n##REF##24748656##\n23\n##\n<sup>]</sup> To reveal clinical significance of AKT expression in GC, analysis of AKT expression in GC tissues was performed and its relationship with prognosis using public databases assessed. The outcomes indicate a significantly elevated level of AKT expression in GC tissues in comparison to normal tissues (<bold>Figure</bold>\n##FIG##1##\n1A##). Furthermore, GC patients with a high level of AKT expression often have a significantly lower overall survival rate compared to those with a low level of AKT expression (Figure ##FIG##1##1B##). To validate this discovery, immunohistochemistry (IHC) analysis was conducted on clinical tissue samples obtained from the West China Hospital (Figure ##SUPPL##0##S1##, Supporting Information). The analysis results (Figure ##FIG##1##1C,D##) are well aligned with the data in Figure ##FIG##1##1A,B##, corroborating the findings reported by Gu et al.<sup>[</sup>\n##REF##24726064##\n24\n##\n<sup>]</sup> Furthermore, previous research findings have demonstrated a strong correlation between the activation of the PI3K/AKT signaling pathway and drug resistance in various tumors.<sup>[</sup>\n##REF##32973135##\n25\n##\n<sup>]</sup>\n</p>", "<p>In this study, out of 100 GC patients, 25 received neoadjuvant chemotherapy, while 75 did not. IHC analysis supports a higher level of AKT expression in GC samples of patients who received neoadjuvant chemotherapy (<italic toggle=\"yes\">p</italic> &lt; 0.001) (Figure ##FIG##1##1E##). In addition, among 25 GC patients who underwent neoadjuvant chemotherapy, those with a lower level of AKT expression exhibit more pronounced tumor regression (Table ##SUPPL##0##S1##, Supporting Information). Western blot results confirm increased expression of AKT in MFC cells after PTX treatment for 24 h (Figure ##FIG##1##1F##). These results suggest chemotherapy could boost the expression of AKT in MFC cells, and the expression of AKT may be related to the inefficacy of chemotherapy. It has been reported that an AKT inhibitor, CAP, can suppress the expression of AKT, leading to an enhanced sensitivity of tumor cells to chemotherapeutic drugs such as PTX.<sup>[</sup>\n##REF##32070411##\n26\n##\n<sup>]</sup> To demonstrate the impact of CAP on the cytotoxic effect of PTX, CAP combined with PTX was applied to treatmouse forestomach carcinoma (MFC) cells and western blot results confirm that AKT expression is inhibited (Figure ##FIG##1##1F,G##). The Cell Counting Kit‐8 (CCK‐8) assay was conducted to assess the cytotoxic effect of CAP combined with free PTX on MFC cells. The results demonstrate that the combination of CAP and PTX exhibits a significantly higher level of cytotoxicity compared to free PTX (Figure ##FIG##1##1H##), which indicates that the inhibition of AKT may be an effective approach to enhancing the efficacy of chemotherapy against GC.</p>", "<p>The synergistic anti‐tumor effect of free CAP and PTX was then comprehensively evaluated. The cytotoxic effects of the combination of free CAP and PTX on MFC cells were assessed at various CAP/PTX weight ratios (CAP: PTX = 4:1, 1:1, and 1:4). The results reveal that almost all synergy indexes for the combination of CAP and PTX at different weight ratios are less than 1, suggesting a synergistic effect of CAP and PTX in killing MFC cells (Figure ##FIG##1##1I##). This demonstrates tremendous potential of the combine therapy of PTX and CAP in treating GC.</p>", "<title>Fabrication and Characterizations of BPGP@CAP</title>", "<p>In this study, we utilized controlled RAFT polymerization and efficient thiol‐ene reaction for designing and synthesizing the cathepsin B‐sensitive branched glycopolymer‐PTX prodrug. As shown in Scheme ##SUPPL##0##S1## (Supporting Information), a crosslinking agent, MA‐GFLG‐MA, and a small molecular prodrug, maleimide‐GFLG‐PTX, were first synthesized. Structural confirmation and purity assessment were performed using <sup>1</sup>H NMR and liquid chromatography‐mass spectrometry (LC‐MS), and the experimental results are presented in Figures ##SUPPL##0##S2–S7## (Supporting Information). After successful preparation of polymerizable monomers and functionalized small molecules, RAFT polymerization was conducted to produce a high‐molecular‐weight chain transfer agent, poly(LAEMA)‐CTA, illustrated in Scheme ##SUPPL##0##S2A## (Supporting Information). An approximate value of 28 kDa is obtained from molecular weight calculation via <sup>1</sup>H NMR and the repeating LAEMA units are ≈61 (Figure ##SUPPL##0##S8##, Supporting Information). Gel permeation chromatography (GPC) analysis reveals a PDI of ≈1.06 for the chain transfer agent (Figure ##SUPPL##0##S13##, Supporting Information), indicative of a narrow molecular weight distribution.</p>", "<p>Subsequently, co‐polymerization of poly(LAEMA)‐CTA, MA‐GFLG‐MA, MA‐PySS, and LAEMA yields an intermediate polymer with a branched architecture (branched poly(LAEMA)‐GFLG‐PySS). The <sup>1</sup>H NMR spectrum of the intermediate polymer displays significant characteristic peaks of pyridine at 7.22 ppm, 7.74 ppm, and 8.31 ppm, indicating successful introduction of MA‐PySS into the polymer structure (Figure ##SUPPL##0##S9##, Supporting Information). After deprotection treatment, the characteristic peak of pyridine in the polymer disappears from the <sup>1</sup>H NMR spectrum, while a characteristic peak of the benzene ring in GFLG is observed at 7.29 ppm (Figure ##SUPPL##0##S10##, Supporting Information). The as‐prepared intermediate polymer was sequentially conjugated with maleimide‐Cy5 and maleimide GFLG PTX, resulting in a product of a branched polymer prodrug, poly(LAEMA<sup>Cy5</sup>)‐GFLG‐PTX (termed as BPGP). Structural confirmation of the product is attained through its <sup>1</sup>H NMR (<bold>Figure</bold>\n##FIG##2##\n2A##). Notably, distinct peaks corresponding to PTX and GFLG are not observed in the <sup>1</sup>H NMR spectrum of BPGP in D<sub>2</sub>O, which is distinctly different from the spectrum of BPGP in DMSO‐<italic toggle=\"yes\">d6</italic>. This disparity suggests BPGP may experience self‐assembly in an aqueous solution (Figure ##SUPPL##0##S11## and ##SUPPL##0##S12##, Supporting Information). As shown in Figure ##FIG##2##2B##, compared with unlabeled branched polymer prodrugs, the characteristic peak of Cy5 can be observed in both ultraviolet visible (UV‐<italic toggle=\"yes\">vis</italic>) and fluorescence spectra, and there is no significant change in the wavelength of the characteristic peak compared to free Cy5, indicating that the optical properties of Cy5 remain after it was covalently coupled to the polymer.</p>", "<p>Due to the presence of hydrophilic segments and hydrophobic drugs in the branched polymer prodrug, the prodrug could self‐assemble into nanoparticles through hydrophilic hydrophobic interactions. We used pyrene as a fluorescence probe to detect its critical micelle concentration (CAC), and its CAC value is found to be ≈2.64 µg mL<sup>−1</sup>, which indicates that the polymer prodrug possesses a remarkable self‐assembly ability (Figure ##FIG##2##2C##). Subsequently, we assessed the potential of the PTX prodrug as a polymeric nanocarrier system for drug delivery. To realize the synergy of chemotherapy and molecular targeted therapy, we utilized a solvent evaporation technique to encapsulate CAP, an AKT inhibitor, into the glycopolymer‐PTX prodrug, resulting in a nanoassembly, BPGP@CAP. Initially, the nanoassembly was fabricated at different PTX‐to‐CAP feed ratios to assess the encapsulation capability of the polymer‐PTX prodrug for CAP. As shown in Figure ##FIG##2##2D##, with an increase in the CAP feed weight, the drug loading of CAP within the nanoassembly progressively augments, signifying a great encapsulation capacity of the nanoassembly. However, it's worth noting that as the drug loading increases, the encapsulation efficiency of the nanoassembly exhibits a gradual decline. Notably, when the weight ratio of PTX to CAP drops below 1:1.5, the encapsulation efficiency of the nanoassembly experiences a substantial reduction. Consequently, the nanoassembly synthesized at a PTX‐to‐CAP weight ratio of 1:1.5 is chosen for subsequent experimental uses. The results of HPLC analysis reveal that 7.5 wt.% of PTX and 8.0 wt.% of CAP are in the nanoassembly of BPGP@CAP. As shown in Figure ##FIG##2##2E,F##, DLS measurements confirm that the hydrodynamic diameter of BPGP is ≈78.83 ± 0.35 nm, and upon encapsulation of CAP, a slight increase in the hydrodynamic size is observed (90.12 ± 0.36 nm). TEM images exhibit a relatively uniform size distribution for both BPGP and BPGP@CAP. Although encapsulation of CAP leads to a marginal size augmentation, the morphology of the nanoassembly remains unchanged. Leveraging the presence of GFLG in the polymer structure, the drug release behavior from the polymer prodrug was probed in a simulated tumor intracellular microenvironment. Since papain and cathepsin B share the same catalytic site, papain was selected to mimic cathepsin B in the tumor microenvironment. As depicted in the Figure ##FIG##2##2G##, under conditions without papain catalysis, the polymer prodrug retains stability with negligible drug release. Conversely, under enzymatic catalysis, the polymer prodrug effectively releases the loaded drug. These findings suggest the polymer prodrug could be used for stable in vivo drug delivery and controlled drug release at tumor sites.</p>", "<title>Cellular Uptake of BPGP@CAP by MFC Cells</title>", "<p>Cellular uptake of polymeric drug delivery systems by tumor cells is a crucial step to exert a drug antitumor effect. The uptake of Cy5‐labeled BPGP@CAP into MFC cells was evaluated using CLSM and flow cytometry techniques. By observing the fluorescence signal of Cy5 in MFC cells after incubation with Cy5‐labeled BPGP@CAP at different durations through CLSM, it is evident that with an increase in the incubation time, the red fluorescence signal from Cy5 gradually accumulates and becomes intensified in the cytoplasm of MFC cells (<bold>Figure</bold>\n##FIG##3##\n3A##; Figure ##SUPPL##0##S14##, Supporting Information). Flow cytometry data for uptake of Cy5‐labeled BPGP@CAP by MFC cells is in agreement with the CLSM images (Figure ##FIG##3##3C##; Figure ##SUPPL##0##S15##, Supporting Information). These results indicate that BPGP@CAP could be efficiently ingested by MFC cells, and this uptake process is time‐dependent.</p>", "<p>To investigate the endocytic pathways of BPGP@CAP into MFC cells, flow cytometry was employed to detect the uptake of BPGP@CAP by MFC cells at a low temperature. The results show that the uptake of BPGP@CAP by MFC cells is significantly inhibited at an inhibition rate of 80.5%, indicating that the internalization of BPGP@CAP is an energy‐dependent process. Furthermore, upon incubating inhibitors with MFC cells, flow cytometry data demonstrate that chlorpromazine, genistein, and amiloride inhibit cellular uptake of BPGP@CAP by 70.2%, 65.4%, and 44.5% respectively. This suggests that clathrin‐mediated, caveolin‐mediated, and icropinocytosis‐mediated endocytic pathways may be involved in the uptake of BPGP@CAP (Figure ##FIG##3##3D##; Figure ##SUPPL##0##S16##, Supporting Information). Moreover, since the lysosomal cathepsin B can cleave the GFLG linker to release PTX,<sup>[</sup>\n##UREF##3##\n27\n##\n<sup>]</sup> we investigated whether BPGP@CAP would be transported to the lysosomes for degradation after cellular uptake. Through lysosomal colocalization experiments (Figure ##FIG##3##3B##), we observe a high overlapping level of the fluorescence signal for BPGP@CAP and lysosomes, suggesting BPGP@CAP may land at lysosomes before it is disintegrated by lysosomal cathepsin B. Combined with the findings from in vitro drug release experiments, it is confirmed that BPGP@CAP can be internalized by MFC cells and release drugs stimulated by lysosomal cathepsin B.</p>", "<title>The Toxicity of BPGP@CAP on MFC Cells</title>", "<p>To assess the toxicity of BPGP@CAP, we conducted CCK‐8 assays to measure the viability of MFC cells subjected to various treatment groups. The results indicate that after the treatment of BPGP@CAP, MFC cells viability significantly decreases. BPGP@CAP has an IC<sub>50</sub> of 0.253 µg mL<sup>−1</sup> in comparison to free PTX with an IC<sub>50</sub> of 2.51 µg mL<sup>−1</sup> and CAP with an IC<sub>50</sub> of 4.74 µg mL<sup>−1</sup>. Furthermore, the cell viability in the group with the treatment of BPGP@CAP is similar to that in the group treated with free PTX+CAP with an IC<sub>50</sub> of 0.43 µg mL<sup>−1</sup>, whereas the cell viability in the group treated with BPGP is comparable to that in the group exposed to free PTX, and the IC<sub>50</sub> value for BPGP and free PTX is 2.52 µg mL<sup>−1</sup> and 2.51 µg mL<sup>−1</sup>, respectively (Figure ##FIG##3##3E##). These findings suggest that BPGP@CAP could effectively release PTX and CAP after disintegration of the nanoassembly structure in the lysosomes, thus exerting an equivalent antitumor effect to a mixture of free PTX and CAP. Additionally, both the groups treated with BPGP@CAP and PTX + CAP exhibit a significantly higher cytotoxic effect on MFC cells than the groups exposed to BPGP and free PTX, indicating that the combination of CAP and PTX displays a synergistic action on MFC cells.</p>", "<p>Microtubules, which are essential cytoskeletal filaments within cells, have a critical function in mitosis and intracellular vesicle transport.<sup>[</sup>\n##REF##30536951##\n28\n##\n<sup>]</sup> It is well‐established that PTX can enhance the polymerization of microtubules, hinder depolymerization, and suppress mitosis of tumor cells.<sup>[</sup>\n##REF##24435445##\n29\n##\n<sup>]</sup> In order to assess the impact of PTX derived from BPGP@CAP on microtubules, we used CLSM to observe morphological changes of microtubules in the MFC cells after various treatments. Microtubules are evenly distributed in the cytoplasm of MFC cells in the control and CAP‐treated groups. However, pronounced aggregation of microtubules is found around the cell nucleus in the groups exposed to PTX and PTX+CAP. Similar morphological changes of microtubules are observed in the groups treated with BPGP and BPGP@CAP (Figure ##FIG##3##3F##). Furthermore, in the control and CAP‐treated groups, the nuclei of MFC cells appear intact, whereas an abnormal nuclear morphology and a multinucleated structure are found in the groups treated with PTX, PTX + CAP, BPGP and BPGP@CAP, indicating that PTX released from BPGP@CAP exerts a similar effect on microtubules as free PTX.</p>", "<p>Furthermore, microfilaments, which are composed of actin proteins, are integral constituents of the cellular cytoskeleton. Through CLSM, the influence of BPGP@CAP on microfilaments of MFC cells was examined. Our results indicate that actin aggregates into clusters or dots near the cell membrane in the BPGP@CAP‐treated group (Figure ##SUPPL##0##S17##, Supporting Information), leading to impaired microfilaments and reduced cell viability.</p>", "<p>Moreover, we utilized flow cytometry to evaluate the impact of BPGP@CAP on the apoptosis of MFC cells. The findings indicate that the percentage of apoptotic cells in the groups exposed to BPGP@CAP (23.8%), BPGP (15.7%), PTX (17.3%), and PTX+CAP (22.3%) is significantly higher than that in the control group (4.7%) (<bold>Figure</bold>\n##FIG##4##\n4A,C##). Additionally, no significant difference is found in the percentage of apoptotic cells between the groups exposed to BPGP@CAP and PTX + CAP. Furthermore, MFC cells have a significantly higher apoptotic percentage after treatment with BPGP@CAP and PTX + CAP than those treated with PTX and CAP, further supporting their synergistic action of inducting apoptosis of MFC cells.</p>", "<p>It is widely recognized that PTX exerts its effects on microtubules, causing inhibition of cell mitosis and resulting in G2/M cell cycle arrest.<sup>[</sup>\n##UREF##4##\n30\n##\n<sup>]</sup> We assessed the influence of PTX released from BPGP@CAP on the cell cycle distribution of MFC cells. As presented in Figure ##FIG##4##4B,D##, the percentages of cells in the G2/M phase in the groups treated with PTX (25.1%), BPGP (20.2%), PTX + CAP (27.8%), and BPGP@CAP (23.6%) are significantly higher than that in the control group (11.0%). Conversely, the proportions cells in the G0/G1 phase in the groups treated with PTX (43.9%), BPGP (52.2%), PTX + CAP (39.0%), and BPGP@CAP (39.6%) are significantly lower than that in the control group (76.6%). These findings support that PTX released from BPGP and BPGP@CAP can lead to cell cycle arrest in the G2/M phase. These results further confirm that BPGP@CAP can effectively releases PTX in the tumor cells, thereby displaying a similar antitumor mechanism of action as free PTX.</p>", "<title>Mechanism Study on the Synergistic Effect of PTX and CAP</title>", "<p>Our in vitro experimental results support the existence of a synergistic effect between PTX and CAP to eliminate MFC cells. To explore the underlying mechanisms behind this synergy, we conducted transcriptome sequencing on MFC cells exposed to BPGP@CAP and compared them with the control group. We detected 2799 differentially expressed genes (DEGs) between BPGP@CAP and control groups. Out of these DEGs, 1678 are upregulated and 1121 downregulated in the BPGP@CAP‐treated group (<bold>Figure</bold>\n##FIG##5##\n5A##; Figure ##SUPPL##0##S18##, Supporting Information). Subsequently, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was employed to uncover the biological pathways impacted by these DEGs. The results suggest that the pathways for apoptosis and PI3K/AKT signaling are significantly upregulated, which indicates that the mechanism underlying the synergistic antitumor effects of PTX and CAP in BPGP@CAP may be related to the PI3K/AKT signaling pathway and apoptosis (Figure ##FIG##5##5B##). It has been evidenced that the PI3K/AKT signaling pathway can regulate apoptosis by modulating the phosphorylation of Bax and Bad and the regulation of their expression levels, the release of cytochrome C, and the activation of caspase ‐ 3 and 9, thus affecting cell survival.<sup>[</sup>\n##REF##23881702##\n31\n##\n<sup>]</sup> Western blot results confirm that CAP inhibits the expression of the PI3K/AKT pathway‐related proteins such as AKT, p‐mTOR, p‐S6, and p‐4EBP1 (Figure ##FIG##5##5C##), indicating that CAP can suppress the PI3K/AKT signaling pathway.</p>", "<p>Furthermore, western blotting was employed to assess the expression of apoptosis‐related proteins, such as cleaved PARP, cleaved caspase‐3, Bax, and Bcl‐2, in various treatment groups. As showed in Figure ##FIG##5##5E,F##, the expression of Bax, cleaved caspase‐3, and cleaved PARP is upregulated in MFC cells after treatment with CAP, which might be credited to apoptosis after the inhibition of AKT. Furthermore, it is known that PTX can induce tumor cell apoptosis by downregulation of Bcl‐2 and upregulation of Bax and cleaved caspase‐3.<sup>[</sup>\n##REF##23735541##\n32\n##\n<sup>]</sup> Our results confirm that the expression levels of Bax, cleaved caspase‐3, and cleaved PARP were elevate, while Bcl‐2 is downregulated in the MFC cells with treatment of PTX and BPGP. In addition, when MFC was treated with the combination of free PTX and CAP or BPGP@CAP, more pronounced changes are observed in the expression of proteins including Bax, cleaved caspase −3, and cleaved PARP. Interestingly, western blot results reveal that the effect of CAP on downregulating the BCL‐2 protein expression is not pronounced as PTX, suggesting that the downregulation of Bcl‐2 may be predominantly induced by PTX, while no apparent correlation is seen between the downregulation of Bcl‐2 and the inhibition of AKT expression. However, the combination of PTX and CAP can induce more significant downregulation of Bcl‐2 compared to their individual effects, which is in agreement with a previous study.<sup>[</sup>\n##REF##32070411##\n26\n##\n<sup>]</sup> It may be explained by that CAP could significantly sensitize MFC cells to PTX‐induced apoptosis, resulting in more prominent downregulation of Bcl‐2.</p>", "<p>The combination of PTX with CAP exerts synergistic effects on MFC cells via the modulation of pro and anti‐apoptotic genes, such as downregulation of Bcl‐2 and upregulation of Bax, cleaved caspase‐3, and cleaved PARP. This could be the underlying mechanism for synergistic promotion of apoptosis by PTX and CAP (Figure ##FIG##5##5G##).</p>", "<title>Antitumor Effect of BPGP@CAP In Vivo</title>", "<title>\n<italic toggle=\"yes\">Distribution of BPGP@CAP</italic> In Vivo</title>", "<p>The accumulation of BPGP@CAP at the site of transplanted tumor plays a critical role in its antitumor efficacy in vivo. Mounting evidence has suggested that nanoparticles exhibit the enhanced permeability and retention (EPR) effect, which can extend the residence time and increase the concentration of drugs in tumors, thus achieving passive drug targeting of tumor cells.<sup>[</sup>\n##UREF##5##\n33\n##\n<sup>]</sup> The characterization results of BPGP@CAP indicate that it possesses a nanoscale size for the EPR effect. To confirm the accumulation of BPGP@CAP in tumor tissues via the EPR effect, we utilized a fluorescence imaging technique to evaluate the distribution of BPGP@CAP in the mice with MFC tumors. By administering Cy5‐labeled BPGP@CAP and free Cy5 intravenously to the tumor‐bearing nude mice, we assessed the distribution of BPGP@CAP at various time intervals using IVIS spectroscopy. The findings reveal that the fluorescence intensity of the tumor in the BPGP@CAP‐treated group is stronger than that in the free Cy5‐treated group as time elapses (<bold>Figure</bold>\n##FIG##6##\n6A##; Figure ##SUPPL##0##S19##, Supporting Information). Specifically, after 24 h, the fluorescence intensity of the tumor in the BPGP@CAP‐treated group still remains strong, while faint fluorescence signal is detected in the tumor of the free Cy5‐treated group. This indicates that BPGP@CAP can accumulate and retain in the tumor site for an extended period. Furthermore, tumor tissues were collected at 24 h post‐injection and visualized using CLSM. The images demonstrate that tumor tissues of the mice after the treatment of free Cy5 show undetectable fluorescence signal, whereas tumor tissues of the mice after the treatment of BPGP@CAP exhibit significantly strong fluorescence intensity (Figure ##FIG##6##6B##). The in vivo imaging results confirm the enrichment of BPGP@CAP in tumor tissues.</p>", "<p>Furthermore, pharmacokinetic analysis in vivo reveals a slower decrease in the Cy5 concentration in the blood of the mice exposed to BPGP@CAP compared to that in the group exposed to free Cy5, and the half‐life of BPGP@CAP and free Cy5 was 488.49 and 160.85 min, respectively (Figure ##FIG##6##6C##; Table ##SUPPL##0##S2##, Supporting Information). The results might be ascribed to a high molecular weight of BPGP@CAP and a prolonged circulation time which may help enhance passive accumulation of BPGP@CAP at the tumor site, thereby improving its therapeutic efficacy against tumors.</p>", "<title>Antitumor Effect of BPGP@CAP</title>", "<p>The mice, which were subcutaneously injected with MFC cells, were divided randomly into six groups, each consisting of 5 mice. The control group were given intravenous injections of saline, while the other groups were intravenously injected with PTX, CAP, PTX + CAP, BPGP, and BPGP@CAP, respectively. The concentrations of PTX remain consistent at 8 mg kg<sup>−1</sup> for each mouse. The treatment schedule is illustrated in Figure ##FIG##6##6D##. The volume of the transplanted tumor and the body weight of each treated mouse were regularly monitored and recorded. The results reveal that the control group has the fastest tumor growth rate, while the BPGP@CAP‐treated group displays the slowest tumor growth (Figure ##FIG##6##6E##). After the treatment, the tumor volume of the control group is 1.45, 1.67, 2.04, 2.48, and 4.13 times that of the group treated with PTX, CAP, PTX+CAP, BPGP, and BPGP@CAP, respectively. The tumor inhibition rates, based on tumor volume measurements, are found to be 31.0%, 40.1%, 51.0%, 59.7%, and 75.8% after treatment with PTX, CAP, PTX + CAP, BPGP, and BPGP@CAP, respectively. In addition, the tumor volumes in the groups with the treatment of free PTX and PTX + CAP are 2.85 times and 2.02 times that of the BPGP@CAP‐treated group, respectively (Figure ##FIG##6##6F##). The tumor volumes of the transplanted tumors harvested from each group are well aligned with those observed in vivo (Figure ##SUPPL##0##S20A##, Supporting Information). Comparison of the transplant tumor masses in the treatment groups reveals that the tumor mass harvested from the BPGP@CAP‐treated mice (0.28 g) is significantly lighter than that of the free control group (1.20 g), the PTX‐treated group (0.84 g), and the PTX + ACP‐treated group (0.57 g) (Figure ##FIG##6##6G##). The tumor inhibition rates, based on tumor mass measurements, are estimated to be 30.2%, 39.1%, 49.6%, 58.6%, and 75.7% for PTX, CAP, PTX + CAP, BPGP, and BPGP@CAP, respectively (Figure ##SUPPL##0##S20B##, Supporting Information). The tumor inhibition rates based on tumor mass measurements are similar to those based on tumor volume measurements in vivo for CAP and/or PTX‐derived formulations. The difference in the tumor inhibition rates among BPGP@CAP and other groups may result from a synergistic effect of PTX and CAP, enrichment of BPGP@CAP in tumor tissues and prolonged circulation in the blood through a nanoscale drug delivery system.</p>", "<p>The antitumor effect of BPGP@CAP was further verified by IHC analysis of tumor tissues. TUNEL assays of the harvested tumors indicate TUNEL‐positive tumor cells in the BPGP@CAP‐treated group are the most populous, confirming that the treatment of BPGP@CAP results in more apoptotic cells compared with other groups (Figure ##FIG##6##6I,J##). Furthermore, the mice treated with BPGP@CAP show a significant reduction in the population of Ki67‐positive tumor cells with comparison to the other groups. This observation suggests that the administration of BPGP@CAP leads to a remarkable suppression of tumor cell proliferation (Figure ##FIG##6##6I,J##), which confirms synergistic inhibition of tumor growth by both agents in vivo. These findings support the excellent anti‐tumor effect of BPGP@CAP.</p>", "<p>Additionally, while the administration of free PTX and PTX + CAP effectively suppresses the growth of transplanted tumors in the mice, it is accompanied by a decrease in the body weight ranging from 9.1% to 6.3% after each administration (Figure ##FIG##6##6H##). This indicates the presence of systemic toxicity associated with free PTX. In contrast, no significant changes in the body weight are found in the BPGP and BPGP@CAP‐treated groups, suggesting that the toxicity of PTX could be remarkably reduced after PTX is delivered via a polymer prodrug. In addition, we conducted H&amp;E staining on the major organs of the mice and analyzed the change of hematological parameters including white blood cells (WBC), red blood cells (RBC), platelets (PLT), alanine aminotransferase (ALT), aspartate aminotransferase (AST), blood urea nitrogen (BUN), and creatinine (CREA) to evaluate the toxicity of BPGP@CAP. The H&amp;E staining images indicate no significant alterations in the major organs, including the heart, liver, spleen, lung, and kidney, across all treatment groups (Figure ##SUPPL##0##S21##, Supporting Information). However, compared to the control group with a WBC count of 8.20×10<sup>9</sup>/L, the WBC count of the mice is found to be 3.19 × 10<sup>9</sup> per L, 3.28 × 10<sup>9</sup> per L, 5.76 × 10<sup>9</sup> per L and 5.69 × 10<sup>9</sup> per L in the group treated free PTX, PTX + CAP, BPGP, and BPGP@CAP, respectively. The most pronounced decreases in the WBC number are seen in the groups treated with PTX and PTX + CAP. Furthermore, when compared to the control group where the ALT level is 21.0 U L<sup>−1</sup>, there is no significant change in the ALT level in the BPGP+CAP‐treated group (22.0 U L<sup>−1</sup>), while a distinctive increase is seen in the PTX group (71.7 U L<sup>−1</sup>) and the PTX+CAP group (63.3 U L<sup>−1</sup>) (Figure ##SUPPL##0##S22##, Supporting Information). These results indicate that systemic administration of free PTX or PTX + CAP can cause hematopoietic system toxicity and liver toxicity, while the use of BPGP@CAP to deliver PTX and CAP can significantly reduce their toxicity.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Expression of AKT in GC Tissues and its Clinical Significance</title>", "<p>Previous studies have validated abnormal activation of the PI3K/AKT signaling pathway in different types of tumors including GC could lead to unfavorable prognoses.<sup>[</sup>\n##REF##32333246##\n22\n##\n<sup>]</sup> The amplification of AKT mutations is believed to contribute to the activation of the PI3K/AKT signaling pathway, serving as one of the important factors responsible for this process.<sup>[</sup>\n##REF##24748656##\n23\n##\n<sup>]</sup> To reveal clinical significance of AKT expression in GC, analysis of AKT expression in GC tissues was performed and its relationship with prognosis using public databases assessed. The outcomes indicate a significantly elevated level of AKT expression in GC tissues in comparison to normal tissues (<bold>Figure</bold>\n##FIG##1##\n1A##). Furthermore, GC patients with a high level of AKT expression often have a significantly lower overall survival rate compared to those with a low level of AKT expression (Figure ##FIG##1##1B##). To validate this discovery, immunohistochemistry (IHC) analysis was conducted on clinical tissue samples obtained from the West China Hospital (Figure ##SUPPL##0##S1##, Supporting Information). The analysis results (Figure ##FIG##1##1C,D##) are well aligned with the data in Figure ##FIG##1##1A,B##, corroborating the findings reported by Gu et al.<sup>[</sup>\n##REF##24726064##\n24\n##\n<sup>]</sup> Furthermore, previous research findings have demonstrated a strong correlation between the activation of the PI3K/AKT signaling pathway and drug resistance in various tumors.<sup>[</sup>\n##REF##32973135##\n25\n##\n<sup>]</sup>\n</p>", "<p>In this study, out of 100 GC patients, 25 received neoadjuvant chemotherapy, while 75 did not. IHC analysis supports a higher level of AKT expression in GC samples of patients who received neoadjuvant chemotherapy (<italic toggle=\"yes\">p</italic> &lt; 0.001) (Figure ##FIG##1##1E##). In addition, among 25 GC patients who underwent neoadjuvant chemotherapy, those with a lower level of AKT expression exhibit more pronounced tumor regression (Table ##SUPPL##0##S1##, Supporting Information). Western blot results confirm increased expression of AKT in MFC cells after PTX treatment for 24 h (Figure ##FIG##1##1F##). These results suggest chemotherapy could boost the expression of AKT in MFC cells, and the expression of AKT may be related to the inefficacy of chemotherapy. It has been reported that an AKT inhibitor, CAP, can suppress the expression of AKT, leading to an enhanced sensitivity of tumor cells to chemotherapeutic drugs such as PTX.<sup>[</sup>\n##REF##32070411##\n26\n##\n<sup>]</sup> To demonstrate the impact of CAP on the cytotoxic effect of PTX, CAP combined with PTX was applied to treatmouse forestomach carcinoma (MFC) cells and western blot results confirm that AKT expression is inhibited (Figure ##FIG##1##1F,G##). The Cell Counting Kit‐8 (CCK‐8) assay was conducted to assess the cytotoxic effect of CAP combined with free PTX on MFC cells. The results demonstrate that the combination of CAP and PTX exhibits a significantly higher level of cytotoxicity compared to free PTX (Figure ##FIG##1##1H##), which indicates that the inhibition of AKT may be an effective approach to enhancing the efficacy of chemotherapy against GC.</p>", "<p>The synergistic anti‐tumor effect of free CAP and PTX was then comprehensively evaluated. The cytotoxic effects of the combination of free CAP and PTX on MFC cells were assessed at various CAP/PTX weight ratios (CAP: PTX = 4:1, 1:1, and 1:4). The results reveal that almost all synergy indexes for the combination of CAP and PTX at different weight ratios are less than 1, suggesting a synergistic effect of CAP and PTX in killing MFC cells (Figure ##FIG##1##1I##). This demonstrates tremendous potential of the combine therapy of PTX and CAP in treating GC.</p>", "<title>Fabrication and Characterizations of BPGP@CAP</title>", "<p>In this study, we utilized controlled RAFT polymerization and efficient thiol‐ene reaction for designing and synthesizing the cathepsin B‐sensitive branched glycopolymer‐PTX prodrug. As shown in Scheme ##SUPPL##0##S1## (Supporting Information), a crosslinking agent, MA‐GFLG‐MA, and a small molecular prodrug, maleimide‐GFLG‐PTX, were first synthesized. Structural confirmation and purity assessment were performed using <sup>1</sup>H NMR and liquid chromatography‐mass spectrometry (LC‐MS), and the experimental results are presented in Figures ##SUPPL##0##S2–S7## (Supporting Information). After successful preparation of polymerizable monomers and functionalized small molecules, RAFT polymerization was conducted to produce a high‐molecular‐weight chain transfer agent, poly(LAEMA)‐CTA, illustrated in Scheme ##SUPPL##0##S2A## (Supporting Information). An approximate value of 28 kDa is obtained from molecular weight calculation via <sup>1</sup>H NMR and the repeating LAEMA units are ≈61 (Figure ##SUPPL##0##S8##, Supporting Information). Gel permeation chromatography (GPC) analysis reveals a PDI of ≈1.06 for the chain transfer agent (Figure ##SUPPL##0##S13##, Supporting Information), indicative of a narrow molecular weight distribution.</p>", "<p>Subsequently, co‐polymerization of poly(LAEMA)‐CTA, MA‐GFLG‐MA, MA‐PySS, and LAEMA yields an intermediate polymer with a branched architecture (branched poly(LAEMA)‐GFLG‐PySS). The <sup>1</sup>H NMR spectrum of the intermediate polymer displays significant characteristic peaks of pyridine at 7.22 ppm, 7.74 ppm, and 8.31 ppm, indicating successful introduction of MA‐PySS into the polymer structure (Figure ##SUPPL##0##S9##, Supporting Information). After deprotection treatment, the characteristic peak of pyridine in the polymer disappears from the <sup>1</sup>H NMR spectrum, while a characteristic peak of the benzene ring in GFLG is observed at 7.29 ppm (Figure ##SUPPL##0##S10##, Supporting Information). The as‐prepared intermediate polymer was sequentially conjugated with maleimide‐Cy5 and maleimide GFLG PTX, resulting in a product of a branched polymer prodrug, poly(LAEMA<sup>Cy5</sup>)‐GFLG‐PTX (termed as BPGP). Structural confirmation of the product is attained through its <sup>1</sup>H NMR (<bold>Figure</bold>\n##FIG##2##\n2A##). Notably, distinct peaks corresponding to PTX and GFLG are not observed in the <sup>1</sup>H NMR spectrum of BPGP in D<sub>2</sub>O, which is distinctly different from the spectrum of BPGP in DMSO‐<italic toggle=\"yes\">d6</italic>. This disparity suggests BPGP may experience self‐assembly in an aqueous solution (Figure ##SUPPL##0##S11## and ##SUPPL##0##S12##, Supporting Information). As shown in Figure ##FIG##2##2B##, compared with unlabeled branched polymer prodrugs, the characteristic peak of Cy5 can be observed in both ultraviolet visible (UV‐<italic toggle=\"yes\">vis</italic>) and fluorescence spectra, and there is no significant change in the wavelength of the characteristic peak compared to free Cy5, indicating that the optical properties of Cy5 remain after it was covalently coupled to the polymer.</p>", "<p>Due to the presence of hydrophilic segments and hydrophobic drugs in the branched polymer prodrug, the prodrug could self‐assemble into nanoparticles through hydrophilic hydrophobic interactions. We used pyrene as a fluorescence probe to detect its critical micelle concentration (CAC), and its CAC value is found to be ≈2.64 µg mL<sup>−1</sup>, which indicates that the polymer prodrug possesses a remarkable self‐assembly ability (Figure ##FIG##2##2C##). Subsequently, we assessed the potential of the PTX prodrug as a polymeric nanocarrier system for drug delivery. To realize the synergy of chemotherapy and molecular targeted therapy, we utilized a solvent evaporation technique to encapsulate CAP, an AKT inhibitor, into the glycopolymer‐PTX prodrug, resulting in a nanoassembly, BPGP@CAP. Initially, the nanoassembly was fabricated at different PTX‐to‐CAP feed ratios to assess the encapsulation capability of the polymer‐PTX prodrug for CAP. As shown in Figure ##FIG##2##2D##, with an increase in the CAP feed weight, the drug loading of CAP within the nanoassembly progressively augments, signifying a great encapsulation capacity of the nanoassembly. However, it's worth noting that as the drug loading increases, the encapsulation efficiency of the nanoassembly exhibits a gradual decline. Notably, when the weight ratio of PTX to CAP drops below 1:1.5, the encapsulation efficiency of the nanoassembly experiences a substantial reduction. Consequently, the nanoassembly synthesized at a PTX‐to‐CAP weight ratio of 1:1.5 is chosen for subsequent experimental uses. The results of HPLC analysis reveal that 7.5 wt.% of PTX and 8.0 wt.% of CAP are in the nanoassembly of BPGP@CAP. As shown in Figure ##FIG##2##2E,F##, DLS measurements confirm that the hydrodynamic diameter of BPGP is ≈78.83 ± 0.35 nm, and upon encapsulation of CAP, a slight increase in the hydrodynamic size is observed (90.12 ± 0.36 nm). TEM images exhibit a relatively uniform size distribution for both BPGP and BPGP@CAP. Although encapsulation of CAP leads to a marginal size augmentation, the morphology of the nanoassembly remains unchanged. Leveraging the presence of GFLG in the polymer structure, the drug release behavior from the polymer prodrug was probed in a simulated tumor intracellular microenvironment. Since papain and cathepsin B share the same catalytic site, papain was selected to mimic cathepsin B in the tumor microenvironment. As depicted in the Figure ##FIG##2##2G##, under conditions without papain catalysis, the polymer prodrug retains stability with negligible drug release. Conversely, under enzymatic catalysis, the polymer prodrug effectively releases the loaded drug. These findings suggest the polymer prodrug could be used for stable in vivo drug delivery and controlled drug release at tumor sites.</p>", "<title>Cellular Uptake of BPGP@CAP by MFC Cells</title>", "<p>Cellular uptake of polymeric drug delivery systems by tumor cells is a crucial step to exert a drug antitumor effect. The uptake of Cy5‐labeled BPGP@CAP into MFC cells was evaluated using CLSM and flow cytometry techniques. By observing the fluorescence signal of Cy5 in MFC cells after incubation with Cy5‐labeled BPGP@CAP at different durations through CLSM, it is evident that with an increase in the incubation time, the red fluorescence signal from Cy5 gradually accumulates and becomes intensified in the cytoplasm of MFC cells (<bold>Figure</bold>\n##FIG##3##\n3A##; Figure ##SUPPL##0##S14##, Supporting Information). Flow cytometry data for uptake of Cy5‐labeled BPGP@CAP by MFC cells is in agreement with the CLSM images (Figure ##FIG##3##3C##; Figure ##SUPPL##0##S15##, Supporting Information). These results indicate that BPGP@CAP could be efficiently ingested by MFC cells, and this uptake process is time‐dependent.</p>", "<p>To investigate the endocytic pathways of BPGP@CAP into MFC cells, flow cytometry was employed to detect the uptake of BPGP@CAP by MFC cells at a low temperature. The results show that the uptake of BPGP@CAP by MFC cells is significantly inhibited at an inhibition rate of 80.5%, indicating that the internalization of BPGP@CAP is an energy‐dependent process. Furthermore, upon incubating inhibitors with MFC cells, flow cytometry data demonstrate that chlorpromazine, genistein, and amiloride inhibit cellular uptake of BPGP@CAP by 70.2%, 65.4%, and 44.5% respectively. This suggests that clathrin‐mediated, caveolin‐mediated, and icropinocytosis‐mediated endocytic pathways may be involved in the uptake of BPGP@CAP (Figure ##FIG##3##3D##; Figure ##SUPPL##0##S16##, Supporting Information). Moreover, since the lysosomal cathepsin B can cleave the GFLG linker to release PTX,<sup>[</sup>\n##UREF##3##\n27\n##\n<sup>]</sup> we investigated whether BPGP@CAP would be transported to the lysosomes for degradation after cellular uptake. Through lysosomal colocalization experiments (Figure ##FIG##3##3B##), we observe a high overlapping level of the fluorescence signal for BPGP@CAP and lysosomes, suggesting BPGP@CAP may land at lysosomes before it is disintegrated by lysosomal cathepsin B. Combined with the findings from in vitro drug release experiments, it is confirmed that BPGP@CAP can be internalized by MFC cells and release drugs stimulated by lysosomal cathepsin B.</p>", "<title>The Toxicity of BPGP@CAP on MFC Cells</title>", "<p>To assess the toxicity of BPGP@CAP, we conducted CCK‐8 assays to measure the viability of MFC cells subjected to various treatment groups. The results indicate that after the treatment of BPGP@CAP, MFC cells viability significantly decreases. BPGP@CAP has an IC<sub>50</sub> of 0.253 µg mL<sup>−1</sup> in comparison to free PTX with an IC<sub>50</sub> of 2.51 µg mL<sup>−1</sup> and CAP with an IC<sub>50</sub> of 4.74 µg mL<sup>−1</sup>. Furthermore, the cell viability in the group with the treatment of BPGP@CAP is similar to that in the group treated with free PTX+CAP with an IC<sub>50</sub> of 0.43 µg mL<sup>−1</sup>, whereas the cell viability in the group treated with BPGP is comparable to that in the group exposed to free PTX, and the IC<sub>50</sub> value for BPGP and free PTX is 2.52 µg mL<sup>−1</sup> and 2.51 µg mL<sup>−1</sup>, respectively (Figure ##FIG##3##3E##). These findings suggest that BPGP@CAP could effectively release PTX and CAP after disintegration of the nanoassembly structure in the lysosomes, thus exerting an equivalent antitumor effect to a mixture of free PTX and CAP. Additionally, both the groups treated with BPGP@CAP and PTX + CAP exhibit a significantly higher cytotoxic effect on MFC cells than the groups exposed to BPGP and free PTX, indicating that the combination of CAP and PTX displays a synergistic action on MFC cells.</p>", "<p>Microtubules, which are essential cytoskeletal filaments within cells, have a critical function in mitosis and intracellular vesicle transport.<sup>[</sup>\n##REF##30536951##\n28\n##\n<sup>]</sup> It is well‐established that PTX can enhance the polymerization of microtubules, hinder depolymerization, and suppress mitosis of tumor cells.<sup>[</sup>\n##REF##24435445##\n29\n##\n<sup>]</sup> In order to assess the impact of PTX derived from BPGP@CAP on microtubules, we used CLSM to observe morphological changes of microtubules in the MFC cells after various treatments. Microtubules are evenly distributed in the cytoplasm of MFC cells in the control and CAP‐treated groups. However, pronounced aggregation of microtubules is found around the cell nucleus in the groups exposed to PTX and PTX+CAP. Similar morphological changes of microtubules are observed in the groups treated with BPGP and BPGP@CAP (Figure ##FIG##3##3F##). Furthermore, in the control and CAP‐treated groups, the nuclei of MFC cells appear intact, whereas an abnormal nuclear morphology and a multinucleated structure are found in the groups treated with PTX, PTX + CAP, BPGP and BPGP@CAP, indicating that PTX released from BPGP@CAP exerts a similar effect on microtubules as free PTX.</p>", "<p>Furthermore, microfilaments, which are composed of actin proteins, are integral constituents of the cellular cytoskeleton. Through CLSM, the influence of BPGP@CAP on microfilaments of MFC cells was examined. Our results indicate that actin aggregates into clusters or dots near the cell membrane in the BPGP@CAP‐treated group (Figure ##SUPPL##0##S17##, Supporting Information), leading to impaired microfilaments and reduced cell viability.</p>", "<p>Moreover, we utilized flow cytometry to evaluate the impact of BPGP@CAP on the apoptosis of MFC cells. The findings indicate that the percentage of apoptotic cells in the groups exposed to BPGP@CAP (23.8%), BPGP (15.7%), PTX (17.3%), and PTX+CAP (22.3%) is significantly higher than that in the control group (4.7%) (<bold>Figure</bold>\n##FIG##4##\n4A,C##). Additionally, no significant difference is found in the percentage of apoptotic cells between the groups exposed to BPGP@CAP and PTX + CAP. Furthermore, MFC cells have a significantly higher apoptotic percentage after treatment with BPGP@CAP and PTX + CAP than those treated with PTX and CAP, further supporting their synergistic action of inducting apoptosis of MFC cells.</p>", "<p>It is widely recognized that PTX exerts its effects on microtubules, causing inhibition of cell mitosis and resulting in G2/M cell cycle arrest.<sup>[</sup>\n##UREF##4##\n30\n##\n<sup>]</sup> We assessed the influence of PTX released from BPGP@CAP on the cell cycle distribution of MFC cells. As presented in Figure ##FIG##4##4B,D##, the percentages of cells in the G2/M phase in the groups treated with PTX (25.1%), BPGP (20.2%), PTX + CAP (27.8%), and BPGP@CAP (23.6%) are significantly higher than that in the control group (11.0%). Conversely, the proportions cells in the G0/G1 phase in the groups treated with PTX (43.9%), BPGP (52.2%), PTX + CAP (39.0%), and BPGP@CAP (39.6%) are significantly lower than that in the control group (76.6%). These findings support that PTX released from BPGP and BPGP@CAP can lead to cell cycle arrest in the G2/M phase. These results further confirm that BPGP@CAP can effectively releases PTX in the tumor cells, thereby displaying a similar antitumor mechanism of action as free PTX.</p>", "<title>Mechanism Study on the Synergistic Effect of PTX and CAP</title>", "<p>Our in vitro experimental results support the existence of a synergistic effect between PTX and CAP to eliminate MFC cells. To explore the underlying mechanisms behind this synergy, we conducted transcriptome sequencing on MFC cells exposed to BPGP@CAP and compared them with the control group. We detected 2799 differentially expressed genes (DEGs) between BPGP@CAP and control groups. Out of these DEGs, 1678 are upregulated and 1121 downregulated in the BPGP@CAP‐treated group (<bold>Figure</bold>\n##FIG##5##\n5A##; Figure ##SUPPL##0##S18##, Supporting Information). Subsequently, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was employed to uncover the biological pathways impacted by these DEGs. The results suggest that the pathways for apoptosis and PI3K/AKT signaling are significantly upregulated, which indicates that the mechanism underlying the synergistic antitumor effects of PTX and CAP in BPGP@CAP may be related to the PI3K/AKT signaling pathway and apoptosis (Figure ##FIG##5##5B##). It has been evidenced that the PI3K/AKT signaling pathway can regulate apoptosis by modulating the phosphorylation of Bax and Bad and the regulation of their expression levels, the release of cytochrome C, and the activation of caspase ‐ 3 and 9, thus affecting cell survival.<sup>[</sup>\n##REF##23881702##\n31\n##\n<sup>]</sup> Western blot results confirm that CAP inhibits the expression of the PI3K/AKT pathway‐related proteins such as AKT, p‐mTOR, p‐S6, and p‐4EBP1 (Figure ##FIG##5##5C##), indicating that CAP can suppress the PI3K/AKT signaling pathway.</p>", "<p>Furthermore, western blotting was employed to assess the expression of apoptosis‐related proteins, such as cleaved PARP, cleaved caspase‐3, Bax, and Bcl‐2, in various treatment groups. As showed in Figure ##FIG##5##5E,F##, the expression of Bax, cleaved caspase‐3, and cleaved PARP is upregulated in MFC cells after treatment with CAP, which might be credited to apoptosis after the inhibition of AKT. Furthermore, it is known that PTX can induce tumor cell apoptosis by downregulation of Bcl‐2 and upregulation of Bax and cleaved caspase‐3.<sup>[</sup>\n##REF##23735541##\n32\n##\n<sup>]</sup> Our results confirm that the expression levels of Bax, cleaved caspase‐3, and cleaved PARP were elevate, while Bcl‐2 is downregulated in the MFC cells with treatment of PTX and BPGP. In addition, when MFC was treated with the combination of free PTX and CAP or BPGP@CAP, more pronounced changes are observed in the expression of proteins including Bax, cleaved caspase −3, and cleaved PARP. Interestingly, western blot results reveal that the effect of CAP on downregulating the BCL‐2 protein expression is not pronounced as PTX, suggesting that the downregulation of Bcl‐2 may be predominantly induced by PTX, while no apparent correlation is seen between the downregulation of Bcl‐2 and the inhibition of AKT expression. However, the combination of PTX and CAP can induce more significant downregulation of Bcl‐2 compared to their individual effects, which is in agreement with a previous study.<sup>[</sup>\n##REF##32070411##\n26\n##\n<sup>]</sup> It may be explained by that CAP could significantly sensitize MFC cells to PTX‐induced apoptosis, resulting in more prominent downregulation of Bcl‐2.</p>", "<p>The combination of PTX with CAP exerts synergistic effects on MFC cells via the modulation of pro and anti‐apoptotic genes, such as downregulation of Bcl‐2 and upregulation of Bax, cleaved caspase‐3, and cleaved PARP. This could be the underlying mechanism for synergistic promotion of apoptosis by PTX and CAP (Figure ##FIG##5##5G##).</p>", "<title>Antitumor Effect of BPGP@CAP In Vivo</title>", "<title>\n<italic toggle=\"yes\">Distribution of BPGP@CAP</italic> In Vivo</title>", "<p>The accumulation of BPGP@CAP at the site of transplanted tumor plays a critical role in its antitumor efficacy in vivo. Mounting evidence has suggested that nanoparticles exhibit the enhanced permeability and retention (EPR) effect, which can extend the residence time and increase the concentration of drugs in tumors, thus achieving passive drug targeting of tumor cells.<sup>[</sup>\n##UREF##5##\n33\n##\n<sup>]</sup> The characterization results of BPGP@CAP indicate that it possesses a nanoscale size for the EPR effect. To confirm the accumulation of BPGP@CAP in tumor tissues via the EPR effect, we utilized a fluorescence imaging technique to evaluate the distribution of BPGP@CAP in the mice with MFC tumors. By administering Cy5‐labeled BPGP@CAP and free Cy5 intravenously to the tumor‐bearing nude mice, we assessed the distribution of BPGP@CAP at various time intervals using IVIS spectroscopy. The findings reveal that the fluorescence intensity of the tumor in the BPGP@CAP‐treated group is stronger than that in the free Cy5‐treated group as time elapses (<bold>Figure</bold>\n##FIG##6##\n6A##; Figure ##SUPPL##0##S19##, Supporting Information). Specifically, after 24 h, the fluorescence intensity of the tumor in the BPGP@CAP‐treated group still remains strong, while faint fluorescence signal is detected in the tumor of the free Cy5‐treated group. This indicates that BPGP@CAP can accumulate and retain in the tumor site for an extended period. Furthermore, tumor tissues were collected at 24 h post‐injection and visualized using CLSM. The images demonstrate that tumor tissues of the mice after the treatment of free Cy5 show undetectable fluorescence signal, whereas tumor tissues of the mice after the treatment of BPGP@CAP exhibit significantly strong fluorescence intensity (Figure ##FIG##6##6B##). The in vivo imaging results confirm the enrichment of BPGP@CAP in tumor tissues.</p>", "<p>Furthermore, pharmacokinetic analysis in vivo reveals a slower decrease in the Cy5 concentration in the blood of the mice exposed to BPGP@CAP compared to that in the group exposed to free Cy5, and the half‐life of BPGP@CAP and free Cy5 was 488.49 and 160.85 min, respectively (Figure ##FIG##6##6C##; Table ##SUPPL##0##S2##, Supporting Information). The results might be ascribed to a high molecular weight of BPGP@CAP and a prolonged circulation time which may help enhance passive accumulation of BPGP@CAP at the tumor site, thereby improving its therapeutic efficacy against tumors.</p>", "<title>Antitumor Effect of BPGP@CAP</title>", "<p>The mice, which were subcutaneously injected with MFC cells, were divided randomly into six groups, each consisting of 5 mice. The control group were given intravenous injections of saline, while the other groups were intravenously injected with PTX, CAP, PTX + CAP, BPGP, and BPGP@CAP, respectively. The concentrations of PTX remain consistent at 8 mg kg<sup>−1</sup> for each mouse. The treatment schedule is illustrated in Figure ##FIG##6##6D##. The volume of the transplanted tumor and the body weight of each treated mouse were regularly monitored and recorded. The results reveal that the control group has the fastest tumor growth rate, while the BPGP@CAP‐treated group displays the slowest tumor growth (Figure ##FIG##6##6E##). After the treatment, the tumor volume of the control group is 1.45, 1.67, 2.04, 2.48, and 4.13 times that of the group treated with PTX, CAP, PTX+CAP, BPGP, and BPGP@CAP, respectively. The tumor inhibition rates, based on tumor volume measurements, are found to be 31.0%, 40.1%, 51.0%, 59.7%, and 75.8% after treatment with PTX, CAP, PTX + CAP, BPGP, and BPGP@CAP, respectively. In addition, the tumor volumes in the groups with the treatment of free PTX and PTX + CAP are 2.85 times and 2.02 times that of the BPGP@CAP‐treated group, respectively (Figure ##FIG##6##6F##). The tumor volumes of the transplanted tumors harvested from each group are well aligned with those observed in vivo (Figure ##SUPPL##0##S20A##, Supporting Information). Comparison of the transplant tumor masses in the treatment groups reveals that the tumor mass harvested from the BPGP@CAP‐treated mice (0.28 g) is significantly lighter than that of the free control group (1.20 g), the PTX‐treated group (0.84 g), and the PTX + ACP‐treated group (0.57 g) (Figure ##FIG##6##6G##). The tumor inhibition rates, based on tumor mass measurements, are estimated to be 30.2%, 39.1%, 49.6%, 58.6%, and 75.7% for PTX, CAP, PTX + CAP, BPGP, and BPGP@CAP, respectively (Figure ##SUPPL##0##S20B##, Supporting Information). The tumor inhibition rates based on tumor mass measurements are similar to those based on tumor volume measurements in vivo for CAP and/or PTX‐derived formulations. The difference in the tumor inhibition rates among BPGP@CAP and other groups may result from a synergistic effect of PTX and CAP, enrichment of BPGP@CAP in tumor tissues and prolonged circulation in the blood through a nanoscale drug delivery system.</p>", "<p>The antitumor effect of BPGP@CAP was further verified by IHC analysis of tumor tissues. TUNEL assays of the harvested tumors indicate TUNEL‐positive tumor cells in the BPGP@CAP‐treated group are the most populous, confirming that the treatment of BPGP@CAP results in more apoptotic cells compared with other groups (Figure ##FIG##6##6I,J##). Furthermore, the mice treated with BPGP@CAP show a significant reduction in the population of Ki67‐positive tumor cells with comparison to the other groups. This observation suggests that the administration of BPGP@CAP leads to a remarkable suppression of tumor cell proliferation (Figure ##FIG##6##6I,J##), which confirms synergistic inhibition of tumor growth by both agents in vivo. These findings support the excellent anti‐tumor effect of BPGP@CAP.</p>", "<p>Additionally, while the administration of free PTX and PTX + CAP effectively suppresses the growth of transplanted tumors in the mice, it is accompanied by a decrease in the body weight ranging from 9.1% to 6.3% after each administration (Figure ##FIG##6##6H##). This indicates the presence of systemic toxicity associated with free PTX. In contrast, no significant changes in the body weight are found in the BPGP and BPGP@CAP‐treated groups, suggesting that the toxicity of PTX could be remarkably reduced after PTX is delivered via a polymer prodrug. In addition, we conducted H&amp;E staining on the major organs of the mice and analyzed the change of hematological parameters including white blood cells (WBC), red blood cells (RBC), platelets (PLT), alanine aminotransferase (ALT), aspartate aminotransferase (AST), blood urea nitrogen (BUN), and creatinine (CREA) to evaluate the toxicity of BPGP@CAP. The H&amp;E staining images indicate no significant alterations in the major organs, including the heart, liver, spleen, lung, and kidney, across all treatment groups (Figure ##SUPPL##0##S21##, Supporting Information). However, compared to the control group with a WBC count of 8.20×10<sup>9</sup>/L, the WBC count of the mice is found to be 3.19 × 10<sup>9</sup> per L, 3.28 × 10<sup>9</sup> per L, 5.76 × 10<sup>9</sup> per L and 5.69 × 10<sup>9</sup> per L in the group treated free PTX, PTX + CAP, BPGP, and BPGP@CAP, respectively. The most pronounced decreases in the WBC number are seen in the groups treated with PTX and PTX + CAP. Furthermore, when compared to the control group where the ALT level is 21.0 U L<sup>−1</sup>, there is no significant change in the ALT level in the BPGP+CAP‐treated group (22.0 U L<sup>−1</sup>), while a distinctive increase is seen in the PTX group (71.7 U L<sup>−1</sup>) and the PTX+CAP group (63.3 U L<sup>−1</sup>) (Figure ##SUPPL##0##S22##, Supporting Information). These results indicate that systemic administration of free PTX or PTX + CAP can cause hematopoietic system toxicity and liver toxicity, while the use of BPGP@CAP to deliver PTX and CAP can significantly reduce their toxicity.</p>" ]
[ "<title>Conclusions</title>", "<p>In this study, a cathepsin B‐responsive drug delivery system has been established for co‐delivery of PTX and CAP using controlled RAFT polymerization and efficient click chemistry, aiming to achieve a synergistic therapeutic outcome from the combine therapy of chemotherapy and targeted therapy for GC. The BPGP@CAP nanoassembly enables targeted delivery of both PTX and CAP into the tumor site through the EPR effect, and precise release of PTX and CAP from BPGP@CAP after intelligently responding to overexpressed cathepsin B in the lysosomes of tumor cells. The released CAP suppresses the expression of AKT and its downstream PI3K/AKT pathway, and it synergizes with the released PTX to exert an enhanced anti‐tumor effect. Meanwhile, the toxicity of PTX and CAP is significantly reduced after their delivery in this glycopolymer‐based drug delivery system. Therefore, this enzyme‐responsive nanomedicine based on glycopolymer prodrugs could be utilized for co‐delivery of multiple therapeutic agents, providing a novel approach for GC treatment.</p>" ]
[ "<title>Abstract</title>", "<p>Combined chemotherapy and targeted therapy holds immense potential in the management of advanced gastric cancer (GC). GC tissues exhibit an elevated expression level of protein kinase B (AKT), which contributes to disease progression and poor chemotherapeutic responsiveness. Inhibition of AKT expression through an AKT inhibitor, capivasertib (CAP), to enhance cytotoxicity of paclitaxel (PTX) toward GC cells is demonstrated in this study. A cathepsin B‐responsive polymeric nanoparticle prodrug system is employed for co‐delivery of PTX and CAP, resulting in a polymeric nano‐drug BPGP@CAP. The release of PTX and CAP is triggered in an environment with overexpressed cathepsin B upon lysosomal uptake of BPGP@CAP. A synergistic therapeutic effect of PTX and CAP on killing GC cells is confirmed by in vitro and in vivo experiments. Mechanistic investigations suggested that CAP may inhibit AKT expression, leading to suppression of the phosphoinositide 3‐kinase (PI3K)/AKT signaling pathway. Encouragingly, CAP can synergize with PTX to exert potent antitumor effects against GC after they are co‐delivered via a polymeric drug delivery system, and this delivery system helped reduce their toxic side effects, which provides an effective therapeutic strategy for treating GC.</p>", "<p>A cathepsin B‐responsive polymeric nanoparticle prodrug system is established for co‐delivery of paclitaxel (PTX) and capivasertib (CAP) to obtain BPGP@CAP, which selectively accumulates in the tumor tissue and releases PTX and CAP in response to overexpressed cathepsin B in lysosomes to exert a synergistic therapeutic effect to eradicate gastric cancer cells.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6766-cit-0060\">\n<string-name>\n<given-names>X.</given-names>\n<surname>Song</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Cai</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Shi</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Zheng</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>Q.</given-names>\n<surname>Gong</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Gu</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Hu</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Luo</surname>\n</string-name>, <article-title>Enzyme‐Responsive Branched Glycopolymer‐Based Nanoassembly for Co‐Delivery of Paclitaxel and Akt Inhibitor toward Synergistic Therapy of Gastric Cancer</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2306230</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202306230</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Materials</title>", "<p>CAP and PTX were obtained from Selleck Chemicals (Shanghai, China). Maleimide cyanine5 was acquired from Confluore Biotech CO. Ltd. (Xian, China). Chlorpromazine hydrochloride, amiloride hydrochloride, and dynasore were bought from APExBIO (Houston, USA). A terminal deoxynucleotidyl transferase‐mediated deoxyuridine triphosphate nick end labeling (TUNEL) Apoptosis Assay Kit was bought from Promega (Beijing, China). Hoechst 33342 and Cell Apoptosis Kit were purchased from Yeasen (Shanghai, China). Actin‐Tracker Green, Tubulin‐Tracker Red and Lyso‐Tracter Green were purchased from Beyotime (Shanghai, China). CCK‐8 was bought from MCE (Shanghai, China).</p>", "<title>Synthesis of LAEMA‐Based Branched Polymeric Prodrug</title>", "<p>\n<italic toggle=\"yes\">Synthesis of Poly (LAEMA)‐CTA</italic>: 4‐cyano‐4‐((phenylcarbonothioyl)thio)pentanoic acid (chain transfer agent, CTA) (18.6 mg, 66.7 µmol) and LAEMA (2001.6 mg, 4.275 mmol) were mixed within a small‐necked 25 mL flask. The flask was subjected to argon purging, and the process was repeated thrice. Under an ice bath condition, an initiator solution containing VA044 (7.2 mg, 22.2 µmol) in a solvent mixture of water and methanol (H<sub>2</sub>O/CH<sub>3</sub>OH = 3:2, 9.1 mL) was introduced into the flask via syringe injection. The reaction mixture was thereafter subjected to bubbling with a continuous stream of argon for a duration of 30 min. The flask was then placed in a light‐protected environment at 45 °C and the reaction continued for 20 h. After the polymerization was completed, the reaction was quenched using liquid nitrogen. The reaction mixture underwent dialysis against deionized water (MWCO 3500 Da) for 1.5 days and was subsequently freeze‐dried to yield the product poly (LAEMA)‐CTA with a 78% yield.</p>", "<p>\n<italic toggle=\"yes\">Synthesis of Branched Poly (LAEMA)‐GFLG‐PySS</italic>: To synthesize the branched polymer poly(LAEMA)‐GFLG‐PySS, poly(LAEMA)‐CTA (270 mg), a monomer MA‐PySS (29 mg, 113 µmol), LAEMA (107 mg, 229 µmol), and a crosslinker MA‐GFLG‐MA (15 mg, 26 µmol) were mixed in a small‐necked 5 mL round‐bottom flask. The flask was purged with argon gas three times. Under an ice bath condition, a solution containing the initiator, VA044 (1.62 mg), in a solvent mixture of water and dimethylformamide (H<sub>2</sub>O/DMF = 2:7, 1.9 mL) was introduced into the flask via syringe injection. The reaction mixture was continuously bubbled with argon for 30 min. The flask was then placed in a light‐protected environment at 45 °C and the reaction continued for 24 h. Upon completion of the reaction, the reaction was quenched using liquid nitrogen. The reaction mixture underwent dialysis against deionized water (MWCO 3500 Da) for a duration of 1.5 days, followed by freeze‐drying to obtain the final product, branched poly(LAEMA)‐GFLG‐PySS, with a yield of 67%.</p>", "<p>\n<italic toggle=\"yes\">Synthesis of Branched Poly(LAEMA)‐GFLG‐PTX</italic>: In a round‐bottom flask, 200 mg of branched poly(LAEMA)‐GFLG‐PySS was accurately weighed and dissolved in 8 mL of a mixture of DMSO:H<sub>2</sub>O (4:1, v/v). After complete dissolution, 30 mg of dithiothreitol (DTT) was introduced, and the reaction mixture underwent 12 h reaction at room temperature. Subsequently, the reaction mixture was subjected to dialysis to remove organic solvents, followed by freeze‐drying to yield the product, branched poly(LAEMA)‐GFLG‐SH.</p>", "<p>Branched poly (LAEMA)‐GFLG‐SH(146 mg) was carefully weighed and dissolved in 8 mL of a mixture of DMSO:H<sub>2</sub>O (4:1, v/v) in a round‐bottom flask. After complete dissolution, 1.4 mg of maleimide‐Cy5 dissolved in DMSO was added to the reaction mixture. The reaction proceeded overnight at room temperature. 48.7 mg of maleimide‐GFLG‐PTX was then introduced into the reaction mixture, and the reaction continued at room temperature for an additional 12 h. After the completion of the reaction, the mixture was sequentially dialyzed with DMF and deionized water (MWCO = 3500 Da). The resulting product was collected, filtered through a membrane, and subjected to freeze‐drying, resulting in the formation of branched poly(LAEMA<sup>Cy5</sup>)‐GFLG‐PTX. The drug loading of PTX in the polymer was determined through HPLC analysis.</p>", "<title>Physicochemical Characterizations of BPGP and BPGP@CAP</title>", "<p>The assessment of the CAC of BPGP was accomplished with the aid of pyrene as a fluorescence agent. Herein, 200 µL of a pyrene‐acetone solution (0.67 × 10<sup>−6</sup> <sc>m</sc>) was introduced into a 10 mL sample vial. After complete evaporation of acetone, an aliquot of the BPGP aqueous solution (ranging from 0.015 to 1000 µg mL<sup>−1</sup>) was added into the sample vial. After 2 h incubation, the fluorescence spectra were captured and recorded via a fluorescence spectrophotometer.</p>", "<p>The AKT inhibitor capivasertib ‐loaded branched poly(LAEMA<sup>Cy5</sup>)‐GFLG‐PTX was prepared using the solvent evaporation method. In brief, a methanol/acetonitrile mixed solution (0.4 mL) containing 1.125 mg of CAP was slowly added dropwise to a 5 mL aqueous solution of BPGP (2 mg mL<sup>−1</sup>, PTX:CAP = 1 (wt):1.5 (wt)) under stirring conditions. The mixture was stirred at room temperature until the organic solvents were completely evaporated. The remaining solution was then filtered through a membrane (0.45 µm) to remove unencapsulated CAP. Finally, the obtained filtrate was freeze‐dried to yield the desired product, BPGP@CAP. BPGP@CAP with different weight ratios of PTX and CAP was prepared by adjusting the weighting ratio of PTX and CAP. The loading contents of CAP in nanoassemblies were determined by HPLC system. The drug loading content (DLC) and the drug loading efficiency (DLE) were calculated using the following equations:</p>", "<p>DLC (wt.%) = (weight of drug loaded/total weight of polymer and loaded drug) × 100</p>", "<p>DLE (wt.%) = (weight of drug loaded/initial weight of drug) × 100</p>", "<p>The hydrodynamic diameter of the obtained nanoassemblies were measured by dynamic light scattering (DLS, Brookhaven ZetaPALS, USA). The morphology of the obtained nanoassemblies was examined under a transmission electron microscope (TEM, Tecnai GF20S‐TWIN, USA). The enzyme‐responsive drug release capacity of nanoassembly was investigated under simulated physiological conditions, with and without the presence of papain.</p>", "<title>Cell Line and Animals</title>", "<p>MFC cell, a cell line derived from GC, was acquired from the Chinese Academy of Medical Sciences (Shanghai, China), which were cultured in a temperature‐controlled incubator at 37 °C with 5% CO<sub>2</sub> in a humidified environment. Male BALB/c nude mice (4‐6 weeks old, weighing 18–20 g) were procured from Hfk Bioscience Co., Ltd (Beijing, China). Subcutaneous GC MFC tumor models were generated through injecting 5 × 10<sup>5</sup> MFC cells into the right back of the mice. Approval for all animal experiments was granted by the Animal Ethics Committee of West China Hospital, Sichuan University (Approval No. 2018154A).</p>", "<title>Clinical Tissue Sampling</title>", "<p>The AKT expression and its relationship was examined with the prognosis of GC using the Gene Expression Omnibus (GEO) (<ext-link xlink:href=\"https://www.ncbi.nlm.nih.gov/geo/\" ext-link-type=\"uri\">https://www.ncbi.nlm.nih.gov/geo/</ext-link>) cohort data via Kaplan‐Meier Plotter (<ext-link xlink:href=\"http://kmplot.com/analysis/index.php?p\" ext-link-type=\"uri\">http://kmplot.com/analysis/index.php?p</ext-link> = background). Tumor and normal tissues of 100 GC patients were collected from the West China Hospital of Sichuan University. IHC was employed for assessing the expression of AKT. Based on the IHC scores, 100 GC patients were categorized into high and low AKT expression groups. The Kaplan–Meier method was used for the survival curve of both groups. This study regarding clinical tissue sampling received approval from the Ethics Committee of The West China Hospital of Sichuan University (2023 Review, No. 549) and all patients provided informed consent for participation in the study.</p>", "<title>Cellular Uptake, Endocytic Pathways, and Subcellular Localization</title>", "<p>MFC cells were inoculated in a confocal chamber (1 × 10<sup>5</sup> cells per well) and incubated overnight. They were then incubated with culture medium containing Cy5‐labeled BPGP@CAP (Cy5: 0.5 µg mL<sup>−1</sup>) for 1, 2, and 4 h, respectively. Following washing with PBS, Hoechst 33342 was added for nucleus staining. Cellular uptake of BPGP@CAP by MFC cells was determined by analyzing the Cy5 signal using laser scanning confocal microscopy (CLSM) (Nikon, Tokyo, Japan). The mean fluorescence intensity was obtained from semi‐quantitative analysis using Image J software. Additionally, flow cytometry (BD FACSCelesta, New Jersey, USA) was employed for detecting cellular uptake of BPGP@CAP by analyzing the Cy5 signal in MFC cells treated with Cy5‐labeled BPGP@CAP for various durations (1 h, 2 h, and 4 h).</p>", "<p>To investigate the endocytic pathways of BPGP@CAP, MFC cells were pre‐treated with the culture medium containing 8 µg mL<sup>−1</sup> chlorpromazine hydrochloride, 0.5 m<sc>m</sc> amiloride hydrochloride or 0.5 m<sc>m</sc> dynasore for 2 h. Subsequently, those MFC cells was incubated with medium containing Cy5‐labeled BPGP@CAP (Cy5: 0.5 µg mL<sup>−1</sup>) for an additional 2 h. Quantitative analysis of cellular uptake of BPGP@CAP was conducted using flow cytometry. Furthermore, to determine if the cellular uptake of BPGP@CAP was relied on energy, cells were exposed in the culture medium with Cy5‐labeled BPGP@CAP (Cy5: 0.5 µg mL<sup>−1</sup>) and incubated at 4 °C for a duration of 2 h and flow cytometry was employed to check the uptake level of BPGP@CAP.</p>", "<p>For subcellular localization studies of BPGP@CAP, MFC cells were first exposed to Cy5‐labeled BPGP@CAP (Cy5: 0.5 µg mL<sup>−1</sup>) for 2 h. Following the staining of MFC cell lysosomes with Lyso Tracker Green and the nucleus with Hoechst 33342 for a duration of 15–20 min, observation and imaging of MFC cells were conducted using CLSM.</p>", "<title>Cell Cytotoxicity Assay</title>", "<p>After MFC cells were inoculated in 96‐well plates (3 × 10<sup>3</sup> cells per well) and grown overnight, MFC cells were exposed to various formulations (such as PTX, CAP, a mixture of PTX and CAP (PTX+CAP), BPGP, and BPGP@CAP) at different concentrations for 48 h. MFC cells treated with fresh culture medium were included as a control group. Following the treatment, those cells were exposed to a medium containing a 10% CCK‐8 solution and incubated at 37 °C for 1 h. A microplate reader (Tecan, Switzerland) was utilized to measure the OD450 value, which was then used to evaluate the relative cell viability.</p>", "<title>Cell Apoptosis and Cell Cycle Assay</title>", "<p>MFC cells were inoculated in a 6‐well plate with 2 × 10<sup>5</sup> cells per well and grown for 12 h. Subsequently, those cells were incubated with the culture medium containing PTX, CAP, PTX + CAP, BPGP, or BPGP@CAP (the PTX concentration: 2.0 µg mL<sup>−1</sup> and the corresponding concentration of CAP: 2.1 µg mL<sup>−1</sup>) for 48 h. MFC cells treated with fresh culture medium were included as a control group. Those cells were collected and stained with an Annexin V‐PI reagent for 30 min. Flow cytometry was employed for assessing apoptosis of MFC cells.</p>", "<p>For cell cycle assays, cells that received treatment with PTX, CAP, PTX + CAP, BPGP, or BPGP@CAP (the PTX concentration: 2.0 µg mL<sup>−1</sup> and the corresponding concentration of CAP: 2.1 µg mL<sup>−1</sup>) for a duration of 48 h were collected and subjected to overnight fixation in 75% ethanol. Following gentle washing with PBS, they were delicately incubated with a 0.5 mL solution of the PI/RNase dye. The flow cytometry was used to discern the cellular distribution at different cell cycle phases. Each experiment had three replicates, and the acquired data was analyzed through the Flowjo software.</p>", "<title>Morphological Examination of Microtubules and Microfilaments</title>", "<p>The culture medium containing PTX, CAP, PTX + CAP, BPGP, or BPGP@CAP was used to treat MFC cells for 24 h to examine the morphology of microtubules. Following washing with PBS, those MFC cells were fixed with a 4% paraformaldehyde solution. After washing with PBS containing 0.1% Triton X‐100, the cells were subjected to Tubulin‐tracker Red staining for 1 h. Subsequently, nucleus staining was performed with DAPI. The cells were then observed and imaged under CLSM. For morphological analysis of microfilaments, MFC cells were stained with Actin‐tracker Green and DAPI and they were then observed and imaged via CLSM.</p>", "<title>Transcriptome Analysis by RNA‐Seq</title>", "<p>MFC cells were inoculated in a 6‐well plate (2 × 10<sup>5</sup> cells per well) and grown for 12 h. Thereafter, they were exposed to BPGP@CAP (the PTX concentration: 2.0 µg mL<sup>−1</sup> and the corresponding concentration of CAP: 2.1 µg mL<sup>−1</sup>) for a duration of 48 h. MFC cells treated with fresh culture medium were included as a control group. Total RNA of MFC cells treated with BPGP@CAP in fresh culture medium was extracted. Genechem Co., Ltd (Shanghai, China) conducted the subsequent steps of quality control, library preparation, and RNA sequencing. Gene Ontology (GO) and KEGG pathway analyses were performed through the R package. Significant differences between the BPGP@CAP treatment group and the control cohort were robustly identified with a <italic toggle=\"yes\">p</italic>‐adjust &lt; 0.05 and a |log2FC| &gt; 1.</p>", "<title>Western Blots</title>", "<p>MFC cells were treated with PTX, CAP, PTX + CAP, BPGP, or BPGP@CAP (the PTX concentration: 2.0 µg mL<sup>−1</sup> and the corresponding concentration of CAP: 2.1 µg mL<sup>−1</sup>) for 48 h. Untreated MFC cells were set as a control group. After collecting the cells from each experimental group, total proteins were collected from cell lysates in a lysis buffer. Subsequently, they underwent SDS‐PAGE gel electrophoresis and were then transferred to a 0.45 µm PVDF membrane (Millipore). Following a blockade using a 5% milk TBST solution, the membrane was subjected to an overnight incubation with primary antibodies in a refrigerator at 4°C. After a thorough TBST wash, HRP‐conjugated secondary antibodies were applied to the membrane and incubated at room temperature for 1 h. Detection of the proteins was achieved through the Syngene GeneGenius gel imaging system (Syngene, Cambridge, UK).</p>", "<title>In Vivo Pharmacokinetics Studies</title>", "<p>Normal male balb/c nude mice were randomly allocated into two groups (n = 5) for intravenous administration of free Cy5 and Cy5‐labelled BPGP@CAP (Cy5: 1.5 mg kg<sup>−1</sup>). At various time points (0 min, 5 min, 15 min, 30 min, 1 h, 2 h, 4 h, 6 h, 8 h, 12 h, 16 h, and 24 h) after injection, blood samples were obtained from the orbital vein and immediately mixed with double distilled water. After the samples were then supplemented with DMSO and refrigerated overnight at 4 °C, they were centrifuged at 12 000 rpm for 15 min, and the supernatant from each sample was transferred to a 96‐well plate for fluorescence measurement using a microplate reader. The pharmacokinetic parameters were calculated using the PKsolver software.</p>", "<title>In Vivo Distribution</title>", "<p>The MFC tumor‐bearing nude mice (<italic toggle=\"yes\">n</italic> = 3) received intravenous injections via the tail with free Cy5 and Cy5‐labeled BPGP@CAP (Cy5: 1.5 mg kg<sup>−1</sup>) in order to assess their in vivo biodistribution. At various time points following the injection (1 h, 2 h, 3 h, 6 h, 9 h, 12 h, and 24 h), the mice were observed and imaged using an IVIS Spectrum (Caliper Life Sciences, Cambridge, UK). Upon completion of the imaging experiment, tumor samples from the mice were obtained and subjected to frozen sectioning. After staining with DAPI to label cell nuclei, the sections were observed and imaged using CLSM.</p>", "<title>In Vivo Anti‐Tumor Study</title>", "<p>The mice with MFC tumors received different formulations via tail vein injection (<italic toggle=\"yes\">n</italic> = 5): (1) Saline; (2) PTX; (3) CAP; (4) PTX + CAP; (5) BPGP; and (6) BPGP@CAP (the PTX concentration: 8.0 mg kg<sup>−1</sup> and the corresponding concentration of CAP: 8.5 mg kg<sup>−1</sup>). The drugs were administered every other day until the completion of the treatment. The body weight of the mice, the length (L) and width (W) of the tumor were regularly recorded. The tumor volume (V) was determined using the formula: V = (L × W<sup>2</sup>)/2.</p>", "<p>After the treatment, the mice were humanely euthanized by cervical dislocation, and their tumors were surgically excised and weighed. Furthermore, the tumors and vital organs underwent a process of fixation, embedding, and sectioning. The tumor sections were subjected to staining with Ki67 and TUNEL to evaluate proliferation and apoptosis of tumor cells. In addition, hematoxylin and eosin (H&amp;E) staining was performed to assess the biocompatibility of these formulations.</p>", "<p>Moreover, the biosafety of these formulations was evaluated in MFC tumor‐bearing nude mice. Hematological and biochemical analyses were conducted using collected whole blood and serum samples. Healthy balb/c nude mice were included as a control group for comparison.</p>", "<title>Statistical Analysis</title>", "<p>GraphPad Prism 9 software was employed to analyze data obtained from at least three independent measurements. The results were presented as the mean ± standard deviation (± S.D.). Statistical significance was determined by performing a two‐tailed t‐test between two groups, and a <italic toggle=\"yes\">P</italic>‐value less than 0.05 was considered to be statistically significant.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>X.S. and H.C. contributed equally to this work. This work was supported by National Natural Science Foundation of China (32271445, 52073193, 82072688, 82202322), 1·3·5 Project for Disciplines of Excellence, West China Hospital, Sichuan University (ZYJC21013, ZYJC21006) and the Sichuan Science and Technology Program (2023NSFSC1592). The authors also thank Li Li, Fei Chen, and Chunjuan Bao (institute of Clinical Pathology, West China Hospital) for their help in processing histological staining. The authors would like to thank Lei Wu and Yaping Wu (Histology and Imaging Platform, Research Core Facility, West China Hospital, Sichuan University) for their help in imaging studies. The authors also thank Qianyu Zhu (Laboratory of Gastric Cancer, West China Hospital, Sichuan University) for her help in data analysis. The authors also acknowledge Qiaorong Huang, Xue Li and Wentong Meng (Laboratory of Stem Cell Biology, West China Hospital, Sichuan University) for help in flow cytometer. Scheme ##FIG##0##1##, Figures ##FIG##5##5G## and ##FIG##6##6D## of contents entry were created with BioRender.com.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6766-fig-0007\"><label>Scheme 1</label><caption><p>Schematic illustration of enzyme‐responsive branched glycopolymer‐based nanoassembly (BPGP@CAP) for synergistic antitumor therapy. A branched poly(LAEMA)‐GFLG‐PTX prodrug self‐assembles through hydrophobic‐hydrophilic interactions and this prodrug encapsulates CAP as an AKT inhibitor to form a stable nanoassembly, BPGP@CAP. Through the enhanced permeability and retention (EPR) effect, BPGP@CAP selectively accumulates at tumor tissues. Within tumor cells, overexpressed cathepsin B triggers specific cleavage of the GFLG peptide in the polymer structure, leading to carrier degradation and concomitant drug release. The released PTX and CAP synergistically exhibit antitumor effects by inducing apoptosis.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6766-fig-0001\"><label>Figure 1</label><caption><p>Clinical significance of AKT in gastric cancer (GC). A) The RNA expression of AKT in GC samples and normal gastric tissues was analyzed by utilizing the GEO cohort data. B) Overall survival rates of GC patients with a high or low level of AKT expression were analyzed through Kaplan‐Meier analysis. C) The AKT expression detected by IHC in GC samples and normal gastric tissues obtained from West China Hospital. D) Kaplan–Meier analysis of overall survival rates of GC patients based on the AKT expression level using the West China Hospital cohort data. E) IHC analysis of AKT expression in GC samples treated with and without neoadjuvant therapy (NAC) in West China Hospital. F) Western blot results of AKT expression in MFC cells treated with PTX (1 µg mL<sup>‐1</sup>) and PTX (1 µg mL<sup>‐1</sup>) + CAP (1 µg mL<sup>‐1</sup>). G) Semiquantitative analysis of the AKT protein level in different groups in Figure ##FIG##1##1F##. H) Cytotoxicity of PTX, CAP, and PTX + CAP toward MFC cells. I) Combination index (CI) of CAP and PTX for treating MFC cells at different CAP/PTX weight ratios (<italic toggle=\"yes\">n</italic> = 5). Data is displayed as mean ± SD. A two‐sided unpaired Student's <italic toggle=\"yes\">t</italic>‐test was employed for assessing statistical significance, ***<italic toggle=\"yes\">p</italic> &lt; 0.001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6766-fig-0002\"><label>Figure 2</label><caption><p>Characterizations of physicochemical properties of BPGP and BPGP@CAP. A) <sup>1</sup>H NMR of the branched poly(LAEMA)‐GFLG‐PTX prodrug in DMSO‐<italic toggle=\"yes\">d6</italic>. B) UV–<italic toggle=\"yes\">vis</italic> and fluorescence spectra of the branched poly(LAEMA)‐GFLG‐PTX prodrug (dissolved in DMSO) with or without Cy5 labeling. The characteristic UV–vis absorption peak of Cy5 appears at 648 nm, and the fluorescence characteristic peak at 667 nm (Ex = 647 nm). C) CAC of the branched poly(LAEMA)‐GFLG‐PTX prodrug. D) The drug loading content (DLC) and the drug loading efficiency (DLE) of CAP in BPGP at various weight ratios of PTX to CAP. E,F) Hydrodynamic diameters and representative TEM images of BPGP and BPGP@CAP, respectively. Scale bars = 100 nm. G) HPLC chromatograms of poly (LAEMA)‐GFLG‐PTX with or without papain, and free PTX as a control.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6766-fig-0003\"><label>Figure 3</label><caption><p>Cellular uptake and cytotoxicity of BPGP@CAP in vitro. A) CLSM images of MFC cells exposed to Cy5‐labelled BPGP@CAP (red: Cy5; blue: nuclei). Scale bar = 20 µm. B) Colocalization of lysosomes and BPGP@CAP in MFC cells. Lyso‐Tracker was used to label and visualize the lysosomes (green), while Hoechst 33342 was employed to stain the nuclei (blue). Scale bar = 20 µm. C) Mean fluorescence intensity (MFI) of MFC cells after exposure to Cy5‐labelled BPGP@CAP for 1 h, 2 h, and 4 h from flow cytometry analysis. D) The inhibitory rate of cellular uptake of BPGP@CAP by MFC cells treated with different inhibitors or at a low temperature. E) Viabilities of MFC cells after treatment with PTX, CAP, PTX + CAP, BPGP and BPGP@CAP. F) Microtubule aggregation in MFC cells induced by various treatments for 24 h. Tubulin Tracker was utilized to stain and detect tubulin (red), while DAPI was employed for staining the nuclei (blue). Scale bar = 20 µm.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6766-fig-0004\"><label>Figure 4</label><caption><p>Analysis of apoptosis and cell cycle arrest in MFC cells after exposure to various treatments through flow cytometry. A,C) Percentages of apoptotic MFC cells after exposure to PTX, CAP, PTX + CAP, BPGP, and BPGP@CAP for 48 h (<italic toggle=\"yes\">n</italic> = 3). B,D) Cell cycle distribution of MFC cells after exposure to PTX, CAP, PTX + CAP, BPGP and BPGP@CAP for 48 h (<italic toggle=\"yes\">n</italic> = 3). Data is displayed as mean ± SD. A two‐sided unpaired Student's <italic toggle=\"yes\">t</italic>‐test was employed for assessing statistical significance, **<italic toggle=\"yes\">p</italic> &lt; 0.01, ***<italic toggle=\"yes\">p</italic> &lt; 0.001 and ns for <italic toggle=\"yes\">p</italic> &gt; 0.05.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6766-fig-0005\"><label>Figure 5</label><caption><p>Mechanisms underlying synergistic effect of PTX and CAP for anticancer treatment. A) Volcano plots of DEGs in BPGP@CAP‐treated MFC cells compared with the control group. B) Top 20 enriched KEGG pathways from DEGs in MFC cells exposed to BPGP@CAP compared to the control cells. C, D) Western blotting analysis of proteins associated with the PI3K/AKT signal pathway in MFC cells treated with CAP, including AKT, p‐mTOR, p‐4E‐BP1, and p‐S6. The proteins in the control group are significantly lower than those in the groups treated with CAP at 0.3 µg mL<sup>‐1</sup> and 1.0 µg mL<sup>‐1</sup>, and the P‐values are less than 0.001. E,F) Western blot results of proteins associated with apoptosis in MFC cells after exposure to PTX, CAP, PTX + CAP, BPGP, and BPGP@CAP, including Bax, Bcl‐2, cleaved‐caspase‐3 and cleavedPARP. The proteins in the control group are significantly lower than those in the groups treated with PTX, CAP, PTX + CAP, BPGP, and BPGP@CAP, and the P‐values are less than 0.001. G) Schematic diagram for the mechanisms for the anticancer effect by the combine therapy with PTX and CAP against GC. Data were displayed as mean ± SD. A two‐sided unpaired Student's <italic toggle=\"yes\">t</italic>‐test was employed for assessing statistical significance, ***<italic toggle=\"yes\">p</italic> &lt; 0.001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6766-fig-0006\"><label>Figure 6</label><caption><p>Biodistribution and tumor growth inhibition of BPGP@CAP in vivo. A) Fluorescent images of the mice with MFC tumors exposed to Cy5‐labelled BPGP@CAP and free Cy5 at different time‐points. B) Immunofluorescence staining images of tumor tissues obtained from the mice treated with free Cy5 and Cy5‐labelled BPGP@CAP for 24 h. Red for Cy5‐labeled BPGP@CAP or free Cy5, and blue for DAPI‐stained cell nuclei. Scale bar = 100 µm. C) Pharmacokinetic curves of the Cy5 concentration after intravenous injection of Cy5‐labelled BPGP@CAP and free Cy5, respectively (<italic toggle=\"yes\">n</italic> = 5). D) Establishment of subcutaneous GC MFC tumor models and therapeutic treatment schedule. E) Growth curves of the tumors in individual mice across different treatment groups (<italic toggle=\"yes\">n</italic> = 5). F) Average tumor growth curves in different treatments groups (<italic toggle=\"yes\">n</italic> = 5). G) Tumor weights of the mice with tumors in different treatment groups (<italic toggle=\"yes\">n</italic> = 5). H) Body weights of the mice with tumors after different treatments (<italic toggle=\"yes\">n</italic> = 5). The statistical difference is obtained from the body weights of the BPGP@CAP‐treated group in comparison with those of the PTX‐treated group and the PTX+CAP‐treated group. I) H&amp;E, TUNEL and Ki67 staining images for tumor tissues from the mice after different treatments (scale bar = 100 µm). J) The proportion of TUNEL and Ki67‐positive cells in the tumors after different treatments. The proportion of TUNEL and Ki67‐positive cells of the BPGP@CAP‐treated group is compared with that in the control group, the PTX‐treated group and the PTX+CAP‐treated group. Data are displayed as mean ± SD. A two‐sided unpaired Student's t‐test was employed for assessing statistical significance, ***<italic toggle=\"yes\">p</italic> &lt; 0.001.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6766-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2306230-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
33
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2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 12; 11(2):2306230
oa_package/10/ac/PMC10787093.tar.gz
PMC10787094
37964412
[ "<title>Introduction</title>", "<p>Over the past few decades, significant efforts have been devoted to developing advanced energy storage devices and new renewable energy sources to cope with the fossil energy crisis and environmental problems. Since the C║LiCoO<sub>2</sub> battery was commercialized by Sony in 1991,<sup>[</sup>\n##REF##11713543##\n1\n##\n<sup>]</sup> lithium‐ion batteries (LIBs) have been used in a wide range of portable electronic devices, hybrid and full electric vehicles and other energy‐storing devices because of their high energy density, long cyclability, low self‐discharge and absence of memory effect.<sup>[</sup>\n##UREF##0##\n2\n##, ##REF##23584142##\n3\n##\n<sup>]</sup> Reducing greenhouse gas emission has now become global consensus in response to the greenhouse effect. For example, in October 2021 the Chinese government has proposed the goals of peak carbon dioxide emissions and carbon neutrality which will be achieved in 2030 and 2060, respectively. In this context, there is no doubt that the new energy technology is inevitable to achieve carbon peak and carbon neutrality. Thus, as a representative of clean energy storage devices, LIBs stand for an ideal candidate due to high energy density, low cost, safety, and environmental sustainability, which are of particular importance.</p>", "<p>LIBs are mainly made of cathode, separator, electrolyte and anode, where the cathode limits the energy density and dominates the final cost of the battery.<sup>[</sup>\n##REF##32214093##\n4\n##, ##UREF##1##\n5\n##, ##UREF##2##\n6\n##\n<sup>]</sup> Up to now, three main types of cathode materials have been commercialized, including layered lithium transition metal oxide LiTMO<sub>2</sub> (TM = Co, Ni, Mn), spinel LiMn<sub>2</sub>O<sub>4</sub>, and olivine‐structure lithium iron phosphate LiFePO<sub>4</sub> (<bold>Figure</bold>\n##FIG##0##\n1a##).<sup>[</sup>\n##REF##24202440##\n7\n##, ##UREF##3##\n8\n##\n<sup>]</sup> In terms of cathode materials, metal elements play an essential role in the advancement of energy storage. As shown in Figure ##FIG##0##1b##, the crustal content of common metals is provided, including nickel (Ni), cobalt (Co), iron (Fe), aluminum (Al) and manganese (Mn), which is related to the cost of batteries. To better compare the characteristics of the state‐of‐the‐art cathodes that are being used in industry today (LiCoO<sub>2</sub>, LiNi<sub>0.33</sub>Co<sub>0.33</sub>Mn<sub>0.33</sub>O<sub>2</sub>, LiNi<sub>0.80</sub>Co<sub>0.15</sub>Al<sub>0.05</sub>O<sub>2</sub>, LiMn<sub>2</sub>O<sub>4</sub>, LiN<sub>i0.5</sub>Mn<sub>1.5</sub>O<sub>4</sub>, LiFePO<sub>4</sub>), Figure ##FIG##0##1c–i## provides the specific parameters of them.<sup>[</sup>\n##REF##34705441##\n9\n##, ##REF##29956705##\n10\n##, ##UREF##4##\n11\n##, ##UREF##5##\n12\n##, ##UREF##6##\n13\n##, ##UREF##7##\n14\n##, ##UREF##8##\n15\n##, ##UREF##9##\n16\n##\n<sup>]</sup>\n</p>", "<p>LiCoO<sub>2</sub> was successfully developed by Goodenough in the 1980s,<sup>[</sup>\n##UREF##10##\n17\n##\n<sup>]</sup> which became the typical layered cathode material and remained the dominant cathode material for the portable electronics market. However, it can be seen that the content of Co is the lowest among above mentioned metals, leading to high cost. Additionally, toxicity and its adverse effects on the environment will be a major constraint on its development.<sup>[</sup>\n##UREF##11##\n18\n##\n<sup>]</sup> Thus, Ni‐layered oxides mixed Co and Mn emerge as the time requires. LiNi<sub>0.80</sub>Co<sub>0.15</sub>Mn<sub>0.05</sub> has an energy density of 760 kw kg<sup>−1</sup> at 4.3 V thanks to the high nickel fraction.<sup>[</sup>\n##UREF##12##\n19\n##\n<sup>]</sup> Nevertheless, A high nickel fraction would promote the cation disorder, resulting in the collapse of the crystal structure and the release of oxygen during the process of cycling.<sup>[</sup>\n##UREF##13##\n20\n##\n<sup>]</sup> That is, although the cost of nickel is lower than that of Co, the low safety of ternary cathode materials mainly caused by the metal Ni cannot be ignored.<sup>[</sup>\n##UREF##14##\n21\n##, ##UREF##15##\n22\n##, ##UREF##16##\n23\n##\n<sup>]</sup>\n</p>", "<p>Therefore, iron and manganese demonstrate great promise for cathode materials owing to their non‐toxicity, abundant resources, and low cost. And from a sustainability perspective, Mn‐based cathodes and LiFePO<sub>4</sub> demonstrate an attractive prospect. Here it should be noted that the sustainability of materials is rated in terms of supply‐demand relations, mining technologies, environmental impacts, waste management, etc,<sup>[</sup>\n##UREF##17##\n24\n##\n<sup>]</sup> and value 5 for sustainability in Figure ##FIG##0##1c## represents the highest level. LiFePO<sub>4</sub> is commonly used in commercial electric vehicles owing to its high level of thermal stability and safety.<sup>[</sup>\n##UREF##18##\n25\n##\n<sup>]</sup> However, the theoretical capacity of olivine LiFePO<sub>4</sub> (170 mAh g<sup>−1</sup>) is significantly lower than that of other cathode materials (LiCoO<sub>2</sub>: 274 mAh g<sup>−1</sup>, LiNi<sub>1−</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">\n<sub>y</sub>\n</italic>Co<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Mn<italic toggle=\"yes\">\n<sub>y</sub>\n</italic>O<sub>2</sub>: 273—285 mAh g<sup>−1</sup>). Moreover, compared with the theoretical density of LiCoO<sub>2</sub>, LiNiO<sub>2</sub>, and LiMn<sub>2</sub>O<sub>4</sub> (5.1, 4.8, 4.2 g cm<sup>−3</sup>, respectively), LiFePO<sub>4</sub> shows much lower theoretical density (3.6 g cm<sup>−3</sup>), which gives a seriously adverse effect on the energy density and specific capacity.<sup>[</sup>\n##UREF##19##\n26\n##\n<sup>]</sup> Meanwhile, LiFePO<sub>4</sub> has poor electronic conductivity and ionic conductivity, leading to initial capacity loss.<sup>[</sup>\n##UREF##20##\n27\n##\n<sup>]</sup> Recently, Co‐free high‐voltage spinel LiN<sub>i0.5</sub>Mn<sub>1.5</sub>O<sub>4</sub> has attracted attention due to its high operating voltage of 4.7 V (vs Li/Li<sup>+</sup>). However, high voltage brings about rapid capacity degradation and the decomposition of electrolytes.<sup>[</sup>\n##UREF##21##\n28\n##, ##UREF##22##\n29\n##, ##UREF##23##\n30\n##\n<sup>]</sup> Hence, manganese‐based cathodes have lately received great attention for the development of Co‐free cathode materials.<sup>[</sup>\n##UREF##24##\n31\n##\n<sup>]</sup> Compared with LiMn<sub>2</sub>O<sub>4</sub> (148 mAh g<sup>−1</sup>), LiMnO<sub>2</sub> possesses a higher theoretical capacity (285 mAh g<sup>−1</sup>).</p>", "<p>As early as 2001, Ammundsen and Paulsen reviewed the progress of LiMnO<sub>2</sub>.<sup>[</sup>\n##UREF##25##\n32\n##\n<sup>]</sup> In the past two decades, more researchers have extensively investigated LiMnO<sub>2</sub> cathode, especially in terms of synthesis methods and modification manners. To get a more comprehensive understanding of LiMnO<sub>2</sub> cathode, we deliver the review. This review is organized as follows. Firstly, in Section <xref rid=\"advs6796-sec-0020\" ref-type=\"sec\">2</xref>, the structural characteristics and drawbacks of LiMnO<sub>2</sub> cathode are presented, as well as the synthesis methods discussed briefly. To improve the weaknesses of LiMnO<sub>2</sub>, modifications like element doping, surface coating, composites designing and finding compatible electrolyte are reviewed in Section <xref rid=\"advs6796-sec-0060\" ref-type=\"sec\">3</xref>. Finally, we describe our conclusions with an outlook for LiMnO<sub>2</sub> cathode in Section <xref rid=\"advs6796-sec-0180\" ref-type=\"sec\">4</xref>.</p>" ]
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[ "<title>Conclusion and Outlook</title>", "<p>It has been 30 years since the commercialization of LIBs in 1991, and seeking for electrodes of low cost, high energy density, high safety and long life is always the primary aim to develop new‐generation LIBs in the future.</p>", "<p>Facing resource depletion and the quest for non‐toxic green resources, lithium manganese oxide as a cathode material shows highly favorable advantages. Previous studies have shown that elemental doping is a good way to keep the LiMnO<sub>2</sub> layers in place by suppressing phase transitions caused by the J–T effect due to high spin Mn<sup>3+</sup>. But it is not even close to commercialization because the charge/discharge mostly remains ≈50 cycles, especially for onefold doping. For another thing, surface coating is another effective approach to resolve the Mn dissolution and improve the cycling stability of LiMnO<sub>2</sub>, however, it also suffers from the complex procedures during coating and electrochemical‐inert coating layers that decrease the capacity of LiMnO<sub>2</sub>.</p>", "<p>Thus, further efforts are still required to address the key issues and make commercialization achievable for LiMnO<sub>2</sub>. Special attention needs to be paid to the following aspects such as design of Li‐rich lithium manganese oxides, multi‐functional coating layers and new liquid electrolytes to achieve higher energy and more stable performance. Meanwhile, from the viewpoint of practical application with high sustainability, all‐solid‐state batteries systems with LiMnO<sub>2</sub> as cathodes should be further exploited and the repairing/recycling techniques of spent LiMnO<sub>2</sub> are necessary to carry forward.\n<list list-type=\"simple\" id=\"advs6796-list-0001\"><list-item><label>1)</label><p>In the LiTMO<sub>2</sub> family, Li‐rich lithium manganese oxides (like Li<sub>1+</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>TM<sub>1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>O<sub>2</sub>) with the disorder‐rocksalt structure are a class of cathode materials that can deliver ultrahigh capacity (&gt; 300 mAh g<sup>−1</sup>) and energy density (&gt;1000 Wh kg<sup>−1</sup>). It is aspired that effective methods could be developed for the controlled preparation of Li‐rich lithium manganese oxides to meet the request in the area of high‐energy applications.</p></list-item><list-item><label>2)</label><p>It is highly desirable to construct multi‐functional coating layers with excellent mechanical stability to avoid Mn dissolution and side reactions, electrochemical activity to contribute capacity and electronic/ionic conductivity to facilitate charge transfer, which needs to design composite coating layers with elaborate element combinations other than traditional ones.</p></list-item><list-item><label>3)</label><p>To reduce side reactions of LiMnO<sub>2</sub> with electrolyte solution and Mn dissolution at most, the design and development of new electrolytes matching LiMnO<sub>2</sub> cathodes is also a good solution.</p></list-item><list-item><label>4)</label><p>All‐solid‐state batteries feature high energy density and high safety. LiMnO<sub>2</sub>‐based all‐solid‐state batteries are deemed to eliminate the problem of Mn dissolution and to deliver higher energy density. However, LiMnO<sub>2</sub>‐based all‐solid‐state batteries have been seldomly reported, which should be paid special attention to and developed as a priority for purpose of practical applications.</p></list-item><list-item><label>5)</label><p>The resource shortage of lithium has raised the price of raw materials of cathode materials as well as the cost of batteries. Therefore, to address the concern in cost as well as the environment, the repairing and recycling techniques are urgent for spent LiMnO<sub>2</sub> cathode materials.</p></list-item></list>\n</p>" ]
[ "<title>Abstract</title>", "<p>Lithium manganese oxides are considered as promising cathodes for lithium‐ion batteries due to their low cost and available resources. Layered LiMnO<sub>2</sub> with orthorhombic or monoclinic structure has attracted tremendous interest thanks to its ultrahigh theoretical capacity (285 mAh g<sup>−1</sup>) that almost doubles that of commercialized spinel LiMn<sub>2</sub>O<sub>4</sub> (148 mAh g<sup>−1</sup>). However, LiMnO<sub>2</sub> undergoes phase transition to spinel upon cycling cause by the Jahn‐Teller effect of the high‐spin Mn<sup>3+</sup>. In addition, soluble Mn<sup>2+</sup> generates from the disproportionation of Mn<sup>3+</sup> and oxygen release during electrochemical processes may cause poor cycle performance. To address the critical issues, tremendous efforts have been made. This paper provides a general review of layered LiMnO<sub>2</sub> materials including their crystal structures, synthesis methods, structural/elemental modifications, and electrochemical performance. In brief, first the crystal structures of LiMnO<sub>2</sub> and synthetic methods have been summarized. Subsequently, modification strategies for improving electrochemical performance are comprehensively reviewed, including element doping to suppress its phase transition, surface coating to resist manganese dissolution into the electrolyte and impede surface reactions, designing LiMnO<sub>2</sub> composites to improve electronic conductivity and Li<sup>+</sup> diffusion, and finding compatible electrolytes to enhance safety. At last, future efforts on the research frontier and practical application of LiMnO<sub>2</sub> have been discussed.</p>", "<p>A LiMnO<sub>2</sub> cathode with high theoretical capacity shows great commercial value due to its low price and nontoxicity. This review summarizes the overall progress and challenges of LiMnO<sub>2</sub>, focusing on crystallographic structures, synthesis and modifications like element doping, surface coating, composites designing, and electrolytes matching for electrochemical performance improvement. Future perspectives on the research frontier and practical application are also discussed.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6796-cit-0158\">\n<string-name>\n<given-names>J.</given-names>\n<surname>Ma</surname>\n</string-name>, <string-name>\n<given-names>T.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Ma</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Yang</surname>\n</string-name>, <article-title>Progress, Challenge, and Prospect of LiMnO<sub>2</sub>: An Adventure toward High‐Energy and Low‐Cost Li‐Ion Batteries</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304938</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304938</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>LiMnO<sub>2</sub>\n</title>", "<title>Crystal Structure and Comparison</title>", "<p>Layered LiMnO<sub>2</sub> and spinel LiMn<sub>2</sub>O<sub>4</sub> are two typical manganese‐based cathodes. The spinel LiMn<sub>2</sub>O<sub>4</sub> belongs to the space group <mml:math id=\"jats-math-1\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>F</mml:mi><mml:mi>d</mml:mi><mml:mover accent=\"true\"><mml:mn>3</mml:mn><mml:mo>¯</mml:mo></mml:mover><mml:mi>m</mml:mi></mml:mrow></mml:mrow></mml:math>, where Li cations occupy the 8a site in 1/8 of the tetrahedron, Mn cations fill in the 16d site in 1/2 of the octahedral void, and O anions arranged by face‐centered cubes (FCC) lie in the 32e site (<bold>Figure</bold>\n##FIG##1##\n2a##).<sup>[</sup>\n##UREF##26##\n33\n##\n<sup>]</sup> In this structure, unoccupied oxygen tetrahedra and oxygen octahedra are connected in a shared plane and line, which forms 3D interconnected channels for the diffusion of Li<sup>+</sup>.<sup>[</sup>\n##UREF##27##\n34\n##\n<sup>]</sup> While layered LiMnO<sub>2</sub> is a polymorphous compound including two quintessentially crystallographic structure (Figure ##FIG##1##2b and c##) and a cation disordered rocksalt polymorph (Figure ##FIG##1##2d##).<sup>[</sup>\n##UREF##1##\n5\n##, ##UREF##28##\n35\n##\n<sup>]</sup> The orthorhombic LiMnO<sub>2</sub> (referred to as o‐LiMnO<sub>2</sub> in the following) having β‐NaMnO<sub>2</sub>‐like structures belongs to Pmnm space group (a = 0.2805 nm; b = 0.5757 nm; c = 0.4572 nm; Z = 2). In the crystal with a close‐packed oxygen lattice, all MnO<sub>6</sub> octahedra shares a common edge with each other,<sup>[</sup>\n##UREF##29##\n36\n##\n<sup>]</sup> as well as MnO<sub>6</sub> and LiO<sub>6</sub> are arranged in a corrugated interaction. The monoclinic LiMnO<sub>2</sub> (herein referred to as m‐LiMnO<sub>2</sub>) is equipped with a structure of α‐NaFeO<sub>2</sub> type, which belongs to the C2/m space group (a = 0.5439 nm; b = 0.2809 nm; c = 0.5395 nm; Z = 2), similar to LiCoO<sub>2</sub> and LiNiO<sub>2</sub>.<sup>[</sup>\n##UREF##30##\n37\n##\n<sup>]</sup> It can also be said that Li and Mn cations alternate to form zigzag layers along the (010) in o‐LiMnO<sub>2</sub>. Different from o‐LiMnO<sub>2</sub>, the Li and Mn cations of m‐LiMnO<sub>2</sub> occupy octahedral site layers that are parallel to the (111) plane of the cubic oxygen sublattice.<sup>[</sup>\n##UREF##31##\n38\n##\n<sup>]</sup> Consequently, Li cations fill in tetrahedral sites and Mn cations are in octahedral sites of the spinel LiMn<sub>2</sub>O<sub>4</sub>, while both Mn and Li cations occupy octahedral sites in the layered structure.<sup>[</sup>\n##REF##15669161##\n39\n##\n<sup>]</sup>\n</p>", "<p>Additionally, Yabuuchi et al. designed a cation‐disordered rocksalt‐type LiMnO<sub>2</sub> by mechanical milling o‐LiMnO<sub>2</sub>. RIETAN‐FP (a software for crystal structure refinement) was used to analyze the structure of the samples before and after milling. The results show that o‐LiMnO<sub>2</sub> is in a zigzag‐type layered structure with a high crystallinity. Whereas the sample lacks the structural features embodied in o‐LiMnO<sub>2</sub> after mechanical milling. Meanwhile, the broad diffraction peaks of X‐ray diffraction (XRD) patterns suggest that the zigzag‐type structure of o‐LiMnO<sub>2</sub> transforms into the cation‐disordered rocksalt phase.<sup>[</sup>\n##UREF##1##\n5\n##\n<sup>]</sup>\n</p>", "<title>Challenges that LiMnO<sub>2</sub> Faced</title>", "<p>Unfortunately, commercial applications of layered LiMnO<sub>2</sub> have been plagued by the following problems. The Mn cations in LiMnO<sub>2</sub> all present as Mn<sup>3+</sup>.<sup>[</sup>\n##UREF##32##\n40\n##\n<sup>]</sup> Three electrons in the d orbitals of high‐spin Mn<sup>3+</sup> stay in the t<sub>2g</sub> orbital with the same spin, and only one electron occupies an e<sub>g</sub> orbital. It is important to note that e<sub>g</sub> orbitals with <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>d</mml:mi><mml:msup><mml:mi>x</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mo>−</mml:mo></mml:mrow></mml:msup></mml:msub><mml:msub><mml:mi>d</mml:mi><mml:msup><mml:mi>y</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:msub><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>and <mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:msub><mml:mi>d</mml:mi><mml:msup><mml:mi>z</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:msub></mml:mrow></mml:math> are doubly degenerate orbitals obtained by splitting 3d orbitals (<bold>Figure</bold>\n##FIG##2##\n3a##). Consequently, this t<sub>2g</sub>\n<sup>3</sup>e<sub>g</sub>\n<sup>1</sup> electronic configuration of Mn<sup>3+</sup> results in the asymmetric occupation of e<sub>g</sub> orbitals. Meanwhile, the electrons in the <mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>d</mml:mi><mml:msup><mml:mi>x</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mo>−</mml:mo></mml:mrow></mml:msup></mml:msub><mml:msub><mml:mi>d</mml:mi><mml:msup><mml:mi>y</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:msub><mml:mspace width=\"0.33em\"/></mml:mrow></mml:mrow></mml:math>and <mml:math id=\"jats-math-5\" display=\"inline\"><mml:mrow><mml:msub><mml:mi>d</mml:mi><mml:msup><mml:mi>z</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:msub></mml:mrow></mml:math> orbitals exhibit shielding for the Mn nucleus to varying degrees in different directions, resulting in an unstable state of central Mn<sup>3+</sup>. In order to maintain the stability of Mn<sup>3+</sup>, the two longitudinal Mn‐O bonds are gradually elongated, accompanying the shrinkage of the other four horizontal Mn‐O bonds (Figure ##FIG##2##3b##). In this case, the symmetry of MnO<sub>6</sub> octahedron changes from O<sub>h</sub> to D<sub>4h</sub>, giving rise to the Jahn–Teller (J–T) distortion.<sup>[</sup>\n##UREF##33##\n41\n##, ##UREF##34##\n42\n##, ##UREF##35##\n43\n##\n<sup>]</sup> Simultaneously, the volume change from the cubic to tetragonal coordination results in the structural degradation of LiMnO<sub>2</sub>. Figure ##FIG##2##3c## illustrates the changes in XRD patterns of the o‐LiMnO<sub>2</sub> electrodes after different cycles. The intensity of the o‐LiMnO<sub>2</sub> peak gradually decreases with the progress of the cycle and some new peaks appear. After three cycles, there are no o‐LiMnO<sub>2</sub> peaks in the XRD patterns, which provides compelling evidence that J–T distortion triggers the rapid structure transformation from layered into the spinel or the rock salt upon cycling.<sup>[</sup>\n##REF##34073268##\n44\n##, ##UREF##36##\n45\n##\n<sup>]</sup> It was confirmed by in situ X‐ray studies that o‐LiMnO<sub>2</sub> was irreversibly converted to spinel structure.<sup>[</sup>\n##UREF##37##\n46\n##\n<sup>]</sup> In addition, high stacking faults induced by structural disorder at Li/Mn sites are more likely to lead to phase transformation to a spinel‐like structure and display capacity fading in 3 V.<sup>[</sup>\n##UREF##38##\n47\n##\n<sup>]</sup> According to the study by Lu et al.,<sup>[</sup>\n##UREF##39##\n48\n##\n<sup>]</sup> additional plateau in the discharging curves (4.0 V) indicated spinel phase Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Mn<sub>2</sub>O<sub>4</sub> was formed from o‐LiMnO<sub>2</sub> (Figure ##FIG##2##3d##). Based on charge/discharge curves analysis and structural studies, Molenda et al. proposed that phase transition (o‐LiMnO<sub>2</sub>↔LiMn<sub>2</sub>O<sub>4</sub>) was reversible in o‐LiMnO<sub>2</sub>.<sup>[</sup>\n##UREF##40##\n49\n##\n<sup>]</sup> However, in‐depth examinations are required to understand the complex kinetics in the process of the phase transition.</p>", "<p>On the other hand, the cycling performance of LiMnO<sub>2</sub> is also restricted by the disproportionation of Mn element (Mn<sup>3+</sup> → Mn<sup>2+</sup> + Mn<sup>4+</sup>) during the discharge process. Seriously, Mn<sup>2+</sup> is freely soluble in electrolyte solution. For one thing, Mn ions migrating and depositing on the anode will have major implications for solid electrolyte interphase (SEI). For another, Mn dissolution leads to the reduction of the active material, directly leading to structural degradation and capacity loss.<sup>[</sup>\n##UREF##41##\n50\n##, ##UREF##42##\n51\n##, ##UREF##43##\n52\n##\n<sup>]</sup>\n</p>", "<p>It is concluded that phase transformation and manganese dissolution are the critical challenges for the application of layered LiMnO<sub>2</sub>. In addition, the loss of oxygen and the preparation of pure‐phase LiMnO<sub>2</sub> also need to be cracked.</p>", "<title>Synthesis and Electrochemical Performance</title>", "<p>The synthetic route has a significant effect on the phase and structure of LiMnO<sub>2</sub> as well as electrochemical properties. Similar to other cathode materials, the main synthesis methods of layered LiMnO<sub>2</sub> include ion‐exchange method, solid‐state process, hydrothermal method, sol‐gel method and co‐precipitation.</p>", "<p>In 1996, Armstrong et al. prepared the stoichiometric m‐LiMnO<sub>2</sub> by the ion‐exchange method.<sup>[</sup>\n##UREF##44##\n53\n##\n<sup>]</sup> First, NaMnO<sub>2</sub> was prepared by heating Na<sub>2</sub>CO<sub>3</sub> and Mn<sub>2</sub>O<sub>3</sub> at high temperatures under the argon atmosphere and then refluxing the mixture of NaMnO<sub>2</sub> and excess lithium compounds (LiCl or LiBr) in n‐hexanol. The initial charge capacity of obtained m‐LiMnO<sub>2</sub> was up to 270 mAh g<sup>−1</sup>. In the same year, Delmas et al. also reported layered m‐LiMnO<sub>2</sub> with metastable character by ion‐exchange process.<sup>[</sup>\n##UREF##45##\n54\n##\n<sup>]</sup> It needs to be pointed out that refluxing experiments are carried out under the argon atmosphere and with a large excess of LiCl to protect the oxidation of any material. A differential scanning calorimetry (DSC) and a high temperature X‐ray diffractometer were applied to evaluate the thermal stability of m‐LiMnO<sub>2</sub>. Both measurement results indicated it is metastable. More specifically, exothermic effects at 300 °C are observed in the DSC curve. Meanwhile, the diffraction lines of o‐LiMnO<sub>2</sub> disappear at 300 °C. In addition, Shao‐Horn et al. obtained a LiMnO<sub>2</sub> material accompanied by spinel phase and orthorhombic LiMnO<sub>2</sub> by ion exchange method.<sup>[</sup>\n##UREF##46##\n55\n##\n<sup>]</sup>\n</p>", "<p>Zhou and co‐workers reported the one‐step synthesis of pure‐phase m‐LiMnO<sub>2</sub> at a lower temperature (450 °C). Electrolytic manganese dioxide (EMD) was used as a manganese precursor to realize carbothermal reduction under the Ar atmosphere.<sup>[</sup>\n##UREF##47##\n56\n##\n<sup>]</sup> An initial reversible capacity of 180 mAh g<sup>−1</sup> is obtained in the synthesized sample. Using one‐step hydrothermal methods, the controlled preparation of LiMnO<sub>2</sub> mixed orthorhombic and monoclinic phases was successfully achieved.<sup>[</sup>\n##UREF##48##\n57\n##\n<sup>]</sup> It presented a higher discharge capacity (112.5 mAh g<sup>−1</sup>) after 50 cycles in a voltage range of 2.0–4.5 V than that of both structures (m‐LiMnO<sub>2</sub>: 94.5 mAh g<sup>−1</sup>, o‐LiMnO<sub>2</sub>: 106.8 mAh g<sup>−1</sup>). The fabrication of pure m‐LiMnO<sub>2</sub> is considered to be relatively difficult because of its thermodynamic instability. Therefore, o‐LiMnO<sub>2</sub> has been extensively investigated.<sup>[</sup>\n##UREF##49##\n58\n##, ##UREF##50##\n59\n##\n<sup>]</sup>\n</p>", "<p>As early as the 1990s, there were studies through high‐temperature solid‐phase approaches to prepare layered LiMnO<sub>2</sub>, which was performed by calcining the mixture of MnO<sub>2</sub> and lithium metal salts (LiOH/Li<sub>2</sub>CO<sub>3</sub>) at high temperatures (600–1000 °C) under an argon atmosphere.<sup>[</sup>\n##UREF##51##\n60\n##, ##UREF##52##\n61\n##\n<sup>]</sup> To prevent manganese from being oxidized to the tetravalent state, a reducing agent like carbon was even required. Despite undergoing a phase transition to spinel in LiMnO<sub>2</sub> during charging and discharging, an interesting phenomenon was found that a small amount of spinel in the original LiMnO<sub>2</sub> cathode could improve electrochemical performance than pure LiMnO<sub>2</sub> cathodes. In addition, its electrochemical performance was better than that of pure LiMnO<sub>2</sub> cathodes. Lee et al. obtained the pure o‐LiMnO<sub>2</sub> phase by a distinctive quenching process, which employed the reaction of LiOH with γ‐MnOOH at 1000 °C in an argon atmosphere.<sup>[</sup>\n##UREF##53##\n62\n##\n<sup>]</sup> It delivered a high discharge capacity of 201 mAh g<sup>−1</sup> in the first cycle and remained 200 mAh g<sup>−1</sup> after 50 cycles at a current density of 0.4 mA cm<sup>−2</sup> between 4.3 and 2.0 V. The group of Wang reported o‐LiMnO<sub>2</sub> with a discharge specific capacity of 180—190 mAh g<sup>−1</sup> by a two‐step solid‐state reaction.<sup>[</sup>\n##UREF##54##\n63\n##\n<sup>]</sup> First, the precursors were prepared by firing mixtures of Mn<sub>2</sub>O<sub>3</sub> and LiOH⋅H<sub>2</sub>O at 450 °C for 5 h, and then at higher 600 °C for 12 h with argon flow. Furthermore, one‐step synthesis by the solid‐state process using glucose as a reducing agent to prepare o‐LiMnO<sub>2</sub> is also feasible.<sup>[</sup>\n##UREF##55##\n64\n##\n<sup>]</sup> MnO<sub>2</sub>, LiOH⋅H<sub>2</sub>O and C<sub>6</sub>H<sub>12</sub>O<sub>6</sub> mixed with a Li/Mn/C molar ratio of 5/4/2 were well ground, and then annealed at 750 °C for 15 hours in a tube furnace under nitrogen flow. In this way, heating temperature and time need to be strictly controlled, otherwise impurity phases are accompanied. However, severe particle agglomeration and high energy consumption are inevitable problems in solid‐phase synthesis.</p>", "<p>The hydrothermal method with low energy consumption is an ideal way to prepare o‐LiMnO<sub>2</sub> for getting uniform and fine particles. In the processes of two‐step hydrothermal synthesis of LiMnO<sub>2</sub>, there are three precursors (γ‐MnOOH, Mn<sub>3</sub>O<sub>4</sub>, and Mn<sub>2</sub>O<sub>3</sub>) formed by the redox reaction of the manganese source. The crystalline o‐LiMnO<sub>2</sub> can be obtained by reacting γ‐MnOOH as the precursor with LiOH solution in a Teflon‐lined autoclave at 180 °C for 24 h.<sup>[</sup>\n##UREF##56##\n65\n##\n<sup>]</sup> The γ‐MnOOH nanorods as precursors were synthesized by magnetically stirring a mixed solution of polyethylene glycol (PEG‐10000) and Mn(NO)<sub>3</sub> at 140 °C for 24 h, namely a novel polymer‐assisted low‐temperature hydrothermal method. The attempts to synthesize o‐LiMnO<sub>2</sub> hydrothermally with Mn<sub>3</sub>O<sub>4</sub> as a precursor were completed by Komaba et al. in 2002.<sup>[</sup>\n##UREF##57##\n66\n##, ##UREF##58##\n67\n##\n<sup>]</sup> Dark brown Mn<sub>3</sub>O<sub>4</sub> powders were prepared by stirring the aqueous mixed solution of Mn(CH<sub>3</sub>COO)<sub>2</sub> and KOH at 80 °C for 24 h with bubbling O<sub>2</sub> gas. It is important to wash the Mn<sub>3</sub>O<sub>4</sub> powders with deionized water until the pH value of 7 for the synthesis of o‐LiMnO<sub>2</sub>. Interestingly, replacing γ‐ MnOOH and Mn<sub>2</sub>O<sub>3</sub> with Mn<sub>3</sub>O<sub>4</sub> as a precursor can obtain highly crystalline o‐LiMnO in hydrothermal synthesis, enabling initial reversible capacity of 210 mAh g<sup>−1</sup>.<sup>[</sup>\n##UREF##59##\n68\n##\n<sup>]</sup> Nanocrystalline Mn<sub>3</sub>O<sub>4</sub> particles can also be prepared through the reduction of high‐valent manganese compounds (KMnO<sub>4</sub>) with methanol or ethanol in an autoclave at the temperature of 80—100 °C for 12–48 h.<sup>[</sup>\n##UREF##60##\n69\n##\n<sup>]</sup> In addition, Yang group introduced a rapid method to synthesize nanosized o‐LiMnO<sub>2</sub>, which was based on microwave‐solvothermal approach. This technique mainly uses α‐Mn<sub>2</sub>O<sub>3</sub> as the precursor mixed with LiOH·H<sub>2</sub>O for ≈30 min at a low temperature of 160 °C.<sup>[</sup>\n##UREF##61##\n70\n##\n<sup>]</sup> The microwave hydrothermal synthesis was carried out in the microwave digestion system. Introducing hydrazine hydrate (N<sub>2</sub>H<sub>4</sub>⋅H<sub>2</sub>O) as a reducing agent in the hydrothermal route, submicron‐sized o‐LiMnO<sub>2</sub> crystals can be successfully prepared by using LiOH and the precursors of porous Mn<sub>2</sub>O<sub>3</sub> at the temperature of 180 °C for 16 h.<sup>[</sup>\n##UREF##62##\n71\n##\n<sup>]</sup> The Mn<sub>2</sub>O<sub>3</sub> precursor was formed by calcining MnCO<sub>3</sub> under the air atmosphere at 620 °C for 6 h. The submicron‐sized o‐LiMnO<sub>2</sub> displayed a superior discharge capacity of 216 mAh g<sup>−1</sup>.</p>", "<p>Nevertheless, the time‐consuming and complex procedures involved in multi‐step processes are the undeniable disadvantages of the two‐step synthesis mentioned above. Hence, the facile and simple one‐step hydrothermal approach was chosen to obtain LiMnO<sub>2</sub> materials.<sup>[</sup>\n##UREF##63##\n72\n##, ##UREF##64##\n73\n##\n<sup>]</sup> This way is conventionally achieved by employing the reactants of Mn source (Mn<sub>2</sub>O<sub>3</sub>/MnO<sub>2</sub>) and LiOH·H<sub>2</sub>O aqueous solution in a Teflon‐lined autoclave. Unfortunately, this method may introduce small amounts of impurities (e.g., Li<sub>2</sub>MnO<sub>3</sub>) in samples.<sup>[</sup>\n##UREF##65##\n74\n##\n<sup>]</sup> Li<sub>2</sub>MnO<sub>3</sub> is also a layered lithium‐manganese oxide with an α‐NaFeO<sub>2</sub> type structure and the C2∖m monoclinic crystal system. In this structure, Li cations occupy the interslab octahedral position in the rock salt structure, and 1/3 of Li cations and 2/3 of Mn cations occupy slab octahedral sites of the transition metal layer,<sup>[</sup>\n##UREF##66##\n75\n##\n<sup>]</sup> so it can also be written as the conventional layered structural formula of Li[Li<sub>1/3</sub>Mn<sub>2/3</sub>]O<sub>2</sub>. There are two hypotheses regarding the explanation of the electrochemical activity of Li<sub>2</sub>MnO<sub>3</sub>. With the aid of flame emission, atomic absorption, X‐ray photoelectron spectroscopy (XPS), thermogravimetric analysis coupled with mass spectrometry (TGA/MS), Bruce et al. investigated the electrochemical activity of Li<sub>2</sub>MnO<sub>3</sub> in organic electrolytes. They indicated that the activity of Li<sub>2</sub>MnO<sub>3</sub> could be attributed to the exchange of Li<sup>+</sup> by H<sup>+</sup> in organic electrolytes rather than removal of O<sup>2−</sup>, and there was no oxidation of Mn<sup>4+</sup> to Mn<sup>5+</sup>.<sup>[</sup>\n##UREF##67##\n76\n##\n<sup>]</sup> Another hypothesis was proposed by Dahn in 2002. They believed oxygen was irreversibly released during the first charge to 4.8 V in Li/Li[Ni<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Li<sub>(1/3‐2</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>/3)</sub>Mn<sub>(2/3‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sub>/3)</sub>]O<sub>2</sub> material.<sup>[</sup>\n##UREF##68##\n77\n##\n<sup>]</sup> In 2006, Armstrong et al. used in situ differential electrochemical mass spectrometry (DEMS) to directly detect the oxidation of O<sup>2−</sup> in Li<sub>2</sub>MnO<sub>3</sub> structure and the accompanying Li<sup>+</sup> extraction, which provided a reliable basis for the mechanism of oxygen loss to the electrochemical activity of Li<sub>2</sub>MnO<sub>3</sub>.<sup>[</sup>\n##REF##16802836##\n78\n##\n<sup>]</sup> Ethylenediaminetetraacetic acid disodium salt (EDTA‐2Na) acted as both a chelating reagent and reducing agent to prepare pure o‐LiMnO<sub>2</sub> via hydrothermal synthesis. EDTA‐2Na not only prevents residual oxygen from oxidation in the reacting system effectively but also ingeniously suppresses the formation of Li<sub>2</sub>MnO<sub>3</sub> (<bold>Figure</bold>\n##FIG##3##\n4a##).<sup>[</sup>\n##UREF##69##\n79\n##\n<sup>]</sup> Figure ##FIG##3##4b,c## show the influence of the concentration of EDTA‐2Na and the reactive temperatures on the appearance of Li<sub>2</sub>MnO<sub>3</sub>, respectively<sub>.</sub>\n</p>", "<p>Particularly, the conditions for soft hydrothermal synthesis can affect the properties of the material. Thus, adjusting the synthesis conditions is an effective way to improve electrochemical performance. A clear understanding of the formation and growth mechanism of materials (including the nucleation time and growth process) is usually expected when conducting synthetic experiments, and in situ hydrothermal synthesis might be a good way to do this.<sup>[</sup>\n##REF##22747718##\n80\n##\n<sup>]</sup>\n</p>", "<p>To the best of our knowledge, the electrochemical performance is heavily affected by the morphology and structure of the material. Accordingly, LiMnO<sub>2</sub> with specific nanostructures and morphologies (e.g., nanoplates, nanoparticles, nanorods, and microcubes) have spurred an intensive search for excellent electrochemical performance (<bold>Figure</bold>\n##FIG##4##\n5\n##).<sup>[</sup>\n##UREF##70##\n81\n##, ##UREF##71##\n82\n##, ##UREF##72##\n83\n##, ##UREF##73##\n84\n##\n<sup>]</sup> In 2007, Liu et al. used needle‐like MnOOH as the precursor to prepare o‐LiMnO<sub>2</sub> with a nanorod‐like shape. Notably, the platy shape, platy with irregular shape and rod‐like crystals corresponded to the appearance of Mn<sub>3</sub>O<sub>4</sub> phase, cubic Li<sub>0.2</sub>Mn<sub>2</sub>O<sub>4</sub> phase, and pure o‐LiMnO<sub>2</sub> after 2 h, 3 and 4 h hydrothermal treatment, respectively (<bold>Figure</bold>\n##FIG##5##\n6\n##).<sup>[</sup>\n##UREF##74##\n85\n##\n<sup>]</sup> It is also a good evidence that LiOH has the two important roles in providing a source of lithium and controlling both morphology and particle size. Xiao et al. prepared orthorhombic LiMnO<sub>2</sub> nanoparticles and LiMnO<sub>2</sub> nanorods by different hydrothermal methods.<sup>[</sup>\n##UREF##75##\n86\n##\n<sup>]</sup> Compared with LiMnO<sub>2</sub> nanoparticles prepared through simple one‐step routes, LiMnO<sub>2</sub> nanorods synthesized by γ‐MnOOH precursors showed a higher discharge capacity (200 mAh g<sup>−1</sup>) as well as better cyclability (180 mAh g<sup>−1</sup> after 30 cycles) due to favorable electronic transport of 1D electronic pathways. Zhao et al. combined Mn<sub>2</sub>O<sub>3</sub> nanorods as a template and thermal decomposition process to prepare o‐LiMnO<sub>2</sub>, which delivered outstanding performance. As a consequence, the one‐dimensional crystalline nanostructure could effectively promote the transport of charge/electron and increase the electrode‐filled ratio.<sup>[</sup>\n##UREF##72##\n83\n##\n<sup>]</sup>\n</p>", "<p>To overcome the difficulty in synthesis of layered LiMnO<sub>2</sub>, there are some novel methods developed, including the emulsion‐drying method, reverse‐microemulsion preparation, microwave irradiation, in.situ oxidation coupling with ion exchange, and in situ carbothermal reduction. It is reported that o‐LiMnO<sub>2</sub> materials by emulsion‐drying method show only a 10% capacity loss after 300 cycles at 45 mA g<sup>−1</sup>. The emulsion‐drying method could mix cations homogeneously at the atomic level and obtain fine single‐crystal oxide cathode materials.<sup>[</sup>\n##UREF##76##\n87\n##\n<sup>]</sup> Reverse‐microemulsion preparation is another nice way to allow cations to mix and interact in an atomic scale. Obtaining a thermodynamically stable and transparent microemulsion, in which nano‐sized water is well dispersed into the oil phase, is the key to reverse microemulsion preparation.<sup>[</sup>\n##UREF##39##\n48\n##\n<sup>]</sup> One of the new technologies based on hydrothermal synthesis is microwave hydrothermal. With the advantage of microwave radiation, it significantly reduces reaction time and temperature in some processes.<sup>[</sup>\n##UREF##77##\n88\n##\n<sup>]</sup> Li et al. described the synthesis of high‐purity and highly crystallized o‐LiMnO<sub>2</sub> via the process of in situ oxidation coupling with ion exchange.<sup>[</sup>\n##UREF##78##\n89\n##\n<sup>]</sup> During the synthesis process, MnOOH was produced by the oxidation of Mn(OH)<sub>2</sub> with the oxidizing agent (NH<sub>4</sub>)<sub>2</sub>S<sub>2</sub>O<sub>8</sub> in a LiOH‐existing strong basic environment. Despite 80 °C, deoxygenated distilled water and nitrogen were required to eliminate the impact of oxygen in the air. Komarnenib's group prepared nanorod‐like o‐LiMnO<sub>2</sub> with high purity and excellent electrochemical behavior by in situ carbothermal reduction.<sup>[</sup>\n##UREF##79##\n90\n##\n<sup>]</sup> In this synthesis process, MnO<sub>2</sub>, LiOH·H<sub>2</sub>O and affordable glucose (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) as a reducing agent were homogeneously mixed followed by high temperature treatment in an argon atmosphere for several hours. Additionally, sol‐gel and co‐precipitation methods have also been used for the synthesis of LiMnO<sub>2</sub>. As for the sol‐gel approach to get LiMnO<sub>2</sub>, citric acid is a common chelating agent.<sup>[</sup>\n##UREF##80##\n91\n##\n<sup>]</sup> Zeng group obtained spherical o‐LiMnO<sub>2</sub> powders with a discharge capacity of 152 mAh g<sup>−1</sup> by a carbonate coprecipitation method using NH<sub>4</sub>HCO<sub>3</sub> and MnCl<sub>2</sub> as raw materials.<sup>[</sup>\n##UREF##81##\n92\n##\n<sup>]</sup>\n</p>", "<p>Briefly, it is relatively difficult to synthesize pure layered LiMnO<sub>2</sub> for its thermodynamic sub‐stability, especially for monoclinic LiMnO<sub>2</sub>. Li<sub>2</sub>MnO<sub>3</sub> and manganese oxide as impurities are frequently seen in the XRD analysis of the product. So, to avoid the various side reactions during synthesis, the use of inert gas is the recommended choice. Both solid‐state synthesis and hydrothermal synthesis should strictly control the Li/Mn ratio, reaction temperature, and reaction time. Moreover, in situ detection techniques can be used for precise material preparation.</p>", "<title>Modifications</title>", "<p>To overcome the drawbacks mentioned in Section <xref rid=\"advs6796-sec-0020\" ref-type=\"sec\">2</xref>, tremendous efforts such as element doping, surface coating, nanocomposite designing and compatible electrolyte have been adopted to improve the electrochemical performance of LiMnO<sub>2</sub> cathode materials.</p>", "<title>Element Doping</title>", "<p>Element doping is one of the most extensive approaches for modifying cathode materials to improve the basic physical properties of materials. The elements doping can suppress phase transitions, and enhance capacity. For LiMnO<sub>2</sub> cathode, the research on doping strategies mainly includes element types, element content, doping sites, synthesis conditions, morphology, and structural effects. The efficacy of element substitution by doping is mainly manifested in the following aspects: 1) inhibiting J–T distortion and making structures stable for improved cycling performance; 2) providing favorable Li<sup>+</sup> diffusion. For substituting at the Mn site, doping ions with smaller radius (Al<sup>3+</sup>, Co<sup>3+</sup>, Cr<sup>3+</sup>) than Mn<sup>3+</sup> result in a contracted crystal lattice and microstrains owing to the shorter and stronger transition metal‐oxygen bonds than Mn─O bonds; substitutes of larger radius (Y<sup>3+</sup>) show larger lattice parameters and lead to the free movement of Li<sup>+</sup> in the oxide, which makes it possible to increase the rate of capability. For substituting at the Li site, the metal element with a larger radius ion can provide a pillaring effect to enhance the stability of cathode materials. For instance, Li<sub>0.53</sub>Na<sub>0.03</sub>MnO<sub>2</sub> with a pseudo‐spinel structure displays an increasing discharge capacity, which reaches 200 mAh g<sup>−1</sup> in the 50th cycle.<sup>[</sup>\n##UREF##82##\n93\n##\n<sup>]</sup> Up to now, various doping elements have been found to improve the electrochemical properties of layered LiMnO<sub>2</sub>, including Na, Cu, Mg, Zn, Fe, Ni, Al, Co, Cr, Y, In, S, Ti, V, Nb, Ru, B, F, BO<sub>3</sub>\n<sup>3−</sup>, PO<sub>4</sub>\n<sup>3−</sup>and SiO<sub>3</sub>\n<sup>3−</sup>.</p>", "<title>Cations Doping</title>", "<title>Divalent Cations</title>", "<p>Transition metal elements usually occupy the Mn site of lithium manganese oxide to improve electrochemical performance. The ionic radius of the doping Cu<sup>2+</sup> (0.072 nm) is larger than that of Mn<sup>3+</sup>, which is beneficial for faster mobility of Li<sup>+</sup> in bulk, contributing to the decreased charge transfer impedance and Warburg impedance of LiMnO<sub>2</sub>. Such lower resistance has an important role in improving high‐rate capability by 65.5%.<sup>[</sup>\n##UREF##83##\n94\n##\n<sup>]</sup> Unlike the doping of transition metal elements, the Mg may occupy both Li and Mn sites. During the charge/discharge cycling, the presence of Mg at the Li sites is beneficial for maintaining the stability of the structure but reduces the electrochemical extraction of lithium ions.<sup>[</sup>\n##UREF##84##\n95\n##\n<sup>]</sup>\n</p>", "<p>Suresh et al. investigated the doping effect of Zn and Fe elements using the ion‐exchange method.<sup>[</sup>\n##UREF##85##\n96\n##\n<sup>]</sup> It was only 5% Zn/Fe (LiMn<sub>0.95</sub>Zn<sub>0.05</sub>O<sub>2</sub>/LiMn<sub>0.95</sub>Fe<sub>0.05</sub>O<sub>2</sub>) substituted into LiMnO<sub>2</sub> that could exhibit a better discharge capacity of 180 and 193 mAh g<sup>−1</sup>, respectively. The substitution of Zn can improve the retention of capacity. However, increasing the content of Zn leads to the capacity fading due to decreasing of electrochemically active Mn<sup>3+</sup>. The decreased intensity of Mn<sup>3+</sup>/Mn<sup>4+</sup> redox peak in the cyclic voltammograms (CV) curves confirms it.</p>", "<title>Mixed Bivalent and Trivalent Cations</title>", "<p>Quine et al. reported that Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Mn<sub>0.95</sub>Ni<sub>0.05</sub>O<sub>2</sub> with the O3 (α‐NaFeO<sub>2</sub>) structure formed via an ion‐exchange route. Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Mn<sub>0.95</sub>Ni<sub>0.05</sub>O<sub>2</sub> delivered a high capacity of 220 mAh g<sup>−1</sup> above 2.5 V.<sup>[</sup>\n##UREF##86##\n97\n##\n<sup>]</sup> Inevitably, a phase transition to spinel occurred after the cycling. In that case, Ni substituted in the layered LiMnO<sub>2</sub> was in a state of Ni<sup>2+</sup> thus accompanied by a reaction from Mn<sup>3+</sup> to Mn<sup>4+</sup>. Drawing support from the x‐ray absorption spectroscopy (XAS) spectrum, Wadati et al. pointed out that Li deficiencies could not be created by the Ni<sup>2+</sup> valence and the change from Mn<sup>3+</sup> to Mn<sup>4+</sup>.<sup>[</sup>\n##UREF##87##\n98\n##\n<sup>]</sup> However, the Ni<sup>3+</sup> was observed in the CV curves, corresponding to anodic peak of 3.05 V.<sup>[</sup>\n##UREF##84##\n95\n##\n<sup>]</sup> In addition, when 5% Ni is substituted, the compound provides the highest capacity of 220 mAh g<sup>−1</sup> but is followed by a rapid capacity decay on repeated cycling. The high Ni contents can provide stable capacity, due to the decrease of Mn<sup>3+</sup> contents, while the loss of capacity is inevitable. Nahm and co‐workers found that O2‐Li<sub>0.7</sub>[Ni<sub>1/6</sub>Mn<sub>5/6</sub>]O<sub>2</sub> instead of Li<sub>0.7</sub>[Li<sub>1/6</sub>Mn<sub>5/6</sub>]O<sub>2</sub> exhibited no phase change after 30 cycles.<sup>[</sup>\n##UREF##88##\n99\n##\n<sup>]</sup> In the first cycle, this sample delivered a discharge capacity of 198 mAh g<sup>−1</sup> between the voltage of 4.6 and 2.0 V. Meanwhile, it exhibited a 96% capacity retention after 25 cycles at 1/3 C. Therefore, Ni doping can exert a positive effect on the stability of the structure and the retention of capacity.</p>", "<title>Trivalent Cations</title>", "<p>In the 1990s and early 2000s, interests in modifying layered LiMnO<sub>2</sub> were focused more on the solid solution formed between LiMnO<sub>2</sub> and LiMO<sub>2</sub> analogues (LiAlO<sub>2</sub>, LiCoO<sub>2</sub>, and LiCrO<sub>2</sub>). Although pure LiAlO<sub>2</sub> is electrochemically inert, the solid solution consisting of LiAlO<sub>2</sub> and other lithiated transition‐metal oxides probably possesses a high intercalation potential, leading to high energy density.<sup>[</sup>\n##UREF##89##\n100\n##\n<sup>]</sup> And two effects can explain why Al<sup>3+</sup> doping can stabilize the monoclinic phase:1) AlO<sub>6</sub> octahedra is not distorted because of non‐J‐T Al<sup>3+</sup>; 2) the smaller size of Al<sup>3+</sup> (0.054 nm) has advantages in building stable transition metal‐oxygen bond.<sup>[</sup>\n##UREF##90##\n101\n##, ##UREF##91##\n102\n##\n<sup>]</sup> Chiang et al. indicated that the Al‐doped LiMnO<sub>2</sub> contained the monoclinic and orthorhombic ordered rock‐salt structures, and exhibited better cycling performance and higher discharge capacities under the test conditions of elevated temperatures.<sup>[</sup>\n##UREF##92##\n103\n##\n<sup>]</sup> But m‐Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Al<sub>0.05</sub>Mn<sub>0.95</sub>O<sub>2</sub> showed a higher discharge capacity of 188 mAh g<sup>−1</sup> as well as higher energy densities of 602 Wh kg<sup>−1</sup> than o‐Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Al<sub>0.05</sub>Mn<sub>0.95</sub>O<sub>2</sub> (146 mAh g<sup>−1</sup> and 465 Wh kg<sup>−1</sup>) at 55 °C. The doping of an element not only directly improves the electrochemical performance of materials, but also affects the structure and morphology of materials. Regan et al. elucidated the impacts of Al doping on the structures and surface properties of material<sup>[</sup>\n##UREF##93##\n104\n##\n<sup>]</sup> The existence of Al favors on Mn‐Li inversion in alternating slabs of the LiAl<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Mn<sub>1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>O<sub>2</sub>. Moreover, it is manifested by XPS that Al is uniformly incorporated in the whole grains up to the limit of its solubility. And no aggregation of Al is observed on the surface. The group of Yang described the facile hydrothermal synthesis of o‐LiMn<sub>1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Al<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>O<sub>2</sub> and investigated the changes in the morphology with varying Al content in the layer.<sup>[</sup>\n##UREF##94##\n105\n##\n<sup>]</sup> The results indicate that Al<sup>3+</sup> in a small content contributes to growth in the b‐axis direction (i.e., (010) direction) and formation of cuboid crystals, but the growth is inhibited and changes to cubic crystals with a high content of Al<sup>3+</sup>. In 1999, Robertson prepared Co‐substituted Li(Mn<sub>1‐</sub>\n<italic toggle=\"yes\">\n<sub>y</sub>\n</italic>Co<italic toggle=\"yes\">\n<sub>y</sub>\n</italic>)O<sub>2</sub> in the range 0≤<italic toggle=\"yes\">y</italic>≤0.5 using a solution‐based route with the assistance of ion exchange.<sup>[</sup>\n##UREF##95##\n106\n##\n<sup>]</sup> On the one hand, it pointed out that Co entered the layered LiMnO<sub>2</sub> as Co<sup>3+</sup> rather than Co<sup>2+</sup>. On the other hand, it indicated that higher content of Co caused somewhat lower capacities, and the best amount of doping was 2.5%.<sup>[</sup>\n##UREF##96##\n107\n##, ##UREF##97##\n108\n##\n<sup>]</sup> The LiMn<sub>1‐</sub>\n<italic toggle=\"yes\">\n<sub>y</sub>\n</italic>Co<italic toggle=\"yes\">\n<sub>y</sub>\n</italic>O<sub>2</sub> from the hydrothermal synthesis gave different optimal doping content (10%).<sup>[</sup>\n##UREF##98##\n109\n##\n<sup>]</sup> Doping of Al, Co, and Cr makes sense in stabilizing LiMnO<sub>2</sub> structure and improving cycle retention. In addition, all doped compounds show contracted crystal lattices by comparison with nonsubstituted LiMnO<sub>2</sub> due to a relatively small radius of doping cations. Although LiMn<sub>1‐y</sub>Co<sub>y</sub>O<sub>2</sub> and LiMn<sub>1‐y</sub>Al<sub>y</sub>O<sub>2</sub> undergo a spinel phase transition at 4 V,<sup>[</sup>\n##UREF##99##\n110\n##, ##UREF##100##\n111\n##\n<sup>]</sup> this has almost no harmful effect on cycling performance and even increases discharge capacity.<sup>[</sup>\n##UREF##101##\n112\n##\n<sup>]</sup> But low levels of Cr<sup>3+</sup>‐substituted materials show insignificant transformation in cycling.<sup>[</sup>\n##UREF##102##\n113\n##\n<sup>]</sup> The key points of Cr doping depend on 1) forming a continuous solid solution in LiMnO<sub>2</sub> across the whole range of composition from LiMnO<sub>2</sub> to LiCrO<sub>2</sub>;<sup>[</sup>\n##UREF##103##\n114\n##\n<sup>]</sup> 2) more regular local coordination symmetry around Cr<sup>3+</sup> than Mn<sup>3+</sup>; 3) higher coordination between Cr<sup>3+</sup> and oxygen than Mn<sup>3+</sup>.<sup>[</sup>\n##UREF##104##\n115\n##\n<sup>]</sup> Furthermore, with the help of <sup>6</sup>Li magic‐angle spinning NMR spectroscopy, it has been found that Cr<sup>3+</sup> doping can partially disrupt the Mn‐Mn antiferromagnetic correlations, which is important for the stabilization of the layered structure over the orthorhombic structure.<sup>[</sup>\n##UREF##103##\n114\n##, ##UREF##105##\n116\n##\n<sup>]</sup> Alternatively, Pang observed that even though Cr doping into o‐LiMnO<sub>2</sub> brought a change in the topography from orthorhombic to monoclinic geometry employing Pechini's synthesis method and XRD patterns,<sup>[</sup>\n##UREF##106##\n117\n##\n<sup>]</sup> it does not matter on improving cycling performance and reversible capacity. Xiao et al. reported the rheological phase method to prepare m‐LiMn<sub>1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Cr<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>O<sub>2</sub>,<sup>[</sup>\n##UREF##107##\n118\n##\n<sup>]</sup> forming ultrafine spherical particles with the size of 60–200 nm. Relative to the preparation through solid‐state reaction at the higher temperature of 1000 °C, LiMn<sub>0.85</sub>Cr<sub>0.15</sub>O<sub>2</sub> by rheological phase method calcined at 800 °C yields a much higher initial discharge capacity (180 mAh g<sup>−1</sup>) and capacity retention as well (94% after 40 cycles).</p>", "<p>Y<sup>3+</sup> as a substituent in place of Mn<sup>3+</sup> in LiMnO<sub>2</sub> was first explored by Zong and partners.<sup>[</sup>\n##UREF##108##\n119\n##\n<sup>]</sup> There is no 4 V plateau associated with spinel LiMn<sub>2</sub>O<sub>4</sub> in the CV and charge/discharge curves of the Li/LiMn<sub>0.98</sub>Y<sub>0.02</sub>O<sub>2</sub> cell, which can be attributed to the pillaring effect of Y<sup>3+</sup>. In addition, doping with a low content of Fe is beneficial for capacity and cycling stability.<sup>[</sup>\n##UREF##85##\n96\n##\n<sup>]</sup> Whereas, Myung found o‐LiMnO<sub>2</sub> of Fe substitution by a hydrothermal reaction obtained much lower capacity than that of undoped one,<sup>[</sup>\n##UREF##109##\n120\n##\n<sup>]</sup> which is down to quasi‐reversible Fe<sup>4+</sup>/Fe<sup>3+</sup> redox couple and gives unimpressive battery performance. The introduction of Ti<sup>3+</sup> into o‐LiMnO<sub>2</sub> is an effective attempt to moderate the phase evolution and stabilize the structure.<sup>[</sup>\n##UREF##110##\n121\n##\n<sup>]</sup> Unfortunately, the secondary phase m‐Li<sub>2</sub>MnO<sub>3</sub> in LiMnO<sub>2</sub> has a low conductivity. By doping Ti<sup>3+</sup> into LiMnO<sub>2</sub>, c‐LiTiO<sub>2</sub> with better electrical conductivity (ca. 10<sup>−6</sup> S cm<sup>−1</sup>) can replace above mentioned secondary phase. And Ti─O bonds are stronger than Mn‐O bonds, which militates in favor of improved structural stability of o‐LiMn<sub>1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Ti<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>O<sub>2</sub>. In addition, B‐doped m‐LiMnO<sub>2</sub> was prepared by carbothermal reduction using LiOH and MnO<sub>2</sub> as reactants under the argon atmosphere.<sup>[</sup>\n##UREF##47##\n56\n##\n<sup>]</sup> Even though the transformation from layer to spinel cannot be suppressed by B‐doping, the cycle performance and Coulombic efficiency are improved. 5% B‐doping (m‐LiB<sub>0.05</sub>Mn<sub>0</sub>.<sub>95</sub>O<sub>2</sub>) gives the best electrochemical performance among B‐doped samples with different ratios, particularly at elevated temperatures (60 °C). The average Coulombic efficiency increases from 69.7% to 99.1% at 60 °C.</p>", "<title>Anions Doping</title>", "<p>Aside from cations doping, doping anions is another feasible approach to modify the LiMnO<sub>2</sub> cathode. The S‐doped LiMnO<sub>2</sub> can deliver a discharge capacity of 220 mAh g<sup>−1</sup> after 50 cycles with a voltage of 2.0–4.6 V.<sup>[</sup>\n##UREF##111##\n122\n##\n<sup>]</sup> The F substitution can stabilize the host structure due to high electronegativity, showing better cycle performance compared with F‐free LiMnO<sub>2</sub>.<sup>[</sup>\n##UREF##112##\n123\n##\n<sup>]</sup> Because the S<sup>2−</sup> (0.184 nm) and F<sup>−</sup> (0.136 nm) are greater than the O<sup>2−</sup> (0.132 nm), the lattice constant of LiMnO<sub>2</sub> doped with S<sup>2</sup> and F<sup>−</sup> increases. However, above mentioned S and F‐doping cannot ultimately suppress the transformation from layer to spinel.</p>", "<p>Larger polyanions (BO<sub>3</sub>\n<sup>3−</sup>, PO<sub>4</sub>\n<sup>3−</sup>and SiO<sub>3</sub>\n<sup>3−</sup>) in place of O<sup>2−</sup> ions in nonstoichiometric Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>MnO<sub>2</sub> can generate an open 3D framework, which enhances the mobility of Li<sup>+</sup> ions. Decreased Warburg impedance is also observed, which is reflected in the improved electrochemical properties of the high‐rate charge/discharge capability. Unfortunately, polyanion doping presents increased charge‐transfer resistance due to the poor electrochemical activity of polyanions relative to cations. Surprisingly, although the discharge capacity of Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>MnO<sub>1.99</sub>X<sub>0.01</sub> (X = BO<sub>3</sub>\n<sup>3−</sup>, PO<sub>4</sub>\n<sup>3−</sup>and SiO<sub>3</sub>\n<sup>3−</sup>) has decreased, the cycling ability has been improved.<sup>[</sup>\n##UREF##83##\n94\n##\n<sup>]</sup>\n</p>", "<title>Co‐Doping</title>", "<p>Furthermore, doping multiple elements into LiMnO<sub>2</sub> endows electrodes with a synergistic effect. Suresh doped 5% Ni and 5% Fe into LiMnO<sub>2</sub>,<sup>[</sup>\n##UREF##113##\n124\n##\n<sup>]</sup> forming a pure and homogeneous phase with a layered structure. The low content of Ni and F exhibited a discharge capacity of 250 mAh g<sup>−1</sup> at the rate of 0.1 C, and improved the cycling stability. The co‐doping of cations and anions, such as Li<sup>+</sup> and F<sup>−</sup> ions, into o‐LiMnO<sub>2</sub> has been realized through a solid‐state reaction.<sup>[</sup>\n##UREF##114##\n125\n##\n<sup>]</sup> Scanning electron microscopy characterization indicates o‐Li<sub>1.07</sub>Mn<sub>0.93</sub>O<sub>1.92</sub>F<sub>0.08</sub> presents a smooth surface even after cycling. Co‐doping of Li<sup>+</sup> and F<sup>−</sup> ions reduces the contact area with the electrolyte as well as suppresses the reaction of the Mn dissolution. Eventually, the products improved cycling stability and rate capability at a higher temperature (55 °C). However, doped LiMnO<sub>2</sub> with multiple elements still shows some reserved disadvantages, such as low specific capacity.</p>", "<p>Su investigated In<sup>3+</sup> and S<sup>2−</sup> co‐doped o‐LiMnO<sub>2</sub> synthesized via the hydrothermal method.<sup>[</sup>\n##UREF##115##\n126\n##\n<sup>]</sup> Compared to pristine and single doping (In or S), dual doping reduced the crystallinity of LiMnO<sub>2</sub>. Meanwhile, In and S dual doping exhibited the partial structural transformation from orthorhombic to spinel after 10 cycles at 50 mA g<sup>−1</sup>, but excellent cycle performance was obtained at various discharge current densities. In brief, In and S dual doping provides a great method to improve the rate performance of LiMnO<sub>2</sub> cathode.</p>", "<title>Theoretical Calculations on Doping Effect</title>", "<p>As a quantum mechanical method for the study of the electronic structure of multi‐electron systems, density functional theory (DFT) is very effective in offering a deeper elaboration of elemental doping. An ab initio study pointed out that 10% Co‐substitution makes the antiferromagnetic spin orthorhombic structure more stable than the monoclinic structure, and 60% substitution helps stabilize the disordered local moment (DLM) rhombohedral layered structure over the ferromagnetic orthorhombic phase and offers easy migration of lithium during intercalation.<sup>[</sup>\n##UREF##116##\n127\n##\n<sup>]</sup>\n</p>", "<p>Prasad et al. reported their first‐principles calculations of doped rhombohedral LiMnO<sub>2</sub> against J–T distortion.<sup>[</sup>\n##UREF##117##\n128\n##\n<sup>]</sup> All calculations indicate that, for dopants, their oxidation state is the first significant factor for effectively stabilizing the rhombohedral structure, and then for a certain oxidation state, the t<sub>2g</sub> or e<sub>g</sub> subshell filling is the second. In addition, results show that divalent dopants (such as Mg, Zn) are more effective in the suppression of the J–T distortion than trivalent dopants because each divalent dopant can remove two Mn<sup>3+</sup> ions from the sublattice.<sup>[</sup>\n##UREF##118##\n129\n##\n<sup>]</sup> Based on generalized gradient approximation, it is found that divalent dopants (Mg and Co) destabilized the monoclinic structure than the trivalent dopant (Fe).<sup>[</sup>\n##UREF##119##\n130\n##\n<sup>]</sup> Using the hybrid eigenvector‐following and DFT approach, Grey groups studied the effect of trivalent dopants on the Mn migration leading to spinel transformation, and found that dopants with a small ionic radius (Al<sup>3+</sup> and Cr<sup>3+</sup>) can raise the migration barrier of Mn, but only Cr<sup>3+</sup> does not move to tetrahedral sites within the Li layer.<sup>[</sup>\n##UREF##120##\n131\n##\n<sup>]</sup> Kong et al. investigated the effects of ten cationic (Mg, Ti, V, Nb, Fe, Ru, Co, Ni, Cu, and Al) and two anionic (N and F) dopants of LiMnO<sub>2</sub> using ab initio DFT simulations.<sup>[</sup>\n##UREF##121##\n132\n##\n<sup>]</sup> The findings indicate that Mg, Ti, V, Nb, Ru as well as F can effectively reduce the redox potential, Ti, V, Nb, and Ru can increase the hole conductivity to inhibit the formation of the hole polaron. However, only Ni can decrease the diffusion batteries of Li<sup>+</sup> by 0.23 V and only the N‐doped phase is thermodynamically unstable. When doping at the Li site, it shows unfavorable thermodynamics than Mn‐site doped configurations.<sup>[</sup>\n##UREF##122##\n133\n##\n<sup>]</sup> Similarly, Khang Hoang indicates that substitutes (Al, Fe) are more favorable at the Mn site.<sup>[</sup>\n##UREF##123##\n134\n##\n<sup>]</sup>\n</p>", "<p>To summarize, a systematical comparison of ionic radius and electrochemical performance of different elements doped into LiMnO<sub>2</sub> is presented in <bold>Table</bold>\n##TAB##0##\n1\n##. Element doping is effective in stabilizing structures and improving the electrochemical performance of LiMnO<sub>2</sub>. To one degree or another, it ameliorates the adverse effects of transformation from a layer to a spinel crystal structure. For Co and Cr doping, it shows good capacity retention upon cycling. However, element doping in LiMnO<sub>2</sub> still suffers from some limitations. For instance, it is inevitable for Al‐doped LiMnO<sub>2</sub> to convert into a spinel phase at 4 V. Keeping the high capacity retention for long cycles is still the biggest problem. Decreasing the amount of Li also needs to be solved during the process of electrochemical extraction, when a dopant occurs at the Li site</p>", "<title>Surface Coating</title>", "<p>Element doping is particularly effective in stabilizing the bulk structure, while coating makes great sense to protect the surface of electrode materials for resisting manganese dissolution into the electrolyte and impeding surface reactions.</p>", "<p>Al<sub>2</sub>O<sub>3</sub>, an ionic and electronic insulation, is often used as a coating for the cathode to prevent active electrode materials from being corroded by electrolytes. Cho et al. confirmed that the capacity loss of the Al<sub>2</sub>O<sub>3</sub>‐coated o‐LiMnO<sub>2</sub> (only 2% after 50 cycles) was significantly lower than that of the bare one (35% loss).<sup>[</sup>\n##UREF##124##\n135\n##\n<sup>]</sup> Most significantly, there are no Li<sub>2</sub>Mn<sub>2</sub>O<sub>4</sub> phases in the Al<sub>2</sub>O<sub>3</sub>‐coated electrode during the process of cycling compared with the uncoated one, implying that the protective coating layer can keep the lattice stable and suppress the J–T distortion. However, the LiMn<sub>1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Al<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>O<sub>2</sub> solid solution or LiAlO<sub>2</sub> may be formed during the process of coating Al<sub>2</sub>O<sub>3</sub> with sol‐gel and heating treatment.<sup>[</sup>\n##UREF##125##\n136\n##\n<sup>]</sup> For the materials prepared at high temperatures (600 °C and 700 °C), the uniform formation of the LiMn<sub>1‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Al<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>O<sub>2</sub> solid solution across the particle instead of staying on the surface may bring the rapid capacity decrease. The LiAlO<sub>2</sub> peak can be observed from the XRD pattern, indicating that the Al<sub>2</sub>O<sub>3</sub> gel solution would react with the o‐LiMnO<sub>2</sub> on the surface of materials. Likewise, similar effects can be observed in CoO‐coated o‐LiMnO<sub>2</sub>.<sup>[</sup>\n##UREF##126##\n137\n##\n<sup>]</sup> Even if CoO‐coated LiMnO<sub>2</sub> exhibits a much lower initial discharge capacity (127 mAh g<sup>−1</sup>) compared to that of the bare one (162 mAh g<sup>−1</sup>), the former presents rapidly increasing capacity (185 mAh g<sup>−1</sup> after 15–20 cycles) and just 12% capacity decay after 50 cycles. A significant amount of Co atoms appears in the range of 2‐µm range near the surface than in the bulk, which is a sign of solid solution formation on the surface. Thanks to the presence of solid solutions, the electrochemical stability of CoO‐coated LiMnO<sub>2</sub> has been improved at 55 °C. In addition, the disappearance of the Li<sub>2</sub>MnO<sub>3</sub> impurity phase after Al<sub>2</sub>O<sub>3</sub>/CoO coating implies that the coating layer lies on the surface of LiMnO<sub>2.</sub>\n<sup>[</sup>\n##UREF##127##\n138\n##\n<sup>]</sup> It may be a reference for the removal of Li<sub>2</sub>MnO<sub>3</sub> impurity that occurred in the synthesis of related lithium‐manganese oxygen cathodes. There are many similar effects in Al<sub>2</sub>O<sub>3</sub> and CoO‐coated o‐LiMnO<sub>2</sub>. However, only CoO‐coated LiMnO<sub>2</sub> displays an additional voltage plateau at 2 V probably causing capacity decay. This phenomenon illustrates the structural disorder of Al<sub>2</sub>O<sub>3</sub>/CoO coating is different.</p>", "<p>Lithium boron oxide (LBO) with good ionic conductivity has been successfully used to coat spinel and binary/ternary layered cathode materials for improving cycling stability. There is no doubt that above mentioned cycling stability is also observed in the LBO‐modified o‐LiMnO<sub>2</sub>. Nagasubramanian et al. studied the cycling performance of the LBO‐coated o‐LiMnO<sub>2</sub> and its potential explanation.<sup>[</sup>\n##UREF##128##\n139\n##\n<sup>]</sup> During the first charge‐discharge, the intercalation/deintercalation behavior of Li<sup>+</sup> is considered to be irreversible, which can be attributed to the structure transformation from the layered to the spinel. But as the phase transition is completed during cycles, the maximum capacity is raised to 189 mAh g<sup>−1</sup> and the electrode retains 91% of the maximum capacities after 70 cycles, while only 77% of capacity can be obtained for uncoated one. By observing the contribution of discharge capacity from different platforms (3 V and 4 V) in the charge/discharge curves before and after coating, it can be seen that the major capacity loss is occurring from the 3 V region. Coupled with significantly reduced charge‐transfer resistance in the corresponding voltage range, it is obvious that LBO is beneficial for Li<sup>+</sup> inserting into the octahedral voids in the LiMn<sub>2</sub>O<sub>4</sub> structure, resulting in less capacity loss.</p>", "<p>In recent years, electrode materials with core‐shell structures have been aggressively developed to resolve the problem of low capacity and poor cyclic instability.<sup>[</sup>\n##REF##21879116##\n140\n##\n<sup>]</sup> Generally speaking, the shell can be formed by coating and acts as a protection layer to make better overall performance of the materials. Guo et al. confirm that designing an o‐LiMnO<sub>2</sub>@Li<sub>2</sub>CO<sub>3</sub> nanosheet array cathode with a core‐shell structure presents better electrochemical behavior.<sup>[</sup>\n##REF##27270124##\n141\n##\n<sup>]</sup> Intriguingly, the o‐LiMnO<sub>2</sub>@Li<sub>2</sub>CO<sub>3</sub> electrode shows 80% and 79% initial capacity after 400 cycles at 2C at 20 °C and 60 °C, respectively (<bold>Figure</bold>\n##FIG##6##\n7a## and ##FIG##5##6b##), yet the control electrode without Li<sub>2</sub>CO<sub>3</sub> coating at 0.5 C only exhibits capacity retention of 18% at 20 °C and less than 1% at 60 °C after 400 cycles (Figure ##FIG##6##7c##). The reasons for the excellent cycling performance of o‐LiMnO<sub>2</sub>@Li<sub>2</sub>CO<sub>3</sub> nanosheet array electrode can be explained in Figure ##FIG##6##7d–f##. First, the outer layer of Li<sub>2</sub>CO<sub>3</sub> on the o‐LiMnO<sub>2</sub> surface can be confirmed by high resolution transmission electron microscope (HRTEM) (Figure ##FIG##6##7d##). The outer layer can significantly minimize or avoid adverse reactions (o‐LMO dissolution and oxygen release) (Figure ##FIG##6##7e##). The Li<sub>2</sub>CO<sub>3</sub> is one of the parts of the SEI layer, the Li<sub>2</sub>CO<sub>3</sub> layer is beneficial to electrochemical stability at elevated temperatures. Second, the nanosheet array structure is not only equipped with a 1D pathway for fast electron transport but also shortens the diffusion length of lithium, which ensures sufficient contact of active material with electrolyte (Figure ##FIG##6##7f##). Huang et al. induced two different core‐shell microstructures of Li‐Mn‐O materials by heating treatment (<bold>Figure</bold>\n##FIG##7##\n8a##).<sup>[</sup>\n##UREF##129##\n142\n##\n<sup>]</sup> The phase transformation is summarized in detail in Figure ##FIG##7##8b##, there are three stages at 300 °C and 700 °C, corresponding to two transformations. TGA analysis was provided in Figure ##FIG##7##8c##. When annealed to 350°C, the oxygen on the surface of Li<sub>1.11</sub>Mn<sub>0.76</sub>O<sub>2</sub> (LMO) is released and the lithium diffuses to form Li<sub>2</sub>O. Thus, the lithium vacancies are occupied by Mn to form spinel, resulting in a layered core and spinel shell. As the annealing proceeds to higher temperatures, the internal Li<sup>+</sup> diffuses to the external spinel, forming a LiMnO<sub>2</sub> shell. That is, a LiMnO<sub>2</sub> shell wrapped around a spinel core is formed at 750 °C. The cycling performance and rate capability of these two core‐shell structural materials are shown in Figure ##FIG##7##8d,e##. Notably, the annealing‐induced synthesis method ensures the homogeneity of the core‐shell structure. Compared with conventional coating methods, this approach presents atomic‐level contacts between the cores and shells.</p>", "<p>In brief, modification by coating has resulted in a relatively feasible solution of optimizing the electrode surface to improve electrochemical performance. For instance, the coating layer reduces phase transformation (from the layer to spinel), decreases capacity loss, facilitates Li<sup>+</sup> transfer, and increases capacities. Particularly, the coating delivers high capacity retention even at elevated temperatures, which may be attributed to impeding the active materials touch with the electrolyte solution, thus the side effects of LiMnO<sub>2</sub> are minimized during cycling, especially manganese dissolution. Maybe coating is just like eggshells, keeping the active material safe in its role. But how to get the depth of the coating to hit the spot in the process of material synthesis still needs further study. Additionally, research on LiMnO<sub>2</sub> coating appears to be slightly less than other cathodes (such as LiCoO<sub>2</sub> and LiMn<sub>2</sub>O<sub>4</sub>). Co‐coating can be considered as a new modification method to improve the electrochemical performance of LiMnO<sub>2</sub>, due to its synergistic effect.</p>", "<title>Composites Designing</title>", "<p>To break through the bottleneck of imperfect LiMnO<sub>2</sub> cathode, introducing other favorable materials to fabricate composites has been investigated in recent years. These materials are conducive to the electrochemical performance of electrodes, especially for carbon materials. LiMnO<sub>2</sub>‐carbon composites are usually prepared by mixing carbon materials (carbon nanotubes (CNTs), reduced graphene oxide (rGO) and graphene nanoplatelet (GNP)) with prepared LiMnO<sub>2</sub> or with raw material for the preparation of LiMnO<sub>2</sub>. The carbon materials in LiMnO<sub>2</sub>‐carbon composites can offer high electronic conductivity and fast Li<sup>+</sup> diffusion, which contributes to enhanced specific capacity, improved capacity retention and reduced electrochemical impedance relative to pristine LiMnO<sub>2</sub>.<sup>[</sup>\n##UREF##130##\n143\n##, ##UREF##131##\n144\n##\n<sup>]</sup>\n</p>", "<p>\n<bold>Figure</bold>\n##FIG##8##\n9\n## is the scheme and scanning electron microscope (SEM) images of orthorhombic LiMnO<sub>2</sub>/CNTs nanocomposites.<sup>[</sup>\n##UREF##132##\n145\n##, ##UREF##133##\n146\n##\n<sup>]</sup> As schematically illustrated in Figure ##FIG##8##9a##, o‐LiMnO<sub>2</sub>/CNTs composites were prepared by a one‐step dynamic hydrothermal way. And the corresponding SEM images show that LiMnO<sub>2</sub> particles are “confined” among CNTs (Figure ##FIG##8##9b,c##).</p>", "<p>Figure ##FIG##8##9a## is the prepared scheme of o‐LiMnO<sub>2</sub>/CNTs composites through a one‐step dynamic hydrothermal way, and the corresponding SEM images show that LiMnO<sub>2</sub> particles are “confined” among CNTs (Figure ##FIG##8##9b,c##). The composite with 5 wt% CNTs brings about the optimum specific capacity of 204.9 mAh g<sup>−1</sup>. The o‐LiMnO<sub>2</sub>‐MWCNTs nanocomposites, where CNTs instead of carbon black worked as an additive material, display the intricate network in Figure ##FIG##8##9d##. The addition of CNTs reduces the charge transfer resistance from 190 to 105 kΩ. The 3D network provided by CNTs increases electronic conductivity of the samples and facilitates the Li<sup>+</sup> diffusion across the interface of electrolyte. Tian et al. synthesized LiMnO<sub>2</sub>@rGO composites via a one‐pot hydrothermal route at 200 °C for 12 h,<sup>[</sup>\n##REF##33043900##\n147\n##\n<sup>]</sup> in which LiMnO<sub>2</sub> nanoparticles were uniformly anchored onto rGO nanosheets. It is rewarding to note that the rGO with superior conductivity provides a stable conductive net, thus the first discharge capacity of LiMnO<sub>2</sub>@rGO could be improved to 175 mAh g<sup>−1</sup>, as well as capacity retention increased from 53.53% to 80.97% after 100 cycles.</p>", "<p>Although manganese‐based cathode materials are of great significance for the sustainability of LIBs, the J–T distortion of Mn<sup>3+</sup> has become a bottleneck to improving their structural stability. Zhu et al first proposed a nice idea to suppress the J–T distortion of Mn<sup>3+</sup> using interfacial orbital ordering.<sup>[</sup>\n##UREF##134##\n148\n##\n<sup>]</sup> As shown in <bold>Figure</bold>\n##FIG##9##\n10a,b##, the in situ electrochemical conversion from Mn<sub>3</sub>O<sub>4</sub> was used to prepare heterostructured spinel‐layered LiMnO<sub>2</sub> (SPL‐LMO). Layered domains within the spinel matrix and the orientation of orbitals at the spinel‐layered interface can be seen in Figure ##FIG##9##10c–e##, where MnO<sub>6</sub> of the layered and spinel phases is linked with an included angle of 83.8°. Significantly, the SPL‐LMO materials exhibit superior rate performance (Figure ##FIG##9##10f##) as well as cycling stability of the full cell at a current density of 1.0 A g<sup>−1</sup> for 1000 cycles (Figure ##FIG##9##10g##), which is superior to layered or spinel LiMnO<sub>2</sub> cathodes reported previously.</p>", "<title>Compatible Electrolyte</title>", "<p>The electrolyte is one of the most important components of the battery, as it endows with the ability to establish ionic conductive channels and block the electronic conductivity between the cathode and anode. The development of electrolytes for LiMnO<sub>2</sub> has been underway for several years.</p>", "<p>In 1997, the group of Davidson researched the electrochemistry of LiMnO<sub>2</sub> over the range of 1.0‐4.6 V with a variety of electrolytes.<sup>[</sup>\n##UREF##135##\n149\n##\n<sup>]</sup> Li/LiMnO<sub>2</sub> cells exhibit a higher discharge capacity in 1 M LiClO<sub>4</sub> ethylene carbonate (EC)/dimethyl carbonate (DMC) electrolyte (257 mAh g<sup>−1</sup>) than that of 1 M LiPF<sub>6</sub> EC/DMC electrolyte (220 mAh g<sup>−1</sup>) between 1.0 and 4.4 V. In addition, the voltage range also has a significant effect on the charge and discharge capacity. For example, with 1 M LiClO<sub>4</sub> in propylene carbonate (PC)/EC, charge and discharge capacities are 253 and 250 mAh g<sup>−1</sup> over the range of 1.0–4.4 V, respectively. But when charging to 4.2 V, it displays only the charge capacity of 228 mAh g<sup>−1</sup>. However, they give no further explanation. Thus, substantial differences occur when varying the electrolytes, which also needs to adjust the voltage range for better compatibility.</p>", "<p>Based on 1, 3‐dioxolane‐LiAsF<sub>6</sub> solutions, Tadiran developed the LiMnO<sub>2</sub> rechargeable battery with excellent electrochemical performance.<sup>[</sup>\n##UREF##136##\n150\n##\n<sup>]</sup> In 1, 3‐dioxolane‐LiAsF<sub>6</sub> solutions, the surface film consisting of Li alkoxides, Li formate, LiF and Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>AsF<italic toggle=\"yes\">\n<sub>y</sub>\n</italic> is formed on the Li anode, which induces uniform and smooth Li deposition. Thus, the smooth morphology of Li deposition provides a high cycle life.</p>", "<p>The layered lithium transition metal oxides tend to release oxygen in a highly delithiated state, possibly accompanied by an exothermic reaction with the electrolyte. These could be the most serious threat to the safety of batteries. Reassuringly, when o‐LiMnO<sub>2</sub> cathode contacts with 1 M LiPF<sub>6</sub> solution in 1:1:1 wt.% EC/diethyl carbonate (DEC)/DMC solvent, DSC measurements show a much lower heat effect during the first process compared with other cathode materials.<sup>[</sup>\n##UREF##137##\n151\n##\n<sup>]</sup>\n</p>", "<p>Solid polymer electrolyte (SPE) has the advantage of excellent processability and flexible tunability. All of these advantages make it particularly valuable in designing and developing high‐energy, long‐life solid state lithium batteries. Lithium polymer batteries (LPBs) involved LiMnO<sub>2</sub> cathode have been investigated in recent years, which relates to SPE such as polyethylene oxide (PEO), polyvinylidene fluoride‐hexafluoropropylene (PVDF‐HFP), and polyvinylidene fluoride (PVDF). Xia et al. evaluated the thermal stability of LiMn<sub>2</sub>O<sub>4</sub> and LiMnO<sub>2</sub> in PEO polymer electrolyte. DSC curves show that delithiated LiMn<sub>2</sub>O<sub>4</sub> decomposes at 230 °C, while the decomposition of LiMnO<sub>2</sub> with partial charge occurs at 350 °C. It is worth noting that the LiMnO<sub>2</sub> cathode displays much higher thermal stability than that of LiMn<sub>2</sub>O<sub>4</sub> when the PEO polymer is used as an electrolyte.<sup>[</sup>\n##UREF##138##\n152\n##\n<sup>]</sup> Gu's group obtained PVDF‐HFP‐PC<sub>10</sub>EC<sub>10</sub>LiClO<sub>4</sub> as SPE to fabricate LiMnO<sub>2</sub>/SPE/Li battery. First, they prepared a mixed solution consisting of LiClO<sub>4</sub>, EC, PC, and 25 wt.% PVDF, and then casting and quickly heating it at 110 °C for 10 min.<sup>[</sup>\n##UREF##139##\n153\n##\n<sup>]</sup> Compared with LiMnO<sub>2</sub>/Li battery with the 1 M LiPF<sub>6</sub> in EC/DMC (EC:DMC = 1:1) liquid electrolyte, LiMnO<sub>2</sub>/SPE/Li battery shows a greater discharge capacity of 124 mAh g<sup>−1</sup>.<sup>[</sup>\n##UREF##140##\n154\n##\n<sup>]</sup> In addition, LiMnO<sub>2</sub>‐PAn‐DMcT composite cathode was prepared by mixing LiMnO<sub>2</sub> powder with polyaniline (PAn), 2,5‐dimercapto‐1,3,4‐thiadiazole (DMcT) and carbon in N‐mehtylpyrrolidinone (NMP).<sup>[</sup>\n##UREF##141##\n155\n##\n<sup>]</sup> LiMnO<sub>2</sub>‐PAn‐DMcT composite cathode can increase the capacity of lithium polymer battery. In addition, PVDF‐based SPE has been intensively studied due to its high mechanical strength and good thermal stability. In 2021, Fouladvand et al. prepared a PVDF/SGO polymer electrolyte by introducing sulfonated graphene oxide (SGO) as an effective nanofiller. LiMnO<sub>2</sub> cathode matched with PVDF/SGO polymer electrolyte obtains a high discharge capacity of 204 mAh g<sup>−1</sup> at 0.1 C.<sup>[</sup>\n##UREF##142##\n156\n##\n<sup>]</sup>\n</p>", "<p>All solid‐state batteries (ASSBs) are the strong contender for the new energy industry due to their longer cycle life, higher energy density and safety compared to conventional liquid batteries. And further research into competitive high energy‐density ASSB is focused on small‐size cathode composite material consisting of active material, solid state electrolyte (SSE) and conductive additive. In order to enhance the charge transfer of Li<sup>+</sup>, active material must bond strongly with SSE by high temperature annealing. Rumpel et al. investigated the thermal stabilities of LiMnO<sub>2</sub> and LiMnPO<sub>4</sub> (LMP) in ASSB, which was assembled with the ceramic electrolyte Li<sub>1.3</sub>Al<sub>0.3</sub>Ti<sub>1.7</sub>(PO<sub>4</sub>)<sub>3</sub> (LATP).<sup>[</sup>\n##UREF##143##\n157\n##\n<sup>]</sup> Unfortunately, LiMnO<sub>2</sub> decomposes into Mn<sub>3</sub>O<sub>4</sub> and LiMn<sub>2</sub>O<sub>4</sub> at &lt;500 °C because of the disproportionation of Mn<sup>3+</sup>. In contrast, LATP remains thermally stable even under 800 °C in an argon atmosphere.</p>", "<p>In conclusion, LiMnO<sub>2</sub> as a cathode can be used in various batteries, including non‐aqueous batteries, LPBs, and ASSBs. To facilitate the commercialization of LiMnO<sub>2</sub> cathode, the design of electrolytes is of great significance. Thus, the application of LiMnO<sub>2</sub> cathode can be researched in more fields.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>" ]
[ "<title>Acknowledgements</title>", "<p>J.M. and T.L. contributed equally to this work. This work was supported by the National Natural Science Foundation (22379114, 51972235), the Natural Science Foundation of Shanghai (22ZR1465600), Innovation Program of Shanghai Municipal Education Commission (2023ZKZD32), and the Fundamental Research Funds for the Central Universities.</p>", "<p>\n<bold>Jin Ma</bold> is currently a Master's student at School of Chemical Sciences and Engineering, Tongji University. Her current research focuses on manganese‐based cathode materials for lithium‐ion batteries.</p>", "<p>\n<bold>Tingting Liu</bold> received her M.S. degree from Ningbo University in 2020 and she is now pursuing her Ph.D. degree at Tongji University. Her current research focuses on cathode materials for rechargeable lithium‐ion batteries.</p>", "<p>\n<bold>Jie Ma</bold> is a Professor in College of Environmental Science and Engineering at Tongji University. He received an M.S. degree from Hefei University of Technology in 2005, a Ph.D. degree from Shanghai Jiaotong University in 2009, and was a visiting scholar in Department of Chemical &amp; Biomolecular Engineering at the University of Akron in 2015–2016. Ma's current research focuses on nanomaterial innovations and electrochemical technology for sustainable environment. He has published 150+ journal papers, with a total citation of 9000+ times and an h‐index of 53.</p>", "<p>\n<bold>Chi Zhang</bold> is a specially‐appointed tenured professor at Tongji University. He received his Ph.D. degree from Nanjing University, and worked at Nagoya University as Research Fellow of Japanese Society for the Promotion of Science and Technical University of Munich as Research Fellow of Alexander von Humboldt Foundation. Zhang's scientific interest is the development of advanced functional materials for optical and energy applications. He has published over 450 SCI papers including Advanced Materials, Journal of the American Chemical Society and Angewandte Chemie International Edition.</p>", "<p>\n<bold>Jinhu Yang</bold> is a specially‐appointed tenured professor at Tongji University. He received his Ph.D. degree from Peking University in 2005. Then, he worked at The Hong Kong University of Science and Technology as a Research Associate from 2005 to 2006, the University of Tokyo as a Foreign Researcher supported by JSPS organization from 2006 to 2008, and Munich University as a Humboldt Research Fellow from 2009 to 2011. His current research focuses on the design and fabrication of advanced electrode materials for rechargeable batteries, supercapacitors, and electrocatalysis.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0001\"><label>Figure 1</label><caption><p>a) Three main types of cathode materials commercialized for lithium‐ion batteries. Reproduced under terms of the CC‐BY license.<sup>[</sup>\n##REF##24202440##\n7\n##\n<sup>]</sup> Copyright 2014, M. Saiful Islam and Craig A. J. Fisher, published by Royal Society of Chemistry. Reproduced with permission.<sup>[</sup>\n##UREF##3##\n8\n##\n<sup>]</sup> Copyright 2017, American Chemical Society. b) Crustal content (marked in blue font) of metal element involved in commercialized cathode materials for LIBs. c) Radar maps for cathode materials commercialized for lithium‐ion batteries.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0002\"><label>Figure 2</label><caption><p>a) LiMn<sub>2</sub>O<sub>4</sub> spinel crystal structure and Li<sup>+</sup> ions diffuse rapidly between face‐sharing octahedral 16c and tetrahedral 8a sites. Reproduced with permission.<sup>[</sup>\n##UREF##19##\n26\n##\n<sup>]</sup> Copyright 2020, Springer Nature. Crystal structure of b) o‐LiMnO<sub>2</sub>, c) m‐LiMnO<sub>2</sub>. Reproduced with permission.<sup>[</sup>\n##UREF##22##\n29\n##\n<sup>]</sup> Copyright 2021, Elsevier. d) Metastable and cation‐disordered rocksalt‐type LiMnO<sub>2</sub>. Reproduced with permission.<sup>[</sup>\n##UREF##1##\n5\n##\n<sup>]</sup> Copyright 2018, Royal Society of Chemistry</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0003\"><label>Figure 3</label><caption><p>a) The molecular orbital energy diagram of the octahedral MnO<sub>6</sub> and the electronic orbitals of Mn<sup>2+</sup>/Mn<sup>3+</sup>/Mn<sup>4+</sup> ions. b) A schematic of the octahedral MnO<sub>6</sub> before and after the J–T distortion. Reproduced with permission.<sup>[</sup>\n##UREF##35##\n43\n##\n<sup>]</sup> Copyright 2021, Elsevier. c) XRD pattern evolution of the o‐LiMnO<sub>2</sub> electrodes after different cycles. Reproduced with permission.<sup>[</sup>\n##UREF##36##\n45\n##\n<sup>]</sup> Copyright 2007, Springer Nature. d) Charge and discharge characteristics of the o‐LiMnO<sub>2</sub> for 30 cycles within the voltage range of 2–4.5 V. Reproduced with permission.<sup>[</sup>\n##UREF##39##\n48\n##\n<sup>]</sup> Copyright 2004, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0004\"><label>Figure 4</label><caption><p>a) The supposed mechanism of the function of EDTA‐2Na in the hydrothermal reaction system to eliminate the Li<sub>2</sub>MnO<sub>3</sub> and form pure o‐LiMnO<sub>2</sub>. XRD patterns of the resulting LiMnO<sub>2</sub> samples at b) different EDTA‐2Na concentrations at 200 °C and c) different hydrothermal temperatures at 0.15 M EDTA‐2Na. Reproduced with permission.<sup>[</sup>\n##UREF##69##\n79\n##\n<sup>]</sup> Copyright 2020, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0005\"><label>Figure 5</label><caption><p>a) SEM images of o‐LiMnO<sub>2</sub> nanoplates. Reproduced with permission.<sup>[</sup>\n##UREF##70##\n81\n##\n<sup>]</sup> Copyright 2009, Elsevier. b) TEM images of LiMnO<sub>2</sub> powders. Reproduced with permission.<sup>[</sup>\n##UREF##71##\n82\n##\n<sup>]</sup> Copyright 2010, Elsevier. c) SEM images of the LiMnO<sub>2</sub> nanorods. Reproduced with permission.<sup>[</sup>\n##UREF##72##\n83\n##\n<sup>]</sup> Copyright 2016, Elsevier. d) Schematic illustration of the preparation of the final LiMnO<sub>2</sub> microcubes (v and vi). Reproduced with permission.<sup>[</sup>\n##UREF##73##\n84\n##\n<sup>]</sup> Copyright 2013, Springer.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0006\"><label>Figure 6</label><caption><p>a) A scheme showing the formation of o‐LiMnO<sub>2</sub> nanorod. b) SEM micrograph of sample powders with different hydrothermal times. i) the MnOOH precursor, ii) 2 h incorporation, iii) 3 h incorporation, and iv) 4 h incorporation). Reproduced with permission.<sup>[</sup>\n##UREF##74##\n85\n##\n<sup>]</sup> Copyright 2007, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0007\"><label>Figure 7</label><caption><p>Cycling performance of the o‐LMO@Li<sub>2</sub>CO<sub>3</sub> nanosheet array cathode at 2 C at a) 20 °C and b) 60 °C. c) Cycling performance of the uncoated o‐LMO cathode at 0.5 C. d) High‐resolution TEM image of o‐LMO@Li<sub>2</sub>CO<sub>3</sub> nanosheet array electrode. e) Proposed interfacial change of the bare o‐LMO electrode and that coated with a Li<sub>2</sub>CO<sub>3</sub> layer during charge/discharge process. f) Pathway of electron transport in the o‐LMO@Li<sub>2</sub>CO<sub>3</sub> nanosheet array electrode. Reproduced with permission.<sup>[</sup>\n##REF##27270124##\n141\n##\n<sup>]</sup> Copyright 2016, American Chemical Society.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0008\"><label>Figure 8</label><caption><p>a) Schematic illustration of core‐shell structural architecture with the annealing treatment. b) The evolution of the phase composition with the temperature based on Rietveld refinements of the corresponding XRD patterns. c) TGA analysis of pristine LMO. d) Cycling stability at 25 °C and 50 mA g<sup>−1</sup> and e) rate capability at a different current density from 10 to 1000 mA g<sup>−1</sup> for the samples Li<sub>2</sub>MnO<sub>3</sub>, LMO, LMO‐PA450, and LMO‐PA750. Reproduced with permission.<sup>[</sup>\n##UREF##129##\n142\n##\n<sup>]</sup> Copyright 2022, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0009\"><label>Figure 9</label><caption><p>a) One‐step dynamic hydrothermal synthesis of o‐LiMnO<sub>2</sub>/CNTs composites. SEM images of b) 1%CNT‐LMO, c) 5%CNT‐LMO with one‐step dynamic hydrothermal synthesis. Reproduced with permission.<sup>[</sup>\n##UREF##132##\n145\n##\n<sup>]</sup> Copyright 2021, Elsevier. d) SEM image of o‐LiMnO<sub>2</sub>‐MWCNTs. Reproduced with permission.<sup>[</sup>\n##UREF##133##\n146\n##\n<sup>]</sup> Copyright 2019, Elsevier.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6796-fig-0010\"><label>Figure 10</label><caption><p>a) Synthesis of SPL‐LMO (CE, counter electrode; RE, reference electrode; WE, working electrode). b) Synthesis of SPL‐LMO/Mn<sub>3</sub>O<sub>4</sub>. c) HAADF‐STEM image for the SPL‐LMO nanoparticle. Scale bar, 5 nm. d) HAADF‐STEM image and e) ABF‐STEM image at the spinel‐layered interface for the SPL‐LMO sample along the [010] zone axis. Scale bar, 1 nm. f) Rate capability and cycle performance of the SPL‐LMO cathode. g) Cycle performance of the SPL‐LMO//graphite full cell. Reproduced with permission.<sup>[</sup>\n##UREF##134##\n148\n##\n<sup>]</sup> Copyright 2021, Springer Nature.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6796-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Comparison of ionic radius and electrochemical performance of different elements doped into LiMnO<sub>2</sub>.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Doping ions</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ionic radius [nm]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Cathode</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Voltage range [V vs Li/Li<sup>+</sup>]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Initial discharge capacity [mAh g<sup>−1</sup>]/current density</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Discharge capacity [mAh g<sup>−1</sup>]/retention/cycles</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Reference</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Na<sup>+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.102</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.53</sub>Na<sub>0.03</sub>MnO<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.4–4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">180/0.2 C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">200/111.1%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##82##93##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cu<sup>2+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.072</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.75</sub>Mn<sub>0.99</sub>Cu<sub>0.012</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">219/60 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈195/89%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##83##94##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mg<sup>2+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.072</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.95</sub>Mg<sub>0.05</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">150/1/7 C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈150/100%/30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##84##95##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Zn<sup>2+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.074</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.95</sub>Zn<sub>0.05</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">185/–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈178/96.2%/30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##85##96##]</td></tr><tr><td rowspan=\"3\" align=\"left\" colspan=\"1\">Ni<sup>2+</sup>/Ni<sup>3+</sup>\n</td><td rowspan=\"3\" align=\"center\" colspan=\"1\">0.069/0.056</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.95</sub>Ni<sub>0.05</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.4–4.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">220/25 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈215/97.7%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##86##97##]</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.95</sub>Ni<sub>0.05</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">220/1/7 C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈180/81.8%/30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##84##95##]</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.7</sub>[Ni<sub>1/6</sub>Mn<sub>5/6</sub>]O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">198/1/3 C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">190/96%/.25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##88##99##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Al<sup>3+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.054</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>m‐Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Al<sub>0.05</sub>Mn<sub>0.95</sub>O<sub>2</sub>\n</p>\n<p>o‐Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Al<sub>0.05</sub>Mn<sub>0.95</sub>O<sub>2</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>2.0–4.4</p>\n<p>2.0–4.4</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>≈150/26.1 mA g<sup>−1</sup>\n</p>\n<p>≈25/75 mA g<sup>−1</sup>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>188/125.3%/50</p>\n<p>146/636.6%/100</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>[##UREF##92##103##]</p>\n<p>[##UREF##92##103##]</p>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"center\" rowspan=\"1\" colspan=\"1\"/><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.93</sub>Mn<sub>0.96</sub>Al<sub>0.04</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">175/0.1 C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">145/82.9%/25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##94##105##]</td></tr><tr><td rowspan=\"3\" align=\"left\" colspan=\"1\">Co<sup>3+</sup>\n</td><td rowspan=\"3\" align=\"center\" colspan=\"1\">0.055</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.9</sub>Mn<sub>0.9</sub>Co<sub>0.1</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.6–4.8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">210/0.1 mA cm<sup>−2</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">162/77.1%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##86##97##]</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Mn<sub>0.975</sub>Co<sub>0.025</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.4–4.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">200/25 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">188/94%/100</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##96##107##]</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.9</sub>Co<sub>0.1</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">71/45 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">170/239.1%/100</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##98##109##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cr<sup>3+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.061</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.9</sub>Cr<sub>0.1</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.5–4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">200/0.1 C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">200/100%/30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##106##117##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"center\" rowspan=\"1\" colspan=\"1\"/><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>R‐LiMn<sub>0.85</sub>Cr<sub>0.15</sub>O<sub>2</sub>\n</p>\n<p>S‐LiMn<sub>0.85</sub>Cr<sub>0.15</sub>O<sub>2</sub>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>2.0–4.4</p>\n<p>2.0–4.4</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>180/50 mA g<sup>−1</sup>\n</p>\n<p>144/50 mA g<sup>−1</sup>\n</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>169/93.9%/40</p>\n<p>121/84%/40</p>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<p>[##UREF##107##118##]</p>\n<p>[##UREF##107##118##]</p>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Y<sup>3+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.090</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.98</sub>Y<sub>0.02</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.4</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">191/25 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">173/90.6%/20</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##108##119##]</td></tr><tr><td rowspan=\"2\" align=\"left\" colspan=\"1\">Fe<sup>3+</sup>\n</td><td rowspan=\"2\" align=\"center\" colspan=\"1\">0.055</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.95</sub>Fe<sub>0.05</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">200/–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈180/90%/30</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##85##96##]</td></tr><tr><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.95</sub>Fe<sub>0.05</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈60/22.5 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈68/113.3%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##109##120##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ti<sup>3+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.076</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">LiMn<sub>0.95</sub>Ti<sub>0.05</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈32/0.2 C</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈132/412.5%/60</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##110##121##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">B<sup>3+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.023</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">m‐LiMn<sub>0.95</sub>B<sub>0.05</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈152/50 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">150/98.7%/100</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##47##56##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Bi<sup>3+</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.096</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.75</sub>Mn<sub>0.99</sub>Bi<sub>0.011</sub>O<sub>2</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">242/60 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈175/72.3%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##83##94##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">S<sup>2−</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.184</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.56</sub>MnO<sub>1.98</sub>S<sub>0.02</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">170/0.4 mA cm<sup>−2</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">220/117.6%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##111##122##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">F<sup>−</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.136</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.8</sub>6MnO<sub>1.98</sub>F<sub>0.02</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">129/50 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">210/162.8%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##112##123##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BO<sub>3</sub>\n<sup>3−</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.64</sub>MnO<sub>1.991</sub>(BO<sub>3</sub>)<sub>0.009</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈209/60 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈163/78%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##83##94##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PO<sub>4</sub>\n<sup>3−</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.67</sub>MnO<sub>1.993</sub>(PO<sub>3</sub>)<sub>0.007</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈221/60 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈137/62%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##83##94##]</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">SiO<sub>3</sub>\n<sup>3−</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">–</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Li<sub>0.65</sub>MnO<sub>1.988</sub>(SiO<sub>3</sub>)<sub>0.012</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">2.0–4.3</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈173/60 mA g<sup>−1</sup>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">≈162/93.6%/50</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">[##UREF##83##94##]</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
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Power Sources"], "year": ["2003"], "volume": ["119"], "fpage": ["686"]}, {"label": ["156"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n"], "given-names": ["M.", "L.", "M.", "A."], "surname": ["Fouladvand", "Naji", "Javanbakht", "Rahmanian"], "source": ["J. Membr. Sci."], "year": ["2021"], "volume": ["636"], "elocation-id": ["119563"]}, {"label": ["157"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["M.", "F.", "L.", "W.", "A.", "O.", "G."], "surname": ["Rumpel", "Nagler", "Appold", "Stracke", "Flegler", "Clemens", "Sextl"], "source": ["Mater. Adv."], "year": ["2022"], "volume": ["3"], "fpage": ["4015"]}]
{ "acronym": [], "definition": [] }
157
CC BY
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2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 14; 11(2):2304938
oa_package/a8/ac/PMC10787094.tar.gz
PMC10787095
37933983
[ "<title>Introduction</title>", "<p>Carbapenem‐resistant <italic toggle=\"yes\">Enterobacterales</italic> (CRE) has been categorized as the highest priority pathogens for treatment by the World Health Organization.<sup>[</sup>\n##REF##30423057##\n1\n##\n<sup>]</sup> Carbapenemase is the main resistance determinant of CRE that renders bacterial resistance to nearly all β‐lactams antibiotics, including carbapenems.<sup>[</sup>\n##REF##22000347##\n2\n##\n<sup>]</sup> New Delhi Metallo‐β‐lactamases (NDMs) are one of the most prevalent carbapenemases and have spread over 70 countries in clinical settings since their discovery in 2009.<sup>[</sup>\n##REF##30700432##\n3\n##\n<sup>]</sup> In particular, the NDMs‐producing CRE can trigger multiple types of severe infection (e.g., pneumonia, septicemia, and abscesses), and kill almost half of infected in‐patients.<sup>[</sup>\n##REF##21623026##\n4\n##\n<sup>]</sup> NDMs is a Zn(II)‐dependent periplasmic enzyme that activates nucleophilic water to destroy the β‐lactam ring of carbapenems, thus resulting in poor clinical outcomes.<sup>[</sup>\n##REF##21507902##\n5\n##\n<sup>]</sup> Considering the existing antibiotic treatment failure combined with new antibiotics void,<sup>[</sup>\n##REF##35203785##\n6\n##\n<sup>]</sup> NDMs‐producing <italic toggle=\"yes\">Enterobacterales</italic> leaves clinicians with few choices from the antibiotic pipeline.</p>", "<p>To date, an economical and effective strategy for tackling NDMs producers is to revitalize existing antibiotics using antibiotic adjuvants.<sup>[</sup>\n##REF##31388008##\n7\n##\n<sup>]</sup> They are usually NDM inhibitors that decrease enzymatic function via kicking out the crucial Zn(II) cofactors, binding with amino acid residue of active sites, or mimicking the NDMs substrates.<sup>[</sup>\n##REF##30959050##\n8\n##\n<sup>]</sup> Among them, inhibitors with Zn(II) deprivation action, such as ethylenediamine‐N,N,N′,N′‐tetraacetate (EDTA), aspergillomarasmine A or bismuth (Bi(III)) compounds, have garnered more attention under their great potential in restoring the susceptibility of NDMs producers to carbapenems.<sup>[</sup>\n##REF##24965651##\n9\n##\n<sup>]</sup> However, such inhibitors indiscriminately displace Zn(II) from commensal bacteria and mammalian cells, therefore impairing many biological functions and triggering high off‐target toxicity in vivo application.<sup>[</sup>\n##REF##24965651##\n9b\n##\n<sup>]</sup> Additionally, the bacterial outer membrane has been recognized as an impermeable barrier, which hindered intracellular antibiotic and adjuvant accumulation.<sup>[</sup>\n##REF##30022160##\n10\n##\n<sup>]</sup> Recently, Nanotechnology has been promising for antibiotic adjuvant development due to its ability to control the loading, delivery, and release of antibiotics and to enhance the antibacterial potency.<sup>[</sup>\n##UREF##0##\n11\n##\n<sup>]</sup> However, spatial and temporal control remains an unresolved obstacle for nanoparticle‐constituent adjuvants due to off‐target distributions, systemic delivery, and limited modulatory effects.</p>", "<p>Bismuth compound has been shown to irreversibly inactive NDMs via replacing zinc ions in the NDMs active site.<sup>[</sup>\n##REF##24965651##\n9b\n##\n<sup>]</sup> Developing a bismuth‐based nanoadjuvant that simultaneously overcome bacterial membrane barrier and precisely inactivate NDMs provides a new opportunity to reverse carbapenems resistance in NDMs producer. However, existing bismuth‐based nanoparticles are faced with a series of shortcomings: the lower loading capacity for ions, uncontrolled release of ions, and synthetic complexity.<sup>[</sup>\n##REF##16444262##\n12\n##\n<sup>]</sup> Here, bismuth potassium citrate (BPC) granule, a low‐price stomach medicine (&lt;1 China Yuan/g), was directly converted into high‐security bismuth nanoclusters (BiNCs) via UV irradiation. BiNCs was found to not only be safe for use in vivo, but also have high bismuth ion loading, ROS‐responsive dissociation, and antibiotic adsorption capabilities. These characteristics are expected to endow BiNCs with an excellent targeted‐NDMs inhibitor.</p>", "<p>Selectively overcoming bacterial outer membrane barrier that delivers BiNCs into bacterial periplasm is another tricky problem. Liposome fusion‐based transport (LiFT) strategy features direct drugs delivery into cells via a vesicle‐cell fusion process, providing a robust tool for breaking outer membrane barrier.<sup>[</sup>\n##UREF##1##\n13\n##\n<sup>]</sup> Although various membrane fusion liposome (MFL) has been developed, most of them was applied into mammalian cell transportation.<sup>[</sup>\n##REF##34094837##\n14\n##\n<sup>]</sup> A deeper excavation and application is urgent in bacterial transportation. Previous studies found that liposome consisting of L‐α‐phosphatidylcholine (EggPC) and cholesterol can fuse with outer membrane of Gram‐negative bacteria,<sup>[</sup>\n##UREF##2##\n15\n##\n<sup>]</sup> in which abundant EggPC provides a moderate phase transition temperature to maintain the fluidity of the lipid shell similar to bacterial membrane for fusion. Additionally, rational designing a bacterial anchored‐MFL further assists in dehydrating the gap between the lipid shell and bacterial membrane, accelerating fusion process. More iomportantly, membrane fusion could change membrane permeability, and then induce the initiation of ROS‐related signal pathway,<sup>[</sup>\n##REF##25962045##\n16\n##\n<sup>]</sup> providing a clue for intracellular bismuth ions release. Hence, pathogen‐targeted LiFT strategy would have a significant potential to selectively overcoming bacterial outer membrane barrier.</p>", "<p>Herein, we designed a pathogen‐primed liposomal antibiotic booster for eradicating NDMs‐producing CRE via specifically inactivating periplasmic NDMs and then potentiating the efficiency of meropenem, a broad‐spectrum carbapenem (<bold>Scheme</bold> ##FIG##0##\n1\n##). High‐security bismuth nanoclusters (BiNCs) act as the core for meropenem loading. The fusion‐type liposome made of L‐α‐phosphatidylcholine (EggPC), cholesterol, and DSPE‐PEG‐maltodextrin (M‐MFL) is used as targeting shell for wrapping the meropenem‐loaded BiNCs (MB). Owing to bacteria‐specific maltodextrin transport pathway, the antibiotic booster could selectively target on pathogen with the assistance of maltodextrin corona. After successfully anchoring to pathogen surface, a rapid membrane fusion behavior between liposome and bacteria broke membrane barrier for direct and efficient intracellular MB accumulation, activated intracellular ROS amplification and then triggered the intracellular‐specific release of Bi(III) and meropenem. Released Bi(III) irreversibly inhibited NDMs via displacing Zn(II) in NDMs active sites, preventing meropenem hydrolyzing. Mice infection models revealed that the antibiotic booster restores meropenem efficacy against clinical NDMs‐producing pathogen. Taken together, we developed a nanoadjuvant‐platform for re‐potentiating meropenem activity with high specificity and effectiveness, to address the severe infections caused by NDMs‐producing CRE.</p>" ]
[]
[ "<title>Results</title>", "<title>The synthesis and characterization of bismuth nanoclusters (BiNCs)</title>", "<p>\n<bold>Figure</bold> ##FIG##1##\n1a## illustrates the preparation approach of BiNCs. A clinically available stomach medicine BPC (oral bismuth potassium citrate granules) was synthesized into BiNCs via a one‐step UV irradiation method.<sup>[</sup>\n##UREF##3##\n17\n##\n<sup>]</sup> The citrate and carboxymethyl cellulose (CMC) used in the synthesis are auxiliary materials in BPC, thereby avoiding the use of harmful reagents and residues of by‐products throughout the synthesis. The buffer containing BPC appeared colorless, whereas BiNCs appeared dark black (Figure ##SUPPL##0##S1##). Dynamic light scattering revealed that the hydrodynamic diameter of BiNCs was 21.04 ± 0.99 nm, and the zeta potential was −57.8 ± 4.27 mV (Figure ##FIG##1##1b##). TEM images showed the spherical morphology of the BiNCs with a typical lattice structure and a spacing of about 0.244 nm with a homogeneous size (Figure ##FIG##1##1c and d##). The peaks at 4f7 and 4f5 in X‐ray photoelectron spectroscopy (XPS) indicated the characteristic peaks of bismuth element (Figure ##FIG##1##1e##). The TEM elemental mappings also showed the uniform distribution of Bi elements in BiNCs (Figure ##FIG##1##1f and g##). Afterward, the X‐ray powder diffraction (XRD) pattern verified that the as‐prepared BiNCs were typical bismuth phases (Figure ##FIG##1##1h##). All these results confirmed the successful preparation of BiNCs.</p>", "<p>Notably, we identified a reactive oxygen species (ROS)‐related Bi(III) release in BiNCs, which was enhanced with the increasing of H<sub>2</sub>O<sub>2</sub> concentration (P &lt; 0.01, Figure ##FIG##1##1i##). Morphological and hydrodynamic diameter changes of BiNCs in the presence of H<sub>2</sub>O<sub>2</sub> also reflected ROS‐responsive disintegration of BiNCs (Figure ##FIG##1##1j##, Figure ##SUPPL##0##S2##). BiNCs also presented excellent photoacoustic (PA) imaging properties (Figure ##FIG##1##1k##), promising to realize visualization of pathogen tracing in vivo. We further verified BiNCs can respond to ROS to resensitize NDMs producers specifically toward meropenem (MEM) in a clinical NDM‐1‐producing <italic toggle=\"yes\">E. coli</italic> isolate EC1322 recovered from peritoneal drainage fluid (Table ##SUPPL##0##S1##, Figure ##SUPPL##0##S3##). Compared with the BiNCs‐MEM group, the BiNCs‐MEM‐H<sub>2</sub>O<sub>2</sub> group exhibited synergistic growth inhibition toward EC1322 with a fractional inhibitory concentration index (FICI) of 0.375 (<bold>Figure</bold> ##FIG##2##\n2a‐c##), and the bacterial amounts plummeted (P &lt; 0.01) and their outgrowth was blocked throughout 4 h exposure (Figure ##FIG##2##2d##). While H<sub>2</sub>O<sub>2</sub> itself, even at 400 µM, showed no growth inhibition and no synergistic interaction with MEM toward EC1322 (Figure ##SUPPL##0##S4##). Additionally, BiNCs could reduce the minimal inhibitory concentration (MIC) values of MEM toward NDM‐1 producer but not NDM‐1 negative strain in the presence of H<sub>2</sub>O<sub>2</sub> (Figure ##SUPPL##0##S5##).</p>", "<p>We further used an engineering <italic toggle=\"yes\">E. coli</italic> BL21 expressing periplasmic NDM‐1 to demonstrate ROS‐powered Bi(III) release from BiNCs inactivating NDMs. Compared with single BiNCs treatment, H<sub>2</sub>O<sub>2</sub>‐pretreated BiNCs presented a more significantly obstructive effect on the hydrolysis rate of MEM in BL21 (Figure ##FIG##2##2e##). The NDM‐1 activity decreased as the 200 µM H<sub>2</sub>O<sub>2</sub>‐pretreated BiNCs concentration escalated (IC<sub>50</sub> = 0.046 mg/mL), ultimately leading to the inhibition of ∼80% activities of NDM‐1 (Figure ##FIG##2##2f## and Figure ##SUPPL##0##S6##). Enzyme kinetics analysis revealed that the apparent Vmax of NDM‐1 decreased from 10.11 to 2.53 µM/s when 200 µM H<sub>2</sub>O<sub>2</sub> – pretreated BiNCs concentration increased from 0 to 100 µg/mL, and a typical non‐competitive or an irreversible inhibition was observed according to the relevant Line‐weaver Burk plot (Figure ##FIG##2##2g##). Next, we found that the appearance of an absorption band at 340 nm after incubating apo‐NDM‐1 (lack of Zn(II)) with H<sub>2</sub>O<sub>2</sub>‐pretreated BiNCs (Figure ##SUPPL##0##S7##), which is characteristic for Bi–S ligand‐to‐metal charge transfer (LMCT) band, suggesting that the Bi(III) from BiNCs could bound to NDM‐1. Moreover, ICP‐MS results further revealed that the addition of increasing amounts of Bi(III) resulted in a Zn(II) removal in NDM‐1, accompanied by Bi(III) bound to NDM‐1 (Figure ##FIG##2##2h## and Figure ##SUPPL##0##S8##). Then, the affinities of Bi(III) from H<sub>2</sub>O<sub>2</sub>‐pretreated BiNCs to NDM‐1 were closely examined by isothermal titration calorimetry (ITC), unveiling that Bi(III) rather than BiNCs have a high affinity to NDM‐1 (Figure ##FIG##2##2i and j##), and the cellular thermal shift assay further reflecting the binding of intracellular BiNCs‐released Bi(III) to NDM‐1 in intact cells (Figure ##FIG##2##2k##). Together, Bi(III) released from BiNCs in response to ROS competitively replaces the Zn(II) to bind to NDM‐1, thereby hampering the activity of NDM‐1 and leading to carbapenem resistance reversal of NDM‐1‐producing <italic toggle=\"yes\">E. coli</italic>. (Figure ##FIG##2##2l##).</p>", "<title>Fabrication and Characterization of Pathogen‐Primed Liposomal Antibiotic Booster</title>", "<p>To integrate pathogen‐targeting, precise intracellular delivery, and site‐specific release of drug capabilities, we produced pathogen‐targeting liposomal antibiotic booster (M‐MFL@MB) using a maltodextrin‐cloaked membrane‐fusion liposome (M‐MFL) as a shell and meropenem‐loaded BiNCs (MB) as a core (<bold>Figure</bold> ##FIG##3##\n3a##). In this system, MEM loaded into BiNCs with a 50% loading yield using an optimal input of 3.2 wt% (Figure ##SUPPL##0##S9##). Maltodextrin (MA)‐PEG‐DSPE successfully anchored to membrane‐fusion liposome (MFL) consisting of L‐α‐phosphatidylcholine (EggPC) and cholesterol via a phospholipids fusion,<sup>[</sup>\n##REF##30657302##\n18\n##\n<sup>]</sup> and the modification rate of MA was counted as 0.52 mg/mL. Then, MB was stored into the lumen of M‐MFL with a 29.5% loading yield (Figure ##SUPPL##0##S9##). M‐MFL@MB (166 nm) was slightly larger than M‐MFL (154 nm) and much larger than naked MB (21 nm). M‐MFL@MB possessed an equivalent surface charge (Figure ##FIG##3##3b##), a uniform and spherical structure with a unilamellar membrane coating, which is similar to that of M‐MFL (Figure ##FIG##3##3c##). Cryo‐TEM revealed the successful cloaking of MB into M‐MFL, reflected by a deeper image lining degree from M‐MFL to M‐MFL@MB (Figure ##FIG##3##3c##). M‐MFL protected MB from disaggregation under physiological (H<sub>2</sub>O<sub>2</sub> concentration = 10 µM) and infectious (H<sub>2</sub>O<sub>2</sub> concentration = 100 µM) microenvironment <sup>[</sup>\n##REF##31218078##\n19\n##\n<sup>]</sup> (Figure ##FIG##3##3d and e##). Once the shell is removed, MB could rapidly release MEM and Bi(III) in an H<sub>2</sub>O<sub>2</sub> concentration‐dependent manner, 73% MEM and 80% Bi(III) were released under the 200 µM H<sub>2</sub>O<sub>2</sub> treatment.</p>", "<p>As a major microbial carbon source, maltodextrin (MA) is selectively internalized into bacterial cells through bacterial‐specific maltodextrin transporter, but hardly enters mammalian cells.<sup>[</sup>\n##REF##21765397##\n20\n##\n<sup>]</sup> As expected, MA corona endowed M‐MFL@MB with a more distinguished bacteria adhesion property than that of MFL@MB (Figure ##FIG##3##3f##). We further imaged M‐MFL@MB and MFL@MB in coculture with green fluorescence protein (GFP)‐expressing <italic toggle=\"yes\">E.coli</italic> and mononuclear macrophages (RAW264.7 cells) (Figure ##FIG##3##3g##), and observed M‐MFL@MB targeted <italic toggle=\"yes\">E.coli</italic> but not RAW264.7 cells (Figure ##FIG##3##3h##). The line‐scan profiles also denoted the specific co‐localization of M‐MFL@MB and bacteria. Whilst MFL@MB did not present differential targeting to <italic toggle=\"yes\">E.coli</italic> and RAW264.7 cells (Figure ##FIG##3##3i##). Additionally, liposomal antibiotic booster also presented an excellent immune escape capability via an obvious reduction of endocytosis by monocyte‐macrophage (Figure ##SUPPL##0##S10a and b##).</p>", "<title>In Situ Bacterial Membrane Fusion, Site‐Specific Drug Transport, and Intracellular ROS Burst</title>", "<p>M‐MFL formulation was first examined for its fusion capability with GFP‐expressing <italic toggle=\"yes\">E. coli</italic> (<bold>Figure</bold> ##FIG##4##\n4a and c##). The intensity of red fluorescence (MFL) in M‐MFL group was higher than that in MFL group, implying MA‐mediated pathogen targeting promotes fusion activity by accelerating bacterial adhesion. Meanwhile, flow cytometer analysis demonstrated the successful fusion (Figure ##SUPPL##0##S11##). Compared with common liposomes constituted by soybean lecithin and cholesterol, M‐MFL exhibited a prominent membrane fusion activity due to a more similar ingredient with bacterial membrane and a higher lipid fluidity <sup>[</sup>\n##REF##27725960##\n21\n##\n<sup>]</sup> (Figure ##SUPPL##0##S12##). Förster resonance energy transfer (FRET) assay further demonstrated the specific bacterial OM fusion of M‐MFL, which was observed successfully fused with <italic toggle=\"yes\">E. coli</italic> but hardly with platelets (Figure ##SUPPL##0##S13##). We then demonstrated membrane fusion strategy could promote intracellular accumulation of drugs. CLSM and flow cytometry reflected that more Cy5 (substituting MB) was located inside the bacteria in M‐MFL group compared with the other groups (Figure ##FIG##4##4b and c##; Figure ##SUPPL##0##S14##). Bio‐TEM assay showed that MB reached inside bacteria with the aid of MFL (Figure ##FIG##4##4d##). TEM elemental mappings and ICP‐MS assay further revealed the presence of abundant bismuth inside bacteria in M‐MFL@MB and MFL@MB groups (Figure ##FIG##4##4d and e##).</p>", "<p>ROS can trigger the dissociation of MB to release MEM and Bi(III). However, the level of ROS, especially H<sub>2</sub>O<sub>2</sub>, inherent within the bacteria is less than 10 µM, only triggering little drug release (Figure ##FIG##3##3d and e##). We identified that MFL‐mediated membrane fusion strategies could endogenously trigger intracellular ROS production (Figure ##FIG##4##4f## and Figure ##SUPPL##0##S15‐16a##). Even at 30 min, the ROS level in M‐MFL and M‐MFL@MB groups still existed steadily with no significant decreasing trend (Figure ##SUPPL##0##S16b##), indicating that membrane fusion strategy initiated a rapid and stable ROS burst inside bacteria. The H<sub>2</sub>O<sub>2</sub> produced inside bacteria was dependent on M‐MFL concentration, and <italic toggle=\"yes\">E.coli</italic> incubated with 1.8 mg/mL M‐MFL produced almost 100 µM H<sub>2</sub>O<sub>2</sub>, which is adequate for MB disintegration (Figure ##FIG##4##4g##). M‐MFL could result in the generation of a variety of bacterial ROS species, including O<sub>2</sub>−•, <sup>1</sup>O<sub>2</sub>, •OH, all of which have high oxidative activity for catalyzing intracellular MB disintegration. In addition, M‐MFL‐mediated membrane fusion strengthened the permeability of outer membrane and inner membrane in <italic toggle=\"yes\">E.coli</italic> due to the impaired integrity of bacterial membrane (Figure ##SUPPL##0##S17a and b##). Enhanced membrane permeability would trigger a change in intracellular osmotic pressure, leading to intra‐ and extracellular ions (e.g., Na<sup>+</sup> and Cl<sup>−</sup>) homeostasis disrupted and then resulted in membrane potential depolarization, which acts as a stimulation trigger, and lastly endogenously activates intracellular ROS amplification (Figure ##SUPPL##0##S17c##).<sup>[</sup>\n##REF##25962045##\n16\n##\n<sup>]</sup> Together, liposomal antibiotic booster can serve as potent NDMs inactivator to reverse MEM resistance by a cascading process: selectivity targeting over bacteria, breaking membrane barrier, specifically accumulating intracellular drugs, endogenously activating ROS amplification for intracellular‐specific release of Bi(III) and MEM (Figure ##FIG##4##4i and j##). Thus, M‐MFL@MB prevents MEM from hydrolyzing in NDM‐1 producer more effectively, compared with MEM, MB and M‐MFL@MEM (P &lt; 0.01, Figure ##SUPPL##0##S18##).</p>", "<title>Liposomal Antibiotic Booster Resensitizes NDM‐1‐Producing <italic toggle=\"yes\">E. Coli</italic> to MEM In Vitro</title>", "<p>The bactericide of targeting liposomal antibiotic booster was evaluated using six NDM‐1‐producing clinical <italic toggle=\"yes\">E. coli</italic> isolates (Table ##SUPPL##0##S1##, Figure ##SUPPL##0##S3##). These strains showed much higher MICs (&gt; 64 to 2 µg/mL) in individual MEM, BiNCs, MB, M‐MFL and M‐MFL@MEM groups, respectively (<bold>Figure</bold> ##FIG##5##\n5a## and Figure ##SUPPL##0##S19##). Whilst M‐MFL@MB exhibited a concentrate‐dependent inhibitory effect (8 to 2 µg/mL) on all tested isolates (Figure ##FIG##5##5b##), indicating that M‐MFL@MB could reverse MEM resistance in NDM producers. Time‐dependent killing of EC1322 showed M‐MFL@MB had excellent bactericidal activity against NDMs producer (Figure ##FIG##5##5c##), also reflected by SEM results (Figure ##FIG##5##5d##). Additionally, M‐MFL@MB destructed more exhaustive bacterial structure than other groups (Figure ##FIG##5##5d##). These results suggested that targeting liposomal antibiotic boosters could resensitize NDM‐1‐producing <italic toggle=\"yes\">E. coli</italic> to MEM in vitro. Notably, the antibiotic booster also showed synergies with ceftazidime (β‐lactam antibiotics) against NDM‐1‐producing <italic toggle=\"yes\">E. coli</italic> isolates, but not with ciprofloxacin (quinolones) and colistin (polypeptide antibiotics), as shown in Fig. ##SUPPL##0##S20 and S21##. The result implied that antibiotic booster mainly induces NDM‐1 inactivation, lastly reversing NDMs producer resistance against β‐lactam antibiotics.</p>", "<title>Liposomal Antibiotic Booster Targets Bacterial Infectious Sites and Restores Meropenem Efficacy In Vivo</title>", "<p>The targeting capability of M‐MFL@MB was evaluated in zebrafish infected with GFP‐expressing <italic toggle=\"yes\">E. coli</italic> (<bold>Figure</bold> ##FIG##6##\n6a##). Compared with MFL group, M‐MFL group showed a more pronounced red fluorescence (RhB) trapped inside the bacteria with green fluorescence in zebrafish, demonstrating the M‐MFL can effectively recognize and adhere to the bacteria under the assist of MA (Figure ##FIG##6##6b1 and b2##). Whilst M‐MFL cannot retained inside the healthy zebrafish (Figure ##FIG##6##6b3##). Moreover, MA crown could distinguish bacterial infection from inflammation in a mouse bacterial and inflammatory co‐infection model. IVIS imaging showed more M‐MFL could accumulate effectively and specifically into the bacterial infectious tissue rather than inflammatory tissue (Figure ##SUPPL##0##S22a‐e##), and ex vivo tissues imaging further verified the MA‐mediated specific bacterial targeting ability of M‐MFL (Figure ##FIG##6##6c and d##). The mouse lung infection model further revealed that M‐MFL could facilitate drugs accumulation at infectious sites, as RhB‐labelled M‐MFL@Cy5, not MFL@Cy5, could be gradually accumulated into infected lung, and presented an excellent co‐location with bacteria in infected tissues (Figure ##FIG##6##6e and f##).</p>", "<p>Pharmacokinetic analysis revealed higher concentrations of M‐MFL@MB (86.32‐15.67 µg/mL) in plasma compared with the free MEM (81.85‐5.25 µg/mL) at the indicating time points (Figure ##SUPPL##0##S23##). Compared with free MEM, the area‐under‐the‐curve (AUC0–∞), half‐life time (t1/2), and mean residence time (MRT0–∞) were distinctly improved in M‐MFL@MB‐injected mice. The blood clearance (CL) rate in M‐MFL@MB group has dropped nearly 10 times compared with MEM group (Figure ##FIG##6##6g##). An excellent photoacoustic imaging ability of M‐MFL@MB was also observed similar to BiNCs. The good PA imaging property jointing with specific targeting ability over bacterial infectious sites endowed M‐MFL@MB with a prominent diagnostic performance (Figure ##FIG##6##6h and i##).</p>", "<p>A panel of biosafety evaluation assays supported the excellent biocompatibility and low toxicity profiles of M‐MFL@MB (Figures ##SUPPL##0##S24–S27##). The bismuth metabolism in vivo showed that the liver and spleen are dominant organs for its accumulation and metabolism, which may be mainly due to RES absorption (Figure ##SUPPL##0##S28##).<sup>[</sup>\n##REF##16444262##\n12b\n##\n<sup>]</sup> A mouse lung infection model (<bold>Figure</bold> ##FIG##7##\n7a##) revealed a remarkable decrease of clinical EC1322 isolates on lung tissue in M‐MFL@MB group (<bold>Figure</bold> ##FIG##8##\n8b##). The body temperature, severed as an important indicator of pneumonia recovery,<sup>[</sup>\n##REF##15127194##\n22\n##\n<sup>]</sup> had the least change in M‐MFL@MB group (Figure ##FIG##7##7c##). Additionally, the obvious decrease trends of three bacterial infectious biomarkers, c‐reactive protein (CRP), serum amyloid A (SAA) and procalcitonin (PCT) were observed after treatment in M‐MFL@MB groups, reflecting the pneumonia control after therapy (Figure ##FIG##7##7d and e##). Hematoxylin‐Eosin (HE) staining further confirmed the recovery of pneumonia mice after M‐MFL@MB treatment (Figure ##FIG##7##7f##).</p>", "<p>We further investigated the systemic therapeutic effect of M‐MFL@MB on a murine sepsis model prepared by the intraperitoneal injection of EC1322 (10<sup>6</sup> CFU) (Figure ##FIG##7##7g##). Neither MEM nor other treatments protected any of the septic mice from death within 96 hours, while 80% septic mice were rescued in M‐MFL@MB group (Figure ##FIG##7##7h##). The bacterial load in the liver, spleen, kidney, and blood in M‐MFL@MB‐treated septic mice was reduced compared with that in the other therapeutic formulation groups. Particularly, M‐MFL@MB treatment resulted in nearly 10<sup>4</sup>, 10<sup>4</sup>, 10<sup>3,</sup> and 10<sup>5</sup> bacterial reductions in the liver, spleen, kidney, and blood compared with MEM group, respectively (P &lt; 0.001) (Figure ##FIG##7##7i##). The stable body temperature and the decreased trends of clinically related infectious indicators were also observed after M‐MLF@MB treatment (Figure ##FIG##7##7j and k##). Together with the dramatic decrease in leukocyte infiltration and relatively normal organizational structure in M‐MFL@MB group compared with other treatments (Figure ##FIG##8##8l##), the in vitro antimicrobial activity of M‐MFL@MB could be converted into in vivo efficacy.</p>", "<title>Liposomal Antibiotic Booster Limits Resistance Dissemination by Blocking OMVs Secretion</title>", "<p>Bacterial outer membrane vesicles (OMVs) can act as vehicle for transferring NDM‐1 protein and <italic toggle=\"yes\">bla</italic>\n<sub>NDM‐1</sub> gene among different pathogens, resulting in resistance spreading.<sup>[</sup>\n##REF##34579567##\n23\n##\n<sup>]</sup> Prevention of OMVs secretion is therefore a feasible strategy for blocking resistance spreading. Inspired by membrane fusion as an effective way of membrane perturbation via fusing with outer membrane,<sup>[</sup>\n##UREF##2##\n15\n##\n<sup>]</sup> we evaluated the interference role of M‐MFL‐induced membrane fusion behavior on OMVs secretion in a clinical NDM‐1 producing <italic toggle=\"yes\">E. coli</italic> isolate (EC1429). The morphology of OMVs upon different treatments was not affected (Figure ##FIG##8##8a##). However, the number of OMVs in M‐MFL group was significantly decreased (Figure ##FIG##8##8a–c##). Compared with other groups, an obvious reduction of NDM‐1 in total protein was found in M‐MFL group (Figure ##FIG##8##8d##). The decrease in enzymatic activity of NDM‐1 also paralleled the decrease in NDM‐1 levels (Figure ##FIG##8##8e##). M‐MFL‐treated <italic toggle=\"yes\">E. coli</italic> secret the OMVs containing the lower level of <italic toggle=\"yes\">bla</italic>\n<sub>NDM‐1</sub> gene abundance, whereas untreated and lipo‐treated <italic toggle=\"yes\">E. coli</italic> had a negligible impact on the level of <italic toggle=\"yes\">bla</italic>\n<sub>NDM‐1</sub> inside OMVs (Figure ##FIG##8##8f## and Figure ##SUPPL##0##S29##). RNA‐seq further revealed the effects of M‐MFL on the RNA expression in EC1429, and 108 differentially expressed genes (DEG) between the control sample and M‐MFL treated sample were verified (Figure ##FIG##8##8g##). The M‐MFL treatment significantly down‐regulated the biosynthetic and metabolic process of EC1349 (Figure ##FIG##8##8h##), including fatty acid biosynthetic process, rRNA methylation, carbohydrate derivative catabolic process and regulation of cellular protein metabolic process, which are closely related to the composition and secretion of OMVs.<sup>[</sup>\n##REF##32722322##\n24\n##\n<sup>]</sup> Above all, liposomal antibiotic booster plays a positive role in blocking resistance dissemination by decreasing both the NDM‐1 production and OMV secretion.</p>" ]
[ "<title>Discussion</title>", "<p>Novel treatments against NDMs‐positive <italic toggle=\"yes\">Enterobacterales</italic>, which exhibited multidrug‐resistant (MDR) or extensively drug‐resistant (XDR) profiles, are urgently needed in clinical practice since colistin and tigecycline were largely compromised due to the emerging and spreading of mobile colistin resistance gene <italic toggle=\"yes\">mcr‐1</italic> and tigecycline resistance genes <italic toggle=\"yes\">tet</italic>(X3) and <italic toggle=\"yes\">tet</italic>(X4).<sup>[</sup>\n##REF##26603172##\n25\n##\n<sup>]</sup> Given that few antimicrobials against Gram‐negative pathogens for entering clinical trials, developing NDMs inhibitors to restore carbapenem activity is a promising strategy. However, the structural diversity in active sites of metallo‐β‐lactamases (MBLs) restricted the development of effective MBL inhibitors.<sup>[</sup>\n##UREF##4##\n26\n##\n<sup>]</sup> As a common active site shared by different types of MBLs (e.g., NDM, IMP, and VIM), Zn(II) is an ideal target for MBL inhibitors. Based on Zn(II)‐binding inhibition mode, two types of MBL inhibitors, metal‐depriving compounds (AMA) and metal ion [Bi(III)] replacing compounds, have been demonstrated.<sup>[</sup>\n##REF##24965651##\n9\n##, ##REF##24965651##\n27\n##\n<sup>]</sup> In the development of clinically useful inhibitors, however, these small‐molecule MBL inhibitors are faced with challenges of metalloenzyme selectivity in vivo and efficient intracellular accumulation.<sup>[</sup>\n##UREF##5##\n28\n##\n<sup>]</sup> Recently, nanomaterial‐based therapeutics with unique advantages in antibacterial effects attracted more attention.<sup>[</sup>\n##REF##33024312##\n29\n##\n<sup>]</sup> It can be served as drug carrier to augment the potency of antibiotics or be used instead of antibiotics to exert entirely new antibacterial actions. Herein, we combined the high NDMs inhibition efficacy of Bi(III) and the advantages of pathogen targeting and membrane barrier breakthrough of nanomaterial‐based therapeutics to design and construct M‐MFL@MB, a liposomal antibiotic booster that can effectively target pathogens and achieve the intracellular co‐delivery of meropenem and Bi(III) through membrane fusion.</p>", "<p>Lipopolysaccharide‐coated outer membrane of Gram‐negative bacteria was considered as a barrier for compounds crossing. Small molecular MBL inhibitors traverse outer membrane mainly through narrow <italic toggle=\"yes\">β</italic>‐barrel porins (eg, OmpF and OmpC).<sup>[</sup>\n##REF##31844257##\n30\n##\n<sup>]</sup> Thus, the cellular accumulation of NDMs inhibitors is an important factor affecting their effectiveness in rescuing carbapenem activity.<sup>[</sup>\n##UREF##5##\n28\n##\n<sup>]</sup> To address this challenge, we chose liposomes to carry adjuvants and antibiotics to break through the out‐membrane barrier via membrane fusion. To date, abundant advantages of commercial liposomes such as mature production and high biocompatibility have been described,<sup>[</sup>\n##REF##31918220##\n31\n##\n<sup>]</sup> and these liposome has been successfully used in clinical or preclinical practice for improving the delivery efficiency of antibiotics or antitumor drugs to disease sites.<sup>[</sup>\n##REF##19010847##\n32\n##\n<sup>]</sup> However, understanding of the capability of bacterial outer membrane penetrability of liposome remains limited. Here, we introduced the targeting membrane fusion liposomes that can effectively reduce in vivo off‐target toxicity of inhibitors and help inhibitors and antibiotics cross the barrier of bacterial outer membrane. Moreover, we found, for the first time, that liposome‐mediated membrane fusion could endogenously activate bacterial intracellular ROS amplification, providing a self‐activated “key” for Bi(III) release into bacterial periplasm, leading to an in‐situ Bi(III)‐mediated Zn(II) deprivation. Additionally, membrane fusion strategy also slowed down NDMs‐related resistance dissemination by decreasing the secretion of bacterial OMVs. Taken together, this strategy improves the effect of Bi(III) on accurately inactivating NDM‐1 in vivo and reduces its off‐target toxicity, therefore is a promising approach for its possible application in clinical settings.</p>", "<p>We acknowledged few limitations existed in this study. First, the visible light‐mediated decomposition of BiNCs needs to be further addressed. Second, more accurate ROS burst mechanisms originating from membrane fusion liposome need to be further elucidated. Third, more evaluations in larger preclinical such as nonhuman primates, are needed to be conducted to advance clinical translation. Nevertheless, all ingredients in the M‐MFL@MB, including liposome, maltodextrin and gastric drug, were FDA‐approved and easily obtained at the kilogram level, which is expected to promote the clinical translation of antibiotic booster.</p>", "<p>In summary, we developed a pathogen‐primed liposomal antibiotic booster, M‐MFL@MB (maltodextrin‐cloaked membrane fusion liposome‐encapsulated meropenem‐loaded BiNCs) for reviving carbapenem efficiency in NDMs‐producing clinical <italic toggle=\"yes\">E. coli</italic> isolates in vitro and in vivo. M‐MFL@MB decreased the mortality of infected mice via its pathogen‐targeting, physical barrier breaks, and ROS‐responsive Bi(III)‐mediated Zn(II) removal. Additionally, membrane fusion strategy mediated by M‐MFL decreased the secretion of bacterial OMVs and slowed down the resistance spreading. Our work offered a potential nano‐adjuvant platform for repurposing carbapenems potency and curing NDMs‐producer infections.</p>" ]
[]
[ "<title>Abstract</title>", "<p>Infections caused by <italic toggle=\"yes\">Enterobacterales</italic> producing New Delhi Metallo‐β‐lactamases (NDMs), Zn(II)‐dependent enzymes hydrolyzing carbapenems, are difficult to treat. Depriving Zn(II) to inactivate NDMs is an effective solution to reverse carbapenems resistance in NDMs‐producing bacteria. However, specific Zn(II) deprivation and better bacterial outer membrane penetrability in vivo are challenges. Herein, authors present a pathogen‐primed liposomal antibiotic booster (M‐MFL@MB), facilitating drugs transportation into bacteria and removing Zn(II) from NDMs. M‐MFL@MB introduces bismuth nanoclusters (BiNCs) as a storage tank of Bi(III) for achieving ROS‐initiated Zn(II) removal. Inspired by bacteria‐specific maltodextrin transport pathway, meropenem‐loaded BiNCs are camouflaged by maltodextrin‐cloaked membrane fusion liposome to cross the bacterial envelope barrier via selectively targeting bacteria and directly outer membrane fusion. This fusion disturbs bacterial membrane homeostasis, then triggers intracellular ROS amplification, which activates Bi(III)‐mediated Zn(II) replacement and meropenem release, realizing more precise and efficient NDMs producer treatment. Benefiting from specific bacteria‐targeting, adequate drugs intracellular accumulation and self‐activation Zn(II) replacement, M‐MFL@MB rescues all mice infected by NDM producer without systemic side effects. Additionally, M‐MFL@MB decreases the bacterial outer membrane vesicles secretion, slowing down NDMs producer's transmission by over 35 times. Taken together, liposomal antibiotic booster as an efficient and safe tool provides new strategy for tackling NDMs producer‐induced infections.</p>", "<p>A pathogen‐primed liposomal antibiotic booster is contructed than can revive carbapenem efficiency in NDMs‐producing clinical <italic toggle=\"yes\">E. coli</italic> isolates in vitro and in vivo, via a cascading process: pathogen‐targeting, membrane fusion‐induced physical barrier breaks, and ROS‐responsive Bi(III)‐mediated Zn(II) removal.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6570-cit-0052\">\n<string-name>\n<given-names>S.</given-names>\n<surname>Wu</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Wei</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Qin</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Shi</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Shen</surname>\n</string-name>, <article-title>Liposomal Antibiotic Booster Potentiates Carbapenems for Combating NDMs‐Producing <italic toggle=\"yes\">Escherichia</italic>\n<italic toggle=\"yes\">c</italic>\n<italic toggle=\"yes\">oli</italic>\n</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304397</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304397</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>S.W., Y.W., and Y.W., contributed equally to this work. S.X.W., J.J.S. and S.S.Q. performed conceptualization, S.X.W. and Y.B.W. performed methodology, Y.B.W. and J.J.S. performed investigation, S.X.W., D.J.L., and Y.B.W. performed visualization, J.J.S., S.S.Q., Y.W., and D.J.L. performed funding acquisition, Z.Z.Z., J.Z.S., and S.S.Q. performed supervision, S.X.W., Y.B.W., and Y.M.W., wrote the original draft, S.X.W., Y.W., J.J.S., S.S.Q., and J.Z.S. wrote, reviewed and edited the manuscripts.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors acknowledge the Modern Analysis and Computing Center of Zhengzhou University for the technical assistance. Additionally, they would like to thank Wang Hui Quan from Shiyanjia Lab (<ext-link xlink:href=\"http://www.shiyanjia.com\" ext-link-type=\"uri\">www.shiyanjia.com</ext-link>) for the test assay. Special thanks go to: National Science Foundation for Distinguished Young Scholars 82222067 (J.J.S), National Natural Science Foundation of China 81874304 (J.J.S), National Natural Science Foundation of China 82073395 (Y.W), Innovation Talent Support Program of Henan Province 19HASTIT006 (J.J.S), Postdoctoral Science Foundation of China 2018T110745 (D.J.L), Training Plan for Young Backbone Teachers in Colleges and Universities in Henan 2021GGJS016 (S.S.Q). All animal studies were carried out following the guidelines of the Regional Ethics Committee for Animal Experiments and the Care Regulations approved by the Institutional Animal Care and Use Committee of Zhengzhou University. The license number of the experimental animal is No.410975211100031648.</p>", "<title>Data Availability Statement</title>", "<p>Research data are not shared.</p>" ]
[ "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6570-fig-0009\"><label>Scheme 1</label><caption><p>Schemes for construction of targeting liposomal antibiotic booster for targeted periplasmic NDMs inactivation via Bi(III)‐mediated Zn(II) removal. The meropenem‐loaded bismuth nanoclusters (MB) are encapsulated in the maltodextrin‐cloaked membrane fusion liposome and precisely delivered to the infectious sites with the assistance of bacteria‐specific maltodextrin transport pathway, where the liposome fuses with bacterial outer membrane, facilitating the periplasmic translocation of MB and intracellular ROS burst. Meanwhile, endogenous ROS amplification triggers the intracellular‐specific release of Bi(III) and meropenem. Released Bi(III) irreversibly inactive NDMs via displacing Zn(II) from NDMs active sites, thus protecting meropenem from hydrolyzation.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6570-fig-0001\"><label>Figure 1</label><caption><p>a) The scheme presenting the synthesis process of Bismuth‐Nano‐Clusters (BiNCs) and ROS‐responsive Bi(III) release from BiNCs. b) Hydrodynamic diameter distribution and zeta potential distribution (inset) obtained for BiNCs. c) Representative TEM image of BiNCs. Scale bar, 10 nm. d) A representative high‐resolution TEM image of BiNCs. Scale bar, 2.5 nm. e) XPS diffraction spectrum of BiNCs. f) STEM‐HAADF image and corresponding EDS elemental mappings of Bi, O, P, N, and C in BiNCs. g) EDS spectrum for bismuth element analysis of BiNCs. h) X‐ray diffraction (XRD) analysis of BiNCs. i) In vitro Bi(III) release from BiNCs against different levels of H<sub>2</sub>O<sub>2</sub>. j) Representative TEM images of BiNCs after 24 h incubation with different levels of H<sub>2</sub>O<sub>2</sub>. Scale bar, 100 nm. k) PA response to different concentrations of BiNCs (0.1, 0.3, 0.6, 0.9, 1.2, and 1.5 mg/mL) (inset: PA imaging of BiNCs). Data are presented as mean values ± SD, n = 3 biologically independent samples. Statistical significance was analyzed by the two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6570-fig-0002\"><label>Figure 2</label><caption><p>a, b) Representative heat plots of microdilution checkerboard assays for the combination of BiNCs and meropenem in the absence (a) or presence (b) of H<sub>2</sub>O<sub>2</sub> against EC1322. c) Isobolograms of the combination of BiNCs and meropenem in the absence or presence of H<sub>2</sub>O<sub>2</sub> against EC1322. The black dotted line shows the ideal isobole, where drugs act additively and independently. Data points below this line reveal synergism. d) Time‐kill curves for meropenem or BiNCs monotherapy, or their combination therapy in the absence or presence of H<sub>2</sub>O<sub>2</sub> against EC1322 during 6 h incubation. The concentrations of meropenem, BiNCs, and H<sub>2</sub>O<sub>2</sub> are used at 8 µg/mL, 125 µg/mL, and 200 µM, respectively. e) Hydrolytic effects of the BiNCs or BiNCs+H<sub>2</sub>O<sub>2</sub> pre‐treated NDM‐1‐producing <italic toggle=\"yes\">E. coli</italic> BL21 on meropenem (n = 3). f) Inhibition of NDM‐1 activity by Bi(III) from 200 µM H<sub>2</sub>O<sub>2</sub>‐pretreated BiNCs with IC<sub>50</sub> of 0.046 mg/mL (n = 3). g) Double reciprocal plot of substrate‐dependent enzyme kinetics on inhibition of NDM‐1 activity by Bi(III) from 200 µM H<sub>2</sub>O<sub>2</sub>‐pretreated BiNCs, reflecting that Bi(III) (released from BiNCs) inhibited NDM‐1 via either a non‐competitive or an irreversible inhibition mode. h) Zn(II) content in Zn<sub>2</sub>‐NDM‐1 and the supernatant after being treated with different concentrations of Bi(III) from H<sub>2</sub>O<sub>2</sub>‐pretreated BiNCs by equilibrium dialysis, respectively. The metal content was determined by ICP‐MS. i, j) ITC thermograms for the binding of Bi(III) from H<sub>2</sub>O<sub>2</sub>‐pretreated BiNCs (i) or BiNCs (j) to NDM‐1. The downward peaks indicate an exothermic process. k) Cellular thermal shift assay demonstrating the binding of Bi(III) to NDM‐1 in NDM‐producing <italic toggle=\"yes\">E. coli</italic> BL21. NDM‐1 melting temperature was shifted from 68.1° to 56.8 °C for control and BiNCs‐H<sub>2</sub>O<sub>2</sub> combination group, respectively. The images show the western blotting result. <bold>l</bold> Schematic diagram of the action mechanism of BiNCs under non‐oxidative stress and oxidative stress on NDM‐1‐producing <italic toggle=\"yes\">E. coli</italic>. Data are presented as mean values ± SD, n = 3 biologically independent samples. Statistical significance was analyzed by the two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6570-fig-0003\"><label>Figure 3</label><caption><p>a) The schematic illustration exhibiting the preparation process of maltodextrin‐decorated membrane fusion liposome that wraps meropenem‐loaded BiNCs (M‐MFL@MB) and the highly specific bacterial targeting mechanism. b) Hydrodynamic diameter and ζ potential of BiNCs, meropenem‐loaded BiNCs (MB), maltodextrin‐decorated membrane fusion liposome (M‐MFL) and M‐MFL@MB (n = 3). c) Representative TEM and cryo‐TEM (inset) images of M‐MFL (left) and M‐MFL@MB (right). Scale bar, 100 nm. d, e) In vitro MEM (d) and Bi(III) (e) release curves of MEM@BiNCs (MB) (upper) and M‐MFL@MB (lower) in PBS containing different concentrations of H<sub>2</sub>O<sub>2</sub> (1, 10, 100 and 200 µM), (n = 3). f) Representative pseudo‐color SEM images of EC1322 after incubation with PBS, M‐MFL@MB, and MFL@MB, respectively. Scale bar, 1 µm. g) The experimental scheme of coculture experiments for verifying the capability of maltodextrin‐mediated specifical targeting to bacteria, not mammalian cells. h, i) Confocal images of mononuclear macrophages (RAW 264.7 cells) cocultured with GFP‐expressing <italic toggle=\"yes\">E. coli</italic> and imaged after labeling with M‐MFL@MB (h) or MFL@MB (i), respectively. Scale bar, 5 µm. The nucleus of RAW 264.7 cells, <italic toggle=\"yes\">E. coli</italic>, and MFL were labeled with DAPI (blue), Green fluorescent protein (green), and Rhodamine (red), respectively. Plot profiles corresponding to white lines are shown on the right. Data are presented as mean values ± SD, n = 3 biologically independent samples. Statistical significance was analyzed by the two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6570-fig-0004\"><label>Figure 4</label><caption><p>a, b) Representative confocal images visualize the membrane fusion interaction between M‐MFL or MFL with <italic toggle=\"yes\">E. coli</italic> (a), and intracellular drug delivery of M‐MFL or MFL into <italic toggle=\"yes\">E.coli</italic> (b). M‐MFL and MFL were labeled with fluorescent dye Rhodamine (red), Cy5 fluorescent dye (pink) was loaded into M‐MFL or MFL for substituting MB, and the <italic toggle=\"yes\">E. coli</italic> could express GFP (green fluorescent protein, green). The control group was incubated with PBS. Scale bar, 100 nm. c) The corresponding fluorescence semi‐quantitative analysis (n = 3), shows membrane fusion and intracellular delivery efficiency of M‐MFL and MFL, respectively. d) Bio‐TEM images and the bismuth element mapping of different nanoparticles‐treated EC1322. Untreated B16‐F10 cells were used as control. Scar bar: 1 µm; Red arrows pointed to BiNCs. e) ICP‐MS analyzes the effect of different treatments on intracellular Bi(III) accumulation of <italic toggle=\"yes\">E. coli</italic> (n = 3). f) Intracellular ROS level after being treated with different nanoparticles was monitored by detection of DCFH‐DA fluorescence intensity using confocal imaging. g) ESR spectrum of M‐MFL‐treated <italic toggle=\"yes\">E. coli</italic>, the untreated <italic toggle=\"yes\">E.coli</italic> was used as control. Scale bar, 30 µm. h) Determination of H<sub>2</sub>O<sub>2</sub> amount in NDM‐1‐EC1322 after different concentrations of M‐MFL treatment (n = 3). i) Hydrolytic effects of the EC1322 on meropenem after different treatments, including MEM, MEM@BiNCs, M‐MFL@MEM and M‐MFL@MB. n = 3. j) Schematic diagram of the action mechanism of targeting liposomal antibiotic booster on NDM‐1 producers. Data are presented as mean values ± SD, n = 3 biologically independent samples. Statistical significance was analyzed by the two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6570-fig-0005\"><label>Figure 5</label><caption><p>a) Measurement of bacterial colony‐forming units, obtained from six clinical isolates of NDM‐1‐producing <italic toggle=\"yes\">E. coli</italic> treated with different concentrations of meropenem (MEM), MB, M‐MFL@MEM and M‐MFL@MB, respectively (n = 6). b) MIC of MEM, MB, M‐MFL@MEM and M‐MFL@MB in six clinical isolates of NDM‐1‐positive <italic toggle=\"yes\">E. coli</italic> (n = 6). c) Time‐kill curves for MEM, BiNCs, M‐MFL, MB, M‐MFL@MEM, and M‐MFL@MB against EC1322 during 6 h incubation, respectively (n = 3). The concentrations of MEM were 8 µg/mL in those groups. The concentrations of BiNCs and M‐MFL were about 53.33 and 177.77 µg/mL, respectively. d) Representative SEM images of EC1322 after treatment with different nanoparticles for 1 h and 6 h, respectively. Scale bar, 0.5 µm. Data are presented as mean values ± SD, n = 3 biologically independent samples. Statistical significance was analyzed by the two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6570-fig-0006\"><label>Figure 6</label><caption><p>a) Experimental scheme of the bacterial‐infected zebrafish model for demonstrating maltodextrin‐mediated adhesion ability. b) Lateral views of the whole bacteria‐infected zebrafish after DiI‐labeled M‐MFL treatment (b1). The bacterial‐infected zebrafish incubated with the DiI‐ labeled MFLipo treatment (b2) and the healthy zebrafish incubated with DiI‐labeled M‐MFL (b3) were used as the control. c, d) Ex‐vivo tissue NIR FL images I and fluorescence semi‐quantitative analysis (d) of mice model of dual infection with LPS and <italic toggle=\"yes\">E. coli</italic> at 22 h post‐injection with M‐MFL@IR783, MFL@IR783, or IR783, respectively (n = 3). e, f) Representative CLSM images I and fluorescence semi‐quantitative analysis (f) of MFL, M‐MFL distribution at different time points after intravenous injection in the <italic toggle=\"yes\">E. coli</italic> infected lung tissues, respectively. The nanoliposome was stained with rhodamine (red). The encapsulated drugs were replaced by cy5 (pink). The nucleus of lung tissues was stained with DAPI (blue). Scar bar, 100 µm. h, i) PA imaging (h) and PA response value (i) of <italic toggle=\"yes\">E. coli</italic>‐infected mice model at different time points after intravenous injection with BiNCs and M‐MFL@MB, respectively. Data are presented as mean values ± SD, n = 3 biologically independent samples. Statistical significance was analyzed by the two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6570-fig-0007\"><label>Figure 7</label><caption><p>a) Schematic diagram of the infection, treatment used in mice with pneumonia. b, c) Bacterial loads (b) and mouse body temperature changes (c) in the pneumonia mice model after different nanoformulations treatment (n = 6). d) Experimental roadmap for detecting inflammation‐related indicators (CRP, SAA and PCT) of mice with pneumonia. e) CRP, SAA and PCT level in the pneumonia mice model after different treatments (n = 6). f) HE staining of infected lung tissues in the pneumonia mice model after different treatments. Scar bar, 100 µm. g) Schematic diagram of the infection, treatment used in mice with sepsis. h, i, j) Survival curves (h), bacterial loads (i) and body temperature changes (j) in the sepsis mice model after different treatments, n = 6. k) CRP, SAA and PCT level in the sepsis mice model after different treatments (n = 6). l) HE staining of infected tissues in the sepsis mice model subjected to different treatments. Scar bar, 100 µm. Data are presented as mean values ± SD, n = 3 biologically independent samples. Statistical significance was analyzed by the two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6570-fig-0008\"><label>Figure 8</label><caption><p>a) an NTA analysis and representative TEM images (inset) of <italic toggle=\"yes\">E. coli</italic> OMVs extracted from <italic toggle=\"yes\">E. coli</italic> incubated with Lipo and M‐MFL, respectively. The OMVs extracted from untreated <italic toggle=\"yes\">E. coli</italic> were used as control. Scar bar, 100 nm. b) Statistics of size and concentration of <italic toggle=\"yes\">E. coli</italic> OMVs extracted from <italic toggle=\"yes\">E. coli</italic> incubated with different nanoparticles. b, c, d) the measurement of total protein content (b, n = 3), NDM‐1 protein content (c, n = 3) and enzymatic activity of NDM‐1 (d, n = 3) of <italic toggle=\"yes\">E. coli</italic> OMVs extracted from <italic toggle=\"yes\">E. coli</italic> incubated with Lipo and M‐MFL, respectively. The OMVs extracted from untreated <italic toggle=\"yes\">E. coli</italic> were used as control. e) Absolute copy number of <italic toggle=\"yes\">bla</italic>\n<sub>NDM‐1</sub> gene in <italic toggle=\"yes\">E. coli</italic> OMVs extracted from <italic toggle=\"yes\">E. coli</italic> incubated with Lipo and M‐MFL, respectively. The OMVs extracted from untreated <italic toggle=\"yes\">E. coli</italic> were used as control. n = 3. f) The MIC of EC15922 after incubation with different <italic toggle=\"yes\">E. coli</italic> OMVs (n = 6). g) Clustering heat map of differentially expressed genes (DEGs) between M‐MFL‐treated <italic toggle=\"yes\">E. coli</italic> and untreated <italic toggle=\"yes\">E. coli</italic>. The abscissa is the sample name, and the ordinate is the normalized value of the DEGs. The redder the color, the higher the expression level, and the bluer the expression level, the lower the expression level. h) KEGG down‐regulated pathway enrichment analysis of differentially expressed genes between M‐MFL and control treatment group. Data are presented as mean values ± SD, n = 3 biologically independent samples. Statistical significance was analyzed by the two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6570-supinfo-0001\" position=\"float\" content-type=\"local-data\"/>", "<supplementary-material id=\"advs6570-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2304397-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
32
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 7; 11(2):2304397
oa_package/76/23/PMC10787095.tar.gz
PMC10787096
37973550
[ "<title>Introduction</title>", "<p>Urethral stricture, which is a narrowing process of urethra lumen caused by fibrosis of the urethra mucosa and the surrounding spongy corpus spongiosum, is often inevitable after urethral injury.<sup>[</sup>\n##UREF##0##\n1\n##, ##UREF##1##\n2\n##, ##REF##28118170##\n3\n##\n<sup>]</sup> It has been reported that 229 to 627 out of 100 000 males suffer from urethral stricture, but the treatment is still limited in the field of urology.<sup>[</sup>\n##REF##17437780##\n4\n##\n<sup>]</sup> Obviously, urethral stricture has a substantial impact on the quality of life in patients with high health costs.<sup>[</sup>\n##REF##17437780##\n4\n##\n<sup>]</sup> Urethroplasty procedures have been considered to be the most effective gold‐standard method, compared to certain micro‐invasive surgeries (e.g., urethral dilation and internal urethrotomy).<sup>[</sup>\n##REF##26631921##\n5\n##, ##REF##21176068##\n6\n##\n<sup>]</sup> A number of challenges indeed exist in the surgical treatment of urethral strictures, such as the use of substitute materials (autologous penile flap or oral mucosa).<sup>[</sup>\n##REF##27940192##\n7\n##\n<sup>]</sup> The autologous substitute materials for urethral reconstruction have limitations, which can cause damage at the harvesting site. Thus, suitable tissue engineering and alternative biomaterials have recently been intensively explored for more effective regenerative medicine in an attempt to overcome such problems of urethral reconstruction.<sup>[</sup>\n##REF##26631921##\n5\n##, ##REF##27940192##\n7\n##, ##REF##25689740##\n8\n##, ##REF##26941491##\n9\n##, ##REF##20477828##\n10\n##\n<sup>]</sup>\n</p>", "<p>It is difficult to mimic an actual urethral structure with the dense mucosal layer and the loose submucosal layer for scarless regeneration. 3D fabrication of biologically functional components is certainly a promising technology, as it adopts the extracellular matrix (ECM) molecules and provides a biomimetic microenvironment for cells.<sup>[</sup>\n##REF##34133940##\n11\n##, ##REF##27315476##\n12\n##\n<sup>]</sup> With its emergence, the synthesis of scaffolds has attracted enormous attention owing to the programmable deposition of biocompatible materials.<sup>[</sup>\n##REF##25093879##\n13\n##, ##REF##31426033##\n14\n##\n<sup>]</sup> Currently, hydrogel biomaterials are routinely used as (bio)inks in extrusion‐based 3D (bio)printing thanks to the printability and cell‐laden capacity.<sup>[</sup>\n##REF##26561931##\n15\n##\n<sup>]</sup> In our previous study, we have shown that the fibrin hydrogels laden with urothelial cells (UCs) and smooth muscle cells (SMCs) could maintain sufficient cell viability and proliferation.<sup>[</sup>\n##REF##27940192##\n7\n##\n<sup>]</sup> Nonetheless, the mechanical properties of fibrin were too weak to function as the urethral scaffold. Thus, a new class of hydrogel biomaterials for urethral reconstruction is strongly necessary.</p>", "<p>SA and Gel, as the natural hydrogel biomaterials that are biocompatible and printable, have been widely used in engineered organs.<sup>[</sup>\n##REF##22318897##\n16\n##, ##REF##27898010##\n17\n##, ##REF##27935198##\n18\n##\n<sup>]</sup> There are some unique characteristics for SA and Gel. The polymer chains of SA can be cross‐linked with Ca<sup>2+</sup> to form a stable structure for mechanical support.<sup>[</sup>\n##UREF##2##\n19\n##\n<sup>]</sup> The microenvironment of urethra is filled with urine that has plenty of calcium ions.<sup>[</sup>\n##REF##23377289##\n20\n##\n<sup>]</sup> It is feasible to realize a second cross‐link of SA to reinforce the strength. Gel is a thermosensitive material that transforms from liquid phase to gel state via physical cross‐linking, and maintains the initial structural stability of the 3D‐printed scaffolds.<sup>[</sup>\n##REF##32948593##\n21\n##\n<sup>]</sup> Meanwhile, due to the arginine‐glycine‐aspartic acid (RGD) sequences intrinsic to the Gel chains, it is considered friendly to the enhanced cell attachment and growth.<sup>[</sup>\n##REF##26523399##\n22\n##, ##UREF##3##\n23\n##\n<sup>]</sup>\n</p>", "<p>For 3D printing, the formulation of the inks is the decisive factor for the successful scaffold fabrication.<sup>[</sup>\n##REF##26561931##\n15\n##\n<sup>]</sup> Zhang et al. have designed the low‐density SA (0.8%) and Gel (4.1%) hybrid bioinks for 3D bioprinting.<sup>[</sup>\n##REF##31426033##\n14\n##\n<sup>]</sup> The results showed that the cell viability for the concentration of 0.8% SA was 84 ± 0.7%. Yet, the mechanical properties, printability, and shape fidelity of the scaffolds were insufficient. The cell viability of 2.3% SA was only 68 ± 1.3%, but the fidelity and mechanical properties of the scaffolds were improved due to the increased viscosity of SA. The optimal concentrations of printability ranged from 0.6 to 2.5%, depending on the viscosity of SA. Several other studies have also optimized the formulation of SA and Gel to satisfy the printability of bioinks and improve the viability of cells.<sup>[</sup>\n##REF##29304429##\n24\n##, ##REF##24157694##\n25\n##, ##UREF##4##\n26\n##, ##REF##31782460##\n27\n##\n<sup>]</sup>\n</p>", "<p>On the other hand, to obtain the desired properties of bioinks, certain nanomaterials (e.g., inorganic and carbon nanomaterials) have been integrated with SA/Gel to prepare the nanocomposite bioinks.<sup>[</sup>\n##REF##33326888##\n28\n##, ##REF##29636985##\n29\n##\n<sup>]</sup> Graphene‐based materials are considered to be the reinforcement nanomaterials: the representative derivatives are GO and rGO, with attributes of favorable antibacterial properties,<sup>[</sup>\n##REF##23586616##\n30\n##, ##REF##32254787##\n31\n##\n<sup>]</sup> angiogenic potential,<sup>[</sup>\n##UREF##5##\n32\n##, ##REF##29428812##\n33\n##\n<sup>]</sup> mechanical strength,<sup>[</sup>\n##REF##33321630##\n34\n##, ##REF##33599084##\n35\n##\n<sup>]</sup> as well as low cytotoxicity.<sup>[</sup>\n##UREF##6##\n36\n##\n<sup>]</sup> Studies have suggested that regulating the surface oxygen content of rGO enhances the cell adhesion and proliferation due to the non‐covalent interactions to improve the surface adsorption of rGO.<sup>[</sup>\n##UREF##7##\n37\n##\n<sup>]</sup> In addition, Mukherjee et al. reported that rGO exhibited considerable angiogenic activity in a dose‐dependent manner.<sup>[</sup>\n##UREF##5##\n32\n##\n<sup>]</sup> Cell proliferation and wound healing were also promoted by the increased concentration of reactive oxygen species (ROS) due to the incorporation of rGO.<sup>[</sup>\n##REF##31534523##\n38\n##, ##REF##33684536##\n39\n##\n<sup>]</sup>\n</p>", "<p>To our knowledge, there are still few studies on fabricating the urethral substitutes by the 3D‐printing technology that would function in the harsh urethral microenvironment. The ideal treatment on urethral stricture should exhibit the following characteristics: i) the match of the patch with the structure of urethral decellularized matrix (Figure ##SUPPL##0##S1##, Supporting Information); ii) angiogenesis and reconstruction of urethral functions; iii) inhibition of bioactive factors on urethral fibrosis and scar hyperplasia. In this study, we design a 3D‐printed SA/Gel/rGO patch, by a double‐freeze‐drying process and also cross‐linked by Ca<sup>2+</sup> with enhanced stability, to characterize its anti‐fibrotic, angiogenic, and epitheliogenic properties in urine (<bold>Scheme</bold>\n##FIG##0##\n1\n##). Systematic experiments in vitro and in vivo were conducted to understand the unique features, which would demonstrate the therapeutic efficacy of the patch for urethral reconstruction.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>rGO Characterizations and Ink Preparation</title>", "<p>Commercially available monolayer rGO powder was used. The rGO was dispersed in water according to the information provided by the manufacturer. The monolayer ratio of rGO powder was up to 80%, the diameters were 0.5–5 µm, and the thicknesses were 0.8–1.2 nm. The morphology of rGO was confirmed under scanning electron microscope (SEM) and transmission electron microscope (TEM) (<bold>Figure</bold>\n##FIG##1##\n1a,b##). The stock rGO dispersion (1 mg mL<sup>−1</sup>) was diluted to concentrations in a series of 0.02, 0.05, 0.1, and 0.2 mg mL<sup>−1</sup>, and all suspensions remained stable and homogeneous for several weeks upon evaluation. With the increasing concentration of rGO, the solution color changed from gray to dark (Figure ##FIG##1##1c##). The solutions were also examined under optical microscopy to show the good dispersion with no obvious aggregation for rGO (Figure ##FIG##1##1d–g##). The area distributions of the rGO were mostly at the 1–50 µm<sup>2</sup> range (Figure ##FIG##1##1h–k##). The mean area rate (%) is from 4% to 28% (Figure ##SUPPL##0##S2##, Supporting Information). The results demonstrate that the rGO distributes evenly in the water solution, and most of the rGO particles do not adhere to each other.</p>", "<title>Characterizations of SA/Gel/rGO Hydrogels</title>", "<p>Raman spectroscopic analysis of SA/Gel/rGO shows two characteristic bands of G‐ and D‐bands (<bold>Figure</bold>\n##FIG##2##\n2a##). The D‐band was at ≈1342 cm<sup>−1</sup> and the G‐band was at ≈1584 cm<sup>−1</sup>. The D‐band reflects the disorder between graphite lamellae due to the interference of <italic toggle=\"yes\">sp<sup>2</sup>\n</italic> hybridization of carbon. The G‐band reflects the symmetry and degree of crystallization due to the <italic toggle=\"yes\">sp<sup>2</sup>\n</italic> hybrid in‐plane stretching vibration of carbon crystals. I<sub>D</sub>/I<sub>G</sub> is the intensity ratio between the D‐ and G‐bands, suggesting the degree of defects in the graphite lamellae<sup>[</sup>\n##REF##33982723##\n40\n##, ##REF##34576956##\n41\n##\n<sup>]</sup>; the higher the intensity ratio is, the more defects the C atomic crystal has. Chakraborty reported that the ID/IG ratios of GO and rGO were 0.9 and 1.1, respectively.<sup>[</sup>\n##REF##35548324##\n42\n##\n<sup>]</sup> To verify the incorporation of rGO into the SA/Gel hydrogels, the composition of the SA/Gel/rGO composite was confirmed through Fourier‐transform infrared (FTIR) spectroscopy (Figure ##FIG##2##2b##). The SA hydroxyl bond (O─H) stretching was at ≈3445 cm<sup>−1</sup>, the CH<sub>2</sub> group stretching was at ≈2935 cm<sup>−1</sup>, and the carbonyl bond (C═O) stretching of amide I was at 1632 cm<sup>−1</sup>. The characteristic bands of SA at ≈1632 and 1401 cm<sup>−1</sup> are associated with the carboxyl (─COOH) bond and asymmetric and symmetric stretching peaks of carboxylate salt groups, respectively. The peak at 1542 cm<sup>−1</sup> is the ─NH group stretching of amide II and the peak at 1238 cm<sup>−1</sup> is the ─NH group stretching of amide III of Gel. The peak at 1177 cm<sup>−1</sup> is the C─O─C asymmetric stretching. The peak at 1028 cm<sup>−1</sup> is the C─O─H stretching of SA. The characteristic peaks of rGO at ≈2930 and 2854 cm<sup>−1</sup> are associated with CH<sub>2</sub> and CH<sub>3</sub> groups, respectively. Interestingly, the strong absorption peaks at ≈2930 and 2854 cm<sup>−1</sup> appeared with the increased concentration of rGO. As such, the FTIR spectra clearly indicated the presence of the rGO in the hybrid hydrogels.</p>", "<p>The swelling behavior of a hydrogel construct plays a crucial role in its surface properties and mechanical integrity for biomaterial applications.<sup>[</sup>\n##REF##32310981##\n43\n##, ##REF##32500887##\n44\n##\n<sup>]</sup> The swelling behaviors of the various hydrogel formulations suggested that the swelling ratio increased when the concentration of SA was elevated (1%, 1.5%, and 2%) and the concentration of rGO was reduced (Figure ##FIG##2##2c##). The higher content of SA enhanced the hydrophilicity of the hydrogel network to improve the equilibrium swelling ratio of SA. For the positive effect of rGO concentration, it was likely due to the ability of rGO to interact with the hydrogen bonds of SA/Gel to act like a multi‐functional cross‐linking agent, therefore increasing the density of the cross‐linked network of the SA/Gel hydrogels at a higher concentration.</p>", "<p>Overtime, the hydrogels would be subjected to hydrolysis and other forms of degradation after being immersed in the liquid environment. The degree of degradation was evaluated by the mass remaining (%) of the hydrogels over 21 days. The various degrees of degradation showed a significant weight reduction in the first 7 days (Figure ##FIG##2##2d##), which might be due to the hydrolysis of the hydrogels. The remaining mass percentages (%) of the hydrogels are ≈42.62 ± 1.98% to 55.58 ± 1.44% in the different groups. In the next few days, there was a slight decrease in the weights of the hydrogels, which might correspond to the reduced degradation of the cross‐linked structure. The total weights of hydrogels had no significant differences between the SA/Gel hydrogels with and without rGO, implying that the incorporation of rGO did not noticeably affect the degradation of the hydrogel formulations.</p>", "<title>Morphological Evaluations on the SA/Gel/rGO Hydrogels</title>", "<p>The colors of the SA/Gel/rGO hydrogels were observed to be darker with the increased concentration of rGO. The SEM images reveal the porous structures of the SA/Gel/rGO hydrogels with different concentrations of rGO (0, 0.02, 0.05, 0.1, and 0.2 mg mL<sup>−1</sup>) (<bold>Figure</bold>\n##FIG##3##\n3a–j##). As the rGO loading increases, the pore size decreases and the pore density increases, further indicating that a high rGO concentration led to a high cross‐linking density, resulting in smaller pore sizes in composite hydrogels (Figure ##FIG##3##3b–j##). The pore size of hydrogels is highly correlated with cell adhesion, growth and proliferation, and nutrient exchange in the matrix. Most importantly, the hydrogels with a porous structure could facilitate efficient biomolecule transport within the environment.<sup>[</sup>\n##REF##35548324##\n42\n##\n<sup>]</sup> However, it should be noted that the pore sizes obtained by SEM observations may not indicate the actual pore sizes of the hydrogels under the hydrated states.</p>", "<p>From the distributions of the pore sizes for the SA/Gel/rGO hydrogels (Figure ##FIG##3##3k–o##), there were network structures with the pore sizes of &lt;100 µm for all the hydrogels. The distributions of the pore sizes of the SA/Gel hydrogel were mainly in the range of 80–200 µm; the pore sizes of the SA/Gel/rGO hydrogels decreased with the increasing concentration of rGO (Figure ##FIG##3##3p##). The pore sizes of the SA/Gel and SA/Gel/rGO<sub>0.02</sub> hydrogels were 92.82 ± 12.60 and 91.59 ± 11.6 µm, respectively . There was significant difference between SA/Gel/rGO<sub>0.05</sub> (69.39 ± 7.97 µm) and SA/Gel/rGO<sub>0.1</sub> (47.20 ± 7.26 µm), compared with the SA/Gel hydrogels. The pore size of SA/Gel/rGO<sub>0.2</sub> was the smallest among all the hydrogels (36.29 ± 17.77 µm, ). These results showed that the incorporation of rGO indeed influenced the pore size of the hydrogels in a dose‐dependent pattern.</p>", "<title>Morphological and Mechanical Evaluations on SA/Gel/rGO Patches</title>", "<p>We 3D‐printed various SA/Gel scaffolds with different concentrations of rGO from 0 to 0.2 mg mL<sup>−1</sup> (<bold>Figure</bold>\n##FIG##4##\n4a##). We used two freeze‐drying and one cross‐linking process to obtain the patches post‐printing. The gross morphologies were not significantly different except that the color changed from white to dark at the rGO concentration was increased. The 3D printer was an Organ Printing United system (Figure ##SUPPL##0##S3a##, Supporting Information). The mechanical properties of the SA/Gel/rGO patches are a valuable element for urethral repair and tissue regeneration. The tensile mechanical characteristics of the SA/Gel/rGO patches with different concentrations of rGO were evaluated by the stretching process of the patches (Figure ##SUPPL##0##S3b##, Supporting Information), the length of the patches that stretched between the upper and lower grips of the tensile machine could be adjusted. Then, each sample was stretched at 10 mm per minute until reaching its breaking points. All the samples exhibited the linear elastic behavior (Figure ##FIG##4##4b##). Compared with the patches containing rGO, the SA/Gel patch without rGO showed a lower modulus, 139.68 ± 0.144 KPa (Figure ##FIG##4##4c##). The tensile strengths of the SA/Gel patches at concentrations of 0, 0.02, 0.05, and 0.2 mg mL<sup>−1</sup> of rGO were in the range of 139.87 ± 1.02–296.65 ± 1.11 KPa (Figure ##FIG##4##4d##). The tensile strength of the SA/Gel/rGO<sub>0.2</sub> patch was higher (296.65 ±1.11 KPa) when the concentration of rGO was increased. The elevation of strain at break in the SA/Gel/rGO<sub>0.05</sub> was 211.10 ± 1.34% (Figure ##FIG##4##4e##). Besides, the patches with appropriate elongation are flexible and elastic. Interestingly, the strain at break of SA/Gel/rGO<sub>0.2</sub> patch was 137.77 ± 0.86% . These observations might be attributed to the SA/Gel patch to become fragile under the higher concentration of rGO. The SA/Gel/rGO patch was saturable and exhibits excellent mechanical properties to fit the requirement of urethral reconstruction. Interestingly, the rGO hybrid patches appeared to possess higher tensile strengths and Young's modulus. The rGO<sub>0.05</sub> was an appropriate concentration to achieve the best mechanical performance among the groups examined.</p>", "<title>Characteristics of Cell Behaviors</title>", "<p>SA/Gel/rGO patches served as the templates for cell adhesion, and proliferation, thus superior cytocompatibility is required. The characteristics of cell survival and proliferation were evaluated through seeding fibroblasts on SA/Gel/rGO hydrogels containing different concentrations of rGO. The live and dead cells were stained with calcein AM and propidium iodides (PI) after 1 day, respectively. The fluorescence of living cells in SA/Gel/rGO hydrogels of 0.1 and 0.2 mg mL<sup>−1</sup> of rGO was less (<bold>Figure</bold>\n##FIG##5##\n5a##). The increased number of dead cells might have been affected in part by the relatively high concentrations of rGO present. The cell morphologies were further observed by SEM, where fibroblasts were generally located within the pores of the 3D‐printed SA/Gel/rGO patches (Figure ##SUPPL##0##S4##, Supporting Information).</p>", "<p>From the expression patterns of differentially expressed proteins (DEPs) by fibroblasts (cell density: 1 × 10<sup>7</sup>) with the different concentrations of rGO (Figure ##FIG##5##5b##), the cells treated with rGO of 0.02, 0.05, and 0.1 mg mL<sup>−1</sup> were compared with the cells with no treatment. The culture time was 72 h. Some biological processes and pathways, which are correlated with tissue regeneration or tissue repair, were observed to be significantly enriched in these DEPs (Figures ##SUPPL##0##S5a,S6a##, and ##SUPPL##0##S7a##, Supporting Information). For example, it is reported that the transmembrane receptor protein tyrosine kinase signaling pathway has a role in promoting sprouting of the angiogenic endothelium.<sup>[</sup>\n##REF##20445537##\n45\n##\n<sup>]</sup> The Ras/MAPK signaling cascade plays an important role in zebrafish heart regeneration.<sup>[</sup>\n##UREF##8##\n46\n##\n<sup>]</sup> The cell proliferation process is required for cardiomyocytes regeneration.<sup>[</sup>\n##REF##28185170##\n47\n##\n<sup>]</sup> In addition, the cellular components related to platelet alpha granule, secretory veside, vesicle lumen, and endomembrane system were enriched in DEPs treated with rGO<sub>0.02</sub> (Figure ##SUPPL##0##S5b##, Supporting Information). Similar situations were observed when treated with rGO<sub>0.05</sub> and treated with rGO<sub>0.1</sub> (Figures ##SUPPL##0##S6b## and ##SUPPL##0##S7b##, Supporting Information). In addition, in molecular functions, the growth factor binding, growth factor activity, receptor‐ligand activity, and signaling receptor activator were enriched (Figures ##SUPPL##0##S5c,S6c##, and ##SUPPL##0##S7c##, Supporting Information). Similarly, the enriched Ras and MAPK signaling pathways were also observed via the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis (Figures ##SUPPL##0##S5d,S6d##, and ##SUPPL##0##S7d##, Supporting Information). The genes involved in these biological processes and pathways might contribute to angiogenesis mediated by rGO. The bubble graph was also shown for gene ontology enrichment treated with rGO of 0.02, 0.05, and 0.1 mg mL<sup>−1</sup> for the biological process, molecular process, and cellular components (Figure ##SUPPL##0##S8a–i##, Supporting Information).</p>", "<p>Scratch assay is a standard for cell migration study in vitro. The migration of fibroblasts for the wound healing process is of great importance; after the injury, fibroblasts were used to proliferate and migrate from neighboring tissues into the wound area.<sup>[</sup>\n##REF##20824344##\n48\n##\n<sup>]</sup> To evaluate the potential of rGO in enhancing the migration of fibroblasts, a time‐dependent experiment was carried out (0–24 h). The results of the scratch assay showed that the migration ability of fibroblasts was greatly improved within 24 h after the treatment with rGO concentrations of 0.02 and 0.05 mg mL<sup>−1</sup> (Figure ##FIG##5##5c##). With the increasing concentration of rGO, the proliferation of fibroblasts and wound healing increased first and then decreased, with a maximum migration rate of 61.18 ± 2.61% for rGO at 0.05 mg mL<sup>−1</sup> (Figure ##FIG##5##5d##). Of note, when the concentration of rGO was set at 0.2 mg mL<sup>−1</sup>, the migration and proliferation of fibroblasts were significantly inhibited (26.39 ± 3.93%).</p>", "<p>Cell counting kit‐8 (CCK‐8) assay was subsequently used to assess the cytotoxic effect of SA/Gel/rGO patches on the fibroblasts (Figure ##FIG##5##5e##). After 1 and 4 days of cell culture, the metabolic activities of cells on the SA/Gel/rGO patches exhibited inhibitory effects. The higher concentration of rGO revealed inhospitable environments to cell metabolic activities during this time point. However, after 7 days of cell culture, the cell metabolic activities on SA/Gel/rGO<sub>0.02</sub> and SA/Gel/rGO<sub>0.05</sub> became higher than the remaining patches close to that for the control patches without rGO. Consequently, it might be undesirably toxic to cells at the concentration of rGO above 0.05 mg mL<sup>−1</sup>, in alignment with the cell viability staining results. Some reports have suggested that GO concentration of 50 µg mL<sup>−1</sup> on fibroblasts led to significant cytotoxicity, while rGO at a concentration higher than 0.1 µg mL<sup>−1</sup> would be toxic to endothelial cells.<sup>[</sup>\n##UREF##5##\n32\n##, ##REF##21082807##\n49\n##\n<sup>]</sup> Our results were overall consistent with the previous studies.</p>", "<title>Urethrogram and Gross Morphology</title>", "<p>The safety and functions of the SA/Gel/rGO patches were further proven in clinically relevant rabbit urethral injury models. According to the results of the in vitro mechanical test and biocompatibility of the scaffold, the patches without rGO were selected as the control group, and the rGO concentration of 0.05 and 0.2 mg mL<sup>−1</sup> was selected as the experimental group. The patches were sutured to the dorsal urethral defect, and the injury model of the urethra and the surgical process of repair are shown in Figure ##SUPPL##0##S9## (Supporting Information). The recovery of the repaired urethras was detected at 4 and 8 weeks after the operation. The 4‐ and 8‐week urethrogram of the SA/Gel group displayed narrow lumens because of scar formation (<bold>Figure</bold>\n##FIG##6##\n6a,d##). The SA/Gel/rGO<sub>0.05</sub> (Figure ##FIG##6##6b,e##) groups showed wide lumens of urethras similar to the normal urethra (Figure ##FIG##6##6g##). In the 4‐week urethrogram, the SA/Gel/rGO<sub>0.2</sub> groups had a narrower urethral lumen, the widths developed larger at 8 weeks (Figure ##FIG##6##6c,f##). The reason might be the inflammation‐related swelling of urethral tissue caused by rGO with high concentration. The blockage rate determines whether and how much urine can flow out. The blockage ratio of the urethras treated with the SA/Gel/rGO<sub>0.05</sub> patches could approach that of normal lumens (Figure ##FIG##6##6i##). After the incision of the ventral urethral wall, the dorsal wall could be exposed. Gross morphology revealed that urethral tissue in the SA/Gel/rGO<sub>0.05</sub> and SA/Gel/rGO<sub>0.2</sub> groups was significantly better than that in the SA/Gel group. The SA/Gel group showed the growth of severe scar‐like tissue in the urethra (Figure ##FIG##6##6j,m##). At 8 weeks, both of SA/Gel/rGO<sub>0.05</sub> (Figure ##FIG##6##6n##) and SA/Gel/rGO<sub>0.2</sub> (Figure ##FIG##6##6o##) groups showed smooth epithelial layer similar to the normal urethra of rabbits (Figure ##FIG##6##6h##). However, SA/Gel/rGO<sub>0.2</sub> group at 4 weeks (Figure ##FIG##6##6i##) revealed red and swollen mucosa compared with that in the SA/Gel/rGO<sub>0.2</sub> group (Figure ##FIG##6##6k##), which is consistent with the lumen width in the urethrogram. Therefore, the treatment of urethral injury could be improved by choosing a low dose of rGO for future application.</p>", "<title>Histological Evaluations</title>", "<p>The histology analyses of urethral reconstruction at 4‐ and 8‐weeks post‐surgery were performed by hematoxylin and eosin (H&amp;E) and Masson's trichrome staining. The SA/Gel patches with/without rGO showed various outcomes. Additionally, there was no significant infection during the experimental period, suggesting good biocompatibility of the patches. According to the histology, the urethras treated with the SA/Gel patches were associated with thinner/uncomplete urothelium layers, fewer blood vessels, and thicker submucosal tissue (<bold>Figure</bold>\n##FIG##7##\n7a–d##). Due to the lack of regenerated urothelium layers, and over‐deposited ECM, the urethra developed to urethral stricture. In contrast, the reconstructed urethra treated with the SA/Gel/rGO patches had the nearly normal urothelium layers, submucosal tissue, and blood vessels. The continuous and complete urothelium layers were formed on the lumen surfaces for the SA/Gel/rGO<sub>0.05</sub> group after 4‐ and 8‐weeks post‐surgery. However, the SA/Gel/rGO<sub>0.2</sub> patches could lead to a short period of swelling and inflammation in 4 weeks. These results suggested that rGO at a lower concentration (0.05 mg mL<sup>−1</sup>) could perform best function in the regeneration of urothelium layers and blood vessels, but not at a higher concentration (0.2 mg mL<sup>−1</sup>). The mucosal coverage ratios by the SA/Gel/rGO patches were measured (Figure ##FIG##7##7e,f##). The urethras treated with the SA/Gel/rGO<sub>0.05</sub> patches had more significant coverages, compared with the other groups. The urethral collagen thicknesses were also measured after the wound healing (Figure ##FIG##7##7g,h##). The SA/Gel/rGO<sub>0.05</sub> patch could induce a less collagen deposition under the mucosa, therefore developing a scar‐less wound healing. The histology showed that an optimal concentration of rGO would promote the regeneration of epithelial cells and decrease submucosal ECM deposition to inhibit urethral fibrosis.</p>", "<title>Immunofluorescence</title>", "<p>The distribution of cytokeratin was investigated based on the expression of epithelial cytokeratin AE1/AE3 (an important membrane surface protein marker of ECs) via immunofluorescence staining of the urethra. The expression level for AE1/AE3 on the SA/Gel/rGO<sub>0.05</sub> at 4‐and 8‐weeks post‐surgery (4W: 16.70 ± 2.66 and 8W: 24.72 ± 2.81) is significantly higher than that in the other groups. Although the continuous urothelium layer is formed, the urothelium layer of the SA/Gel/rGO<sub>0.2</sub> group is thinner than that of the SA/Gel/rGO<sub>0.05</sub> group. The expression of cytokeratin in the SA/Gel group is low (4W: 8.19 ± 1.72 and 8W: 8.29 ± 1.65), there is no complete regeneration of a discontinuous urothelium layer (<bold>Figure</bold>\n##FIG##8##\n8a,e##). It suggests that the introduction of rGO has the potential to promote the regeneration of urothelium layers. Studies have shown that the significant pro‐angiogenic properties of rGO depend on its concentration.<sup>[</sup>\n##UREF##5##\n32\n##, ##REF##29892387##\n50\n##\n<sup>]</sup> In the results of fluorescence staining at 4‐weeks post‐surgery, the SA/Gel/rGO<sub>0.05</sub> group showed a number of CD 31‐positive cells (the blood vessels labeled by CD 31), which were more than them in the SA/Gel and SA/Gel/rGO<sub>0.2</sub> group. At the beginning process of urethral regeneration with inflammation, the vessels in tissue would be much more obvious that is consistent with the results.<sup>[</sup>\n##REF##12490959##\n51\n##\n<sup>]</sup> For SA/Gel/rGO<sub>0.05</sub> and SA/Gel/rGO<sub>0.2</sub> groups, the number of CD 31‐positive cells at 8 weeks (SA/Gel/rGO<sub>0.05</sub>: 14.10 ± 3.99 and SA/Gel/rGO<sub>0.2</sub>: 8.63 ± 1.23) are lower than them at 4 weeks (SA/Gel/rGO<sub>0.05</sub>: 15.35 ± 4.55 and SA/Gel/rGO<sub>0.2</sub>: 14.77 ± 3.07) (Figure ##FIG##8##8b,f##).</p>", "<p>Different degrees of inflammation response at the injured sites would appear because of the transplantation of external scaffolds. CD 206 is used to label M2 macrophages.<sup>[</sup>\n##REF##31903147##\n52\n##\n<sup>]</sup> The results showed that the number of CD206‐positive cells in the SA/Gel group was the lowest. The number of CD206 positive cells in the SA/Gel/rGO<sub>0.05</sub> group in 4‐and 8‐weeks post‐surgery (4W: 36.36 ± 3.54 and 8W: 40.74 ± 2.23) were significantly higher than them in the other groups, indicating that the lower level of local inflammatory response was caused by the rGO treated group (Figure ##FIG##8##8c,g##). This indicated that rGO appeared to promote the transition of M2 macrophages and inhibit the inflammatory response during the urethral repair. Meanwhile, the low inflammatory response might promote the proliferation and activation of fibroblasts. The positive expression of proliferating cell nuclear antigen (PCNA) was obviously increased in the SA/Gel/rGO<sub>0.05</sub> group at 4‐and 8‐weeks post‐surgery (4W: 7.77 ± 0.25 and 8W: 8.46 ± 0.94) (Figure ##FIG##8##8d,h##).</p>", "<title>Flow Cytometric Analysis of RAW264.7 Surface Markers</title>", "<p>To evaluate the macrophages polarization status, the M1 surface markers (CD68, CD86) and M2 surface markers (CD206) in RAW 264.7 macrophages were further analyzed by flow cytometric (<bold>Figure</bold>\n##FIG##9##\n9a##). The results revealed that more than 90% of the cells strongly expressed surface antigens such as CD68. The inflammatory cell density was evaluated by CD86 staining. The CD86 inflammatory cell density in the 0.02rGO and 0.1rGO groups was no significant difference in the control group. However, as the amount of rGO increases, it leads to the increase of CD206‐positive macrophages. The expression of CD86 in M1 type was significantly increased by LPS + INF‐r, and the expression of CD206‐positive macrophages was significantly higher than that in the control group after the introduction of rGO (Figure ##FIG##9##9b##). The results of flow cytometry analysis showed that the addition of rGO promoted the polarization of macrophages to the M2 phenotype in vivo.</p>", "<title>qRT‐PCR Analysis of mRNA Levels of the Markers in Tissue and RAW 264.7 Cells</title>", "<p>The gene expression of Arg1, Fizz, and Ym1 in the 0.02rGO group and the 0.1rGO group was significantly higher than that in the control group, and the gene expression of iNOS and TGF‐β in the 0.02 rGO group and the 0.1rGO group was significantly lower than that in the control group (<bold>Figure</bold>\n##FIG##10##\n10a##). At the mRNA level, rGO treatment was associated with significant increases in Arg1, Fizz, and Ym1 expression compared to the control and M1 groups, and the gene expression of iNOS and TGF‐β in the 0.02 rGO group and the 0.1rGO group was significantly lower than that in the M1 group (Figure ##FIG##10##10b##). These results suggest that rGO may also have an inducing effect on the macrophage anti‐inflammatory phenotype in vivo. The expression of SA/Gel/rGO<sub>0.05</sub> α‐SMA, COL1A1, COL3A1, CD206, CD31, TGF‐β2 was significantly higher than that in the control group. The expression of TGFBR1, β‐catenin, and VWF was no significant difference in the control group (Figure ##FIG##10##10c–i##). Overall, the low‐dose rGO effectively promoted epithelization and neovascularization while reducing inflammation. These results suggested that rGO can promote urethral healing and regeneration.</p>" ]
[ "<title>Results and Discussion</title>", "<title>rGO Characterizations and Ink Preparation</title>", "<p>Commercially available monolayer rGO powder was used. The rGO was dispersed in water according to the information provided by the manufacturer. The monolayer ratio of rGO powder was up to 80%, the diameters were 0.5–5 µm, and the thicknesses were 0.8–1.2 nm. The morphology of rGO was confirmed under scanning electron microscope (SEM) and transmission electron microscope (TEM) (<bold>Figure</bold>\n##FIG##1##\n1a,b##). The stock rGO dispersion (1 mg mL<sup>−1</sup>) was diluted to concentrations in a series of 0.02, 0.05, 0.1, and 0.2 mg mL<sup>−1</sup>, and all suspensions remained stable and homogeneous for several weeks upon evaluation. With the increasing concentration of rGO, the solution color changed from gray to dark (Figure ##FIG##1##1c##). The solutions were also examined under optical microscopy to show the good dispersion with no obvious aggregation for rGO (Figure ##FIG##1##1d–g##). The area distributions of the rGO were mostly at the 1–50 µm<sup>2</sup> range (Figure ##FIG##1##1h–k##). The mean area rate (%) is from 4% to 28% (Figure ##SUPPL##0##S2##, Supporting Information). The results demonstrate that the rGO distributes evenly in the water solution, and most of the rGO particles do not adhere to each other.</p>", "<title>Characterizations of SA/Gel/rGO Hydrogels</title>", "<p>Raman spectroscopic analysis of SA/Gel/rGO shows two characteristic bands of G‐ and D‐bands (<bold>Figure</bold>\n##FIG##2##\n2a##). The D‐band was at ≈1342 cm<sup>−1</sup> and the G‐band was at ≈1584 cm<sup>−1</sup>. The D‐band reflects the disorder between graphite lamellae due to the interference of <italic toggle=\"yes\">sp<sup>2</sup>\n</italic> hybridization of carbon. The G‐band reflects the symmetry and degree of crystallization due to the <italic toggle=\"yes\">sp<sup>2</sup>\n</italic> hybrid in‐plane stretching vibration of carbon crystals. I<sub>D</sub>/I<sub>G</sub> is the intensity ratio between the D‐ and G‐bands, suggesting the degree of defects in the graphite lamellae<sup>[</sup>\n##REF##33982723##\n40\n##, ##REF##34576956##\n41\n##\n<sup>]</sup>; the higher the intensity ratio is, the more defects the C atomic crystal has. Chakraborty reported that the ID/IG ratios of GO and rGO were 0.9 and 1.1, respectively.<sup>[</sup>\n##REF##35548324##\n42\n##\n<sup>]</sup> To verify the incorporation of rGO into the SA/Gel hydrogels, the composition of the SA/Gel/rGO composite was confirmed through Fourier‐transform infrared (FTIR) spectroscopy (Figure ##FIG##2##2b##). The SA hydroxyl bond (O─H) stretching was at ≈3445 cm<sup>−1</sup>, the CH<sub>2</sub> group stretching was at ≈2935 cm<sup>−1</sup>, and the carbonyl bond (C═O) stretching of amide I was at 1632 cm<sup>−1</sup>. The characteristic bands of SA at ≈1632 and 1401 cm<sup>−1</sup> are associated with the carboxyl (─COOH) bond and asymmetric and symmetric stretching peaks of carboxylate salt groups, respectively. The peak at 1542 cm<sup>−1</sup> is the ─NH group stretching of amide II and the peak at 1238 cm<sup>−1</sup> is the ─NH group stretching of amide III of Gel. The peak at 1177 cm<sup>−1</sup> is the C─O─C asymmetric stretching. The peak at 1028 cm<sup>−1</sup> is the C─O─H stretching of SA. The characteristic peaks of rGO at ≈2930 and 2854 cm<sup>−1</sup> are associated with CH<sub>2</sub> and CH<sub>3</sub> groups, respectively. Interestingly, the strong absorption peaks at ≈2930 and 2854 cm<sup>−1</sup> appeared with the increased concentration of rGO. As such, the FTIR spectra clearly indicated the presence of the rGO in the hybrid hydrogels.</p>", "<p>The swelling behavior of a hydrogel construct plays a crucial role in its surface properties and mechanical integrity for biomaterial applications.<sup>[</sup>\n##REF##32310981##\n43\n##, ##REF##32500887##\n44\n##\n<sup>]</sup> The swelling behaviors of the various hydrogel formulations suggested that the swelling ratio increased when the concentration of SA was elevated (1%, 1.5%, and 2%) and the concentration of rGO was reduced (Figure ##FIG##2##2c##). The higher content of SA enhanced the hydrophilicity of the hydrogel network to improve the equilibrium swelling ratio of SA. For the positive effect of rGO concentration, it was likely due to the ability of rGO to interact with the hydrogen bonds of SA/Gel to act like a multi‐functional cross‐linking agent, therefore increasing the density of the cross‐linked network of the SA/Gel hydrogels at a higher concentration.</p>", "<p>Overtime, the hydrogels would be subjected to hydrolysis and other forms of degradation after being immersed in the liquid environment. The degree of degradation was evaluated by the mass remaining (%) of the hydrogels over 21 days. The various degrees of degradation showed a significant weight reduction in the first 7 days (Figure ##FIG##2##2d##), which might be due to the hydrolysis of the hydrogels. The remaining mass percentages (%) of the hydrogels are ≈42.62 ± 1.98% to 55.58 ± 1.44% in the different groups. In the next few days, there was a slight decrease in the weights of the hydrogels, which might correspond to the reduced degradation of the cross‐linked structure. The total weights of hydrogels had no significant differences between the SA/Gel hydrogels with and without rGO, implying that the incorporation of rGO did not noticeably affect the degradation of the hydrogel formulations.</p>", "<title>Morphological Evaluations on the SA/Gel/rGO Hydrogels</title>", "<p>The colors of the SA/Gel/rGO hydrogels were observed to be darker with the increased concentration of rGO. The SEM images reveal the porous structures of the SA/Gel/rGO hydrogels with different concentrations of rGO (0, 0.02, 0.05, 0.1, and 0.2 mg mL<sup>−1</sup>) (<bold>Figure</bold>\n##FIG##3##\n3a–j##). As the rGO loading increases, the pore size decreases and the pore density increases, further indicating that a high rGO concentration led to a high cross‐linking density, resulting in smaller pore sizes in composite hydrogels (Figure ##FIG##3##3b–j##). The pore size of hydrogels is highly correlated with cell adhesion, growth and proliferation, and nutrient exchange in the matrix. Most importantly, the hydrogels with a porous structure could facilitate efficient biomolecule transport within the environment.<sup>[</sup>\n##REF##35548324##\n42\n##\n<sup>]</sup> However, it should be noted that the pore sizes obtained by SEM observations may not indicate the actual pore sizes of the hydrogels under the hydrated states.</p>", "<p>From the distributions of the pore sizes for the SA/Gel/rGO hydrogels (Figure ##FIG##3##3k–o##), there were network structures with the pore sizes of &lt;100 µm for all the hydrogels. The distributions of the pore sizes of the SA/Gel hydrogel were mainly in the range of 80–200 µm; the pore sizes of the SA/Gel/rGO hydrogels decreased with the increasing concentration of rGO (Figure ##FIG##3##3p##). The pore sizes of the SA/Gel and SA/Gel/rGO<sub>0.02</sub> hydrogels were 92.82 ± 12.60 and 91.59 ± 11.6 µm, respectively . There was significant difference between SA/Gel/rGO<sub>0.05</sub> (69.39 ± 7.97 µm) and SA/Gel/rGO<sub>0.1</sub> (47.20 ± 7.26 µm), compared with the SA/Gel hydrogels. The pore size of SA/Gel/rGO<sub>0.2</sub> was the smallest among all the hydrogels (36.29 ± 17.77 µm, ). These results showed that the incorporation of rGO indeed influenced the pore size of the hydrogels in a dose‐dependent pattern.</p>", "<title>Morphological and Mechanical Evaluations on SA/Gel/rGO Patches</title>", "<p>We 3D‐printed various SA/Gel scaffolds with different concentrations of rGO from 0 to 0.2 mg mL<sup>−1</sup> (<bold>Figure</bold>\n##FIG##4##\n4a##). We used two freeze‐drying and one cross‐linking process to obtain the patches post‐printing. The gross morphologies were not significantly different except that the color changed from white to dark at the rGO concentration was increased. The 3D printer was an Organ Printing United system (Figure ##SUPPL##0##S3a##, Supporting Information). The mechanical properties of the SA/Gel/rGO patches are a valuable element for urethral repair and tissue regeneration. The tensile mechanical characteristics of the SA/Gel/rGO patches with different concentrations of rGO were evaluated by the stretching process of the patches (Figure ##SUPPL##0##S3b##, Supporting Information), the length of the patches that stretched between the upper and lower grips of the tensile machine could be adjusted. Then, each sample was stretched at 10 mm per minute until reaching its breaking points. All the samples exhibited the linear elastic behavior (Figure ##FIG##4##4b##). Compared with the patches containing rGO, the SA/Gel patch without rGO showed a lower modulus, 139.68 ± 0.144 KPa (Figure ##FIG##4##4c##). The tensile strengths of the SA/Gel patches at concentrations of 0, 0.02, 0.05, and 0.2 mg mL<sup>−1</sup> of rGO were in the range of 139.87 ± 1.02–296.65 ± 1.11 KPa (Figure ##FIG##4##4d##). The tensile strength of the SA/Gel/rGO<sub>0.2</sub> patch was higher (296.65 ±1.11 KPa) when the concentration of rGO was increased. The elevation of strain at break in the SA/Gel/rGO<sub>0.05</sub> was 211.10 ± 1.34% (Figure ##FIG##4##4e##). Besides, the patches with appropriate elongation are flexible and elastic. Interestingly, the strain at break of SA/Gel/rGO<sub>0.2</sub> patch was 137.77 ± 0.86% . These observations might be attributed to the SA/Gel patch to become fragile under the higher concentration of rGO. The SA/Gel/rGO patch was saturable and exhibits excellent mechanical properties to fit the requirement of urethral reconstruction. Interestingly, the rGO hybrid patches appeared to possess higher tensile strengths and Young's modulus. The rGO<sub>0.05</sub> was an appropriate concentration to achieve the best mechanical performance among the groups examined.</p>", "<title>Characteristics of Cell Behaviors</title>", "<p>SA/Gel/rGO patches served as the templates for cell adhesion, and proliferation, thus superior cytocompatibility is required. The characteristics of cell survival and proliferation were evaluated through seeding fibroblasts on SA/Gel/rGO hydrogels containing different concentrations of rGO. The live and dead cells were stained with calcein AM and propidium iodides (PI) after 1 day, respectively. The fluorescence of living cells in SA/Gel/rGO hydrogels of 0.1 and 0.2 mg mL<sup>−1</sup> of rGO was less (<bold>Figure</bold>\n##FIG##5##\n5a##). The increased number of dead cells might have been affected in part by the relatively high concentrations of rGO present. The cell morphologies were further observed by SEM, where fibroblasts were generally located within the pores of the 3D‐printed SA/Gel/rGO patches (Figure ##SUPPL##0##S4##, Supporting Information).</p>", "<p>From the expression patterns of differentially expressed proteins (DEPs) by fibroblasts (cell density: 1 × 10<sup>7</sup>) with the different concentrations of rGO (Figure ##FIG##5##5b##), the cells treated with rGO of 0.02, 0.05, and 0.1 mg mL<sup>−1</sup> were compared with the cells with no treatment. The culture time was 72 h. Some biological processes and pathways, which are correlated with tissue regeneration or tissue repair, were observed to be significantly enriched in these DEPs (Figures ##SUPPL##0##S5a,S6a##, and ##SUPPL##0##S7a##, Supporting Information). For example, it is reported that the transmembrane receptor protein tyrosine kinase signaling pathway has a role in promoting sprouting of the angiogenic endothelium.<sup>[</sup>\n##REF##20445537##\n45\n##\n<sup>]</sup> The Ras/MAPK signaling cascade plays an important role in zebrafish heart regeneration.<sup>[</sup>\n##UREF##8##\n46\n##\n<sup>]</sup> The cell proliferation process is required for cardiomyocytes regeneration.<sup>[</sup>\n##REF##28185170##\n47\n##\n<sup>]</sup> In addition, the cellular components related to platelet alpha granule, secretory veside, vesicle lumen, and endomembrane system were enriched in DEPs treated with rGO<sub>0.02</sub> (Figure ##SUPPL##0##S5b##, Supporting Information). Similar situations were observed when treated with rGO<sub>0.05</sub> and treated with rGO<sub>0.1</sub> (Figures ##SUPPL##0##S6b## and ##SUPPL##0##S7b##, Supporting Information). In addition, in molecular functions, the growth factor binding, growth factor activity, receptor‐ligand activity, and signaling receptor activator were enriched (Figures ##SUPPL##0##S5c,S6c##, and ##SUPPL##0##S7c##, Supporting Information). Similarly, the enriched Ras and MAPK signaling pathways were also observed via the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis (Figures ##SUPPL##0##S5d,S6d##, and ##SUPPL##0##S7d##, Supporting Information). The genes involved in these biological processes and pathways might contribute to angiogenesis mediated by rGO. The bubble graph was also shown for gene ontology enrichment treated with rGO of 0.02, 0.05, and 0.1 mg mL<sup>−1</sup> for the biological process, molecular process, and cellular components (Figure ##SUPPL##0##S8a–i##, Supporting Information).</p>", "<p>Scratch assay is a standard for cell migration study in vitro. The migration of fibroblasts for the wound healing process is of great importance; after the injury, fibroblasts were used to proliferate and migrate from neighboring tissues into the wound area.<sup>[</sup>\n##REF##20824344##\n48\n##\n<sup>]</sup> To evaluate the potential of rGO in enhancing the migration of fibroblasts, a time‐dependent experiment was carried out (0–24 h). The results of the scratch assay showed that the migration ability of fibroblasts was greatly improved within 24 h after the treatment with rGO concentrations of 0.02 and 0.05 mg mL<sup>−1</sup> (Figure ##FIG##5##5c##). With the increasing concentration of rGO, the proliferation of fibroblasts and wound healing increased first and then decreased, with a maximum migration rate of 61.18 ± 2.61% for rGO at 0.05 mg mL<sup>−1</sup> (Figure ##FIG##5##5d##). Of note, when the concentration of rGO was set at 0.2 mg mL<sup>−1</sup>, the migration and proliferation of fibroblasts were significantly inhibited (26.39 ± 3.93%).</p>", "<p>Cell counting kit‐8 (CCK‐8) assay was subsequently used to assess the cytotoxic effect of SA/Gel/rGO patches on the fibroblasts (Figure ##FIG##5##5e##). After 1 and 4 days of cell culture, the metabolic activities of cells on the SA/Gel/rGO patches exhibited inhibitory effects. The higher concentration of rGO revealed inhospitable environments to cell metabolic activities during this time point. However, after 7 days of cell culture, the cell metabolic activities on SA/Gel/rGO<sub>0.02</sub> and SA/Gel/rGO<sub>0.05</sub> became higher than the remaining patches close to that for the control patches without rGO. Consequently, it might be undesirably toxic to cells at the concentration of rGO above 0.05 mg mL<sup>−1</sup>, in alignment with the cell viability staining results. Some reports have suggested that GO concentration of 50 µg mL<sup>−1</sup> on fibroblasts led to significant cytotoxicity, while rGO at a concentration higher than 0.1 µg mL<sup>−1</sup> would be toxic to endothelial cells.<sup>[</sup>\n##UREF##5##\n32\n##, ##REF##21082807##\n49\n##\n<sup>]</sup> Our results were overall consistent with the previous studies.</p>", "<title>Urethrogram and Gross Morphology</title>", "<p>The safety and functions of the SA/Gel/rGO patches were further proven in clinically relevant rabbit urethral injury models. According to the results of the in vitro mechanical test and biocompatibility of the scaffold, the patches without rGO were selected as the control group, and the rGO concentration of 0.05 and 0.2 mg mL<sup>−1</sup> was selected as the experimental group. The patches were sutured to the dorsal urethral defect, and the injury model of the urethra and the surgical process of repair are shown in Figure ##SUPPL##0##S9## (Supporting Information). The recovery of the repaired urethras was detected at 4 and 8 weeks after the operation. The 4‐ and 8‐week urethrogram of the SA/Gel group displayed narrow lumens because of scar formation (<bold>Figure</bold>\n##FIG##6##\n6a,d##). The SA/Gel/rGO<sub>0.05</sub> (Figure ##FIG##6##6b,e##) groups showed wide lumens of urethras similar to the normal urethra (Figure ##FIG##6##6g##). In the 4‐week urethrogram, the SA/Gel/rGO<sub>0.2</sub> groups had a narrower urethral lumen, the widths developed larger at 8 weeks (Figure ##FIG##6##6c,f##). The reason might be the inflammation‐related swelling of urethral tissue caused by rGO with high concentration. The blockage rate determines whether and how much urine can flow out. The blockage ratio of the urethras treated with the SA/Gel/rGO<sub>0.05</sub> patches could approach that of normal lumens (Figure ##FIG##6##6i##). After the incision of the ventral urethral wall, the dorsal wall could be exposed. Gross morphology revealed that urethral tissue in the SA/Gel/rGO<sub>0.05</sub> and SA/Gel/rGO<sub>0.2</sub> groups was significantly better than that in the SA/Gel group. The SA/Gel group showed the growth of severe scar‐like tissue in the urethra (Figure ##FIG##6##6j,m##). At 8 weeks, both of SA/Gel/rGO<sub>0.05</sub> (Figure ##FIG##6##6n##) and SA/Gel/rGO<sub>0.2</sub> (Figure ##FIG##6##6o##) groups showed smooth epithelial layer similar to the normal urethra of rabbits (Figure ##FIG##6##6h##). However, SA/Gel/rGO<sub>0.2</sub> group at 4 weeks (Figure ##FIG##6##6i##) revealed red and swollen mucosa compared with that in the SA/Gel/rGO<sub>0.2</sub> group (Figure ##FIG##6##6k##), which is consistent with the lumen width in the urethrogram. Therefore, the treatment of urethral injury could be improved by choosing a low dose of rGO for future application.</p>", "<title>Histological Evaluations</title>", "<p>The histology analyses of urethral reconstruction at 4‐ and 8‐weeks post‐surgery were performed by hematoxylin and eosin (H&amp;E) and Masson's trichrome staining. The SA/Gel patches with/without rGO showed various outcomes. Additionally, there was no significant infection during the experimental period, suggesting good biocompatibility of the patches. According to the histology, the urethras treated with the SA/Gel patches were associated with thinner/uncomplete urothelium layers, fewer blood vessels, and thicker submucosal tissue (<bold>Figure</bold>\n##FIG##7##\n7a–d##). Due to the lack of regenerated urothelium layers, and over‐deposited ECM, the urethra developed to urethral stricture. In contrast, the reconstructed urethra treated with the SA/Gel/rGO patches had the nearly normal urothelium layers, submucosal tissue, and blood vessels. The continuous and complete urothelium layers were formed on the lumen surfaces for the SA/Gel/rGO<sub>0.05</sub> group after 4‐ and 8‐weeks post‐surgery. However, the SA/Gel/rGO<sub>0.2</sub> patches could lead to a short period of swelling and inflammation in 4 weeks. These results suggested that rGO at a lower concentration (0.05 mg mL<sup>−1</sup>) could perform best function in the regeneration of urothelium layers and blood vessels, but not at a higher concentration (0.2 mg mL<sup>−1</sup>). The mucosal coverage ratios by the SA/Gel/rGO patches were measured (Figure ##FIG##7##7e,f##). The urethras treated with the SA/Gel/rGO<sub>0.05</sub> patches had more significant coverages, compared with the other groups. The urethral collagen thicknesses were also measured after the wound healing (Figure ##FIG##7##7g,h##). The SA/Gel/rGO<sub>0.05</sub> patch could induce a less collagen deposition under the mucosa, therefore developing a scar‐less wound healing. The histology showed that an optimal concentration of rGO would promote the regeneration of epithelial cells and decrease submucosal ECM deposition to inhibit urethral fibrosis.</p>", "<title>Immunofluorescence</title>", "<p>The distribution of cytokeratin was investigated based on the expression of epithelial cytokeratin AE1/AE3 (an important membrane surface protein marker of ECs) via immunofluorescence staining of the urethra. The expression level for AE1/AE3 on the SA/Gel/rGO<sub>0.05</sub> at 4‐and 8‐weeks post‐surgery (4W: 16.70 ± 2.66 and 8W: 24.72 ± 2.81) is significantly higher than that in the other groups. Although the continuous urothelium layer is formed, the urothelium layer of the SA/Gel/rGO<sub>0.2</sub> group is thinner than that of the SA/Gel/rGO<sub>0.05</sub> group. The expression of cytokeratin in the SA/Gel group is low (4W: 8.19 ± 1.72 and 8W: 8.29 ± 1.65), there is no complete regeneration of a discontinuous urothelium layer (<bold>Figure</bold>\n##FIG##8##\n8a,e##). It suggests that the introduction of rGO has the potential to promote the regeneration of urothelium layers. Studies have shown that the significant pro‐angiogenic properties of rGO depend on its concentration.<sup>[</sup>\n##UREF##5##\n32\n##, ##REF##29892387##\n50\n##\n<sup>]</sup> In the results of fluorescence staining at 4‐weeks post‐surgery, the SA/Gel/rGO<sub>0.05</sub> group showed a number of CD 31‐positive cells (the blood vessels labeled by CD 31), which were more than them in the SA/Gel and SA/Gel/rGO<sub>0.2</sub> group. At the beginning process of urethral regeneration with inflammation, the vessels in tissue would be much more obvious that is consistent with the results.<sup>[</sup>\n##REF##12490959##\n51\n##\n<sup>]</sup> For SA/Gel/rGO<sub>0.05</sub> and SA/Gel/rGO<sub>0.2</sub> groups, the number of CD 31‐positive cells at 8 weeks (SA/Gel/rGO<sub>0.05</sub>: 14.10 ± 3.99 and SA/Gel/rGO<sub>0.2</sub>: 8.63 ± 1.23) are lower than them at 4 weeks (SA/Gel/rGO<sub>0.05</sub>: 15.35 ± 4.55 and SA/Gel/rGO<sub>0.2</sub>: 14.77 ± 3.07) (Figure ##FIG##8##8b,f##).</p>", "<p>Different degrees of inflammation response at the injured sites would appear because of the transplantation of external scaffolds. CD 206 is used to label M2 macrophages.<sup>[</sup>\n##REF##31903147##\n52\n##\n<sup>]</sup> The results showed that the number of CD206‐positive cells in the SA/Gel group was the lowest. The number of CD206 positive cells in the SA/Gel/rGO<sub>0.05</sub> group in 4‐and 8‐weeks post‐surgery (4W: 36.36 ± 3.54 and 8W: 40.74 ± 2.23) were significantly higher than them in the other groups, indicating that the lower level of local inflammatory response was caused by the rGO treated group (Figure ##FIG##8##8c,g##). This indicated that rGO appeared to promote the transition of M2 macrophages and inhibit the inflammatory response during the urethral repair. Meanwhile, the low inflammatory response might promote the proliferation and activation of fibroblasts. The positive expression of proliferating cell nuclear antigen (PCNA) was obviously increased in the SA/Gel/rGO<sub>0.05</sub> group at 4‐and 8‐weeks post‐surgery (4W: 7.77 ± 0.25 and 8W: 8.46 ± 0.94) (Figure ##FIG##8##8d,h##).</p>", "<title>Flow Cytometric Analysis of RAW264.7 Surface Markers</title>", "<p>To evaluate the macrophages polarization status, the M1 surface markers (CD68, CD86) and M2 surface markers (CD206) in RAW 264.7 macrophages were further analyzed by flow cytometric (<bold>Figure</bold>\n##FIG##9##\n9a##). The results revealed that more than 90% of the cells strongly expressed surface antigens such as CD68. The inflammatory cell density was evaluated by CD86 staining. The CD86 inflammatory cell density in the 0.02rGO and 0.1rGO groups was no significant difference in the control group. However, as the amount of rGO increases, it leads to the increase of CD206‐positive macrophages. The expression of CD86 in M1 type was significantly increased by LPS + INF‐r, and the expression of CD206‐positive macrophages was significantly higher than that in the control group after the introduction of rGO (Figure ##FIG##9##9b##). The results of flow cytometry analysis showed that the addition of rGO promoted the polarization of macrophages to the M2 phenotype in vivo.</p>", "<title>qRT‐PCR Analysis of mRNA Levels of the Markers in Tissue and RAW 264.7 Cells</title>", "<p>The gene expression of Arg1, Fizz, and Ym1 in the 0.02rGO group and the 0.1rGO group was significantly higher than that in the control group, and the gene expression of iNOS and TGF‐β in the 0.02 rGO group and the 0.1rGO group was significantly lower than that in the control group (<bold>Figure</bold>\n##FIG##10##\n10a##). At the mRNA level, rGO treatment was associated with significant increases in Arg1, Fizz, and Ym1 expression compared to the control and M1 groups, and the gene expression of iNOS and TGF‐β in the 0.02 rGO group and the 0.1rGO group was significantly lower than that in the M1 group (Figure ##FIG##10##10b##). These results suggest that rGO may also have an inducing effect on the macrophage anti‐inflammatory phenotype in vivo. The expression of SA/Gel/rGO<sub>0.05</sub> α‐SMA, COL1A1, COL3A1, CD206, CD31, TGF‐β2 was significantly higher than that in the control group. The expression of TGFBR1, β‐catenin, and VWF was no significant difference in the control group (Figure ##FIG##10##10c–i##). Overall, the low‐dose rGO effectively promoted epithelization and neovascularization while reducing inflammation. These results suggested that rGO can promote urethral healing and regeneration.</p>" ]
[ "<title>Conclusion</title>", "<p>In this study, the SA/Gel/rGO patches were synthesized by 3D printing with printable, degradation, and tunable mechanical features for urethral reconstruction. Our results were interesting in that the physical and biological properties of SA/Gel/rGO patches were controllable by adjusting the concentration of rGO. rGO with proper intermediate concentrations turned out to promote cell migration, proliferation, and urothelium layer formation. In addition, the fibrosis of the urethra was inhibited by introducing low‐dose rGO. The urethral reconstruction in rabbits model using the optimized SA/Gel/rGO<sub>0.05</sub> patches led to the scar‐less urethral regeneration. Totally, our study provided a systematic evaluation of the application potential of rGO‐based scaffold on the urological and other organ defects’ treatment.</p>" ]
[ "<title>Abstract</title>", "<p>The nasty urine microenvironment (UME) is an inherent obstacle that hinders urethral repair due to fibrosis and swelling of the oftentimes adopted hydrogel‐based biomaterials. Here, using reduced graphene oxide (rGO) along with double‐freeze‐drying to strengthen a 3D‐printed patch is reported to realize scarless urethral repair. The sodium alginate/gelatin/reduced graphene oxide (SA/Gel/rGO) biomaterial features tunable stiffness, degradation profile, and anti‐fibrosis performance. Interestingly, the 3D‐printed alginate‐containing composite scaffold is able to respond to Ca<sup>2+</sup> present in the urine, leading to enhanced structural stability and strength as well as inhibiting swelling. The investigations present that the swelling behaviors, mechanical properties, and anti‐fibrosis efficacy of the SA/Gel/rGO patch can be modulated by varying the concentration of rGO. In particular, rGO in optimal concentration shows excellent cell viability, migration, and proliferation. In‐depth mechanistic studies reveal that the activation of cell proliferation and angiogenesis‐related proteins, along with inhibition of fibrosis‐related gene expressions, play an important role in scarless repair by the 3D‐printed SA/Gel/rGO patch via promoting urothelium growth, accelerating angiogenesis, and minimizing fibrosis in vivo. The proposed strategy has the potential of resolving the dilemma of necessary biomaterial stiffness and unwanted fibrosis in urethral repair.</p>", "<p>A sodium alginate/gelatin/rGO biomimetic patch is created with printable, degradable, and adjustable mechanical properties. The inclusion of rGO with the appropriate concentration can promote cell migration, and proliferation, and inhibit urethral fibrosis and the formation of the urothelium. This strategy demonstrates great potential in addressing the dilemma of necessary biomaterial stiffness and unwanted fibrosis in urethral repair.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6803-cit-0055\">\n<string-name>\n<given-names>L.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Niu</surname>\n</string-name>, <string-name>\n<given-names>W.</given-names>\n<surname>Zhao</surname>\n</string-name>, <string-name>\n<given-names>W.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>Q.</given-names>\n<surname>Fu</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Zhang</surname>\n</string-name>, <article-title>Urethral Microenvironment Adapted Sodium Alginate/Gelatin/Reduced Graphene Oxide Biomimetic Patch Improves Scarless Urethral Regeneration</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2302574</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202302574</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Inks preparation and rGO characterization</title>", "<p>The rGO was dispersed (1 mg mL<sup>−1</sup>) in water, and the solution was prepared according to the instructions. Briefly, the graphene powder (rGO, 20 mg, XFNANO, Nanjing, China) was dispersed in 20 mL double‐distilled water. And the aqueous suspension was obtained by ultrasonication at 40 KHz for 2 h. Polyvinyl pyrrolidone (PVP, MW = 58 000, 100 mg, Aladdin, Shanghai, China) was added to rGO aqueous suspension for sonication at ambient temperature for 2 h. After that, the rGO suspension was diluted to 0.02, 0.05, 0.1, and 0.2 mg mL<sup>−1</sup>, respectively.</p>", "<p>SA powder (2% weight/volume, from brown algae, Sigma–Aldrich, USA) and Gel powder (2% w/v, from porcine skin, Tape A, gel strength ≈300 g Bloom, Sigma–Aldrich, USA) were added to sterile water to prepare the 0 rGO group as a control. Five GA/Gel/rGO hybrid ink solutions containing different rGO concentrations, 0, 0.02, 0.05, 0.1, and 0.2 mg mL<sup>−1</sup> rGO, were named as SA/Gel, SA/Gel/rGO<sub>0.02</sub>, SA/Gel/rGO<sub>0.05</sub>, SA/Gel/rGO<sub>0.1</sub>, and SA/Gel/rGO<sub>0.2</sub>, respectively. To keep the same SA and Gel concentrations, different volumes of sterile water and rGO dispersion were prepared. The amounts of chemicals used for preparing the different SA/Gel/rGO hybrid ink solution are listed (Table ##SUPPL##0##S1##, Supporting Information). As an example, to prepare the SA/Gel/rGO<sub>0.05</sub> ink solution, 1.0 mL rGO solution (1 mg mL<sup>−1</sup>) was mixed with 19 mL sterile water to a homogeneous solution. Then, 400 mg SA and 400 mg Gel were dissolved in the above solution at 37 °C for 24 h. The mixture was kept standing to homogenize, sufficiently dissolve the polymer, and eliminate air bubbles. The rGO morphology was studied by using TEM (FEI, Hillsboro, USA) and SEM (Hitachi TM‐100, Tokyo, Japan). The spatial distribution of rGO was observed under an inverted phase contrast microscope (Olympus, Japan).</p>", "<title>Characterizations of SA/Gel/rGO hydrogel</title>", "<p>\n<list list-type=\"simple\" id=\"advs6803-list-0001\"><list-item><label>1.</label><p>\n<italic toggle=\"yes\">Raman Shift</italic>: The rGO incorporation into the hydrogel was analyzed qualitatively via Raman spectroscopy (DXR 2Xi, ThermoFisher, United States).</p></list-item><list-item><label>2.</label><p>\n<italic toggle=\"yes\">Fourier‐Transform Infrared (FTIR)</italic>: The functional groups of hydrogels were analyzed by FTIR (iS50, ThermoFisher, United States). The hydrogel was freeze‐dried in a vacuum freeze‐dryer (SCIENTZ‐10N, Ningbo, China) to obtain the powder. The hydrogel powder was finely grounded with KBr and compressed into slices for FTIR measurements, over the range of 500–4000 cm<sup>−1</sup>.</p></list-item><list-item><label>3.</label><p>\n<italic toggle=\"yes\">Swelling Ratio</italic>: The swelling property was assessed after immersion in double‐distilled water for 5 days by the general gravimetric method, which was referred to by Liu.<sup>[</sup>\n##UREF##9##\n53\n##\n<sup>]</sup> Three different concentrations of SA (1%, 1.5%, and 2%) and rGO hybrid hydrogel were investigated (<italic toggle=\"yes\">n</italic> = 4 per group). The freeze‐dried hydrogels samples were weighed (<italic toggle=\"yes\">W</italic>\n<sub>d</sub>) and placed in a 24‐well plate filled with double‐distilled water at room temperature. Then, the samples were taken out and rubbed with filter paper to remove the excess water. Finally, the samples were weighed (<italic toggle=\"yes\">W</italic>\n<sub>w</sub>) at the point of swelling equilibrium. The swelling ratio was calculated according to the following formula:\n\n</p></list-item></list>\n</p>", "<p>Where <italic toggle=\"yes\">W</italic>\n<sub>d</sub> represents the weights of freeze‐dried hydrogel samples, <italic toggle=\"yes\">W</italic>\n<sub>w</sub> stands for the weights of hydrogels after absorbing water.\n<list list-type=\"simple\" id=\"advs6803-list-0002\"><list-item><label>4.</label><p>\n<italic toggle=\"yes\">In Vitro Degradation</italic>: The degradable properties of SA/Gel hydrogel with different concentrations of rGO were examined via quantifying the mass remaining in vitro. These samples were immersed in double‐distilled water and lyophilized for 7, 14, and 21 days. Then, the lyophilized samples were weighed. W<sub>I</sub> was the initial dry weights of the sample and W<sub>T</sub> was the weights after T days of immersion in water (T = 7, 14, and 21 days). Finally, the remaining weights were calculated by the following formula. These experiments were performed in triplicates and repeated thrice.\n\n</p></list-item></list>\n</p>", "<title>Scanning Electron Microscope (SEM)</title>", "<p>The morphology of the hybrid hydrogel samples was observed by SEM. Briefly, the samples were prepared in a 24‐well plate (0.4 cm in height), frozen at 4 °C and −80 °C for 2 h, respectively, and then lyophilized overnight in a vacuum freeze‐dryer (SCIENTZ‐10N, Ningbo, China). Next, the freeze‐dried hydrogel samples were cross‐linked with 5% CaCl<sub>2</sub> for 30 min and washed thoroughly with sterile water. Then, they were freeze‐dried and stored in a vacuum container. The distribution of pore size and porosity of hydrogels was counted using Image J visualization software (National Institutes of Health, Bethesda, MD, USA) (<italic toggle=\"yes\">n</italic> = 10) from SEM images.</p>", "<title>Cell Culture</title>", "<p>Human fibroblasts were obtained from the human foreskin dermal tissue from the National Collection of Authenticated Cell Culture. The cells were cultured in a T‐75 flask (Corning, USA) with high‐glucose Dulbecco's modified Eagle's medium (DMEM, Hyclone, UT), and supplemented with 10% fetal bovine serum (FBS, Gibco, USA) and 1% penicillin‐streptomycin in an incubator (37°C, 5% CO<sub>2</sub>). The complete medium was updated every 2 days. After 85–90% confluence, the passage of 10 to 15 cells was used for subsequent experiments. The growth and proliferation of cells were observed with an inverted phase contrast microscope (CKX53, Olympus, Japan).</p>", "<title>In Vitro Cell Biocompatibility Measurements</title>", "<p>Fibroblasts were used to test cell adhesion and proliferation on the hydrogel. The cells at a density of 5 × 10<sup>4</sup> cells mL<sup>−1</sup> were seeded on the surface of SA/Gel hydrogel. Cell viability was identified by 2 µ<sc>m</sc> Calcein AM (live cell stain, 490 nm) (Life Technologies, USA) and 4 µ<sc>m</sc> propidium iodides (dead cell stain, 535 nm) (PI, Life Technologies, USA). The living and dead cells were marked in green and red, respectively. Samples were washed three times by PBS and stained with Calcein AM and PI for 30 min in the dark. Then, they were washed with PBS solution. A fluorescence microscope with an imaging system (IX73, Olympus, Japan) was used for image acquisition. The cell cytotoxicity of rGO for fibroblasts was evaluated by the CCK‐8 (Dojindo, Japan) at days 1, 4, and 7 after seeding according to the protocol. Briefly, fibroblasts seeded on hydrogel with or without rGO were washed with PBS three times. Then, 100 µL of CCK‐8 and 1 mL of complete culture medium were added to each well, followed by incubation in the dark for 4 h at 37 °C. 200 µL of the medium was transferred into a 96‐well plate after incubation. Each group contained five replicate wells. The CCK‐8 medium was used as the black control. The optical density (OD) was read by the multifunctional enzyme marker (Varioskan Flash, Thermo Fisher Scientific, USA) at 450 nm. five samples were tested for each group.</p>", "<p>Cell Migration: Wound scratch assay was used for the cell migration study. The fibroblasts at the density were 2 × 10<sup>5</sup> cells well<sup>−1</sup> were seeded on the 24‐well plate. A scratch wound was formed using a pipette tip of 1000 µL when the confluence of cells reached 80–90%. Then, cells were washed with PBS. The distance of scratches was observed and recorded with an inverted phase contrast microscope (<italic toggle=\"yes\">W</italic>\n<sub>d0</sub>). The rGO dispersion in a certain volume ratio blended with the complete medium was added to the wells. The cells were cultured for 24 h and observed under the microscope again. And the distance of scratches (<italic toggle=\"yes\">W</italic>\n<sub>dt</sub>) was recorded. Wound contraction was quantified from the images by the following equation. Experiments were repeated in triplicates.\n\n</p>", "<title>Printing of Acellular SA/Gel/rGO Patches</title>", "<p>In this study, the SA/Gel/rGO patches were printed using the Organ Printing United system (OPUS, Novaprint Therapeutics Suzhou Co., Ltd, Suzhou, China); it includes multi‐nozzle printing and multi‐material mixing. The patch model was a lattice‐rod structure with 15 mm ×15 mm × 0.75 mm, which was converted into a G‐Code file using Slic3r with the layer height of 0.15 mm (5 layers), the pore size of 1.5 mm. An inner diameter of 200 µm of the printing nozzle was selected. The ink solution was liquid at 37 °C and introduced into a special printing syringe (3 cc), but it cannot be printed in this state. Therefore, the printing syringe with the ink was placed and cooled at 4 °C for 8–10 min. And the temperature of the printer chamber was set to 19 °C. The SA/Gel/rGO patches were printed in a layer‐by‐layer deposition fashion on the printer platform. After printing each patch, they were cooled to −80 °C. Briefly, the above printed acellular patches (15 mm × 15 mm) were frozen at −80 °C, and then lyophilized overnight in a vacuum freeze‐dryer. Next, the freeze‐dried patches were cross‐linked with 5% CaCl<sub>2</sub> for 30 min and washed thoroughly with sterile water. The patches were freeze‐dried again and stored in a vacuum container.</p>", "<title>Patch Mechanics</title>", "<p>Multifunctional materials testing machine (HD‐5000B, Yangzhou, China) was used to characterize the tensile behavior of the SA/Gel/rGO patches. The SA/Gel patch was used as the control material. The patch samples of longitudinal strips with a length of 50 mm and a width of 20 mm were prepared. Then, the distance between the clamps was measured. The patches were stretched at a speed of 10 mm per minute at room temperature until reaching their breaking points. Five samples were measured in each group, and the average value and standard deviation were calculated. The final tensile strength was calculated in the following formula.\nwhere <italic toggle=\"yes\">δ</italic> was the tensile strength, <italic toggle=\"yes\">F</italic> was the maximum force at the breaking points and <italic toggle=\"yes\">S</italic> was the cross‐sectional area of patch.</p>", "<title>Cell Morphologies on Patches</title>", "<p>The patches after the final freeze‐drying were sterilized with UV for 8 h and put on a 6‐well plate. Fibroblasts were seeded onto the patches at a density of 2 × 10<sup>5</sup> cells cm<sup>−2</sup> and incubated at 5% CO<sub>2</sub> and 37 °C for 3 days. Additionally, the cell culture medium was updated every 2 days. Then, the cells with patches were fixed in 2.5% glutaraldehyde for 2 h at room temperature and then rinsed with PBS. The patches were then vacuum‐dried. The patches were sputter‐coated with gold for 30 sec and examined under a scanning electron microscope at 15 kV (SU8100, Hitachi, Japan).</p>", "<title>Protein Detection</title>", "<p>The total protein of fibroblasts was extracted using ice‐cold Cell &amp; Tissue Protein Extraction Reagent (Kang Chen. Shanghai, China). Then, according to the manufacturer's protocol, the protein concentration was determined using BCA Protein Assay Kit (Kang Chen, Shanghai, China). Briefly, protein array membranes were blocked in blocking buffer for 30 min and incubated with samples at room temperature for 2 h. Then samples were decanted, and membranes were washed. Next, membranes were incubated with diluted biotin‐conjugated antibodies at room temperature for 2 h. The membranes were washed with washing buffer and reacted with HRP‐conjugated streptavidin (1:1000 dilution) at room temperature for 2 h. Membranes were washed thoroughly and exposed to detection buffer in the dark. After acting to detect buffer, the membranes were exposed to X‐ray film. The image was developed using a film scanner. Relative expression levels of cytokines were made by comparing the signal intensities and quantified by densitometry. Positive controls were used to standardize the results from different membranes. And fold changes were calculated in protein expression.</p>", "<title>Gene Ontology and KEGG Enrichment Analysis</title>", "<p>Gene ontology (<ext-link xlink:href=\"http://www.geneontology.org\" ext-link-type=\"uri\">http://www.geneontology.org</ext-link>) a systematical approach for gene and protein annotation in terms of biological process, molecular process, aisnd cellular component.<sup>[</sup>\n##REF##10802651##\n54\n##\n<sup>]</sup> Kyoto Encyclopedia of Genes and Genomes (KEGG; <ext-link xlink:href=\"http://www.genome.jp/kegg/\" ext-link-type=\"uri\">http://www.genome.jp/kegg/</ext-link>) is an online database depositing biological pathways of genes and biochemicals. The enriched GO terms and KEGG pathways were annotated using the R package cluster Profiler.</p>", "<title>Urethroplasty and Postoperative Examinations in Rabbit</title>", "<p>To verify the biocompatibility of the 3D printed SA/Gel/rGO patches in vivo, the patches were placed in the urethral defect of rabbits for in vivo experiments. Nine adult New Zealand white rabbits had an average weight of ≈2.5 kg and were randomly divided into three groups for the urethral defect and subsequent urethroplasty. Rabbits in group 1 (<italic toggle=\"yes\">n</italic> = 3) were repaired with the SA/Gel patch. Rabbits in group 2 (<italic toggle=\"yes\">n</italic> = 3) were repaired with the SA/Gel/rGO<sub>0.05</sub> patch. Rabbits in group 3 (<italic toggle=\"yes\">n</italic> = 3) were repaired with the SA/Gel/rGO<sub>0.2</sub> patch. These rabbits were first performed by general anesthesia with intravenous injection of pentobarbital, then the rabbit's urethras were disinfected with alcohol. The skins were sectioned at ≈3 cm proximal to the external urethral orifices, and the urethral lumens were exposed. Ventral urethral defects with a mean length × width of 2.0 cm × 0.8 cm were created in the anterior urethra of rabbits. The scaffolds with a length × width of 1.5 cm × 0.5 cm were sutured to the edge of the defect using 6‐0 absorbable polyglactin sutures (Ethicon, USA), and the whole urethral defects were sutured with 6‐0 absorbable polyglactin sutures. The rabbits were observed twice a day.</p>", "<p>To observe the urethral leakage and stricture of the three groups of rabbits, the contrast solution was injected into the urethral lumens at 4‐ and 8‐weeks post‐surgery. Meanwhile, the rabbits were undertaken contrast‐enhanced urethrogram tests to check the condition of lumen in the urethra at 4‐ and 8‐weeks post‐surgery. The rabbits were euthanized after retrograde urethrograms at 4‐ and 8‐ weeks, and the urethral tissue for the following histology staining was collected. All the animal experiments were in accordance with the guidelines for animal care. The animal protocol (SYXK 2017‐0240) was approved by the Institutional Animal Care and Use Committee of the Shanghai Jiao Tong University Affiliated Sixth People's Hospital.</p>", "<title>Histology Assessment and Immunofluorescence</title>", "<p>The urethras were harvested after 4 weeks and 8 weeks postoperatively for histology analysis. Hematoxylin and eosin staining (H&amp;E) and Masson's trichrome staining tests were conducted to identify the epithelial layer and collagen distribution of urethra. The specimens were fixed in 4% paraformaldehyde for 30 min at room temperature. Then, they were dehydrated with different grades of alcohol and embedded in the paraffin blocks. Histological sections were prepared and observed using an optical microscope. To further demonstrate the repair of urethral function, the samples were stained for immunofluorescence for epithelial cytokeratin AE1/AE3 (Santa Cruz Biotechnology, Inc.), CD31 (blood vessels, 1:100, Proteintech Group, Inc), CD206 (1:500, Proteintech Group, Inc), and PCNA (Proliferating Cell Nuclear Antigen 1:500, Abcam plc). Nuclei were stained with DAPI (1:500, Life Technologies). Afterward, the specimens were imaged and observed by an optical microscope.</p>", "<title>Flow cytometry</title>", "<p>After 85–90% confluence, leukemia cells in mouse macrophage (RAW 264.7 cells) were digested with pancreatic enzyme, and centrifuged at 1000 rpm for 5 min. Then the supernatant was removed, and cells were resuspended with a complete medium. RAW264.7 cells were seeded in 6‐well plates (5 × 10<sup>5</sup> cells/well), and placed in a CO<sub>2</sub> incubator at 37 °C overnight. After 1 day, cells were divided into two groups when the cell density reached ≈40–50%. Group 1 (Control; 0.02rGO; 0.1rGO) was temporarily not treated. Group 2 (Control; M1; M1 + 0.02rGO; M1 + 0.1rGO), where M1; M1 + 0.02rGO; M1+ 0.1rGO, first treated with LPS (100 ng/mL) + INF‐r (50 ng mL<sup>−1</sup>) for 24 h to induce M1 type. On the third day, when the cell density reaches ≈70–80%, the corresponding concentration of rGO was added to the two groups, which were 0.02rGO, 0.1rGO, and treated for 24 h. RAW264.7 cells in the two groups of plates were collected separately for flow cytometry and RT‐PCR detection after 24 h. Flow cytometry was used to determine the effect of graphene on the polarization of Raw264.7 to M1, M2. Fluorescently labeled antibodies CD68, CD86, and CD206 were added to both groups of cells. Before staining, Raw264.7 cells were fixed and broken, then mixed with antibodies and incubated at 4 °C for 30 min in the dark. Then, the cells were resuspended with a cell staining buffer, followed by centrifugation for 5 min at 300 g, and discard the supernatant. Finally, the cells were resuspended by 200 µL cell stained buffer for detection and analysis with flow cytometry (Sysmex, CyFlow Cube8).</p>", "<title>RT‐PCR</title>", "<p>Relative quantification for mRNA gene expression studies. Extraction of mRNA with Invitrogen's trizol. The extracted mRNA was then reverse‐transcribed to become a cDNA template. Finally, a real‐time PCR experiment was performed using cDNA as a template.</p>", "<title>Statistical Analysis</title>", "<p>All the statistical significance for the experiments was analyzed using the one‐way ANOVA and paired‐samples t‐test. The error bar represents the mean ± standard deviation (SD) of measurements performed on each sample group. It was a statistically significant difference based on <italic toggle=\"yes\">p</italic> &lt;0.05 (*<italic toggle=\"yes\">p</italic> &lt;0.05, **<italic toggle=\"yes\">p</italic> &lt;0.01, ***<italic toggle=\"yes\">p</italic> &lt;0.001, and ****<italic toggle=\"yes\">p</italic> &lt;0.0001).</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>L.W., K.W., and M.Y contributed equally to this work. This work was supported by the following grants: National Key Research and Development Program of China (2018YFA0703100), Jiangsu Key Technology Research Development Program (BE2017664), Shanghai Jiao Tong University Biomedical Engineering Cross Research Foundation (YG2022ZD022 and YG2017QN15) and the National Natural Science Foundation of China (82072217 and 81772135). Shanghai health committee (20184Y0053), Shanghai “Rising stars of medical talent” Youth development program, Shanghai Jiao Tong University K. C. Wong Medical Fellowship Fund, and Shanghai sixth people's hospital foundational research program. National Natural Science Foundation of China (Grant No. 62374107), The Talent Progrom of Shanghai University of Engineering Science (QNTD202104), Shanghai Local University Capacity Building Project of Science and Technology Innovation Action Program (21010501700), Class III Peak Discipline of Shanghai‐Materials Science and Engineering (High‐Energy Beam Intelligent Processing and Green Manufacturing). Natural Science Foundation of Shanghai(20ZR1442100).</p>", "<title>Data Availability Statement</title>", "<p>Research data are not shared.</p>" ]
[ "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6803-fig-0011\"><label>Scheme 1</label><caption><p>Schematics on the development of 3D‐printed SA/Gel/rGO patches for urethral repair. The SA/Gel/rGO patches were prepared by a 3D‐printing system and cross‐linked by Ca<sup>2+</sup>. The patches were then sutured in the damaged urethra of rabbits, wherein the rGO component facilitated regeneration of mucosa, promoted vascularization, and exhibited anti‐fibrotic activity.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0001\"><label>Figure 1</label><caption><p>Morphologies of rGO and optical images of rGO/hydrogel‐precursor dispersions. a) SEM and b) TEM images of rGO. c) Photographs of different concentrations of rGO/hydrogel‐precursor suspensions at rGO concentrations of 0.02, 0.05, 0.1, and 0.2 mg mL<sup>−1</sup>. d–g) Corresponding optical microscopy images. h–k) Area counts of the rGO distributed in the corresponding suspensions; *<italic toggle=\"yes\">p</italic> &lt;0.05, ****<italic toggle=\"yes\">p</italic> &lt;0.0001, n.s. means not significant.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0002\"><label>Figure 2</label><caption><p>Physicochemical characterizations of the SA/Gel/rGO hydrogels. a) Raman spectra of SA, SA/Gel, and SA/Gel/rGO hydrogels. b) FTIR spectra of i) SA/Gel hydrogel, ii) SA/Gel/rGO<sub>0.02</sub> hydrogel, iii) SA/Gel/rGO<sub>0.05</sub> hydrogel, and iv) SA/Gel/rGO<sub>0.2</sub> hydrogel. c) Swelling ratios of the different concentrations of SA and SA/Gel/rGO composite inks at different concentrations of rGO. d) Degradation profiles of the hydrogels.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0003\"><label>Figure 3</label><caption><p>SEM images and gross appearances of SA/Gel/rGO hydrogels with various concentrations of rGO: 0, 0.02, 0.05, 0.1, and 0.2 mg mL<sup>−1</sup>. a–e) SEM images at 1000× magnification and optical images of the hydrogels; f–j) SEM images at 300× magnification. k–o) Distributions of pore sizes of the different hydrogels. p) Average pore sizes of the different hydrogels; **<italic toggle=\"yes\">p</italic> &lt;0.01; ***p &lt;0.001; ****p &lt;0.0001; n.s. means not significant.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0004\"><label>Figure 4</label><caption><p>a) Morphology of the 3D‐printed SA/Gel/rGO patches containing different concentrations of rGO, and the double‐freeze‐drying process. b) Tensile stress‐strain curves; c) Young's moduli; d) tensile strengths at break; and e) strains at the break for the different 3D‐printed patches; **<italic toggle=\"yes\">p</italic> &lt;0.01; ***<italic toggle=\"yes\">p</italic> &lt;0.001; and ****<italic toggle=\"yes\">p</italic> &lt;0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0005\"><label>Figure 5</label><caption><p>In vitro cytocompatibility of rGO and rGO composite hydrogel. a) Cell viability of fibroblasts seeded on different concentrations of SA/Gel/rGO hydrogels at day 1. Living cells are depicted in green and dead cells in red. b) Heat map of DEPs. Red and green colors indicate high and low expressions, respectively. c) wound healing was observed in fibroblast cells treated with the different concentrations of rGO (0, 0.02, 0.05, 0.1, and 0.2 mg mL<sup>−1</sup>). fibroblast cells treated without rGO were used as a positive control experiment. The scale bar at the right lower corner is 500 µm. d) The percentage of wound contraction was measured using Image J analysis software. Statistical significance was calculated by using a t‐test. e) Cell proliferation of fibroblasts cultured on hydrogels for 1, 4, and 7 days; n = 6, **<italic toggle=\"yes\">p</italic> &lt;0.01, ***<italic toggle=\"yes\">p</italic> &lt;0.001, ****<italic toggle=\"yes\">p</italic> &lt;0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0006\"><label>Figure 6</label><caption><p>Urethrography examinations and appearances of urethral repair from the biomaterial with SA/Gel, SA/Gel/rGO<sub>0.05</sub>, and SA/Gel/rGO<sub>0.2</sub>. The results of urethras from a,d,g,j) SA/Gel, b,e,h,k) SA/Gel/rGO<sub>0.05</sub>, and c,f,i,l) SA/Gel/rGO<sub>0.2</sub> at 4‐ and 8‐weeks post‐surgery. The red arrows indicate the lumen of the urethra. The red dotted boxes indicate the urethral epithelial layer. *<italic toggle=\"yes\">p</italic> &lt;0.05, ****<italic toggle=\"yes\">p</italic> &lt;0.0001, n.s. means not significant.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0007\"><label>Figure 7</label><caption><p>Histological examination of the regenerated tissues at the damaged urethra sites after staining the sections with H&amp;E and Masson's Trichrome. Representative images of urethral cross‐sections of the reconstructed urethra using SA/Gel, SA/Gel/rGO<sub>0.05</sub>, and SA/Gel/rGO<sub>0.2</sub> of a,c) at 4 weeks and b,d) at 8 weeks. The mucosal coverage of urethra at 4 weeks (a) and at 8 weeks (b); The collagen thickness of urethra at 4 weeks (a) and at 8 weeks (b). The green dotted lines indicate the border line of collagen thickness. Data are means ± standard error, <italic toggle=\"yes\">n</italic> = 3; **<italic toggle=\"yes\">p</italic> &lt;0.01, ***<italic toggle=\"yes\">p</italic> &lt;0.001, ****<italic toggle=\"yes\">p</italic> &lt;0.0001, n.s. means not significant.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0008\"><label>Figure 8</label><caption><p>Immunofluorescence staining of specific biomarkers in the SA/Gel, SA/Gel/rGO<sub>0.05</sub>, and SA/Gel/rGO<sub>0.2</sub> repair after 4‐ and 8‐weeks post‐surgery. Representative immunofluorescence images of a) AE1/AE3, b) CD31, c) CD206, d) PCNA. Scale bar: 50 µm. Blue: Nuclei. e) Quantification of expression levels of epithelial cytokeratin AE1/AE3, f) the blood vessels based on the CD 31, g) the inflammation based on CD206 (M2 macrophages), and h) cell proliferation based on PCNA. Data are mean ± standard error, <italic toggle=\"yes\">n</italic> = 3; *<italic toggle=\"yes\">p</italic> &lt;0.05, **<italic toggle=\"yes\">p</italic> &lt;0.01, ***p &lt;0.001; ****<italic toggle=\"yes\">p</italic> &lt;0.0001, n.s. means not significant.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0009\"><label>Figure 9</label><caption><p>Flow cytometric analysis of RAW264.7 surface markers (CD68, CD86, and CD206). a) group 1 (Control; 0.02rGO; 0.1rGO). b) group 2 (Control; M1; M1 + 0.02rGO; M1 + 0.1rGO), where, M1; M1 + 0.02rGO; M1+ 0.1rGO, first treated with LPS (100 ng mL<sup>−1</sup>) + INF‐r (50 ng/mL) for 24 h to induce M1 type.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6803-fig-0010\"><label>Figure 10</label><caption><p>qRT‐PCR analysis of mRNA levels of the indicated macrophage markers in rGO co‐cultured with the RAW 264.7 cells and/or factors. The gene expression levels of a) iNOS, TGF‐α, Arg‐1, Fizz, Ym1, and b) iNOS, TGF‐α, Arg‐1, Fizz, Ym1. qRT‐PCR analysis of mRNA levels of the markers and factors in tissue. The gene expression levels of c) α‐SMA, d) COL1A1, e) COL3A1, f) CD206, g) PCNA, h) TGFBR1, i) CD31, j) β‐catenin, k) TGF‐β2, l) VWF. *<italic toggle=\"yes\">p</italic> &lt;0.05, **<italic toggle=\"yes\">p</italic> &lt;0.01, ***<italic toggle=\"yes\">p</italic> &lt;0.001, ****<italic toggle=\"yes\">p</italic> &lt;0.0001, n.s. means not significant.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6803-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2302574-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
54
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 16; 11(2):2302574
oa_package/fe/8e/PMC10787096.tar.gz
PMC10787098
37933980
[ "<title>Introduction</title>", "<p>Plastic products have become deeply rooted in human society. Globally, more than 100 million tons of plastic waste are annually discarded into the environment, which are landfilled, incinerated, or discharged into the ocean, resulting in serious ecological damages.<sup>[</sup>\n##REF##32703909##\n1\n##\n<sup>,2]</sup> Epoxy resins (EPs), derived from petroleum, are cost‐effective thermosetting materials that are ubiquitously used in aerospace, transportation, architecture, and electronic and electrical devices.<sup>[</sup>\n##UREF##0##\n3\n##, ##UREF##1##\n4\n##\n<sup>]</sup> However, thermosets have a limited capacity to degrade and recycle than thermoplastics or supramolecular plastics due to their three‐dimensional (3D) crosslinked structure.<sup>[</sup>\n##REF##36163266##\n5\n##, ##REF##28386008##\n6\n##, ##UREF##2##\n7\n##, ##UREF##3##\n8\n##\n<sup>]</sup> Once cured, it will cause permanent plastic wastes that require hundreds of years to naturally clean up. To resolve the problem, tremendous efforts are still necessitated toward degradable and closed‐loop cycling epoxies as alternatives to traditional ones,<sup>[</sup>\n##UREF##4##\n9\n##, ##UREF##5##\n10\n##\n<sup>]</sup> such as developing bio‐based monomers.<sup>[</sup>\n##UREF##6##\n11\n##\n<sup>]</sup> However, there still remain intractable challenges for these structures such as their high cost, and how to make a trade‐off between high structural strength and easy degradability, as well as further realize multifunctional material purposes.<sup>[</sup>\n##UREF##7##\n12\n##, ##UREF##8##\n13\n##\n<sup>]</sup>\n</p>", "<p>Alternatively, dynamic‐covalent and/or non‐covalent crosslinking strategies are particularly attractive for the designs of next‐generation materials with healable and chemical recycling properties.<sup>[</sup>\n##UREF##9##\n14\n##, ##REF##32999924##\n15\n##, ##UREF##10##\n16\n##, ##REF##33393759##\n17\n##, ##REF##22890548##\n18\n##, ##UREF##11##\n19\n##, ##UREF##12##\n20\n##, ##REF##32699399##\n21\n##, ##UREF##13##\n22\n##\n<sup>]</sup> This fact derives a new class of polymers named vitrimers, which merge the combinative features of thermoplastics and thermosets.<sup>[</sup>\n##REF##22096195##\n23\n##, ##UREF##14##\n24\n##, ##REF##28386008##\n25\n##, ##UREF##15##\n26\n##, ##REF##31565382##\n27\n##, ##UREF##16##\n28\n##\n<sup>]</sup> Epoxy vitrimers are emerging and explored as the time demand for programming degradable and recyclable epoxies and even their thermosets.<sup>[</sup>\n##REF##36299449##\n29\n##, ##UREF##17##\n30\n##\n<sup>]</sup> Vitrimers are generally constructed by dynamic‐covalent bonds linked with polymer networks (DCPNs), wherein bond reversion is driven by catalysts or external stimuli.<sup>[</sup>\n##UREF##18##\n31\n##, ##UREF##19##\n32\n##, ##UREF##20##\n33\n##\n<sup>]</sup> In many cases, the control exerted over the crosslinked structure by governing dynamic covalent bonds tends to compromise their natural thermosetting virtues (for example, thermal and chemical resistance, and mechanical robustness). Therefore, a holistic perspective involving supramolecular modes and covalent adaptable modes will contribute to an in‐depth understanding of crosslinking behavior from chemical bonds to linear monomers, and even to the whole crosslinked structure of polymer networks.<sup>[</sup>\n##UREF##21##\n34\n##, ##UREF##22##\n35\n##, ##UREF##23##\n36\n##, ##UREF##24##\n37\n##\n<sup>]</sup>\n</p>", "<p>Unlike classical linear polymers, hyperbranched polymers (HBPs) possess spatial molecular configurations with 3D‐branched architecture and abundant external terminals.<sup>[</sup>\n##UREF##25##\n38\n##, ##REF##25902871##\n39\n##\n<sup>]</sup> They can be easily functionalized for polymer modification and are a well‐established strategy for achieving high strength and toughness of thermoset polymers.<sup>[</sup>\n##UREF##26##\n40\n##\n<sup>]</sup> Considerable progress has been made in developing various hyperbranched structures and prototyping them in relevant functional applications.<sup>[</sup>\n##REF##25902871##\n41\n##, ##UREF##27##\n42\n##, ##REF##33492940##\n43\n##, ##UREF##28##\n44\n##, ##UREF##29##\n45\n##, ##UREF##30##\n46\n##\n<sup>]</sup> Benefiting the virtue of their hyperbranched architecture, HBPs with broad intramolecular cavities can reduce network density to accommodate solvent molecules, thus driving dynamic behaviors. Hence, they hold promise for tailoring degradable and in‐processable vitrimers from native thermosets. The interpenetrating networks formed by HBPs and epoxy matrices, characterized by network topologies and dynamic linkages, are poised to bestow upon thermoset polymers unique and exceptional characteristics. Moreover, they offer ease of functionalization, particularly in compensating for the lack of mechanical robustness.</p>", "<p>Herein, we report hyperbranched dynamic crosslinking networks (HDCNs) to program an industrial thermoset into a degradable and reconfigurable vitrimer. The conceptual basis underlying this approach is depicted in <bold>Figure</bold> ##FIG##0##\n1\n##. The HDCNs are structured with multiple dynamics via introducing a hyperbranched macromonomer (HBPPB) bearing dynamic units and reactive terminals. Through the integration of boron and phosphorus units, the molecular configuration can be well stretched into a topology, exploiting the planar‐like nature (sp2 hybridization) of boron and the sp3 hybridization of phosphorus esters. This hybridized structure establishes covalent crosslinks with DGEBA monomer (ring‐opening) and anhydride monomer (forming ester bond), as well as supramolecular crosslinking via H‐bonding (Figure ##FIG##0##1c##). Consequently, the installation of HDCNs makes a thermoset network from a permanently 3D structure to a dynamic topologically crosslinked architecture, wherein the branching architecture benefits an expanded crosslinking network (low‐crosslink‐density, Figure ##FIG##3##4c##) that is capable of adapting solvent molecule entrance to drive the dynamic bond exchange. Such structural features render HDCNs susceptible to mild solvent‐dissolved degradation (room temperature, Figure ##FIG##0##1b##) and confer transformative material property<sup>[</sup>\n##UREF##31##\n47\n##, ##UREF##32##\n48\n##, ##REF##23579959##\n49\n##\n<sup>]</sup> from a rigid vitrimer to an elastomer upon heating in ethanol (See Movie ##SUPPL##1##S1##, Supporting Information). More attractively, the after‐treated vitrimer showcases a suprahigh modulus (5.45 GPa) at extremely low temperature (−150 °C), posing them and even their composites supranormal uses for astrospace, superconducting energy storage, medical equipment, and beyond. Furthermore, the vitrimer exhibits high flexural modulus and toughness, and excellent thermal stability, among other high added values, demonstrating an extension of existing vitrimers and vitrimer properties. In light, this design principle via HDCNs may hold promise for the breakthrough of conventional concepts toward the next generation of sustainable and advanced thermoset polymers.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Synthesis and Characterization of HDCNs</title>", "<p>The synthesis of HDCNs is straightforward via introducing a hyperbranched dynamic macromonomer into a traditional epoxy thermoset network as a dynamic crosslinker. The hyperbranched macromonomer (HBPPB) was synthesized via A<sub>2</sub>+B<sub>2</sub>+C<sub>3</sub> polycondensation (Section ##SUPPL##0##S1.3a##, Supporting Information). In parallel, a linear poly‐phosphate/borate structure (LPPB), a hyperbranched polyborate (HBPB), and a hyperbranched polyphosphate (HBPP) were synthesized as controls to compare with HDCNs. Synthesis details are described in Sections ##SUPPL##0##S1.4## and ##SUPPL##0##S1.5## (Supporting Information). The molecular structure of the synthetic polymers was characterized using multiple analytical techniques, including Fourier transform infrared (FT‐IR), <sup>1</sup>H, <sup>13</sup>C, and <sup>31</sup>P nuclear magnetic resonance (NMR) spectroscopies, gel permeation chromatography (GPC) (see Section ##SUPPL##0##S1.3b##, Supporting Information). The concentration of hydroxyl groups (─OH) in HBPPB was quantified via a standard titration experiment, yielding a value of 7.97 × 10<sup>−3</sup> mol g<sup>−1</sup> (Section ##SUPPL##0##S1.3c## and Table ##SUPPL##0##S2##, Supporting Information), indicating the high abundance of ─OH groups.</p>", "<p>The polymer matrix comprised of a petroleum‐based epoxy (diglycidyl ether bisphenol A, DGEBA, E51) a commercially used anhydride‐type curing agent (methyl tetrahydrophthalic anhydride, MTHPA), and a certain amount of HBPPB. A facile thermosetting workflow was employed to cast EP‐x samples, where <italic toggle=\"yes\">x</italic> represents the mass concentration of HBPPB. The curing performance was evaluated using isothermal differential scanning calorimetry (Figure ##SUPPL##0##S21c##, Supporting Information), which showed a homogeneous and single peak among all pre‐polymer systems, indicating well compatibility among the three constituents. The natural EP and EP‐9 underwent full curing as proved in its time‐sweep curves by rheology (Figure ##SUPPL##0##S22##, Supporting Information). For subsequent analysis, the epoxy samples containing HBPPB equal to or greater than 9 wt.% were donated as vitrimers due to their degradable and/or reconfigurable dynamic behavior. The other samples were categorized as thermosets due to their predominant thermoset nature. To facilitate comparative investigations, epoxy vitrimers containing varying mass fractions of LPPB, HBPB, and HBPP were prepared using the same procedure as HDCNs, and a comparison of their material properties is presented in Sections ##SUPPL##0##S2.5## and ##SUPPL##0##S2.6## (Supporting Information).</p>", "<p>The dynamic nature of HDCNs was characterized extensively through stress relaxation (see Section ##SUPPL##0##S2.3##, Supporting Information) and creep‐recovery test (Section ##SUPPL##0##S2.4##, Supporting Information) in tensile mode.<sup>[</sup>\n##REF##31433176##\n50\n##, ##REF##35590755##\n51\n##, ##REF##35607118##\n52\n##, ##REF##29733205##\n53\n##, ##REF##28557428##\n54\n##\n<sup>]</sup> In EP‐12, the time‐ and temperature‐dependent modulus revealed a partial relaxation to a plateau regime that deviates from classical linear‐viscoelastic vitrimers. This unique relaxation signifies that HDCNs not only behave with liquid‐like viscoelasticity due to the activation of dynamic exchange above the topology‐freezing transition temperature (<italic toggle=\"yes\">T</italic>\n<sub>v</sub>, described by Arrhenius and Williams−Landel−Ferry law), but also retain the resilience and recovery capabilities like an elastic body subjected to Hooke's law. By fitting the results on an Arrhenius plot, a linear correlation between ln(<italic toggle=\"yes\">τ*</italic>) (relaxation time) and 1000/T (inverse temperature) was observed, enabling the calculation of an activation energy (<italic toggle=\"yes\">E</italic>\n<sub>a</sub>) of 78.1 kJ mol<sup>−1</sup> and <italic toggle=\"yes\">T</italic>\n<sub>v</sub> of 71.7 °C (Figures ##SUPPL##0##S24## and ##SUPPL##0##S25##, Supporting Information). It is noteworthy that several examples of vitrimers with <italic toggle=\"yes\">T</italic>\n<sub>g</sub> &gt; <italic toggle=\"yes\">T</italic>\n<sub>v</sub> have been reported.<sup>[</sup>\n##UREF##33##\n55\n##, ##REF##28991493##\n56\n##\n<sup>]</sup> Consequently, the material exhibits dynamic vitrimer behavior, albeit with reduced dynamic capabilities compared to fully relaxed vitrimers. Nonetheless, it demonstrates exceptional dimensional stability and mechanical strength even above the glass‐transition temperature (<italic toggle=\"yes\">T</italic>\n<sub>g</sub>) and <italic toggle=\"yes\">T</italic>\n<sub>v</sub>. This behavior can be attributed to the presence of permanently crosslinked sites and potentially relates to the network topologies, thereby underlying further understanding of vitrimers and their dynamic behaviors.</p>", "<title>Cleavable and Topological Crosslinks Control over Degradable HDCNs</title>", "<p>Thermoset polymers are generally considered non‐degradable and hard to reprocess, particularly when in comparison to thermoplastic or weakly crosslinked supramolecular plastics.<sup>[</sup>\n##REF##36318511##\n57\n##, ##UREF##34##\n58\n##\n<sup>]</sup> However, inserting topological crosslinks and cleavable bonds into the thermoset network via HDCNs leads to the formation of vitrimers that exhibit distinctive behavior upon exposure to solvents (<bold>Figure</bold> ##FIG##1##\n2\n##; Section ##SUPPL##0##S1.7##, Supporting Information). In this study, a commonly used aprotic solvent (dimethylacetamide, DMAc) was employed to fully immerse the samples. EP‐12, as the most prominent case for degradation, underwent swelling and fragmentation within a mere 2 days at room temperature (Figure ##FIG##1##2a,b##), in stark contrast to the natural thermoset EP, which retained its intact and rigid shape. Moreover, an increasing concentration of HBPPB can accelerate the process. In fact, a rapid degradation was observed within 6 hours when the system temperature was raised to 95 °C in DMAc (Figure ##SUPPL##0##S13##, Supporting Information). Based on these differences, we infer that the solvent‐assisted degradation was associated with cleavable crosslinks in HDCNs.</p>", "<p>Unlike classic thermoset networks or degradable covalent networks, most of them are specialized for the degradation of weakly crosslinked materials such as thermoplastics and supramolecular plastics but are often helpless for highly crosslinked thermoset networks.<sup>[</sup>\n##REF##31011169##\n59\n##, ##UREF##35##\n60\n##\n<sup>]</sup> Whereas HDCNs benefit the stretching of molecular configurations for topological crosslinking purposes, which not only consists of several cleavable units but, more importantly, enables a topologically expanded network interspace that allows solvent molecular entrance to drive dynamic behaviors. The crosslinking density of HDCNs is relatively lower than their thermoset EP counterpart (Figure ##FIG##3##4c##). To assert the breakages when degrading, a schematic model describes the possible mechanisms in Figure ##FIG##1##2e##. Such a structure model encompasses three types of cleavable bonds. The first involves two kinds of carbonic ester bonds (mark a) that result from the reaction between the anhydride with HBPPB and the epoxy monomer (Figure ##SUPPL##0##S10##, Supporting Information). The second breakage is attributed to the boronic ester group (BO<sub>3</sub>)<sup>[</sup>\n##REF##29733205##\n53\n##, ##REF##25945818##\n61\n##, ##REF##27387198##\n62\n##\n<sup>]</sup> and the phosphate group (PO<sub>3</sub>)<sup>[</sup>\n##UREF##36##\n63\n##\n<sup>]</sup> upon the molecular backbone of the hyperbranched crosslinker. Third, non‐covalent H‐bonds are also susceptible to cleavage when the solvent is diffused.</p>", "<p>To monitor the aforementioned breakages, both EP‐12 and the solvent were subjected to FT‐IR analysis, as shown in Figure ##FIG##1##2f##. The results reveal distinct spectral features, notably the emergence of a newly detected C═O absorption (mark a) and C─H signals within the substituted benzene moiety in the DMAc spectrum after degradation, indicating the species of anhydride‐contained substrates are partially dissolved in DMAc, primarily indicating the cleavage of these carboxyl ester bonds. Furthermore, the degraded sample exhibits a diminished C─O─B/P absorption (mark b), which corresponds to the depolymerization of HBPPB. Complementary insights from the X‐ray photoelectron spectroscopy (XPS, details in Section ##SUPPL##0##S2.8##, Supporting Information) reveal that the beta‐hydroxy ester (formed through the reaction of the anhydride with ‐OH and epoxy groups) underwent breakage, as evidenced by its heightened and broader O─H/COOH intensity in the O1s spectra, as well as the relatively lower signals of C═O and C─O─C in the C1s spectra. More importantly, the degraded sample shows very weak signals of B and P in its high‐resolution XPS, thus further confirming the depolymerized HBPPB. Consequently, a highly cross‐linked network experienced fragmentation as a result of cleavages of these bonds.</p>", "<p>The degraded products were subsequently processed into fine powder through grinding and drying (Figure ##FIG##1##2c##). Notably, by mixing 1 g of degraded powder with ≈5 g of our pristine epoxy resin (refer to Section ##SUPPL##0##S1.7##, Supporting Information) and curing following the same procedure, we obtained the post‐cycled EP with impact strength and flexural strength comparable to the original (Figure ##FIG##1##2d##). Despite the cleavable bonds being introduced, we note that in thermosetting materials with only adapting additively crosslinked cleavable units, theoretically, it is difficult in practice to realize entirely or closed‐loop recycling of monomers once all of the crosslinks are formed.<sup>[</sup>\n##REF##36864144##\n64\n##, ##REF##37023198##\n65\n##, ##REF##37100913##\n66\n##\n<sup>]</sup> In this system, although the native EP thermoset also contains ester dynamic bonds, it remains non‐degradable or slowly degradable compared to the vitrimer. Thus, both the cleavable units and topological crosslinks control the degradation.</p>", "<p>Regarding the recovery uses (Figure ##FIG##1##2g–i##), carbon fiber composites have been explored for high‐performance applications, while the costly embedded carbon fibers (CFs) cannot be retrieved from bulk materials.<sup>[</sup>\n##UREF##37##\n67\n##, ##REF##35549086##\n68\n##\n<sup>]</sup> In this implementation, when carbon fiber fabrics were embedded into HDCNs to fabricate a composite, we were able to quantitatively recover the CFs while effectively separating the end‐of‐use epoxy powders from the composite. The Raman spectrum of the recovered fibers shows a carbon peak closely resembling those of the native fibers, indicating minimal surface impact on the carbon fibers (Figure ##FIG##1##2j##). These results hint at promising opportunities for the cyclic utilization of end‐of‐use epoxy resins and composites.</p>", "<title>Reconstructed HDCNs Enable Reconfigurable Elastic Vitrimer</title>", "<p>Next, by a chance following‐up, we note that when the samples were immersed in ethanol following a heating (95 °C, 6 h), the vitrimer sample (EP‐9) via forming HDCNs displayed elastomeric‐like feature upon cooling to room temperature, which allowed for a casual deformation and recovery as well (see Movie ##SUPPL##1##S1##, Supporting Information; <bold>Figure</bold> ##FIG##2##\n3a,b##), whereas the native thermoset (EP) still remains its rigid stiffness (Figure ##FIG##2##3c##). In our further study, we denoted EP‐9 as an example with suitable elasticity compared to EP‐12. Such transformation in elastomeric characteristics is exciting considering the inherent highly crosslinked nature of its bulk thermosets, especially for industrial epoxy commodities. This suggests that hyperbranched cross‐linking may alter the crosslinking mode of the thermoset network. We coined this type of vitrimer as “reconfigurable” vitrimers,<sup>[</sup>\n##UREF##10##\n16\n##, ##REF##23579959##\n49\n##\n<sup>]</sup> that is, a thermosetting network – whose crosslinked structure should be permanent – but can be reconstructed through solvent‐assisted reconfiguration. As illustrated in Figure ##FIG##2##3d,e##, we reasoned the ester‐exchange driving the reconstruction of HDCNs,<sup>[</sup>\n##REF##35640074##\n69\n##, ##REF##31469270##\n70\n##\n<sup>]</sup> whereby the ester bonds and hydrogen bonds can be rearranged since the ethanol serves as a single ─OH blocking molecule to substitute the ─OH site from those of hyperbranched crosslinks. The reorganized structure (Figure ##FIG##2##3j##) is corroborated by FT‐IR before‐ and after‐ethanol, temperature‐dependent IR, and dynamic thermomechanometry (Figure ##FIG##2##3g–i##). In particular, Figure ##FIG##2##3g## demonstrates a blueshift in the hydroxyl stretching vibration at 3400 cm<sup>−1</sup>, along with an increased width and intensity, indicating the transition of hydroxyl groups from a “free” state to an “associated” state. Furthermore, the reduction in peak intensity of C─O─C<sub>sym</sub> verifies the occurrence of ester exchange in HDCNs since symmetric ether structures (C─O─C<sub>sym</sub>, 1200–1150 cm<sup>−1</sup>) typically exhibit an increase in peak intensity. Additional evidence from model reactions (Section ##SUPPL##0##S1.8##, Supporting Information)<sup>[</sup>\n##REF##31433176##\n50\n##, ##REF##29733205##\n53\n##\n<sup>]</sup> and the XPS survey (Section ##SUPPL##0##S2.8##, Supporting Information) further supports the ester exchange should be the main mechanism to drive the reconfigurable behavior of the material. Ultimately, the reconstruction of HDCNs introduces polymer chain mobility and reduces the crosslinked structure, leading to the transformation in material nature.</p>", "<p>To further investigate the network dynamics of HDCNs, dynamic thermomechanometry was investigated over a wide temperature from −150 to 150 °C (Figure ##FIG##2##3i##; Figure ##SUPPL##0##S23##, Supporting Information) to record flexural modulus at three‐point bending mode. As the temperature decreases, the loss modulus exhibits a double‐relaxation of heat dissipation when the material is deformed. The lower (mark 1) relaxation involves a glass‐to‐elastic transition that unfreezes the side chains and groups, resulting in a rapid increase in flexural storage modulus from 3.2 to 5.4 GPa (Figure ##SUPPL##0##S23a##, Supporting Information). This increase is attributed to the ethyl ester (forming by ethanol exchange) occupying the initial crosslinked site of carbonic ester for network reconstruction (Figure ##FIG##2##3j##). The second relaxation (mark 2) signifies an elastic‐to‐liquid transition as the vitrimer network flows and relaxes due to dynamic bond exchange. Real‐temperature IR analysis confirms the defreezing temperature of H‐bonds in close proximity to this transition, as indicated by a significant increase in the normalized intensity of hydroxyl groups, shifting from the “associated” state to the “free” state upon temperature elevation from 0 °C (Figure ##FIG##2##3h##),<sup>[</sup>\n##UREF##38##\n71\n##\n<sup>]</sup> while the intensity remains almost unchanged from −50 to 0 °C.</p>", "<p>In this term, the reconstructed HDCNs display a stronger H‐bonding crosslinked network compared with that of native EP at lower temperature areas, where the polymer segments are frozen and tightly constrained by H‐bonding.<sup>[</sup>\n##UREF##39##\n72\n##\n<sup>]</sup> Consequently, we observe a significant increase in <italic toggle=\"yes\">G’</italic> with decreasing temperature (Figure ##SUPPL##0##S23a##, Supporting Information), recording as high as 5.45 GPa at −150 °C. This represents an exceptionally high flexural modulus for polymeric materials and approximately twice that of native EP under the same condition. The exceptional modulus at ultra‐low temperatures empowers this polymeric material with supernormal applications in astrospace material, superconducting energy storage, and medical equipment.</p>", "<title>General Properties and Multifunctional Performance of HDCNs</title>", "<p>\n<bold>Figure</bold> ##FIG##3##\n4\n## provides a comprehensive analysis of the multifaceted performance of the material in harnessing the advantages of HDCNs. First, the glass transition temperature (<italic toggle=\"yes\">T</italic>\n<sub>g</sub>, Figure ##SUPPL##0##S21a## and Table ##SUPPL##0##S6##, Supporting Information) of EP, EP‐3, EP‐6, EP‐9, and EP‐12 are 131, 121, 118, 104, and 94 <sup>°</sup>C, respectively, indicating they are glassy polymers at room temperature. The slight decrease in <italic toggle=\"yes\">T</italic>\n<sub>g</sub> can be attributed to the amorphous structure of HBPPB.<sup>[</sup>\n##UREF##25##\n38\n##\n<sup>]</sup> Upon crosslinking a hyperbranched macromolecular, network topologies are physically expanded.<sup>[</sup>\n##UREF##40##\n73\n##, ##REF##27634530##\n74\n##\n<sup>]</sup> However, the heat loss of chains motion is intensified below <italic toggle=\"yes\">T</italic>\n<sub>g</sub> due to increased friction and constraints imposed by the HBPPB within the network (increased loss modulus (Figure ##FIG##3##4a##). Conversely, above <italic toggle=\"yes\">T</italic>\n<sub>g</sub> and <italic toggle=\"yes\">T</italic>\n<sub>v</sub>, the friction between epoxy chains with HBPPB is reduced due to dynamic bond exchange, and the network flows more easily thus existing a reduced loss modulus. Note that inserting poorly rigid chains often compromises the modulus and strength. Remarkably, the vitrimer, upon introducing an aliphatic hyperbranched crosslinker, demonstrates an even higher storage modulus (<italic toggle=\"yes\">E’</italic>) compared to that of native EP (Figure ##FIG##3##4b##). Specifically, the addition of 3% HBPPB elevates <italic toggle=\"yes\">E’</italic> from 2.38 GPa of native EP up to 3.15 GPa (Figure ##SUPPL##0##S21b##, Supporting Information), followed by a decline with further increasing HBPPB, which substantiates the reinforcement effect of HDCNs. This enhancement can be attributed to that the hyperbranched structure acts as a “supramolecular rivet” to facilitate a robust supramolecular/epoxy interpenetrating network through H‐bonds and covalent bonds (Figure ##FIG##3##4d##).<sup>[</sup>\n##UREF##41##\n75\n##, ##UREF##42##\n76\n##\n<sup>]</sup> The branching molecular topology enables an expanded network interspace, resulting in a reduced network crosslinking density (Figure ##FIG##3##4c##), as elaborated in Section ##SUPPL##0##S2.1## (Supporting Information). Consequently, the hyperbranched crosslinker holds significant promise as a topological crosslinking tool for programming low‐crosslinking yet high‐strength polymers.</p>", "<p>Measurements of impact toughness, flexural strength, and tensile strength were carried out to facilitate a comprehensive understanding of mechanical performance (Figure ##FIG##3##4e,f##; details in Section ##SUPPL##0##S2.6##, Supporting Information). The high crosslinking density and rigid polymer chains render thermosets susceptible to impact failure, resulting in a microscopic “river‐like” brittle fracture (Figure ##SUPPL##0##S30##, Supporting Information) with 12.94 kJ m<sup>−2</sup> of impact strength. However, EP‐3 shows a superior increase (98.5%) from 12.94 up to 25.69 kJ m<sup>−2</sup>, accompanied by obvious “dimple‐fracture” features that promote energy absorption. Thought‐out relevant works regarding hyperbranched polymer‐reinforced thermosets, a supramolecular network‐induced energy dissipation mechanism could be supposed.<sup>[</sup>\n##UREF##43##\n77\n##, ##REF##35042887##\n78\n##\n<sup>]</sup> The network topologies furnish cross‐linked polymers with enhanced properties without altering their chemical composition.<sup>[</sup>\n##REF##35894294##\n79\n##\n<sup>]</sup> It is worth noting that the increase in impact strength surpasses that of flexural strength, which can be attributed to the presence of flexible aliphatic chains that mitigate the network stiffness. Both the flexural and tensile strength show a consistent and noteworthy improvement from 106.1 up to 132 MPa, and 52.1 up to 81.2 MPa, respectively (Table ##SUPPL##0##S7##, Supporting Information). Notably, the tensile strain‐stress curves indicate that vitrimers are more stretchable than that of native thermoset epoxy (Figure ##SUPPL##0##S31##, Supporting Information). This finding holds great promise for the fabrication of carbon fiber reinforced polymers (CFRPs), where the stress should primarily reside in the fibers rather than the resins. This attribute ensures the exceptional mechanical strength of CFRPs (Section ##SUPPL##0##S2.6.3##, Supporting Information).</p>", "<p>In this contribution, both the strength and modulus depend on a tightly crosslinked network. The HBPPB, which terminates abundant ─OH groups, acts as a “rivet” within the network through covalent bonding and non‐covalent H‐bonding. The observed increase in <italic toggle=\"yes\">E’</italic> is also in agreement with the flexural results. Unfortunately, the optimal mechanical system does not maintain a consistent HBPPB concentration with the degradable and recyclable sample. Despite overloading HBPPB causing deteriorated mechanical strength, it still outperforms native EP. The reduction in impact and flexural strength can be attributed to the local agglomeration of hyperbranched polymers.<sup>[</sup>\n##UREF##29##\n45\n##, ##UREF##30##\n46\n##\n<sup>]</sup> Supplementary thermal and thermomechanical parameters are provided in Table ##SUPPL##0##S6## (Supporting Information). The vitrimers exhibit improved <italic toggle=\"yes\">T</italic>\n<sub>max</sub> values and char yields, indicating superior thermal stability of HDCNs, which is primarily attributed to the presence of the inert boron component in the system.</p>", "<p>We next sought to probe the functional performance of materials. Good fire safety is a crucial consideration for real‐world applications of polymeric materials.<sup>[</sup>\n##UREF##44##\n80\n##, ##UREF##45##\n81\n##\n<sup>]</sup> Overall, our results demonstrate that the vitrimer sample exhibits superior fire safety performance compared to the native EP. Specifically, the vitrimer samples, EP‐9 and EP‐12, exhibit reduced thermal hazards and smoke production, along with increased resistance to ignition (higher limit oxygen index), and self‐extinguishing properties in an air atmosphere (Figure ##FIG##3##4g##). A comprehensive investigation was conducted through a full‐scale study of the fire‐retardant performance (Section ##SUPPL##0##S2.10## and Figure ##SUPPL##0##S41##, Supporting Information). The cone calorimeter test, which simulates a real fire scenario, provided crucial parameters to elucidate the flame‐retardant effect and mechanism.<sup>[</sup>\n##UREF##46##\n82\n##\n<sup>]</sup> Additionally, XPS analysis and Raman spectra (Figure ##SUPPL##0##S42##, Supporting Information) revealed the condensed fire‐retardant actions. The HDCNs constructed in our materials accumulate two types of flame‐retardant elements (phosphorus and boron) within the hyperbranched backbone for synergistic fire‐retarding action, ensuring the fire safety of the material.</p>", "<p>One of the facts is that the materials, specifically EP‐9 and EP‐12, exhibit significantly superior transparency and lighter coloration than their native thermoset. The transmittance of materials was measured using UV–vis spectrophotometer (See Figure ##SUPPL##0##S40##, Supporting Information). The average transmittance in both 280–380 nm (UV region) and 380–780 nm (visible region) was acquired in Figure ##FIG##3##4h##, showing significant increases in transmittance to both UV and visible light. The exceptional transparency of these materials can be attributed to the unique construction of HDCNs and the optical properties of HBPPB. Excitingly, this type of hyperbranched polymer has been reported as a class of non‐traditional aggregation‐induced emission luminogens (AIEgens),<sup>[</sup>\n##UREF##47##\n83\n##, ##UREF##48##\n84\n##\n<sup>]</sup> posing a promising pathway toward understanding the polymer crosslinking via fluorescent visualization methods. Besides, the exceptional transparency and lightness impart this polymeric material high added‐values for application in packaging materials, photoelectric materials, and flexible electronics.<sup>[</sup>\n##UREF##49##\n85\n##, ##REF##22789123##\n86\n##\n<sup>]</sup>\n</p>" ]
[ "<title>Results and Discussion</title>", "<title>Synthesis and Characterization of HDCNs</title>", "<p>The synthesis of HDCNs is straightforward via introducing a hyperbranched dynamic macromonomer into a traditional epoxy thermoset network as a dynamic crosslinker. The hyperbranched macromonomer (HBPPB) was synthesized via A<sub>2</sub>+B<sub>2</sub>+C<sub>3</sub> polycondensation (Section ##SUPPL##0##S1.3a##, Supporting Information). In parallel, a linear poly‐phosphate/borate structure (LPPB), a hyperbranched polyborate (HBPB), and a hyperbranched polyphosphate (HBPP) were synthesized as controls to compare with HDCNs. Synthesis details are described in Sections ##SUPPL##0##S1.4## and ##SUPPL##0##S1.5## (Supporting Information). The molecular structure of the synthetic polymers was characterized using multiple analytical techniques, including Fourier transform infrared (FT‐IR), <sup>1</sup>H, <sup>13</sup>C, and <sup>31</sup>P nuclear magnetic resonance (NMR) spectroscopies, gel permeation chromatography (GPC) (see Section ##SUPPL##0##S1.3b##, Supporting Information). The concentration of hydroxyl groups (─OH) in HBPPB was quantified via a standard titration experiment, yielding a value of 7.97 × 10<sup>−3</sup> mol g<sup>−1</sup> (Section ##SUPPL##0##S1.3c## and Table ##SUPPL##0##S2##, Supporting Information), indicating the high abundance of ─OH groups.</p>", "<p>The polymer matrix comprised of a petroleum‐based epoxy (diglycidyl ether bisphenol A, DGEBA, E51) a commercially used anhydride‐type curing agent (methyl tetrahydrophthalic anhydride, MTHPA), and a certain amount of HBPPB. A facile thermosetting workflow was employed to cast EP‐x samples, where <italic toggle=\"yes\">x</italic> represents the mass concentration of HBPPB. The curing performance was evaluated using isothermal differential scanning calorimetry (Figure ##SUPPL##0##S21c##, Supporting Information), which showed a homogeneous and single peak among all pre‐polymer systems, indicating well compatibility among the three constituents. The natural EP and EP‐9 underwent full curing as proved in its time‐sweep curves by rheology (Figure ##SUPPL##0##S22##, Supporting Information). For subsequent analysis, the epoxy samples containing HBPPB equal to or greater than 9 wt.% were donated as vitrimers due to their degradable and/or reconfigurable dynamic behavior. The other samples were categorized as thermosets due to their predominant thermoset nature. To facilitate comparative investigations, epoxy vitrimers containing varying mass fractions of LPPB, HBPB, and HBPP were prepared using the same procedure as HDCNs, and a comparison of their material properties is presented in Sections ##SUPPL##0##S2.5## and ##SUPPL##0##S2.6## (Supporting Information).</p>", "<p>The dynamic nature of HDCNs was characterized extensively through stress relaxation (see Section ##SUPPL##0##S2.3##, Supporting Information) and creep‐recovery test (Section ##SUPPL##0##S2.4##, Supporting Information) in tensile mode.<sup>[</sup>\n##REF##31433176##\n50\n##, ##REF##35590755##\n51\n##, ##REF##35607118##\n52\n##, ##REF##29733205##\n53\n##, ##REF##28557428##\n54\n##\n<sup>]</sup> In EP‐12, the time‐ and temperature‐dependent modulus revealed a partial relaxation to a plateau regime that deviates from classical linear‐viscoelastic vitrimers. This unique relaxation signifies that HDCNs not only behave with liquid‐like viscoelasticity due to the activation of dynamic exchange above the topology‐freezing transition temperature (<italic toggle=\"yes\">T</italic>\n<sub>v</sub>, described by Arrhenius and Williams−Landel−Ferry law), but also retain the resilience and recovery capabilities like an elastic body subjected to Hooke's law. By fitting the results on an Arrhenius plot, a linear correlation between ln(<italic toggle=\"yes\">τ*</italic>) (relaxation time) and 1000/T (inverse temperature) was observed, enabling the calculation of an activation energy (<italic toggle=\"yes\">E</italic>\n<sub>a</sub>) of 78.1 kJ mol<sup>−1</sup> and <italic toggle=\"yes\">T</italic>\n<sub>v</sub> of 71.7 °C (Figures ##SUPPL##0##S24## and ##SUPPL##0##S25##, Supporting Information). It is noteworthy that several examples of vitrimers with <italic toggle=\"yes\">T</italic>\n<sub>g</sub> &gt; <italic toggle=\"yes\">T</italic>\n<sub>v</sub> have been reported.<sup>[</sup>\n##UREF##33##\n55\n##, ##REF##28991493##\n56\n##\n<sup>]</sup> Consequently, the material exhibits dynamic vitrimer behavior, albeit with reduced dynamic capabilities compared to fully relaxed vitrimers. Nonetheless, it demonstrates exceptional dimensional stability and mechanical strength even above the glass‐transition temperature (<italic toggle=\"yes\">T</italic>\n<sub>g</sub>) and <italic toggle=\"yes\">T</italic>\n<sub>v</sub>. This behavior can be attributed to the presence of permanently crosslinked sites and potentially relates to the network topologies, thereby underlying further understanding of vitrimers and their dynamic behaviors.</p>", "<title>Cleavable and Topological Crosslinks Control over Degradable HDCNs</title>", "<p>Thermoset polymers are generally considered non‐degradable and hard to reprocess, particularly when in comparison to thermoplastic or weakly crosslinked supramolecular plastics.<sup>[</sup>\n##REF##36318511##\n57\n##, ##UREF##34##\n58\n##\n<sup>]</sup> However, inserting topological crosslinks and cleavable bonds into the thermoset network via HDCNs leads to the formation of vitrimers that exhibit distinctive behavior upon exposure to solvents (<bold>Figure</bold> ##FIG##1##\n2\n##; Section ##SUPPL##0##S1.7##, Supporting Information). In this study, a commonly used aprotic solvent (dimethylacetamide, DMAc) was employed to fully immerse the samples. EP‐12, as the most prominent case for degradation, underwent swelling and fragmentation within a mere 2 days at room temperature (Figure ##FIG##1##2a,b##), in stark contrast to the natural thermoset EP, which retained its intact and rigid shape. Moreover, an increasing concentration of HBPPB can accelerate the process. In fact, a rapid degradation was observed within 6 hours when the system temperature was raised to 95 °C in DMAc (Figure ##SUPPL##0##S13##, Supporting Information). Based on these differences, we infer that the solvent‐assisted degradation was associated with cleavable crosslinks in HDCNs.</p>", "<p>Unlike classic thermoset networks or degradable covalent networks, most of them are specialized for the degradation of weakly crosslinked materials such as thermoplastics and supramolecular plastics but are often helpless for highly crosslinked thermoset networks.<sup>[</sup>\n##REF##31011169##\n59\n##, ##UREF##35##\n60\n##\n<sup>]</sup> Whereas HDCNs benefit the stretching of molecular configurations for topological crosslinking purposes, which not only consists of several cleavable units but, more importantly, enables a topologically expanded network interspace that allows solvent molecular entrance to drive dynamic behaviors. The crosslinking density of HDCNs is relatively lower than their thermoset EP counterpart (Figure ##FIG##3##4c##). To assert the breakages when degrading, a schematic model describes the possible mechanisms in Figure ##FIG##1##2e##. Such a structure model encompasses three types of cleavable bonds. The first involves two kinds of carbonic ester bonds (mark a) that result from the reaction between the anhydride with HBPPB and the epoxy monomer (Figure ##SUPPL##0##S10##, Supporting Information). The second breakage is attributed to the boronic ester group (BO<sub>3</sub>)<sup>[</sup>\n##REF##29733205##\n53\n##, ##REF##25945818##\n61\n##, ##REF##27387198##\n62\n##\n<sup>]</sup> and the phosphate group (PO<sub>3</sub>)<sup>[</sup>\n##UREF##36##\n63\n##\n<sup>]</sup> upon the molecular backbone of the hyperbranched crosslinker. Third, non‐covalent H‐bonds are also susceptible to cleavage when the solvent is diffused.</p>", "<p>To monitor the aforementioned breakages, both EP‐12 and the solvent were subjected to FT‐IR analysis, as shown in Figure ##FIG##1##2f##. The results reveal distinct spectral features, notably the emergence of a newly detected C═O absorption (mark a) and C─H signals within the substituted benzene moiety in the DMAc spectrum after degradation, indicating the species of anhydride‐contained substrates are partially dissolved in DMAc, primarily indicating the cleavage of these carboxyl ester bonds. Furthermore, the degraded sample exhibits a diminished C─O─B/P absorption (mark b), which corresponds to the depolymerization of HBPPB. Complementary insights from the X‐ray photoelectron spectroscopy (XPS, details in Section ##SUPPL##0##S2.8##, Supporting Information) reveal that the beta‐hydroxy ester (formed through the reaction of the anhydride with ‐OH and epoxy groups) underwent breakage, as evidenced by its heightened and broader O─H/COOH intensity in the O1s spectra, as well as the relatively lower signals of C═O and C─O─C in the C1s spectra. More importantly, the degraded sample shows very weak signals of B and P in its high‐resolution XPS, thus further confirming the depolymerized HBPPB. Consequently, a highly cross‐linked network experienced fragmentation as a result of cleavages of these bonds.</p>", "<p>The degraded products were subsequently processed into fine powder through grinding and drying (Figure ##FIG##1##2c##). Notably, by mixing 1 g of degraded powder with ≈5 g of our pristine epoxy resin (refer to Section ##SUPPL##0##S1.7##, Supporting Information) and curing following the same procedure, we obtained the post‐cycled EP with impact strength and flexural strength comparable to the original (Figure ##FIG##1##2d##). Despite the cleavable bonds being introduced, we note that in thermosetting materials with only adapting additively crosslinked cleavable units, theoretically, it is difficult in practice to realize entirely or closed‐loop recycling of monomers once all of the crosslinks are formed.<sup>[</sup>\n##REF##36864144##\n64\n##, ##REF##37023198##\n65\n##, ##REF##37100913##\n66\n##\n<sup>]</sup> In this system, although the native EP thermoset also contains ester dynamic bonds, it remains non‐degradable or slowly degradable compared to the vitrimer. Thus, both the cleavable units and topological crosslinks control the degradation.</p>", "<p>Regarding the recovery uses (Figure ##FIG##1##2g–i##), carbon fiber composites have been explored for high‐performance applications, while the costly embedded carbon fibers (CFs) cannot be retrieved from bulk materials.<sup>[</sup>\n##UREF##37##\n67\n##, ##REF##35549086##\n68\n##\n<sup>]</sup> In this implementation, when carbon fiber fabrics were embedded into HDCNs to fabricate a composite, we were able to quantitatively recover the CFs while effectively separating the end‐of‐use epoxy powders from the composite. The Raman spectrum of the recovered fibers shows a carbon peak closely resembling those of the native fibers, indicating minimal surface impact on the carbon fibers (Figure ##FIG##1##2j##). These results hint at promising opportunities for the cyclic utilization of end‐of‐use epoxy resins and composites.</p>", "<title>Reconstructed HDCNs Enable Reconfigurable Elastic Vitrimer</title>", "<p>Next, by a chance following‐up, we note that when the samples were immersed in ethanol following a heating (95 °C, 6 h), the vitrimer sample (EP‐9) via forming HDCNs displayed elastomeric‐like feature upon cooling to room temperature, which allowed for a casual deformation and recovery as well (see Movie ##SUPPL##1##S1##, Supporting Information; <bold>Figure</bold> ##FIG##2##\n3a,b##), whereas the native thermoset (EP) still remains its rigid stiffness (Figure ##FIG##2##3c##). In our further study, we denoted EP‐9 as an example with suitable elasticity compared to EP‐12. Such transformation in elastomeric characteristics is exciting considering the inherent highly crosslinked nature of its bulk thermosets, especially for industrial epoxy commodities. This suggests that hyperbranched cross‐linking may alter the crosslinking mode of the thermoset network. We coined this type of vitrimer as “reconfigurable” vitrimers,<sup>[</sup>\n##UREF##10##\n16\n##, ##REF##23579959##\n49\n##\n<sup>]</sup> that is, a thermosetting network – whose crosslinked structure should be permanent – but can be reconstructed through solvent‐assisted reconfiguration. As illustrated in Figure ##FIG##2##3d,e##, we reasoned the ester‐exchange driving the reconstruction of HDCNs,<sup>[</sup>\n##REF##35640074##\n69\n##, ##REF##31469270##\n70\n##\n<sup>]</sup> whereby the ester bonds and hydrogen bonds can be rearranged since the ethanol serves as a single ─OH blocking molecule to substitute the ─OH site from those of hyperbranched crosslinks. The reorganized structure (Figure ##FIG##2##3j##) is corroborated by FT‐IR before‐ and after‐ethanol, temperature‐dependent IR, and dynamic thermomechanometry (Figure ##FIG##2##3g–i##). In particular, Figure ##FIG##2##3g## demonstrates a blueshift in the hydroxyl stretching vibration at 3400 cm<sup>−1</sup>, along with an increased width and intensity, indicating the transition of hydroxyl groups from a “free” state to an “associated” state. Furthermore, the reduction in peak intensity of C─O─C<sub>sym</sub> verifies the occurrence of ester exchange in HDCNs since symmetric ether structures (C─O─C<sub>sym</sub>, 1200–1150 cm<sup>−1</sup>) typically exhibit an increase in peak intensity. Additional evidence from model reactions (Section ##SUPPL##0##S1.8##, Supporting Information)<sup>[</sup>\n##REF##31433176##\n50\n##, ##REF##29733205##\n53\n##\n<sup>]</sup> and the XPS survey (Section ##SUPPL##0##S2.8##, Supporting Information) further supports the ester exchange should be the main mechanism to drive the reconfigurable behavior of the material. Ultimately, the reconstruction of HDCNs introduces polymer chain mobility and reduces the crosslinked structure, leading to the transformation in material nature.</p>", "<p>To further investigate the network dynamics of HDCNs, dynamic thermomechanometry was investigated over a wide temperature from −150 to 150 °C (Figure ##FIG##2##3i##; Figure ##SUPPL##0##S23##, Supporting Information) to record flexural modulus at three‐point bending mode. As the temperature decreases, the loss modulus exhibits a double‐relaxation of heat dissipation when the material is deformed. The lower (mark 1) relaxation involves a glass‐to‐elastic transition that unfreezes the side chains and groups, resulting in a rapid increase in flexural storage modulus from 3.2 to 5.4 GPa (Figure ##SUPPL##0##S23a##, Supporting Information). This increase is attributed to the ethyl ester (forming by ethanol exchange) occupying the initial crosslinked site of carbonic ester for network reconstruction (Figure ##FIG##2##3j##). The second relaxation (mark 2) signifies an elastic‐to‐liquid transition as the vitrimer network flows and relaxes due to dynamic bond exchange. Real‐temperature IR analysis confirms the defreezing temperature of H‐bonds in close proximity to this transition, as indicated by a significant increase in the normalized intensity of hydroxyl groups, shifting from the “associated” state to the “free” state upon temperature elevation from 0 °C (Figure ##FIG##2##3h##),<sup>[</sup>\n##UREF##38##\n71\n##\n<sup>]</sup> while the intensity remains almost unchanged from −50 to 0 °C.</p>", "<p>In this term, the reconstructed HDCNs display a stronger H‐bonding crosslinked network compared with that of native EP at lower temperature areas, where the polymer segments are frozen and tightly constrained by H‐bonding.<sup>[</sup>\n##UREF##39##\n72\n##\n<sup>]</sup> Consequently, we observe a significant increase in <italic toggle=\"yes\">G’</italic> with decreasing temperature (Figure ##SUPPL##0##S23a##, Supporting Information), recording as high as 5.45 GPa at −150 °C. This represents an exceptionally high flexural modulus for polymeric materials and approximately twice that of native EP under the same condition. The exceptional modulus at ultra‐low temperatures empowers this polymeric material with supernormal applications in astrospace material, superconducting energy storage, and medical equipment.</p>", "<title>General Properties and Multifunctional Performance of HDCNs</title>", "<p>\n<bold>Figure</bold> ##FIG##3##\n4\n## provides a comprehensive analysis of the multifaceted performance of the material in harnessing the advantages of HDCNs. First, the glass transition temperature (<italic toggle=\"yes\">T</italic>\n<sub>g</sub>, Figure ##SUPPL##0##S21a## and Table ##SUPPL##0##S6##, Supporting Information) of EP, EP‐3, EP‐6, EP‐9, and EP‐12 are 131, 121, 118, 104, and 94 <sup>°</sup>C, respectively, indicating they are glassy polymers at room temperature. The slight decrease in <italic toggle=\"yes\">T</italic>\n<sub>g</sub> can be attributed to the amorphous structure of HBPPB.<sup>[</sup>\n##UREF##25##\n38\n##\n<sup>]</sup> Upon crosslinking a hyperbranched macromolecular, network topologies are physically expanded.<sup>[</sup>\n##UREF##40##\n73\n##, ##REF##27634530##\n74\n##\n<sup>]</sup> However, the heat loss of chains motion is intensified below <italic toggle=\"yes\">T</italic>\n<sub>g</sub> due to increased friction and constraints imposed by the HBPPB within the network (increased loss modulus (Figure ##FIG##3##4a##). Conversely, above <italic toggle=\"yes\">T</italic>\n<sub>g</sub> and <italic toggle=\"yes\">T</italic>\n<sub>v</sub>, the friction between epoxy chains with HBPPB is reduced due to dynamic bond exchange, and the network flows more easily thus existing a reduced loss modulus. Note that inserting poorly rigid chains often compromises the modulus and strength. Remarkably, the vitrimer, upon introducing an aliphatic hyperbranched crosslinker, demonstrates an even higher storage modulus (<italic toggle=\"yes\">E’</italic>) compared to that of native EP (Figure ##FIG##3##4b##). Specifically, the addition of 3% HBPPB elevates <italic toggle=\"yes\">E’</italic> from 2.38 GPa of native EP up to 3.15 GPa (Figure ##SUPPL##0##S21b##, Supporting Information), followed by a decline with further increasing HBPPB, which substantiates the reinforcement effect of HDCNs. This enhancement can be attributed to that the hyperbranched structure acts as a “supramolecular rivet” to facilitate a robust supramolecular/epoxy interpenetrating network through H‐bonds and covalent bonds (Figure ##FIG##3##4d##).<sup>[</sup>\n##UREF##41##\n75\n##, ##UREF##42##\n76\n##\n<sup>]</sup> The branching molecular topology enables an expanded network interspace, resulting in a reduced network crosslinking density (Figure ##FIG##3##4c##), as elaborated in Section ##SUPPL##0##S2.1## (Supporting Information). Consequently, the hyperbranched crosslinker holds significant promise as a topological crosslinking tool for programming low‐crosslinking yet high‐strength polymers.</p>", "<p>Measurements of impact toughness, flexural strength, and tensile strength were carried out to facilitate a comprehensive understanding of mechanical performance (Figure ##FIG##3##4e,f##; details in Section ##SUPPL##0##S2.6##, Supporting Information). The high crosslinking density and rigid polymer chains render thermosets susceptible to impact failure, resulting in a microscopic “river‐like” brittle fracture (Figure ##SUPPL##0##S30##, Supporting Information) with 12.94 kJ m<sup>−2</sup> of impact strength. However, EP‐3 shows a superior increase (98.5%) from 12.94 up to 25.69 kJ m<sup>−2</sup>, accompanied by obvious “dimple‐fracture” features that promote energy absorption. Thought‐out relevant works regarding hyperbranched polymer‐reinforced thermosets, a supramolecular network‐induced energy dissipation mechanism could be supposed.<sup>[</sup>\n##UREF##43##\n77\n##, ##REF##35042887##\n78\n##\n<sup>]</sup> The network topologies furnish cross‐linked polymers with enhanced properties without altering their chemical composition.<sup>[</sup>\n##REF##35894294##\n79\n##\n<sup>]</sup> It is worth noting that the increase in impact strength surpasses that of flexural strength, which can be attributed to the presence of flexible aliphatic chains that mitigate the network stiffness. Both the flexural and tensile strength show a consistent and noteworthy improvement from 106.1 up to 132 MPa, and 52.1 up to 81.2 MPa, respectively (Table ##SUPPL##0##S7##, Supporting Information). Notably, the tensile strain‐stress curves indicate that vitrimers are more stretchable than that of native thermoset epoxy (Figure ##SUPPL##0##S31##, Supporting Information). This finding holds great promise for the fabrication of carbon fiber reinforced polymers (CFRPs), where the stress should primarily reside in the fibers rather than the resins. This attribute ensures the exceptional mechanical strength of CFRPs (Section ##SUPPL##0##S2.6.3##, Supporting Information).</p>", "<p>In this contribution, both the strength and modulus depend on a tightly crosslinked network. The HBPPB, which terminates abundant ─OH groups, acts as a “rivet” within the network through covalent bonding and non‐covalent H‐bonding. The observed increase in <italic toggle=\"yes\">E’</italic> is also in agreement with the flexural results. Unfortunately, the optimal mechanical system does not maintain a consistent HBPPB concentration with the degradable and recyclable sample. Despite overloading HBPPB causing deteriorated mechanical strength, it still outperforms native EP. The reduction in impact and flexural strength can be attributed to the local agglomeration of hyperbranched polymers.<sup>[</sup>\n##UREF##29##\n45\n##, ##UREF##30##\n46\n##\n<sup>]</sup> Supplementary thermal and thermomechanical parameters are provided in Table ##SUPPL##0##S6## (Supporting Information). The vitrimers exhibit improved <italic toggle=\"yes\">T</italic>\n<sub>max</sub> values and char yields, indicating superior thermal stability of HDCNs, which is primarily attributed to the presence of the inert boron component in the system.</p>", "<p>We next sought to probe the functional performance of materials. Good fire safety is a crucial consideration for real‐world applications of polymeric materials.<sup>[</sup>\n##UREF##44##\n80\n##, ##UREF##45##\n81\n##\n<sup>]</sup> Overall, our results demonstrate that the vitrimer sample exhibits superior fire safety performance compared to the native EP. Specifically, the vitrimer samples, EP‐9 and EP‐12, exhibit reduced thermal hazards and smoke production, along with increased resistance to ignition (higher limit oxygen index), and self‐extinguishing properties in an air atmosphere (Figure ##FIG##3##4g##). A comprehensive investigation was conducted through a full‐scale study of the fire‐retardant performance (Section ##SUPPL##0##S2.10## and Figure ##SUPPL##0##S41##, Supporting Information). The cone calorimeter test, which simulates a real fire scenario, provided crucial parameters to elucidate the flame‐retardant effect and mechanism.<sup>[</sup>\n##UREF##46##\n82\n##\n<sup>]</sup> Additionally, XPS analysis and Raman spectra (Figure ##SUPPL##0##S42##, Supporting Information) revealed the condensed fire‐retardant actions. The HDCNs constructed in our materials accumulate two types of flame‐retardant elements (phosphorus and boron) within the hyperbranched backbone for synergistic fire‐retarding action, ensuring the fire safety of the material.</p>", "<p>One of the facts is that the materials, specifically EP‐9 and EP‐12, exhibit significantly superior transparency and lighter coloration than their native thermoset. The transmittance of materials was measured using UV–vis spectrophotometer (See Figure ##SUPPL##0##S40##, Supporting Information). The average transmittance in both 280–380 nm (UV region) and 380–780 nm (visible region) was acquired in Figure ##FIG##3##4h##, showing significant increases in transmittance to both UV and visible light. The exceptional transparency of these materials can be attributed to the unique construction of HDCNs and the optical properties of HBPPB. Excitingly, this type of hyperbranched polymer has been reported as a class of non‐traditional aggregation‐induced emission luminogens (AIEgens),<sup>[</sup>\n##UREF##47##\n83\n##, ##UREF##48##\n84\n##\n<sup>]</sup> posing a promising pathway toward understanding the polymer crosslinking via fluorescent visualization methods. Besides, the exceptional transparency and lightness impart this polymeric material high added‐values for application in packaging materials, photoelectric materials, and flexible electronics.<sup>[</sup>\n##UREF##49##\n85\n##, ##REF##22789123##\n86\n##\n<sup>]</sup>\n</p>" ]
[ "<title>Conclusion</title>", "<p>In summary, we concept a hyperbranched dynamic crosslinked network (HDCNs) featuring multi‐dynamic bonds and topological crosslinking network architecture. Such a unique structure not only allows the penetration of solvent molecules for dynamic responsiveness, but also integrates exceptional mechanical strength, high transparency, and fire‐retardant functions into a single material. Through the construction of HDCNs, this work engineers a commercial petroleum‐based epoxy thermoset into a degradable and reconfigurable vitrimer by the breakages of dynamic units and the reconstruction of dynamic networks. The vitrimer showcases mild solvent degradation at room‐temperature and powder reprocessable performance, enabling the recovery of carbon fiber and resin powder from composite. More remarkably, we have made an exciting discovery that HDCNs display reconfigurable behavior via ester‐exchange triggered by ethanol, resulting in a flexible elastomer at 25 °C and a supra‐high flexural modulus of 5.45 GPa at ultralow temperature (−150 °C), thus offering the potential for extraordinary applications. The utilization of HDCNs as a building strategy opens up many inspirations toward designing and customizing sustainable polymeric materials, while also uncovering their fascinating material nature.</p>" ]
[ "<title>Abstract</title>", "<p>Degradation and reprocessing of thermoset polymers have long been intractable challenges to meet a sustainable future. Star strategies via dynamic cross‐linking hydrogen bonds and/or covalent bonds can afford reprocessable thermosets, but often at the cost of properties or even their functions. Herein, a simple strategy coined as hyperbranched dynamic crosslinking networks (HDCNs) toward in‐practice engineering a petroleum‐based epoxy thermoset into degradable, reconfigurable, and multifunctional vitrimer is provided. The special characteristics of HDCNs involve spatially topological crosslinks for solvent adaption and multi‐dynamic linkages for reversible behaviors. The resulting vitrimer displays mild room‐temperature degradation to dimethylacetamide and can realize the cycling of carbon fiber and epoxy powder from composite. Besides, they have supra toughness and high flexural modulus, high transparency as well as fire‐retardancy surpassing their original thermoset. Notably, it is noted in a chance‐following that ethanol molecule can induce the reconstruction of vitrimer network by ester‐exchange, converting a stiff vitrimer into elastomeric feature, and such material records an ultrahigh modulus (5.45 GPa) at −150 °C for their ultralow‐temperature condition uses. This is shaping up to be a potentially sustainable advanced material to address the post‐consumer thermoset waste, and also provide a newly crosslinked mode for the designs of high‐performance polymer.</p>", "<p>Hyperbranched dynamic crosslinking networks (HDCNs) convert a thermoset network from permanently three‐dimensional‐structure to dynamically topological‐crosslinked architecture, programming a petroleum‐based thermoset into degradable, reconfigurable and multifunctional vitrimer. They are capable of room‐temperature degradation to solvent, and exhibit reconfigurability from stiff vitrimer to elastomer. Vitrimers also display enhanced modulus, toughness, flame‐retardancy, and high transparency when compared to native commodity thermosets.\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6607-cit-0087\">\n<string-name>\n<given-names>Y.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Yan</surname>\n</string-name>, <string-name>\n<given-names>R.</given-names>\n<surname>Yu</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Yuan</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Yang</surname>\n</string-name>, <string-name>\n<given-names>R.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>He</surname>\n</string-name>, <string-name>\n<given-names>W.</given-names>\n<surname>Feng</surname>\n</string-name>, <string-name>\n<given-names>W.</given-names>\n<surname>Tian</surname>\n</string-name>, <article-title>Hyperbranched Dynamic Crosslinking Networks Enable Degradable, Reconfigurable, and Multifunctional Epoxy Vitrimer</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2306350</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202306350</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was sponsored by National Natural Science Foundation of China (Grants 21875188, 22175143, and 22022107), Key Research and Development Project of Shaanxi (Grants 2022GY‐353), Science Center for Gas Turbine Project (Grants P2022‐DB‐V‐001‐001), and Fundamental Research Funds for the Central Universities (D5000230114). Many thanks to the Analytical &amp; Testing Center of Northwestern Polytechnical University for testing assistance.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6607-fig-0001\"><label>Figure 1</label><caption><p>The conceptual basis of this work. a) The HDCNs forming strategy via a hyperbranched macromonomer bearing ─OH terminal and dynamic bonds to co‐crosslink with industrial thermoset epoxy. b) The schematic model describing HDCNs enables a strong and tough epoxy vitrimer with reconfigurable and degradable performance. c) Network features: from double topologically crosslinking modes to reduce network density for adapting solvents, as well as multiple dynamic linkages involving covalent PO<sub>3</sub>/BO<sub>3</sub>, ester bonds, and non‐covalent hydrogen bonds.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6607-fig-0002\"><label>Figure 2</label><caption><p>Degradation and cycling case of HDCNs. a,b) Samples immersed in DMAc for the solvent‐degradation varying the concentration of HBPPB. c) degradation product underwent drying and grinding into epoxy powder. d) cycling epoxy powder with virgin epoxy resin at a ratio of ≈1:5 for comparable mechanical strength. e) HDCNs braking modes: multiple cleavable units upon the HDCNs. f) IR spectrum before‐ and after‐ degradation. g–i) cycling case for end‐of‐use carbon fiber and epoxy resin from composite. j) Raman spectra of the recovered carbon fiber.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6607-fig-0003\"><label>Figure 3</label><caption><p>Reconstructed HDCNs enable a reconfigurable yet tough vitrimer. a) Samples immersed in ethanol for the reconstruction of HDCNs. b,c) digital photographs of the elastomeric vitrimer (EP‐9) versus rigid thermoset (EP). d,e) ethanol‐induced reconstruction of HDCNs from ester‐exchange. f) <italic toggle=\"yes\">E’</italic> showing an ultrahigh flexural modulus at −150 °C for low‐temperature application. g) FTIR spectra of the vitrimer before‐ and after‐ ethanol treatment. h) 2D temperature‐dependent FTIR upon heating from −50 to 150 °C. i) loss modulus (<italic toggle=\"yes\">G’’</italic>) corresponds to double‐relaxation behaviors. J) Possible HDCNs reconstruction mechanism: reorganized H‐bonds and dynamic ester bonds.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6607-fig-0004\"><label>Figure 4</label><caption><p>General and multifunctional performance of material. DMA determination for a) temperature‐dependent loss modulus and b) storage modulus of materials. c) Crosslinking density showing the reduction in network density due to network topology. d) Simultaneously strengthening and toughening effect through HDCNs. e,f) Impact toughness and flexural strength improvement. g) Self‐extinguishing performance and reduced smoke production for fire‐retardancy. h) Digital photos of typical samples (EP, EP‐9, EP‐12 from left to right) and average transmittance in visible (220–380 nm) and UV region (380–780 nm).</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6607-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6607-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Movie 1</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2306350-s002.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2306350-s001.mp4\" mimetype=\"video\" mime-subtype=\"mp4\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
86
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 7; 11(2):2306350
oa_package/9a/a8/PMC10787098.tar.gz
PMC10787099
37946681
[ "<title>Introduction</title>", "<p>Since the seminal work of Bloch in 1929,<sup>[</sup>\n##UREF##0##\n1\n##\n<sup>]</sup> electron–phonon coupling has emerged as one of the most important topics in modern condensed matter physics. In conventional superconductors, electron‐phonon coupling underlies Cooper pairing. In semiconductors, it sets an upper bound for electron mobility. Electron–phonon coupling also governs numerous thermal and spin relaxation processes in solids. In ionic crystals with f orbitals, spin‐orbit coupling and the crystal electric field (CEF) associated with the ionic or ligand environment split the electronic wavefunction eigenstates into manifolds. Atomic displacements can change the ligand environment and hence the orbital manifolds. This change is typically treated within the adiabatic Born–Oppenheimer approximation, in which atomic motion is slow relative to the electronic degrees of freedom. However, when phonon‐CEF coupling is nearly resonant, the Born–Oppenheimer approximation is inadequate and a new state—a vibronic bound state (VBS), with both orbital character and phonon character—can form.</p>", "<p>Phonons can carry pseudo‐angular momentum when the 2D eigenvibration can be represented by a circular basis, as shown in <bold>Figure</bold> ##FIG##0##\n1a##.<sup>[</sup>\n##UREF##1##\n2\n##, ##REF##26406841##\n3\n##, ##UREF##2##\n4\n##, ##UREF##3##\n5\n##, ##UREF##4##\n6\n##, ##UREF##5##\n7\n##, ##REF##29420291##\n8\n##, ##UREF##6##\n9\n##\n<sup>]</sup> The conceptual difference between angular momentum and pseudo angular momentum is similar to that between linear momentum and pseudo linear momentum. The prefix <italic toggle=\"yes\">pseudo</italic> is unnecessary for elementary particles in a vacuum and distinguishes that from motion in a medium, such as a lattice. Regular angular momentum exhibits rotational invariance under the rotation of the entire system while <italic toggle=\"yes\">pseudo</italic> angular momentum is invariant under the rotation of the field.<sup>[</sup>\n##UREF##7##\n10\n##\n<sup>]</sup>\n</p>", "<p>The ability to control angular‐momentum transfer between phonons and electronic degrees of freedom may unlock new opportunities in quantum information processing by providing new interfaces with spins in materials. However, the transfer of angular momentum between photons, electronic spin, orbital excitations, and phonons is still not well understood. It has been studied, for instance, in the context of paramagnetic spin relaxation,<sup>[</sup>\n##UREF##8##\n11\n##, ##UREF##9##\n12\n##\n<sup>]</sup> ultra‐fast demagnetization processes,<sup>[</sup>\n##REF##31501328##\n13\n##, ##UREF##10##\n14\n##\n<sup>]</sup> and recently <italic toggle=\"yes\">angulon</italic> quasiparticles.<sup>[</sup>\n##UREF##11##\n15\n##\n<sup>]</sup> Phononic angular momentum is key to several fundamental effects in physics, including the microscopic explanation of the phonon Hall effect,<sup>[</sup>\n##REF##16241740##\n16\n##\n<sup>]</sup> the Einstein‐de Haas effect,<sup>[</sup>\n##UREF##12##\n17\n##, ##REF##30602792##\n18\n##, ##REF##35110761##\n19\n##\n<sup>]</sup> and zero‐point energies of chiral phonons.<sup>[</sup>\n##UREF##12##\n17\n##\n<sup>]</sup>\n</p>", "<p>NaYbSe<sub>2</sub>\n<sup>[</sup>\n##UREF##13##\n20\n##, ##UREF##14##\n21\n##, ##UREF##15##\n22\n##, ##UREF##16##\n23\n##, ##UREF##17##\n24\n##\n<sup>]</sup> belongs to the family of the form A<sup>1 +</sup>Yb<sup>3 +</sup>X<mml:math id=\"jats-math-12\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mrow/><mml:mn>2</mml:mn><mml:mrow><mml:mn>2</mml:mn><mml:mo>−</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math> that have been identified as quantum spin liquid (QSL) candidates. 14 members of this family have been identified to date.<sup>[</sup>\n##UREF##14##\n21\n##, ##UREF##15##\n22\n##, ##UREF##16##\n23\n##, ##UREF##18##\n25\n##, ##UREF##19##\n26\n##, ##UREF##20##\n27\n##, ##UREF##21##\n28\n##, ##UREF##22##\n29\n##, ##UREF##23##\n30\n##, ##UREF##24##\n31\n##, ##UREF##25##\n32\n##, ##UREF##26##\n33\n##, ##UREF##27##\n34\n##, ##UREF##28##\n35\n##, ##UREF##29##\n36\n##, ##UREF##30##\n37\n##\n<sup>]</sup> They all have planar triangular lattices decorated by antiferromagnetically coupled spins making them susceptible to geometric frustration, resulting in a lack of long‐range magnetic order down to the lowest probed temperatures. This family of candidate QSLs is objectively less defect prone than Yb(Mg, Ga)O<sub>4</sub>,<sup>[</sup>\n##UREF##16##\n23\n##\n<sup>]</sup> and the breadth of substitutional composites in the family makes it an ideal platform for the study and control of QSL excitations.</p>", "<p>The effective spin S<sub>eff</sub> = 1/2 of the system comes from the Yb<sup>3 +</sup> ion, which has the [Xe]4f<sup>13</sup> electronic configuration. Yb<sup>3 +</sup>, like all the elements in the 4f block, has weak exchange coupling and strong spin‐orbit coupling compared to the 3d‐block elements. The ground state spin‐orbit manifold of Yb<sup>3 +</sup> has total spin <italic toggle=\"yes\">J</italic> = 7/2. The next manifold <italic toggle=\"yes\">J</italic> = 5/2 is more than an eV above the ground state manifold.<sup>[</sup>\n##UREF##31##\n38\n##, ##UREF##32##\n39\n##\n<sup>]</sup> The ground state spin‐orbit manifold <italic toggle=\"yes\">J</italic> = 7/2 splits into four Kramers pairs <mml:math id=\"jats-math-13\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-14\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-15\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-16\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, where the <italic toggle=\"yes\">z</italic>‐component of the total angular momentum in the system can take values of m<sub>J</sub> = ±1/2, ±3/2, ±5/2, and ±7/2. CEF1, CEF2, and CEF3 describe the transition between the excited doublets and the ground state <mml:math id=\"jats-math-17\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, respectively. The CEF splitting within the ground‐state manifold is typically only tens of meV due to the well‐shielded nature of the 4f electrons. Structurally, NaYbSe<sub>2</sub> has less distortion in its YbSe<sub>6</sub> octahedra than other members in the A<sup>1 +</sup>Yb<sup>3 +</sup>X<mml:math id=\"jats-math-18\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mrow/><mml:mn>2</mml:mn><mml:mrow><mml:mn>2</mml:mn><mml:mo>−</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math> family.<sup>[</sup>\n##UREF##18##\n25\n##\n<sup>]</sup> Its ground states are reported to be described by spinon excitations<sup>[</sup>\n##UREF##14##\n21\n##\n<sup>]</sup> or ferrimagnetic quasistatic and dynamic excitations within a QSL matrix.<sup>[</sup>\n##UREF##33##\n40\n##\n<sup>]</sup> While pristine NaYbSe<sub>2</sub> is insulating, with increasing pressure it exhibits increased conductivity and eventually demonstrates a dip in resistivity attributed to a possible superconducting state.<sup>[</sup>\n##UREF##13##\n20\n##, ##UREF##17##\n24\n##\n<sup>]</sup>\n</p>", "<p>Elementary excitations in solids like magnons, phonons, and CEFs are usually considered decoupled and determined independently. However, strong coupling between normally decoupled excitations can result in fundamentally new material functionality. Thalmeier and Fulde<sup>[</sup>\n##UREF##34##\n41\n##\n<sup>]</sup> first theoretically described how a bound state between a crystal field excitation and phonons may form, but VBSs have only been reported in a handful of intermetallics<sup>[</sup>\n##UREF##34##\n41\n##, ##REF##30894488##\n42\n##, ##REF##31107079##\n43\n##, ##UREF##35##\n44\n##, ##UREF##36##\n45\n##, ##REF##23003286##\n46\n##, ##UREF##37##\n47\n##\n<sup>]</sup> and oxides,<sup>[</sup>\n##REF##10044073##\n48\n##, ##UREF##38##\n49\n##, ##UREF##39##\n50\n##\n<sup>]</sup> including Tb<sub>2</sub>Ti<sub>2</sub>O<sub>7</sub>\n<sup>[</sup>\n##UREF##40##\n51\n##\n<sup>]</sup> another geometrically frustrated magnet whose quantum spin liquid state is not yet fully understood.<sup>[</sup>\n##REF##24483925##\n52\n##, ##UREF##41##\n53\n##\n<sup>]</sup> Here we report the presence of a VBS in NaYbSe<sub>2</sub> and a change of angular momentum Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = ±1ℏ in an orbital excitation due to phononic coupling.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<p>We first verify the primary CEF excitations and phonon modes with temperature‐dependent Raman spectroscopy. The temperature dependence of the relevant Raman features is depicted in Figure ##FIG##0##1c## while the full spectra are shown in Figures ##SUPPL##0##S2## and ##SUPPL##0##S3##, Supporting Information. Consistent with earlier neutron scattering and Raman reports,<sup>[</sup>\n##UREF##16##\n23\n##, ##UREF##28##\n35\n##\n<sup>]</sup> strong CEF modes are observed at 117.2 cm<sup>−1</sup> (CEF1), 197.8 cm<sup>−1</sup> (CEF2), and 247.0 cm<sup>−1</sup> (CEF3). These become significantly stronger in intensity and soften (shift toward lower energy) as the temperature decreases. NaYbSe<sub>2</sub> also has two Raman‐active phonon modes: <italic toggle=\"yes\">E</italic>\n<sub>g</sub> at 124.4 cm<sup>−1</sup> and <italic toggle=\"yes\">A</italic>\n<sub>1g</sub> at 172.8 cm<sup>−1</sup> within this frequency space. The intensity and energy of these phonon modes exhibit a substantially weaker temperature dependence. Figure ##FIG##0##1b## shows a classical <italic toggle=\"yes\">spinning top</italic> representation of the spin‐orbit eigenstates for <mml:math id=\"jats-math-19\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> as well as the relative weights <mml:math id=\"jats-math-20\" display=\"inline\"><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:msub></mml:mrow></mml:math> for <mml:math id=\"jats-math-21\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-22\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-23\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-24\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> as |ψ〉= <mml:math id=\"jats-math-25\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mo>∑</mml:mo><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mo>−</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mtext>…</mml:mtext><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:msub><mml:msub><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. Empty (filled) circles represent <mml:math id=\"jats-math-26\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:mrow></mml:math> (<mml:math id=\"jats-math-27\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:msub><mml:mo>≠</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:mrow></mml:math>). The blue (pink) cones represent the + (−) branch. Note that the <italic toggle=\"yes\">E</italic>\n<sub>g</sub> and CEF1 modes exist at similar energies. This is the case for NaYbSe<sub>2</sub>,<sup>[</sup>\n##UREF##16##\n23\n##\n<sup>]</sup> CsYbSe<sub>2</sub>,<sup>[</sup>\n##UREF##28##\n35\n##\n<sup>]</sup> and KYbSe<sub>2</sub>.<sup>[</sup>\n##UREF##30##\n37\n##\n<sup>]</sup> Using Bayesian inference with a Hamiltonian Monte Carlo model in <monospace>PyMC3</monospace>,<sup>[</sup>\n##UREF##42##\n54\n##\n<sup>]</sup> we track the peak parameters from the experimental data shown in Figure ##FIG##0##1c##. The extracted peak positions for CEF1 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub> are shown in Figure ##FIG##0##1d##. The symbols represent the median values from the Bayesian inference. The darker shaded bands illustrate the 68% (corresponding to 1σ in the central limit) highest density intervals (HDIs), and the lighter shaded bands illustrate the 95% (corresponding to 2σ) HDIs. Other selected modes are described in the Supporting Information. The model has larger error bars from <italic toggle=\"yes\">T</italic> = 175 to 255 K, but the modes are well resolved elsewhere.</p>", "<p>A previously unreported mode is clearly seen in our data at 151.2 cm<sup>−1</sup>. Labeled ω in Figure ##FIG##0##1c,d##, this mode has characteristics in common with both CEFs and phonons: ω has a significantly stronger structure factor at low temperatures, just as the CEFs do, but it does not exhibit the strong softening at lower temperatures that the CEF modes exhibit. Instead, it hardens in a manner consistent with slight phonon hardening in NaYbSe<sub>2</sub> at low temperatures. We therefore assign ω as a VBS with parent states CEF1 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub>. Earlier Raman spectra in this temperature range<sup>[</sup>\n##UREF##16##\n23\n##\n<sup>]</sup> were only helicity‐resolved at room temperature, where ω is weak.</p>", "<p>In order to better understand the origin of the ω mode, we calculated the phonon dispersion relationship for NaYbSe<sub>2</sub> using density functional theory (DFT) and Perdew–Burke–Ernzerhof (PBE) exchange energy, as shown in Figure ##SUPPL##0##S1##, Supporting Information. These calculations suggest that no optical or acoustic phonons are present near ω. If anything, PBE normally overestimates the in‐plane lattice constants, resulting in softer in‐plane vibrations (<italic toggle=\"yes\">E</italic>\n<sub>g</sub>) than those measured. Comparing these calculations to published data (and the data in this manuscript) the calculated <italic toggle=\"yes\">E</italic>\n<sub>g</sub> at the gamma point is indeed 15 cm<sup>−1</sup> softer than that measured. The <italic toggle=\"yes\">A</italic>\n<sub>1g</sub> mode is also calculated to be softer than the measured mode, 135 cm<sup>−1</sup> compared to the measured 172.8 cm<sup>−1</sup>. Between these two energies, there are very few modes at the gamma point, and halfway between them there are no phonon branches.</p>", "<p>In fact, most models have no phonons throughout the Brillouin zone around 150 cm<sup>−1</sup>. Additionally, published neutron scattering data suggests there are no phonons in this frequency space. Specifically, figure S3J in ref. [##UREF##14##21##] reveals a decrease in spectral weight as the temperature increases. Additionally, Zhang et al.<sup>[</sup>\n##UREF##16##\n23\n##\n<sup>]</sup> could not model extra spectral weight at ≈19 meV (see figure ##FIG##1##2## of that manuscript) when the temperature decreased below 100 K. Notably, these neutron data have momentum transfer dependence like a phonon, but the temperature dependence of a crystal field, consistent with a vibronic bound state.</p>", "<p>The mode ω is present in both NaYbSe<sub>2</sub> and CsYbSe<sub>2</sub>, although it is far less prominent in CsYbSe<sub>2</sub>.<sup>[</sup>\n##UREF##28##\n35\n##\n<sup>]</sup> This is likely because in NaYbSe<sub>2</sub>, Na is both smaller and lighter. The lattice is therefore more tightly‐packed. The lighter Na also has larger vibrational displacements. Both effects increase the coupling strength, resulting in a VBS far stronger than that in CsYbSe<sub>2</sub>. Fitting to the Thalmeier–Fulde description of a magnetoelastic vibronic bound state<sup>[</sup>\n##UREF##34##\n41\n##\n<sup>]</sup> yields a coupling strength of 32.0 cm<sup>−1</sup> (3.97 meV) for NaYbSe<sub>2</sub>, which is stronger than the 23.6 cm<sup>−1</sup> (2.93 meV) coupling strength reported for CsYbSe<sub>2</sub> and comparable to the roughly 34.0 cm<sup>−1</sup> (4.22 meV) coupling strength reported for Ce<sub>2</sub>O<sub>3</sub>.<sup>[</sup>\n##REF##31107079##\n43\n##\n<sup>]</sup>\n</p>", "<p>To gain a deeper understanding of the CEF and the ω Raman modes, we studied the helicity dependence and magnetic field dependence of Raman spectra of NaYbSe<sub>2</sub>. During the Raman scattering process, the energy transferred from the photons can be used to excite a variety of (quasi)particles in the system, including electronic orbitals, phonons, and their hybridized states, as indicated by the schematic illustration in <bold>Figure</bold> ##FIG##1##\n2a##. Figure ##FIG##1##2b## shows helicity‐resolved Raman spectra acquired at <italic toggle=\"yes\">T</italic> = 4 K, with CEF1, CEF2, CEF3, <italic toggle=\"yes\">E</italic>\n<sub>g</sub>, <italic toggle=\"yes\">A</italic>\n<sub>1g</sub>, and ω highlighted. Here, we can simultaneously observe electronic orbital excitations (CEF1, CEF2, and CEF3), phononic excitations (<italic toggle=\"yes\">E</italic>\n<sub>g</sub> and <italic toggle=\"yes\">A</italic>\n<sub>1g</sub>), and the entangled state ω between the orbital and phononic excitations by low‐temperature Raman spectroscopy. Furthermore, we discovered that these (quasi)particles exhibit different responses to the helicity of photons. While <italic toggle=\"yes\">A</italic>\n<sub>1g</sub> and ω (along with the Rayleigh scattering; see Figure ##SUPPL##0##S7##, Supporting Information) are stronger in the co‐circular polarization configuration, CEF1–CEF3 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub> are stronger in the cross‐circular polarization configuration.</p>", "<p>We also performed magnetic field‐dependent Raman spectroscopy with <bold>B</bold> || <bold>c</bold>, which lifts the degeneracy within each of the Kramers pairs and therefore provides further information on the orbital excitations corresponding to CEF1–3. Magnetization and specific heat measurements have been previously used to show that no field‐induced ordering is present in NaYbSe<sub>2</sub> for <bold>B</bold> || <bold>c</bold> for <italic toggle=\"yes\">B</italic> &lt; 9 T at <italic toggle=\"yes\">T</italic> = 4 K.<sup>[</sup>\n##UREF##15##\n22\n##\n<sup>]</sup> Therefore, with the 6 T magnetic fields accessible here, no field‐induced transition is expected. <bold>Figure</bold> ##FIG##2##\n3\n## shows the magnetic field dependence of the CEF levels for CEF1 (Figure ##FIG##2##3a##), CEF2 (Figure ##FIG##2##3b##), ω (Figure ##FIG##2##3c##), and CEF3 (Figure ##FIG##2##3d##) measurements. Again, the CEF levels only show up in cross‐circular polarization configurations, (σ<sup>+</sup>, σ<sup>−</sup>) and (σ<sup>−</sup>, σ<sup>+</sup>), while the ω mode only appears in co‐circular polarization configurations, (σ<sup>+</sup>, σ<sup>+</sup>) and (σ<sup>−</sup>, σ<sup>−</sup>). Note that in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration and with increasing positive magnetic field, CEF1 and CEF2 increase in energy while CEF3 decreases. This dependence is inverted if the magnetic field is reversed (<italic toggle=\"yes\">B</italic> → −<italic toggle=\"yes\">B</italic>) or the helicity is reversed ((σ<sup>+</sup>, σ<sup>−</sup>) → (σ<sup>−</sup>, σ<sup>+</sup>)).</p>", "<p>The observed circular polarization dependence and magnetic field dependence of CEF1–3 and ω in Figures ##FIG##1##2## and ##FIG##2##3## clearly indicate different underlying optical selection rules that can be understood based on angular momentum conservation. Each left (right) circularly polarized σ<sup>+</sup> (σ<sup>−</sup>) photon carries angular momentum +ℏ (−ℏ).<sup>[</sup>\n##UREF##43##\n55\n##\n<sup>]</sup> The link between helicity and circular polarization is given by <italic toggle=\"yes\">h</italic> = <bold>σ</bold> · <bold>k</bold>, where <bold>k</bold> is the momentum of the photon, and <italic toggle=\"yes\">h</italic> the helicity.<sup>[</sup>\n##REF##29956970##\n56\n##\n<sup>]</sup> Absorption of a σ<sup>+</sup> photon increases the angular momentum of the system by +ℏ, corresponding to being acted on by operator <italic toggle=\"yes\">J</italic>\n<sub>+</sub>, while scattering a σ<sup>+</sup> photon corresponds to <italic toggle=\"yes\">J</italic>\n<sub>−</sub> acting on the system. Therefore, if one considers Raman spectra acquired in the (σ<sub>incident</sub>, σ<sub>scatter</sub>) = (σ<sup>+</sup>, σ<sup>−</sup>) configuration where the change of angular momentum in photons is Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = −2ℏ, the system could obtain +2ℏ of angular momentum from the photons (i.e., Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = +2ℏ), corresponding to <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub> acting on the system (a generalization of the closure condition in Axe et al.,<sup>[</sup>\n##UREF##44##\n57\n##\n<sup>]</sup> which contracts ∑<sub>virtual</sub>||〈ψ<sub>final</sub>|<italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">i</italic>\n</sub>|ψ<sub>virtual</sub>〉〈ψ<sub>virtual</sub>|<italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">j</italic>\n</sub>|ψ<sub>initial</sub>〉|| to ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">i</italic>\n</sub>\n<italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">j</italic>\n</sub>|ψ<sub>initial</sub>〉|| for any dipolar transition <italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">i</italic>\n</sub>, <italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">j</italic>\n</sub>). Therefore, a mode that is active in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration could have dominant matrix‐element contributions from ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub>|ψ<sub>initial</sub>〉||. However, it is important to note that in an analog to the Umklapp process, the threefold rotational symmetry in NaYbSe<sub>2</sub>\n<sup>[</sup>\n##UREF##45##\n58\n##\n<sup>]</sup> allows for discrete angular momentum conservation as long as |Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> + Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub>|/ℏ = 0 (modulo 3). In other words, the angular momentum conservation rule is relaxed so that the total change of angular momentum can be either zero or a multiple of 3ℏ due to the threefold rotational symmetry.<sup>[</sup>\n##UREF##46##\n59\n##, ##UREF##47##\n60\n##, ##UREF##48##\n61\n##\n<sup>]</sup> This means that in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration where Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = −2ℏ, Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> can be +2ℏ or −ℏ to satisfy the relaxed angular momentum conservation rule. For Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = +2ℏ, it corresponds to the operation of <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub>, while for Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = −ℏ, it corresponds to <italic toggle=\"yes\">J</italic>\n<sub>−</sub>. Therefore, a mode that is active in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration could also have dominant matrix‐element contributions from ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">J</italic>\n<sub>−</sub>|ψ<sub>initial</sub>〉||. In contrast, in the (σ<sub>incident</sub>, (σ<sup>−</sup>, σ<sup>+</sup>) configuration where Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = +2ℏ, the system could lose 2ℏ of angular momentum to the photons (Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = −2ℏ), corresponding to <italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub> acting on the system, or Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = +ℏ, corresponding to <italic toggle=\"yes\">J</italic>\n<sub>+</sub> acting on the system. Hence, a mode that is active in the (σ<sup>−</sup>, σ<sup>+</sup>) configuration should have dominant matrix‐element contributions from ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub>|ψ<sub>initial</sub>〉|| or ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">J</italic>\n<sub>+</sub>|ψ<sub>initial</sub>〉||.</p>", "<p>Since all the CEF modes are enhanced in the cross‐circular channel and suppressed in the co‐circular channel, all of them should have a finite change of angular momentum after the orbital transitions. As discussed above, Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF</sub> = +2ℏ or −ℏ in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration, while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF</sub> = −2ℏ or +ℏ in the (σ<sup>−</sup>, σ<sup>+</sup>) configuration. Considering that an additional Zeeman dependence <italic toggle=\"yes\">H</italic>\n<sub>\n<bold>B</bold>\n</sub> = −<italic toggle=\"yes\">g</italic>\n<sub>\n<italic toggle=\"yes\">J</italic>\n</sub>μ<sub>B</sub>\n<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> · <bold>B</bold> is added when a magnetic field is applied, the change of the sign of Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF</sub> from (σ<sup>+</sup>, σ<sup>−</sup>) to (σ<sup>−</sup>, σ<sup>+</sup>) explains why the magnetic field dependence of CEF1–3 is inverted when the helicity is reversed in Figure ##FIG##2##3##. Another intriguing finding from Figure ##FIG##2##3## is that the magnetic field dependence of CEF1 and CEF2 is opposite to that of CEF3 regardless of the helicity, suggesting that Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> and Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> share the same sign, whereas Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> has the opposite sign. More specifically, in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration, we should have Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> = +2ℏ while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = −ℏ, or Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> = −ℏ while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = +2ℏ. Note that Δ<italic toggle=\"yes\">J</italic> = −ℏ is allowed for a CEF level due to the threefold rotational symmetry that relaxes the angular momentum conservation rule, but we expect that Δ<italic toggle=\"yes\">J</italic> = +2ℏ that satisfies the strict angular momentum conservation should have a higher probability and stronger Raman signals. Since CEF1 and CEF2 have much stronger Raman intensities than CEF3 (Figure ##FIG##1##2b##), it is natural to conclude that Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> = +2ℏ while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = −ℏ in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration. Similarly, Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> = −2ℏ while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = +ℏ in the (σ<sup>−</sup>, σ<sup>+</sup>) configuration. In terms of matrix operations, <mml:math id=\"jats-math-28\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-29\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-30\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-31\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-32\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, and <mml:math id=\"jats-math-33\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math> should be significant while <mml:math id=\"jats-math-34\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-35\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-36\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-37\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-38\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-39\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-40\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, and <mml:math id=\"jats-math-41\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math> should all be small or zero (the last six matrix elements correspond to the co‐circular polarization).</p>", "<p>As shown in Figure ##FIG##0##1b##, the eigenstates of CEF levels are linear combinations of multiplets <italic toggle=\"yes\">m</italic>\n<sub>\n<italic toggle=\"yes\">J</italic>\n</sub> = −7/2…7/2: |ψ<sup>±</sup>〉 = <mml:math id=\"jats-math-42\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mo>∑</mml:mo><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mo>−</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mtext>…</mml:mtext><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:msub><mml:msubsup><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. Typically, CEF parameters are fit to a CEF Hamiltonian with Stevens operators given by the symmetry of the ionic environment of the 4f orbitals, as described in the Experimental Section. The procedure is frequently under‐constrained, and there are enough degrees of freedom to fit experimentally observed CEF energy levels with more than one set of CEF parameters that minimize the error that may exist. The order of the eigenstates may not be the same across those sets. However, once the constraints imposed by the optical selection rules discussed above are taken into account, we are able to find a set of CEF parameters, as indicated by filled and empty circles in Figure ##FIG##0##1b##, that can explain the observed helicity and magnetic field dependence in Figures ##FIG##1##2## and ##FIG##2##3##, and we can make final assignments of CEF1‐3. As illustrated in <bold>Figure</bold> ##FIG##3##\n4a##, CEF1 comes from <mml:math id=\"jats-math-43\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration, where Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = −2ℏ and Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = +2ℏ, or <mml:math id=\"jats-math-44\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> in the (σ<sup>−</sup>, σ<sup>+</sup>) configuration, where Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = +2ℏ and Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = −2ℏ (see the arrows for the transitions). We note that the transition of <mml:math id=\"jats-math-45\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> with Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = −ℏ is allowed in (σ<sup>+</sup>, σ<sup>−</sup>) and the transition of <mml:math id=\"jats-math-46\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> with Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = +ℏ is allowed in (σ<sup>−</sup>, σ<sup>+</sup>), since Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = −3ℏ and +3ℏ, respectively, which satisfies the discrete angular momentum conservation. However, these transitions allowed by the crystal threefold rotational symmetry are of a higher order and should be much weaker. Similar transitions apply for CEF2, although they correspond to <mml:math id=\"jats-math-47\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-48\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. For CEF3 in Figure ##FIG##3##4b##, however, any transition with Δ<italic toggle=\"yes\">J</italic> = −2ℏ or +2ℏ is impossible; hence, the transition of <mml:math id=\"jats-math-49\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> with Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = −ℏ is the only one allowed in (σ<sup>+</sup>, σ<sup>−</sup>) where Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = −3ℏ, and the transition of <mml:math id=\"jats-math-50\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> with Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = +ℏ is the only one allowed in (σ<sup>−</sup>, σ<sup>+</sup>) where Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = +3ℏ. This could explain why CEF3 is much weaker than CEF1 and CEF2.</p>", "<p>As for the phonon Raman modes, in general, a nondegenerate Γ‐point phonon (like the <italic toggle=\"yes\">A</italic>\n<sub>1g</sub> Raman mode in NaYbSe<sub>2</sub>) cannot have angular momentum since the eigenvector is a real number. It is therefore only observed in the co‐circular polarization configuration, as shown in Figure ##FIG##1##2b##. However, when the Γ‐point phonon is doubly degenerate, the two real eigenvectors can be reconstructed by a complex superposition as shown in Figure ##FIG##0##1a##. Therefore, doubly degenerate modes like the <italic toggle=\"yes\">E</italic>\n<sub>g</sub> Raman mode in NaYbSe<sub>2</sub> can have (pseudo)angular momentum of ±ℏ.<sup>[</sup>\n##REF##26406841##\n3\n##, ##UREF##6##\n9\n##, ##UREF##47##\n60\n##, ##UREF##49##\n62\n##\n<sup>]</sup> With nonzero angular momentum, it can change the chirality of incident photons and appear in the cross‐circular polarization configuration. As shown in Figure ##FIG##3##4c##, in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration, Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = −2ℏ and <mml:math id=\"jats-math-59\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>J</mml:mi><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:mo>−</mml:mo><mml:mi>ℏ</mml:mi></mml:mrow></mml:mrow></mml:math>, so it is allowed by the discrete angular momentum conservation as Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = −3ℏ; In the (σ<sup>−</sup>, σ<sup>+</sup>) configuration, Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = +2ℏ and <mml:math id=\"jats-math-60\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>J</mml:mi><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:mo>+</mml:mo><mml:mi>ℏ</mml:mi></mml:mrow></mml:mrow></mml:math>, giving rise to Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = +3ℏ. Such an optical selection rule is similar to that shown for CEF3 in Figure ##FIG##3##4b##, which explains why both are observed in the cross‐circular polarization. Similar results have been reported for <italic toggle=\"yes\">E</italic> symmetry Raman modes in TMDs, CrBr<sub>3</sub>, and quartz, among other materials.<sup>[</sup>\n##UREF##6##\n9\n##, ##UREF##47##\n60\n##, ##UREF##48##\n61\n##\n<sup>]</sup>\n</p>", "<p>Finally, moving on to the VBS ω, it is much stronger in the co‐circular polarization configuration and its magnetic field dependence is weak (Figures ##FIG##1##2## and ##FIG##2##3##), in stark contrast to CEF1‐3. This indicates that the change in angular momentum for ω is zero: Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = 0. Since it is a coupled state between the CEF1 and the <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode, we consider the 2 × ~2 dimensional space <mml:math id=\"jats-math-61\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>±</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. As the angular momentum change Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> for CEF1 is finite (Figure ##FIG##3##4a##), the phonon subsystem has to carry additional angular momentum (Figure ##FIG##3##4c##) in order to yield zero angular momentum for ω. Therefore, the circular basis {$E$<sub>g, +</sub>, $E$<sub>g, $‐$</sub>} is the natural choice for describing the eigenvibration. As discussed previously, CEF1 can arise from four possible transitions while <italic toggle=\"yes\">E</italic>\n<sub>g</sub> can be $E$<sub>g, +</sub> and $E$<sub>g, $‐$</sub>, which gives rise to a total of eight possible transitions for ω. Based on the angular momentum conservation rule, however, we found that two states, <mml:math id=\"jats-math-62\" display=\"inline\"><mml:mrow><mml:mrow><mml:msup><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msup><mml:mrow><mml:mo>=</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-63\" display=\"inline\"><mml:mrow><mml:mrow><mml:msup><mml:mi>ω</mml:mi><mml:mo>−</mml:mo></mml:msup><mml:mrow><mml:mo>=</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, are the most probable (see more details in the Supporting Information). As shown in Figure ##FIG##3##4d##, due to the angular momentum transfer between the CEF1 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode, the excited state of ω, <mml:math id=\"jats-math-64\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-65\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, has the <italic toggle=\"yes\">z</italic>‐component of the angular momentum effectively raised or lowered by ℏ compared to the <mml:math id=\"jats-math-66\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-67\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> shown in Figure ##FIG##3##4a##, respectively. As a result, the transitions of <mml:math id=\"jats-math-68\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-69\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> have Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = 0 to satisfy the selection rule in the co‐circular polarization configuration and explain the weak magnetic field dependence.</p>", "<p>\n<bold>Figure</bold> ##FIG##4##\n5a,b## illustrates the two states, <mml:math id=\"jats-math-70\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-71\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> based on the observations described above. In Figure ##FIG##4##5a##, when the ground state is <mml:math id=\"jats-math-72\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> (shown in light pink), the <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub> or <italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub> operator excites the system to the + branch, <mml:math id=\"jats-math-73\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> (where the CEF excitation corresponds to the + branch and the phononic excitation corresponds to + angular momentum). Figure ##FIG##4##5b## shows the same effect for <mml:math id=\"jats-math-74\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> to <mml:math id=\"jats-math-75\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. Because the transition is degenerate for <mml:math id=\"jats-math-76\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>∓</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo></mml:mrow><mml:msup><mml:mi>ω</mml:mi><mml:mo>±</mml:mo></mml:msup></mml:mrow></mml:mrow></mml:math> with <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub> or <italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub>, this eigenspace, in principle, can be transduced from a QSL ground state. If the QSL ground state is written as <mml:math id=\"jats-math-77\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mo>∑</mml:mo><mml:mi>j</mml:mi></mml:msub><mml:msub><mml:mo>∏</mml:mo><mml:mi>i</mml:mi></mml:msub><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:msub><mml:mi>σ</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>j</mml:mi></mml:mrow></mml:msub></mml:msubsup></mml:mrow></mml:mrow></mml:math> – where <italic toggle=\"yes\">i</italic> is the site index, <italic toggle=\"yes\">j</italic> the configuration index, and σ<sub>\n<italic toggle=\"yes\">ij</italic>\n</sub> = +, − is the branch—then <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub> or <italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub> should bring the system into <mml:math id=\"jats-math-78\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mo>∑</mml:mo><mml:mi>j</mml:mi></mml:msub><mml:msub><mml:mo>∏</mml:mo><mml:mi>i</mml:mi></mml:msub><mml:msup><mml:mi>ω</mml:mi><mml:msub><mml:mi>σ</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>j</mml:mi></mml:mrow></mml:msub></mml:msup></mml:mrow></mml:mrow></mml:math> within the point spread volume of the excitation beam, transducing the possible ground state entanglement to the VBS ω<sup>±</sup>.</p>", "<p>It is worth noting that, in the original Thalmeier–Fulde model, two VBS modes are expected to emerge from the hybridization of a CEF mode and a phonon mode.<sup>[</sup>\n##UREF##34##\n41\n##\n<sup>]</sup> Besides the two most probable VBS transitions shown in Figure ##FIG##3##4d## that give rise to the observed ω peak in the Raman spectra, there are six other transitions that could contribute to the other VBS mode that is not observed in our Raman measurements (see Equation (##SUPPL##0##S1##), Supporting Information). Since the picture of how orbital and phononic excitations couple is not entirely clear, a definitive answer to why other transitions and the other VBS mode do not appear in Raman scattering is beyond the scope of this work. It is expected that the electron–phonon coupling may be more complicated compared to the conventional coupling between orbital angular momentum and spin angular momentum.<sup>[</sup>\n##UREF##50##\n63\n##\n<sup>]</sup> Therefore, we hypothesize that the coupling between the CEF1 and the E<sub>g</sub> mode is not the same as the conventional coupling between orbital and spin angular momenta. There is a coupling coefficient before the derived Δ<italic toggle=\"yes\">J</italic>\n<sub>ω</sub> (see Equation (##SUPPL##0##S1##), Supporting Information), leading to non‐integer Δ<italic toggle=\"yes\">J</italic>\n<sub>ω</sub> unless it is zero to begin with. As a consequence, only <mml:math id=\"jats-math-81\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-82\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-83\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, and <mml:math id=\"jats-math-84\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> that have zero angular momentum can satisfy the angular momentum conservation rule in the co‐circular polarization configuration, and other transitions are forbidden in any polarization channel. Moreover, as discussed previously, since <mml:math id=\"jats-math-85\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-86\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> are of a higher order and much less probable, only <mml:math id=\"jats-math-87\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-88\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> have detectable signals (see Figure ##FIG##3##4d##). This could explain why other transitions and the other VBS modes are not observed.</p>" ]
[ "<title>Results and Discussion</title>", "<p>We first verify the primary CEF excitations and phonon modes with temperature‐dependent Raman spectroscopy. The temperature dependence of the relevant Raman features is depicted in Figure ##FIG##0##1c## while the full spectra are shown in Figures ##SUPPL##0##S2## and ##SUPPL##0##S3##, Supporting Information. Consistent with earlier neutron scattering and Raman reports,<sup>[</sup>\n##UREF##16##\n23\n##, ##UREF##28##\n35\n##\n<sup>]</sup> strong CEF modes are observed at 117.2 cm<sup>−1</sup> (CEF1), 197.8 cm<sup>−1</sup> (CEF2), and 247.0 cm<sup>−1</sup> (CEF3). These become significantly stronger in intensity and soften (shift toward lower energy) as the temperature decreases. NaYbSe<sub>2</sub> also has two Raman‐active phonon modes: <italic toggle=\"yes\">E</italic>\n<sub>g</sub> at 124.4 cm<sup>−1</sup> and <italic toggle=\"yes\">A</italic>\n<sub>1g</sub> at 172.8 cm<sup>−1</sup> within this frequency space. The intensity and energy of these phonon modes exhibit a substantially weaker temperature dependence. Figure ##FIG##0##1b## shows a classical <italic toggle=\"yes\">spinning top</italic> representation of the spin‐orbit eigenstates for <mml:math id=\"jats-math-19\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> as well as the relative weights <mml:math id=\"jats-math-20\" display=\"inline\"><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:msub></mml:mrow></mml:math> for <mml:math id=\"jats-math-21\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-22\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-23\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-24\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> as |ψ〉= <mml:math id=\"jats-math-25\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mo>∑</mml:mo><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mo>−</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mtext>…</mml:mtext><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:msub><mml:msub><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:msub><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. Empty (filled) circles represent <mml:math id=\"jats-math-26\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:mrow></mml:math> (<mml:math id=\"jats-math-27\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub></mml:msub><mml:mo>≠</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:mrow></mml:math>). The blue (pink) cones represent the + (−) branch. Note that the <italic toggle=\"yes\">E</italic>\n<sub>g</sub> and CEF1 modes exist at similar energies. This is the case for NaYbSe<sub>2</sub>,<sup>[</sup>\n##UREF##16##\n23\n##\n<sup>]</sup> CsYbSe<sub>2</sub>,<sup>[</sup>\n##UREF##28##\n35\n##\n<sup>]</sup> and KYbSe<sub>2</sub>.<sup>[</sup>\n##UREF##30##\n37\n##\n<sup>]</sup> Using Bayesian inference with a Hamiltonian Monte Carlo model in <monospace>PyMC3</monospace>,<sup>[</sup>\n##UREF##42##\n54\n##\n<sup>]</sup> we track the peak parameters from the experimental data shown in Figure ##FIG##0##1c##. The extracted peak positions for CEF1 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub> are shown in Figure ##FIG##0##1d##. The symbols represent the median values from the Bayesian inference. The darker shaded bands illustrate the 68% (corresponding to 1σ in the central limit) highest density intervals (HDIs), and the lighter shaded bands illustrate the 95% (corresponding to 2σ) HDIs. Other selected modes are described in the Supporting Information. The model has larger error bars from <italic toggle=\"yes\">T</italic> = 175 to 255 K, but the modes are well resolved elsewhere.</p>", "<p>A previously unreported mode is clearly seen in our data at 151.2 cm<sup>−1</sup>. Labeled ω in Figure ##FIG##0##1c,d##, this mode has characteristics in common with both CEFs and phonons: ω has a significantly stronger structure factor at low temperatures, just as the CEFs do, but it does not exhibit the strong softening at lower temperatures that the CEF modes exhibit. Instead, it hardens in a manner consistent with slight phonon hardening in NaYbSe<sub>2</sub> at low temperatures. We therefore assign ω as a VBS with parent states CEF1 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub>. Earlier Raman spectra in this temperature range<sup>[</sup>\n##UREF##16##\n23\n##\n<sup>]</sup> were only helicity‐resolved at room temperature, where ω is weak.</p>", "<p>In order to better understand the origin of the ω mode, we calculated the phonon dispersion relationship for NaYbSe<sub>2</sub> using density functional theory (DFT) and Perdew–Burke–Ernzerhof (PBE) exchange energy, as shown in Figure ##SUPPL##0##S1##, Supporting Information. These calculations suggest that no optical or acoustic phonons are present near ω. If anything, PBE normally overestimates the in‐plane lattice constants, resulting in softer in‐plane vibrations (<italic toggle=\"yes\">E</italic>\n<sub>g</sub>) than those measured. Comparing these calculations to published data (and the data in this manuscript) the calculated <italic toggle=\"yes\">E</italic>\n<sub>g</sub> at the gamma point is indeed 15 cm<sup>−1</sup> softer than that measured. The <italic toggle=\"yes\">A</italic>\n<sub>1g</sub> mode is also calculated to be softer than the measured mode, 135 cm<sup>−1</sup> compared to the measured 172.8 cm<sup>−1</sup>. Between these two energies, there are very few modes at the gamma point, and halfway between them there are no phonon branches.</p>", "<p>In fact, most models have no phonons throughout the Brillouin zone around 150 cm<sup>−1</sup>. Additionally, published neutron scattering data suggests there are no phonons in this frequency space. Specifically, figure S3J in ref. [##UREF##14##21##] reveals a decrease in spectral weight as the temperature increases. Additionally, Zhang et al.<sup>[</sup>\n##UREF##16##\n23\n##\n<sup>]</sup> could not model extra spectral weight at ≈19 meV (see figure ##FIG##1##2## of that manuscript) when the temperature decreased below 100 K. Notably, these neutron data have momentum transfer dependence like a phonon, but the temperature dependence of a crystal field, consistent with a vibronic bound state.</p>", "<p>The mode ω is present in both NaYbSe<sub>2</sub> and CsYbSe<sub>2</sub>, although it is far less prominent in CsYbSe<sub>2</sub>.<sup>[</sup>\n##UREF##28##\n35\n##\n<sup>]</sup> This is likely because in NaYbSe<sub>2</sub>, Na is both smaller and lighter. The lattice is therefore more tightly‐packed. The lighter Na also has larger vibrational displacements. Both effects increase the coupling strength, resulting in a VBS far stronger than that in CsYbSe<sub>2</sub>. Fitting to the Thalmeier–Fulde description of a magnetoelastic vibronic bound state<sup>[</sup>\n##UREF##34##\n41\n##\n<sup>]</sup> yields a coupling strength of 32.0 cm<sup>−1</sup> (3.97 meV) for NaYbSe<sub>2</sub>, which is stronger than the 23.6 cm<sup>−1</sup> (2.93 meV) coupling strength reported for CsYbSe<sub>2</sub> and comparable to the roughly 34.0 cm<sup>−1</sup> (4.22 meV) coupling strength reported for Ce<sub>2</sub>O<sub>3</sub>.<sup>[</sup>\n##REF##31107079##\n43\n##\n<sup>]</sup>\n</p>", "<p>To gain a deeper understanding of the CEF and the ω Raman modes, we studied the helicity dependence and magnetic field dependence of Raman spectra of NaYbSe<sub>2</sub>. During the Raman scattering process, the energy transferred from the photons can be used to excite a variety of (quasi)particles in the system, including electronic orbitals, phonons, and their hybridized states, as indicated by the schematic illustration in <bold>Figure</bold> ##FIG##1##\n2a##. Figure ##FIG##1##2b## shows helicity‐resolved Raman spectra acquired at <italic toggle=\"yes\">T</italic> = 4 K, with CEF1, CEF2, CEF3, <italic toggle=\"yes\">E</italic>\n<sub>g</sub>, <italic toggle=\"yes\">A</italic>\n<sub>1g</sub>, and ω highlighted. Here, we can simultaneously observe electronic orbital excitations (CEF1, CEF2, and CEF3), phononic excitations (<italic toggle=\"yes\">E</italic>\n<sub>g</sub> and <italic toggle=\"yes\">A</italic>\n<sub>1g</sub>), and the entangled state ω between the orbital and phononic excitations by low‐temperature Raman spectroscopy. Furthermore, we discovered that these (quasi)particles exhibit different responses to the helicity of photons. While <italic toggle=\"yes\">A</italic>\n<sub>1g</sub> and ω (along with the Rayleigh scattering; see Figure ##SUPPL##0##S7##, Supporting Information) are stronger in the co‐circular polarization configuration, CEF1–CEF3 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub> are stronger in the cross‐circular polarization configuration.</p>", "<p>We also performed magnetic field‐dependent Raman spectroscopy with <bold>B</bold> || <bold>c</bold>, which lifts the degeneracy within each of the Kramers pairs and therefore provides further information on the orbital excitations corresponding to CEF1–3. Magnetization and specific heat measurements have been previously used to show that no field‐induced ordering is present in NaYbSe<sub>2</sub> for <bold>B</bold> || <bold>c</bold> for <italic toggle=\"yes\">B</italic> &lt; 9 T at <italic toggle=\"yes\">T</italic> = 4 K.<sup>[</sup>\n##UREF##15##\n22\n##\n<sup>]</sup> Therefore, with the 6 T magnetic fields accessible here, no field‐induced transition is expected. <bold>Figure</bold> ##FIG##2##\n3\n## shows the magnetic field dependence of the CEF levels for CEF1 (Figure ##FIG##2##3a##), CEF2 (Figure ##FIG##2##3b##), ω (Figure ##FIG##2##3c##), and CEF3 (Figure ##FIG##2##3d##) measurements. Again, the CEF levels only show up in cross‐circular polarization configurations, (σ<sup>+</sup>, σ<sup>−</sup>) and (σ<sup>−</sup>, σ<sup>+</sup>), while the ω mode only appears in co‐circular polarization configurations, (σ<sup>+</sup>, σ<sup>+</sup>) and (σ<sup>−</sup>, σ<sup>−</sup>). Note that in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration and with increasing positive magnetic field, CEF1 and CEF2 increase in energy while CEF3 decreases. This dependence is inverted if the magnetic field is reversed (<italic toggle=\"yes\">B</italic> → −<italic toggle=\"yes\">B</italic>) or the helicity is reversed ((σ<sup>+</sup>, σ<sup>−</sup>) → (σ<sup>−</sup>, σ<sup>+</sup>)).</p>", "<p>The observed circular polarization dependence and magnetic field dependence of CEF1–3 and ω in Figures ##FIG##1##2## and ##FIG##2##3## clearly indicate different underlying optical selection rules that can be understood based on angular momentum conservation. Each left (right) circularly polarized σ<sup>+</sup> (σ<sup>−</sup>) photon carries angular momentum +ℏ (−ℏ).<sup>[</sup>\n##UREF##43##\n55\n##\n<sup>]</sup> The link between helicity and circular polarization is given by <italic toggle=\"yes\">h</italic> = <bold>σ</bold> · <bold>k</bold>, where <bold>k</bold> is the momentum of the photon, and <italic toggle=\"yes\">h</italic> the helicity.<sup>[</sup>\n##REF##29956970##\n56\n##\n<sup>]</sup> Absorption of a σ<sup>+</sup> photon increases the angular momentum of the system by +ℏ, corresponding to being acted on by operator <italic toggle=\"yes\">J</italic>\n<sub>+</sub>, while scattering a σ<sup>+</sup> photon corresponds to <italic toggle=\"yes\">J</italic>\n<sub>−</sub> acting on the system. Therefore, if one considers Raman spectra acquired in the (σ<sub>incident</sub>, σ<sub>scatter</sub>) = (σ<sup>+</sup>, σ<sup>−</sup>) configuration where the change of angular momentum in photons is Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = −2ℏ, the system could obtain +2ℏ of angular momentum from the photons (i.e., Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = +2ℏ), corresponding to <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub> acting on the system (a generalization of the closure condition in Axe et al.,<sup>[</sup>\n##UREF##44##\n57\n##\n<sup>]</sup> which contracts ∑<sub>virtual</sub>||〈ψ<sub>final</sub>|<italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">i</italic>\n</sub>|ψ<sub>virtual</sub>〉〈ψ<sub>virtual</sub>|<italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">j</italic>\n</sub>|ψ<sub>initial</sub>〉|| to ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">i</italic>\n</sub>\n<italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">j</italic>\n</sub>|ψ<sub>initial</sub>〉|| for any dipolar transition <italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">i</italic>\n</sub>, <italic toggle=\"yes\">M</italic>\n<sub>\n<italic toggle=\"yes\">j</italic>\n</sub>). Therefore, a mode that is active in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration could have dominant matrix‐element contributions from ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub>|ψ<sub>initial</sub>〉||. However, it is important to note that in an analog to the Umklapp process, the threefold rotational symmetry in NaYbSe<sub>2</sub>\n<sup>[</sup>\n##UREF##45##\n58\n##\n<sup>]</sup> allows for discrete angular momentum conservation as long as |Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> + Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub>|/ℏ = 0 (modulo 3). In other words, the angular momentum conservation rule is relaxed so that the total change of angular momentum can be either zero or a multiple of 3ℏ due to the threefold rotational symmetry.<sup>[</sup>\n##UREF##46##\n59\n##, ##UREF##47##\n60\n##, ##UREF##48##\n61\n##\n<sup>]</sup> This means that in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration where Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = −2ℏ, Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> can be +2ℏ or −ℏ to satisfy the relaxed angular momentum conservation rule. For Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = +2ℏ, it corresponds to the operation of <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub>, while for Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = −ℏ, it corresponds to <italic toggle=\"yes\">J</italic>\n<sub>−</sub>. Therefore, a mode that is active in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration could also have dominant matrix‐element contributions from ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">J</italic>\n<sub>−</sub>|ψ<sub>initial</sub>〉||. In contrast, in the (σ<sub>incident</sub>, (σ<sup>−</sup>, σ<sup>+</sup>) configuration where Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = +2ℏ, the system could lose 2ℏ of angular momentum to the photons (Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = −2ℏ), corresponding to <italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub> acting on the system, or Δ<italic toggle=\"yes\">J</italic>\n<sub>system</sub> = +ℏ, corresponding to <italic toggle=\"yes\">J</italic>\n<sub>+</sub> acting on the system. Hence, a mode that is active in the (σ<sup>−</sup>, σ<sup>+</sup>) configuration should have dominant matrix‐element contributions from ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub>|ψ<sub>initial</sub>〉|| or ||〈ψ<sub>final</sub>|<italic toggle=\"yes\">J</italic>\n<sub>+</sub>|ψ<sub>initial</sub>〉||.</p>", "<p>Since all the CEF modes are enhanced in the cross‐circular channel and suppressed in the co‐circular channel, all of them should have a finite change of angular momentum after the orbital transitions. As discussed above, Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF</sub> = +2ℏ or −ℏ in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration, while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF</sub> = −2ℏ or +ℏ in the (σ<sup>−</sup>, σ<sup>+</sup>) configuration. Considering that an additional Zeeman dependence <italic toggle=\"yes\">H</italic>\n<sub>\n<bold>B</bold>\n</sub> = −<italic toggle=\"yes\">g</italic>\n<sub>\n<italic toggle=\"yes\">J</italic>\n</sub>μ<sub>B</sub>\n<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> · <bold>B</bold> is added when a magnetic field is applied, the change of the sign of Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF</sub> from (σ<sup>+</sup>, σ<sup>−</sup>) to (σ<sup>−</sup>, σ<sup>+</sup>) explains why the magnetic field dependence of CEF1–3 is inverted when the helicity is reversed in Figure ##FIG##2##3##. Another intriguing finding from Figure ##FIG##2##3## is that the magnetic field dependence of CEF1 and CEF2 is opposite to that of CEF3 regardless of the helicity, suggesting that Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> and Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> share the same sign, whereas Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> has the opposite sign. More specifically, in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration, we should have Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> = +2ℏ while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = −ℏ, or Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> = −ℏ while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = +2ℏ. Note that Δ<italic toggle=\"yes\">J</italic> = −ℏ is allowed for a CEF level due to the threefold rotational symmetry that relaxes the angular momentum conservation rule, but we expect that Δ<italic toggle=\"yes\">J</italic> = +2ℏ that satisfies the strict angular momentum conservation should have a higher probability and stronger Raman signals. Since CEF1 and CEF2 have much stronger Raman intensities than CEF3 (Figure ##FIG##1##2b##), it is natural to conclude that Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> = +2ℏ while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = −ℏ in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration. Similarly, Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF2</sub> = −2ℏ while Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = +ℏ in the (σ<sup>−</sup>, σ<sup>+</sup>) configuration. In terms of matrix operations, <mml:math id=\"jats-math-28\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-29\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-30\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-31\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-32\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, and <mml:math id=\"jats-math-33\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math> should be significant while <mml:math id=\"jats-math-34\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-35\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-36\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-37\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-38\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-39\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-40\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math>, and <mml:math id=\"jats-math-41\" display=\"inline\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">⟨</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">|</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo stretchy=\"false\">|</mml:mo><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:math> should all be small or zero (the last six matrix elements correspond to the co‐circular polarization).</p>", "<p>As shown in Figure ##FIG##0##1b##, the eigenstates of CEF levels are linear combinations of multiplets <italic toggle=\"yes\">m</italic>\n<sub>\n<italic toggle=\"yes\">J</italic>\n</sub> = −7/2…7/2: |ψ<sup>±</sup>〉 = <mml:math id=\"jats-math-42\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mo>∑</mml:mo><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mo>−</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mtext>…</mml:mtext><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:msub><mml:msubsup><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. Typically, CEF parameters are fit to a CEF Hamiltonian with Stevens operators given by the symmetry of the ionic environment of the 4f orbitals, as described in the Experimental Section. The procedure is frequently under‐constrained, and there are enough degrees of freedom to fit experimentally observed CEF energy levels with more than one set of CEF parameters that minimize the error that may exist. The order of the eigenstates may not be the same across those sets. However, once the constraints imposed by the optical selection rules discussed above are taken into account, we are able to find a set of CEF parameters, as indicated by filled and empty circles in Figure ##FIG##0##1b##, that can explain the observed helicity and magnetic field dependence in Figures ##FIG##1##2## and ##FIG##2##3##, and we can make final assignments of CEF1‐3. As illustrated in <bold>Figure</bold> ##FIG##3##\n4a##, CEF1 comes from <mml:math id=\"jats-math-43\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration, where Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = −2ℏ and Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = +2ℏ, or <mml:math id=\"jats-math-44\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> in the (σ<sup>−</sup>, σ<sup>+</sup>) configuration, where Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = +2ℏ and Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = −2ℏ (see the arrows for the transitions). We note that the transition of <mml:math id=\"jats-math-45\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> with Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = −ℏ is allowed in (σ<sup>+</sup>, σ<sup>−</sup>) and the transition of <mml:math id=\"jats-math-46\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> with Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF1</sub> = +ℏ is allowed in (σ<sup>−</sup>, σ<sup>+</sup>), since Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = −3ℏ and +3ℏ, respectively, which satisfies the discrete angular momentum conservation. However, these transitions allowed by the crystal threefold rotational symmetry are of a higher order and should be much weaker. Similar transitions apply for CEF2, although they correspond to <mml:math id=\"jats-math-47\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-48\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. For CEF3 in Figure ##FIG##3##4b##, however, any transition with Δ<italic toggle=\"yes\">J</italic> = −2ℏ or +2ℏ is impossible; hence, the transition of <mml:math id=\"jats-math-49\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> with Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = −ℏ is the only one allowed in (σ<sup>+</sup>, σ<sup>−</sup>) where Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = −3ℏ, and the transition of <mml:math id=\"jats-math-50\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> with Δ<italic toggle=\"yes\">J</italic>\n<sub>CEF3</sub> = +ℏ is the only one allowed in (σ<sup>−</sup>, σ<sup>+</sup>) where Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = +3ℏ. This could explain why CEF3 is much weaker than CEF1 and CEF2.</p>", "<p>As for the phonon Raman modes, in general, a nondegenerate Γ‐point phonon (like the <italic toggle=\"yes\">A</italic>\n<sub>1g</sub> Raman mode in NaYbSe<sub>2</sub>) cannot have angular momentum since the eigenvector is a real number. It is therefore only observed in the co‐circular polarization configuration, as shown in Figure ##FIG##1##2b##. However, when the Γ‐point phonon is doubly degenerate, the two real eigenvectors can be reconstructed by a complex superposition as shown in Figure ##FIG##0##1a##. Therefore, doubly degenerate modes like the <italic toggle=\"yes\">E</italic>\n<sub>g</sub> Raman mode in NaYbSe<sub>2</sub> can have (pseudo)angular momentum of ±ℏ.<sup>[</sup>\n##REF##26406841##\n3\n##, ##UREF##6##\n9\n##, ##UREF##47##\n60\n##, ##UREF##49##\n62\n##\n<sup>]</sup> With nonzero angular momentum, it can change the chirality of incident photons and appear in the cross‐circular polarization configuration. As shown in Figure ##FIG##3##4c##, in the (σ<sup>+</sup>, σ<sup>−</sup>) configuration, Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = −2ℏ and <mml:math id=\"jats-math-59\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>J</mml:mi><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:mo>−</mml:mo><mml:mi>ℏ</mml:mi></mml:mrow></mml:mrow></mml:math>, so it is allowed by the discrete angular momentum conservation as Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = −3ℏ; In the (σ<sup>−</sup>, σ<sup>+</sup>) configuration, Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> = +2ℏ and <mml:math id=\"jats-math-60\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>J</mml:mi><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub></mml:msub><mml:mo>=</mml:mo><mml:mo>+</mml:mo><mml:mi>ℏ</mml:mi></mml:mrow></mml:mrow></mml:math>, giving rise to Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = +3ℏ. Such an optical selection rule is similar to that shown for CEF3 in Figure ##FIG##3##4b##, which explains why both are observed in the cross‐circular polarization. Similar results have been reported for <italic toggle=\"yes\">E</italic> symmetry Raman modes in TMDs, CrBr<sub>3</sub>, and quartz, among other materials.<sup>[</sup>\n##UREF##6##\n9\n##, ##UREF##47##\n60\n##, ##UREF##48##\n61\n##\n<sup>]</sup>\n</p>", "<p>Finally, moving on to the VBS ω, it is much stronger in the co‐circular polarization configuration and its magnetic field dependence is weak (Figures ##FIG##1##2## and ##FIG##2##3##), in stark contrast to CEF1‐3. This indicates that the change in angular momentum for ω is zero: Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = 0. Since it is a coupled state between the CEF1 and the <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode, we consider the 2 × ~2 dimensional space <mml:math id=\"jats-math-61\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>±</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. As the angular momentum change Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> for CEF1 is finite (Figure ##FIG##3##4a##), the phonon subsystem has to carry additional angular momentum (Figure ##FIG##3##4c##) in order to yield zero angular momentum for ω. Therefore, the circular basis {$E$<sub>g, +</sub>, $E$<sub>g, $‐$</sub>} is the natural choice for describing the eigenvibration. As discussed previously, CEF1 can arise from four possible transitions while <italic toggle=\"yes\">E</italic>\n<sub>g</sub> can be $E$<sub>g, +</sub> and $E$<sub>g, $‐$</sub>, which gives rise to a total of eight possible transitions for ω. Based on the angular momentum conservation rule, however, we found that two states, <mml:math id=\"jats-math-62\" display=\"inline\"><mml:mrow><mml:mrow><mml:msup><mml:mi>ω</mml:mi><mml:mo>+</mml:mo></mml:msup><mml:mrow><mml:mo>=</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-63\" display=\"inline\"><mml:mrow><mml:mrow><mml:msup><mml:mi>ω</mml:mi><mml:mo>−</mml:mo></mml:msup><mml:mrow><mml:mo>=</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, are the most probable (see more details in the Supporting Information). As shown in Figure ##FIG##3##4d##, due to the angular momentum transfer between the CEF1 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode, the excited state of ω, <mml:math id=\"jats-math-64\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-65\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, has the <italic toggle=\"yes\">z</italic>‐component of the angular momentum effectively raised or lowered by ℏ compared to the <mml:math id=\"jats-math-66\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-67\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> shown in Figure ##FIG##3##4a##, respectively. As a result, the transitions of <mml:math id=\"jats-math-68\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-69\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> have Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = 0 to satisfy the selection rule in the co‐circular polarization configuration and explain the weak magnetic field dependence.</p>", "<p>\n<bold>Figure</bold> ##FIG##4##\n5a,b## illustrates the two states, <mml:math id=\"jats-math-70\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-71\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> based on the observations described above. In Figure ##FIG##4##5a##, when the ground state is <mml:math id=\"jats-math-72\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> (shown in light pink), the <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub> or <italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub> operator excites the system to the + branch, <mml:math id=\"jats-math-73\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> (where the CEF excitation corresponds to the + branch and the phononic excitation corresponds to + angular momentum). Figure ##FIG##4##5b## shows the same effect for <mml:math id=\"jats-math-74\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> to <mml:math id=\"jats-math-75\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. Because the transition is degenerate for <mml:math id=\"jats-math-76\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>∓</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo></mml:mrow><mml:msup><mml:mi>ω</mml:mi><mml:mo>±</mml:mo></mml:msup></mml:mrow></mml:mrow></mml:math> with <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub> or <italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub>, this eigenspace, in principle, can be transduced from a QSL ground state. If the QSL ground state is written as <mml:math id=\"jats-math-77\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mo>∑</mml:mo><mml:mi>j</mml:mi></mml:msub><mml:msub><mml:mo>∏</mml:mo><mml:mi>i</mml:mi></mml:msub><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:msub><mml:mi>σ</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>j</mml:mi></mml:mrow></mml:msub></mml:msubsup></mml:mrow></mml:mrow></mml:math> – where <italic toggle=\"yes\">i</italic> is the site index, <italic toggle=\"yes\">j</italic> the configuration index, and σ<sub>\n<italic toggle=\"yes\">ij</italic>\n</sub> = +, − is the branch—then <italic toggle=\"yes\">J</italic>\n<sub>+</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>−</sub> or <italic toggle=\"yes\">J</italic>\n<sub>−</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>+</sub> should bring the system into <mml:math id=\"jats-math-78\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mo>∑</mml:mo><mml:mi>j</mml:mi></mml:msub><mml:msub><mml:mo>∏</mml:mo><mml:mi>i</mml:mi></mml:msub><mml:msup><mml:mi>ω</mml:mi><mml:msub><mml:mi>σ</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>j</mml:mi></mml:mrow></mml:msub></mml:msup></mml:mrow></mml:mrow></mml:math> within the point spread volume of the excitation beam, transducing the possible ground state entanglement to the VBS ω<sup>±</sup>.</p>", "<p>It is worth noting that, in the original Thalmeier–Fulde model, two VBS modes are expected to emerge from the hybridization of a CEF mode and a phonon mode.<sup>[</sup>\n##UREF##34##\n41\n##\n<sup>]</sup> Besides the two most probable VBS transitions shown in Figure ##FIG##3##4d## that give rise to the observed ω peak in the Raman spectra, there are six other transitions that could contribute to the other VBS mode that is not observed in our Raman measurements (see Equation (##SUPPL##0##S1##), Supporting Information). Since the picture of how orbital and phononic excitations couple is not entirely clear, a definitive answer to why other transitions and the other VBS mode do not appear in Raman scattering is beyond the scope of this work. It is expected that the electron–phonon coupling may be more complicated compared to the conventional coupling between orbital angular momentum and spin angular momentum.<sup>[</sup>\n##UREF##50##\n63\n##\n<sup>]</sup> Therefore, we hypothesize that the coupling between the CEF1 and the E<sub>g</sub> mode is not the same as the conventional coupling between orbital and spin angular momenta. There is a coupling coefficient before the derived Δ<italic toggle=\"yes\">J</italic>\n<sub>ω</sub> (see Equation (##SUPPL##0##S1##), Supporting Information), leading to non‐integer Δ<italic toggle=\"yes\">J</italic>\n<sub>ω</sub> unless it is zero to begin with. As a consequence, only <mml:math id=\"jats-math-81\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-82\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-83\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, and <mml:math id=\"jats-math-84\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> that have zero angular momentum can satisfy the angular momentum conservation rule in the co‐circular polarization configuration, and other transitions are forbidden in any polarization channel. Moreover, as discussed previously, since <mml:math id=\"jats-math-85\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-86\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> are of a higher order and much less probable, only <mml:math id=\"jats-math-87\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-88\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> have detectable signals (see Figure ##FIG##3##4d##). This could explain why other transitions and the other VBS modes are not observed.</p>" ]
[ "<title>Conclusion</title>", "<p>We have used polarized field‐dependent Raman spectroscopy to elucidate a vibronic bound state in the quantum spin liquid, NaYbSe<sub>2</sub>. Of course, future direct infrared excitation of the modes explored in this manuscript could prove to be a more efficient method for direct control of angular momentum transfer. We have measured quantized angular momentum transfer Δ<italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = ±ℏ between an orbital and a phonon subsystem due to strong coupling between orbitals and <italic toggle=\"yes\">E</italic>\n<sub>g</sub> phonons. This was verified by observing clean selection rules between the ground and excited‐state orbital levels as well as the vibronic bound state. This transfer of angular momentum may enable the on‐demand creation of phonon condensates carrying macroscopic angular momentum, though the quantum many‐body physics of the orbital‐phonon interactions does require further study. If the phonon band structure is modified by this coupling, it may also be possible to access the resulting Berry curvature and probe the robustness of potential topological invariants. Additionally, the observation of photon‐ and CEF‐mediated angular‐momentum transfer suggests that there may be many more possible routes to the creation and control of phononic angular momentum by coupling to electronic, spin, and orbital degrees of freedom in a given system. This finding thus creates a framework that may ultimately enable the transduction of possible QSL ground states to experimentally accessible VBSs.</p>" ]
[ "<title>Abstract</title>", "<p>The notion that phonons can carry pseudo‐angular momentum has many major consequences, including topologically protected phonon chirality, Berry curvature of phonon band structure, and the phonon Hall effect. When a phonon is resonantly coupled to an orbital state split by its crystal field environment, a so‐called vibronic bound state forms. Here, a vibronic bound state is observed in NaYbSe<sub>2</sub>, a quantum spin liquid candidate. In addition, field and polarization dependent Raman microscopy is used to probe an angular momentum transfer of Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = ±ℏ between phonons and the crystalline electric field mediated by the vibronic bound stat. This angular momentum transfer between electronic and lattice subsystems provides new pathways for selective optical addressability of phononic angular momentum via electronic ancillary states.</p>", "<p>Angular momentum transfer between phonons and the crystal electric field in a candidate quantum spin liquid is observed with polarization‐ and magnetic‐field‐dependent Raman microscopy. These results provide a new framework for selective optical addressability of phononic angular momentum via electronic, spin, and orbital degrees of freedom in emerging quantum materials.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6818-cit-0070\">\n<string-name>\n<given-names>Y.‐Y.</given-names>\n<surname>Pai</surname>\n</string-name>, <string-name>\n<given-names>C. E.</given-names>\n<surname>Marvinney</surname>\n</string-name>, <string-name>\n<given-names>G.</given-names>\n<surname>Pokharel</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Xing</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Chilcote</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Brahlek</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Lindsay</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Miao</surname>\n</string-name>, <string-name>\n<given-names>A. S.</given-names>\n<surname>Sefat</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Parker</surname>\n</string-name>, <string-name>\n<given-names>S. D.</given-names>\n<surname>Wilson</surname>\n</string-name>, <string-name>\n<given-names>J. S.</given-names>\n<surname>Gardner</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Liang</surname>\n</string-name>, <string-name>\n<given-names>B. J.</given-names>\n<surname>Lawrie</surname>\n</string-name>, <article-title>Angular‐Momentum Transfer Mediated by a Vibronic‐Bound‐State</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304698</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304698</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Sample Details</title>", "<p>Single crystals of NaYbSe<sub>2</sub> were synthesized from NaCl (crystalline powder, <mml:math id=\"jats-math-89\" display=\"inline\"><mml:mrow><mml:mrow><mml:mn>99</mml:mn><mml:mo>+</mml:mo><mml:mo>%</mml:mo></mml:mrow></mml:mrow></mml:math>), Yb (ingot, 99.9%), and Se (powder, 99.999%) via the flux method. The finely ground flux mixtures of NaCl, Yb, and Se with a molar ratio of 20:1:2.4 were heated slowly to 850 °C in a vacuum. After 2 weeks, the furnace was cooled to room temperature at a rate of 40 °C h<sup>−1</sup>. The laboratory‐grown single crystals of NaYbSe<sub>2</sub> were separated from excess alkali halide flux by washing with deionized water and isopropyl alcohol inside a fume‐hood. CsYbSe<sub>2</sub> single crystals were grown using a related flux method that is described in more detail in previous work.<sup>[</sup>\n##UREF##27##\n34\n##\n<sup>]</sup>\n</p>", "<title>Raman Spectroscopy</title>", "<p>Variable temperature Raman spectra were acquired in a Montana Instruments closed‐cycle cryostat using an in‐vacuum objective with a numerical aperture of 0.85. A 1.5 mW, 532.03 nm continuous wave laser excited the sample in an out‐of‐plane back scattering geometry (beam path ‖ <bold>c</bold>). Rayleigh scattering was minimized with either a set of three Optigrate volume Bragg gratings or a set of Semrock RazorEdge ultrasteep dichroic and long‐pass edge filters with cutoff at 90 cm<sup>−1</sup>, and spectra were acquired with a 30 s exposure time.</p>", "<p>Magnetic‐field‐dependent Raman spectra were acquired at a fixed temperature of <italic toggle=\"yes\">T</italic> = 4 K for <bold>H</bold> ‖ <bold>c</bold> in a customized Leiden dilution refrigerator with free space optical access to the sample at the mixing chamber stage.<sup>[</sup>\n##UREF##51##\n64\n##\n<sup>]</sup> The spectra were taken with an Andor Kymera 193 spectrograph (2400 line mm<sup>−1</sup> grating) and a Newton EMCCD DU970P‐BV camera. The same laser and filters were used as with the variable temperature measurements, with the laser power set to 1.0 mW and a typical exposure time of 300 s per spectrum. Achromatic half‐wave plates and quarter‐wave plates were mounted on rotators for automated polarization control in both microscopes.</p>", "<title>Crystal Field Hamiltonian</title>", "<p>For a review of the approaches used here, see, for example, Baqrtolomé et al.<sup>[</sup>\n##UREF##52##\n65\n##\n<sup>]</sup> The CEF Hamiltonian for NaYbSe<sub>2</sub> within the point charge approximation<sup>[</sup>\n##UREF##16##\n23\n##, ##UREF##18##\n25\n##, ##UREF##25##\n32\n##, ##UREF##53##\n66\n##\n<sup>]</sup> that described the ground state manifold <italic toggle=\"yes\">J</italic> = 7/2 is\n\n</p>", "<p>The expected helicity dependence of the CEF excitations follows from the selection rule bridging the two relevant states. The eigenstates for the energy levels described in Equation (##FORMU##0##1##) are:\nwhere the relative weights <mml:math id=\"jats-math-92\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>±</mml:mo></mml:msubsup></mml:mrow></mml:math> are determined by <mml:math id=\"jats-math-93\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>B</mml:mi><mml:mn>2</mml:mn><mml:mn>0</mml:mn></mml:msubsup></mml:mrow></mml:math>, <mml:math id=\"jats-math-94\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>B</mml:mi><mml:mn>4</mml:mn><mml:mn>0</mml:mn></mml:msubsup></mml:mrow></mml:math>, <mml:math id=\"jats-math-95\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>B</mml:mi><mml:mn>4</mml:mn><mml:mn>3</mml:mn></mml:msubsup></mml:mrow></mml:math>, <mml:math id=\"jats-math-96\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>B</mml:mi><mml:mn>6</mml:mn><mml:mn>0</mml:mn></mml:msubsup></mml:mrow></mml:math>, <mml:math id=\"jats-math-97\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>B</mml:mi><mml:mn>6</mml:mn><mml:mn>3</mml:mn></mml:msubsup></mml:mrow></mml:math>, and <mml:math id=\"jats-math-98\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>B</mml:mi><mml:mn>6</mml:mn><mml:mn>6</mml:mn></mml:msubsup></mml:mrow></mml:math>. The eigenstates are shown in Figure ##FIG##0##1b##. Due to the threefold symmetry of the Yb<sup>3 +</sup> environment, a threefold periodicity and hence angular momentum folding, analogous to the the Umklapp process for linear momentum<sup>[</sup>\n##UREF##49##\n62\n##\n<sup>]</sup> was expected. Without further constraints, the six parameters have enough degrees of freedom to fit experimentally observed energy levels. More than one set of CEF parameters that minimize the error might exist and the order of the eigenstates might not be the same across those sets. For example, the little group spanned by the special pair with single angular momentum eigenstate <mml:math id=\"jats-math-99\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mfrac><mml:mn>3</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-100\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mo>−</mml:mo><mml:mfrac><mml:mn>3</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> was assigned to CEF1 in Zhang et al.<sup>[</sup>\n##UREF##16##\n23\n##\n<sup>]</sup> and CEF2 in Scheie et al.<sup>[</sup>\n##UREF##30##\n37\n##\n<sup>]</sup> Schimidt et al. pointed out that they cannot be the ground state due to observed in‐plane field dependence at low temperatures.<sup>[</sup>\n##UREF##18##\n25\n##\n<sup>]</sup> In addition to the Zeeman dependence <italic toggle=\"yes\">H</italic>\n<sub>\n<bold>B</bold>\n</sub> = −<italic toggle=\"yes\">g</italic>\n<sub>\n<italic toggle=\"yes\">J</italic>\n</sub>μ<sub>\n<italic toggle=\"yes\">B</italic>\n</sub>\n<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> · <bold>B</bold>, several additional corrections have been considered in the literature. For example, Pocs et al.<sup>[</sup>\n##UREF##25##\n32\n##\n<sup>]</sup> considered an <italic toggle=\"yes\">H</italic>\n<sub>XXZ</sub> term. Zhang et al. considered anisotropic spin–spin interactions.<sup>[</sup>\n##UREF##54##\n67\n##\n<sup>]</sup>\n</p>", "<p>In the context of magnetostrictive coupling with CEF modes, Callan et al. considered an additional term <mml:math id=\"jats-math-101\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>H</mml:mi><mml:mtext>me</mml:mtext></mml:msub><mml:mo>=</mml:mo><mml:mo>−</mml:mo><mml:msub><mml:mo>∑</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi>ν</mml:mi></mml:msub></mml:msub><mml:mi>ζ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi>ν</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mspace width=\"0.28em\"/><mml:mi>u</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi>ν</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mspace width=\"0.28em\"/><mml:mi>Q</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi>ν</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> where ζ is the coupling strength, <italic toggle=\"yes\">u</italic>(Γ<sub>ν</sub>) are phonon operators, and <italic toggle=\"yes\">Q</italic>(Γ<sub>ν</sub>) is the transformed phonon mode octupolar operator on the CEF manifold. The Callen–Callen<sup>[</sup>\n##UREF##55##\n68\n##, ##UREF##56##\n69\n##\n<sup>]</sup> magnetoelastic interaction is quadruplar. The quadruple operator (<italic toggle=\"yes\">l</italic> = 2) is given by <italic toggle=\"yes\">A</italic>\n<sub>1g</sub> + 2<italic toggle=\"yes\">E</italic>\n<sub>g</sub>. Hence,\n\n</p>", "<p>For <mml:math id=\"jats-math-103\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>Q</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:msubsup><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi><mml:mtext>II</mml:mtext></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math>, since <mml:math id=\"jats-math-104\" display=\"inline\"><mml:mrow><mml:mrow><mml:msubsup><mml:mi>J</mml:mi><mml:mi>x</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>−</mml:mo><mml:msubsup><mml:mi>J</mml:mi><mml:mi>y</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>=</mml:mo><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mo>−</mml:mo></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>/</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:mrow></mml:math>, it induced Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = ±2ℏ, while for <italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub> + <italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">y</italic>\n</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub> = <italic toggle=\"yes\">iJ</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>, Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = 0. For <mml:math id=\"jats-math-105\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>Q</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:msubsup><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi><mml:mi mathvariant=\"normal\">I</mml:mi></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math>, <italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub> + <italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> and <italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub> + <italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">x</italic>\n</sub>\n<italic toggle=\"yes\">J</italic>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> both induces Δ<bold>J</bold>\n<sub>\n<italic toggle=\"yes\">z</italic>\n</sub> = ±1ℏ.</p>", "<title>Fitting Experimental Helicitiy‐Resolved Data to a CEF Hamiltonian</title>", "<p>To fit the experimental data, a general non‐linear model normalization procedure in Mathematica was used. To start, a general set of eigenvalues and eigenvectors as a function of the CEF parameters was obtained by direct diagonalization of the CEF Hamiltonian. The eigenvectors were sorted based on their eigenvalues for each test parameter space. Then the cost function was defined by the sum of the squared errors between transitions and the data, with both inter‐branch and intra‐branch transitions considered. The selection rules were added as a term in the cost function when necessary. The final CEF parameters were the set that minimized the cost function. However, it was noted that the field dependence of the model was only qualitatively accurate not quantitatively: the experimentally observed levels were only 30% to 60% of the level shift in magnetic field. It was reported that there was non‐negligible magnetoelastic coupling and the field dependence needed to include corresponding terms in the Hamiltonian.</p>", "<title>Bayesian Inference</title>", "<p>Bayesian inference was employed to extract spectral parameters such as peak positions and widths. This approach is based on Bayes' rule: <mml:math id=\"jats-math-106\" display=\"inline\"><mml:mrow><mml:mrow><mml:mi>P</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>θ</mml:mi><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>y</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>P</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>y</mml:mi><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>θ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mi>P</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>θ</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mi>P</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>y</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>. In the context of spectral data, the priors <italic toggle=\"yes\">P</italic>(θ) were the <italic toggle=\"yes\">true</italic> distribution of the parameters such as peak position, peak height, and peak width. The likelihood <italic toggle=\"yes\">P</italic>(<italic toggle=\"yes\">y</italic>|θ) was the experimental data. The posterior <italic toggle=\"yes\">P</italic>(θ|<italic toggle=\"yes\">y</italic>) was the conditional distribution of the experiment parameters given the experimental data. <italic toggle=\"yes\">P</italic>(<italic toggle=\"yes\">y</italic>) was a normalization factor. The distribution of the priors of the parameters was assumed to be Gaussian or uniform. Additional noise, offset, and slope were added to capture backgrounds unrelated to the peak parameters. To carry out the inference, the Hamiltonian Monte Carlo Python package <monospace>PyMC3</monospace>\n<sup>[</sup>\n##UREF##42##\n54\n##\n<sup>]</sup> was used. A hierarchical model was constructed to concurrently extract peak parameters from a family of spectra, such as the temperature dependence or magnetic field dependence. A no U‐Turns (NUTS) sampler was used with four chains with 3000 samples per chain. It takes between 20 min to 3 h for a peak over a dataset to converge.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>All authors discussed the results thoroughly. Y.‐Y.P., C.E.M., and B.J.L. performed magneto‐Raman measurements. L.L. performed Raman tensor analysis. G.P. and J.X. grew the samples. Y.‐Y.P and L.L. did the data analysis with inputs from L.L., M.C., J.S.G., and B.J.L. X.L. and L.L. performed DFT calculations. A.S.S., D.P., S.W., and B.J.L initiated and oversaw the project. Y.‐Y.P., L.L. and B.J.L wrote most of the manuscript with contributions from all authors.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors would like to acknowledge insightful discussion with Michael A. McGuire, Allen Scheie, Xinshu Zhang, Yi Luo, Cristian Batista, Alan Tennant, and Vyacheslav Bryantsev. This research was sponsored by the U. S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division. Some of the first‐principles phonon calculations and all of the variable‐temperature, zero‐field Raman microscopy were performed at the Center for Nanophase Materials Sciences, which is a U.S. Department of Energy Office of Science User Facility. S.D.W. and G.P. acknowledge support by the US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE‐SC0017752. Postdoctoral research support was provided by the Intelligence Community Postdoctoral Research Fellowship Program at the Oak Ridge National Laboratory, administered by Oak Ridge Institute for Science and Education through an interagency agreement between the U.S. Department of Energy and the Office of the Director of National Intelligence.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6818-fig-0001\"><label>Figure 1</label><caption><p>a) The <italic toggle=\"yes\">E</italic>\n<sub>g</sub> eigenspace is spanned by the basis {$E$<sub>g, $x$</sub>, $E$<sub>g, $y$</sub>}, which can also be spanned by {$E$<sub>g, +</sub>, $E$<sub>g, $‐$</sub>} = {$E$<sub>g, $x$</sub> + <italic toggle=\"yes\">i</italic>$E$<sub>g, $y$</sub>, $E$<sub>g, $x$</sub> − <italic toggle=\"yes\">i</italic>$E$<sub>g, $y$</sub>}. b) Representations of the CEF eigenstates <mml:math id=\"jats-math-1\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, <mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, and <mml:math id=\"jats-math-4\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. The eigenstates are linear combinations of multiplets <italic toggle=\"yes\">m</italic>\n<sub>\n<italic toggle=\"yes\">J</italic>\n</sub> = −7/2…7/2. For example, <mml:math id=\"jats-math-5\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>=</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mfrac><mml:mn>3</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> is represented by precessing cones with <mml:math id=\"jats-math-6\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:mfrac><mml:mn>3</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:msub><mml:mo>≠</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:mrow></mml:math> for <mml:math id=\"jats-math-7\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>=</mml:mo></mml:mrow><mml:msub><mml:mi>c</mml:mi><mml:mfrac><mml:mn>3</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:msub><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mi>J</mml:mi><mml:mo>,</mml:mo><mml:mfrac><mml:mn>3</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. Hence, all but the <mml:math id=\"jats-math-8\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>J</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mfrac><mml:mn>3</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:mrow></mml:math> cones are transparent (and all but the <mml:math id=\"jats-math-9\" display=\"inline\"><mml:mrow><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>J</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mfrac><mml:mn>3</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:mrow></mml:math> circles are empty). The same follows for <mml:math id=\"jats-math-10\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and <mml:math id=\"jats-math-11\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mrow><mml:mn>0</mml:mn><mml:mo>,</mml:mo><mml:mn>2</mml:mn><mml:mo>,</mml:mo><mml:mn>3</mml:mn></mml:mrow><mml:mo>±</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. c) Temperature dependent Raman spectra for CEF1, $E$<sub>g</sub>, and the VBS, ω, from <italic toggle=\"yes\">T</italic> = 3.3 K to <italic toggle=\"yes\">T</italic> = 260 K. d) Peak positions for CEF1, <italic toggle=\"yes\">E</italic>\n<sub>g</sub> and ω extracted from Bayesian inference. The symbols are medians of the posterior distribution, and the 68% and 95% HDIs are represented by darker and lighter shading, respectively.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6818-fig-0002\"><label>Figure 2</label><caption><p>a) Schematic illustration of Raman scattering where CEF1‐3, phonon modes, and ω can be excited in the process. b) Helicity‐resolved Raman spectra at <italic toggle=\"yes\">T</italic> = 4 K, <italic toggle=\"yes\">B</italic> = 0 T. Four prominent modes are CEF1 (with an <italic toggle=\"yes\">E</italic>\n<sub>g</sub> phonon mode at its shoulder), ω, CEF2, and CEF3. The Rayleigh scattering and ω are of (σ<sup>+</sup>, σ<sup>+</sup>) and (σ<sup>−</sup>, σ<sup>−</sup>) co‐circular scattering channels, while CEF1‐3 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub> are of (σ<sup>+</sup>, σ<sup>−</sup>) and (σ<sup>−</sup>, σ<sup>+</sup>) cross‐circular channels.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6818-fig-0003\"><label>Figure 3</label><caption><p>Helicity‐resolved magnetic field dependence of CEFs and ω for NaYbSe<sub>2</sub> at <italic toggle=\"yes\">T</italic> = 4 K. a) CEF1, b) CEF2, c) ω, and d) CEF3. The 68% and 95% HDIs are represented by darker and lighter shading, respectively. See Supporting Information for the raw spectra that the peak positions were extracted from.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6818-fig-0004\"><label>Figure 4</label><caption><p>a) Selection rule for CEF1 corresponding to <mml:math id=\"jats-math-51\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-52\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. A similar rule applies for CEF2, although the transition corresponds to <mml:math id=\"jats-math-53\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-54\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>2</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. b) Selection rule for CEF3 corresponding to <mml:math id=\"jats-math-55\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-56\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>3</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>. Note that the threefold rotational symmetry in NaYbSe<sub>2</sub> allows for discrete angular momentum conservation: |Δ<italic toggle=\"yes\">J</italic>\n<sub>photon</sub> + Δ<italic toggle=\"yes\">J</italic>\n<sub>particle</sub>|/ℏ = 0 (modulo 3). Here Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = −3ℏ or Δ<italic toggle=\"yes\">J</italic>\n<sub>total</sub> = 3ℏ. c) Selection rule for the doubly degenerate <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode that can have (pseudo)angular momentum of ±ℏ. d) Selection rule for the vibronic bound state ω. Due to the angular momentum transfer between the CEF1 and <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode, the excited state of ω, <mml:math id=\"jats-math-57\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-58\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>, has a completely different helicity selection rule and magnetic field dependence than CEF1.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6818-fig-0005\"><label>Figure 5</label><caption><p>Schematic illustrations of the vibronic bound state ω: a) <mml:math id=\"jats-math-79\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mtext>g,+</mml:mtext></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> and b) <mml:math id=\"jats-math-80\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>0</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>→</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mn>1</mml:mn><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo><mml:mo>⊗</mml:mo><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mrow><mml:mtext>g,</mml:mtext><mml:mo>−</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math>.</p></caption></fig>" ]
[]
[ "<disp-formula id=\"advs6818-disp-0001\">\n<label>(1)</label>\n<mml:math id=\"jats-math-90\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:msub><mml:mi>H</mml:mi><mml:mtext>CEF</mml:mtext></mml:msub></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msubsup><mml:mi>B</mml:mi><mml:mn>2</mml:mn><mml:mn>0</mml:mn></mml:msubsup><mml:msubsup><mml:mi mathvariant=\"bold\">O</mml:mi><mml:mn>2</mml:mn><mml:mn>0</mml:mn></mml:msubsup><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msubsup><mml:mi>B</mml:mi><mml:mn>4</mml:mn><mml:mn>0</mml:mn></mml:msubsup><mml:msubsup><mml:mi mathvariant=\"bold\">O</mml:mi><mml:mn>4</mml:mn><mml:mn>0</mml:mn></mml:msubsup><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msubsup><mml:mi>B</mml:mi><mml:mn>4</mml:mn><mml:mn>3</mml:mn></mml:msubsup><mml:msubsup><mml:mi mathvariant=\"bold\">O</mml:mi><mml:mn>4</mml:mn><mml:mn>3</mml:mn></mml:msubsup></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd/><mml:mtd columnalign=\"left\"><mml:mrow><mml:mspace width=\"1em\"/><mml:mo linebreak=\"badbreak\">+</mml:mo><mml:msubsup><mml:mi>B</mml:mi><mml:mn>6</mml:mn><mml:mn>0</mml:mn></mml:msubsup><mml:msubsup><mml:mi mathvariant=\"bold\">O</mml:mi><mml:mn>6</mml:mn><mml:mn>0</mml:mn></mml:msubsup><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msubsup><mml:mi>B</mml:mi><mml:mn>6</mml:mn><mml:mn>3</mml:mn></mml:msubsup><mml:msubsup><mml:mi mathvariant=\"bold\">O</mml:mi><mml:mn>6</mml:mn><mml:mn>3</mml:mn></mml:msubsup><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msubsup><mml:mi>B</mml:mi><mml:mn>6</mml:mn><mml:mn>6</mml:mn></mml:msubsup><mml:msubsup><mml:mi mathvariant=\"bold\">O</mml:mi><mml:mn>6</mml:mn><mml:mn>6</mml:mn></mml:msubsup></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6818-disp-0002\">\n<label>(2)</label>\n<mml:math id=\"jats-math-91\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mtext>0, 1, 2, 3</mml:mtext><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mo>−</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mo>−</mml:mo><mml:mfrac><mml:mn>5</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mtext>…</mml:mtext><mml:mfrac><mml:mn>5</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:munder><mml:msubsup><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>+</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo></mml:mrow><mml:msubsup><mml:mi>ψ</mml:mi><mml:mtext>0, 1, 2, 3</mml:mtext><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:munder><mml:mo>∑</mml:mo><mml:mrow><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mo>−</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mo>−</mml:mo><mml:mfrac><mml:mn>5</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mtext>…</mml:mtext><mml:mfrac><mml:mn>5</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:munder><mml:msubsup><mml:mi>c</mml:mi><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo>−</mml:mo></mml:msubsup><mml:mrow><mml:mo stretchy=\"false\">|</mml:mo><mml:mfrac><mml:mn>7</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mo>,</mml:mo><mml:msub><mml:mi>m</mml:mi><mml:mi>j</mml:mi></mml:msub><mml:mo stretchy=\"false\">⟩</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6818-disp-0003\">\n<label>(3)</label>\n<mml:math id=\"jats-math-102\" display=\"block\"><mml:mrow><mml:mtable displaystyle=\"true\"><mml:mtr><mml:mtd columnalign=\"right\"><mml:msub><mml:mi>H</mml:mi><mml:mtext>me</mml:mtext></mml:msub></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mo>−</mml:mo><mml:munder><mml:mo>∑</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi>ν</mml:mi></mml:msub></mml:munder><mml:mi>ζ</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi>ν</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mspace width=\"0.28em\"/><mml:mi>u</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi>ν</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mspace width=\"0.28em\"/><mml:mi>Q</mml:mi><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi mathvariant=\"normal\">Γ</mml:mi><mml:mi>ν</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>Q</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>A</mml:mi><mml:mtext>1g</mml:mtext></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mn>3</mml:mn><mml:msubsup><mml:mi>J</mml:mi><mml:mi>z</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:msup><mml:mi>J</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>Q</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:msubsup><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi><mml:mi mathvariant=\"normal\">I</mml:mi></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mi>z</mml:mi></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mi>z</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mi>y</mml:mi></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mi>z</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mi>z</mml:mi></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mi>y</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd columnalign=\"right\"><mml:mrow><mml:mi>Q</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:msubsup><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi><mml:mtext>II</mml:mtext></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mtd><mml:mtd columnalign=\"left\"><mml:mrow><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mn>3</mml:mn></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msubsup><mml:mi>J</mml:mi><mml:mi>x</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:msubsup><mml:mi>J</mml:mi><mml:mi>y</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>α</mml:mi><mml:mn>4</mml:mn></mml:msub><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mi>y</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:msub><mml:mi>J</mml:mi><mml:mi>y</mml:mi></mml:msub><mml:msub><mml:mi>J</mml:mi><mml:mi>x</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:math>\n</disp-formula>" ]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
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[ "<supplementary-material id=\"advs6818-supl-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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Y."], "surname": ["Lawrie", "Feldman", "Marvinney", "Pai"], "article-title": ["arXiv:2103.06851"], "year": ["2021"]}, {"label": ["65"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["E.", "A.", "J.", "J.", "F.", "E."], "surname": ["Bartolom\u00e9", "Arauzo", "Luz\u00f3n", "Bartolom\u00e9", "Bartolom\u00e9", "Br\u00fcck"], "source": ["Handbook of Magnetic Materials"], "person-group": ["\n"], "volume": ["26"], "publisher-name": ["Elsevier"], "publisher-loc": ["Amsterdam"], "year": ["2017"], "fpage": ["1"], "lpage": ["289"]}, {"label": ["66"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n"], "given-names": ["J.", "A.", "B."], "surname": ["Jensen", "Mackintosh", "Mackintosh"], "article-title": ["Rare Earth Magnetism: Structures and Excitations", "International Series of Monographs on Physics"], "publisher-name": ["Clarendon Press"], "publisher-loc": ["Oxford"], "year": ["1991"]}, {"label": ["67"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["Z.", "J.", "W.", "Z.", "J.", "F.", "R.", "J.", "X.", "J.", "Q."], "surname": ["Zhang", "Li", "Liu", "Zhang", "Ji", "Jin", "Chen", "Wang", "Wang", "Ma", "Zhang"], "source": ["Phys. 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{ "acronym": [], "definition": [] }
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2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 9; 11(2):2304698
oa_package/98/33/PMC10787099.tar.gz
PMC10787100
37984865
[ "<title>Introduction</title>", "<p>Electron–phonon coupling (EPC) is essential in condensed matter physics, leading to pivotal phenomena such as superconductivity,<sup>[</sup>\n##UREF##0##\n1\n##, ##REF##27015504##\n3\n##\n<sup>‐3]</sup> ultrahigh thermal conductivity,<sup>[</sup>\n##UREF##2##\n4\n##\n<sup>]</sup> charge density wave,<sup>[</sup>\n##REF##11328180##\n5\n##\n<sup>]</sup> colossal magneto‐resistant,<sup>[</sup>\n##UREF##3##\n6\n##\n<sup>]</sup> etc. To date, there has been rarely reports on experimental determination of the EPC strength in transition metal perovskites, except for superconducting oxides.<sup>[</sup>\n##UREF##4##\n7\n##\n<sup>]</sup> Needless to say, understanding the EPC is also important for such non‐superconducting oxides to reveal their underlying microscopic mechanisms.<sup>[</sup>\n##UREF##5##\n8\n##, ##UREF##6##\n9\n##\n<sup>]</sup>\n</p>", "<p>Transition‐metal perovskite LaCoO<sub>3</sub> exhibits a diamagnetic insulating low‐spin phase (<mml:math id=\"jats-math-1\" display=\"inline\"><mml:mrow><mml:mrow><mml:msubsup><mml:mi>t</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi mathvariant=\"normal\">g</mml:mi></mml:mrow><mml:mn>6</mml:mn></mml:msubsup><mml:msubsup><mml:mi>e</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi><mml:mn>0</mml:mn></mml:msubsup><mml:mo>,</mml:mo><mml:mrow><mml:mspace width=\"0.33em\"/><mml:mi mathvariant=\"normal\">S</mml:mi><mml:mspace width=\"0.33em\"/><mml:mspace width=\"0.33em\"/></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mspace width=\"0.33em\"/><mml:mspace width=\"0.33em\"/></mml:mrow><mml:mn>0</mml:mn></mml:mrow></mml:mrow></mml:math>) at low temperatures, whereas it becomes metallic at higher temperature with the Co ions assuming a higher spin state (<mml:math id=\"jats-math-2\" display=\"inline\"><mml:mrow><mml:mrow><mml:msubsup><mml:mi>t</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi mathvariant=\"normal\">g</mml:mi></mml:mrow><mml:mn>4</mml:mn></mml:msubsup><mml:msubsup><mml:mi>e</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>,</mml:mo><mml:mrow><mml:mspace width=\"0.33em\"/><mml:mi mathvariant=\"normal\">S</mml:mi><mml:mspace width=\"0.33em\"/></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mspace width=\"0.33em\"/><mml:mspace width=\"0.33em\"/></mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:mrow></mml:math> or <mml:math id=\"jats-math-3\" display=\"inline\"><mml:mrow><mml:mrow><mml:msubsup><mml:mi>t</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mi mathvariant=\"normal\">g</mml:mi></mml:mrow><mml:mn>5</mml:mn></mml:msubsup><mml:msubsup><mml:mi>e</mml:mi><mml:mi mathvariant=\"normal\">g</mml:mi><mml:mn>1</mml:mn></mml:msubsup><mml:mo>,</mml:mo><mml:mrow><mml:mspace width=\"0.33em\"/><mml:mi mathvariant=\"normal\">S</mml:mi><mml:mspace width=\"0.33em\"/></mml:mrow><mml:mo>=</mml:mo><mml:mrow><mml:mspace width=\"0.33em\"/><mml:mspace width=\"0.33em\"/></mml:mrow><mml:mn>1</mml:mn></mml:mrow></mml:mrow></mml:math>).<sup>[</sup>\n##UREF##7##\n10\n##, ##UREF##8##\n11\n##, ##UREF##9##\n12\n##, ##REF##17280319##\n13\n##\n<sup>]</sup> Recently, it was found that epitaxial tensile‐strained LaCoO<sub>3</sub> thin films become ferromagnetic below 85 K,<sup>[</sup>\n##UREF##10##\n15\n##, ##REF##33929867##\n16\n##, ##UREF##11##\n17\n##, ##UREF##12##\n18\n##\n<sup>]</sup> exhibiting application potentials in magnetic devices. To date, the EPC strength in LaCoO<sub>3</sub> has rarely been measured, especially for thin film samples, although the EPC is one of the primary concerns.<sup>[</sup>\n##UREF##9##\n12\n##, ##UREF##10##\n15\n##\n<sup>]</sup> Moreover, the phonon–phonon scattering (PPS) in LaCoO<sub>3</sub> has rarely been investigated either.</p>", "<p>It has rarely been reported whether the EPC and PPS are spatially separated in such oxides or other solids, although it is well known that these two processes are largely detached temporally by exhibiting different characteristic lifetimes.<sup>[</sup>\n##UREF##13##\n19\n##, ##REF##12618781##\n20\n##\n<sup>]</sup> Ultrafast time‐resolved pump‐probe spectroscopy is the most viable experimental tool to detect both the EPC and PPS in quantum materials.<sup>[</sup>\n##UREF##1##\n2\n##, ##REF##27015504##\n3\n##, ##UREF##14##\n21\n##, ##REF##34852544##\n22\n##\n<sup>]</sup> In parallel, coherent phonon can also be generated and detected by ultrafast pump‐probe spectroscopy.<sup>[</sup>\n##UREF##15##\n23\n##, ##REF##25031087##\n24\n##, ##UREF##16##\n25\n##\n<sup>]</sup>\n</p>", "<p>In this work, we investigate the fluence‐dependent photo‐carriers dynamics in a 40 nm thick LaCoO<sub>3</sub> film on a SrTiO<sub>3</sub> substrate. Two distinct relaxation processes with lifetimes <italic toggle=\"yes\">τ</italic>\n<sub>fast</sub> = 0.2 ps and <italic toggle=\"yes\">τ</italic>\n<sub>slow</sub> = 0.9 ps are experimentally observed. The nominal EPC strength <italic toggle=\"yes\">λ<sub>E</sub>\n</italic>\n<sub>g</sub> is experimentally determined to be 0.30. We also detected a coherent acoustic phonon in our experiment. Significantly, we identify that the EPC and PPS are basically spatially separated by the interface of the sample.</p>" ]
[]
[ "<title>Results</title>", "<title>Photo‐Carrier Relaxation Dynamics in LaCoO<sub>3</sub>/SrTiO<sub>3</sub>\n</title>", "<p>We detect the relative transient differential reflectivity Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub> of LaCoO<sub>3</sub>/SrTiO<sub>3</sub> as a function of delay time, for which the data recorded at various pump fluences are presented in <bold>Figure</bold>\n##FIG##0##\n1\n##. In Figure ##FIG##0##1a##, the dots are the experimental results and the solid curves are fitting results (see a latter paragraph for a quantitative description). The signal we measure is proportional to the density of the photo‐excited carriers (abbreviated as photo‐carriers), which is intrinsically due to the Fermi transition and obeys the Fermi golden rule.<sup>[</sup>\n##UREF##1##\n2\n##, ##UREF##17##\n26\n##\n<sup>]</sup> Upon the pump pulse excitation, the density of the photo carriers reaches a maximum value at time <italic toggle=\"yes\">t</italic> = 0 fs, then decays through various relaxation channels, including the EPC, PPS, electron‐hole recombination, etc.<sup>[</sup>\n##UREF##14##\n21\n##\n<sup>]</sup>\n</p>", "<p>In the inset of Figure ##FIG##0##1a## we summarize the max value of |Δ<italic toggle=\"yes\">R</italic>/<italic toggle=\"yes\">R</italic>\n<sub>0</sub>| as a function of the excitation fluence. The value |Δ<italic toggle=\"yes\">R</italic>/<italic toggle=\"yes\">R</italic>\n<sub>0</sub>|<sub>max </sub> increases with fluence and a linear fit (solid line) to the signal |Δ<italic toggle=\"yes\">R</italic>/<italic toggle=\"yes\">R</italic>\n<sub>0</sub>|<sub>max </sub> can cover most of the range of the experimental condition. At above 3.2 mJ cm<sup>−2</sup> an off‐linear behavior arises, which indicates the occurrence of a thermal effect in the experiment. Note that the off‐linear (i.e., saturation) behavior in |Δ<italic toggle=\"yes\">R</italic>/<italic toggle=\"yes\">R</italic>\n<sub>0</sub>|<sub>max</sub> is a strict criterion for identifying whether there is a thermal effect (for details, see the Supporting Information of ref. [##UREF##1##2##] and references therein). The thermal (pink) and non‐thermal (blue) effect regimes are depicted by different colors as a guide for the identification.</p>", "<p>To better reveal the fluence dependence of the photo‐carriers ultrafast dynamics, the normalized Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub> is shown in Figure ##FIG##0##1b##. The data are normalized to the |Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub>|<sub>max</sub> value at the highest fluence excitation. To see the initial dynamics clearly, we illustrate a higher temporal resolution view of the scanning trace in the inset of Figure ##FIG##0##1b##. With increasing fluence, the normalized Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub> exhibits prominent changes, whereby the relaxation becomes more gradual. This reveals that the ultrafast photo‐carriers relaxation in LaCoO<sub>3</sub>/SrTiO<sub>3</sub> is clearly dependent on the pump fluence. Note that all the data in this work are one identical set of experimental results, although they are presented in different ways to emphasize different aspects. The transient reflectivity of the SrTiO<sub>3</sub> substrate is also measured, which is significantly different from that of the LaCoO<sub>3</sub>/SrTiO<sub>3</sub> sample (Figure ##SUPPL##0##S2##, Supporting Information). The control experiment demonstrates that the photo‐carriers relaxation dynamics in Figure ##FIG##0##1a## is mainly attributed to the LaCoO<sub>3</sub> thin film.</p>", "<p>We quantitatively analyze the experimental results. Because the electron–phonon interaction has a characteristic lifetime at the order of 1 ps,<sup>[</sup>\n##UREF##1##\n2\n##, ##UREF##2##\n4\n##, ##UREF##13##\n19\n##, ##REF##12618781##\n20\n##\n<sup>]</sup> and the presence of a hump centered at 10 ps in the dynamics<sup>[</sup>\n##UREF##18##\n27\n##\n<sup>]</sup> may affect the assignment of the relaxation components, we choose the data fitting range to be from −0.7 to 3.6 ps to minimize the interference of the hump. Before we do the quantitative data fitting, we use a log‐scale coordinate to show Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub> (Figure ##SUPPL##0##S4##, Supporting Information), which more clearly reveals how many components are present in the photo‐carriers relaxation dynamics. As seen, there are three components, and the slowest one is very flat, which can be reasonably represented by a constant term. A convoluted exponential‐decay function is employed to fit the photo‐carriers relaxation dynamics, along with a decaying cosine function to fit the coherent phonon, as:\nwhere <italic toggle=\"yes\">A</italic> and <italic toggle=\"yes\">τ</italic> represent the amplitude and lifetime, respectively, the subscript fast, slow, and 0 mark the three components, <mml:math id=\"jats-math-5\" display=\"inline\"><mml:mrow><mml:mrow><mml:mfrac><mml:mn>1</mml:mn><mml:msqrt><mml:mrow><mml:mn>2</mml:mn><mml:mi>π</mml:mi><mml:mi>p</mml:mi></mml:mrow></mml:msqrt></mml:mfrac><mml:msup><mml:mi>e</mml:mi><mml:mrow><mml:msup><mml:mi>t</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mo>/</mml:mo><mml:mn>2</mml:mn><mml:msup><mml:mi>p</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:msup></mml:mrow></mml:mrow></mml:math>is the Gaussian response function,<sup>[</sup>\n<sup>28]</sup> Ω is the angular frequency of the coherent phonon, and <italic toggle=\"yes\">φ</italic> is the initial phase of the coherent phonon. The fitting results compare well with our data [Figure ##FIG##0##1a##].</p>", "<p>The quantitative analysis of the fluence‐dependent results yields fluence‐dependent amplitudes and lifetimes, which are summarized in <bold>Figure</bold>\n##FIG##1##\n2\n##. The <italic toggle=\"yes\">A</italic>\n<sub>fast</sub> and <italic toggle=\"yes\">A</italic>\n<sub>slow</sub> exhibit positive correlations with the fluence in the non‐thermal effect regime [Figures ##FIG##1##2a,c##], which is in line with the results shown in the inset of Figure ##FIG##0##1##. The value of <italic toggle=\"yes\">τ</italic>\n<sub>fast</sub> slightly increases with fluence (Figure ##FIG##1##2b##), and <italic toggle=\"yes\">τ</italic>\n<sub>slow</sub> is nearly a constant (Figure ##FIG##1##2d##). Following the convention, the fast component is dominated by the EPC, and the slow component is mainly connected to the PPS. <sup>[</sup>\n##UREF##1##\n2\n##, ##REF##27015504##\n3\n##, ##UREF##2##\n4\n##\n<sup>]</sup> Such assignment is based on the characteristic interaction times for different processes (Figure ##SUPPL##0##S5##, Supporting Information),<sup>[</sup>\n##UREF##13##\n19\n##\n<sup>]</sup> which is experimentally tested true and consistent in previous investigations. From the fast component, we can obtain the explicit value of the EPC strength <italic toggle=\"yes\">λ</italic>.</p>", "<title>Obtaining the EPC Strength <italic toggle=\"yes\">λ</italic>\n</title>", "<p>In a recent work,<sup>[</sup>\n<sup>4]</sup> we developed a method to obtain <italic toggle=\"yes\">λ</italic> by the fluence dependence of the fast component, for which the advantages are two‐folded: 1) one can obtain the EPC strength <italic toggle=\"yes\">λ</italic> at room temperature, which usually does not vary much with temperature, and 2) one can circumvent the frequently encountered dilemma that the light penetration depth and the heat capacity coefficient of a material are usually unavailable. The initial work<sup>[</sup>\n##UREF##19##\n28\n##\n<sup>]</sup> is developed for low temperature and medium‐high fluence regime. Later on, we have developed a more comprehensive version, which is extended to room temperature (thus easier to implement) and can also be applied to medium‐high fluence regime.<sup>[</sup>\n##UREF##2##\n4\n##\n<sup>]</sup> We name this model as fluence‐dependence model (FDM).<sup>[</sup>\n##UREF##2##\n4\n##, ##UREF##19##\n28\n##\n<sup>]</sup> The FDM is indeed derived from the Allen model.<sup>[</sup>\n##UREF##20##\n29\n##\n<sup>]</sup> There have also been several other sophisticated discussions and models along this direction.<sup>[</sup>\n##UREF##21##\n30\n##, ##REF##21231613##\n31\n##, ##UREF##22##\n32\n##, ##UREF##23##\n33\n##\n<sup>]</sup> In our FDM approach, the value of <italic toggle=\"yes\">λ</italic> is related to the fast component lifetime <italic toggle=\"yes\">τ</italic>\n<sub>fast</sub> by \nwhere <italic toggle=\"yes\">k<sub>B</sub>\n</italic> is the Boltzmann constant, <italic toggle=\"yes\">T<sub>L</sub>\n</italic> is the lattice temperature, Ω is the angular frequency of the phonon (usually optical phonon<sup>[</sup>\n##UREF##24##\n34\n##\n<sup>]</sup>), and Θ is an effective absorption coefficient of fluence (when a laser beam of fluence <italic toggle=\"yes\">F</italic> is incident on the sample, the electron temperature increases from the equilibrium temperature <italic toggle=\"yes\">T<sub>L</sub>\n</italic> to <mml:math id=\"jats-math-7\" display=\"inline\"><mml:mrow><mml:msqrt><mml:mrow><mml:msubsup><mml:mi>T</mml:mi><mml:mi>L</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>+</mml:mo><mml:mi mathvariant=\"normal\">Θ</mml:mi><mml:mi>F</mml:mi></mml:mrow></mml:msqrt></mml:mrow></mml:math>). At medium‐high fluence regime whereby the sample assumes the non‐thermal regime (i.e., the density of photocarriers is proportional to the fluence, see the inset of Figure ##FIG##0##1a##), Θ is a constant.</p>", "<p>Using the equation of FDM, the fitting curve compares well with the experimental results at various fluences [Figure ##FIG##1##2b##]. We obtain that <italic toggle=\"yes\">λ</italic>˂Ω<sup>3</sup>&gt;/&lt;Ω&gt; = 294.9 ± 25.4 ps<sup>−2</sup> (i.e., 129.3 ± 11.1 meV<sup>2</sup>). Usually, we take the lowest energy optical phonon mode as an example to obtain the nominal EPC strength for a quantum material. For our LaCoO<sub>3</sub>/SrTiO<sub>3</sub> sample, it has four <italic toggle=\"yes\">E</italic>\n<sub>g</sub> modes, where the lowest energy <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode is the lowest energy optical phonon mode (<italic toggle=\"yes\">E</italic>\n<sub>g</sub>) for the material. The second highest energy <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode is related to the orbital‐phonon coupling and the Jahn–Teller distortion.<sup>[</sup>\n##REF##15524742##\n35\n##\n<sup>]</sup> Still, in the Raman result, the second lowest <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode is much more prominent than the lowest energy <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode, and it is the second lowest energy optical phonon mode (another <italic toggle=\"yes\">A</italic>\n<sub>gg</sub> mode is silent).<sup>[</sup>\n##UREF##25##\n36\n##\n<sup>]</sup> We take the second lowest <italic toggle=\"yes\">E</italic>\n<sub>g</sub> mode (with a frequency of 175.3 cm<sup>−1 [</sup>\n##REF##15524742##\n35\n##, ##UREF##25##\n36\n##, ##UREF##26##\n37\n##\n<sup>]</sup>) to be the characteristic phonon mode to obtain the nominal EPC strength. In such a way, we obtain <italic toggle=\"yes\">λ<sub>E</sub>\n</italic>\n<sub>g</sub> = 0.30. Note that the EPC strength of LaCoO<sub>3</sub>/SrTiO<sub>3</sub> we obtain here is close to those of superconducting oxides YBa<sub>2</sub>Cu<sub>3</sub>O<sub>6.5</sub> (<italic toggle=\"yes\">λ</italic> ≥ 0.25) and La<sub>1.85</sub>Sr<sub>0.15</sub>CuO<sub>4</sub> (<italic toggle=\"yes\">λ</italic> ≥ 0.5).<sup>[</sup>\n##REF##21231613##\n31\n##\n<sup>]</sup> The <italic toggle=\"yes\">λ</italic> = 0.30 is a regular EPC value, in the middle of the various EPC values reported. Such an EPC strength is enough to cause significant Jahn–Teller distortion.<sup>[</sup>\n##UREF##9##\n12\n##, ##UREF##10##\n15\n##\n<sup>]</sup>\n</p>", "<title>Coherent Phonon in Thin Film LaCoO<sub>3</sub>/SrTiO<sub>3</sub>\n</title>", "<p>Furthermore, as seen in Figure ##FIG##0##1b##, there is a coherent oscillation that is unambiguously observed in our fluence‐dependent Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub> signal. We re‐plot one of the signals (with the fluence of 1.41 mJ cm<sup>−2</sup>) in <bold>Figure</bold>\n##FIG##2##\n3a##. Here, Figure ##FIG##2##3a## shows the data with a longer temporal range than that of Figure ##FIG##0##1##. The data at a relatively longer time scale are fitted by a red wavy curve using a decaying cosine function, which corresponds to the phonon term in Equation (##FORMU##0##1##). A regular periodic oscillation is clearly seen. The inset of Figure ##FIG##2##3a## provides a closer zoom‐in view of the oscillation and the fitting curve compares well with the data. A broad hump is observed at the 4–30 ps range, which is not a part of the coherent phonon oscillation, due to the opposite phase. Previous investigations in cobalt perovskite had assigned it to the propagation of the photo‐induced metallic domain.<sup>[</sup>\n##REF##19659241##\n38\n##, ##UREF##27##\n39\n##\n<sup>]</sup> In this work we mainly focus on the coherent phonon, rather than this hump.</p>", "<p>In Figures ##FIG##2##3b‐d##, we present the quantitative analysis of the coherent phonon. To better reveal the coherent oscillation, we subtract the photo‐carriers relaxation from the Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub> signal. The coherent oscillations at different fluences are illustrated in Figure ##FIG##2##3b##, which are offset for clarity. Each experimental oscillation trace is fitted by the decaying cosine function in Equation (##FORMU##0##1##). All the values of <italic toggle=\"yes\">A</italic>\n<sub>phonon</sub>, <italic toggle=\"yes\">τ</italic>\n<sub>phonon</sub>, <italic toggle=\"yes\">φ</italic>, and Ω (see Equation (##FORMU##0##1##)) are obtained through the data fitting in Figure ##FIG##2##3b##. The phonon frequency Ω is shown in Figure ##FIG##2##3c##, whose average value is 45.3 GHz, nearly unchanged even up to the high fluence regime whereby the thermal effect inaugurates. The value of the phonon frequency is much smaller than a regular optical phonon frequency. We attribute it to be a coherent acoustic phonon, which is generated by the transient thermal strain induced by the ultrafast light pulses.<sup>[</sup>\n##REF##25031087##\n24\n##, ##UREF##28##\n40\n##, ##UREF##29##\n41\n##\n<sup>]</sup> Here the phonon frequency is independent of the film thickness (Figure ##SUPPL##0##S8##, Supporting Information).<sup>[</sup>\n##REF##25031087##\n24\n##, ##UREF##30##\n42\n##\n<sup>]</sup> The phonon amplitudes <italic toggle=\"yes\">A</italic>\n<sub>phonon</sub> are summarized in Figure ##FIG##2##3d##, which increase linearly with fluence. Thus, unlike that for the photo‐carriers dynamics (Figure ##FIG##0##1a## and Figure ##FIG##1##2a##), no prominent saturation on coherent phonons is observed in the thermal effect regime. This indicates the lattice does not experience irreversible damage by shining the ultrafast light pulses on. Similar property has also been found in other materials (e.g., in Cd<sub>3</sub>As<sub>2</sub>\n<sup>[</sup>\n##UREF##16##\n25\n##\n<sup>]</sup>).</p>", "<p>Significantly, we investigate the effect of the substrate on the photo‐carriers relaxation dynamics by comparing the ultrafast dynamics of two different samples. In the control experiment, the second sample is a 40 nm thickness LaCoO<sub>3</sub> on a (100) LaAlO<sub>3</sub> substrate. The pump and probe beam fluences are 0.86 and 0.14 mJ cm<sup>−2</sup>, respectively. The dynamics we obtain is shown in <bold>Figure</bold>\n##FIG##3##\n4a##, which is normalized to compare with that of the LaCoO<sub>3</sub>/SrTiO<sub>3</sub> sample. The data for LaCoO<sub>3</sub>/SrTiO<sub>3</sub> are obtained under a pump fluence of 0.91 mJ cm<sup>−2</sup> and a probe fluence of 0.13 mJ cm<sup>−2</sup>, which are nearly identical to those for the LaCoO<sub>3</sub>/LaAlO<sub>3</sub> sample. In the longer temporal range, the dynamics of these two samples exhibit an apparent difference. However, for the shorter temporal range, the dynamics for the two samples nearly overlap in the initial range (see the inset of Figure ##FIG##3##4a## for better revealed the ultrafast relaxation at initial stage). This indicates that the fast and slow components behave in a different way. To better illaustrate the data, following the aforementioned procedures (Equation (##FORMU##0##1##)), we display the fast and slow components for both samples in Figure ##FIG##3##4b##, along with a normalized version in its inset. The solid curves are fast components and the dashed curves are slow components. The fast components for the two samples are nearly overlapped; as a contrast, the slow components for the two samples are clearly different. While the lifetime <italic toggle=\"yes\">τ</italic>\n<sub>fast</sub> = 0.17 ± 0.03 ps is nearly identical for both samples (<italic toggle=\"yes\">τ</italic>\n<sub>fast</sub> for the LaCoO<sub>3</sub>/SrTiO<sub>3</sub> sample is 0.18 ps (Figure ##FIG##1##2b##), the lifetime <italic toggle=\"yes\">τ</italic>\n<sub>slow</sub> = 0.67 ± 0.18 ps is different from that for the other sample (<italic toggle=\"yes\">τ</italic>\n<sub>slow</sub> = 0.90 ± 0.17 ps (Figure ##FIG##1##2d##) for the LaCoO<sub>3</sub>/SrTiO<sub>3</sub> sample). These results indicate that the EPC strength for the two samples is very close; however, the PPS rate in LaCoO<sub>3</sub>/SrTiO<sub>3</sub> is noticeably lower than in LaCoO<sub>3</sub>/LaAlO<sub>3</sub>.</p>", "<p>In the control experiment, we follow the same procedure to analyze the coherent acoustic phonon in the LaCoO<sub>3</sub>/LaAlO<sub>3</sub> sample. The oscillations were obtained by subtracting the photo‐carriers relaxation in Figure ##FIG##3##4a##, and are presented in Figure ##FIG##3##4c##, both fitted with cosine decaying functions. The frequency domain results are obtained through Fast Fourier Transformation (FFT) (see Figure ##FIG##3##4d##). Interestingly, the two frequency domain peaks are located at 33.3 (for LaCoO<sub>3</sub>/LaAlO<sub>3</sub>) and 45.6 GHz (for LaCoO<sub>3</sub>/SrTiO<sub>3</sub>), respectively. While these two values are different, we find that the value for LaCoO<sub>3</sub>/LaAlO<sub>3</sub> is in well agreement with that in Fe<sub>2</sub>O<sub>3</sub>/LaAlO<sub>3</sub>,<sup>[</sup>\n##UREF##31##\n43\n##\n<sup>]</sup> and that for LaCoO<sub>3</sub>/SrTiO<sub>3</sub> is in agreement with that in Fe<sub>2</sub>O<sub>3</sub>/SrTiO<sub>3</sub> and LaRhO<sub>3</sub>/SrTiO<sub>3</sub>.<sup>[</sup>\n##UREF##30##\n42\n##, ##UREF##31##\n43\n##\n<sup>]</sup>\n</p>" ]
[ "<title>Discussion</title>", "<p>We summarize a few typical reported coherent acoustic phonon frequencies in oxides thin films, as well as in some semiconductor thin films, in <bold>Table</bold>\n##TAB##0##\n1\n##. All these values are obtained at room temperature and probed with 800 nm light pulses. From the table, the coherent acoustic phonon frequency is nearly identical for samples with identical substrates, regardless of the material of the thin films. This indicates that the coherent acoustic phonons are all mainly generated in the substrate. Note that for Figure ##FIG##2##3b## by sample we mean the whole heterostructure including the film and substrate. All these results are in consensus with each other, indicating that the coherent acoustic phonons are mainly determined by the substrate. It is very plausible that the coherent acoustic phonons are generated (especially at a few atomic layers in the substrate nearby the interface) and detected in the substrates (Figure ##SUPPL##0##S9##, Supporting Information). The penetration depth of LaCoO<sub>3</sub> is reported to be 110 nm,<sup>[</sup>\n##UREF##32##\n44\n##\n<sup>]</sup> which allows for the prominent transmission through a 40 nm thick thin film. In such a scenario, the pump pulse generates a transient thermal strain, producing longitudinal temperature gradients that spread at the interface between the film and substrate to generate the coherent acoustic phonon.<sup>[</sup>\n##UREF##28##\n40\n##, ##UREF##33##\n45\n##\n<sup>]</sup> Note that the coherent acoustic phonon in a bare SrTiO<sub>3</sub> substrate is not easy to observe.<sup>[</sup>\n##UREF##30##\n42\n##\n<sup>]</sup> Usually, one needs the interference between the reflections from the surface and the strain wave to detect the coherent acoustic phonon (Figure ##SUPPL##0##S9##, Supporting Information).<sup>[</sup>\n##UREF##30##\n42\n##\n<sup>]</sup>\n</p>", "<p>We schematically illustrate the scenario underlying the whole process in <bold>Figure</bold>\n##FIG##4##\n5\n##. The photo‐carriers are excited to the excited states and then relax through the coupling with optical phonons in the thin films (not mainly in the substrate).<sup>[</sup>\n##UREF##2##\n4\n##, ##UREF##24##\n34\n##\n<sup>]</sup> Energy is exchanged between the photo‐carriers and the thin film crystal lattice. Consequently, the thin film lattice absorbs the energy from the photo‐carriers, generating a vast quantity of non‐equilibrium optical phonons, which relax mainly through PPS, decaying into lower energy acoustic phonons. The deviation in the PPS rate in LaCoO<sub>3</sub>/SrTiO<sub>3</sub> and LaCoO<sub>3</sub>/LaAlO<sub>3</sub> suggests that this OP→AP relaxation process mainly occurs in the substrate, especially at the several atomic layers in the substrate nearby the interface, instead of the thin film. Note that the inset of Figure ##FIG##3##4b## shows a very similar EPC relaxation rate, indicating that strain<sup>[</sup>\n##REF##30778061##\n48\n##\n<sup>]</sup> does not affect EPC (Figure ##SUPPL##0##S6##, Supporting Information); also, possible effects caused by interfacial structural configuration or band alignment<sup>[</sup>\n##UREF##36##\n49\n##, ##UREF##37##\n50\n##\n<sup>]</sup> will be masked by our LaCoO<sub>3</sub> 40 nm thick film, thus becoming negligible (Figure ##SUPPL##0##S7##, Supporting Information).</p>", "<p>Assuming that it is other than the above scenario—supposing the EPC and PPS occur both in the thin film or substrate, we should observe nearly identical <italic toggle=\"yes\">τ</italic>\n<sub>fast</sub> and <italic toggle=\"yes\">τ</italic>\n<sub>slow</sub> in the control experiment, which is apparently not the fact. Hence, we conclude that the EPC and PPS are spatially separated by the interface. This scenario is also confirmed by the distinctive coherent acoustic phonons observed in samples with distinctive substrates. Owing to such a scenario, the OP→AP decaying process inevitably penetrates the interface, which is in line with the longitudinal nature of the acoustic phonons.<sup>[</sup>\n##REF##25031087##\n24\n##, ##UREF##16##\n25\n##\n<sup>]</sup> As a result, the penetration and annihilation/creation of phonons perpendicular to the interface<sup>[</sup>\n##REF##27015504##\n3\n##, ##REF##30822064##\n51\n##, ##UREF##38##\n52\n##, ##REF##30770805##\n53\n##\n<sup>]</sup> naturally occur. A temporal evolution for the ultrafast processes is depicted in the caption.</p>" ]
[]
[ "<title>Abstract</title>", "<p>Electron–phonon coupling (EPC) and phonon–phonon scattering (PPS) are at the core of the microscopic physics mechanisms of vast quantum materials. However, to date, there are rarely reports that these two processes can be spatially separated, although they are usually temporally detached with different characteristic lifetimes. Here, by employing ultrafast spectroscopy to investigate the photo‐carrier ultrafast dynamics in a LaCoO<sub>3</sub> thin film on a (100) SrTiO<sub>3</sub> substrate, intriguing evidence is found that the two interactions are indeed spatially separated. The EPC mainly occurs in the thin film, whereas PPS is largely in the substrate, especially at the several atomic layers near the interface. Across‐interface penetration and decay of optical phonons into acoustic phonons thus naturally occur. An EPC strength <italic toggle=\"yes\">λ<sub>Eg</sub>\n</italic> = 0.30 is also obtained and an acoustic phonon mode at 45.3 GHz is observed. The finding lays out a cornerstone for future quantum nano device designs.</p>", "<p>Electron–phonon coupling (EPC) and phonon‐phonon scattering (PPS) are at the core of the microscopic physics mechanisms of vast quantum materials. Here, evidence of spatially separated EPC and PPS is unveiled by using ultrafast spectroscopy on a 40 nm LaCoO<sub>3</sub> thin films grown on SrTiO<sub>3</sub> substrate. The EPC mainly occurs in thin film and the PPS occurs largely in the substrate, especially at the several atomic layers in the substrate nearby the interface.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6841-cit-0054\">\n<string-name>\n<given-names>W.</given-names>\n<surname>Hao</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Gu</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Tian</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Fu</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Meng</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Guo</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Zhao</surname>\n</string-name>, <article-title>Separated Electron–Phonon and Phonon–Phonon Scatterings Across Interface in Thin Film LaCoO<sub>3</sub>/SrTiO<sub>3</sub>\n</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305900</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305900</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Summary</title>", "<p>In summary, we investigate the ultrafast dynamics of LaCoO<sub>3</sub>/SrTiO<sub>3</sub> and perform the control experiment with a LaCoO<sub>3</sub>/LaAlO<sub>3</sub> sample. By the lifetime of the fast photo‐carriers relaxation component, we obtain the EPC strength in the LaCoO<sub>3</sub> thin film to be <italic toggle=\"yes\">λ</italic>˂Ω<sup>3</sup>&gt;/&lt;Ω&gt; = 129.3 ± 11.1 meV<sup>2</sup>, which corresponds to a nominal EPC strength of <italic toggle=\"yes\">λ<sub>E</sub>\n</italic>\n<sub>g</sub>  = 0.30. A coherent acoustic phonon mode with a frequency of 45.3 GHz is also generated and detected. We attribute it to light pulse‐induced thermal strain. Intriguingly, through the control experiment, we discover that the EPC mainly occurs in the thin film and the PPS is dominated by the substrate, especially at the several atomic layers in the substrate nearby the interface, whereby the optical phonons penetrate across the interface to decay into acoustic phonons. Our findings reveal a rarely observed/reported phenomena that can hardly be detected by any other experimental means, and lays down an important physics mechanism foundation for the relevant future designs of quantum nano devices.</p>", "<title>Experimental Section</title>", "<p>Ultrafast laser pulses with 800 nm central wavelength, 70 fs pulse duration, and 250 kHz repetition rate were used. The spot diameters of the pump and probe beams were 60 and 55 µm, respectively, on the sample surface. The pump fluence ranges from 0.16 to 4.81 mJ cm<sup>−2</sup>, while the probe fluence was kept at 0.13 mJ cm<sup>−2</sup>. The fluences <italic toggle=\"yes\">F</italic> were obtained through <italic toggle=\"yes\">F</italic>= 4<italic toggle=\"yes\">W</italic>/<italic toggle=\"yes\">R<sub>r</sub>\n</italic>π<italic toggle=\"yes\">d</italic>\n<sup>2</sup>, where <italic toggle=\"yes\">W</italic> was the laser beam power, <italic toggle=\"yes\">R<sub>r</sub>\n</italic> was the repetition rate of the laser, and <italic toggle=\"yes\">d</italic> was the beam spot diameter. Cross‐polarization detection was implemented in order to reduce noise. We conducted all the experiments at room temperature (i.e., 298 K).</p>", "<p>Our samples were grown by using the pulsed laser deposition method, where two ≈100 unit‐cell‐thick (approximately 40 nm) LaCoO<sub>3</sub> films were grown on twin‐polished SrTiO<sub>3</sub>(100) and LaAlO<sub>3</sub>(100) substrates, respectively. The oxygen partial pressure was optimized at 15 Pa and the growth temperature was 670 °C. After in‐situ annealing for 1 h, the samples were cooled down to room temperature under the same oxygen pressure (15 Pa). The substrates were 5 × 5 × 0.5 mm<sup>3</sup> in volume. The general grown method, X‐ray diffraction, and reflection high‐energy electron diffraction characterizations were presented in Supporting Information, Figure ##SUPPL##0##S1##. Our magnetic and electrical characterizations shown that there was no prominent oxygen vacancy (or in‐gap state) in the SrTiO<sub>3</sub>(100) and LaAlO<sub>3</sub>(100) substrates (Figure ##SUPPL##0##S3## Supporting Information ##SUPPL##1##S1##).</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>J.Z. conceived the idea and supervised the project. W.H. and J.Z. conducted the ultrafast spectroscopy experiment. M.G., M.M., and J.G. fabricated the sample and did the characterization. W.H., Z.T., S.F., and J.Z. analyzed the data. With constructive inputs from H.Z. and J.G., W.H. prepared the draft and J.Z. wrote the paper.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was supported by the National Key Research and Development Program of China (Grant Nos. 2021YFA1400201 and 2017YFA0303600), the CAS Project for Young Scientists in Basic Research (Grant No. YSBR‐059), the Beijing Natural Science Foundation (Grant No. 4191003), the National Natural Science Foundation of China (Grant Nos. 11774408 and 11974253), the Strategic Priority Research Program of CAS (Grant No. XDB30000000), the International Partnership Program of Chinese Academy of Sciences (Grant No. GJHZ1826), and CAS Interdisciplinary Innovation Team.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6841-fig-0001\"><label>Figure 1</label><caption><p>Relative transient differential reflectivity of LaCoO<sub>3</sub>/SrTiO<sub>3</sub>. a) Fluence‐dependent relative differential reflectivity Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub>. Solid curves: fitting results using Equation (##FORMU##0##1##). The arrow marks the increase in pump fluence. Inset: fluence‐dependence of |Δ<italic toggle=\"yes\">R</italic>/<italic toggle=\"yes\">R</italic>\n<sub>0</sub>|<sub>max</sub>. Blue and pink colors: non‐thermal and thermal effect regimes. Solid line: linear fit. b) Normalized Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub>. Inset: zoom‐in view of the normalized signal Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub>.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6841-fig-0002\"><label>Figure 2</label><caption><p>Fluence‐dependence of the amplitudes and lifetimes. Quantitatively obtained fitting results: a) <italic toggle=\"yes\">A</italic>\n<sub>fast</sub>, b) <italic toggle=\"yes\">τ</italic>\n<sub>fast</sub>, c) <italic toggle=\"yes\">A</italic>\n<sub>slow</sub>, and d) <italic toggle=\"yes\">τ</italic>\n<sub>slow</sub>. Solid curve in b): Fitted curve using a FDM<sup>[</sup>\n##UREF##2##\n4\n##\n<sup>]</sup> of obtaining the EPC strength at room temperature.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6841-fig-0003\"><label>Figure 3</label><caption><p>Pump fluence dependence of the coherent phonon oscillation. a) Ultrafast photo‐carriers relaxation dynamics under 1.41 mJ cm<sup>−2</sup> pump fluence. Red wave: fitting curve of the coherent phonon oscillation with relaxation. b) Coherent phonon oscillation at different fluences (data are offset for clarity). Solid curves: decaying cosine functions. c,d) Fluence dependence of the phonon frequency and amplitude. Dark red lines: constant and linear fits to the data.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6841-fig-0004\"><label>Figure 4</label><caption><p>Photo‐carriers relaxation dynamics of LaCoO<sub>3</sub>/SrTiO<sub>3</sub> and LaCoO<sub>3</sub>/LaAlO<sub>3</sub>. a) Normalized differential reflectivity Δ<italic toggle=\"yes\">R/R</italic>\n<sub>0</sub> under close pump and probe fluences. Inset: zoom‐in view for initial temporal range. b) The fitting components for fast and slow components in the inset of 5a. Inset: Normalized components. c) Coherent phonon oscillation with cosine decay fitting (offset for clarity). d) Fourier transformation of the oscillations. Note, for LaCoO<sub>3</sub>/SrTiO<sub>3</sub>, the pump fluence is 0.91 mJ cm<sup>−2</sup> and the probe fluence is 0.13 mJ cm<sup>−2</sup>.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6841-fig-0005\"><label>Figure 5</label><caption><p>Schematic illustration of the separated EPC and PPS processes across the interface. The vibrational balls depict the real‐space atomic position fluctuations. OP: optical phonons; AP: acoustic phonons. The pump laser pulses instantly generate excited state photo‐carriers (within femtoseconds), which then excite optical phonons mainly within the thin film (with a typical interaction lifetime of 0.15–0.25 ps, see Figure ##FIG##1##2##). Concomitantly, these optical phonons annihilate to create acoustic phonons mainly within the substrate, especially at the several atomic layers in the substrate nearby the interface (with a characteristic interaction lifetime of 0.8–1.2 ps, see Figure ##FIG##1##2##). Such a process naturally involves the penetration of phonons across the interface.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6841-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Coherent acoustic phonon frequencies in various oxide and semiconductor thin film samples (from this work and adapted from<sup>[</sup>\n##UREF##30##\n42\n##, ##UREF##31##\n43\n##, ##UREF##34##\n46\n##, ##UREF##35##\n47\n##\n<sup>]</sup>).</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Sample</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Phonon frequency [GHz]</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LaRhO<sub>3</sub>/SrTiO<sub>3</sub>(110)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">45<sup>[</sup>\n##UREF##30##\n42\n##\n<sup>]</sup>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LaCoO<sub>3</sub>/SrTiO<sub>3</sub>(100)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">45.3<sup>[this work]</sup>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fe<sub>2</sub>O<sub>3</sub>/SrTiO<sub>3</sub>(100)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">44.7<sup>[</sup>\n##UREF##31##\n43\n##\n<sup>]</sup>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fe<sub>2</sub>O<sub>3</sub>/BaTiO<sub>3</sub>(100)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">30.9<sup>[</sup>\n##UREF##31##\n43\n##\n<sup>]</sup>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LaCoO<sub>3</sub>/LaAlO<sub>3</sub>(100)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">33.3<sup>[this work]</sup>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fe<sub>2</sub>O<sub>3</sub>/LaAlO<sub>3</sub>(100)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">33.9<sup>[</sup>\n##UREF##31##\n43\n##\n<sup>]</sup>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">LaRhO<sub>3</sub>/(LaAlO<sub>3</sub>)<sub>0.3</sub>(Sr<sub>2</sub>TaAlO<sub>6</sub>)<sub>0.7</sub>(110)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">35.05<sup>[</sup>\n##UREF##30##\n42\n##\n<sup>]</sup>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">GaSb/GaAs</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">43<sup>[</sup>\n##UREF##34##\n46\n##\n<sup>]</sup>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Co<sub>2</sub>MnAl/GaAs</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">43.5<sup>[</sup>\n##UREF##35##\n47\n##\n<sup>]</sup>\n</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
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[ "<supplementary-material id=\"advs6841-supinfo-0001\" position=\"float\" content-type=\"local-data\"/>", "<supplementary-material id=\"advs6841-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6841-tbl1-note-0001\"><p>The phonon frequencies in samples with identical substrates exhibit close values, not depending on the thin film material. Identical thin films on different substrates exhibit different frequency values. These facts indicate that the acoustic phonons are dominated by the substrates.</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2305900-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
53
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2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 20; 11(2):2305900
oa_package/b5/30/PMC10787100.tar.gz
PMC10787101
37957540
[ "<title>Introduction</title>", "<p>Liver fibrosis is a common feature of chronic liver diseases, associated with advanced disease progression and poor prognosis. Unless effectively treated, fibrosis tends to develop into cirrhosis and subsequently into liver failure, requiring transplantation.<sup>[</sup>\n##REF##31590120##\n1\n##\n<sup>]</sup> The underlying etiologies of liver fibrosis include hepatitis B and C infections, alcohol abuse, non‐alcoholic fatty liver disease (NAFLD), and cholestatic injury.<sup>[</sup>\n##REF##34923653##\n2\n##\n<sup>]</sup> Hepatic stellate cells (HSCs) play a crucial role in the development of fibrotic processes as they possess the ability to undergo activation and trans‐differentiation into myofibroblast‐like cells. These cells are a primary source of the extracellular matrix (ECM).<sup>[</sup>\n##REF##28487545##\n3\n##\n<sup>]</sup> The activation of HSCs involves a complex interaction with other resident cells and their secreted profibrotic mediators, including chemokines, growth factors, reactive oxygen species, and metabolic products.<sup>[</sup>\n##UREF##0##\n4\n##\n<sup>]</sup> Although numerous studies have contributed to our understanding of the pathogenesis of liver fibrosis, the intercellular crosstalk between dysregulated hepatocyte metabolism and HSC activation remains unclear.</p>", "<p>Bile acids (BAs) are the end products of cholesterol catabolism in hepatocytes. They are known for liver cholesterol secretion and intestine lipid absorption.<sup>[</sup>\n##REF##35165436##\n5\n##\n<sup>]</sup> However, dysregulated BAs homeostasis may result in chronic liver diseases.<sup>[</sup>\n##REF##34555862##\n6\n##\n<sup>]</sup> Recent studies have reported increased BAs levels with increasing fibrosis stage.<sup>[</sup>\n##REF##30506692##\n7\n##\n<sup>]</sup> The composition of BAs in patients with cirrhosis has been previously reported to be abnormal.<sup>[</sup>\n##REF##25964117##\n8\n##, ##REF##33754726##\n9\n##\n<sup>]</sup> The accumulation of BAs in the liver may lead to hepatocyte mitochondrial injury, cholangiocyte proliferation, or macrophage activation, which result in cholestatic liver injuries and inflammatory responses.<sup>[</sup>\n##REF##33987435##\n10\n##, ##REF##28120434##\n11\n##, ##REF##33724957##\n12\n##\n<sup>]</sup> Defects in specific genes involved in BAs metabolism contribute to chronic cholestatic liver fibrosis.<sup>[</sup>\n##REF##35229330##\n13\n##\n<sup>]</sup>\n</p>", "<p>Solute carrier family 27 member 5 (SLC27A5), also known as long‐chain fatty acid transport protein 5 (FATP5), is mainly expressed in the liver, specifically in the basement membrane of hepatocytes, where it participates in fatty acid transport.<sup>[</sup>\n##REF##16618416##\n14\n##\n<sup>]</sup> SLC27A5 exhibits bile acid‐CoA ligase (BAL) activity, which converts unconjugated BAs to their CoA thioester derivatives and catalyzes the conjugation of BAs with amino acids.<sup>[</sup>\n##REF##12454267##\n15\n##, ##REF##16618417##\n16\n##\n<sup>]</sup> Mice lacking SLC27A5 have shown to exhibit higher levels of unconjugated BAs and lower levels of conjugated BAs, as compared to normal mice.<sup>[</sup>\n##REF##16618417##\n16\n##, ##REF##21826528##\n17\n##\n<sup>]</sup> This is consistent with elevated unconjugated BAs observed in patients with genetic defects in SLC27A5.<sup>[</sup>\n##REF##22089923##\n18\n##, ##REF##23415802##\n19\n##\n<sup>]</sup> Silencing of SLC27A5 in mice corresponds to the high proportion of unconjugated BAs reported in these patients. Notably, a neonate with a homozygotic missense mutation in SLC27A5 was found to develop extensive liver fibrosis.<sup>[</sup>\n##REF##22089923##\n18\n##\n<sup>]</sup> Additionally, Enooku et al. demonstrated that lower SLC27A5 expression is associated with the progression of ballooning and fibrosis in patients with NAFLD.<sup>[</sup>\n##REF##31602526##\n20\n##\n<sup>]</sup> However, the specific mechanisms underlying SLC27A5 deficiency in liver fibrosis remain unclear.</p>", "<p>Therefore, we aimed to elucidate the role of SLC27A5 in regulating BAs conjugation during the progression of liver fibrosis. Furthermore, we monitored the effect of the lack of SLC27A5 in mice on the activation of HSCs and liver fibrosis and investigated the associated molecular mechanisms. We believe that our findings can provide mechanistic insights into the role of SLC27A5 in regulating liver fibrosis.</p>" ]
[]
[ "<title>Results</title>", "<title>SLC27A5 Expression is Downregulated in Human and Murine Liver Fibrosis</title>", "<p>To evaluate the role of SLC27A5 in the development of liver fibrosis, we analyzed <italic toggle=\"yes\">SLC27A5</italic> mRNA expression levels in normal and fibrotic liver biopsy samples from the Gene Expression Omnibus (GEO) database. We observed downregulation of hepatic <italic toggle=\"yes\">SLC27A5</italic> mRNA expression in patients with NAFLD coupled with fibrosis, non‐alcoholic steatohepatitis (NASH) with fibrosis, and cirrhosis, as displayed in <bold>Figure</bold>\n##FIG##0##\n1A##. We also observed a stepwise decrease in the level of SLC27A5 transcript from fibrosis stages 0 to 4 in a cohort of patients with hepatitis B virus (HBV)‐related liver fibrosis (Figure ##FIG##0##1A##). Analyzing the cirrhosis dataset (GSE25097) revealed that the expression of SLC27A5 was negatively correlated with that of fibrosis‐related genes such as <italic toggle=\"yes\">ACTA2</italic>, <italic toggle=\"yes\">COL1A1</italic>, and <italic toggle=\"yes\">COL3A1</italic> (Figure ##SUPPL##0##S1A##, Supporting Information). Consistently, human cirrhotic tissue samples (Figure ##FIG##0##1B##; Figure ##SUPPL##0##S1B,C##, Supporting Information) and mouse models of liver fibrosis induced by carbon tetrachloride (CCI<sub>4</sub>) and thioacetamide (TAA) (Figure ##SUPPL##0##S1D–I##, Supporting Information) also revealed reduced SLC27A5 expression compared with that in the control trials.</p>", "<p>To identify the putative transcription factors (TFs) responsible for the downregulation of SLC27A5 in liver fibrosis, we analyzed the potential promoter region of <italic toggle=\"yes\">SLC27A5</italic> using the JASPAR database considering the 2‐kb upstream sequence of the transcription start site of <italic toggle=\"yes\">SLC27A5</italic>.<sup>[</sup>\n##REF##34850907##\n21\n##\n<sup>]</sup> Further analysis helped identify five TFs (NR2C2, REST, RXRA, HNF4α, and RUNX2) that may bind to the <italic toggle=\"yes\">SLC27A5</italic> promoter region (Figure ##SUPPL##0##S2A,B##, Supporting Information). Notably, qRT‐PCR demonstrated a significant upregulation of <italic toggle=\"yes\">Runx2</italic> mRNA levels in CCI<sub>4</sub>‐induced fibrotic liver tissues of mice, whereas <italic toggle=\"yes\">Hnf4a</italic> and <italic toggle=\"yes\">Rest</italic> indicated only minor changes (Figure ##FIG##0##1C##). Additionally, substantially elevated RUNX2 expression was observed in the liver tissues of patients with cirrhosis and fibrosis model mice (Figure ##FIG##0##1D##; Figure ##SUPPL##0##S2C–F##, Supporting Information).</p>", "<p>Subsequently, we investigated whether RUNX2 was involved in the transcriptional regulation of SLC27A5. According to the prediction made using JASPAR, RUNX2 may bind the promoter of <italic toggle=\"yes\">SLC27A5</italic> at several possible sites (Figure ##FIG##0##1E##). To determine regulatory regions of RUNX2, the <italic toggle=\"yes\">SLC27A5</italic> promoter regions containing different RUNX2 binding sites were cloned into the pGL3 basic vector to perform luciferase reporter assay. We truncated the full‐length region of the <italic toggle=\"yes\">SLC27A5</italic> promoter into two fragments, −2023/+366 (pGL3‐P1) and −1001/+182 (pGL3‐P2) (Figure ##FIG##0##1E##). Notably, RUNX2 substantially decreased the activity of both <italic toggle=\"yes\">SLC27A5</italic> promoter fragments in the normal human liver cell line MIHA, which further indicates that SLC27A5 is transcriptionally inhibited by RUNX2 (Figure ##FIG##0##1F##). Chromatin immunoprecipitation assay confirmed the binding of RUNX2 to the <italic toggle=\"yes\">SLC27A5</italic> promoter (Figure ##FIG##0##1G##). RUNX2 overexpression significantly downregulated SLC27A5 expression in MIHA cells (Figure ##FIG##0##1H##), whereas the inhibition of RUNX2 by shRNA led to elevated expression of SLC27A5 (Figure ##FIG##0##1I##). These findings suggest that RUNX2 is responsible for the downregulation of SLC27A5.</p>", "<p>The upregulation of RUNX2 was verified in the cirrhosis, NAFLD, NASH and HBV‐related fibrosis datasets (Figure ##FIG##0##1J##; Figure ##SUPPL##0##S2G–I##, Supporting Information). <italic toggle=\"yes\">RUNX2</italic> expression was negatively correlated with <italic toggle=\"yes\">SLC27A5</italic> mRNA levels in cirrhotic tissues (GSE25097) (Figure ##FIG##0##1K##). These results indicate that the elevated expression of the repressor RUNX2 impairs SLC27A5 transcription in patients with liver fibrosis and mouse models.</p>", "<title>SLC27A5 Deficiency Induces Spontaneous Hepatic Fibrosis in 24‐Month‐Old Mice</title>", "<p>We used the CRISPR‐Cas9 system to generate whole‐body SLC27A5 knockout (<italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup>) mice by deleting the protein‐coding exons of <italic toggle=\"yes\">Slc27a5</italic> (Figure ##SUPPL##0##S3A##, Supporting Information) to investigate the loss‐of‐function effect of SLC27A5 in vivo. The genotypes of the mice were determined through PCR analysis of tail DNA (Figure ##SUPPL##0##S3B##, Supporting Information). The serum ALT, AST and ALP levels showed a mild increase in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice at 12 months compared to WT littermates (Figure ##SUPPL##0##S3C##, Supporting Information). The mRNA levels of inflammatory genes (<italic toggle=\"yes\">Tnfa</italic>, <italic toggle=\"yes\">Il6</italic>, <italic toggle=\"yes\">Il1b</italic>, <italic toggle=\"yes\">Ccl2</italic>, <italic toggle=\"yes\">Adgre1</italic>) were substantially upregulated in the livers of 12‐month‐old <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice (Figure ##SUPPL##0##S3D##, Supporting Information). These results indicated that <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice developed liver injury and inflammatory response at 12 months of age.</p>", "<p>We then maintained wild‐type (WT) and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice for 24 months and observed an increase in the size of gallbladders in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice (<bold>Figure</bold>\n##FIG##1##\n2A##). <italic toggle=\"yes\">SLC27A5</italic>\n<sup>−/−</sup> mice exhibited a significant increase in the liver‐to‐body weight ratio and elevated serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and total bilirubin (TBil) compared with that in WT littermates (Figure ##FIG##1##2B##; Figure ##SUPPL##0##S3E,F##, Supporting Information). Histological analysis using H&amp;E and Sirius red staining revealed mild collagen deposition in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice at 12 months old (Figure ##FIG##1##2C,D##). With aging, <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice displayed a massive diffuse ECM and pseudo‐lobular nodule formation at 18 and 24 months, respectively (Figure ##FIG##1##2C,D##). We observed that mRNA levels of profibrotic genes (<italic toggle=\"yes\">Acta2</italic>, <italic toggle=\"yes\">Col1a1</italic>, <italic toggle=\"yes\">Col3a1</italic>, <italic toggle=\"yes\">Timp1</italic>, and <italic toggle=\"yes\">Vim</italic>) and inflammatory genes were substantially upregulated in the livers of 24‐month‐old <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice (Figure ##FIG##1##2E,F##). Liver hydroxyproline (HYP) levels were also increased in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice (Figure ##SUPPL##0##S3G##, Supporting Information). Western blotting analysis demonstrated a significant increase in the expression of activated HSCs marker α‐SMA and collagen deposition markers COL1A1 and COL3A1 in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice liver tissues (Figure ##SUPPL##0##S3H##, Supporting Information). Furthermore, the expression levels of hepatic genes involved in bile acid synthesis, including <italic toggle=\"yes\">Cyp7a1</italic>, <italic toggle=\"yes\">Cyp8b1</italic>, and <italic toggle=\"yes\">Cyp27a1</italic>, were significantly increased in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice (Figure ##FIG##1##2G##). These findings demonstrate that <italic toggle=\"yes\">Slc27a5</italic> deficiency in mice induces spontaneous liver fibrosis at 24 months of age.</p>", "<title>SLC27A5 Deficiency Promotes Liver Fibrosis in Chemical‐Induced Fibrosis Murine Models</title>", "<p>To further examine the role of SLC27A5 in liver fibrosis, we investigated fibrogenesis in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice subjected to CCl<sub>4</sub> and TAA treatment. We observed an increase in the liver‐to‐body weight ratio in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice after six weeks of CCl<sub>4</sub> treatment (<bold>Figure</bold>\n##FIG##2##\n3A##; Figure ##SUPPL##0##S4A##, Supporting Information). Furthermore, H&amp;E, Sirius red staining, α‐SMA, and F4/80 immunostaining revealed elevated collagen deposition, fibrogenesis, and macrophage infiltration in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice (Figure ##FIG##2##3B,C##). Hydroxyproline measurements confirmed increased collagen deposition in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice (Figure ##SUPPL##0##S4B##, Supporting Information). Compared with WT mice, <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice displayed significantly higher levels of serum ALT, AST, ALP, and total bilirubin, indicating increased liver injury (Figure ##FIG##2##3D##; Figure ##SUPPL##0##S4C##, Supporting Information). The upregulation of profibrotic and inflammatory genes were also observed in the livers of <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice (Figure ##SUPPL##0##S4D–F##, Supporting Information). Eight weeks after TAA injection (Figure ##FIG##2##3E##), <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice demonstrated increased collagen deposition, α‐SMA expression, and liver injury (Figure ##FIG##2##3F–H##; Figure ##SUPPL##0##S4G–I##, Supporting Information). Similar to the CCl<sub>4</sub> treatment, the hepatic expression of profibrotic and inflammatory genes increased in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice compared with that in WT controls (Figure S##FIG##3##4J–L##, Supporting Information). These findings collectively suggest that SLC27A5 deficiency exacerbates liver fibrosis in mouse models.</p>", "<title>SLC27A5 Loss in Hepatocytes Promotes HSC Activation</title>", "<p>We compared the primary HSCs isolated from <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> and WT mice to assess their culture‐induced activation. The HSCs from <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice exhibited enhanced activation, as evidenced by changes in cell morphology, loss of lipid droplets, and a myofibroblast‐like appearance (<bold>Figure</bold>\n##FIG##3##\n4A##). The expression of fibrogenic marker genes was induced in these cells (Figure ##FIG##3##4B–D##). We further determined the sensitivity of <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> HSCs to the transforming growth factor β1 (TGFβ1), which is regarded as a critical factor in the HSCs activation. The primary HSCs derived from <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice displayed increased sensitivity to TGFβ1‐stimulated activation compared with that of WT HSCs (Figure ##SUPPL##0##S5A–C##, Supporting Information). These findings suggest that primary HSCs from <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice exhibit enhanced culture‐induced activation and increased sensitivity to TGFβ1 stimulation in vitro.</p>", "<p>The crosstalk between hepatocytes and HSCs generates a permissive fibrotic microenvironment that contributes to fibrosis.<sup>[</sup>\n##UREF##0##\n4\n##\n<sup>]</sup> Given that SLC27A5 mainly functions in hepatocytes,<sup>[</sup>\n##REF##16618416##\n14\n##\n<sup>]</sup> we first examined the expression of SLC27A5 in primary mouse hepatocytes (PMHs) and primary HSCs of WT mice, and observed that SLC27A5 was only expressed in PMHs but not in primary HSCs (Figure ##SUPPL##0##S5D##, Supporting Information). We next investigated the contribution of <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> PMHs to fibrotic progression. The WT or <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> PMH supernatant was added to a primary culture of WT mice HSCs for 48 h (Figure ##FIG##3##4E##). Our results demonstrated a significant up‐regulation of fibrogenic markers in WT HSCs exposed to <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> PMH supernatant (Figure ##FIG##3##4F–H##). Next, we performed a co‐culture experiment using a combination of the human HSC cell line LX‐2 and MIHA cells in a contact‐independent manner (Figure ##FIG##3##4I##). The increased expression of fibrogenic genes in LX‐2 cells co‐cultured with SLC27A5‐KO MIHA cells was similar to those observed earlier in this study (Figure ##FIG##3##4J,K##; Figure ##SUPPL##0##S5E,F##, Supporting Information). These findings indicate that the loss of SLC27A5 in hepatocytes contributes to HSC activation and increased sensitivity to fibrosis.</p>", "<title>Elevated Unconjugated Cholic Acid (CA) Activates HSCs in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> Mouse</title>", "<p>SLC27A5 is required for bile acid conjugation and plays an essential role in regulating BAs homeostasis in the liver.<sup>[</sup>\n##REF##32760200##\n22\n##\n<sup>]</sup> In this study, we observed an increase in unconjugated BAs, including cholic acid (CA), deoxycholic acid (DCA), and muricholic acid (MCA) in 6‐month‐old <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice liver tissues and serum (Figure ##SUPPL##0##S6A–D##, Supporting Information). Furthermore, analysis of the bile acid composition of 24‐month‐old <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice revealed a significant increase in CA and DCA (<bold>Figure</bold>\n##FIG##4##\n5A,B##), two major bile acids present in both mice and humans. The reported range of BA levels in human portal venous plasma or serum is 9—43 µм.<sup>[</sup>\n##REF##31616073##\n23\n##\n<sup>]</sup> To determine whether the elevated BAs in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice contribute to the activation of HSCs, we treated human HSC cell line LX‐2 with CA or DCA at concentrations of 25, 50, and 100 µм. Interestingly, CA treatment upregulated the expression of HSCs activation markers in a dose‐dependent manner (Figure ##FIG##4##5C##; Figure ##SUPPL##0##S6E,F##, Supporting Information). This was further confirmed in primary HSCs from WT mice treated with CA at 50 µм. (Figure ##FIG##4##5D–F##). However, DCA supplementation did not strongly affect LX‐2 activation (Figure ##SUPPL##0##S6G–H##, Supporting Information). The mRNA and protein expression of fibrogenic genes were also increased in primary HSCs from <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice after CA treatment (Figure ##SUPPL##0##S6I,J##, Supporting Information). Furthermore, the serum levels of CA, but not DCA, were significantly increased in patients with cirrhosis (Figure ##FIG##4##5G##). Consistent with these, CA levels were also higher in SLC27A5‐KO MIHA cells and primary mouse hepatocytes (PMHs) compared with that in controls (Figure ##FIG##4##5H,I##). Based on these observations, we concluded that the abnormal elevation of unconjugated CA in mouse models and patients with cirrhosis promotes HSC activation.</p>", "<p>To determine whether the inhibition of CA levels could diminish the activation of HSCs induced by the supernatant of <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> PMHs, WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice were treated with BSH‐IN‐1, a covalent pan‐inhibitor of gut bacterial bile salt hydrolases (BSHs),<sup>[</sup>\n##REF##32042200##\n24\n##\n<sup>]</sup> which decreased unconjugated bile acids (especially CA in Slc27a5<sup>−/−</sup> mice) in vivo (Figure ##SUPPL##0##S7A##, Supporting Information). Then, the supernatant was added to HSCs from normal WT mice (Figure ##SUPPL##0##S7B##, Supporting Information). The results suggested that the expression of profibrotic genes in primary HSCs was decreased by the treatment of conditional medium from primary PMHs of <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice with BSH‐IN‐1 gavage (Figure ##SUPPL##0##S7C##, Supporting Information). The CA levels were also decreased in the conditional medium of BSH‐IN‐1 group, whereas the TCA levels were increased in the same medium (Figure ##SUPPL##0##S7D,E##, Supporting Information). Taken together, these results indicate that inhibition of unconjugated CA levels could decrease the expression of profibrotic genes in primary HSCs co‐cultured with the supernatant of <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> PMHs.</p>", "<title>Cholic Acid‐Triggered Upregulation of Early Growth Response (EGR3) Promotes HSC Activation</title>", "<p>To investigate how CA induced the activation of HSCs, we performed RNA‐seq analysis on LX‐2 cells treated with CA at a concentration of 50 µм or vehicle controls. The treatment with CA effectively increased the expression of regulatory genes associated with fibrosis in LX‐2 cells (<bold>Figure</bold>\n##FIG##5##\n6A##). Among the upregulated genes in LX‐2 cells, we observed the most significant upregulation in the expression of pro‐fibrotic transcription factor EGR3 following CA treatment (Figure ##FIG##5##6B##). However, taurodeoxycholate (TDCA), DCA, or taurocholic acid (TCA) supplementation did not significantly affect EGR3 expression (Figure ##SUPPL##0##S8A##, Supporting Information). EGR3 is upregulated in the fibrotic dermis of mice with scleroderma, and increased EGR3 expression contributes to the upregulation of fibrotic genes such as <italic toggle=\"yes\">ACTA2</italic> and <italic toggle=\"yes\">COL1A1</italic>.<sup>[</sup>\n##REF##23906810##\n25\n##\n<sup>]</sup> To determine the role of EGR3 in CA‐induced activation of HSCs, we performed ChIP assay to confirm the binding of EGR3 on the promoter of <italic toggle=\"yes\">ACTA2</italic> and <italic toggle=\"yes\">COL1A1</italic> gene in LX‐2 cells. The data indicated that EGR3 could bind the promoter of <italic toggle=\"yes\">ACTA2</italic> and <italic toggle=\"yes\">COL1A1</italic> directly, and the recruitment of EGR3 on <italic toggle=\"yes\">ACTA2</italic> and <italic toggle=\"yes\">COL1A1</italic> promoter was increased by CA stimulation (Figure ##SUPPL##0##S8B##, Supporting Information). Based on these results, we investigated whether CA triggers HSC activation in an EGR3‐dependent manner. Treatment of LX‐2 cells with CA induced the expression of fibrotic genes. However, the induction of these genes was significantly compromised by EGR3 silencing (Figure ##FIG##5##6C,D##). Furthermore, immunofluorescence assays demonstrated that sh<italic toggle=\"yes\">EGR3</italic> treatment attenuated the CA‐induced expression of α‐SMA (Figure ##FIG##5##6E##). Notably, the upregulation of α‐SMA, COL1A1, and COL3A1 was similarly compromised by EGR3 silencing in primary mouse HSCs (Figure ##FIG##5##6F–H##). We also utilized the MIHA and LX‐2 cells to explore the role of EGR3. As displayed in Figure ##SUPPL##0##S8B–D## (Supporting Information), EGR3 silencing inhibited LX‐2 cell activation induced by SLC27A5‐KO MIHA cell co‐culture. Our findings thus indicate that CA‐induced HSCs activation depends on the transcription factor EGR3.</p>", "<title>Overexpression of SLC27A5 or Inhibition of Intestinal Bile Acid Absorption Ameliorates CCl<sub>4</sub>‐Induced Liver Fibrosis</title>", "<p>Based on our observations, we observed that SLC2A75 expression was downregulated in human and mouse liver fibrosis tissues (Figure ##FIG##0##1##). Furthermore, we noted that SLC27A5 deficiency promoted liver fibrosis (Figure ##FIG##2##3##). We thus hypothesize that SLC27A5 overexpression might protect against liver fibrosis. To test this hypothesis, specifically overexpressed SLC27A5 in the livers of WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> (KO) mice through tail vein injection of adeno‐associated virus (AAV) harboring <italic toggle=\"yes\">Slc27a5</italic> (AAV‐<italic toggle=\"yes\">Slc27a5</italic>) or AAV‐Control (AAV‐Con) in a CCl<sub>4</sub>‐induced liver fibrosis model (<bold>Figure</bold>\n##FIG##6##\n7A##). Concordantly, the re‐expression of SLC27A5 in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice alleviated collagen deposition, fibrosis, and liver injury (Figure ##FIG##6##7B–F## and Figure ##SUPPL##0##S9A–E##, Supporting Information). Both serum and liver CA accumulation was reduced in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice injected with AAV‐<italic toggle=\"yes\">Slc27a5</italic> (Figure ##FIG##6##7G,H##). Notably, WT mice with SLC27A5 overexpression exhibited a mild alleviation of liver fibrosis compared with those injected with AAV‐Control (Figure ##FIG##6##7B–E##). These results suggest that the AAV‐mediated restoration of hepatic SLC27A5 protects against CCl<sub>4</sub>‐induced liver fibrosis in mice.</p>", "<p>To further investigate the potential therapeutic strategies for liver fibrosis, we examined the effect of A4250, a specific ASBT inhibitor that decreases hepatic bile acid levels by inhibiting intestinal bile acid absorption,<sup>[</sup>\n##REF##35780808##\n26\n##\n<sup>]</sup> on CCl<sub>4</sub>‐induced liver fibrosis. We subjected WT and <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice to CCl<sub>4</sub> injection and treated them with A4250 through gavage (Figure ##FIG##6##7I##). After administering the A4250, we observed an evident improvement in liver fibrosis in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice (Figure ##SUPPL##0##S9F##, Supporting Information). Furthermore, the attenuation of hepatic collagen deposition and α‐SMA expression, along with the improvement of liver function, were evident in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice with A4250 administration (Figure ##FIG##6##7J–N##; Figure ##SUPPL##0##S9G–##J, Supporting Information). Moreover, both serum and liver CA levels were markedly decreased in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice following the A4250 treatment (Figure ##FIG##6##7O,P##). Overall, these findings suggest that the re‐expression of SLC27A5 or inhibition of CA accumulation ameliorates the pathogenesis of liver fibrosis, providing a potential strategy for treating this condition.</p>" ]
[ "<title>Discussion</title>", "<p>In the present study, we identified SLC27A5 as a novel regulator of liver fibrosis progression. Our findings demonstrate that the expression of SLC27A5 is diminished in the livers of cirrhotic patients and mice with liver fibrosis. Moreover, SLC27A5 deficiency aggravates the progression of liver fibrosis by activating hepatic stellate cells (HSCs) via the regulation of bile acid (BA) conjugation (<bold>Figure</bold> ##FIG##7##\n8\n##). These results provide important insights into the role of unconjugated BAs in liver fibrosis.</p>", "<p>The abnormal metabolism of BAs has been associated with various causes of liver fibrosis.<sup>[</sup>\n##REF##32498677##\n27\n##, ##REF##32243703##\n28\n##, ##UREF##1##\n29\n##\n<sup>]</sup> However, the specific roles of BAs metabolic enzymes in liver fibrosis have not been systematically explored. In our study, we observed that the expression of the bile acid‐CoA ligase SLC27A5 was decreased in patients with cirrhosis and fibrosis mouse models. A recent study found that SLC27A5 mRNA levels were upregulated in patients with NAFLD and a NAFLD rat model;<sup>[</sup>\n##REF##36851897##\n30\n##\n<sup>]</sup> however, SLC27A5 expression decreased as fibrosis progressed.<sup>[</sup>\n##REF##31602526##\n20\n##\n<sup>]</sup> Lower expression of Slc27a5 was related to chronic CCl<sub>4</sub>‐induced liver fibrosis.<sup>[</sup>\n##UREF##2##\n31\n##\n<sup>]</sup> Similarly, we previously suggested that SLC27A5 expression was downregulated in HCC tissues owing to DNA hypermethylation.<sup>[</sup>\n##REF##31367013##\n32\n##\n<sup>]</sup> This lower expression may be useful for predicting HCC prognosis.<sup>[</sup>\n##REF##33777129##\n33\n##\n<sup>]</sup> These findings suggest that the downregulation of SLC27A5 plays a vital role in disease progression, particularly in the development of liver fibrosis, cirrhosis, and HCC.<sup>[</sup>\n##REF##35124283##\n34\n##\n<sup>]</sup>\n</p>", "<p>The maintenance of BAs homeostasis is regulated by the farnesoid X receptor (FXR) via transcriptional repression of key enzymes involved in BAs synthesis, such as cholesterol 7α­hydroxylase (CYP7A1) and sterol 12α‐hydroxylase (CYP8B1).<sup>[</sup>\n##REF##34555862##\n6\n##\n<sup>]</sup>\n<italic toggle=\"yes\">SLC27A5</italic> mRNA expression was upregulated after FXR agonist GW4064 treatment.<sup>[</sup>\n##REF##30520052##\n35\n##\n<sup>]</sup> However, the underlying mechanisms of SLC27A5 downregulation in liver fibrosis remain unclear. In this study, we identified RUNX2 as a transcriptional repressor of SLC27A5. The RUNX2 is a master transcription factor in regulating osteoblast differentiation, angiogenesis, cancer metastasis, and, in particular, the fibrosis response.<sup>[</sup>\n##REF##32788656##\n36\n##, ##REF##37108164##\n37\n##, ##REF##27242197##\n38\n##\n<sup>]</sup> The upregulation of RUNX2 promotes aortic and pulmonary fibrosis.<sup>[</sup>\n##REF##26208651##\n39\n##, ##REF##28986417##\n40\n##\n<sup>]</sup> Several fibrosis‐related genes, such as <italic toggle=\"yes\">COL1A1</italic> and <italic toggle=\"yes\">TIMP1</italic>, are regulated by RUNX2.<sup>[</sup>\n##UREF##3##\n41\n##, ##REF##15051730##\n42\n##\n<sup>]</sup> Notably, putative RUNX2‐binding sites are localized in the <italic toggle=\"yes\">SLC27A5</italic> promoter, and SLC27A5 expression is repressed by RUNX2, which offers at least one underlying reason for SLC27A5 downregulation in patients with cirrhosis and mice with liver fibrosis. These findings suggest SLC27A5 as a potential diagnostic marker of liver fibrosis.</p>", "<p>Another important finding of this study was the physiological role of SLC27A5 in liver fibrosis. This finding is supported by several lines of evidence. The experimental <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice exhibited significantly increased collagen deposition and α‐SMA expression, with an abundance of unconjugated BAs in the serum and liver. This is consistent with a previous report of a child with a homozygous mutation in <italic toggle=\"yes\">SLC2A75</italic> who developed extensive fibrosis.<sup>[</sup>\n##REF##22089923##\n18\n##\n<sup>]</sup> Although SLC27A5 expression was not reduced in the liver biopsy, over 85% of the unconjugated BAs were present in the plasma of this child, leading us to speculate that the deficiency of BAs conjugation may result in liver fibrosis.</p>", "<p>Patients with disrupted BAs conjugation exhibited fat‐soluble vitamin deficiency, whereas some developed liver disease.<sup>[</sup>\n##REF##23415802##\n19\n##\n<sup>]</sup> Meanwhile, increased levels of DCA, an unconjugated bile acid from the gut microbiota, promote liver cancer through the senescence of HSCs.<sup>[</sup>\n##REF##23803760##\n43\n##\n<sup>]</sup> Elevated BAs levels induce cholestatic disease and fibrosis, which may be attributed to hepatocyte injury or cholangiopathy.<sup>[</sup>\n##REF##33987435##\n10\n##, ##REF##36899928##\n44\n##\n<sup>]</sup> However, the role of BAs in HSC activation has not been fully explored.</p>", "<p>TCA is significantly increased in patients with cirrhosis and promotes HSC activation.<sup>[</sup>\n##REF##29996772##\n45\n##, ##REF##36800698##\n46\n##\n<sup>]</sup> Increased levels of conjugated BAs such as TDCA and glycodeoxycholate (GDCA) in patients with NASH and fibrosis mouse models could also increase the protein expression of fibrosis‐related markers in LX‐2 cells.<sup>[</sup>\n##REF##33752128##\n47\n##\n<sup>]</sup> However, elevated serum BAs of normal composition may not lead to liver injury or fibrosis, which is supported by the fact that patients with Na<sup>+</sup>‐taurocholate co‐transporting polypeptide (NTCP) deficiency present with significantly elevated levels of conjugated BAs in the plasma without distinct clinical symptoms.<sup>[</sup>\n##REF##24867799##\n48\n##\n<sup>]</sup> In this study, we demonstrated that SLC27A5 knockout in mice substantially increased hepatic and serum‐unconjugated CA levels; this subsequently promoted HSC activation and liver fibrosis. Meanwhile, male C57BL/6J mice fed a chow diet supplemented with 0.5% (w/w) CA reportedly exhibit significant liver fibrosis.<sup>[</sup>\n##REF##35326188##\n49\n##\n<sup>]</sup> Although unconjugated DCA was also increased in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice, the DCA may not promote HSCs activation, which is consistent with the unchanged levels of DCA in cirrhotic patients as previously reported.<sup>[</sup>\n##REF##29996772##\n45\n##\n<sup>]</sup>\n</p>", "<p>Furthermore, attenuation of BA levels alleviated CCI<sub>4</sub>‐induced liver fibrosis in <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice. Bile acids are synthesized in the liver and secreted into the intestine to facilitate the absorption of lipophilic nutrients, with 95% of BAs being reabsorbed via the ASBT transporter.<sup>[</sup>\n##REF##35165436##\n5\n##\n<sup>]</sup> Thus, the interruption of ASBT has been suggested as a promising strategy to attenuate bile acid‐related diseases.<sup>[</sup>\n##REF##32201314##\n50\n##\n<sup>]</sup> Recently, the novel ASBT inhibitor A4250 has demonstrated promise in patients with progressive familial intrahepatic cholestasis.<sup>[</sup>\n##REF##34499340##\n51\n##, ##REF##35780807##\n52\n##\n<sup>]</sup> This study suggests that A4250 reduced CA levels and liver fibrosis progression in CCI<sub>4</sub>‐treated <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice. Although A4250 did not specifically reduce CA levels in mice, the presence of abundant CA in the liver and serum of <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice suggests that it can be an effective therapy. Hence, we conclude that SLC27A5 deficiency promotes liver fibrosis progression by upregulating unconjugated CA levels.</p>", "<p>Various BAs can induce the proliferation of activated rat HSCs via the epidermal growth factor receptor (EGFR) pathway. Notably, these bile acids did not affect the expression of collagen I.<sup>[</sup>\n##REF##15825085##\n53\n##\n<sup>]</sup> Furthermore, BAs stimulate the expression of early growth response (EGR) genes and protein kinase C signal transduction pathways in HSCs.<sup>[</sup>\n##REF##8670150##\n54\n##\n<sup>]</sup> However, the precise details and functions of this signaling mechanism are yet to be determined. The EGR family of transcription factors comprises four members that play a role in immune regulation.<sup>[</sup>\n##REF##20035903##\n55\n##\n<sup>]</sup> Notably, a specific member of this family, EGR3, reportedly modulates TGF‐β1 transcription in T cells.<sup>[</sup>\n##REF##33011290##\n56\n##\n<sup>]</sup> This member also exerts a profibrotic role in skin and cardiac fibroblasts by stimulating the expression of <italic toggle=\"yes\">ACTA2</italic> and <italic toggle=\"yes\">COL1A1</italic> genes.<sup>[</sup>\n##REF##23906810##\n25\n##, ##REF##36182775##\n57\n##\n<sup>]</sup> Our RNA‐seq data revealed a significant upregulation of EGR3 in CA‐treated LX‐2 cells. To further determine the specific role of EGR3, we conducted an experiment to knock down EGR3 using shRNA. The results suggested that the knockdown of EGR3 attenuated the activation of HSCs induced by CA treatment, indicating the importance of unconjugated CA in HSC activation and fibrosis. However, the specific mechanism underlying the upregulation of EGR3 in CA‐treated HSCs requires further investigation.</p>", "<p>In the present study, we have mainly focused on the role of SLC27A5 in regulation of BAs conjugation during the progression of liver fibrosis. However, other functions of SLC27A5, such as transportation of LCFA <sup>[</sup>\n##REF##16618416##\n14\n##\n<sup>]</sup> in liver fibrosis, need further investigation. Additionally, the injection of AAV‐<italic toggle=\"yes\">Slc27a5</italic> at an earlier time point may be a better choice to investigate the effects of SLC27A5 overexpression on the treatment of liver fibrosis.</p>", "<p>In summary, these results suggest that SLC27A5 deficiency in mice promotes liver fibrosis by inhibiting BAs conjugation. This leads to the accumulation of unconjugated CA in the liver, which activates HSCs via EGR3. These findings provide novel insights into the role of SLC27A5 in the progression of fibrosis. The dysregulation of BAs composition is thus suggested to be closely linked to HSC activation. Therefore, the restoration of SLC27A5 expression in hepatocytes and repression of profibrotic CA levels represent potential applications in the treatment of fibrosis.</p>" ]
[]
[ "<title>Abstract</title>", "<p>Although the dysregulation of bile acid (BA) composition has been associated with fibrosis progression, its precise roles in liver fibrosis is poorly understood. This study demonstrates that solute carrier family 27 member 5 (SLC27A5), an enzyme involved in BAs metabolism, is substantially downregulated in the liver tissues of patients with cirrhosis and fibrosis mouse models. The downregulation of SLC27A5 depends on RUNX family transcription factor 2 (RUNX2), which serves as a transcriptional repressor. The findings reveal that experimental SLC27A5 knockout (<italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic>) mice display spontaneous liver fibrosis after 24 months. The loss of SLC27A5 aggravates liver fibrosis induced by carbon tetrachloride (CCI<sub>4</sub>) and thioacetamide (TAA). Mechanistically, SLC27A5 deficiency results in the accumulation of unconjugated BA, particularly cholic acid (CA), in the liver. This accumulation leads to the activation of hepatic stellate cells (HSCs) by upregulated expression of early growth response protein 3 (EGR3). The re‐expression of hepatic SLC27A5 by an adeno‐associated virus or the reduction of CA levels in the liver using A4250, an apical sodium‐dependent bile acid transporter (ASBT) inhibitor, ameliorates liver fibrosis in Slc27a5<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice. In conclusion, SLC27A5 deficiency in mice drives hepatic fibrosis through CA‐induced activation of HSCs, highlighting its significant implications for liver fibrosis treatment.</p>", "<p>The authors propose a novel mechanism of aberrant bile acid metabolism in liver fibrosis. Loss of solute carrier family 27 member 5 (SLC27A5) accumulates cholic acids (CA) in the liver and promotes hepatic stellate cells activation via early growth response protein 3 (EGR3). Re‐expression of SLC27A5 or inhibition of CA levels could be a promising strategy for liver fibrosis treatment.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6770-cit-0065\">\n<string-name>\n<given-names>K.</given-names>\n<surname>Wu</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Xia</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Liang</surname>\n</string-name>, <string-name>\n<given-names>F.</given-names>\n<surname>Xu</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Nie</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Tang</surname>\n</string-name>, <string-name>\n<given-names>A.</given-names>\n<surname>Huang</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>N.</given-names>\n<surname>Tang</surname>\n</string-name>, <article-title>Loss of SLC27A5 Activates Hepatic Stellate Cells and Promotes Liver Fibrosis via Unconjugated Cholic Acid</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304408</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304408</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Clinical Samples</title>", "<p>Liver tissue samples from healthy controls (n = 14) and cirrhotic patients (n = 20) were obtained from the Second Affiliated Hospital of Chongqing Medical University. Fasting serum samples were collected from healthy controls (n = 18) and cirrhotic patients (n = 18) recruited from the Second Affiliated Hospital of Chongqing Medical University. Fasting blood specimens were collected from all volunteers and centrifuged at 2000 g for 10 min at 4 °C. The resulting sera were collected and stored at −80 °C until analysis. Clinical characteristics of participants were summarized in Table ##SUPPL##0##S1## (Supporting Information). Informed consents were obtained from all involved participants. This study was approved by the Research Ethics Committee of Chongqing Medical University (Approval number: 2022054).</p>", "<title>Cell Cultures and Reagents</title>", "<p>Human hepatic stellate cell line LX‐2 was obtained from the China Center for Type Culture Collection (CCTC, Wuhan, China). An immortalized human liver cell line MIHA was kindly provided by Prof. Ben C. B. Ko (The Hong Kong Polytechnic University, Hong Kong, China).<sup>[</sup>\n##REF##25708728##\n58\n##\n<sup>]</sup> Cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco, Grand Island, NY, USA) supplemented with 10% FBS (Corning, NY, USA), and 1% penicillin‐streptomycin (MedChemExpress, NJ, USA) at 37 °C containing 5% CO<sub>2</sub>.</p>", "<p>For the bile acid treatment experiments, LX‐2 cells were seeded in 6‐well plates, and cells were stimulated by fresh 2% FBS medium with or without individual BAs (Sigma‐Aldrich, St Louis, MO, USA) at 25, 50, 75, and 100 µм for 48 h, and DMSO were used as a vehicle control.</p>", "<p>For co‐culture experiments, LX‐2 cells were seeded in 12‐well plates at densities of 50000 cells cm<sup>−2</sup>. MIHA cells were seeded and adhered to the porous polyester (PET) membrane surface of trans‐well inserts (0.4 µm pores, BIOFIL, Guangzhou, China) at a density of 100000 cells cm<sup>−2</sup>. Inserts containing MIHA cells were incubated overnight to adapt to the new conditions before being placed in 12‐well plates containing HSCs. The co‐culture system was incubated for 48 h in DMEM medium with 2% FBS. Trans‐well inserts were then carefully removed and the LX‐2 cells in 12‐well plates were immediately collected for analysis.</p>", "<title>Animals</title>", "<p>Heterozygous C57BL/6N‐Slc27a5<sup>em1cyagen</sup> mice were created using the CRISPR‐Cas9 technology by Cyagen Biosciences (Suzhou, China) and were crossed to breed wild‐type (WT) and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice. The genotype of WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice was confirmed by PCR amplification of tail DNA (PCR primers were listed in Table ##SUPPL##0##S2##, Supporting Information). All mice were maintained under specific pathogen‐free conditions in the laboratory animal center of Chongqing Medical University. All animal experiments were performed under the guidelines of the institutional Animal Care and Use Committee at Chongqing Medical University. All animal procedures were also approved by the Animal Experimentation Ethics Committees of Chongqing Medical University (Approval number: 2022054).</p>", "<p>For the carbon tetrachloride (CCl<sub>4</sub>) model of liver fibrosis, 6‐ to 8‐week‐old male WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice were given intraperitoneal (i.p.) injections of CCl<sub>4</sub> (1.0 mL kg<sup>−1</sup> body weight, dissolved in corn oil at a ratio of 1:9) (Macklin, Shanghai, China) or vehicle (corn oil) twice a week for 6 weeks (n = 5 per group). For the thioacetamide (TAA) model of liver fibrosis, 6‐ to 8‐week‐old male WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice were intraperitoneally injected with phosphate‐buffered saline (PBS) or TAA (100 mg kg<sup>−1</sup> body weight) (Macklin, Shanghai, China) three times a week for 8 weeks (n = 5 per group). The mice were starved overnight and sacrificed 2 days after the final injection. The mouse livers and serum were collected for subsequent experiments. Mouse serum ALT, AST, ALP. and TBil were detected using an automatic biochemical analyzer (Catalyst One, IDEXX, USA).</p>", "<p>For overexpression of SLC27A5, AAV8‐TBG‐control or AAV8‐TBG‐<italic toggle=\"yes\">Slc27a5</italic> (OBiO Technology, Corp., Ltd. Shanghai, China) was injected via tail vein of WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> male mice at 8 weeks of age (2 × 10<sup>11</sup> genome copies per mouse). After 8 weeks of CCI<sub>4</sub> injection, mice were starved overnight and sacrificed for analysis.</p>", "<p>For inhibition of the hepatic CA accumulation, 8‐week‐old male WT and <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice were subjected to the CCl<sub>4</sub> injection for 6 weeks and treated with vehicle or bile acid transporter inhibitor A4250 (10 mg kg<sup>−1</sup> body weight) (HY‐109120, MedChemExpress) by daily gavages in the last 4 weeks. After 4 weeks of A4250 treatment, mice were starved overnight and sacrificed for analysis.</p>", "<p>For treatment of BSH‐IN‐1, Adult male WT or <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice were gavaged with a single dose of BSH‐IN‐1 (10 mg kg<sup>−1</sup>, TargetMol, USA) or vehicle control (n = 3 per group). The primary mice hepatocytes were isolated after 24 h of the gavage to perform the co‐culture experiment.</p>", "<title>Extraction and Profiling of Bile Acids</title>", "<p>Serum bile acids extraction was performed by mixing 50 µL of serum with 500 µL of methanol containing 20 µL of 1 µg mL<sup>−1</sup> of Cholic acid‐d4 (CDN Isotopes Inc, Pointe‐Claire, Canada) used as the internal standard. For liver bile acid extraction, ≈60 mg of frozen liver samples was weighed and homogenized in 600 mL of methanol. An amount of 500 µL of liver homogenate was spiked with 20 µL of internal standards. The serum or liver mixture was then vortexed at 12000 g at 4 °C for 30 seconds and incubated for 30 min at 65 °C. The samples were then heated on boiling water bath for 3 min and cooled to room temperature. The mixture was centrifuged at 12,000 g for 10 min at 4 °C, and the supernatant was collected. The pellet was resuspended in 500 µL of methanol, vortexed for 2 min, and centrifuged at 12,000 g for 10 min at 4 °C. The supernatant was combined with that collected earlier, and dried under vacuum. The residue was redissolved with 50% methanol to a final volume of 100 µL. After centrifugation at 12000 g at for 10 min at 4 °C, an aliquot of 70 µL of supernatant was used for liquid chromatography‐tandem mass spectrometry (LC‐MS) analysis as previously described.<sup>[</sup>\n##REF##36379100##\n59\n##\n<sup>]</sup> Briefly, the separation and detection were performed on a Waters ACQUITY UPLC CSH C18 column (2.1 ×100 mm, 1.7 µm) with an Agilent 1290—6495 C ultra performance liquid chromatography‐triple quadrupole tandem mass spectrometry system. Ammonium formate solution of 5 mм with 0.1% formic acid was used as mobile phase A, and methanol was chosen as mobile phase B. The dynamic multiple reaction monitoring (DMRM) was used for MS analysis.</p>", "<p>For bile acid quantitation, calibration curves of standard samples containing various bile acids were used according to recently published methods.<sup>[</sup>\n##REF##36379100##\n59\n##\n<sup>]</sup> Serial standard mixtures were obtained by gradient dilution (4 ×). The standard mixtures were then mixed with internal standard and underwent the same sample preparation as the test samples. Bile acid quantitation was based on the peak area ratio of the targeted bile acids to Cholic acid‐d4. The bile acids concentrations of test samples were quantified using slopes, but not intercepts, of the calibration curves to deduct background signals.</p>", "<title>Primary Mouse Liver Cell Isolation and Culture</title>", "<p>Primary murine hepatocytes were isolated from the livers of male WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice aged 8–12 weeks according to a reported protocol <sup>[</sup>\n##UREF##4##\n60\n##\n<sup>]</sup> with some modification that includes the following steps: in situ pronase (P5147, Sigma‐Aldrich) /collagenase (V900893, Sigma‐Aldrich) perfusion of mouse liver, perfused livers were minced, filtered through 70 µm cell strainer (BS‐70‐XBS, Biosharp, Beijing, China), and centrifuged at 40 g for 5 min at 4 °C to separate hepatocytes. Hepatocytes were plated in Dulbecco's modified Eagle's medium with 1 g L<sup>−1</sup> glucose (DMEM‐low glucose, SH30021.01, HyClone) supplemented with 5% FBS, 15 mmol L<sup>−1</sup> HEPES (H1095, Solarbio, Beijing, China), and 1% penicillin‐streptomycin. Cells were maintained overnight in serum‐free DMEM containing 1 g L<sup>−1</sup> glucose. After 48 h of cell seeding in coated plates, medium was collected and concentrated by a speed‐vacuum to measure bile acids by LC‐MS.</p>", "<p>HSCs were isolated according to a previously published method,<sup>[</sup>\n##REF##25612230##\n61\n##\n<sup>]</sup> and the supernatant was further centrifuged at 580 g for 10 min at 4 °C, resuspended in density gradient‐based Nycodenz (1002424‐1, Alere Technologios AS), and centrifuged at 1400 g for 17 min at 4 °C. HSCs were collected from the interface and cultured in DMEM with 10% FBS and 1% penicillin‐streptomycin.</p>", "<p>The 48 h culture supernatant from primary hepatocytes of WT or <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice was collected and centrifuged at 2000 g for 5 min to prepare it for the conditional culture. The supernatant was collected and labelled as conditioned medium. Twenty‐four hours post isolation, the medium of the primary HSCs was replaced by the conditioned medium from WT or <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> mice primary hepatocytes and incubated for another 48 h. For TGFβ1 treatment, the primary HSCs after 24 h isolation were treated with and without TGFβ1 (4 ng mL<sup>−1</sup>, Novoprotein, Beijing, China) for another 48 h. For CA treatment, the primary HSCs after 24 h isolation were treated with CA (50 µм) for another 48 h.</p>", "<title>Western Blotting</title>", "<p>Proteins were extracted from cells or liver tissues in the lysis buffer (Beyotime, Shanghai, China) consisting of protease inhibitor cocktail (1:100, TargetMol, MA, USA). The concentration of proteins was determined using BCA Protein Assay kit (Beyotime). The extracted proteins were separated by 10% SDS/PAGE and electro‐transferred to PVDF membranes (Millipore, Billerica, MA, USA). After blocking in 5% milk for 1 h, the membranes were probed with primary antibodies against SLC27A5 (1:1000, NBP2‐37412, Novus Biologicals, CO, USA), α‐SMA (1:1000, ER1003, Huabio, Hangzhou, China), COL1A1 (1:1000, WL0088, Wanleibio, Shenyang, China), COL3A1 (1:1000, 22734‐1‐AP, Proteintech, IL, USA), RUNX2 (1:1000, 20700‐1‐AP, Proteintech, IL, USA), EGR3 (1:500, sc‐390967, Santa Cruz Biotechnology, USA), β‐actin (1:3000, BL005B, Biosharp), or GAPDH (1:3000, AG019‐1, Beyotime, Shanghai, China) at 4 °C overnight. Membranes were then incubated with horseradish peroxidase‐conjugated secondary antibody (Abcam, Cambridge, UK). The staining was visualized using ClarityTM Western ECL Substrate (Bio‐Rad, CA, USA).</p>", "<title>Liver histological and Immunohistological (IHC) Staining</title>", "<p>Liver specimens were fixed in 4% paraformaldehyde, embedded in paraffin and cut into 4 µm sections. Then, the specimens were deparaffinized, hydrated and stained by standard methods. To examine hepatic morphology and assess liver fibrosis, H&amp;E and Sirius Red staining were performed. Sections were immune‐stained for SLC27A5 (1:500, NBP2‐37412, Novus Biologicals, CO, USA), α‐SMA (1:300, 19245T, CST, MA, USA), F4/80 (1:300, 70076T, CST), or RUNX2 (1:300, 20700‐1‐AP, Proteintech, IL, USA) overnight at 4 °C. Sections were then incubated with a secondary anti‐rabbit or anti‐mouse IgG (ZSGB‐BIO, Beijing, China) and stained using 3,3′‐diaminobenzidine (ZSGB‐BIO). Stained slides were scanned with a Pannoramic Scan 250 Flash and images were acquired using Pannoramic Viewer 1.15.2 (3DHistech, Budapest, Hungary). Immunostaining and Sirius Red staining were quantified by threshold analysis using the NIH ImageJ software. The immunohistochemical staining of SLC27A5 and RUNX2 was semi‐quantitatively analyzed using the immunoreactive scoring system.<sup>[</sup>\n##REF##34921145##\n62\n##\n<sup>]</sup>\n</p>", "<title>Hepatic Hydroxyproline (HYP) Measurement</title>", "<p>The HYP levels of fresh liver samples of mice were quantified. Concentration was calculated by a standard curve using the HYP Content Assay Kit (BC0255, Solarbio, China) according to the manufacturer protocol.</p>", "<title>Immunofluorescence</title>", "<p>HSCs were seeded and treated with CA (50 µм) in slide chambers. After being fixed in 4% paraformaldehyde, cells were permeabilized in 0.5% Triton X‐100 for 10 min. After being blocked in 5% goat serum for 1 h, slides were incubated with primary antibody against α‐SMA (1:300, 19245T, CST) overnight at 4 °C. The slides were then washed 5 times in PBS and incubated with goat anti‐rabbit conjugated with Alexa Fluor 488 or 552 secondary antibody (1:100, ZF‐0311, ZSGB‐bio) for 1 h at 37 °C. Nucleus was stained using 1 µg mL<sup>−1</sup> 4′,6‐diamidino‐2‐phenylindole (DAPI,1:2000, Roche, Basel, Switzerland). Stained sections were observed by a laser‐scanning confocal microscope (Leica TCS SP8, Solms, Germany).</p>", "<title>Quantitative Reverse Transcriptase PCR (qRT‐PCR)</title>", "<p>Total RNA of tissue or cells was isolated with Trizol reagent (Invitrogen, Rockville, MD). Reverse transcription (RT) reactions were performed using PrimeScript RT Reagent Kit (RR047A, TaKaRa, TKY, Japan). Real‐time PCR was carried out using Bio‐Rad CFX96 machine (Bio‐Rad, Hercules, CA, USA). The level of GAPDH or β‐actin RNA expression was used to normalize the data. The sequences of qRT‐PCR primers were listed in Table ##SUPPL##0##S2## (Supporting Information).</p>", "<title>Construction of Plasmids</title>", "<p>The expression vector of human <italic toggle=\"yes\">RUNX2</italic> was inserted into the <italic toggle=\"yes\">Sal</italic> I and <italic toggle=\"yes\">Xba</italic> I sites of the shuttle vector pAdTrack‐TO4 (from Dr T‐C He, University of Chicago, USA). The 5′‐flanking region (from −2023 to +366 nt) of <italic toggle=\"yes\">SLC27A5</italic> gene was inserted into the <italic toggle=\"yes\">Hind</italic> III and <italic toggle=\"yes\">Xho</italic> I sites of the pGL3‐Basic vector (Promega, Madison, WI, USA), named pGL3‐P1. To construct another length of luciferase reporter plasmid of SLC27A5, the region from −1001 to +182 nt of <italic toggle=\"yes\">SLC27A5</italic> gene was inserted into the pGL3‐Basic vector, named pGL3‐P2. Oligonucleotide sequences were listed in Table ##SUPPL##0##S2## (Supporting Information).</p>", "<title>Lentivirus‐Meditated RNA Interference</title>", "<p>The small double‐strand hairpin shRNA expressing constructs (sh<italic toggle=\"yes\">RUNX2</italic>, sh<italic toggle=\"yes\">EGR3</italic>, and sh<italic toggle=\"yes\">Egr3</italic>) were designed and annealed into the <italic toggle=\"yes\">Hpa</italic> I and <italic toggle=\"yes\">Xho</italic> I sites of pLL3.7 lentivirus vector (kindly provided by Prof. Bing Sun, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China). A negative control construct (shCon) was also generated. The lentiviral supernatants were produced in HEK293T cells as previously described.<sup>[</sup>\n##REF##34650217##\n63\n##\n<sup>]</sup> Oligonucleotide sequences were listed in Table ##SUPPL##0##S2## (Supporting Information).</p>", "<title>CRISPR/Cas9‐Mediated Knockout Cells</title>", "<p>SLC27A5‐knockout cells were constructed by the CRISPR‐Cas9 system provided by Prof. Ding Xue (Tsinghua University, Beijing, China), as previously described.<sup>[</sup>\n##REF##31367013##\n32\n##\n<sup>]</sup> The Knockout of SLC27A5 in MIHA cells were validated by immunoblotting. The sgRNA target sequences were listed in Table ##SUPPL##0##S2## (Supporting Information).</p>", "<title>Luciferase Reporter Assay</title>", "<p>MIHA cells were transfected in twelve‐well plates containing 4 µL of Lipofectamine 8000, 0.5 µg of pADTrack‐TO4 control or pADTrack‐RUNX2 overexpression vectors, 0.5 µg of each luciferase reporter plasmids pGL3‐basic (Promega, Madison, WI, USA), pGL3‐P1 (from −2023 to +366 nt of the promoter region of the <italic toggle=\"yes\">SLC27A5</italic> gene), or pGL3‐P2 (from −1001 to +182 nt of the promoter region of the <italic toggle=\"yes\">SLC27A5</italic> gene), and 10 ng of pRL‐TK‐Renilla (as transfection control) for 48 h. Cells were harvested and assayed for luciferase activity using the Dual Luciferase Assay Kit (Promega, Madison, WI, USA). All experiments were performed at least three times and expressed as mean ± SEM.</p>", "<title>Chromatin Immunoprecipitation (ChIP) Assay</title>", "<p>MIHA cells of 6 × 10<sup>6</sup> were cross‐linked using 1% paraformaldehyde for 8 min at 37 °C. Cell lysates were sonicated at 30% power for 10 cycles (15 seconds ON and 15 seconds OFF). Supernatants were separated and incubated with anti‐RUNX2 (20700‐1‐AP, Proteintech, IL, USA), anti‐EGR3 (sc‐390967, Santa Cruz Biotechnology, USA), or control IgG overnight at 4 °C. Chromatin‐antibody complexes were collected by protein A/G agarose beads (Millipore), washed and then eluted. Real‐time PCR was used to analyze the RUNX2‐binding DNA fragments from ChIP assays. The ChIP and ChIP‐qPCR assays were performed as previously described.<sup>[</sup>\n##REF##34650217##\n63\n##\n<sup>]</sup> Primers were listed in Table ##SUPPL##0##S2## (Supporting Information).</p>", "<title>RNA‐Seq Analysis</title>", "<p>Total RNA was extracted in LX‐2 cells treated with CA (50 µм) or vehicle for 48 h using Trizol reagent and subjected to library preparation. RNA‐seq was performed by Majorbio Bio‐pharm Technology Co.,Ltd (Shanghai, China). Differential expression genes (DEGs) were analyzed using the DESeq2. Heatmap of DEGs was performed using the “ggplot2” packages in R (v4.2.1, The R Project for Statistical Computing, Vienna, Austria).</p>", "<title>Online Database Analysis</title>", "<p>UCSC (<ext-link xlink:href=\"https://genome.ucsc.edu/\" ext-link-type=\"uri\">https://genome.ucsc.edu/</ext-link>) was used to predict transcriptional factors (TFs) that could affect SLC27A5.<sup>[</sup>\n##REF##36420891##\n64\n##\n<sup>]</sup> JASPAR (<ext-link xlink:href=\"http://jaspar.genereg.net/\" ext-link-type=\"uri\">http://jaspar.genereg.net/</ext-link>) was used to predict the potential binding sites of TFs on <italic toggle=\"yes\">SLC27A5</italic> promoter.<sup>[</sup>\n##REF##34850907##\n21\n##\n<sup>]</sup>\n</p>", "<title>Gene Expression Omnibus Database Mining</title>", "<p>Four data sets from GEO database (<ext-link xlink:href=\"https://www.ncbi.nlm.nih.gov/geo/\" ext-link-type=\"uri\">https://www.ncbi.nlm.nih.gov/geo/</ext-link>) were analyzed with GEO2R to profile gene expression between different samples, such as mild fibrosis versus advanced fibrosis in NAFLD patients (GSE31803), control versus NASH patients (GSE48452), normal versus cirrhosis patients (GSE25097), and different stage of fibrosis in HBV infected patients (GSE84044).</p>", "<title>Statistical Analysis</title>", "<p>All data were presented as the means ± SEM. Tests used to examine the differences between groups include Student's <italic toggle=\"yes\">t</italic> test, one‐way ANOVA and with the Tukey's post hoc test, and two‐way ANOVA with Tukey's multiple comparisons test. Pearson correlation coefficient (r) was used to test the linear correlation. <italic toggle=\"yes\">P</italic>‐values &lt; 0.05 were considered statistically significant. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001. Statistical analyses were conducted using GraphPad Prism 8.0 software (La Jolla, CA, USA).</p>", "<title>Ethics Approval Statement</title>", "<p>This study was approved by the Research Ethics Committee of Chongqing Medical University (approval number: 2022054). All animal experiments were performed under the guidelines of the institutional Animal Care and Use Committee at Chongqing Medical University.</p>", "<title>Patient Consent Statement</title>", "<p>Informed consents were obtained from all involved participants.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>K.W., Y.L., J.X., and J.L. contributed equally to this work. N.T., C.C. and A.H. conceived and designed the study. K.W., Y.L., J.X., and J.L. performed most experiments and analyzed the data. K.W. provided suggestions and designed primer sequence. H.L. constructed plasmids. F.X., D.L., D.N., and X.T. assisted with mice experiments. C.C. provided technical assistance. K.W. and N.T. wrote the manuscript with all authors providing feedback. The order of the co‐first authors was determined on the basis of their relative contributions to the study.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank Dr. T.‐C He (University of Chicago, USA) for providing the pAdEasy system. The authors were grateful that Prof. Ding Xue (Tsinghua University, Beijing, China) supplied the CRISPR‐Cas9 system. This work was supported by the China National Natural Science Foundation (grant no. U20A20392, 82272975, 82072286, 82071671), the 111 Project (No. D20028), the Innovative and Entrepreneurial Team of Chongqing Talents Plan, Chongqing Medical Scientific Research Project (Joint project of Chongqing Health Commission and Science and Technology Bureau, 2023DBXM007), Senior Medical Talents Program of Chongqing for Young and Middle‐aged, the Kuanren talents program and the DengFeng program of the second affiliated hospital of Chongqing Medical University, and the Future Medical Youth Innovation Team of Chongqing Medical University (W0036, W0101).</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6770-fig-0001\"><label>Figure 1</label><caption><p>SLC27A5 expression is generally down‐regulated in the livers of cirrhosis patients and CCI<sub>4</sub>‐treated mice A) Box plots of relative <italic toggle=\"yes\">SLC27A5</italic> mRNA levels in GSE31803, GSE48452, GSE25097, and GSE84044 datasets. B) Representative liver histology of H&amp;E, Sirius Red staining, SLC27A5, and α‐SMA IHC in consecutive sections of normal and cirrhotic human livers, and its statistical summary (n = 10 per group). Scale bar, 100 µm. C) The <italic toggle=\"yes\">Runx2</italic>, <italic toggle=\"yes\">Hnf4a</italic>, <italic toggle=\"yes\">Rxra</italic>, <italic toggle=\"yes\">Rest</italic>, and <italic toggle=\"yes\">Nr2c2</italic> expression levels were detected using qRT‐PCR in WT mice livers subjected to CCl<sub>4</sub> treatment (n = 4 per group). D) Representative H&amp;E and RUNX2 IHC in liver sections from healthy controls and patients with cirrhosis, and its statistical summary (n = 10 per group). Scale bar: 50 µm. E) Putative binding sites of RUNX2 (black spots) in the <italic toggle=\"yes\">SLC27A5</italic> gene promoter (−2023/+366). F) MIHA cells were co‐transfected with the <italic toggle=\"yes\">SLC27A5</italic> promoter luciferase reporter and expression plasmids for RUNX2, and the luciferase activity was monitored as described in the panel (n = 3 per group). G) ChIP‐qPCR analysis to determine the binding of RUNX2 protein to the SLC27A5 promoter in MIHA cells. Diagram of the SLC27A5 gene promoter (−1001/+182) depicting the location of the amplified region (−396/−280) (n = 3 per group). H) MIHA cells were transfected with vector or RUNX2‐overexpressing plasmid. The protein levels of RUNX2 and SLC27A5 were analyzed using Western blotting. I) MIHA cells were transfected with shControl or shRUNX2. The expression of RUNX2 and SLC27A5 was detected. J) Box plots of relative mRNA levels of <italic toggle=\"yes\">RUNX2</italic> in the GSE25097 dataset. K) Correlation of hepatic <italic toggle=\"yes\">RUNX2</italic> mRNA with <italic toggle=\"yes\">SLC27A5</italic> in patients with cirrhosis (n = 40 for GSE25097). Data are presented as mean ± SEM. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ns., not significant. Data in (A) (left three panels), (B–D), (F–G), and (J) were analyzed using two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test. One‐way ANOVA analyzed data in (A) (right panel) with Tukey's post hoc test. Data in (K) was analyzed using Pearson correlation coefficient analysis.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6770-fig-0002\"><label>Figure 2</label><caption><p>SLC27A5 deficiency in mice develops liver fibrosis after 24 months of age A) Representative pictures of livers from 24‐month‐old WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice. Scale bar, 2 mm. B) Serum ALT, AST, and ALP levels from 24‐month‐old WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice (n  =  5 per group). C) Representative images of H&amp;E and Sirius Red staining from liver tissues of WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice at 12, 18, and 24 months (n  =  5 per group). Scale bar, 50 µm. D) Quantification of Sirius red staining is described in (C). E,F) Relative mRNA levels of profibrotic genes (E) and inflammatory genes (F) of liver tissues from 24‐month‐old WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice (n  =  5 per group). G) The hepatic mRNA levels of gene expression of bile acids synthesis in 24‐month‐old WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice (n  =  5 per group). Data are presented as mean ± SEM. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ns., not significant, two‐tailed Student's <italic toggle=\"yes\">t</italic> test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6770-fig-0003\"><label>Figure 3</label><caption><p>SLC27A5 deficiency promotes CCl<sub>4</sub>‐ and TAA‐induced liver fibrosis in mice A–D) Eight‐week‐old male WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice were injected with CCl<sub>4</sub> for six weeks (n  =  5 per group). E–H) Eight‐week‐old male WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice were injected with TAA for eight weeks (n  =  5 per group). (A,E) The experimental approach of the animal model establishment. (B,F) Representative histology of H&amp;E, Sirius Red, and IHC staining (α‐SMA, F4/80) from each group. Scale bar, 50 µm. (C) Quantification of Sirius red, F4/80, and α‐SMA IHC staining are described in (B). G) Quantification of Sirius red, F4/80, and α‐SMA IHC staining are described in (F). (D,H) Serum levels of ALT, AST, and ALP were measured. Data are presented as mean ± SEM. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, two‐tailed Student's <italic toggle=\"yes\">t</italic> test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6770-fig-0004\"><label>Figure 4</label><caption><p>SLC27A5 loss in hepatocytes promotes HSCs activation in vitro. A) Primary mouse HSCs were isolated from WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice and culture‐activated for the indicated duration. Cell morphology as observed under light‐field microscopy. Scale bar: 50 µm. B–D) Primary HSCs isolated from WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice were culture‐activated for 72 h (n = 3 per group). mRNA expression of fibrogenic genes (B), protein expression of α‐SMA, COL1A1, and COL3A1 (C), and immunofluorescence of α‐SMA (D) are displayed. Scale bar, 25 µm. DAPI, 4′,6‐diamidino‐2‐phenylindole. E) Schematic of co‐culture experiments. F–H) Primary HSCs from WT mice were incubated with the supernatant from WT or <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> PMHs for 48 h. mRNA expression of fibrogenic genes (F), protein expression of α‐SMA, COL1A1, and COL3A1 (G), and immunofluorescence of α‐SMA (H) are displayed. Scale bar, 25 µm. I) Schematic flow chart of co‐culture models. (J‐K) LX‐2 cells were co‐cultured with parental and SLC27A5‐KO MIHA cells for 48 h. Protein expression of α‐SMA, COL1A1, and COL3A1 J), and immunofluorescence of α‐SMA K) are displayed. Scale bar, 25 µm. Data are presented as mean ± SEM. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, two‐tailed Student's <italic toggle=\"yes\">t</italic> test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6770-fig-0005\"><label>Figure 5</label><caption><p>Elevation of unconjugated CA promotes HSCs activation. A) Serum CA and DCA levels in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> and WT mice at 24 months of age (n = 5 per group). B) Liver CA and DCA levels in <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> and WT mice at 24 months of age (n = 5 per group). C) LX‐2 cells were treated with CA at 25, 50, and 100 µм for 48 h. The expression of α‐SMA was measured using immunostaining. D–F) WT mice HSCs were treated with CA at 50 µм for 48 h. mRNA expression of fibrogenic genes (D), protein expression of α‐SMA, COL1A1, and COL3A1 (E), and α‐SMA immunostaining (F) are displayed. G) The serum levels of CA and DCA in healthy individuals and patients with cirrhosis (n = 18 per group). H) CA levels were measured in media from parental and SLC27A5‐KO MIHA cells (n = 3 per group). I) CA levels were measured in PMHs supernatant from WT and <italic toggle=\"yes\">Slc27a5</italic>\n<sup>−/−</sup> mice (n = 3 per group). Data are presented as mean ± SEM. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, two‐tailed Student's <italic toggle=\"yes\">t</italic> test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6770-fig-0006\"><label>Figure 6</label><caption><p>CA‐triggered activation of HSC is dependent on EGR3. A) Expression profile of regulatory genes of fibrosis in LX‐2 cells treated with 50 µм CA or vehicle controls based on RNA‐seq data (n = 3 per group). B) qRT‐PCR was performed to validate the expression of fibrosis‐regulated genes in vehicle‐ and CA‐treated LX‐2 cells (n = 3 per group). C–E) LX‐2 cells were transfected with Control (shCon) or shEGR3 plasmid in the presence of 50 µм CA for 48 h. Expression of the fibrotic genes was analyzed using qRT‐PCR (C), Western blotting (D), or immunofluorescence (E). Scale bar, 25 µm. F–H) Primary mouse HSCs were isolated from WT mice and transfected with Control (shCon) or shEgr3 plasmid in 50 µм CA for 48 h. Expression of the fibrotic genes was analyzed using qRT‐PCR (F), Western blotting (G), or immunofluorescence (H). Scale bar, 25 µm. Data are presented as mean ± SEM. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ns., not significant. Two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic> test was used to analyze data in (B). Data in (C) and (F) were analyzed using one‐way ANOVA with Tukey's post hoc test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6770-fig-0007\"><label>Figure 7</label><caption><p>Overexpression of SLC27A5 or inhibition of intestinal bile acid absorption ameliorates CCl<sub>4</sub>‐induced liver fibrosis A–H) Eight‐week‐old male WT and <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> (KO) mice were subjected to CCl<sub>4</sub> treatment and injected with AAV‐Control (AAV‐Con) or AAV‐<italic toggle=\"yes\">Slc27a5</italic> (n = 5 per group). I–P) Eight‐week‐old male WT and <italic toggle=\"yes\">Slc27a5</italic>\n<italic toggle=\"yes\">\n<sup>−/−</sup>\n</italic> (KO) mice were subjected to CCl<sub>4</sub> model and treated with vehicle or A4250 by daily gavages as outlined in (I) (n = 5 per group). (A,I) The experimental approach of the animal model establishment. (B,J) Representative liver histology of H&amp;E, Sirius Red, and α‐SMA IHC staining. Scale Bar, 50 µm. (C,D,K,L) Quantification of Sirius red (C,K) and α‐SMA IHC (D,L) staining described in (B,J). (E,M) Hepatic hydroxyproline content was measured. (F,N) Serum levels of ALT, AST, and ALP were measured. (G,H,O,P) CA levels in serum (G,O) and liver (H,P). Data are presented as mean ± SEM. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ns., not significant, one‐way ANOVA with Tukey's post hoc test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6770-fig-0008\"><label>Figure 8</label><caption><p>Underlying mechanisms of SLC27A5 deficiency promotes HSCs activation and fibrosis via CA. SLC27A5 was downregulated in liver fibrosis tissues via RUNX2. The loss of SLC27A5 in mice resulted in accumulating unconjugated CA in hepatocytes and subsequently activated HSCs via EGR3. Re‐expression of SLC27A5 or inhibition of CA accumulation may represent a potential strategy for liver fibrosis treatment. SLC27A5, solute carrier family 27 member 5; RUNX2, RUNX family transcription factor 2; CA, cholic acid; TCA, taurocholic acid; BSH, bile salt hydrolases; ASBT, apical sodium‐dependent bile acid transporter; EGR3, early growth response protein 3; HSC, hepatic stellate cell.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6770-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6770-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2304408-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2304408-s002.xlsx\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
64
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 13; 11(2):2304408
oa_package/a4/c5/PMC10787101.tar.gz
PMC10787102
37997163
[ "<title>Introduction</title>", "<p>Epilepsy, a common neurological disorder,<sup>[</sup>\n##UREF##0##\n1\n##\n<sup>]</sup> is caused by the failure of neuronal inhibition, which disperses epileptic responses over broad brain regions.<sup>[</sup>\n##REF##30317911##\n2\n##\n<sup>]</sup> The primary features of antiepileptic therapies, such as antiepileptic drugs (AEDs),<sup>[</sup>\n##REF##16581409##\n3\n##, ##REF##31348240##\n4\n##\n<sup>]</sup> vagus nerve stimulation (VNS),<sup>[</sup>\n##REF##29670050##\n5\n##, ##REF##31085961##\n6\n##\n<sup>]</sup> deep brain stimulation (DBS),<sup>[</sup>\n##REF##29670050##\n5\n##, ##REF##31697763##\n7\n##\n<sup>]</sup> transcranial magnetic stimulation (TMS), and transcranial direct/alternating current stimulation (tD/ACS),<sup>[</sup>\n##REF##29670050##\n5\n##, ##REF##19332316##\n8\n##, ##UREF##1##\n9\n##, ##REF##35989912##\n10\n##\n<sup>]</sup> involve alleviation of cortical hyper‐excitabilities by either enhancing γ‐Aminobutyric acid (GABA)ergic neurons or blocking excitatory amino acid neurotransmission. Optimal stimulation sequences for these conventional therapeutic approaches have been empirically investigated because their performance in seizure suppression relies on stimulation parameters, such as stimulus strength, length, and intervals. In addition, certain combinations of these parameters in AEDs,<sup>[</sup>\n##REF##30875668##\n11\n##, ##REF##20067500##\n12\n##\n<sup>]</sup> VNS,<sup>[</sup>\n##REF##19427651##\n13\n##\n<sup>]</sup> DBS,<sup>[</sup>\n##UREF##2##\n14\n##\n<sup>]</sup> and TMS<sup>[</sup>\n##REF##7106219##\n15\n##, ##REF##28359831##\n16\n##, ##REF##26642974##\n17\n##\n<sup>]</sup> can exacerbate epileptic symptoms. Meanwhile, transcranial‐focused ultrasound (tFUS) is a recent therapeutic approach that has gained significant attention for its antiepileptic effects in drug‐induced small animal epilepsy models,<sup>[</sup>\n##REF##21144673##\n18\n##, ##REF##21375781##\n19\n##, ##REF##31575487##\n20\n##, ##UREF##3##\n21\n##, ##REF##30166265##\n22\n##, ##REF##31002886##\n23\n##, ##UREF##4##\n24\n##, ##REF##31109842##\n25\n##\n<sup>]</sup> and there are expectations that tFUS may be more efficient in antiepileptic therapeutic approach owing to its ability to stimulate deep brain structures within millimeter‐scale lesions. Despite the successful induction of suppressive effects and several efforts to optimize the stimulation parameters for tFUS, its efficacy in prior studies remains vague. In addition, some studies have indicated that the reliability of the neuromodulation effects may not be sufficient for clinical use because the sonication time for tFUS is too short to cause persistent modulation effects.<sup>[</sup>\n##UREF##3##\n21\n##, ##REF##31002886##\n23\n##, ##UREF##4##\n24\n##\n<sup>]</sup> Furthermore, similar to other stimulation approaches, bidirectional neuromodulation can be induced by tFUS. Care should be taken to avoid side effects because ultrasound stimulation also works on inhibitory pathways by activating GABAergic neurons or blocking ion channels, like other conventional stimulant methods,<sup>[</sup>\n##UREF##3##\n21\n##, ##REF##30166265##\n22\n##, ##REF##31002886##\n23\n##, ##UREF##4##\n24\n##\n<sup>]</sup> and may exacerbate epileptic symptoms.</p>", "<p>In the present study, repetitive tFUS (rtFUS) having the longer repetition ratio of tens of seconds had been explored to empirically demonstrate significant suppressive effects on epileptiform activities in a pentylenetetrazole (PTZ)‐induced acute generalized epilepsy model.<sup>[</sup>\n##UREF##5##\n26\n##\n<sup>]</sup> As repetitive TMS (rTMS) exerts longer neuromodulatory effects than single‐pulse TMS in the treatment of major depressive disorders,<sup>[</sup>\n##REF##35396023##\n27\n##, ##UREF##6##\n28\n##, ##REF##32973560##\n29\n##\n<sup>]</sup> similar repetitive stimulus sequences in ultrasound brain stimulation have recently been reported to have long‐lasting inhibitory effects on the anti‐saccade motion of non‐human primates.<sup>[</sup>\n##REF##32973560##\n29\n##, ##REF##30747105##\n30\n##\n<sup>]</sup> Instead of a single stimulation burst, burst trains can be more effective in suppressing epileptiform activities, eventually resulting in symptoms that are comparable to those in the baseline. Therefore, the prolonged sustainability of the antiepileptic effects of rtFUS can be compared with that of single‐burst tFUS. Furthermore, paradoxical proconvulsive effects and even a transition from anticonvulsive to proconvulsive effects may be discovered by navigating changes in rtFUS parameters, such as the interval between stimulus bursts, burst duration, and strength because these parameters are known to affect GABA secretion and induce bidirectional epileptiform activities in other stimulation methods (such as tDCS and TMS<sup>[</sup>\n##REF##30317911##\n2\n##, ##UREF##2##\n14\n##, ##UREF##7##\n31\n##, ##REF##23882212##\n32\n##, ##UREF##8##\n33\n##, ##UREF##9##\n34\n##\n<sup>]</sup>). The exploratory studies for comparison in epileptic activities between different acoustic parameters of rtFUS (e.g., stronger vs weaker bursts, longer vs shorter burst length, or burst interval) will help in identifying the optimal transmission conditions to perform antiepileptic effects.</p>", "<p>Furthermore, we assessed the sustainability and bidirectional modulations in epileptic activities with rtFUS using electroencephalography (EEG) and optical measurements of cerebral blood volume (CBV) changes in the prefrontal cortex, where epileptiform activities in the hippocampus are reflected through the limbic system.<sup>[</sup>\n##REF##24445927##\n35\n##\n<sup>]</sup> Immunohistochemistry (IHC) was performed to visualize the excitatory and inhibitory activation of neurons in the hippocampus. In addition, changes in the amounts of excitatory (glutamate) and inhibitory (GABA) neurotransmitters during bidirectional modulation of epileptiform activities were assessed through multitemporal harvesting of interstitial fluid (ISF) from stimulated locations via microdialysis.</p>" ]
[]
[ "<title>Results</title>", "<p>Ultrasound stimulation was applied using a custom‐made focused ultrasound transducer over the right hemisphere of the midbrain to target the anterior thalamic nucleus (ATN). EEG was performed before, during, and after sonication. IHC was performed on brain samples harvested from the model animals. Optical measurements of CBV changes and microdialysis for proteomic analysis of neurotransmitters were performed in separate trials to measure the responses to the stimulation. The detailed repetitive transcranial ultrasound stimulation transmission sequences used in the experiment are shown in <bold>Figure</bold>\n##FIG##0##\n1\n##. The detailed experimental configurations are described in the Experimental Section and Supporting Information figures (Figures ##SUPPL##0##S1## and ##SUPPL##0##S2##, Supporting Information).</p>", "<title>Repeated Transcranial Low‐Intensity Elongated Ultrasound Stimulations for Sustainable Full Suppression of Epileptiform Activities</title>", "<p>Changes in epileptiform activities were compared between the two stimulant sequences. The first sequence (TXH_0.25_30) comprised eleven repetitions of a stronger (1 MPa) and shorter (0.25 s) burst with a burst interval of 30 s. The second sequence (TXL_40_40) consisted of six repetitions of weaker (0.25 MPa) but longer (40 s) burst with a burst interval of 40 s (Figure ##FIG##0##1##). First, epileptiform activities were reliably induced in a PTZ‐control group that received PTZ, a drug used for acute seizure induction, without ultrasound stimulation. While sparsely located discharge peaks in the EEG signal were identified during the baseline period, the signal was transformed into ictal shapes that demonstrated repetitive high‐frequency discharge peaks in the PTZ‐control group (<bold>Figure</bold>\n##FIG##1##\n2A##). The relative number of epileptic spikes increased 2.6‐fold in the first 10 min after PTZ injection in the PTZ‐control group. The number then decreased for 7 min and saturated at 2.3 times the baseline (Figure ##FIG##1##2B##). Although the number decreased slightly from 10 to 17 min after the PTZ injection, this decrease was not statistically significant at 17 min after the PTZ injection compared to 10 min after the PTZ injection (<italic toggle=\"yes\">p</italic> = 0.588; two‐tailed paired <italic toggle=\"yes\">t</italic>‐test) where the number of epileptic spikes ratio still remained significantly different at 17 min after the PTZ injection compared to the baseline period (<italic toggle=\"yes\">p</italic> = 0.014; two‐tailed paired <italic toggle=\"yes\">t</italic>‐test). Following stimulation with TXH_0.25_30, the amplitude of the discharge pattern slightly reduced but gradually became comparable to that of the PTZ‐control group. During the period between 0 and 10 min post‐stimulation (10AS) and 20 and 30 min post‐stimulation (30AS), the number of epileptic spikes ratio in the TXH_0.25_30 group was not significantly different from that of the PTZ‐control (<italic toggle=\"yes\">p</italic> = 0.524 and 0.724 at 10AS and 30AS, respectively; two‐tailed Mann–Whitney U test) (Figure ##FIG##1##2C##). Meanwhile, the discharging patterns following TXL_40_40 became similar to those of the baseline, and the suppressive effect lasted until the end of the EEG recording. TXL_40_40 administration resulted in the maintenance of the number of epileptic spikes ratio similar to that of the baseline, and a suppressive effect was still found at 10AS and 30AS (<italic toggle=\"yes\">p</italic> = 0.030 and 0.030 at 10AS and 30AS compared with that of PTZ‐control, respectively; two‐tailed Mann–Whitney U test). In the delta band between 1 and 3 Hz, the spectral power with TXH_0.25_30 at 30AS was not significantly different from that of the PTZ control (<italic toggle=\"yes\">p</italic> = 0.833; two‐tailed Mann‐Whitney U test). However, the relative spectral power followed by TXL_40_40 was 1.19 at 30AS, indicating that this level was close to the baseline. TXL_40_40 also demonstrated strong suppressive effects on the theta band between 4 and 7 Hz (<italic toggle=\"yes\">p</italic> = 0.019 at 30AS compared with that of PTZ‐control; two‐tailed Mann–Whitney U test), whereas TXH_0.25_30 demonstrated mild effects (<italic toggle=\"yes\">p</italic> = 0.093 at 30AS compared with that of PTZ‐control; two‐tailed Mann–Whitney U test) (Figure ##FIG##1##2D##). However, with a single transmission of an elongated (40 s), low pressure (0.25 MPa) burst, the number of epileptic spikes ratio became similar to that of the PTZ‐control group, although the suppressive effects were briefly observed for 5 min immediately after the stimulation (Figure ##FIG##1##2B,C##). In the CBV measurements, while the total hemoglobin amount (Δ[Hb]) barely changed in the normal control group (that did not receive PTZ or ultrasound stimulations), Δ[Hb] sharply increased in the PTZ‐control group after drug administration. The increase in Δ[Hb] was as low as that in the normal control group when TXL_40_40 was used (<italic toggle=\"yes\">p</italic> = 0.699 at 20AS compared with that of normal control; two‐tailed Mann–Whitney U‐test), while the low Δ[Hb] level was maintained until the end of the recording. Following TXH_0.25_30, the Δ[Hb] level was similar to that of the PTZ control (<italic toggle=\"yes\">p</italic> = 0.180 at 20AS; two‐tailed Mann–Whitney U test), although a gradual decay pattern was observed after the sonication was completed (Figure ##FIG##1##2E##).</p>", "<title>Efficacy of rtFUS for Epilepsy Treatment is Dependent on the Burst Length in the rtFUS Sequence</title>", "<p>To investigate the effects of burst length changes in rtFUS, the modulation effects were compared for the sequences with burst lengths of 10 s (TXL_10_50), 20 s (TXL_20_40), and 40 s (TXL_40_40). The burst was repeated six times at intervals of 50, 40, and 40 s for TXL_10_50, TXL_20_40, and TXL_40_40, respectively (Figure ##FIG##0##1##). For TXL_10_50, the frequency of the discharge peaks increased in the EEG waveform (<bold>Figure</bold>\n##FIG##2##\n3A##). The number of epileptic spikes with TXL_10_50 was statistically comparable with that in the PTZ‐control group at the post‐stimulation periods from 10AS to 30AS (<italic toggle=\"yes\">p</italic> = 0.435, 0.354, and 0.435 at 10AS, 20AS, and 30AS, respectively; two‐tailed Mann–Whitney U test). As the stimulation length elongated from 10 to 40 s (TXL_10_50, TXL_20_40, TXL_40_40), the number of epileptic spikes decreased from 2.63, 1.94, 1.07 times the baseline, respectively, at 10AS while the difference in the number of epileptic spikes ratio between that of the PTZ‐control was only significant in the TXL_40_40 group (<italic toggle=\"yes\">p</italic> = 0.435, 0.943 and 0.030 at 10AS for TXL_10_50, TXL_20_40, and TXL_40_40, respectively; two‐tailed Mann–Whitney U test) (Figure ##FIG##2##3B,C##). In the delta band, the spectral power of the EEG for the TXL_10_50 condition was comparable to that for the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.524 at 30AS; two‐tailed Mann–Whitney U test) while that of the EEG for TXL_40_40 condition was lower than that for the PTZ‐control group. (<italic toggle=\"yes\">p</italic> = 0.045 at 30AS; two‐tailed Mann–Whitney U test) (Figure ##FIG##2##3D##). In the theta band, the spectral power of the EEG for the TXL_10_50 condition was comparable to that for the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.524 at 30AS; two‐tailed Mann–Whitney U test). However, the trend of reduction in the theta power was significant as the burst length was increased to 20 and 40 s (<italic toggle=\"yes\">p</italic> = 0.171 and 0.019 at 30AS for TXL_20_40 and TXL_40_40, respectively, compared to PTZ‐control; two‐tailed Mann–Whitney U test) (Figure ##FIG##2##3D##). In the CBV curve, with TXL_10_50, Δ[Hb] was sharply increased by + 12.89% at 20AS compared to that in the baseline and was maintained at a higher level than that in the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.699 at 20AS; two‐tailed Mann‐Whitney U‐test), while the CBV with TXL_40_40 was similar to that of the normal control (<italic toggle=\"yes\">p</italic> = 0.699 at 20AS; two‐tailed Mann–Whitney U‐test) (Figure ##FIG##2##3E##).</p>", "<title>Upregulation and Downregulation of Epileptiform Activities Selected by Adjusting the Interval Between Bursts in the rtFUS Sequence</title>", "<p>The epileptiform activity changes by TXL_40_40 were compared with that by TXL_40_20, which also had a burst length of 40 s; however, the interval between the bursts was reduced from 40 to 20 s (Figure ##FIG##0##1##). TXL_40_20 stimulation demonstrated rebound excitatory effects in the post‐stimulus period (<bold>Figure</bold>\n##FIG##3##\n4A##). TXL_40_20 generated a similar number of epileptic spikes as that in the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.943, 0.833, and 0.943 at 10AS, 20AS, and 30AS, respectively; two‐tailed Mann–Whitney U test). In contrast, TXL_40_40 stimulation demonstrated prominent suppressive effects both during and after stimulation (Figure ##FIG##3##4B,C##). The spectral density in the delta band was higher with TXL_40_20 at 30AS than that in the PTZ control. However, the difference was not significant owing to large deviations with TXL_40_20 (<italic toggle=\"yes\">p</italic> = 0.833; two‐tailed Mann–Whitney U test) (Figure ##FIG##3##4D##). While the CBV response of TXL_40_20 was similar to that of TXL_40_40 during the stimulation period, the Δ[Hb] sharply increased after TXL_40_20, unlike the CBV responses after TXL_40_40, ultimately becoming higher than that of the PTZ control (Figure ##FIG##3##4E##).</p>", "<title>Transformation from Suppressive to Excitatory States Through a Hybrid Sequence</title>", "<p>As shown in previous studies, TXL_40_40 demonstrated strong suppressive effects. In contrast, the insignificant suppressive effects observed with TXH_0.25_30 – that showed suppressive effects with low statistical significance [19.91% less epileptic spikes ratio (<italic toggle=\"yes\">p</italic> = 0.724), 16.61% less delta PSD (<italic toggle=\"yes\">p</italic> = 0.833) and 38.79% less theta PSD (<italic toggle=\"yes\">p</italic> = 0.093) than that of the PTZ‐control at 30AS]. Although the single use of TXL_40_40 maintained the suppressive effect for more than 30 min, the epileptiform activities were sharply transformed into the excitatory state with the use of TXH_0.25_30, followed by a 3 min resting time after TXL_40_40 (TX_HYBRID, <bold>Figure</bold>\n##FIG##4##\n5A##). The number of epileptic spikes ratio in the TX_HYBRID group was always comparable with the PTZ‐control group across all post‐stimulation periods at 10AS, 20AS, and 30AS (<italic toggle=\"yes\">p</italic> = 0.943, 0.943, and 0.622, respectively; two‐tailed Mann–Whitney U test) (Figure ##FIG##4##5B,C##). The elevations of the power spectral densities in the delta and theta band after TX_HYBRID (30AS) were comparable to that of the PTZ‐control group (Figure ##FIG##4##5D##) (<italic toggle=\"yes\">p</italic> = 1.000 and 0.622 at 30AS, respectively; two‐tailed Mann–Whitney U test). Regarding CBV changes, the Δ[Hb] was reduced after TXL_40_40 sonication, whereas TXH_0.25_30 increased the blood volume, approaching that of the PTZ control (Figure ##FIG##4##5E##).</p>", "<title>Immunohistochemistry Results</title>", "<p>\n<bold>Figure</bold>\n##FIG##5##\n6A## shows the immunohistochemical results of the samples harvested from sacrificed animals immediately after each experiment. While c‐Fos‐expressed cells were rarely found in the normal control group, c‐Fos‐labeled cells were abundant in the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.002; two‐tailed Mann–Whitney U test). The increase of the proportion of c‐Fos‐positive cells in the TXL_10_50 group was trending toward significance to that in the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.093; two‐tailed Mann–Whitney U test). As shown in the bar graph, 82.58% (standard error of the mean [SEM] = 1.83%) of neuronal cells expressed c‐Fos with TXL_10_50, and 77.14% (SEM = 2.12%) of cells expressed c‐Fos in the PTZ‐control group. TXL_20_40 (<italic toggle=\"yes\">p</italic> = 0.240; two‐tailed Mann–Whitney U test), TXL_40_20 (<italic toggle=\"yes\">p</italic> = 0.394; two‐tailed Mann–Whitney U test) and TXH_0.25_30 (<italic toggle=\"yes\">p</italic> = 0.394; two‐tailed Mann–Whitney U test) demonstrated c‐Fos‐positive cell ratios comparable to those of the PTZ‐control group. Furthermore, TX_HYBRID presented an even higher value of ≈87.47% (SEM = 1.25%) than that of PTZ‐control (<italic toggle=\"yes\">p</italic> = 0.004; two‐tailed Mann–Whitney U test). In contrast, the expression ratio was drastically reduced to 11.11% with TXL_40_40 compared with the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.002; two‐tailed Mann‐Whitney U test).</p>", "<p>Although the normal and PTZ‐control cases barely exhibited glutamic acid decarboxylase 65‐kilodalton isoform (GAD65)‐positive cells, the sonicated conditions exhibited a greater number of GAD65‐expressed cells. The GAD65‐positive cell density with TXL_40_40 (mean = 15.88 cells mm<sup>−2</sup>; SEM = 1.53 cells mm<sup>−2</sup>) was ≈6.2‐fold higher than that in the PTZ‐control group (mean = 2.56 cells mm<sup>−2</sup>; SEM = 0.42 cells mm<sup>−2</sup>). Although sharing the same burst duration, TXL_40_20 exhibited a lower expression of GAD65‐positive cells (mean = 7.27 cells mm<sup>−2</sup>; SEM = 0.61 cells mm<sup>−2</sup>) than that of TXL_40_40 (mean = 15.88 cells mm<sup>−2</sup>; SEM = 1.53 cells mm<sup>−2</sup>), while both groups showed statistically significant difference compared to the PTZ‐control (<italic toggle=\"yes\">p</italic> = 0.002 and 0.002, respectively; two‐tailed Mann–Whitney U test). The GAD65‐expressed cell densities for TXL_10_50 (mean = 5.60 cells mm<sup>−2</sup>; SEM = 0.71 cells mm<sup>−2</sup>) and TXL_40_20 (mean   7.27 cells mm<sup>−2</sup>; SEM = 0.61 cells mm<sup>−2</sup>) were lower than the cell density with TXL_40_40 (mean = 15.88 cells mm<sup>−2</sup>; SEM = 1.53 cells mm<sup>−2</sup>) and TX_HYBRID (mean = 14.89 cells mm<sup>−2</sup>; SEM = 0.81 cells mm<sup>−2</sup>).</p>", "<p>While the ionized calcium‐binding adaptor molecule 1 (Iba1)‐expressed cell density in the normal control group was 39.30 cells mm<sup>−2</sup> (SEM = 0.89 cells mm<sup>−2</sup>), the number increased to 55.62 cells mm<sup>−2</sup> (SEM = 1.79 cells mm<sup>−2</sup>) in the PTZ‐control group. The density of activated cells with TXL_40_40 was 49.36 cells mm<sup>−2</sup> (SEM = 0.59 cells mm<sup>−2</sup>), which was significantly lower than that of the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.009, two‐tailed Mann–Whitney U test). The Iba1‐expressed cell densities in TXH_0.25_30, TXL_10_50, TXL_20_40 and TXL_40_20 were 54.13 cells mm<sup>−2</sup> (SEM = 1.68 cells mm<sup>−2</sup>), 60.50 cells mm<sup>−2</sup> (SEM = 2.61 cells mm<sup>−2</sup>), 54.07 cells mm<sup>−2</sup> (SEM = 1.58 cells mm<sup>−2</sup>) and 57.91 cells mm<sup>−2</sup> (SEM = 2.95 cells mm<sup>−2</sup>), respectively. However, those values were not statistically different (<italic toggle=\"yes\">p</italic> = 0.394, 0.240, 0.699, 0.589 for TXH_0.25_30, TXL_10_50, TXL_20_40 and TXL_40_20, respectively, two‐tailed Mann–Whitney U test) from the one with PTZ‐control. TX_HYBRID induced the highest Iba1‐expression level at 69.72 cells mm<sup>−2</sup> (SEM = 3.51 cells mm<sup>−2</sup>) among all the experimental groups, and the increase was significant compared with PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.009, two‐tailed Mann–Whitney U test).</p>", "<p>In the glial fibrillary acidic protein (GFAP) responses indicating astrocytic reactivity, GFAP density increased to 51.76 cells mm<sup>−2</sup> (SEM = 1.96 cells mm<sup>−2</sup>) in the PTZ‐control group, unlike the normal control group, which presented a density of 39.71 cells mm<sup>−2</sup> (SEM = 1.23 cells mm<sup>−2</sup>) (<italic toggle=\"yes\">p</italic> = 0.002; two‐tailed Mann–Whitney U test). Furthermore, the GFAP‐positive cell densities of TXL_10_50, TXL_20_40, and TXL_40_40 gradually decreased to 62.58 (SEM = 2.52), 52.59 (SEM = 0.82), and 47.30 cells mm<sup>−2</sup> (SEM = 1.82 cells mm<sup>−2</sup>), respectively, while the GFAP‐positive cell densities with TXL_20_40 and TXL_40_40 were comparable with that with PTZ‐control (<italic toggle=\"yes\">p</italic> = 0.004, 0.937 and 0.132, respectively, compared to that of PTZ‐control; two‐tailed Mann–Whitney U test). In contrast, TXL_40_20 demonstrated a higher density of 58.85 cells mm<sup>−2</sup> (SEM = 2.06 cells mm<sup>−2</sup>) than that of PTZ‐control (<italic toggle=\"yes\">p</italic> = 0.041; two‐tailed Mann–Whitney U test). The degree of GFAP expression with TXH_0.25_30 was similar to that with PTZ‐control (<italic toggle=\"yes\">p</italic> = 0.485; two‐tailed Mann–Whitney U test), demonstrating a reduced level of 50.18 cells mm<sup>−2</sup> (SEM = 2.08 cells mm<sup>−2</sup>). TX_HYBRID presented a higher GFAP‐density level of 66.43 cells mm<sup>−2</sup> (SEM = 2.36 cells mm<sup>−2</sup>) than the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.002; two‐tailed Mann–Whitney U test).</p>", "<title>Multitemporal Neurotransmitter Analysis Through Microdialysis</title>", "<p>Changes in neurotransmitters through bidirectional neuromodulation were measured using proteomic analysis of ISF samples at baseline and 0, 8, and 16 min after sonication (Figure ##SUPPL##0##S2A–C##, Supporting Information). In hybrid transmission, an additional ISF sample was acquired between the two transmissions. For comparison, the changes in the neurotransmitter levels were divided by the baseline values. In the PTZ‐control group, the levels of glutamate were observed to be increased, while that of GABA was observed to be decreased (Figure ##FIG##5##6B##) compared to the baseline levels after PTZ injection. In contrast, the use of TXL_40_40 significantly reversed the pattern of GABA concentration changes observed in the PTZ‐control (<italic toggle=\"yes\">p</italic> = 0.030; two‐tailed Mann–Whitny U test) while a decrease in glutamate was not significant compared with that in the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.530; two‐tailed Mann–Whitney U test). After the stimulation, GABA levels became similar with that in the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.343 and <italic toggle=\"yes\">p</italic> = 1.000 at 0 – 8 min and 20 – 28 min after rtFUS, respectively; two‐tailed Mann–Whitny U test). The glutamate concentration decreased during TXL_40_20 was trending toward significance (<italic toggle=\"yes\">p</italic> = 0.073 compared to that of PTZ‐control; two‐tailed Mann–Whitny U test) while the GABA decrease during TXL_40_20 application was not significant (<italic toggle=\"yes\">p</italic> = 0.202 compared to that of PTZ‐control; two‐tailed Mann–Whitny U test). However, the GABA concentration in TXL_40_20 group at 20–29 min after rtFUS dropped significantly compared to that in the PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.018, compared to that of the PTZ‐control; two‐tailed Mann–Whitny U test) while glutamate levels were similar between two groups. With hybrid transmission, both GABA and glutamate levels became lower during the second transmission (TXH_0.25_30) than PTZ‐control (<italic toggle=\"yes\">p</italic> = 0.030 and 0.048 for GABA and glutamate, respectively, compared to that of the PTZ‐control; two‐tailed Mann–Whitny U test), but immediately became similar with that in PTZ‐control group (<italic toggle=\"yes\">p</italic> = 0.876 and 0.343 for GABA and glutamate, respectively, compared to that of the PTZ‐control; two‐tailed Mann–Whitny U test).</p>" ]
[ "<title>Discussion</title>", "<p>In previous studies, tFUS that sonicated a brain region a single time was more or less effective in lowering epileptiform activities. In the current study, rtFUS, which involves the repetitive transmission of elongated bursts, was first introduced. In contrast to tFUS, rtFUS was able to fully suppress epileptic discharge, resulting in a state comparable to baseline brain responses as measured by EEG and CBV. Surprisingly, the c‐Fos response in the IHC study was barely expressed in the brain samples receiving TXL_40_40 stimulation, whereas the response rate of GAD65 was highest with TXL_40_40 that repeated to transmit a 40 s long low‐intensity burst six times with an interval of 40 s. In microdialysis studies, GABA levels during stimulation with TXL_40_40 were prominently increased, and this observation could support the highest number of GAD65 stains after stimulation with TXL_40_40. Meanwhile, the use of a single transmission of a 40 s long burst suppressed epileptiform activities for a brief period and eventually resulting in symptoms similar to those of the PTZ‐control group. These results suggested that repetitive ultrasonic stimulation with elongated bursts can provide reliable and sustainable suppressive effects by modulating GABA release.</p>", "<p>In contrast to TXL_40_40, which induced seizure‐suppressive effects, shorter bursting intervals of 20 s (TXL_40_20) could exacerbate epileptiform activities, as shown by EEG, CBV, and IHC. The interval between ultrasound stimulation might not be sufficient for 20 s and needs to be longer than 40 s to maintain a reasonable GABA level for suppression. This is supported by previous findings that reported an excretion time for GABA with electrical stimulation exceeding 40 s in a mouse model.<sup>[</sup>\n##REF##32728074##\n36\n##\n<sup>]</sup> This assumption was verified by performing multitemporal measurements of neurotransmitters because the GABA level after TXL_40_20 was continuously decreased and eventually became significantly lower than that with PTZ‐control (Figure ##FIG##5##6B##). Furthermore, in immunohistochemical studies, the number of c‐Fos‐expressing cells was reduced by 85.6% in samples treated with TXL_40_40 compared to the PTZ‐control. In comparison, GAD65 expression increased by 520% compared to that in the PTZ‐control group (Figure ##FIG##5##6A##). However, with TXL_40_20, the expression of GAD65 was significantly reduced by 54.2% compared to that with TXL_40_40 whereas c‐Fos expression was comparable to that in the PTZ‐control group.</p>", "<p>Our results further demonstrated that burst pressure and length also influenced these suppressive effects. rtFUS using a sequence repeating a shorter (0.25 s) but stronger pressure (1 MPa) burst at every 30 s for eleven times (TXH_0.25_30) demonstrated only mild antiepileptic effects. Considering previous studies that reported neuronal activation with high‐pressure stimulation, TXH_0.25_30 may simultaneously activate excitatory and inhibitory neurons and reduce the net suppressive effect. As shown in the IHC results, the expression ratio of GAD65 with TXH_0.25_30 was 2.74 times higher than that of the PTZ‐Control, while the expression levels of c‐Fos, Iba‐1 and GFAP with TXH_0.25_30 were comparable with those in the PTZ‐control. Interestingly, TXH_0.25_30 induced an excitatory response when the transmit sequence was applied after TXL_40_40. Therefore, controlling the progressive direction of epileptiform activities with short‐ and high‐intensity stimulation was challenging. In contrast, burst lengths longer than 40 s clearly demonstrated seizure suppressive effects. c‐Fos expression decreased drastically, and GAD65 expression gradually increased as the burst length increased from 10 to 40 s with low stimulation pressure levels. These results indicated that the burst pressure and length of rtFUS could be key parameters in determining the progressive direction of epileptiform activities in animal models of drug‐induced epilepsy.</p>", "<p>In addition to generating different epileptiform activities for different burst lengths or intervals in rtFUS, the suppressive effects could be cleared and translated to excitatory states, worsening epileptic activity by hybrid transmission. The application of TX_HYBRID, comprising a back‐to‐back transmission of TXL_40_40 and TXH_0.25_30 with a 3 min interval, induced the transformation of the suppressant effect into a paradoxically proconvulsant cortical response (Figure ##FIG##4##5B##), although TXL_40_40 and TXH_0.25_30 alone induced strong and mild suppressive effects (Figure ##FIG##1##2B##). In the IHC experiments, the expression rates of GAD65 and c‐Fos with TX_HYBRID were higher than those in PTZ‐control. In the multitemporal neurotransmitter analysis, the elevated GABA level induced by TXL_40_40 also immediately decreased after TXH_0.25_30 treatment, becoming similar to that of the PTZ‐control. Therefore, both inhibitory and excitatory responses were induced by highly conjugated and compensatory regulation, which may also be explained by an increase in GAD65 and c‐Fos expression. Amplified excitation by TX_HYBRID also induced more extensive hippocampal damages than the responses in other animals receiving sole stimulation types. The numbers of both Iba1‐ and GFAP‐expressing cells were the highest in the TX_HYBRID group compared to that in the PTZ‐control group.</p>", "<p>Although the EEG and CBV measurement of brain activities for temporal lobe epilepsy were not located around the hippocampus, but mostly in the prefrontal cortex, the measured signals should reflect deep brain activities because of the prefrontal limbic network connection to deep brain structures.<sup>[</sup>\n##UREF##10##\n37\n##\n<sup>]</sup> Because a four‐channel EEG can measure both the frontal and midbrain regions in both hemispheres, a simple topography revealing the number of discharge peaks could be acquired by linear interpolation among the numbers from the four channels. As shown in the Supporting Information figure (Figure ##SUPPL##0##S3##, Supporting Information) and videos, the excitatory brain response to PTZ injection was initially identified in the prefrontal region, and the signal was stronger than that in the midbrain region. Furthermore, the GABA and glutamate levels measured in the deep brain region using microdialysis demonstrated temporal patterns similar to epidural electrical signal changes. In future work, deep brain electrode recordings may help acquire direct proof of the seizure modulation capability of rtFUS.</p>", "<p>The number of Iba1‐positive cells, which are reactive near‐damaged neuronal cells sharply increased in the PTZ control group compared to that of the normal control group. The amount of activation increased with TX_HYBRID and decreased with TXL_40_40 compared with PTZ‐control. Therefore, rtFUS sequences that induce more frequent EEG discharges could induce higher cellular damage than that of other sequences. In contrast, other sequences suppressing epileptiform activities could preserve neuronal cells, although they could not fully recover from the damage caused by suppressive treatments. To confirm that the damage to neuronal cells was caused by the proconvulsant effect and not by the delivery of ultrasonic energy, Cresyl Violet staining was performed on the normal control and PTZ‐/rtFUS+ groups. The Nissl‐stained brain slice images demonstrated no damage to the rat brain after TXH_0.25_30 and TXL_40_40 stimulations, which may be the worst cases for sonication amplitude and time, respectively (Figure ##SUPPL##0##S4##, Supporting Information).</p>", "<p>Bidirectional neuromodulation was achieved by adjusting the acoustic parameters of stimulation strength, length, and the interval of stimulus repetition. For instance, post‐stimulus extracellular GABA level was lowered by shorter intervals of longer stimulation length (TXL_40_20) that might cause GABA depletion because post‐stimulus GABA release took tens of seconds to occur, as demonstrated in a prior study using electrical stimulation<sup>[</sup>\n##UREF##4##\n24\n##\n<sup>]</sup> and the stimulation before the GABA recovery might reduce extracellular GABA. Meanwhile, a longer interval (TXL_40_40) could elevate extracellular GABA by allowing sufficient post‐stimulus GABA recovery time. Although we demonstrated the changes in GABA over time using protein analysis with microdialysis, further analysis using a device that presents the changes in GABA with higher time resolution, such as an implantable electrochemical GABA sensor,<sup>[</sup>\n##REF##32728074##\n36\n##\n<sup>]</sup> may be needed to prove the depletion and recovery of post‐stimulus GABA over time. Moreover, molecular mechanistic studies are required to extend bidirectional control to other applications. A study has shown that the astrocytic mechanosensitive TRPA1 channel plays a significant role in inducing neuronal activation and eventually releasing glutamate by low‐intensity ultrasound stimulation,<sup>[</sup>\n##REF##32155416##\n38\n##\n<sup>]</sup> while there are only limited molecular mechanistic studies investigating pathways of GABA release in response to ultrasound stimulation. The navigation of possible pathways that activate GABA excretion with ultrasound stimulation should be planned to clearly understand bidirectional neuromodulation.</p>", "<p>We demonstrated the effectiveness of rtFUS in modulating acutely elevated neuronal responses in a chemically induced epilepsy model. As both anticonvulsive and proconvulsive effects were immediately acquired and sustained for at least 30 min using low‐intensity rtFUS, the pulse sequence may be applied to treat epilepsy in the clinic. To achieve this, a seizure detection system, such as a closed‐loop system with EEG, will need to be combined with rtFUS to rapidly suppress signals by sonication as soon as epileptiform activities are detected. Furthermore, this technology may be applicable to other neuronal disorders originating from a dysfunction in the control of neurotransmitters, such as depression and drug addiction.<sup>[</sup>\n##REF##30946828##\n39\n##, ##REF##37041107##\n40\n##, ##REF##30569209##\n41\n##, ##UREF##11##\n42\n##\n<sup>]</sup> As introduced in a previous review,<sup>[</sup>\n##UREF##12##\n43\n##\n<sup>]</sup> ultrasound neuromodulations with tFUS are highlighted to be effective in brain therapeutics while the efficacies in some results were mild. The use of different ultrasound pulse sequences modulates different outcomes in treating Alzheimer's disease.<sup>[</sup>\n##UREF##13##\n44\n##\n<sup>]</sup> Therefore, we expect that the efficacies of ultrasound neuromodulation can be amplified and prolonged by using rtFUS.</p>" ]
[ "<title>Conclusion</title>", "<p>In our study, the bidirectional modulation of epileptiform brain activity was first demonstrated by changing the burst duration, interval, and amplitude of rtFUS. A stimulation train repeating elongated bursts with sufficiently long intervals was shown to effectively suppress epileptiform activities. In contrast, stimulation transmitting the same burst length with a shorter interval worsened the epileptic responses. Furthermore, the suppressive effect achieved by the long burst could be reversed using a short, strong burst train, leading to a shift from a suppressive to an excitatory state. The IHC and proteomic analyses conducted in this study allowed us to conclude that bidirectional modulation of epileptiform activity with rtFUS was achieved by controlling the excretion of GABA in sonicated brain tissue.</p>" ]
[ "<title>Abstract</title>", "<p>Repetitive stimulation procedures are used in neuromodulation techniques to induce persistent excitatory or inhibitory brain activity. The directivity of modulation is empirically regulated by modifying the stimulation length, interval, and strength. However, bidirectional neuronal modulations using ultrasound stimulations are rarely reported. This study presents bidirectional control of epileptiform activities with repetitive transcranial‐focused ultrasound stimulations in a rat model of drug‐induced acute epilepsy. It is found that repeated transmission of elongated (40 s), ultra‐low pressure (0.25 MPa) ultrasound can fully suppress epileptic activities in electro‐encephalography and cerebral blood volume measurements, while the change in bursting intervals from 40 to 20 s worsens epileptic activities even with the same burst length. Furthermore, the suppression induced by 40 s long bursts is transformed to excitatory states by a subsequent transmission. Bidirectional modulation of epileptic seizures with repeated ultrasound stimulation is achieved by regulating the changes in glutamate and γ‐Aminobutyric acid levels, as confirmed by measurements of expressed c‐Fos and GAD65 and multitemporal analysis of neurotransmitters in the interstitial fluid obtained via microdialysis.</p>", "<p>Bidirectional control of epileptiform activities can be achieved by changing stimulus parameters for repetitive transcranial focused ultrasound. The repeated sonication of elongated burst with longer intervals can increase extracellular GABA and induce suppressive effects while the same burst with shorter intervals returns opposite responses. Furthermore, the suppressed epileptiform transforms the excitatory state by following stronger short bursts.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6900-cit-0053\">\n<string-name>\n<given-names>T.</given-names>\n<surname>Choi</surname>\n</string-name>, <string-name>\n<given-names>M.</given-names>\n<surname>Koo</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Joo</surname>\n</string-name>, <string-name>\n<given-names>T.</given-names>\n<surname>Kim</surname>\n</string-name>, <string-name>\n<given-names>Y.‐M.</given-names>\n<surname>Shon</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Park</surname>\n</string-name>, <article-title>Bidirectional Neuronal Control of Epileptiform Activity by Repetitive Transcranial Focused Ultrasound Stimulations</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2302404</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202302404</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<p>All animal experiments were performed in accordance with the Korean Ministry of Food and Drug Safety Guide for the Care and Use of Laboratory Animals and were conducted according to protocols approved by the Institutional Animal Care and Use Committees (IACUC). This study was reviewed and approved by the IACUC of Samsung Biomedical Research Institute (SBRI) and WOOJUNG BIO (Approval Numbers: SBRIIACUC20200109003 and IACUC2301‐025). SBRI and WOOJUNG BIO are Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC International) accredited facility and abide by the Institute of Laboratory Animal Resources (ILAR) guide.</p>", "<title>Animal Preparation and Epileptic Induction</title>", "<p>Fifty‐nine 8‐week‐old male Sprague–Dawley rats weighing 300–320 g (Orient Bio, Inc.) were used in the experiments. For the EEG, eight rats were chosen for the non‐stimulated PTZ+/tFUS‐control (PTZ‐control) group, and five rats were chosen for each stimulated experimental group. IHC was performed within the EEG group for five rats in each of the PTZ‐control and stimulated experimental groups, and five additional rats were evaluated as the PTZ‐/tFUS‐control (normal control) group. For wide‐field optical imaging, six rats each from the PTZ control, normal control, and stimulated experimental groups were evaluated. For the microdialysis, eight rats were chosen for PTZ‐control, and five rats were chosen for each group of TXL_40_40, TXL_40_20 and TX_Hybrid. (<bold>Table</bold>\n##TAB##0##\n1\n##) Animals were anesthetized using urethane (1.25 g kg<sup>−1</sup> body weight in 1.25 g 4 mL<sup>−1</sup> saline; Sigma–Aldrich, U‐2500‐500G) and pentylenetetrazol (100 mg kg<sup>−1</sup> body weight in 10 mg 0.1 mL<sup>−1</sup> saline; Sigma–Aldrich, P6500‐25G), administered acutely and intraperitoneally to induce epileptic seizures.</p>", "<title>Ultrasound Transducer Fabrication</title>", "<p>A lead zirconate titanate (Del Piezo Specialties LLC., DL‐47) 690 kHz single‐element ring transducer with inner and outer diameters of 10 and 31 mm, respectively, was fabricated with a focal distance of 45 mm and a bandwidth of 25%. An acoustic coupling gel‐filled cone‐shaped beam guide was attached to the front side of the transducer. The beam was focused 5 mm ahead of the tip of the collimator with −3 dB beam sizes of 4.7 and 2.2 mm along the axial and lateral directions, respectively (Figure ##SUPPL##0##S1A##, Supporting Information). By placing the tip of the transducer above the parietal bone, the acoustic beam was delivered to the right anterior thalamic nuclei (ATN) (AP = −1.5 mm, ML = + 1.5 mm, DV = 5.0–5.5 mm; AP denotes the anterior (+) or posterior (−) distance from the bregma; ML denotes the lateral distance from the bregma; and DV denotes the dorsoventral distance from the bregma). The beam pathway was confirmed by overlaying the beam profile on the Paxinos rat brain atlas<sup>[</sup>\n##UREF##14##\n45\n##\n<sup>]</sup> along the sagittal and coronal planes (Figure ##SUPPL##0##S1B,C##, Supporting Information).</p>", "<title>Sonication and Monitoring Protocol</title>", "<p>The stimuli were classified into two types to simplify the ultrasonic conditions and mimic electrical stimulations generating rebound excitations: one with a low‐pressure (0.25 MPa) consecutive burst train (TXL sequences), and the other with shorter, high‐pressure (1.0 MPa) bursts (TXH sequence) with a 50% duty cycle of 100 Hz pulse repetition frequency. TX_HYBRID, a back‐to‐back transmission of TXL_40_40 and TXH_0.25_30 was generated assuming that rebound excitation could be artificially induced using brief excitation followed by inhibitory stimulation.</p>", "<p>Figure ##SUPPL##0##S1D## (Supporting Information) depicts the entire experimental platform for delivering ultrasonic energy to the target region and recording EEG signals. The rats were anchored to a custom‐made stereotaxic frame (Scitech Korea, Inc.), and ultrasound pulsation was generated using two function generators. The first function generator (Tektronix, AFG3252) sent out a pulse train of 100 Hz, and the second function generator (Agilent, 33250A) transmitted a 5 ms, 3450 cycle, 690 kHz burst to secure a 50% duty cycle (Figure ##SUPPL##0##S1D##, Supporting Information) at every rising edge in the pulse train from the first function generator. The generated waveform was then passed through a radiofrequency power amplifier (Electronics and Innovation, 350 L) and applied to the transducer. The experimental protocol involved: 1) anesthesia; 2) pre‐tFUS (baseline) monitoring; 3) PTZ injection and sonication; 4) post‐tFUS monitoring; and 5) euthanization and brain tissue harvesting. Figure ##FIG##0##1## shows the overall timeline of sonication and data acquisition.</p>", "<title>EEG Recording</title>", "<p>The rats were stereotactically implanted with five cortical screw electrodes (Fine Science Tools, 19010‐00 screws) to record the EEG signals (Figure ##SUPPL##0##S1A##, Supporting Information). The implantation coordinates were adopted based on a stereotactic atlas<sup>[</sup>\n##UREF##14##\n45\n##, ##UREF##15##\n46\n##\n<sup>]</sup>: C4/C3 (primary motor cortex; A = + 2.2 mm, L = ± 3.2 mm) and T6/T5 (temporal association cortex; A = −8.3 mm, L = ± 5.8 mm). A reference ground electrode was implanted on the posterior side of the lambda. EEG was performed to monitor changes in neuronal activity using a four‐channel commercial EEG acquisition system (Natus, NicoletOne vEEG) at a sampling rate of 500 Hz. The ratio of the number of epileptic spikes at baseline to the number at specific time points was calculated to assess the epileptic severity. Epileptic spikes were defined as local maximum points with amplitudes greater than twice the standard deviation from individual baseline EEG activities lasting 70 ms. The discharge peaks of the EEG signal were counted every 30 s in a 1 min segment across the monitoring period and averaged every 10 min for each animal. The power spectral density values were computed for every 1 min segment using Welch's method and also averaged every 10 min for each animal. Pairwise comparison was made at each time period for the statistical analysis where each value represented a single value from a single animal.</p>", "<title>Immunohistochemistry</title>", "<p>IHC was performed using c‐Fos, GAD65, Iba‐1, and GFAP staining of rat brain sections. The rats were euthanized after the EEG recording and transcardially perfused with saline to obtain brain tissue samples. The ratio of c‐Fos‐positive cells to total cells in the granular layer of the dentate gyrus was quantified using ImageJ software (National Institutes of Health, 1.53c) to compare the degree of excitatory responses generated under ultrasonic stimulus conditions. To compare inhibitory synaptic transmission, GAD65‐positive cell densities were measured in the molecular and granular layers of the dentate gyrus. Staining for Iba1 and GFAP was performed to investigate the reactivity of microglia and astrocytes, respectively, by computing the Iba1‐ and GFAP‐positive cell densities. All values were measured three times independently from a different person in a random order to avoid biased erroneous measurement and averaged in a single value for each animal. A pairwise comparison was made where each value represented a single value from a single antibody‐stained brain slice from a single animal.</p>", "<title>Cerebral Blood Volume Measurement</title>", "<p>Craniotomies were performed on isoflurane‐anesthetized rats secured in a custom‐made stereotaxic frame. The cranial window region was created above the left ATN (A = −1.5 mm, L = −1.5 mm), such that the rtFUS stimulus could be applied on the right ATN while simultaneously imaging the cranial window (Figure ##SUPPL##0##S2C,D##, Supporting Information). After an overnight recovery, urethane (1.25 mg kg<sup>−1</sup> body weight) was injected intraperitoneally for wide‐field optical imaging.</p>", "<p>Optical measurement was conducted for the normal control, PTZ‐control, and tFUS‐stimulated groups to examine the regional hemodynamic response of cerebral blood volume (CBV). The imaging system consisted of a macro‐zoom microscope (Olympus, MVX10), an sCMOS camera (Andor, Zyla 5.5), and a light‐emitting diode source (Figure ##SUPPL##0##S2C##, Supporting Information). For the experiment, raw reflectance data were collected under green (530 nm) light, as 530 nm is primarily sensitive to changes in the local total blood volume, denoted as the HbT.<sup>[</sup>\n##REF##31834545##\n47\n##, ##UREF##16##\n48\n##\n<sup>]</sup> Each imaging trial was recorded for 30 min, including a 2 min baseline (pre‐PTZ/tFUS).</p>", "<title>Microdialysis</title>", "<p>Microdialysis analysis was conducted to determine the amount of neurotransmitter secreted during the alterations in epileptiform activities generated by the rtFUS transmission sequences (Figure ##SUPPL##0##S2A##, Supporting Information) to demonstrate the cause of bidirectional modulation in animal models of drug‐induced epilepsy. The guide cannula was implanted in twenty male Sprague‐Dawley rats weighing 300–320 g (Koatech, Inc.) under respiratory anesthesia using a hand drill at the target coordinates of the hippocampal region CA2/CA3 (Coordinates −3.80 mm posterior (AP), −4.40 mm lateral (ML), and −2.20 mm ventral (DV), 26 degrees lateral) (Figure ##SUPPL##0##S2B##, Supporting Information). After the guide cannula reached the target coordinates, dental cement was applied for fixation, avoiding the position of the ultrasound transducer, and the incision site was sutured with a silk suture for the recovery period. For proteomic analysis, five rats were chosen for the PTZ‐control group (PTZ+/tFUS‐) and five rats were chosen for each experimental group: TXL_40_40, TXL_40_20, and TX_HYBRID.</p>", "<p>Two days after the guide cannula insertion surgery, the recovered rats were intraperitoneally anesthetized with urethane (1.25 g kg<sup>−1</sup> body weight in 1.25 g 4 mL<sup>−1</sup> saline; Sigma–Aldrich, U‐2500‐500G). After the anesthetized rats were secured to the stereotaxic frame, the dummy was removed from the guide cannula and a CMA12 1‐mm membrane probe (CMA Microdialysis) was inserted. A 5 mL glass syringe filled with aCSF (M dialysis AB) was mounted on a syringe pump (KD Scientific) and connected to the probe inlet. The tubing was connected to the probe outlet to collect the interstitial fluid (ISF) in a sample collector (BASi, U.S.A). After ≈1 h of stabilization (1 point 8 min<sup>−1</sup>), Interstitial fluid (ISF) was collected by sampling for 1 h. For microdialysis, samples were collected for 8 min at a flow rate of 1.3 µL min<sup>−1</sup> in order to obtain a sufficient amount (minimum 10 µL) of ISF for the neurotransmitter analysis. The sample collection time was minimized to match the sonication duration (440 s/340 s), but due to the fixed flow rate and the minimum required collection volume, the sample collection time was inevitably longer than the sonication duration. Therefore, a portion of the baseline (40 s for TXL_40_40 and 140 s for TXL_40_20) was collected together when analyzing the neurotransmitter concentration during the rtFUS. All samples were stored in a freezer at −80 °C.</p>", "<p>Neurotransmitter analysis of the microdialysis samples was conducted using LC‐MS/MS in NeuroVIS (Chungcheongnam‐do, Republic of Korea). <bold>Table</bold>\n##TAB##1##\n2\n## presents the analytical conditions of the LC‐MS/MS instrument. To separate GABA and glutamate in the LC‐MS/MS system composed of ExionLC Series UHPLC, AB SCIEX Triple Quadrupole 6500+, and ESI (SCIEX, Framingham), an ACQUITY UPLC HSS T3 column (2.1 × 100 mm, 1.8 µm, Waters, Milford, MA, USA) at 50 °C was used. The mobile phase consisted of 1) water containing 0.1% FA and 5 m<sc>m</sc> ammonium formate and 2) a 1:1 mixture of methanol and acetonitrile containing 5 m<sc>m</sc> ammonium formate. The flow rate was adjusted at 0.3 mL min<sup>−1</sup>, and a 7 µL per sample was injected in LC‐MS/MS. Multiple reaction monitoring (MRM) was performed in the positive mode for each NTs. The experiment was conducted at an ion transfer temperature of 500 °C, and a positive ion spray voltage of 5000 V.</p>", "<title>Statistical Analyses</title>", "<p>All experimental data were analyzed using statistics software (IBM, SPSS Statistics 27). In order to determine whether the data from each group follows a normal distribution, the Shapiro‐Wilk test<sup>[</sup>\n##UREF##17##\n49\n##\n<sup>]</sup> was performed. Once the normality was confirmed, the statistical significance of the difference between a sonicated group and the PTZ‐control group was assessed by <italic toggle=\"yes\">t</italic>‐test. For the <italic toggle=\"yes\">t</italic>‐test, a paired <italic toggle=\"yes\">t</italic>‐test was employed in case the data were compared by time within the same group. If the distribution of the data departed significantly from the normality, a non‐parametric Mann–Whitney U test was performed to compare the significance of the difference. The type of test used for the statistical analysis was presented along with the p‐values throughout the paper. The purpose of experiments in this paper was to find either upregulating or downregulating effects for each stimulation sequence independently by comparing the effect with the control group. The neuromodulation effect for each stimulation sequence was only observed from a rat group of PTZ‐control that did not receive other stimulation sequences. Therefore, two‐sided Mann–Whitney U test was employed without considering multiple comparison corrections. <italic toggle=\"yes\">p</italic> &lt;0.05 was considered statistically significant and was marked as ** <italic toggle=\"yes\">p</italic> &lt;0.10 was considered trending toward statistical significance and was marked as *<italic toggle=\"yes\">p</italic> &gt; 0.10 was considered non‐significant and was marked as NS throughout the paper. Although <italic toggle=\"yes\">p</italic> &lt; 0.05 was the typical standard significance threshold in the general scientific community, the differences <italic toggle=\"yes\">p</italic> &lt;0.10 were also provisioned on the figures as providing the information may still identify potential trends – especially considering the small sample sizes – and suggest a potentially meaningful relationship that warrants further study.<sup>[</sup>\n##UREF##18##\n50\n##\n<sup>]</sup> Effects with significance of <italic toggle=\"yes\">p</italic> &lt;0.10 were termed as “mild” throughout the paper. The sample sizes were determined by using the resource equation method.<sup>[</sup>\n##UREF##19##\n51\n##, ##REF##24250214##\n52\n##\n<sup>]</sup>\n</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>T.C. and M.K. contributed equally to this work. This work was supported in part by grants from the National Research Foundation of Korea (NRF) funded by the Korean government (MIST) NRF‐2020R1A2C2011808 (J.P.), NRF‐2021R1A4A1028713 (J.P.), and NRF‐2019M3C1B8090805 (J.P.). Also, this research was partially supported by the K‐Brain Project of National Research Foundation (NRF) funded by the Korean government (MIST) (RS‐2023‐00265524) and a grant of the Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea (grant number: HR21C0885)</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available from the corresponding author upon reasonable request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6900-fig-0001\"><label>Figure 1</label><caption><p>Sonication and EEG recording protocol. A) Summary of the overall experimental protocols for sonication and EEG recording. B) Detailed timeline of rtFUS stimulation and EEG recording for all transmit condition groups. <underline underline-style=\"single\">TXH_0.25_30</underline> is a sequence repeating eleven times of 1 MPa, 0.25 s bursts with 30 s intervals. <underline underline-style=\"single\">TXL_40_40</underline> is a sequence repeating six times of 0.25 MPa, 40 s bursts with 40 s intervals. <underline underline-style=\"single\">TXL_10_50</underline> is a sequence repeating six times of 0.25 MPa, 10 s bursts with 50 s intervals. <underline underline-style=\"single\">TXL_20_40</underline> is a sequence repeating six times of 0.25 MPa, 20 s bursts with 40 s intervals. <underline underline-style=\"single\">TXL_40_20</underline> is a sequence repeating six times of 0.25 MPa, 40 s bursts with 20 s intervals. <underline underline-style=\"single\">TX_HYBRID</underline> is a sequence that consecutively applies TXL_40_40 and TXH_0.25_30 with 3 min resting period in between the two sequences.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6900-fig-0002\"><label>Figure 2</label><caption><p>Changes in epileptiform activities during and after TXH_0.25_30, TXL_40_40, and TXL_40_Single. A) Time courses of EEG signals in the PTZ‐control and stimulated experimental groups. B) Time courses of the number of epileptic spikes ratio in each group (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). C) Ratio of the number of epileptic spikes measured at time periods of 0–10 min (10AS) and 10–20 min (20AS) (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). D) Power spectral density ratio of EEG signals at the delta (0.5–3 Hz) and theta (4–7 Hz) frequency bands (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). E) Changes in the cerebral blood volume [Hb] calculated from 530 nm reflectance data (PTZ‐control: <italic toggle=\"yes\">n</italic> = 6, TX groups: <italic toggle=\"yes\">n</italic> = 6). Data presented as mean ± SEM, <italic toggle=\"yes\">p</italic>‐values calculated via two‐tailed Mann–Whitney U test, <bold>\n<sup>**</sup>\n</bold> : <italic toggle=\"yes\">p</italic> &lt;0.05, * : <italic toggle=\"yes\">p</italic> &lt;0.10, NS : <italic toggle=\"yes\">p</italic>&gt; 0.10. <italic toggle=\"yes\">p</italic> = ① 0.036 ② 0.030 ③ 0.030 ④ 0.045 ⑤ 0.019 ⑥ 0.093.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6900-fig-0003\"><label>Figure 3</label><caption><p>Changes in epileptiform activities during and after TXL_10_50, TXL_20_40, and TXL_40_40. A) Time courses of EEG signals in the PTZ‐control and stimulated experimental groups. B) Time courses of the number of epileptic spikes ratio in each group (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). C) Ratio of the number of epileptic spikes measured at time periods of 0–10 min (10AS) and 10–20 min (20AS) (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). D) Power spectral density ratio of EEG signals at the delta (0.5–3 Hz) and theta (4–7 Hz) frequency bands (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). E) Changes in the cerebral blood volume [Hb] calculated from 530 nm reflectance data (PTZ‐control: <italic toggle=\"yes\">n</italic> = 6, TX groups: <italic toggle=\"yes\">n</italic> = 6). Data presented as mean ± SEM, <italic toggle=\"yes\">p</italic>‐values calculated via two‐tailed Mann‐Whitney U test, ** : <italic toggle=\"yes\">p</italic> &lt;0.05, * : <italic toggle=\"yes\">p</italic> &lt;0.10, NS : <italic toggle=\"yes\">p</italic>&gt; 0.10. <italic toggle=\"yes\">p</italic> = ① 0.030 ② 0.030 ③ 0.045 ④ 0.019.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6900-fig-0004\"><label>Figure 4</label><caption><p>Changes in epileptiform activities during and after TXL_40_20 and TXL_40_40. A) Time courses of EEG signals in the PTZ‐control and stimulated experimental groups. B) Time courses of the number of epileptic spikes ratio in each group (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). C) Ratio of the number of epileptic spikes measured at time periods of 0–10 min (10AS) and 10–20 min (20AS) (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). D) Power spectral density ratio of EEG signals at the delta (0.5–3 Hz) and theta (4–7 Hz) frequency bands (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). E) Changes in the cerebral blood volume [Hb] calculated from 530 nm reflectance data (PTZ‐control: <italic toggle=\"yes\">n</italic> = 6, TX groups: <italic toggle=\"yes\">n</italic> = 6). Data presented as mean ± SEM, <italic toggle=\"yes\">p</italic>‐values calculated via two‐tailed Mann–Whitney U test, ** : <italic toggle=\"yes\">p</italic> &lt;0.05, * : <italic toggle=\"yes\">p</italic> &lt;0.10, NS : <italic toggle=\"yes\">p</italic>&gt; 0.10. <italic toggle=\"yes\">p</italic> = ① 0.030 ② 0.030 ③ 0.045 ④ 0.019.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6900-fig-0005\"><label>Figure 5</label><caption><p>Changes in epileptiform activities during and after TX_HYBRID (consecutive transmits of TXL_40_40 and TXH_0.25_30). A) Time courses of EEG signals in the PTZ‐control and the stimulated experimental groups. B) Time courses of the number of epileptic spikes ratio in each group (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). C) Ratio of the number of epileptic spikes measured at time periods of 0–10 min (10AS) and 10–20 min (20AS) (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). D) Power spectral density ratio of EEG signals at the delta (0.5–3 Hz) and theta (4–7 Hz) frequency bands (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). E) Changes in the cerebral blood volume [Hb] calculated from 530 nm reflectance data (PTZ‐control: <italic toggle=\"yes\">n</italic> = 6, TX groups: <italic toggle=\"yes\">n</italic> = 6). Data presented as mean ± SEM, <italic toggle=\"yes\">p</italic>‐values calculated via two‐tailed Mann–Whitney U test, ** : <italic toggle=\"yes\">p</italic> &lt;0.05, * : <italic toggle=\"yes\">p</italic> &lt;0.10, NS : <italic toggle=\"yes\">p</italic>&gt; 0.10.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6900-fig-0006\"><label>Figure 6</label><caption><p>Immunohistochemistry results and multitemporal neurotransmitter analysis from microdialysis. A) Representative slice images and quantitative measurements from c‐Fos‐, GAD65‐, Iba1‐, and GFAP‐stained brain tissue at the dentate gyrus. Quantitative measurements were made in the stained cell ratio for c‐Fos and the stain‐positive cell density for GAD65, Iba1, and GFAP (PTZ‐control: <italic toggle=\"yes\">n</italic> = 6, TX groups: <italic toggle=\"yes\">n</italic> = 6). B) Changes in the normalized glutamate and GABA concentration (%) during and after TXL_40_40, TX_40_20 and TX_HYBRID compared to the baseline (PTZ‐control: <italic toggle=\"yes\">n</italic> = 8, TX groups: <italic toggle=\"yes\">n</italic> = 5). Data presented as mean ± SEM, <italic toggle=\"yes\">p</italic>‐values calculated via two‐tailed Mann–Whitney U test, ** : <italic toggle=\"yes\">p</italic> &lt;0.05, * : <italic toggle=\"yes\">p</italic> &lt; 0.10, NS : <italic toggle=\"yes\">p</italic>&gt; 0.10. <italic toggle=\"yes\">p</italic> = ① 0.002 ② 0.002 ③ 0.093 ④ 0.004 ⑤ 0.004 ⑥ 0.002 ⑦ 0.015 ⑧ 0.002 ⑨ 0.002 ⑩ 0.002 ⑪ 0.002 ⑫ 0.009 ⑬ 0.009 ⑭ 0.002 ⑮ 0.004 ⑯ 0.041 ⑰ 0.002 ⑱ 0.048 ⑲ 0.073 ⑳ 0.062 ㉑ 0.088 ㉒ 0.073 ㉓ 0.003 ㉔ 0.030 ㉕ 0.018.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6900-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>Animal Allocation for Each Experimental Group and Studies.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\"/><th align=\"center\" rowspan=\"1\" colspan=\"1\">Normal Control</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">PTZ‐Control</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">TXH_0.25_30</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">TXL_10_50</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">TXL_20_40</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">TXL_40_40</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">TXL_40_20</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">TX_HYBRID</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">EEG/IHC<xref rid=\"advs6900-tbl1-note-0001\" ref-type=\"table-fn\">\n<sup>a)</sup>\n</xref>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 0/6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 8/6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 5/6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 5/6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 5/6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 5/6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 5/6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 5/6</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">CBV</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">‐</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 6</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 6</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Microdialysis</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">‐</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 8</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">‐</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">‐</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">‐</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 5</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">n = 5</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>", "<table-wrap position=\"float\" id=\"advs6900-tbl-0002\" content-type=\"Table\"><label>Table 2</label><caption><p>MRM transitions, retention times, and other conditions of GABA and glutamate.</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Analyte</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Q1 Mass (<italic toggle=\"yes\">m/z</italic>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Q3 Mass (<italic toggle=\"yes\">m/z</italic>)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">CE (V)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">CXP (V)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Retention time (min)</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Ionization polarity</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">GABA</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">104</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">87</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">15</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.97</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Positive</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Glutamate</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">148</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">84</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">25</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">0.98</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">Positive</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
[]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
[]
[]
[]
[ "<supplementary-material id=\"advs6900-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6900-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 1</p></caption></supplementary-material>", "<supplementary-material id=\"advs6900-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 2</p></caption></supplementary-material>", "<supplementary-material id=\"advs6900-supitem-0004\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 3</p></caption></supplementary-material>", "<supplementary-material id=\"advs6900-supitem-0005\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 4</p></caption></supplementary-material>", "<supplementary-material id=\"advs6900-supitem-0006\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 5</p></caption></supplementary-material>", "<supplementary-material id=\"advs6900-supitem-0007\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 6</p></caption></supplementary-material>", "<supplementary-material id=\"advs6900-supitem-0008\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Video 7</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn id=\"advs6900-tbl1-note-0001\"><label>\n<sup>a)</sup>\n</label><p>Immunohistochemical analyses were performed with n = 6 for each staining method. Additionally, the safety of focused ultrasound stimulation was evaluated in the PTZ‐/rtFUS+ group (n = 3), where TXH_0.25_30 was applied to the left hemisphere and TXL_40_40 was applied to the right hemisphere (Figure ##SUPPL##0##S4##, Supporting Information).</p></fn></table-wrap-foot>" ]
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[ "<media xlink:href=\"ADVS-11-2302404-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2302404-s007.avi\" mimetype=\"video\" mime-subtype=\"x-msvideo\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2302404-s002.avi\" mimetype=\"video\" mime-subtype=\"x-msvideo\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2302404-s004.avi\" mimetype=\"video\" mime-subtype=\"x-msvideo\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2302404-s005.avi\" mimetype=\"video\" mime-subtype=\"x-msvideo\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2302404-s006.avi\" mimetype=\"video\" mime-subtype=\"x-msvideo\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2302404-s003.avi\" mimetype=\"video\" mime-subtype=\"x-msvideo\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2302404-s008.avi\" mimetype=\"video\" mime-subtype=\"x-msvideo\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
52
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 23; 11(2):2302404
oa_package/12/5a/PMC10787102.tar.gz
PMC10787103
37953462
[ "<title>Introduction</title>", "<p>Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with high mortality rate and poor prognosis.<sup>[</sup>\n##REF##30970190##\n1\n##, ##REF##33479224##\n2\n##\n<sup>]</sup> The five‐year overall survival rate exceeds 70% for early‐stage HCC, while the median survival of advanced (metastatic) HCC patients is ≈1.5 years.<sup>[</sup>\n##REF##33479224##\n2\n##\n<sup>]</sup> Metastatic HCC is less effective for surgical treatment and more resistant to drug therapy.<sup>[</sup>\n##REF##32017145##\n3\n##, ##REF##24700742##\n4\n##\n<sup>]</sup> Metastasis is a pivotal process, frequently accompanied by dynamic metabolic alterations.<sup>[</sup>\n##REF##35821160##\n5\n##, ##REF##33899000##\n6\n##\n<sup>]</sup> During the progress of metastasis, cancer cells utilize multiple mechanisms including lipid accumulation to favor cancer cell survival and provide energy to distant metastasis.<sup>[</sup>\n##REF##33462499##\n7\n##\n<sup>]</sup> Lipid metabolism reprogramming is actually another cancer hallmark, which is a complex cascade controlled by various factors, and AMP‐activated protein kinase (AMPK) and acetyl‐CoA carboxylase (ACC) are two key regulators among them.<sup>[</sup>\n##REF##35022204##\n8\n##, ##UREF##0##\n9\n##, ##REF##23446547##\n10\n##\n<sup>]</sup> AMPK is a metabolic sensor in mammals activated by the increased cellular ratio of AMP/ATP.<sup>[</sup>\n##REF##36316383##\n11\n##\n<sup>]</sup> ACC is the rate‐limiting enzyme for fatty acid synthesis, and can be inhibited by AMPK.<sup>[</sup>\n##UREF##0##\n9\n##, ##REF##36316383##\n11\n##, ##REF##30244972##\n12\n##\n<sup>]</sup>\n</p>", "<p>Circular RNAs (circRNAs) are a class of endogenous RNA transcripts, generated by back‐splicing from linear precursor RNAs or other RNA circularization mechanisms.<sup>[</sup>\n##REF##34865956##\n13\n##, ##REF##31395983##\n14\n##, ##REF##31973951##\n15\n##, ##REF##32048164##\n16\n##, ##REF##25664725##\n17\n##\n<sup>]</sup> Most circRNAs localize to the cytoplasm in an Exportin 4 dependent mechanism,<sup>[</sup>\n##REF##36182935##\n18\n##\n<sup>]</sup> and cytoplasmic circRNAs mainly function through sponging miRNAs, modulating RNA binding proteins (RBPs), and serving as translation templates.<sup>[</sup>\n##REF##34865956##\n13\n##, ##REF##23446348##\n19\n##, ##UREF##1##\n20\n##, ##REF##31619685##\n21\n##, ##REF##33664496##\n22\n##, ##REF##31027518##\n23\n##\n<sup>]</sup> Compiling studies have been carried out to investigate the molecular and cellular functions of circRNAs, although only a handful of circRNAs have been studied for the physiological roles with genetically manipulated mice, in which the expression of the corresponding circRNAs is missing or at a low level.<sup>[</sup>\n##REF##34865956##\n13\n##, ##REF##31395983##\n14\n##, ##REF##31973951##\n15\n##\n<sup>]</sup> The mammalian conserved circRNA <italic toggle=\"yes\">CDR1as</italic> impacts brain development and function by sequestering <italic toggle=\"yes\">miR‐7</italic>.<sup>[</sup>\n##REF##23446348##\n19\n##, ##UREF##1##\n20\n##\n<sup>]</sup>\n<italic toggle=\"yes\">CircBoule</italic>, a circRNA conserved in metazoan, plays roles in the antistress reaction of sperm by regulating the stability of heat shock proteins.<sup>[</sup>\n##UREF##2##\n24\n##\n<sup>]</sup>\n<italic toggle=\"yes\">Cia‐cGAS</italic> regulates the differentiation of hematopoietic stem cells by binding and inhibiting cGAS in bone marrow.<sup>[</sup>\n##REF##29625897##\n25\n##\n<sup>]</sup>\n</p>", "<p>In cancers, an array of circRNAs have been shown to play regulatory roles.<sup>[</sup>\n##REF##34912049##\n26\n##, ##UREF##3##\n27\n##\n<sup>]</sup> For example, <italic toggle=\"yes\">circNSUN2</italic> interacts with IGF2BP2 to form a circNSUN2‐IGF2BP2‐HMGA2 ternary complex to promote liver metastasis of colorectal cancer.<sup>[</sup>\n##REF##31619685##\n21\n##\n<sup>]</sup> The circRNA <italic toggle=\"yes\">FECR1</italic> induces extensive DNA demethylation in the FLI1 genomic locus, thereby enhancing its expression to promote metastasis of breast cancer.<sup>[</sup>\n##REF##30537986##\n28\n##\n<sup>]</sup>\n<italic toggle=\"yes\">CircTP63</italic> upregulates FOXM1 by competitively binding to <italic toggle=\"yes\">miR‐873‐3p</italic> to facilitate cell cycle progression in lung squamous cell carcinoma.<sup>[</sup>\n##REF##31324812##\n29\n##\n<sup>]</sup> Multiple circRNAs have also been reported to play roles in HCC.<sup>[</sup>\n##REF##31027518##\n23\n##, ##REF##28520103##\n30\n##, ##UREF##4##\n31\n##\n<sup>]</sup> For example, <italic toggle=\"yes\">circMTO1</italic> suppresses HCC progression by serving as an <italic toggle=\"yes\">miR‐9</italic> sponge to promote the expression of p21.<sup>[</sup>\n##REF##28520103##\n30\n##\n<sup>]</sup>\n<italic toggle=\"yes\">CircPABPC1</italic> represses both intrahepatic and distant metastases in HCC through the degradation of ITGB1 in a ubiquitination‐independent manner.<sup>[</sup>\n##UREF##4##\n31\n##\n<sup>]</sup>\n<italic toggle=\"yes\">Circβ‐catenin</italic> promotes the HCC cell growth and metastasis via encoding a small protein, which stabilizes the full‐length β‐catenin to activate the Wnt pathway.<sup>[</sup>\n##REF##31027518##\n23\n##\n<sup>]</sup> CircRNAs can participate in HCC in multiple ways,<sup>[</sup>\n##REF##31027518##\n23\n##, ##REF##28520103##\n30\n##, ##UREF##4##\n31\n##\n<sup>]</sup> although there is so far no circRNA identified to regulate HCC metastasis by modulating lipid metabolism.</p>", "<p>Most of the studies in cancer circRNAs have been carried out with tumor cell lines, with associated clinical specimens and data, and sometimes with nude mice models.<sup>[</sup>\n##REF##34912049##\n26\n##, ##UREF##3##\n27\n##, ##UREF##5##\n32\n##\n<sup>]</sup> Lots of circRNAs with identified functions in cancer are not conserved between human and mice, which in some way hampers in‐depth investigations for roles of circRNAs and the underlying mechanisms with animal models. Identification of conserved circRNAs with critical roles in HCC yields meaningful insights into potential biomarkers and therapeutic targets.</p>", "<p>In an effort to explore the roles of circRNAs in HCC metastasis, we have identified a mammalian conserved circRNA <italic toggle=\"yes\">circLARP1B</italic>. With a series of bioinformatics, molecular, biochemical, and cellular analyses, and very importantly by using genetically modified mice, we have provided data to support roles of <italic toggle=\"yes\">circLARP1B</italic> in HCC. We have uncovered that <italic toggle=\"yes\">circLARP1B</italic> disturbs heterogeneous nuclear ribonucleoprotein D (HNRNPD) from the binding to 3′ UTR of <italic toggle=\"yes\">liver kinase B1</italic> (<italic toggle=\"yes\">LKB1</italic>), which leads to destabilizing <italic toggle=\"yes\">LKB1</italic> mRNA and then modulating a pathway pivotal to HCC metastasis and lipid metabolism.</p>" ]
[]
[ "<title>Results</title>", "<title>\n<italic toggle=\"yes\">CircLARP1B</italic> as a Mammalian Conserved CircRNA Is Identified in HCC Metastasis</title>", "<p>In order to investigate the functional roles of conserved circRNAs in HCC, we performed ribosomal RNA depleted RNA‐sequencing (RNA‐seq) of six HCC specimens, among which three HCC patients were metastatic and the other three were nonmetastatic (<bold>Figure</bold> ##FIG##0##\n1a##). 4614 circRNAs with back‐splicing junction (BSJ) reads &gt;2 were detected, and 48 of them were with over fourfold changes in expression levels between the two groups (Figure ##FIG##0##1a##; Table ##SUPPL##1##S1##, Supporting Information). 38 of these circRNAs were with lower levels, and 10 out of the 48 were with higher levels in metastatic HCC (Figure ##FIG##0##1a##). Then we aligned the 48 circRNA sequences to annotated murine circRNAs from the circAtlas database to identify conserved circRNAs with a stringent criterion (full‐length and BSJ sequences &gt;75% identical).<sup>[</sup>\n##REF##32345360##\n33\n##\n<sup>]</sup>\n<italic toggle=\"yes\">CircLARP1B</italic> was the most differentially expressed and also the only metastasis upregulated circRNA among the five conserved circRNAs identified (Figure ##FIG##0##1a##). <italic toggle=\"yes\">CircLARP1B</italic> is highly conserved with ≈86% sequence identity between human and mice, and consists of exons 2–4 from the La ribonucleoprotein 1B (<italic toggle=\"yes\">LARP1B)</italic> gene, with a deduced size of 294 nt in both human and mice (Figure ##FIG##0##1b##; Figure ##SUPPL##0##S1a##, Supporting Information). <italic toggle=\"yes\">CircLARP1B</italic> and <italic toggle=\"yes\">LARP1B</italic> mRNA exhibited distinct expression patterns in human tissues analyzed from the NCBI and circAtlas databases; for example, <italic toggle=\"yes\">LARP1B</italic> mRNA but not <italic toggle=\"yes\">circLARP1B</italic> was expressed in thyroid tissue (Figure ##SUPPL##0##S1b##, Supporting Information). LARP1B itself is an RBP that regulates the translation of certain mRNAs.<sup>[</sup>\n##REF##28650797##\n34\n##\n<sup>]</sup> The overall survival rate showed no significant difference between the two groups of HCC patients with higher <italic toggle=\"yes\">LARP1B</italic> expression and lower expression (Figure ##SUPPL##0##S1c##, Supporting Information), indicating that <italic toggle=\"yes\">LARP1B</italic> mRNA may not be a key regulator in HCC. The <italic toggle=\"yes\">circLARP1B</italic> BSJ was validated by PCR amplification and confirmed by Sanger sequencing in a human HCC cell line PLC and mouse liver, to verify the circular nature of <italic toggle=\"yes\">circLARP1B</italic> (Figure ##SUPPL##0##S1d##, Supporting Information). Then, the actinomycin D chase assay revealed that <italic toggle=\"yes\">circLARP1B</italic> was stable compared to <italic toggle=\"yes\">LARP1B</italic> mRNA (Figure ##SUPPL##0##S1e##, Supporting Information). By Northern blotting, bands corresponding to the deduced size of <italic toggle=\"yes\">circLARP1B</italic> were detected, and the estimated copy numbers per cell in two HCC cell lines PLC and HepG2 were ≈136 and ≈158, respectively (Figure ##FIG##0##1b##; Figure ##SUPPL##0##S1f##, Supporting Information). Copy numbers of more than 100 are high for circRNAs or even for mRNAs. Single molecular fluorescence in situ hybridization (smFISH) of <italic toggle=\"yes\">circLARP1B</italic> in PLC cells revealed that this circRNA localized predominately in the cytoplasm (Figure ##FIG##0##1c##; Figure ##SUPPL##0##S1g,h##, Supporting Information). The specificity of smFISH to <italic toggle=\"yes\">circLARP1B</italic> was demonstrated with significantly decreased smFISH signals upon shcircLARP1B knockdown of the circRNA (Figure ##SUPPL##0##S1i–k##, Supporting Information). With a thyroid cell line (K1 cells), which exhibited considerable <italic toggle=\"yes\">LARP1B</italic> mRNA levels but no <italic toggle=\"yes\">circLARP1B</italic> expression, the specificity of smFISH to <italic toggle=\"yes\">circLARP1B</italic> or <italic toggle=\"yes\">LARP1B</italic> mRNA was further proofed (Figure ##SUPPL##0##S1l##, Supporting Information). More than 85% of <italic toggle=\"yes\">circLARP1B</italic> were found to be cytoplasmic in one murine HCC cell line Hepa1‐6 and the two human HCC cell lines (Figure ##FIG##0##1d##). Furthermore, smFISH of <italic toggle=\"yes\">circLARP1B</italic> in mouse liver also showed cytoplasmic enrichment (Figure ##FIG##0##1e##).</p>", "<p>Higher <italic toggle=\"yes\">circLARP1B</italic> levels in metastatic compared to nonmetastatic HCC specimens were revealed by smFISH analysis (Figure ##FIG##0##1f##). We collected HCC specimens from 90 patients, and found that higher <italic toggle=\"yes\">circLARP1B</italic> levels were associated with 23 metastatic specimens as against the 67 nonmetastatic specimens (Figure ##FIG##0##1g##). Except 5 specimens without information of prognostic stage, these clinical samples could be divided into 65 specimens with prognostic TNM stage I–II and 20 specimens with TNM stage III–IV, and higher <italic toggle=\"yes\">circLARP1B</italic> levels were significantly correlated with advanced TNM stages (III–IV) (Figure ##FIG##0##1h##). HCC patients with higher <italic toggle=\"yes\">circLARP1B</italic> levels in tumors had significantly lower five‐year overall survival (OS) and disease‐free survival (DFS) rates (Figure ##FIG##0##1i,j##).</p>", "<p>Collectively, these results demonstrated that <italic toggle=\"yes\">circLARP1B</italic> as a mammalian conserved and highly expressed circRNA might play promoting roles in HCC metastasis as supported by data from clinical specimens.</p>", "<title>\n<italic toggle=\"yes\">CircLARP1B</italic> Regulates Cell Invasion and Lipid Accumulation via Fatty Acid Synthesis</title>", "<p>To explore the cellular functions of <italic toggle=\"yes\">circLARP1B</italic>, we applied the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technique to generate <italic toggle=\"yes\">circLARP1B</italic> deficient (circLARP1B‐Def) PLC cells (<bold>Figure</bold> ##FIG##1##\n2a##). Flanking introns of circularized exons contain <italic toggle=\"yes\">Alu</italic> elements and <italic toggle=\"yes\">B1</italic> repeats in human and mice, respectively, which both belong to reverse complementary sequences, known to facilitate circRNA biogenesis (Figure ##SUPPL##0##S2a##, Supporting Information).<sup>[</sup>\n##REF##34865956##\n13\n##, ##REF##33514913##\n35\n##\n<sup>]</sup> To generate circLARP1B‐Def PLC cells, repeat sequences including four proximal <italic toggle=\"yes\">Alu</italic> elements in the fourth intron of human <italic toggle=\"yes\">LARP1B</italic> were deleted, but functional intronic elements such as the splice sites and pyrimidine tract remained unaltered (Figure ##FIG##1##2a##). The resulted circLARP1B‐Def PLC cells exhibited significantly decreased <italic toggle=\"yes\">circLARP1B</italic> levels with no alteration in <italic toggle=\"yes\">LARP1B</italic> mRNA levels, compared to the wildtype (WT) PLC cells (Figure ##FIG##1##2b##).</p>", "<p>CircLARP1B‐Def PLC cells compared to WT cells showed significantly reduced invasion, when examined with Transwell invasion assay (Figure ##FIG##1##2c##). No significant difference in growth curve and colony formation was observed between the circLARP1B‐Def and WT cells (Figure ##SUPPL##0##S2b–d##, Supporting Information). Invasion ability is directly related to metastasis, and growth curve and colony formation are associated with cell growth and proliferation.</p>", "<p>We then assessed the potential metabolic alterations in circLARP1B‐Def PLC cells by liquid chromatography‐mass spectrometry (LC‐MS) untargeted metabolomics (Figure ##FIG##1##2d##). A total of 366 metabolites and lipid classes (including 44 lipid classes) were detected, and 105 of them, 42 increased and 63 decreased, were significantly dysregulated (variable importance in the projection, VIP &gt;1; <italic toggle=\"yes\">P</italic>‐value &lt;0.05) upon <italic toggle=\"yes\">circLARP1B</italic> deficiency in PLC cells (Figure ##SUPPL##0##S2e##; Table ##SUPPL##2##S2##, Supporting Information). KEGG pathway analysis of these dysregulated metabolites revealed that lipid metabolism, among the 6 metabolic pathways significantly affected, was perturbed the most (Figure ##FIG##1##2e##). For the 24 lipid classes enriched in lipid metabolism of KEGG analysis, 18 ones were decreased, and 6 were increased in circLARP1B‐Def cells (Figure ##SUPPL##0##S2e##, Supporting Information). We then performed lipidomics to examine lipid class composition, and identified 2709 lipid species that compose the 24 dysregulated lipid classes detected in the metabolomics. 273 lipid species covering all these 24 lipid classes were significantly changed upon <italic toggle=\"yes\">circLARP1B</italic> deficiency (Figure ##FIG##1##2f##; Table ##SUPPL##2##S2##, Supporting Information). Components of lipid droplets (LDs) including lipid classes such as phosphatidylcholine (PC), phosphatidylethanolamine (PE), diglyceride (DG), triglyceride (TG), and phosphatidylinositol (PI) were among the metabolites with lower levels in circLARP1B‐Def cells (Figure ##SUPPL##0##S2e##, Supporting Information).<sup>[</sup>\n##REF##24220094##\n36\n##\n<sup>]</sup> LDs examined by Nile red staining were markedly decreased in circLARP1B‐Def cells compared to WT cells (Figure ##FIG##1##2g##).</p>", "<p>To further explore the mechanism of lipid accumulation promoted by <italic toggle=\"yes\">circLARP1B</italic>, we performed metabolic labeling with <sup>13</sup>C‐labeled targeted metabolic flux analysis to assess the incorporation of <sup>13</sup>C‐labeled glucose and glutamine into lipid in circLARP1B‐Def and WT PLC cells (Figure ##FIG##1##2h,i##).<sup>[</sup>\n##REF##32101748##\n37\n##\n<sup>]</sup> Targeted metabolic flux analyses were performed, and we totally detected 17 kinds of fatty acids with <sup>13</sup>C labeling, and found that all of them were significantly reduced in circLARP1B‐Def cells (Figure ##FIG##1##2h##; Table ##SUPPL##3##S3##, Supporting Information), indicating a promoting effect of <italic toggle=\"yes\">circLARP1B</italic> in fatty acid synthesis (FAS). Glucose and glutamine are first converted to two‐carbon acetyl‐CoA, which serves as a substrate for ACC1 enzyme in FAS, and <sup>13</sup>C‐labeled two‐carbon units from <sup>13</sup>C‐glucose or <sup>13</sup>C‐glutamine into palmitate can thus be examined to reveal FAS from glucose or glutamine. As expected, the distributions of <sup>13</sup>C‐labeled palmitate isotopologs (M12, M14, and M16) in circLARP1B‐Def cells, compared to WT cells were significantly lower (Figure ##FIG##1##2i##). We further evaluated the involvement of <italic toggle=\"yes\">circLARP1B</italic> in fatty acid oxidation (FAO) with oxygen consumption rate (OCR) assays after supplementing cells with exogenous free fatty acids (FFAs; palmitate was supplied). CircLARP1B‐Def cells showed similar OCR compared with WT cells (Figure ##SUPPL##0##S2f##, Supporting Information). Unc‐51 like autophagy activating kinase 1 (ULK1) is a key regulator in lipophagy initiation, and phosphorylation of Ser555 of ULK1 induces lipophagy.<sup>[</sup>\n##REF##32863214##\n38\n##\n<sup>]</sup> The ULK1 and phosphorylated ULK1 (p‐ULK1) levels exhibited no significant alternation between circLARP1B‐Def and WT cells (Figure ##FIG##1##2j##). Together, these findings suggested that <italic toggle=\"yes\">circLARP1B</italic> facilitated lipid accumulation by FAS, not through regulating FAO or lipophagy.</p>", "<p>The activity of ACC1 is inhibited by phosphorylation of Ser79,<sup>[</sup>\n##UREF##0##\n9\n##, ##REF##36316383##\n11\n##\n<sup>]</sup> and we observed that the phosphorylated ACC1 (p‐ACC1) levels were substantially upregulated in circLARP1B‐Def cells (Figure ##FIG##1##2j##). AMPK is the major kinase that catalyzes the phosphorylation of ACC1, and AMPK itself is initially activated by phosphorylation at Thr172.<sup>[</sup>\n##REF##36316383##\n11\n##\n<sup>]</sup> The phosphorylated AMPK (p‐AMPK) levels were also significantly higher in circLARP1B‐Def cells than WT cells (Figure ##FIG##1##2j##). Therefore, higher levels of p‐AMPK and then p‐ACC1 would repress lipogenesis and lead to decreased amount of LDs in circLARP1B‐Def cells. AMPK activation also causes a range of metabolites changed in HCC.<sup>[</sup>\n##REF##28355557##\n39\n##, ##REF##33690219##\n40\n##, ##REF##30468782##\n41\n##\n<sup>]</sup> From the literature we searched, 12 of circLARP1B‐modulated metabolites have been reported to be regulated by AMPK signaling in HCC,<sup>[</sup>\n##REF##28355557##\n39\n##, ##REF##33690219##\n40\n##, ##REF##30468782##\n41\n##\n<sup>]</sup> and 8 of these metabolites exhibit consistent changes between <italic toggle=\"yes\">circLARP1B</italic> deficiency and AMPK activation (Figure ##SUPPL##0##S2g##, Supporting Information).</p>", "<p>Additionally, we examined the effects of <italic toggle=\"yes\">circLARP1B</italic> on the other downstream processes known to be regulated by AMPK, such as the mTOR pathway, angiogenesis, TGF‐β, and mitochondrial activity.<sup>[</sup>\n##REF##36316383##\n11\n##, ##REF##22576211##\n42\n##, ##REF##31974393##\n43\n##, ##REF##30425336##\n44\n##\n<sup>]</sup> AMPK activation led to phosphorylation of the mTORC1 subunit RAPTOR to inhibit mTOR pathway,<sup>[</sup>\n##REF##36316383##\n11\n##\n<sup>]</sup> and significantly increased phosphorylated RAPTOR (p‐RAPTOR) levels were observed in circLARP1B‐Def cells compared to WT cells (Figure ##SUPPL##0##S2h##, Supporting Information). Once activated, AMPK is reported to increase the protein level of VEGFA (an angiogenesis driver) and inhibit TGF‐β signaling,<sup>[</sup>\n##REF##36316383##\n11\n##, ##REF##22576211##\n42\n##, ##REF##31974393##\n43\n##\n<sup>]</sup> and the VEGFA and TGF‐β protein levels did not demonstrate significant change in circLARP1B‐Def cells compared to WT cells (Figure ##SUPPL##0##S2h##, Supporting Information). As another substrate of AMPK, mitochondrial fission factor (MFF) is phosphorylated by AMPK to promote mitochondrial fission,<sup>[</sup>\n##REF##36316383##\n11\n##\n<sup>]</sup> and the MFF/p‐MFF protein levels remained unaltered upon <italic toggle=\"yes\">circLARP1B</italic> deficiency in PLC cells (Figure ##SUPPL##0##S2h##, Supporting Information). Moreover, basal respiration, ATP production, and maximum respiration revealing mitochondrial activity examined by OCR assays demonstrated no significant difference between circLARP1B‐Def cells and WT cells (Figure ##SUPPL##0##S2i##, Supporting Information). Our results demonstrated that both ACC1 and the mTOR signaling directly regulated by AMPK were modulated by <italic toggle=\"yes\">circLARP1B</italic> through a mechanism awaiting characterization in PLC cells. Both ACC1 and the mTOR signaling are known to promote fatty acid synthesis,<sup>[</sup>\n##UREF##0##\n9\n##, ##REF##30425336##\n44\n##\n<sup>]</sup> we focused on examining ACC1/p‐ACC1 as a readout of downstream effects of AMPK, owing to the fact that ACC1 is the rate‐limiting enzyme for FAS.<sup>[</sup>\n##UREF##0##\n9\n##\n<sup>]</sup>\n</p>", "<p>We also manipulated levels of <italic toggle=\"yes\">circLARP1B in trans</italic> by either RNA interference knockdown or plasmid overexpression, and in human PLC cells or murine Hepa1‐6 cells. ShRNA‐mediated <italic toggle=\"yes\">circLARP1B</italic> knockdown suppressed cell invasion and formation of LDs, and increased p‐AMPK and p‐ACC1 levels in both PLC and Hepa1‐6 cells (Figure ##SUPPL##0##S3a–h##, Supporting Information). <italic toggle=\"yes\">CircLARP1B</italic> overexpression promoted cell invasion and LDs formation, and decreased the p‐AMPK and p‐ACC1 levels in PLC cells (Figure ##SUPPL##0##S3i–l##, Supporting Information).</p>", "<p>Roles of lipid metabolism in the promoting effects of <italic toggle=\"yes\">circLARP1B</italic> on HCC cell invasion were then investigated. Fatty acid synthase (FASN), which is the human lipogenic enzyme for de novo fatty acid synthesis,<sup>[</sup>\n##UREF##0##\n9\n##\n<sup>]</sup> was overexpressed in circLARP1B‐Def PLC cells (Figure ##FIG##1##2k,l##). FASN overexpression enhanced formation of LDs in circLARP1B‐Def PLC cells, and rescued the inhibitory effect on cell invasion caused by <italic toggle=\"yes\">circLARP1B</italic> deficiency (Figure ##FIG##1##2k,l##). Then, we treated circLARP1B‐overexpressing PLC cells with IPI‐9119, a potent FASN inhibitor,<sup>[</sup>\n##REF##30578319##\n45\n##\n<sup>]</sup> and found that FASN inhibition blocked the promoting effect of <italic toggle=\"yes\">circLARP1B</italic> on the formation of LDs and cell invasion (Figure ##SUPPL##0##S3m,n##, Supporting Information).</p>", "<p>Taken together, these findings demonstrated that <italic toggle=\"yes\">circLARP1B</italic> stimulated HCC invasion through remodeling lipid metabolism at the cellular level, and promoted FAS via modulating the AMPK and its downstream targets including ACC1.</p>", "<title>\n<italic toggle=\"yes\">CircLARP1B</italic> Interacts with HNRNPD Protein</title>", "<p>We set out to elucidate the functional mechanism of <italic toggle=\"yes\">circLARP1B</italic> through inspecting its potential interacting molecules. Several putative miRNA binding sites on <italic toggle=\"yes\">circLARP1B</italic> were predicted using CircInteractome (Figure ##SUPPL##0##S4a##, Supporting Information),<sup>[</sup>\n##REF##26669964##\n46\n##\n<sup>]</sup> however, RNA immunoprecipitation (RIP) of AGO2, which mediates the interaction between target RNA and miRNA,<sup>[</sup>\n##REF##34865956##\n13\n##\n<sup>]</sup> showed no enrichment of <italic toggle=\"yes\">circLARP1B</italic> in PLC cells (Figure ##SUPPL##0##S4b##, Supporting Information). Furthermore, we applied ribosome profiling assay and found no obvious binding of <italic toggle=\"yes\">circLARP1B</italic> to polysomes (Figure ##SUPPL##0##S4c##, Supporting Information), indicating that <italic toggle=\"yes\">circLARP1B</italic> did not function as a template for protein translation. Both human and murine <italic toggle=\"yes\">circLARP1B</italic> also displayed low coding possibilities in CPAT predicting tool (Figure ##SUPPL##0##S4d##, Supporting Information).<sup>[</sup>\n##REF##23335781##\n47\n##\n<sup>]</sup> Therefore, <italic toggle=\"yes\">circLARP1B</italic> is noncoding and does not function as miRNA sponge.</p>", "<p>We then performed RNA pull‐down with the cytoplasmic fraction of PLC cells with a biotinylated oligo against the BSJ of <italic toggle=\"yes\">circLARP1B</italic>, which showed effective and specific capture of <italic toggle=\"yes\">circLARP1B</italic> (<bold>Figure</bold> ##FIG##2##\n3a##). Cytoplasmic fraction was used due to the predominately cytoplasmic localization of <italic toggle=\"yes\">circLARP1B</italic> (Figure ##FIG##0##1c–e##). The proteins co‐pulled down with <italic toggle=\"yes\">circLARP1B</italic> were separated with SDS‐PAGE, followed by silver staining and mass spectrometry (MS) to disclose the specific <italic toggle=\"yes\">circLARP1B</italic> binding band (Figure ##FIG##2##3a##). HNRNPD, also known as AU‐rich element RNA‐binding factor 1 (AUF1), was identified as the circLARP1B‐interacting protein in human cells (Figure ##FIG##2##3a##; Figure ##SUPPL##0##S4e##, Supporting Information). HNRNPD is an RBP with both cytoplasmic and nuclear roles.<sup>[</sup>\n##REF##1901943##\n48\n##, ##REF##19033365##\n49\n##\n<sup>]</sup> In the cytoplasm, HNRNPD regulates the stability of some mRNAs, e.g., <italic toggle=\"yes\">CCND1</italic> mRNA, through binding to the AU‐rich region in 3′ UTR.<sup>[</sup>\n##REF##1901943##\n48\n##, ##REF##19033365##\n49\n##, ##REF##33444453##\n50\n##\n<sup>]</sup> HNRNPD undergoes alternative splicing to produce four protein variants (p37, p40, p42, and p45) that are expressed with cell type‐specificity,<sup>[</sup>\n##REF##19033365##\n49\n##, ##REF##21956942##\n51\n##\n<sup>]</sup> and two variants (p37 and p40) were further confirmed as major HNRNPD isoforms in PLC cells (Figure ##SUPPL##0##S4f##, Supporting Information). RNA pull‐down of <italic toggle=\"yes\">circLARP1B</italic> and HNRNPD RIP assays using the cytoplasmic fraction of PLC cells further verified their interaction (Figure ##FIG##2##3b,c##). Using mouse liver as the experimental material, RNA pull‐down of murine <italic toggle=\"yes\">circLARP1B</italic> could co‐pull down Hnrnpd, and Hnrnpd RIP acquired <italic toggle=\"yes\">circLARP1B</italic> (Figure ##FIG##2##3d,e##). Therefore, <italic toggle=\"yes\">circLARP1B</italic> and HNRNPD interact in both human and murine cells.</p>", "<p>To map the binding sites of HNRNPD in <italic toggle=\"yes\">circLARP1B</italic>, we uncovered two motifs (motif 1 and motif 2) conserved in human and murine <italic toggle=\"yes\">circLARP1B</italic> via RBPmap (Figure ##FIG##2##3f##), a tool for predicting RBP binding sites in an RNA sequence.<sup>[</sup>\n##REF##24829458##\n52\n##\n<sup>]</sup> Both sites (Positions 143–151 and 158–166 from BSJ) are also AU‐rich, consistent with the HNRNPD binding preference to AU‐rich region.<sup>[</sup>\n##REF##19033365##\n49\n##\n<sup>]</sup> Mutation of either motif 1 or motif 2 in <italic toggle=\"yes\">circLARP1B</italic> decreased the interaction between <italic toggle=\"yes\">circLARP1B</italic> and HNRNPD in PLC cells (Figure ##FIG##2##3g##). Mutation of both motifs (double<sup>mut</sup>) abolished the interaction (Figure ##FIG##2##3g##). The 5′ portion of <italic toggle=\"yes\">LARP1B</italic> mRNA possessing the same nucleic acid sequences as <italic toggle=\"yes\">circLARP1B</italic> also has the HNRNPD binding site sequences present in <italic toggle=\"yes\">circLARP1B</italic>, although HNRNPD RIP followed by semiquantitative RT‐PCR and real‐time quantification PCR (RT‐qPCR) analyses revealed that HNRNPD did not bind to <italic toggle=\"yes\">LARP1B</italic> mRNA in PLC cells and mouse liver (Figure ##FIG##2##3c,e##; Figure ##SUPPL##0##S5a##, Supporting Information). The 5′ portion of <italic toggle=\"yes\">LARP1B</italic> mRNA is heavily bound by ribosomes through analyzing available ribosome profiling sequencing (Ribo‐seq) data from HCC cell lines (GSE125757, GSE128320, and GSE147840) (Figure ##SUPPL##0##S5b##, Supporting Information).<sup>[</sup>\n##REF##31240521##\n53\n##, ##REF##34728628##\n54\n##, ##REF##35609991##\n55\n##\n<sup>]</sup> One possibility is that <italic toggle=\"yes\">LARP1B</italic> mRNA is actively involved in translation, and the HNRNPD sites present in its 5′ are thus not available for HNRNPD binding.</p>", "<p>HNRNPD binding to mRNA would modulate RNA stability,<sup>[</sup>\n##REF##1901943##\n48\n##, ##REF##33444453##\n50\n##, ##REF##10702317##\n56\n##\n<sup>]</sup> and we found out that knocking down of HNRNPD with siRNA did not affect levels of <italic toggle=\"yes\">circLARP1B</italic>, indicating that HNRNPD did not regulate the stability of <italic toggle=\"yes\">circLARP1B</italic> (Figure ##SUPPL##0##S5c##, Supporting Information). Knocking down of <italic toggle=\"yes\">circLARP1B</italic> with shRNA also did not affect levels of <italic toggle=\"yes\">HNRNPD</italic> mRNA and protein (Figure ##SUPPL##0##S5d,e##, Supporting Information). Consistent with previous reports,<sup>[</sup>\n##REF##10702317##\n56\n##, ##REF##30799487##\n57\n##, ##REF##22633954##\n58\n##\n<sup>]</sup> immunofluorescence (IF) analysis demonstrated that most HNRNPD localized in the nucleus, and ≈20% HNRNPD localized in the cytoplasm in PLC cells, which affected better visualization of cytoplasmic HNRNPD signals (Figure ##FIG##2##3h##). By using a condition to reduce the nuclear permeability to decrease the nuclear signals and thus to highlight the cytoplasmic HNRNPD signals,<sup>[</sup>\n##REF##34549195##\n59\n##, ##REF##31508410##\n60\n##\n<sup>]</sup> we observed that more than 70% <italic toggle=\"yes\">circLARP1B</italic> signals overlapped with HNRNPD protein signals in the cytoplasm (Figure ##FIG##2##3i##). A binding assay with FLAG‐tagged HNRNPD protein purified from HEK293 cells and synthesized <italic toggle=\"yes\">circLARP1B</italic> RNA demonstrated the direct binding between <italic toggle=\"yes\">circLARP1B</italic> and HNRNPD in vitro (Figure ##FIG##2##3j##). With over ≈100 copies in the cytoplasm, <italic toggle=\"yes\">circLARP1B</italic> with two functional sites can bind to a substantial portion of cytoplasmic HNRNPD protein. Collectively, we concluded that <italic toggle=\"yes\">circLARP1B</italic> with two functional sites and reasonable abundance could interact with a substantial portion of cytoplasmic HNRNPD, and <italic toggle=\"yes\">circLARP1B</italic> and HNRNPD did not reciprocally regulate their expression or stability.</p>", "<title>HNRNPD and HNRNPD Binding Are Essential for <italic toggle=\"yes\">CircLARP1B</italic> Functions</title>", "<p>We then set out to investigate the roles of HNRNPD binding in the functionality of <italic toggle=\"yes\">circLARP1B</italic>. Overexpression of WT but not double<sup>mut</sup>\n<italic toggle=\"yes\">circLARP1B</italic> could rescue the phenotypes in cell invasion and formation of LDs of circLARP1B‐Def cells (<bold>Figure</bold> ##FIG##3##\n4a,b##; Figure ##SUPPL##0##S5f##, Supporting Information). At the molecular level, overexpression of WT but not double<sup>mut</sup>\n<italic toggle=\"yes\">circLARP1B</italic> restored the p‐AMPK and p‐ACC1 levels in circLARP1B‐Def cells (Figure ##FIG##3##4c##). Overexpression of HNRNPD inhibited cell invasion and formation of LDs (Figure ##FIG##3##4d,e##; Figure ##SUPPL##0##S5g##, Supporting Information), and levels of p‐AMPK and p‐ACC1 were also increased in PLC cells (Figure ##FIG##3##4f##). WT but not double<sup>mut</sup>\n<italic toggle=\"yes\">circLARP1B</italic> that overexpressed together with HNRNPD blocked the effects of HNRNPD on cell invasion, formation of LDs, and levels of p‐AMPK and p‐ACC1 (Figure ##FIG##3##4d–f##). Taking these results together, we concluded that the interaction between HNRNPD and <italic toggle=\"yes\">circLARP1B</italic> was essential to regulatory functions of this circRNA, and it is possible that <italic toggle=\"yes\">circLARP1B</italic> might function through binding to and modulating HNRNPD.</p>", "<title>\n<italic toggle=\"yes\">CircLARP1B</italic> Destabilizes <italic toggle=\"yes\">LKB1</italic> mRNA via Perturbing HNRNPD</title>", "<p>To provide further insights into the molecular mechanisms of <italic toggle=\"yes\">circLARP1B</italic> and HNRNPD in HCC cells, we extracted cytoplasmic fractions of PLC cells and performed HNRNPD RIP of endogenously expressed HNRNPD, and the RNAs from RIP were subjected to RNA‐seq (RIP‐seq) (Figure ##SUPPL##0##S6a,b##, Supporting Information). Distribution of RIP‐seq reads on mRNA targets revealed predominate 3′ UTR counts (Figure ##SUPPL##0##S6a##, Supporting Information), consistent with the functional roles of cytoplasmic HNRNPD in regulating mRNA stability by binding to 3′ UTR.<sup>[</sup>\n##REF##1901943##\n48\n##, ##REF##33444453##\n50\n##, ##REF##10702317##\n56\n##\n<sup>]</sup> Comparison of RIP‐seq data from circLARP1B‐Def cells and <italic toggle=\"yes\">circLARP1B</italic> overexpression cells to those from the corresponding control cells, identified 216 mRNAs with contrast changes of HNRNPD bindings on their 3′ UTR upon <italic toggle=\"yes\">circLARP1B</italic> deficiency or overexpression (<bold>Figure</bold> ##FIG##4##\n5a##; Table ##SUPPL##4##S4##, Supporting Information). We have reanalyzed the HNRNPD PAR‐CLIP data (GSE52977) from HEK293 cells,<sup>[</sup>\n##REF##25366541##\n61\n##\n<sup>]</sup> and found that the 216 mRNAs sensitive to <italic toggle=\"yes\">circLARP1B</italic> had significantly lower HNRNPD PAR‐CLIP binding signals in the 3′ UTRs, compared to the other HNRNPD PAR‐CLIP targets (Figure ##SUPPL##0##S6c##, Supporting Information). These results indicated that the subset of mRNAs impacted by changes in <italic toggle=\"yes\">circLARP1B</italic> levels might be with disadvantage in competing for the pool of HNRNPD, due to either relatively weaker binding ability to the protein or unfavorable cellular distribution and/or ratio of the corresponding mRNA/HNRNPD protein.</p>", "<p>Gene ontology (GO) analysis for these target genes illustrated biological processes such as peptidyl‐Thr phosphorylation, protein stability, and mRNA metabolic process (Figure ##FIG##4##5b##). Peptidyl‐Thr phosphorylation was the most significantly (with the lowest <italic toggle=\"yes\">P</italic>‐value) enriched process, among which LKB1 also known as serine/threonine kinase 11 (STK11) showed the most overall HNRNPD binding signals (the sum of binding signals from all four types of cells) on the 3′ UTR (Figure ##FIG##4##5c##). This indicated that its 3′ UTR occupied the most HNRNPD protein out of the 3′ UTRs of the six genes enriched in this GO term. With mouse liver, we found that Hnrnpd RIP could also pull down <italic toggle=\"yes\">Lkb1</italic> mRNA (Figure ##SUPPL##0##S6d##, Supporting Information). LKB1 is well known to directly catalyze the phosphorylation of Thr172 of AMPK, which is required for AMPK activation.<sup>[</sup>\n##REF##12847291##\n62\n##, ##REF##14985505##\n63\n##, ##REF##14614828##\n64\n##\n<sup>]</sup> Directly based on the RIP‐seq data, <italic toggle=\"yes\">circLARP1B</italic> deficiency resulted in more HNRNPD bindings, and <italic toggle=\"yes\">circLARP1B</italic> overexpression led to less HNRNPD bindings, to the 3′ UTR of <italic toggle=\"yes\">LKB1</italic> mRNA (Figure ##FIG##4##5d##). We also found that the endogenous HNRNPD protein bound more <italic toggle=\"yes\">circLARP1B</italic> upon <italic toggle=\"yes\">circLARP1B</italic> overexpression and less <italic toggle=\"yes\">circLARP1B</italic> in circLARP1B‐Def cells (Figure ##FIG##4##5e##). Furthermore, HNRNPD RIP revealed that <italic toggle=\"yes\">circLARP1B</italic> deficiency but not knockdown of <italic toggle=\"yes\">LARP1B</italic> mRNA resulted in significantly more HNRNPD binding to the 3′ UTR of <italic toggle=\"yes\">LKB1</italic> mRNA (Figure ##SUPPL##0##S6e–g##, Supporting Information). A recent study demonstrated that HNRNPD bound to the <italic toggle=\"yes\">c‐MYC</italic> 3′ UTR and promoted the c‐MYC expression in colorectal cancer.<sup>[</sup>\n##REF##35940521##\n65\n##\n<sup>]</sup> HNRNPD RIP‐qPCR revealed that HNRNPD also bound to the <italic toggle=\"yes\">c‐MYC</italic> 3′ UTR, and siRNA‐mediated HNRNPD knockdown significantly increased the c‐MYC protein levels in PLC cells (Figure ##SUPPL##0##S6h,i##, Supporting Information). c‐MYC was not in the 216 targets sensitive to <italic toggle=\"yes\">circLARP1B</italic> (Figure ##FIG##4##5a##; Table ##SUPPL##4##S4##, Supporting Information), and the opposite effect of HNRNPD on c‐MYC expression in colorectal cancer and HCC cells required further investigation.</p>", "<p>We examined the effect of LKB1 in HCC cells directly by overexpression, and we found that the overexpressed LKB1 blocked the effect of <italic toggle=\"yes\">circLARP1B</italic> in promoting cell invasion and formation of LDs (Figure ##FIG##4##5f,g##). Overexpressed LKB1 also nearly abolished the effects of <italic toggle=\"yes\">circLARP1B</italic> on p‐AMPK and p‐ACC1 levels (Figure ##FIG##4##5h##). Lower LKB1 protein levels were observed in metastatic compared to nonmetastatic HCC specimens (Figure ##FIG##4##5i##). These results indicated that <italic toggle=\"yes\">LKB1</italic> mRNA was a downstream target of <italic toggle=\"yes\">circLARP1B</italic> with robust contributions to the effects of <italic toggle=\"yes\">circLARP1B</italic>.</p>", "<title>\n<italic toggle=\"yes\">CircLARP1B</italic> Competes with <italic toggle=\"yes\">LKB1</italic> mRNA for HNRNPD Binding and Leads to <italic toggle=\"yes\">LKB1</italic> mRNA Instability</title>", "<p>HNRNPD has complex regulatory effects on the stability of mRNAs, with some stabilized and the others destabilized.<sup>[</sup>\n##REF##1901943##\n48\n##, ##REF##33444453##\n50\n##, ##REF##10702317##\n56\n##\n<sup>]</sup> We observed that the steady levels but not nascent levels of <italic toggle=\"yes\">LKB1</italic> mRNA were significantly increased, upon <italic toggle=\"yes\">circLARP1B</italic> deficiency or knockdown in human and murine cells (Figure ##SUPPL##0##S6j,k##, Supporting Information). We then examined whether and how HNRNPD and <italic toggle=\"yes\">circLARP1B</italic> regulated the steady levels of <italic toggle=\"yes\">LKB1</italic> mRNA. Knocking down HNRNPD with siRNA resulted in significant decrease in half‐life of <italic toggle=\"yes\">LKB1</italic> mRNA and also LKB1 protein levels in PLC and Hepa1‐6 cells (<bold>Figure</bold> ##FIG##5##\n6a–d##), indicating that HNRNPD stabilized <italic toggle=\"yes\">LKB1</italic> mRNA. HNRNPD has been reported to bind to the 3′ UTR and simultaneously interact with translation initiation factor eIF4G1 and cap‐binding protein eIF4E to form a ternary complex, which could bring the 5′ and 3′ ends of the mRNA together to form a loop.<sup>[</sup>\n##REF##21956942##\n51\n##\n<sup>]</sup> We wondered whether HNRNPD looped <italic toggle=\"yes\">LKB1</italic> mRNA through this mechanism. We performed eIF4G1 and eIF4E RIP followed by RT‐qPCR with specific primers to detect the 3′ UTR of <italic toggle=\"yes\">LKB1</italic> mRNA in PLC cells with or without HNRNPD knockdown.<sup>[</sup>\n##REF##25826658##\n66\n##, ##REF##27437580##\n67\n##\n<sup>]</sup> HNRNPD knockdown resulted in decreased binding signal of both eIF4G1 and eIF4E to the <italic toggle=\"yes\">LKB1</italic> 3′ UTR (Figure ##FIG##5##6e,f##). These results demonstrated that HNRNPD enhanced the mRNA looping and stabilized <italic toggle=\"yes\">LKB1</italic> mRNA.</p>", "<p>In circLARP1B‐Def PLC cells, compared to the WT cells, <italic toggle=\"yes\">LKB1</italic> mRNA stability was increased, and the steady levels of LKB1 protein were also increased (Figure ##FIG##5##6g,h##). Overexpression of <italic toggle=\"yes\">circLARP1B</italic> in PLC cells destabilized <italic toggle=\"yes\">LKB1</italic> mRNA, and led to lower levels of LKB1 protein (Figure ##SUPPL##0##S6l,m##, Supporting Information). In mouse Hepa1‐6 cells, the stability of <italic toggle=\"yes\">Lkb1</italic> mRNA was markedly enhanced, and the steady levels of Lkb1 protein were significantly increased upon <italic toggle=\"yes\">circLARP1B</italic> knockdown with shRNA (Figure ##FIG##5##6i,j##). Dual‐luciferase reporter using the 3′ UTR of <italic toggle=\"yes\">LKB1</italic> mRNA as the 3′ UTR of firefly luciferase mRNA showed that WT <italic toggle=\"yes\">circLARP1B</italic> but not the double<sup>mut</sup>\n<italic toggle=\"yes\">circLARP1B</italic> could partially block the promoting effect on HNRNPD‐mediated stabilization of <italic toggle=\"yes\">LKB1</italic> 3′ UTR (Figure ##SUPPL##0##S7a##, Supporting Information). Fluorescent in situ hybridization (FISH) of <italic toggle=\"yes\">LKB1</italic> mRNA and the HNRNPD IF staining revealed that circLARP1B‐Def compared to WT PLC cells, exhibited significantly more colocalization of <italic toggle=\"yes\">LKB1</italic> mRNA signals and HNRNPD protein signals in the cytoplasm (Figure ##SUPPL##0##S7b##, Supporting Information). ≈459 and ≈663 copies of <italic toggle=\"yes\">LKB1</italic> mRNA per cell were estimated in PLC and HepG2 cells, respectively (Figure ##SUPPL##0##S7c##, Supporting Information). The cytoplasmic copies of <italic toggle=\"yes\">circLARP1B</italic> and <italic toggle=\"yes\">LKB1</italic> mRNA were evaluated in PLC cells, and the molecular ratio was ≈1:3 (Figure ##SUPPL##0##S7d##, Supporting Information). A competing assay, in which purified HNRNPD was incubated with equal moles of in vitro synthesized <italic toggle=\"yes\">circLARP1B</italic> and <italic toggle=\"yes\">LKB1</italic> 3′ UTR, was set up (Figure ##FIG##5##6k##). It was found that HNRNPD had much higher (≈18‐fold) binding affinity to <italic toggle=\"yes\">circLARP1B</italic> than to the 3′ UTR of <italic toggle=\"yes\">LKB1</italic> mRNA (Figure ##FIG##5##6k##).</p>", "<p>A 24‐nt antisense oligodeoxynucleotide (ODN) complementary to the two HNRNPD binding sites in <italic toggle=\"yes\">circLARP1B</italic> was synthesized to examine as an inhibitor of <italic toggle=\"yes\">circLARP1B</italic>. The antisense ODN was modified with phosphorothioate (PS) and 2′‐<italic toggle=\"yes\">O</italic>‐methyl (2′‐OMe),<sup>[</sup>\n##REF##15064360##\n68\n##\n<sup>]</sup> and termed ODN‐AS. ODN‐AS transfection in PLC cells increased the HNRNPD binding to <italic toggle=\"yes\">LKB1</italic> 3′ UTR and upregulated LKB1 protein levels (Figure ##FIG##5##6l,m##). 5‐methylcytosine (m<sup>5</sup>C) modified sense single‐stranded RNA oligos (m<sup>5</sup>C‐ssRNA) containing the HNRNPD binding sites of <italic toggle=\"yes\">circLARP1B</italic> were also tested.<sup>[</sup>\n##UREF##6##\n69\n##\n<sup>]</sup> m<sup>5</sup>C‐ssRNA did not affect either the HNRNPD binding to <italic toggle=\"yes\">LKB1</italic> 3′ UTR or LKB1 protein levels (Figure ##SUPPL##0##S7e,f##, Supporting Information). These results indicated that the small m<sup>5</sup>C‐ssRNA oligos somehow could not function as a <italic toggle=\"yes\">circLARP1B</italic> mimics in cells. On the other hand, the interaction between HNRNPD and <italic toggle=\"yes\">circLARP1B</italic> could be blocked by ODN‐AS, and the potential effects of ODN‐AS in lipid metabolism, HCC metastasis, and even therapeutics could be further investigated.</p>", "<title>\n<italic toggle=\"yes\">CircLARP1B</italic> Deficiency in Mice Causes Liver Changes Attributable to Lkb1 Surplus</title>", "<p>To directly investigate the physiological roles of <italic toggle=\"yes\">circLARP1B</italic> in animals, we used CRISPR/Cas9 to generate <italic toggle=\"yes\">circLARP1B</italic> deficient mice, in which repeat sequences in intron 4 of murine <italic toggle=\"yes\">Larp1b</italic> gene were deleted (<italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic>), with functional intronic elements such as the splice sites and pyrimidine tract remained unaltered (<bold>Figure</bold> ##FIG##6##\n7a##). The mutant mice did not show statistically significant difference in body weight or litter size, when compared age‐matched WT mice (Figure ##SUPPL##0##S8a,b##, Supporting Information). The <italic toggle=\"yes\">circLARP1B</italic> expression was significantly decreased in livers of <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> mice compared to WT mice, while the total and nascent levels of <italic toggle=\"yes\">Larp1b</italic> mRNA were unaltered (Figure ##FIG##6##7b##; Figure ##SUPPL##0##S8c##, Supporting Information). The levels of <italic toggle=\"yes\">HNRNPD</italic> mRNA and protein also showed no significant difference in livers of WT and <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> mice (Figure ##SUPPL##0##S8d##, Supporting Information). Liver was the focus due to that it is the organ giving rise to HCC, and a central organ of metabolism in the body.</p>", "<p>\n<italic toggle=\"yes\">CircLARP1B<sup>−/−</sup>\n</italic> mice compared to WT mice had significantly reduced LDs in livers, examined by Oil red O staining (Figure ##FIG##6##7c##). Protein levels of Lkb1, p‐Ampk, and p‐Acc1 were significantly increased in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> livers (Figure ##FIG##6##7d,e##; Figure ##SUPPL##0##S8e##, Supporting Information). Further, we performed tail vein injection of 8‐week‐old <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> mice with hepatocyte‐directed adeno‐associated virus 8 (AAV8) to express shRNA against Lkb1 (AAV8‐shLkb1) or the corresponding control (AAV8‐shCtrl). When examined 3 weeks after the infection, AAV8‐shLkb1 resulted in effective Lkb1 knockdown in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> livers, and Lkb1 depletion recovered the LDs levels in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> livers to the levels in WT livers (Figure ##FIG##6##7f,g##). The increased p‐Ampk and p‐Acc1 levels in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> liver were also restored nearly to the levels in WT liver (Figure ##FIG##6##7h,i##; Figure ##SUPPL##0##S8f##, Supporting Information).</p>", "<title>\n<italic toggle=\"yes\">CircLARP1B</italic> Deficiency in Mice Impedes HCC Metastasis and Lipid Accumulation</title>", "<p>To examine physiological roles of <italic toggle=\"yes\">circLARP1B</italic> in HCC at the whole organismal level, we induced HCC in mice with diethylnitrosamine (DEN), which is well established to cause severe liver damage and eventually hepatocarcinogenesis (<bold>Figure</bold> ##FIG##7##\n8a##).<sup>[</sup>\n##REF##22265403##\n70\n##\n<sup>]</sup> After DEN induction for 10 weeks, liver inflammation examined by H&amp;E staining was significantly lower in livers of <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> mice than that of WT mice (Figure ##SUPPL##0##S8g##, Supporting Information). mRNA levels of <italic toggle=\"yes\">Il6</italic> and <italic toggle=\"yes\">Tnf</italic> (as inflammation indicators) were also decreased in livers of <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> mice (Figure ##SUPPL##0##S8h##, Supporting Information). The presence of bridging fibrosis was also examined, and it was found that <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> mice had fewer Masson and Sirius Red signals in the portal areas (Figure ##SUPPL##0##S8i,j##, Supporting Information). Consistently, mRNA levels of fibrosis‐related markers, <italic toggle=\"yes\">Col1a1</italic>, <italic toggle=\"yes\">Tgfb1</italic>, and <italic toggle=\"yes\">Mmp2</italic> were decreased in livers of <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> mice (Figure ##SUPPL##0##S8k##, Supporting Information). After DEN induction for 18 weeks (HCC mice), <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> mice exhibited fewer and smaller tumor nodes in livers, and significantly smaller lung metastatic nodes, compared with WT mice (Figure ##FIG##7##8b,c##). HNRNPD levels demonstrated no significant difference in liver tumors between WT and <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice, while in HCC liver tumors of both genotypes, Hnrnpd levels were significantly higher than livers from age‐matched WT mice (Figure ##SUPPL##0##S8l,m##, Supporting Information). Immunohistochemistry (IHC) of liver tumor nodes revealed that the prometastasis marker Vimentin (Vim) was lower and the antimetastasis marker E‐cadherin (Ecad) was higher in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice (Figure ##FIG##7##8d##). In consistence with HCC severity, the serum concentrations of alpha‐fetoprotein (AFP), a biomarker for HCC, was significantly lower in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice (Figure ##FIG##7##8e##). Alanine transaminase (ALT) and aspartate transaminase (AST), two markers of liver injury, were also significantly lower in the serum of <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice (Figure ##FIG##7##8f,g##). <italic toggle=\"yes\">CircLARP1B<sup>−/−</sup>\n</italic> HCC mice exhibited lower triglyceride (TG) and total cholesterol (TC) levels in serum, and significantly fewer LDs in liver tumor nodes (Figure ##FIG##7##8h–j##). Meanwhile, levels of Lkb1, p‐Ampk, and p‐Acc1 were significantly higher in liver tumor nodes from <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice (Figure ##FIG##7##8k,l##; Figure ##SUPPL##0##S9a##, Supporting Information).</p>", "<p>To provide further insights for HCC metastatic roles of <italic toggle=\"yes\">circLARP1B</italic> in liver cells, we infused hepatocyte‐directed AAV8 expressing shRNA against <italic toggle=\"yes\">circLARP1B</italic> (AAV8‐shcircLARP1B) or the corresponding negative control (AAV8‐shCtrl) into WT mice after DEN induction for 10 weeks (<bold>Figure</bold> ##FIG##8##\n9a##; Figure ##SUPPL##0##S3e##, Supporting Information).<sup>[</sup>\n##REF##12192090##\n71\n##\n<sup>]</sup> In livers of WT mice infused with AAV8‐shcircLARP1B, effective knockdown of <italic toggle=\"yes\">circLARP1B</italic> was observed, while the <italic toggle=\"yes\">Larp1b</italic> mRNA was unaltered (Figure ##FIG##8##9b##). Consistent with results from <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> mice, AAV8‐shcircLARP1B injection resulted in fewer and smaller tumor nodes in livers, and smaller lung metastatic nodes, compared to AAV8‐shCtrl injection in WT mice (Figure ##FIG##8##9c,d##). The Vim IHC signals were lower, and the Ecad IHC signals were higher in liver tumors of WT mice with AAV8‐shcircLARP1B (Figure ##FIG##8##9e##). Serum AFP, ALT, AST, TG, and TC levels were also significantly lower in HCC mice with AAV8‐shcircLARP1B (Figure ##FIG##8##9f–j##). WT HCC mice infused with AAV8‐shcircLARP1B exhibited significantly fewer LDs and markedly higher levels of Lkb1, p‐Ampk, and p‐Acc1 in liver tumor nodes (Figure ##FIG##8##9k–m##; Figure ##SUPPL##0##S9b##, Supporting Information). Even these results were based on AAV8‐mediated hepatocyte specific <italic toggle=\"yes\">circLARP1B</italic> knockdown, in the real case of HCC, effects of the niche, immune cells, and other unaccounted parameters could still contribute to the overall effects of <italic toggle=\"yes\">circLARP1B</italic> on metastasis.</p>", "<p>Taken together, these results demonstrated that lower <italic toggle=\"yes\">circLARP1B</italic> levels were unfavorable to HCC progression, lipid accumulation, and metastasis in mouse models, by affecting the same <italic toggle=\"yes\">circLARP1B–</italic>HNRNPD–<italic toggle=\"yes\">LKB1</italic>–AMPK regulatory pathway identified in HCC cell lines.</p>", "<title>Lkb1 Is the Key Factor for the Effect of <italic toggle=\"yes\">CircLARP1B</italic> in HCC Mouse Model</title>", "<p>We then performed tail vein injection with AAV8‐shLkb1 or the AAV8‐shCtrl once in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice also at the 10th week after DEN induction. Hepatic Lkb1 protein was successfully knocked down (Figure ##SUPPL##0##S9c##, Supporting Information). We found that AAV8‐shLkb1 injection led to more and larger liver tumors, and larger lung metastatic nodes compared to AAV8‐shCtrl injection in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice (<bold>Figure</bold> ##FIG##9##\n10a,b##). In <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice upon AAV8‐shLkb1 application, liver tumor number and size, and lung metastases were as worse as what happened in the WT HCC mice (Figure ##FIG##9##10a,b##), indicating strongly that Lkb1 was the key downstream factor in hepatocytes for the effects of <italic toggle=\"yes\">circLARP1B</italic>.</p>", "<p>Lkb1 knockdown led to the increased Vim levels and the decreased Ecad levels in liver tumor nodes in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice (Figure ##FIG##9##10c##). Meanwhile, Lkb1 knockdown reversed these changes in Vim and Ecad levels caused by <italic toggle=\"yes\">circLARP1B</italic> deficiency (Figure ##FIG##9##10c##). Lkb1 silencing nearly restored the circLARP1B‐deficient mediated suppressive effects on the levels of serum markers AFP, ALT, and AST in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice (Figure ##SUPPL##0##S9d–f##, Supporting Information). Furthermore, Lkb1 depletion almost completely restored the inhibitory effects of <italic toggle=\"yes\">circLARP1B</italic> deficiency on lipid accumulation in liver tumor nodes and serum TG and TC levels (Figure ##FIG##9##10d##; Figure ##SUPPL##0##S9g,h##, Supporting Information). Increased levels of p‐Ampk and p‐Acc1 observed in the liver of <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice were also eradicated upon Lkb1 knockdown (Figure ##FIG##9##10e##; Figure ##SUPPL##0##S9i,j##, Supporting Information). Therefore, Lkb1 was the key factor in hepatocytes for the molecular regulatory pathway of <italic toggle=\"yes\">circLARP1B</italic> in HCC lipid metabolism and metastasis.</p>", "<title>Clinical Significance of HNRNPD, LKB1, and AMPK in HCC</title>", "<p>Levels of <italic toggle=\"yes\">HNRNPD</italic> mRNA were significantly higher in the 23 metastatic specimens compared to 67 nonmetastatic specimens we collected (Figure ##SUPPL##0##S10a##, Supporting Information), and higher <italic toggle=\"yes\">HNRNPD</italic> mRNA levels were positively associated with shorter OS and DFS analyzed based on these 90 HCC specimens (Figure ##FIG##9##10f##). HCC patients with higher <italic toggle=\"yes\">LKB1</italic> mRNA levels in tumors had significantly longer OS and DFS (Figure ##FIG##9##10g##). On the other hand, levels of <italic toggle=\"yes\">LKB1</italic> mRNA showed no statistically significant difference in metastatic versus nonmetastatic specimens (Figure ##SUPPL##0##S10b##, Supporting Information). Presumably upstream mechanisms might upregulate both HNRNPD and <italic toggle=\"yes\">circLARP1B</italic> in metastatic HCC (Figure ##FIG##0##1g##), and the two regulators had opposite effects on the levels of <italic toggle=\"yes\">LKB1</italic> mRNA, with HNRNPD enhancing and <italic toggle=\"yes\">circLARP1B</italic> destabilizing <italic toggle=\"yes\">LKB1</italic> mRNA. Therefore, these regulations might lead to the balance of <italic toggle=\"yes\">LKB1</italic> mRNA levels in metastatic versus nonmetastatic HCC. The <italic toggle=\"yes\">AMPK</italic> mRNA levels demonstrated statistically significant increase in metastatic HCC, but its levels had no significant correlation to the OS and DFS of HCC patients (Figure ##SUPPL##0##S10c,d##, Supporting Information). AMPK was reported to either promote or suppress HCC,<sup>[</sup>\n##REF##36316383##\n11\n##, ##REF##32631382##\n72\n##, ##REF##23942093##\n73\n##, ##REF##30853530##\n74\n##\n<sup>]</sup> and in the <italic toggle=\"yes\">circLARP1B</italic>–HNRNPD–<italic toggle=\"yes\">LKB1</italic>–AMPK axis, the levels of p‐AMPK rather than the overall AMPK levels would be more relevant to HCC.</p>" ]
[ "<title>Discussion</title>", "<p>Roles of circRNAs in human diseases are a field with extensive studies,<sup>[</sup>\n##REF##35821160##\n5\n##, ##REF##34865956##\n13\n##, ##REF##31395983##\n14\n##, ##REF##31973951##\n15\n##\n<sup>]</sup> although further understandings of circRNAs with strong functions and in‐depth circRNA functional mechanisms are still required. In this study, a mammalian conserved circRNA <italic toggle=\"yes\">circLARP1B</italic> is identified through the inspection of clinical specimens with different metastasis and prognostic features. Each <italic toggle=\"yes\">circLARP1B</italic> molecule possesses two HNRNPD binding sites, and with more than 100 copies in the cytoplasm, <italic toggle=\"yes\">circLARP1B</italic> can absolve a considerable portion of HNRNPD, and perturb the HNRNPD from binding to <italic toggle=\"yes\">LKB1</italic> mRNA. <italic toggle=\"yes\">LKB1</italic> mRNA is remarkably sensitive to low availability of HNRNPD, which leads to instability of this mRNA and then low LKB1 protein level. LKB1 as a kinase activates another mighty kinase AMPK that regulates downstream targets including the phosphorylation of ACC1 to constrain FAS and metastasis in HCC. Through this regulatory pathway, high levels of <italic toggle=\"yes\">circLARP1B</italic> result in high level of FAS and metastasis in HCC (Figure ##SUPPL##0##S10e##, Supporting Information).</p>", "<p>CircRNAs are pervasively expressed and can be conserved across species,<sup>[</sup>\n##REF##34865956##\n13\n##, ##REF##31395983##\n14\n##, ##REF##31973951##\n15\n##, ##REF##32345360##\n33\n##, ##REF##32694641##\n75\n##\n<sup>]</sup> and several conserved circRNAs such as <italic toggle=\"yes\">CDR1as</italic> in mammals and <italic toggle=\"yes\">circBoule</italic> in metazoans have been investigated with animal models.<sup>[</sup>\n##REF##23446348##\n19\n##, ##UREF##1##\n20\n##, ##UREF##2##\n24\n##\n<sup>]</sup> As for HCC or even cancers, almost all reported circRNAs are either not conserved or not subjected to examinations with genetically manipulated animal models.<sup>[</sup>\n##REF##35821160##\n5\n##, ##REF##34865956##\n13\n##\n<sup>]</sup> A previous report has revealed that the <italic toggle=\"yes\">p21</italic> mRNA stability is enhanced by <italic toggle=\"yes\">circPCNX</italic>, which inhibits HNRNPD's binding to <italic toggle=\"yes\">p21</italic> mRNA in human HeLa cells,<sup>[</sup>\n##REF##33444453##\n50\n##\n<sup>]</sup> although <italic toggle=\"yes\">circPCNX</italic> is not conserved in mice. Another circRNA, <italic toggle=\"yes\">circURI1</italic> also functions as a protein sponge of HNRNPM to modulate alternative splicing of genes such as VEGF1 to inhibit gastric cancer metastasis,<sup>[</sup>\n##UREF##5##\n32\n##\n<sup>]</sup> and <italic toggle=\"yes\">circURI1</italic> is again not conserved in mice. The nature that <italic toggle=\"yes\">circLARP1B</italic> is a mammalian conserved circRNA facilitates our study, especially enables detailed investigations of <italic toggle=\"yes\">circLARP1B</italic> functions and functional mechanisms at the whole organismal level. It is evident that <italic toggle=\"yes\">circLARP1B</italic> utilizes a conserved mechanism to play roles in regulating a cascade that dictates lipid synthesis in HCC, and maybe also in other physiological events or disorders.</p>", "<p>Cancer metastasis is always coupled with lipid metabolism reprogramming.<sup>[</sup>\n##REF##35022204##\n8\n##, ##UREF##0##\n9\n##, ##REF##23446547##\n10\n##\n<sup>]</sup> Take LDs as an example, besides other metastasis promoting functions, increased storage of lipids as LDs at least provide energy reservoir for metastatic cloning.<sup>[</sup>\n##REF##33462499##\n7\n##, ##REF##32506038##\n76\n##\n<sup>]</sup> A recent study has demonstrated that ND‐654, as a liver‐specific ACC inhibitor, constrains hepatic de novo lipogenesis and HCC development by mimicking the effects of ACC phosphorylation.<sup>[</sup>\n##REF##30244972##\n12\n##\n<sup>]</sup> Besides the regulation of ACC activity in lipid biosynthesis, both LKB1 and AMPK are potent kinases, and LKB1/AMPK pathway has an array of known functionalities in HCC and cancers.<sup>[</sup>\n##REF##36316383##\n11\n##, ##REF##19629071##\n77\n##\n<sup>]</sup> In addition to ACC1, the mTOR signaling has been known to promote FAS and is relevant to liver tumorigenesis,<sup>[</sup>\n##UREF##0##\n9\n##, ##REF##30425336##\n44\n##\n<sup>]</sup> which seems also regulated by <italic toggle=\"yes\">circLARP1B</italic> through the AMPK pathway (Figure ##SUPPL##0##S2h##, Supporting Information). mTOR has been subjected to extensive investigations, although the involvement of mTOR signaling in the effects of <italic toggle=\"yes\">circLARP1B</italic> in HCC metastasis and lipid metabolism needs further exploration. Data from PLC cells demonstrate that FAS, but not FAO or lipophagy, is the process that regulated by <italic toggle=\"yes\">circLARP1B</italic> (Figure ##FIG##1##2d–j##; Figure ##SUPPL##0##S2e–i##, Supporting Information).</p>", "<p>\n<italic toggle=\"yes\">CircLARP1B</italic> deficiency leads to the dysregulation of a series of lipid classes (Figure ##FIG##1##2f##). PC, PE, PI, phosphatidylglycerol, and cardiolipin decreased in circLARP1B‐Def PLC cells belong to glycerophospholipids, which are associated with drug‐resistance in multiple cancers.<sup>[</sup>\n##REF##31846838##\n78\n##\n<sup>]</sup> For instance, colorectal cancer patients with abnormal biosynthesis of PC are resistant to oxaliplatin and 5‐fluorouracil.<sup>[</sup>\n##REF##31846838##\n78\n##\n<sup>]</sup> DG, TG, and monoglyceride that are also decreased in circLARP1B‐Def PLC cells belong to glycerolipids, which function as secondary messengers to activate downstream oncogenic signaling.<sup>[</sup>\n##REF##35764645##\n79\n##\n<sup>]</sup> Sphingomyelin (SM), <italic toggle=\"yes\">N</italic>‐acetylhexosyl ceramide (CerG2GNAc1), ceramides phosphate, and phytosphingosine with increased levels in circLARP1B‐Def cells belong to sphingolipids, which are enriched in the lipid rafts localized in cellular membranes, and play critical roles in tumor metastasis, such as EMT and angiogenesis.<sup>[</sup>\n##REF##32999001##\n80\n##\n<sup>]</sup> It is highly possible that these molecules are not just substrates or products of lipid metabolism but also modulators that contribute to the effects of <italic toggle=\"yes\">circLARP1B</italic> in HCC.</p>", "<p>We have provided lines of evidence to reveal roles of <italic toggle=\"yes\">circLARP1B</italic> in hepatocytes with cell lines, knockout mice, and hepatocyte‐directed <italic toggle=\"yes\">circLARP1B</italic> knockdown mice, although the effects of the niche, immune cells, and other unaccounted parameters could also contribute to the final effects observed in HCC. For the effects of hepatocytic Lkb1 depletion in <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> HCC mice (Figure ##FIG##9##10a–c##), the restoration of liver tumor numbers and the Vim and Ecad IHC in liver tumors indicate that Lkb1 depletion in hepatocytes promotes malignant transformation; the restoration of liver tumor size indicates that Lkb1 depletion also promotes tumor growth. Hepatocyte‐directed AAV8‐mediated <italic toggle=\"yes\">circLARP1B</italic> knockdown significantly inhibits HCC metastasis and relevant traits in mice, providing valuable insights for developing this circRNA as a therapeutic target of HCC.</p>", "<p>We have provided experimental data from multiple levels to support that <italic toggle=\"yes\">LKB1</italic> mRNA is the key downstream target of <italic toggle=\"yes\">circLARP1B</italic> via perturbing HNRNPD in both human and mice. Even hepatocytic knockdown of <italic toggle=\"yes\">LKB1</italic> seems sufficient to abolish effects of <italic toggle=\"yes\">circLARP1B</italic> absence in HCC (Figure ##FIG##9##10a–e##; Figure ##SUPPL##0##S9c–j##, Supporting Information), it is possible that the other mRNAs sensitive to <italic toggle=\"yes\">circLARP1B</italic> and HNRNPD may also take part in the regulatory effects of <italic toggle=\"yes\">circLARP1B</italic> to some degree. HNRNPD, a well‐recognized and conserved RBP with multiple post‐translational modifications, is upregulated in various human cancers including HCC, and is associated with poor prognosis and drug resistance.<sup>[</sup>\n##REF##1901943##\n48\n##, ##REF##19033365##\n49\n##, ##REF##21956942##\n51\n##, ##REF##35178834##\n81\n##, ##REF##37060820##\n82\n##, ##UREF##7##\n83\n##, ##REF##33016643##\n84\n##\n<sup>]</sup> In the cytoplasm, HNRNPD can promote the decay of some mRNAs, and on the other hand stabilize some mRNA targets (e.g., <italic toggle=\"yes\">PTH</italic> and <italic toggle=\"yes\">VHL</italic>).<sup>[</sup>\n##REF##1901943##\n48\n##, ##REF##33444453##\n50\n##, ##REF##10702317##\n56\n##\n<sup>]</sup> Intriguingly, for <italic toggle=\"yes\">c‐MYC</italic> mRNA, HNRNPD promotes its degradation in human lymphoblast cell line K562 and PLC liver cancer cells, and increases its stability in murine fibroblast 3T3 and human colorectal cancer cell line HCT116 indicating that the effect of HNRNPD may depend on the overall interactions among proteins bound to the mRNA.<sup>[</sup>\n##REF##35940521##\n65\n##, ##REF##16391004##\n85\n##\n<sup>]</sup> We have demonstrated clinical significance of <italic toggle=\"yes\">circLARP1B</italic>, HNRNPD, and <italic toggle=\"yes\">LKB1</italic> in HCC. As for AMPK, it may play complex regulatory roles through various downstream signaling networks in cancers. In this study, p‐AMPK has been shown to play critical roles in regulating HCC metastasis through remodeling lipid metabolism, and further investigation concentrating on clinical relevance of the kinase role of AMPK in HCC is required.</p>", "<p>Starting from screening with clinical specimens collected, we have identified the functional roles and mechanisms of the mammalian conserved <italic toggle=\"yes\">circLARP1B</italic> in HCC metastasis and lipid metabolism. Data from both human and mice have revealed a pathway of <italic toggle=\"yes\">circLARP1B</italic>–HNRNPD–<italic toggle=\"yes\">LKB1</italic>–AMPK with potent regulatory effects in HCC lipid metabolism and metastasis. As it is closely associated with progression and prognosis, <italic toggle=\"yes\">circLARP1B</italic> may be explored as a diagnostic marker or even a therapeutic target for HCC.</p>" ]
[]
[ "<title>Abstract</title>", "<p>Circular RNAs (circRNAs) have emerged as crucial regulators in physiology and human diseases. However, evolutionarily conserved circRNAs with potent functions in cancers are rarely reported. In this study, a mammalian conserved circRNA <italic toggle=\"yes\">circLARP1B</italic> is identified to play critical roles in hepatocellular carcinoma (HCC). Patients with high <italic toggle=\"yes\">circLARP1B</italic> levels have advanced prognostic stage and poor overall survival. <italic toggle=\"yes\">CircLARP1B</italic> facilitates cellular metastatic properties and lipid accumulation through promoting fatty acid synthesis in HCC. <italic toggle=\"yes\">CircLARP1B</italic> deficient mice exhibit reduced metastasis and less lipid accumulation in an induced HCC model. Multiple lines of evidence demonstrate that <italic toggle=\"yes\">circLARP1B</italic> binds to heterogeneous nuclear ribonucleoprotein D (HNRNPD) in the cytoplasm, and thus affects the binding of HNRNPD to sensitive transcripts including <italic toggle=\"yes\">liver kinase B1</italic> (<italic toggle=\"yes\">LKB1</italic>) mRNA. This regulation causes decreased <italic toggle=\"yes\">LKB1</italic> mRNA stability and lower LKB1 protein levels. Antisense oligodeoxynucleotide complementary to theHNRNPD binding sites in <italic toggle=\"yes\">circLARP1B</italic> increases the HNRNPD binding to <italic toggle=\"yes\">LKB1</italic> mRNA. Through the HNRNPD–LKB1–AMPK pathway, <italic toggle=\"yes\">circLARP1B</italic> promotes HCC metastasis and lipid accumulation. Results from AAV8‐mediated hepatocyte‐directed knockdown of <italic toggle=\"yes\">circLARP1B</italic> or Lkb1 in mouse models also demonstrate critical roles of hepatocytic <italic toggle=\"yes\">circLARP1B</italic> regulatory pathway in HCC metastasis and lipid accumulation, and indicate that <italic toggle=\"yes\">circLARP1B</italic> may be potential target of HCC treatment.</p>", "<p>The mammalian conserved <italic toggle=\"yes\">circLARP1B</italic> promotes hepatocellular carcinoma metastasis and lipid accumulation. <italic toggle=\"yes\">CircLARP1B</italic> functions by sequestering cytoplasmic heterogeneous nuclear ribonucleoprotein D (HNRNPD) to decrease HNRNPD binding to sensitive transcripts including <italic toggle=\"yes\">liver kinase B1</italic> (<italic toggle=\"yes\">LKB1</italic>) mRNA, leading to decreased <italic toggle=\"yes\">LKB1</italic> mRNA stability and lower protein levels. Hepatocyte‐directed knockdown of <italic toggle=\"yes\">circLARP1B</italic> or Lkb1 in mice impedes hepatocellular carcinoma metastasis and lipid accumulation.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6779-cit-0097\">\n<string-name>\n<given-names>J.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Shi</surname>\n</string-name>, <string-name>\n<given-names>B.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Sheng</surname>\n</string-name>, <string-name>\n<given-names>S.</given-names>\n<surname>Chang</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Cai</surname>\n</string-name>, <string-name>\n<given-names>G.</given-names>\n<surname>Shan</surname>\n</string-name>, <article-title>A Mammalian Conserved Circular RNA <italic toggle=\"yes\">CircLARP1B</italic> Regulates Hepatocellular Carcinoma Metastasis and Lipid Metabolism</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305902</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305902</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Clinical Specimens</title>", "<p>All fresh HCC tumor tissues were collected from Sir Run Run Shaw Hospital, which was approved by the Human Research Ethics Committee of Sir Run Run Shaw Hospital (SRRSHLS2022Y0312). Written informed consent was obtained from each patient for this study. All samples were frozen and stored in liquid nitrogen after removal from the operation followed by washing with PBS twice.</p>", "<title>Mice</title>", "<p>All mice were housed in an enriched environment under the standard conditions (23–25 °C temperature, 40–60% humidity) with a 12‐h light‐dark cycle (lights on from 08:00 to 20:00) at the Specific‐Pathogen‐Free facility with unrestricted access to food and water for the duration of the experiment, unless specified in the corresponding situation. All animal protocols were approved by the Animal Care and Use Committee of the University of Science and Technology of China (USTCACUC212201037). For genetically engineered mice, whole‐body <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice were generated with the CRISPR/Cas9 system as previously described.<sup>[</sup>\n##REF##36182935##\n18\n##\n<sup>]</sup> sgRNAs targeting <italic toggle=\"yes\">Larp1b</italic> intron 4 were designed by CRISPick web‐server (<ext-link xlink:href=\"https://portals.broadinstitute.org/gppx/crispick/public\" ext-link-type=\"uri\">https://portals.broadinstitute.org/gppx/crispick/public</ext-link>). The synthesized <italic toggle=\"yes\">Cas9</italic> mRNA and sgRNAs were coinjected into fertilized embryos of C57BL/6J mice and 100 zygotes were implanted into five ICR strain surrogate mice. All F0 founders were genotyped at 2 weeks after birth with PCR amplification followed by Sanger sequencing. Specific primers for PCR were included in Table ##SUPPL##5##S5## of the Supporting Information. Positive F0 founders were backcrossed to C57BL/6 mice to obtain deficient allele heritable heterozygous F1 mice, which were further intercrossed to generate <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> homozygous mice. All <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice used for analyses were in parallel with age‐ and gender‐matched wildtype littermates (as the control group). Male mice were used for experiments in this study.<sup>[</sup>\n##REF##37005415##\n86\n##, ##REF##32182125##\n87\n##\n<sup>]</sup>\n</p>", "<title>Library Preparation for RNA‐seq</title>", "<p>Total RNA from frozen tissues or cultured cells was extracted with the TRIzol reagent (Invitrogen) according to the manufacturer's protocols. Libraries were prepared with the TruSeq Ribo Profile Library Prep Kit (Illumina) according to the manufacturer's instructions and then subjected to sequencing in an Illumina Nova‐PE150 system (Novogene). Each library generated ≈100 million 150‐nt paired‐end read pairs.</p>", "<title>CircRNA Identification</title>", "<p>The circRNA candidates were identified with CIRI2 and the BSJ reads per million were used to calculate circRNA levels. Briefly, the adapters were removed with Cutadapt (‐e 0.1 ‐O 5) to obtain clean reads. The reads continuously aligned to the human reference genome (hg19) were filtered with Bowtie (‐v 1) allowing one mismatch. The remaining reads were used to predict circRNA candidates with CIRI2 with default parameters. The differentially expressed circRNAs were determined by DEseq2 with a criterion (fold change &gt;4 or &lt;0.25, <italic toggle=\"yes\">P</italic>‐value &lt;0.05). For conservation analysis of circRNAs, the circRNA sequences were aligned to annotated murine circRNAs from the circAtlas database with Blast. Conserved circRNAs between human and mice were determined with a stringent cutoff (full‐length and BSJ sequences &gt;75% identical).</p>", "<title>Cell Culture and Cell Transfection</title>", "<p>The PLC/PRF/5 (PLC) cells were kindly provided by Dr. Yide Mei (USTC). HepG2, HEK293T, K1, and Hepa1‐6 cells all originated from the American Type Culture Collection. All above cells were maintained under standard conditions with the DMEM medium containing 10% FBS (CLARK, FB25015) and 1% penicillin/streptomycin (Beyotime, C0222) at 37 °C under 5% CO<sub>2</sub>. A PCR‐based method and DAPI staining were used to ensure cells without contamination of mycoplasma. All cell lines were authenticated by short‐tandem‐repeat profiling. Transfection of plasmids and siRNAs was conducted with Lipofectamine 2000 (Invitrogen) according to the manufacturer's protocol.</p>", "<title>CRISPR/Cas9‐Mediated CircLARP1B Deficient Cells</title>", "<p>Two sgRNAs targeting the intron 4 of human LARP1B were designed based on <ext-link xlink:href=\"http://crispr.mit.edu\" ext-link-type=\"uri\">http://crispr.mit.edu</ext-link> to knockout <italic toggle=\"yes\">circLARP1B</italic>. After transfection of 2 µg pX330 plasmids expressing <italic toggle=\"yes\">Cas9</italic> mRNA and targeted sgRNAs for two days, hundreds of mCherry‐positive single‐cell clones were sorted through the BD FACSAria III cell sorting system. Two weeks later, the colonies were split into two identical plates and one plate was harvested for PCR‐mediated genotype and confirmation by Sanger sequencing. The primer sequences are listed in Table ##SUPPL##5##S5## of the Supporting Information.</p>", "<title>OCR Measurements</title>", "<p>The OCR analyses were performed using the Agilent Seahorse XF Cell Mito Stress Test Kit (Agilent, 103015‐100) as previously described.<sup>[</sup>\n##REF##33758188##\n88\n##\n<sup>]</sup> Briefly, 20 000 cells per well were seeded in a 96‐well XF cell culture microplate in the growth medium overnight at 37 °C in 5% CO<sub>2</sub>. OCR was measured with an XF96 analyzer in XF DMEM medium (Agilent, 103575‐100) containing 1 m<sc>m</sc> pyruvate, 2 m<sc>m</sc> glutamine, and 10 m<sc>m</sc> glucose, followed by sequential addition of 1.5 µ<sc>m</sc> oligomycin (ATP synthase inhibitor), 1.0 µ<sc>m</sc> FCCP (membrane potential uncoupler), 0.5 µ<sc>m</sc> rotenone (Complex I inhibitor), and 0.5 µ<sc>m</sc> antimycin A (Complex III inhibitor). Data were analyzed by the Seahorse XF Cell Mito Stress Test Report Generator package.</p>", "<title>FAO Rate Measurements</title>", "<p>The FAO rate analyses were performed using the Agilent Seahorse XF Cell Mito Stress Test Kit (Agilent, 103015‐100) as previously described.<sup>[</sup>\n##REF##31155494##\n89\n##\n<sup>]</sup> Briefly, 15 000 cells per well were seeded in a 96‐well XF cell culture microplate in the growth medium overnight at 37 °C in 5% CO<sub>2</sub>. Then, cells were starved by incubating with substrate‐limited DMEM supplemented with 0.5 m<sc>m</sc> glucose, 1 m<sc>m</sc> glutamate, 0.5 m<sc>m</sc> carnitine, and 1% FBS. After 24‐h starvation, the medium was replaced by FAO assay medium (111 m<sc>m</sc> NaCl, 4.7 m<sc>m</sc> KCl, 1.25 m<sc>m</sc> CaCl<sub>2</sub>, 2 m<sc>m</sc> MgSO<sub>4</sub>, 1.2 m<sc>m</sc> NaH<sub>2</sub>PO<sub>4</sub> supplemented with 2.5 m<sc>m</sc> glucose, 0.5 m<sc>m</sc> carnitine, and 5 m<sc>m</sc> HEPES, pH 7.4). Finally, BSA‐conjugated palmitate (Agilent, 102720‐100) was added to a final concentration of 50 m<sc>m</sc>, followed by sequential addition of 1.5 µ<sc>m</sc> oligomycin, 1.0 µ<sc>m</sc> FCCP, 0.5 µ<sc>m</sc> rotenone, and 0.5 µ<sc>m</sc> antimycin A. Data were analyzed by the Seahorse XF Cell Mito Stress Test Report Generator package.</p>", "<title>\n<sup>13</sup>C‐Labeled Targeted Metabolic Flux Analysis</title>", "<p>\n<sup>13</sup>C‐labeled targeted metabolic flux analysis was carried out as previously described with minor modifications.<sup>[</sup>\n##REF##32101748##\n37\n##\n<sup>]</sup> In brief, 10<sup>7</sup> PLC cells were washed with 0.9% saline three times and incubated in substrate‐limited DMEM supplemented with 15  m<sc>m</sc>\n<sup>13</sup>C‐glucose, 4  m<sc>m</sc>\n<sup>13</sup>C‐glutamine, and 10% FBS for 24 h before metabolite extraction. After washing with cold 0.9% saline twice, cells were incubated with 500 µL cold extraction buffer (methanol:acetonitrile:water, 2:2:1, v/v/v). Harvested cells were sonicated for 2 min, centrifuged at 14 000 × <italic toggle=\"yes\">g</italic> for 5 min at 4 °C and cell supernatants were transferred to new tubes. 400 µL chloroform was added and the tubes were vortexed, centrifuged at 14 000 × <italic toggle=\"yes\">g</italic> for 5 min at 4 °C. The resulting phase separation resulted in an aqueous upper phase containing polar metabolites and an organic lower phase containing nonpolar metabolites. The aqueous upper phase was transferred to tubes and the lower chloroform phase was transferred to a glass tube. For reverse phase liquid chromatography separation, ACQUITY UPLC BEH C18 (100 × 2.1 mm, 1.7 µm, Waters) was used. Mass spectrometric data were acquired with a Q‐Exactive plus hybrid quadrupole–orbitrap mass spectrometer (Thermo) using negative ion electrospray ionization. The scan range was from 50 to 1000 <italic toggle=\"yes\">m</italic>/<italic toggle=\"yes\">z</italic>. The scan time for each function was set to 0.2 s. Ion monitoring conditions were defined as a capillary voltage of 2.0 kV, source temperature of 120 °C, and desolvation temperature of 500 °C. Data processing and ion annotation based on accurate mass were performed in TraceFinder 5.0 (Thermo) and Xcalibur 4.0 (Thermo). Metabolite mass isotopomer distribution was determined based on the ratio of the integrated peak areas of the chosen isotopomer to the sum of all the integrated peak areas of the possible isotopomers for the given metabolites.</p>", "<title>Plasmids Construction</title>", "<p>All plasmids were constructed with restriction‐enzyme digestion and ligation or with recombinant methods (Vazyme, c113‐02). For <italic toggle=\"yes\">circLARP1B</italic> overexpression in human, the circularized exons and the endogenous flanking sequences including one <italic toggle=\"yes\">Alu</italic> pair were inserted into the pcDNA3 vector. The backbone vector of p3×FLAG‐Myc was used for constructing FLAG‐tagged HNRNPD and LKB1. The shRNA against the BSJ of human or murine <italic toggle=\"yes\">circLARP1B</italic> was cloned into the vector pLKO.1 (Sigma) and the negative‐control shRNA (shCtrl, MFCD07785395) was obtained from the MISSION shRNA Library (Sigma). The sgRNAs for human or murine <italic toggle=\"yes\">circLARP1B</italic> were inserted into the <italic toggle=\"yes\">Cas9‐</italic> and sgRNA‐expressing backbone (pX330), which was engineered with expressing mCherry and a puromycin selectable marker. All plasmids have been sequenced for confirmation and further information about these plasmids is available upon request. Oligonucleotide sequences for primers used in plasmids construction, along with other oligo sequences used in probe preparation, siRNA, and biotin‐labeled nucleic acids were listed in Table ##SUPPL##5##S5## of the Supporting Information.</p>", "<title>Northern Blotting</title>", "<p>Northern blotting was performed as previously described.<sup>[</sup>\n##REF##29322446##\n90\n##\n<sup>]</sup> The digoxigenin‐labeled RNA probe with antisense sequences to the <italic toggle=\"yes\">circLARP1B</italic> BSJ was synthesized with a DIG Northern Starter Kit (Roche, 12039672910) according to the manufacturer's protocol. The primers for probe preparation were listed in Table ##SUPPL##5##S5## of the Supporting Information.</p>", "<title>Single‐Molecule Fluorescence In Situ Hybridization</title>", "<p>The smFISH was carried out as previously described with minor modifications.<sup>[</sup>\n##UREF##8##\n91\n##\n<sup>]</sup> Cells or tissues were fixed with 4% PFA for 10 min at room temperature and permeabilized with ice‐cold 70% ethanol overnight at −20 °C. For hybridization, cells or tissues were prehybridized at 37 °C for 30 min in hybridization buffer (30% formamide, 5× SSC, 9 m<sc>m</sc> citric acid, pH 6.0, 0.1% Tween‐20, 50 µg mL<sup>−1</sup> heparin, 1× Denhardt's solution, and 10% dextran sulfate) after washing with 2× SSC twice. Then, samples were hybridized with 2 pmol probes overnight at 37 °C in the hybridization buffer. For the amplification stage, 18 pmol hairpins were heated at 95 °C for 90 s and cooled to room temperature in a dark drawer for 30 min. Samples were incubated with the denatured probes overnight at room temperature followed by three 5 min washes in 2× SSC buffer. After a 10 min incubation in DAPI (5 mg mL<sup>−1</sup>), the sections were washed three times for 5 min in 2× SSC buffer. The images were captured using the laser confocal microscopy LSM880 (Zeiss). The ImageJ was used to further process the data, and the ImageJ Plot Profile tool was applied to calculate signal intensity. All probe sequences were included in Table ##SUPPL##5##S5## of the Supporting Information.</p>", "<title>PCR Reactions</title>", "<p>For RT‐PCR, 500 ng total RNA was reverse‐transcribed into complementary DNA (cDNA) with the GoScript Reverse Transcription System (Promega, A5001) according to the manufacturer's protocol. For PCR with genomic DNA (gDNA) as the template, gDNA was isolated by phenol/chloroform extraction. For semiquantitative RT‐PCR gels, 25–30 cycles were carried out. The RT‐qPCR was performed using GoTaq SYBR Green qPCR Master Mix (Promega, A6001) on a PikoReal 96 real‐time PCR system (Thermo). All PCR products were confirmed by Sanger sequencing. All used primer sequences are included in Table ##SUPPL##5##S5## of the Supporting Information.</p>", "<title>Nuclear/Cytosolic Fractionation</title>", "<p>Cellular fractionation was carried out as previously described with minor modifications.<sup>[</sup>\n##REF##36182935##\n18\n##\n<sup>]</sup> Briefly, cells were incubated with hypotonic buffer (10 m<sc>m</sc> Tris‐HCl, pH 8.0, 140 m<sc>m</sc> NaCl, 1.5 m<sc>m</sc> MgCl<sub>2</sub>, 0.5% NP‐40, 1 m<sc>m</sc> DTT, and 0.1 U µL<sup>−1</sup> RNase inhibitor (Promega, N2615)) on ice for 20 min after washing with PBS twice. After centrifugation at 1000 × <italic toggle=\"yes\">g</italic> for 5 min at 4 °C, the supernatant was collected as the cytoplasmic fraction. The pellets were then resuspended in nuclear resuspension buffer (20 m<sc>m</sc> HEPES, pH 7.9, 400 m<sc>m</sc> NaCl, 1 m<sc>m</sc> EGTA, 1 m<sc>m</sc> EDTA, 1 m<sc>m</sc> DTT, and 0.1 U µL<sup>−1</sup> RNase inhibitor followed by the incubation at 4 °C for 30 min. Nuclear fraction was collected after removing insoluble membrane debris by centrifugation at 12 000 × <italic toggle=\"yes\">g</italic> for 15 min.</p>", "<title>Quantification of RNA Copy Number per Cell</title>", "<p>The protocol was carried out as previously described.<sup>[</sup>\n##UREF##5##\n32\n##\n<sup>]</sup> Total RNA was extracted from 10<sup>6</sup> PLC and HepG2 cells, and cDNA was synthesized. The standard curve was used to calculate the copy numbers per cell in each cell line based on cell numbers and Ct values.</p>", "<title>Transwell Assay</title>", "<p>Transwell invasion assay was performed using the chamber with Matrigel (BD Biosciences). Cells were seeded into the upper chamber cultured with the serum‐free DMEM medium, and DMEM containing 10% FBS was added to the lower chamber. After 24 h, the migrated cells on the outer membrane were stained with 0.1% crystal violet for 10 min. Images were captured with an inverted microscope (Olympus) and the number of invaded cells was quantified by ImageJ.</p>", "<title>Cell Viability and Number Measurement and Colony Formation</title>", "<p>The cell viability was detected using MTT cell proliferation and Cytotoxicity Detection Kit (KeyGEN, KGA311). Cell numbers were measured by trypan blue assay using Trypan Blue Staining Cell Viability Assay Kit (Beyotime, C0011). For colony formation, cells were seeded into 6‐well plates (500 cells per well) and then were fixed and stained with 0.1% crystal violet for 10 min after two weeks.</p>", "<title>Nile Red Staining</title>", "<p>To visualize lipid droplets, cells were washed with PBS twice, fixed with 4% PFA, and stained with 0.05 mg mL<sup>−1</sup> Nile red solution for 10 min. The nuclei were further stained with Hoechst 33342, and images were captured using laser confocal microscopy LSM880 (Zeiss). For FASN inhibition, 50 n<sc>m</sc> IPI‐9119 (Selleck, E2667) was incubated with PLC cells for 72 h. The Nile red signal is defined as the mean gray value per cell (integrated density/area) quantified by ImageJ.</p>", "<title>Untargeted Metabolomics and Lipidomics</title>", "<p>The untargeted metabolomics and lipidomics were carried out as previously described with minor modifications.<sup>[</sup>\n##REF##29663480##\n92\n##\n<sup>]</sup> All cells were maintained under standard conditions with DMEM medium containing 10% FBS for 48 h and then subjected to metabolomics analysis. 10<sup>7</sup> cells were incubated with 800 µL cold methanol for protein removal and metabolite extraction after two PBS washes. The mixture was collected and centrifuged at 12 000 × <italic toggle=\"yes\">g</italic> for 20 min, and the supernatant was further dried in a vacuum centrifuge. For LC‐MS analysis, samples were redissolved in 100 µL acetonitrile/water (1:1, v/v) solvent and centrifuged at 14 000 × <italic toggle=\"yes\">g</italic> at 4 °C for 15 min. Then the supernatant was subjected to AB Triple TOF 6600 (AB SCIEX) and Q Exactive HF‐X (Thermo) for metabolomics and lipidomics, respectively (Shanghai Applied Protein Technology). For statistical analysis, the VIP value of each variable in the orthogonal partial least‐squares discriminant analysis model was calculated to indicate its contribution to the classification. The significantly differential metabolites were identified with the cutoff (VIP &gt;1, <italic toggle=\"yes\">P</italic>‐value &lt;0.05). <italic toggle=\"yes\">P</italic>‐values were generated by the two‐tailed Student's <italic toggle=\"yes\">t</italic>‐test.</p>", "<title>Western Blotting</title>", "<p>For western blots, samples were separated on SDS‐PAGE gels and then transferred to PVDF membranes (Millipore). Membranes were processed according to the ECL western blotting protocol (GE Healthcare). The grayscale statistics of western blotting were performed by ImageJ. The following antibodies were used in western blots: anti‐AMPK (CST, 5832), anti‐p‐AMPK (CST, 2535), anti‐ACC1 (CST, 3676), anti‐p‐ACC1 (CST, 3661), anti‐RAPTOR (CST, 2280), anti‐p‐RAPTOR (CST, 89146), anti‐VEGFA (Proteintech, 9003‐1‐AP), anti‐TGF‐β (Immunoway, YT4632), anti‐MFF (Proteintech, 17090‐1‐AP), anti‐p‐MFF (Immunoway, YP1403), anti‐p‐ULK1 (CST, 5869), anti‐ULK1 (CST, 8054), anti‐LKB1 (Immunoway, YT2573), anti‐HNRNPD (Thermo, PA5‐99469), anti‐AGO2 (Sigma, SAB4200085), anti‐eIF4G1 (CST, 8701), anti‐eIF4E (Abcam, ab33768), anti‐c‐MYC (CST, 9402), and anti‐ACTB (TransGen, HC201). Antibody validation is provided on the manufacturers’ websites.</p>", "<title>RNA Pull‐Down and RNA Immunoprecipitation</title>", "<p>RNA pull‐down with 5′‐biotinylated antisense oligos and RIP were carried out as previously described with minor modifications.<sup>[</sup>\n##REF##27694840##\n93\n##\n<sup>]</sup> PLC cells and murine liver cells were cross‐linked (a total of 0.4 J cm<sup>−2</sup>) in a UV cross‐linker. Cells were harvested in ice‐cold lysis buffer (20 m<sc>m</sc> HEPES, pH 7.4, 10 m<sc>m</sc> KCl, 2 m<sc>m</sc> MgCl<sub>2</sub>, 0.5% NP‐40, 1 m<sc>m</sc> DTT, 1× Protease Inhibitor Cocktail, and 0.1 U µL<sup>−1</sup> RNase inhibitor (Promega, N2615)) for 30 min on ice. The supernatant was collected after centrifugation at 1000 × <italic toggle=\"yes\">g</italic> for 5 min at 4 °C, and subjected to sonication on ice for 5 min with a Sonics Vibra‐Cell (3 s on, 6 s off, 30%). 100 pmol biotinylated AS oligos (for pull‐down) or 2 µg antibody (for RIP) was added to the supernatant. After rotation 4 h at 4 °C, 50 µL M‐280 Streptavidin Dynabeads (Invitrogen, 11206D, for RNA pulldown) or Protein G Dynabeads (Invitrogen, 10004D, for RIP), which were blocked with 500 ng µL<sup>−1</sup> yeast total RNA and 1 mg mL<sup>−1</sup> BSA for 1 h at room temperature were added. After rotation 4 h at 4 °C, washing once with lysis buffer, twice with high salt lysis buffer (20 m<sc>m</sc> HEPES, pH 7.4, 10 m<sc>m</sc> KCl, 500 m<sc>m</sc> NaCl, 2 m<sc>m</sc> MgCl<sub>2</sub>, 0.5% NP‐40, 1 m<sc>m</sc> DTT, 1× Protease Inhibitor Cocktail, and 0.1 U µL<sup>−1</sup> RNase inhibitor). The purified RNAs were analyzed by RT‐qPCR. The purified proteins were analyzed by MS after silver staining using Protein Stains K kit (Sangon Biotech, C500021‐0010) or western blot. The following antibodies were used: anti‐HNRNPD (Thermo, PA5‐99469); anti‐AGO2 (Sigma, SAB4200085). For HNRNPD RIP, <italic toggle=\"yes\">CCND1</italic> and <italic toggle=\"yes\">Mef2c</italic> mRNAs were used as positive controls in human and mice, respectively.<sup>[</sup>\n##REF##33444453##\n50\n##, ##REF##24891619##\n94\n##\n<sup>]</sup> For AGO2 RIP, <italic toggle=\"yes\">TNFRSF12A</italic> mRNA was used as a positive control.<sup>[</sup>\n##REF##29458013##\n95\n##\n<sup>]</sup>\n</p>", "<title>Ribosome Profiling and Ribo‐seq Analysis</title>", "<p>The ribosome profiling assay was conducted as previously described with minor modifications.<sup>[</sup>\n##UREF##5##\n32\n##\n<sup>]</sup> The curve was generated with optical scanning at 254 nm using a Gradient Profiler (BioComp). <italic toggle=\"yes\">GAPDH</italic> mRNA is a positive control, and <italic toggle=\"yes\">circHIPK3</italic>, a negative control, is known to be noncoding.<sup>[</sup>\n##REF##27050392##\n96\n##\n<sup>]</sup> For Ribo‐seq analysis from previous studies (GSE147840, GSE125757, and GSE128320), the adapters were trimmed to obtain clean reads. The left reads with lengths ranging from 28 to 32 nt were then aligned to the human genome (hg19) with Bowtie (‐v 1) allowing one mismatch. Ribo‐seq signals shown in Figure ##SUPPL##0##S5b## of the Supporting Information were presented by IGV visualization.</p>", "<title>Protein Mass Spectrometry</title>", "<p>The specific silver‐stained band was cut, cleaned, and digested in gel with the digestion buffer (100 m<sc>m</sc> NH<sub>4</sub>HCO<sub>3</sub>, pH 8.5) containing trypsin (Promega, V5111). The samples were analyzed using an LC‐ESI‐MS/MS system after extraction and purification. Protech's ProtQuest software suite was used to search the mass spectrometric data against the UniProt protein database.</p>", "<title>ImmunofluorescenceStaining</title>", "<p>PLC cells or HCC tissues were fixed with methanol/glacial acetic acid (3:1, v/v) at room temperature for 10 min after washing with PBS twice, and permeabilized with fresh PBS containing 1% Triton X‐100 on ice for 10 min. After blocking with 1% BSA for 30 min at room temperature, samples were incubated with the anti‐HNRNPD antibody (Thermo, PA5‐99469) or anti‐LKB1 antibody (Proteintech, 10746‐1‐AP) (1:200 dilution in 1% BSA) for 4 h at room temperature. With three 5 min washes in PBST buffer (PBS with 0.4% Tween‐20), samples were incubated with Goat Anti‐Rabbit Secondary Antibody Alexa Fluor 488 (Abcam, ab150077) (1:200 diluted in 1% BSA) for 2 h at room temperature, protected from light. After three 5 min washes in PBST buffer, nuclei were stained with DAPI, and the images were captured using laser confocal microscopy LSM880 (Zeiss).</p>", "<title>RIP‐seq and Data Analysis</title>", "<p>RIP‐seq was carried out as previously described with minor modifications.<sup>[</sup>\n##REF##36182935##\n18\n##, ##UREF##2##\n24\n##\n<sup>]</sup> 5 × 10<sup>7</sup> PLC cells were ultraviolet cross‐linked (a total of 0.4 J cm<sup>−2</sup>) in a UVP cross‐linker and harvested in ice‐cold lysis buffer (20 m<sc>m</sc> HEPES, pH 7.4, 10 m<sc>m</sc> KCl, 2 m<sc>m</sc> MgCl<sub>2</sub>, 0.5% NP‐40, 1 m<sc>m</sc> DTT, 1× Protease Inhibitor Cocktail, and 0.1 U µL<sup>−1</sup> RNase inhibitor (Promega, N2615)) for 30 min on ice. The supernatant was collected after centrifugation at 1000 × <italic toggle=\"yes\">g</italic> for 5 min at 4 °C, and subjected to sonication on ice for 5 min with a Sonics Vibra‐Cell (3 s on, 6 s off, 30%). The HNRNPD‐binding complexes were isolated by anti‐HNRNPD (Thermo, PA5‐99469) coupled with Protein G Dynabeads (Life Technology, 10004D). After one wash with lysis buffer, two washes with high salt lysis buffer (20 m<sc>m</sc> HEPES, pH 7.4, 10 m<sc>m</sc> KCl, 500 m<sc>m</sc> NaCl, 2 m<sc>m</sc> MgCl<sub>2</sub>, 0.5% NP‐40, 1 m<sc>m</sc> DTT, 1× Protease Inhibitor Cocktail, and 0.1 U µL<sup>−1</sup> RNase inhibitor) and treatment of proteinase K, the mixture was subjected to RNA extraction with TRIzol reagent according to standard protocol. For RIP‐seq cDNA library preparation, the purified RNAs were ligated to adapters, reverse transcribed, PCR‐amplified for ≈25 cycles, and then subjected to high‐throughput sequencing using an Illumina Novoseq platform with a 150‐nt run length. For data analysis, the adapters were first trimmed to obtain clean reads, and the left reads were then mapped to the human genome (hg19) with Bowtie2. After the alignment, duplicates were removed and MACS2 was used for peak calling. The genome distribution of HNRNPD RIP‐seq signals was annotated according to the gene transfer format file from UCSC. For <italic toggle=\"yes\">circLARP1B</italic>, all <italic toggle=\"yes\">circLARP1B</italic> reads including the BSJ reads from the HNRNPD RIP‐seq were used for IGV visualization. For HNRNPD PAR‐CLIP reanalysis from previous studies (GSE52977), HNRNPD signals in the 3′ UTRs of targeted mRNAs were used for comparison.</p>", "<title>KEGG and GO Analysis</title>", "<p>For KEGG pathway analysis, the metabolites were blasted against the online KEGG database (<ext-link xlink:href=\"https://www.genome.jp/kegg/\" ext-link-type=\"uri\">https://www.genome.jp/kegg/</ext-link>) to annotate the corresponding pathways. For GO analysis of HNRNPD binding targets regulated by <italic toggle=\"yes\">circLARP1B</italic>, GOrilla web‐server (<ext-link xlink:href=\"https://cbl-gorilla.cs.technion.ac.il/\" ext-link-type=\"uri\">https://cbl‐gorilla.cs.technion.ac.il/</ext-link>) with default parameters was visualized by the ggplot2 package in R software.</p>", "<title>mRNA Stability Assay</title>", "<p>For mRNA stability assay, cells were cultured with fresh DMEM at 37 °C for 12 h before being treated with 5 mg mL<sup>−1</sup> Actinomycin D (Sigma, A4262). The samples were harvested at indicated times and then subjected to RT‐qPCR analysis.</p>", "<title>EIF4E and eIF4G1 RIP Assays</title>", "<p>EIF4E and eIF4G1 RIP assays were performed as previously described with minor modifications.<sup>[</sup>\n##REF##25826658##\n66\n##\n<sup>]</sup> 5 × 10<sup>7</sup> PLC cells were ultraviolet cross‐linked (a total of 0.4 J cm<sup>−2</sup>) in a UV cross‐linker, and harvested in ice‐cold RIPA buffer (50  m<sc>m</sc> Tris‐HCl, pH 8.0, 150  m<sc>m</sc> NaCl, 5  m<sc>m</sc> EDTA, 1% NP‐40, 0.1% SDS, 1 m<sc>m</sc> DTT, 1× Protease Inhibitor Cocktail) for 30 min on ice. The lysate was then subjected to sonication on ice for 5 min with a Sonics Vibra‐Cell (3 s on, 6 s off, 30%) and the supernatant was collected after centrifugation at 12 000 × <italic toggle=\"yes\">g</italic> for 5 min at 4 °C. After the measurement of the absorbance at 260 nm, the supernatant was incubated with 3 U of RNase I (Invitrogen, AM2294) per A260 unit (Absorbance at 260 nm × volume in mL). An aliquot of the digestion reaction was saved as the input sample. The left supernatant was incubated with Protein G beads preconjugated antibody for the immunoprecipitation procedures. The bead–lysate mixture was rotated at room temperature (25 °C) for 30 min, and the input sample was placed alongside it. After collection on a magnetic rack at 4 °C, beads were rinsed briefly in 1 mL ice‐cold RIPA buffer, then collected and washed twice for 5 min each with rotating. Meanwhile, the bead supernatant and the input sample were aliquoted into two samples each (for RNA and protein isolation) and frozen. The RNA samples were subjected to TRIzol extraction. For further RT‐qPCR detection, primers used were included in Table ##SUPPL##5##S5## of the Supporting Information. The following antibodies were used: anti‐eIF4E (Abcam, ab33768); anti‐eIF4G1 (CST, 8701).</p>", "<title>Dual‐Luciferase Reporter Assay</title>", "<p>The 3′ UTR sequence of <italic toggle=\"yes\">LKB1</italic> mRNA was used as the 3′ UTR of firefly luciferase in the vector pGL3 (Promega, HG‐VQP0122). Vector expressing renilla luciferase was used as a loading control. After transfection in HEK293T cells for 24 h, relative luciferase activities were determined using a Dual‐Luciferase Reporter Assay System (Promega, E1910) according to the manufacturer's instructions.</p>", "<title>Immunofluorescence Combined with Fluorescence In Situ Hybridization</title>", "<p>The IF combined with FISH assay was performed as previously described with several modifications.<sup>[</sup>\n##REF##32048164##\n16\n##, ##REF##31508410##\n60\n##\n<sup>]</sup> PLC cells were fixed with methanol/glacial acetic acid (3:1, v/v) at room temperature for 10 min after washing with PBS twice and then permeabilized with freshly made PBS containing 0.01% Triton X‐100 (v/v) and 0.1 U µL<sup>−1</sup> RNase inhibitor (Promega, N2615) on ice for 20 min. After blocking with 1% BSA for 30 min at room temperature, samples were incubated with the anti‐HNRNPD antibody (Thermo, PA5‐99469) (1:200 dilution in 1% BSA) for 3 h at room temperature. With three 5 min washes in PBST buffer (PBS with 0.4% Tween‐20), samples were incubated with Donkey anti‐Rabbit IgG Secondary Antibody Alexa Fluor 546 (Invitrogen, A10040) (1:200 diluted in 1% BSA) for 1 h at room temperature in dark. For <italic toggle=\"yes\">LKB1</italic> mRNA FISH, probes were generated with Transcript Aid T7 High Yield Transcription Kit (Thermo, K0441), and then labeled with Alexa Fluor 488 by using the ULYSIS Nucleic Acid Labeling Kit (Invitrogen, 2161899) according to manufacturer's instructions. RNA probes were denatured at 80 °C for 5 min and placed on ice immediately. After washing with PBST buffer twice and 2× SSC once in dark, samples were incubated with RNA probes mixed with 20 ng µL<sup>−1</sup> human Cot‐1 DNA (Invitrogen, 15279011), 500 ng µL<sup>−1</sup> yeast total RNA (Invitrogen, AM7118) and 0.1 U µL<sup>−1</sup> RNase inhibitor in 2× hybridization buffer (4× SSC, 40% dextran sulfate) at 37 °C for 15–17 h. Slides were washed with 2× SSC containing 0.1% Triton X‐100 at 45 °C. Nuclei were stained with DAPI and the images were captured using laser confocal microscopy LSM880 (Zeiss). The regain of interest (ROI) was drawn as a small rectangle and colocalization percentage of HNRNPD protein and <italic toggle=\"yes\">LKB1</italic> mRNA in 15 ROIs was measured by using ImageJ plugin Coloc2.</p>", "<title>In Vitro RNA Circularization</title>", "<p>Linear RNA fragment was generated with Transcript Aid T7 High Yield Transcription Kit (Thermo, K0441). In brief, 1 µg PCR‐amplified template, 2 µL T7 RNA polymerase enzyme, 0.5 m<sc>m</sc> NTPs, and 2 m<sc>m</sc> GMP were mixed and incubated for 4 h at 37 °C. After DNase I treatment, transcribed linear RNA was purified using phenol/chloroform (pH 4.5). For in vitro circularization, 50 µg linear RNA was incubated with T4 RNA ligase 1 (NEB, M0204) in 500 µL reaction buffer for overnight at 16 °C. After separation on 5% Urea PAGE gel, circularized RNA was cut in the corresponding band and eluted overnight in elution buffer (20 m<sc>m</sc> Tris‐HCl, pH 7.5, 250 m<sc>m</sc> NaOAc, 1 m<sc>m</sc> EDTA, and 0.25% SDS). The eluted RNA was then purified using phenol/chloroform (pH 4.5).</p>", "<title>In Vitro Binding/Competing Assay</title>", "<p>In vitro synthesized <italic toggle=\"yes\">circLARP1B</italic>, <italic toggle=\"yes\">ACTB</italic> fragment, and <italic toggle=\"yes\">LKB1</italic> 3′ UTR fragment RNAs were heated in RNA‐folding buffer (10 m<sc>m</sc> HEPES, pH 7.4 and 10 m<sc>m</sc> MgCl<sub>2</sub>) for 5 min at 65 °C and slowly cooled down over the course of 40 min to room temperature. For in vitro binding assay, equal amounts (10 pmol) of folded <italic toggle=\"yes\">circLARP1B</italic> or <italic toggle=\"yes\">ACTB</italic> RNAs were incubated with 1 µg purified Flag‐tagged HNRNPD protein (OriGene, TP320809) in 0.2 mL Binding buffer (50 m<sc>m</sc> HEPES, pH 7.4, 150 m<sc>m</sc> NaCl, 10 m<sc>m</sc> MgCl<sub>2</sub>, 1 m<sc>m</sc> DTT, 1× Protease Inhibitor Cocktail, and 0.1 U µL<sup>−1</sup> RNase inhibitor) for 2 h at 4 °C. For in vitro competing assay, 5 pmol folded <italic toggle=\"yes\">circLARP1B</italic> and 5 pmol <italic toggle=\"yes\">LKB1</italic> 3′ UTR fragment RNA were incubated with 1 µg purified Flag‐tagged HNRNPD protein in 0.2 mL Binding buffer for 2 h at 4 °C. For both assays, one tenth of incubated solution was saved as input. The HNRNPD–RNA complex was purified with Protein G beads (Invitrogen, 10004D) preconjugated anti‐FLAG antibody (Sigma, F1804). After one Binding buffer wash and one high‐salt Binding buffer (50 m<sc>m</sc> HEPES, pH 7.4, 500 m<sc>m</sc> NaCl, 10 m<sc>m</sc> MgCl<sub>2</sub>, 1 m<sc>m</sc> DTT, 1× Protease Inhibitor Cocktail, and 0.1 U µL<sup>−1</sup> RNase inhibitor) wash at 4 °C for 5 min, the interacted RNA was extracted with TRIzol according to the manufacturer's protocol for further analysis.</p>", "<title>DEN‐Induced HCC Mouse Model</title>", "<p>Diethylnitrosamine (DEN)‐induced HCC mouse model was established as described previously.<sup>[</sup>\n##REF##22265403##\n70\n##\n<sup>]</sup> In brief, 2‐week‐old mice were injected with DEN (20 mg k<sup>−1</sup>g body weight, Sigma, N0258) to start the growth of tumors. The phenobarbital‐like inducer TCPOBOP (3 mg k<sup>−1</sup>g body weight; ApexBio, B8576) was injected every 2 weeks (a total of 8 times) to accelerate HCC progression after DEN injection for 2 weeks. All mice were kept in a controlled environment (23–25 °C with a 12‐h light‐dark cycle and lights on at 8:00 AM), on normal diet feeding with free access to water. For Figure ##SUPPL##0##S8g–k## of the Supporting Information to examine liver inflammation and fibrosis, all data were collected from mice at 9:00 AM. For the other HCC mouse model, mice were fasted for 12 h before bleeding and sacrifice at 9:00 AM.</p>", "<title>Liver‐Directed AAV8‐Mediated CircLARP1B and Lkb1 Silencing</title>", "<p>For preparing AAV8 to silence <italic toggle=\"yes\">circLARP1B</italic> or Lkb1, shRNA was inserted into the p‐AAV‐MCS plasmid. AAV8‐shcircLARP1B, AAV8‐shLkb1 or AAV8‐shCtrl was generated with the AAV Helper‐Free System and infected mice with tail vein injection (10<sup>12</sup> vg AAV8/mouse). For evaluating Lkb1's roles in normal livers as shown in Figure ##FIG##6##7f–i## and Figure ##SUPPL##0##S8f## (Supporting Information), 8‐week‐old <italic toggle=\"yes\">circLARP1B<sup>−/−</sup>\n</italic> or WT male mice were injected with AAV8‐shLkb1 or AAV8‐shCtrl, and sacrificed after 3 weeks. For AAV treatment in HCC mice models, AAV8 expressing shcircLARP1B, shLKB1 or shCtrl was injected once at 10 weeks after DEN injection and TCPOBOP was also injected into mice at the time point.</p>", "<title>Nuclear Run‐On Assay</title>", "<p>For nuclear isolation, cells were harvested in ice‐cold solution I (10 m<sc>m</sc> Tris‐HCl, pH 7.5, 150 m<sc>m</sc> KCl, 4 m<sc>m</sc> Mg(OAc)<sub>2</sub>) and placed on ice for 10 min. After centrifugation at 1000 × <italic toggle=\"yes\">g</italic> for 10 min, pellets were resuspended in solution II (10 m<sc>m</sc> Tris‐HCl, pH 7.5, 150 m<sc>m</sc> KCl, 4 m<sc>m</sc> Mg(OAc)<sub>2</sub>, 0.5% NP‐40, 10% glycerol, and 1 U µL<sup>−1</sup> RNase inhibitor (Promega, N2615)) followed by intermittent shaking on ice for 20 min. The nuclear run‐on mixture (10 m<sc>m</sc> ATP, CTP, GTP, BrUTP, and the crude nuclei) was incubated at 30 °C for 5 min in the run‐on buffer (10 m<sc>m</sc> Tris‐HCl, pH 7.5, 5 m<sc>m</sc> MgCl<sub>2</sub>, 150 m<sc>m</sc> KCl, 1% Sarkosyl, and 2 m<sc>m</sc> DTT) in the presence of RNase inhibitor. The RNA was isolated with TRIzol reagent (Invitrogen) based on the manufacturer's instructions. Nascent transcripts were immunoprecipitated with anti‐BrdU antibody (Novus, NB500‐235) and converted to cDNA for use in RT‐qPCR assays.</p>", "<title>Oil Red O Staining</title>", "<p>Frozen sections of liver tissues or tumor samples were washed with PBS twice followed by fixing with 4% PFA. After one ddH<sub>2</sub>O wash, samples were stained with freshly prepared 3 µg mL<sup>−1</sup> Oil Red O for 1 h at room temperature. Nuclei were counterstained with hematoxylin. Images were captured using an inverted microscope (Olympus). The percentage of Oil Red O positive area is calculated by image‐Pro plus.</p>", "<title>Immunohistochemistry</title>", "<p>For IHC staining, paraffin sections of murine tissues were deparaffinized with xylene and rehydrated with ethanol at decreasing concentrations. Then, samples were incubated with the indicated antibodies overnight at 4 °C followed by incubating with the correspondent secondary antibodies for 1 h at room temperature. Nuclei were stained with hematoxylin and images were captured using an inverted microscope (Olympus). The following antibodies were used in IHC: anti‐ACC1 (CST, 3676), anti‐p‐ACC1 (CST, 3661), anti‐AMPK (CST, 5832), anti‐p‐AMPK (CST, 2535), anti‐LKB1 (Immunoway, YT2573), anti‐Vim (Bioss, bs‐8533R), anti‐Ecad (Bioss, bs‐10009R), anti‐HNRNPD (Thermo, PA5‐99469). The average optical density (AOD) is calculated by ImageJ to indicate the IHC signal.</p>", "<title>H&amp;E, Masson, and Sirius Red Staining</title>", "<p>The lung or liver tissues were soaked in 10% formalin, dehydrated with graded alcohols, and then embedded in paraffin wax for sections. The paraffin sections were deparaffinized and rehydrated after being immersed in xylene. H&amp;E Staining Kit (Abcam, ab245880) was used for H&amp;E staining. The Fontana‐Masson Stain Kit (Abcam, ab150669) was used for Masson staining. The Picro Sirius Red Stain Kit (Abcam, ab150681) was used for Sirius Red staining. Images were captured using an inverted microscope (Olympus). The percentage of Masson and Sirius Red positive area is calculated by ImageJ.</p>", "<title>Measurement of Serum AFP, ALT, AST, TG, and TC</title>", "<p>The serum AFP level was measured with Alpha‐fetoprotein ELISA Kit (NJJC, H226‐1‐1). The ALT and AST levels in serum were detected with Micro Glutamic‐pyruvic Transaminase Assay Kit (Solarbio, BC1555) and Micro Glutamic‐oxalacetic Transaminase Assay Kit (Solarbio, BC1565), respectively. The serum TG and TC levels were examined by Triglycerides Assay Kit (NJJC, F001‐1‐1) and Total Cholesterol Assay Kit (NJJC, F002‐1‐1), respectively.</p>", "<title>Image Processing</title>", "<p>All images of the Nile Red staining, smFISH, and IF were taken by confocal microscope LSM880 (Zeiss). All images of the Transwell assay, Oil red O staining, and IHC were taken with an inverted fluorescence microscope IX73 (Olympus). Image processing and quantification were performed by ImageJ or Image‐Pro plus (as stated specifically in the corresponding method).</p>", "<title>Statistical Analysis</title>", "<p>Statistical analysis was carried out using GraphPad Prism version 8.0. Either Student's <italic toggle=\"yes\">t</italic>‐tests, two‐way ANOVA tests were used to calculate <italic toggle=\"yes\">P</italic>‐values, as indicated in the figure legends. For Student's <italic toggle=\"yes\">t</italic>‐tests, the values reported in the graphs represent averages with error bars showing S.D. After analysis of variance with F tests, the statistical significance and <italic toggle=\"yes\">P</italic>‐values were evaluated with Student's <italic toggle=\"yes\">t</italic>‐tests. Statistical significance was defined as <italic toggle=\"yes\">P</italic>‐value &lt; 0.05. The detailed statistical analysis applied to each experiment is included in the figure legends. The sample size (<italic toggle=\"yes\">N</italic>) was represented in the corresponding figure legends.</p>", "<title>Conflict of Interest</title>", "<p>J.L., X.W., and G.S. have an ownership interest in a patent related to this research.</p>", "<title>Author Contributions</title>", "<p>J.L. and X.W. contributed equally to this work. G.S. conceived of and designed this project. J.L., X.W., and S.C. performed experiments. J.L. and X.W. performed bioinformatics analyses of RNA‐seq data, circRNA profiling, and RIP‐seq. X.C., L.S., B.L., and Z.S. provided clinical specimens. X.W., X.C., and G.S. analyzed the results. J.L., X.W., and G.S., wrote the manuscript. All authors have discussed the results and made comments on the manuscript. All authors approved the final manuscript.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank Dr. Yide Mei (USTC) for providing PLC cells. The authors thank the Bioinformatics Center of the USTC, School of Life Sciences, for providing supercomputing resources, and also thank the Laboratory Animal Research Center of USTC for technique supports. This study was supported by the National Key R&amp;D Program of China (2019YFA0802600) and the National Natural Science Foundation of China (31930019 and 32200431).</p>", "<title>Data Availability Statement</title>", "<p>All high‐throughput sequencing data in this study have been deposited to the Gene Expression Omnibus (GEO) database and are available under Accession No. GSE217403. All metabolomics, lipidomics, and metabolic flux data in this study are available in Metabolomics Workbench with the sproject (DOI: 10.21228/M8CM5D). All experimental materials generated in this study are available upon request.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0001\"><label>Figure 1</label><caption><p>Characterization of mammalian‐conserved <italic toggle=\"yes\">circLARP1B</italic> in HCC metastasis. a) Heatmap and volcano plot illustrating the differentially expressed circRNAs in three metastasis (metas) versus three nonmetastasis (nonmetas) specimens. In the volcano plot, red dots indicate significantly upregulated circRNAs, and blue ones represent downregulated circRNAs. Filled and empty dots indicate conserved and unconserved circRNAs, respectively. Specimens are in situ HCC from patients with or without metastasis. b) Northern blotting analysis of <italic toggle=\"yes\">circLARP1B</italic> in human cells (PLC and HepG2) and murine Hepa1‐6 cells with or without RNase R treatment. The hybridization probe against the back‐splicing junction (BSJ) of <italic toggle=\"yes\">circLARP1B</italic> is shown. <italic toggle=\"yes\">ACTB</italic> mRNA is a control for the effect of RNase R, which digests linear RNAs. c) Representative smFISH images of <italic toggle=\"yes\">circLARP1B</italic> (green) and <italic toggle=\"yes\">LARP1B</italic> mRNA (red) in PLC cells. Blue, DAPI staining of nuclei. Scale bar: 10 µm. d) RT‐qPCR analysis of <italic toggle=\"yes\">circLARP1B</italic> in the nuclear/cytoplasmic fraction of human cells (PLC and HepG2) and murine Hepa1‐6 cells. e) Representative smFISH images of <italic toggle=\"yes\">circLARP1B</italic> (green) in the liver from wildtype mice. DAPI (nuclei, blue). Scale bar: 10 µm. f) RNA smFISH of <italic toggle=\"yes\">circLARP1B</italic> (green) in nonmetas and metas specimens. Quantification of positive dots of <italic toggle=\"yes\">circLARP1B</italic> smFISH is shown (right). <italic toggle=\"yes\">N</italic> = 15 views. Scale bar: 10 µm. g,h) RT‐qPCR analysis of <italic toggle=\"yes\">circLARP1B</italic> expressions in HCC specimens. <italic toggle=\"yes\">ACTB</italic> mRNA is the endogenous control for normalization. i,j) Kaplan–Meier analysis of overall survival (i) and disease‐free survival (j) for 90 HCC patients collected. The red curve indicates survival in patients with higher HCC <italic toggle=\"yes\">circLARP1B</italic> levels, and the blue line indicates survival in patients with lower HCC <italic toggle=\"yes\">circLARP1B</italic> levels. (d) Data are shown as mean ± SD from three independent experiments. (f–h) <italic toggle=\"yes\">P</italic>‐values are from two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test. (i,j) <italic toggle=\"yes\">P</italic>‐values are calculated by the log‐rank test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0002\"><label>Figure 2</label><caption><p>\n<italic toggle=\"yes\">CircLARP1B</italic> modulates cell invasion and fatty acid synthesis in mammalian cells. a) Strategy of deleting intronic reverse‐complementary repeats in human <italic toggle=\"yes\">LARP1B</italic> using CRISPR/Cas9 in PLC cells. Genomic PCR validation of WT and circLARP1B‐Def PLC cells is shown, and the corresponding amplifications are confirmed by Sanger sequencing. WT, wildtype; circLARP1B‐Def, <italic toggle=\"yes\">circLARP1B</italic> deficient. b) RT‐qPCR analysis of <italic toggle=\"yes\">circLARP1B</italic> and <italic toggle=\"yes\">LARP1B</italic> mRNA expressions in WT and circLARP1B‐Def PLC cells. c) Transwell assays of WT and circLARP1B‐Def PLC cells. Quantification of invasive cells is shown (right). Scale bar: 100 µm. d) Schematic procedure of the untargeted metabolomics. All cells were maintained with standard DMEM medium containing 10% FBS for 48 h and then subjected to metabolomics analysis. e) KEGG pathway analysis of dysregulated metabolites in circLARP1B‐Def versus WT PLC cells. The number of significantly changed metabolites in the corresponding pathway is included in the brackets. f) Heatmap of the significantly changed lipid species (VIP &gt;1, <italic toggle=\"yes\">P</italic>‐value &lt; 0.05) corresponding to 24 lipid classes enriched in lipid metabolism (e) from untargeted lipidomics of WT and circLARP1B‐Def PLC cells. VIP, variable importance in the projection. <italic toggle=\"yes\">N</italic> = 5 samples for each cell type. g) Representative Nile red (red) and Hoechst 33342 (for nuclei, blue) staining of WT and circLARP1B‐Def PLC cells. <italic toggle=\"yes\">N</italic> = 15. Scale bar: 20 µm. h) The distribution of <sup>13</sup>C‐label fatty acids from <sup>13</sup>C‐labeled targeted metabolic flux analysis of WT and circLARP1B‐Def PLC cells measured by liquid chromatography‐mass spectrometry (LC‐MS) following a 24 h <sup>13</sup>C‐glucose and <sup>13</sup>C‐glutamine incubation. A total of 17 <sup>13</sup>C‐label fatty acids are detected and three replicates are performed for each group. i) Schematic depicting of the incorporation of uniformly labeled <sup>13</sup>C‐glucose or <sup>13</sup>C‐glutamine (<sup>13</sup>C is indicated by gray circle) into the fatty acid palmitate. Two representative palmitate isotopologs are indicated (top). The distribution of <sup>13</sup>C‐label in even palmitate isotopologs in WT and circLARP1B‐Def PLC cells measured by LC‐MS is shown (bottom). j) Western blots and the quantification of p‐ULK1, ULK1, p‐ACC1, ACC1, p‐AMPK, and AMPK proteins in WT and circLARP1B‐Def PLC cells. ACTB, Actin b protein used as a loading control. The grayscale statistics of western blotting were performed by ImageJ. k) Representative Nile red (red) and Hoechst 33342 (nuclei, blue) staining of WT or circLARP1B‐Def PLC cells with overexpressing FASN (FASN OE) or not. EV, empty vector. <italic toggle=\"yes\">N</italic> = 15. Scale bar: 20 µm. l) Transwell assays of WT or circLARP1B‐Def PLC cells with overexpressing FASN or not. Scale bar: 100 µm. (g,k) Nile red signal is defined as the mean gray value per cell quantified by ImageJ. (b,c,i,j,l) Data are shown as mean ± SD from three independent experiments. (b,c,g,i–l) <italic toggle=\"yes\">P</italic>‐values by two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test. (h) <italic toggle=\"yes\">P</italic>‐values by two‐tailed paired Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0003\"><label>Figure 3</label><caption><p>\n<italic toggle=\"yes\">CircLARP1B</italic> interacts with HNRNPD via two binding sites of the circRNA. a) Pull‐down efficiency of <italic toggle=\"yes\">circLARP1B</italic> in the cytoplasmic fraction of PLC cells (left). Biotinylated oligonucleotide antisense to the <italic toggle=\"yes\">circLARP1B</italic> back‐splicing junction (BSJ) is indicated. Silver staining shows the proteins co‐pulled down. The red arrow denotes the band identified as HNRNPD by mass spectrometry. Scr, negative control of biotin‐labeled oligo with scrambled sequences; Oligo, biotin‐labeled oligo with antisense sequences to the <italic toggle=\"yes\">circLARP1B</italic> BSJ. The pull‐down efficiency of <italic toggle=\"yes\">circLARP1B</italic> is shown with bar figure. b) Western blot of HNRNPD to demonstrate that RNA pull‐down of <italic toggle=\"yes\">circLARP1B</italic> co‐pulls down HNRNPD in the cytoplasmic fraction of PLC cells. ACTB is a negative control. c) RIP with an antibody against HNRNPD in the cytoplasmic fraction of PLC cells pulls down <italic toggle=\"yes\">circLARP1B</italic>. Western blots showing efficient pull‐down of HNRNPD with ACTB as a negative control. Gel images demonstrate the semiquantitative RT‐PCR products of RIP RNAs. RT‐qPCR analyses show the enrichment of RIP RNAs. <italic toggle=\"yes\">CCND1</italic> mRNA is a known target of HNRNPD and a positive control.<sup>[</sup>\n##REF##33444453##\n50\n##\n<sup>]</sup>\n<italic toggle=\"yes\">ACTB</italic> mRNA is a negative control. d,e) <italic toggle=\"yes\">circLARP1B</italic> RNA pull‐down (d) and Hnrnpd RIP with the cytoplasmic fraction (e) using mouse liver. <italic toggle=\"yes\">Mef2c</italic> mRNA is a known target of Hnrnpd in mice and a positive control examined in Hnrnpd RIP (e).<sup>[</sup>\n##REF##24891619##\n94\n##\n<sup>]</sup> f) Conserved binding motifs of HNRNPD in <italic toggle=\"yes\">circLARP1B</italic>. The conserved motif 1 (purple) and motif 2 (orange) are mutated separately to motif 1<sup>mut</sup> and motif 2<sup>mut</sup>, or mutated together as double<sup>mut</sup>. Both sites (Positions 143–151 and 158–166 from the BSJ) are located in the exon 4 of the <italic toggle=\"yes\">LARP1B</italic> gene. g) Association of <italic toggle=\"yes\">circLARP1B</italic> examined by RT‐qPCR of HNRNPD RIP in PLC cells with overexpression of the corresponding forms of <italic toggle=\"yes\">circLARP1B</italic>. Enrichment, normalized to IgG. EV, empty vector. Western blot images indicate successful IP of HNRNPD protein. h) Immunofluorescence (IF) of HNRNPD (green) in PLC cells. Nuclei were stained with DAPI (blue). Quantification of nuclear (Nuc)/cytoplasmic (Cyto) HNRNPD signals is shown as bar figure. <italic toggle=\"yes\">N</italic> = 15. Scale bar: 10 µm. i) Representative images of <italic toggle=\"yes\">circLARP1B</italic> FISH together with HNRNPD IF in PLC cells. A permeabilization condition was used to reduce the nuclear HNRNPD signals,<sup>[</sup>\n##REF##34549195##\n59\n##, ##REF##31508410##\n60\n##\n<sup>]</sup> thereby highlighting cytoplasmic signals in PLC cells. Boxed areas are enlarged. The colocalization between <italic toggle=\"yes\">circLARP1B</italic> (G, green) and HNRNPD (R, red) is shown (<italic toggle=\"yes\">N</italic> = 15 randomly selected areas). R/G, proportion of red signal to green signal colocalization; G/R, proportion of green signal to red signal colocalization. IF, immunofluorescence. Scale bar: 10 and 1 µm (enlarged areas). j) In vitro binding assay of synthesized <italic toggle=\"yes\">circLARP1B</italic> and FLAG‐tagged HNRNPD protein purified from HEK293 cells. An illustration of the assay was shown (left) and semiquantitative RT‐PCR for <italic toggle=\"yes\">circLARP1B</italic> or <italic toggle=\"yes\">ACTB</italic> mRNA fragment was indicated (right). (a–e,g) Data are shown as mean ± SD from three independent experiments; <italic toggle=\"yes\">P</italic>‐values by two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0004\"><label>Figure 4</label><caption><p>Effects of <italic toggle=\"yes\">circLARP1B</italic> depend on the interaction with HNRNPD. a) Transwell assays of WT or circLARP1B‐Def PLC cells with overexpressing <italic toggle=\"yes\">circLARP1B</italic> or double<sup>mut</sup>\n<italic toggle=\"yes\">circLARP1B</italic>. The quantification of invaded cells is analyzed. double<sup>mut</sup>, <italic toggle=\"yes\">circLARP1B</italic> two HNRNPD‐binding sites mutated. Scale bar: 100 µm. b) Representative Nile red (red) and Hoechst 33342 (for nuclei, blue) staining of WT or circLARP1B‐Def PLC cells with overexpressing <italic toggle=\"yes\">circLARP1B</italic> or double<sup>mut</sup>\n<italic toggle=\"yes\">circLARP1B</italic>. <italic toggle=\"yes\">N</italic> = 15. Scale bar: 20 µm. c) Western blot images and the quantification of the indicated proteins in WT or circLARP1B‐Def PLC cells with the overexpression of <italic toggle=\"yes\">circLARP1B</italic> or double<sup>mut</sup>. d) Transwell assays in PLC cells with HNRNPD overexpression. Cells with HNRNPD overexpression are examined upon co‐overexpression of <italic toggle=\"yes\">circLARP1B</italic> or double<sup>mut</sup>\n<italic toggle=\"yes\">circLARP1B</italic>. The quantification of invaded cells is shown. Scale bar: 100 µm. e) Representative Nile red (red) and Hoechst 33342 (for nuclei, blue) staining in PLC cells with HNRNPD overexpression. Cells with HNRNPD overexpression are examined upon co‐overexpression of <italic toggle=\"yes\">circLARP1B</italic> or double<sup>mut</sup>\n<italic toggle=\"yes\">circLARP1B</italic>. <italic toggle=\"yes\">N</italic> = 15. Scale bar: 20 µm. f) Western blot images and quantification of the proteins in PLC cells overexpressed HNRNPD, with co‐overexpression of <italic toggle=\"yes\">circLARP1B</italic> or double<sup>mut</sup>. (b,e) The Nile red signal is defined as the mean gray value per cell quantified by ImageJ. (c,f) The grayscale statistics of western blotting was performed by ImageJ. (a,c,d,f) Data are shown as mean ± SD from three independent experiments. (a–f) <italic toggle=\"yes\">P</italic>‐values by two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test. EV, empty vector.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0005\"><label>Figure 5</label><caption><p>\n<italic toggle=\"yes\">LKB1</italic> mRNA is a functional downstream target of <italic toggle=\"yes\">circLARP1B</italic>. a) Heatmap showing HNRNPD RIP‐seq signals on the 3′ UTRs of 216 mRNAs that demonstrate significant sensitivity to <italic toggle=\"yes\">circLARP1B</italic> levels. EV, PLC cells transfected with empty vector; <italic toggle=\"yes\">circLARP1B</italic> OE, cells with <italic toggle=\"yes\">circLARP1B</italic> overexpression; WT, wildtype PLC cells; circLARP1B‐Def, <italic toggle=\"yes\">circLARP1B</italic> deficient PLC cells. b) Gene ontology (GO) analysis of 216 HNRNPD targets significantly sensitive to changes in <italic toggle=\"yes\">circLARP1B</italic> levels. c) Total HNRNPD binding signals of four PLC cells (EV, <italic toggle=\"yes\">circLARP1B</italic> OE, WT, circLARP1B‐Def) for six genes enriched in the biological process of peptidyl‐Thr phosphorylation. d) HNRNPD binding signals on <italic toggle=\"yes\">LKB1</italic>’s 3′ UTR in four PLC cells. e) HNRNPD binding signals on <italic toggle=\"yes\">circLARP1B</italic> (All reads including the BSJ reads are counted) in four PLC cells. Enlarged IGV visualization demonstrated HNRNPD binding signals around two functional motifs. f) Transwell assays of PLC cells with <italic toggle=\"yes\">circLARP1B</italic> overexpression alone or with <italic toggle=\"yes\">circLARP1B</italic> and LKB1 overexpression together. The quantification of invaded cells by ImageJ is shown. Scale bar: 100 µm. g) Representative Nile red (red) and Hoechst 33342 (nuclei, blue) staining of PLC cells with <italic toggle=\"yes\">circLARP1B</italic> overexpression or co‐overexpressing of <italic toggle=\"yes\">circLARP1B</italic> and LKB1. Nile red signal is defined as the mean gray value per cell quantified by ImageJ. <italic toggle=\"yes\">N</italic> = 15. Scale bar: 20 µm. h) Western blot images and quantification of proteins in PLC cells with <italic toggle=\"yes\">circLARP1B</italic> overexpression or co‐overexpressing of <italic toggle=\"yes\">circLARP1B</italic> and LKB1. The grayscale statistics of western blotting was performed by ImageJ. i) Representative immunohistochemistry (IHC) staining and the quantification of LKB1 proteins in nonmetas and metas HCC specimens (<italic toggle=\"yes\">N</italic> = 3). The IHC signal is defined as the average optical density (AOD) calculated by ImageJ. Scale bar: 50 µm. (f–h) EV, empty vector control. (f,h) Data are shown as mean ± SD from three independent experiments. (f–i) <italic toggle=\"yes\">P</italic>‐values by two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0006\"><label>Figure 6</label><caption><p>\n<italic toggle=\"yes\">CircLARP1B</italic> destabilizes <italic toggle=\"yes\">LKB1</italic> mRNA via perturbing HNRNPD. a–d) Stability assay of <italic toggle=\"yes\">LKB1</italic> mRNA and the steady levels of LKB1 protein (examined by western blotting) in human PLC cells (a,b) and murine Hepa1‐6 cells (c,d) treated siRNA against HNRNPD. siNC, negative control siRNA with scrambled sequences. e) Overall experimental strategy of eIF4E and eIF4G1 RIP assays. RNase I is introduced to digest unprotected RNAs across the IP procedure. Western blots showing HNRNPD knockdown efficiency and efficient IPs of eIF4E and eIF4G1 in PLC cells treated with siRNA against HNRNPD (right). ACTB protein acted as the loading control. f) Primers against various regions of <italic toggle=\"yes\">LKB1</italic> mRNA (top) and enrichment of <italic toggle=\"yes\">LKB1</italic> mRNA regions with eIF4E or eIF4G1 by RT‐qPCR (bottom). g,h) Stability assay of <italic toggle=\"yes\">LKB1</italic> mRNA (g) and the steady levels of LKB1 protein (h) in WT or circLARP1B‐Def PLC cells. i,j) Stability assay of <italic toggle=\"yes\">Lkb1</italic> mRNA (i) and the steady levels of Lkb1 protein (j) in Hepa1‐6 cells treated with shcircLARP1B or shCtrl. shCtrl, shRNA control that generates siRNA of scrambled sequences; shcircLARP1B, shRNA against the murine <italic toggle=\"yes\">circLARP1B</italic> BSJ. k) In vitro competing assay of purified HNRNPD protein for equal moles of in vitro synthesized <italic toggle=\"yes\">circLARP1B</italic> and <italic toggle=\"yes\">LKB1</italic> 3′ UTR. An illustration of the assay was shown (top). Semiquantitative RT‐PCR gels and RT‐qPCR for <italic toggle=\"yes\">circLARP1B</italic> and <italic toggle=\"yes\">LKB1</italic> 3′ UTR were indicated (bottom). <italic toggle=\"yes\">LKB1</italic> 3′ UTR, in vitro transcribed <italic toggle=\"yes\">LKB1</italic> 3′ UTR fragments with the HNRNPD binding sequence. l) Association of <italic toggle=\"yes\">LKB1</italic> mRNA examined by RT‐qPCR of HNRNPD RIP in PLC cells treated with oligodeoxynucleotide antisense to two HNRNPD binding motifs in <italic toggle=\"yes\">circLARP1B</italic> (ODN‐AS) or the control (ODN‐Ctrl, ODN with scrambled sequences). Two motifs with reverse complementary sequences were indicated with underlines. PS, phosphorothioate; 2′‐OMe, 2′‐<italic toggle=\"yes\">O</italic>‐methyl. Western blot images indicate successful IP of HNRNPD protein. Enrichment, normalized to IgG. m) Western blotting and the corresponding quantification showing the steady level of LKB1 protein in PLC cells transfected with ODN‐AS or ODN‐Ctrl. (b,d,h,j,m) The grayscale statistics of western blotting were performed by ImageJ. (a–d,f–m) Data are shown as mean ± SD from three independent experiments. (a,c,g,i) <italic toggle=\"yes\">P</italic>‐values by two‐way ANOVA test. (b,d,f,h,j,l,m) <italic toggle=\"yes\">P</italic>‐values by two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0007\"><label>Figure 7</label><caption><p>\n<italic toggle=\"yes\">CircLARP1B</italic> deficiency in mice causes liver changes attributable to Lkb1 surplus. a) Strategy of knockout (KO) reverse‐complementary sequence in mouse <italic toggle=\"yes\">Larp1b</italic> intron 4 using CRISPR‐Cas9. PCR products of mouse genotyping are shown. WT, wildtype; <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup>, KO of the intronic reverse‐complementary sequences; B1, mouse B1 repeat. b) RT‐qPCR analysis of the steady levels and nascent levels (with nuclear run‐on assay) of <italic toggle=\"yes\">circLARP1B</italic> and <italic toggle=\"yes\">Larp1b</italic> mRNA in WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mouse liver. Data are from three independent experiments. c) Representative Oil Red O staining and the quantification in WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mouse liver (<italic toggle=\"yes\">N</italic> = 5 per group). Nuclei stained with hematoxylin (blue). Scale bar: 50 µm. d) Representative IHC staining and quantification of the proteins in liver from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice (<italic toggle=\"yes\">N</italic> = 5 per group). Scale bar: 50 µm. AOD, average optical density. e) Western blot of the indicated proteins in livers from WT or <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice. f) Representative Lkb1 IHC staining in livers from WT or <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice with the intravenous tail injection of AAV8‐shCtrl or AAV8‐shLkb1 for three weeks (<italic toggle=\"yes\">N</italic> = 5 per group). Scale bar: 50 µm. g) Representative Oil Red O staining in liver from WT or <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice with AAV8‐shCtrl or AAV8‐shLkb1 injection (<italic toggle=\"yes\">N</italic> = 5 per group). shCtrl, negative control shRNA construct that gives rise to siRNA with scrambled sequences. Nuclei stained with hematoxylin (blue). Scale bar: 50 µm. h) Representative IHC staining of the indicated proteins in liver from WT or <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice with AAV8‐shCtrl or AAV8‐shLkb1 injection (<italic toggle=\"yes\">N</italic> = 5 per group). Scale bar: 50 µm. i) Western blot of the indicated proteins in livers from WT or <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice with AAV8‐shCtrl or AAV8‐shLkb1 injection. Data are shown as mean ± SD. (c,g) Lipid level is defined as the percentage of Oil Red positive area calculated by Image‐Pro plus. (d,f,h) The IHC signal is defined as the average optical density (AOD) calculated by ImageJ. (e,i) The grayscale statistics of western blotting was performed by ImageJ. (c–i) All animals were kept in a controlled environment (23–25 °C with a 12‐h light‐dark cycle and lights on at 8:00 AM), on normal diet feeding with free access to water; all data were from mice at 9:00 AM. (b–d,f–h) <italic toggle=\"yes\">P</italic>‐values by two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0008\"><label>Figure 8</label><caption><p>\n<italic toggle=\"yes\">CircLARP1B</italic> deficiency impedes HCC metastasis and lipid accumulation in mice. a) Schematic illustration for generating the DEN‐induced mice HCC model. b) Representative images and H&amp;E staining of liver tumor nodes from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice (<italic toggle=\"yes\">N</italic> = 5 per group) after DEN‐induction for 18 weeks. Statistical analysis of liver tumor node numbers and diameters of the largest tumor node are shown. Scale bar: 2 mm. c) Representative H&amp;E staining and the quantification of lung metastases in WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> HCC mice (<italic toggle=\"yes\">N</italic> = 5 per group). Scale bar: 400 µm. d) Representative Vim (Vimentin, a prometastasis marker) and Ecad (E‐cadherin, an antimetastasis marker) IHC staining of liver tumors from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> HCC mice (<italic toggle=\"yes\">N</italic> = 5 per group). Scale bar: 50 µm. e–i) The serum AFP (e), ALT (f), AST (g), TG (h), and TC (i) levels in WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> HCC mice (<italic toggle=\"yes\">N</italic> = 5 per group). AFP, alpha‐fetoprotein (a biomarker for HCC); ALT, alanine aminotransferase; AST, aspartate aminotransferase; TG, triglyceride; TC, total cholesterol. j) Representative Oil Red O staining images and the quantification in liver tumors from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> HCC mice (<italic toggle=\"yes\">N</italic> = 5 per group). Lipid level is defined as the percentage of Oil Red positive area calculated by Image‐Pro plus. Scale bar: 100 µm. k) Representative Lkb1, p‐Ampk, and p‐Acc1 IHC staining of liver tumors from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> HCC mice (<italic toggle=\"yes\">N</italic> = 5 per group). Scale bar: 50 µm. l) Western blot of the indicated proteins of liver tumors from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> HCC mice. The grayscale statistics of western blotting was performed by ImageJ. (b–l) All animals were kept in a controlled environment (23–25 °C with a 12‐h light‐dark cycle and lights on at 8:00 AM), on normal diet feeding with free access to water, and fasted for 12 h before bleeding and sacrifice at 9:00 AM. All data are shown as mean ± SD. (d,k) The IHC signal is defined as the average optical density (AOD) calculated by ImageJ. (b–k) <italic toggle=\"yes\">P</italic>‐values by two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0009\"><label>Figure 9</label><caption><p>Hepatocyte‐directed <italic toggle=\"yes\">circLARP1B</italic> knockdown impedes HCC metastasis and lipid accumulation in mice. a) Schematic illustration for generating the DEN‐induced mice HCC model. Hepatocyte‐directed AAV8 expressing shcircLARP1B and AAV8‐shCtrl were injected after induction for 10 weeks. b) RT‐qPCR analysis of <italic toggle=\"yes\">circLARP1B</italic> and <italic toggle=\"yes\">Larp1b</italic> mRNA levels of livers from WT mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shcircLARP1B injection. c) Representative images and H&amp;E staining of liver nodes from WT mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shcircLARP1B injection after DEN‐induction for 18 weeks. Statistical analysis of liver tumor node numbers and diameters of the largest tumor node are shown. Scale bar: 2 mm. d) Representative H&amp;E staining and the quantification of lung metastases in WT mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shcircLARP1B injection. Scale bar: 400 µm. e) Representative Vim (Vimentin, a prometastasis marker) and Ecad (E‐cadherin, an antimetastasis marker) IHC staining of liver tumors from WT mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shcircLARP1B injection. Scale bar: 50 µm. f–j) The serum AFP (f), ALT (g), AST (h), TG (i), and TC (j) levels in WT mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shcircLARP1B injection. k) Representative Oil Red O staining images and the quantification in liver tumors from WT mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shcircLARP1B injection. Lipid level is defined as the percentage of Oil Red positive area calculated by Image‐Pro plus. Scale bar: 100 µm. l) Representative Lkb1, p‐Ampk, and p‐Acc1 IHC staining of liver tumors from WT mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shcircLARP1B injection. Scale bar: 50 µm. m) Western blot of the indicated proteins of liver tumors from WT HCC mice with AAV8‐shCtrl or AAV8‐shcircLARP1B injection. The grayscale statistics of western blotting was performed by ImageJ. (b–m) All animals were kept in a controlled environment (23–25 °C with a 12‐h light‐dark cycle and lights on at 8:00 AM), on normal diet feeding with free access to water, and fasted for 12 h before bleeding and sacrifice at 9:00 AM. Data are shown as mean ± SD. (e,l) The IHC signal is defined as the average optical density (AOD) calculated by ImageJ. (b–l) <italic toggle=\"yes\">P</italic>‐values by two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6779-fig-0010\"><label>Figure 10</label><caption><p>LKB1 is a key target for the roles of <italic toggle=\"yes\">circLARP1B</italic> in HCC. a) Representative images and H&amp;E staining of liver tumors from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shLkb1 injection after DEN induction for 10 weeks. Statistical analysis of liver tumor numbers and diameter of the largest tumor is shown. Scale bar: 2 mm. b) Representative H&amp;E staining and the quantification of lung metastases in WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> HCC mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shLkb1 injection. Scale bar: 400 µm. c) Representative Vim (Vimentin, prometastasis marker) and Ecad (E‐cadherin, antimetastasis marker) IHC staining of liver tumors from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shLkb1 injection. The quantification of IHC is shown. Scale bar: 50 µm. d) Representative Oil Red O staining of liver tumors from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shLkb1 injection. Lipid level is defined as the percentage of Oil Red positive area calculated by Image‐Pro plus. Scale bar: 100 µm. e) Representative p‐Ampk and p‐Acc1 IHC staining of liver tumors from WT and <italic toggle=\"yes\">circLARP1B</italic>\n<sup>−/−</sup> mice (<italic toggle=\"yes\">N</italic> = 5 per group) with AAV8‐shCtrl or AAV8‐shLkb1 injection (top). The corresponding quantification is analyzed (bottom). Scale bar: 50 µm. f) Kaplan–Meier analysis of OS (left) and DFS (right) for 90 HCC patients collected. The red curve indicates survival in patients with higher HCC <italic toggle=\"yes\">HNRNPD</italic> mRNA levels, and the blue line indicates survival in patients with lower HCC <italic toggle=\"yes\">HNRNPD</italic> mRNA levels. g) Kaplan–Meier analysis of OS (left) and DFS (right) for 90 HCC patients with <italic toggle=\"yes\">LKB1</italic> mRNA levels. (a–e) All animals were kept in a controlled environment (23–25 °C with a 12‐h light‐dark cycle and lights on at 8:00 AM), on normal diet feeding with free access to water, and fasted for 12 h before bleeding and sacrifice at 9:00 AM. Data are shown as mean ± SD. (c,e) The quantification of IHC as average optical density (AOD) calculated by ImageJ is shown. (a–e) <italic toggle=\"yes\">P</italic>‐values by two‐tailed unpaired Student's <italic toggle=\"yes\">t</italic>‐test. (f,g) <italic toggle=\"yes\">P</italic>‐values are calculated by the log‐rank test.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6779-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>", "<supplementary-material id=\"advs6779-supitem-0002\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Table 1</p></caption></supplementary-material>", "<supplementary-material id=\"advs6779-supitem-0003\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Table 2</p></caption></supplementary-material>", "<supplementary-material id=\"advs6779-supitem-0004\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Table 3</p></caption></supplementary-material>", "<supplementary-material id=\"advs6779-supitem-0005\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Table 4</p></caption></supplementary-material>", "<supplementary-material id=\"advs6779-supitem-0006\" position=\"float\" content-type=\"local-data\"><caption><p>Supplemental Table 5</p></caption></supplementary-material>" ]
[]
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[ "<media xlink:href=\"ADVS-11-2305902-s006.pdf\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305902-s002.xlsx\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305902-s004.xlsx\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305902-s003.xlsx\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305902-s001.xlsx\"><caption><p>Click here for additional data file.</p></caption></media>", "<media xlink:href=\"ADVS-11-2305902-s005.xlsx\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
96
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 12; 11(2):2305902
oa_package/a5/8b/PMC10787103.tar.gz
PMC10787104
38217044
[ "<title>INTRODUCTION</title>", "<p>Multidirectional interaction among organ systems is an integral aspect of the development and physiology of mammalian organisms. Factors, including hormones, cytokines, and chemokines, are produced by diverse cells in the body and participate in interorgan communication (Castillo‐Armengol et al., ##REF##31423716##2019##). The mammalian gut is not an exception in the production of factors that mediate interorgan crosstalk for maintaining a healthy homeostatic state and for the normal functioning of several organ systems, including the musculoskeletal and cardiovascular systems (Hu et al., ##REF##35932976##2022##; Lucas et al., ##UREF##2##2018##).</p>", "<p>The gut microbiome encompasses a diverse array of gene batteries whose products (i.e., postbiotics) are continuously being characterized to participate in important aspects of hosts physiology, including gut (Martin‐Gallausiaux et al., ##REF##32238208##2021##), cardiovascular (Razavi et al., ##REF##31182162##2019##; Yang et al., ##REF##31803054##2019##) and bone health (Lucas et al., ##UREF##2##2018##). More so, gut colonization with microbiota is critical for shaping the mucosal immune system and results in either a homeostatic or abnormal immune reactivity (Al Bander et al., ##REF##33086688##2020##; Brandsma et al., ##REF##30582442##2019##). Importantly, the mammalian gut has evolved to guard against the translocation of unwanted substances, including toxins and pathogens, into the systemic circulation. In addition, ~70% of our immune cells reside in the gut, functioning in antigen sampling, and producing pathogen‐specific immune responses (Wiertsema et al., ##REF##33803407##2021##). Aging‐induced alterations in the mammalian gut microbiome and immune cell function increase chronic inflammation (i.e., inflammaging) in the gut and increase the risk of chronic diseases, including cardiovascular disorders (CVDs) and osteoporosis (Bosco &amp; Noti, ##REF##33875817##2021##; Fasano, ##REF##32742638##2020##; Gibon et al., ##REF##29094003##2017##; Li et al., ##UREF##1##2019##; Liberale et al., ##REF##35210039##2022##).</p>", "<p>Interleukin (IL)‐10 is a well‐known pleiotropic anti‐inflammatory cytokine (Sabat et al., ##REF##21115385##2010##). The partial or total loss of this cytokine, as in the IL‐10 knockout (KO) mouse, models inflammaging and is associated with spontaneous enterocolitis (Kühn et al., ##REF##8402911##1993##), osteopenia and increased bone fragility (Dresner‐Pollak et al., ##REF##15362035##2004##), and cardiac events including thrombosis, (Caligiuri et al., ##REF##12765335##2003##), atherosclerosis (Mallat et al., ##REF##10521249##1999##), arterial stiffness and cardiac dysfunction (Sikka et al., ##REF##23159957##2013##). Additionally, a role for inflammatory response mediators, including interleukin (IL)‐6 and tumor necrosis factor (TNF) in CVDs and bone resorption have been reported (Epsley et al., ##REF##33584321##2021##; Willerson &amp; Ridker, ##UREF##6##2004##). Research also supports an anti‐inflammatory role for certain postbiotics such as butyrate (Säemann et al., ##REF##11024006##2000##). However, other roles of gut microbiota in reducing inflammation and the crosstalk between the gut, bone, and cardiovascular system are still poorly understood.</p>", "<p>Fibroblast growth factor (FGF)‐23 and estrogen are hormones derived mainly from the bone and ovaries (testes in males), respectively, and are important regulators of bone metabolism and cardiovascular outcomes (Lu &amp; Hu, ##REF##28785560##2017##; Quarles, ##REF##22421513##2012##). Whereas inflammation, directly and indirectly, increases phosphaturic FGF23 (Francis &amp; David, ##REF##27191351##2016##), an anti‐inflammatory role has been mainly attributed to estrogen (Chakrabarti et al., ##REF##18409173##2008##; Josefsson et al., ##REF##1586960##1992##), a hormone that prevents bone loss (Kameda et al., ##REF##9254647##1997##; Nakamura et al., ##REF##17803905##2007##) and reduces vascular injuries and atherosclerosis (Arnal et al., ##REF##20631350##2010##; Meng et al., ##REF##33364052##2021##; Xing et al., ##REF##19221203##2009##). Egli‐Spichtig et al. (##REF##31301888##2019##) reported increased serum intact FGF23 (iFGF23) in IL‐10 KO mice at 12–14 weeks of age. However, the clinical significance of this finding in relation to skeletal and cardiovascular outcomes has not been investigated.</p>", "<p>An important aspect of estrogen metabolism is the recycling of its conjugated form by gut bacterial, β‐glucuronidase (Baker et al., ##REF##28778332##2017##). While aging causes an alteration in the metabolic signature of the gut microbiome, the role of inflammation in estrogen recycling and signaling has not been investigated. We aimed to examine the crosstalk between the gut, bone, and cardiovascular system in an IL‐10 KO mouse model. We hypothesized that the anti‐inflammatory cytokine IL‐10 is critical for fine‐tuning gut‐microbial derived factors, including deconjugated estrogen and inflammatory stimuli, which in turn play critical roles in normal bone remodeling and cardiovascular function.</p>" ]
[ "<title>METHODS</title>", "<title>Animals</title>", "<p>Animals were maintained at the Oklahoma State University Laboratory Animal Research facility under humidity‐ and temperature‐controlled conditions and a 12‐h light–12‐h dark cycle.</p>", "<p>Six‐week‐old male and female IL‐10 KO mice (KO) and their wild type (WT) counterpart of C57BL/6 background were (Jackson Laboratories, Bar Harbor, ME) maintained on a semi‐purified rodent growth diet (AIN‐93G) for the first 3 months following weaning and then changed to maintenance diet (AIN‐93M) for the final 3 months of the study. Mice had access to food and water ad libitum. Weekly food intake and body weight were monitored during the study period.</p>", "<title>Sample collection and tissue processing</title>", "<p>Fecal samples were collected per cage and stored at −80°C after 3 and 6 months on the AIN‐93 diet. At the end of each time point, mice were fasted for ~3 h and anesthetized with a ketamine and xylazine cocktail (100 mg and 10 mg, kg<sup>−1</sup> body weight, respectively). Whole‐body dual‐energy x‐ray absorptiometry (DXA) scans were performed to determine bone mineral content (BMC) and bone mineral density (BMD) using a whole‐body densitometer (Piximus; GE Medical System Lunar, Madison, WI). Serum was processed from blood collected from the carotid artery and stored at −80°C. The heart, aorta, and white adipose tissue (WAT) were excised and snap‐frozen in liquid nitrogen. Lamina propria (LP) was collected from saline‐flushed ileum and stored in RNALater. A femur from each mouse was flushed with ice cold PBS and the marrow‐free bone was snap‐frozen and cryo‐stored until analyses.</p>", "<title>Serum <styled-content style=\"fixed-case\" toggle=\"no\">17β‐estradiol</styled-content> and cecal content β‐glucuronidase activity</title>", "<p>Serum unconjugated 17β‐estradiol (E2) was assessed using an ELISA kit (Biovision; Milpitas, CA) following the manufacturer's instructions.</p>", "<p>Bacterial β‐glucuronidase activity in cecal content was assessed with slight modifications to previous protocols (Flores et al., ##REF##23259758##2012##; Walsh et al., ##REF##32146834##2020##). Briefly, approximately 300 mg of frozen cecal content was homogenized in 1 mL ice‐cold PBS. Lysates were centrifuged at 2000 rpm for 5 min at 4°C and the supernatant was further centrifuged at 10,000 rpm for 20 min. Enzyme activity was assessed in the supernatant by mixing 25 μL of supernatant, 50 μL PBS, and 50 μL 4‐nitrophenyl‐β‐d‐glucuronide (1 mM, dissolved in PBS; Sigma‐Aldrich, St. Louis, MO # 10344‐94‐2). The resulting mixture was incubated at 37°C for 15 min, followed by the addition of 125 μL sodium hydroxide (NaOH, 0.5 N, ThermoFisher #BP359) to stop the reaction. The absorbance was read at 405 nm on a Biotek HTX microplate reader. Enzymatic concentrations were extrapolated from a standard curve of a serially diluted pure enzyme purchased from Sigma‐Aldrich (# G7646). Enzyme activities were normalized by the total protein content in each sample.</p>", "<title>X‐ray micro‐computed tomography (μCT) analyses</title>", "<p>μCT analyses (μCT40; SCANCO Medical, Brüttisellen, Switzerland) were performed on the lumbar vertebral body (L6), distal femur metaphysis, and the femur mid‐diaphysis to determine alterations in trabecular and cortical bone microarchitecture. Femur specimens were scanned at a high resolution of 2048 × 2048 pixels. Analysis of the distal femur was performed on a volume of interest (VOI) that included a region of secondary spongiosa that was 60 μm from the growth plate and extended in the proximal direction 600 μm (100 images). A 180 μm (30 images) VOI at the mid‐point of the femur was used for cortical bone analysis. Scanning of the vertebra was performed at medium resolution or 1024 × 1024 pixels. The VOI included a region of secondary spongiosa that was approximately 2.56 mm (160 images × 16 μm ea). Analysis of all specimens was performed at the threshold of 360, a sigma of 1.2, and a support setting of 2. The trabecular analysis for the distal femur metaphysis and vertebral body included the following: relative bone volume (BV/TV), trabecular number (TbN), trabecular thickness (TbTh), trabecular separation (TbSp), connectivity density (ConnDens), structural model index (SMI), apparent density, material density, and degree of anisotropy. Cortical analyses of the tibial mid‐diaphysis included cortical thickness, cortical area, medullary area, and porosity.</p>", "<title>Gene expression analysis</title>", "<p>Total RNA was isolated from ileum LP, WAT, heart, aorta, ovary, bone marrow, and femur by rupturing tissues in Trizol RNA isolation reagent (ThermoFisher, Waltham, MA, #10‐296‐028) and precipitating chloroform‐separated clear phase in isopropanol as earlier described (Peirson &amp; Butler, ##UREF##3##2007##). cDNA was synthesized following a standardized protocol (Peterson &amp; Freeman, ##UREF##4##2009##), and the relative abundance of genes was determined by quantitative reverse transcriptase‐polymerase chain reaction (qRT‐PCR) using SYBR green chemistry (Applied Biosystems, #A25742) on a CFX Opus RT‐PCR System (Bio‐Rad, Hercules, CA). Gene targets included interleukin (<italic toggle=\"yes\">Il</italic>)<italic toggle=\"yes\">‐17a</italic>, <italic toggle=\"yes\">Il1b</italic>, <italic toggle=\"yes\">Il6</italic>, <italic toggle=\"yes\">Tnf</italic>, and <italic toggle=\"yes\">Tgfb</italic>, estrogen receptor (<italic toggle=\"yes\">Esr</italic>)<italic toggle=\"yes\">‐1</italic> and <italic toggle=\"yes\">2</italic>, tight junction protein 1 (<italic toggle=\"yes\">Tjp1</italic>) and occludin (<italic toggle=\"yes\">Ocln</italic>) in the ileum. <italic toggle=\"yes\">Il17a</italic>, <italic toggle=\"yes\">Tnf</italic>, <italic toggle=\"yes\">Il6</italic>, <italic toggle=\"yes\">Il1b</italic>, intercellular and vascular cell adhesion molecule 1 (<italic toggle=\"yes\">Icam1</italic> and <italic toggle=\"yes\">Vcam1</italic>), <italic toggle=\"yes\">Esr1</italic>, adhesion G protein‐coupled receptor E1 (<italic toggle=\"yes\">Adgre1</italic>), and arginase 1 (<italic toggle=\"yes\">Arg1</italic>) were assessed in cardiac tissues. Dentin matrix protein 1 (<italic toggle=\"yes\">Dmp1</italic>), phosphate regulating endopeptidase homolog X‐linked (<italic toggle=\"yes\">Phex</italic>), <italic toggle=\"yes\">Fgf23</italic>, <italic toggle=\"yes\">Il6</italic>, wingless‐type MMTV integration site family member 10B (<italic toggle=\"yes\">Wnt10b</italic>), osteoprotegerin (<italic toggle=\"yes\">Opg</italic>), <italic toggle=\"yes\">Rankl</italic>, collagen type 1 alpha 1 (<italic toggle=\"yes\">Col1a1</italic>), bone gamma‐carboxyglutamate protein 2 (<italic toggle=\"yes\">Bglap2</italic>), secreted phosphoprotein 1 (<italic toggle=\"yes\">Spp1</italic>), and sclerostin (<italic toggle=\"yes\">Sost</italic>) were assessed in the bone tissue. <italic toggle=\"yes\">Esr 1</italic> and <italic toggle=\"yes\">2</italic>, <italic toggle=\"yes\">Cyp19a1</italic> (aromatase), and <italic toggle=\"yes\">Cyp11a1</italic> were assessed in the WAT and ovary. The data were analyzed using the 2−ΔΔCt method (Schmittgen &amp; Livak, ##REF##18546601##2008##), with glyceraldehyde‐3‐phosphate dehydrogenase (<italic toggle=\"yes\">Gapdh</italic>) serving as the invariant control. Primers were either derived from previous reports in the literature or designed in our laboratory and then validated in our hands before gene expression analyses were performed. Table ##SUPPL##0##S1## contains the list of primer sequences.</p>", "<title>Immunoblotting</title>", "<p>Total protein was extracted and quantified from heart tissue using the radioimmunoprecipitation assay (RIPA) buffer containing 0.5% protease and phosphatase inhibitor cocktails (Sigma‐Aldrich, #P8340 #P0044). Proteins were denatured and separated on polyacrylamide gels (BioRad, #4561093EDU) using SDS‐PAGE before transfer on PVDF membranes (ThermoScientific, Waltham, MA, #PI88585) as previously described (Ojo et al., ##REF##33144228##2021##). Membranes were incubated overnight at 4°C in primary antibodies: (p‐eNOS Ser1119 [ThermoFisher, #PIPA564613]; NOS3 [ThermoFisher, #4904]; p‐IKB [Santa Cruz Biotechnology, Dallas, TX, #SC‐8404]; PI3K [Santa Cruz Biotechnology, #SC‐365290]; IKB [Santa Cruz Biotechnology, #SC‐1643]; p‐NFkBp65 Ser536 [#sc‐136548, Santa Cruz Biotechnology]; NFkBp65 [Santa Cruz Biotechnology, #SC‐8008]; and GAPDH [#60004–1, Proteintech, Rosemont IL]) diluted in 5% bovine serum albumin (BSA). Membranes were washed in PBS and incubated for 1 h in anti‐rabbit (Cell Signaling Technology, Danvers, MA #7074) or anti‐mouse (Cell Signaling Technology, #7076) IgG HRP‐linked antibody diluted in 5% milk solution. Proteins were detected using the SuperSignal West Femto Maximum Sensitivity Substrate (ThermoScientific, #34095). Band signals were captured with the ChemiDoc imaging system (BioRad) and quantified with the Image J software, v 1.8.0.</p>", "<title>Cell culture experiments</title>", "<p>Intestinal lymphocytes were isolated from the ileum of 14 month‐old female KO and WT mice (<italic toggle=\"yes\">n</italic> = 4/strain) maintained on standard chow as previously described with minor modifications (Sheridan &amp; Lefrançois, ##UREF##5##2012##). Briefly, tissues were flushed with RPMI medium (ThermoFisher, #61‐870‐036) supplemented with 2% FBS and 1 mM dithiothreitol (DTT, Sigma‐Aldrich, #D9779). Ileal samples were opened longitudinally and incubated at room temperature in Hanks' balanced salt solution (HBSS) with 2 mM EDTA. Epithelia‐free samples were digested with collagenase type VIII (Sigma‐Aldrich #C2139) and filtered through a 70 μm cell strainer. Lymphocytes were subsequently separated, by differential centrifugation, as an interphase between Percoll gradients (40% and 80%, Sigma‐Aldrich, #GE17‐0891‐01). Cells were collected, washed twice, and incubated for 40 min in a 10% FBS‐supplemented RPMI with or without E2 (100 nM, Sigma‐Aldrich, #E2758).</p>", "<p>For 3‐dimensional cultures, intestinal crypts were isolated from the ileum of 14 month‐old female KO and WT mice and developed into organoids as previously described (Sato et al., ##REF##19329995##2009##) with minor modifications. Briefly, the small intestine was excised, opened longitudinally and gently flushed with cold PBS. Tissues were cut into small pieces (~2 mm) and gently washed several times in PBS until the supernatant became clear (~20 times). Tissues were digested at room temperature in gentle cell dissociation reagent (Stemcell Technologies, Cambridge, MA, #07174), resuspended in cold 0.1% BSA‐containing PBS, pipetted up and down three times, and allowed to settle under gravity. The wash, digestion, and dissociation step were repeated three times. Crypt‐enriched fractions derived by passing supernatant from the fourth digestion through a 70 μm strainer was centrifuged and resuspended in complete mouse intesticult organoid growth medium (Stemcell Technologies, #06005) and geltrex basement membrane matrix (Thermofisher, #A1413302) before plating in triplicate in a 24‐well plate. Once solidified, organoids were formed in complete mouse intesticult organoid growth medium treated with or without E2 (100 nM).</p>", "<title>Statistical analyses</title>", "<p>Data were evaluated for conformity to normal distribution. Two‐group comparisons of IL‐10 KO and their sex‐matched WT control were performed for all outcome variables using the independent Student <italic toggle=\"yes\">t</italic>‐test in SAS version 9.4 (SAS Institute, Cary, NC). Data are presented as mean ± standard deviation (SD), and <italic toggle=\"yes\">p</italic> value &lt;0.05 was considered statistically significant.</p>" ]
[ "<title>RESULTS</title>", "<title>Gut inflammation increased in IL‐10 KO mice</title>", "<p>Compared to their WT gender‐matched counterparts, body weight was significantly lower (<italic toggle=\"yes\">p</italic> &lt; 0.01) in KO male mice from Week 6 to 24 (Figure ##FIG##0##1a##). In contrast, the female KO mice maintained similar body weight as the WT counterparts until Week 19, and then exhibited reduced body weight (<italic toggle=\"yes\">p</italic> &lt; 0.05) until the end of the experiment (Figure ##FIG##0##1b##). The reduced body weight in the male and female KO mice corresponds with lower food intake (Figure ##SUPPL##0##S1a##) and most likely be due to the increase in gut inflammation observed in these mice.</p>", "<p>We next examined the relative mRNA abundance of inflammatory cytokines in the ileal LP as an index of inflammation. The anti‐inflammatory cytokine, <italic toggle=\"yes\">Tgfb</italic>, increased in KO male at 3 months (<italic toggle=\"yes\">p</italic> = 0.00014), but decreased in KO female at both time points (<italic toggle=\"yes\">p</italic> &lt; 0.01, Figure ##FIG##0##1c##). There were no significant differences in <italic toggle=\"yes\">Il6</italic> gene expressions for either sex compared with WT controls (Figure ##FIG##0##1d##). However, <italic toggle=\"yes\">Il17</italic> and <italic toggle=\"yes\">Tnf</italic> mRNA increased significantly in both male (<italic toggle=\"yes\">p</italic> &lt; 0.05) and female KO (<italic toggle=\"yes\">p</italic> &lt; 0.01) mice at both timepoints compared to their WT sex‐matched counterparts (Figure ##FIG##0##1e,f##). As inflammation is crucial to compromising intestinal integrity, we examined tight junction gene expression. At the 3 month timepoint, ileal expression of <italic toggle=\"yes\">Tjp1</italic> was lowered in male (<italic toggle=\"yes\">p</italic> &lt; 0.0001) and <italic toggle=\"yes\">Ocln</italic> in female (<italic toggle=\"yes\">p</italic> = 0.027) KO compared to their WT counterpart (Figure ##FIG##0##1g##). However, by the 6 month timepoint, there were no differences in the expression of <italic toggle=\"yes\">Tjp1</italic> and <italic toggle=\"yes\">Ocln</italic> (Figure ##FIG##0##1g,h##).</p>", "<title>Increased inflammation and FGF23 are associated with osteopenia in IL‐10 KO mice</title>", "<p>To confirm the effects of <italic toggle=\"yes\">Il10</italic> KO on bone parameters, we performed a whole‐body DXA scan. At 3 and 6 months, both male and female KO mice had lower (<italic toggle=\"yes\">p</italic> &lt; 0.05) BMD than their WT counterparts (Figure ##FIG##1##2a##). The significant loss of BMC in the KO male mice (Figure ##SUPPL##0##S1b##) is primarily responsible for the reduced BMD since bone mineral area (BMA) was either somewhat reduced or not affected in these mice (Figure ##SUPPL##0##S1c##). However, both BMC and BMA were significantly reduced in female KO mice at both time points (Figure ##SUPPL##0##S1b,c##).</p>", "<p>Next, we evaluated the alterations in trabecular bone in the distal femur metaphysis and vertebral body using microCT. At the 3 month timepoint, vertebral BV/TV was lower in male and female KO mice by ~20% and 40% compared to their respective WT controls (Figure ##FIG##1##2b##). By 6 months, the magnitude of the difference in vertebral bone of the male and female KO compared to WT controls was even greater, with an ~40% and 60% decline, respectively. The lower vertebral BV/TV was associated with significant reductions (<italic toggle=\"yes\">p</italic> &lt; 0.05) in TbN and TbTh with a corresponding increase in TbSp in KO mice versus WT controls (Figure ##SUPPL##0##S2a–c##). Similarly, the reduction in BV/TV within the distal femur metaphysis of male KO mice was ~30%–33% at 3 and 6 months, whereas female KO mice exhibited a trend at 3 months (<italic toggle=\"yes\">p</italic> = 0.065; ~27% reduction) and a statistically significant reduction (<italic toggle=\"yes\">p</italic> &lt; 0.0001; 44%) at 6 months compared to WT counterpart (Figure ##FIG##1##2c##). The reduced femoral trabecular bone volume was attributed to a corresponding lower TbTh in KO mice in both sexes at both timepoints (Figure ##SUPPL##0##S2d##). Conversely, there were no statistically significant differences in the femur TbN and TbSp for the strains of mice that were compared (Figure ##SUPPL##0##S2e,f##).</p>", "<p>Cortical bone was also compromised in the IL‐10 KO mice, with ~10% reduction (<italic toggle=\"yes\">p</italic> &lt; 0.05) in femoral cortical area and thickness at the 3 month timepoint, and ~20% reduction (<italic toggle=\"yes\">p</italic> &lt; 0.01) in these parameters at the 6 month timepoint (Figure ##FIG##1##2d,e##). At the transcriptional level, the relative abundance of <italic toggle=\"yes\">Sost</italic>, the Wnt signaling inhibitor, was lower in the femur (<italic toggle=\"yes\">p</italic> &lt; 0.05) of male KO mice at 6 months and at both timepoints in the female KO mice compared to their WT controls (Figure ##FIG##1##2f##). Interestingly, <italic toggle=\"yes\">Wnt10b</italic> mRNA was also repressed (<italic toggle=\"yes\">p</italic> &lt; 0.05) in male KO at both timepoints and upregulated in female KO mice at 6 months versus WT mice (Figure ##SUPPL##0##S2g##). Assessment of the mRNA expression of extracellular matrix proteins revealed similar <italic toggle=\"yes\">Col1a1</italic> mRNA level in both WT and KO mice (Figure ##SUPPL##0##S2h##), whereas <italic toggle=\"yes\">Opn</italic> and <italic toggle=\"yes\">Bglap2</italic> had at least ~1.5‐fold increased expression in KO mice compared to gender‐matched WT mice at both the 3 and 6 month timepoints (Figure ##FIG##1##2g,h##). Next, we assessed the gene expression of receptor activator of nuclear factor kappa B ligand (RANKL), which regulates the catabolic activity of bone and OPG, a decoy receptor that inhibits RANKL‐RANK interaction. The relative abundance of <italic toggle=\"yes\">RankL</italic> was reduced (Figure ##SUPPL##0##S2i##) with a corresponding lower <italic toggle=\"yes\">Opg</italic> gene expression (<italic toggle=\"yes\">p</italic> &lt; 0.05) in both male and female KO compared to WT control mice at both timepoints (Figure ##SUPPL##0##S2j##). These data support an attempt to down‐regulate osteolytic activity in the bone of the KO mice.</p>", "<p>We next examined gene expression of the endopeptidase, phosphate‐regulating endopeptidase X‐linked (PHEX) and its sibling protein, dentine matrix acidic phosphoprotein 1 (DMP1), both produced by osteocytes and participating in bone mineralization (Schaffler &amp; Kennedy, ##REF##22552701##2012##). <italic toggle=\"yes\">Phex</italic> was significantly reduced at 6 months and <italic toggle=\"yes\">Dmp1</italic> was reduced at both timepoints in KO mice compared with sex‐matched WT control (Figure ##FIG##1##2i,j##). DMP1 and Phex are involved in the regulation of <italic toggle=\"yes\">Fgf23</italic> (Martin et al., ##REF##21507898##2011##). As expected, <italic toggle=\"yes\">Fgf23</italic> mRNA increased (<italic toggle=\"yes\">p</italic> &lt; 0.05) with reducing <italic toggle=\"yes\">Phex</italic> and <italic toggle=\"yes\">Dmp1</italic> in KO mice at both timepoints compared to their WT control (Figure ##FIG##1##2k##). Importantly, <italic toggle=\"yes\">Il6</italic> mRNA tended to increase at 6 months in male KO, and was significantly increased (<italic toggle=\"yes\">p</italic> &lt; 0.05) at both timepoints in female KO mice compared to WT control (Figure ##FIG##1##2l##).</p>", "<title>Loss of <styled-content style=\"fixed-case\" toggle=\"no\">IL</styled-content>‐10 is associated with increased cardiac inflammation and fibrosis in mice</title>", "<p>Motivated by the reported role of excessive FGF23 in inducing left ventricular hypertrophy, cardiac fibrosis, and vascular calcification (Böckmann et al., ##REF##31540546##2019##; Faul et al., ##REF##21985788##2011##; Hao et al., ##REF##27579618##2016##; Jimbo et al., ##REF##24088960##2014##), we next examined transverse cross‐section of the heart for histological changes. Masson's trichrome staining revealed increased fibrosis in the cardiac tissue of KO mice at 6 months compared with WT control mice (Figure ##FIG##2##3a##). Cardiac gene expression of the inflammatory marker, <italic toggle=\"yes\">Tnf</italic>, only reached statistical significance at 6 months in female KO mice (Figure ##FIG##2##3b##). Similarly, the <italic toggle=\"yes\">Il6</italic> transcript was significantly elevated (<italic toggle=\"yes\">p</italic> &lt; 0.05) in the KO mice at the 6 months timepoint in both sexes compared to their respective WT control (Figure ##FIG##2##3c##). In contrast, the relative abundance of <italic toggle=\"yes\">Il1b</italic> expression was higher (<italic toggle=\"yes\">p</italic> &lt; 0.05) in the cardiac tissue of KO mice at both timepoints (Figure ##FIG##2##3d##). Gene expression of adhesion molecules, including, vascular cell adhesion protein 1 (VCAM‐1) and intercellular adhesion molecule‐1 (ICAM‐1) was increased (<italic toggle=\"yes\">p</italic> &lt; 0.05) in the cardiac tissue of female KO mice at the 6 month timepoint. (Figure ##SUPPL##0##S3a,b##). Gene expression of the receptor <italic toggle=\"yes\">Adgre1</italic>, a macrophage marker, increased significantly in the cardiac tissues of KO mice at 6 months (Figure ##FIG##2##3e##). The M2 macrophage marker, <italic toggle=\"yes\">Arg1</italic>, tended to be reduced (0.05 &lt; <italic toggle=\"yes\">p</italic> &lt; 0.1) in female KO mice at 3 months, but was reduced (<italic toggle=\"yes\">p</italic> &lt; 0.05) in the cardiac tissue of male KO mice at both timepoints compared with WT control (Figure ##SUPPL##0##S3c##).</p>", "<p>Next, we assessed the protein expression/activation of the redox‐sensitive transcription factor, NF‐κB and key components of its signaling pathway. Inhibitor of nuclear factor kappa B (IκB), which prevents the nuclear translocation of NF‐κB, was reduced (<italic toggle=\"yes\">p</italic> &lt; 0.05) in both sexes of KO mice at the 3 and 6 month timepoints (Figure ##FIG##2##3f,g##), with female KO exhibiting reduced phosphorylation (<italic toggle=\"yes\">p</italic> &lt; 0.01) of IκB at 6 months (Figure ##FIG##2##3f,h##). The ratio of phosphorylated to total IκB increased (<italic toggle=\"yes\">p</italic> &lt; 0.05) at both time points in male KO (Figure ##FIG##2##3f,i##). The reduced phosphorylation of IκB at 6 months in female KO mice correlates with a reduced (<italic toggle=\"yes\">p</italic> &lt; 0.05) phospho‐NFκB (Ser<sup>536</sup>) in these mice at this timepoint (Figure ##FIG##2##3f,j,k##).</p>", "<p>We further assessed the protein expression of endothelial nitric oxide synthase (NOS)‐3, whose Ser<sup>1119</sup> phosphorylation is critical in nitric oxide‐mediated vasodilation. KO mice had a reduced expression of NOS3 (<italic toggle=\"yes\">p</italic> &lt; 0.05) at the 6 month timepoint (Figure ##FIG##2##3l,m##). Reduced activation of this enzyme as indicated by its reduced Ser<sup>1119</sup> phosphorylation coincided with a reduction in phosphoinositide 3‐kinase (PI3K), which lies downstream of the NOS3 signaling, at both timepoints compared with respective WT control (Figure ##FIG##2##3m–o##).</p>", "<title>Loss of <styled-content style=\"fixed-case\" toggle=\"no\">IL</styled-content>‐10 is associated with reduced estrogen signaling in mice</title>", "<p>Considering the role of estrogen as an activator of NOS3 (Chen et al., ##REF##9927501##1999##) and the role of this hormone in reducing inflammation (Liberale et al., ##REF##35210039##2022##), cardiac dysfunction, and bone loss (Arnal et al., ##REF##20631350##2010##; Meng et al., ##REF##33364052##2021##; Xing et al., ##REF##19221203##2009##), we compared serum 17β‐estradiol (E2) in KO mice with WT control mice. Serum E2 was lower (<italic toggle=\"yes\">p</italic> &lt; 0.05) in female KO mice and tended to be reduced (0.05 &lt; <italic toggle=\"yes\">p</italic> &lt; 0.1) in male KO mice at both timepoints compared with WT controls (Figure ##FIG##3##4a##). Following this serendipitous finding of reduced E2 in the KO mice, we assessed estrogen synthesis in the ovaries of 14 month‐old mice. Concurrently, mRNA levels of <italic toggle=\"yes\">Cyp11a1</italic> and <italic toggle=\"yes\">Cyp19a1</italic>, which are involved in estrogen synthesis, were significantly reduced in the ovaries of 14 month‐old KO mice compared with WT counterparts of the same age (Figure ##FIG##3##4b##). Similar reductions in mRNA levels were also observed in the WAT, another source of endogenous E2, of KO mice at the 3 and 6 month timepoints (Figure ##FIG##3##4c,d##). The activity of microbial β‐glucuronidase within the gut, which deconjugates estrogen in the intestinal lumen, was reduced at both time points in KO mice (Figure ##FIG##3##4e##). Estrogen could mediate its effects in several ways, one of which is binding to receptors, including ESR1 and ESR2, to mediate a membrane response or genomic response (Heldring et al., ##REF##17615392##2007##). <italic toggle=\"yes\">Esr2</italic> was not expressed in the heart (data not shown), whereas <italic toggle=\"yes\">Esr1</italic> mRNA was not different between groups compared at both timepoints (Figure ##SUPPL##0##S4a##). Contrarily, ileal and WAT <italic toggle=\"yes\">Esr1</italic> mRNA were significantly reduced (<italic toggle=\"yes\">p</italic> &lt; 0.05) in KO mice at both timepoints (Figure ##FIG##3##4f##; Figure ##SUPPL##0##S4b##), while the reduction in ileal <italic toggle=\"yes\">Esr2</italic> mRNA only reached statistical significance in the ileum tissue at the 6 month timepoint (Figure ##FIG##3##4g##). <italic toggle=\"yes\">Esr1</italic> was highly expressed at the 6 month timepoint in the bone marrow of female KO, while <italic toggle=\"yes\">Esr2</italic> was repressed within the bone marrow at both timepoints in KO mice compared to WT control mice (Figure ##FIG##3##4h,i##).</p>", "<p>To further confirm if IL‐10 is required for estrogen to modulate gut inflammation, lymphocytes from the ileum of 14 month‐old‐female WT and KO mice were isolated and treated with conditioned media with or without E2 (100 nM). E2 treatment lowered lymphocytic <italic toggle=\"yes\">Tnf</italic> and <italic toggle=\"yes\">Il17</italic> mRNA in WT, but not in the KO mice (Figure ##FIG##4##5a,b##). We further assessed the effect of E2 treatment (100 nM) on intestinal crypt‐derived organoids from female KO and WT mice. E2‐treated organoids were faster in developing complex structures (crypt domain) in both WT and KO groups (Figure ##FIG##4##5c##). The mRNA expression of <italic toggle=\"yes\">Vil1</italic> and <italic toggle=\"yes\">Alpi</italic>, which are highly expressed in the intestine, were not affected by E2 treatment in both organoid from WT and KO mice (Figure ##SUPPL##0##S5a,b##). In contrast, E2 treatment increased gene expression of <italic toggle=\"yes\">Tjp1</italic> in the KO‐derived organoid (Figure ##FIG##4##5d##), and <italic toggle=\"yes\">Ocln</italic> in organoid from both WT and KO mice (Figure ##FIG##4##5e##). These data support an estrogenic effect on the enterocytes and not the lymphocytes of old IL‐10 KO mice.</p>" ]
[ "<title>DISCUSSION</title>", "<p>In addition to its role in balancing gut immune reactivity, IL‐10 plays a critical role in interorgan communication (Madsen et al., ##REF##9207273##1997##; Miyoshi et al., ##REF##32835897##2021##; Oshima et al., ##REF##11162203##2001##). The mammalian gut participates in several interorgan communications in the mammalian system (Forkosh &amp; Ilan, ##REF##31168383##2019##; Tripathi et al., ##REF##29748586##2018##; Zaiss et al., ##REF##31305265##2019##). Aging‐associated alterations in these interorgan communications contribute to chronic diseases, including cardiovascular and musculoskeletal disorders. Using the IL‐10 KO frail mouse model (Walston et al., ##REF##18426963##2008##), this study investigated the role of IL‐10 in mediating interplay between the gastrointestinal, skeletal, and cardiovascular systems. We reported a proinflammatory signature in the gut, bone loss and higher bone <italic toggle=\"yes\">Fgf23</italic> mRNA, lower serum estrogen, and increased cardiac fibrosis in the absence of IL‐10.</p>", "<p>The highly expressed <italic toggle=\"yes\">Il17a</italic> and <italic toggle=\"yes\">Tnfa</italic> mRNA in the gut of the IL‐10 KO mice is expected, as IL‐10 suppresses both Th1 and Th17 immune responses in regulating immune reactivity (Chaudhry et al., ##REF##21511185##2011##; Couper et al., ##REF##18424693##2008##; Gu et al., ##REF##18506885##2008##). Berg et al. (##REF##8770874##1996##) has also reported a role for Th1 immune response in driving enterocolitis in IL‐10 KO mice. It is noteworthy that the higher gene expression of these proinflammatory cytokines in the female IL‐10 KO mice corresponds with their reduced <italic toggle=\"yes\">Tgfb</italic> mRNA. TGF‐β impinges on Th1 differentiation by repressing <italic toggle=\"yes\">Tbx21</italic> and <italic toggle=\"yes\">Stat5a</italic>, which encode the master transcription factors for Th1 cells (Gorelik &amp; Flavell, ##REF##10714683##2000##; Lin et al., ##REF##15879087##2005##). The proinflammatory gut signature of the IL‐10 KO mouse could contribute to the loss of epithelial tight junction (Capaldo &amp; Nusrat, ##REF##18952050##2009##; Ma et al., ##REF##14766535##2004##). The repression of <italic toggle=\"yes\">Tjp1</italic> and <italic toggle=\"yes\">Ocln</italic> in male and female IL‐10 KO mice, respectively, at 3 months supports the early onset of inflammaging and further suggests a potential sex‐based difference in the expression of these tight junctions. A compromised gut is critical to the commonly reported increased systemic inflammation in the IL‐10 KO mice (Alake et al., ##REF##36813578##2023##; Kühn et al., ##REF##8402911##1993##).</p>", "<p>As anticipated, both the female and male IL‐10 KO mice exhibited a bone phenotype characterized by lower cortical and trabecular bone mass. Relative to the WT control mice, alterations in <italic toggle=\"yes\">Rankl</italic> and <italic toggle=\"yes\">Wnt10b</italic> in the IL‐10 KO mice suggest greater osteoclastogenesis and reduced osteoblastogenesis contributed to this phenotype. Osteocytes are a major source of IL‐6 in the bone which has been reported to be increased in rodent models of IBD (Metzger et al., ##REF##27796050##2017##). The higher <italic toggle=\"yes\">Il6</italic> mRNA noted in the IL‐10 KO mice have the potential to stimulate osteoclast bone resorption (Ishimi et al., ##REF##2121824##1990##; Löwik et al., ##REF##2548501##1989##) and upregulate the expression of the phosphaturic hormone, FGF23 (Durlacher‐Betzer et al., ##REF##29861060##2018##). This response occurs in conjunction with the IL‐10 KO mice's reduced expression of bone <italic toggle=\"yes\">Phex</italic> and <italic toggle=\"yes\">Dmp1</italic>, which encode for PHEX and DMP1 and regulate FGF23 (Ling et al., ##REF##16294270##2005##; Martin et al., ##REF##21507898##2011##). PHEX represses Fgf23 gene expression mainly through the FGF receptor signaling (Bär et al., ##REF##31199502##2019##; Lu &amp; Feng, ##REF##21404002##2011##; Martin et al., ##REF##21507898##2011##). More so, PHEX and DMP1 are interaction partners and evidence support the importance of their interaction in lowering plasma FGF23 (Martin et al., ##REF##22930691##2012##). Importantly, the increased expression of osteopontin and osteocalcin in the bone tissue also contributes to the bone phenotype in the IL‐10 KO mice. Osteocalcin appears to facilitate bone resorption (Ducy et al., ##REF##8684484##1996##), whereas osteopontin is a substrate for PHEX and it is known for inhibiting bone mineralization (Barros et al., ##REF##22991293##2013##). The reduced PHEX expression in the IL‐10 KO mice therefore explains the increase in <italic toggle=\"yes\">Opn</italic> expression and the reduced bone phenotype in IL‐10 KO mice.</p>", "<p>The increased cardiac fibrosis in IL‐10 KO mice at 6 months could be partly attributed to an increase FGF23 in these mice. Egli‐Spichtig et al. (##REF##31301888##2019##) had previously reported an increased serum iFGF23 in IL‐10 KO mice. Higher serum FGF23 had also been reported to mediate cardiovascular pathologies, including left ventricular hypertrophy, cardiac fibrosis, and vascular calcification (Böckmann et al., ##REF##31540546##2019##; Faul et al., ##REF##21985788##2011##; Hao et al., ##REF##27579618##2016##; Jimbo et al., ##REF##24088960##2014##). Furthermore, we reported a reduced E2 signaling in the cardiac tissue of KO mice, as indicated by a reduced phosphorylation of NOS3 as well as a reduced PI3K expression in the cardiac tissue of the IL10 KO mice. Haynes et al. (##REF##11029403##2000##) had earlier demonstrated that the E2 activation of NOS3 occurs via the PI3K‐Akt pathway and it involves the phosphorylation and activation of Ser<sup>1119</sup> residue of NOS3. More so, the anti‐inflammatory potential of E2 was reported to be mediated by an increased IκBα and the prevention of NFκB nuclear translocation or binding (Ghisletti et al., ##REF##15798185##2005##; Xing et al., ##REF##22723832##2012##). In addition, an increased Ser<sup>536</sup> phosphorylation of NFκB reportedly inhibits p65 signaling and inflammation (Pradère et al., ##REF##27555662##2016##). Our findings, including the reduced expression of IκBα and phospho Ser<sup>536</sup> NFκB in the cardiac tissue of IL‐10 KO mice, therefore support a reduced activation of NOS3 and increased inflammation due to reduced E2 signaling in the cardiac tissue of these mice.</p>", "<p>In this study, we also demonstrated that IL‐10 KO mice had lower circulating 17‐ β estradiol. 17‐ β estradiol mediates an anti‐inflammatory response in various tissues, including the gut, bone, and vascular endothelium (Goodman et al., ##REF##32632016##2020##; Nilsson, ##REF##17659431##2007##; Weitzmann &amp; Pacifici, ##REF##16670759##2006##). Therefore, the increased gene expression of IL‐6 in the bone and cardiac tissue could be partly attributed to estrogen deficiency in the IL‐10 KO mice. The lowered serum 17‐β estradiol in these mice is explained in part by reduced estrogen synthesis in the ovaries and in adipose tissue as evidenced by a reduced ovarian and WAT <italic toggle=\"yes\">Cyp17a1</italic> and <italic toggle=\"yes\">Cyp11a1</italic> mRNA. These genes encode for two cytochrome P450 enzymes, both catalyzing important steps in the conversion of cholesterol to estrogens. However, recycling of estrogen was also altered in the KO mice as indicated by reduced activity of microbial β‐glucuronidase. β‐glucuronidase increases serum estrogen by deconjugating the glucuronide‐complex and increasing the bioavailability of estrogen (Baker et al., ##REF##28778332##2017##). Interestingly, <italic toggle=\"yes\">Lactobacillus rhamnosus</italic>, which has β‐glucuronidase activity (Biernat et al., ##REF##30696850##2019##) had been reported to prevent bone loss and reduce intestinal inflammation and gut permeability in sex‐steroid‐deficient mice (Li et al., ##REF##27111232##2016##). However, our finding contradicted a phylogenetic prediction of an increased β‐glucuronidase in female IL‐10 KO mice that was earlier reported by Son et al. (##REF##31624723##2019##) using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) software. This difference might be due to the incomprehensive nature of the 16S sequencing data that was used in those predictions. Moreover, such predictions are gene‐level based suggesting the transcriptional, posttranscriptional and translational regulation of gut bacterial β‐glucuronidase warrants further investigation.</p>", "<p>The estrogen receptor, ESR2 mediates the anti‐inflammatory role of E2 as well as its role in intestinal organoid regeneration (Goodman et al., ##REF##32632016##2020##; Hases et al., ##REF##32711097##2020##; Lee et al., ##UREF##0##2019##). Our result showed that E2 treatment does not affect the proinflammatory phenotype in isolated lymphocytes from IL‐10 KO mice. However, E2 treatment increased the transcription of tight junctions in intestinal organoids. These findings suggest an interference of E2 signaling by other factors that are present in an inflamed gut. Interestingly, Pierdominici et al. (##REF##26497217##2015##) had previously reported significant repression of <italic toggle=\"yes\">Esr2</italic> mRNA in T lymphocytes and intestinal epithelial cells exposed to IL‐6. More so, the role of IL‐10 in suppressing IL‐6 production has been previously reported (Hempel et al., ##REF##7725065##1995##). Therefore, the lack of IL‐10 favored the dominance of proinflammatory molecules that could act partially by suppressing the expression of estrogen receptors to increase proinflammatory response in the gut of IL‐10 KO mice.</p>", "<p>There are a few limitations in this study. First, the utilization of a global KO model makes it seemingly impossible to fully understand the tissue‐specific role of IL‐10. Future experiments should consider utilizing tissue‐specific KO models to understand the specific roles of IL‐10 in the tissues that were studied and how IL‐10 affects interorgan communication in these tissues. The gene expression of tight junctions does not necessarily determine their localization pattern; however, we are unable to confirm the localization pattern in the tissues that are available. Even though no differences were detected in Tjp1 and Ocln gene expression, future studies should include immunostaining techniques to determine if localization patterns are altered in the IL‐10KO mice since these changes can occur without alterations in overall gene expression. Our supporting in vitro experiments on the effect of E2 in LP lymphocytes and intestinal organoid was limited to female retired breeders. It will be interesting to perform similar experiment at a younger age in both male and female mice. In addition, since lowered E2 was a serendipitous finding at the end of the study and only retired breeders were available, we could not compare the expression level of <italic toggle=\"yes\">Cyp2a1</italic> and <italic toggle=\"yes\">Cyp2a11</italic> for the age group of mice that were studied. Lastly, whereas it is tempting to assume that E2 was lowered due to the deficiency in IL10, further research is needed to understand the mechanism by which reduced recycling and synthesis of E2 occurs in the IL‐10 KO mice.</p>", "<p>Based on our findings, including a gut proinflammatory phenotype, an increased bone <italic toggle=\"yes\">Fgf23</italic> with corresponding reduced <italic toggle=\"yes\">Dmp1</italic> and <italic toggle=\"yes\">Phex</italic> mRNA, a reduced serum E2 and gut bacterial β‐glucuronidase, as well as a reduced expression of estrogen receptor or downstream target of E2, we conclude that it is likely the combination of reduced IL‐10 and E2 signaling that promote an inflammatory phenotype which increases the secretion of FGF23. As a result, both factors mediate the interorgan communication that leads to gut inflammation and compromised barrier integrity, cardiac dysfunction and decrements in bone mass in the IL‐10 KO mouse.</p>" ]
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[ "<title>Abstract</title>", "<p>Characterization of the interleukin (IL)‐10 knockout (KO) mouse with chronic gut inflammation, cardiovascular dysfunction, and bone loss suggests a critical role for this cytokine in interorgan communication within the gut, bone, and cardiovascular axis. We sought to understand the role of IL‐10 in the cross‐talk between these systems. Six‐week‐old IL‐10 KO mice and their wild type (WT) counterparts were maintained on a standard rodent diet for 3 or 6 months. Gene expression of proinflammatory markers and <italic toggle=\"no\">Fgf23</italic>, serum 17β‐estradiol (E2), and cardiac protein expression were assessed. Ileal <italic toggle=\"no\">Il17a</italic> and <italic toggle=\"no\">Tnf</italic> mRNA increased while <italic toggle=\"no\">Il6</italic> mRNA increased in the bone and heart by at least 2‐fold in IL‐10 KO mice. Bone <italic toggle=\"no\">Dmp1</italic> and <italic toggle=\"no\">Phex</italic> mRNA were repressed at 6 months in IL‐10 KO mice, resulting in increased <italic toggle=\"no\">Fgf23</italic> mRNA (~4‐fold) that contributed to increased fibrosis. In the IL‐10 KO mice, gut bacterial β‐glucuronidase activity and ovarian <italic toggle=\"no\">Cyp19a1</italic> mRNA were lower (<italic toggle=\"no\">p</italic> &lt; 0.05), consistent with reduced serum E2 and reduced cardiac pNOS3 (Ser<sup>1119</sup>) in these mice. Treatment of ileal lymphocytes with E2 reduced gut inflammation in WT but not IL‐10 KO mice. In conclusion, our data suggest that diminished estrogen and defective bone mineralization increased FGF23 which contributed to cardiac fibrosis in the IL‐10 KO mouse.</p>", "<p>Unlike the WT (C57BL6) mouse, IL‐10 KO mouse exhibited tissue (gut, and consequently bone and cardiac) proinflammatory signature and reduced gut bacterial β‐glucuronidase activity. Proinflammatory cytokines favor increased bone production of FGF23, whose action (potentiated by reduced PHEX activity) could increase cardiac fibrosis. The reduced gut bacterial β‐glucuronidase activity decreases conjugated estrogen recycling into its active form, favoring reduced bone mass and cardiac phenotype in the IL‐10 KO mouse.\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"PHY215914-cit-2001\">\n<string-name>\n<surname>Alake</surname>, <given-names>S. E.</given-names>\n</string-name>, <string-name>\n<surname>Ice</surname>, <given-names>J.</given-names>\n</string-name>, <string-name>\n<surname>Robinson</surname>, <given-names>K.</given-names>\n</string-name>, <string-name>\n<surname>Price</surname>, <given-names>P.</given-names>\n</string-name>, <string-name>\n<surname>Hatter</surname>, <given-names>B.</given-names>\n</string-name>, <string-name>\n<surname>Wozniak</surname>, <given-names>K.</given-names>\n</string-name>, <string-name>\n<surname>Lin</surname>, <given-names>D.</given-names>\n</string-name>, <string-name>\n<surname>Chowanadisai</surname>, <given-names>W.</given-names>\n</string-name>, <string-name>\n<surname>Smith</surname>, <given-names>B. J.</given-names>\n</string-name>, &amp; <string-name>\n<surname>Lucas</surname>, <given-names>E. A.</given-names>\n</string-name> (<year>2024</year>). <article-title>Reduced estrogen signaling contributes to bone loss and cardiac dysfunction in interleukin‐10 knockout mice</article-title>. <source>Physiological Reports</source>, <volume>12</volume>, <elocation-id>e15914</elocation-id>. <pub-id pub-id-type=\"doi\">10.14814/phy2.15914</pub-id>\n<pub-id pub-id-type=\"pmid\">38217044</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>AUTHOR CONTRIBUTIONS</title>", "<p>Edralin A. Lucas and Brenda J. Smith funding acquisition; Sanmi E. Alake, Karen Wozniak, Dingbo Lin, Winyoo Chowanadisai, Brenda J. Smith, and Edralin A. Lucas designed research; Sanmi E. Alake, John Ice, Kara Robinson, Payton Price, Bethany Hatter, Brenda J. Smith, and Edralin A. Lucas conducted research; Sanmi E. Alake, Brenda J. Smith and Edralin A. Lucas analyzed the data, wrote the paper, and had primary responsibility for the final content. All authors read and approved the final manuscript.</p>", "<title>FUNDING INFORMATION</title>", "<p>This study was funded by the Oklahoma Agricultural Experiment Station (Project # OKL03104 and OKL03105) and the Jim and Lynn Williams Professorship (1‐156560).</p>", "<title>CONFLICT OF INTEREST STATEMENT</title>", "<p>All authors declared no conflicts of interest.</p>", "<title>ETHICS STATEMENT</title>", "<p>All procedures were approved and followed strict guidelines set by the Institution Animal Care of Oklahoma State University (Protocol #IACUC 22‐02‐STW).</p>", "<title>Supporting information</title>" ]
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[ "<fig position=\"float\" fig-type=\"FIGURE\" id=\"phy215914-fig-0001\"><label>FIGURE 1</label><caption><p>Weekly body weight of male (a) and female (b) mice, and ileum gene expression of inflammatory cytokines, <italic toggle=\"yes\">Tgfb</italic> (c), <italic toggle=\"yes\">Il6</italic> (d), <italic toggle=\"yes\">Il17a</italic> (e), <italic toggle=\"yes\">Tnf</italic> (f), and tight junctions, <italic toggle=\"yes\">Tjp1</italic> (g), and <italic toggle=\"yes\">Ocln</italic> (h) in WT mice and IL‐10 KO (KO) mice fed a semi‐purified diet for 3 or 6 months. Values are mean ± SD, <italic toggle=\"yes\">n</italic> = 12–16 mice/group for a and b, <italic toggle=\"yes\">n</italic> = 6 mice/group for c and d, <italic toggle=\"yes\">n</italic> = 12–16 mice/group for e, and <italic toggle=\"yes\">n</italic> = 6 mice/group for f–h. Based on data analysis using Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"FIGURE\" id=\"phy215914-fig-0002\"><label>FIGURE 2</label><caption><p>Skeletal response of male and female WT and IL‐10 KO (KO) mice fed a semi‐purified diet for 3 or 6 months: whole body bone mineral density, BMD (a), trabecular bone volume/total volume (BV/TV) of the lumbar vertebra body (b) and distal femur metaphysis (c), femur cortical area (d) and thickness (e), and gene expression of <italic toggle=\"yes\">Sost</italic> (f), <italic toggle=\"yes\">Opn</italic> (g), <italic toggle=\"yes\">Bglap2</italic> (h) <italic toggle=\"yes\">Phex</italic> (i) <italic toggle=\"yes\">Dmp1</italic> (j), <italic toggle=\"yes\">Fgf23</italic> (k), and <italic toggle=\"yes\">Il6</italic> (l). Values are mean ± SD, <italic toggle=\"yes\">n</italic> = 12–16 mice/group for a, <italic toggle=\"yes\">n</italic>‐8–13 mice/group for b–e, <italic toggle=\"yes\">n</italic> = 6 mice/group for f–l. Based on data analysis using Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"FIGURE\" id=\"phy215914-fig-0003\"><label>FIGURE 3</label><caption><p>Representative trichrome staining of fixed heart tissue, with blue coloration indicating fibrosis (a), cardiac gene expression of inflammatory markers: <italic toggle=\"yes\">Tnf</italic> (b), <italic toggle=\"yes\">Il6</italic> (c), <italic toggle=\"yes\">Il1b</italic> (d), and the macrophage marker <italic toggle=\"yes\">Adgre1</italic> (e). Representative blots (f), showing cardiac protein expression of: IκB (g), phosphorylated IκB (h), Ratio of pIκB to total IκB (i), phosphorylated NFκB (j), and NFκB (k). Also, representative blots (l) for cardiac protein expression of NOS3 (m), phosphorylated NOS3 (n), and PI3K (o) in WT mice and IL‐10 KO (KO) mice fed a semi‐purified diet for 3 or 6 months. Values are mean ± SD, <italic toggle=\"yes\">n</italic> = 6 mice/group for a–e, <italic toggle=\"yes\">n</italic> = 4–5 mice/group for f–o. Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"FIGURE\" id=\"phy215914-fig-0004\"><label>FIGURE 4</label><caption><p>Serum 17β‐estradiol (a). Gene expression of <italic toggle=\"yes\">Cyp19a1</italic> and <italic toggle=\"yes\">Cyp11a1</italic> in the ovary (b), and white adipose (WAT; c and d, respectively). β‐glucuronidase enzyme activity in the cecal contents (e), and estrogen receptor gene expression in the ileum, Esr1 (f) and Esr2 (g) and bone marrow (h and i) in WT mice and IL‐10 KO (KO) mice fed a semi‐purified diet for 3 or 6 months. Values are mean ± SD, <italic toggle=\"yes\">n</italic> = 8–10 mice/group for a, <italic toggle=\"yes\">n</italic> = 5 mice/group for b, <italic toggle=\"yes\">n</italic> = 6 mice/group for c and d, <italic toggle=\"yes\">n</italic> = 7 mice/group for e, <italic toggle=\"yes\">n</italic> = 5–6 mice/group for f–i. Based on data analysis using Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>", "<fig position=\"float\" fig-type=\"FIGURE\" id=\"phy215914-fig-0005\"><label>FIGURE 5</label><caption><p>Gene expression of proinflammatory cytokines in E2‐treated (100 nM) ileal‐derived lymphocytes isolated from 14 month‐old‐female KO and WT mice: <italic toggle=\"yes\">Tnf</italic> (a), and <italic toggle=\"yes\">Il17</italic> (b). Representative image of intestinal organoids, Day 6, developed from crypt cells derived from 14 month‐old female KO and WT mice, with or without E2 treatment (c). Gene expression of tight junctions in E2‐treated intestinal organoids: <italic toggle=\"yes\">Tjp1</italic> (d), and <italic toggle=\"yes\">Ocln</italic> (e). Values are mean ± SD, <italic toggle=\"yes\">n</italic> = 3 mice/group for a, b, <italic toggle=\"yes\">n</italic> = 3 mice/group and replicate = 3/mouse for c–e. Based on data analysis using Student's <italic toggle=\"yes\">t</italic>‐test.</p></caption></fig>" ]
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[ "<supplementary-material id=\"phy215914-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>\nData S1.\n</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"PHY2-12-e15914-s001.docx\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
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2024-01-14 23:41:57
Physiol Rep. 2024 Jan 12; 12(1):e15914
oa_package/4e/71/PMC10787104.tar.gz
PMC10787105
38032131
[ "<title>Introduction</title>", "<p>Sphingolipids are structural molecules of cell membranes that play an important role in maintaining barrier function and fluidity. Sphingolipids were first isolated and identified from brain tissues in the 19th century by German biochemist Johann L. W. Thudichum, who named them after the Sphinx, a creature from Greek mythology, because of their enigmatic nature.<sup>[</sup>\n##REF##26747648##\n2\n##\n<sup>]</sup> Sphingolipid metabolites, ceramide (Cer), ceramide‐1‐phosphate (C1P), and sphingosine‐1‐phosphate (S1P) have been recognized as important signaling molecules that regulate cell growth, survival, immune cell trafficking, and vascular and epithelial cell integrity and are particularly important in inflammation and cancer.<sup>[</sup>\n##REF##35420948##\n1\n##, ##REF##24899305##\n3\n##\n<sup>]</sup> In addition, sphingosine (Sph), another sphingolipid metabolite, constitutes a class of natural products containing a long aliphatic chain with a polar 2‐amino‐1,3‐diol terminus (2‐amino‐4‐trans‐octadecene‐1,3‐diol), which is generated from ceramides.<sup>[</sup>\n##REF##16782799##\n4\n##\n<sup>]</sup> It occurs in the cell membranes of all animals and many plants and plays an important role in a variety of complex biological processes, such as DNA damage,<sup>[</sup>\n##REF##26943039##\n5\n##\n<sup>]</sup> apoptosis,<sup>[</sup>\n##REF##19797232##\n6\n##\n<sup>]</sup> (including hippocampal neuron and astrocyte apoptosis),<sup>[</sup>\n##REF##21660956##\n7\n##\n<sup>]</sup> cell growth,<sup>[</sup>\n##REF##23221613##\n8\n##\n<sup>]</sup> differentiation, autophagic processes, and development.<sup>[</sup>\n##REF##25697338##\n9\n##\n<sup>]</sup> Significantly, abnormal sphingosine metabolism can induce various diseases, such as cancers and neurodegenerative diseases, including NPC (Niemann‐Pick disease type C), AD (Alzheimer's disease),<sup>[</sup>\n##REF##18547682##\n10\n##\n<sup>]</sup> and others.<sup>[</sup>\n##REF##27830727##\n11\n##\n<sup>]</sup> Based on the above, developing suitable probes or chemical tools to study sphingolipids and their metabolites and decipher their roles in cellular biology is urgently needed.</p>", "<p>A plethora of approaches have been developed to detect cellular sphingolipids and metabolites. With respect to instrumental development, liquid chromatography‐mass spectrometry (LC‐MS), mass spectrometry (MS) and imaging mass spectrometry (IMS) techniques have become the method of choice for the detection and quantification of sphingolipid metabolites.<sup>[</sup>\n##REF##23359681##\n12\n##\n<sup>]</sup> Alternatively, sphingomyelin can be stained by fluorescent protein conjugates such as recombinant lysenin and equinatoxin.<sup>[</sup>\n##REF##25389132##\n13\n##\n<sup>]</sup> More interestingly and importantly, based on the widespread applications of fluorescence imaging technology in chemical biology, numerous methods for fluorescently labeling sphingolipids and metabolites have been developed and extensively used as sphingolipid probes to study the subcellular localization and metabolism of sphingolipids using fluorescence microscopy.<sup>[</sup>\n##REF##33496698##\n14\n##\n<sup>]</sup> Although there are many ways to label sphingolipids and metabolites, such as sphingosine, few methods have been developed for the direct detection of sphingolipids and metabolites, especially sphingosine.<sup>[</sup>\n##REF##23359681##\n12\n##, ##REF##25389132##\n13\n##, ##REF##34509716##\n15\n##\n<sup>]</sup> In 2020, Devaraj et al. first developed an ingenious fluorescently labeled aldehyde probe that chemoselectively reacts with terminal 1,2‐amino alcohol to detect endogenous Sph.<sup>[</sup>\n##REF##33044062##\n16\n##\n<sup>]</sup> Hence, the development of a simple and efficient novel method for highly selective and ultrasensitive detection of sphingosine in living cells remains highly useful and desirable.</p>", "<p>In contrast to other sphingolipids, sphingosine has a unique terminal amino alcohol structure similar to that of norepinephrine (NE). Notably, Yin et al. pioneered the highly powerful “protect‐deprotect” strategy for NE detection.<sup>[</sup>\n##REF##33000941##\n17\n##\n<bold>\n<sup>]</sup>\n</bold> Herein, a series of fluorogenic probes, <bold>DMS‐X</bold> (X = 2F, F, Cl, Br, I), with thiocarbonate protecting groups were developed (<bold>Scheme</bold> ##FIG##0##\n1\n##). Different halo substituents were introduced to control the reactivity between the probes and Sph. The results indicated that the 2,6‐difluoro‐substituted probe <bold>DMS‐2F</bold> can specifically and selectively detect sphingosine in a short time with good response sensitivity compared to other probes. Interestingly, neurotransmitters (NE, EP, and DA) did not interfere with the response of <bold>DMS‐2F</bold> to Sph. Furthermore, the results of intracellular studies suggest that <bold>DMS‐2F</bold> allows fluorescent imaging of exogenous and endogenous Sph, especially can monitor the Aβ<sub>42</sub> oligomers‐induced Sph variation in live neutral cells and zebrafish in vivo. Based on the characteristics of reactive fluorescence probes, which largely avoid the background interference of probe molecules, this new NIR fluorogenic probe provides a new research idea for the selective and sensitive detection of sphingosine in vitro and in vivo.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<p>The detailed synthesis procedure (Scheme ##SUPPL##0##S1##, Supporting Information) and structural characterization (Figures ##SUPPL##0##S1–S30##, Supporting Information) of fluorogenic probes <bold>DMS‐X</bold> are provided in the Supporting Information.</p>", "<p>To evaluate the stability of <bold>DMS‐X</bold> (<bold>DMS‐2F</bold>, <bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>), solutions of <bold>DMS‐X</bold> in PBS buffer were first exposed to a UV lamp (365 nm), and the change in fluorescence intensities of <bold>DMS‐X</bold> was monitored separately at different times. As shown in Figure ##SUPPL##0##S31a## (Supporting Information), the fluorescence intensities of <bold>DMS‐X</bold> were almost unchanged after 52 h of exposure to a UV lamp. The investigation of fluorescent changes of <bold>DMS‐X</bold> in different pH buffers at different times also showed excellent stability (Figure ##SUPPL##0##S31b–f##, Supporting Information). These results indicate that the <bold>DMS‐X</bold> probes have good photostability and acid‐base resistance properties.</p>", "<p>Next, the ability of <bold>DMS‐X</bold> probes (<bold>DMS‐2F</bold>, <bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>) to react with Sph under physiological conditions (pH 7.4, 37 °C) was tested using the vesicles of DMPC to mimic biological membranes. After reacting with Sph, the fluorescent emission results showed that only <bold>DMS‐2F</bold> had significant fluorescence enhancement at 660 nm (<bold>Figure</bold> ##FIG##1##\n1a##), while the other probes (<bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>) exhibited only slight fluorescence changes (Figure ##SUPPL##0##S32a–h##, Supporting Information). To further validate the superiority of <bold>DMS‐2F</bold> in detecting sphingosine, the fluorescence changes of <bold>DMS‐X</bold> were examined when incubated with Sph for different times in the DMPC system (with or without Sph). As shown in Figure ##FIG##1##1b##, an obvious fluorescence enhancement (I/I<sub>0</sub> = 21.08) was detected in the <bold>DMS‐2F</bold> and Sph system when incubated at 37 °C for 10 min. With increasing incubation time, the fluorescence intensity of <bold>DMS‐2F</bold> gradually increased, reaching the highest intensity at 4 h (I/I<sub>0</sub> = 57.60) (Figure ##FIG##1##1c##), which was fivefold faster than that reported for the Sph probe.<sup>[</sup>\n##REF##33044062##\n16\n##\n<sup>]</sup> However, the other probes (<bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>) did not show significant fluorescence changes even after 6 h of incubation with Sph (Figure ##FIG##1##1b##; Figure ##SUPPL##0##S33##, Supporting Information). These findings suggest that <bold>DMS‐2F</bold> can be used as a highly efficient fluorogenic probe in response to Sph.</p>", "<p>To evaluate the appropriate pH range for the Sph recognition process of <bold>DMS‐2F</bold>, pH control experiments were carefully carried out in PBS‐buffered solutions (pH 3 to 9). After incubation with 200 µ<sc>m</sc> Sph in buffer solutions of different pH values for 30 min at 37 °C, the fluorescence of <bold>DMS‐2F</bold> at 660 nm was significantly enhanced when the pH ranged from 6 to 9 (Figure ##SUPPL##0##S34##, Supporting Information), indicating that <bold>DMS‐2F</bold> could efficiently fluorogenically detect Sph in the physiological pH range.</p>", "<p>Concentration‐dependent fluorescence experiments were subsequently performed by incubating <bold>DMS‐2F</bold> (5 µ<sc>m</sc>) with various concentrations of Sph (0–200 µ<sc>m</sc>) in DMPC vesicles for 30 min at 37 °C. The results showed that the fluorescence intensity of <bold>DMS‐2F</bold> at 660 nm gradually increased with increasing Sph concentrations (Figure ##FIG##1##1d##). Moreover, an excellent linear relationship between the emission intensities was observed in the range of 0–110 µ<sc>m</sc> (Figure ##FIG##1##1e##). The limit of detection (LOD) of <bold>DMS‐2F</bold> for Sph was calculated as 9.33 ± 0.41 n<sc>m</sc> according to the 3σ/m method. These findings suggest that <bold>DMS‐2F</bold> has the capability for ultrasensitive detection of Sph.</p>", "<p>To further determine whether <bold>DMS‐2F</bold> could selectively detect Sph in living cells, <bold>DMS‐2F</bold> (5 ε<sc>m</sc>) was incubated in DMPC vesicles composed of several naturally abundant lipid species and other possible interferents (including amino acids with structures similar to Sph, such as cysteine (Cys), lysine (Lys), serine (Ser), threonine (Thr), tyrosine (Tyr) (260 ε<sc>m</sc>) and glutathione (GSH) (2 m<sc>m</sc>); naturally abundant lipid species, sphingomyelin (SM, 200 ε<sc>m</sc>) and ceramide (Cer, 200 ε<sc>m</sc>); and neurotransmitters: NE (norepinephrine, 200 ε<sc>m</sc>), DA (dopamine, 200 ε<sc>m</sc>), and EP (epinephrine, 200 ε<sc>m</sc>) for 30 min at 37 °C. The results showed that a significant fluorescence turn‐on was observed when <bold>DMS‐2F</bold> (5 ε<sc>m</sc>) was incubated with Sph (200 ε<sc>m</sc>). However, when <bold>DMS‐2F</bold> was incubated with another analyte, there was a weak change in fluorescence intensity compared to the untreated <bold>DMS‐2F</bold> probe (Figure ##FIG##1##1f##). These results are consistent with the design of the <bold>DMS‐2F</bold> probe to selectively detect Sph in the DMPC system.</p>", "<p>The specific response mechanism of <bold>DMS‐2F</bold> to Sph was confirmed by liquid chromatograph mass spectrometer (LC‐MS), high‐resolution mass spectrometry (HR‐MS), fluorescence spectroscopy, UV‐Visible spectroscopy, and theoretical calculation. <bold>DMS‐2F</bold> was exposed to Sph for 6 h at 37 °C, followed by LC−MS analysis and the reaction products of a five‐membered cyclic oxazolidinone‐based Sph compound (0.83 min) and the fluorophore <bold>DM‐2F</bold> (3.57 min) were successfully detected (<bold>Figure</bold> ##FIG##2##\n2a–c##). In addition, HR‐MS experiments again confirmed that the fluorophore was released after <bold>DMS‐2F</bold> reacted with Sph, producing a five‐membered cyclic oxazolidinone‐based Sph compound (Figure ##SUPPL##0##S35##, Supporting Information). Subsequently, the UV−vis and fluorescence response of <bold>DMS‐2F</bold> to Sph were determined by adding 200 ε<sc>m</sc> Sph to 1 mL of PBS buffer containing 5 ε<sc>m</sc>\n<bold>DMS‐2F</bold> and incubating at 37 °C for 6 h. As illustrated in Figure ##FIG##2##2d##, incubation with Sph resulted in a decrease in the UV‒vis absorption of <bold>DMS‐2F</bold> at 408 nm and an increase in absorption at 463 nm. The spectral properties of the system after reaction with Sph were in good agreement with the fluorophore <bold>DM‐2F</bold>. These results indicated that the response mechanism of <bold>DMS‐2F</bold> to Sph should be attributed to the nucleophilic addition and elimination reaction between ─NH<sub>2</sub> of Sph and the thiocarbonate‐ester group of <bold>DMS‐2F</bold>. When the reaction is triggered, the fluorophore <bold>DM‐2F</bold> is released and emits significant fluorescence. The probable response mechanism of <bold>DMS‐2F</bold> to Sph is shown in Scheme ##FIG##0##1##. According to the proposed mechanism above, the bond cleavage between the carbon atom of the carbonyl group (C<sup>20</sup>) and the aryl oxide (O<sup>21</sup>) in probes is the key factor for the fluorogenic response of <bold>DMS‐X</bold> to Sph. Therefore, the bond energy of C<sup>20</sup>─O<sup>21</sup> was a determining factor for screening the optimal probe for the response of Sph. To further understand the response priority of <bold>DMS‐2F</bold> and other probes (<bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>) to Sph, theoretical calculations were carried out. The structures of <bold>DMS‐X</bold> were optimized by density functional theory (DFT) studies using the B3LYP 6–31G (d, p) levels (Figure ##FIG##2##2f,g##: Figure ##SUPPL##0##S36##, Supporting Information), and the bond lengths of C<sup>20</sup>─O<sup>21</sup> in <bold>DMS‐X</bold> were evaluated. As shown in Figure ##FIG##2##2e##, the bond length of <bold>DMS‐2F</bold> is significantly longer than that of the other probes, which further indicates that <bold>DMS‐2F</bold> has a better response effect than the other probes. Additionally, the ground‐state geometry structures of Sph and NE were optimized by DFT at the B3LYP/6‐31G levels to investigate the selective response mechanism of <bold>DMS‐2F</bold> toward Sph. The calculation results indicate that there are hydrogen bonding interactions between the amino group of NE and its neighboring hydroxyl group (Figure ##SUPPL##0##S37a##, Supporting Information), which was detrimental to the <bold>DMS‐2F</bold> response to NE, whereas such interactions are absent in the structure of Sph (Figure ##SUPPL##0##S37b##, Supporting Information). Additionally, the electrostatic surface potential (ESP) maps reveal that the amino moieties of Sph possess higher electronegativity compared to those of NE (Figures ##SUPPL##0##S37c,d##, Supporting Information). These findings suggest that Sph can readily react with <bold>DMS‐2F</bold>, leading to its selective response.</p>", "<p>These promising in vitro results prompted us to explore the imaging effect of <bold>DMS‐X</bold> in living cells. Using MTT assays, it was confirmed that <bold>DMS‐X</bold> was non‐toxic to different cell lines (Figures ##SUPPL##0##S38## and ##SUPPL##0##S39##, Supporting Information). First, to determine whether <bold>DMS‐2F</bold> could react with Sph in live cells, A549 cells were incubated with <bold>DMS‐2F</bold> (10 ε<sc>m</sc>) for 30 min, and then the cell medium was exchanged with a new medium containing 40 ε<sc>m</sc> Sph and incubated for different amounts of time (30–150 min). As shown in Figure ##SUPPL##0##S40## (Supporting Information), as the Sph incubation time increased, the cells showed a gradual enhancement in red fluorescence emission within 1.5 h. To assess whether the response of <bold>DMS‐2F</bold> to Sph is concentration‐dependent in living cells, <bold>DMS‐2F</bold>‐pretreated A549 and HepG2 cells were incubated with different concentrations of Sph (0, 5, 10, and 20 εM). After 2 h of incubation, cells treated with exogenous Sph showed a dose‐dependent fluorescence enhancement signal (Figure ##SUPPL##0##S41##, Supporting Information). Furthermore, to confirm that the observed increase in cellular fluorescence was a result of the release of the fluorophore <bold>DM‐2F</bold> after the reaction between <bold>DMS‐2F</bold> and Sph, A549 cells were further treated with <bold>DM‐2F</bold> (10 ε<sc>m</sc>) (Figure ##SUPPL##0##S42##, Supporting Information). Cells treated with <bold>DM‐2F</bold> exhibited a fluorescent imaging pattern consistent with that observed in cells treated with <bold>DMS‐2F</bold> and Sph. These results indicate that <bold>DMS‐2F</bold> could react with Sph in living cells within a short period of time and release an enhanced fluorescence signal by generating the fluorophore <bold>DM‐2F</bold> in a dose‐dependent manner.</p>", "<p>Since elevated sphingosine in mammalian cells is closely associated with apoptosis, to evaluate the response ability of <bold>DMS‐2F</bold> to endogenous Sph levels in live cells, cancer cells (rat adrenal pheochromocytoma PC12 cells, human non‐small cell lung cancer A549 cells, and brain glioma U87 cell lines) and normal lung fibroblast MRC‐5 cells were exposed to serum‐free medium (opti‐MEM containing 10 ε<sc>m</sc>\n<bold>DMS‐2F</bold>), which could result in elevated Sph levels. As shown in Figure ##SUPPL##0##S43a,b## (Supporting Information), after 2 h of incubation, the fluorescence of live cells treated with opti‐MEM all showed a significant increase. Taken together, these results suggest that <bold>DMS‐2F</bold> is sensitive enough to probe native sphingosine in various live cells, and can be used for imaging differences in sphingosine levels in living cells.</p>", "<p>Abnormal sphingolipid metabolism has been reported to induce Alzheimer's disease (AD), and substantial evidence also support that amyloid‐β (Aβ<sub>42</sub>) plays an important role in AD. In vitro, Aβ<sub>42</sub> has been shown to induce apoptosis via the sphingomyelin pathway in various brain cells, including PC12 cells, etc.<sup>[</sup>\n##REF##18547682##\n10\n##, ##REF##14748735##\n18\n##\n<sup>]</sup> Accordingly, we attempted to assess whether the level of Sph will be changed in PC12 cells after treatment with Aβ<sub>42</sub> peptide. We first treated PC12 cells with 10 ε<sc>m</sc> Aβ<sub>42</sub> oligomers for different times and then incubated them with <bold>DMS‐2F</bold>, as shown in Figure ##SUPPL##0##S44## (Supporting Information), the fluorescence of PC12 cells treated with Aβ<sub>42</sub> oligomers was significantly increased. These observations undoubtedly revealed that intracellular Sph was up‐regulated when neuronal cells were challenged by Aβ<sub>42</sub> oligomers. To further correlate Sph generation with Aβ<sub>42</sub> oligomers, PC12 cells were treated with different concentrations of Aβ<sub>42</sub> oligomers and Aβ<sub>42</sub> monomers. After 12 h of incubation, a gradual increase in fluorescence was observed in PC12 cells treated with Aβ<sub>42</sub> oligomers, however, weak fluorescence changes were observed in Aβ<sub>42</sub> monomers treated cells (<bold>Figure</bold> ##FIG##3##\n3a,b,d,e##). Together, these findings suggested that neuronal cells experienced overexpression of Sph during Aβ<sub>42</sub> administration and that the up‐regulated Sph levels correlated with both the incubation time and dosage of Aβ<sub>42</sub> oligomers, indicating that the abnormal sphingolipid metabolism in neuronal cells is tightly related to the stimulation of Aβ<sub>42</sub> oligomers.</p>", "<p>Since the overexpression of Aβ protein induces mitochondrial oxidative stress and activates the intrinsic apoptotic cascade, and previous studies have illustrated that H<sub>2</sub>O<sub>2</sub> could induce neurotoxicity in PC12 cells,<sup>[</sup>\n##REF##14748735##\n18\n##, ##REF##22133762##\n19\n##\n<sup>]</sup> we further investigated the Sph variations induced by H<sub>2</sub>O<sub>2</sub>. PC12 cells were treated with different concentrations of H<sub>2</sub>O<sub>2</sub>, after 4 h of incubation, a gradual increase in fluorescence was detected in PC12 cells treated with H<sub>2</sub>O<sub>2</sub> (Figure ##FIG##3##3c,f##), suggesting that the Sph variation occurred during the oxidative stress process. In addition, the changes of Sph levels after being treated with Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> in other cell lines were also assessed. U87, A549, HepG2, and MRC5 cells were treated with Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> for 12 and 4 h, respectively, and then incubated with <bold>DMS‐2F</bold> for 2 h. As shown in Figure ##SUPPL##0##S45## (Supporting Information), significant fluorescence enhancement was exhibited in PC12 and U87 cells, while the fluorescence in other cell lines was not evident. These results indicate that the fluorogenic probe <bold>DMS‐2F</bold> can successfully monitor the level changes of Sph during Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub>‐induced apoptosis in neuronal cells.</p>", "<p>Since changes in Sph levels are associated with the abnormal sphingolipid metabolism in cells, to investigate the possible mechanisms of Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub>‐induced changes in Sph levels, we further investigated intracellular sphingomyelinase and ceramidase activities in Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> treated cells. PC12 cells were preincubated for 2 h in the presence of 10 µ<sc>m</sc> amitriptyline hydrochloride (AMI, an acid sphingomyelinase inhibitor<sup>[</sup>\n##UREF##0##\n20\n##\n<sup>]</sup>), 20 µ<sc>m</sc> GW4869 (a neutral sphingomyelinase inhibitor<sup>[</sup>\n##REF##20629193##\n21\n##\n<sup>]</sup>), 10 µ<sc>m</sc> LCL‐521 (an acid ceramidase inhibitor<sup>[</sup>\n##REF##25456083##\n22\n##\n<sup>]</sup>), 500 µ<sc>m</sc> N‐acetyl‐cysteine (NAC, an efficient antioxidant<sup>[</sup>\n##UREF##1##\n23\n##\n<sup>]</sup>) and 1 m<sc>m</sc> Trolox (a reactive oxygen scavenger <sup>[</sup>\n##REF##17013382##\n24\n##\n<sup>]</sup>), and then treated with Aβ<sub>42</sub> oligomers (10 µ<sc>m</sc>, 12 h) or H<sub>2</sub>O<sub>2</sub> (50 µ<sc>m</sc>, 4 h), respectively. As shown in <bold>Figure</bold> ##FIG##4##\n4a,c##, the fluorescence of the cells preincubated with the inhibitors prior to the treatment with Aβ<sub>42</sub> oligomers was lower than that of the control group. This suggests that the Aβ<sub>42</sub> oligomers increase Sph levels by elevating intracellular ROS and enhancing intracellular acidic and neutral sphingomyelinase and acidic ceramidase activities. However, the increase in intracellular Sph levels in H<sub>2</sub>O<sub>2</sub>‐treated cells appeared to be more correlated with neutral sphingomyelinase activity. This is supported by the reduced imaging intensity observed in cells pretreated with the nerve sphingomyelinase inhibitor, GW4869, as well as the reactive oxygen scavengers, NAC and Trolox (Figure ##FIG##4##4b,d##). Therefore, it is hypothesized that the possible mechanism of Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub>‐induced up‐regulation of intracellular Sph levels is as follows: Aβ<sub>42</sub> oligomers induced an increase in intracellular ROS levels, which then activated neutral sphingomyelinase (NSMase), leading to the hydrolysis of sphingomyelin (SM) and the production of ceramides (Cer). This process ultimately results in an increase in intracellular Sph levels. Moreover, Aβ<sub>42</sub> oligomers can activate acidic sphingomyelinase (ASMase) and acidic ceramidase (ACDase), which also contribute to the hydrolysis of SM and Cer, thereby increasing Sph levels (Figure ##FIG##4##4e##).</p>", "<p>To further validate the possible mechanisms proposed above, changes in ROS levels after different times of treatment of PC12 cells with Aβ<sub>42</sub> oligomers were monitored using a ROS specific probe. We found that changes of ROS levels in cellular mitochondria upon Aβ<sub>42</sub> oligomers treatment showed a gradual increase and reached the peak at 1 h. With prolonged treatment time, the ROS levels gradually decreased and eventually returned to the initial level (<bold>Figure</bold> ##FIG##5##\n5a–c##; Figure ##SUPPL##0##S46##, Supporting Information). The activations of SMase and CDase were then investigated. The treatment of PC12 cells with 1 µ<sc>m</sc> Aβ<sub>42</sub> oligomers and 50 µ<sc>m</sc> H<sub>2</sub>O<sub>2</sub> induced a time‐dependent increase in SMase activity and reached maximum levels at 6 and 3 h, respectively (Figure ##FIG##5##5d,e##; Figure ##SUPPL##0##S47##, Supporting Information). Notably, the widely used ASMase and NSMase inhibitors AMI and GW4869 strongly inhibited Aβ<sub>42</sub> oligomers‐induced SMase activation, respectively, while only GW4869 inhibited H<sub>2</sub>O<sub>2</sub>‐induced SMase activation, and the ROS scavenger NAC and Trolox inhibited both the Aβ<sub>42</sub> oligomers‐ and H<sub>2</sub>O<sub>2</sub>‐induced SMase activation (Figure ##FIG##5##5f,g##). Immunoblotting and immunofluorescence experiments provided additional support for the aforementioned experimental results (Figure ##FIG##5##5h–j##; Figure ##SUPPL##0##S48##, Supporting Information). This suggests that Aβ<sub>42</sub> oligomers can induce the activation of ASMase and NSMase, respectively, whereas H<sub>2</sub>O<sub>2</sub> can only induce the activation of NSMase. In addition, the ELISA test results for CDase indicated that the intracellular ceramidase level reached a maximum after 4 h of treatment with Aβ<sub>42</sub> oligomers. It was observed that H<sub>2</sub>O<sub>2</sub> did not activate intracellular CDase, but had an inhibitory effect, which aligns with the findings reported in the literature,<sup>[</sup>\n##REF##34459070##\n25\n##\n<sup>]</sup> (Figure ##FIG##5##5l,m##; Figure ##SUPPL##0##S49##, Supporting Information). Moreover, the activation effect of ROS scavenger to Aβ<sub>42</sub> oligomers induced CDase activity and immunoblotting experiments on ACDase further supported that Aβ<sub>42</sub> oligomers can activate ACDase, while H<sub>2</sub>O<sub>2</sub> inhibits its activity (Figure ##FIG##5##5h,k##; Figure ##SUPPL##0##S50##, Supporting Information). Taken together, these results suggest that Aβ<sub>42</sub> oligomers directly activate ASMase and ACDase, and also increase ROS levels, which activate NSMase and ultimately accelerate sphingolipid metabolism and increase the level of Sph.</p>", "<p>Encouraged by the excellent results of live cell imaging, we further investigated the in vivo detection in a living animal model. The transparent zebrafish larva was selected as a model because zebrafish are optically transparent and have a high degree of homology with mammals.<sup>[</sup>\n##REF##21240407##\n26\n##\n<sup>]</sup> Zebrafish larvae (3 days old) were incubated with Aβ<sub>42</sub> oligomers (10 ε<sc>m</sc>) for 12 h and then treated with <bold>DMS‐2F</bold> (10 ε<sc>m</sc>) for 2 h. As shown in <bold>Figure</bold> ##FIG##6##\n6\n##, zebrafish treated with <bold>DMS‐2F</bold> without Aβ<sub>42</sub> oligomers exhibited weak fluorescence, and notably, the Aβ<sub>42</sub> oligomers treated zebrafish showed bright red fluorescence in the brain, yolk sac, and intestine. However, the fluorescence intensity of zebrafish pretreated with inhibitors (AMI, GW4869, LCL‐521, and Trolox) and further treated with Aβ<sub>42</sub> oligomers and <bold>DMS‐2F</bold> was significantly weaker than that of zebrafish treated without inhibitors. Based on these results, it is shown that in vivo, Aβ<sub>42</sub> oligomers can still induce the upregulation of Sph levels by the same mechanism as in neuronal cells. Hence, this new probe <bold>DMS‐2F</bold> successfully realized the detection of Sph in vivo.</p>" ]
[ "<title>Results and Discussion</title>", "<p>The detailed synthesis procedure (Scheme ##SUPPL##0##S1##, Supporting Information) and structural characterization (Figures ##SUPPL##0##S1–S30##, Supporting Information) of fluorogenic probes <bold>DMS‐X</bold> are provided in the Supporting Information.</p>", "<p>To evaluate the stability of <bold>DMS‐X</bold> (<bold>DMS‐2F</bold>, <bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>), solutions of <bold>DMS‐X</bold> in PBS buffer were first exposed to a UV lamp (365 nm), and the change in fluorescence intensities of <bold>DMS‐X</bold> was monitored separately at different times. As shown in Figure ##SUPPL##0##S31a## (Supporting Information), the fluorescence intensities of <bold>DMS‐X</bold> were almost unchanged after 52 h of exposure to a UV lamp. The investigation of fluorescent changes of <bold>DMS‐X</bold> in different pH buffers at different times also showed excellent stability (Figure ##SUPPL##0##S31b–f##, Supporting Information). These results indicate that the <bold>DMS‐X</bold> probes have good photostability and acid‐base resistance properties.</p>", "<p>Next, the ability of <bold>DMS‐X</bold> probes (<bold>DMS‐2F</bold>, <bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>) to react with Sph under physiological conditions (pH 7.4, 37 °C) was tested using the vesicles of DMPC to mimic biological membranes. After reacting with Sph, the fluorescent emission results showed that only <bold>DMS‐2F</bold> had significant fluorescence enhancement at 660 nm (<bold>Figure</bold> ##FIG##1##\n1a##), while the other probes (<bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>) exhibited only slight fluorescence changes (Figure ##SUPPL##0##S32a–h##, Supporting Information). To further validate the superiority of <bold>DMS‐2F</bold> in detecting sphingosine, the fluorescence changes of <bold>DMS‐X</bold> were examined when incubated with Sph for different times in the DMPC system (with or without Sph). As shown in Figure ##FIG##1##1b##, an obvious fluorescence enhancement (I/I<sub>0</sub> = 21.08) was detected in the <bold>DMS‐2F</bold> and Sph system when incubated at 37 °C for 10 min. With increasing incubation time, the fluorescence intensity of <bold>DMS‐2F</bold> gradually increased, reaching the highest intensity at 4 h (I/I<sub>0</sub> = 57.60) (Figure ##FIG##1##1c##), which was fivefold faster than that reported for the Sph probe.<sup>[</sup>\n##REF##33044062##\n16\n##\n<sup>]</sup> However, the other probes (<bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>) did not show significant fluorescence changes even after 6 h of incubation with Sph (Figure ##FIG##1##1b##; Figure ##SUPPL##0##S33##, Supporting Information). These findings suggest that <bold>DMS‐2F</bold> can be used as a highly efficient fluorogenic probe in response to Sph.</p>", "<p>To evaluate the appropriate pH range for the Sph recognition process of <bold>DMS‐2F</bold>, pH control experiments were carefully carried out in PBS‐buffered solutions (pH 3 to 9). After incubation with 200 µ<sc>m</sc> Sph in buffer solutions of different pH values for 30 min at 37 °C, the fluorescence of <bold>DMS‐2F</bold> at 660 nm was significantly enhanced when the pH ranged from 6 to 9 (Figure ##SUPPL##0##S34##, Supporting Information), indicating that <bold>DMS‐2F</bold> could efficiently fluorogenically detect Sph in the physiological pH range.</p>", "<p>Concentration‐dependent fluorescence experiments were subsequently performed by incubating <bold>DMS‐2F</bold> (5 µ<sc>m</sc>) with various concentrations of Sph (0–200 µ<sc>m</sc>) in DMPC vesicles for 30 min at 37 °C. The results showed that the fluorescence intensity of <bold>DMS‐2F</bold> at 660 nm gradually increased with increasing Sph concentrations (Figure ##FIG##1##1d##). Moreover, an excellent linear relationship between the emission intensities was observed in the range of 0–110 µ<sc>m</sc> (Figure ##FIG##1##1e##). The limit of detection (LOD) of <bold>DMS‐2F</bold> for Sph was calculated as 9.33 ± 0.41 n<sc>m</sc> according to the 3σ/m method. These findings suggest that <bold>DMS‐2F</bold> has the capability for ultrasensitive detection of Sph.</p>", "<p>To further determine whether <bold>DMS‐2F</bold> could selectively detect Sph in living cells, <bold>DMS‐2F</bold> (5 ε<sc>m</sc>) was incubated in DMPC vesicles composed of several naturally abundant lipid species and other possible interferents (including amino acids with structures similar to Sph, such as cysteine (Cys), lysine (Lys), serine (Ser), threonine (Thr), tyrosine (Tyr) (260 ε<sc>m</sc>) and glutathione (GSH) (2 m<sc>m</sc>); naturally abundant lipid species, sphingomyelin (SM, 200 ε<sc>m</sc>) and ceramide (Cer, 200 ε<sc>m</sc>); and neurotransmitters: NE (norepinephrine, 200 ε<sc>m</sc>), DA (dopamine, 200 ε<sc>m</sc>), and EP (epinephrine, 200 ε<sc>m</sc>) for 30 min at 37 °C. The results showed that a significant fluorescence turn‐on was observed when <bold>DMS‐2F</bold> (5 ε<sc>m</sc>) was incubated with Sph (200 ε<sc>m</sc>). However, when <bold>DMS‐2F</bold> was incubated with another analyte, there was a weak change in fluorescence intensity compared to the untreated <bold>DMS‐2F</bold> probe (Figure ##FIG##1##1f##). These results are consistent with the design of the <bold>DMS‐2F</bold> probe to selectively detect Sph in the DMPC system.</p>", "<p>The specific response mechanism of <bold>DMS‐2F</bold> to Sph was confirmed by liquid chromatograph mass spectrometer (LC‐MS), high‐resolution mass spectrometry (HR‐MS), fluorescence spectroscopy, UV‐Visible spectroscopy, and theoretical calculation. <bold>DMS‐2F</bold> was exposed to Sph for 6 h at 37 °C, followed by LC−MS analysis and the reaction products of a five‐membered cyclic oxazolidinone‐based Sph compound (0.83 min) and the fluorophore <bold>DM‐2F</bold> (3.57 min) were successfully detected (<bold>Figure</bold> ##FIG##2##\n2a–c##). In addition, HR‐MS experiments again confirmed that the fluorophore was released after <bold>DMS‐2F</bold> reacted with Sph, producing a five‐membered cyclic oxazolidinone‐based Sph compound (Figure ##SUPPL##0##S35##, Supporting Information). Subsequently, the UV−vis and fluorescence response of <bold>DMS‐2F</bold> to Sph were determined by adding 200 ε<sc>m</sc> Sph to 1 mL of PBS buffer containing 5 ε<sc>m</sc>\n<bold>DMS‐2F</bold> and incubating at 37 °C for 6 h. As illustrated in Figure ##FIG##2##2d##, incubation with Sph resulted in a decrease in the UV‒vis absorption of <bold>DMS‐2F</bold> at 408 nm and an increase in absorption at 463 nm. The spectral properties of the system after reaction with Sph were in good agreement with the fluorophore <bold>DM‐2F</bold>. These results indicated that the response mechanism of <bold>DMS‐2F</bold> to Sph should be attributed to the nucleophilic addition and elimination reaction between ─NH<sub>2</sub> of Sph and the thiocarbonate‐ester group of <bold>DMS‐2F</bold>. When the reaction is triggered, the fluorophore <bold>DM‐2F</bold> is released and emits significant fluorescence. The probable response mechanism of <bold>DMS‐2F</bold> to Sph is shown in Scheme ##FIG##0##1##. According to the proposed mechanism above, the bond cleavage between the carbon atom of the carbonyl group (C<sup>20</sup>) and the aryl oxide (O<sup>21</sup>) in probes is the key factor for the fluorogenic response of <bold>DMS‐X</bold> to Sph. Therefore, the bond energy of C<sup>20</sup>─O<sup>21</sup> was a determining factor for screening the optimal probe for the response of Sph. To further understand the response priority of <bold>DMS‐2F</bold> and other probes (<bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br,</bold> and <bold>DMS‐I</bold>) to Sph, theoretical calculations were carried out. The structures of <bold>DMS‐X</bold> were optimized by density functional theory (DFT) studies using the B3LYP 6–31G (d, p) levels (Figure ##FIG##2##2f,g##: Figure ##SUPPL##0##S36##, Supporting Information), and the bond lengths of C<sup>20</sup>─O<sup>21</sup> in <bold>DMS‐X</bold> were evaluated. As shown in Figure ##FIG##2##2e##, the bond length of <bold>DMS‐2F</bold> is significantly longer than that of the other probes, which further indicates that <bold>DMS‐2F</bold> has a better response effect than the other probes. Additionally, the ground‐state geometry structures of Sph and NE were optimized by DFT at the B3LYP/6‐31G levels to investigate the selective response mechanism of <bold>DMS‐2F</bold> toward Sph. The calculation results indicate that there are hydrogen bonding interactions between the amino group of NE and its neighboring hydroxyl group (Figure ##SUPPL##0##S37a##, Supporting Information), which was detrimental to the <bold>DMS‐2F</bold> response to NE, whereas such interactions are absent in the structure of Sph (Figure ##SUPPL##0##S37b##, Supporting Information). Additionally, the electrostatic surface potential (ESP) maps reveal that the amino moieties of Sph possess higher electronegativity compared to those of NE (Figures ##SUPPL##0##S37c,d##, Supporting Information). These findings suggest that Sph can readily react with <bold>DMS‐2F</bold>, leading to its selective response.</p>", "<p>These promising in vitro results prompted us to explore the imaging effect of <bold>DMS‐X</bold> in living cells. Using MTT assays, it was confirmed that <bold>DMS‐X</bold> was non‐toxic to different cell lines (Figures ##SUPPL##0##S38## and ##SUPPL##0##S39##, Supporting Information). First, to determine whether <bold>DMS‐2F</bold> could react with Sph in live cells, A549 cells were incubated with <bold>DMS‐2F</bold> (10 ε<sc>m</sc>) for 30 min, and then the cell medium was exchanged with a new medium containing 40 ε<sc>m</sc> Sph and incubated for different amounts of time (30–150 min). As shown in Figure ##SUPPL##0##S40## (Supporting Information), as the Sph incubation time increased, the cells showed a gradual enhancement in red fluorescence emission within 1.5 h. To assess whether the response of <bold>DMS‐2F</bold> to Sph is concentration‐dependent in living cells, <bold>DMS‐2F</bold>‐pretreated A549 and HepG2 cells were incubated with different concentrations of Sph (0, 5, 10, and 20 εM). After 2 h of incubation, cells treated with exogenous Sph showed a dose‐dependent fluorescence enhancement signal (Figure ##SUPPL##0##S41##, Supporting Information). Furthermore, to confirm that the observed increase in cellular fluorescence was a result of the release of the fluorophore <bold>DM‐2F</bold> after the reaction between <bold>DMS‐2F</bold> and Sph, A549 cells were further treated with <bold>DM‐2F</bold> (10 ε<sc>m</sc>) (Figure ##SUPPL##0##S42##, Supporting Information). Cells treated with <bold>DM‐2F</bold> exhibited a fluorescent imaging pattern consistent with that observed in cells treated with <bold>DMS‐2F</bold> and Sph. These results indicate that <bold>DMS‐2F</bold> could react with Sph in living cells within a short period of time and release an enhanced fluorescence signal by generating the fluorophore <bold>DM‐2F</bold> in a dose‐dependent manner.</p>", "<p>Since elevated sphingosine in mammalian cells is closely associated with apoptosis, to evaluate the response ability of <bold>DMS‐2F</bold> to endogenous Sph levels in live cells, cancer cells (rat adrenal pheochromocytoma PC12 cells, human non‐small cell lung cancer A549 cells, and brain glioma U87 cell lines) and normal lung fibroblast MRC‐5 cells were exposed to serum‐free medium (opti‐MEM containing 10 ε<sc>m</sc>\n<bold>DMS‐2F</bold>), which could result in elevated Sph levels. As shown in Figure ##SUPPL##0##S43a,b## (Supporting Information), after 2 h of incubation, the fluorescence of live cells treated with opti‐MEM all showed a significant increase. Taken together, these results suggest that <bold>DMS‐2F</bold> is sensitive enough to probe native sphingosine in various live cells, and can be used for imaging differences in sphingosine levels in living cells.</p>", "<p>Abnormal sphingolipid metabolism has been reported to induce Alzheimer's disease (AD), and substantial evidence also support that amyloid‐β (Aβ<sub>42</sub>) plays an important role in AD. In vitro, Aβ<sub>42</sub> has been shown to induce apoptosis via the sphingomyelin pathway in various brain cells, including PC12 cells, etc.<sup>[</sup>\n##REF##18547682##\n10\n##, ##REF##14748735##\n18\n##\n<sup>]</sup> Accordingly, we attempted to assess whether the level of Sph will be changed in PC12 cells after treatment with Aβ<sub>42</sub> peptide. We first treated PC12 cells with 10 ε<sc>m</sc> Aβ<sub>42</sub> oligomers for different times and then incubated them with <bold>DMS‐2F</bold>, as shown in Figure ##SUPPL##0##S44## (Supporting Information), the fluorescence of PC12 cells treated with Aβ<sub>42</sub> oligomers was significantly increased. These observations undoubtedly revealed that intracellular Sph was up‐regulated when neuronal cells were challenged by Aβ<sub>42</sub> oligomers. To further correlate Sph generation with Aβ<sub>42</sub> oligomers, PC12 cells were treated with different concentrations of Aβ<sub>42</sub> oligomers and Aβ<sub>42</sub> monomers. After 12 h of incubation, a gradual increase in fluorescence was observed in PC12 cells treated with Aβ<sub>42</sub> oligomers, however, weak fluorescence changes were observed in Aβ<sub>42</sub> monomers treated cells (<bold>Figure</bold> ##FIG##3##\n3a,b,d,e##). Together, these findings suggested that neuronal cells experienced overexpression of Sph during Aβ<sub>42</sub> administration and that the up‐regulated Sph levels correlated with both the incubation time and dosage of Aβ<sub>42</sub> oligomers, indicating that the abnormal sphingolipid metabolism in neuronal cells is tightly related to the stimulation of Aβ<sub>42</sub> oligomers.</p>", "<p>Since the overexpression of Aβ protein induces mitochondrial oxidative stress and activates the intrinsic apoptotic cascade, and previous studies have illustrated that H<sub>2</sub>O<sub>2</sub> could induce neurotoxicity in PC12 cells,<sup>[</sup>\n##REF##14748735##\n18\n##, ##REF##22133762##\n19\n##\n<sup>]</sup> we further investigated the Sph variations induced by H<sub>2</sub>O<sub>2</sub>. PC12 cells were treated with different concentrations of H<sub>2</sub>O<sub>2</sub>, after 4 h of incubation, a gradual increase in fluorescence was detected in PC12 cells treated with H<sub>2</sub>O<sub>2</sub> (Figure ##FIG##3##3c,f##), suggesting that the Sph variation occurred during the oxidative stress process. In addition, the changes of Sph levels after being treated with Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> in other cell lines were also assessed. U87, A549, HepG2, and MRC5 cells were treated with Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> for 12 and 4 h, respectively, and then incubated with <bold>DMS‐2F</bold> for 2 h. As shown in Figure ##SUPPL##0##S45## (Supporting Information), significant fluorescence enhancement was exhibited in PC12 and U87 cells, while the fluorescence in other cell lines was not evident. These results indicate that the fluorogenic probe <bold>DMS‐2F</bold> can successfully monitor the level changes of Sph during Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub>‐induced apoptosis in neuronal cells.</p>", "<p>Since changes in Sph levels are associated with the abnormal sphingolipid metabolism in cells, to investigate the possible mechanisms of Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub>‐induced changes in Sph levels, we further investigated intracellular sphingomyelinase and ceramidase activities in Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> treated cells. PC12 cells were preincubated for 2 h in the presence of 10 µ<sc>m</sc> amitriptyline hydrochloride (AMI, an acid sphingomyelinase inhibitor<sup>[</sup>\n##UREF##0##\n20\n##\n<sup>]</sup>), 20 µ<sc>m</sc> GW4869 (a neutral sphingomyelinase inhibitor<sup>[</sup>\n##REF##20629193##\n21\n##\n<sup>]</sup>), 10 µ<sc>m</sc> LCL‐521 (an acid ceramidase inhibitor<sup>[</sup>\n##REF##25456083##\n22\n##\n<sup>]</sup>), 500 µ<sc>m</sc> N‐acetyl‐cysteine (NAC, an efficient antioxidant<sup>[</sup>\n##UREF##1##\n23\n##\n<sup>]</sup>) and 1 m<sc>m</sc> Trolox (a reactive oxygen scavenger <sup>[</sup>\n##REF##17013382##\n24\n##\n<sup>]</sup>), and then treated with Aβ<sub>42</sub> oligomers (10 µ<sc>m</sc>, 12 h) or H<sub>2</sub>O<sub>2</sub> (50 µ<sc>m</sc>, 4 h), respectively. As shown in <bold>Figure</bold> ##FIG##4##\n4a,c##, the fluorescence of the cells preincubated with the inhibitors prior to the treatment with Aβ<sub>42</sub> oligomers was lower than that of the control group. This suggests that the Aβ<sub>42</sub> oligomers increase Sph levels by elevating intracellular ROS and enhancing intracellular acidic and neutral sphingomyelinase and acidic ceramidase activities. However, the increase in intracellular Sph levels in H<sub>2</sub>O<sub>2</sub>‐treated cells appeared to be more correlated with neutral sphingomyelinase activity. This is supported by the reduced imaging intensity observed in cells pretreated with the nerve sphingomyelinase inhibitor, GW4869, as well as the reactive oxygen scavengers, NAC and Trolox (Figure ##FIG##4##4b,d##). Therefore, it is hypothesized that the possible mechanism of Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub>‐induced up‐regulation of intracellular Sph levels is as follows: Aβ<sub>42</sub> oligomers induced an increase in intracellular ROS levels, which then activated neutral sphingomyelinase (NSMase), leading to the hydrolysis of sphingomyelin (SM) and the production of ceramides (Cer). This process ultimately results in an increase in intracellular Sph levels. Moreover, Aβ<sub>42</sub> oligomers can activate acidic sphingomyelinase (ASMase) and acidic ceramidase (ACDase), which also contribute to the hydrolysis of SM and Cer, thereby increasing Sph levels (Figure ##FIG##4##4e##).</p>", "<p>To further validate the possible mechanisms proposed above, changes in ROS levels after different times of treatment of PC12 cells with Aβ<sub>42</sub> oligomers were monitored using a ROS specific probe. We found that changes of ROS levels in cellular mitochondria upon Aβ<sub>42</sub> oligomers treatment showed a gradual increase and reached the peak at 1 h. With prolonged treatment time, the ROS levels gradually decreased and eventually returned to the initial level (<bold>Figure</bold> ##FIG##5##\n5a–c##; Figure ##SUPPL##0##S46##, Supporting Information). The activations of SMase and CDase were then investigated. The treatment of PC12 cells with 1 µ<sc>m</sc> Aβ<sub>42</sub> oligomers and 50 µ<sc>m</sc> H<sub>2</sub>O<sub>2</sub> induced a time‐dependent increase in SMase activity and reached maximum levels at 6 and 3 h, respectively (Figure ##FIG##5##5d,e##; Figure ##SUPPL##0##S47##, Supporting Information). Notably, the widely used ASMase and NSMase inhibitors AMI and GW4869 strongly inhibited Aβ<sub>42</sub> oligomers‐induced SMase activation, respectively, while only GW4869 inhibited H<sub>2</sub>O<sub>2</sub>‐induced SMase activation, and the ROS scavenger NAC and Trolox inhibited both the Aβ<sub>42</sub> oligomers‐ and H<sub>2</sub>O<sub>2</sub>‐induced SMase activation (Figure ##FIG##5##5f,g##). Immunoblotting and immunofluorescence experiments provided additional support for the aforementioned experimental results (Figure ##FIG##5##5h–j##; Figure ##SUPPL##0##S48##, Supporting Information). This suggests that Aβ<sub>42</sub> oligomers can induce the activation of ASMase and NSMase, respectively, whereas H<sub>2</sub>O<sub>2</sub> can only induce the activation of NSMase. In addition, the ELISA test results for CDase indicated that the intracellular ceramidase level reached a maximum after 4 h of treatment with Aβ<sub>42</sub> oligomers. It was observed that H<sub>2</sub>O<sub>2</sub> did not activate intracellular CDase, but had an inhibitory effect, which aligns with the findings reported in the literature,<sup>[</sup>\n##REF##34459070##\n25\n##\n<sup>]</sup> (Figure ##FIG##5##5l,m##; Figure ##SUPPL##0##S49##, Supporting Information). Moreover, the activation effect of ROS scavenger to Aβ<sub>42</sub> oligomers induced CDase activity and immunoblotting experiments on ACDase further supported that Aβ<sub>42</sub> oligomers can activate ACDase, while H<sub>2</sub>O<sub>2</sub> inhibits its activity (Figure ##FIG##5##5h,k##; Figure ##SUPPL##0##S50##, Supporting Information). Taken together, these results suggest that Aβ<sub>42</sub> oligomers directly activate ASMase and ACDase, and also increase ROS levels, which activate NSMase and ultimately accelerate sphingolipid metabolism and increase the level of Sph.</p>", "<p>Encouraged by the excellent results of live cell imaging, we further investigated the in vivo detection in a living animal model. The transparent zebrafish larva was selected as a model because zebrafish are optically transparent and have a high degree of homology with mammals.<sup>[</sup>\n##REF##21240407##\n26\n##\n<sup>]</sup> Zebrafish larvae (3 days old) were incubated with Aβ<sub>42</sub> oligomers (10 ε<sc>m</sc>) for 12 h and then treated with <bold>DMS‐2F</bold> (10 ε<sc>m</sc>) for 2 h. As shown in <bold>Figure</bold> ##FIG##6##\n6\n##, zebrafish treated with <bold>DMS‐2F</bold> without Aβ<sub>42</sub> oligomers exhibited weak fluorescence, and notably, the Aβ<sub>42</sub> oligomers treated zebrafish showed bright red fluorescence in the brain, yolk sac, and intestine. However, the fluorescence intensity of zebrafish pretreated with inhibitors (AMI, GW4869, LCL‐521, and Trolox) and further treated with Aβ<sub>42</sub> oligomers and <bold>DMS‐2F</bold> was significantly weaker than that of zebrafish treated without inhibitors. Based on these results, it is shown that in vivo, Aβ<sub>42</sub> oligomers can still induce the upregulation of Sph levels by the same mechanism as in neuronal cells. Hence, this new probe <bold>DMS‐2F</bold> successfully realized the detection of Sph in vivo.</p>" ]
[ "<title>Conclusion</title>", "<p>In summary, we have developed a series of easily synthesized fluorogenic probes, named <bold>DMS‐X</bold>, by introducing different halogen substituents and thiocarbonate protecting groups. <bold>DMS‐2F</bold> can specifically detect sphingosine in a short period of time (within 4 h) and has excellent response sensitivity (LOD, 9.33 n<sc>m</sc>). <bold>DMS‐2F</bold> is capable of fluorescence tracing and imaging of exogenous and endogenous sphingosine in living cells. Importantly, we, for the first time, evaluated the Sph levels during Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub>‐induced apoptosis of PC12 cells by fluorescent imaging approach and further verified that Aβ<sub>42</sub> oligomers can induce abnormal sphingolipid metabolism by increasing the intracellular ROS levels and inducing the activation of sphingomyelinase and ceramidase during sphingolipid metabolism, which ultimately led to the increase of Sph level. Finally, we successfully realized the in vivo detection of Aβ<sub>42</sub> oligomers‐induced Sph in a living zebrafish model. Based on the properties of reactive fluorogenic probes, this new probe greatly avoids the background interference of probe molecules and provides a novel strategy for monitoring sphingosine in living cells and in vivo.</p>" ]
[ "<title>Abstract</title>", "<p>Sphingosine (Sph) plays important roles in various complex biological processes. Abnormalities in Sph metabolism can result in various diseases, including neurodegenerative disorders. However, due to the lack of rapid and accurate detection methods, understanding sph metabolic in related diseases is limited. Herein, a series of near‐infrared fluorogenic probes <bold>DMS‐X</bold> (X = 2F, F, Cl, Br, and I) are designed and synthesized. The fast oxazolidinone ring formation enables the <bold>DMS‐2F</bold> to detect Sph selectively and ultrasensitively, and the detection limit reaches 9.33 ± 0.41 n<sc>m</sc>. Moreover, it is demonstrated that <bold>DMS‐2F</bold> exhibited a dose‐ and time‐dependent response to Sph and can detect sph in living cells. Importantly, for the first time, the changes in Sph levels induced by Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> are assessed through a fluorescent imaging approach, and further validated the physiological processes by which Aβ<sub>42</sub> oligomers and reactive oxygen species (ROS)‐induce changes in intracellular Sph levels. Additionally, the distribution of Sph in living zebrafish is successfully mapped by in vivo imaging of a zebrafish model. This work provides a simple and efficient method for probing Sph in living cells and in vivo, which will facilitate investigation into the metabolic process of Sph and the connection between Sph and disease pathologies.</p>", "<p>A novel fluorogenic probe for specifical sphingosine detecting is constructed via a rational molecular design strategy. The probe could image Aβ<sub>42</sub> oligomers‐induced Sph in neural cells and in vivo.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6946-cit-0067\">\n<string-name>\n<given-names>Y.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>T.</given-names>\n<surname>Hao</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>W.</given-names>\n<surname>Wei</surname>\n</string-name>, <string-name>\n<given-names>J.</given-names>\n<surname>Zhao</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Qian</surname>\n</string-name>, <article-title>A Near‐Infrared Fluorogenic Probe for Rapid, Specific, and Ultrasensitive Detection of Sphingosine in Living Cells and In Vivo</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2307598</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202307598</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was supported by the National Key Research Program 2019YFA0905801, the National Natural Science Foundation of China (22025701, 22207053, 22177048 and 22074065), the National Science Fund for Excellent Young Scholars (22222704), the Natural Science Foundation of Jiangsu Province (BK20202004 and BK20220764), Shenzhen Basic Research Program (JCYJ20170413150538897, JCYJ20180508182240106), the National Key Research and Development Program of China (2017YFA0208200, 2016YFB0700600, 2015CB659300), The Fundamental Research Funds for the Central Universities, 2021 Strategic Research Project of the Science and Technology Commission of the Ministry of Education of China.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available in the supplementary material of this article.</p>" ]
[ "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6946-fig-0007\"><label>Scheme 1</label><caption><p>a) The response process of <bold>DMS‐2F</bold> with Sph; b) Designed structure of the fluorogenic probes <bold>DMS‐X</bold> and c) Structure of Sph and oxazolidinone‐based Sph after reacting with <bold>DMS‐2F</bold>.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6946-fig-0001\"><label>Figure 1</label><caption><p>a) Fluorescence spectra of <bold>DMS‐2F</bold> in PBS and DMPC vesicles (with/without Sph), inset: histograms for fluorescent intensity at 660 nm; b,c) Fluorescence results of <bold>DMS‐X</bold> (<bold>DMS‐2F</bold>, <bold>DMS‐F</bold>, <bold>DMS‐Cl</bold>, <bold>DMS‐Br</bold> and <bold>DMS‐I</bold>) for Sph under physiological conditions and incubated for different times: b) 10 min, c) 0–360 min, respectively; d) Concentration response of <bold>DMS‐2F</bold> to Sph from 0 to 200 µ<sc>m</sc>; e) Fluorescence spectrum linear range for Sph from 0 to 110 µ<sc>m</sc>; f) Fluorescence intensity ratios of <bold>DMS‐2F</bold> and <bold>DMS‐2F</bold> toward various analytes (<italic toggle=\"yes\">λ</italic>\n<sub>ex</sub> = 540 nm, <italic toggle=\"yes\">λ</italic>\n<sub>em</sub> = 660 nm, slit = 10/10 nm, pH 7.4, 37 °C.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6946-fig-0002\"><label>Figure 2</label><caption><p>a,b,c) The LC‐MS of <bold>DMS‐2F</bold> (5 m<sc>m</sc>) in MeOH after reacting with Sph (100 m<sc>m</sc>) for 6 h at 37 °C; d) UV‒vis absorption spectra of <bold>DM‐2F</bold> (5 µ<sc>m</sc>), <bold>DMS‐2F</bold> (5 µ<sc>m</sc>) and <bold>DMS‐2F</bold> (5 µ<sc>m</sc>) reacted with Sph (200 µ<sc>m</sc>) in PBS buffer; e) Bond length between C<sup>21</sup>─O<sup>20</sup> in <bold>DMS‐X</bold> evaluated by theoretical calculations, inset: the chemical structure of <bold>DMS‐X</bold>; f) View of the energy‐optimized structure and g) The molecular electrostatic potential (ESP) surface for <bold>DMS‐2F</bold> from Gauss View.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6946-fig-0003\"><label>Figure 3</label><caption><p>Fluorescence images of PC12 cells treated with different concentrations of a) Aβ<sub>42</sub> monomers and b) Aβ<sub>42</sub> oligomers for 12 h and then incubated with 10 ε<sc>m</sc>\n<bold>DMS‐2F</bold> for 2 h. c) Fluorescence images of PC12 cells treated with different concentrations of H<sub>2</sub>O<sub>2</sub> for 4 h and then incubated with 10 µ<sc>m</sc>\n<bold>DMS‐2F</bold> for 2 h. d,e,f) Mean fluorescent intensities of PC12 cells in panels (a), (b), and (c), respectively. Scale bar: 20 µ<sc>m</sc>. The data are expressed as the mean ± SD. One‐way ANOVA was used to compare multiple groups: <sup>*</sup>\n<italic toggle=\"yes\">P</italic> ≤0.05, <sup>**</sup>\n<italic toggle=\"yes\">P</italic> ≤0.01, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> ≤0.001, <sup>****</sup>\n<italic toggle=\"yes\">P</italic> ≤0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6946-fig-0004\"><label>Figure 4</label><caption><p>Fluorescence images of PC12 cells preincubated with different inhibitors and then treated with a) 10 ε<sc>m</sc> Aβ<sub>42</sub> oligomers for 12 h and b) 50 ε<sc>m</sc> H<sub>2</sub>O<sub>2</sub> for 4 h, and then incubated with 10 ε<sc>m</sc>\n<bold>DMS‐2F</bold> for 2 h, scale bar: 10 µ<sc>m</sc>; c,d) Mean fluorescent intensities of PC12 cells in panels (a) and (b), respectively; e) Schematic pathway proposed for the Aβ<sub>42</sub> oligomers, ROS, and sphingolipid changes in the PC12 cells. All values are expressed as the mean ± SD of triplicates. One‐way ANOVA was used to compare multiple groups: ns <italic toggle=\"yes\">P</italic>&gt; 0.05, <sup>*</sup>\n<italic toggle=\"yes\">P</italic> ≤0.05, <sup>**</sup>\n<italic toggle=\"yes\">P</italic> ≤0.01, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> ≤0.001, <sup>****</sup>\n<italic toggle=\"yes\">P</italic> ≤0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6946-fig-0005\"><label>Figure 5</label><caption><p>a) Fluorescence image of ROS in PC12 cells induced by Aβ<sub>42</sub> oligomers at different time, scale bar: 5 µ<sc>m</sc>; b,c) Mean fluorescent intensities of PC12 cells in panels (a); d,e). The level of SMase released in the supernatant of PC12 cells treated with Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> for different durations measured by ELISA; f,g). The level of SMase released in the supernatant of PC12 cells pretreated with different inhibitors and then incubated by Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> measured by ELISA; h) WB blot analysis of the expression of ASMase and ACDase in PC12 cells after incubation with Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> at different times; i) Immunofluorescence analysis of ASMase in Aβ<sub>42</sub> oligomers‐incubated PC12 cells pretreated or not pretreated with inhibitors AMI and NAC, scale bar: 10 µ<sc>m</sc>; j) Mean fluorescent intensities of PC12 cells in panels Figure ##FIG##5##5(h)##; k) The level of CDase released in the supernatant of PC12 cells pretreated with different inhibitors and then incubated by Aβ<sub>42</sub> oligomers measured by ELISA; l,m). The level of CDase released in the supernatant of PC12 cells treated with Aβ<sub>42</sub> oligomers and H<sub>2</sub>O<sub>2</sub> for different durations measured by ELISA; All values are expressed as the mean ± SD of triplicates. One‐way ANOVA was used to compare multiple groups: <sup>*</sup>\n<italic toggle=\"yes\">P</italic> ≤0.05, <sup>**</sup>\n<italic toggle=\"yes\">P</italic> ≤0.01, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> ≤0.001, <sup>****</sup>\n<italic toggle=\"yes\">P</italic> ≤0.0001.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6946-fig-0006\"><label>Figure 6</label><caption><p>a) Fluorescence images of zebrafish preincubated with/without different inhibitors (20 µ<sc>m</sc> AMI, 40 µ<sc>m</sc> GW4869, 20 µ<sc>m</sc> LCL‐521, and 1m<sc>m</sc> Trolox) and treated with 10 ε<sc>m</sc> Aβ<sub>42</sub> oligomers for 12 h and then incubated with 10 ε<sc>m</sc>\n<bold>DMS‐2F</bold> for 2 h, scale bar: 200 µ<sc>m</sc>; Mean fluorescent intensities of zebrafish position b) brain, c) yolk sac, and d) intestine, respectively. All values are expressed as the mean ± SD of triplicates. One‐way ANOVA was used to compare multiple groups: ns <italic toggle=\"yes\">P</italic>&gt; 0.05, <sup>*</sup>\n<italic toggle=\"yes\">P</italic> ≤0.05, <sup>**</sup>\n<italic toggle=\"yes\">P</italic> ≤0.01, <sup>***</sup>\n<italic toggle=\"yes\">P</italic> ≤0.001, <sup>****</sup>\n<italic toggle=\"yes\">P</italic> ≤0.0001.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6946-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2307598-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
[{"label": ["20"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["Y.", "J.", "L.", "C.", "J.", "H.", "H.", "S.", "S.", "B.", "C.", "S.", "Y."], "surname": ["Ji", "Chen", "Pang", "Chen", "Ye", "Liu", "Chen", "Zhang", "Liu", "Liu", "Cheng", "Liu", "Zhong"], "source": ["Cardiovasc Drugs Ther."], "year": ["2022"], "pub-id": ["10.1007/s10557-022-07378-0"]}, {"label": ["23"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["J. C. Y. J.", "F.", "X. L.", "M. M.", "N. N.", "C. Y.", "Y.", "F.", "M.", "Y. W.", "L. M."], "surname": ["Shen", "Sun", "Cai", "Li", "Zheng", "Qu", "Zhang", "Shen", "Zhou", "Chen", "Xu"], "source": ["World J. Gastroenterol"], "year": ["2018"], "volume": ["24"], "fpage": ["2219"]}]
{ "acronym": [], "definition": [] }
26
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 30; 11(2):2307598
oa_package/85/3f/PMC10787105.tar.gz
PMC10787106
37964763
[ "<title>Introduction</title>", "<p>The branched‐chain amino acids (BCAAs) valine, leucine, and isoleucine are essential amino acids containing non‐linear aliphatic side chains. Apart from their roles in protein synthesis and as metabolic precursors for the tricarboxylic acid (TCA) cycle and other pathways,<sup>[</sup>\n##REF##31084571##\n1\n##\n<sup>]</sup> BCAAs also function as molecular signals to activate mammalian target of rapamycin complex 1 (mTORC1),<sup>[</sup>\n##REF##26449471##\n2\n##, ##REF##31937935##\n3\n##\n<sup>]</sup> a crucial regulator of cell growth and metabolism. Despite their widespread use as dietary supplements to potentially improve exercise performance and muscle growth,<sup>[</sup>\n##UREF##0##\n4\n##\n<sup>]</sup> their roles in aging and inflammatory diseases are complex and remain controversial.<sup>[</sup>\n##REF##33132154##\n5\n##\n<sup>]</sup> While some studies suggest that BCAA supplementation may improve skeletal muscle function in middle‐aged mice,<sup>[</sup>\n##REF##20889128##\n6\n##\n<sup>]</sup> others suggest that high BCAA intake can impair health and lifespan.<sup>[</sup>\n##REF##31656947##\n7\n##\n<sup>]</sup> In addition, low BCAA intake has been associated with improved metabolic health and extended longevity in mice,<sup>[</sup>\n##REF##31656947##\n7\n##, ##REF##27346343##\n8\n##\n<sup>]</sup> as well as higher survival rates and better performance in Alzheimer's disease models.<sup>[</sup>\n##UREF##1##\n9\n##\n<sup>]</sup> However, because most of these previous studies were based on manipulating dietary or medium BCAA availability to investigate their potential roles in these contexts, any intrinsic alterations in BCAA metabolism that might occur during the aging process remain largely unknown.</p>", "<p>Cellular senescence is an irreversible cell cycle arrest phenotype<sup>[</sup>\n##REF##13905658##\n10\n##\n<sup>]</sup> that is induced by various stresses, including DNA damage, oxidative stress, and oncogene activation.<sup>[</sup>\n##REF##28729727##\n11\n##\n<sup>]</sup> Senescent cells accumulate in aged and inflammatory tissues where they drive age‐associated and inflammatory phenotypes primarily through the senescence‐associated secretory phenotype (SASP).<sup>[</sup>\n##REF##26646499##\n12\n##, ##REF##7568133##\n13\n##\n<sup>]</sup> Known SASP factors include various cytokines, chemokines, and proteases, which together produce a proinflammatory microenvironment promoting tissue deterioration.<sup>[</sup>\n##REF##26646499##\n12\n##, ##REF##24848057##\n14\n##\n<sup>]</sup> Targeting senescence has been shown to delay the aging‐related phenotypes<sup>[</sup>\n##REF##22048312##\n15\n##, ##REF##26840489##\n16\n##, ##UREF##2##\n17\n##, ##UREF##3##\n18\n##, ##UREF##4##\n19\n##, ##REF##30728521##\n20\n##\n<sup>]</sup> and relieve the progression of various diseases including liver fibrosis,<sup>[</sup>\n##REF##32555459##\n21\n##, ##REF##37169907##\n22\n##\n<sup>]</sup> osteoarthritis,<sup>[</sup>\n##REF##28436958##\n23\n##\n<sup>]</sup> and COVID‐19.<sup>[</sup>\n##REF##34517409##\n24\n##, ##REF##34103349##\n25\n##\n<sup>]</sup> However, the molecular pathways that distinguish senescence from alternative cell fates such as quiescence and apoptosis, as well as those molecules responsible for establishing and maintaining the SASP, remain incompletely understood. Previous studies have shown that senescent cells undergo metabolic reprogramming,<sup>[</sup>\n##REF##30526768##\n26\n##, ##REF##31920721##\n27\n##, ##REF##27591812##\n28\n##\n<sup>]</sup> which involves broad changes in glucose,<sup>[</sup>\n##REF##6127343##\n29\n##, ##REF##19302375##\n30\n##, ##REF##24577087##\n31\n##, ##REF##12943534##\n32\n##, ##REF##6509159##\n33\n##\n<sup>]</sup> nucleotide,<sup>[</sup>\n##REF##23562156##\n34\n##, ##REF##31138644##\n35\n##\n<sup>]</sup> and lipid metabolism.<sup>[</sup>\n##REF##22421146##\n36\n##, ##REF##29090099##\n37\n##, ##REF##30962418##\n38\n##, ##REF##36864206##\n39\n##\n<sup>]</sup> Although some studies have revealed an altered abundance and possible functions of certain amino acids in senescent cells,<sup>[</sup>\n##UREF##5##\n40\n##, ##REF##33446552##\n41\n##, ##REF##18656976##\n42\n##, ##REF##28264926##\n43\n##, ##REF##18317946##\n44\n##, ##REF##24223226##\n45\n##, ##REF##27922824##\n46\n##, ##UREF##6##\n47\n##\n<sup>]</sup> the intrinsic changes in amino acid metabolism that underlie these alterations have remained obscure, such that it remains unclear whether and how senescent cells alter amino acid metabolism and how these changes might impact senescence.</p>", "<p>In this study, we discovered consistent upregulation of BCAA transporters and reduced BCAA catabolism in senescent cells. These intrinsic alterations lead to intracellular BCAA accumulation and mTORC1 activation in senescent cells to promote SASP establishment. Importantly, manipulating these BCAA regulators is sufficient to block SASP factor expression in vitro and in vivo. Together, these findings uncover BCAA buildup as upstream of mTORC1 in senescent cells and provide new therapeutic targets for senescence‐ and age‐related inflammatory disorders.</p>" ]
[]
[ "<title>Results</title>", "<title>Alterations in BCAA Metabolism during Cellular Senescence</title>", "<p>We previously found that epidermal growth factor receptor (EGFR) signaling inhibition causes senescence of normal human bronchial epithelial (NHBE) cells in vitro and premature aging in vivo.<sup>[</sup>\n##REF##37169907##\n22\n##, ##REF##25367123##\n48\n##, ##REF##29808012##\n49\n##, ##REF##28189533##\n50\n##, ##REF##29777051##\n51\n##\n<sup>]</sup> Using this senescence model, we used the EGFR inhibitor erlotinib to induce senescence and conducted unbiased transcriptional profiling to characterize proliferating, quiescent, and senescent populations of NHBE cells.<sup>[</sup>\n##REF##29808012##\n49\n##\n<sup>]</sup> Interestingly, after confirming the previously reported reprogramming of lipid and glucose metabolism in senescent NHBE cells (Figure ##SUPPL##0##S1a,b##, Supporting Information),<sup>[</sup>\n##REF##30526768##\n26\n##, ##REF##31920721##\n27\n##, ##REF##27591812##\n28\n##\n<sup>]</sup> we noticed significant changes in pathways related to amino acid transport and metabolism (<bold>Figure</bold>\n##FIG##0##\n1a##). Specifically, we identified the amino acid transporter Solute Carrier Family 6 member 14 (SLC6A14) as one of the most highly upregulated genes; conversely, the branched chain amino acid transaminase 1 (BCAT1) was significantly decreased upon senescence induction among the amino acid‐related metabolic pathways (Figure ##FIG##0##1b## and Figure ##SUPPL##0##S1c,d##, Supporting Information).</p>", "<p>SLC6A14 is a Na<sup>+</sup> and Cl<sup>−</sup>‐dependent broad spectrum amino acids transporter that mediates the uptake of neutral and cationic amino acids, with high affinities for BCAAs.<sup>[</sup>\n##REF##11306607##\n52\n##\n<sup>]</sup> It is primarily expressed in epithelial cells of the digestive tract and lung to mediate nutrient uptake and fluid homeostasis.<sup>[</sup>\n##REF##25613900##\n53\n##, ##REF##30004386##\n54\n##\n<sup>]</sup> BCAT1 mediates the reversible deamination of BCAA to produce branched‐chain α‐keto acids via the conversion of α‐ketoglutarate into glutamate.<sup>[</sup>\n##REF##31084571##\n1\n##, ##UREF##7##\n55\n##\n<sup>]</sup> BCAT1‐produced branched‐chain α‐keto acids can be further processed by a series of enzymes and shuttled into different metabolic pathways, including TCA cycle, lipid synthesis, and gluconeogenesis.<sup>[</sup>\n##REF##31084571##\n1\n##, ##UREF##7##\n55\n##\n<sup>]</sup> Although BCAT catalysis is theoretically reversible, animals cannot <italic toggle=\"yes\">de novo</italic> synthesize branched‐chain α‐keto acids; thus, BCAT1 primarily catalyzes BCAA catabolism.<sup>[</sup>\n##REF##31084571##\n1\n##, ##UREF##7##\n55\n##\n<sup>]</sup> Therefore, we postulated that elevated expression of SLC6A14 and reduced BCAT1 should have interconnected impacts on senescent cell metabolism resulting in increased intracellular BCAAs.</p>", "<p>To demonstrate this, we first validated these gene expression changes in senescent cells. Consistent with our transcriptome data, the increase of SLC6A14 and decrease of BCAT1 expression was observed in senescent epithelial cells (Figure ##FIG##0##1c,d## and Figure ##SUPPL##0##S2a##, Supporting Information). This phenomenon is further supported by published datasets of senescent human IMR90 fibroblasts,<sup>[</sup>\n##REF##24647599##\n56\n##\n<sup>]</sup> one of the most commonly used cellular senescence models. In senescent IMR90 cells,<sup>[</sup>\n##REF##24647599##\n56\n##\n<sup>]</sup> we also observed a consistent decrease in BCAT1, although we did not detect elevated SLC6A14 expression. Instead, upon senescence induction we found an increase in SLC6A15, a family member that shares similar functions with SLC6A14. This difference is likely explained by cell type heterogeneity, since the functions of these transporters are redundant and they exhibit distinct tissue distributions.<sup>[</sup>\n##REF##11306607##\n52\n##, ##REF##25613900##\n53\n##, ##REF##24098498##\n57\n##, ##REF##16226721##\n58\n##, ##REF##16185194##\n59\n##\n<sup>]</sup> In support of this, the single cell type Atlas indicates that SLC6A14 is mainly expressed in epithelial and endocrine cells, while SLC6A15 is expressed in neuronal cells, melanocytes, and fibroblasts.<sup>[</sup>\n##REF##28495876##\n60\n##\n<sup>]</sup> To confirm this data mining, we used three independent methods to induce senescence in human IMR90 fibroblasts: overexpression of the oncogene HRasV12 (HRas proto‐oncogene with G12V mutation), treatment with the DNA‐damage inducer etoposide, and replicative exhaustion. Indeed, both immunoblotting and quantitative reverse transcription PCR (RT‐qPCR) showed that SLC6A15 is significantly upregulated and BCAT1 reduced in all three senescent fibroblast models (Figure ##FIG##0##1e–j##, Figure ##SUPPL##0##S2b–g##, Supporting Information). Together, these results demonstrate consistently increased BCAA transporter expression and reduced BCAA transamination machinery in diverse senescent cell models.</p>", "<title>Suppressing BCAA Accumulation Blocks the SASP</title>", "<p>To assess a possible functional role for BCAA metabolism during cellular senescence, we first blocked SLC6A15 expression using short hairpin RNA and assessed senescence establishment using a variety of senescent cell models. Interestingly, SLC6A15 depletion had no effect on cell cycle arrest, as indicated by high p16 (Cyclin Dependent Kinase Inhibitor 2A) expression, reduced Lamin B1, and senescence‐associated‐beta‐galactosidase (SA‐β‐Gal) positivity in senescent IMR90 fibroblasts (<bold>Figure</bold>\n##FIG##1##\n2a,b,d## and Figure ##SUPPL##0##S3a,c,e##, Supporting Information). However, we noticed that reduced expression of SLC6A15 significantly inhibited the production of prominent SASP factors, including interleukin 6 (IL6) and interleukin 8 (IL8) (Figure ##FIG##1##2a,b,d##). Indeed, RT‐qPCR analysis revealed that SLC6A15 depletion blocks the induction of a large number of proteins known to comprise the SASP (Figure ##FIG##1##2b## and Figure ##SUPPL##0##S4a,c##, Supporting Information), suggesting that BCAA transport is a requirement for SASP generation during senescence induction. Similarly, ectopic BCAT1 expression also reduced the expression of the majority of SASP factors without affecting the levels of p16, Lamin B1, or SA‐β‐Gal (Figure ##FIG##1##2c,e##, and Figures ##SUPPL##0##S3b,d,f## and ##SUPPL##0##S4b,d##, Supporting Information). To further explore the functional role of BCAAs in cellular senescence, we utilized the SLC6A15 inhibitor loratadine.<sup>[</sup>\n##REF##25318072##\n61\n##\n<sup>]</sup> Immunoblots and RT‐qPCR both showed that loratadine treatment phenocopies SLC6A15 knockdown in senescent cells: upon inducing senescence with either oncogene activation or DNA damage, pharmacological SLC6A15 inhibition blocks the upregulation of several major SASP factors including IL6, IL8, Interleukin 1 alpha (IL1A), and Interleukin 1 beta (IL1B) in a dose‐dependent manner, without significantly altering the levels of p16, p21 (Cyclin Dependent Kinase Inhibitor 1A), or Lamin B1 (Figure ##SUPPL##0##S5a–f##, Supporting Information). These data suggest that either suppressing BCAA transport (via SLC6A15 inhibition) or activating BCAA catabolism (via BCAT1 expression) both suppress the SASP program in various senescent cell models.</p>", "<p>In senescent cells, the cell‐cycle arrest phenotype is induced by the p53‐p21‐phospho‐retinoblastoma protein (RB) and p16‐pRB signaling pathways, while SASP factor expression is thought to be mediated by the Nuclear factor‐κB and CCAAT/enhancer‐binding protein beta transcription factors.<sup>[</sup>\n##REF##23140366##\n62\n##\n<sup>]</sup> Despite the existence of crosstalk between these mechanisms controlling cell cycle arrest and the SASP, our results suggest that their regulation can be uncoupled due to the involvement of these distinct signaling pathways, a notion that is consistent with findings from several other recent studies.<sup>[</sup>\n##REF##29777051##\n51\n##, ##REF##28976970##\n63\n##, ##REF##26280535##\n64\n##, ##REF##30778219##\n65\n##, ##REF##26147250##\n66\n##, ##REF##33795874##\n67\n##\n<sup>]</sup>\n</p>", "<title>BCAA Regulators Drive SASP Factor Production by Activating mTORC1 Signaling</title>", "<p>To determine the molecular mechanism by which BCAAs mediate SASP production, we first analyzed BCAA levels in senescent cells using an enzymatic assay. As expected, we observed significantly elevated intracellular BCAA levels in all tested senescence models as compared with proliferating cells (<bold>Figure</bold>\n##FIG##2##\n3a–c##). Moreover, overexpression of SLC6A14 or SLC6A15 in HEK293T cells resulted in increased BCAA level (Figure ##FIG##2##3d##), while BCAT1 downregulation produced a similar effect (Figure ##FIG##2##3e##). Conversely, suppressing SLC6A15 upregulation or restoring BCAT1 expression in senescent cells significantly reduced BCAA accumulation (Figure ##FIG##2##3f,g##). Together, these results validate that elevated BCAA uptake through SLC6A transporters and reduced BCAT1 catabolism both function to increase BCAA levels in senescent cells.</p>", "<p>We next investigated whether increased cellular BCAAs affect SASP establishment by culturing cells in BCAA‐restricted media. This revealed that reducing BCAA levels to 25% of the standard concentration did not affect cell growth (Figure ##SUPPL##0##S6a##, Supporting Information), but significantly inhibited the expression of multiple important SASP factors (Figure ##SUPPL##0##S6b–d##, Supporting Information); this is consistent with phenotypes observed upon manipulating BCAA regulators in senescent cells. To further explore metabolic changes in senescent cells, we performed high‐performance liquid chromatography‐mass spectrometry (HPLC‐MS)‐based metabolite profiling. Interestingly, this revealed that, in addition to BCAAs, other essential amino acids are also elevated in two senescent cell models (Figure ##SUPPL##0##S7a##, Supporting Information); this might be due to broad‐spectrum transport by SLC6A14/15, which mediates the uptake of other essential amino acids in addition to having a high affinity for BCAAs.<sup>[</sup>\n##REF##11306607##\n52\n##, ##REF##16226721##\n58\n##, ##REF##16185194##\n59\n##\n<sup>]</sup> Consistent with this, transient overexpression of SLC6A14 or SLC6A15 increased intracellular levels of essential amino acids (Figure ##SUPPL##0##S7c##, Supporting Information), whereas sustained SLC6A15 knockdown significantly reduced nearly all essential amino acids (Figure ##SUPPL##0##S7b##, Supporting Information). To assess the impact of specific amino acids on SASP establishment, we individually increased the levels of essential amino acids known to be transported by SLC6A14/15, as well as two non‐essential amino acids. This revealed that, among the eight tested amino acids, increasing the levels of BCAAs and tryptophan promotes heightened expression of the SASP factors IL6 and IL8 during senescence (Figure ##SUPPL##0##S7d##, Supporting Information). Based on these amino acid restriction and supplementation results, we conclude that BCAA accumulation via increased BCAA transport and reduced BCAA catabolism is both necessary for full SASP factor production and also sufficient to induce the expression of key SASP proteins in senescent cells.</p>", "<p>BCAAs, particularly leucine, are potent activators of mTORC1,<sup>[</sup>\n##REF##26449471##\n2\n##\n<sup>]</sup> and recent studies have shown that mTORC1 signaling drives the SASP program in senescent cells.<sup>[</sup>\n##REF##26280535##\n64\n##, ##REF##26147250##\n66\n##, ##REF##21512002##\n68\n##, ##REF##33823141##\n69\n##\n<sup>]</sup> This occurs both through regulating the translation of mitogen‐activated protein kinase‐activated protein kinase 2 (MAPKAPK2) and IL1A to increase the mRNA levels of SASP factors, and also through directly promoting the translation of those mRNAs.<sup>[</sup>\n##REF##26280535##\n64\n##, ##REF##26147250##\n66\n##\n<sup>]</sup> We therefore investigated whether changes in SLC6A15 and BCAT1 influence the mTORC1 signaling pathway. Indeed, SLC6A15 knockdown (Figure ##FIG##2##3h## and Figure ##SUPPL##0##S8a##, Supporting Information) or forced BCAT1 expression (Figure ##FIG##2##3i## and Figure ##SUPPL##0##S8b##, Supporting Information) inhibited mTORC1 signaling activation during the onset of senescence, suggesting that BCAA buildup is the upstream activator of this pathway. To further confirm that mTORC1 functions downstream of SLC6A15 and BCAT1, we knocked down DEP domain‐containing 5 (DEPDC5) protein, an inhibitory component of the mTORC1 pathway, to reactivate mTORC1.<sup>[</sup>\n##REF##23723238##\n70\n##\n<sup>]</sup> This revealed that, even after depleting SLC6A15 or overexpressing BCAT1, rescuing mTORC1 signaling restores the expression of multiple prominent SASP factors (Figure ##FIG##2##3j,k,m## and Figure ##SUPPL##0##S8c,d##, Supporting Information). Together, these data suggest that elevated SLC6A15 and reduced BCAT1 expression in senescent cells control SASP establishment via the BCAA‐mTORC1 signaling pathway (Figure ##FIG##2##3l##).</p>", "<title>Upregulating BCAA Transporters Induces Age‐Related Phenotypes in <italic toggle=\"yes\">Drosophila melanogaster</italic>\n</title>", "<p>SASP factors have been shown to have deleterious effects by promoting paracrine senescence, which contributes to aging and inflammatory diseases as the immune system becomes less effective in removing senescent cells.<sup>[</sup>\n##REF##23770676##\n71\n##, ##REF##18555778##\n72\n##, ##REF##18555777##\n73\n##, ##REF##35902645##\n74\n##\n<sup>]</sup> To investigate the effects of alterations in BCAA metabolism on the aging process, we turned to <italic toggle=\"yes\">Drosophila melanogaster</italic>, which has a shorter lifespan and shares conserved signaling pathways in cellular senescence and aging with mammals.<sup>[</sup>\n##REF##25584795##\n75\n##, ##UREF##8##\n76\n##, ##REF##32130880##\n77\n##\n<sup>]</sup> Furthermore, recent <italic toggle=\"yes\">Drosophila</italic> studies demonstrated that BCAA‐restricted diet extends lifespan,<sup>[</sup>\n##REF##30891588##\n78\n##, ##UREF##9##\n79\n##\n<sup>]</sup> highlighting the role of BCAA metabolism during physiological aging in <italic toggle=\"yes\">Drosophila</italic>.</p>", "<p>Based on protein similarity,<sup>[</sup>\n##REF##9254694##\n80\n##\n<sup>]</sup> while we could not find an ortholog of human SLC6A14 in fruit flies, we identified two possible orthologs of human SLC6A15: <italic toggle=\"yes\">CG43066</italic> (43.8% identity) and <italic toggle=\"yes\">CG10804</italic> (41.2% identity). Based on the Alliance algorithm,<sup>[</sup>\n##REF##31796553##\n81\n##\n<sup>]</sup> the top predicted ortholog for <italic toggle=\"yes\">CG43066</italic> (hereafter termed <italic toggle=\"yes\">dSlc6a15‐a</italic>) is indeed SLC6A15. For <italic toggle=\"yes\">CG10804</italic> (hereafter <italic toggle=\"yes\">dSlc6a15‐b</italic>), the predicted orthologs are SLC6A15, SLC6A17, and SLC6A18. As the functions of these two proteins have not been characterized in flies, and the three mammalian SLC6 family transporters are similar and likely redundant,<sup>[</sup>\n##REF##23506866##\n82\n##\n<sup>]</sup> we tested the effects of manipulating the expression of <italic toggle=\"yes\">dSlc6a15‐a</italic> and <italic toggle=\"yes\">dSlc6a15‐b</italic> on fly aging. Specifically, we mimicked the increased BCAA transporter expression observed in senescent mammalian cells by inducing overexpression of <italic toggle=\"yes\">dSlc6a15‐a</italic> or <italic toggle=\"yes\">dSlc6a15‐b</italic> in adult flies using the <italic toggle=\"yes\">actin</italic>‐transcription activator protein Gal4/ Upstream Activation Sequence (Gal4/UAS) system (<bold>Figure</bold>\n##FIG##3##\n4a,b##). We used female fruit flies in these experiments, based on our preliminary findings that they were more responsive to the BCAA‐restricted diet and showed a greater lifespan extension compared to male flies, which is consistent with a previous study.<sup>[</sup>\n##UREF##9##\n79\n##\n<sup>]</sup> Strikingly, overexpression of either transporter significantly shortened fly lifespan (Figure ##FIG##3##4c##) and led to age‐related decline in climbing ability (Figure ##FIG##3##4d##).<sup>[</sup>\n##REF##18515028##\n83\n##\n<sup>]</sup> Additionally, overexpression of <italic toggle=\"yes\">dSlc6a15‐a</italic> or <italic toggle=\"yes\">dSlc6a15‐b</italic> induced cellular senescent hallmarks, including upregulation of the cyclin‐dependent kinase inhibitor <italic toggle=\"yes\">dacapo</italic> (<italic toggle=\"yes\">d</italic>p21) (Figure ##FIG##3##4e##), and increased expression of the inflammatory cytokine unpaired 2 (<italic toggle=\"yes\">Upd2</italic>) (Figure ##FIG##3##4f##) in elderly flies. These results suggest that hyper‐expression of BCAA transporters is sufficient to accelerate fly aging, possibly through increased cellular senescence and a pro‐inflammatory SASP.</p>", "<p>Previous studies have shown that the expression of antimicrobial peptides is upregulated in aged fruit flies, possibly due to Janus kinase/signal transducers and activators of transcription signaling activation by SASP factors as well as increased exposure to environmental bacteria during aging.<sup>[</sup>\n##REF##12361567##\n84\n##, ##REF##23236133##\n85\n##, ##REF##17681150##\n86\n##, ##REF##34502551##\n87\n##\n<sup>]</sup> Strikingly, we observed massive increases in antimicrobial peptide expression in elderly transgenic flies overexpressing BCAA transporters as compared with GFP‐overexpression control flies (Figure ##FIG##3##4g##). While the detailed mechanism of how this pathway contribute to fly aging needs to be further resolved in future studies, our findings support the notion that increasing BCAA transport shortens fly lifespan and induces senescent as well as aging‐related phenotypes at the organismal level.</p>", "<title>Blocking BCAA Accumulation Attenuates the Senescence‐Associated Inflammatory Response in Mouse Liver</title>", "<p>To investigate the impact of BCAA regulators on the senescence‐associated inflammatory response in the mammalian system, we utilized an established oncogene‐induced senescence model to study the immune‐mediated clearance of senescent mouse hepatocytes.<sup>[</sup>\n##REF##22080947##\n88\n##\n<sup>]</sup> This sleeping‐beauty transposon system, which is introduced into mouse liver via hydrodynamic tail vein injection, enables the simultaneous manipulation of multiple genes; here, we knocked down SLC6A15 and overexpressed BCAT1 to reduce intracellular BCAA levels, while also inducing senescence via NRasV12 (NRas proto‐oncogene with G12V mutation) overexpression (<bold>Figure</bold>\n##FIG##4##\n5a,b##). Samples were collected on days 6 and 12 to evaluate the effects of BCAA metabolism on SASP gene expression and senescent cell immune clearance, respectively (Figure ##FIG##4##5b##).</p>", "<p>As expected, NRasV12 activation (as indicated in brown) (Figure ##FIG##4##5d##) induced senescence in hepatocytes, resulting in the rapid production of proinflammatory factors: day 6 analysis revealed high expression of SASP components in the control group (GFP‐ShN) (Figure ##FIG##4##5c##), along with a large number of protein tyrosine phosphatase receptor type C (CD45)‐positive immune cell clusters (as indicated in red) (Figure ##FIG##4##5d##). Conversely, in the animals with depleted SLC6A15 and overexpressed BCAT1 (BCAT1‐SLC6A15_KD), we observed significantly attenuated expression of canonical SASP factors (Figure ##FIG##4##5c##), with few immune cell clusters present (as indicated in red) (Figure ##FIG##4##5d##). These results suggest that, if BCAA accumulation is impaired, senescence can still be induced by oncogene activation, but SASP factor production is blocked such that senescent cells are not efficiently cleared by the immune system. Consistent with this, on day 12, significantly fewer NRasV12‐positive cells (as indicated in brown) were observed in the control group (GFP‐ShN) as compared with the experimental group (BCAT1‐SLC6A15_KD) (Figure ##FIG##4##5e##). Collectively, these findings support the notion that elevated BCAA levels are required for the senescence‐associated inflammatory response and immune clearance of senescent cells in vivo.</p>", "<p>To explore whether BCAA metabolism is also involved in the mammalian aging process, we examined the relationship between expression of SLC6A14/15 and BCAT1/2 with a panel of established SASP transcripts across various human datasets obtained from the Genotype‐Tissue Expression (GTEx) portal.<sup>[</sup>\n##REF##23715323##\n89\n##\n<sup>]</sup> This analysis revealed a positive correlation between SLC6A14 and SLC6A15 and the SASP signature score, whereas BCAT1 and BCAT2 levels showed a negative correlation with the SASP signature score across multiple aged human tissues, including lung, pancreas, and stomach (Figure ##SUPPL##0##S9a–e##, Supporting Information). These findings indicate that elevated BCAA transport and reduced BCAA degradation are associated with enhanced pro‐inflammatory cytokine expression during the aging process, suggesting that altered BCAA metabolism could play an important role in age‐related chronic inflammation in humans.</p>" ]
[ "<title>Discussion</title>", "<p>While previous studies have reported that circulating BCAA levels are altered during physiological aging and age‐related diseases,<sup>[</sup>\n##REF##33132154##\n5\n##, ##UREF##10##\n90\n##, ##REF##29570613##\n91\n##, ##REF##19356713##\n92\n##, ##REF##29051501##\n93\n##, ##REF##27036001##\n94\n##\n<sup>]</sup> including obesity, type 2 diabetes, cardiovascular disease, and Alzheimer's disease, the metabolic pathways underlying altered BCAA abundance in these settings have remained largely obscure. Moreover, while BCAAs are a popular dietary supplement with purported benefits for physical exercise,<sup>[</sup>\n##UREF##0##\n4\n##\n<sup>]</sup> liver disease,<sup>[</sup>\n##REF##20071143##\n95\n##\n<sup>]</sup> and brain function,<sup>[</sup>\n##UREF##11##\n96\n##\n<sup>]</sup> their roles in aging and inflammation‐related diseases remain controversial. This controversy is due to various factors,<sup>[</sup>\n##REF##33132154##\n5\n##\n<sup>]</sup> including an unclear causality between blood BCAA levels and disease onset or progression, poor correlation between dietary BCAA intake and blood availability, variability in BCAA requirements among organs, and the fact that BCAAs in the blood do not always reflect those in cells. Therefore, it is important to understand the intrinsic regulation of BCAA metabolism in these contexts in order to develop more precise nutritional interventions or combination therapies. Here, we discovered that senescent cells reprogram BCAA metabolism by increasing BCAA uptake and decreasing catabolism; together, these intrinsic metabolic alterations may contribute to the changes in blood BCAA levels observed in age‐ and inflammation‐related diseases. This has important implications for these age‐related disorders, as senescence plays a crucial role in them.<sup>[</sup>\n##REF##32555459##\n21\n##, ##REF##37169907##\n22\n##, ##REF##28436958##\n23\n##, ##REF##34517409##\n24\n##, ##REF##34103349##\n25\n##\n<sup>]</sup> SASP is akin to a double‐edged sword. On the one hand, SASP factors play a beneficial role by recruiting immune cells to eliminate senescent cells triggered by oncogene expression, DNA damage, or other stressors, potentially preventing oncogenesis in young and healthy populations.<sup>[</sup>\n##REF##13905658##\n10\n##, ##REF##28729727##\n11\n##, ##REF##26646499##\n12\n##, ##REF##7568133##\n13\n##, ##REF##24848057##\n14\n##\n<sup>]</sup> However, as the immune system's efficacy diminishes with age and stress stimuli accumulate, there is a decreased efficiency in the clearance of senescent cells. This results in prolonged SASP activity, which can culminate in detrimental inflammation and expedite disease progression.<sup>[</sup>\n##REF##13905658##\n10\n##, ##REF##28729727##\n11\n##, ##REF##26646499##\n12\n##, ##REF##7568133##\n13\n##, ##REF##24848057##\n14\n##\n<sup>]</sup> It is also worth noting that BCAA supplementation should be used with caution in the elderly and those with inflammatory diseases, as intracellular BCAA accumulation is shown here to promote a senescence‐associated‐inflammatory response.</p>", "<p>In addition to their impact on the SASP during aging, BCAAs also influence other aging‐related signaling pathways. One of the hallmarks of aging is diminished mitochondrial functionality.<sup>[</sup>\n##REF##36047448##\n97\n##\n<sup>]</sup> BCAAs, along with related metabolites, have been shown to modulate mitochondrial biogenesis and functions.<sup>[</sup>\n##REF##36047448##\n97\n##\n<sup>]</sup> The underlying mechanisms for these modulations are evidently associated with the mTORC1 and Sirtuin 1 pathways and the regulation of TCA cycle enzyme activities.<sup>[</sup>\n##REF##36047448##\n97\n##\n<sup>]</sup> Furthermore, BCAA restriction has shown promise in improving insulin resistance and reducing body fat by modulating the energy‐regulating hormone fibroblast growth factor 21 (FGF21) to enhance metabolic health.<sup>[</sup>\n##REF##35526271##\n98\n##\n<sup>]</sup>\n</p>", "<p>BCAAs are often studied collectively due to their shared structural and metabolic features. However, a closer examination reveals both overlapping and distinct roles for individual BCAAs across various age‐related diseases. For instance, dietary restriction of all or each of the three BCAAs results in improved metabolic health, primarily through modulation of FGF21.<sup>[</sup>\n##REF##35526271##\n98\n##, ##REF##33887198##\n99\n##, ##REF##28855637##\n100\n##\n<sup>]</sup> Notably, among BCAAs, isoleucine restriction stands out as the most potent.<sup>[</sup>\n##REF##35526271##\n98\n##, ##REF##33887198##\n99\n##, ##REF##28855637##\n100\n##\n<sup>]</sup> In atherosclerosis, leucine uniquely demonstrates anti‐atherogenic properties through reducing macrophage triglyceride content to decrease macrophage foam cell formation, a critical step in the development of atherosclerosis.<sup>[</sup>\n##REF##29944113##\n101\n##\n<sup>]</sup> In Alzheimer's disease research, a salient decline in circulating valine levels has been consistently documented, and this appears intricately linked to cognitive degeneration.<sup>[</sup>\n##UREF##10##\n90\n##\n<sup>]</sup> While the exact mechanisms underlying this association remain to be elucidated, it is noteworthy that dietary BCAA restriction manifests favorable outcomes, whereas BCAA supplementation appears deleterious in Alzheimer's disease mouse models.<sup>[</sup>\n##UREF##1##\n9\n##\n<sup>]</sup> Given the intricacies of these findings, further research is essential to unravel both the collective and distinct roles played by each BCAA in the context of age‐related disorders.</p>", "<p>Although they did not report BCAAs’ specific role in inducing the SASP, previous studies have shown these amino acids’ involvement in various age‐ and inflammation‐related diseases. For example, deletion of SLC6A15 has been shown to improve motor performance in aged mice<sup>[</sup>\n##REF##17931606##\n102\n##\n<sup>]</sup> and its expression has been found to positively correlate with neuropathic and inflammatory pain.<sup>[</sup>\n##REF##36291662##\n103\n##\n<sup>]</sup> Similarly, depletion of SLC6A19, another member of the SLC6 family that is enriched in kidney, leads to reduced senescent markers and inflammation in aristolochic acid‐induced kidney injury.<sup>[</sup>\n##UREF##12##\n104\n##\n<sup>]</sup> Additionally, a loss in BCAT1 has been observed in aged mouse brains and Alzheimer's disease models,<sup>[</sup>\n##REF##29802157##\n105\n##\n<sup>]</sup> while its knockdown has been reported to cause Parkinson's disease‐like progressive motor deficits and neurodegeneration with age in <italic toggle=\"yes\">Caenorhabditis elegans</italic>.<sup>[</sup>\n##REF##33024014##\n106\n##\n<sup>]</sup> These findings support our discovery that enhanced BCAA transporter expression or reduced BCAA catabolism promotes senescence and inflammation. In addition, we observed that the expression of BCAA regulators correlates with inflammation signatures in multiple aged human tissues. Therefore, small molecules that enhance BCAA catabolism<sup>[</sup>\n##REF##24895126##\n107\n##\n<sup>]</sup> or inhibit BCAA transporters<sup>[</sup>\n##REF##25318072##\n61\n##, ##REF##18522536##\n108\n##\n<sup>]</sup> should be investigated for their potential efficacy in treating various age‐related and inflammatory conditions.</p>", "<p>While our study provides new insights into the role of BCAA regulators in the SASP and their impact on senescence‐associated inflammation, it is important to acknowledge its limitations. BCAA regulators may have additional roles in the aging process by modulating various signaling pathways.<sup>[</sup>\n##REF##26620638##\n109\n##\n<sup>]</sup> For example, recent research revealed that BCAT regulates isoleucine abundance in neurons to influence the feeling of hunger and affect the lifespan of fruit flies.<sup>[</sup>\n##UREF##9##\n79\n##\n<sup>]</sup> Moreover, SLC6A15 knockdown was shown to impact appetite and weight gain in mice,<sup>[</sup>\n##REF##24023709##\n110\n##\n<sup>]</sup> which may affect their life span and metabolic health in the long term. These findings highlight the need for further research to explore the complex roles of BCAA regulators in organismal aging. These complexities notwithstanding, our findings uncover an essential role for intrinsic metabolic reprogramming, leading to BCAA accumulation, in establishing the pro‐inflammatory SASP upon senescence induction, with important implications for human aging and inflammation‐related diseases.</p>" ]
[]
[ "<title>Abstract</title>", "<p>The essential branched‐chain amino acids (BCAAs) leucine, isoleucine, and valine play critical roles in protein synthesis and energy metabolism. Despite their widespread use as nutritional supplements, BCAAs’ full effects on mammalian physiology remain uncertain due to the complexities of BCAA metabolic regulation. Here a novel mechanism linking intrinsic alterations in BCAA metabolism is identified to cellular senescence and the senescence‐associated secretory phenotype (SASP), both of which contribute to organismal aging and inflammation‐related diseases. Altered BCAA metabolism driving the SASP is mediated by robust activation of the BCAA transporters Solute Carrier Family 6 Members 14 and 15 as well as downregulation of the catabolic enzyme BCAA transaminase 1 during onset of cellular senescence, leading to highly elevated intracellular BCAA levels in senescent cells. This, in turn, activates the mammalian target of rapamycin complex 1 (mTORC1) to establish the full SASP program. Transgenic <italic toggle=\"yes\">Drosophila</italic> models further indicate that orthologous BCAA regulators are involved in the induction of cellular senescence and age‐related phenotypes in flies, suggesting evolutionary conservation of this metabolic pathway during aging. Finally, experimentally blocking BCAA accumulation attenuates the inflammatory response in a mouse senescence model, highlighting the therapeutic potential of modulating BCAA metabolism for the treatment of age‐related and inflammatory diseases.</p>", "<p>Upregulation of the branched‐chain amino acid (BCAA) transporters, solute carrier Family 6 member 14/15 (SLC6A14/15), coupled with the downregulation of the catabolic enzyme BCAA transaminase 1 (BCAT1), drives the establishment of senescence‐associated secreted phenotypes (SASP) through BCAA–mammalian target of rapamycin complex 1 (mTORC1) signaling pathway in cellular senescence and promotes senescence‐related inflammatory responses in fruit flies and mice.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6749-cit-0117\">\n<string-name>\n<given-names>Y.</given-names>\n<surname>Liang</surname>\n</string-name>, <string-name>\n<given-names>C.</given-names>\n<surname>Pan</surname>\n</string-name>, <string-name>\n<given-names>T.</given-names>\n<surname>Yin</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>X.</given-names>\n<surname>Gao</surname>\n</string-name>, <string-name>\n<given-names>E.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Quang</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Huang</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Tan</surname>\n</string-name>, <string-name>\n<given-names>K.</given-names>\n<surname>Xiang</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Wang</surname>\n</string-name>, <string-name>\n<given-names>P. B.</given-names>\n<surname>Alexander</surname>\n</string-name>, <string-name>\n<given-names>Q.‐J.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>T.‐P.</given-names>\n<surname>Yao</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Zhang</surname>\n</string-name>, <string-name>\n<given-names>X.‐F.</given-names>\n<surname>Wang</surname>\n</string-name>, <article-title>Branched‐Chain Amino Acid Accumulation Fuels the Senescence‐Associated Secretory Phenotype</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2303489</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202303489</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Experimental Section</title>", "<title>Cell Culture</title>", "<p>Human IMR90 lung diploid fibroblasts and HEK293T cells were purchased from Duke University's Cell Culture Facility (originally from American Type Culture Collection (ATCC). Normal human bronchial epithelial (NHBE) cells derived from healthy donors were purchased from LONZA. IMR90 cells were cultured in Eagle's minimum essential medium (MEM) supplemented with 10% fetal bovine serum (FBS), 1 x MEM non‐essential amino acids, 1 × 10<sup>‐3</sup>\n<sc>m</sc> pyruvate, and 100 U mL<sup>‐1</sup> penicillin‐streptomycin. HEK293T cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented 10% fetal bovine serum (FBS) and 100 U mL<sup>‐1</sup> penicillin‐streptomycin. NHBE cells were cultured in basal epithelial growth medium (BEGM). All cells were maintained at 37 °C incubator with 5% CO<sub>2</sub>.</p>", "<title>Plasmids</title>", "<p>ShRNA vectors targeting SLC6A15 and DEPDC5 were purchased from Sigma‐Aldrich. Coding sequences of human SLC6A14, SLC6A15, and BCAT1 were subcloned into pSIN‐lentiviral vector using Gibson Assembly Master Mix kit (E2611S, NEB). The CDS sequences of human HRasV12 were inserted into the lentiviral vector pCDH‐TetOne‐MCS‐EF1‐Puro.<sup>[</sup>\n##REF##29808012##\n49\n##\n<sup>]</sup> PAX2 (Addgene, 12 260) and VSV‐G (Addgene, 12 259) were gifts from D. Trono. The shRNA targeting sequences and the primers used for cloning were provided in Table ##SUPPL##0##S1## (Supporting Information).</p>", "<title>Stable Cell Lines</title>", "<p>HEK293T cells were seeded and transfected with lentiviral plasmids together with PAX2 and VSV‐G using Lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer's protocol. Virus‐containing media were collected 48 hours post‐transfection and filtered using 0.45 × 10<sup>‐6</sup>\n<sc>m</sc> PVDF filters to remove cells. These media were used to infect target cells for 12 hours. Two days later, infected cells were subjected to puromycin treatment for 2 to 4 d to establish stable lines.</p>", "<title>RT‐qPCR</title>", "<p>Total RNA was extracted using RNeasy Mini Kit (QIAGEN). Equal amounts of RNA were reverse transcribed using the iScript gDNA Clear cDNA Synthesis Kit (Bio‐Rad). Synthesized cDNA was analyzed by quantitative PCR with SYBR Green (Roche). Primer sequences for all tested genes are provided in Table ##SUPPL##0##S2## (Supporting Information).</p>", "<title>Western Blotting and Antibodies</title>", "<p>Cell pellets were lysed using RIPA buffer with protease and phosphatase inhibitor cocktails (Thermo Fisher Scientific) and 1% SDS. The resulting cell lysates were boiled for 10 min, and protein concentrations were determined by BCA Protein Assay (Thermo Fisher Scientific). Volumes were adjusted to ensure that all samples had equivalent protein concentrations, and samples were boiled in 1x loading and reducing buffer (Thermo Fisher Scientific). Samples were loaded onto denaturing SDS polyacrylamide gels and separated proteins were transferred onto polyvinylidene difluoride membranes. Membranes were blocked with 5% BSA in TBS buffer and then incubated with primary antibodies overnight. Corresponding HRP‐conjugated secondary antibodies and chemiluminescent horseradish peroxidase substrate (Thermo Fisher Scientific) were used for signal detection.</p>", "<p>Antibodies used in this study are as follows: Beta Actin (Proteintech, 66009‐1‐Ig, 1:5000), p16 (BD, 551154, 1:1000), p21 (Cell Signaling, 2947, 1:1000), p21 (Mouse Preferred) (Cell Signaling, 64016, 1:1000), IL‐6 (Cell Signaling, 12153, 1:1000), IL‐8 (Abcam, ab18672 1:1000), Ras (G12V Mutant Specific) (Cell Signaling, 14412, 1:1000), SLC6A14 (Sigma‐Aldrich, HPA003193, 1:1000), SLC6A15 (Abcam, ab191192, 1:1000), BCAT1 (Proteintech, 13640‐1‐AP, 1:1000), BCAT2 (Proteintech, 16417‐1‐AP, 1:1000), Lamin B1 (Proteintech, 12987‐1‐AP, 1:1000), Phospho‐p70 S6 Kinase (Cell Signaling, 9205, 1:1000), p70 S6 Kinase (Cell Signaling, 2708, 1:1000), Phospho‐S6 Ribosomal Protein (Ser240/244) (Cell Signaling, 5364, 1:1000), S6 Ribosomal Protein (Cell Signaling, 2317, 1:1000), Phospho‐4E‐BP1 (Thr37/46) (Cell Signaling, 2855, 1:1000), 4E‐BP1 (Cell Signaling, 9644, 1:1000), Dacapo (<italic toggle=\"yes\">d</italic>p21)(Developmental Studies Hybridoma Bank, NP1, AB_10805540), Anti‐mouse HRP (Cell Signaling, 7076, 1:5000), Anti‐Rabbit HRP (Thermo Fisher, G‐21234, 1:5000).</p>", "<title>IHC Staining</title>", "<p>Mouse liver tissues were collected and fixed in 10% formalin overnight and then embedded in paraffin and sectioned into 8 µm slices. Slides were deparaffinized and rehydrated in graded ethanol followed by antigen retrieval in Decloaker buffer (Biocare Medical). Next, slides were treated with 3% H<sub>2</sub>O<sub>2</sub> to block endogenous peroxidase activity. 5% BSA was then used to block non‐specific binding. Primary antibodies were added and incubated overnight. After 3 washes with TBST, corresponding secondary antibodies were added and incubated for 1 h. DAB substrate (Dako) and Vibrant Red (Cell Signaling) were used to detect signals, and hematoxylin (Vector Laboratories) was used to stain the nucleus. Images were taken under an Olympus CK40 microscope (Center Valley). The following primary antibodies were used for IHC staining: Ras (G12V Mutant Specific) (Cell Signaling, 14412, 1:100), CD45 (BioLegend, 103101, 1:100), Anti‐Rabbit HRP (Dako, K4003), Anti‐Rat (Invitrogen, A18868, 1:100).</p>", "<title>Induction of Senescence and SA‐β‐Gal Assays</title>", "<p>Induction of senescence was performed as described previously.<sup>[</sup>\n##REF##29808012##\n49\n##\n<sup>]</sup> Erlotinib‐induced senescence: NHBE were treated with the EGFR inhibitor erlotinib (1 × 10<sup>‐6</sup>\n<sc>m</sc>) for 48 h and then collected at day 7. Oncogene induced senescence: IMR90 cells with Tet‐on HRasV12 were treated with doxycycline (1 µg mL<sup>‐1</sup>) for 9 d. DNA damage‐induced senescence: IMR90 cells were treated with 100 × 10<sup>‐6</sup>\n<sc>m</sc> etoposide for 24 hours to induce DNA damage and then cultured for another 8 d. SA‐β‐Gal assays were conducted using a Senescence‐β‐Galactosidase Staining Kit (Cell Signaling) according to the manufacturer's protocol. In brief, cells were rinsed twice in PBS and fixed with 1 x fixative solution for 5 min. Fixed cells were washed once with PBS and incubated in 1x staining solution with X‐Gal overnight. The staining solution was then removed and switched to 70% glycerol. Photographs were taken using an Olympus CK40 microscope (Center Valley).</p>", "<title>BCAA Analysis</title>", "<p>BCAA levels were measured using a BCAA Assay Kit (Abcam) according to the manufacturer's protocol. Briefly, cells were trypsinized and pelleted. BCAA assay buffer was added to lyse the cells followed by full‐speed centrifugation for 10 min to remove cell debris. Reaction reagents were mixed and added to the cell lysates. After 30 min of incubation, the OD was read using a plate reader at 450 nm. BCAA concentrations were calculated using a standard curve.</p>", "<title>Metabolite Measurements</title>", "<p>Metabolite extraction has been described previously.<sup>[</sup>\n##REF##29590619##\n111\n##\n<sup>]</sup> In brief, equivalent numbers of cells were seeded on six‐well plates and cultured overnight. To extract polar metabolites, 1 mL of prechilled 80% ethanol (HPLC grade) was added to each well after removing the culture medium. The plates were then placed on dry ice and immediately transferred to −80 °C. After incubation for 15 minutes, cells were scraped off with the solvent and transferred to 1.5 mL Eppendorf tube for centrifugation at 20 000 × <italic toggle=\"yes\">g</italic> for 10 min at 4 °C. Next, the resulting supernatant was split into two new tubes and dried in a vacuum concentrator. The dried pellets were reconstituted in 30 µL of sample solvent (water:methanol:acetonitrile, 2:1:1, v/v/v) for analysis by HPLC coupled with Orbitrap Exploris 480 Mass Spectrometer (Thermo). Raw data were analyzed using Compound Discoverer 3.3 software (Thermo).</p>", "<title>Mouse Studies</title>", "<p>Eight‐week‐old female C57BL/6 mice were purchased from Charles River Laboratories. The mice were housed in a temperature‐controlled room (72°F) with a humidity range of 30–70% and a 12 h:12 h light:dark cycle. All animal procedures were conducted following institutional and National Institutes of Health guidelines and approved by Duke University's Animal Care and Use Committee (A044‐23‐02). The research involving animals followed all applicable ethical regulations. The induction of senescence in mouse liver using the Sleeping Beauty transposon system was conducted as described in a previous paper.<sup>[</sup>\n##REF##22080947##\n88\n##\n<sup>]</sup> In brief, 8‐12 weeks old female mice were injected with 80 µg of NRasV12‐GFP‐ShN (or NRasV12‐BCAT1‐SLC6A15_KD, as indicated) and 40 µg of transposase plasmids diluted in Ringer solution through the tail vein (<italic toggle=\"yes\">n</italic> = 5 per group). The volume of Ringer solution used for injection was 10% of the mouse's body weight, not exceeding 2.5 mL if the mouse weighed over 25 grams. Mice were dissected on days 6 and 12 post‐injection, and livers were collected for further analysis.</p>", "<title>Fruit Fly Studies</title>", "<p>Flies were maintained at 22 °C with standard fly food (Archon Scientific). Full‐length <italic toggle=\"yes\">D. melanogaster dSlc6a15‐a</italic> and <italic toggle=\"yes\">dSlc6a15‐b</italic> were cloned into a pPFMW vector by using gateway cloning technology (Thermo) and the resulting plasmids were used to generate transgenic flies (Model System Injections, Duke University). Male transgenic flies were mated with virgin female flies with balancer chromosomes, and offspring with specific phenotypes were selected to generate the stable lines. To study the effects of <italic toggle=\"yes\">dSlc6a15‐a</italic> and <italic toggle=\"yes\">dSlc6a15‐b</italic> on the aging process, stable transgenic flies were crossed with driver lines carrying <italic toggle=\"yes\">actin‐Gal4</italic> and <italic toggle=\"yes\">tubulin‐Gal80<sup>ts</sup>\n</italic> and raised at 18 °C. Hatching flies were collected within 24 h. Male and female flies were separated and transferred to 30 °C with 1SY food<sup>[</sup>\n##REF##24240321##\n112\n##\n<sup>]</sup> after 48 h of mating. For lifespan analysis, female flies were switched into fresh vials daily while dead flies were counted and recorded, <italic toggle=\"yes\">n</italic> = 70–75. For climbing assays, 4 week old female flies were transferred to an empty vial with a line drawn 6 centimeters from the bottom, <italic toggle=\"yes\">n</italic> = 30–40. The vial was tapped gently three times to ensure all flies were on the bottom and kept vertically for about 15 s. Videos were then recorded to analyze the number of flies crossing the 6 cm line within 10 s. The assay was repeated three times and averages were calculated.</p>", "<title>Signaling Pathway Analysis</title>", "<p>Microarray expression datasets for proliferative cells and erlotinib‐induced senescent cells were downloaded from GSE100014.<sup>[</sup>\n##REF##29808012##\n49\n##\n<sup>]</sup> The differential expression analysis between proliferating and senescent cells was performed by limma (V 3.54.2).<sup>[</sup>\n##REF##25605792##\n113\n##\n<sup>]</sup> Gene set enrichment analysis (GSEA) was performed using the R package cluster Profiler (V 4.2.2),<sup>[</sup>\n##REF##34557778##\n114\n##\n<sup>]</sup> based on the metric of ‐log(<italic toggle=\"yes\">P</italic> value)*sign(log2 fold change), and the pathway of interests were retrieved from gsea‐msigdb online repository. <italic toggle=\"yes\">P</italic>‐values in the ridgeplot were corrected using the Benjamini‐Hochberg method.</p>", "<title>GSVA and Correlation Analysis</title>", "<p>To investigate the correlation between the BCAA regulators and the SASP signature, we performed GSVA<sup>[</sup>\n##REF##23323831##\n115\n##\n<sup>]</sup> for the SASP genes. Thirty prominent SASP factors<sup>[</sup>\n##UREF##13##\n116\n##\n<sup>]</sup> (Table ##SUPPL##0##S3##, Supporting Information) were used to generate a gene set and queried its score in different tissues present in GTEx.<sup>[</sup>\n##REF##23715323##\n89\n##\n<sup>]</sup> Human donors with ages greater than 60 were characterized as “aged” and included into the analysis. The correlation test between the GSVA score and the gene of interest was carried out by Pearson correlation.</p>", "<title>Code Availability</title>", "<p>Microarray data retrieval, differential expression analysis, GSEA analysis, GSVA analysis, and signature correlation were performed using R package.</p>", "<title>Statistical Analysis</title>", "<p>The ImageJ software was used to measure the band intensity for western blotting quantitation. RT‐qPCR and western blot signals were normalized to housekeeping genes/proteins, <italic toggle=\"yes\">n</italic> = 3. BCAA concentrations were normalized by cell numbers, <italic toggle=\"yes\">n</italic> = 3. Further data statistical analyses were conducted using GraphPad Prism software. Significance of results was determined by unpaired two‐tailed student's t‐test, one‐way Analysis of Variance (ANOVA) with Dunnett's multiple comparisons, or Two‐way ANOVA with Tukey's multiple comparisons as indicated in the figure legends. Fly survival was analyzed by Log‐rank (Mantel‐Cox) test, <italic toggle=\"yes\">n</italic> = 70–75. For the climbing assay, data were analyzed by one‐way ANOVA with Dunnett's multiple comparisons, <italic toggle=\"yes\">n</italic> = 30–40. For mouse studies, data were analyzed with a two‐tailed Student's t‐test, <italic toggle=\"yes\">n</italic> = 5. Data were presented as mean ± SD, <italic toggle=\"yes\">P</italic> values below 0.05 were considered statistically significant and are represented in the figures by asterisks, where * denotes <italic toggle=\"yes\">P</italic> &lt; 0.05, ** denotes <italic toggle=\"yes\">P</italic> &lt; 0.01, *** denotes <italic toggle=\"yes\">P</italic> &lt; 0.001, and **** denotes <italic toggle=\"yes\">P</italic> &lt; 0.0001. All of the experiments were repeated with a minimum of two independent repeats with similar results unless otherwise noted.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>X.F.W., P.B.A., and Y.L. conceived the project. Y.L. performed the majority of the experiments. C.P. contributed to the establishment of in vitro cellular senescence models. T.Y. performed the hydrodynamic tail vein injection. L.W. and Z.Z. contributed to the generation of transgenic flies. X.G. and H.Q. performed HPLC‐MS analysis. E.W. performed the bioinformatic analysis. D.H., L.T., and K.X. contributed to cell culture experiments. Y.W. contributed to the construction of Sleeping Beauty transposon system. Q.J.L. and T.P.Y. contributed to data analysis and experimental design. X.F.W., P.B.A., and Y.L. composed the manuscript. All authors discussed the results and reviewed the manuscript.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>The authors thank Drs. Kris C. Wood, and Lifeng Yuan for valuable discussions and suggestions. This work was supported by CA244564 and GM144497 from the NCI (NIH) and NIGMS (NIH) to X.F.W. and T.P.Y., GM141018 from the NIGMS (NIH) to Z.Z., CA237618 (NCI) and Cancer Prevention and Research Institute of Texas Scholar Award (PR210056) to X.G.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available in the supplementary material of this article.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6749-fig-0001\"><label>Figure 1</label><caption><p>Altered BCAA metabolism in senescent cells. a) Altered amino acid metabolic pathways in senescent NHBE cells. b) Top differentially expressed genes in amino acid‐related metabolic pathways between senescent NHBE cells and proliferative cells. c) Immunoblots and d) RT‐qPCR showing increased SLC6A14 and decreased BCAT1 in senescent NHBE cells. Cells were induced to senescence by treatment with the EGFR inhibitor erlotinib (1 × 10<sup>‐6</sup>\n<sc>m</sc>). e,f) Increased SLC6A15 and reduced BCAT1 in oncogene‐induced senescence. IMR90 cells with Tet‐on HRasV12 were treated with doxycycline (1 µg mL<sup>‐1</sup>) for 9 d. g,h) Increased SLC6A15 and reduced BCAT1 in DNA damage‐induced senescence. IMR90 cells were treated with 100 × 10<sup>‐6</sup>\n<sc>m</sc> etoposide for 24 h to induce DNA damage and then cultured for another 8 d. i,j) Increased SLC6A15 and reduced BCAT1 in replicative senescence. Early (passage doubling: 38) and late passage (passage doubling: 78) IMR90 cells were collected for immunoblotting and RT‐qPCR. d,f,h,j) <italic toggle=\"yes\">n</italic> = 3, mean ± SD, two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.05, ***<italic toggle=\"yes\">P</italic> &lt; 0.001. SLC6A14: solute carrier family 6 member 14; CLIC3: chloride intracellular channel 3; ASS1: argininosuccinate synthetase 1; OCA2: oculocutaneous albinism II; KMO: kynurenine 3‐monooxygenase; BCAT1: branched chain amino acid transaminase 1; CHAC1: ChaC glutathione specific gamma‐glutamylcyclotransferase 1; DDAH1: dimethylarginine dimethylaminohydrolase 1; PFAS: phosphoribosylformyl‐glycinamidine synthase; SLC39A8: solute carrier family 39 member 8; SLC6A15: solute carrier family 6 member 15; CDKN1A(p21): cyclin dependent kinase inhibitor 1A; CDKN2A(p16): cyclin dependent kinase inhibitor 2A; ACTB: actin beta; HRasV12: HRas proto‐oncogene with G12V mutation.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6749-fig-0002\"><label>Figure 2</label><caption><p>SLC6A15 and BCAT1 regulate the SASP. a,c) Immunoblots showing that a) SLC6A15 knockdown or c) BCAT1 overexpression impairs expression of IL6 and IL8 in oncogene‐induced senescence. IMR90 cells with Tet‐on HRasV12 were treated with doxycycline (1 µg mL<sup>‐1</sup>) for 9 d to induce senescence. Cells were infected with lentivirus to express ShN, SLC6A15 shRNA, GFP, or BCAT1, as indicated. b) RT‐qPCR analysis showing that SLC6A15 knockdown inhibits IL6 and IL8 expression in oncogene‐induced senescence. <italic toggle=\"yes\">n</italic> = 3, mean ± SD, one‐way ANOVA test with Dunnett's multiple comparisons, *<italic toggle=\"yes\">P</italic> &lt; 0.05, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001. d) SLC6A15 knockdown or e) BCAT1 overexpression impairs the expression of IL6 and IL8 in DNA damage‐induced senescence. IMR90 cells were treated with 100 × 10<sup>‐6</sup>\n<sc>m</sc> etoposide for 24 h and cultured for 8 d before collecting samples. Cells were infected with lentivirus to express ShN, SLC6A15 shRNA, GFP, or BCAT1, as indicated. Eto.: Etoposide; IL6: interleukin 6; IL8: interleukin 8.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6749-fig-0003\"><label>Figure 3</label><caption><p>BCAA accumulation drives the SASP by activating mTORC1 signaling. BCAA metabolite assay showing that intracellular BCAA levels increase in a) replicative, b) oncogene‐induced, and c) DNA damage‐induced senescence. Relative BCAA levels were quantified by normalizing to cell number and then to the proliferative control for each condition. d) SLC6A14 or SLC6A15 overexpression increases intracellular BCAA levels in HEK293T cells. e) BCAT1 knockdown in HEK293T cells increases intracellular BCAA levels. a–e) <italic toggle=\"yes\">n</italic> = 3, mean ± SD, a) two‐tailed Student's t‐test or b–e) one‐way ANOVA test with Dunnett's multiple comparisons. *<italic toggle=\"yes\">P</italic> &lt; 0.05, ***<italic toggle=\"yes\">P</italic> &lt; 0.001, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001, ns, not significant. f) SLC6A15 knockdown impairs BCAA accumulation in senescent IMR90 cells. g) BCAT1 rescue impairs BCAA accumulation in senescent IMR90 cells. f,g) <italic toggle=\"yes\">n</italic> = 3, mean ± SD, two‐way ANOVA test with Tukey's multiple comparisons. **<italic toggle=\"yes\">P</italic> &lt; 0.01, ****<italic toggle=\"yes\">P</italic> &lt; 0.0001. h) SLC6A15 knockdown or i) BCAT1 overexpression inhibits mTORC1 activation. j,k,m) mTORC1 activation via DEPDC5 knockdown rescues SASP production in j,m) SLC6A15‐depleted or k) BCAT‐overexpressing senescent cells. m) <italic toggle=\"yes\">n</italic> = 3, mean ± SD, two‐way ANOVA test with Tukey's multiple comparisons. The symbol “#” indicates statistical significance (<italic toggle=\"yes\">P</italic> &lt; 0.05) compared to the HRasV12‐ShN‐ShN group. l) Schematic of BCAA‐dependent SASP induction. Increase amino acid transport through SLC6A14 or SLC6A15 together with reduced BCAT1‐mediated catabolism leads to BCAA accumulation in senescent cells. BCAA buildup then activates mTORC1 signaling to promote SASP factor production. RS: replicative senescence; p4EBP(T37/46): eukaryotic translation initiation factor 4E‐binding protein 1 phosphorylated at threonine 37 and/or threonine 46; 4EBP: eukaryotic translation initiation factor 4E‐binding protein 1; pS6RP(S240/244): S6 ribosomal protein phosphorylated at serine 240 and serine 244; S6RP: S6 ribosomal protein; DEPDC5: DEP domain–containing 5; IL1A: interleukin 1 alpha; IL1B: interleukin 1 beta; CXCL1: chemokine (C‐X‐C motif) ligand 1; CXCL2: chemokine (C‐X‐C motif) ligand 2.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6749-fig-0004\"><label>Figure 4</label><caption><p>BCAA metabolism regulates cellular senescence and age‐related phenotypes in <italic toggle=\"yes\">Drosophila</italic>. a) Overexpression of dSlc6a15‐a or b) dSlc6a15‐b in transgenic fruit flies using the actin‐Gal4/UAS system. <italic toggle=\"yes\">n</italic> = 3, mean ± SD, two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01. c) dSlc6a15‐a or dSlc6a15‐b overexpression shortens fly lifespans and d) impairs climbing ability in 4‐week‐old female flies. c) <italic toggle=\"yes\">n</italic> = 70–75, log‐rank test, ***<italic toggle=\"yes\">P</italic> &lt; 0.001. d) <italic toggle=\"yes\">n</italic> = 30–40, One‐way ANOVA, *<italic toggle=\"yes\">P</italic> &lt; 0.05, **** <italic toggle=\"yes\">P</italic> &lt; 0.0001. e–g) dSlc6a15‐a or dSlc6a15‐b overexpression induces expression of e) <italic toggle=\"yes\">Drosophila</italic> dacapo (dp21), f) Upd2, and g) multiple antimicrobial peptides. <italic toggle=\"yes\">n</italic> = 3, mean ± SD. SE: short exposure; LE: long exposure; Upd2: Unpaired 2; Attc: Attacin‐C; CecA1: Cecropin A1; CecA2: Cecropin A2; CecB: Cecropin B; Mtk: Metchnikowin; DptA: Diptericin A; DptB: Diptericin B; Dro: Drosocin.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6749-fig-0005\"><label>Figure 5</label><caption><p>BCAA inhibition abrogates SASP factor production and senescent cell immune clearance in mice. Schematic illustrations of a) sleeping‐beauty transposon plasmids and b) experimental design. c) RT‐qPCR analysis showing that BCAT1 overexpression and SLC6A15 knockdown reduce SASP factor expression and immune cell markers on day 6. Representative images and quantification of liver tissue immunohistochemical staining for NRasV12 (brown) and CD45 (red) expression on d) days 6 and e) 12 in GFP‐ShN control and BCAT1‐15KD groups, as indicated. c–e) <italic toggle=\"yes\">n</italic> = 5, mean ± SD, two‐tailed Student's t‐test. *<italic toggle=\"yes\">P</italic> &lt; 0.05, **<italic toggle=\"yes\">P</italic> &lt; 0.01, ***P &lt; 0.001, ns, not significant. Scale bar = 100 µm. IR: inverted repeat; NRasV12: NRas proto‐oncogene with G12V mutation; EF1: elongation factor‐1 promoter; PGK: phosphoglycerate kinase promoter; U6: U6 promoter; Il6: interleukin 6; Il1a: interleukin 1 alpha; Il1b: interleukin 1 beta; Tnf: tumor necrosis factor; Ptprc: protein tyrosine phosphatase receptor type c; CD45: protein tyrosine phosphatase receptor type C.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6749-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2303489-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
116
CC BY
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2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 15; 11(2):2303489
oa_package/6a/c6/PMC10787106.tar.gz
PMC10787107
37922524
[ "<title>Introduction</title>", "<p>The search for materials with high ionic mobility and diffusivity, so‐called fast ionic conductors (FICs), remains an ongoing quest. FICs are essential components for electrochemical energy conversion devices, such as solid oxide fuel cells, electrolyzers, and solid‐state batteries.<sup>[</sup>\n##UREF##0##\n1\n##, ##UREF##1##\n2\n##, ##UREF##2##\n3\n##\n<sup>]</sup> The commercialization of these devices could constitute important aspects of the development of green energy. All of these applications require high ionic conductivity. To achieve these objectives, it is crucial to fully understand the peculiarities in ion transport mechanisms. The temperature dependence of ionic conductivity in solids often follows the Arrhenius law, which is characterized by constant activation energy and prefactor,<sup>[</sup>\n##UREF##3##\n4\n##\n<sup>]</sup> written as:\nwhere σ is the conductivity, <italic toggle=\"yes\">T</italic> is the temperature, σ<sub>0</sub> is the prefactor, <italic toggle=\"yes\">E</italic>\n<sub>a</sub> is the activation energy, and <italic toggle=\"yes\">k</italic>\n<sub>B</sub> is the Boltzmann constant.</p>", "<p>It is frequently assumed that decreasing the activation energy (lowering the activation barrier) of ionic conductors will improve their conductivity. However, the improvement in ionic conductivity due to the reduced activation energy may be less than expected, because the prefactor is also lower, and compensates the decrease in activation energy. In some cases, the ionic conductivity is even lower when the activation energy is reduced.<sup>[</sup>\n##UREF##4##\n5\n##\n<sup>]</sup> Since the 1920s, numerous examples of such compensation have been found. This compensation effect in the prefactor is found to be proportional to <italic toggle=\"yes\">E<sub>a</sub>\n</italic>, or to Δ<italic toggle=\"yes\">H</italic>, the activation enthalpy.<sup>[</sup>\n##UREF##5##\n6\n##, ##UREF##6##\n7\n##, ##UREF##7##\n8\n##, ##REF##18518230##\n9\n##, ##UREF##8##\n10\n##, ##UREF##9##\n11\n##\n<sup>]</sup> This results in the intersection of the Arrhenius plots for different activation energies of related samples at an isokinetic temperature. This observation is sufficiently common to be called<sup>[</sup>\n##UREF##8##\n10\n##\n<sup>]</sup> the compensation law (compensation effect<sup>[</sup>\n##UREF##10##\n12\n##\n<sup>]</sup>), the isokinetic law, and the MNR, for the authors who reported its observation in disordered solids.<sup>[</sup>\n##UREF##7##\n8\n##\n<sup>]</sup> In particular, such an effect is frequently observed in electronic and ion conduction and in atomic and ionic diffusion.<sup>[</sup>\n##REF##30981228##\n13\n##, ##UREF##11##\n14\n##, ##REF##32022546##\n15\n##, ##UREF##12##\n16\n##, ##UREF##13##\n17\n##, ##UREF##14##\n18\n##, ##UREF##15##\n19\n##\n<sup>]</sup>\n<bold>Figure</bold>\n##FIG##0##\n1a## shows an example Arrhenius plot for conductivity of garnet‐structured lithium ionic conductors Li<sub>6</sub>MLa<sub>2</sub>Ta<sub>2</sub>O<sub>12</sub> (M = Ba, Ca, Sr, and Sr<sub>0.5</sub>Ba<sub>0.5</sub>) with variations of dopant or dopant concentration. In terms of Equation (##FORMU##0##1##), with logarithm applied, we may write</p>", "<p>\nwhere σ<sub>00</sub> is the isokinetic prefactor, which is determined by parameters related to elementary ion hopping in FICs, and is discussed in detail in Section <xref rid=\"advs6678-sec-0060\" ref-type=\"sec\">6</xref>. <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> is the isokinetic temperature, and <italic toggle=\"yes\">k<sub>B</sub>T<sub>iso</sub>\n</italic> is also known as Meyer‐Neldel energy, sometimes denoted as Δ<sub>0</sub>.</p>", "<p>The activation energy and prefactor are determined from the slope and intercept of the Arrhenius plot, as shown in Figure ##FIG##0##1a##.The point of isokinetic temperature is also shown in Figure ##FIG##0##1a##. By fitting the prefactor as a function of activation energy using Equation (##FORMU##1##2##), that is, the Meyer‐Neldel plot (M‐N plot), as shown for the garnet family Li<sub>6</sub>MLa<sub>2</sub>Ta<sub>2</sub>O<sub>12</sub> in Figure ##FIG##0##1b##, <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> is obtained from the inverse slope of the linear least square fit to the data, as discussed below.</p>", "<p>The MNR indicates that when the activation energy changes, the prefactor changes accordingly, compensating for the change in activation energy, reducing the improvement in conductivity. Therefore, researchers have been trying to break the limitation of the MNR<sup>[</sup>\n##UREF##17##\n21\n##\n<sup>]</sup> or look for materials which do not show a compensation effect.<sup>[</sup>\n##UREF##18##\n22\n##\n<sup>]</sup> However, since the ionic conductivity is affected by multiple factors related to the material structure, a comprehensive understanding of the MNR in ion transport has been challenging.</p>", "<p>Here, we review the contribution of entropy and lattice dynamics to the ionic conductivity within the framework of the MNR. After briefly introduce the physical meaning of the MNR and the condition under which this rule is applied, we then discuss the material parameters that determine the isokinetic prefactor based on the fundamental physics of ion transport, and the effort to apply the MNR to improving the ionic conductivity by controlling the isokinetic temperature. Then we evaluate the approaches to determination of the isokinetic temperature, and the relationship between lattice vibration and isokinetic temperature. Finally, we investigate the origin of the relationship between isokinetic temperature and isokinetic prefactor and examine the mechanism of conductivity in FICs.</p>" ]
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[ "<title>Conclusion</title>", "<p>It has been shown that MNR is the result of entropy‐enthalpy compensation, and it has been proposed that multi‐excitation entropy, MEE compensates the lack of thermal energy to overcome the energy barrier to ion transport in FICs. Within this framework, the dependence of Arrhenius prefactor on the activation energy may be applied to closely related systems, in which the material parameters, including mobile ion concentration, ion jump distance, and attempt frequency, do not differ greatly. Applying these constraints, we have investigated the roles of entropy, of isokinetic temperature, <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, and the contribution of lattice dynamics in the ion transport processes in FICs.</p>", "<p>The value of operating temperature <italic toggle=\"yes\">T</italic> compared to <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> determines the strategy for improving the conductivity by tuning the activation energy. When <italic toggle=\"yes\">T</italic> &lt; <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, the conductivity can be improved by decreasing the activation energy. When <italic toggle=\"yes\">T</italic> &gt; <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, it can be improved by increasing it. Since MNR applies to closely related systems, caution must be taken to determine its value. <italic toggle=\"yes\">T</italic>\n<sub>\n<italic toggle=\"yes\">iso</italic>\n</sub> may be determined experimentally, using an Arrhenius plot or a M‐N plot, using Equation (##FORMU##1##2##). The pressure‐tuning method is an effective approach for measuring <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> in FICs. Controlling its value remains challenging, due to the lack of theoretical models. The MEE model suggests that <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> is proportional to the excitation phonon frequency, given by Equation (##FORMU##15##16##). The general validity of this prediction, in particular its applicability to FICs continues to be investigated.</p>", "<p>Finally, we have proposed that for FICs, the critical energy <italic toggle=\"yes\">E<sub>n</sub>\n</italic>, determined from the relationship between isokinetic prefactor σ<sub>00</sub> and isokinetic temperature <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, is related to the configurational entropy change between the initial and transition sites. A positive <italic toggle=\"yes\">E<sub>n</sub>\n</italic> suggests that the charge carriers behave as polarons. The new understanding will add insights to develop new FICs.</p>" ]
[ "<title>Abstract</title>", "<p>Ion transport in crystalline solids is an essential process for many electrochemical energy converters such as solid‐state batteries and fuel cells. Empirical data have shown that ion transport in crystal lattices obeys the Meyer‐Neldel Rule (MNR). For similar, closely related materials, when the material properties are changed by doping or by strain, the measured ionic conductivities showing different activation energies intersect on the Arrhenius plot, at an isokinetic temperature. Therefore, the isokinetic temperature is a critical parameter for improving the ionic conductivity. However, a comprehensive understanding of the fundamental mechanism of MNR in ion transport is lacking. Here the physical significance and applicability of MNR is discussed, that is, of activation entropy‐enthalpy compensation, in crystalline fast ionic conductors, and the methods for determining the isokinetic temperature. Lattice vibrations provide the excitation energy for the ions to overcome the activation barrier. The multi‐excitation entropy model suggests that isokinetic temperature can be tuned by modulating the excitation phonon frequency. The relationship between isokinetic temperature and isokinetic prefactor can provide information concerning conductivity mechanisms. The need to effectively determine the isokinetic temperature for accelerating the design of new fast ionic conductors with high conductivity is highlighted.</p>", "<p>Ionic conductivities in crystal lattices often obey the Meyer‐Neldel Rule, that is, the entropy‐enthalpy compensation. In closely related materials, the ionic conductivities showing different activation energies intersect on the Arrhenius plot, at an isokinetic temperature. Here, the physical significance and applicability of is compensation effect in fast ionic conductors are discussed, and the methods for determining the isokinetic temperature.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6678-cit-0069\">\n<string-name>\n<given-names>P.</given-names>\n<surname>Du</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Zhu</surname>\n</string-name>, <string-name>\n<given-names>A.</given-names>\n<surname>Braun</surname>\n</string-name>, <string-name>\n<given-names>A.</given-names>\n<surname>Yelon</surname>\n</string-name>, <string-name>\n<given-names>Q.</given-names>\n<surname>Chen</surname>\n</string-name>, <article-title>Entropy and Isokinetic Temperature in Fast Ion Transport</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2305065</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202305065</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Activation Entropy and Isokinetic Temperature in MNR</title>", "<p>It has been known since the work of Eyring<sup>[</sup>\n##UREF##19##\n23\n##\n<sup>]</sup> in the 1920s, that a more rigorous form of the Arrhenius equation for any activated process is given by\nwhere the free energy of activation, Δ<italic toggle=\"yes\">G</italic>, is given by\n\n</p>", "<p>In Equation (##FORMU##3##4##), Δ<italic toggle=\"yes\">H</italic> and Δ<italic toggle=\"yes\">S</italic> are the activation enthalpy and entropy. It has been observed that the activation enthalpy and entropy of chemical reactions often show a linear relation, the slope of which has been defined as the isokinetic temperature. But caution must be practiced to not over‐interpret the outcome of such mathematical construction.<sup>[</sup>\n##UREF##20##\n24\n##, ##UREF##21##\n25\n##, ##UREF##22##\n26\n##\n<sup>]</sup> The activation entropy, Δ<italic toggle=\"yes\">S</italic>, for movement of a carrier, electronic or ionic, called the migration entropy, is expressed as<sup>[</sup>\n##UREF##23##\n27\n##, ##UREF##24##\n28\n##\n<sup>]</sup>\nwhere <mml:math id=\"jats-math-6\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>v</mml:mi><mml:mi>i</mml:mi><mml:mi>I</mml:mi></mml:msubsup></mml:mrow></mml:math> and <mml:math id=\"jats-math-7\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>v</mml:mi><mml:mi>i</mml:mi><mml:mi>S</mml:mi></mml:msubsup></mml:mrow></mml:math> are the vibrational frequencies of the initial state and the transition state of the ion hopping process, respectively. Equation (##FORMU##4##5##) shows that Δ<italic toggle=\"yes\">S</italic> depends only upon the ratio of vibrational distribution functions of the initial and transition states.</p>", "<p>It is now generally recognized<sup>[</sup>\n##UREF##8##\n10\n##\n<sup>]</sup> that MNR occurs in closely related systems. It has recently been shown<sup>[</sup>\n##REF##22555217##\n29\n##\n<sup>]</sup> that it is obeyed when the free energy of the samples considered is a linear function of <italic toggle=\"yes\">T</italic> and of one other physical variable, such as in a structure‐property relationship. We take this to be the condition for “closely related systems”. Further, <mml:math id=\"jats-math-8\" display=\"inline\"><mml:mrow><mml:mrow><mml:mfrac><mml:mn>1</mml:mn><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>s</mml:mi><mml:mi>o</mml:mi></mml:mrow></mml:msub></mml:mfrac><mml:mo>&gt;</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:mrow></mml:math> when Δ<italic toggle=\"yes\">H</italic> is large compared to <italic toggle=\"yes\">k<sub>B</sub>T</italic> and to the excitation energies of the system under study, and that it is an entropic effect. That is, if the process obeys MNR, there is a contribution to Δ<italic toggle=\"yes\">S</italic> that compensates Δ<italic toggle=\"yes\">H</italic>, and is given by:\n\n</p>", "<p>Δ<italic toggle=\"yes\">S<sub>M</sub>\n</italic> has been called multi‐excitation entropy. The multi‐excitation entropy model<sup>[</sup>\n##UREF##8##\n10\n##\n<sup>]</sup> (MEE model) suggests that, when the thermal energy is too small to provide the excitation energy for ion transport, Δ<italic toggle=\"yes\">S<sub>M</sub>\n</italic> is associated with the collected excitations which provide the energy needed in order to overcome the barrier.</p>", "<p>For a given Δ<italic toggle=\"yes\">H</italic>, at low <italic toggle=\"yes\">T</italic>, <italic toggle=\"yes\">X</italic> is larger than it would be if such compensation did not exist. At <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, <italic toggle=\"yes\">X</italic> is independent of Δ<italic toggle=\"yes\">H</italic>. If the data of Figure ##FIG##0##1a##, are extrapolated to <mml:math id=\"jats-math-10\" display=\"inline\"><mml:mrow><mml:mrow><mml:mfrac><mml:mn>1</mml:mn><mml:mi>T</mml:mi></mml:mfrac><mml:mo>=</mml:mo><mml:mn>0</mml:mn></mml:mrow></mml:mrow></mml:math>, we may obtain the log or ln of the experimental prefactors. If the latter is plotted as a function of <italic toggle=\"yes\">E<sub>a</sub>\n</italic>, the inverse slope of the best linear fit yields <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> as in Figure ##FIG##0##1b##, the M‐N plot. As discussed in Section <xref rid=\"advs6678-sec-0050\" ref-type=\"sec\">5</xref>, this is generally a more accurate determination of <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, than can be made from Figure ##FIG##0##1a##. Then, Δ<italic toggle=\"yes\">S<sub>M</sub>\n</italic> can be calculated using Equation (##FORMU##5##6##). However, there may be a contribution to Δ<italic toggle=\"yes\">S</italic> that is independent of Δ<italic toggle=\"yes\">H</italic>, which we call the change of configurational entropy, Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic>, between the transition and initial states. Then\n\n</p>", "<p>It is not generally feasible to accurately calculate Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic> from computational or experimental data. However, a comparison between Li‐ion conductors LiTi<sub>2</sub>(PS<sub>4</sub>)<sub>3</sub> (LTPS) and Li<sub>10</sub>GeP<sub>2</sub>S<sub>12</sub> (LGPS) suggests that a smooth energy landscape can lead to a larger entropy of the transition state.<sup>[</sup>\n##UREF##18##\n22\n##\n<sup>]</sup> Fortunately, we can frequently determine the sign of Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic>.<sup>[</sup>\n##UREF##8##\n10\n##, ##UREF##25##\n30\n##\n<sup>]</sup> In the great majority of experimental circumstances, Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic> is small, or positive. In a typical kinetic process, the disorder, that is, the configurational entropy, of the transition state is likely to be very little different from that of the initial state. The atoms or molecules in a chemical reaction, the mobile species in a diffusion or conduction process can move in many directions. Thus, at some <italic toggle=\"yes\">T</italic> below <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, either Δ<italic toggle=\"yes\">G</italic> becomes zero, so that Arrhenius no longer applies (the process is no longer activated), or the condition <italic toggle=\"yes\">k<sub>B</sub>T</italic> ≪ Δ<italic toggle=\"yes\">H</italic> is no longer valid, so that MNR no longer applies.</p>", "<p>In a small fraction of experiments, most notably on fast ionic conduction, as discussed below, and on relaxation of polymeric glasses,<sup>[</sup>\n##UREF##25##\n30\n##\n<sup>]</sup> Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic> is negative. Then, Δ<italic toggle=\"yes\">G</italic> is negative at <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, that is, the phenomenon continues to be activated, with higher Δ<italic toggle=\"yes\">H</italic> yielding a more rapid process. If the controlling mechanism does not change, and <italic toggle=\"yes\">k<sub>B</sub>T</italic> ≪ Δ<italic toggle=\"yes\">H</italic> continues to be valid, this situation continues until a temperature, approximately:\nis reached, so that Δ<italic toggle=\"yes\">G</italic> becomes zero. For entropy to be lower in the transition than in the initial state, this motion must be constrained. This is precisely the case for the two notable examples of negative Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic> which we have cited. In glass‐forming polymers, a molecule is normally intertwined with its neighbors. For two neighboring molecules to move with respect to each other, most likely they are in a particular relative position. In each of the relaxations of a polymer glass, there are distinct values of <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> and of negative Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic> associated with the molecular segments which move.<sup>[</sup>\n##UREF##25##\n30\n##\n<sup>]</sup> For the relaxation at the highest temperature, α relaxation, for example, large portions of neighboring molecules must be close to parallel.</p>", "<p>It is now well established that FICs, such as perovskite‐type oxides, behave as they do because of particular paths in their crystal structure,<sup>[</sup>\n##REF##31873227##\n31\n##\n<sup>]</sup> through which the ions can move readily. The price of this logistic advantage is their confinement, and the associated low entropy. Their conductivities above <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> may behave in a way which is quite different from that of typical semiconducting or insulating materials, whose carrier densities are activated, and carrier mobilities decrease slowly with <italic toggle=\"yes\">T</italic>. In FICs, both maybe activated.</p>", "<title>Applicability of MNR in Solid State Ionics</title>", "<p>We now examine the fundamental physics of ion transport, in order to understand the effect of MNR, and especially, of <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>\n<sub>,</sub> on ionic conductivity at <italic toggle=\"yes\">T</italic>. The conductivity, σ, is given by:\nwhere <italic toggle=\"yes\">c</italic> is the mobile ion concentration, <italic toggle=\"yes\">q</italic> is the ionic charge, and <italic toggle=\"yes\">μ</italic> is the ionic mobility.</p>", "<p>The ionic mobility <italic toggle=\"yes\">μ</italic> is related to the macroscopic long‐range diffusion coefficient <italic toggle=\"yes\">D</italic>\n<sub>σ</sub> by the Nernst‐Einstein equation:<sup>[</sup>\n##UREF##26##\n32\n##\n<sup>]</sup>\n\n</p>", "<p>The classical model of ion diffusion in solids considers that the ion hopping events are random, that is, the ion hopping direction is independent of the previous hopping direction. This model applies when the ion concentration is low.<sup>[</sup>\n##UREF##27##\n33\n##\n<sup>]</sup> When ion transport is uncorrelated and independent, one can treat <italic toggle=\"yes\">D</italic>\n<sub>σ</sub> as the random diffusion coefficient <italic toggle=\"yes\">D<sub>r</sub>\n</italic>:\nwhere <italic toggle=\"yes\">a</italic> is the ion jump distance, <italic toggle=\"yes\">ν</italic> is the ion jump frequency for successful jumps which leads to macroscopic diffusion, <italic toggle=\"yes\">b</italic> is a geometric factor, for 1D, 2D, or 3D diffusion, <italic toggle=\"yes\">b</italic> is 2, 4, or 6 respectively.</p>", "<p>The ion jump frequency ν is described by:\nwhere ν<sub>0</sub> is the attempt frequency which includes both the successful jumps and unsuccessful jumps.</p>", "<p>According to Equation (##FORMU##8##9##) to Equation (##FORMU##11##12##), the complexity of temperature‐dependent ionic conductivity σ can be mathematically illustrated by:<sup>[</sup>\n##REF##32347715##\n34\n##\n<sup>]</sup>\nwhere the enthalpy Δ<italic toggle=\"yes\">H</italic> is also called activation energy (denoted as <italic toggle=\"yes\">E<sub>a</sub>\n</italic>). Comparing Equation (##FORMU##0##1##), and Equation (##FORMU##12##13##), the prefactor is written as:<sup>[</sup>\n##UREF##4##\n5\n##\n<sup>]</sup>\n\n</p>", "<p>From Equation (##FORMU##13##14##), one may see that, in addition to the entropy, the prefactor is affected by many parameters, including the mobile ion concentration, ion jump distance, and attempt frequency. Therefore, it is worth noting that MNR applies only to “closely related systems”, when the material candidates have similar composition and structure, so that other parameters do not differ much between different samples or for variable measurement parameters, as discussed in the literature on chemical reactions<sup>[</sup>\n##UREF##20##\n24\n##, ##UREF##21##\n25\n##, ##UREF##28##\n35\n##\n<sup>]</sup> and in the previous and following sections. However, when the ion concentration changes, the defect formation energy may also vary, causing changes in the activation energy. The variation in ion concentration adds difficulties to the determination of <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, and may be one reason for the scattering of data. Therefore, we propose that <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> can be more rigorously determined using the diffusion coefficients instead of ionic conductivities, when the influence of concentration is excluded.</p>", "<title>Improving the Ionic Conductivity According to the MNR</title>", "<p>Reducing the activation energy has been considered to be an effective method for improving ionic conductivity. However, the MNR shows that lower activation energy is not always related to high ionic conductivity. Here, we consider how activation energy determines the ionic conductivity according to MNR.</p>", "<p>Because of the entropy‐enthalpy compensation suggested by the MNR, we can use <italic toggle=\"yes\">E<sub>a</sub>\n</italic> to replace Δ<italic toggle=\"yes\">S<sub>M</sub>\n</italic> to formally describe the ionic conductivity. That is, combining Equation (##FORMU##1##2##), Equation (##FORMU##5##6##), Equation (##FORMU##6##7##), and Equation (##FORMU##12##13##), the conductivity becomes:\nwhere <italic toggle=\"yes\">T</italic> is the measurement temperature, or the operating temperature. Equation (##FORMU##14##15##) suggests that the argument <mml:math id=\"jats-math-20\" display=\"inline\"><mml:mrow><mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mfrac><mml:msub><mml:mi>E</mml:mi><mml:mi>a</mml:mi></mml:msub><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:mfrac><mml:mrow><mml:mi>T</mml:mi><mml:mo>−</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>s</mml:mi><mml:mi>o</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>s</mml:mi><mml:mi>o</mml:mi></mml:mrow></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:mrow></mml:math> in the exponent may be considered to be an indicator for modulating the material conductivity. If <italic toggle=\"yes\">T</italic> &gt; <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, the measured conductivity falls in Region I in <bold>Figure</bold>\n##FIG##1##\n2a##. That is, the ionic conductivity is higher when <italic toggle=\"yes\">E<sub>a</sub>\n</italic> is larger. When <italic toggle=\"yes\">T</italic> &lt; <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> and the measured conductivity is located in Region II in Figure ##FIG##1##2b##, it is necessary to decrease <italic toggle=\"yes\">E<sub>a</sub>\n</italic> to improve the ionic conductivity. When <italic toggle=\"yes\">T</italic> = <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>, the conductivity is independent of <italic toggle=\"yes\">E<sub>a</sub>\n</italic>.</p>", "<p>In Figure ##FIG##1##2## we show examples of the behavior described above. In Figure ##FIG##1##2b##, the conductivity of Na<sub>3</sub>PS<sub>4‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Se<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> decreases with the increase of <italic toggle=\"yes\">E<sub>a</sub>\n</italic>, whereas that of Li<sub>1‐3x</sub>Ga<sub>x</sub>Zr<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub> (LGZP) increases with the increase of <italic toggle=\"yes\">E<sub>a</sub>\n</italic> in Figure ##FIG##1##2c##. The <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> of LGZP<sup>[</sup>\n##UREF##29##\n36\n##\n<sup>]</sup> and Na<sub>3</sub>PS<sub>4‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Se<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>\n<sup>[</sup>\n##REF##30284822##\n37\n##\n<sup>]</sup> are presented in <bold>Table</bold>\n##TAB##0##\n1\n##. According to the above discussion, the conductivity of LGZP and Na<sub>3</sub>PS<sub>4‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Se<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> should fall in Region I and Region II of Figure ##FIG##1##2a##, respectively. This is confirmed by the measured conductivity, as shown in Figure ##FIG##1##2b,c##. The proton conductivity of BaZr<sub>0.9</sub>Y<sub>0.1</sub>O<sub>3</sub> under high pressure<sup>[</sup>\n##UREF##30##\n38\n##\n<sup>]</sup> shows the same behavior as in the Na‐ion conductivity of Na<sub>3</sub>PS<sub>4‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Se<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>. More data from various lithium‐ion and proton conductors are presented in Tables ##SUPPL##0##S1## and ##SUPPL##0##S2## (Supporting Information). For most of the materials investigated, <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> is higher than the measurement temperature.</p>", "<p>The activation energy can be affected by multiple factors including crystal symmetry, defects, and lattice softness.<sup>[</sup>\n##REF##32347715##\n34\n##\n<sup>]</sup> For related material systems, the activation energy is lower when the crystal structure exhibits higher symmetry and less disorder. A softer lattice is generally considered to be related to lower activation energy.<sup>[</sup>\n##UREF##17##\n21\n##\n<sup>]</sup> In practice, the activation energy can be tuned by doping,<sup>[</sup>\n##REF##33150740##\n39\n##\n<sup>]</sup> applying strain,<sup>[</sup>\n##UREF##31##\n40\n##\n<sup>]</sup> by modifying the vibration frequency,<sup>[</sup>\n##UREF##17##\n21\n##\n<sup>]</sup> and the density of grain boundaries.<sup>[</sup>\n##UREF##32##\n41\n##\n<sup>]</sup>\n</p>", "<p>Notably, interesting results have been found in recent investigations whose objective was to reduce the activation energy. For instance, in the materials that manifest mobile ion disordering, the frustration in the LTPS framework enlarges the ionic jump distances compared to LGPS.<sup>[</sup>\n##UREF##18##\n22\n##\n<sup>]</sup> As a result, LTPS exhibits a larger prefactor but a lower activation energy, which deviates from the MNR. Thus, the disorder in the material offers an alternative approach to significantly increasing the ionic conductivity.</p>", "<title>Determination and Physical Significance of Isokinetic Temperature in Fast Ion Conductors: The Role of Lattice Vibrations</title>", "<p>In Section <xref rid=\"advs6678-sec-0030\" ref-type=\"sec\">3</xref>, we have suggested that isokinetic temperature is affected by the material structure, lattice parameters, and composition. All these factors vary when the dopant concentration changes, thus makes the determination of isokinetic temperature challenging. Most often, the investigation of MNR of a property of a family of similar materials involves the preparation of a material by different techniques, or of similar composition, for example, by element substitution and doping.<sup>[</sup>\n##UREF##13##\n17\n##, ##REF##33150740##\n39\n##\n<sup>]</sup> Conduction in FICs may also be investigated using a single sample by imposing strain in the material (e.g., with pressure<sup>[</sup>\n##UREF##30##\n38\n##\n<sup>]</sup>). For instance, <bold>Figure</bold>\n##FIG##2##\n3\n## shows a M‐N plot demonstrating the strain‐induced variation in <italic toggle=\"yes\">E<sub>a</sub>\n</italic> and σ<sub>0</sub> under high compressive strain.<sup>[</sup>\n##UREF##33##\n42\n##\n<sup>]</sup> Then <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> is calculated from Equation (##FORMU##1##2##) according to experimental data.</p>", "<p>It is evident from Figure ##FIG##2##3## that under these circumstances, of a single material under varying pressure, MNR is rigorously obeyed, as predicted by Sapunov.<sup>[</sup>\n##UREF##28##\n35\n##\n<sup>]</sup> In contrast, in Figure ##FIG##0##1b##, in which garnets containing different ions are compared, the criterion of “closely related systems” is not completely satisfied. When tuning the material composition, the adjustment in lattice parameters leads to changes in migration entropy. We cannot use MNR to determine the properties of these materials. However, it can still be used as a rule of thumb to suggest that such systems may be expected to exhibit similar values of <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>\n<sub>.</sub>\n<sup>[</sup>\n##UREF##13##\n17\n##, ##UREF##33##\n42\n##, ##REF##31753075##\n43\n##\n<sup>]</sup>\n</p>", "<p>A recent molecular dynamics (MD) study of MNR in atomic diffusion in simple metals<sup>[</sup>\n##REF##32770040##\n44\n##\n<sup>]</sup> strongly suggests that the phenomenon is quite complicated, with substantial changes in vibrational densities of states between the initial and the transition state during diffusion, and that this provides the entropy for the compensation. Density functional theory and other first principles computational methods can only obtain the entropy, <italic toggle=\"yes\">S</italic>, and activation energy <italic toggle=\"yes\">E<sub>a</sub>\n</italic>, of the initial state, but not Δ<italic toggle=\"yes\">S<sub>M</sub>\n</italic>.<sup>[</sup>\n##REF##32347715##\n34\n##, ##UREF##33##\n42\n##\n<sup>]</sup> Therefore, isokinetic temperature cannot be calculated from such theories, for now. To date, there have been no MD studies of MNR in ion conduction. Thus, we rely upon simple models or experiments to clarify the situation.</p>", "<p>Within the simple, phenomenological, MEE model,<sup>[</sup>\n##UREF##8##\n10\n##, ##REF##10003136##\n45\n##\n<sup>]</sup> inspired by microscopic models for particular processes, a prediction for <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> has been proposed. It assumes that one excitation of the system is most strongly coupled to that process which takes place, when Δ<italic toggle=\"yes\">H</italic> is large, a number of these excitations must be accumulated to overcome the barrier. This concentration results in Δ<italic toggle=\"yes\">S<sub>M</sub>\n</italic>.<sup>[</sup>\n##UREF##8##\n10\n##\n<sup>]</sup> For optical phonons it is proposed that:\nwhere <italic toggle=\"yes\">h</italic> is Planck's constant, <italic toggle=\"yes\">hv</italic> is the excitation energy, and <italic toggle=\"yes\">κ</italic> is a coupling constant. It has been suggested that <italic toggle=\"yes\">ln</italic>\n<italic toggle=\"yes\">κ</italic> for polaronic materials, particularly ionic polarons, is related to the characteristic phonon occupation,<sup>[</sup>\n##UREF##34##\n46\n##\n<sup>]</sup> that is, the phonon number in a specific excitation state of vibrational mode.</p>", "<p>The MEE model prediction<sup>[</sup>\n##UREF##8##\n10\n##\n<sup>]</sup> for <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> of a material, in which the only excitations are acoustic phonons, is different from Equation (##FORMU##15##16##). In that case, it does not predict a particular frequency within the broad spectrum, for a situation such as that considered in ref.[##REF##32770040##44##]. In experiments concerning a number of phenomena, it has been possible to identify excitations which satisfy Equation (##FORMU##15##16##), assuming<sup>[</sup>\n##UREF##8##\n10\n##\n<sup>]</sup> that <italic toggle=\"yes\">ln</italic>κ ranges between 0.5 and 2. These include studies of chemical reactions,<sup>[</sup>\n##UREF##35##\n47\n##\n<sup>]</sup> where the excitations are those of molecular vibrations; relaxations,<sup>[</sup>\n##UREF##36##\n48\n##\n<sup>]</sup> where they are the energies of the relaxing entities, conduction of FICs,<sup>[</sup>\n##UREF##13##\n17\n##, ##UREF##14##\n18\n##, ##REF##31753075##\n43\n##\n<sup>]</sup> where they are optical phonons.</p>", "<p>It is still not clear whether Equation (##FORMU##15##16##) is widely applicable. For example, in Y‐doped BaMO<sub>3</sub> (M = Zr or Ce) proton conductors, the relation between isokinetic temperature and average M‐O stretch vibration follows Equation (##FORMU##15##16##), as shown in <bold>Figure</bold>\n##FIG##3##\n4a##.<sup>[</sup>\n##UREF##13##\n17\n##\n<sup>]</sup> In contrast, in lithium superionic conductors (LISICON) and olivine compounds, the phonon band center decreases with the increase of Meyer‐Neldel energy, as illustrated in Figure ##FIG##3##4b##.<sup>[</sup>\n##UREF##37##\n49\n##\n<sup>]</sup> It is possible that the excitations responsible for <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> are not Li phonons in these lithium conductors. However, recent work on garnet‐type lithium conductors using isotope substitution have demonstrated that lower lithium vibration frequency corresponds to higher ionic conductivity.<sup>[</sup>\n##UREF##38##\n50\n##\n<sup>]</sup> Clearly, further investigation as to whether Equation (##FORMU##15##16##) is universally applicable to FICs is needed. If it is, it is important to identify the phonons which contribute the excitation that determines the isokinetic temperature. One promising experimental method to perform this task could be nuclear resonant vibration spectroscopy (NRVS).<sup>[</sup>\n##UREF##39##\n51\n##\n<sup>]</sup> New developments in synchrotron based x‐ray methods permit the determination of element‐specific vibration spectra, provided the element is available as a Mössbauer active isotope.<sup>[</sup>\n##UREF##39##\n51\n##\n<sup>]</sup>\n</p>", "<title>Relationship between Isokinetic Temperature and Isokinetic Prefactor</title>", "<p>Over the past several decades, it has been observed<sup>[</sup>\n##UREF##8##\n10\n##\n<sup>]</sup> that for some families of electronic and ionic conductors obeying MNR, there is a correlation, that is, an approximate relationship between the isokinetic prefactor, σ<sub>00</sub> and the isokinetic temperature <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>,<sup>[</sup>\n##UREF##8##\n10\n##, ##UREF##13##\n17\n##, ##REF##31753075##\n43\n##, ##UREF##40##\n52\n##, ##UREF##41##\n53\n##\n<sup>]</sup>\nwhere <mml:math id=\"jats-math-23\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>σ</mml:mi><mml:mn>00</mml:mn><mml:mo>′</mml:mo></mml:msubsup></mml:mrow></mml:math> and <italic toggle=\"yes\">E<sub>n</sub>\n</italic> are empirical constants, discussed below. From Equation (##FORMU##15##16##) we see that <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> is inversely proportional to <italic toggle=\"yes\">κ</italic>, the coupling to excitations. On this basis, it has been proposed<sup>[</sup>\n##UREF##8##\n10\n##, ##REF##31753075##\n43\n##\n<sup>]</sup> that positive <italic toggle=\"yes\">E<sub>n</sub>\n</italic> corresponds to polaronic conduction, while negative <italic toggle=\"yes\">E<sub>n</sub>\n</italic> corresponds to trap‐limited conduction. This has led to the identification of polaronic conduction in numerous materials. These include electronic conduction in chalcogenide glasses,<sup>[</sup>\n##UREF##42##\n54\n##\n<sup>]</sup> proton conductivity in minerals,<sup>[</sup>\n##UREF##15##\n19\n##\n<sup>]</sup> and ionic conductivity in perovskite‐type oxides.<sup>[</sup>\n##UREF##13##\n17\n##\n<sup>]</sup>\n<bold>Figure</bold>\n##FIG##4##\n5\n## shows other examples from the literature.<sup>[</sup>\n##UREF##43##\n55\n##, ##UREF##44##\n56\n##, ##UREF##45##\n57\n##, ##UREF##46##\n58\n##, ##UREF##47##\n59\n##, ##UREF##48##\n60\n##, ##UREF##49##\n61\n##, ##REF##34169722##\n62\n##, ##UREF##50##\n63\n##, ##UREF##51##\n64\n##, ##UREF##52##\n65\n##\n<sup>]</sup>\n</p>", "<p>Figure ##FIG##4##5a## shows the isokinetic prefactor σ<sub>00</sub> as a function of the reciprocal of isokinetic temperature <italic toggle=\"yes\">T<sub>iso</sub>\n</italic> for some perovskite‐type proton conductors. Neutron scattering experiments have also confirmed that for perovskite proton conductors, the proton jump time follows a polaron model.<sup>[</sup>\n##REF##28613274##\n66\n##, ##UREF##53##\n67\n##\n<sup>]</sup> Figure ##FIG##4##5b## shows a similar relationship for the LGPS family Li‐ion conductors with variable compositions. Note that the data points scatter because the criterion of closely related system is not completely satisfied, for instance, the mobile ion concentration, attempt frequency, or other parameters change. Now, let us consider the significance of Equation (##FORMU##16##17##) and the physical meaning of <mml:math id=\"jats-math-24\" display=\"inline\"><mml:mrow><mml:msubsup><mml:mi>σ</mml:mi><mml:mn>00</mml:mn><mml:mo>′</mml:mo></mml:msubsup></mml:mrow></mml:math> and <italic toggle=\"yes\">E<sub>n</sub>\n</italic>.</p>", "<p>Applying Equation (##FORMU##1##2##), Equation (##FORMU##5##6##), and Equation (##FORMU##6##7##) to Equation (##FORMU##13##14##), yields\n\n</p>", "<p>Therefore, in random and uncorrelated ion hopping processes, the isokinetic parameter, σ<sub>00</sub>, is determined by the ion concentration, jump distance, attempt frequency, and Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic>. As discussed in Section <xref rid=\"advs6678-sec-0020\" ref-type=\"sec\">2</xref>, Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic> is positive or small for most properties of most materials. However, as shown in Figure ##FIG##1##2##, it is negative and non‐negligible for conductivity of FICs. As we may see, σ<sub>00</sub> depends exponentially upon Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic>. There is no reason to expect the linear terms in Equation (##FORMU##7##8##) to exhibit large changes from one member of a family to another. This leads us to suggest that, for FICs:\nand <italic toggle=\"yes\">E<sub>n</sub>\n</italic> is expressed by:\n\n</p>", "<p>Therefore, <italic toggle=\"yes\">E<sub>n</sub>\n</italic> is related to the change of configurational entropy between initial and translational states, Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic>. It has been suggested that the value of <italic toggle=\"yes\">E<sub>a</sub>\n</italic> compared to <italic toggle=\"yes\">E<sub>n</sub>\n</italic> can determine the direction to modulate the isokinetic temperature in order to tune the ionic conductivity.<sup>[</sup>\n##UREF##13##\n17\n##\n<sup>]</sup> and thus <italic toggle=\"yes\">E<sub>n</sub>\n</italic> is called the critical energy of materials.<sup>[</sup>\n##UREF##13##\n17\n##\n<sup>]</sup>\n</p>", "<p>Nevertheless, the extent to which the model we have proposed here may apply to other materials, including isotropic ionic conductors, is not evident. As pointed out in Section <xref rid=\"advs6678-sec-0030\" ref-type=\"sec\">3</xref>, most properties which obey MNR exhibit positive or very small Δ<italic toggle=\"yes\">S<sub>C</sub>\n</italic>\n<sub>,</sub> which should then not determine the sign of <italic toggle=\"yes\">E<sub>n</sub>\n</italic>\n<sub>.</sub> However, in Figure ##FIG##4##5##, the calculated <italic toggle=\"yes\">E<sub>n</sub>\n</italic> according to Equation (##FORMU##16##17##) is 0.32 ± 0.06 eV for perovskite‐type proton conductors and 0.38 ± 0.01 eV for Li‐ion conductors, respectively, indicating that <italic toggle=\"yes\">E<sub>n</sub>\n</italic> differs among different types of ionic conductors and can also be large. This also requires further investigation.</p>", "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>Q.C. and P.D. acknowledge support from the National Natural Science Foundation of China (Grant No. 52272227) and the Shanghai Natural Science Foundation (Grant No. 22ZR1428800). A.B. and Q.C. acknowledge support from the Swiss National Science Foundation (Grant No. 200021‐188588). P.D. and Q.C. thank Shouhang Bo, Yanming Wang (Shanghai Jiao Tong University), and Donglin Han (Soochow University) for valuable suggestions.</p>" ]
[ "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6678-fig-0001\"><label>Figure 1</label><caption><p>Arrhenius plot a) and Meyer‐Neldel plot b) of garnet Li<sub>6</sub>MLa<sub>2</sub>Ta<sub>2</sub>O<sub>12</sub> (M = Ba, Ca, Sr, and Sr<sub>0.5</sub>Ba<sub>0.5</sub>) lithium ionic conductors.<sup>[</sup>\n##UREF##16##\n20\n##\n<sup>]</sup> The <italic toggle=\"yes\">\n<bold>T</bold>\n</italic>\n<sub>\n<italic toggle=\"yes\">\n<bold>iso</bold>\n</italic>\n</sub> is shown as asterisk and the grey dash dot line indicates the value of <italic toggle=\"yes\">\n<bold>T</bold>\n</italic>\n<sub>\n<italic toggle=\"yes\">\n<bold>iso</bold>\n</italic>\n</sub>. The solid line in (b) is the least square fit line according to Equation (##FORMU##1##2##).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6678-fig-0002\"><label>Figure 2</label><caption><p>a) The role of <italic toggle=\"yes\">\n<bold>T</bold>\n</italic>\n<sub>\n<italic toggle=\"yes\">\n<bold>iso</bold>\n</italic>\n</sub> in ionic conductivity. Region I (blue) and Region II (pink) represent the cases of measurement temperature larger and smaller than <bold>\n<italic toggle=\"yes\">T</italic>\n<sub>iso</sub>\n</bold>. The lines i, ii, and iii represent three conductivity lines with activation energies and prefactors decreasing sequentially. b) the lithium‐ion conductivity of Li<sub>1‐3</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Ga<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Zr<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub> (<italic toggle=\"yes\">x</italic> = 0, 0.02, 0.05, 0.1). Reproduced with permission.<sup>[</sup>\n##UREF##29##\n36\n##\n<sup>]</sup> Copyright 2021, The Royal Society of Chemistry. c) The sodium ionic conductivity of Na<sub>3</sub>PS<sub>4‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Se<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> (<italic toggle=\"yes\">x</italic> = 0, 2, 4). Reproduced with permission.<sup>[</sup>\n##REF##30284822##\n37\n##\n<sup>]</sup> Copyright 2018, American Chemical Society.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6678-fig-0003\"><label>Figure 3</label><caption><p>Meyer‐Neldel plot of Li<sub>6.4</sub>La<sub>3</sub>Zr<sub>1.4</sub>Ta<sub>0.6</sub>O<sub>12</sub> under variable pressure.<sup>[</sup>\n##UREF##33##\n42\n##\n<sup>]</sup>\n</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6678-fig-0004\"><label>Figure 4</label><caption><p>a) The relationship between Meyer–Neldel energy or isokinetic temperature and the average M‐O stretch vibration 〈ν〉 for BaZr<sub>0.9</sub>Y<sub>0.1</sub>O<sub>3−δ</sub>, BaZr<sub>0.8−x</sub>Ce<sub>x</sub>Y<sub>0.2</sub>O<sub>3−δ</sub> (<italic toggle=\"yes\">x</italic> = 0, 0.1, 0.2), and BaCe<sub>0.8</sub>Y<sub>0.2</sub>O<sub>3−δ</sub>. Reproduced with permission.<sup>[</sup>\n##UREF##13##\n17\n##\n<sup>]</sup> Copyright 2021, Wiley‐VCH. b) The relationship between Meyer–Neldel energy (<italic toggle=\"yes\">\n<bold>Δ</bold>\n</italic>\n<sub>0</sub>) and Li‐band center for Li<sub>3.25</sub>Ge<sub>0.25</sub>P<sub>0.75</sub>S<sub>4</sub>, Li<sub>3.25</sub>Ge<sub>0.25</sub>V<sub>0.75</sub>O<sub>4</sub>, Li<sub>3</sub>VO<sub>4</sub>, Li<sub>3</sub>PO<sub>4,</sub> and Li<sub>0.325</sub>Ge<sub>0.25</sub>P<sub>0.75</sub>O<sub>4</sub>. Reproduced with permission.<sup>[</sup>\n##UREF##37##\n49\n##\n<sup>]</sup> Copyright 2018, American Chemical Society.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6678-fig-0005\"><label>Figure 5</label><caption><p>Correlation between isokinetic prefactor <italic toggle=\"yes\">\n<bold>σ</bold>\n</italic>\n<sub>\n<bold>00</bold>\n</sub> and isokinetic temperature <italic toggle=\"yes\">\n<bold>T</bold>\n</italic>\n<sub>\n<italic toggle=\"yes\">\n<bold>iso</bold>\n</italic>\n</sub> for various compositions of perovskite‐type proton conductors a), and lithium‐ion conductors b).<sup>[</sup>\n##UREF##43##\n55\n##, ##UREF##44##\n56\n##, ##UREF##45##\n57\n##, ##UREF##46##\n58\n##, ##UREF##47##\n59\n##, ##UREF##48##\n60\n##, ##UREF##49##\n61\n##, ##REF##34169722##\n62\n##, ##UREF##50##\n63\n##, ##UREF##51##\n64\n##, ##UREF##52##\n65\n##\n<sup>]</sup> The solid lines are the fit according to Equation (##FORMU##16##17##). In (a), the solid, hollow, and semi‐solid symbols correspond to the grain, grain boundary, and total conductivity. (All the relevant data obtained from literature which is found in Tables ##SUPPL##0##S1## and ##SUPPL##0##S2##, Supporting Information).</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"advs6678-tbl-0001\" content-type=\"Table\"><label>Table 1</label><caption><p>The measurement temperature <italic toggle=\"yes\">\n<bold>T</bold>\n</italic>, isokinetic temperature <italic toggle=\"yes\">\n<bold>T</bold>\n</italic>\n<sub>\n<italic toggle=\"yes\">\n<bold>iso</bold>\n</italic>\n</sub>, and <italic toggle=\"yes\">\n<bold>T vs</bold>\n</italic>.<italic toggle=\"yes\">\n<bold> T</bold>\n</italic>\n<sub>\n<italic toggle=\"yes\">\n<bold>iso</bold>\n</italic>\n</sub> of Li<sub>1‐3</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Ga<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Zr<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub>\n<sup>[</sup>\n##REF##30284822##\n37\n##\n<sup>]</sup> and Na<sub>3</sub>PS<sub>4‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Se<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> (<italic toggle=\"yes\">x</italic> = 0, 2, 4).<sup>[</sup>\n##UREF##29##\n36\n##\n<sup>]</sup>\n</p></caption><table frame=\"hsides\" rules=\"groups\"><col align=\"left\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><col align=\"center\" span=\"1\"/><thead><tr style=\"border-bottom:solid 1px #000000\"><th align=\"left\" rowspan=\"1\" colspan=\"1\">Material</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">Operating temperature <italic toggle=\"yes\">T</italic> [K]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">T<sub>iso</sub>\n</italic> [K]</th><th align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">T</italic> \n<italic toggle=\"yes\">vs</italic>. <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>\n</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Li<sub>1‐3</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Ga<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Zr<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub>\n</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">293–363</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">224.9</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">T</italic> &gt; <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Na<sub>3</sub>PS<sub>4‐</sub>\n<italic toggle=\"yes\">\n<sub>x</sub>\n</italic>Se<italic toggle=\"yes\">\n<sub>x</sub>\n</italic> (<italic toggle=\"yes\">x</italic>=0, 2, 4)</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">250–330</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">396.7</td><td align=\"center\" rowspan=\"1\" colspan=\"1\">\n<italic toggle=\"yes\">T</italic> &lt; <italic toggle=\"yes\">T<sub>iso</sub>\n</italic>\n</td></tr></tbody></table><permissions><copyright-holder>John Wiley &amp; Sons, Ltd.</copyright-holder></permissions></table-wrap>" ]
[ "<disp-formula id=\"advs6678-disp-0001\">\n<label>(1)</label>\n<mml:math id=\"jats-math-1\" display=\"block\"><mml:mrow><mml:mrow><mml:mspace width=\"80.0pt\"/><mml:mi>σ</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:msub><mml:mi>σ</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mi>T</mml:mi></mml:mfrac><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mo linebreak=\"badbreak\">−</mml:mo><mml:mfrac><mml:msub><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">a</mml:mi></mml:msub><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0002\">\n<label>(2)</label>\n<mml:math id=\"jats-math-2\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>ln</mml:mi><mml:msub><mml:mi>σ</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mo 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linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mi>ln</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mrow><mml:msubsup><mml:mo>∏</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mspace width=\"0.33em\"/><mml:mn>1</mml:mn></mml:mrow><mml:mrow><mml:mn>3</mml:mn><mml:mi>N</mml:mi></mml:mrow></mml:msubsup><mml:msubsup><mml:mi>v</mml:mi><mml:mi>i</mml:mi><mml:mi>I</mml:mi></mml:msubsup></mml:mrow><mml:mrow><mml:msubsup><mml:mo>∏</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mspace width=\"0.33em\"/><mml:mo>=</mml:mo><mml:mspace width=\"0.33em\"/><mml:mn>1</mml:mn></mml:mrow><mml:mrow><mml:mn>3</mml:mn><mml:mi>N</mml:mi><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msubsup><mml:msubsup><mml:mi>v</mml:mi><mml:mi>i</mml:mi><mml:mi>S</mml:mi></mml:msubsup></mml:mrow></mml:mfrac></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0006\">\n<label>(6)</label>\n<mml:math id=\"jats-math-9\" display=\"block\"><mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>S</mml:mi><mml:mi>M</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>H</mml:mi></mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi>iso</mml:mi></mml:msub></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0007\">\n<label>(7)</label>\n<mml:math id=\"jats-math-11\" display=\"block\"><mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>S</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>S</mml:mi><mml:mi>M</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">+</mml:mo><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>S</mml:mi><mml:mi>C</mml:mi></mml:msub></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0008\">\n<label>(8)</label>\n<mml:math id=\"jats-math-12\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>T</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>H</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>S</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0009\">\n<label>(9)</label>\n<mml:math id=\"jats-math-13\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>σ</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi>cq</mml:mi><mml:mi>μ</mml:mi></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0010\">\n<label>(10)</label>\n<mml:math id=\"jats-math-14\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>μ</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:mi>q</mml:mi><mml:msub><mml:mi>D</mml:mi><mml:mi>σ</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0011\">\n<label>(11)</label>\n<mml:math id=\"jats-math-15\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>D</mml:mi><mml:mi>r</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:msup><mml:mi>a</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mi>ν</mml:mi></mml:mrow><mml:mi>b</mml:mi></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0012\">\n<label>(12)</label>\n<mml:math id=\"jats-math-16\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>ν</mml:mi><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:msub><mml:mi>ν</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mo linebreak=\"badbreak\">−</mml:mo><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>G</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mfenced><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:msub><mml:mi>ν</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>S</mml:mi></mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac></mml:mfenced><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mo linebreak=\"badbreak\">−</mml:mo><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>H</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0013\">\n<label>(13)</label>\n<mml:math id=\"jats-math-17\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>σ</mml:mi><mml:mfenced open=\"(\" close=\")\"><mml:mi>T</mml:mi></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mi>b</mml:mi></mml:mfrac><mml:mfrac><mml:mrow><mml:mi>c</mml:mi><mml:msup><mml:mi>q</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac><mml:msup><mml:mi>a</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:msub><mml:mi>υ</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>S</mml:mi></mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac></mml:mfenced><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mo linebreak=\"badbreak\">−</mml:mo><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>H</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0014\">\n<label>(14)</label>\n<mml:math id=\"jats-math-18\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mi>b</mml:mi></mml:mfrac><mml:mfrac><mml:mrow><mml:mi>c</mml:mi><mml:msup><mml:mi>q</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac><mml:msup><mml:mi>a</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:msub><mml:mi>υ</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:mi>S</mml:mi></mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0015\">\n<label>(15)</label>\n<mml:math id=\"jats-math-19\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>σ</mml:mi><mml:mfenced open=\"(\" close=\")\"><mml:mi>T</mml:mi></mml:mfenced><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mi>b</mml:mi></mml:mfrac><mml:mfrac><mml:mrow><mml:mi>c</mml:mi><mml:msup><mml:mi>q</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac><mml:msup><mml:mi>a</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:msub><mml:mi>υ</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>S</mml:mi><mml:mi>C</mml:mi></mml:msub></mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac></mml:mfenced><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"[\" close=\"]\"><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:msub><mml:mi>E</mml:mi><mml:mi>a</mml:mi></mml:msub><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac></mml:mfenced><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mrow><mml:mi>T</mml:mi><mml:mo>−</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mi>iso</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>T</mml:mi><mml:mi>iso</mml:mi></mml:msub><mml:mi>T</mml:mi></mml:mrow></mml:mfrac></mml:mfenced></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0016\">\n<label>(16)</label>\n<mml:math id=\"jats-math-21\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>s</mml:mi><mml:mi>o</mml:mi></mml:mrow></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mrow><mml:mi>h</mml:mi><mml:mi>v</mml:mi></mml:mrow><mml:mrow><mml:mi>l</mml:mi><mml:mi>n</mml:mi><mml:mi>κ</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0017\">\n<label>(17)</label>\n<mml:math id=\"jats-math-22\" display=\"block\"><mml:mrow><mml:mrow><mml:mi>ln</mml:mi><mml:msub><mml:mi>σ</mml:mi><mml:mn>00</mml:mn></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mi>ln</mml:mi><mml:msubsup><mml:mi>σ</mml:mi><mml:mn>00</mml:mn><mml:msup><mml:mrow/><mml:mo>′</mml:mo></mml:msup></mml:msubsup><mml:mo linebreak=\"goodbreak\">−</mml:mo><mml:mfrac><mml:msub><mml:mi>E</mml:mi><mml:mi mathvariant=\"normal\">n</mml:mi></mml:msub><mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi mathvariant=\"normal\">B</mml:mi></mml:msub><mml:msub><mml:mi>T</mml:mi><mml:mi>iso</mml:mi></mml:msub></mml:mrow></mml:mfrac></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0018\">\n<label>(18)</label>\n<mml:math id=\"jats-math-25\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>σ</mml:mi><mml:mn>00</mml:mn></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mi>b</mml:mi></mml:mfrac><mml:mfrac><mml:mrow><mml:mi>c</mml:mi><mml:msup><mml:mi>q</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac><mml:msup><mml:mi>a</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:msub><mml:mi>υ</mml:mi><mml:mn>0</mml:mn></mml:msub><mml:mi>exp</mml:mi><mml:mfenced separators=\"\" open=\"(\" close=\")\"><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>S</mml:mi><mml:mi>C</mml:mi></mml:msub></mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac></mml:mfenced></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0019\">\n<label>(19)</label>\n<mml:math id=\"jats-math-26\" display=\"block\"><mml:mrow><mml:mrow><mml:msubsup><mml:mi>σ</mml:mi><mml:mn>00</mml:mn><mml:msup><mml:mrow/><mml:mo>′</mml:mo></mml:msup></mml:msubsup><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mi>b</mml:mi></mml:mfrac><mml:mfrac><mml:mrow><mml:mi>c</mml:mi><mml:msup><mml:mi>q</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow><mml:msub><mml:mi>k</mml:mi><mml:mi>B</mml:mi></mml:msub></mml:mfrac><mml:msup><mml:mi>a</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:msub><mml:mi>υ</mml:mi><mml:mn>0</mml:mn></mml:msub></mml:mrow></mml:mrow></mml:math>\n</disp-formula>", "<disp-formula id=\"advs6678-disp-0020\">\n<label>(20)</label>\n<mml:math id=\"jats-math-27\" display=\"block\"><mml:mrow><mml:mrow><mml:msub><mml:mi>E</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo linebreak=\"badbreak\">=</mml:mo><mml:mo>−</mml:mo><mml:msub><mml:mi>T</mml:mi><mml:mrow><mml:mi>i</mml:mi><mml:mi>s</mml:mi><mml:mi>o</mml:mi></mml:mrow></mml:msub><mml:mi mathvariant=\"normal\">Δ</mml:mi><mml:msub><mml:mi>S</mml:mi><mml:mi>C</mml:mi></mml:msub></mml:mrow></mml:mrow></mml:math>\n</disp-formula>" ]
[ "<boxed-text position=\"anchor\" content-type=\"graphic\"></boxed-text>" ]
[]
[]
[]
[ "<supplementary-material id=\"advs6678-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
[]
[ "<graphic xlink:href=\"ADVS-11-2305065-g006.jpg\" position=\"anchor\" id=\"jats-graphic-1\"/>", "<graphic xlink:href=\"ADVS-11-2305065-g001\" position=\"anchor\" id=\"jats-graphic-3\"/>", "<graphic xlink:href=\"ADVS-11-2305065-g003\" position=\"anchor\" id=\"jats-graphic-5\"/>", "<graphic xlink:href=\"ADVS-11-2305065-g002\" position=\"anchor\" id=\"jats-graphic-7\"/>", "<graphic xlink:href=\"ADVS-11-2305065-g004\" position=\"anchor\" id=\"jats-graphic-9\"/>", "<graphic xlink:href=\"ADVS-11-2305065-g005\" position=\"anchor\" id=\"jats-graphic-11\"/>" ]
[ "<media xlink:href=\"ADVS-11-2305065-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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{ "acronym": [], "definition": [] }
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2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 3; 11(2):2305065
oa_package/91/d2/PMC10787107.tar.gz
PMC10787108
37933988
[ "<title>Introduction</title>", "<p>With the increase in the aging population, the incidence of bone fractures and orthopedic‐related injuries is rising every year, resulting in enormous medical and economic burdens as well as impaired quality of life.<sup>[</sup>\n##UREF##0##\n1\n##\n<sup>]</sup> Generally, the regeneration of damaged bone tissue, especially for large bone defects, is a complex cascade reaction process, requiring initiation of the immune system and microenvironment regulation, activation of vascular ingrowth, and subsequent osteogenic differentiation. At the initial stage of bone defect repair, the implantation of bone graft substitute materials triggers local inflammation and the immune microenvironment, recruiting multiple immune cells (e.g., neutrophils, natural killer cells, macrophages, dendritic cells, and T and B lymphocytes) to participate in inflammation development and regulation.<sup>[</sup>\n##REF##35504180##\n2\n##\n<sup>]</sup> Among these, macrophages, as the most common effector immune cells at the inflammatory phase, participate in all phases of bone healing. According to classical theory, macrophages can be divided into proinflammatory macrophages (M1) and anti‐inflammatory macrophages (M2) in response to diverse signal stimuli. More specifically, M1‐type macrophages induce excessive fibrosis and healing disorders by secreting proinflammatory cytokines and reactive oxygen species (ROS), while M2 macrophages tend to promote angiogenesis and osteogenic differentiation through the secretion of multiple anti‐inflammatory and pro‐healing cytokines.<sup>[</sup>\n##REF##33984633##\n3\n##, ##UREF##1##\n4\n##\n<sup>]</sup> Unfortunately, excessive or prolonged inflammation can result in macrophage polarization to a proinflammatory M1 phenotype, with the formation of granulomas and fibrotic scar tissue, which further aggravate the inflammatory response following injury and thus compromise cell proliferation and tissue regeneration. Therefore, it is likely that timely shifting of the macrophage phenotype toward the M2 phenotype (i.e., immunomodulation) at the early stages of bone regeneration would create a suitable immune microenvironment (anti‐inflammatory and M2‐polarizing) for high‐performance bone repair.</p>", "<p>Once the proper timing activation of M2 phenotype macrophages is achieved, immediately following vascular reconstruction and osteogenesis are coupled in bone formation.<sup>[</sup>\n##UREF##2##\n5\n##\n<sup>]</sup> Advances in materiobiology have recently suggested that angiogenesis and osteogenesis are two critical events in bone fracture healing and remodeling, in which the development of internal blood vessels is essential for the success of tissue engineering and bone regeneration.<sup>[</sup>\n##REF##35870263##\n6\n##\n<sup>]</sup> Furthermore, accelerated vascular ingrowth can provide nutrients and transport metabolites essential for osteogenesis and may recruit osteoprogenitors to the injury area, promoting bone tissue regeneration by establishing cell and nutrient transport channels. Conversely, the impaired blood supply of implanted bone repair material results in delayed tissue healing, which has become a serious obstacle to its application.<sup>[</sup>\n##UREF##3##\n7\n##\n<sup>]</sup> Recent research has also highlighted the importance of neovascularization in skeletal development and bone repair.<sup>[</sup>\n##REF##35114373##\n8\n##\n<sup>]</sup> Therefore, a promising strategy for bone augmentation is the utilization of tissue‐engineered biomaterials to recreate a conducive immune microenvironment at the inflammation stage and subsequently coordinate angiogenesis and osteogenesis in an intelligent manner, thereby achieving optimized tissue healing outcomes.</p>", "<p>Among various bone tissue engineering scaffolds developed thus far, biocompatible 3D hydrogels have been considered to be excellent artificial bone graft materials owing to their similarity to the extracellular matrix (ECM) in physical and chemical properties as well as their extraordinary capacity to serve as drug loading (encapsulated or bonded) and delivery vehicles.<sup>[</sup>\n##UREF##4##\n9\n##\n<sup>]</sup> The vast majority of previously developed hydrogels have solely been used as carriers to encapsulate various biological products, failing to satisfy the proper timing manipulation of macrophage activation, angiogenesis, and osteogenesis.<sup>[</sup>\n##UREF##5##\n10\n##\n<sup>]</sup> Thus, it is still challenging to develop a biocompatible hydrogel with programmed release‐specific actives to sequentially modulate specific biological functions (e.g., immune response, vessel formation, and subsequent osteogenic differentiation) during bone repair. Although loading exogenous biological agents is a facile and promising strategy that has resulted in significant improvement in the overall performance of biomaterials, improper release behavior leads to delayed or dysfunctional bone regeneration.<sup>[</sup>\n##REF##31670079##\n11\n##\n<sup>]</sup> In addition, these therapeutic strategies are limited by initial burst release and easy inactivation of cytokines, drug‐associated complications, high production cost and sophisticated manufacturing. Of note, the dynamic and complex microenvironment in vivo together with the biosafety and short half‐life of these traditional biologically active molecules also make it difficult to match the physiological process of bone repair, inevitably delaying bone healing.<sup>[</sup>\n##REF##35986434##\n12\n##\n<sup>]</sup> It is thus of great significance to develop a smart drug delivery system with controlled release for the sequential promotion of immune regulation, vascularization, and recruitment of bone marrow stem cells (BMSCs) and skeletal progenitors, which could meet the complex and ordered process in bone regeneration.</p>", "<p>Herein, based on the above introduction, we rationally designed smart‐responsive multifunctional hydrogels with mild photothermal activity to promote bone regeneration through sequential activation of M2 macrophage polarization, angiogenesis, and osteogenesis. The hydrogel platform (denoted as GA/BPPD) was fabricated based on gelatin methacrylate (GelMA)/sodium methacrylic acid alginate (Alg‐MA) hybrid hydrogel (GA) system and further incorporated with black phosphorus (BP)‐based nanocomposite (BPPD), coated with polydopamine (PDA) and loaded with deferoxamine (DFO). As a rising star on the horizon of 2D layered biomaterials, BP nanosheets possess fantastic physiochemical properties, biocompatibility, and superior efficiency in near‐infrared (NIR)‐thermal conversion, leading to their wide application in the fields of biomedical engineering, such as drug delivery, cancer therapy and tissue engineering.<sup>[</sup>\n##REF##35072461##\n13\n##\n<sup>]</sup> Additionally, the large specific surface area and unique layered structure endow BP nanosheets with high performance in guest molecule (drug, protein, and gene) delivery, which potentiates the efficient treatment of bone defect‐associated diseases.<sup>[</sup>\n##REF##36920036##\n14\n##\n<sup>]</sup> In the physiological environment, the oxidization degradation products of BP nanosheets are usually non‐toxic phosphate ions, which have been reported to promote bone regeneration spontaneously by accelerating cell proliferation, differentiation, and signal transduction, as well as participating in bone metabolism.<sup>[</sup>\n##REF##34704438##\n15\n##, ##REF##34464823##\n16\n##\n<sup>]</sup> Due to various biological functions and easy availability, 2D BP and 2D BP‐based materials combined with a mild NIR‐based photothermal strategy can produce a synergistic effect on promoting bone regeneration, although the efficiency still needs improvement. As reported, BP nanosheets are not stable in aqueous environments and can rapidly degrade into orthophosphate ions under ambient conditions, severely impeding their potential applications in biomedicine.<sup>[</sup>\n##REF##36125961##\n17\n##\n<sup>]</sup> Emerging evidence has revealed that the surface modification of BP nanosheets with PDA can not only effectively protect BP from fast degradation and allow for sustained PO<sub>4</sub>\n<sup>3−</sup> release that promotes bone regeneration, but also enhance interfacial bonding between pristine BP nanosheets and the polymer matrix to improve stability.<sup>[</sup>\n##UREF##6##\n18\n##, ##REF##37080119##\n19\n##\n<sup>]</sup> As a synthetic melanin‐like biopolymer, the abundant presence of catechols, amine, and aromatic rings in the PDA structure would enable a high loading and controlled release of therapeutic molecules via hydrogen bonding or π−π stacking interactions.<sup>[</sup>\n##REF##36278256##\n20\n##\n<sup>]</sup> In the present work, DFO, as a Food and Drug Administration (FDA)‐approved iron‐chelating agent, was chosen as a bioactive small molecule to be loaded in the PDA‐modified BP (BP@PDA) carrier because of its promoting effects on vascularization and osteogenesis. A growing number of studies have demonstrated that DFO can regulate hypoxia‐inducible factor (HIF‐1α)/vascular endothelial growth cell (VEGF) signaling, thereby enhancing angiogenesis and tissue perfusion.<sup>[</sup>\n##REF##30415019##\n21\n##\n<sup>]</sup> More interestingly, each raw material, including BP, PDA, and DFO, was demonstrated to have a direct effect on scavenging free radicals, which could synergistically help protect tissue from oxidative damage and thus suppress reactive oxygen species (ROS)‐induced inflammatory status.<sup>[</sup>\n##UREF##7##\n22\n##, ##UREF##8##\n23\n##\n<sup>]</sup> It was recently reported that a pro‐healing immune microenvironment could be achieved by PDA and mild heat stimulation‐mediated macrophage reprogramming.<sup>[</sup>\n##REF##35986434##\n12\n##\n<sup>]</sup> We envision that the as‐prepared BPPD nanocomposite with photothermal and therapeutic effects could serve as a smart delivery system to release DFO and PO<sub>4</sub>\n<sup>3−</sup> in a pH‐ and thermal‐stimuli‐dependent manner, which holds significant incentives for spatiotemporal manipulation of the immune response, vascular development, and bone regeneration.</p>", "<p>As shown in <bold>Scheme</bold> ##FIG##0##\n1\n##, gelatin methacrylate (GelMA)/sodium methacrylic acid alginate (Alg‐MA) hybrid hydrogel (GA) system was selected as the model substrate for cranial defect repair, which could be utilized to reinforce the impaired bone tissue and serve as a carrier for delivering therapeutic drugs/ions from bioactive BPPD nanocomposites. Previous studies have shown that GA hydrogels can not only maintain good stability under physiological conditions but also form a natural 3D polymeric structure in the presence of photoinitiators and ultraviolet light.<sup>[</sup>\n##REF##35633590##\n24\n##\n<sup>]</sup> After loading in GA, self‐degradation of the BPPD nanocomposite could be greatly inhibited due to the protective effect of the hydrogel matrix, thereby better exerting its biological activities to meet the sequential demands of cellular response and tissue regeneration. Under internal stimulation of pH and external NIR laser irradiation, sequential release of DFO and PO<sub>4</sub>\n<sup>3−</sup> from the BPPD‐loaded GA hybrid hydrogel was observed because these factors significantly affected the desorption of DFO as well as the release of PO<sub>4</sub>\n<sup>3−</sup> from BPPD, thereby providing a pro‐regenerative microenvironment. In the present work, we systematically investigated the physicochemical structure and properties, in vitro drug loading and on‐demand release behavior, and in vitro cellular response, including adhesion, proliferation, migration, osteogenic differentiation, angiogenic effects, and macrophage polarization. The subcutaneous implantation of this kind of photothermal hydrogel platform in rats further confirmed its enormous potential in regulating the immune response and promoting revascularization in tissue engineering applications. Finally, the bone regeneration ability of the bioactive nanocomposite hydrogel on bone healing was validated using a critical‐sized calvaria bone defect model under NIR light irradiation. Together, our strategy of integrating bioactive BPPD nanomaterials within a biocompatible GA hydrogel provides a new insight into the design of smart biomaterials for the whole management of bone tissue regeneration (Scheme ##FIG##0##1##). To the best of our knowledge, this study is the first report that utilizes a smart‐responsive photothermal hydrogel platform to sequentially modulate the immune response, vascularization, and osteogenesis through a combination of physical (mild photothermal treatment) and chemical (drug/ion delivery) interventions.</p>" ]
[]
[ "<title>Results and Discussion</title>", "<title>Preparation and Characterization of the Hybrid Hydrogels</title>", "<p>To realize the spatiotemporal regulation of the immune microenvironment, angiogenesis, and osteogenesis, we designed and constructed a bioactive BPPD nanocomposite‐incorporated hybrid hydrogel with strong photothermal effect and desirable NIR‐triggered drug‐releasing capability in the current study. As shown in Scheme ##FIG##0##1##, the obtained smart delivery hydrogel system can synchronously realize multifunctionality for the treatment of bone defects by combining long‐term physical (photothermal) and continuous chemical (drug/ion delivery) intervention, so as to provide a bone‐friendly microenvironment for sequential activation of M2 macrophage polarization, vascularization, and MSC recruitment, resulting in enhanced bone regeneration.</p>", "<p>For preparation of smart‐responsive multifunctional hydrogels, BPPD nanocomposites, which served as NIR/pH dual‐triggered drug release nanoplatforms, were prepared through BP crystal exfoliation, PDA modification, and DFO loading. A schematic illustration of the preparation process of BPPD is shown in <bold>Figure</bold> ##FIG##1##\n1A##. The raw BP nanosheets were first exfoliated by a sonication‐assisted top‐down strategy. PDA was then decorated on the surface of the BP nanosheets by the self‐polymerization reaction of DA using BP nanosheets as a template. Lines of evidence have shown that mussel‐inspired polymerization of DA to form PDA coatings on various biomaterials has emerged as a diverse surface functionalization method for biomedical applications.<sup>[</sup>\n##UREF##9##\n25\n##\n<sup>]</sup> Introducing PDA layer on BP nanosheets could avoid agglomeration induced by high surface energy, achieving not only better physiological stability and interface compatibility with the hydrogel matrix but also good biocompatibility and ROS scavenging capacity as well as strong drug loading capacity.<sup>[</sup>\n##UREF##6##\n18\n##, ##REF##34237507##\n26\n##\n<sup>]</sup> Previous studies have also shown that the introduction of polyphenols, such as PDA, not only promotes cell migration, adhesion, proliferation, and differentiation but also regulates the inflammatory and immune microenvironment in the early stages of implantation, thus accelerating the subsequent tissue regeneration process.<sup>[</sup>\n##REF##36890691##\n27\n##, ##UREF##10##\n28\n##\n<sup>]</sup> In the present work, the introduction of PDA endowed this hybrid nanocomposite with improved biocompatibility and simultaneously provided a stable glue to conjugate BP nanosheets and DFO molecules.</p>", "<p>Thereafter, the angiogenic drug DFO was introduced to the BP@PDA nanosystem (BPPD) by the interaction between DFO (‐NH<sub>2</sub>) and the rich functional moieties of PDA (e.g., catechols, amine, and aromatic rings). The interaction mechanism between DFO and BP@PDA was mainly attributed to a series of noncovalent forces (physical adsorption, hydrogen bonding, π−π stacking, electrostatic interactions, etc.). It should also be noted that, as a common melanin‐like biopolymer, PDA with enriched catechol groups has excellent photothermal conversion efficiency, which endows BPPD with NIR‐controlled drug release behavior for efficient bone regeneration.</p>", "<p>As revealed by transmission electron microscopy (TEM) images, BPPD is a typical 2D multilayered structure with well‐defined edges (Figure ##FIG##1##1B##). Similarly, the atomic force microscopy (AFM) results reveal the thicknesses of BPPD with a layer height of ≈16 nm (Figure ##FIG##1##1C##). The successful synthesis of the BPPD nanomaterial was verified by zeta potential and Fourier transform infrared spectrometer (FTIR) analysis. As shown in Figure ##SUPPL##0##S1## (Supporting Information), it could be observed that the surface zeta potential of raw BP nanosheets (−30.6 mV) decreased to −56 mV after the in situ polymerization of PDA on BP nanosheets, which was ascribed to the introduction of negatively charged hydroxyl groups from the PDA structure, consistent with previous reports.<sup>[</sup>\n##REF##37080119##\n19\n##\n<sup>]</sup> After loading DFO, BP@PDA presented a less negative potential (−42 mV) than unmodified BP@PDA (−56 mV). The increase in zeta potential was ascribed to the immobilization of positively charged DFO onto negatively charged BP@PDA nanosheets. This phenomenon suggested that DFO can be assembled on the surface of BP@PDA nanospheres by electrostatic adsorption, which agrees with previous studies.<sup>[</sup>\n##REF##30415019##\n21\n##\n<sup>]</sup> The FTIR spectra of pristine BP exhibited three absorption peaks located at ≈1491, 1010, and 815 cm<sup>−1</sup>, which could be attributed to the stretching vibration of P = O and P‐O bonds, further confirming the successful preparation of BP nanosheets (Figure ##FIG##1##1D##). After PDA modification, new additional peaks appeared at 1633, 1457 and 1372 cm<sup>−1</sup> corresponding to the C = C stretching vibration, N‐H scissoring vibration and C‐O stretching vibration of PDA, respectively, demonstrating the successful polymerization of DA in the system. Meanwhile, compared to the FTIR spectrum of BP@PDA, the peaks of BPPD at 1195, 1264, 1461, 1566, and 1628 cm<sup>−1</sup> are slightly stronger because DFO contains more amide bonds, verifying the successful preparation of the BPPD nanocomposite (Figure ##FIG##1##1D##).</p>", "<p>To realize the controlled release of dual factors to match the immune response, angiogenic and osteogenic progressions, different amounts of BPPD nanocomposite were added into the GA pre‐gel solution followed by photo‐polymerization under UV irradiation, forming a photo‐triggered covalent bond network. Both GelMA and Alg‐MA are well‐known photosensitive hydrogels with the advantages of good biocompatibility and biodegradability, which have the ability to mimic the natural ECM of bone to encapsulate bioactive molecules or cells and integrate well with the surrounding tissue.<sup>[</sup>\n##UREF##11##\n29\n##\n<sup>]</sup> The favorable 3D microenvironment provided by the GA hydrogel could accelerate the formation of bone tissue owing to the presence of cell attachment‐promoting arginine‐glycine‐aspartic acid (RGD) sequences.<sup>[</sup>\n##UREF##12##\n30\n##\n<sup>]</sup> As major building blocks for the GA/BPPD hydrogel, photo‐cross‐linkable GelMA and Alg‐MA prepolymers were designed and synthesized by modifying gelatin and Alg with reactive methacrylate groups, as illustrated in Figure ##FIG##1##1E,F##. The successful preparation of methacrylated gelatin and Alg products was confirmed by proton‐1 nuclear magnetic resonance (<sup>1</sup>H NMR) and FTIR. As shown in Figure ##FIG##1##1G,H##, the methyl (‐CH = CH<sub>2</sub>) proton peak was observed in the spectra of GelMA (5.46 and 5.67 ppm) and Alg‐MA (5.65 and 6.08 ppm), indicating the successful introduction of double bonds into gelatin and Alg and the successful synthesis of GelMA and Alg‐MA. FTIR spectra also verified the success of GelMA synthesis, where, in comparison with the gelatin spectrum, we observed that the C = O stretching of amide I shifted to 1660 cm<sup>−1</sup> (Figure ##FIG##1##1I##), which is due to the overlapping of the stretching signals at 1695 cm<sup>−1</sup> (C = C band) from methacrylate. A similar result was also observed in the FTIR spectrum of Alg‐MA (Figure ##SUPPL##0##S2##, Supporting Information), indicating the successful synthesis of the Alg‐MA monomer. Next, the mixture of BPPD nanocomposite and GA was cured under 405 nm visible light to form a nanocomposite hydrogel (<bold>Figure</bold> ##FIG##2##\n2A##). The BPPD nanocomposite together with PDA chains would facilitate interaction with the GA network via both covalent (free‐radical photo‐polymerization) and noncovalent (hydrogen bonds and π–π stacking between catechol groups of PDA chains) forces.</p>", "<p>For bone tissue engineering scaffolds, porous structures that promote cell migration and adhesion are essential, so the morphological structure of the as‐prepared hydrogels was examined, as shown in Figure ##FIG##2##2B##. From the macroscopic photographs, the GA hydrogels were initially opalescent in color, while the BPPD loading did not significantly change the color, probably due to a very small amount of loading. The cross‐sectional scanning electron microscopy (SEM) images showed that all hydrogels exhibited a highly interconnected and porous structure with relatively smooth pore walls, which is similar to that of bone ECM. No obvious BPPD was observed in the pore walls of the hydrogel, probably because of the good interfacial compatibility between the GA matrix and BPPD nanocomposites. Such a porous 3D network structure (e.g., interconnected pores and high porosity) provided an ECM‐mimicking environment (Figure ##FIG##2##2C##), which was demonstrated to contribute to cell adhesion, migration, and transport of nutrients and metabolic wastes. Micro‐CT reconstruction and parameter analysis showed that all hydrogels had almost the same 3D porous structures and porosity (Figure ##FIG##2##2D,E##), which holds great potential for facilitating vascular formation and bone regeneration. It is worth noting that the GA/BPPDH hydrogel seemed denser than the other hydrogels, and this phenomenon may be explained by the introduction of PDA increasing the additional crosslinking density in the hydrogel matrix. These results demonstrated that the global structure of the GA hydrogels did not change considerably after BPPD loading, which could be considered as a stable carrier for BPPD.</p>", "<p>The material surface hydrophilicity will influence cellular behaviors on the interface between the implant surface and host surrounding tissues. In view of this, the hydrophilicity of all hydrogels was evaluated by measuring their water contact angle. As shown in Figure ##FIG##2##2F##, the water contact angle was 74.3 ± 3.1° for GA, 61.7 ± 2.5 ± 4.3° for GA/BPPDL, 37.3 ± 2.1° for GA/BPPDM, and 31.3 ± 2.1 for GA/BPPDH, indicating the improved hydrophilicity of these hydrogels after the introduction of BPPD. The excellent hydrophilicity of the GA/BPPD hybrid hydrogels was strongly ascribed to the hydrophilic properties of the PDA and BP components, which was consistent with those of findings reported previously.<sup>[</sup>\n##REF##36996420##\n31\n##, ##REF##36469414##\n32\n##\n<sup>]</sup> Thus, the GA/BPPDM and GA/BPPDH hydrogels showed better wettability than the other hydrogel groups, which were expected to exhibit high performance in favor of cell adhesion, proliferation, growth, spreading, and differentiation.</p>", "<p>To achieve successful bone regeneration, the ideal implanted bone materials should possess long‐term structural stability and mechanical support. As shown in Figure ##FIG##2##2G##, the hybrid hydrogels could maintain their integrity and recover to their original shape without obvious breakage or collapse after repeated compression. The oscillatory rheology of the hydrogels was further tested to investigate their mechanical properties and stability, as shown in Figure ##FIG##2##2H##. As the oscillation frequency increased, the values of G′ (storage modulus) were consistently greater than G″ (loss modulus), showing good elasticity and mechanical stability of the hydrogel. Meanwhile, the G′ of the hydrogel increased with the addition of BPPD, indicating that the mechanical strength of the hydrogel increased with the increase of the crosslinked network. Notably, increasing the amount of BPPD from 0.5 wt.% to 1 wt.% did not further improve its mechanical properties but rather reduced the elastic modulus. This may be attributed to the reduction of the covalent crosslinking density in the GelMA hydrogel as the amount of BPPD was increased.</p>", "<p>The compressive properties of the hydrogels were also investigated, as shown in Figure ##FIG##2##2I,J##. The compressive stress‐strain curve indicated that the mechanical strength of the hydrogel increased with increasing BPPD concentration, which was due to the improved cross‐linking network. In detail, among all hydrogel groups, the GA hydrogel shows low compressive strength according to the stress‐strain curves. With subsequent BPPD loading, the compressive strength of the hydrogels gradually increased, which was consistent with the rheological results. In particular, the compressive strength of the as‐prepared GA/BPPDM hydrogel (45.1 ± 3.1 MPa) was higher than that of the GA (5.3 ± 1.2 MPa), GA/BPPDL (14.3 ± 1.2 MPa), and GA/BPPDH (26.3 ± 2.6 MPa) hydrogels. The results of the mechanical test demonstrated that the incorporation of BP‐based materials in the hydrogel showed significant improvement in the mechanical strength, which was consistent with previous studies.<sup>[</sup>\n##REF##31008576##\n33\n##\n<sup>]</sup> Notably, the enhanced stiffness might regulate cell adhesion, cell growth, and osteogenic differentiation by the enhanced mechanotransduction effect.<sup>[</sup>\n##REF##33260094##\n34\n##\n<sup>]</sup> However, increased BPPD concentration may lead to an inhomogeneous distribution in the GA matrix, resulting in the compromised mechanical strength of GA/BPPDH compared with GA/BPPDM. Through rheological and mechanical performance tests, it can be found that the GA/BPPDM hydrogel has a larger energy storage modulus and mechanical strength, so it is more resistant to external deformation and less susceptible to damage.</p>", "<p>In addition to desirable structural and mechanical properties, the swelling and degradation profiles of hydrogels play an important role in maintaining the stability of implants and promoting tissue regeneration. As shown in Figure ##FIG##2##2K##, the swelling of all hydrogels increased rapidly within 60 min and reached equilibrium within 48 h. The swelling ratios of GA, GA/BPPDL, GA/BPPDM, and GA/BPPDH were 1329 ± 50%, 958 ± 36%, 726 ± 40%, and 598 ± 36%, respectively, after 48 h, implying that the swelling ratio of hydrogels decreased with increasing concentrations of BPPD. The declined equilibrium swelling capacities of GA/BPPD may be due to their high crosslinking densities, preventing greater swelling of the hydrogel and buffer diffusion. To observe the in vitro degradation of hydrogels, freeze‐dried samples were collected and weighted after immersion into PBS solution in the presence of lysozyme (100 mg mL<sup>−1</sup>). All hydrogels gradually degraded with prolonged immersion time, and the degradation of GA/BPPD was retarded owing to the increased cross‐linking density in the hydrogel matrix caused by BPPD loading (Figure ##FIG##2##2L##). The results showed similar trends in the degradation and swelling behavior of the hydrogels. Collectively, GA/BPPD hydrogels with low swelling ratio and slow biodegradation rate are suitable for bone regeneration applications.</p>", "<title>Photothermal Performance and Drug Release Behaviors of the Hydrogels</title>", "<p>Recently, photothermal therapy (PTT) has emerged as a promising treatment modality to accelerate bone repair because of its remote controllability, non‐invasive properties, good therapeutic effectiveness, and strong tissue penetration depth.<sup>[</sup>\n##REF##35358870##\n35\n##\n<sup>]</sup> Both BP and PDA have been proven to have good photothermal effects.<sup>[</sup>\n##REF##37080119##\n19\n##\n<sup>]</sup> To evaluate the photothermal conversion efficiency of GA/BPPD, all hydrogel samples were irradiated with 808 nm NIR light at 1 W cm<sup>−2</sup>. As depicted in <bold>Figure</bold> ##FIG##3##\n3A##, upon NIR irradiation, the temperature of the GA/BPPD hydrogels increased gradually, while the GA hydrogel group showed no obvious temperature variation recorded by an infrared thermogram. After 5 min of NIR irradiation, the temperature was 36.7 ± 0.2 °C for the GA/BPPDL group, 43.8 ± 0.1 °C for the GA/BPPDM group, and 48.9 ± 0.2 °C for the GA/BPPDH group (Figure ##FIG##3##3B##). Notably, with expending irradiation time, the temperature of GA/BPPDM can eventually reach an equilibrium temperature (≈45 °C), meeting the basic biosafety requirements of mild photothermal biomaterials in promoting tissue regeneration. Moreover, the photothermal stability of the GA/BPPD hydrogel was investigated, as illustrated in Figure ##FIG##3##3C##. The corresponding results showed that the GA/BPPD hydrogels could be heated and cooled to fixed values without significant attenuation after four cycles of laser on/off, indicating high photostability and great potential to act as NIR‐controlled PTT. Previous studies have found that mild heat stimulation (≈45 °C) can not only promote angiogenesis and osteogenesis but also induce M2 phenotype polarization of macrophages.<sup>[</sup>\n##REF##35986434##\n12\n##, ##REF##36321923##\n36\n##\n<sup>]</sup> Significantly, the temperature of NIR‐triggered efficient mild PTT treatment was usually controlled to be below 45 °C to avoid side effects on normal tissues. In summary, after combining mechanical characterization and the requirement of mild‐temperature PTT (≈45 °C), we selected the GA/BPPDM hydrogel group as a suitable specification for subsequent experiments due to comprehensive consideration.</p>", "<p>To realize an appropriate regenerative microenvironment for bone regeneration, it is essential to develop controlled release formulations that can deliver multiple bioactive factors to manipulate cellular functions. The in vitro release kinetics of DFO from GA/BPPD were calculated by UV–vis spectrophotometry at a wavelength of 485 nm. Moreover, the drug loading capacity of DFO was characterized according to the standard calibration curve and is shown in Figure ##SUPPL##0##S3## (Supporting Information), with a loading efficiency of DFO reaching 79.8%. As shown in Figure ##FIG##3##3D##, GA/BPPDM showed typical dual NIR/pH‐dual‐responsive release behavior, and both NIR laser irradiation and the acidic environment could considerably accelerate the release of DFO, showing a similar phenomenon to previous studies.<sup>[</sup>\n##REF##36278256##\n20\n##, ##REF##31702885##\n37\n##\n<sup>]</sup> It is known that the initial physiological characteristics of bone injury are mainly a slightly acidic pH (pH≈6.5), whereas the pH of healthy tissues is 7.3–7.4.<sup>[</sup>\n##REF##35870263##\n6\n##\n<sup>]</sup> As such, the pH‐responsive drug release from GA/BPPDM was monitored under neutral (pH = 7.4) and slightly acidic (pH = 6.5) conditions to mimic the healthy and bone injury‐related physiological microenvironments, respectively. The cumulative release of DFO was only ≈21.3% at pH = 7.4 after 48 h, whereas at pH = 6.5, the amount released in 48 h reached ≈36%. Such acid‐accelerated DFO release behavior was ascribed to the pH sensitivity of the PDA layer and protonation of amine groups, which could result in the disruption of π−π interactions between DFO and PDA. As displayed in Figure ##FIG##3##3E,F##, the release peak of DFO appeared in the first two days and then quickly decayed, indicating that DFO was quickly released within a short time frame (≈7 days). Since bone remodeling requires rapid angiogenesis to provide adequate nutrition delivery, which is conducive to the formation of new bone and the survival of deep bone tissue, the relatively quick release of DFO from hydrogels is favorable for stimulating timely neovascularization and subsequently robust bone formation.</p>", "<p>In addition, the NIR‐responsive release behavior of DFO was investigated. Compared with internal pH stimuli, using NIR as external stimuli for drug delivery control exhibits several advantages, such as high tissue penetration, low tissue harm, easy operation, and spatiotemporal precise control of treatment.<sup>[</sup>\n##REF##37080119##\n19\n##\n<sup>]</sup> As can be seen from Figure ##FIG##3##3E,F##, the heat effect generated by NIR laser irradiation obviously affected DFO release. Burst drug release occurred after NIR laser irradiation was applied for 5 min at predetermined time intervals under different pH values. Under the action of the photothermal effect, the final cumulative release percentage of DFO reached ≈66.7% and 84.7% at pH values of 7.4 and 6.5, respectively, during the initial 48 h. In the following release time, the release rate of DFO slowed significantly, and the cumulative release percentage was 73.3% and 89.3% at pH values of 7.4 and 6.5, respectively. These curves presented a burst release in the first 7 days, followed by a slow and plateaued DFO release. The reason for the controlled drug release mode was probably associated with the enhanced diffusion effect under elevated temperature. This result indicated that GA/BPPDM with photothermal function could further trigger DFO release in a thermal‐stimuli manner. Then, the release of PO<sub>4</sub>\n<sup>3−</sup> from the GA/BPPDM hydrogel was investigated by ion chromatography. As shown in Figure ##SUPPL##0##S4## (Supporting Information), the cumulative release percentage of PO<sub>4</sub>\n<sup>3−</sup> from the hydrogel increased over the soaking time, and a relatively fast release of PO<sub>4</sub>\n<sup>3−</sup> within 10 days was observed. Although the release rate of PO<sub>4</sub>\n<sup>3−</sup> slowed down with an increase in immersion time, the cumulative release curve suggested that PO<sub>4</sub>\n<sup>3−</sup> release could continue for up to 28 days in vitro under NIR or without NIR treatment. This sustained release behavior was mainly because the protective effects of the hydrogel matrix and organic coating composed of PDA and DFO synergistically reduced the release of PO<sub>4</sub>\n<sup>3−</sup> from the BPPD nanocomposites. A sustainable and slow release of PO<sub>4</sub>\n<sup>3−</sup> has been shown to be better for osteogenic differentiation, while the relatively fast release of DFO is preferred for angiogenesis.<sup>[</sup>\n##UREF##3##\n7\n##, ##REF##34704438##\n15\n##\n<sup>]</sup> These results directly confirmed that the GA/BPPDM hydrogel had both intelligent controlled‐release (DFO) and sustained‐release (PO<sub>4</sub>\n<sup>3−</sup>) capacities, which made the GA/BPPDM hydrogel as a desirable platform to promote bone regeneration over a long‐term period. From the above results, it was suggested that our nanocomposite hydrogel has a “smart” drug release feature, that is, “switching on” enhanced drug release under both NIR laser irradiation and slightly acidic conditions to enhance bone regeneration efficacy. With the assistance of external NIR photothermal stimuli and bone injury site environmental changes, such as pH, codelivery of DFO/PO<sub>4</sub>\n<sup>3−</sup> for synergistic immunomodulation, revascularization and efficient bone regeneration could be achieved. Considering the above rationale, the smart‐responsive GA/BPPDM hydrogels will be promising in the applications of bone defect treatment and even other tissue regeneration.</p>", "<title>In Vitro Evaluation of Cytocompatibility</title>", "<p>In the following experiments, both MC3T3‐E1 cells and HUVECs were used to evaluate the influence of the nanocomposite hydrogels on cell viability and proliferation, as they are the major and important cell sources for bone formation and vascular regeneration.<sup>[</sup>\n##UREF##13##\n38\n##, ##UREF##14##\n39\n##\n<sup>]</sup> The results of the CCK‐8 assay revealed that the OD values of the four hydrogel groups increased with the culture time prolonging (<bold>Figure</bold> ##FIG##4##\n4A,C##), indicating that the cells maintained good viability and proliferation ability. More specifically, cell proliferation on day 1 was similar for all groups and the cells co‐cultured on the hydrogels proliferated over time. After 2 days of co‐incubation, compared to the GA hydrogel, the hydrogels loaded with active BPPD nanocomposites showed a slightly improved cell proliferation rate, although there was no obvious difference among the four groups of GA, GA/BPPDL, GA/BPPDM, and GA/BPPDH. When it came to 3 days, the highest cell proliferation rate was found in GA/BPPDM, followed by GA/BPPDL and GA/BPPDH, then GA, revealing that the hydrogel group loaded with BPPD, especially 0.5 wt.%, was more beneficial for promoting cell proliferation. The excellent cell affinity of these hydrogels was also confirmed by live/dead staining assay, as shown in Figure ##FIG##4##4B,D##. After co‐culturing for 3 days, almost all MC3T3‐E1 cells and HUVECs were alive (green fluorescence) in the GA, GA/BPPDL, GA/BPPDM, and GA/BPPDH hydrogels, with only a few dead cells present (red fluorescence), indicating that the composite hydrogels could support cell survival and growth (viability &gt; 90%). According to the quantitative results, all hydrogels had excellent cytocompatibility for both MC3T3‐E1 cells and HUVECs, and the existence of BPPD substantially increased the cell density and the percentage of living cells (Figure ##FIG##4##4G,I##), improving the bioactivity of the hydrogel. Notably, significantly promoted proliferation of cells was observed in the GA/BPPDM hydrogel group compared with GA/BPPDL and GA/BPPDH, which was in accordance with the results of the CCK‐8 analysis. Both GelMA and Alg‐MA have high biocompatibility and mimic the chemical properties of the ECM; meanwhile, BP and PDA have shown excellent biocompatibility in previously reported studies.<sup>[</sup>\n##REF##36125961##\n17\n##, ##UREF##11##\n29\n##\n<sup>]</sup> The enhanced cell proliferation was likely due to phosphate and DFO release into the culture medium, which was consistent with literature reports.<sup>[</sup>\n##REF##34894585##\n40\n##\n<sup>]</sup> However, with a concentration higher than 0.5 wt.%, no obvious enhancement was observed, mostly because higher concentrations of phosphate and DFO disturbed normal cell activity. This implied that at an appropriate level, BPPD nanomaterials might promote cell growth, which can also explain why cells on GA/BPPDM are well proliferated and widely distributed.</p>", "<p>The adhesion and spreading morphologies of the cells were further observed by cytoskeleton staining. After being co‐cultured for 3 days, the cytoskeletal morphology of MC3T3‐E1 cells revealed that the cells in the GA group had only a few pseudopodia and had not completely spread on the hydrogel. In contrast, the cells adhered to the GA/BPPD hydrogels exhibited better stretched morphology with well‐developed cell cytoskeletons and clusters, extending numerous branchy filamentous pseudopods and tightly interleaving with each other (Figure ##FIG##4##4E##; Figure ##SUPPL##0##S5A##, Supporting Information). In particular, the cells on the GA/BPPDM hydrogel spread well with a typical elongated‐spindle and osteoblastic‐like morphology, indicating a favorable growth status, which may be attributed to its optimal BPPD concentration and hydrophilicity. Additionally, we also observed increased numbers of cell colonies on GA/BPPDM samples compared to pure GA, which allowed for more cell attachment and spreading, revealing the positive effects of BPPD on improving cell migration and proliferation, which is consistent with the results of cell toxicity and proliferation assays. Recent studies have found that cell morphology plays a vital role in regulating the phenotype of cells, and an elongated spindle‐shaped morphology has been found to be tightly correlated with the adhesion, proliferation, and differentiation of osteoblast‐related cells and endothelial cells.<sup>[</sup>\n##UREF##15##\n41\n##, ##UREF##16##\n42\n##\n<sup>]</sup> The enlarged confocal laser scanning microscopy (CLSM) images further verified the good cell adhesion and spreading behaviors on the GA/BPPDM hydrogel (Figure ##SUPPL##0##S5A##, Supporting Information), as evidenced by the stretched filopodia and cytoskeletal rearrangement. According to the CLSM observation (Figure ##FIG##4##4E##) and quantitative results (Figure ##FIG##4##4G,H##), more cells adhered to the GA/BPPDM hydrogel not only exhibited the highest spreading area, but the actin filaments that make up the cytoskeleton were also highly expressed, implying a strong interaction between cells and the GA/BPPDM hydrogel. Concomitantly, similar results were also detected in HUVECs grown on the hydrogels, in which the HUVECs grown on the GA/BPPDM hydrogel presented well‐stretched morphology and favorable proliferation (Figure ##FIG##4##4F,I,J##; Figure ##SUPPL##0##S5B##, Supporting Information). These encouraging results suggested that the incorporation of moderate BPPD contributed to the adhesion behavior of MC3T3‐E1 cells and HUVECs due to the nature of each raw material, including PDA, DFO, and BP nanosheets, which demonstrated good cell affinity and improved cell crawling and adhesion properties.<sup>[</sup>\n##UREF##3##\n7\n##, ##REF##34704438##\n15\n##, ##UREF##17##\n43\n##\n<sup>]</sup> With high bioactivity and hydrophilicity, BPPD nanomaterials might serve as cell adhesion sites that promote cell growth, spreading, and differentiation. Overall, our data showed that all fabricated GA/BPPD nanocomposite hydrogels, especially GA/BPPDM, possessed remarkably positive effects on MC3T3‐E1 cell and HUVEC proliferation, survival, and growth. Considering the vital role of cell proliferation in cell differentiation and subsequent tissue formation, we chose the GA/BPPDM hydrogel to further verify its osteogenesis, angiogenesis, and immunomodulatory capability in vivo and in vitro.</p>", "<title>In Vitro and In Vivo Immunomodulatory Properties</title>", "<p>Although multiple immune cell types are involved in the immune response and microenvironment regulation, macrophages have been demonstrated to play a prominent role in tissue regeneration and remodeling. Following bone injury, macrophages predominate as proinflammatory phenotypes (M1) at the inflammation stage and contribute to the characteristics of high ROS in response to local inflammatory signals.<sup>[</sup>\n##UREF##18##\n44\n##\n<sup>]</sup> Unfortunately, excessive inflammatory response‐induced overproduction of ROS in the bone defect region has a detrimental impact on bone regeneration. Increased levels of ROS in the bone defect can not only cause cell death in osteoblast precursor cells and mature osteoblasts but also reduce the expression of osteogenic markers and mineralization, leading to prolonged and unhealed bone injury.<sup>[</sup>\n##REF##35870263##\n6\n##\n<sup>]</sup> Therefore, the development of functional biomaterials with excellent immunomodulatory effects and ROS‐scavenging capacity is of great significance to promote the regeneration of bone tissue (<bold>Figure</bold> ##FIG##5##\n5A##). In this work, RAW264.7 cells were selected as the model of macrophages and then treated with LPS (a component of Gram‐negative bacterial cell walls) to imitate acute inflammatory responses and induce macrophages to the M1 phenotype, thus leading to the production of numerous free radicals (i.e., ROS) and long‐term inflammation. Macrophages were co‐cultured with different hydrogels, and the macrophage response was then assessed via immunofluorescence staining and flow cytometry. As shown in Figure ##SUPPL##0##S6A## (Supporting Information), the highest expression level of ROS was observed in the control group exposed to LPS, suggesting that cellular oxidative stress was successfully induced. Interestingly, both GA/BPPDM and GA/BPPDM+NIR effectively inhibited LPS‐provoked ROS generation, as evidenced by the decreased 2′,7′‐dichlorofluorescein diacetate (DCFH‐DA) fluorescent signals and the shift of its relative fluorescence intensity to the left (Figure ##SUPPL##0##S6B##, Supporting Information). More importantly, cells treated with GA/BPPDM plus NIR irradiation exerted the most significant inhibitory effects on total ROS generation, showing negligible green fluorescence, which indicated a strong ability to protect cells from ROS‐induced oxidative damage. Thus, these results demonstrated that GA/BPPDM combined with mild photothermal treatment through NIR irradiation could reduce the excessive oxidative stress of cells induced by the inflammation‐related response, showing protective effect on cell function. Studies have shown that in addition to a notable promoting effect on osteogenesis, BP has a strong ROS‐scavenging capability and high bioactivity, showing great prospects for application in promoting tissue repair and regeneration.<sup>[</sup>\n##UREF##19##\n45\n##\n<sup>]</sup> Additionally, owing to the presence of abundant catechol groups, PDA could efficiently eliminate intracellular ROS and thus exhibit anti‐inflammatory ability by regulating the proportion of M1/M2 macrophages,<sup>[</sup>\n##REF##34237507##\n26\n##, ##REF##36736645##\n46\n##\n<sup>]</sup> and the anti‐inflammatory effect of DFO has been reported more frequently.<sup>[</sup>\n##UREF##7##\n22\n##\n<sup>]</sup> The anti‐inflammatory effect of DFO was achieved through its excellent iron‐chelating ability, which enabled it to scavenge free radicals and ROS generated after acute inflammation. Furthermore, the mild photothermal effect (41 ± 1 °C) triggered by NIR irradiation could further enhance the radical scavenging ability of the hybrid hydrogel, which may be related to accelerated disassembly of BPPD, thus facilitating adequate contact between reductive components and free radical detection reagents, consistent with the results of previous work.<sup>[</sup>\n##REF##35759676##\n47\n##\n<sup>]</sup> On the basis of previously published studies, our current findings supported the excellent antioxidant ability of the GA/BPPDM hydrogel system because of the combined effects of bioactive components (BP, PDA, and DFO) and mild photothermal activity upon NIR irradiation.</p>", "<p>Accumulating data show that M1‐type macrophages aggravate inflammation, while M2‐type macrophages with anti‐inflammatory effects can ameliorate the local inflammatory microenvironment and promote tissue regeneration.<sup>[</sup>\n##UREF##10##\n28\n##\n<sup>]</sup> Thus, guiding the polarization of macrophages toward the regenerative M2 phenotype is more likely to achieve immune‐mediated bone regeneration. To evaluate the effect of the GA/BPPDM hydrogel platform on macrophage reprogramming, we first collected RAW264.7 cells and investigated the morphological changes by cytoskeleton staining. As shown in Figure ##FIG##5##5B##, macrophages cultured on GA/BPPDM hydrogels under NIR laser irradiation appeared as elongated and flattened spindle‐like cells, which are the morphological characteristics of M2 macrophages. Subsequently, the effects of the hydrogels with or without NIR radiation on the 3D migration of macrophages were investigated by cytoskeleton staining. Recent studies have reported that macrophage infiltration is the initial and critical step in the process of regeneration, while promoting macrophage infiltration accelerates hard callus formation and ossification.<sup>[</sup>\n##REF##34325336##\n48\n##\n<sup>]</sup> As displayed in Figure ##FIG##5##5C##, 3D‐reconstructed CLSM images demonstrated that the macrophages not only adhered to the surface of the hydrogels but also gradually infiltrated into the 3D network of the hydrogel matrix. Importantly, the cells treated with GA/BPPDM+NIR exhibited the strongest migration and penetration capabilities, followed by the GA/BPPDM group. In sharp contrast, cell infiltration was almost invisible inside the GA hydrogel, in which cells mainly grew on the top surface of the hydrogel.</p>", "<p>To validate the phenotypes of polarized macrophages after treatment, the M1 and M2 phenotypes of macrophages were labeled with CD86 and CD206, respectively, and then detected by flow cytometry. As shown in Figure ##FIG##5##5D##, a significant increase of CD86 (an M1 marker) expression was observed in RAW264.7 cells after treatment with LPS, while the expression of CD86 in the GA, GA/BPPDM and GA/BPPDM+NIR groups was reduced, indicating the activation of macrophage polarization toward the M2 phenotype. Specifically, higher levels of CD206 (an M2 marker) expression were observed in the GA/BPPDM group than in the LPS and GA groups, and this effect was even more pronounced after periodic and appropriate NIR irradiation. According to the statistical results in Figure ##FIG##5##5E,F##, significantly higher ratios of M2 macrophages (CD206<sup>+</sup> cells) and decreased M1 macrophages (CD86<sup>+</sup> cells) were observed in the GA/BPPDM+NIR group with better immunomodulatory ability. These results demonstrated that the combined therapy of GA/BPPDM plus mild PTT treatment was beneficial for switching the macrophage phenotype from M1 toward M2, leading to the creation of an anti‐inflammatory microenvironment. Immunofluorescence staining further confirmed that GA/BPPDM plus mild photothermal effect was more conducive to macrophage M2 polarization than GA and GA/BPPDM alone (Figure ##FIG##5##5G##). The quantitative fluorescence intensity also showed that the GA/BPPDM+NIR group presented higher CD206<sup>+</sup> expression and lower iNOS<sup>+</sup> expression (Figure ##SUPPL##0##S7##, Supporting Information). According to our in vitro results, GA/BPPDM combined with mild thermal stimulation at 41 ± 1 °C could promote M2 polarization of macrophages and inhibit the expression of M1 macrophages under NIR irradiation conditions, showing huge potential to shorten the inflammation phase and shift it into the proliferation phase during bone regeneration. To further reveal the role of GA/BPPDM and NIR treatment in the immune response, the expression of a series of inflammatory and pro‐healing cytokines was evaluated in the cell supernatant by ELISA. As expected, GA/BPPDM was associated with increased secretion of anti‐inflammatory IL‐10 and IL‐4 and decreased secretion of proinflammatory TNF‐α and IL‐6 under thermal stimulation provided by NIR irradiation (Figure ##SUPPL##0##S8##, Supporting Information). More significantly, compared with the other groups, the GA/BPPDM+NIR group secreted much more pro‐osteogenic (BMP‐2, TGF‐β1) and pro‐angiogenic (VEGF, bFGF) factors, followed by the GA/BPPDM and GA groups (Figure ##SUPPL##0##S9##, Supporting Information). Previous studies have found that M2‐type macrophages can participate in bone regeneration by regulating the release of growth factors (BMP‐2, TGF‐β1, VEGF, and bFGF) and paracrine signals.<sup>[</sup>\n##REF##33984633##\n3\n##\n<sup>]</sup> The GA/BPPDM+NIR hydrogel system is able to polarize macrophages to an anti‐inflammatory M2 phenotype, which is consistent with the results of flow cytometry, resulting in the release of pro‐regenerative factors associated with osteogenesis and angiogenesis. Likewise, both real‐time polymerase chain reaction (qRT‐PCR) and Western blot results confirmed that M2 phenotypic markers, such as IL‐4, IL‐10, Arg‐1, and CD206, were significantly upregulated in the GA/BPPDM+NIR group (Figure ##FIG##5##5H##; Figure ##SUPPL##0##S10##, Supporting Information). On the contrary, the expression of M1 phenotypic markers, such as CD86, IL‐6, TNF‐α, and iNOS, was relatively lower in the GA/BPPDM+NIR group than in the GA/BPPDM group (Figure ##FIG##5##5I##; Figure ##SUPPL##0##S10##, Supporting Information). These results suggested that the GA/BPPDM hydrogel system together with NIR‐triggered drug release had the potential to synergistically alleviate the inflammatory reaction and induce tissue regeneration through the transition of M1‐to‐M2 macrophage polarization.</p>", "<p>Previous studies have shown that mild hyperthermia triggered by NIR irradiation could induce an increase in anti‐inflammatory cytokine secretion, ROS scavenging, and the transformation of the M1‐M2 phenotype of macrophages via activation of the PI3K/Akt1 signaling pathway, leading to a favorable regenerative microenvironment for tissue regeneration.<sup>[</sup>\n##REF##35986434##\n12\n##, ##UREF##20##\n49\n##\n<sup>]</sup> The role of the PI3K/Akt1 signaling pathway in the regulation of macrophage polarization has been well studied, and PI3K is an upstream regulator of protein kinase B (Akt) and has been demonstrated to modulate the phenotype of M2 macrophages.<sup>[</sup>\n##UREF##21##\n50\n##\n<sup>]</sup> Given that, the PI3K/Akt1 signaling pathway was subsequently verified via Western blot analysis. As shown in Figure ##SUPPL##0##S11## (Supporting Information), the GA/BPPDM+NIR group remarkably enhanced the PI3K, Akt1, and p‐Akt1 protein expression of RAW264.7 cells, indicating that PI3K/Akt1 signaling is activated, which may be important to promote cascading macrophage M2 polarization. These results further suggested that the photothermal GA/BPPDM hydrogel system may therapeutically alleviate inflammation and induce the polarization of macrophages toward the M2 phenotype by activating the PI3K/Akt1 signaling pathway to downregulate the expression of inflammatory cytokines.</p>", "<p>To further identify the immunomodulatory ability during the early stage of implantation, we evaluated the macrophage phenotypes in subcutaneously embedded tissue sections on day 7 as mentioned above (Figure ##FIG##5##5J##). Real‐time infrared thermal images were captured after irradiating the implanted hydrogel samples with an 808 nm NIR laser. Consistent with the in vitro polarization of macrophages, immunohistochemical staining confirmed that the GA/BPPDM+NIR group was more conducive to macrophage M2 polarization than the GA/BPPDM group (Figure ##FIG##5##5K##). Quantitative analysis showed higher CD206<sup>+</sup> expression and lower iNOS<sup>+</sup> expression in the GA/BPPDM+NIR group than in the GA/BPPDM group (Figure ##SUPPL##0##S12##, Supporting Information). The proteins of the cells in the subcutaneously embedded hydrogel were extracted and processed for ELISA measurement. The GA/BPPDM hydrogel with NIR stimulation showed higher expression of the anti‐inflammatory factor IL‐10 and lower expression of the proinflammatory factor TNF‐α (Figure ##SUPPL##0##S13##, Supporting Information), which is also consistent with the in vitro tests. The GA/BPPDM photothermal therapeutic platform effectively alleviated inflammation and altered the secretion of cytokines in the microenvironment through immunomodulation compared to the GA/BPPDM and GA groups alone. Based on these in vitro and in vivo results, it is summarized that the GA/BPPDM hydrogel could modulate macrophage polarization and promote anti‐inflammatory processes under on‐demand NIR irradiation, thus shortening the inflammatory phase.</p>", "<title>In Vitro and In Vivo Angiogenesis Assay</title>", "<p>Accumulating evidence has well‐established that angiogenesis is essential for the reconstruction processes of bone healing, which helps to promote new bone formation by accelerating the transportation of nutrients, signaling molecules, and so on.<sup>[</sup>\n##UREF##14##\n39\n##, ##REF##32215404##\n51\n##\n<sup>]</sup> In view of this, satisfactory pro‐angiogenic activities are required for advanced functional biomaterials to satisfy the demands for bone healing. To evaluate the potential effects of NIR‐triggered drug release of the hydrogels on angiogenesis, HUVECs cultured with the hydrogels with or without NIR irradiation were subjected to angiogenic differentiation assay (<bold>Figure</bold> ##FIG##6##\n6A##). The effect of the hydrogel on HUVEC migration was first evaluated by wound healing experiments. Cell migration appeared in all groups and was much better in the GA/BPPDM and GA/BPPDM+NIR groups than in the GA group (Figure ##FIG##6##6B##). The GA/BPPDM+NIR group displayed better wound closure at 24 h, in which the scratch was almost closed, followed by the GA/BPPDM group. The quantitative analysis further indicated better wound closure in the GA/BPPDM+NIR groups than in the GA/BPPDM and GA groups at 24 h (Figure ##FIG##6##6C##), which was mainly ascribed to the accumulated release of DFO triggered by periodic NIR irradiation. In vitro Transwell migration assay was also performed to investigate the potential of the hydrogel system to induce HUVEC migration. As shown in Figure ##SUPPL##0##S14## (Supporting Information), both the GA/BPPDM and GA/BPPDM+NIR groups could exert a chemotaxis effect on recruiting more HUVECs than the GA group. Additionally, the migration ability was considerably improved by the GA/BPPDM hydrogel upon NIR irradiation, as indicated by the highest number of transmembrane cells observed in the GA/BPPDM+NIR group. Here, the wound healing and Transwell migration assays revealed better migration ability for HUVECs in the GA/BPPDM group, but the promotive effect was not as strong as that of the GA/BPPDM+NIR group. Collectively, these results indicated that the migration ability of HUVECs was effectively improved by GA/BPPDM together with on‐demand NIR irradiation, which was also beneficial for vascular regeneration and bone formation.</p>", "<p>The in vitro tube formation assay was further conducted to evaluate the pro‐angiogenic activity of the prepared hydrogels using Matrigel because angiogenesis is a key factor in bone healing, and the ability to promote angiogenesis can accelerate the repair process. As shown in Figure ##FIG##6##6D##, little tubule formation was observed in the GA group, suggesting that the vasculogenic ability of the cells was limited. As expected, the formation of tubular frameworks was detected in the GA/BPPDM and GA/BPPDM+NIR groups; however, compared with the GA/BPPDM group, more mature and intact tubular structures as well as a higher density of cell junctions were observed in the GA/BPPDM+NIR group. In terms of the quantitative analysis, both the vessel percentage area and total number of junctions were significantly increased in the GA/BPPDM+NIR group, followed by the GA/BPPDM group (Figure ##FIG##6##6E,F##), indicating that enhanced vessel formation likely occurred because of the cumulative effect of sustainedly released DFO from GA/BPPDM with the assistance of NIR irradiation. The rapid establishment of vessel networks can promote the recruitment of nutrients and related growth factors at the defect area, thereby accelerating the repair process. These results indicated that the outstanding pro‐angiogenic potential of the GA/BPPDM+NIR group was mainly due to continuous NIR‐triggered DFO release, which can effectively induce cell migration and tubule formation in vitro, benefiting the repair and angiogenesis of impaired tissues.</p>", "<p>Vascularization during bone healing is known to be regulated by growth factors such as VEGF and bFGF and other downstream angiogenic molecules, including eNOS and HIF‐1α expressed by endothelial cells.<sup>[</sup>\n##REF##35946874##\n52\n##\n<sup>]</sup> In view of this, the expression of angiogenesis‐related factors in HUVECs was further studied by qRT‐PCR analysis. As expected, HUVECs in the GA/BPPDM+NIR group owned the highest expression levels of Ang‐1, bFGF, eNOS, HIF‐1α, and VEGF (Figure ##FIG##6##6G##); this was because of the continuous accumulation of DFO from the GA/BPPDM hydrogel with the help of NIR irradiation. It has been verified that DFO is beneficial for the stimulation of angiogenesis. Meanwhile, DFO can stabilize HIF‐1α expression, followed by upregulating the expression of angiogenic factors such as VEGF.<sup>[</sup>\n##REF##34894585##\n40\n##\n<sup>]</sup> As for the GA/BPPDM group, due to the incorporation of BPPD, a significant promotion effect on angiogenic activity was demonstrated. Next, the angiogenic capacity of different hydrogels was further verified by immunofluorescence staining of CD31, VEGF, and HIF‐1α. After 7 days of co‐incubation, the protein expression of CD31 was significantly increased in both the GA/BPPDM and GA/BPPDM+NIR groups, especially in the GA/BPPDM+NIR group, in which the fluorescence signal of CD31 displayed the highest expression level (Figure ##FIG##6##6H##), suggesting enhanced vascularization. Unsurprisingly, the results of VEGF and HIF‐1α protein expression showed the same tendency that the GA/BPPDM+NIR groups exhibited the most significant expression of VEGF and HIF‐1α protein markers, followed by the GA/BPPDM and GA groups (Figure ##FIG##6##6I##). The quantitative results of fluorescence intensity also demonstrated the most significant expression of angiogenic protein markers in the GA/BPPDM+NIR group (Figure ##SUPPL##0##S15##, Supporting Information), indicating enhanced angiogenic activity. From the above results, it was concluded that the GA/BPPDM+NIR group might activate the HIF‐1α pathway and promote the expression of angiogenesis‐related genes/proteins, including Ang‐1, bFGF, eNOS, and VEGF, in HUVECs, which led to the rapid angiogenesis process in vitro.</p>", "<p>In bone tissue engineering, early blood vessel formation can provide sufficient nutrient supply and accelerate new bone formation. To evaluate the impacts of hydrogels on the angiogenesis process in vivo, samples were implanted subcutaneously into the backs of rats to observe new blood vessel formation (Figure ##FIG##6##6J##). During NIR laser irradiation, the temperature changes and corresponding thermal images of the implanted site were recorded by an infrared thermograph, as shown in Figure ##FIG##6##6K##. After 7 days of implantation, the tissues surrounding the implanted hydrogels were subjected to histological observation. The results of hematoxylin and eosin (H&amp;E) staining showed that quite a lot of surrounding tissue cells could be detected around and within the GA/BPPDM+NIR group (Figure ##FIG##6##6L##), implying that the GA/BPPDM hydrogel and mild heat stimulation contributed to the fast ingrowth of the surrounding tissues (red arrows), especially to timely vascular growth, which is essential for tissue remodeling. Owing to the biodegradable hydrogel matrix and bioactive BPPD nanomaterial as well as mild heat stimulation, the cells could migrate into the hydrogels rapidly after in vivo implantation. As a result, the GA/BPPDM+NIR group exhibited excellent tissue integration. The in vivo angiogenic abilities of the implanted hydrogels were further investigated by immunohistochemical analyses of CD31 and α‐SMA, as shown in Figure ##FIG##6##6M##. It is obviously found that there were a greater number of newly formed CD31<sup>+</sup> and α‐SMA<sup>+</sup> blood vessels (yellow arrows) around the GA/BPPDM and GA/BPPDM+NIR groups than around the GA group, implying a higher vascular regeneration improvement. The reason might be that the release of DFO in the early stage was demonstrated to improve the angiogenic activity of the hydrogel and promote angiogenesis in vivo, consistent with previously reported studies.<sup>[</sup>\n##UREF##22##\n53\n##\n<sup>]</sup> Significantly, the expression of CD31 and α‐SMA in the GA/BPPDM+NIR group was the highest among the three groups, which was ascribed to the ability of the on‐demand NIR‐assisted mild heat stimulation to promote adhesion, migration, and angiogenesis as well as induce fast DFO release to a greater extent than the hydrogel without NIR treatment. Accordingly, the quantitative results further verified the formation and quantity of blood vessels in the different groups, supporting the robust stimulation of angiogenesis in the initial inflammatory phase by the GA/BPPDM+NIR group (Figure ##FIG##6##6N,O##), which was consistent with the in vitro results. The above evidence showed that GA/BPPDM could effectively induce the formation of microvessels, and on‐demand NIR irradiation could further accelerate neovascularization due to the synergetic effect of mild heat stimulation and NIR‐triggered DFO release.</p>", "<title>In Vitro Evaluation of Osteogenic Differentiation</title>", "<p>The ability to recruit endogenous cells from surrounding areas is critical for initiating efficient vessel and bone regeneration. To investigate the effect of the as‐prepared hydrogel platform on recruiting osteoblast precursor cells, a Transwell migration assay was conducted with or without NIR irradiation. As shown in Figure ##SUPPL##0##S16## (Supporting Information), with burst release of PO<sub>4</sub>\n<sup>3‐</sup> and DFO from the hydrogels upon NIR irradiation, the GA/BPPDM+NIR group significantly improved the recruitment of MC3TE‐E1 cells in vitro. After being co‐cultured for 24 h, the cell numbers recruited by the GA/BPPDM+NIR group were 3.8‐fold and 1.8‐fold that of the GA/BPPDM and GA groups, respectively, demonstrating that BPPD loading and NIR treatment efficiently enhanced MC3TE‐E1 cell recruitment. Previous studies have demonstrated that BP‐incorporated biomaterials display a positive effect on osteogenesis by modulating osteogenic cytokine secretion to recruit osteoblasts and promote osteogenic activity.<sup>[</sup>\n##REF##36996420##\n31\n##, ##UREF##23##\n54\n##\n<sup>]</sup> Meanwhile, DFO can be rapidly released from the GA/BPPDM hydrogel with the assistance of NIR irradiation and synergize with BP to further promote the proliferation, migration and osteogenic differentiation of cells. This suggested that the NIR‐induced photothermal effect could trigger the release of large amounts of drug/ion quickly to promote cell migration, as evidenced by the results of the release behaviors in vitro.</p>", "<p>We next assessed the effect of the hydrogel platform on the osteogenic differentiation of MC3TE‐E1 cells. A cell co‐culture system was established using a Transwell device, in which the hydrogels were placed in the upper chamber and MC3TE‐E1 cells in the lower chamber under NIR laser irradiation (<bold>Figure</bold> ##FIG##7##\n7A##). As a hallmark of osteogenic differentiation in the early stage, alkaline phosphatase (ALP) activity was first evaluated by qualitative and quantitative measurements in vitro. As illustrated in Figure ##FIG##7##7B##, the GA/BPPDM+NIR group exhibited the deepest ALP staining, followed by the GA/BPPDM and GA groups, which confirmed that the GA/BPPDM hydrogel with NIR‐induced PTT treatment promoted the early osteogenic differentiation of MC3TE‐E1 cells. Correspondingly, through the quantitative analysis of ALP activity, both the GA/BPPDM and GA/BPPDM+NIR groups caused a significant increase in ALP production compared with the GA group (Figure ##FIG##7##7D##). In particular, the ALP activities in the GA/BPPDM+NIR group were significantly higher than those in the other groups on days 7 and 14, demonstrating the synergistic effects of BPPD and NIR‐triggered drug/ion release on inducing osteogenic differentiation in vitro.</p>", "<p>The deposition of calcium minerals, as an important indicator of the later stage of osteogenic differentiation, was evaluated by Alizarin red S (ARS) staining. Consistent with the results of ALP activity, both macroscopic and microscopic images showed that the GA/BPPDM+NIR group presented the highest amounts of bone‐mineralized nodules with an enhanced degree of positive staining among all groups (Figure ##FIG##7##7C##), indicating better osteogenic potential. In a previous study, Shao et al. found that irradiation with NIR light not only accelerated the degradation of BP‐incorporated hydrogels into PO<sub>4</sub>\n<sup>3−</sup>, but also enhanced the biological activity to facilitate the reaction between PO<sub>4</sub>\n<sup>3−</sup> and Ca<sup>2+</sup>, thus promoting bone regeneration through in situ biomineralization.<sup>[</sup>\n##UREF##24##\n55\n##\n<sup>]</sup> In line with the qualitative results, higher levels of mineral matrix formation were detected in the GA/BPPDM and GA/BPPDM+NIR groups, especially in the GA/BPPDM+NIR group (Figure ##FIG##7##7E##). To further assess the in vitro osteogenic potential of the photothermal hydrogel platform, rat BMSCs were also selected for this study because they are the major and important cell source for bone repair and regeneration (Figure ##SUPPL##0##S17A##, Supporting Information). Unsurprisingly, the GA/BPPDM+NIR group showed the highest ALP activity and mineralized nodule formation compared with any other group, followed by the GA/BPPDM and GA groups (Figure ##SUPPL##0##S17B–E##, Supporting Information). These data strongly implied that the incorporation of BPPD could promote osteogenic differentiation in vitro, and NIR‐triggered PO<sub>4</sub>\n<sup>3‐</sup> and DFO release further exerted a potent synergistic effect on osteogenesis. Thus, the GA/BPPDM+NIR group could promote osteogenic differentiation and accelerate mineralized matrix formation in both MC3TE‐E1 cells and BMSCs.</p>", "<p>It has been reported that Col‐1, OPN, and OCN are important components of the ECM of bone, and Runx2 is a critical transcription factor regulating the expression of osteogenesis‐related genes.<sup>[</sup>\n##REF##36469414##\n32\n##\n<sup>]</sup> Therefore, the effects of GA/BPPDM and NIR‐triggered DFO on the osteogenic differentiation of both MC3T3‐E1 cells and BMSCs were investigated through genetic‐ and protein‐level analyses. As illustrated in Figure ##FIG##7##7F–H## and Figure ##SUPPL##0##S17F## (Supporting Information), the expression levels of ALP, Runx2, Col‐1, OPN, and OCN substantially increased in the GA/BPPDM and GA/BPPDM+NIR groups compared with the GA group, indicating that BPPD plays an important role in upregulating the expression of osteogenic markers. Interestingly, in comparison with the GA and GA/BPPDM groups, the GA/BPPDM+NIR group showed the strongest improvement in inducing osteogenic marker expression, consistent with the ALP and ARS evaluation; this result demonstrated that the BPPD and NIR‐triggered DFO and PO<sub>4</sub>\n<sup>3−</sup> release had a synergistic effect on promoting the expression of both early and late osteogenic markers. It is acknowledged that BP not only can be used as a photothermal agent, but also has biological activity and participates in the mineralization process, which induces osteogenesis by activating multiple signaling pathways, including the Wnt/β‐catenin and Ras/MAPK signaling pathways.<sup>[</sup>\n##REF##36920036##\n14\n##\n<sup>]</sup> On the other hand, the DFO released from the on‐demand delivery hydrogel also contributed to the enhancement of osteogenic activity.<sup>[</sup>\n##REF##35946874##\n52\n##\n<sup>]</sup> Similar trends were also detected for osteogenic marker protein expression in the immunofluorescence staining assay. As displayed in Figure ##FIG##7##7I## and Figure ##SUPPL##0##S17G## (Supporting Information), the immunofluorescence staining assay revealed that both MC3T3‐E1 cells and BMSCs in the GA/BPPDM group secreted more osteogenic (Runx2 and OPN) proteins than those in the GA group, which also revealed the pro‐osteogenic activity of BPPD. More importantly, among all the groups, the GA/BPPDM hydrogel with heat stimulation showed the highest expression of Runx2 and OPN upon NIR irradiation (Figure ##SUPPL##0##S18##, Supporting Information), which represented an excellent improvement in bone formation. Overall, these data demonstrated that the GA/BPPDM+NIR group had a prominent stimulatory effect on the osteogenic differentiation of both MC3T3‐E1 cells and BMSCs and probably promoted bone healing by upregulating the gene expression of ALP, Runx2, Col‐1, OPN, and OCN.</p>", "<title>In Vitro Evaluation of the Effect of Immunomodulation on Angiogenesis and Osteogenesis</title>", "<p>During the process of bone regeneration, activated M2 macrophages participate in the clearance of debris, suppression of inflammation, and regulation of angiogenesis and osteogenesis.<sup>[</sup>\n##REF##36031402##\n56\n##\n<sup>]</sup> As mentioned in the previous sections, the photoactivated GA/BPPDM hydrogel platform with excellent anti‐inflammatory and immunomodulatory properties could not only promote M2 macrophage polarization but also produce a conducive immune microenvironment through the secretion of various cytokines, such as IL‐4, IL‐10, BMP‐2, TGF‐β1, VEGF, and bFGF. Consequently, in this section, we used conditioned medium to assess the effect of macrophage phenotype reprogramming on angiogenic and osteogenic responses, as shown in the schematic illustration (<bold>Figure</bold> ##FIG##8##\n8A##). The conditioned medium derived from macrophages treated with GA, GA/BPPDM and GA/BPPDM plus NIR irradiation was collected and used for subsequent in vitro wound healing, tube formation, ALP activity and ARS staining assays. In terms of angiogenic activity, the GA/BPPDM+NIR group elicited a robust ability to promote HUVEC migration and tube formation, as indicated by the enhanced wound healing rate and vessel percentage area (Figure ##FIG##8##8B–E##). Meanwhile, the ALP activity and calcium mineral deposition of MC3T3‐E1 cells in the GA/BPPDM+NIR group were significantly higher than those in the other groups (Figure ##FIG##8##8F–I##), which was mainly related to the anti‐inflammatory and therapeutic cytokines secreted by M2 macrophages. Another reason behind the angiogenic and osteogenic activities may also be attributed to the presence of BP and DFO.</p>", "<p>Taken together, these in vitro results suggested that the GA/BPPDM hydrogel system could not only directly promote osteogenic and angiogenic differentiation, thus accelerating bone regeneration but also indirectly increase the secretion of various pro‐healing cytokines in the microenvironment through immunomodulation, thereby accelerating osteogenesis and angiogenesis. This was consistent with previous studies showing that M2 macrophages played a positive role in recruiting mesenchymal progenitor cells, boosting angiogenesis and osteogenic differentiation by secreting various factors such as BMP‐2 and VEGF.<sup>[</sup>\n##REF##35523800##\n57\n##\n<sup>]</sup> As illustrated in Figure ##FIG##8##8J##, we elucidated the underlying mechanism of GA/BPPDM hydrogel‐mediated anti‐inflammation, macrophage phenotype reprogramming and immunomodulatory function. Under the action of BPPD and mild PTT treatment, the GA/BPPDM hydrogel resulted in inhibited oxidative stress and diminished secretion of proinflammatory cytokines (CD86, IL‐6, TNF‐α, and iNOS) by activating the PI3K/Akt1 signaling pathway. As reported, the upregulation of the PI3K/Akt1 signaling pathway has been identified to be associated with the activation of M2 macrophages.<sup>[</sup>\n##REF##33811079##\n58\n##\n<sup>]</sup> In addition, ROS was one of the factors that could regulate the transformation of M1/M2 macrophages, while reducing local levels of ROS benefits the transformation of macrophages from the M1 phenotype to the M2 phenotype, leading to the secretion of a diverse array of anti‐inflammatory and pro‐healing signals for accelerated tissue regeneration,<sup>[</sup>\n##REF##36890691##\n27\n##\n<sup>]</sup> which is consistent with our in vitro immunomodulation results. Consequently, the NIR‐irradiated GA/BPPDM hydrogel system with favorable immunomodulatory and antioxidant activity could orchestrate M2 macrophage polarization and promote the production of anti‐inflammatory, angiogenic and osteogenic cytokines, recreating a favorable regenerative microenvironment for vascularization and osteogenesis. The results from both direct and indirect evaluations suggested that the GA/BPPDM hydrogel system not only had good biocompatibility, pro‐angiogenic and pro‐osteogenic activities, and ROS scavenging ability but also induced anti‐inflammatory M2‐type macrophage polarization to remodel the damaged microenvironment into a pro‐healing microenvironment for enhanced angiogenesis and osteogenesis.</p>", "<title>In Vivo Immunomodulatory Properties, Angiogenesis, and Bone Regeneration Capabilities in SD Rat Skull Defect Models</title>", "<p>Based on the results described above, our prepared GA/BPPDM hydrogels possessed favorable osteogenic and angiogenic capabilities as well as efficient immunomodulatory performance, showing great potential in accelerating bone tissue repair. However, whether these beneficial effects can be achieved in vivo remains unclear. In this study, a critical‐sized skull defect model (Φ = 5 mm) in rats was constructed to further evaluate the influence of GA/BPPDM with NIR irradiation on regulating the regenerative microenvironment and accelerating bone healing. A schematic diagram of our in vivo study is illustrated in <bold>Figure</bold> ##FIG##9##\n9A##. The GA/BPPDM hydrogel was implanted into the defect sites as a photoactivated material followed by NIR laser irradiation to maintain a local temperature of 41 ± 1 °C (Figure ##FIG##9##9B##), which is suitable for tissue regeneration without additional photothermal injury.<sup>[</sup>\n##REF##35358870##\n35\n##\n<sup>]</sup> During the early stage of bone defects and material implantation, the inflammatory response initially occurs and further determines the fate of bone healing by inducing immune cells to migrate toward wound sites to accommodate the immune microenvironment.<sup>[</sup>\n##REF##35667249##\n59\n##\n<sup>]</sup> Therefore, at 7 days after the operation, the immunomodulatory ability of GA/BPPDM+NIR on the bone defect microenvironment was investigated by immunofluorescence staining. iNOS and Arg‐1 were chosen as typical surface markers for M1 or M2 macrophages, respectively. As shown in Figure ##FIG##9##9C##, a substantial increase of iNOS‐positive macrophages was detected in the control group after bone defect modeling, indicating a serious inflammatory state. Simultaneously, the three experimental groups not only significantly decreased the percentage of iNOS‐positive macrophages but also increased the percentage of CD206‐positive macrophages infiltrated in the defect sites, especially in the GA/BPPDM+NIR group, which exhibited the highest M2 expression, implying a weakened inflammatory state. These data suggested that the GA/BPPDM+NIR group could convert proinflammatory M1 macrophages to anti‐inflammatory M2 macrophages, thus efficiently reducing the local inflammatory response during bone healing. The fluorescence intensity also showed that GA/BPPDM+NIR exhibited higher CD206<sup>+</sup> expression and lower iNOS<sup>+</sup> expression (Figure ##FIG##9##9D,E##), which was consistent with the decreased M1 phenotype markers (CD86, IL‐6, TNF‐α, and iNOS) and improved levels of M2 phenotype markers (IL‐4, IL‐10, Arg‐1, and CD206) measured by qRT‐PCR assay (Figure ##SUPPL##0##S19##, Supporting Information). To further validate the regulatory effect of the implanted hydrogels on macrophage polarization in the defect area, the representative proinflammatory cytokine TNF‐α and anti‐inflammatory cytokine IL‐10 were investigated on day 7. As presented in Figure ##FIG##9##9F##, the defect site in the control group induced the highest expression of TNF‐α, suggesting a serious inflammatory response. As expected, downregulated proinflammatory cytokine (TNF‐α) and upregulated anti‐inflammatory cytokine (IL‐10) were observed in both the GA/BPPDM and GA/BPPDM+NIR groups in comparison with the control and GA groups. And this was particularly obvious in the GA/BPPDM+NIR group, which exhibited significantly higher expression of IL‐10 (Figure ##FIG##9##9G,H##), indicating an excellent anti‐inflammatory effect. The role of PDA and mild heat stimulation in anti‐inflammation and macrophage polarization has been widely studied.<sup>[</sup>\n##REF##35533294##\n60\n##\n<sup>]</sup> Researchers found that NIR‐derived mild thermal stimulation at 41 ± 1 °C was able to protect cells from ROS‐induced oxidative damage through inhibition of the NF‐κB signaling pathway, thus promoting tissue regeneration under chronic inflammatory conditions.<sup>[</sup>\n##REF##35759676##\n47\n##\n<sup>]</sup> Besides, the combination of PDA and mild PTT triggered by NIR laser irradiation could significantly reprogram macrophages from the M1 phenotype to the M2 phenotype, thereby suppressing inflammatory responses and producing a pro‐regenerative microenvironment for bone healing. Combined with the previous results both in vitro and in vivo, it was demonstrated that the GA/BPPDM hydrogel was beneficial for polarizing macrophages toward the M2 phenotype, and mild heat stimulation further ameliorated the inflammatory environment, thus creating a conducive microenvironment for subsequent tissue regeneration.</p>", "<p>There is substantial evidence that the presence of M2 macrophages can induce high expression of BMP‐2 and VEGF in the regenerative microenvironment, acting as potent inducers of osteogenesis and angiogenesis to stabilize bone and blood vessel formation.<sup>[</sup>\n##REF##35523800##\n57\n##\n<sup>]</sup> The early pro‐osteogenic and pro‐angiogenic capacities of different hydrogels were further verified by immunohistochemical staining, including BMP‐2, VEGF, and HIF‐1α (<bold>Figure</bold> ##FIG##10##\n10A##). Owing to the synergistic interaction of the GA/BPPDM hydrogel system and mild heat stimulation, the GA/BPPDM+NIR group effectively enhanced the secretion of pro‐regenerative factors in the microenvironment of bone defects, with significant BMP‐2 and VEGF marker expression observed at week 2 post‐treatment (Figure ##FIG##10##10B,C##). Similarly, HIF‐1α, as an upstream regulator that can activate the transcription of VEGF, was also remarkably upregulated in the GA/BPPDM+NIR group (Figure ##FIG##10##10D##). Multiple studies have identified that BMP‐2 and VEGF are the most effective cytokines in promoting osteogenesis and vascular regeneration, respectively, while BMP‐2 can indirectly promote angiogenesis by stimulating VEGF.<sup>[</sup>\n##UREF##25##\n61\n##\n<sup>]</sup> Furthermore, as an important regulator of angiogenesis, HIF‐1α can stimulate the growth of new blood vessels and provoke transcription of its downstream molecule VEGF.<sup>[</sup>\n##REF##35550764##\n62\n##\n<sup>]</sup> The quantitative analysis results further showed that the expression of BMP‐2, VEGF, and HIF‐1α was significantly higher in the GA/BPPDM+NIR group than in the other groups (Figure ##FIG##10##10B–D##), which could beneficially achieve enhanced cellular responses for rapid neovascularization, promoted recruitment of MSCs to the defect site, and enhanced ECM biosynthesis during the proliferation phase.</p>", "<p>In the process of bone development and bone remodeling, enhanced neovascularization and endogenous stem cell recruitment were demonstrated to accelerate new bone formation.<sup>[</sup>\n##REF##36996420##\n31\n##\n<sup>]</sup> After 2 weeks of bone defect modeling, there was degradation of the residual hydrogels to various degrees in the defect area, which integrated well with the surrounding tissues without obvious displacement. Moreover, all hydrogel‐treated groups presented newly formed blood vessels (yellow arrows) within the defect area, in remarkable contrast to the limited vascularization observed in the control group (Figure ##FIG##10##10E##). Notably, the GA group showed a small amount of vascular network, while the GA/BPPDM and GA/BPPDM+NIR groups displayed a more obvious vascular structure, indicating abundant blood vessel infiltration, which is also consistent with the results of in vitro tube formation and subcutaneous embedding experiments. Especially in the GA/BPPDM+NIR group, abundant microvessel ingrowth was detected throughout the whole defect area (Figure ##FIG##10##10E##), resulting in a complete vascular network, which was mainly due to the secreted VEGF and HIF‐1α as well as the presence of an M2 macrophage‐enriched pro‐healing microenvironment. Meanwhile, by detecting the expression of CD31 (a specific marker of vascular endothelial cells) and CD90 (a specific surface marker of stem cells), we further analyzed angiogenesis as well as the recruitment and migration of endogenous stem cells during the repair of the defect site. The results of immunofluorescence staining showed that almost no signals for stem cell accumulation (CD90<sup>+</sup>, green) and only a small amount of host vascular endothelial cells (CD31<sup>+</sup>, red) with sporadic distribution were detected in the control group at 2 weeks (Figure ##FIG##10##10E,F##). Conversely, both GA/BPPDM and GA/BPPDM+NIR promoted endogenous stem cell recruitment and newly formed blood vessel infiltration into the defect area, especially for GA/BPPDM+NIR, which showed a more developed ring‐shaped vascular system and higher enrichment of CD90<sup>+</sup> MSCs. Quantitative results for CD31 and CD90 expression also confirmed that GA/BPPDM plus mild heat stimulation could facilitate the ingrowth of host blood vessels as well as the recruitment of endogenous stem cells (Figure ##FIG##10##10G##; Figure ##SUPPL##0##S20##, Supporting Information), which were crucial for the osseointegration of host bone tissue and implanted material in the early stage of bone repair. Herein, Figure ##FIG##10##10H## illustrates the osteoimmunomodulatory mechanism of the GA/BPPDM therapeutic platform. Benefiting from the combination of GA/BPPDM and mild PTT treatment, GA/BPPDM+NIR could recreate a favorable osteoimmunomodulatory microenvironment (anti‐inflammatory and M2‐polarizing) and drive the production of osteogenic/angiogenic factors (BMP‐2 and VEGF) to induce endogenous MSC recruitment and blood vessel formation, thereby initiating robust osteogenesis and angiogenesis. Collectively, owing to bioactive components and functional properties, the GA/BPPDM photothermal hydrogel could effectively transform the tissue microenvironment from inflammatory to reparative by polarizing macrophages recruited at the defect to the M2 type and promoting the secretion of anti‐inflammatory and pro‐healing cytokines, thereby achieving augmented bone regeneration.</p>", "<p>Then, the bone regeneration performance was analyzed using micro‐CT, histological staining, and immunohistochemical staining. A schematic diagram of the bone regeneration capacity experiment is presented in <bold>Figure</bold> ##FIG##11##\n11A##. From 2D‐ and 3D‐reconstructed micro‐CT images, only a small amount of new bone distributed around the rim of the defect areas could be found in the control group at both 4 and 8 weeks. As expected, a critical‐sized skull defect model was successfully established in the present study. In sharp contrast, a significantly greater amount of new bone ingrowth was detected in the GA/BPPDM and GA/BPPDM+NIR groups at 4 weeks, which subsequently formed a more complete bone structure at 8 weeks (Figure ##FIG##11##11B##). Especially in the GA/BPPDM+NIR group, the density of newly formed bone tissue was dramatically increased, with the defect site almost completely healed at 8 weeks, while only sporadic new bone tissue appeared in the GA group. The examination of the coronal view also reflected the same result, showing that a complete bone bridge connecting the defects could be detected in the GA/BPPDM+NIR group. However, visible and obvious defects were still present in the GA and control groups without such apparent bone formation at the defect edge due to the limited self‐healing capacity. These results further highlighted the synergistic role of the GA/BPPDM hydrogel combined with mild photothermal treatment in promoting osteogenesis and tissue regeneration in vivo. It is worth noting that the micro‐CT results in the GA group were better than those in the control group in vivo, which is mainly attributed to the fact that GA with biomimetic bone ECM structure could also promote bone regeneration despite without any modification, consistent with previous studies.<sup>[</sup>\n##UREF##1##\n4\n##\n<sup>]</sup>\n</p>", "<p>Accordingly, quantitative analysis of the micro‐CT examination is shown in Figure ##FIG##11##11C##, revealing the formation of new bone in the defect area. The analysis of bone regeneration‐related parameters, including the bone tissue volume/total tissue volume (BV/TV), trabecular thickness (Tb.Th), trabecular number (Tb.N), and bone mineral density (BMD), was consistent with the micro‐CT results. The BV/TV of the GA/BPPDM+NIR group reached 50.01 ± 3.04% at 8 weeks, which was significantly higher than that of the GA/BPPDM group (34.01 ± 1.77%), GA group (12.49 ± 1.97%), and control group (7.35 ± 0.97%), indicating that the presence of BPPD and mild PTT can promote new bone formation in vivo. Furthermore, the critical index for evaluating bone regeneration efficacy, including Tb.Th (0.64 0.04 mm), Tb.N (1.44 ± 0.0.5 mm<sup>−1</sup>), and BMD (0.46 ± 0.03 g cm<sup>−3</sup>) in the GA/BPPDM+NIR group showed the highest value, followed by the GA/BPPDM and GA groups at 8 weeks, similar to the results of the BV/TV analysis, further verifying a fulfilled effect in the promotion of bone mass. Owing to the excellent NIR/pH‐dual‐responsive properties, the photothermal effect can increase the release of DFO rapidly to promote vascularization in the early stage of bone healing and sustainably release PO<sub>4</sub>\n<sup>3−</sup> from the GA/BPPDM hydrogels to induce bone regeneration through in situ biomineralization during the long‐term bone repair period. Additionally, previous studies have reported that the combination of on‐demand mild hyperthermia (≈45 °C) and BP‐incorporated scaffolds could synergistically promote bone regeneration due to the alteration of cytoskeleton and integrin signaling as well as the upregulation of heat shock protein.<sup>[</sup>\n##REF##30550998##\n63\n##\n<sup>]</sup> Our study further proved that NIR‐induced mild PTT combined with the dual‐sensitive drug/ion delivery GA/BPPDM hydrogel platform had a significant promotion effect on bone healing in vivo. Taken together, relying on the sequential modulation of the immune microenvironment, revascularization, and osteogenesis, the NIR‐irradiated GA/BPPDM hydrogel platform can effectively promote bone regeneration in vivo, and the newly formed bone possesses excellent mineral density and intact bone structure.</p>", "<p>Subsequently, the histopathological structures of the regenerated new bone in the defect sites were verified by H&amp;E, Masson's trichrome (MST), and Goldner's trichrome staining. As seen from the histological images, the defect areas of the control group showed predominantly fibrous tissue formation bridging the edge of the host bone at 4 and 8 weeks (Figure ##FIG##11##11D##), implying poor bone regeneration potential, consistent with the results of the micro‐CT analysis. In contrast, there were numerous continuously regenerated lamellar bone with newborn bone lacunae and central canals observed in the GA/BPPDM and GA/BPPDM+NIR groups, which exhibited a relatively complete laminar structure. In particular, the defect areas of the GA/BPPDM+NIR group were almost completely occupied by dense and mature newly formed bone tissue, and the thickness was similar to that of the original bone at 8 weeks after implantation. MST staining further demonstrated that only a few collagen fibers were sparsely deposited within the defect area of the control group, while with the treatment of GA/BPPDM plus mild PTT, abundant collagen with dense and continuous structures was observed in the GA/BPPDM+NIR group, demonstrating the formation of mature lamellar bone. It is worth mentioning that the residual hydrogel material was almost replaced with fibrous tissue and surrounded by internal newly formed bone islands due to the ECM‐mimicking 3D microenvironment and proper degradation rate, which allowed space for new bone formation and ingrowth. Another possible reason is the creation of favorable regenerative microenvironment by the combined effect of GA/BPPDM and mild PTT (Figure ##FIG##10##10H##), which is conducive to tissue ingrowth and microcirculation, consequently accelerating the catabolism of the implanted hydrogel.<sup>[</sup>\n##UREF##26##\n64\n##\n<sup>]</sup> These results indicated that the GA/BPPDM hydrogel combined with mild heat stimulation could promote cell ingrowth and facilitate material‐neo‐bone tissue integration, thus leading to quicker and better bone healing with bone‐like structures. Goldner's trichrome staining was further performed to evaluate the degree of bone maturation at 8 weeks after implantation (Figure ##FIG##11##11E##). Compared with the control and GA groups, a significantly greater amount of mature lamellar bone tissues (green) together with less immature bone (osteoid, orange/red) was observed in the GA/BPPDM group, indicating that the GA/BPPDM hydrogels facilitated bone mineralization and remodeling. Furthermore, after treatment with mild PTT, considerable, green‐stained mature bone tissues were observed to grow from the edges of defective regions toward the central areas, which meant that the new bone was gradually calcified and matured. This phenomenon fully demonstrated that new bone tissue tended to regenerate from the margin toward the center of defects, benefiting from the guiding and promoting role of the GA/BPPDM hydrogel and NIR‐triggered mild PTT on osteoprogenitor cell recruitment, migration, differentiation, and biomineralization. Hydrogel biodegradation in vivo was also assessed by H&amp;E staining at 8 weeks after implantation. It could be found that the residual hydrogel material (yellow arrows) gradually degraded, and some tissue cells were observed within the interior of the hydrogels, indicating good compatibility and long‐term biodegradability in vivo (Figure ##SUPPL##0##S21##, Supporting Information), which is beneficial for cell infiltration in the bone defect areas. Furthermore, the residual GA/BPPDM hydrogel was surrounded by internal newly formed bone islands, indicating the ability of the GA/BPPDM scaffold plus mild heat stimulation to facilitate bone tissue ingrowth and promote material‐tissue integration. To verify the ability of the smart‐responsive photothermal hydrogel platform to promote osteogenesis and biomineralization during bone repair, immunohistochemical staining of Col‐1, Runx2, OPN, and OCN was conducted at 8 weeks post‐implantation. As displayed in Figure ##FIG##11##11F##, the expression of these osteogenic markers in both the GA/BPPDM and GA/BPPDM+NIR groups was significantly higher than that in the control and GA groups. In particular, the GA/BPPDM+NIR group exhibited the strongest positive staining of Col‐1, Runx2, OPN, and OCN proteins, followed by those in the GA/BPPDM and GA groups (Figure ##SUPPL##0##S22##, Supporting Information), indicating that the mild photothermal effect of GA/BPPDM could facilitate matrix maturation and mineralization during bone regeneration and remodeling. As mentioned above, GA/BPPDM plus NIR treatment can improve the local microenvironment and realize stimuli‐responsive release of DFO and PO<sub>4</sub>\n<sup>3−</sup>, resulting in the continuous secretion of these ECM proteins in the defect sites, thus accelerating tissue repair and regeneration. In addition, compared with the control group, no obvious pathological changes in major organs, including the heart, lung, liver, spleen, and kidney, were observed for all experimental groups, suggesting good biosafety of the hydrogels in vivo (Figure ##SUPPL##0##S23##, Supporting Information). In this work, the superior performance of the GA/BPPDM hydrogel platform in the bone augmentation effect is mainly attributed to its multifunctional therapeutic features (<bold>Figure</bold> ##FIG##12##\n12\n##). i) Owing to the combined action of BP, PDA, and DFO, GA/BPPDM could continuously maintain a conducive pro‐regenerative microenvironment in the repair process because of its superior osteogenic and angiogenic activities, which are vital for bone defect repair. ii) Under mild NIR irradiation, GA/BPPDM could modulate the polarization of macrophages toward the M2 phenotype and promote the production of anti‐inflammatory, angiogenic and osteogenic cytokines, thereby enhancing neovascularization and endogenous stem cell recruitment, which played a key role in the early stage of the healing process. Meanwhile, BPPD, as an important component of GA/BPPDM, could endow the hydrogel with mild photothermal activity and pH‐responsive and NIR laser‐triggered drug/ion release behavior for efficient bone regeneration. iii) Under the combined long‐term effect of physical (mild hyperthermia) and chemical (drug/ion delivery) interventions, the smart‐responsive multifunctional therapeutic system achieved improved regenerative microenvironment and efficient bone regeneration. Overall, the photoactivated GA/BPPDM hydrogel was a promising biomaterial scaffold that could augment the repair and regeneration of large bone defects, as indicated by accumulated M2‐type macrophages, reduced inflammation, promoted angiogenesis, and enhanced bone matrix deposition.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Preparation and Characterization of the Hybrid Hydrogels</title>", "<p>To realize the spatiotemporal regulation of the immune microenvironment, angiogenesis, and osteogenesis, we designed and constructed a bioactive BPPD nanocomposite‐incorporated hybrid hydrogel with strong photothermal effect and desirable NIR‐triggered drug‐releasing capability in the current study. As shown in Scheme ##FIG##0##1##, the obtained smart delivery hydrogel system can synchronously realize multifunctionality for the treatment of bone defects by combining long‐term physical (photothermal) and continuous chemical (drug/ion delivery) intervention, so as to provide a bone‐friendly microenvironment for sequential activation of M2 macrophage polarization, vascularization, and MSC recruitment, resulting in enhanced bone regeneration.</p>", "<p>For preparation of smart‐responsive multifunctional hydrogels, BPPD nanocomposites, which served as NIR/pH dual‐triggered drug release nanoplatforms, were prepared through BP crystal exfoliation, PDA modification, and DFO loading. A schematic illustration of the preparation process of BPPD is shown in <bold>Figure</bold> ##FIG##1##\n1A##. The raw BP nanosheets were first exfoliated by a sonication‐assisted top‐down strategy. PDA was then decorated on the surface of the BP nanosheets by the self‐polymerization reaction of DA using BP nanosheets as a template. Lines of evidence have shown that mussel‐inspired polymerization of DA to form PDA coatings on various biomaterials has emerged as a diverse surface functionalization method for biomedical applications.<sup>[</sup>\n##UREF##9##\n25\n##\n<sup>]</sup> Introducing PDA layer on BP nanosheets could avoid agglomeration induced by high surface energy, achieving not only better physiological stability and interface compatibility with the hydrogel matrix but also good biocompatibility and ROS scavenging capacity as well as strong drug loading capacity.<sup>[</sup>\n##UREF##6##\n18\n##, ##REF##34237507##\n26\n##\n<sup>]</sup> Previous studies have also shown that the introduction of polyphenols, such as PDA, not only promotes cell migration, adhesion, proliferation, and differentiation but also regulates the inflammatory and immune microenvironment in the early stages of implantation, thus accelerating the subsequent tissue regeneration process.<sup>[</sup>\n##REF##36890691##\n27\n##, ##UREF##10##\n28\n##\n<sup>]</sup> In the present work, the introduction of PDA endowed this hybrid nanocomposite with improved biocompatibility and simultaneously provided a stable glue to conjugate BP nanosheets and DFO molecules.</p>", "<p>Thereafter, the angiogenic drug DFO was introduced to the BP@PDA nanosystem (BPPD) by the interaction between DFO (‐NH<sub>2</sub>) and the rich functional moieties of PDA (e.g., catechols, amine, and aromatic rings). The interaction mechanism between DFO and BP@PDA was mainly attributed to a series of noncovalent forces (physical adsorption, hydrogen bonding, π−π stacking, electrostatic interactions, etc.). It should also be noted that, as a common melanin‐like biopolymer, PDA with enriched catechol groups has excellent photothermal conversion efficiency, which endows BPPD with NIR‐controlled drug release behavior for efficient bone regeneration.</p>", "<p>As revealed by transmission electron microscopy (TEM) images, BPPD is a typical 2D multilayered structure with well‐defined edges (Figure ##FIG##1##1B##). Similarly, the atomic force microscopy (AFM) results reveal the thicknesses of BPPD with a layer height of ≈16 nm (Figure ##FIG##1##1C##). The successful synthesis of the BPPD nanomaterial was verified by zeta potential and Fourier transform infrared spectrometer (FTIR) analysis. As shown in Figure ##SUPPL##0##S1## (Supporting Information), it could be observed that the surface zeta potential of raw BP nanosheets (−30.6 mV) decreased to −56 mV after the in situ polymerization of PDA on BP nanosheets, which was ascribed to the introduction of negatively charged hydroxyl groups from the PDA structure, consistent with previous reports.<sup>[</sup>\n##REF##37080119##\n19\n##\n<sup>]</sup> After loading DFO, BP@PDA presented a less negative potential (−42 mV) than unmodified BP@PDA (−56 mV). The increase in zeta potential was ascribed to the immobilization of positively charged DFO onto negatively charged BP@PDA nanosheets. This phenomenon suggested that DFO can be assembled on the surface of BP@PDA nanospheres by electrostatic adsorption, which agrees with previous studies.<sup>[</sup>\n##REF##30415019##\n21\n##\n<sup>]</sup> The FTIR spectra of pristine BP exhibited three absorption peaks located at ≈1491, 1010, and 815 cm<sup>−1</sup>, which could be attributed to the stretching vibration of P = O and P‐O bonds, further confirming the successful preparation of BP nanosheets (Figure ##FIG##1##1D##). After PDA modification, new additional peaks appeared at 1633, 1457 and 1372 cm<sup>−1</sup> corresponding to the C = C stretching vibration, N‐H scissoring vibration and C‐O stretching vibration of PDA, respectively, demonstrating the successful polymerization of DA in the system. Meanwhile, compared to the FTIR spectrum of BP@PDA, the peaks of BPPD at 1195, 1264, 1461, 1566, and 1628 cm<sup>−1</sup> are slightly stronger because DFO contains more amide bonds, verifying the successful preparation of the BPPD nanocomposite (Figure ##FIG##1##1D##).</p>", "<p>To realize the controlled release of dual factors to match the immune response, angiogenic and osteogenic progressions, different amounts of BPPD nanocomposite were added into the GA pre‐gel solution followed by photo‐polymerization under UV irradiation, forming a photo‐triggered covalent bond network. Both GelMA and Alg‐MA are well‐known photosensitive hydrogels with the advantages of good biocompatibility and biodegradability, which have the ability to mimic the natural ECM of bone to encapsulate bioactive molecules or cells and integrate well with the surrounding tissue.<sup>[</sup>\n##UREF##11##\n29\n##\n<sup>]</sup> The favorable 3D microenvironment provided by the GA hydrogel could accelerate the formation of bone tissue owing to the presence of cell attachment‐promoting arginine‐glycine‐aspartic acid (RGD) sequences.<sup>[</sup>\n##UREF##12##\n30\n##\n<sup>]</sup> As major building blocks for the GA/BPPD hydrogel, photo‐cross‐linkable GelMA and Alg‐MA prepolymers were designed and synthesized by modifying gelatin and Alg with reactive methacrylate groups, as illustrated in Figure ##FIG##1##1E,F##. The successful preparation of methacrylated gelatin and Alg products was confirmed by proton‐1 nuclear magnetic resonance (<sup>1</sup>H NMR) and FTIR. As shown in Figure ##FIG##1##1G,H##, the methyl (‐CH = CH<sub>2</sub>) proton peak was observed in the spectra of GelMA (5.46 and 5.67 ppm) and Alg‐MA (5.65 and 6.08 ppm), indicating the successful introduction of double bonds into gelatin and Alg and the successful synthesis of GelMA and Alg‐MA. FTIR spectra also verified the success of GelMA synthesis, where, in comparison with the gelatin spectrum, we observed that the C = O stretching of amide I shifted to 1660 cm<sup>−1</sup> (Figure ##FIG##1##1I##), which is due to the overlapping of the stretching signals at 1695 cm<sup>−1</sup> (C = C band) from methacrylate. A similar result was also observed in the FTIR spectrum of Alg‐MA (Figure ##SUPPL##0##S2##, Supporting Information), indicating the successful synthesis of the Alg‐MA monomer. Next, the mixture of BPPD nanocomposite and GA was cured under 405 nm visible light to form a nanocomposite hydrogel (<bold>Figure</bold> ##FIG##2##\n2A##). The BPPD nanocomposite together with PDA chains would facilitate interaction with the GA network via both covalent (free‐radical photo‐polymerization) and noncovalent (hydrogen bonds and π–π stacking between catechol groups of PDA chains) forces.</p>", "<p>For bone tissue engineering scaffolds, porous structures that promote cell migration and adhesion are essential, so the morphological structure of the as‐prepared hydrogels was examined, as shown in Figure ##FIG##2##2B##. From the macroscopic photographs, the GA hydrogels were initially opalescent in color, while the BPPD loading did not significantly change the color, probably due to a very small amount of loading. The cross‐sectional scanning electron microscopy (SEM) images showed that all hydrogels exhibited a highly interconnected and porous structure with relatively smooth pore walls, which is similar to that of bone ECM. No obvious BPPD was observed in the pore walls of the hydrogel, probably because of the good interfacial compatibility between the GA matrix and BPPD nanocomposites. Such a porous 3D network structure (e.g., interconnected pores and high porosity) provided an ECM‐mimicking environment (Figure ##FIG##2##2C##), which was demonstrated to contribute to cell adhesion, migration, and transport of nutrients and metabolic wastes. Micro‐CT reconstruction and parameter analysis showed that all hydrogels had almost the same 3D porous structures and porosity (Figure ##FIG##2##2D,E##), which holds great potential for facilitating vascular formation and bone regeneration. It is worth noting that the GA/BPPDH hydrogel seemed denser than the other hydrogels, and this phenomenon may be explained by the introduction of PDA increasing the additional crosslinking density in the hydrogel matrix. These results demonstrated that the global structure of the GA hydrogels did not change considerably after BPPD loading, which could be considered as a stable carrier for BPPD.</p>", "<p>The material surface hydrophilicity will influence cellular behaviors on the interface between the implant surface and host surrounding tissues. In view of this, the hydrophilicity of all hydrogels was evaluated by measuring their water contact angle. As shown in Figure ##FIG##2##2F##, the water contact angle was 74.3 ± 3.1° for GA, 61.7 ± 2.5 ± 4.3° for GA/BPPDL, 37.3 ± 2.1° for GA/BPPDM, and 31.3 ± 2.1 for GA/BPPDH, indicating the improved hydrophilicity of these hydrogels after the introduction of BPPD. The excellent hydrophilicity of the GA/BPPD hybrid hydrogels was strongly ascribed to the hydrophilic properties of the PDA and BP components, which was consistent with those of findings reported previously.<sup>[</sup>\n##REF##36996420##\n31\n##, ##REF##36469414##\n32\n##\n<sup>]</sup> Thus, the GA/BPPDM and GA/BPPDH hydrogels showed better wettability than the other hydrogel groups, which were expected to exhibit high performance in favor of cell adhesion, proliferation, growth, spreading, and differentiation.</p>", "<p>To achieve successful bone regeneration, the ideal implanted bone materials should possess long‐term structural stability and mechanical support. As shown in Figure ##FIG##2##2G##, the hybrid hydrogels could maintain their integrity and recover to their original shape without obvious breakage or collapse after repeated compression. The oscillatory rheology of the hydrogels was further tested to investigate their mechanical properties and stability, as shown in Figure ##FIG##2##2H##. As the oscillation frequency increased, the values of G′ (storage modulus) were consistently greater than G″ (loss modulus), showing good elasticity and mechanical stability of the hydrogel. Meanwhile, the G′ of the hydrogel increased with the addition of BPPD, indicating that the mechanical strength of the hydrogel increased with the increase of the crosslinked network. Notably, increasing the amount of BPPD from 0.5 wt.% to 1 wt.% did not further improve its mechanical properties but rather reduced the elastic modulus. This may be attributed to the reduction of the covalent crosslinking density in the GelMA hydrogel as the amount of BPPD was increased.</p>", "<p>The compressive properties of the hydrogels were also investigated, as shown in Figure ##FIG##2##2I,J##. The compressive stress‐strain curve indicated that the mechanical strength of the hydrogel increased with increasing BPPD concentration, which was due to the improved cross‐linking network. In detail, among all hydrogel groups, the GA hydrogel shows low compressive strength according to the stress‐strain curves. With subsequent BPPD loading, the compressive strength of the hydrogels gradually increased, which was consistent with the rheological results. In particular, the compressive strength of the as‐prepared GA/BPPDM hydrogel (45.1 ± 3.1 MPa) was higher than that of the GA (5.3 ± 1.2 MPa), GA/BPPDL (14.3 ± 1.2 MPa), and GA/BPPDH (26.3 ± 2.6 MPa) hydrogels. The results of the mechanical test demonstrated that the incorporation of BP‐based materials in the hydrogel showed significant improvement in the mechanical strength, which was consistent with previous studies.<sup>[</sup>\n##REF##31008576##\n33\n##\n<sup>]</sup> Notably, the enhanced stiffness might regulate cell adhesion, cell growth, and osteogenic differentiation by the enhanced mechanotransduction effect.<sup>[</sup>\n##REF##33260094##\n34\n##\n<sup>]</sup> However, increased BPPD concentration may lead to an inhomogeneous distribution in the GA matrix, resulting in the compromised mechanical strength of GA/BPPDH compared with GA/BPPDM. Through rheological and mechanical performance tests, it can be found that the GA/BPPDM hydrogel has a larger energy storage modulus and mechanical strength, so it is more resistant to external deformation and less susceptible to damage.</p>", "<p>In addition to desirable structural and mechanical properties, the swelling and degradation profiles of hydrogels play an important role in maintaining the stability of implants and promoting tissue regeneration. As shown in Figure ##FIG##2##2K##, the swelling of all hydrogels increased rapidly within 60 min and reached equilibrium within 48 h. The swelling ratios of GA, GA/BPPDL, GA/BPPDM, and GA/BPPDH were 1329 ± 50%, 958 ± 36%, 726 ± 40%, and 598 ± 36%, respectively, after 48 h, implying that the swelling ratio of hydrogels decreased with increasing concentrations of BPPD. The declined equilibrium swelling capacities of GA/BPPD may be due to their high crosslinking densities, preventing greater swelling of the hydrogel and buffer diffusion. To observe the in vitro degradation of hydrogels, freeze‐dried samples were collected and weighted after immersion into PBS solution in the presence of lysozyme (100 mg mL<sup>−1</sup>). All hydrogels gradually degraded with prolonged immersion time, and the degradation of GA/BPPD was retarded owing to the increased cross‐linking density in the hydrogel matrix caused by BPPD loading (Figure ##FIG##2##2L##). The results showed similar trends in the degradation and swelling behavior of the hydrogels. Collectively, GA/BPPD hydrogels with low swelling ratio and slow biodegradation rate are suitable for bone regeneration applications.</p>", "<title>Photothermal Performance and Drug Release Behaviors of the Hydrogels</title>", "<p>Recently, photothermal therapy (PTT) has emerged as a promising treatment modality to accelerate bone repair because of its remote controllability, non‐invasive properties, good therapeutic effectiveness, and strong tissue penetration depth.<sup>[</sup>\n##REF##35358870##\n35\n##\n<sup>]</sup> Both BP and PDA have been proven to have good photothermal effects.<sup>[</sup>\n##REF##37080119##\n19\n##\n<sup>]</sup> To evaluate the photothermal conversion efficiency of GA/BPPD, all hydrogel samples were irradiated with 808 nm NIR light at 1 W cm<sup>−2</sup>. As depicted in <bold>Figure</bold> ##FIG##3##\n3A##, upon NIR irradiation, the temperature of the GA/BPPD hydrogels increased gradually, while the GA hydrogel group showed no obvious temperature variation recorded by an infrared thermogram. After 5 min of NIR irradiation, the temperature was 36.7 ± 0.2 °C for the GA/BPPDL group, 43.8 ± 0.1 °C for the GA/BPPDM group, and 48.9 ± 0.2 °C for the GA/BPPDH group (Figure ##FIG##3##3B##). Notably, with expending irradiation time, the temperature of GA/BPPDM can eventually reach an equilibrium temperature (≈45 °C), meeting the basic biosafety requirements of mild photothermal biomaterials in promoting tissue regeneration. Moreover, the photothermal stability of the GA/BPPD hydrogel was investigated, as illustrated in Figure ##FIG##3##3C##. The corresponding results showed that the GA/BPPD hydrogels could be heated and cooled to fixed values without significant attenuation after four cycles of laser on/off, indicating high photostability and great potential to act as NIR‐controlled PTT. Previous studies have found that mild heat stimulation (≈45 °C) can not only promote angiogenesis and osteogenesis but also induce M2 phenotype polarization of macrophages.<sup>[</sup>\n##REF##35986434##\n12\n##, ##REF##36321923##\n36\n##\n<sup>]</sup> Significantly, the temperature of NIR‐triggered efficient mild PTT treatment was usually controlled to be below 45 °C to avoid side effects on normal tissues. In summary, after combining mechanical characterization and the requirement of mild‐temperature PTT (≈45 °C), we selected the GA/BPPDM hydrogel group as a suitable specification for subsequent experiments due to comprehensive consideration.</p>", "<p>To realize an appropriate regenerative microenvironment for bone regeneration, it is essential to develop controlled release formulations that can deliver multiple bioactive factors to manipulate cellular functions. The in vitro release kinetics of DFO from GA/BPPD were calculated by UV–vis spectrophotometry at a wavelength of 485 nm. Moreover, the drug loading capacity of DFO was characterized according to the standard calibration curve and is shown in Figure ##SUPPL##0##S3## (Supporting Information), with a loading efficiency of DFO reaching 79.8%. As shown in Figure ##FIG##3##3D##, GA/BPPDM showed typical dual NIR/pH‐dual‐responsive release behavior, and both NIR laser irradiation and the acidic environment could considerably accelerate the release of DFO, showing a similar phenomenon to previous studies.<sup>[</sup>\n##REF##36278256##\n20\n##, ##REF##31702885##\n37\n##\n<sup>]</sup> It is known that the initial physiological characteristics of bone injury are mainly a slightly acidic pH (pH≈6.5), whereas the pH of healthy tissues is 7.3–7.4.<sup>[</sup>\n##REF##35870263##\n6\n##\n<sup>]</sup> As such, the pH‐responsive drug release from GA/BPPDM was monitored under neutral (pH = 7.4) and slightly acidic (pH = 6.5) conditions to mimic the healthy and bone injury‐related physiological microenvironments, respectively. The cumulative release of DFO was only ≈21.3% at pH = 7.4 after 48 h, whereas at pH = 6.5, the amount released in 48 h reached ≈36%. Such acid‐accelerated DFO release behavior was ascribed to the pH sensitivity of the PDA layer and protonation of amine groups, which could result in the disruption of π−π interactions between DFO and PDA. As displayed in Figure ##FIG##3##3E,F##, the release peak of DFO appeared in the first two days and then quickly decayed, indicating that DFO was quickly released within a short time frame (≈7 days). Since bone remodeling requires rapid angiogenesis to provide adequate nutrition delivery, which is conducive to the formation of new bone and the survival of deep bone tissue, the relatively quick release of DFO from hydrogels is favorable for stimulating timely neovascularization and subsequently robust bone formation.</p>", "<p>In addition, the NIR‐responsive release behavior of DFO was investigated. Compared with internal pH stimuli, using NIR as external stimuli for drug delivery control exhibits several advantages, such as high tissue penetration, low tissue harm, easy operation, and spatiotemporal precise control of treatment.<sup>[</sup>\n##REF##37080119##\n19\n##\n<sup>]</sup> As can be seen from Figure ##FIG##3##3E,F##, the heat effect generated by NIR laser irradiation obviously affected DFO release. Burst drug release occurred after NIR laser irradiation was applied for 5 min at predetermined time intervals under different pH values. Under the action of the photothermal effect, the final cumulative release percentage of DFO reached ≈66.7% and 84.7% at pH values of 7.4 and 6.5, respectively, during the initial 48 h. In the following release time, the release rate of DFO slowed significantly, and the cumulative release percentage was 73.3% and 89.3% at pH values of 7.4 and 6.5, respectively. These curves presented a burst release in the first 7 days, followed by a slow and plateaued DFO release. The reason for the controlled drug release mode was probably associated with the enhanced diffusion effect under elevated temperature. This result indicated that GA/BPPDM with photothermal function could further trigger DFO release in a thermal‐stimuli manner. Then, the release of PO<sub>4</sub>\n<sup>3−</sup> from the GA/BPPDM hydrogel was investigated by ion chromatography. As shown in Figure ##SUPPL##0##S4## (Supporting Information), the cumulative release percentage of PO<sub>4</sub>\n<sup>3−</sup> from the hydrogel increased over the soaking time, and a relatively fast release of PO<sub>4</sub>\n<sup>3−</sup> within 10 days was observed. Although the release rate of PO<sub>4</sub>\n<sup>3−</sup> slowed down with an increase in immersion time, the cumulative release curve suggested that PO<sub>4</sub>\n<sup>3−</sup> release could continue for up to 28 days in vitro under NIR or without NIR treatment. This sustained release behavior was mainly because the protective effects of the hydrogel matrix and organic coating composed of PDA and DFO synergistically reduced the release of PO<sub>4</sub>\n<sup>3−</sup> from the BPPD nanocomposites. A sustainable and slow release of PO<sub>4</sub>\n<sup>3−</sup> has been shown to be better for osteogenic differentiation, while the relatively fast release of DFO is preferred for angiogenesis.<sup>[</sup>\n##UREF##3##\n7\n##, ##REF##34704438##\n15\n##\n<sup>]</sup> These results directly confirmed that the GA/BPPDM hydrogel had both intelligent controlled‐release (DFO) and sustained‐release (PO<sub>4</sub>\n<sup>3−</sup>) capacities, which made the GA/BPPDM hydrogel as a desirable platform to promote bone regeneration over a long‐term period. From the above results, it was suggested that our nanocomposite hydrogel has a “smart” drug release feature, that is, “switching on” enhanced drug release under both NIR laser irradiation and slightly acidic conditions to enhance bone regeneration efficacy. With the assistance of external NIR photothermal stimuli and bone injury site environmental changes, such as pH, codelivery of DFO/PO<sub>4</sub>\n<sup>3−</sup> for synergistic immunomodulation, revascularization and efficient bone regeneration could be achieved. Considering the above rationale, the smart‐responsive GA/BPPDM hydrogels will be promising in the applications of bone defect treatment and even other tissue regeneration.</p>", "<title>In Vitro Evaluation of Cytocompatibility</title>", "<p>In the following experiments, both MC3T3‐E1 cells and HUVECs were used to evaluate the influence of the nanocomposite hydrogels on cell viability and proliferation, as they are the major and important cell sources for bone formation and vascular regeneration.<sup>[</sup>\n##UREF##13##\n38\n##, ##UREF##14##\n39\n##\n<sup>]</sup> The results of the CCK‐8 assay revealed that the OD values of the four hydrogel groups increased with the culture time prolonging (<bold>Figure</bold> ##FIG##4##\n4A,C##), indicating that the cells maintained good viability and proliferation ability. More specifically, cell proliferation on day 1 was similar for all groups and the cells co‐cultured on the hydrogels proliferated over time. After 2 days of co‐incubation, compared to the GA hydrogel, the hydrogels loaded with active BPPD nanocomposites showed a slightly improved cell proliferation rate, although there was no obvious difference among the four groups of GA, GA/BPPDL, GA/BPPDM, and GA/BPPDH. When it came to 3 days, the highest cell proliferation rate was found in GA/BPPDM, followed by GA/BPPDL and GA/BPPDH, then GA, revealing that the hydrogel group loaded with BPPD, especially 0.5 wt.%, was more beneficial for promoting cell proliferation. The excellent cell affinity of these hydrogels was also confirmed by live/dead staining assay, as shown in Figure ##FIG##4##4B,D##. After co‐culturing for 3 days, almost all MC3T3‐E1 cells and HUVECs were alive (green fluorescence) in the GA, GA/BPPDL, GA/BPPDM, and GA/BPPDH hydrogels, with only a few dead cells present (red fluorescence), indicating that the composite hydrogels could support cell survival and growth (viability &gt; 90%). According to the quantitative results, all hydrogels had excellent cytocompatibility for both MC3T3‐E1 cells and HUVECs, and the existence of BPPD substantially increased the cell density and the percentage of living cells (Figure ##FIG##4##4G,I##), improving the bioactivity of the hydrogel. Notably, significantly promoted proliferation of cells was observed in the GA/BPPDM hydrogel group compared with GA/BPPDL and GA/BPPDH, which was in accordance with the results of the CCK‐8 analysis. Both GelMA and Alg‐MA have high biocompatibility and mimic the chemical properties of the ECM; meanwhile, BP and PDA have shown excellent biocompatibility in previously reported studies.<sup>[</sup>\n##REF##36125961##\n17\n##, ##UREF##11##\n29\n##\n<sup>]</sup> The enhanced cell proliferation was likely due to phosphate and DFO release into the culture medium, which was consistent with literature reports.<sup>[</sup>\n##REF##34894585##\n40\n##\n<sup>]</sup> However, with a concentration higher than 0.5 wt.%, no obvious enhancement was observed, mostly because higher concentrations of phosphate and DFO disturbed normal cell activity. This implied that at an appropriate level, BPPD nanomaterials might promote cell growth, which can also explain why cells on GA/BPPDM are well proliferated and widely distributed.</p>", "<p>The adhesion and spreading morphologies of the cells were further observed by cytoskeleton staining. After being co‐cultured for 3 days, the cytoskeletal morphology of MC3T3‐E1 cells revealed that the cells in the GA group had only a few pseudopodia and had not completely spread on the hydrogel. In contrast, the cells adhered to the GA/BPPD hydrogels exhibited better stretched morphology with well‐developed cell cytoskeletons and clusters, extending numerous branchy filamentous pseudopods and tightly interleaving with each other (Figure ##FIG##4##4E##; Figure ##SUPPL##0##S5A##, Supporting Information). In particular, the cells on the GA/BPPDM hydrogel spread well with a typical elongated‐spindle and osteoblastic‐like morphology, indicating a favorable growth status, which may be attributed to its optimal BPPD concentration and hydrophilicity. Additionally, we also observed increased numbers of cell colonies on GA/BPPDM samples compared to pure GA, which allowed for more cell attachment and spreading, revealing the positive effects of BPPD on improving cell migration and proliferation, which is consistent with the results of cell toxicity and proliferation assays. Recent studies have found that cell morphology plays a vital role in regulating the phenotype of cells, and an elongated spindle‐shaped morphology has been found to be tightly correlated with the adhesion, proliferation, and differentiation of osteoblast‐related cells and endothelial cells.<sup>[</sup>\n##UREF##15##\n41\n##, ##UREF##16##\n42\n##\n<sup>]</sup> The enlarged confocal laser scanning microscopy (CLSM) images further verified the good cell adhesion and spreading behaviors on the GA/BPPDM hydrogel (Figure ##SUPPL##0##S5A##, Supporting Information), as evidenced by the stretched filopodia and cytoskeletal rearrangement. According to the CLSM observation (Figure ##FIG##4##4E##) and quantitative results (Figure ##FIG##4##4G,H##), more cells adhered to the GA/BPPDM hydrogel not only exhibited the highest spreading area, but the actin filaments that make up the cytoskeleton were also highly expressed, implying a strong interaction between cells and the GA/BPPDM hydrogel. Concomitantly, similar results were also detected in HUVECs grown on the hydrogels, in which the HUVECs grown on the GA/BPPDM hydrogel presented well‐stretched morphology and favorable proliferation (Figure ##FIG##4##4F,I,J##; Figure ##SUPPL##0##S5B##, Supporting Information). These encouraging results suggested that the incorporation of moderate BPPD contributed to the adhesion behavior of MC3T3‐E1 cells and HUVECs due to the nature of each raw material, including PDA, DFO, and BP nanosheets, which demonstrated good cell affinity and improved cell crawling and adhesion properties.<sup>[</sup>\n##UREF##3##\n7\n##, ##REF##34704438##\n15\n##, ##UREF##17##\n43\n##\n<sup>]</sup> With high bioactivity and hydrophilicity, BPPD nanomaterials might serve as cell adhesion sites that promote cell growth, spreading, and differentiation. Overall, our data showed that all fabricated GA/BPPD nanocomposite hydrogels, especially GA/BPPDM, possessed remarkably positive effects on MC3T3‐E1 cell and HUVEC proliferation, survival, and growth. Considering the vital role of cell proliferation in cell differentiation and subsequent tissue formation, we chose the GA/BPPDM hydrogel to further verify its osteogenesis, angiogenesis, and immunomodulatory capability in vivo and in vitro.</p>", "<title>In Vitro and In Vivo Immunomodulatory Properties</title>", "<p>Although multiple immune cell types are involved in the immune response and microenvironment regulation, macrophages have been demonstrated to play a prominent role in tissue regeneration and remodeling. Following bone injury, macrophages predominate as proinflammatory phenotypes (M1) at the inflammation stage and contribute to the characteristics of high ROS in response to local inflammatory signals.<sup>[</sup>\n##UREF##18##\n44\n##\n<sup>]</sup> Unfortunately, excessive inflammatory response‐induced overproduction of ROS in the bone defect region has a detrimental impact on bone regeneration. Increased levels of ROS in the bone defect can not only cause cell death in osteoblast precursor cells and mature osteoblasts but also reduce the expression of osteogenic markers and mineralization, leading to prolonged and unhealed bone injury.<sup>[</sup>\n##REF##35870263##\n6\n##\n<sup>]</sup> Therefore, the development of functional biomaterials with excellent immunomodulatory effects and ROS‐scavenging capacity is of great significance to promote the regeneration of bone tissue (<bold>Figure</bold> ##FIG##5##\n5A##). In this work, RAW264.7 cells were selected as the model of macrophages and then treated with LPS (a component of Gram‐negative bacterial cell walls) to imitate acute inflammatory responses and induce macrophages to the M1 phenotype, thus leading to the production of numerous free radicals (i.e., ROS) and long‐term inflammation. Macrophages were co‐cultured with different hydrogels, and the macrophage response was then assessed via immunofluorescence staining and flow cytometry. As shown in Figure ##SUPPL##0##S6A## (Supporting Information), the highest expression level of ROS was observed in the control group exposed to LPS, suggesting that cellular oxidative stress was successfully induced. Interestingly, both GA/BPPDM and GA/BPPDM+NIR effectively inhibited LPS‐provoked ROS generation, as evidenced by the decreased 2′,7′‐dichlorofluorescein diacetate (DCFH‐DA) fluorescent signals and the shift of its relative fluorescence intensity to the left (Figure ##SUPPL##0##S6B##, Supporting Information). More importantly, cells treated with GA/BPPDM plus NIR irradiation exerted the most significant inhibitory effects on total ROS generation, showing negligible green fluorescence, which indicated a strong ability to protect cells from ROS‐induced oxidative damage. Thus, these results demonstrated that GA/BPPDM combined with mild photothermal treatment through NIR irradiation could reduce the excessive oxidative stress of cells induced by the inflammation‐related response, showing protective effect on cell function. Studies have shown that in addition to a notable promoting effect on osteogenesis, BP has a strong ROS‐scavenging capability and high bioactivity, showing great prospects for application in promoting tissue repair and regeneration.<sup>[</sup>\n##UREF##19##\n45\n##\n<sup>]</sup> Additionally, owing to the presence of abundant catechol groups, PDA could efficiently eliminate intracellular ROS and thus exhibit anti‐inflammatory ability by regulating the proportion of M1/M2 macrophages,<sup>[</sup>\n##REF##34237507##\n26\n##, ##REF##36736645##\n46\n##\n<sup>]</sup> and the anti‐inflammatory effect of DFO has been reported more frequently.<sup>[</sup>\n##UREF##7##\n22\n##\n<sup>]</sup> The anti‐inflammatory effect of DFO was achieved through its excellent iron‐chelating ability, which enabled it to scavenge free radicals and ROS generated after acute inflammation. Furthermore, the mild photothermal effect (41 ± 1 °C) triggered by NIR irradiation could further enhance the radical scavenging ability of the hybrid hydrogel, which may be related to accelerated disassembly of BPPD, thus facilitating adequate contact between reductive components and free radical detection reagents, consistent with the results of previous work.<sup>[</sup>\n##REF##35759676##\n47\n##\n<sup>]</sup> On the basis of previously published studies, our current findings supported the excellent antioxidant ability of the GA/BPPDM hydrogel system because of the combined effects of bioactive components (BP, PDA, and DFO) and mild photothermal activity upon NIR irradiation.</p>", "<p>Accumulating data show that M1‐type macrophages aggravate inflammation, while M2‐type macrophages with anti‐inflammatory effects can ameliorate the local inflammatory microenvironment and promote tissue regeneration.<sup>[</sup>\n##UREF##10##\n28\n##\n<sup>]</sup> Thus, guiding the polarization of macrophages toward the regenerative M2 phenotype is more likely to achieve immune‐mediated bone regeneration. To evaluate the effect of the GA/BPPDM hydrogel platform on macrophage reprogramming, we first collected RAW264.7 cells and investigated the morphological changes by cytoskeleton staining. As shown in Figure ##FIG##5##5B##, macrophages cultured on GA/BPPDM hydrogels under NIR laser irradiation appeared as elongated and flattened spindle‐like cells, which are the morphological characteristics of M2 macrophages. Subsequently, the effects of the hydrogels with or without NIR radiation on the 3D migration of macrophages were investigated by cytoskeleton staining. Recent studies have reported that macrophage infiltration is the initial and critical step in the process of regeneration, while promoting macrophage infiltration accelerates hard callus formation and ossification.<sup>[</sup>\n##REF##34325336##\n48\n##\n<sup>]</sup> As displayed in Figure ##FIG##5##5C##, 3D‐reconstructed CLSM images demonstrated that the macrophages not only adhered to the surface of the hydrogels but also gradually infiltrated into the 3D network of the hydrogel matrix. Importantly, the cells treated with GA/BPPDM+NIR exhibited the strongest migration and penetration capabilities, followed by the GA/BPPDM group. In sharp contrast, cell infiltration was almost invisible inside the GA hydrogel, in which cells mainly grew on the top surface of the hydrogel.</p>", "<p>To validate the phenotypes of polarized macrophages after treatment, the M1 and M2 phenotypes of macrophages were labeled with CD86 and CD206, respectively, and then detected by flow cytometry. As shown in Figure ##FIG##5##5D##, a significant increase of CD86 (an M1 marker) expression was observed in RAW264.7 cells after treatment with LPS, while the expression of CD86 in the GA, GA/BPPDM and GA/BPPDM+NIR groups was reduced, indicating the activation of macrophage polarization toward the M2 phenotype. Specifically, higher levels of CD206 (an M2 marker) expression were observed in the GA/BPPDM group than in the LPS and GA groups, and this effect was even more pronounced after periodic and appropriate NIR irradiation. According to the statistical results in Figure ##FIG##5##5E,F##, significantly higher ratios of M2 macrophages (CD206<sup>+</sup> cells) and decreased M1 macrophages (CD86<sup>+</sup> cells) were observed in the GA/BPPDM+NIR group with better immunomodulatory ability. These results demonstrated that the combined therapy of GA/BPPDM plus mild PTT treatment was beneficial for switching the macrophage phenotype from M1 toward M2, leading to the creation of an anti‐inflammatory microenvironment. Immunofluorescence staining further confirmed that GA/BPPDM plus mild photothermal effect was more conducive to macrophage M2 polarization than GA and GA/BPPDM alone (Figure ##FIG##5##5G##). The quantitative fluorescence intensity also showed that the GA/BPPDM+NIR group presented higher CD206<sup>+</sup> expression and lower iNOS<sup>+</sup> expression (Figure ##SUPPL##0##S7##, Supporting Information). According to our in vitro results, GA/BPPDM combined with mild thermal stimulation at 41 ± 1 °C could promote M2 polarization of macrophages and inhibit the expression of M1 macrophages under NIR irradiation conditions, showing huge potential to shorten the inflammation phase and shift it into the proliferation phase during bone regeneration. To further reveal the role of GA/BPPDM and NIR treatment in the immune response, the expression of a series of inflammatory and pro‐healing cytokines was evaluated in the cell supernatant by ELISA. As expected, GA/BPPDM was associated with increased secretion of anti‐inflammatory IL‐10 and IL‐4 and decreased secretion of proinflammatory TNF‐α and IL‐6 under thermal stimulation provided by NIR irradiation (Figure ##SUPPL##0##S8##, Supporting Information). More significantly, compared with the other groups, the GA/BPPDM+NIR group secreted much more pro‐osteogenic (BMP‐2, TGF‐β1) and pro‐angiogenic (VEGF, bFGF) factors, followed by the GA/BPPDM and GA groups (Figure ##SUPPL##0##S9##, Supporting Information). Previous studies have found that M2‐type macrophages can participate in bone regeneration by regulating the release of growth factors (BMP‐2, TGF‐β1, VEGF, and bFGF) and paracrine signals.<sup>[</sup>\n##REF##33984633##\n3\n##\n<sup>]</sup> The GA/BPPDM+NIR hydrogel system is able to polarize macrophages to an anti‐inflammatory M2 phenotype, which is consistent with the results of flow cytometry, resulting in the release of pro‐regenerative factors associated with osteogenesis and angiogenesis. Likewise, both real‐time polymerase chain reaction (qRT‐PCR) and Western blot results confirmed that M2 phenotypic markers, such as IL‐4, IL‐10, Arg‐1, and CD206, were significantly upregulated in the GA/BPPDM+NIR group (Figure ##FIG##5##5H##; Figure ##SUPPL##0##S10##, Supporting Information). On the contrary, the expression of M1 phenotypic markers, such as CD86, IL‐6, TNF‐α, and iNOS, was relatively lower in the GA/BPPDM+NIR group than in the GA/BPPDM group (Figure ##FIG##5##5I##; Figure ##SUPPL##0##S10##, Supporting Information). These results suggested that the GA/BPPDM hydrogel system together with NIR‐triggered drug release had the potential to synergistically alleviate the inflammatory reaction and induce tissue regeneration through the transition of M1‐to‐M2 macrophage polarization.</p>", "<p>Previous studies have shown that mild hyperthermia triggered by NIR irradiation could induce an increase in anti‐inflammatory cytokine secretion, ROS scavenging, and the transformation of the M1‐M2 phenotype of macrophages via activation of the PI3K/Akt1 signaling pathway, leading to a favorable regenerative microenvironment for tissue regeneration.<sup>[</sup>\n##REF##35986434##\n12\n##, ##UREF##20##\n49\n##\n<sup>]</sup> The role of the PI3K/Akt1 signaling pathway in the regulation of macrophage polarization has been well studied, and PI3K is an upstream regulator of protein kinase B (Akt) and has been demonstrated to modulate the phenotype of M2 macrophages.<sup>[</sup>\n##UREF##21##\n50\n##\n<sup>]</sup> Given that, the PI3K/Akt1 signaling pathway was subsequently verified via Western blot analysis. As shown in Figure ##SUPPL##0##S11## (Supporting Information), the GA/BPPDM+NIR group remarkably enhanced the PI3K, Akt1, and p‐Akt1 protein expression of RAW264.7 cells, indicating that PI3K/Akt1 signaling is activated, which may be important to promote cascading macrophage M2 polarization. These results further suggested that the photothermal GA/BPPDM hydrogel system may therapeutically alleviate inflammation and induce the polarization of macrophages toward the M2 phenotype by activating the PI3K/Akt1 signaling pathway to downregulate the expression of inflammatory cytokines.</p>", "<p>To further identify the immunomodulatory ability during the early stage of implantation, we evaluated the macrophage phenotypes in subcutaneously embedded tissue sections on day 7 as mentioned above (Figure ##FIG##5##5J##). Real‐time infrared thermal images were captured after irradiating the implanted hydrogel samples with an 808 nm NIR laser. Consistent with the in vitro polarization of macrophages, immunohistochemical staining confirmed that the GA/BPPDM+NIR group was more conducive to macrophage M2 polarization than the GA/BPPDM group (Figure ##FIG##5##5K##). Quantitative analysis showed higher CD206<sup>+</sup> expression and lower iNOS<sup>+</sup> expression in the GA/BPPDM+NIR group than in the GA/BPPDM group (Figure ##SUPPL##0##S12##, Supporting Information). The proteins of the cells in the subcutaneously embedded hydrogel were extracted and processed for ELISA measurement. The GA/BPPDM hydrogel with NIR stimulation showed higher expression of the anti‐inflammatory factor IL‐10 and lower expression of the proinflammatory factor TNF‐α (Figure ##SUPPL##0##S13##, Supporting Information), which is also consistent with the in vitro tests. The GA/BPPDM photothermal therapeutic platform effectively alleviated inflammation and altered the secretion of cytokines in the microenvironment through immunomodulation compared to the GA/BPPDM and GA groups alone. Based on these in vitro and in vivo results, it is summarized that the GA/BPPDM hydrogel could modulate macrophage polarization and promote anti‐inflammatory processes under on‐demand NIR irradiation, thus shortening the inflammatory phase.</p>", "<title>In Vitro and In Vivo Angiogenesis Assay</title>", "<p>Accumulating evidence has well‐established that angiogenesis is essential for the reconstruction processes of bone healing, which helps to promote new bone formation by accelerating the transportation of nutrients, signaling molecules, and so on.<sup>[</sup>\n##UREF##14##\n39\n##, ##REF##32215404##\n51\n##\n<sup>]</sup> In view of this, satisfactory pro‐angiogenic activities are required for advanced functional biomaterials to satisfy the demands for bone healing. To evaluate the potential effects of NIR‐triggered drug release of the hydrogels on angiogenesis, HUVECs cultured with the hydrogels with or without NIR irradiation were subjected to angiogenic differentiation assay (<bold>Figure</bold> ##FIG##6##\n6A##). The effect of the hydrogel on HUVEC migration was first evaluated by wound healing experiments. Cell migration appeared in all groups and was much better in the GA/BPPDM and GA/BPPDM+NIR groups than in the GA group (Figure ##FIG##6##6B##). The GA/BPPDM+NIR group displayed better wound closure at 24 h, in which the scratch was almost closed, followed by the GA/BPPDM group. The quantitative analysis further indicated better wound closure in the GA/BPPDM+NIR groups than in the GA/BPPDM and GA groups at 24 h (Figure ##FIG##6##6C##), which was mainly ascribed to the accumulated release of DFO triggered by periodic NIR irradiation. In vitro Transwell migration assay was also performed to investigate the potential of the hydrogel system to induce HUVEC migration. As shown in Figure ##SUPPL##0##S14## (Supporting Information), both the GA/BPPDM and GA/BPPDM+NIR groups could exert a chemotaxis effect on recruiting more HUVECs than the GA group. Additionally, the migration ability was considerably improved by the GA/BPPDM hydrogel upon NIR irradiation, as indicated by the highest number of transmembrane cells observed in the GA/BPPDM+NIR group. Here, the wound healing and Transwell migration assays revealed better migration ability for HUVECs in the GA/BPPDM group, but the promotive effect was not as strong as that of the GA/BPPDM+NIR group. Collectively, these results indicated that the migration ability of HUVECs was effectively improved by GA/BPPDM together with on‐demand NIR irradiation, which was also beneficial for vascular regeneration and bone formation.</p>", "<p>The in vitro tube formation assay was further conducted to evaluate the pro‐angiogenic activity of the prepared hydrogels using Matrigel because angiogenesis is a key factor in bone healing, and the ability to promote angiogenesis can accelerate the repair process. As shown in Figure ##FIG##6##6D##, little tubule formation was observed in the GA group, suggesting that the vasculogenic ability of the cells was limited. As expected, the formation of tubular frameworks was detected in the GA/BPPDM and GA/BPPDM+NIR groups; however, compared with the GA/BPPDM group, more mature and intact tubular structures as well as a higher density of cell junctions were observed in the GA/BPPDM+NIR group. In terms of the quantitative analysis, both the vessel percentage area and total number of junctions were significantly increased in the GA/BPPDM+NIR group, followed by the GA/BPPDM group (Figure ##FIG##6##6E,F##), indicating that enhanced vessel formation likely occurred because of the cumulative effect of sustainedly released DFO from GA/BPPDM with the assistance of NIR irradiation. The rapid establishment of vessel networks can promote the recruitment of nutrients and related growth factors at the defect area, thereby accelerating the repair process. These results indicated that the outstanding pro‐angiogenic potential of the GA/BPPDM+NIR group was mainly due to continuous NIR‐triggered DFO release, which can effectively induce cell migration and tubule formation in vitro, benefiting the repair and angiogenesis of impaired tissues.</p>", "<p>Vascularization during bone healing is known to be regulated by growth factors such as VEGF and bFGF and other downstream angiogenic molecules, including eNOS and HIF‐1α expressed by endothelial cells.<sup>[</sup>\n##REF##35946874##\n52\n##\n<sup>]</sup> In view of this, the expression of angiogenesis‐related factors in HUVECs was further studied by qRT‐PCR analysis. As expected, HUVECs in the GA/BPPDM+NIR group owned the highest expression levels of Ang‐1, bFGF, eNOS, HIF‐1α, and VEGF (Figure ##FIG##6##6G##); this was because of the continuous accumulation of DFO from the GA/BPPDM hydrogel with the help of NIR irradiation. It has been verified that DFO is beneficial for the stimulation of angiogenesis. Meanwhile, DFO can stabilize HIF‐1α expression, followed by upregulating the expression of angiogenic factors such as VEGF.<sup>[</sup>\n##REF##34894585##\n40\n##\n<sup>]</sup> As for the GA/BPPDM group, due to the incorporation of BPPD, a significant promotion effect on angiogenic activity was demonstrated. Next, the angiogenic capacity of different hydrogels was further verified by immunofluorescence staining of CD31, VEGF, and HIF‐1α. After 7 days of co‐incubation, the protein expression of CD31 was significantly increased in both the GA/BPPDM and GA/BPPDM+NIR groups, especially in the GA/BPPDM+NIR group, in which the fluorescence signal of CD31 displayed the highest expression level (Figure ##FIG##6##6H##), suggesting enhanced vascularization. Unsurprisingly, the results of VEGF and HIF‐1α protein expression showed the same tendency that the GA/BPPDM+NIR groups exhibited the most significant expression of VEGF and HIF‐1α protein markers, followed by the GA/BPPDM and GA groups (Figure ##FIG##6##6I##). The quantitative results of fluorescence intensity also demonstrated the most significant expression of angiogenic protein markers in the GA/BPPDM+NIR group (Figure ##SUPPL##0##S15##, Supporting Information), indicating enhanced angiogenic activity. From the above results, it was concluded that the GA/BPPDM+NIR group might activate the HIF‐1α pathway and promote the expression of angiogenesis‐related genes/proteins, including Ang‐1, bFGF, eNOS, and VEGF, in HUVECs, which led to the rapid angiogenesis process in vitro.</p>", "<p>In bone tissue engineering, early blood vessel formation can provide sufficient nutrient supply and accelerate new bone formation. To evaluate the impacts of hydrogels on the angiogenesis process in vivo, samples were implanted subcutaneously into the backs of rats to observe new blood vessel formation (Figure ##FIG##6##6J##). During NIR laser irradiation, the temperature changes and corresponding thermal images of the implanted site were recorded by an infrared thermograph, as shown in Figure ##FIG##6##6K##. After 7 days of implantation, the tissues surrounding the implanted hydrogels were subjected to histological observation. The results of hematoxylin and eosin (H&amp;E) staining showed that quite a lot of surrounding tissue cells could be detected around and within the GA/BPPDM+NIR group (Figure ##FIG##6##6L##), implying that the GA/BPPDM hydrogel and mild heat stimulation contributed to the fast ingrowth of the surrounding tissues (red arrows), especially to timely vascular growth, which is essential for tissue remodeling. Owing to the biodegradable hydrogel matrix and bioactive BPPD nanomaterial as well as mild heat stimulation, the cells could migrate into the hydrogels rapidly after in vivo implantation. As a result, the GA/BPPDM+NIR group exhibited excellent tissue integration. The in vivo angiogenic abilities of the implanted hydrogels were further investigated by immunohistochemical analyses of CD31 and α‐SMA, as shown in Figure ##FIG##6##6M##. It is obviously found that there were a greater number of newly formed CD31<sup>+</sup> and α‐SMA<sup>+</sup> blood vessels (yellow arrows) around the GA/BPPDM and GA/BPPDM+NIR groups than around the GA group, implying a higher vascular regeneration improvement. The reason might be that the release of DFO in the early stage was demonstrated to improve the angiogenic activity of the hydrogel and promote angiogenesis in vivo, consistent with previously reported studies.<sup>[</sup>\n##UREF##22##\n53\n##\n<sup>]</sup> Significantly, the expression of CD31 and α‐SMA in the GA/BPPDM+NIR group was the highest among the three groups, which was ascribed to the ability of the on‐demand NIR‐assisted mild heat stimulation to promote adhesion, migration, and angiogenesis as well as induce fast DFO release to a greater extent than the hydrogel without NIR treatment. Accordingly, the quantitative results further verified the formation and quantity of blood vessels in the different groups, supporting the robust stimulation of angiogenesis in the initial inflammatory phase by the GA/BPPDM+NIR group (Figure ##FIG##6##6N,O##), which was consistent with the in vitro results. The above evidence showed that GA/BPPDM could effectively induce the formation of microvessels, and on‐demand NIR irradiation could further accelerate neovascularization due to the synergetic effect of mild heat stimulation and NIR‐triggered DFO release.</p>", "<title>In Vitro Evaluation of Osteogenic Differentiation</title>", "<p>The ability to recruit endogenous cells from surrounding areas is critical for initiating efficient vessel and bone regeneration. To investigate the effect of the as‐prepared hydrogel platform on recruiting osteoblast precursor cells, a Transwell migration assay was conducted with or without NIR irradiation. As shown in Figure ##SUPPL##0##S16## (Supporting Information), with burst release of PO<sub>4</sub>\n<sup>3‐</sup> and DFO from the hydrogels upon NIR irradiation, the GA/BPPDM+NIR group significantly improved the recruitment of MC3TE‐E1 cells in vitro. After being co‐cultured for 24 h, the cell numbers recruited by the GA/BPPDM+NIR group were 3.8‐fold and 1.8‐fold that of the GA/BPPDM and GA groups, respectively, demonstrating that BPPD loading and NIR treatment efficiently enhanced MC3TE‐E1 cell recruitment. Previous studies have demonstrated that BP‐incorporated biomaterials display a positive effect on osteogenesis by modulating osteogenic cytokine secretion to recruit osteoblasts and promote osteogenic activity.<sup>[</sup>\n##REF##36996420##\n31\n##, ##UREF##23##\n54\n##\n<sup>]</sup> Meanwhile, DFO can be rapidly released from the GA/BPPDM hydrogel with the assistance of NIR irradiation and synergize with BP to further promote the proliferation, migration and osteogenic differentiation of cells. This suggested that the NIR‐induced photothermal effect could trigger the release of large amounts of drug/ion quickly to promote cell migration, as evidenced by the results of the release behaviors in vitro.</p>", "<p>We next assessed the effect of the hydrogel platform on the osteogenic differentiation of MC3TE‐E1 cells. A cell co‐culture system was established using a Transwell device, in which the hydrogels were placed in the upper chamber and MC3TE‐E1 cells in the lower chamber under NIR laser irradiation (<bold>Figure</bold> ##FIG##7##\n7A##). As a hallmark of osteogenic differentiation in the early stage, alkaline phosphatase (ALP) activity was first evaluated by qualitative and quantitative measurements in vitro. As illustrated in Figure ##FIG##7##7B##, the GA/BPPDM+NIR group exhibited the deepest ALP staining, followed by the GA/BPPDM and GA groups, which confirmed that the GA/BPPDM hydrogel with NIR‐induced PTT treatment promoted the early osteogenic differentiation of MC3TE‐E1 cells. Correspondingly, through the quantitative analysis of ALP activity, both the GA/BPPDM and GA/BPPDM+NIR groups caused a significant increase in ALP production compared with the GA group (Figure ##FIG##7##7D##). In particular, the ALP activities in the GA/BPPDM+NIR group were significantly higher than those in the other groups on days 7 and 14, demonstrating the synergistic effects of BPPD and NIR‐triggered drug/ion release on inducing osteogenic differentiation in vitro.</p>", "<p>The deposition of calcium minerals, as an important indicator of the later stage of osteogenic differentiation, was evaluated by Alizarin red S (ARS) staining. Consistent with the results of ALP activity, both macroscopic and microscopic images showed that the GA/BPPDM+NIR group presented the highest amounts of bone‐mineralized nodules with an enhanced degree of positive staining among all groups (Figure ##FIG##7##7C##), indicating better osteogenic potential. In a previous study, Shao et al. found that irradiation with NIR light not only accelerated the degradation of BP‐incorporated hydrogels into PO<sub>4</sub>\n<sup>3−</sup>, but also enhanced the biological activity to facilitate the reaction between PO<sub>4</sub>\n<sup>3−</sup> and Ca<sup>2+</sup>, thus promoting bone regeneration through in situ biomineralization.<sup>[</sup>\n##UREF##24##\n55\n##\n<sup>]</sup> In line with the qualitative results, higher levels of mineral matrix formation were detected in the GA/BPPDM and GA/BPPDM+NIR groups, especially in the GA/BPPDM+NIR group (Figure ##FIG##7##7E##). To further assess the in vitro osteogenic potential of the photothermal hydrogel platform, rat BMSCs were also selected for this study because they are the major and important cell source for bone repair and regeneration (Figure ##SUPPL##0##S17A##, Supporting Information). Unsurprisingly, the GA/BPPDM+NIR group showed the highest ALP activity and mineralized nodule formation compared with any other group, followed by the GA/BPPDM and GA groups (Figure ##SUPPL##0##S17B–E##, Supporting Information). These data strongly implied that the incorporation of BPPD could promote osteogenic differentiation in vitro, and NIR‐triggered PO<sub>4</sub>\n<sup>3‐</sup> and DFO release further exerted a potent synergistic effect on osteogenesis. Thus, the GA/BPPDM+NIR group could promote osteogenic differentiation and accelerate mineralized matrix formation in both MC3TE‐E1 cells and BMSCs.</p>", "<p>It has been reported that Col‐1, OPN, and OCN are important components of the ECM of bone, and Runx2 is a critical transcription factor regulating the expression of osteogenesis‐related genes.<sup>[</sup>\n##REF##36469414##\n32\n##\n<sup>]</sup> Therefore, the effects of GA/BPPDM and NIR‐triggered DFO on the osteogenic differentiation of both MC3T3‐E1 cells and BMSCs were investigated through genetic‐ and protein‐level analyses. As illustrated in Figure ##FIG##7##7F–H## and Figure ##SUPPL##0##S17F## (Supporting Information), the expression levels of ALP, Runx2, Col‐1, OPN, and OCN substantially increased in the GA/BPPDM and GA/BPPDM+NIR groups compared with the GA group, indicating that BPPD plays an important role in upregulating the expression of osteogenic markers. Interestingly, in comparison with the GA and GA/BPPDM groups, the GA/BPPDM+NIR group showed the strongest improvement in inducing osteogenic marker expression, consistent with the ALP and ARS evaluation; this result demonstrated that the BPPD and NIR‐triggered DFO and PO<sub>4</sub>\n<sup>3−</sup> release had a synergistic effect on promoting the expression of both early and late osteogenic markers. It is acknowledged that BP not only can be used as a photothermal agent, but also has biological activity and participates in the mineralization process, which induces osteogenesis by activating multiple signaling pathways, including the Wnt/β‐catenin and Ras/MAPK signaling pathways.<sup>[</sup>\n##REF##36920036##\n14\n##\n<sup>]</sup> On the other hand, the DFO released from the on‐demand delivery hydrogel also contributed to the enhancement of osteogenic activity.<sup>[</sup>\n##REF##35946874##\n52\n##\n<sup>]</sup> Similar trends were also detected for osteogenic marker protein expression in the immunofluorescence staining assay. As displayed in Figure ##FIG##7##7I## and Figure ##SUPPL##0##S17G## (Supporting Information), the immunofluorescence staining assay revealed that both MC3T3‐E1 cells and BMSCs in the GA/BPPDM group secreted more osteogenic (Runx2 and OPN) proteins than those in the GA group, which also revealed the pro‐osteogenic activity of BPPD. More importantly, among all the groups, the GA/BPPDM hydrogel with heat stimulation showed the highest expression of Runx2 and OPN upon NIR irradiation (Figure ##SUPPL##0##S18##, Supporting Information), which represented an excellent improvement in bone formation. Overall, these data demonstrated that the GA/BPPDM+NIR group had a prominent stimulatory effect on the osteogenic differentiation of both MC3T3‐E1 cells and BMSCs and probably promoted bone healing by upregulating the gene expression of ALP, Runx2, Col‐1, OPN, and OCN.</p>", "<title>In Vitro Evaluation of the Effect of Immunomodulation on Angiogenesis and Osteogenesis</title>", "<p>During the process of bone regeneration, activated M2 macrophages participate in the clearance of debris, suppression of inflammation, and regulation of angiogenesis and osteogenesis.<sup>[</sup>\n##REF##36031402##\n56\n##\n<sup>]</sup> As mentioned in the previous sections, the photoactivated GA/BPPDM hydrogel platform with excellent anti‐inflammatory and immunomodulatory properties could not only promote M2 macrophage polarization but also produce a conducive immune microenvironment through the secretion of various cytokines, such as IL‐4, IL‐10, BMP‐2, TGF‐β1, VEGF, and bFGF. Consequently, in this section, we used conditioned medium to assess the effect of macrophage phenotype reprogramming on angiogenic and osteogenic responses, as shown in the schematic illustration (<bold>Figure</bold> ##FIG##8##\n8A##). The conditioned medium derived from macrophages treated with GA, GA/BPPDM and GA/BPPDM plus NIR irradiation was collected and used for subsequent in vitro wound healing, tube formation, ALP activity and ARS staining assays. In terms of angiogenic activity, the GA/BPPDM+NIR group elicited a robust ability to promote HUVEC migration and tube formation, as indicated by the enhanced wound healing rate and vessel percentage area (Figure ##FIG##8##8B–E##). Meanwhile, the ALP activity and calcium mineral deposition of MC3T3‐E1 cells in the GA/BPPDM+NIR group were significantly higher than those in the other groups (Figure ##FIG##8##8F–I##), which was mainly related to the anti‐inflammatory and therapeutic cytokines secreted by M2 macrophages. Another reason behind the angiogenic and osteogenic activities may also be attributed to the presence of BP and DFO.</p>", "<p>Taken together, these in vitro results suggested that the GA/BPPDM hydrogel system could not only directly promote osteogenic and angiogenic differentiation, thus accelerating bone regeneration but also indirectly increase the secretion of various pro‐healing cytokines in the microenvironment through immunomodulation, thereby accelerating osteogenesis and angiogenesis. This was consistent with previous studies showing that M2 macrophages played a positive role in recruiting mesenchymal progenitor cells, boosting angiogenesis and osteogenic differentiation by secreting various factors such as BMP‐2 and VEGF.<sup>[</sup>\n##REF##35523800##\n57\n##\n<sup>]</sup> As illustrated in Figure ##FIG##8##8J##, we elucidated the underlying mechanism of GA/BPPDM hydrogel‐mediated anti‐inflammation, macrophage phenotype reprogramming and immunomodulatory function. Under the action of BPPD and mild PTT treatment, the GA/BPPDM hydrogel resulted in inhibited oxidative stress and diminished secretion of proinflammatory cytokines (CD86, IL‐6, TNF‐α, and iNOS) by activating the PI3K/Akt1 signaling pathway. As reported, the upregulation of the PI3K/Akt1 signaling pathway has been identified to be associated with the activation of M2 macrophages.<sup>[</sup>\n##REF##33811079##\n58\n##\n<sup>]</sup> In addition, ROS was one of the factors that could regulate the transformation of M1/M2 macrophages, while reducing local levels of ROS benefits the transformation of macrophages from the M1 phenotype to the M2 phenotype, leading to the secretion of a diverse array of anti‐inflammatory and pro‐healing signals for accelerated tissue regeneration,<sup>[</sup>\n##REF##36890691##\n27\n##\n<sup>]</sup> which is consistent with our in vitro immunomodulation results. Consequently, the NIR‐irradiated GA/BPPDM hydrogel system with favorable immunomodulatory and antioxidant activity could orchestrate M2 macrophage polarization and promote the production of anti‐inflammatory, angiogenic and osteogenic cytokines, recreating a favorable regenerative microenvironment for vascularization and osteogenesis. The results from both direct and indirect evaluations suggested that the GA/BPPDM hydrogel system not only had good biocompatibility, pro‐angiogenic and pro‐osteogenic activities, and ROS scavenging ability but also induced anti‐inflammatory M2‐type macrophage polarization to remodel the damaged microenvironment into a pro‐healing microenvironment for enhanced angiogenesis and osteogenesis.</p>", "<title>In Vivo Immunomodulatory Properties, Angiogenesis, and Bone Regeneration Capabilities in SD Rat Skull Defect Models</title>", "<p>Based on the results described above, our prepared GA/BPPDM hydrogels possessed favorable osteogenic and angiogenic capabilities as well as efficient immunomodulatory performance, showing great potential in accelerating bone tissue repair. However, whether these beneficial effects can be achieved in vivo remains unclear. In this study, a critical‐sized skull defect model (Φ = 5 mm) in rats was constructed to further evaluate the influence of GA/BPPDM with NIR irradiation on regulating the regenerative microenvironment and accelerating bone healing. A schematic diagram of our in vivo study is illustrated in <bold>Figure</bold> ##FIG##9##\n9A##. The GA/BPPDM hydrogel was implanted into the defect sites as a photoactivated material followed by NIR laser irradiation to maintain a local temperature of 41 ± 1 °C (Figure ##FIG##9##9B##), which is suitable for tissue regeneration without additional photothermal injury.<sup>[</sup>\n##REF##35358870##\n35\n##\n<sup>]</sup> During the early stage of bone defects and material implantation, the inflammatory response initially occurs and further determines the fate of bone healing by inducing immune cells to migrate toward wound sites to accommodate the immune microenvironment.<sup>[</sup>\n##REF##35667249##\n59\n##\n<sup>]</sup> Therefore, at 7 days after the operation, the immunomodulatory ability of GA/BPPDM+NIR on the bone defect microenvironment was investigated by immunofluorescence staining. iNOS and Arg‐1 were chosen as typical surface markers for M1 or M2 macrophages, respectively. As shown in Figure ##FIG##9##9C##, a substantial increase of iNOS‐positive macrophages was detected in the control group after bone defect modeling, indicating a serious inflammatory state. Simultaneously, the three experimental groups not only significantly decreased the percentage of iNOS‐positive macrophages but also increased the percentage of CD206‐positive macrophages infiltrated in the defect sites, especially in the GA/BPPDM+NIR group, which exhibited the highest M2 expression, implying a weakened inflammatory state. These data suggested that the GA/BPPDM+NIR group could convert proinflammatory M1 macrophages to anti‐inflammatory M2 macrophages, thus efficiently reducing the local inflammatory response during bone healing. The fluorescence intensity also showed that GA/BPPDM+NIR exhibited higher CD206<sup>+</sup> expression and lower iNOS<sup>+</sup> expression (Figure ##FIG##9##9D,E##), which was consistent with the decreased M1 phenotype markers (CD86, IL‐6, TNF‐α, and iNOS) and improved levels of M2 phenotype markers (IL‐4, IL‐10, Arg‐1, and CD206) measured by qRT‐PCR assay (Figure ##SUPPL##0##S19##, Supporting Information). To further validate the regulatory effect of the implanted hydrogels on macrophage polarization in the defect area, the representative proinflammatory cytokine TNF‐α and anti‐inflammatory cytokine IL‐10 were investigated on day 7. As presented in Figure ##FIG##9##9F##, the defect site in the control group induced the highest expression of TNF‐α, suggesting a serious inflammatory response. As expected, downregulated proinflammatory cytokine (TNF‐α) and upregulated anti‐inflammatory cytokine (IL‐10) were observed in both the GA/BPPDM and GA/BPPDM+NIR groups in comparison with the control and GA groups. And this was particularly obvious in the GA/BPPDM+NIR group, which exhibited significantly higher expression of IL‐10 (Figure ##FIG##9##9G,H##), indicating an excellent anti‐inflammatory effect. The role of PDA and mild heat stimulation in anti‐inflammation and macrophage polarization has been widely studied.<sup>[</sup>\n##REF##35533294##\n60\n##\n<sup>]</sup> Researchers found that NIR‐derived mild thermal stimulation at 41 ± 1 °C was able to protect cells from ROS‐induced oxidative damage through inhibition of the NF‐κB signaling pathway, thus promoting tissue regeneration under chronic inflammatory conditions.<sup>[</sup>\n##REF##35759676##\n47\n##\n<sup>]</sup> Besides, the combination of PDA and mild PTT triggered by NIR laser irradiation could significantly reprogram macrophages from the M1 phenotype to the M2 phenotype, thereby suppressing inflammatory responses and producing a pro‐regenerative microenvironment for bone healing. Combined with the previous results both in vitro and in vivo, it was demonstrated that the GA/BPPDM hydrogel was beneficial for polarizing macrophages toward the M2 phenotype, and mild heat stimulation further ameliorated the inflammatory environment, thus creating a conducive microenvironment for subsequent tissue regeneration.</p>", "<p>There is substantial evidence that the presence of M2 macrophages can induce high expression of BMP‐2 and VEGF in the regenerative microenvironment, acting as potent inducers of osteogenesis and angiogenesis to stabilize bone and blood vessel formation.<sup>[</sup>\n##REF##35523800##\n57\n##\n<sup>]</sup> The early pro‐osteogenic and pro‐angiogenic capacities of different hydrogels were further verified by immunohistochemical staining, including BMP‐2, VEGF, and HIF‐1α (<bold>Figure</bold> ##FIG##10##\n10A##). Owing to the synergistic interaction of the GA/BPPDM hydrogel system and mild heat stimulation, the GA/BPPDM+NIR group effectively enhanced the secretion of pro‐regenerative factors in the microenvironment of bone defects, with significant BMP‐2 and VEGF marker expression observed at week 2 post‐treatment (Figure ##FIG##10##10B,C##). Similarly, HIF‐1α, as an upstream regulator that can activate the transcription of VEGF, was also remarkably upregulated in the GA/BPPDM+NIR group (Figure ##FIG##10##10D##). Multiple studies have identified that BMP‐2 and VEGF are the most effective cytokines in promoting osteogenesis and vascular regeneration, respectively, while BMP‐2 can indirectly promote angiogenesis by stimulating VEGF.<sup>[</sup>\n##UREF##25##\n61\n##\n<sup>]</sup> Furthermore, as an important regulator of angiogenesis, HIF‐1α can stimulate the growth of new blood vessels and provoke transcription of its downstream molecule VEGF.<sup>[</sup>\n##REF##35550764##\n62\n##\n<sup>]</sup> The quantitative analysis results further showed that the expression of BMP‐2, VEGF, and HIF‐1α was significantly higher in the GA/BPPDM+NIR group than in the other groups (Figure ##FIG##10##10B–D##), which could beneficially achieve enhanced cellular responses for rapid neovascularization, promoted recruitment of MSCs to the defect site, and enhanced ECM biosynthesis during the proliferation phase.</p>", "<p>In the process of bone development and bone remodeling, enhanced neovascularization and endogenous stem cell recruitment were demonstrated to accelerate new bone formation.<sup>[</sup>\n##REF##36996420##\n31\n##\n<sup>]</sup> After 2 weeks of bone defect modeling, there was degradation of the residual hydrogels to various degrees in the defect area, which integrated well with the surrounding tissues without obvious displacement. Moreover, all hydrogel‐treated groups presented newly formed blood vessels (yellow arrows) within the defect area, in remarkable contrast to the limited vascularization observed in the control group (Figure ##FIG##10##10E##). Notably, the GA group showed a small amount of vascular network, while the GA/BPPDM and GA/BPPDM+NIR groups displayed a more obvious vascular structure, indicating abundant blood vessel infiltration, which is also consistent with the results of in vitro tube formation and subcutaneous embedding experiments. Especially in the GA/BPPDM+NIR group, abundant microvessel ingrowth was detected throughout the whole defect area (Figure ##FIG##10##10E##), resulting in a complete vascular network, which was mainly due to the secreted VEGF and HIF‐1α as well as the presence of an M2 macrophage‐enriched pro‐healing microenvironment. Meanwhile, by detecting the expression of CD31 (a specific marker of vascular endothelial cells) and CD90 (a specific surface marker of stem cells), we further analyzed angiogenesis as well as the recruitment and migration of endogenous stem cells during the repair of the defect site. The results of immunofluorescence staining showed that almost no signals for stem cell accumulation (CD90<sup>+</sup>, green) and only a small amount of host vascular endothelial cells (CD31<sup>+</sup>, red) with sporadic distribution were detected in the control group at 2 weeks (Figure ##FIG##10##10E,F##). Conversely, both GA/BPPDM and GA/BPPDM+NIR promoted endogenous stem cell recruitment and newly formed blood vessel infiltration into the defect area, especially for GA/BPPDM+NIR, which showed a more developed ring‐shaped vascular system and higher enrichment of CD90<sup>+</sup> MSCs. Quantitative results for CD31 and CD90 expression also confirmed that GA/BPPDM plus mild heat stimulation could facilitate the ingrowth of host blood vessels as well as the recruitment of endogenous stem cells (Figure ##FIG##10##10G##; Figure ##SUPPL##0##S20##, Supporting Information), which were crucial for the osseointegration of host bone tissue and implanted material in the early stage of bone repair. Herein, Figure ##FIG##10##10H## illustrates the osteoimmunomodulatory mechanism of the GA/BPPDM therapeutic platform. Benefiting from the combination of GA/BPPDM and mild PTT treatment, GA/BPPDM+NIR could recreate a favorable osteoimmunomodulatory microenvironment (anti‐inflammatory and M2‐polarizing) and drive the production of osteogenic/angiogenic factors (BMP‐2 and VEGF) to induce endogenous MSC recruitment and blood vessel formation, thereby initiating robust osteogenesis and angiogenesis. Collectively, owing to bioactive components and functional properties, the GA/BPPDM photothermal hydrogel could effectively transform the tissue microenvironment from inflammatory to reparative by polarizing macrophages recruited at the defect to the M2 type and promoting the secretion of anti‐inflammatory and pro‐healing cytokines, thereby achieving augmented bone regeneration.</p>", "<p>Then, the bone regeneration performance was analyzed using micro‐CT, histological staining, and immunohistochemical staining. A schematic diagram of the bone regeneration capacity experiment is presented in <bold>Figure</bold> ##FIG##11##\n11A##. From 2D‐ and 3D‐reconstructed micro‐CT images, only a small amount of new bone distributed around the rim of the defect areas could be found in the control group at both 4 and 8 weeks. As expected, a critical‐sized skull defect model was successfully established in the present study. In sharp contrast, a significantly greater amount of new bone ingrowth was detected in the GA/BPPDM and GA/BPPDM+NIR groups at 4 weeks, which subsequently formed a more complete bone structure at 8 weeks (Figure ##FIG##11##11B##). Especially in the GA/BPPDM+NIR group, the density of newly formed bone tissue was dramatically increased, with the defect site almost completely healed at 8 weeks, while only sporadic new bone tissue appeared in the GA group. The examination of the coronal view also reflected the same result, showing that a complete bone bridge connecting the defects could be detected in the GA/BPPDM+NIR group. However, visible and obvious defects were still present in the GA and control groups without such apparent bone formation at the defect edge due to the limited self‐healing capacity. These results further highlighted the synergistic role of the GA/BPPDM hydrogel combined with mild photothermal treatment in promoting osteogenesis and tissue regeneration in vivo. It is worth noting that the micro‐CT results in the GA group were better than those in the control group in vivo, which is mainly attributed to the fact that GA with biomimetic bone ECM structure could also promote bone regeneration despite without any modification, consistent with previous studies.<sup>[</sup>\n##UREF##1##\n4\n##\n<sup>]</sup>\n</p>", "<p>Accordingly, quantitative analysis of the micro‐CT examination is shown in Figure ##FIG##11##11C##, revealing the formation of new bone in the defect area. The analysis of bone regeneration‐related parameters, including the bone tissue volume/total tissue volume (BV/TV), trabecular thickness (Tb.Th), trabecular number (Tb.N), and bone mineral density (BMD), was consistent with the micro‐CT results. The BV/TV of the GA/BPPDM+NIR group reached 50.01 ± 3.04% at 8 weeks, which was significantly higher than that of the GA/BPPDM group (34.01 ± 1.77%), GA group (12.49 ± 1.97%), and control group (7.35 ± 0.97%), indicating that the presence of BPPD and mild PTT can promote new bone formation in vivo. Furthermore, the critical index for evaluating bone regeneration efficacy, including Tb.Th (0.64 0.04 mm), Tb.N (1.44 ± 0.0.5 mm<sup>−1</sup>), and BMD (0.46 ± 0.03 g cm<sup>−3</sup>) in the GA/BPPDM+NIR group showed the highest value, followed by the GA/BPPDM and GA groups at 8 weeks, similar to the results of the BV/TV analysis, further verifying a fulfilled effect in the promotion of bone mass. Owing to the excellent NIR/pH‐dual‐responsive properties, the photothermal effect can increase the release of DFO rapidly to promote vascularization in the early stage of bone healing and sustainably release PO<sub>4</sub>\n<sup>3−</sup> from the GA/BPPDM hydrogels to induce bone regeneration through in situ biomineralization during the long‐term bone repair period. Additionally, previous studies have reported that the combination of on‐demand mild hyperthermia (≈45 °C) and BP‐incorporated scaffolds could synergistically promote bone regeneration due to the alteration of cytoskeleton and integrin signaling as well as the upregulation of heat shock protein.<sup>[</sup>\n##REF##30550998##\n63\n##\n<sup>]</sup> Our study further proved that NIR‐induced mild PTT combined with the dual‐sensitive drug/ion delivery GA/BPPDM hydrogel platform had a significant promotion effect on bone healing in vivo. Taken together, relying on the sequential modulation of the immune microenvironment, revascularization, and osteogenesis, the NIR‐irradiated GA/BPPDM hydrogel platform can effectively promote bone regeneration in vivo, and the newly formed bone possesses excellent mineral density and intact bone structure.</p>", "<p>Subsequently, the histopathological structures of the regenerated new bone in the defect sites were verified by H&amp;E, Masson's trichrome (MST), and Goldner's trichrome staining. As seen from the histological images, the defect areas of the control group showed predominantly fibrous tissue formation bridging the edge of the host bone at 4 and 8 weeks (Figure ##FIG##11##11D##), implying poor bone regeneration potential, consistent with the results of the micro‐CT analysis. In contrast, there were numerous continuously regenerated lamellar bone with newborn bone lacunae and central canals observed in the GA/BPPDM and GA/BPPDM+NIR groups, which exhibited a relatively complete laminar structure. In particular, the defect areas of the GA/BPPDM+NIR group were almost completely occupied by dense and mature newly formed bone tissue, and the thickness was similar to that of the original bone at 8 weeks after implantation. MST staining further demonstrated that only a few collagen fibers were sparsely deposited within the defect area of the control group, while with the treatment of GA/BPPDM plus mild PTT, abundant collagen with dense and continuous structures was observed in the GA/BPPDM+NIR group, demonstrating the formation of mature lamellar bone. It is worth mentioning that the residual hydrogel material was almost replaced with fibrous tissue and surrounded by internal newly formed bone islands due to the ECM‐mimicking 3D microenvironment and proper degradation rate, which allowed space for new bone formation and ingrowth. Another possible reason is the creation of favorable regenerative microenvironment by the combined effect of GA/BPPDM and mild PTT (Figure ##FIG##10##10H##), which is conducive to tissue ingrowth and microcirculation, consequently accelerating the catabolism of the implanted hydrogel.<sup>[</sup>\n##UREF##26##\n64\n##\n<sup>]</sup> These results indicated that the GA/BPPDM hydrogel combined with mild heat stimulation could promote cell ingrowth and facilitate material‐neo‐bone tissue integration, thus leading to quicker and better bone healing with bone‐like structures. Goldner's trichrome staining was further performed to evaluate the degree of bone maturation at 8 weeks after implantation (Figure ##FIG##11##11E##). Compared with the control and GA groups, a significantly greater amount of mature lamellar bone tissues (green) together with less immature bone (osteoid, orange/red) was observed in the GA/BPPDM group, indicating that the GA/BPPDM hydrogels facilitated bone mineralization and remodeling. Furthermore, after treatment with mild PTT, considerable, green‐stained mature bone tissues were observed to grow from the edges of defective regions toward the central areas, which meant that the new bone was gradually calcified and matured. This phenomenon fully demonstrated that new bone tissue tended to regenerate from the margin toward the center of defects, benefiting from the guiding and promoting role of the GA/BPPDM hydrogel and NIR‐triggered mild PTT on osteoprogenitor cell recruitment, migration, differentiation, and biomineralization. Hydrogel biodegradation in vivo was also assessed by H&amp;E staining at 8 weeks after implantation. It could be found that the residual hydrogel material (yellow arrows) gradually degraded, and some tissue cells were observed within the interior of the hydrogels, indicating good compatibility and long‐term biodegradability in vivo (Figure ##SUPPL##0##S21##, Supporting Information), which is beneficial for cell infiltration in the bone defect areas. Furthermore, the residual GA/BPPDM hydrogel was surrounded by internal newly formed bone islands, indicating the ability of the GA/BPPDM scaffold plus mild heat stimulation to facilitate bone tissue ingrowth and promote material‐tissue integration. To verify the ability of the smart‐responsive photothermal hydrogel platform to promote osteogenesis and biomineralization during bone repair, immunohistochemical staining of Col‐1, Runx2, OPN, and OCN was conducted at 8 weeks post‐implantation. As displayed in Figure ##FIG##11##11F##, the expression of these osteogenic markers in both the GA/BPPDM and GA/BPPDM+NIR groups was significantly higher than that in the control and GA groups. In particular, the GA/BPPDM+NIR group exhibited the strongest positive staining of Col‐1, Runx2, OPN, and OCN proteins, followed by those in the GA/BPPDM and GA groups (Figure ##SUPPL##0##S22##, Supporting Information), indicating that the mild photothermal effect of GA/BPPDM could facilitate matrix maturation and mineralization during bone regeneration and remodeling. As mentioned above, GA/BPPDM plus NIR treatment can improve the local microenvironment and realize stimuli‐responsive release of DFO and PO<sub>4</sub>\n<sup>3−</sup>, resulting in the continuous secretion of these ECM proteins in the defect sites, thus accelerating tissue repair and regeneration. In addition, compared with the control group, no obvious pathological changes in major organs, including the heart, lung, liver, spleen, and kidney, were observed for all experimental groups, suggesting good biosafety of the hydrogels in vivo (Figure ##SUPPL##0##S23##, Supporting Information). In this work, the superior performance of the GA/BPPDM hydrogel platform in the bone augmentation effect is mainly attributed to its multifunctional therapeutic features (<bold>Figure</bold> ##FIG##12##\n12\n##). i) Owing to the combined action of BP, PDA, and DFO, GA/BPPDM could continuously maintain a conducive pro‐regenerative microenvironment in the repair process because of its superior osteogenic and angiogenic activities, which are vital for bone defect repair. ii) Under mild NIR irradiation, GA/BPPDM could modulate the polarization of macrophages toward the M2 phenotype and promote the production of anti‐inflammatory, angiogenic and osteogenic cytokines, thereby enhancing neovascularization and endogenous stem cell recruitment, which played a key role in the early stage of the healing process. Meanwhile, BPPD, as an important component of GA/BPPDM, could endow the hydrogel with mild photothermal activity and pH‐responsive and NIR laser‐triggered drug/ion release behavior for efficient bone regeneration. iii) Under the combined long‐term effect of physical (mild hyperthermia) and chemical (drug/ion delivery) interventions, the smart‐responsive multifunctional therapeutic system achieved improved regenerative microenvironment and efficient bone regeneration. Overall, the photoactivated GA/BPPDM hydrogel was a promising biomaterial scaffold that could augment the repair and regeneration of large bone defects, as indicated by accumulated M2‐type macrophages, reduced inflammation, promoted angiogenesis, and enhanced bone matrix deposition.</p>" ]
[ "<title>Conclusion</title>", "<p>In summary, in this study, a smart‐responsive multifunctional hydrogel platform combined with NIR‐triggered mild PTT was developed for spatiotemporally manipulating macrophage polarization and vascular development for rapid bone regeneration. Owing to the photothermal conversion performance of BP and PDA as well as the pH sensitivity of the PDA layer, the as‐prepared dual‐drug delivery hydrogel system possessed spatial distributions of angiogenic (DFO) and osteogenic (PO<sub>4</sub>\n<sup>3−</sup>) factors under on‐demand NIR irradiation, thus achieving a synergistic therapeutic effect of immunomodulation, angiogenesis, and osteogenesis. The in vitro evaluation and in vivo subcutaneous implantation experiments demonstrated that combined with mild PTT under appropriate NIR irradiation, the GA/BPPDM therapeutic system had excellent biocompatibility, pro‐osteogenic and pro‐angiogenic capacities, as well as outstanding ROS‐scavenging capacities and immunomodulatory functions. The in vivo experiments further confirmed that NIR‐assisted GA/BPPDM could promote multiple regenerative processes in the healing process of a critical‐sized bone defect model in rats, including M2 polarization of macrophages, neovascularization, osteogenesis, and tissue remodeling. In conclusion, by combining physical (mild PTT treatment) and chemical (drug/ion delivery) interventions, the hydrogel ensured a rapid transformation from M1 to M2 macrophages at the early stage of inflammation and the secretion of pro‐osteogenic and pro‐angiogenic factors, which efficiently stimulated vascular tissue growth and endogenous stem cell recruitment and ultimately accelerated the bone repair process. This study offers an amazing strategy for bone regeneration through the combination of smart responsive design and bioactive factors, and multifunctional hydrogels provide broad implications for bone defect repair applications.</p>" ]
[ "<title>Abstract</title>", "<p>The treatment of bone defects remains a substantial clinical challenge due to the lack of spatiotemporal management of the immune microenvironment, revascularization, and osteogenic differentiation. Herein, deferoxamine (DFO)‐loaded black phosphorus nanosheets decorated by polydopamine layer are prepared (BPPD) and compounded into gelatin methacrylate/sodium alginate methacrylate (GA) hybrid hydrogel as a smart‐responsive therapeutic system (GA/BPPD) for accelerated bone regeneration. The BPPD nanocomposites served as bioactive components and near‐infrared (NIR) photothermal agents, which conferred the hydrogel with excellent NIR/pH dual‐responsive properties, realizing the stimuli‐responsive release of DFO and PO<sub>4</sub>\n<sup>3 −</sup> during bone regeneration. Under the action of NIR‐triggered mild photothermal therapy, the GA/BPPD hydrogel exhibited a positive effect on promoting osteogenesis and angiogenesis, eliminating excessive reactive oxygen species, and inducing macrophage polarization to the M2 phenotype. More significantly, through macrophage M2 polarization‐induced osteoimmune microenvironment, this hydrogel platform could also drive functional cytokine secretion for enhanced angiogenesis and osteogenesis. In vivo experiments further demonstrated that the GA/BPPD system could facilitate bone healing by attenuating the local inflammatory response, increasing the secretion of pro‐healing factors, stimulating endogenous cell recruitment, and accelerating revascularization. Collectively, the proposed intelligent photothermal hydrogel platform provides a promising strategy to reshape the damaged tissue microenvironment for augmented bone regeneration.</p>", "<p>A smart‐responsive multifunctional therapeutic system composed of DFO‐loaded BP nanosheets decorated by PDA layer and GA composite hydrogel is designed and constructed to achieve the stimuli‐responsive release of DFO and PO<sub>4</sub>\n<sup>3−</sup> under the action of NIR‐triggered mild photothermal treatment for spatiotemporal management of the immune regulation, revascularization, and osteogenic differentiation during bone healing.\n\n</p>", "<p content-type=\"self-citation\">\n<mixed-citation publication-type=\"journal\" id=\"advs6575-cit-0065\">\n<string-name>\n<given-names>M.</given-names>\n<surname>Wu</surname>\n</string-name>, <string-name>\n<given-names>H.</given-names>\n<surname>Liu</surname>\n</string-name>, <string-name>\n<given-names>D.</given-names>\n<surname>Li</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Zhu</surname>\n</string-name>, <string-name>\n<given-names>P.</given-names>\n<surname>Wu</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>F.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>Y.</given-names>\n<surname>Chen</surname>\n</string-name>, <string-name>\n<given-names>Z.</given-names>\n<surname>Deng</surname>\n</string-name>, <string-name>\n<given-names>L.</given-names>\n<surname>Cai</surname>\n</string-name>, <article-title>Smart‐Responsive Multifunctional Therapeutic System for Improved Regenerative Microenvironment and Accelerated Bone Regeneration via Mild Photothermal Therapy</article-title>. <source>Adv. Sci.</source>\n<year>2024</year>, <volume>11</volume>, <elocation-id>2304641</elocation-id>. <pub-id pub-id-type=\"doi\">10.1002/advs.202304641</pub-id>\n</mixed-citation>\n</p>" ]
[ "<title>Conflict of Interest</title>", "<p>The authors declare no conflict of interest.</p>", "<title>Author Contributions</title>", "<p>M.W., H.L., D.L., and Y.Z. contributed equally to this work. M.W. performed conceptualization, methodology, investigation, wrote the original draft, and project administration. H.L., D.L., Y.Z., performed conceptualization, methodology, investigation, and wrote the original draft. P.W., Z.C., F.C., Y.C., performed investigation. Z.D. performed conceptualization, methodology, wrote the original draft, and supervised. L.C. performed conceptualization, methodology, wrote the original draft, supervised, and funding acquisition.</p>", "<title>Supporting information</title>" ]
[ "<title>Acknowledgements</title>", "<p>This work was supported by the National Natural Science Foundation of China (NFSC) for Young Scientists (Grant No. 82302392), China Postdoctoral Science Foundation Funded Project (2023M732711), Translational Medicine and Interdisciplinary Research Joint Fund of Zhongnan Hospital of Wuhan University (Grant No. ZNLH202202), and the Knowledge Innovation Program of Wuhan‐Shuguang (2022020801020491). The authors thank the Experimental Teaching Center of Basic Medical Sciences, Wuhan University, for technical support. The procedures of all animal studies in this study were approved by the Animal Ethical Committee of Wuhan University, and the methods in the current work were carried out in strict accordance with “Guiding Opinions on the Treatment of Animals (09/30/2006)” published by the Ministry of Science and Technology of the People's Republic of China.</p>", "<title>Data Availability Statement</title>", "<p>The data that support the findings of this study are available in the supplementary material of this article.</p>" ]
[ "<fig position=\"float\" fig-type=\"Scheme\" id=\"advs6575-fig-0013\"><label>Scheme 1</label><caption><p>Schematic illustration for fabrication and application of smart‐responsive multifunctional therapeutic system with mild photothermal activity for augmented bone regeneration through spatiotemporal manipulation of the immune microenvironment, stem cell recruitment and vascular development, and osteogenic differentiation throughout the whole healing process.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0001\"><label>Figure 1</label><caption><p>A) Schematic diagram of the fabrication of BPPD. B) TEM and C) AFM images of BPPD. D) FTIR spectra of BP, BP@PDA, BPPD, and DFO. Schematic illustration for the fabrication of E) GelMA and F) Alg‐MA. <sup>1</sup>H NMR spectra of G) GelMA and H) Alg‐MA. I) FTIR spectra of gelatin and GelMA. Scale bar: 500 nm (B), 1 µm (C).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0002\"><label>Figure 2</label><caption><p>A) Schematic illustration of the fabrication of the GA/BPPD hydrogel. B) SEM and D) micro‐CT images of the lyophilized GA/BPPD hydrogel. Mean C) pore size, E) porosity, and F) water contact angle of the GA/BPPD hydrogel. G) Photographs of the GA/BPPD hydrogel before and after compression. H) Rheological analysis of the GA/BPPD hydrogel. I) Strain–stress curves and J) compressive strength of the GA/BPPD hydrogel. K) Swelling ratio of the hydrogels in PBS solution. L) Degradation behavior of the hydrogels in the presence of 100 mg mL<sup>−1</sup> lysozyme. Scale bar: 200 µm (low‐magnification SEM images in B), 5 µm (high‐magnification SEM images in B), 300 µm (D). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3). *<italic toggle=\"yes\">p</italic> &lt; 0.05 and **<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA group. <sup>#</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05 and <sup># #</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA/BPPDM group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0003\"><label>Figure 3</label><caption><p>A) Real‐time infrared thermal images and B) photothermal heating curves of the GA/BPPD hydrogel with mild NIR irradiation powers (808 nm, 1 W cm<sup>−2</sup>). C) Photothermal stability of the GA/BPPD hydrogel with four on/off cycles. D) Schematic diagram of the NIR/pH dual‐triggered drug/ion release behavior of the GA/BPPDM hydrogel. E,F) Cumulative release of DFO from the GA/BPPDM hydrogel at different pH values with or without NIR irradiation (808 nm, 1 W cm<sup>−2</sup>). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3).</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0004\"><label>Figure 4</label><caption><p>A) CCK‐8 assay and B) live/dead staining of MC3T3‐E1 cells cultured on the hydrogels. C) CCK‐8 assay and D) live/dead staining of HUVECs cultured on the hydrogels. Cytoskeleton fluorescence staining of F‐actin and DAPI in E) MC3T3‐E1 cells and F) HUVECs cultured on the hydrogels for 3 days. Quantitative analysis of G) cell density and H) cell spreading area of MC3T3‐E1 cells. Quantitative analysis of I) cell density and J) cell spreading area of HUVECs. Scale bar: 200 µm (B,D), 75 µm (E,F). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3). *<italic toggle=\"yes\">p</italic> &lt; 0.05 and **<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA group. <sup>#</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05 and <sup># #</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA/BPPDM group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0005\"><label>Figure 5</label><caption><p>A) Schematic diagram of exploring the effect of GA/BPPDM hydrogels combined with NIR irradiation on ROS scavenging and immunomodulation. B) Immunofluorescence staining of F4/80 and F‐actin in RAW264.7 macrophages after different treatments. C) 3D z‐stack images of RAW264.7 macrophage penetration depth after incubation for 4 days. D) Flow cytometry analysis and E,F) quantification of CD86 and CD206 expression in RAW264.7 macrophages. G) Immunofluorescence staining of iNOS and CD206 in RAW264.7 macrophages. H,I) Relative mRNA expression of inflammation‐related genes in RAW264.7 macrophages. J,K) Immunohistochemical staining of iNOS and CD206 in different hydrogels on day 7 after implantation in the rat subcutaneous model (M: material residue). Scale bar: 5 µm (B), 200 µm (C), 20 µm (G), 50 µm (K). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3). *<italic toggle=\"yes\">p</italic> &lt; 0.05 and **<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the control group. <sup>#</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05 and <sup># #</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA/BPPDM+NIR group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0006\"><label>Figure 6</label><caption><p>A) Schematic diagram of exploring the effect of GA/BPPDM hydrogels combined with NIR irradiation on the angiogenic differentiation of HUVECs. B) Crystal violet staining and C) quantitative analysis of the scratch wound healing assay. D) CLSM images of the tube formation assay and E,F) quantitative analysis of tube formation, including the average vessel percentage area and the total number of junctions. G) Relative mRNA expression of angiogenesis‐related genes in HUVECs, including Ang‐1, bFGF, eNOS, HIF‐1α, and VEGF. H,I) Immunofluorescence staining of CD31, VEGF, and HIF‐1α in HUVECs. J) Schematic diagram of the rat subcutaneous implantation model and the process of blood vessel formation. K) Real‐time infrared thermal images of rats implanted with GA/BPPDM hydrogel under NIR irradiation for 5 min (1 W cm<sup>−2</sup>, 808 nm). L) H&amp;E staining and M) immunohistochemical staining for CD31 and α‐SMA at 14 days after implantation (M: material residue, red arrow: infiltration of host cells, yellow arrow: newly formed blood vessels). N,O) Quantitative analysis of the CD31‐positive expression area and microvessel density. Scale bar: 200 µm (B, D), 50 µm (H, I), 100 µm (L,M). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3). *<italic toggle=\"yes\">p</italic> &lt; 0.05 and **<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA group. <sup>#</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05 and <sup># #</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA/BPPDM+NIR group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0007\"><label>Figure 7</label><caption><p>A) Schematic diagram of exploring the effect of GA/BPPDM hydrogels combined with NIR irradiation on the osteogenic differentiation of MC3T3‐E1 cells. Macroscopic and microscopic images of B) ALP staining and C) ARS staining of MC3T3‐E1 cells. Quantitative analysis of D) ALP activity and E) ARS staining. F) Relative mRNA expression of osteogenesis‐related genes in MC3T3‐E1 cells, including ALP, Runx2, Col‐1, OPN, and OCN. G,H) Western blot analysis and quantification of osteogenic protein expression, including ALP, Runx2, Col‐1, OPN, and OCN. I) Immunofluorescence staining of Runx2 and OPN in MC3T3‐E1 cells. Scale bar: 200 µm (B, C), 20 µm (I). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3). *<italic toggle=\"yes\">p</italic> &lt; 0.05 and **<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA group. <sup>#</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05 and <sup># #</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA/BPPDM+NIR group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0008\"><label>Figure 8</label><caption><p>A) Schematic diagram of exploring the effect of conditioned medium collected from activated macrophages on angiogenesis and osteogenesis. B) Crystal violet staining and D) quantitative analysis of the wound healing assay. C) CLSM images of the tube formation assay and E) quantitative analysis of vessel percentage area. F,G) Macroscopic and microscopic images of ALP staining and ARS staining of MC3T3‐E1 cells. Quantitative analysis of H) ALP activity and I) mineralization level of MC3T3‐E1 cells. J) Schematic illustration of the potential mechanism of anti‐inflammation and M2‐type macrophage polarization and the subsequent guiding effect on vascularization and osteogenic differentiation by the GA/BPPDM hydrogel under mild NIR irradiation. Scale bar: 200 µm (B,C,G). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3). *<italic toggle=\"yes\">p</italic> &lt; 0.05 and **<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the control group. <sup>#</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05 and <sup># #</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA/BPPDM+NIR group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0009\"><label>Figure 9</label><caption><p>A) Schematic diagram for analysis of the early immune response, neovascularization, and stem cell recruitment. B) Real‐time infrared thermal images of rats implanted with GA/BPPDM hydrogel under NIR irradiation for 5 min (1 W cm<sup>−2</sup>, 808 nm). C) Immunofluorescence staining and D,E) quantitative analysis of iNOS and Arg‐1. F) Immunohistochemical staining and G,H) quantitative analysis of TNF‐α and IL‐10. Scale bar: 100 µm (C,F). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3). *<italic toggle=\"yes\">p</italic> &lt; 0.05 and **<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the control group. <sup>#</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05 and <sup># #</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA/BPPDM+NIR group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0010\"><label>Figure 10</label><caption><p>A) Immunohistochemical staining and B–D) quantitative analysis of BMP‐2, VEGF, and HIF‐1α. E) Photographs and immunofluorescence staining of CD31 in the defect region. F) Immunofluorescence staining of CD90 in the defect region. G) Quantitative analysis of CD31‐positive blood vessels. H) Schematic diagram of early immunomodulation and subsequent promotion effect on neovascularization and endogenous stem cell recruitment. Scale bar: 100 µm (A), 200 µm (E,F). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3). *<italic toggle=\"yes\">p</italic> &lt; 0.05 and **<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the control group. <sup>#</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05 and <sup># #</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA/BPPDM+NIR group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0011\"><label>Figure 11</label><caption><p>A) Schematic diagram for the analysis of bone regeneration. B) 2D‐ and 3D‐reconstructed micro‐CT images, including transverse and coronal sections, in the defect sites at 4 and 8 weeks after implantation. C) Quantitative analysis of micro‐CT results, including BV/TV, Tb.Th, Tb.N, and BMD. D,E) Histological analysis, including H&amp;E staining, MST staining, and Goldner's trichrome staining, of regenerated bone tissue in the defect sites (FT: fibrous tissue, NB: newly formed bone tissue, HB: host bone, black arrow: newly formed bone lacunae, yellow arrow: newly formed central canal, black circle: residual hydrogel, MB: mineralized/mature bone (green), blue circle: immature bone (osteoid, red)). F) Immunohistochemical staining of Col‐1, Runx2, OPN, and OCN in the defect area. Scale bar: 1 mm (B), 200 µm (D,E), 100 µm (F). Data are presented as the mean ± SD (<italic toggle=\"yes\">n</italic> = 3). *<italic toggle=\"yes\">p</italic> &lt; 0.05 and **<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the control group. <sup>#</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.05 and <sup># #</sup>\n<italic toggle=\"yes\">p</italic> &lt; 0.01 indicate significant differences compared with the GA/BPPDM+NIR group.</p></caption></fig>", "<fig position=\"float\" fig-type=\"Figure\" id=\"advs6575-fig-0012\"><label>Figure 12</label><caption><p>Schematic diagram of the possible mechanism by which the smart‐responsive multifunctional GA/BPPDM therapeutic system promotes bone regeneration.</p></caption></fig>" ]
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[ "<supplementary-material id=\"advs6575-supitem-0001\" position=\"float\" content-type=\"local-data\"><caption><p>Supporting Information</p></caption></supplementary-material>" ]
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[ "<media xlink:href=\"ADVS-11-2304641-s001.pdf\"><caption><p>Click here for additional data file.</p></caption></media>" ]
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J."], "year": ["2023"], "volume": ["466"], "elocation-id": ["143173"]}, {"label": ["53"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["X.", "M.", "B.", "Q.", "J.", "H.", "L.", "P.", "W.", "W."], "surname": ["Han", "Sun", "Chen", "Saiding", "Zhang", "Song", "Deng", "Wang", "Gong", "Cui"], "source": ["Bioactive Mater."], "year": ["2021"], "volume": ["6"], "fpage": ["1639"]}, {"label": ["54"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["X.", "Y.", "C.", "C.", "K.", "L.", "F.", "Y."], "surname": ["Wang", "Yu", "Yang", "Shao", "Shi", "Shang", "Ye", "Zhao"], "source": ["Adv. Funct. Mater."], "year": ["2021"], "volume": ["31"], "elocation-id": ["2105190"]}, {"label": ["55"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n"], "given-names": ["J.", "C.", "H.", "P. K.", "X.\u2010F."], "surname": ["Shao", "Ruan", "Xie", "Chu", "Yu"], "source": ["Adv. Sci."], "year": ["2020"], "volume": ["7"], "elocation-id": ["2000439"]}, {"label": ["61"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["H.", "Z.", "Z.", "J.", "A. C.", "Y.", "L.", "Y.", "L.", "C.", "X.", "Y.", "W.", "B.", "G."], "surname": ["Xue", "Zhang", "Lin", "Su", "Panayi", "Xiong", "Hu", "Hu", "Chen", "Yan", "Xie", "Shi", "Zhou", "Mi", "Liu"], "source": ["Bioactive Mater."], "year": ["2022"], "volume": ["18"], "fpage": ["552"]}, {"label": ["64"], "mixed-citation": ["\n"], "string-name": ["\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n"], "given-names": ["X.", "L.", "Y.", "Z.", "H.", "T.", "Z.", "Y.", "X.", "A. E. d. 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{ "acronym": [], "definition": [] }
64
CC BY
no
2024-01-14 23:41:57
Adv Sci (Weinh). 2023 Nov 7; 11(2):2304641
oa_package/e0/a8/PMC10787108.tar.gz
PMC10787109
0
[ "<title>Introduction</title>", "<p id=\"Par2\">Pathogenesis of multi-organ complications associated with diabetes [##UREF##2##4##], alcohol abuse [##REF##28988577##16##], and cART use [##UREF##8##17##] is via oxidative stress and inflammation [##UREF##9##18##, ##REF##28956285##19##]. Oxidative stress and inflammation are interlinked, stimulate the occurrence of one another [##REF##34576205##14##] and incidentally are the commonest factors in male reproductive dysfunctions [##UREF##10##20##, ##REF##29136166##21##]. Moreover, a high number of reproductive age males are diabetic [##REF##29887834##1##], involved in a lifestyle of alcohol abuse [##UREF##0##2##], and are on chronic (HIV-infected) combination antiretroviral therapy (cART) or its prophylaxis [##UREF##1##3##]. Unfortunately, diabetes [##REF##29887834##1##, ##UREF##2##4##], alcohol [##UREF##3##5##, ##UREF##4##6##], and cART [##REF##27818734##7##, ##REF##30132391##8##] have been reported to cause alternations in reproductive hormone levels, testicular structure, and sperm parameters.</p>", "<p id=\"Par3\">Previous studies have demonstrated decreased tubule diameter, reduced height and derangement of germinal epithelium cell layers, spermatogenic cell loss, sloughed epithelium, and karyolysis in diabetic or/and alcohol-exposed or/and cART-treated animals [##REF##29654715##9##, ##UREF##5##10##]. Corroborating findings reported from seminal fluid analysis, include reduced sperm count, motility, and viability and an increase in abnormal sperm morphology and DNA fragmentation in diabetic condition [##REF##29887834##1##, ##UREF##2##4##, ##UREF##6##11##] alcohol consumption [##UREF##3##5##, ##UREF##4##6##, ##UREF##7##12##], and cART treatment [##REF##27818734##7##, ##REF##30132391##8##, ##REF##21722892##13##]. Testicular and spermatozoa alternations have been linked to increased reactive oxygen species (ROS), and oxidative stress [##REF##34576205##14##, ##REF##30569652##15##]. Markedly, nitric oxide synthases (NOS) are established to mediate testicular oxidative stress induction in several testis disorders including cryptorchidism, testicular torsion, varicocele, and toxicity [##UREF##11##22##, ##UREF##12##23##].</p>", "<p id=\"Par4\">The three NOS isoforms viz. endothelial NOS (eNOS or NOS3), inducible NOS (iNOS or NOS2), and neuronal NOS (nNOS or NOS1) catalyze the production of nitric oxide from L-arginine [##REF##18567643##24##]. Nitric oxide (NO) is a free radical recognized to play a regulatory role in the process of spermatogenesis at low concentrations [##REF##11058531##25##, ##UREF##13##26##], but at elevated levels leads to formation of nitrogen-based reactive oxygen species (ROS), which are detrimental to the testicular tissue [##REF##18567643##24##, ##UREF##14##27##]. Unlike eNOS and nNOS, iNOS is calcium-independent and produces NO in larger quantities than other isoforms. Therefore, upregulation (NO) is clinically important in the induction of testicular oxidative stress [##UREF##11##22##, ##REF##19404589##28##].</p>", "<p id=\"Par5\">Evidently, the testis is particularly vulnerable to oxidative stress because of high mitochondrial oxygen consumption to support the inherent spermatogenic cell divisions and steroidogenesis [##REF##28658802##29##]. Testicular tissue is further predisposed to oxidative stress because of poor vascularization and relatively high amounts of unsaturated fatty acids [##UREF##10##20##, ##REF##24795696##30##]. Therefore, based on previous reports which showed that diabetes [##REF##29371661##31##], alcohol [##UREF##3##5##], and cART [##UREF##15##32##] can independently induce oxidative stress and inflammation, this study evaluated the testicular effects of co-existence of cART and alcohol abuse in diabetic conditions relative to inducible nitric oxide synthase (iNOS) activity, oxidative stress, inflammation, apoptosis, and cell proliferation.</p>" ]
[ "<title>Materials and methods</title>", "<title>Chemical and reagents</title>", "<p id=\"Par6\">Streptozotocin (STZ) (S0130) was procured from Sigma-Aldrich Chemical Company (St. Louis, MO, USA) and Atripla, a fixed-dose combination antiretroviral drug (cART) was purchased from Bristol-Myers Squibb and Gilead Sciences (Foster City, CA, USA). The primary antibodies interleukin-1beta (IL-1β) (ab2105), interleukin-6 (IL-6) (ab9324), tumor necrosis factor-alpha (TNF-α) (ab6671), inducible nitric oxide synthase (iNOS) (ab115819), malondialdehyde (MDA) (ab243066), 8-hydroxydeoxyguanosine (8-OHDG) (ab62623), caspase 3 (ab4051), and Ki-67 (ab15580) were purchased from Abcam (Cambridge, MA, USA). The biotinylated goat anti-rabbit (BA-1000) and goat anti-mouse (BA-9200) secondary antibodies, and Avidin–Biotin Complex kit (ABC) (PK-6100) were purchased from Vector Laboratories (Burlingame, CA, USA).</p>", "<title>Ethical clearance</title>", "<p id=\"Par7\">The Animal Research Ethics Committee (AREC) of the University of Witwatersrand (Wits) approved the study protocol with approval number 2018/011/58/C. All experiments were carried out at Wits Animal Research Facility (WARF) per the guidelines of AREC.</p>", "<title>Animal husbandry</title>", "<p id=\"Par8\">In this study, 30 adult male Sprague Dawley rats (10 weeks old; weighing 330–370 g) were used. Every rat was housed individually in a sterile plastic cage at a room temperature of 21–23 °C, with a 12/12-h light/dark cycle, and allowed free access to rat chow and water. Throughout the 90 days treatment duration, the animals freely accessed drinking water or alcohol, and rat chow according to respective treatment groupings.</p>", "<title>Induction of type 2 diabetes</title>", "<p id=\"Par9\">Type 2 diabetes was induced using a modified procedure described by Wilson &amp; Islam, 2012 [##REF##22580529##33##]. Briefly, animals were fed on a 20% fructose reconstituted rat chow diet for two weeks, after which a single injection of freshly prepared 40 mg/kg STZ in 0.05 M (pH 4.5) citrate buffer was administered intraperitoneally. Then, blood glucose (non-fasting) levels were measured 72 h after STZ administration, and rats with glucose levels ≥ 250 mg/dl were regarded diabetic. Once the diabetic state was confirmed in animals, they were placed on a standard rat chow diet.</p>", "<title>Experimental design</title>", "<p id=\"Par10\">The animals were divided into five groups, each with six animals, as follows. Control group, diabetic (DM) group, diabetic animals treated with 10% v/v alcohol daily (DM + A) group, diabetic animals treated with an extrapolated human recommended dose of 23.22 mg/kg of cART [##REF##16906786##34##] in gelatine cubes daily (DM + cART), and diabetic animals treated with both alcohol and cART (DM + A + cART) group. The animals were treated for 90 days, after which the animals were weighed, anesthetized with 240 mg/ml pentobarbitone, and terminated. The testes were then extracted and preserved in 10% neutral buffered formalin for subsequent processing.</p>", "<title>Food and fluid intake</title>", "<p id=\"Par11\">The amount of food and fluid consumed by each rat was recorded daily throughout the experimental period.</p>", "<title>Body weight and gonadosomatic index</title>", "<p id=\"Par12\">The animals were weighed before termination (final body weight) and testis weight was recorded immediately after their extraction. Then, the final body and testis weights were used to calculate the gonadosomatic index, using the formula previously reported by Olasile et al., 2018 [##REF##30627377##35##]</p>", "<title>Immunohistochemistry for oxidative stress, inflammatory, apoptosis, and proliferation biomarkers</title>", "<p id=\"Par13\">The harvested and fixed testes were dehydrated sequentially in 70–100% alcohol grades and embedded in molten paraffin wax and sectioned at 5 μm thickness using a Leica RM 2125 rotatory microtome. The sections were floated in a warm water bath (45 °C) for 60 s, then mounted onto silane-coated glass slides for antibody immunolabeling. The sections were dried overnight, followed by deparaffinizing in xylene, hydrating in a series of decreasing alcohol concentrations, and rinsing in running tap water for 5 min. The sections were incubated in citrate buffer overnight in a water bath at 60 °C for antigen retrieval. Thereafter, sections were rinsed in phosphate-buffered saline (PBS) for 5 min, then, immersed in 1% hydrogen peroxide in methanol for 20 min to inhibit endogenous peroxidase. After rinsing in phosphate-buffered saline (PBS) for three changes of five minutes each, 5% normal goat serum was added to the sections to block nonspecific antibody binding. This was tapped off after 30 min, and the primary antibody added subsequently (1:100 for anti-TNF-α and anti-iNOS, 1:200 for anti-IL-1β, anti-IL-6, anti-MDA, and anti-caspase 3, and 1:1000 for anti-8-OHDG and anti-Ki-67) and left overnight (approximately 16 h) at 4 °C. Afterward, the sections were rinsed in PBS and incubated with the secondary antibody (1:1000 biotinylated goat anti-rabbit for the IL-1β, TNF-α, iNOS, caspase 3, and Ki-67 antibodies and 1: 1000 biotinylated goat anti-mouse for IL-6, MDA, and 8-OHDG antibodies) for 30 min. Followed by rinsing in PBS, then avidin–biotin complex (ABC) reagent was added for 30 min. Subsequently, the sections were rinsed in PBS and incubated with 3, 3’-diaminobenzidine tetrachloride (DAB) for five minutes. DAB was then washed off under running tap water for five minutes and the slides were dipped in hematoxylin for one minute to counterstain. Followed by rinsing in running tap water to remove excess stain, dehydration of slides in alcohol series, and coverslip with Dibutylphthalate Polystyrene Xylene (DPX). For the antibodies with immunoreactivity localized to cell nuclei (IL-6, 8-OHDG, caspase 3, and Ki-67), the total number of cell nuclei expressing immunoreactivity were counted in 20 rounded seminiferous tubules for each animal (i.e., 120 tubules for each group) at × 400. The images of antibodies with immunoreactivity localized to both cell nucleus and cytoplasm (IL-1β, TNF-α, iNOS, and MDA) were captured in 144 microscopic fields at × 100 for each group and the ilastik software (v1.3.3; <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ilastik.org\">https://www.ilastik.org</ext-link>) was used for image segmentation. Then Fiji software (v1.52e; <ext-link ext-link-type=\"uri\" xlink:href=\"https://imagej.net/Fiji\">https://imagej.net/Fiji</ext-link>) was used to quantify immunostaining in the image segments as we previously described [##REF##36759974##36##]. Below is the procedure for quantifying Ki-67 staining intensity.</p>", "<title>IHC staining intensity quantification</title>", "<p id=\"Par14\">The Fiji software (v1.52e; <ext-link ext-link-type=\"uri\" xlink:href=\"https://imagej.net/Fiji\">https://imagej.net/Fiji</ext-link>) was used to measure the mean gray values (MGV) of selected stained regions of interest (ROI) as shown in Fig. ##FIG##0##1## [##UREF##16##37##, ##REF##33731967##38##]. Worth noting is that the darker stained areas have a low MGV and the lightly stained areas have a high MGV, thus the staining intensity is equal to the reciprocal of MGV [##REF##33731967##38##]. The steps followed for Ki-67 staining intensity quantification were as follows; opening the image in Fiji: File &gt; Open &gt; Select the image &gt; Open; setting the scale: Analyze &gt; Set scale &gt; Ok; drawing an ROI: Edit &gt; Selection &gt; Specify &gt; Ok; selecting the parameters: Analyze &gt; Set measurement (check the MGV box) &gt; Ok; taking the measurement: Analyze &gt; Measure; opening the next image: File &gt; Open next; choosing the same ROI size and shape: Edit &gt; Selection &gt; Restore selection; proceed to take the measurement: Analyze &gt; Measure; save the results as a CVS file for statistical analysis.</p>", "<p id=\"Par15\">The staining intensity of Ki-67 was calculated as follows. [##REF##33731967##38##]</p>", "<title>Data analysis</title>", "<p id=\"Par16\">The data were analyzed using the Windows version of GraphPad Prism 6 and the data was presented as Mean ± SEM. The different group means were compared using one-way analysis of variance (ANOVA), and the Bonferroni post hoc test was performed for multiple comparisons. Deeming <italic>p</italic> &lt; 0.05 value statistically significant.</p>" ]
[ "<title>Results</title>", "<title>Food and fluid intake</title>", "<p id=\"Par17\">A general reduction in food intake was recorded in all treated groups relative to the control group but was significant in the DM + A (<italic>p</italic> = 0.0455) and DM + A + cART (<italic>p</italic> = 0.0090) treated groups only (Fig. ##FIG##1##2##). In comparison with the control, fluid intake increased significantly (<italic>p</italic> &lt; 0.0001) in DM and DM + cART treated groups; however, an insignificant increase (<italic>p</italic> &gt; 0.05) was recorded in DM + A and DM + A + cART treated groups. Further, the fluid intake in DM and DM + cART was significantly increased (<italic>p</italic> &lt; 0.0001) relative to DM + A and DM + A + cART (Fig. ##FIG##1##2##).</p>", "<title>Body weight and gonadosomatic index (GSI)</title>", "<p id=\"Par18\">All treated groups showed a decrease in final body weight compared to the control, but a significant decrease was recorded in only the DM + A (<italic>p</italic> = 0.0197) and DM + A + cART (<italic>p</italic> = 0.0357) treated groups (Fig. ##FIG##1##2##). Gonadosomatic index increased significantly in DM + A + cART group relative to control (<italic>p</italic> = 0.0306) and DM + A (<italic>p</italic> = 0.0190). However, the gonadosomatic index of DM + A treated group was insignificantly deceased (<italic>p</italic> &gt; 0.05) compared to the control. Further, a non-significant increase (<italic>p</italic> &gt; 0.05) was recorded in the gonadosomatic index of DM and DM + cART treated groups relative to the control group (Fig. ##FIG##1##2##).</p>", "<title>Oxidative stress biomarker immunoexpression</title>", "<p id=\"Par19\">Expression of iNOS was found in the testicular interstitial cells, Leydig cells, and macrophages of the control and treated groups (Fig. ##FIG##2##3##). The DM, DM + cART, and DM + A + cART) treated groups had significantly increased iNOS expression compared to the control (<italic>p</italic> &lt; 0.0001 for all) and DM + A (<italic>p</italic> = 0.0005, <italic>p</italic> &lt; 0.0001, and <italic>p</italic> &lt; 0.0001 respectively). The DM + A treated group iNOS expression increased significantly (<italic>p</italic> = 0.0041) relative to the control group. Further, iNOS expression in DM + A + cART group was significantly increased compared to DM (<italic>p</italic> &lt; 0.0001) and DM + cART (<italic>p</italic> = 0.0003) treated groups. Similarly, immunostaining of MDA was detected in the Leydig cells and macrophages (Fig. ##FIG##2##3##). Compared to the control, the expression of MDA significantly increased in all treated groups (DM: <italic>p</italic> &lt; 0.0001, DM + A: <italic>p</italic> &lt; 0.0001, DM + cART: (<italic>p</italic> = 0.0041, and DM + A + cART: <italic>p</italic> &lt; 0.0001). Also, the MDA expression in DM + A treated group increased significantly (<italic>p</italic> &lt; 0.0001) compared to the other treated groups. Furthermore, MDA expression in DM treated group was significantly increased (<italic>p</italic> = 0.0004) compared to DM + cART. The control and treated groups showed 8-OHDG immunostaining in the spermatogenic cells (Fig. ##FIG##2##3##). The 8-OHDG immunostaining of all treated groups increased significantly (<italic>p</italic> &lt; 0.0001) compared to control, whilst the expression in the DM + A treated group was respectively significantly increased (<italic>p</italic> &lt; 0.0001) compared to the other treated groups (DM, DM + cART, and DM + A + cART).</p>", "<title>Proinflammatory cytokine immunoexpression</title>", "<p id=\"Par20\">The interleukin-1beta (IL-1β) immunostaining was observed in the testicular interstitial cells, macrophages, and Leydig cells of the control and treated groups, except in DM + A treated group that showed IL-1β immunostaining in the germinal epithelium as well (Fig. ##FIG##3##4##). All treated groups (DM, DM + A, DM + cART, and DM + A + cART) showed significant increases in IL-1β expression in comparison with the control group (<italic>p</italic> &lt; 0.0001, <italic>p</italic> &lt; 0.0001, <italic>p</italic> = 0.0389, and <italic>p</italic> = 0.0095 respectively). Moreso, the expression of IL-1β in the DM group was significantly increased compared to DM + A (<italic>p</italic> = 0.0005), DM + cART (<italic>p</italic> &lt; 0.0001), and DM + A + cART (<italic>p</italic> &lt; 0.0001) treated groups. The interleukin-6 (IL-6) immunostaining in both control and treated groups was detected in Sertoli cells, macrophages, and Leydig cells, except the DM + A group which had immunostaining in only a few Sertoli cells (Fig. ##FIG##3##4##). For this study, only immunostained Sertoli cells were quantified. The IL-6 expression in DM, DM + cART, and DM + A + cART treated groups increased significantly (<italic>p</italic> &lt; 0.0001) compared to control and DM + A. However, DM + A treated group had a significantly decreased (<italic>p</italic> &lt; 0.0001) IL-6 expression compared to control. Additionally, DM + cART group IL-6 expression was significantly increased compared to DM (<italic>p</italic> &lt; 0.0001) and DM + A + cART (<italic>p</italic> = 0.0001), but the IL-6 expression in DM + A + cART was increased significantly (<italic>p</italic> &lt; 0.0001) compared to DM group. Further, tumor necrosis factor-alpha (TNF-α) immunostaining was similar to that of IL-1β mentioned above. In comparison with control, TNF-α expression increased significantly in all treated groups (DM: <italic>p</italic> = 0.0016, DM + A: <italic>p</italic> &lt; 0.0001, DM + cART: <italic>p</italic> &lt; 0.0001, and DM + A + cART: <italic>p</italic> = 0.0019) (Fig. ##FIG##3##4##).</p>", "<title>Apoptosis marker, caspase 3 immunoexpression</title>", "<p id=\"Par21\">Caspase 3 immunostaining was detected in the germinal epithelium cells of both control and treated groups (Fig. ##FIG##4##5##). Compared to the control, all treated groups showed a significant increase (<italic>p</italic> &lt; 0.0001) in the number of germ cells expressing caspase 3. However, the expression of caspase 3 was significantly increased in DM + A treated group in comparison with other treated groups (DM: <italic>p</italic> = 0.0385, DM + cART: <italic>p</italic> &lt; 0.0001, and DM + A + cART: <italic>p</italic> &lt; 0.0001). and the expression in DM treated group increased significantly (<italic>p</italic> = 0.0002) compared to DM + A + cART treated group.</p>", "<title>Proliferation marker, Ki-67 immunoexpression</title>", "<p id=\"Par22\">The Ki-67 expression was found in germ cells, majorly the spermatocytes and round spermatids of the control and treated groups (Fig. ##FIG##5##6##). A significant reduction in the number of germ cells expressing Ki-67 was detected in all treated groups (<italic>p</italic> &lt; 0.0001) in comparison with control. Ki-67 expression in DM + A treated group reduced significantly (<italic>p</italic> &lt; 0.0001) compared to the other treated groups, and the expression in DM group was also significantly reduced (<italic>p</italic> &lt; 0.0001) respectively when compared with DM + cART and DM + A + cART treated groups. However, Ki-67 staining intensity increased significantly (<italic>p</italic> &lt; 0.0001) in all treated groups compared to the control. The intensity of Ki-67 in DM + A group was significantly increased (<italic>p</italic> &lt; 0.0001) in comparison with the other treated groups, and the intensity in DM and DM + A + cART treated groups increased significantly (<italic>p</italic> &lt; 0.0001) compared with DM + cART treated group.</p>" ]
[ "<title>Discussion</title>", "<p id=\"Par23\">Diabetes and combination antiretroviral therapy (cART) regimen due to HIV infection are a huge public health concern [##REF##33382732##39##], and alcohol abuse as a lifestyle is also prevalent in society [##UREF##17##40##]. The prevalence of these trio (diabetes, alcohol abuse, and cART use) and their co-existence in one individual is rising in sub-Saharan Africa, especially in males of reproductive age [##REF##29887834##1##–##UREF##1##3##]. Consistent with previous studies [##REF##30627377##35##, ##UREF##18##41##], our results showed a decreased food intake but increased fluid intake in treated groups when compared to the control group. Further, the final body weight of all treated groups decreased, resulting in increased gonadosomatic index (GSI), except the DM + A (diabetic and alcohol) treated group which showed a slight GSI decrease compared to control. Both increased and decreased GSI implicate impairment in testicular structure and function [##REF##34233693##42##, ##REF##31468683##43##]. Conversely, increased GSI suggests an increase in testicular weight due to fibrosis and/or inflammation [##REF##31468683##43##], but a decreased GSI reflects a reduction in testis weight that could have resulted from tissue degeneration [##REF##34233693##42##, ##REF##31600920##44##].</p>", "<p id=\"Par24\">In this study, the oxidative stress biomarkers evaluated (inducible nitric oxide synthase (iNOS), malondialdehyde (MDA), and 8-hydroxydeoxyguanosine (8-OHDG)) were significantly upregulated in the testis of all treated groups relative to control. Oxidative stress plays a major role in the pathogenesis of testicular dysfunctions [##REF##34576205##14##, ##REF##32093059##45##], and incidentally, diabetes, alcohol, and cART are well-established oxidative stress inducers [##UREF##3##5##, ##UREF##9##18##, ##REF##28956285##19##]. Corroborating with the results of this study, increased expression of iNOS has previously been reported in testis of diabetic rats [##REF##26566682##46##], rats exposed to alcohol [##UREF##12##23##], and those treated with cART [##REF##34118364##47##]. Additionally, a clinical study by Coştur et al. [##REF##22050043##48##] observed an intense iNOS expression in testis of azoospermic patients. Remarkably, iNOS was greatly upregulated in diabetic animals treated with both alcohol and cART compared to other treated and control groups, suggesting a heightened oxidative stress induction due to alcohol-cART-diabetes interaction.</p>", "<p id=\"Par25\">Earlier studies have established that iNOS plays a key role in induction of testicular oxidative stress through catalysis of nitric oxide production [##UREF##14##27##, ##REF##19404589##28##, ##REF##24551570##49##]. Though nitric oxide (NO) level was not determined in the present study, the upregulation of iNOS would imply an increase in nitric oxide level [##REF##31600920##44##, ##REF##22050043##48##]. At low concentrations (&lt; 1 µM), NO promotes homeostasis, cell proliferation, and survival, but elevated NO levels (&gt; 1 µM) which may occur following induction of oxidative stress by chemical insults stimulate spermatogenic cell proliferation arrest and apoptosis [##REF##18567643##24##, ##REF##24551570##49##, ##REF##31583254##50##]. This conforms with the significant germ cell loss and distortions of seminiferous tubules observed in the testis of treated animals.</p>", "<p id=\"Par26\">Furthermore, testis tissue has relatively high amounts of unsaturated fatty acids compared to other tissues [##REF##28658802##29##, ##REF##24795696##30##]. In addition, Leydig cell utilizes high amounts of fatty acids during the biosynthesis of testosterone [##UREF##19##51##] and thus, are very susceptible to lipid peroxidation [##REF##28747539##52##]. Moreover, macrophages which are a main source of iNOS/NO lie adjacent to Leydig cells in the testicular interstitium, making the Leydig cells immediate targets of iNOS/NO activity [##REF##19404589##28##, ##REF##22050043##48##]. Consequently, high testicular iNOS/NO levels stimulate lipid peroxidation leading to production of unsaturated reactive aldehyde, malondialdehyde (MDA) [##REF##31583254##50##, ##REF##10495477##53##]. Accordingly, elevated MDA levels were recorded in all treated groups, the diabetic animals treated with alcohol (DM + A group) had the highest MDA levels. Our findings agree with previous studies that recorded increased MDA levels in testis tissue homogenate of rats that were diabetic [##UREF##20##54##], exposed to alcohol [##UREF##4##6##], and treated with cART [##UREF##15##32##]. However, in the present study, elevated MDA levels were recorded not only in diabetic animals but in all the treatment combinations. Elevation of MDA levels is an evidence of lipid peroxidation and causes testicular cell disintegration, subsequently resulting in impairments of steroidogenesis and spermatogenesis [##UREF##13##26##, ##REF##10495477##53##, ##REF##31737171##55##].</p>", "<p id=\"Par27\">Additionally, testicular iNOS/NO upregulation stimulates an increased formation of reactive oxygen species (ROS) and lowers cellular antioxidant production [##UREF##13##26##]. ROS is a potent mediator of DNA oxidation, consequently leading to DNA breakdown and generation of 8-hydroxydeoxyguanosine (8-OHDG) [##REF##10701694##56##]. Conversely, increased nuclear 8-OHDG is an indicator of testicular oxidative stress [##REF##34576205##14##, ##REF##32093059##45##], and has been suggested to induce several mutations such as transitions, deletions, frameshifts, and epigenetic changes that subsequently lead to infertility and genetic disorders in offspring [##REF##32093059##45##, ##REF##10701694##56##]. Therefore, the increased levels of 8-OHDG observed in the testis of treated animal groups suggests severe oxidative stress induced by the treatments. Further, previous studies have reported increased testicular DNA fragmentation in rats treated with alcohol [##UREF##12##23##] and cART [##REF##34118364##47##], which adversely affect the male reproductive capacity.</p>", "<p id=\"Par28\">Furthermore, earlier studies reported that elevated iNOS/NO levels stimulate testicular inflammation via the nuclear factor- kβ (NF-kβ) pathway [##UREF##13##26##, ##REF##31737171##55##], leading to the release of cytokines such as interleukin-1β (IL-1β), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and interferons (IFNs) [##REF##31600920##44##, ##REF##24551570##49##]. Although NF-kβ antibody immunostaining was nonspecific (not reported) in the present study, previous studies have demonstrated increased testicular NF- kβ in conditions associated with testicular oxidative stress and inflammation [##REF##34576205##14##, ##UREF##9##18##]. We found significantly elevated levels of testicular pro-inflammatory cytokines such as IL-1β, IL-6, and TNF-α in the treated groups, except in the DM + A group (diabetic animals treated with alcohol) that showed a significantly decreased IL-6 expression relative to the control group. This suggests induction of testicular inflammation in line with previous reports of elevated levels of proinflammatory cytokines (IL-1β and TNF-α) in testicular tissue homogenate of diabetic rats [##UREF##20##54##] and those treated with cART [##REF##34118364##47##].</p>", "<p id=\"Par29\">Earlier studies have reported increased levels of pro-inflammatory cytokines in testicular injury, infection, ischemia, and toxicosis [##REF##19527232##57##–##REF##29250030##59##]. Upregulation of testicular cytokines is associated with suppressed steroidogenesis, disruption of blood-testis barrier (BTB) integrity, and diminished spermatozoa viability, which subsequently lead to spermatogenesis and fertility impairments [##REF##24584780##60##, ##REF##34075113##61##]. Furthermore, studies show that both increase and decrease in the expression of IL-1β [##REF##34515835##62##] and TNF-α [##REF##18832037##63##] can be detrimental to Leydig cell function, through inhibition of Leydig cell cytochrome P450 steroidogenic enzymes (CYP11A1 and CYP17A1) [##REF##34515835##62##, ##REF##18832037##63##]. The alternations in testicular cytokines recorded in this study corroborates with earlier reports and conform with the testicular structure and cellular derangements, that will eventually cause steroidogenesis and spermatogenesis failure.</p>", "<p id=\"Par30\">Consequently, accumulation of ROS (oxidative stress) and cytokines (inflammation) are both triggers of testicular cell apoptosis [##REF##31600920##44##, ##REF##34401644##64##]. Our results revealed that immuno-expression of caspase 3, an executioner of cell apoptosis increased significantly in testis of treated groups relative to the control, which implies increased apoptosis due to the treatments. Additionally, previous studies have reported apoptosis in the testis of animals that are diabetic [##REF##31600920##44##, ##REF##24771956##65##], exposed to alcohol [##REF##30048695##66##, ##REF##32141651##67##], and treated with cART [##REF##34118364##47##, ##REF##24919589##68##]. Further, a significant decrease in the number of germ cells expressing Ki-67 but with strong staining intensity was recorded in the treated groups suggesting a disruption of germ cell proliferation and spermatogenesis dysfunction. Similar findings have been demonstrated in cryptorchidism [##REF##25628730##69##] and fluoride-induced testicular toxicity [##REF##29748930##70##].</p>", "<p id=\"Par31\">In conclusion, this study demonstrated that diabetes, alcohol, cART, and their concurrency trigger testicular oxidative stress, inflammation, apoptosis, and disruption of spermatogenic cell proliferation, leading to testis structural and spermatogenesis derangement. Our results suggest that the deleterious impacts of alcohol consumption or/and cART use in diabetic condition on the testis may be mediated through iNOS activity upregulation. The current study highlights the possible critical male reproductive health impairments that may arise amongst diabetic patients who are on cART therapy and consume alcohol regularly.</p>" ]
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[ "<p id=\"Par1\">Diabetes, alcohol abuse, and combination antiretroviral therapy (cART) use have been reported to cause multi-organ complications via induction of oxidative stress and inflammation. Moreover, these are the most common factors implicated in male reproductive dysfunctions. This study evaluated testicular oxidative stress, inflammation, apoptosis, and germ cell proliferation in diabetic rats receiving alcohol or cART and their combination. Thirty adult male Sprague Dawley rats were divided into five groups, each consisting of six rats; control, diabetic only (DM), diabetic treated with alcohol (DM + A), diabetic treated with cART (DM + cART), and diabetic treated with both alcohol and cART (DM + A + cART). After 90 days of treatment, the rats were terminated, and the testes were extracted and processed for immunohistochemistry analysis for oxidative stress, inflammatory cytokines, apoptosis, and cell proliferation marker. In comparison to the control, oxidative stress markers, inducible nitric oxide synthase (iNOS), malondialdehyde (MDA), and 8-hydroxydeoxyguanosine (8-OHDG) increased significantly in all treated groups. Expression of testicular proinflammatory cytokines, interleukin-1β, and tumor necrosis factor-α was upregulated in all treated groups, but interleukin-6 was upregulated in DM, DM + cART, and DM + A + cART treated groups and was downregulated in the DM + A treated group. All treated animal groups showed an upregulation of apoptotic marker (caspase 3) and a downregulation of proliferation marker (Ki-67). However, Ki-67 staining intensity significantly increased in treated animals compared to the control. These findings suggest that diabetes, alcohol abuse, cART use, and their combination via iNOS activity upregulation can induce inflammation and oxidative stress in testicular tissue, stimulating germ cell apoptosis and proliferation inhibition leading to failure of spermatogenesis.</p>", "<title>Keywords</title>", "<p>Open access funding provided by University of the Witwatersrand.</p>" ]
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[ "<title>Acknowledgements</title>", "<p>We appreciate the collaborative efforts of our colleagues Jaclyn Asouzu Johnson, Idemudia Eguavoen, and Vaughan Perry and extend special appreciation to Hasiena Ali for her laboratory assistance.</p>", "<title>Author contributions</title>", "<p>Conceptualization: EO and EFM.; Data acquisition: EO, and EFM; Data analysis or interpretation: EO and PN and EFM; Drafting of the manuscript: EO and EFM.; Critical revision of the manuscript: EO, PN, and EFM; All authors read and approved the final manuscript.</p>", "<title>Funding</title>", "<p>Open access funding provided by University of the Witwatersrand. This research was funded partly by Professor Mbajiorgu’s Wits Faculty of Health Sciences Research Publication Incentive (RINC) grant (grant number; 001.167.8421101.5122201/4228) and supplemented by the Wits School of Anatomical Sciences Research grant (grant number; School is 001.251.8421101.5122201/4708).</p>", "<title>Data availability</title>", "<p>The minimal dataset for the results from this study will be made available through a University of the Witwatersrand archived link.</p>", "<title>Declarations</title>", "<title>Conflict of interest</title>", "<p id=\"Par32\">The authors declare no conflicts of interest.</p>" ]
[ "<fig id=\"Fig1\"><label>Fig. 1</label><caption><p>Representative Ki-67 image quantified in Fiji, the mean gray values of a selected region of interest (ROI) illustrated with a thick arrow</p></caption></fig>", "<fig id=\"Fig2\"><label>Fig. 2</label><caption><p>Graphs showing the food and fluid intake, final body weight, and gonadosomatic index. Different symbols *, π, and Ф represent significant differences (<italic>p</italic> &lt; 0.05) as analyzed by a Bonferroni’s multiple comparison test; ‘*’ significantly different compared to control, ‘π’ significantly increased compared to DM + A, and ‘Ф’ significantly increased compared to DM + A + cART. DM, diabetes; DM + A, diabetes and alcohol; DM + cART, diabetes and combination antiretroviral therapy; DM + A + cART, diabetes and alcohol and combination antiretroviral therapy</p></caption></fig>", "<fig id=\"Fig3\"><label>Fig. 3</label><caption><p>Photomicrographs of oxidative stress markers immunoexpression and respective mean of expression graphs. Representative immunoreactivity is indicated with red arrowheads. (i) iNOS photomicrograph and a graph showing the percentage area of iNOS expression. (ii) MDA photomicrograph and a graph showing the percentage area of MDA expression. (iii) 8-OHDG photomicrograph and a graph showing the number of cells expressing 8-OHDG. Different symbols *, #, π, α, and Ф represent significant differences (<italic>p</italic> &lt; 0.05) as analyzed by a Bonferroni’s multiple comparison test; ‘*’ significantly increased compared to control, ‘#’ significantly increased compared to DM, ‘π’ significantly increased compared to DM + A, ‘α’ significantly increased compared to DM + cART, and ‘Ф’ significantly increased compared to DM + A + cART. Magnification, × 400; scale bar, 50 μm. Key: Images in panel: <bold>a</bold> control group, <bold>b</bold> DM group, <bold>c</bold> DM + A group, <bold>d</bold> DM + cART group, and <bold>e</bold> DM + A + cART group. Treatment groups: DM (diabetes); DM + A (diabetes and alcohol); DM + cART (diabetes and combination antiretroviral therapy); DM + A + cART (diabetes and alcohol and combination antiretroviral therapy)</p></caption></fig>", "<fig id=\"Fig4\"><label>Fig. 4</label><caption><p>Photomicrographs of cytokine expression and respective mean of expression graphs. Representative immunoreactivity is indicated with red arrowheads. (i) IL-1β photomicrograph and a graph showing the percentage area of IL-1β expression. (ii) TNF-α photomicrograph and a graph showing the percentage area of TNF-α expression. (iii) IL-6 photomicrograph and a graph showing the number of cells expressing IL-6. Different symbols *, #, π, α, and Ф represent significant differences (<italic>p</italic> &lt; 0.05) as analyzed by a Bonferroni’s multiple comparison test; ‘*’ significantly different compared to control, ‘#’ significantly increased compared to DM, ‘π’ significantly increased compared to DM + A, ‘α’ significantly increased compared to DM + cART, and ‘Ф’ significantly increased compared to DM + A + cART. Magnification, × 400; scale bar, 50 μm. Key: Images in panel: <bold>a</bold> control group, <bold>b</bold> DM group, <bold>c</bold> DM + A group, <bold>d</bold> DM + cART group, and <bold>e</bold> DM + A + cART group. Treatment groups: DM (diabetes); DM + A (diabetes and alcohol); DM + cART (diabetes and combination antiretroviral therapy); DM + A + cART (diabetes and alcohol and combination antiretroviral therapy)</p></caption></fig>", "<fig id=\"Fig5\"><label>Fig. 5</label><caption><p>Representative photomicrographs showing caspase 3 expression (red arrowheads) and a graph showing the number of immunostained cells. Different symbols *, #, α, and Ф represent significant differences (<italic>p</italic> &lt; 0.05) as analyzed by a Bonferroni’s multiple comparison test; ‘*’ significantly increased compared to control, ‘#’ significantly increased compared to DM, ‘α’ significantly increased compared to DM + cART, and ‘Ф’ significantly increased compared to DM + A + cART. Magnification, × 400; scale bar, 50 μm. Key: Images in panel: <bold>a</bold> control group, <bold>b</bold> DM group, <bold>c</bold> DM + A group, <bold>d</bold> DM + cART group, and <bold>e</bold> DM + A + cART group. Treatment groups: DM (diabetes); DM + A (diabetes and alcohol); DM + cART (diabetes and combination antiretroviral therapy); DM + A + cART (diabetes and alcohol and combination antiretroviral therapy)</p></caption></fig>", "<fig id=\"Fig6\"><label>Fig. 6</label><caption><p>Representative photomicrographs showing Ki-67 expression (red arrowheads) and respective graphs of the number of immunostained cells and staining intensity. Different symbols *, #, α, and Ф represent significant differences (<italic>p</italic> &lt; 0.05) as analyzed by a Bonferroni’s multiple comparison test; ‘*’ significantly different compared to control, ‘#’ significantly different compared to DM, ‘α’ significantly different compared to DM + cART, and ‘Ф’ significantly different compared to DM + A + cART. Magnification, × 400; scale bar, 50 μm. Key: Images in panel: <bold>a</bold> control group, <bold>b</bold> DM group, <bold>c</bold> DM + A group, <bold>d</bold> DM + cART group, and <bold>e</bold> DM + A + cART group. Treatment groups: DM (diabetes); DM + A (diabetes and alcohol); DM + cART (diabetes and combination antiretroviral therapy); DM + A + cART (diabetes and alcohol and combination antiretroviral therapy)</p></caption></fig>" ]
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InTech.\u00a010.5772/67562"]}, {"label": ["32."], "surname": ["Ikekpeazu", "Orji", "Uchendu", "Ezeanyika"], "given-names": ["JE", "OC", "IK", "LUS"], "article-title": ["Mitochondrial and oxidative impacts of short and long-term administration of HAART on HIV patients"], "source": ["Curr Clin Pharmacol"], "year": ["2019"], "volume": ["15"], "fpage": ["110"], "lpage": ["124"], "pub-id": ["10.2174/1574884714666190905162237"]}, {"label": ["37."], "surname": ["Jensen"], "given-names": ["EC"], "article-title": ["Quantitative analysis of histological staining and fluorescence using imageJ"], "source": ["Anat Rec"], "year": ["2013"], "volume": ["296"], "fpage": ["378"], "lpage": ["381"], "pub-id": ["10.1002/ar.22641"]}, {"label": ["40."], "surname": ["Trangenstein", "Morojele", "Lombard", "Jernigan", "Parry"], "given-names": ["PJ", "NK", "C", "DH", "CDH"], "article-title": ["Heavy drinking and contextual risk factors among adults in South Africa: findings from the International Alcohol Control study"], "source": ["Subst Abus Treat Prev Policy"], "year": ["2018"], "volume": ["13"], "fpage": ["43"], "pub-id": ["10.1186/s13011-018-0182-1"]}, {"label": ["41."], "surname": ["Sultan", "Butt", "Karim", "Zia-Ul-Haq", "Batool", "Ahmad", "Aliberti", "De Feo"], "given-names": ["MT", "MS", "R", "M", "R", "S", "L", "V"], "italic": ["Nigella sativa"], "source": ["Evid Based Complement Altern Med"], "year": ["2014"], "volume": ["2014"], "fpage": ["1"], "lpage": ["8"], "pub-id": ["10.1155/2014/826380"]}, {"label": ["51."], "surname": ["Koganti", "Tu", "Selvaraj"], "given-names": ["PP", "LN", "V"], "article-title": ["Functional metabolite reserves and lipid homeostasis revealed by the MA-10 Leydig cell metabolome"], "source": ["PNAS Nexus"], "year": ["2022"], "volume": ["1"], "fpage": ["1"], "lpage": ["14"], "pub-id": ["10.1093/pnasnexus/pgac215"]}, {"label": ["54."], "surname": ["Khairuddin", "Sudirman", "Huang", "Kong"], "given-names": ["K", "S", "L", "Z-L"], "italic": ["Caulerpa lentillifera"], "source": ["Appl Sci"], "year": ["2020"], "volume": ["10"], "fpage": ["8768"], "pub-id": ["10.3390/app10248768"]}]
{ "acronym": [], "definition": [] }
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2024-01-14 23:41:58
Toxicol Res. 2023 Aug 3; 40(1):31-43
oa_package/51/b5/PMC10787109.tar.gz
PMC10787110
37804081
[ "<title>I. INTRODUCTION</title>", "<p>\n##REF##31922579##Heath (2020##, 86) “initiate[s] a discussion about the moral dimension of physician billing” and raises several challenging cases. He characterizes billing “gamesmanship” as a violation of the integrity of professionals as fiduciaries; when physicians game the system, they act for selfish, greedy ends, rather than being fiduciaries who put client-patients’ interests first; when the entire profession promotes gamesmanship, it acts as a cartel, not a self-regulating group of experts upholding trust with client-patients. To curb this, physicians should self-regulate by encouraging integrity in billing, rather than mere compliance with documentation requirements.</p>", "<p>Heath builds his argument within a theoretical framework that develops the functions and limitations of instrumental forms of rationality in social situations, including the conduct of professionals selling health services. This framework is generally fecund, but unfortunately, in the case of medical billing, Heath applies the wrong parts of it. The wrongness of gamesmanship is not explained by physicians’ fiduciary responsibilities or features of health insurance as a commodity; the wrongness of gamesmanship is better explained by how it distorts prices and reduces the efficiency of healthcare markets. This explanation works from within Heath’s framework but departs from his analysis about which elements to apply. I argue physicians should not free-ride on the more common billing practices of <italic toggle=\"yes\">other physicians</italic>. Otherwise, physicians are permitted to press insurance claims to the full letter of the contract with insurers. Thus, I agree with Heath about integrity’s importance, but I disagree about how best to exercise it. This affects how the medical profession polices its members and promotes billing integrity.</p>" ]
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[ "<title>IV. CONCLUSION</title>", "<p>Physicians sell services to patients, who pay their bills via insurers; physicians maintain billing contracts with these insurers and submit claims to them for services provided to patients. Physicians have distinct duties to their patients and the insurers with whom they contract. They also have duties to their colleagues and to the well functioning of the profession in the healthcare marketplace. It is important to disentangle which duties physicians have to which parties. The purpose of this convoluted payment system is no different from any other market: to direct resources to where they are most needed. Billing gamesmanship violates the spirit of this institution; it is a form of legal cheating that distorts the price mechanism and interferes with the point of this market. The best way for physicians to detect gamesmanship is to ask themselves, “Could other physicians bill the same way that I am billing?” If the answer is “no,” then they should ask themselves, “Does this way of billing benefit patients and exercise a competitive advantage against other physicians?” If the answer to the second question is also “no,” then they should refrain from the practice. Otherwise, physicians are permitted to press their claims against insurers to the maximum extent. Physicians and their professional organizations should encourage uniformity in billing practices in order to minimize price distortions, and they should reinforce the importance of integrity in avoiding gamesmanship. These duties are not unique to <italic toggle=\"yes\">medical</italic> or even <italic toggle=\"yes\">professional ethics</italic>; they are just good business practice.</p>" ]
[ "<title>Abstract</title>", "<p>This paper proposes that billing gamesmanship occurs when physicians free-ride on the billing practices of other physicians. Gamesmanship is non-universalizable and does not exercise a competitive advantage; consequently, it distorts prices and allocates resources inefficiently. This explains why gamesmanship is wrong. This explanation differs from the recent proposal of Heath (2020. Ethical issues in physician billing under fee-for-service plans. J. Med. Philos. 45(1):86–104) that gamesmanship is wrong because of specific features of health care and of health insurance. These features are aggravating factors but do not explain gamesmanship’s primary wrong-making feature, which is to cause diffuse harm not traceable to any particular patient or insurer. This conclusion has important consequences for how medical schools and professional organizations encourage integrity in billing. To avoid free-riding, physicians should ask themselves, “could all physicians bill this way?” and if not, “does the patient benefit from the distinctive service I am providing under this code?” If both answers are “no,” physicians should refrain from the billing practice in question.</p>" ]
[ "<title>II. HEATH’S FRAMEWORK</title>", "<p>Heath raises examples of “fiddles”—clinical, administrative, or paperwork maneuvers whose only purpose is to secure higher monetary compensation. With some plausibility, Heath proposes that trust is eroded not only when fiddles break the law’s letter by practicing billing fraud, but also when they violate its “spirit”—the “purpose or intent underlying the rules,” the clauses in insurance contracts (##REF##31922579##2020##, 92).<xref rid=\"fn0001\" ref-type=\"fn\"><sup>1</sup></xref> Heath assigns fiddles to the categories of <italic toggle=\"yes\">true fraud</italic>, <italic toggle=\"yes\">honest fraud</italic>,<xref rid=\"fn0002\" ref-type=\"fn\"><sup>2</sup></xref><italic toggle=\"yes\">gamesmanship</italic>, and <italic toggle=\"yes\">creative billing,</italic> based on whether a fiddle obeys the letter or spirit (##TAB##0##Table 1##).</p>", "<p>He emphasizes the difference between <italic toggle=\"yes\">creative billing</italic>, which is permissible, and <italic toggle=\"yes\">gamesmanship</italic>, which violates the spirit of contractual clauses. Gamesmanship is cheating without lying.</p>", "<p>The letter/spirit distinction is a major theme in Heath’s general approach to institutional ethics, especially business ethics.<xref rid=\"fn0004\" ref-type=\"fn\"><sup>4</sup></xref> It underlies his comparisons between markets and other institutions like the law and sports,<xref rid=\"fn0005\" ref-type=\"fn\"><sup>5</sup></xref> which are structured as internal competitions among adversaries that serve larger social goals: legal contests serve the goal of justice; athletic contests serve the goals of teamwork and health, among others; business contests improve product quality, lower prices, and promote overall efficiency (##UREF##6##Heath, 2014##, 100–10). In contrast, contests with no redeeming social value, like dueling or gambling, are prohibited or curtailed. In adversarial institutions, adversaries are allowed to break some conventions of everyday interpersonal morality (boxers punch each other, prosecutors attack witnesses’ character, businesses steal each other’s customers), but there are rules that constrain otherwise antisocial behavior and direct it toward the institution’s broader, prosocial purpose. The limitation of rules is that they are inherently crude and challenging to enforce, such that adversaries can one-up each other in ways that satisfy the letter of the rules but that still contradict their spirit—the larger purpose of the competition itself. Hence, there are competitive circumstances where adversaries are freed by the rules of the contest to break everyday social prohibitions, but nevertheless should exercise restraint.</p>", "<p>With particular business practices, the letter/spirit distinction supports Heath’s contention that even when business managers are not <italic toggle=\"yes\">contractually</italic> forbidden (by the law’s letter) from certain adversarial practices in their relationships with employees or other constituency groups within the firm, they are still <italic toggle=\"yes\">ethically</italic> forbidden (by its spirit) because of the firm’s larger purpose, which is to instill social cohesion sheltered from naked self-interest. If managers want to take this adversarial approach with intrafirm groups like employees, then it is better to replace them with extra firm, independent contractors. Heath disparages the suggestion that managers can exploit employees as far as the letter of contracts permits as the “let them eat contracts” thesis (##UREF##6##2014##, Chapter 5). The flipside of Heath’s objection to this thesis is that managers <italic toggle=\"yes\">are</italic> permitted to play hardball with groups <italic toggle=\"yes\">outside of the firm</italic> such as investors, suppliers, and customers, to whom the firm is joined only by contract. Indeed, the adversarial negotiation of prices is where markets as an institution are supposed to fulfill their efficiency-maximizing purpose. I return to this important point when discussing the billing relationship between physicians and insurers.</p>", "<title>Heath’s Examples</title>", "<p>Heath raises seven examples in order to illustrate the difference between gamesmanship, which breaks the rules’ spirit, and creative billing, which does not.</p>", "<title>Creative billing</title>", "<p>(A) Redescription of laparoscopic colon resection</p>", "<p>(B) Billing a left hemicolectomy with anterior resection as an anterior resection</p>", "<title>Gamesmanship</title>", "<p>(1) Manipulating the timing of surgery</p>", "<p>(2) Calculating obesity</p>", "<p>(3) Scheduling follow-up care</p>", "<p>(4) Billing liver biopsy as resection &lt;5cm</p>", "<p>(5) Cholecystectomy with add-on hernia repair</p>", "<p>In creative billing cases, the billing codes enable the surgeon to describe the same surgery in different ways with different remunerative consequences. In (A), the difference comes from applying a code for encouraging surgeons to perform procedures laparoscopically (hence, less invasively, which benefits patients). In (B), Heath infers that the difference is due to an “oversight in the billing codes” (##REF##31922579##2020##, 92) in which the generic description bills $18 more than the specific one, which seems superfluous. Thus, surgeons who upcode in (A) are fulfilling the rules’ spirit, while surgeons who upcode in (B) are merely not violating that spirit.</p>", "<p>Heath’s cases of putative gamesmanship are more complicated. Only one captures unequivocal gamesmanship. Let us start with this successful example. In case (1), surgeons can bill 50%–75% more for operations that <italic toggle=\"yes\">commence</italic> at an “unsocial hour” (10 p.m. to 7 a.m.), whereas no extra compensation applies to cases that commence during normal hours but that cross into an unsocial hour. Heath alleges that surgeons who prepone surgery until just before 7 a.m. in order to secure extra compensation are not committing fraud, but are gaming the billing system by contravening the purpose of this additional compensation. In contrast, postponing surgery until after 10 p.m. just to bill more is malpractice, because it endangers the patient and violates fiduciary responsibility. There are borderline cases where the surgeon can postpone surgery for a few hours, but still prepone it by sneaking it in before the 7 a.m. threshold in order to secure extra compensation; these borderline cases must be disambiguated according to the surgeon’s intention. Heath does not say what the spirit of the extra compensation is, but presumably, it is to credit surgeons for undertaking more acute cases to benefit patients at the expense of the surgeon’s rest, not to enable surgeons to charge a surcharge for their first case just because they arrived at work a few minutes early. Certainly, it could not be to compensate surgeons just for working longer hours, because if that were true, cases that run after 10 p.m. would also be credited. This example demonstrates how the letter and spirit come apart.</p>", "<p>In (2), surgeons bill 25% more for obese patients, whose BMI is over 40. The purpose is to compensate for greater surgical complexity. When a patient’s weight is close to this threshold, the surgeon can weigh the patient after surgery, after they have received intravenous fluids, which may tip the measurement over the threshold. By selecting the time to weigh patients, surgeons are not misrepresenting patients’ weights, hence, are not committing fraud; but they are manipulating<xref rid=\"fn0006\" ref-type=\"fn\"><sup>6</sup></xref> patients’ information for their own personal advantage, not patients’ advantage.</p>", "<p>In (3), surgeons can schedule follow-up appointments just past the 365-day threshold so that they can bill follow-ups as new patient appointments, which pay more. However, this is not really gamesmanship, because it is inconsistent with the law’s letter: in Ontario, new patient appointments require new referrals; thus, this fiddle amounts to fraud (##REF##31922579##Heath, 2020##, 93).</p>", "<p>In (4), the surgical procedure is describable in two ways, but unlike case (B), the difference in compensation is larger (about $250), and one code is not obviously superfluous, because neither description is a subset of the other. Liver biopsies can be done via a needle (pays $87.10) or via an incision ($102.10), and the intent is purely diagnostic, not therapeutic. Typically, the target is tissue that is clearly diseased; so, including the margins of normal tissue is less useful. In contrast, an excisional biopsy is a therapeutic attempt to remove affected tissue and manifests a concern for the margins of normal tissue.<xref rid=\"fn0007\" ref-type=\"fn\"><sup>7</sup></xref> Billing code S269 (“Hepatectomy—local excision of a lesion [less than 5 cm]) pays $350.65 and is part of a connected set of codes (e.g., S275, S270, S267, S271) that involve higher rates for larger resections, which are clearly therapeutic in intent. This situation in the billing codes presents a dilemma: a small, laparoscopic liver excision for purely diagnostic purposes could be billed as “biopsy via incision” or as “local excision of a lesion (less than 5cm)” (##REF##31922579##Heath, 2020##, 94).<xref rid=\"fn0008\" ref-type=\"fn\"><sup>8</sup></xref> It’s hard to discern the purpose behind this difference in billing codes: is it to compensate more for riskier, more invasive techniques that tend to be done in inpatient facilities? Or to compensate more for more complex therapeutic interventions with concern for margins than merely diagnostic ones? It is not clear, but the large difference in remuneration creates the strong presumption that, unlike (B), the difference between these codes is not an oversight but instead reflects some intended purpose, however, inchoate. Therefore, this case seems to straddle the line between creative billing and gamesmanship.</p>", "<p>In (5), surgeons can bill $100 more for the repair of hernias discovered mid operation (code E764). Heath complains that this enables payment for the repair of hernias that are “clinically insignificant” (94) and “entirely incidental to the intervention and would never have provided a reason to operate” (95). Heath suggests that the surgeon who bills for such incidental hernia repairs is not violating the letter of the rules (the surgeon performed the procedure), but is violating their spirit, which, he feels, is to compensate for two independent procedures done conjointly. Like case (4), the spirit seems more indeterminate than Heath allows. A herniotomy that provides an independent reason to operate (S333) pays $222.76, which is almost twice as much as the cost of add-on hernia repair. It seems unlikely that add-on hernia repairs must be sufficient to justify surgery to merit compensation; more likely, the purpose of the billing code for add-on hernia repair is to compensate surgeons for the additional time and effort that goes into identifying and repairing these hernias, whether incidental or not. The real problem is whether to count hernias which are very small and require almost no time or effort to repair; but this is less a problem with the spirit of the rules, as a problem of vagueness in their letter: the billing codes could easily specify a threshold according to which remuneration applies only to hernias of a certain size or time to repair. Like case (3) and cases of honest fraud, the problem is not that the rules’ spirit has been violated, but that their letter is unartfully inexact.</p>", "<p>Let us review. Case (1) is the only clear case of genuine gamesmanship, where the letter is met but the spirit violated. Cases (2) and (3) come close; like case (1), they turn on manipulating a numerical threshold, but in (2) the threshold is arbitrary and does not reflect the spirit of the rules with any precision, while in (3) crossing the threshold amounts to genuine fraud because of other safeguards in the rules’ letter. Case (4) bears some resemblance to creative billing because it turns on two overlapping descriptions, each of which satisfies the rules’ letter, but the difference in their spirit is unclear and is not an obvious consequence of oversight in the construction of the letter. Likewise, the rule’s spirit is open to interpretation in case (5): the letter is insufficiently precise to distinguish between distinct purposes. The end result is that cases of unequivocal gamesmanship are restricted to case (1).</p>", "<title>II. EXERCISING INTEGRITY WHEN THE SPIRIT OF THE RULES IS UNCLEAR</title>", "<p>Our examination of these cases is consistent with Heath’s claim that there is a “moral grey zone” between fraud and creative billing (##REF##31922579##2020##, 92). Heath contends that <italic toggle=\"yes\">integrity</italic> deserves renewed emphasis in this zone, but our analysis shows that this recommendation is premature. When the rules’ spirit is unclear, it is difficult to discern genuine gamesmanship and distinguish it from creative billing; hence, integrity provides little guidance. Appeals to integrity cannot enforce uniformity on billing practices where sincere minds can disagree about the rules’ spirit. Integrity is an executive virtue, and in general, executive virtues like courage, self-control, and prudence are <italic toggle=\"yes\">amplifiers</italic> of moral virtues and vices, while executive vices are <italic toggle=\"yes\">attenuators</italic>. The importance of executive virtues like integrity is conspicuous only when the appropriate exercise of moral virtues and vices is clear. Thus, Heath’s appeal to integrity is hollow.</p>", "<p>There are three ways to clarify the role of integrity. First, brighten the line between gamesmanship and creative billing. For example, require physicians to discern the spirit according to general principles of professionalism (which is roughly Heath’s position) or of business ethics (my position). Second, <italic toggle=\"yes\">maximal permission</italic>: when the line between creative billing and gamesmanship is unclear, then physicians are permitted to press insurance claims up to the point of fraud. This proposal endorses <italic toggle=\"yes\">legalism</italic>, the thesis that the letter of the rules exhausts moral obligations in billing. A conspicuous problem with this proposal is that it fails to generalize to other adversarial social institutions: for example, it implies rejecting sportsmanship in athletics. Third, <italic toggle=\"yes\">maximal prohibition</italic>: when the spirit is unclear, physicians should err on the side of caution and follow integrity by avoiding the temptations of greed as far as possible. In effect, this enjoins physicians to reflexively downcode in order to avoid any appearance of greed. It renders impermissible not only in all cases of putative gamesmanship, but also of creative billing. This proposal suffers from problems of scope similar to the last. Maximal prohibition under- and over-generalizes: under because no other professions (e.g., lawyers or accountants) are subject to similar constraints in submitting claims to clients’ insurers; and over because it demands unreasonable asceticism of physicians. While maximal permission eliminates sportsmanship, maximal prohibition exaggerates it—in effect, implying that boxers should turn the other cheek. Thus, maximal permission and prohibition are unsavory extremes that depart from Heath’s framework. With this in mind, let us examine how Heath might develop the first option.</p>", "<title>The Argument from Fiduciary Responsibility</title>", "<p>Suppose a physician “games” patients by inflating prices in violation of the spirit of the billing contract. Patients are not in a position to know that the prices have been inflated, because of lower medical literacy. If patients discover the physician’s gamesmanship, it will undermine trust in the medical profession and harm all physicians as a result. Therefore, the “information asymmetry” between physicians and patients generates an obligation for physicians to avoid gamesmanship. This is Heath’s Argument from Fiduciary Responsibility in a nutshell.<xref rid=\"fn0009\" ref-type=\"fn\"><sup>9</sup></xref></p>", "<p>This argument is sound, but limited: strictly speaking, it implies only a <italic toggle=\"yes\">specific</italic> obligation to eschew gamesmanship in cases of information asymmetry, cases which never arise in common, “real world” billing contexts. Heath’s own examples illustrate how rarely information asymmetries arise: they do not arise in cases (1), (2), and (3), which all involve numerical thresholds; no special <italic toggle=\"yes\">medical</italic> knowledge is required to understand that the patient’s weight can be measured twice and the higher number selected, or that an appointment can be scheduled just after the 365-day threshold. Physicians who game their patients in these ways could at most be accused of being price-gouging jerks who charge capricious prices, not of violating any special, <italic toggle=\"yes\">fiduciary responsibility</italic> to patients. A patient who did not like any of these billing arrangements could easily have walked away or negotiated an agreement where the letter of the agreement operationalized the spirit more precisely. <italic toggle=\"yes\">Caveat emptor</italic>.</p>", "<p>A fiduciary responsibility to distinguish gamesmanship from creative billing potentially arises only in cases like (A), (B), (4), and (5), where the same medical service satisfies the letter of distinct billing codes. Luckily, this kind of situation never arises when physicians are negotiating directly with patients, because patients do not have sufficient medical knowledge to author <italic toggle=\"yes\">codes</italic> in the first place.<xref rid=\"fn0010\" ref-type=\"fn\"><sup>10</sup></xref> In the rare circumstance where patients do negotiate directly with physicians, they form a one-off contract where there is little room for slippage between the letter and spirit of the agreement. In all other cases, billing codes are an artifact of insurers, who hire <italic toggle=\"yes\">other physicians</italic> to help craft and apply billing codes. If a physician who works for the insurer crafts a billing code and another physician submits a claim that satisfies that code’s letter but possibly not its spirit, which is unclear, then because of the information <italic toggle=\"yes\">symmetry</italic> between the two physicians, it is false to claim that the physician submitting the claim has a special obligation to draw bright lines between gamesmanship and creative billing. Rather, the physician who is the code’s author and the insurer who employs that physician would seem to have the weight of responsibility in ensuring that there is no daylight between the code’s letter and spirit. Indeed, insurers employ physicians to oversee the application of billing codes—hence, contested claims pass through successive rounds of “peer to peer” evaluation, where the doctor submitting the claim and a doctor working for the insurer discuss the details of the case.<xref rid=\"fn0011\" ref-type=\"fn\"><sup>11</sup></xref><italic toggle=\"yes\">Such processes eliminate the information asymmetry between the billing party and the billed party</italic>, or at least substantially attenuate it; <italic toggle=\"yes\">where there is no information asymmetry, there can be no special obligation not to exploit it. As such</italic>, fiduciary responsibility is irrelevant.</p>", "<p>Heath may have overemphasized fiduciary responsibility in particular<xref rid=\"fn0012\" ref-type=\"fn\"><sup>12</sup></xref> as the most prominent of several duties of professionalism (##REF##31922579##2020##, 99), which are intended to promote trust and extend beyond information asymmetries alone. For example, physicians can collectively agree that felonies like arson should be professionally disqualifying, even though the wrongness of arson does not turn on an information asymmetry, or even on fiduciary responsibility more generally; arson is disqualifying because having felons among the professional ranks would reduce patient trust in the medical profession. Similarly, general duties of professionalism may support prohibitions on billing gamesmanship, even when gamesmanship itself does not turn on information asymmetry. Insofar as Heath alleges that gamesmanship exists in a “moral grey zone” between fraud and creative billing, he seems to concede that one cannot expect the gamesmanship/creative-billing distinction to be enforced strictly; rather, professionalism enforces it loosely through integrity-based culture (##REF##31922579##2020##, 98–9). This culture prevents mischief in the grey zone but does not necessarily ensure uniformity of practice.</p>", "<p>There are two overlapping problems with a professionalism amendment to Heath’s primary argument. First, it lacks defined scope and so threatens to under- and over-generalize about billing restrictions in the same ways as the maximal prohibition proposal, thereby conflicting with Heath’s framework. For instance, when Heath says that professionalism enjoins physicians to “refrain from acting opportunistically, thereby creating trust” (##REF##31922579##2020##, 98), the limits of “opportunistic” action are undefined. It satisfies one sense of “opportunistic” for physicians to charge capricious prices and offer “tiered” care (concierge medicine, VIP floors in hospitals, “Medicaid clinics,” etc.), but typically these have no appreciable effect on patient trust. Also, opportunism should not generate distrust if it is part of general business dealings; any professional prohibition on opportunism cannot be so strong that it turns doctors into suckers, but it’s unclear how professionalism as such could formulate a prohibition of the right strength and scope. Consider a patient who overhears the physician on the telephone, but it is unclear whether the physician is pressing a health insurance claim on the <italic toggle=\"yes\">patient’s</italic> behalf, pressing the same claim for <italic toggle=\"yes\">the physician’s own</italic> gain, or pressing a property insurance claim for the physician’s own gain because of water damage in the clinic’s bathroom. The patient, the patient’s insurer, and the physician’s property insurer are all external contractors of the physician’s business venture. The professionalism amendment aims to reach the conclusion that patient trust would not be affected by physician greed as such (i.e., not for high concierge prices, or for the physician’s own gain against the property insurer), nor by gamesmanship as such (i.e., not against the patient’s insurer for the patient’s gain), but would be affected only in the combined case when the physician is pressing a claim for the physician’s own gain <italic toggle=\"yes\">against the patient’s insurer</italic>. It is hard to see how professionalism as such strikes this delicate balance; it is unlikely that the patient overhearing the doctor on the phone would be listening attentively for such subtle details in order to condemn or absolve the physician. Rather than strike this right balance, appealing to professionalism would seem to smuggle interpersonal morality into adversarial institutions through the back door: rather than tell boxers to avoid blows to the back of the head, it would tell them “punch softly”; and rather than tell football players to avoid unnecessary roughness, it would tell them “tackle gently.” The prescriptions are close, but insufficiently precise and with the wrong emphasis.</p>", "<p>Second, it is an <italic toggle=\"yes\">empirical</italic> question as to what extent billing gamesmanship affects patient trust.<xref rid=\"fn0013\" ref-type=\"fn\"><sup>13</sup></xref> Indeed, it is highly dubious that patient trust is <italic toggle=\"yes\">generally</italic> undermined by gamesmanship, especially in cases where physicians violate the billing code’s spirit <italic toggle=\"yes\">in order to benefit the patient</italic>. More generally, patient trust is affected by how gamesmanship is framed in terms of the wider context. When characterizing this context, Heath paints in broad strokes: he characterizes physicians who practice gamesmanship as greedy cheaters who exploit the Ontario Health Insurance Program (OHIP), the people’s champion. He contends physicians rationalize sharp billing practices with sanitizing language; they amplify grievances over their compensation, which he portrays as ample; and they practice what psychologists call “moral disengagement,”<xref rid=\"fn0014\" ref-type=\"fn\"><sup>14</sup></xref> against which integrity is a bulwark. These points are less developed and more controversial than he acknowledges. Under this tendentious characterization, it is easy to see how patient trust could be jeopardized. Of course, its tendentiousness is why Heath does not lean heavily on it; instead, he raises his second argument for why physicians have a special obligation to distinguish gamesmanship from creative billing. This argument serves two roles: it adds color to the wider context, and it highlights independent reasons to sharply distinguish gamesmanship from creative billing.</p>", "<title>The Argument from the Susceptibility of Insurers to Inflated Claims</title>", "<p>Heath contends that anyone filing an insurance claim has a distinctive obligation not to exaggerate or inflate the claim (##REF##31922579##2020##, 97). He observes that insurers are especially susceptible to inflated claims because the extra cost is divided between all of the premium payers, and humans are psychologically predisposed to downplay harms when they are diffused. Heath urges that the temptation to downplay diffuse harms should be resisted, and this resistance requires exercising integrity. Heath recommends that claimants test their integrity by asking whether they would pursue the inflated claim if it were passed on to a single individual, instead of diffused across all of the premium payers. When physicians file a claim with an insurer, they should ask themselves whether they would be comfortable justifying the inflation of the claim to the individual patient—in other words, since the insurer is the proxy of patient interests, the effects of diffusing harm can be filtered out by substituting a single patient for the insurer. In (1), physicians who start surgery at 6:59 a.m. in order to bill more would find themselves unable to justify this practice to a singular patient and so would recognize that the practice is wrong.</p>", "<p>There are two parts to this argument: the observation that insurers are susceptible to inflated claims; and a test for identifying when a claim has exploited this susceptibility. The first part does not <italic toggle=\"yes\">show</italic> that inflating claims is wrong; it just shows that <italic toggle=\"yes\">when</italic> the insurer has been harmed, this is less likely to be noticed than when a single patient has been harmed. Heath develops this part by discussing fraud and “white collar crime,” and then tries to generalize the point to any inflated claim, including gamesmanship. He insinuates that the same considerations that support a distinctive obligation to exercise vigilance in avoiding fraud support an obligation to avoid gamesmanship, but he never identifies these considerations: fraud is wrong because it is <italic toggle=\"yes\">theft by pretense</italic>, but by definition, gamesmanship contains no pretense, hence, no fraud. This part of the argument succeeds only if the wrong-making feature of gamesmanship is supplied from elsewhere, such as the argument from fiduciary responsibility, or the second part of the susceptibility argument, the single-patient substitution test. In the last section, we defused the former. Here, we show that the latter fails because insurers are not proxies of patients’ interests.</p>", "<p>Heath’s substitution test is problematic in principle (even after we put aside the practical dissimilarities between patients and insurers<xref rid=\"fn0015\" ref-type=\"fn\"><sup>15</sup></xref>). In order to screen out any diffusion of harm, Heath’s test turns on switching from the indirect billing context, where the insurer is billed, to the direct billing context, where the individual patient is billed. This test works in the case of fraud since the same grounds of harm hold in both the direct and indirect billing contexts. Now in the case of gamesmanship, the transition from one context to another removes not only the diffusion of harm, but also the grounds of harm in the first place. When a surgeon is in a price negotiation with a single patient, the surgeon can request a surcharge for cases begun during unsocial hours; if the patient does not want to pay the surcharge, then the patient can ask for a cheaper surgery time or simply find another surgeon who does not charge this surcharge. If the patient agrees to pay it, <italic toggle=\"yes\">then no wrong has been committed</italic>. In the direct billing scenario, the surgeon is only guilty of setting capricious prices, which is the surgeon’s prerogative in the medical marketplace; the surgeon has not obviously harmed or wronged the patient, especially by being unprofessional.<xref rid=\"fn0016\" ref-type=\"fn\"><sup>16</sup></xref> So, even if physician gamesmanship harms the <italic toggle=\"yes\">insurer</italic>, where this goes unnoticed because of the diffusion of harm, it does not help to transpose the same practice to the direct billing context, where the <italic toggle=\"yes\">patient</italic> is <italic toggle=\"yes\">not</italic> harmed—hence no wrong committed.</p>", "<p>The direct scenario described above might seem like an outlier because typically patients cannot shop for surgeons. Except with elective surgeries, surgeries are urgent/emergent cases that come via ambulance to the emergency department without any patient choice in the matter. In these more typical contexts, it might seem ethically problematic for a surgeon to request a surcharge after preponing a patient’s case from 7:15 to 6:45 (recall that the surgeon cannot <italic toggle=\"yes\">postpone</italic> the case solely to increase payment without committing malpractice): the patient seems to have no ability to bargain. There are at least two problems with this objection. First, emergency situations prompt generalizations to the worst case; so, they should not be used as a counterexample that health services are traded in a true market (compare this argument with the similar argument that flooded basements are not good grounds to argue that there is no true market for plumbing services). The more general phenomenon is that the demand for health care is very price elastic in the long run (patients defer cheap health maintenance) and very inelastic in the short run (patients want their current medical problems solved immediately regardless of cost); emergency situations are a limiting case. Second, even when the patient cannot shop around between surgeons, the patient can still bargain: if the surgery is being preponed for a surcharge, the patient can make the decision whether it is worth saving the additional money to delay surgery—a delay, which, by hypothesis, is not medically significant because otherwise the surgeon would have been prohibited from offering it. So, no matter how it is specified, the patient is not harmed or wronged in the direct scenario. Because no harm/wrong has been done to the patient in the direct billing scenario, no harm/wrong has been done to the insurer in the indirect scenario either—the insurer expresses the same preference for earlier surgery, but on a larger scale.</p>", "<title>Disentangling the Arguments</title>", "<p>Now we are in a position to disentangle Heath’s two arguments. These arguments turn on two asymmetries between physicians and the parties they are billing. When these asymmetries are teased apart, it becomes clear that each asymmetry on its own is insufficient to establish an obligation to eschew gamesmanship and that putting them together does not gain any additional traction. The Argument from the Susceptibility of Insurers to Inflated Claims aims to generate a responsibility to eschew the gamesmanship of <italic toggle=\"yes\">insurers</italic>, and the Argument from Fiduciary Responsibility (with its professionalism amendment) aims to generate a responsibility to eschew the gamesmanship of <italic toggle=\"yes\">patients</italic>. The substitution test tries to connect them by transferring physician’s fiduciary/professional responsibility from being directed toward patients to being directed toward insurers; conversely, the susceptibility of insurers to inflated claims affects the wider context in which patient trust is formed and in which physicians exercise their professional responsibility to patients. Thus, the two arguments have interlocking features; in conjunction, they form a larger argument for physicians’ responsibility to root out gamesmanship. When this is characterized as physicians greedily exploiting nonprofit OHIP, then the wrongness of gamesmanship seems not just obvious, but so egregious that integrity deserves renewed emphasis.</p>", "<p>The analysis presented here shows why the two arguments must be separated: the fiduciary responsibility that physicians have to patients does not apply in almost any practically relevant billing contexts, and even then, it is not absolute; it must be considered alongside other factors affecting patient trust. The professionalism amendment extends these duties to prohibit gamesmanship, but at the cost of indeterminacy and unclear scope that threatens to conflict with Heath’s framework. The susceptibility of insurers to inflated claims generates an obligation to vigilantly avoid fraud, violations of insurance contracts’ <italic toggle=\"yes\">letter</italic>. However, without the argument from fiduciary responsibility, it does not extend to gamesmanship, violations of their <italic toggle=\"yes\">spirit</italic>. Moreover, it is fallacious to treat insurers as proxies of patient interests such that obligations to patients carry over to insurers. Each argument on its own is insufficient to show that billing gamesmanship is wrong, let alone that physicians have a responsibility to detect and avoid it. Accordingly, the emphasis on integrity is premature.</p>", "<title>III. WHEN AND WHY GAMESMANSHIP IS WRONG: THE PRIMARY-FUNCTION-OF-PRICES ARGUMENT</title>", "<p>I borrow from Heath’s framework the insight that gamesmanship is wrong because it violates the spirit of insurance contracts. Where Heath construes spirit in terms of fiduciary/professional responsibility, I construe it more broadly as markets’ primary function, which is to carry information about where resources are needed, and more narrowly as undistorted pricing. By price “distortion,” I mean that a physician submits insurance claims to intentionally exploit a loophole that is not universally available to other physicians (hence “free-rides” on standard practice) and which the physician believes does not represent an improvement in service compared with less remunerative codes. In short, it is unequal pricing that fails to produce a pareto improvement. When successful, this attempt to exercise market power produces a deadweight loss that foils the purpose of the market. Compared with Heath’s proposal, mine is much more permissive.</p>", "<p>Let us work up to this conclusion by reexamining Heath’s cases—which cases are ethically problematic and why? Case (1) seems the most problematic, even though the physician does not take advantage of an information asymmetry, violate patient trust, or flagrantly exploit the susceptibility of insurers to inflated claims. There are indications that this practice is ethically wrong: the physician who schedules early surgery for extra compensation acts unseemly; physicians would hardly be proud of this practice (indicating “consciousness of guilt”). I hypothesize that the gamesmanship in (1) is wrong because it is not correctible in principle, hence distorts the prices of a medical service. This transmits the wrong information to the market and produces a deadweight loss. The result is that the function of the healthcare market is foiled.</p>", "<p>Health care is a commodity, but it is not traded in a classical market. Patients bundle their demand for health care and pay for health services through insurers. Bundling is more efficient than saving for health care individually, because economy of scale reduces the variance in each individual’s expected healthcare expenditures. Currently, the insurance market is dominated by publicly administered companies, like OHIP and Medicare, which enjoy a (near-)monopoly over health <italic toggle=\"yes\">insurance</italic>, and a (near-)monopsony for health <italic toggle=\"yes\">care</italic>. In this respect, they effectively set prices and resemble “buyer cartels.”<xref rid=\"fn0017\" ref-type=\"fn\"><sup>17</sup></xref> Despite the intricacies of the quasi-market for health care, its price structure still displays important features of prototypical markets.</p>", "<p>The main function of prices is to carry information about the demand to suppliers and about supply to consumers: when prices go up, the market effectively says, “produce more” and “consume less”; when prices go down, it says, “produce less” and “consume more.” This is true even in the quasi-market for health care,<xref rid=\"fn0018\" ref-type=\"fn\"><sup>18</sup></xref> but it can be obscured by the interposition of insurers between the physician (the supplier) and the patient (the end consumer). Suppose that when insurers like OHIP or CMS update their fee schedules, they increase payments for 10 p.m. to 7 a.m. surgery; this tells surgeons, “produce more 10 p.m. to 7 a.m. surgery,” and tells patients and their insurers, “consume less.” However, the demand for such surgery <italic toggle=\"yes\">among insured patients</italic> does not change <italic toggle=\"yes\">directly</italic> because they are shielded from prices. Instead, their insurers, who are exposed to the price increase, pass it along to patients <italic toggle=\"yes\">indirectly</italic> in the form of increased premiums, co-pays, or deductibles (or taxes, with public insurers); or insurers fiddle with the “effective price” (i.e., limiting consumption on patients’ behalf) by adding various restrictions on supply, such as through “step algorithms.” In the limit, insurers drop coverage for certain kinds of care, in which case patients become uninsured. Uninsured patients limit their own consumption as in classical markets. Although the price mechanism in health care is different from in classical markets, it still has the same primary function, just with clunkier execution.<xref rid=\"fn0019\" ref-type=\"fn\"><sup>19</sup></xref></p>", "<p>Gamesmanship like that in case (1) produces <italic toggle=\"yes\">noise</italic> in the price information stream. The fiddle in case (1) is not universalizable; it is possible only in small surgical centers where individual surgeons have discretion over work hours; at large institutions, where nursing and staff work schedules are tightly regulated, surgeons do not have the unilateral authority to perform this fiddle, and if this practice were adopted system-wide at such institutions, insurers would easily take notice and restrict the code to explicitly acute cases (e.g., claims for surgeries during unsocial hours might require additional documentation stating that delay posed an urgent danger). This kind of correction is what happens in case (2), where insurers require new referrals for new patient visits, because insurers realize that it is possible to schedule appointments just past the 365-day threshold. The corresponding correction is practically impossible in case (1). Re-organizing a large hospital’s surgery schedule is like asking, “please move the hospital a little to the left.” After extensive negotiations with nursing, pharmacy, anesthesia, etc., over many months, the change could be implemented, but it would be foreseeably futile since insurers would foil it easily. It would be a massive but ultimately pointless undertaking. In contrast, small surgical centers can fly under insurers’ radar.<xref rid=\"fn0020\" ref-type=\"fn\"><sup>20</sup></xref> There may be borderline cases of “near-universal” or “almost correctible” billing practices that require special treatment, but case (1) does not seem like one of them. Consequently, (1) is a case of parasitic free-riding on other physicians’ billing practices. When small surgical practices capture the payment bump for 6:45 a.m. surgery, their income increases until a new equilibrium with surgical demand is reached. From here, the story takes one of two turns, which are indistinguishable from society’s point of view: either society tolerates this increase and shifts production away from other sectors to surgery; or it does not, in which case, insurers indiscriminately slash reimbursement for surgery. If there were palpable benefits to pre-7 a.m. surgery (e.g., patients could return to work earlier), then this shift in production might be worth it, but in case (1) patients do not benefit. Gamesmanship draws more resources to health care without any consumer benefit; compared with the market-clearing price, this exercise of market power yields a deadweight loss.</p>", "<p>Now, even if I am wrong about the facts of case (1), this error would not undermine universalizability as a prohibition criterion. Ultimately, gamesmanship turns on the physician’s state of mind: if any physician sincerely believes that the maxim of his action is universalizable, then the act does not amount to gamesmanship. In contrast to gamesmanship, “creative billing” consists of fiddles that are licit because the physician believes they either represent an improvement in product quality or are universalizable, hence, correctible, and do not distort prices. Consider case (A). When new techniques like laparoscopy<xref rid=\"fn0021\" ref-type=\"fn\"><sup>21</sup></xref> are first introduced, they are usually available only at large academic centers; the new technique is diffused through the rest of the surgical community. During the transition, some centers can perform the new procedure and apply the more remunerative billing code, while others cannot. But the surgical techniques and their associated billing codes are not impossible to universalize in principle; the limitation is only temporary. Moreover, even if this differential existed in principle (which might be the case with services like proton beam therapy for cancer, for example), it would still be justified because it benefits patients. This is just the exercise of competitive advantage.</p>", "<p>Even when a billing practice does not benefit patients, it can still be licit because it is universalizable, hence, correctible. Consider case (B): even though patients do not benefit when the same procedure is billed as “anterior resection” instead of “left hemicolectomy with anterior resection,” this difference is universalizable; all physicians could apply the generic code instead of the specific one. When universally adopted, insurers are able to assess whether they are paying too much for the generic code, and simply correct the amount they are willing to pay, in which case the price might return to what it would be had everyone billed for the lesser code. When services are billed <italic toggle=\"yes\">uniformly</italic>, the market bears the same price for the same service. That is, even though the difference in case (B) does not represent any improvement in quality, it is universally possible to adopt the higher billing code, and the resulting uniformity allows the price to return to the right equilibrium. Similarly, in cases (3), (4), and (5), if all physicians applied the more remunerative code, then insurers could assess whether they were paying more than they were willing to for these services and adjust payments accordingly. Therefore, these cases are not ethically problematic. They provoke suspicion of “gamesmanship” only because of the opportunity to apply the codes nonuniformly, but this suspicion does not survive scrutiny.</p>", "<p>The preceding argument presupposes that insurers can adjust prices flexibly, which is not necessarily the case. For example, OHIP updates its schedule every four years; CMS annually. With such delays, there is a perpetual gap for mischief, a gap which insurers play catch-up to close. Excusing upcoding during such periods might seem similar to excusing pollution when the government has not (yet) outlawed it. However, such worries should not be overblown. Annual updates are reasonable for prices affecting 10%–20% of GDP; more frequent updates might have unforeseen but problematic consequences. Furthermore, insurers are not necessarily playing catch-up; they have ample opportunity to anticipate trends. Poor business management (e.g., delayed updates) is never a reason to demand generosity in an adversarial contractual negotiation.</p>", "<p>On my hypothesis, when physicians are seeking to detect and avoid gamesmanship, they should ask themselves, “could all other physicians bill the way I am billing?” and, if not, “does the more remunerative code reflect a genuine competitive advantage?” If the answer to both questions is “no,” then they should refrain from the practice. This set of questions comprise a test that is different from Heath’s substitution test, in which physicians ask themselves, “would I bill this individual patient the same way I am billing the insurer?” There is some overlap between the two tests, insofar as it would pass both tests for physicians to apply a more remunerative code that reflects a benefit to patients (e.g., case [A]), or not (e.g., case [1]). But in muddy cases like (B), (3), (4), and (5), Heath’s test is less reliable; it requires physicians to indirectly test their own motives by speculating about the reactions of patients, who are ignorant of billing codes and the billing process. In contrast, my test requires physicians to ask themselves whether they believe potential nonuniformities in billing are due to a genuine improvement in service. Not only is this test easier for physicians to apply, but also it discriminates which practices are licit more decisively. Heath’s test produces uncertain results for cases (B), (3), (4), and (5), whereas my test delivers the clear verdict that physicians are permitted to bill aggressively.</p>", "<p>So long as they do not distort prices, physicians are permitted to press billing claims, just as insurers can resist them in return. This is one of the important lessons of Heath’s framework that we developed in Section <xref rid=\"s1\" ref-type=\"sec\">I</xref> outside of the firm, the rigorous and exacting enforcement of the letter of contracts enables markets to function efficiently. The spirit of contracts matters too, but the relevant aspect of “spirit” concerns the possibility of uniform pricing. Restraint is called for when physicians can flout the spirit of billing codes in ways that distort prices—in the first instance, non-universalizable ways that do not reflect a benefit to patients.</p>", "<p>In my analysis, gamesmanship is wrong because physicians free-ride on other physicians, not because they are cheating insurers or patients. Gamesmanship is not necessarily against physicians’ collective self-interest. Physician A can adopt gamesmanship practice alpha to free-ride on the billing practices of physician B, who can in turn adopt gamesmanship practice beta to free-ride on the billing practices of A. Each physician benefits personally, and physicians benefit overall. So free-riding need not result in overall harm to physicians. But the gamesmanship is still wrong, because it distorts prices in the healthcare market. The vice at issue in gamesmanship is <italic toggle=\"yes\">cheating society without lying</italic>; integrity is a bulwark against this vice, but the way integrity must be exercised is different than if the relevant vices were exploitation, lying, stealing, breaking promises, or other ways of contravening fiduciary responsibilities.</p>", "<p>My analysis explains what Heath’s analysis gets right and wrong. The <italic toggle=\"yes\">Cui Bono</italic> (who is benefitted?) of gamesmanship is clear: physicians. But the <italic toggle=\"yes\">Cui Malo</italic> (who is harmed?) is not. Heath tries to tie the harm to the insurer (via the Argument from the Susceptibility of Inflated Claims) and to the patient (via fiduciary responsibility, or professionalism). The problem is that the insurer, who is directly harmed, has no basis for complaint, since the insurer wrote the rules by which the physician is billing; and the patient, who is indirectly harmed via increased prices/premiums, has no control over the billing codes. Consequently, gamesmanship is not wrong because it is a violation of these “first-order” duties to insurers and patients. The more compelling part of Heath’s analysis is when he suggests that gamesmanship is wrong because of how it affects the <italic toggle=\"yes\">generic</italic> patient, as the payer of premiums, and OHIP, as the insurance market writ large. The insight here is not that individual patients or OHIP are harmed in an indirect way; the insight is that gamesmanship impairs the function of the healthcare market within the entire society; these shifts in production harm society’s nonhealthcare projects.</p>", "<p>Once the wrong-making feature of gamesmanship has been successfully identified, only then does the susceptibility of insurers to inflated claims matter: when many small price distortions are diffused among premium payers through their premiums, it is harder to identify the harm, and the wrongness of gamesmanship <italic toggle=\"yes\">qua</italic> cheating is easy to overlook. Now when physicians cheat billing codes in ways that increase premiums, this can have an indirect effect on patient trust. Neither of these effects of gamesmanship is sufficient to explain why gamesmanship is wrong on its own, but both are aggravating factors that make it <italic toggle=\"yes\">worse</italic>.</p>", "<p>My analysis provides guidance for professional schools and organizations teaching and policing their members. Gamesmanship is wrong because it foils the function of the healthcare market. Therefore, the profession as a whole has an interest in squashing it. When physicians share advice on billing tips and tricks to maximize payment, or when professional organizations host seminars to avoid “leaving money on the table,” these educational activities induce billing <italic toggle=\"yes\">uniformity</italic> and reduce opportunities for free-riding. This uniformity aspires to maximize compensation, which can cross into crass opportunism, but it also has the benign purpose of educating physicians and correcting their tendency to underbill. Many physicians struggle to recoup full payment for their work. Not only do they fail to submit billing for some cases, but also a substantial portion of their bills is denied; insurers “claw back” payments years later for reasons that are difficult for physicians to rebut so long after the original service. In this cutthroat billing environment, it makes sense for physicians to promulgate billing advice widely and to encourage uniformly maximal claims. While preparing future physicians for this environment, medical schools should teach students the tests for identifying gamesmanship proposed here.</p>" ]
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[ "<table-wrap position=\"float\" id=\"T1\"><label>Table 1.</label><caption><p>Types of fiddles<xref rid=\"fn0003\" ref-type=\"fn\"><sup>3</sup></xref></p></caption><table frame=\"hsides\" rules=\"groups\" width=\"100%\" border=\"1\"><colgroup span=\"1\"><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/><col align=\"left\" span=\"1\"/></colgroup><thead><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\"/><th align=\"left\" rowspan=\"1\" colspan=\"1\">Consistent with the rules</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Violates the rules</th></tr></thead><tbody><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Consistent with the spirit</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Creative Billing</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Honest Fraud</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Violates the spirit</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Gamesmanship</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fraud</td></tr></tbody></table></table-wrap>" ]
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[ "<fn-group><title>Footnotes</title><fn id=\"fn0001\"><label>1</label><p>Gamesmanship involves <italic toggle=\"yes\">intentional</italic> malfeasance, which is different from <italic toggle=\"yes\">abuse</italic>, which involves <italic toggle=\"yes\">unintentionally</italic> erroneous billing that violates billing codes’ letter. Cf., the ##UREF##1##American Medical Association’s (2017)##<italic toggle=\"yes\">Principles of CPT Coding, 9</italic><sup><italic toggle=\"yes\">th</italic></sup><italic toggle=\"yes\">Ed.</italic></p></fn><fn id=\"fn0002\"><label>2</label><p>Heath does not elaborate on honest fraud because it is a species of fraud; he includes it in his taxonomy to illustrate the letter/spirit distinction. He insinuates that honest fraud is less seriously wrong than true fraud because it reflects “a problem with the rules, such that when applied literally they do not provide fair compensation” (##REF##31922579##2020##, 93).</p></fn><fn id=\"fn0003\"><label>3</label><p>Reproduced from (##REF##31922579##Heath, 2020##: Table 1).</p></fn><fn id=\"fn0004\"><label>4</label><p>Cf., ##UREF##6##Heath (2014)##, Chapter 4.</p></fn><fn id=\"fn0005\"><label>5</label><p>Cf., ##UREF##5##Heath (2019)##.</p></fn><fn id=\"fn0006\"><label>6</label><p>Heath is not completely convinced that this is gamesmanship. He acknowledges that the difference in surgical difficulty between a BMI of 39 and 41 is negligible and that 40 is an arbitrary threshold. He proposes a graduated billing scheme might operationalize the spirit of this compensation regime better. The problem is like that of honest fraud (cf., footnote 2), the difference being that in this case there is no deception, hence no violation of the letter.</p></fn><fn id=\"fn0007\"><label>7</label><p>One surgical guideline notes that excisional biopsy is “often used for biopsying lesions found fortuitously at routine laparoscopic surgery,” though it adds, “some centres in the USA perform laparoscopic liver biopsy on outpatient basis” (##REF##10485854##Grant and Neuberger, 1999##, IV2), where this suggests the biopsies are preplanned, not fortuitous.</p></fn><fn id=\"fn0008\"><label>8</label><p>Heath says that upcoding for a diagnostic liver resection “is obviously right on the border between gaming and fraud” (##REF##31922579##2020##, 94), but this characterization seems mistaken: it presumes that the spirit of the rules has “obviously” been violated, and the open question is whether the letter has been broken, too. But actually, the situation seems to be the reverse: small excisions clearly satisfy the letter of the more remunerative billing code; its spirit is unclear.</p></fn><fn id=\"fn0009\"><label>9</label><p>The argument is spread over section IV of ##REF##31922579##Heath (2020)##, but is concentrated in the last full paragraph on page 100: “[I]t is easy to see what the problem with the current attitudes toward billing [is] in the medical profession. Just as in the case of patient care, the fundamental issue involves an information asymmetry.”</p></fn><fn id=\"fn0010\"><label>10</label><p>Indeed, the patient’s comparative medical illiteracy is one of the critical reasons that physicians submit claims to insurers directly, rather than having patients seek reimbursement.</p></fn><fn id=\"fn0011\"><label>11</label><p>There is another feature of these cases that underscores that physicians do not enjoy an informational advantage. In many practices, physicians do not submit claims themselves, but hire practice managers as professional coders to review clinical documentation and submit the most remunerative set of codes. Despite their knowledge of billing codes, practice managers do not have more <italic toggle=\"yes\">medical</italic> knowledge than physicians—the knowledge relevant to exercising fiduciary responsibility. Hence, compared with physicians employed by insurers, practice managers are at an informational <italic toggle=\"yes\">disadvantage</italic>; if there is any asymmetry in medical information, it would be in <italic toggle=\"yes\">the insurer’s favor</italic>. Moreover, practice managers are deputized agents of physicians, while insurers are deputized agents of patients. As Heath argues elsewhere (##UREF##6##2014##, Chapter 10, esp. 247), agents are bound by all of the principal’s obligations and prohibitions (although agents can have additional obligations and prohibitions that are only permissions of the principal). If physicians exercise fiduciary responsibility in medical billing, then, as their agents, practice managers would, too. This would fly in the face of current practice, where practice managers show limited concern for patients’ interests (cf., ##UREF##0##AHIMA Standard of Ethical Coding, 2016##). Current practice may be wrong, but I submit that the more natural interpretation of current practice is that because the fiduciary relationship is irrelevant in the direct billing scenario between physician and patient, it is not carried over to the doubly indirect billing scenarios between practice managers and insurers.</p></fn><fn id=\"fn0012\"><label>12</label><p>As previously mentioned, Heath says, “the <italic toggle=\"yes\">fundamental issue</italic> involves an information asymmetry” (emphasis added). To my ear, “fundamental” gives the distinct impression that he thinks the wrongness of gamesmanship turns on an information asymmetry, though he also discusses general duties of professionalism (##REF##31922579##Heath, 2020##, 98–9).</p></fn><fn id=\"fn0013\"><label>13</label><p>The reaction of patients is relevant because it reflects genuine trustworthiness, which in turn establishes limits for professional duties. Thus, I am <italic toggle=\"yes\">not</italic> claiming that doctors are permitted to practice gamesmanship so long as they “get away with it”; I am merely claiming that patients’ reactions serve as a barometer of trustworthiness in this case.</p></fn><fn id=\"fn0014\"><label>14</label><p>Cf., ##UREF##2##Bandura (2002)##.</p></fn><fn id=\"fn0015\"><label>15</label><p>On the practical level, insurers are not proxies of patient interests because insurers have their own agenda, especially for profit insurers, who serve their bottom line, not patient interests. Physicians enter into contracts with commercial insurers that are negotiated within the marketplace, and physicians are permitted to “play hardball” by holding insurers to the letter of these contracts, just as any other business does, such as when Wal-Mart levies fines against vendors who fail to satisfy contracts precisely (##UREF##4##Gerstein, 2017##). Any dollar that a physician “leaves on the table” goes into the insurer’s pocket, not back into the patient’s. In practice, physicians have limited ability to play hardball with commercial insurers when it comes to recouping claims. American physicians regularly and intentionally “overbill” on claims that they submit to commercial insurers, because they have no idea what proportion of the charge the insurer will actually pay; if the physician charges less than what the insurer actually pays, then the physician “leaves money on the table” and incurs a self-inflicted loss. (This is described with concrete examples in Chapter 5 of ##UREF##3##Belk and Belk, 2020##.) As described in Section <xref rid=\"s1\" ref-type=\"sec\">I</xref>, Heath’s approach to business ethics implies that hardball billing practices with insurers are permissible because markets achieve their efficiency-maximizing function through such self-interested price negotiations. There is no difference when physicians bill aggressively according to the letter of contracts, than when one boxer punches another in the face—this is part of the adversarial institution. The suggestion that doctors “play nice” with insurers thus risks committing an error that Heath objects to elsewhere, viz. it is fallacious to transplant the norms of “everyday” morality into institutional contexts that are self-consciously adversarial. So, in both the formation of contracts and their performance, physicians interact with insurers in ways unlike the way they interact with patients. It is inappropriate to treat insurers as proxies of patients; the substitution test is not apt. These practical problems with Heath’s test are obscured by his test case: physicians in Ontario, Canada, who do not negotiate prices with commercial insurers but rather accept a price schedule from the Ontario Health Insurance Program (##UREF##9##OHIP##), which is nonprofit and publicly administered. (In this respect, Heath’s insistence [##REF##31922579##2020##, 87–8] that the situation of these physicians generalizes to physicians at large is strained). But even nonprofit, publicly administered health insurers like OHIP or Medicare are not straightforward proxies of patient interests. As Heath points out elsewhere (##UREF##7##2003##, ##UREF##6##2014##, Chapter 2, section 2.4 “Lessons from Public Management”), public insurers are not charities; they sell a commodity and have governance structure like commercial firms. To the extent they are enmeshed in the political bureaucracy, they serve multiple stakeholders, such as politicians, academic medicine, research consortiums, physician groups, pharmaceutical companies, and private insurers. They are a funny mirror reflection of patient interests, not a window onto them.</p></fn><fn id=\"fn0016\"><label>16</label><p>To help see this, imagine an inverted scenario, where a surgeon bills the “regular price” from 10 p.m. to 7 a.m., but offers a “discount” from 7 a.m. to 10 p.m.. A patient is offered the “regular price” at 6:59 might be disappointed that they missed out on the “discount,” but they have not been wronged or harmed because they missed it.</p></fn><fn id=\"fn0017\"><label>17</label><p>I stress this point because Heath compares professional organizations to seller cartels, but does not mention the demand side mirror image of buyer cartels.</p></fn><fn id=\"fn0018\"><label>18</label><p>\n##REF##29302693##Frakt and Chernew (2018##, E1) observe: “Prices are signals, and even in health care, many individuals follow them in some circumstances. The problem in health care is not that prices play a role – that is unavoidable. The problem is that prices are distorted in ways that result in an inefficient allocation of healthcare resources.”</p></fn><fn id=\"fn0019\"><label>19</label><p>There are many complications with this story: public-private subsidization and “cost-shifting”; “queue jumping” and crossed financial streams; connections between Canadian and US health care (e.g., OHIP patients getting “buffaloed”); vertical integration between physicians and insurers (e.g., health maintenance organizations) or between physicians (e.g., accountable care organizations), which can resemble “seller-cartels.”</p></fn><fn id=\"fn0020\"><label>20</label><p>Another possibility: large surgical centers might consider taking a “if you can’t beat ‘em, join ‘em” approach and distribute some of their case load to smaller centers who could adopt this practice and with whom they could form partnerships. But, the profits from such ventures would likely either be too low to offset the administrative efforts or would again attract attention from insurers.</p></fn><fn id=\"fn0021\"><label>21</label><p>This is a fictionalized version of the history of laparoscopy, which evolved over many years. Cf. ##UREF##8##Kelley (2008)##.</p></fn></fn-group>" ]
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[{"mixed-citation": ["\n"], "collab": ["American Health Management Association"], "year": ["2016"], "italic": ["Standards of Ethical Coding"], "ext-link": ["http://bok.ahima.org/codingstandards#.X_XSWeQ8IIQ"], "comment": ["July 26, 2023"]}, {"mixed-citation": ["\n"], "collab": ["American Medical Association"], "year": ["2017"], "source": ["Principles of CPT Coding"], "edition": ["9"], "publisher-loc": ["Chicago"], "publisher-name": ["American Medical Association"]}, {"mixed-citation": ["\n"], "person-group": ["\n"], "string-name": ["\n"], "surname": ["Bandura"], "given-names": ["A."], "year": ["2002"], "article-title": ["Selective moral disengagement in the exercise of moral agency"], "source": ["Journal of Moral Education"], "volume": ["31"], "issue": ["2"], "fpage": ["101"], "lpage": ["19"]}, {"mixed-citation": ["\n"], "person-group": ["\n"], "string-name": ["\n"], "surname": ["Belk", "Belk"], "given-names": ["D.", "P."], "year": ["2020"], "source": ["The Great American Healthcare Scam: How Kickbacks, Collusion and Propaganda Have Exploded Healthcare Costs in the United States"]}, {"mixed-citation": ["\n"], "person-group": ["\n"], "string-name": ["\n"], "surname": ["Gerstein"], "given-names": ["M."], "year": ["2017"], "article-title": ["Is Wal-Mart an abusive customer"], "source": ["Forbes"], "ext-link": ["https://www.forbes.com/sites/marcgerstein/2017/07/13/is-wal-mart-an-abusive-customer/?sh=5a9ff4383c42"], "comment": ["July 27, 2023"]}, {"mixed-citation": ["\u2003\u2003\u2003\u200a. "], "year": ["2019"], "article-title": ["The moral status of profit"], "source": ["The Oxford Handbook of Ethics and Economics"], "publisher-loc": ["Oxford, United Kingdom"], "publisher-name": ["Oxford University Press"]}, {"mixed-citation": ["\u2003\u2003\u2003. "], "year": ["2014"], "source": ["Morality, Competition, and the Firm: The Market Failures Approach to Business Ethics"], "publisher-loc": ["New York"], "publisher-name": ["Oxford University Press"]}, {"mixed-citation": ["\u2003\u2003\u2003. "], "year": ["2003"], "article-title": ["Les soins de sant\u00e9 comme merchandises"], "source": ["\u00c9thique Publique"], "volume": ["5"], "issue": ["1"], "fpage": ["84"], "lpage": ["9"]}, {"mixed-citation": ["\n"], "person-group": ["\n"], "string-name": ["\n"], "surname": ["Kelley"], "given-names": ["W. E."], "year": ["2008"], "article-title": ["The evolution of laparoscopy and the revolution in surgery in the decade of the 1990s"], "source": ["Journal of the Society of Laparoscopic and Robotic Surgeons"], "volume": ["12"], "issue": ["4"], "fpage": ["351"], "lpage": ["7"]}, {"mixed-citation": ["\n"], "collab": ["Ontario Ministry of Health and Long-Term Care (OHIP)"], "italic": ["Schedule of Benefits: Physician Services under the Health Insurance"], "ext-link": ["https://www.health.gov.on.ca/en/pro/programs/ohip/sob/"], "comment": ["July 27, 2023"]}]
{ "acronym": [], "definition": [] }
13
CC BY
no
2024-01-14 23:41:58
J Med Philos. 2023 Oct 6; 49(1):72-84
oa_package/4a/79/PMC10787110.tar.gz
PMC10787112
37863386
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[ "<p id=\"p0005\">More than 170 distinct chemical modifications have been identified in non-coding and coding RNAs. Accumulating evidence suggests that RNA modifications play pivotal roles at both the molecular and physiological levels. Dysregulation of RNA-modifying enzymes has been linked to various human cancers and developmental diseases. The expanding understanding of RNA modifications in molecular and cellular functions further suggests promising prospects for therapeutic applications. Recently, the creation of effective mRNA vaccines against coronavirus disease 2019 (COVID-19), based on RNA base modification, was honored with the Nobel Prize in Physiology or Medicine 2023 (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.nobelprize.org/prizes/medicine/2023/press-release/\" id=\"ir005\">https://www.nobelprize.org/prizes/medicine/2023/press-release/</ext-link>). Aiming to provide a forum for emerging advances in detection and functional studies of epitranscriptomic modifications, we have organized a special issue “RNA Modifications and Epitranscriptomics” for the journal <italic>Genomics, Proteomics &amp; Bioinformatics</italic> (GPB). This special issue encompasses a wide range of topics, including: (1) dynamic landscapes of RNA modifications in various organisms, including animals, plants, and viruses; (2) mechanistic regulation of m<sup>6</sup>A and m<sup>5</sup>C modifications in human diseases and plant responses to stresses; (3) an online platform for unveiling the context-specific m<sup>6</sup>A methylation and m<sup>6</sup>A-affecting mutation; and (4) the regulatory role of non-coding RNAs (ncRNAs), including tRNAs and circular RNAs (circRNAs), in gene expression regulation.</p>", "<p id=\"p0010\">We are pleased to present 14 articles selected for publication in this special issue, comprising eleven original research articles, one review, one letter, and one database article. An overview of the studies included in this issue is provided as follows.</p>", "<p id=\"p0015\">Yafen Wang and Xiang Zhou reviewed the writer, reader, and eraser proteins involved in m<sup>6</sup>A modification, describing their mechanism of action during viral replication and infection. Moreover, the authors provided an overview of current detection methods for m<sup>6</sup>A, shedding light on the development of vaccines and antiviral drugs by examining the role of epigenetic modifications in viral processes ##REF##35835441##[1]##.</p>", "<p id=\"p0020\">Yixian Cun et al. uncovered a novel role of serine/arginine-rich splicing factor 7 (SRSF7) in regulating m<sup>6</sup>A and its impact on glioblastoma (GBM) progression. The authors found that SRSF7 specifically influenced m<sup>6</sup>A levels on genes associated with cell proliferation and migration, exhibiting oncogenic roles by recruiting the m<sup>6</sup>A methyltransferase complexes. This study highlights the significance of RNA-binding protein (RBP)-mediated specific regulation of m<sup>6</sup>A in determining cellular functions ##REF##34954129##[2]##.</p>", "<p id=\"p0025\">Xiao Han et al. presented the inaugural landscapes of dynamic DNA 5hmC and RNA m<sup>5</sup>C modifications across a variety of samples, including heart, kidney, liver, and lung, from human fetuses at 13–28 weeks. The authors identified 70,091 and 503 organ- and stage-specific differentially hydroxymethylated regions (DhMRs) and m<sup>5</sup>C-modified mRNAs, respectively. The integrated studies revealed a potential link between DNA modification and RNA methylation, illustrating the epigenetic dynamics during human fetal organogenesis ##REF##35644351##[3]##.</p>", "<p id=\"p0030\">Feng Yu et al. presented a study on the complexity of epitranscriptomic dynamics in rice by identifying RNA modifications using direct RNA sequencing (DRS) technology. Besides identifying tissue-specific genes and transcript expression, the authors also mapped the m<sup>6</sup>A and m<sup>5</sup>C modifications on RNA across six developmental tissues of rice, offering a thorough understanding of the rice transcriptome and epitranscriptome ##REF##36775055##[4]##.</p>", "<p id=\"p0035\">Peng Yu et al. explored the relationship between tRNA abundance and translational efficiency in mammals, as well as the contribution of tRNA expression to tissue-specific proteomes. The authors measured tRNA expression using demethylase-tRNA sequencing (DM-tRNA-seq) and mRNA translational efficiencies using ribosome-tagging sequencing (RiboTag-seq) in the mouse brain, heart, and testis. They showed tRNA expression variations among tissues and provided insights into the dynamics of tRNAs and their roles in translational regulation ##REF##35952936##[5]##.</p>", "<p id=\"p0040\">Shuai Chen et al. studied the presence and role of circRNAs in stress granules (SGs), which are cytoplasmic ribonucleoprotein assemblies formed under stress conditions. The authors used improved total RNA sequencing to identify both linear and circular RNAs in purified SG cores and found that circRNAs with higher SG-related RBP binding abilities are more likely to be enriched in SGs. They also identified differentially expressed SG-enriched circRNAs in hepatocellular carcinoma (HCC) and adjacent tissues, suggesting a regulatory role of circRNAs and SGs in HCC ##REF##35085777##[6]##.</p>", "<p id=\"p0045\">Bowen Song et al. presented m6A-TSHub, a comprehensive online platform designed to explore tissue-specific m<sup>6</sup>A RNA methylation patterns and related genetic mutations. This platform encompasses four core tools: m6A-TSDB, which curates extensive m<sup>6</sup>A site data from human tissues and tumors; m6A-TSFinder, a predictive server for tissue-specific m<sup>6</sup>A sites using deep learning; m6A-TSVar, evaluating genetic variant impacts on m<sup>6</sup>A modifications; and m6A-CAVar, cataloging mutations affecting m<sup>6</sup>A in various cancers. This serves as a pivotal resource for specialized m<sup>6</sup>A epitranscriptome studies ##REF##36096444##[7]##.</p>", "<p id=\"p0050\">Zidong Liu et al. uncovered the m<sup>6</sup>A modification dynamics during porcine spermatogenesis. Analyzing m<sup>6</sup>A distribution across spermatogonia, spermatocytes, and round spermatids, they identified a globally conserved m<sup>6</sup>A pattern in genes related to spermatogenesis. Enrichment of m<sup>6</sup>A in genes encoding metabolic enzymes and regulators was observed, showcasing its regulatory role. This study provides novel insights into the transcriptional regulation of lifelong male fertility in non-rodent mammals, enhancing our understanding of spermatogenesis in large animals ##REF##34543723##[8]##.</p>", "<p id=\"p0055\">Lorane Le Franc et al. employed the methylated RNA immunoprecipitation sequencing (MeRIP-seq) method to map m<sup>6</sup>A RNA methylomes during oyster development. Their analysis revealed dynamic and stage-specific m<sup>6</sup>A modifications in mRNA and lncRNA classes, displaying unique methylation patterns compared to transposon transcripts. The observed shifts in methylation profiles corresponded to expression changes across developmental stages such as cleavage, gastrulation, and organogenesis. These findings highlight the potential regulatory role of m<sup>6</sup>A in oyster development, offering novel insights into the control and evolution of developmental processes in lophotrochozoan organisms ##REF##36496129##[9]##.</p>", "<p id=\"p0060\">Ying Lv et al. deciphered the pattern and function of m<sup>6</sup>A modification during sexual reproduction in <italic>Chlamydomonas</italic> and also revealed its frequent occurrence in the DRAC motif and its main enrichment in the 3′ untranslated region (UTR) of mRNAs. The study found that m<sup>6</sup>A levels negatively correlate with gene expression, particularly affecting the microtubule-associated pathway. This study offers evolutionary insights into the role of m<sup>6</sup>A in <italic>Chlamydomonas</italic> and sheds light on its evolutionary significance in plant sexual reproduction ##REF##35550876##[10]##.</p>", "<p id=\"p0065\">Dan Song et al. highlighted that HCC tissues exhibit increased m<sup>5</sup>C methylation, particularly influencing phosphokinase signaling pathways. NOP2/Sun RNA methyltransferase (NSUN2) is notably overexpressed in HCC, impacting the expression of several genes and HCC cell sensitivity to the drug sorafenib. The study revealed innovative insights into the impact of RNA epigenetic modification on HCC progression, which might help to discover more effective HCC treatment targets and strategies ##REF##36183976##[11]##.</p>", "<p id=\"p0070\">Boyang Shi et al. employed the psoralen analysis of RNA interactions and structures method (PARIS) to map RNA structures in non-small cell lung cancer (NSCLC) cells, shedding light on epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) resistance mechanisms. They found that RNA structures, particularly in UTRs, correlate with translation efficiency, and the RNA structure of the gene encoding yrdC <italic>N</italic><sup>6</sup>-threonylcarbamoyltransferase domain containing (YDRC) impacts EGFR-TKI sensitivity by modulating its translation. Disrupting the RNA structure in <italic>YRDC</italic> 3′ UTR with antisense oligonucleotide (ASO) presents a potential therapeutic strategy. This unveils a novel RNA structure-driven mechanism controlling EGFR-TKI resistance, providing valuable therapeutic perspectives ##REF##36435452##[12]##.</p>", "<p id=\"p0075\">Chen Zhu et al. explored the m<sup>6</sup>A-mediated regulatory impact on tea flavor-related metabolic pathways during solar-withering processes. Through integrated transcriptome analysis, the study revealed that two m<sup>6</sup>A erasers control global m<sup>6</sup>A levels, influencing terpenoid biosynthesis and spliceosome pathways. This m<sup>6</sup>A-mediated mechanism affects volatile terpenoid accumulation and flavonoid content. This study uncovered a novel epitranscriptomic layer in tea flavor formation, enhancing our understanding of tea flavor evolution during solar-withering ##REF##36791953##[13]##.</p>", "<p id=\"p0080\">Yongsheng Wang et al. systematically explored circRNAs in moso bamboo seedlings, especially in relation to gibberellin (GA) and auxin (NAA) treatments. They also developed a custom degradome sequencing method to detect microRNA-mediated cleavage of circRNAs. Their study revealed insights into the biogenesis, function, and microRNA-mediated degradation of circRNAs, emphasizing their significance in regulating hormone metabolism. The findings provided a deeper understanding of the role of circRNAs in plant biology, especially in moso bamboo ##REF##36805531##[14]##.</p>", "<p id=\"p0085\">These 14 articles in this special issue collectively broaden our understanding of RNA epitranscriptomics. They elucidate the roles of RNA modifications in gene regulation, diseases, and developmental processes across a range of organisms and tissues. We envision that new breakthrough in epitranscriptomics will underscore the complexity and importance of RNA modifications in determining cellular functions and hint at potential novel clinical applications.</p>", "<title>Completing interests</title>", "<p id=\"p0090\">Both authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0095\"><bold>Chengqi Yi:</bold> Conceptualization, Writing – original draft, Writing – review &amp; editing. <bold>Jianhua Yang:</bold> Conceptualization, Writing – original draft, Writing – review &amp; editing. Both authors have read and approved the final manuscript.</p>" ]
[ "<title>Acknowledgments</title>", "<p id=\"p0100\">We thank all authors, reviewers, and editors for their contributions to this special issue.</p>" ]
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[ "<fn-group><fn id=\"d35e9\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn></fn-group>" ]
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{ "acronym": [], "definition": [] }
14
CC BY
no
2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Aug 19; 21(4):675-677
oa_package/8c/29/PMC10787112.tar.gz
PMC10787114
35085777
[ "<title>Introduction</title>", "<p id=\"p0005\">Stress granules (SGs) are membrane-less condensates that are dynamically and reversibly formed with ribonucleoproteins by phase separation ##REF##27289443##[1]##. SGs usually assemble in response to stress conditions ##REF##27821493##[2]##. Recent studies have shown that SGs are associated with cellular biological processes and various human diseases, such as degenerative diseases and malignant tumors ##UREF##0##[3]##, ##REF##34460104##[4]##, ##UREF##1##[5]##. Some RNA-binding proteins (RBPs) like Ras GTPase-activating protein-binding protein (G3BP), TIA-1, and TAR are proved to be essential in SG assembly, and G3BP1 serves as the core component of SGs ##REF##10613902##[6]##, ##REF##12642610##[7]##, ##REF##32302571##[8]##. In addition to proteins, RNAs are associated with SG formation as well. A fraction of translationally proceeded or arrested mRNAs is localized in SGs ##REF##33308477##[9]##, ##REF##19461665##[10]##. Moreover, the principle of mRNA and non-coding RNA (ncRNA) accumulation in SGs is revealed in the transcriptome of SG cores ##REF##29129640##[11]##. However, these studied SG-related RNAs are all linear transcripts. Circular RNAs (circRNAs) specifically recruited to SGs have not been elucidated.</p>", "<p id=\"p0010\">To address this issue, we improved the purification and sequencing approach of total RNA in SGs and screened circRNAs in SGs from the transcriptome of purified SG cores induced from mammalian cells. We identified 130 SG-enriched circRNAs and 2462 SG-depleted circRNAs, which revealed the specific accumulation of circRNAs in SGs. The circRNAs enriched in SGs exhibited stronger ability to interact with SG-related RBPs, even the SG core component G3BP2. In addition, some SG-enriched circRNAs were differentially expressed in hepatocellular carcinoma (HCC) and adjacent tissues, indicating the potential role of circRNAs and SGs in HCC.</p>" ]
[ "<title>Materials and methods</title>", "<title>Cell culture and stress conditions</title>", "<p id=\"p0055\">HCC SMMC-7721 cells were cultured in the cell culture medium containing Dulbecco’s modified Eagle’s medium (DMEM; Catalog No. C11995500BT, Gibco, Carlsbad, CA), 10% fetal bovine serum (FBS; Catalog No. 10270-106, Gibco), and 1% penicillin–streptomycin (Catalog No. 15140-122, Gibco) at 37 °C and 5% CO<sub>2</sub>. For stress experiments, cells were treated with 0.5 mM NaAsO<sub>2</sub> (Catalog No. S7400-100g, Sigma-Aldrich, Saint Louis, MO) for 1 h at 37 °C and 5% CO<sub>2</sub>.</p>", "<title>Isolation of SGs</title>", "<p id=\"p0060\">Isolation of SGs was performed as described in a previous study ##REF##29196162##[26]##. SMMC-7721 cells were seeded on 15-cm culture dishes (Catalog No. 430599, Corning, Cambridge, MA) and grown to 80% confluence. Cell culture medium was exchanged with fresh culture medium 1 h prior to the stress treatment. After treating with NaASO<sub>2</sub>, cells were washed once with 1× PBS (137 mM NaCl, 2.7 mM KCl, 10 mM Na<sub>2</sub>HPO<sub>4</sub>, 2 mM KH<sub>2</sub>PO<sub>4</sub>, and pH 7.4), collected by scraping and pelleted by centrifugalization at 1500 <italic>g</italic> for 3 min. Cells were re-suspended in 1 ml SG lysis buffer [50 mM Tris-HCl pH 7.4, 2 mM MgOAc, 100 mM KOAc, 50 μg/ml Heparin, 0.5 mM DTT, 0.5% NP40, 1 U/μl Recombinant RNase Inhibitor (Catalog No. 2313A, Takara, Tokyo, Japan), and EDTA-free protease inhibitor cocktail tablets (Catalog No. 04693132001, Roche, Basel, Switzerland)] and passed through a 25G 5/8 needle 7 times to lyse cells. Cell debris were removed after centrifugalizing at 1000 <italic>g</italic> for 5 min at 4 °C. Then, 50 μl of the lysate supernatant was collected to isolate total RNA or perform Western blot. The remaining lysate was spun at 1,8000 <italic>g</italic> for 20 min at 4 °C to pellet SG cores. The pellets were re-suspended by SG lysis buffer and incubated with 25 μl protein A/G magnetic beads (Catalog No. 88802, ThermoFisher Scientific, Waltham, MA) twice for 30 min at 4 °C with gentle rotation to remove nonspecific binding proteins. Magnetic beads were removed using a magnet. The supernatants were incubated with G3BP1 antibodies (Catalog No. 13057-2-AP, Proteintech, Rosemont, IL) for 1 h at 4 °C followed by incubating with 25 μl protein A/G magnetic beads for 3 h at 4 °C with gentle rotation. The supernatants were collected to isolate supernatant RNA or perform Western blot. Beads were then washed three times with wash buffer 1 (20 mM Tris-HCl pH 8.0, 200 mM NaCl, and 1 U/μl Recombinant RNase Inhibitor), wash buffer 2 (20 mM Tris-HCl pH 8.0, 500 mM NaCl, and 1 U/μl Recombinant RNase Inhibitor), and wash buffer 3 (SG lysis buffer and 2 M Urea). The beads were then eluted to acquire SG proteins or resuspended with 200 μl Proteinase K buffer (1× TE buffer, 2 M Urea, and 1 U/μl Recombinant RNase Inhibitor) for 15 min at 37 °C, and the supernatants were collected to isolate SG RNAs.</p>", "<title>RNA isolation, library construction, and RNA-seq</title>", "<p id=\"p0065\">RNA was isolated using TRIzol LS reagent (Catalog No. 15596026, Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol, and was dissolved in 10 μl RNase-free water. The concentration of RNA was assessed using Qubit (Catalog No. 2061412, ThermoFisher Scientific).</p>", "<p id=\"p0070\">Ribosomal RNAs (rRNAs) were depleted using KAPA RiboErase Kit (Catalog No. 07962266001, KAPA biosystem, Wilmington, MA). cDNA libraries from 10 ng ribosomal-depleted RNA were prepared using KAPA RNA HyperPrep kit (Catalog No. 7962428001, KAPA biosystem) according to the manufacturer’s protocol. The cDNA libraries (3 from cell lysates, 3 from SGs, and 3 from supernatants without SGs) were sequenced on the Illumina NovaSeq 6000 platform with 150 bp pair-end reads.</p>", "<title>RNA FISH and immunofluorescence assay</title>", "<p id=\"p0075\">RNA FISH was performed using the biotin-labeled RNA probes in the exon junction region of mRNAs and the back-splice region of circRNAs. The sense and antisense DNA oligos containing T7 promoters and probes were synthesized and annealed (<xref rid=\"s0105\" ref-type=\"sec\">Table S3</xref>). Biotin-labeled RNA probes were transcribed from the annealed products using a HiScribe T7 Quick High Yield RNA Synthesis Kit (Catalog No. E2050S, New England Biolabs, Ipswich, MA) and biotin RNA labeling mix (Catalog No. 11685597910, Roche) according to the manufacturers’ protocols. Cells were seeded on glass coverslips and grown to 60%–80% confluent. Cells were washed with 1× PBS, fixed with 4% paraformaldehyde, and permeabilized with 0.3% Triton-X 100. The prehybridization and hybridization experiments were performed using Fluorescent <italic>In Situ</italic> Hybridization Kit (Catalog No. C10910, Ribobio, Guangzhou, China) according to the manufacturer’s protocol. Signals were detected using FITC labeled anti-biotin antibody (Catalog No. ab6650, Abcam, Cambridge, UK).</p>", "<p id=\"p0080\">For immunofluorescence assay, the RNA probe incubated cells were blocked with 5% bovine serum albumin (BSA; Catalog No. 36103ES25, YEASEN, Shanghai, China). Antibodies were diluted in 1× PBS containing 0.3% Triton-X 100 and 1% BSA. Cells were incubated with mouse anti-G3BP1 (Catalog No. 66486-1-Ig, Proteintech) primary antibody for 2 h at room temperature, followed by three times of washes with 1× PBS. Cells were then incubated with Alexa Fluor 555 goat anti-rabbit (Catalog No. 4413, Cell Signaling Technology, Beverly, MA) primary antibody for 2 h at room temperature, followed by three times of washes with 1× PBS. The nucleus was stained using Hochest33342. The cell slices were mounted and images were acquired using Olympus IX83 confocal microscope (Olympus, Tokyo, Japan).</p>", "<title>Western blot</title>", "<p id=\"p0085\">Protein samples were separated by SDS–PAGE and transferred onto polyvinylidene fluoride membrane (Catalog No. ISEQ00010, Millipore, Billerica, MA). The membranes were blocked with 5% nonfat dried milk in TBST buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% Tween-20, and pH 7.6) for 1 h at room temperature and incubated with protein-specific primary antibodies for 1 h at room temperature, followed by three times of washes with TBST buffer. The membranes were then incubated with HRP-conjugated secondary antibodies, followed by three times of washes with TBST buffer. The detailed information for the primary and secondary antibodies used in this analysis is provided in <xref rid=\"s0105\" ref-type=\"sec\">Table S4</xref>. The protein signals were visualized using ECL chemiluminescence reagents (Catalog No. BE6706-100, EASYBIO, Beijing, China), and images were acquired using Tanon 5200 chemiluminescent imaging system (Tanon, Shanghai, China).</p>", "<title>Quality control of RNA-seq data</title>", "<p id=\"p0090\">Quality control was performed using FastQC (v0.11.9), and results were aggregated and visualized using MultiQC (v1.7) ##REF##27312411##[27]##. Sequencing adapter and low-quality sequences were trimmed using Trim_galore (v.0.6.6) with ‘stringency 6’ parameter. The human rRNA sequences were downloaded from the NCBI Nucleotide database using keyword ““<italic>Homo sapiens</italic>”[Organism] AND biomol_rrna[PROP]”. Trimmed reads were aligned to rRNA sequences using bowtie2 (v2.3.4.3) ##REF##22388286##[28]## with ‘--very-sensitive’ parameter, and aligned reads were depleted using samtools (v1.10) ##UREF##3##[29]##.</p>", "<title>RNA-seq data analysis</title>", "<p id=\"p0095\">The reference human genome and annotation (release 19, GRCh37.p13) were downloaded from GENCODE project. CIRI2 (v2.0.6) and CIRIquant (v1.1.2) were used for detection, quantification, and differential expression analysis of circRNAs in the RNA-seq libraries ##REF##28334140##[14]##, ##REF##31900416##[13]##. Gene expression values were calculated using the HISAT2 (v2.1.0) and StringTie (v2.0.5) pipelines ##REF##25751142##[30]##, ##REF##25690850##[31]##. Gene differential expression analysis was performed using the GLM model in edgeR (v.3.26.8) package ##REF##19910308##[32]##. PCA was performed using ‘sklearn.decomposition.PCA’ function in the scikit-learn package ##UREF##4##[33]##.</p>", "<title>circRNA characterization and RBP analysis</title>", "<p id=\"p0100\">The full-length sequences of circRNAs were downloaded from the circAtlas (v2.0) database ##REF##32345360##[17]##. Only circRNAs that included in circAtlas database were kept for downstream analysis. The binding sites of human RPBs were predicted using the RBPmap (v1.2) webserver with high stringency level and conservation filter, and results were parsed using custom scripts ##UREF##2##[19]##. The expression levles of circRNAs in HCC dataset were obtained from a previous study ##REF##31900416##[13]##. SG-related protein database was downloaded from PhaSepDB 2.0 ##REF##31584089##[34]##. GO analysis was calculated using Enrichr ##REF##27141961##[35]##.</p>" ]
[ "<title>Results</title>", "<title>RNA transcripts enriched in SG cores</title>", "<p id=\"p0015\">To determine the transcriptome of SG cores, we isolated total RNA from purified SG cores in triplicates from SMMC-7721 cells, followed by RNA sequencing (RNA-seq) analysis (##FIG##0##Figure 1##A). Since only few SGs formed in cells grown under normal conditions, we induced SGs by incubating cells with 0.5 mM NaAsO<sub>2</sub> for 1 h. Immunofluorescence analysis of G3BP1 protein identified cytoplasmic SG condensates after stimulation (##FIG##0##Figure 1##B). Then, SGs were separated from cell lysates by differential centrifugation and purified by immunoprecipitation (IP) with G3BP1-specific antibodies. Western blot analysis of IP products showed that the SG core component G3BP1 and another SG-associated protein CAPRIN1 could be enriched by specific antibodies (##FIG##0##Figure 1##C). For each sample, RNA was isolated for RNA-seq from purified SGs, 5% of cell lysates, and the supernatants without SGs of the IP solution, which are referred to as SG-RNA, total-RNA, and sup-RNA, respectively (##FIG##0##Figure 1##A).</p>", "<p id=\"p0020\">Pairwise correlation analysis of the transcriptomes of the three RNA groups demonstrated the high reproducibility between experimental replicates in the same group (<italic>R</italic><sup>2</sup> &gt; 0.9; ##FIG##0##Figure 1##D). Moreover, both SG-RNA and sup-RNA transcriptomes showed low correlations with total-RNA transcriptomes (<italic>R</italic><sup>2</sup> &lt; 0.5), suggesting that SG-RNA transcriptomes are different from total-RNA transcriptomes. In addition, principal component analysis (PCA) also highlighted the similarities within each transcriptome triplicates of SG-RNA, total-RNA, and sup-RNA as well as the differences between these three RNA groups (##FIG##0##Figure 1##E). Therefore, these findings demonstrate that SGs contain specific transcriptomes compared with cytosolic total RNA and the RNAs outside of SGs.</p>", "<title>SG-enriched RNAs are longer and have higher GC content</title>", "<p id=\"p0025\">Since there were differences between the transcriptomes of SG-RNA, sup-RNA, and total-RNA, we thought to identify the specific transcripts that are enriched or depleted in SGs. According to the general analysis of RNA profiles in these transcriptomes, more fraction of mRNA transcripts was detected in SG-RNA than in total-RNA and sup-RNA, while long non-coding RNA (lncRNA) and circRNA transcripts were fewer (##FIG##1##Figure 2##A; <xref rid=\"s0105\" ref-type=\"sec\">Table S1</xref>), indicating the translation regulation roles of SGs. Furthermore, differential expression analysis indicated that 1413 transcripts were significantly enriched in SGs, while 4577 transcripts were significantly depleted in SGs compared with the total-RNA group (adjusted <italic>P</italic> &lt; 0.05; ##FIG##1##Figure 2##B). RNA fluorescence <italic>in situ</italic> hybridization (FISH) of two SG-enriched genes, <italic>ANKRD11</italic> and <italic>COL7A1</italic>, together with immunofluorescence showed that both mRNAs were colocalized with SGs (##FIG##1##Figure 2##C). Gene Ontology (GO) analysis for SG-enriched and SG-depleted transcripts showed that the SG-enriched transcripts were involved in regulating RNA transcription, while the SG-depleted transcripts were associated with membrane targeting of proteins (##FIG##1##Figure 2##D). These findings demonstrated the transcription regulation role of SGs, which was supported by a previous study ##REF##33784494##[12]##, as transcription of most genes is inhibited under stress conditions. We also examined the molecular features of RNAs in SGs. The SG-enriched RNAs tended to be longer (2267 nt <italic>versus</italic> 1252 nt on average) and had higher GC content than SG-depleted RNAs (##FIG##1##Figure 2##E and F).</p>", "<title>SG-enriched circRNAs have stronger ability to bind SG-related RBPs</title>", "<p id=\"p0030\">As increasing studies have highlighted the importance of circRNAs in various biological processes, we further used the CIRI software ##REF##31900416##[13]##, ##REF##28334140##[14]##, ##REF##27350239##[15]##, ##REF##25583365##[16]## to identify and quantify the circRNAs that were recruited to SGs. According to the differential expression analysis, 130 circRNAs were significantly enriched in SGs, while 2462 were significantly depleted in SGs, compared to those in the total-RNA group (<italic>P</italic> &lt; 0.05) (##FIG##2##Figure 3##A). Among the enriched circRNAs, 66 have the sequence and annotation information in the circAtlas database ##REF##32345360##[17]##, ##REF##30893614##[18]## (<xref rid=\"s0105\" ref-type=\"sec\">Table S2</xref>). We also validated the localization of two circRNAs, <italic>circSLTM</italic> and <italic>circARHGAP5</italic>, in SGs by RNA FISH and immunofluorescence (##FIG##2##Figure 3##B).</p>", "<p id=\"p0035\">To uncover the characteristics of enriched circRNAs in SGs, we performed analysis on the sequence features and molecular functions of these circRNAs. Although longer mRNA transcripts tended to be enriched in SGs (##FIG##1##Figure 2##E), SG-enriched circRNAs (average length = 413 nt) were significantly shorter than SG-depleted circRNAs (average length = 537 nt) (<italic>P</italic> &lt; 0.001, Wilcoxon test) (##FIG##2##Figure 3##C). In addition, there was no significant difference in GC content between SG-enriched and SG-depleted circRNAs (##FIG##2##Figure 3##D), indicating that GC content is not associated with SG accumulation of circRNAs. Given that RNAs that bind more SG-related RBPs are more likely to be localized into SGs, whether SG-enriched RNAs exhibit higher RBP binding ability were evaluated. RBP-binding sites prediction by RBPmap web server ##UREF##2##[19]## found that there was no significant difference in RBP types between SG-enriched RNAs and SG-depleted RNAs (##FIG##2##Figure 3##E). However, SG-enriched circRNAs could bind fewer types of RBPs than SG-depleted circRNAs (##FIG##2##Figure 3##F). Surprisingly, we observed that the proportion of binding sites of SG-related RBPs were higher in SG-enriched RNAs than in SG-depleted RNAs (##FIG##2##Figure 3##G), as well as higher in SG-enriched circRNAs than in SG-depleted circRNAs (##FIG##2##Figure 3##H). Furthermore, analysis of the top 15 RBPs with higher binding density on SG-enriched circRNAs showed that most of them were SG-related RBPs (##FIG##2##Figure 3##I). Among them, G3BP2 was a core component of SGs, indicating the role of circRNAs in regulating SG formation. Taken together, these results demonstrate that circRNAs with higher capability of binding SG-related RBPs show a stronger preference to be recruited into SGs and circRNAs are involved in the formation of SGs through binding to their component proteins.</p>", "<title>Differentially expressed SG-enriched circRNAs in HCC</title>", "<p id=\"p0040\">Previous studies demonstrate that SGs are associated with human diseases like cancer ##REF##34502337##[20]##. We further examined whether there are SGs-enriched circRNAs associated with HCC, since the SG transcriptomes were purified from HCC cells. We screened 35 SG-enriched circRNAs that were expressed in HCC and adjacent tissues, and found three circRNAs, <italic>circEXOC6B</italic>, <italic>circCALD1</italic>, and <italic>circVAMP3</italic> that were significantly down-regulated in HCC tissues (<xref rid=\"s0105\" ref-type=\"sec\">Figure S1</xref>). These results indicate the potential roles of mutual interplay between these circRNAs and SGs in HCC.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0045\">Assembly of SGs can be influenced by stress stimulation, as well as regulated by proteins and RNAs. RBPs are reported to play important roles in the formation of SGs ##REF##27821493##[2]##, while RNAs are thought to act as scaffolds to bind RBPs and thus to regulate SG assembly. It has been reported that GIRGL lncRNA interacts with CAPRIN1 to drive SG formation ##REF##33762340##[21]##. As SG-enriched circRNAs exhibit higher ability of binding SG-related RBPs, <italic>e.g.</italic>, G3BP2, these circRNAs are presumed to be related to the formation of SGs. Although it has been assumed that RNAs can be recruited to SGs through the SG-related RBPs, there is no direct evidence to support this hypothesis. Moreover, RNA translation inhibition is also reported to be relevant to SG assembly ##REF##22718973##[22]##. However, no translation potential was detected in SG-enriched circRNAs (<xref rid=\"s0105\" ref-type=\"sec\">Table S2</xref>), suggesting that the localization of circRNAs in SGs should not be due to translation. Although longer RNAs are more likely to be enriched in SGs, we observed that SG-enriched circRNAs are shorter than SG-depleted circRNAs. According to our previous study, most of circRNAs are less than 600 nt in length ##REF##33707777##[23]##, ##REF##30660194##[24]##. Considering that the length difference between SG-enriched and SG-depleted circRNAs is limited, it may have little effect on the SG-related RBP binding of circRNAs. It should be noted that as SGs are dynamic condensates, high speed of centrifugation may affect the stability of SGs. Some SG components with weak interactions may be missed by differential centrifugation without crosslinking. However, the internal core components in SGs are more stable ##REF##26777405##[25]##, which can be effectively captured using the approach developed in this study.</p>", "<p id=\"p0050\">In summary, our study provides novel insights into SG-related circRNAs through transcriptome analysis of SG cores. The ability of binding SG-related RBPs of circRNAs is related to their localization in SGs, suggesting the role of circRNAs in SG formation. Also, some SG-enriched circRNAs are differentially expressed between HCC and adjacent tissues. Further studies are still needed to elucidate the specific mechanisms and cellular consequences of circRNAs in SG formation.</p>" ]
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[ "<p id=\"np010\">Equal contribution.</p>", "<p><bold>Stress granules</bold> (SGs) are cytoplasmic ribonucleoprotein assemblies formed under stress conditions and are related to various biological processes and human diseases. Previous studies have reported the regulatory role of some proteins and linear RNAs in SG assembly. However, the relationship between <bold>circular RNAs</bold> (circRNAs) and SGs has not been discovered. Here, we screened both linear RNAs and circRNAs in SGs using improved total RNA sequencing of purified SG cores in mammalian cells and identified circular transcripts specifically localized in SGs. circRNAs with higher SG-related RNA-binding protein (RBP) binding abilities are more likely to be enriched in SGs. Furthermore, some SG-enriched circRNAs are differentially expressed in <bold>hepatocellular carcinoma</bold> (HCC) and adjacent tissues. These results suggest the regulatory role of circRNAs in SG formation and provide insights into the biological function of circRNAs and SGs in HCC.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Chengqi Yi</p>" ]
[ "<title>Data availability</title>", "<p id=\"p0105\">The raw sequence data in this study have been deposited in the Genome Sequence Archive for Human ##REF##34400360##[36]## at the National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (GSA-Human: HRA001512), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa-human/\" id=\"ir401\">https://ngdc.cncb.ac.cn/gsa-human/</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0110\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0115\"><bold>Shuai Chen:</bold> Conceptualization, Validation, Investigation, Writing – original draft. <bold>Jinyang Zhang:</bold> Formal analysis, Data curation, Writing – original draft. <bold>Fangqing Zhao:</bold> Conceptualization, Writing – review &amp; editing, Supervision, Project administration, Funding acquisition. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0130\">The following are the Supplementary data to this article:</p>", "<p id=\"p0135\">\n\n</p>", "<p id=\"p0140\">\n\n</p>", "<p id=\"p0145\">\n\n</p>", "<p id=\"p0150\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0120\">This work was supported by grants from the <funding-source id=\"gp005\">National Key R&amp;D Program</funding-source> of China (Grant Nos. 2021YFA1300500 and 2021YFA1302000) and the <funding-source id=\"gp010\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100001809</institution-id><institution>National Natural Science Foundation of China</institution></institution-wrap></funding-source> (Grant Nos. 32130020, 32025009, and 91940306).</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Screening SG-specific transcripts in SGs of SMMC-7721 cells</bold></p><p><bold>A</bold><bold>.</bold> The schematic workflow of inducing, isolating, and purifying SGs and sequencing of RNAs in SGs. Total-RNA indicates the RNA from cell lysates (excluding nucleus and debris); SG-RNA indicates the RNA from purified SGs; and sup-RNA indicates the RNA from the supernatants without SGs of the IP solution. <bold>B</bold><bold>.</bold> Immunofluorescence of SGs in control and NaAsO<sub>2</sub>-stimulated cells. Scale bar, 20 μm. <bold>C</bold><bold>.</bold> Western blot of SG core protein G3BP1 in purified SGs and supernatants. <bold>D</bold><bold>.</bold> Pairwise Pearson correlation coefficients between replicates of SG-RNA, total-RNA, and sup-RNA. <bold>E</bold>. PCA of individual replicates of SG-RNA, total-RNA, and sup-RNA. SG, stress granule; IP, immunoprecipitation; WB, Western blot; PCA, principal component analysis; PC, principal component.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Characterization of all types of RNAs in SGs</bold></p><p><bold>A.</bold> Composition of the transcriptomes of SG-RNA, total-RNA, and sup-RNA groups. <bold>B.</bold> Volcano plot depicting abundance of all types of transcripts in SG-RNA <italic>versus</italic> total-RNA. Red and blue dots indicate RNAs that are significantly enriched or depleted in SGs, respectively. <bold>C</bold><bold>.</bold> RNA FISH validation of RNAs enriched in SGs (<italic>ANKRD11</italic> and <italic>COL7A1</italic>). Scale bar, 5 μm. <bold>D</bold><bold>.</bold> GO analysis for SG-enriched and SG-depleted RNAs. <bold>E</bold><bold>.</bold> and <bold>F</bold><bold>.</bold> Violin plots depicting the difference in transcript length (E) and GC content (F) between all types of SG-enriched and SG-depleted RNAs. ***, <italic>P</italic> &lt; 0.001. LincRNA, long intergenic non-coding RNA; misc_RNA, miscellaneous RNA; mt-tRNA, mitochondrial transfer RNA; circRNA, circular RNA; snRNA, small nuclear RNA; mt-rRNA, mitochondrial ribosomal RNA; snoRNA, small nucleolar RNA; miRNA, microRNA; rRNA, ribosomal RNA; FISH, fluorescence <italic>in situ</italic> hybridization; GO, Gene Ontology.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Characterization of circRNAs</bold><bold>enriched</bold><bold>in SGs</bold></p><p><bold>A</bold><bold>.</bold> Volcano plot showing circRNA abundance in SG-RNA <italic>versus</italic> total-RNA. Red and blue dots indicate circRNAs that are significantly enriched or depleted in SGs, respectively. <italic>P</italic> values were calculated using GLM test in edgeR. <bold>B</bold><bold>.</bold> RNA FISH validation of circRNAs enriched in SGs (<italic>circSLTM</italic> and <italic>circARHGAP5</italic>). Scale bar, 5 μm. <bold>C</bold><bold>.</bold>–<bold>H</bold><bold>.</bold> Violin plots showing the difference in transcript length (C), GC content (D), number of RBP types (F), and proportion of SG-related RBP-binding sites (H) between SG-enriched and SG-depleted circRNAs, as well as the number of RBP types (E) and proportion of SG-related RBP-binding sites (G) between all types of SG-enriched and SG-depleted RNAs. <bold>I</bold><bold>.</bold> Box plot showing the binding density of top 15 RBPs with higher binding ability to SG-enriched circRNAs. The symbols on the top shows whether these RBPs are targeted to SGs. **, <italic>P</italic> &lt; 0.01; ***, <italic>P</italic> &lt; 0.001; NS, not significant.</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Figure S1</title><p><bold>SG-enriched circRNAs in HCC and adjacent tissues</bold>. *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; ***, <italic>P</italic> &lt; 0.001.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S1</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S2</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S3</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S4</title></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e113\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China</p></fn><fn id=\"s0100\" fn-type=\"supplementary-material\"><p id=\"p0125\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.01.003\" id=\"ir005\">https://doi.org/10.1016/j.gpb.2022.01.003</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["3"], "surname": ["Mahboubi", "Stochaj"], "given-names": ["H.", "U."], "article-title": ["Cytoplasmic stress granules: dynamic modulators of cell signaling and disease"], "source": ["Biochim Biophy Acta Mol Basis Dis"], "volume": ["1863"], "year": ["2017"], "fpage": ["884"], "lpage": ["895"]}, {"label": ["5"], "surname": ["Dudman", "Qi"], "given-names": ["J.", "X."], "article-title": ["Stress granule dysregulation in amyotrophic lateral sclerosis"], "source": ["Front Cell Neurosci"], "volume": ["14"], "year": ["2020"], "object-id": ["598517"]}, {"label": ["19"], "mixed-citation": ["Paz I, Kosti I, Ares M, Cline M, Mandel-Gutfreund Y. RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res 2014;42:W361\u20137."]}, {"label": ["29"], "surname": ["Bonfield", "Marshall", "Danecek", "Li", "Ohan", "Whitwham"], "given-names": ["J.K.", "J.", "P.", "H.", "V.", "A."], "article-title": ["C library for reading/writing high-throughput sequencing data"], "source": ["Gigascience"], "volume": ["10"], "year": ["2021"], "object-id": ["giab007"]}, {"label": ["33"], "surname": ["Pedregosa", "Varoquaux", "Gramfort", "Michel", "Thirion", "Grisel"], "given-names": ["F.", "G.", "A.", "V.", "B.", "O."], "article-title": ["Scikit-learn: machine learning in Python"], "source": ["J Mach Learn Res"], "volume": ["12"], "year": ["2011"], "fpage": ["2825"], "lpage": ["2830"]}]
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36
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2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Aug 25; 21(4):886-893
oa_package/c0/2f/PMC10787114.tar.gz
PMC10787115
36183976
[ "<title>Introduction</title>", "<p id=\"p0005\">Liver cancer accounts for the sixth most common cancer and the third leading cause of cancer mortality worldwide ##REF##33538338##[1]##. The main type of liver cancer is hepatocellular carcinoma (HCC), which is a primary malignant tumor originating from the liver epithelial tissue or mesenchymal tissue ##REF##28043904##[2]##. Various kinase-related signaling pathways are aberrantly activated in HCC, such as the Ras/Raf/MAPK/Erk pathway (Ras pathway) and the PI3K/Pten/Akt/mTOR pathway (PI3K-Akt pathway) ##REF##19038007##[3]##, ##REF##31684995##[4]##. The Ras pathway regulates the proliferation, apoptosis, and differentiation of HCC cells ##REF##31657972##[5]##. This kinase pathway recruits the GRB2/SHC/SOS complex and promotes the phosphorylation of Ras and Raf when the membrane surface receptor of the epidermal growth factor receptor (EGFR) receives the stimulation signal. Then, a high level of phosphorylated Erk (p-Erk), as an activation marker, translocates into the nucleus and combines with other transcription initiation factors to promote oncogene expression ##UREF##0##[6]##. As the first-line molecular-targeted drug for HCC, sorafenib can specifically inhibit Raf phosphorylation in the Ras pathway and plays an important role in inhibiting HCC cell proliferation and angiogenesis ##REF##33197225##[7]##, ##REF##30030148##[8]##.</p>", "<p id=\"p0010\">The 5-methylcytosine (m<sup>5</sup>C) modification occurs in many types of RNAs, including mRNAs and non-coding RNAs. NOP2/Sun RNA methyltransferase (NSUN2) mainly catalyzes the formation of m<sup>5</sup>C as a writer protein ##REF##33438329##[9]##, induces the differentiation of epidermal and neural stem cells ##REF##31186410##[10]##, ##REF##28041877##[11]##, and directly affects gene expression in viruses by regulating the splicing of HIV-1 RNA ##REF##31358969##[12]##. Modified RNAs are recognized by Y-box binding protein 1 (YBX1) and Aly/REF export factor (ALYREF). YBX1 and ALYREF promote mRNA stability ##REF##22395603##[13]## and nuclear translocation ##REF##28418038##[14]## as the readers of m<sup>5</sup>C. No m<sup>5</sup>C eraser has been identified yet, although some proteins are involved in m<sup>5</sup>C oxidation. For example, AlkB homolog 1 (ALKBH1) and ten-eleven translocation (TET) family proteins have been identified as dioxygenases that catalyze the conversion of m<sup>5</sup>C to hm<sup>5</sup>C, which regulates RNA degradation and mitochondrial activity ##REF##29483655##[15]##, ##REF##28472312##[16]##.</p>", "<p id=\"p0015\">As a critical RNA m<sup>5</sup>C catalytic enzyme, the functions of NSUN2 have been described in multiple types of cancer. NSUN2 affects the mRNA stability of the heparin-binding growth factor (HDGF) by catalyzing m<sup>5</sup>C modification in its 3′-untranslated region (3′-UTR), which promotes the pathogenesis of bladder cancer ##REF##31358969##[12]##. Additionally, NSUN2 is overexpressed in breast cancer (BRCA) and hypopharyngeal squamous cell carcinoma (HPSCC) ##UREF##1##[17]##, ##REF##19740597##[18]##. Pan-cancer analysis showed that NSUN2 is positively correlated with DNA copy number and mRNA expression, which are associated with poor prognosis ##REF##19740597##[18]##, ##REF##31957540##[19]##. NSUN2 can regulate the m<sup>5</sup>C modification of H19 lncRNA and promote the occurrence and development of HCC by recruiting G3BP stress granule assembly factor 1 (G3BP1) ##REF##32978516##[20]##. The m<sup>5</sup>C profiles of circular RNA and mRNA were discovered in HCC ##REF##33042451##[21]##, ##REF##32571340##[22]##. However, the biological significance of NSUN2 and the characteristics of the m<sup>5</sup>C modification in HCC have not been fully investigated.</p>", "<p id=\"p0020\">In this study, we analyzed the characteristics of the mRNA m<sup>5</sup>C modification in HCC tissues compared to those in the adjacent tissues at the single-nucleotide resolution. The mechanism by which NSUN2 regulates the expression of multiple target genes was determined at the bioinformatic and experimental levels. We examined the effect of NSUN2 on regulating HCC cell sensitivity to sorafenib by affecting the activity of the Ras pathway. Additionally, the down-regulation of NSUN2 in HCC cells arrested the cell cycle. The mechanisms of m<sup>5</sup>C regulated by NSUN2 were involved in the progression of HCC.</p>" ]
[ "<title>Materials and methods</title>", "<title>Cell lines and tissues</title>", "<p id=\"p0075\">Human HCC cell lines (QGY-7703, Huh 7, and SMMC-7721) were cultured in Dulbecco's modified eagle medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in 5% CO<sub>2</sub> at 37 °C. For sensitivity analysis of sorafenib, QGY-7703 cells were seeded in six-well plates and treated with 10 µM sorafenib for 24 h. The Huh7 cells were treated with 8 µM sorafenib for 24 h.</p>", "<title>Plasmids, antibodies, and real-time PCR primers</title>", "<p id=\"p0080\">PLKO.1-shcontrol (NC), pLKO.1-shNSUN2, psPAX2, and pMD2 were used for <italic>NSUN2</italic> knockdown in HCC cells. The sequence of shNSUN2 was 5′-CCGGGCTGGCACAGGAGGGAATATACTCGAGTATATTCCCTCCTGTGCCAGCTTTTTG-3′. The sequence of siNSUN2 was: 5′-CACGUGUUCACUAAACCCUAUTT-3′.</p>", "<p id=\"p0085\">The antibodies used in this study were anti-NSUN2 (Catalog No. 44056S, Cell Signaling Technology, Danvers, MA), anti-GAPDH (Catalog No. GB12002, Servicebio, Wuhan, China), anti-pErk (Catalog No. 4370s, Cell Signaling Technology), and anti-Erk (Catalog No. 4695s, Cell Signaling Technology). Real-time PCR primers for target gene quantification used in this study are as follows: <italic>RNF115</italic> (forward 5′-CGGCAGTCGGATAGACAATAC-3′, reverse 5′-TGTCAGGACGAGAACTTCCTC-3′), <italic>GRB2</italic> (forward 5′-CTGGGTGGTGAAGTTCAATTCT-3′, reverse 5′-GTTCTATGTCCCGCAGGAATATC-3′), <italic>ADAM15</italic> (forward 5′-CCCTGAATGTACGAGTGGCAC-3′, reverse 5′-GGAGGAAGTTTTCGAGGGTGA-3′), <italic>AATF</italic> (forward 5′-TCAGCCTCCCTCTTGGACA-3′, reverse 5′-TCATCAGACGATCCTGGCAGA-3′), <italic>NSUN2</italic> (forward 5′-GGTATCCTGAAGAACTTGCC-3′, reverse 5′-ATCTTATGATGAGGCCGCA-3′), and <italic>GAPDH</italic> (forward 5′-CGCTCTCTGCTCCTCCTGTTC-3′, reverse 5′-ATCCGTTGACTCCGACCTTCAC-3′).</p>", "<title>RNA-BisSeq and RNA-seq for HCC tissues and adjacent tissues</title>", "<p id=\"p0090\">Tissues were frozen in liquid nitrogen and broken using Qiagen tissue lyser II (Catalog No. 69982, Qiagen, Hilden, Germany). Then, 1 ml TRIzol was added to the broken tissues, and total RNA was extracted with chloroform-isopropyl alcohol. Next, the HCC mRNAs were enriched using the Dynabeads mRNA Purification Kit (Catalog No. 61006, Ambion, Waltham, MA), and samples were treated with DNase (Catalog No. AM22222, ThermoFisher Scientific, Waltham, MA) at 37 °C for 20 min to remove genomic DNA. After DNase treatment, mRNAs were fragmented by a fragmentation reagent (Catalog No. AM8740, Ambion), and then the alcohol method was used to precipitate the samples.</p>", "<p id=\"p0095\">After alcohol precipitation, 10 ng of mRNA samples were taken for the transcription library, and 100–200 ng of mRNA samples were taken for bisulfite treatment, according to an earlier published method ##REF##30539560##[32]##. Finally, we used the KAPA stranded RNA-seq library preparation kit (Catalog No. KR1139, KAPA, Potters Bar, UK) for library construction. Sequencing was performed on an Illumina HiSeq PE150 sequencing system with a paired-end 150 bp read length.</p>", "<title>UHPLC-MS/MS analysis</title>", "<p id=\"p0100\">The UHPLC-MS/MS analysis was performed by a previously reported method ##REF##22395603##[13]##. Total RNA or mRNA (100–200 ng) was extracted from the QGY-7703 and SMMC-7721 cells, which were digested with 0.1 U nuclease P1 (Catalog No. M0660, New England Biolabs, Ipswich, MA) and 1.0 U calf intestinal alkaline phosphatase (Catalog No. 18009019, Invitrogen) at 37 °C overnight. Then, the mixture was filtered through a 3 K Omega membrane tube (Catalog No. OD010C35, PALL, New York, NY). Finally, we detected rm<sup>5</sup>C, rC, rU, rG, and rA using UHPLC-MS/MS.</p>", "<title>Immunohistochemistry</title>", "<p id=\"p0105\">The tissues were fixed with 5 ml of formaldehyde fixative solution. Then, they were dehydrated by adding molten paraffin wax at 58 °C. Tissues were cut into 15-µm sections using a rotary microtome, suspended in a water bath at 56 °C, and mounted onto gelatin-coated histological slides. The slides were dried overnight at room temperature. Then, we performed an immunohistochemistry analysis. The samples were incubated with anti-NSUN2 (1:100) overnight at 4 °C. Finally, the expression of NSUN2 in HCC tissues was visualized under a microscope using bright-field illumination.</p>", "<title>Ras activation assay</title>", "<p id=\"p0110\">RAS activity was analyzed with a Ras activation assay biochem kit (Catalog No. BK008, Cytoskeleton, Männedorf, Switzerland). The QGY-7703 cell lines containing the control group, the <italic>NSUN2</italic>-KO6 group, the <italic>NSUN2</italic>-KO10 group, and the <italic>NSUN2</italic>-Res group were prepared in advance, and equal concentrations of cells were collected and spread in a six-well plate. After 24 h, 500 µl of cell lysate was added to each well and centrifuged at 10,000 r/min at 4 °C for 2 min, and the supernatant protein was collected. The Bradford protein quantification kit (Catalog No. 23236, Invitrogen) was used to quantify the protein, and each group was diluted with cell lysate to equal volume and density. Then, 20 µl of whole-cell lysate was added to 5 µl of 5× sodium dodecyl sulfate (SDS) loading buffer, and the sample was boiled at 95 °C for 10 min as an input sample. The remaining samples were added with the same amount of Raf-RBD beads and rotated at 4 °C for 1 h. The beads were collected at 4 °C and centrifuged at 5000 <italic>g</italic> for 1 min. Then, 90% of the supernatant was removed, and the beads were cleaned three times with 500 µl of wash buffer. Finally, 1× SDS loading buffer was added, and the sample was boiled at 95 °C for 10 min as an immunoprecipitation (IP) sample. The samples were subjected to Western blot analysis, and the pan-RAS antibody was used to quantitatively identify the active Ras.</p>", "<title>Flow cytometry analysis</title>", "<p id=\"p0115\">The NC group and the shNSUN2 group cells were seeded in a six-well plate. The cell confluence reached 80% through overnight culture. Then, the cells were treated with sorafenib for 24 h. The cells were harvested and washed once with precooled phosphate buffer saline (PBS). According to the protocol of the dead cell apoptosis kit (Catalog No. V13241, Invitrogen), 5× annexin-binding buffer was diluted to 1× with deionized water, and the propidium iodide (PI) staining solution was diluted to 100 µg/ml. After the buffer was prepared, the cells were resuspended in 100 µl 1× annexin-binding buffer, 5 µl Alexa Fluor 488-annexin V, and 1 µl PI (100 µg/ml). The cells were incubated for 15 min at room temperature. Then, 400 µl of 1× annexin-binding buffer was added and gently mixed before flow cytometry analysis. All the experiments were repeated at least three times.</p>", "<title>RNA-seq data analysis</title>", "<p id=\"p0120\">The raw data were trimmed for adaptors by the Cutadapt software (v3.0), and low-quality bases were removed by the Trimmomatic software (v0.39) ##UREF##2##[33]##, ##REF##24695404##[34]##. The filtered clean reads were mapped to the hg19 genome with HISAT2 (v2.0) ##REF##25751142##[35]##. The HTSeq (v0.12.4) software was used to count reads mapped to each Ensembl gene ##REF##25260700##[36]##. Differentially expressed genes were calculated using DESeq2 (v1.30.1) ##REF##25516281##[37]##. The differential fold change cutoff was 1.2, and the false discovery rate (FDR) cutoff was 0.05.</p>", "<title>RNA-BisSeq data analysis</title>", "<p id=\"p0125\">The Cutadapt and Trimmomatic software were used to trim adaptors and remove low-quality bases ##UREF##2##[33]##, ##REF##24695404##[34]##. The clean reads were mapped to the hg19 genome by meRanGh from meRanTK (v1.2.0) ##REF##26543174##[38]##.</p>", "<p id=\"p0130\">The m<sup>5</sup>C sites were called by meRanCall from meRanTK. The luciferase spike-in conversion rates were evaluated to be over 99%. The sample-credible m<sup>5</sup>C sites satisfied coverage depth ≥ 30, methylated cytosine depth ≥ 5, and methylation level ≥ 0.1. The differential m<sup>5</sup>C methylation analysis criteria comprised coverage ≥ 10 for all samples and were used to compare methylation levels between tumor and normal samples. The differential m<sup>5</sup>C sites were defined as follows: mean m<sup>5</sup>C level difference ≥ 0.05 (tumor and normal samples) and <italic>P</italic> &lt; 0.05 (Wilcoxon test). The m<sup>5</sup>C sites were annotated using bedtools (v2.26.0) intersectBed ##REF##20110278##[39]##.</p>", "<title>Pathway analysis</title>", "<p id=\"p0135\">Hypermethylated and hypomethylated genes were used as input for DAVID (v6.8) (<ext-link ext-link-type=\"uri\" xlink:href=\"https://david.ncifcrf.gov/\" id=\"ir005\">https://david.ncifcrf.gov/</ext-link>).</p>", "<title>Statistical analysis</title>", "<p id=\"p0140\">Data were analyzed using the Python and GraphPad Prism (v8) software. Two-way analysis of variance and Student’s <italic>t</italic>-test were performed to determine statistical significance. The error bars, when present, represent the mean ± SD. The experiments were repeated at least three times independently. Statistical significance was considered at <italic>P</italic> &lt; 0.05.</p>" ]
[ "<title>Results</title>", "<title>mRNAs are frequently <bold>m</bold><bold><sup>5</sup></bold>C-hypermethylated in HCC tissues</title>", "<p id=\"p0025\">To reveal the m<sup>5</sup>C modification features in HCC, we collected 20 pairs of HCC tumor samples and analyzed the transcriptome (RNA sequencing; RNA-seq) data and RNA bisulfite sequencing (RNA-BisSeq) data. The m<sup>5</sup>C sites were enriched in mRNAs in the HCC tumor tissues and the adjacent tissues (<xref rid=\"s0125\" ref-type=\"sec\">Figure S1</xref>A). The distribution characteristics of the m<sup>5</sup>C modifications in HCC mRNAs were found to be enriched downstream of the translation initiation site in the mRNA coding sequence (CDS) region (##FIG##0##Figure 1##A). The distribution pattern was consistent with other mammalian cells previously reported ##REF##22395603##[13]##. The proportion of the m<sup>5</sup>C modification in different regions of the mRNA was statistically analyzed. The m<sup>5</sup>C sites covered in the 3′-UTR, CDS, and 5′-UTR were similar in cancer tissues and adjacent tissues, and the CDS region contained the highest number of m<sup>5</sup>C sites (##FIG##0##Figure 1##B). A sequence frequency logo displayed an embedding feature of m<sup>5</sup>C sites in CG-rich environments (<xref rid=\"s0125\" ref-type=\"sec\">Figure S1</xref>B). Our RNA-BisSeq data identified 2482 m<sup>5</sup>C sites in mRNAs with differential methylation levels (as shown in <xref rid=\"s0125\" ref-type=\"sec\">Table S1</xref>). Additionally, we found that mRNA m<sup>5</sup>C modification in HCC tissues was significantly higher than that in the adjacent tissues for the overall methylation level (##FIG##0##Figure 1##C). We found 1548 and 934 sites for hypermethylated and hypomethylated, respectively. The ratio of hypermethylated sites in tumor tissues was 62.36%, and the ratio of hypomethylated sites was 37.63% relative to that in the normal tissues (##FIG##0##Figure 1##D). The heatmap analysis showed the differential methylation level of the m<sup>5</sup>C sites between the adjacent tissues and HCC tissues (##FIG##0##Figure 1##E). In summary, mRNAs are frequently m<sup>5</sup>C-hypermethylated in HCC.</p>", "<title>Multiple <bold>m<sup>5</sup></bold>C-hypermethylated genes related to NSUN2 participate in oncogenic pathways</title>", "<p id=\"p0030\">To further investigate the effect of m<sup>5</sup>C on the progress of HCC, we identified differentially expressed mRNAs with hypermethylated m<sup>5</sup>C sites in HCC tissues. We detected 255 hypermethylated sites, covering 124 genes with high mRNA expression (##FIG##1##Figure 2##A). Through the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of highly m<sup>5</sup>C-modified genes, several tumor-related pathways, including the PI3K-Akt, ErbB, and Ras signaling pathways, were found to be enriched in m<sup>5</sup>C modifications (##FIG##1##Figure 2##B). Moreover, these highly m<sup>5</sup>C-modified genes were found to be involved in the progression of cell migration, apoptosis, and cell cycle (<xref rid=\"s0125\" ref-type=\"sec\">Figure S1</xref>C). We investigated the genes (<italic>GRB2</italic>, <italic>AATF</italic>, <italic>RNF115</italic>, <italic>ADAM15</italic>, <italic>RTN3</italic>, and <italic>HDGF</italic>) that are highly expressed in HCC and modified by m<sup>5</sup>C (<xref rid=\"s0125\" ref-type=\"sec\">Figure S1</xref>D and E). To further determine whether the specific m<sup>5</sup>C-modified genes are regulated by NSUN2 in HCC, first, we analyzed the correlation between the mRNA expression level of target genes and their m<sup>5</sup>C modification level (##FIG##1##Figure 2##C). Then, we analyzed the correlation between the <italic>NSUN2</italic> mRNA expression and the mRNA expression of the target genes (##FIG##1##Figure 2##D). The results showed that the mRNA expression of the target genes was related to their m<sup>5</sup>C modification level and also to the <italic>NSUN2</italic> mRNA expression level (##FIG##1##Figure 2##C and D). Additionally, the results of the TCGA analysis indicated that higher expression levels of these target genes (<italic>GRB2</italic>, <italic>AATF</italic>, <italic>RNF115</italic>, <italic>ADAM15</italic>, <italic>RTN3</italic>, and <italic>HDGF</italic>) were associated with a poor prognosis of HCC (##FIG##1##Figure 2##E, <xref rid=\"s0125\" ref-type=\"sec\">Figure S1</xref>F). The aforementioned results suggest that multiple hypermethylated genes associated with NSUN2 participate in oncogenic pathways.</p>", "<title>NSUN2 is highly expressed in HCC and regulates mRNA <bold>m</bold><bold><sup>5</sup></bold>C modification</title>", "<p id=\"p0035\">Transcriptome data analysis showed that m<sup>5</sup>C-related writer and reader proteins were highly expressed in HCC tissues (<xref rid=\"s0125\" ref-type=\"sec\">Figure S2</xref>A). Previous studies have shown that NSUN2 is involved in the regulation of m<sup>5</sup>C modification and affects tumor progression ##REF##32978516##[20]##, ##REF##32708015##[23]##. Here we focused on the regulatory relationship between NSUN2 and m<sup>5</sup>C-modified target genes in the progression of HCC. Expression data displayed that <italic>NSUN2</italic> mRNA was overexpressed in HCC tissues (##FIG##2##Figure 3##A). We confirmed the protein expression of NSUN2 in some of the HCC tissue cohorts (<italic>n</italic> = 6) through Western blot (##FIG##2##Figure 3##B). The results of the immunohistochemical analysis showed that NSUN2 had a higher expression in HCC tissues than that in the adjacent normal tissues (##FIG##2##Figure 3##C). Additionally, the m<sup>5</sup>C modification level of total RNA and mRNAs in the HCC cell lines (QGY-7703 and SMMC-7721) were analyzed by ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry (UHPLC-MS/MS). We used siRNAs to knock down <italic>NSUN2</italic> and its family members (<italic>NSUN1/5</italic>). NSUN2 was found to be an important methyltransferase for mRNAs in HCC cells (##FIG##2##Figure 3##D, <xref rid=\"s0125\" ref-type=\"sec\">Figure S2</xref>B). Real-time PCR revealed that the mRNA expression levels of <italic>GRB2</italic>, <italic>RNF115</italic>, and <italic>AATF</italic> were significantly decreased in the <italic>NSUN2</italic>-knockdown HCC cells (##FIG##2##Figure 3##E, <xref rid=\"s0125\" ref-type=\"sec\">Figure S2</xref>C). The integrative genomics viewer (IGV) tracks displayed the read coverage of the <italic>GRB2</italic> mRNA in the RNA-seq and RNA-BisSeq data, and showed the up-regulation of m<sup>5</sup>C modifications and mRNA abundance in <italic>GRB2</italic> in HCC tissues compared to that in the adjacent tissues (<xref rid=\"s0125\" ref-type=\"sec\">Figure S2</xref>D). We concluded that NSUN2 plays a critical role in regulating the m<sup>5</sup>C modification of the target genes (<italic>GRB2</italic>, <italic>RNF115</italic>, and <italic>AATF</italic>) in HCC.</p>", "<title>NSUN2 affects the sensitivity of HCC cells to sorafenib by regulating the activity of the Ras pathway</title>", "<p id=\"p0040\">The activity of the Ras pathway is abnormally high in most HCC patients, which leads to a poor prognosis ##REF##33579428##[24]##. The phosphorylation of Raf is one of the crucial targets of sorafenib ##REF##30061739##[25]##. GRB2 is a critical upstream linker that promotes Raf phosphorylation that is regulated by NSUN2 in esophageal squamous cell carcinoma. A previous study has reported that GRB2 is a key upstream regulator of Raf phosphorylation and is regulated by NSUN2 ##REF##8386805##[26]##. To confirm the effect of the regulation of m<sup>5</sup>C by NSUN2 on the activity of the Ras pathway in HCC, the m<sup>5</sup>C modification levels of genes (such as <italic>GRB2</italic>, <italic>MAPK3</italic>, and <italic>PIK3R2</italic>) in the Ras pathway were analyzed. These genes were hypermethylated in HCC tissues (##FIG##3##Figure 4##A). A heatmap analysis showed that the m<sup>5</sup>C modification levels of these genes were increased in HCC tissues (##FIG##3##Figure 4##B). According to the results of the TCGA data analysis, HCC patients with higher expression of <italic>NSUN2</italic> and <italic>GRB2</italic> had the worst prognosis (##FIG##3##Figure 4##C).</p>", "<p id=\"p0045\">To further investigate the effect of NSUN2 on the level of active Ras, we constructed two <italic>NSUN2</italic>-konckout cell lines (<italic>NSUN2</italic>-KO6/KO10) and one <italic>NSUN2</italic>-rescued stable cell line (<italic>NSUN2</italic>-Res). The identification of <italic>NSUN2</italic> knockout at the genome level and the mRNA expression level are shown in <xref rid=\"s0125\" ref-type=\"sec\">Figure S3</xref>. We found that the level of active Ras protein in <italic>NSUN2</italic>-knockout cells was significantly decreased, which could be rescued by wild-type <italic>NSUN2</italic> (##FIG##3##Figure 4##D). The level of phosphorylated-Erk (p-Erk) is an important indicator of the activity of the Ras pathway. p-Erk decreased in HCC cells without changing the Erk protein level in <italic>NSUN2</italic>-knockout cells, and rescued by wild-type <italic>NSUN2</italic>. The changing of the p-Erk level cannot be rescued by mutant <italic>NSUN2</italic> (##FIG##3##Figure 4##E).</p>", "<p id=\"p0050\">Sorafenib is a molecular inhibitor for the phosphorylation of Raf, and inhibits Ras activity, which is widely used in the systemic therapy of HCC. We investigated whether NSUN2 affects the sensitivity of sorafenib in HCC cell lines. Through flow cytometry analysis of the apoptotic HCC cells in the <italic>NSUN2</italic>-knockout group and the control group under sorafenib stress, the proportion of apoptotic HCC cells treated with sorafenib was significantly higher, compared to the proportion of apoptotic cells in the control group (##FIG##3##Figure 4##F). Data statistics are shown in ##FIG##3##Figure 4##G. Similar results were obtained in the <italic>NSUN2</italic>-knockdown cells (<xref rid=\"s0125\" ref-type=\"sec\">Figure S4</xref>A and B). We observed that knockdown of <italic>NSUN2</italic> did not increase the apoptotic rate of QGY-7703 cells but affected that of Huh7 cells. The increased sensitivity of these cell lines to sorafenib was consistent when <italic>NSUN2</italic> is knocked down (<xref rid=\"s0125\" ref-type=\"sec\">Figure S4</xref>C). Additionally, we found that the down-regulation of <italic>NSUN2</italic> was associated with cell cycle arrest (<xref rid=\"s0125\" ref-type=\"sec\">Figure S4</xref>D and E). In summary, NSUN2 affects the sensitivity of HCC cells to sorafenib by regulating the activity of the Ras pathway.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0055\">In recent years, many RNA modifications have been identified ##REF##34631286##[27]##. As an essential epigenetic modification of RNA, m<sup>5</sup>C participates in different regulatory mechanisms and biological functions, especially in cancers ##REF##28472312##[16]##, ##UREF##1##[17]##, ##REF##19740597##[18]##, ##REF##31957540##[19]##, ##REF##32978516##[20]##, ##REF##33042451##[21]##, ##REF##32571340##[22]##. In this study, the distribution characteristics of the m<sup>5</sup>C modification in HCC were studied. We discovered high levels of m<sup>5</sup>C modification and NSUN2 expression in HCC. The hypermethylated target genes (<italic>GRB2</italic>, <italic>AATF</italic>, and <italic>RNF115</italic>) participate in the carcinogenic pathways. NSUN2 affects the sensitivity of HCC cells to sorafenib by regulating the activity of the Ras pathway.</p>", "<p id=\"p0060\">NSUN2 is highly expressed in multiple tumor types, such as gastric cancer and esophageal squamous cell carcinoma ##REF##19740597##[18]##, ##REF##29763634##[28]##, ##REF##32332707##[29]##. Here, we found that <italic>NSUN2</italic> was overexpressed in HCC. Moreover, NSUN2 in HCC tissues was strongly correlated with the high methylation and expression of target genes, including <italic>GRB2</italic>, <italic>RNF115</italic>, <italic>AATF</italic>, <italic>ADAM15</italic>, <italic>RTN3</italic>, and <italic>HDGF</italic>. Li et al. found that NSUN2 coordinates with lin-28B, a novel m<sup>5</sup>C recognition protein, to catalyze the m<sup>5</sup>C modification of <italic>GRB2</italic> and stabilize its mRNA expression. High levels of GRB2 promote the activation of the PI3K/Akt and Ras pathways in esophageal squamous cell carcinoma ##REF##34345012##[30]##. We demonstrated that NSUN2 inhibited the Ras activation and decreased the p-Erk level in HCC, which led to the increased sensitivity of HCC cells to sorafenib.</p>", "<p id=\"p0065\">A previous study has reported that nascent RNA with m<sup>5</sup>C modification can regulate chromatin structures and recruit transcription factors. The m<sup>5</sup>C-mediated complex leads to 5-azacitidine resistance in leukemia cells, which provides new insights into the treatment of leukemia ##REF##29563491##[31]##. In our study, because of the critical role of NSUN2 in regulating the m<sup>5</sup>C modification and the expression of mRNAs related to the Ras pathway, the sensitivity of HCC cells to sorafenib was increased, which has great significance for the treatment of HCC patients. RNA epigenetics, especially m<sup>5</sup>C, can potentially regulate drug sensitivity.</p>", "<p id=\"p0070\">Overall, we reveal the m<sup>5</sup>C landscape in HCC at a single-nucleotide resolution and verified the correlation between m<sup>5</sup>C-hypermethylated genes and HCC tumor characteristics. NSUN2 has been reported to be involved in various tumor-related cell processes, including affecting proliferation, apoptosis, and sorafenib sensitivity in HCC cells. Our study provides novel mechanisms for the effect of RNA epigenetic modification on HCC progression, which might help discover more effective HCC treatment targets and strategies.</p>" ]
[]
[ "<p id=\"np010\">Equal contribution.</p>", "<p>RNA modifications affect many biological processes and physiological diseases. The <bold>5-methylcytosine</bold> (m<sup>5</sup>C) modification regulates the progression of multiple tumors. However, its characteristics and functions in <bold>hepatocellular carcinoma</bold> (HCC) remain largely unknown. Here, we found that HCC tissues had a higher m<sup>5</sup>C methylation level than the adjacent normal tissues. Transcriptome analysis revealed that the hypermethylated genes mainly participated in the phosphokinase signaling pathways, such as the Ras and PI3K-Akt pathways. The m<sup>5</sup>C methyltransferase <bold>NSUN2</bold> was highly expressed in HCC tissues. Interestingly, the expression of many genes was positively correlated with the expression of <italic>NSUN2</italic>, including <italic>GRB2</italic>, <italic>RNF115</italic>, <italic>AATF</italic>, <italic>ADAM15</italic>, <italic>RTN3</italic>, and <italic>HDGF</italic>. Real-time PCR assays further revealed that the expression of the mRNAs of <italic>GRB2</italic>, <italic>RNF115</italic>, and <italic>AATF</italic> decreased significantly with the down-regulation of <italic>NSUN2</italic> expression in HCC cells. Furthermore, NSUN2 could regulate the cellular sensitivity of HCC cells to <bold>sorafenib</bold> via modulating the Ras signaling pathway. Moreover, knocking down <italic>NSUN2</italic> caused cell cycle arrest. Taken together, our study demonstrates the vital role of NSUN2 in the progression of HCC.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Jianhua Yang</p>" ]
[ "<title>Ethical statement</title>", "<p id=\"p0145\">Human samples in this study were collected from the Biobank of the First Affiliated Hospital of Zhengzhou University, China. The study was approved by the Ethics Committee of Scientific Research and Clinical Trial of the First Affiliated Hospital of Zhengzhou University, China (Approval No. 2019-KY-0024-001). All participants provided written informed consent according to the institutional guidelines.</p>", "<title>Data availability</title>", "<p id=\"p0150\">The raw sequence data reported in this study have been deposited in the Genome Sequence Archive for Human ##REF##34400360##[40]## at the National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (GSA-Human: HRA001101), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa-human/\" id=\"ir010\">https://ngdc.cncb.ac.cn/gsa-human/</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0155\">The authors declare no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0160\"><bold>Dan Song:</bold> Methodology, Validation, Investigation, Writing – original draft, Writing – review &amp; editing. <bold>Ke An:</bold> Formal analysis, Data curation, Writing – original draft, Writing – review &amp; editing. <bold>Wenlong Zhai:</bold> Resources, Methodology, Investigation, Writing – review &amp; editing. <bold>Luyao Feng:</bold> Validation, Investigation. <bold>Yingjie Xu:</bold> Validation, Investigation. <bold>Ran Sun:</bold> Validation. <bold>Yueqin Wang:</bold> Methodology, Investigation. <bold>Yun-Gui Yang:</bold> Methodology, Supervision, Project administration. <bold>Quancheng Kan:</bold> Conceptualization, Project administration. <bold>Xin Tian:</bold> Conceptualization, Supervision, Funding acquisition, Project administration, Writing – review &amp; editing. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0175\">The following are the Supplementary material to this article:</p>", "<p id=\"p0180\">\n\n</p>", "<p id=\"p0185\">\n\n</p>", "<p id=\"p0190\">\n\n</p>", "<p id=\"p0195\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0165\">We thank Prof. Jiaxue Wu from School of Life Sciences Fudan University for providing HCC cell lines. This study was financially supported by grants from the <funding-source id=\"gp005\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100001809</institution-id><institution>National Natural Science Foundation of China</institution></institution-wrap></funding-source> (Grant Nos. 32170594 and 31870809), the <funding-source id=\"gp010\">Province and Ministry Coconstruction Major Program of Medical Science and Technique Foundation of Henan Province</funding-source> (Grant No. SBGJ202001007), and the <funding-source id=\"gp015\">Special Fund for Young and Middle School Leaders of Henan Health Commission</funding-source> (Grant No. HNSWJW-2020017), China.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>mRNAs are frequently</bold><bold>m<sup>5</sup>C-</bold><bold>hypermethylated in HCC tissues</bold><bold>A.</bold> Distribution pattern of the m<sup>5</sup>C sites on mRNAs in the HCC tissues (tumor) and the adjacent tissues (normal). <bold>B.</bold> Different proportions of m<sup>5</sup>C modifications in regions of mRNA between the HCC tissues and the adjacent tissues. <bold>C.</bold> The overall m<sup>5</sup>C modification level is higher in the HCC tissues than in the adjacent tissues, as determined by the BisSeq data analysis. Statistical significance was calculated by Wilcoxon test (****, <italic>P</italic> = 5.116E−09). <bold>D.</bold> Difference in the m<sup>5</sup>C modification levels between the HCC tissues and the adjacent tissues. <bold>E.</bold> Heatmap showing the differential m<sup>5</sup>C methylation levels between the HCC tissues and the adjacent tissues. HCC, hepatocellular carcinoma; m<sup>5</sup>C, 5-methylcytidine; CDS, coding sequence; UTR, untranslated region.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Multiple</bold><bold>m</bold><sup><bold>5</bold></sup><bold>C-</bold><bold>hypermethylated genes related to NSUN2 participate in the oncogenic pathways</bold><bold>A.</bold> The distribution of mRNAs with a significant change in the m<sup>5</sup>C methylation level and the gene expression level in HCC tissues and the adjacent tissues. <bold>B.</bold> The KEGG analysis showed that m<sup>5</sup>C-hypermethylated genes with high expression levels in the HCC tissues were enriched in oncogenic signaling pathways. <bold>C.</bold> A relation analysis showed that the expression levels of <italic>GRB2</italic>, <italic>RNF115</italic>, and <italic>AATF</italic> were positively correlated with their m<sup>5</sup>C modification levels. <bold>D.</bold> The expression levels of <italic>GRB2</italic>, <italic>RNF115</italic>, and <italic>AATF</italic> were positively correlated with the <italic>NSUN2</italic> expression level. <bold>E.</bold> The overall survival analysis indicates the correlation of the mRNA expression of <italic>GRB2</italic>, <italic>RNF115</italic>, and <italic>AATF</italic> with poor prognosis in HCC patients. <italic>P</italic> values were calculated by Student’s <italic>t</italic>-test. KEGG, Kyoto Encyclopedia of Genes and Genomes; TPM, transcripts per kilobase of exon model per million mapped reads.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>NSUN2 is highly expressed in HCC and regulates mRNA m<sup>5</sup>C modification</bold><bold>A.</bold> The expression of <italic>NSUN2</italic> mRNA was higher in HCC tissues than in the adjacent tissues determined by transcriptome analysis. <bold>B.</bold> Western blot analysis showed the higher expression of NSUN2 in HCC tissues than in the adjacent tissues. GAPDH was used as a reference control. “T” indicates a tumor smaple, and “N” indicates the adjacent tissue. <bold>C.</bold> Immunohistochemical analysis showed the higher expression of NSUN2 in HCC tissues than in the adjacent tissues. <bold>D.</bold> In HCC cells, UHPLC-MS/MS analysis showed that the down-regulation of <italic>NSUN2</italic> significantly decreased the density of m<sup>5</sup>C/C in mRNAs. <bold>E.</bold> The real-time PCR analysis showed that the mRNA expression of <italic>GRB2</italic>, <italic>RNF115</italic>, and <italic>AATF</italic> was significantly decreased when <italic>NSUN2</italic> was silenced in QGY-7703 cells. Data were represented by mean ± SD. Statistical significance was determined by Student’s <italic>t</italic>-test (*, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; ***, <italic>P</italic> &lt; 0.001; ****, <italic>P</italic> &lt; 0.0001). UHPLC-MS/MS, ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>NSUN2 affects the sensitivity of HCC cells to sorafenib by regulating the activity of the Ras pathway</bold><bold>A.</bold> Box plots showing the mRNA m<sup>5</sup>C levels of the Ras pathway-related genes. <bold>B.</bold> Heatmap showing the differential mRNA m<sup>5</sup>C levels of the Ras pathway-related genes in HCC tissues and the adjacent tissues. <bold>C.</bold> The overall survival analysis indicated that the high expression of <italic>NSUN2</italic> and <italic>GRB2</italic> was correlated with the worst prognosis in HCC patients (****, <italic>P</italic> &lt; 0.0001). <bold>D.</bold> Western blot showing the Ras activity detected in wild-type QGY-7703 cells (WT), <italic>NSUN2</italic>-knockout cells (<italic>NSUN2</italic>-KO6/KO10), and <italic>NSUN2</italic>-rescued cells (<italic>NSUN2</italic>-Res). <bold>E.</bold> Western blot of Erk and p-Erk in <italic>NSUN2</italic>-knockout cells (<italic>NSUN2</italic>-KO6/KO10) and <italic>NSUN2</italic>-rescued cells (<italic>NSUN2</italic>-Res, <italic>NSUN2</italic>-C271A, and <italic>NSUN2</italic>-DM). <italic>NSUN2</italic>-Res, <italic>NSUN2</italic>-C271A, and <italic>NSUN2</italic>-DM indicate wild-type rescued, binding site mutant rescued, and binding site and catalytic site double mutant rescued, respectively. GAPDH was used as a reference control. <bold>F.</bold> Sorafenib treatment and flow cytometry analysis of the apoptosis of QGY-7703 cells when <italic>NSUN2</italic> was knockout or rescued. <bold>G</bold><bold>.</bold> The statistical analysis of the apoptosis ratio shown in (F). Data were represented by mean ± SD. Statistical significance was determined by Student’s <italic>t</italic>-test (*, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; ns, not significant). Raf RBD, Ras-binding domain of Raf; IP, immunoprecipitation; p-Erk, phosphorylated-Erk; PI, propidium iodide.</p></caption></fig>", "<fig id=\"f0025\" position=\"anchor\"><label>Supplementary Figure S1</label><caption><p><bold>Distribution characteristics of m5C in HCC and expression pattern of target genes</bold>. <bold>A.</bold> The type and proportion of RNA in the sequencing library. <bold>B.</bold> The sequences are proximal to the mRNA m<sup>5</sup>C sites in HCC tissues and the adjacent tissues. <bold>C.</bold> The m<sup>5</sup>C hypermethylated and highly expressed genes in HCC tissues were involved in different cellular processes, determined by the GO functional analysis. <bold>D.</bold> and <bold>E.</bold> The expression of target genes, including GRB2, AATF, RNF115, ADAM15, RTN3, and HDGF, was higher in HCC tissues than that in the adjacent tissues, determined by transcriptome analysis, ****, <italic>P</italic> &lt; 0.0001. <bold>F.</bold> The overall survival analysis showed that the higher expression of ADAM15, RTN3, and HDGF was correlated with a poor prognosis in HCC patients; ADAM15 (*, <italic>P</italic> = 0.0097), RTN3 (**, <italic>P</italic> = 0.00018), HDGF (*, <italic>P</italic> = 0.0092). TPM, transcripts per kilobase of exon model per million mapped reads; HCC, hepatocellular carcinoma; GO, gene ontology.</p></caption></fig>", "<fig id=\"f0030\" position=\"anchor\"><label>Supplementary Figure S2</label><caption><p><bold>NSUN2 regulates downstream target gene expression, especially GRB2</bold>. <bold>A.</bold> The mRNA expression of m<sup>5</sup>C writers and readers in HCC tissues was higher than that in the adjacent tissues, determined by the transcriptomic analysis, ***, <italic>P</italic> &lt; 0.001. <bold>B.</bold> In HCC cell lines, the UHPLC-MS/MS analysis showed that downregulation of NSUN2 did not change the density of m5C/C in total RNA. <bold>C.</bold> Real-time PCR analysis showed that the mRNA expression levels of GRB2, RNF115, and AATF were significantly lower in Huh7 <italic>NSUN2</italic> knockdown cells, *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01. <bold>D.</bold> The m<sup>5</sup>C modification in the 3′ UTR and the expression of GRB2 mRNA were analyzed by IGV visualization in HCC tissues and the adjacent tissues. UHPLC-MS/MS, ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry; UTR, untranslated region; IGV, itegrative genomics viewer.</p></caption></fig>", "<fig id=\"f0035\" position=\"anchor\"><label>Supplementary Figure S3</label><caption><p><bold>Identification of NSUN2 knockout efficiency at the genome level and transcriptome level</bold>. <bold>A.</bold> NSUN2 knockout characteristics were identified by Sanger sequencing in the QGY-7703 cell genome. <bold>B.</bold> The mRNA expression levels of NSUN2 in NSUN2 knockout cells (KO6/KO10) and NSUN2 reconstituted cells were evaluated by real-time PCR. WT, wilg type ; KO, knock out ; Res, rescue.</p></caption></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary Figure S4</label><caption><p><bold>Apoptosis and cycle analysis of NSUN2 on HCC cells</bold>. <bold>A.</bold> and <bold>B.</bold> After sorafenib treatment, flow cytometry analyses of the apoptosis of HCC cells rate when NSUN2 knockdown. The statistical analyses of the apoptosis ratio are shown in (<bold>C</bold>), **, <italic>P</italic> &lt; 0.01. <bold>D.</bold> Flow cytometry analyses of the cell cycle of Huh 7 cells. These cells were arrested in the G1 phase when NSUN2 was knocked down. The statistical analyses of the arrest ratio are shown in (<bold>E</bold>), *, <italic>P</italic> &lt; 0.05. Statistical significance was calculated by Student’s t-test, mean ± SD. shNC, nonsense control-shRNA.</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S1</title><p>The list of mRNA m<sup>5</sup>C sites in HCC.</p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e231\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0120\" fn-type=\"supplementary-material\"><p id=\"p0170\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.09.007\" id=\"ir015\">https://doi.org/10.1016/j.gpb.2022.09.007</ext-link>.</p></fn></fn-group>" ]
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{ "acronym": [], "definition": [] }
40
CC BY
no
2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Aug 30; 21(4):823-833
oa_package/a3/d5/PMC10787115.tar.gz
PMC10787120
35550876
[ "<title>Introduction</title>", "<p id=\"p0005\">In eukaryotes, sexual reproduction consists of two sequential events: haploid gametes fusing to form diploid zygotes after fertilization and diploid zygotes producing haploid progenies by meiosis ##REF##23449590##[1]##. Unlike animals and plants, the unicellular green alga <italic>Chlamydomonas reinhardtii</italic> (hereafter <italic>Chlamydomonas</italic>) has unicellular haploid and diploid bodies like the gametophytes and sporophytes of land plants, respectively ##REF##23449590##[1]##, ##REF##31368133##[2]##, ##REF##11641281##[3]##. <italic>Chlamydomonas</italic> is known as “Green Yeast”, and it has been introduced as a model organism to study fundamental processes such as photosynthesis, nutrient metabolism, flagella biology, cell cycle, and sexual reproduction ##REF##17932292##[4]##, ##REF##19264963##[5]##, ##REF##25752440##[6]##, ##REF##25690512##[7]##, ##REF##22715041##[8]##, ##REF##30382941##[9]##, ##UREF##0##[10]##. Because <italic>Chlamydomonas</italic> possesses both animal and plant features, studying the cell cycle and sexual reproduction of <italic>Chlamydomonas</italic> can yield important insights into evolution ##REF##23449590##[1]##. Many studies have shown that its mitotic cell cycle has a long G1 phase and rapidly alternating S/M phases, which allow <italic>Chlamydomonas</italic> to produce 2<sup><italic>n</italic></sup> (<italic>n</italic> = 1–5) daughter cells in one cell cycle ##REF##25690512##[7]##, ##REF##26475866##[11]##. In <italic>Chlamydomonas</italic>, the cell cycle is mainly controlled by two major cyclin-dependent kinases (CDKs), namely CDKA1 and CDKB1 ##REF##18421551##[12]##, ##REF##33909603##[13]##, and other critical proteins reported previously ##REF##25690512##[7]##. The <italic>Chlamydomonas</italic> vegetative cells can be induced by nitrogen deficiency to produce two kinds of isogametes: mating type minus (mt−) and mating type plus (mt+) ##REF##17643326##[14]##; further, many mating type-specific genes are induced during this process ##REF##9215892##[15]##, ##REF##18487630##[16]##, ##REF##18510927##[17]##. Gamete-specific agglutinins encoded by the mt+-specific gene (<italic>SAG1</italic>) and the mt−-specific gene (<italic>SAD1</italic>) facilitate the interactions between two different mating type gametes ##REF##15659633##[18]##. Different mating type gametes adhere together to initiate the zygote formation process, which includes increased cAMP levels as a signal, flagellar tip activation, loss of the cell wall, and mating structure activation accompanied by actin polymerization ##REF##28235200##[19]##, ##REF##20335357##[20]##, ##REF##12808049##[21]##, ##REF##2824527##[22]##. After clumping together, the mating type-specific structures are formed, and this process is controlled by gamete fusion protein 1 (FUS1) in mt+ gametes and hapless 2 (HAP2)/generative cell specific 1 (GCS1) in mt− gametes, respectively ##REF##12808049##[21]##, ##REF##25655701##[23]##. Simultaneously, the expression of zygote-specific genes such as <italic>early zygote expressed</italic> (<italic>EZY</italic>) genes is up-regulated ##REF##26450704##[24]##, and the transcription factors gamete-specific homeodomain protein (GSP1) in mt+ gametes and gamete-specific minus 1 (GSM1) in mt− gametes accumulate to regulate the transition from haploid cells to the diploid zygotes ##REF##31368133##[2]##, ##REF##11641281##[3]##, ##REF##22715041##[8]##, ##REF##18510927##[17]##.</p>", "<p id=\"p0010\">In eukaryotes, RNA modifications are crucial for the fate determination of RNA ##REF##28622506##[25]##. As the most prevalent regulator found within eukaryotic mRNAs, m<sup>6</sup>A modification is involved in mRNA alternative splicing, nuclear export, stability, translation, and degradation ##REF##26876937##[26]##, ##REF##28984244##[27]##, ##REF##27558897##[28]##, ##REF##24284625##[29]##, ##REF##28106072##[30]##, ##REF##28106076##[31]##. In mammals, m<sup>6</sup>A modification is catalyzed by a large RNA methyltransferase complex (MTase) as writer proteins, which is composed of methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14), Wilms’ tumor 1-associating protein (WTAP), virilizer like m<sup>6</sup>A methyltransferase associated protein (VIRMA), Casitas B-lineage lymphoma-transforming sequence-like protein 1 (CBLL1, also known as HAKAI), RNA-binding protein 15/15B (RBM15/15B), and zinc finger CCCH domain-containing protein 13 (ZC3H13) ##REF##29789545##[32]##, ##REF##31100245##[33]##, ##REF##9409616##[34]##, ##REF##24407421##[35]##, ##REF##24316715##[36]##, ##REF##29507755##[37]##, ##REF##29535189##[38]##, ##REF##11836526##[39]##. The removal of methyl groups is performed by two RNA demethylases that act as eraser proteins: alkylated DNA repair protein alkB homolog 5 (ALKBH5) and fat mass and obesity-associated protein (FTO) ##REF##17434869##[40]##, ##REF##22002720##[41]##, ##REF##23177736##[42]##. Furthermore, the functions of m<sup>6</sup>A modification in mammalian mRNA metabolic processes mainly depend on diverse reader proteins, including YTH domain-containing family (YTHDF1–3 and YTHDC1–2), heterogeneous nuclear ribonucleoproteins (HNRNPC, HNRNPG, and HNRNPA2B1), and IGF2 mRNA binding protein family (IGF2BP1–3) ##REF##26876937##[26]##, ##REF##24284625##[29]##, ##REF##28106072##[30]##, ##REF##26321680##[43]##, ##REF##28809393##[44]##, ##REF##25719671##[45]##, ##REF##26046440##[46]##. Malfunctions of these proteins cause disorders in m<sup>6</sup>A modification and further affect spermatogenesis and embryo development in animals ##REF##23177736##[42]##, ##REF##25569111##[47]##, ##REF##29799838##[48]##, ##UREF##1##[49]##. Consistently, m<sup>6</sup>A modification is also detected in plants, and their counterparts of animal writers, erasers, and readers have also been identified to play critical roles ##REF##31748418##[50]##, ##REF##33515769##[51]##, ##REF##33515768##[52]##. Functional studies have shown that m<sup>6</sup>A is also important for embryo development and sporogenesis in plants ##REF##31748418##[50]##, ##REF##18505803##[53]##, ##REF##31863849##[54]##, ##REF##31116744##[55]##, ##REF##31387610##[56]##. These findings suggest that m<sup>6</sup>A modification may have critical conserved roles in the sexual reproduction of mammals and plants ##REF##23177736##[42]##, ##UREF##1##[49]##, ##REF##18505803##[53]##. However, whether and how m<sup>6</sup>A modification is involved in sexual reproduction and life cycle regulation of <italic>Chlamydomonas</italic> remains unknown.</p>", "<p id=\"p0015\">Here, we first performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) to depict the m<sup>6</sup>A modification landscapes on six samples (mt+ vegetative cells, mt− vegetative cells, mt+ gametes, mt− gametes, zygotes at day 1, and zygotes at day 7) during the sexual life cycle of <italic>Chlamydomonas</italic> with two biological replicates, and RNA sequencing (RNA-seq) was conducted simultaneously to analyze the associated transcriptional variation. The results show that m<sup>6</sup>A peaks appear widely in <italic>Chlamydomonas</italic> mRNAs, while m<sup>6</sup>A peaks are mainly enriched in the 3′ untranslated regions (3′UTRs) of mRNAs. DRAC (where D represents G/A/U, R represents A/G, and A represents m<sup>6</sup>A) is the main motif of the m<sup>6</sup>A modification peak that occurs among different stages. Moreover, the combined analyses of MeRIP-seq and RNA-seq show that <italic>Chlamydomonas</italic> m<sup>6</sup>A modification is negatively correlated with the abundance of transcripts. In particular, the genes involved in the microtubule-associated pathway display significantly negative correlations between gene expression and m<sup>6</sup>A modification level, suggesting that m<sup>6</sup>A modification regulates microtubule-based movement during sexual reproduction in the <italic>Chlamydomonas</italic> life cycle. Finally, CrMETTL3 and CrMETTL14 are potential m<sup>6</sup>A methyltransferases responsible for m<sup>6</sup>A formation in <italic>Chlamydomonas</italic>. Overall, our findings reveal the distribution of m<sup>6</sup>A modification and its potential regulatory functions during sexual reproduction and the life cycle of <italic>Chlamydomonas</italic>.</p>" ]
[ "<title>Materials and methods</title>", "<title>Strains and growth conditions</title>", "<p id=\"p0090\"><italic>Chlamydomonas</italic> strains CC-620 and CC-621 were cultivated on a solid TAP medium with photoperiod 12 h light/12 h dark, 22 °C, 50 μmol photons·m<sup>−2</sup>·s<sup>−1</sup>. The cells were resuspended in 60 ml TAP liquid medium with 4–6 × 10<sup>7</sup> cells per ml for further sample collection.</p>", "<title>Sample preparation</title>", "<p id=\"p0095\">Sample preparation was performed as described previously ##REF##26450704##[24]## with slight modifications. Fifteen milliliter <italic>Chlamydomonas</italic> cell suspensions were collected as vegetative cell samples after 2 h under light. The remaining cells were resuspended in 45-ml TAP-N medium, and 15 ml of the cells were harvested as gamete cells after culturing in the light for 21 h, while the remaining 30-ml cells were resuspended in ultrapure water. After being shaken slowly for 30 min under low light, the two strains were mixed in equal amounts and placed under normal light for 2 h to complete the mating. The cell mating status was confirmed by optical microscopic inspection. The zygotes were transferred to a TAP medium containing 3% agar, and half of the cells were collected as a 1d zygote sample after 1 day in the light, while the remaining half was placed in the dark for 6 days and collected as a 7d zygote sample. Before collecting the zygote samples, the lawn on the solid agar surface with vegetative cells was scraped off with a spatula, and the zygotes were collected with a scalpel and resuspended in Tris-EDTA-NaCl (TEN) buffer with 0.2% (v/v) Nonidet P-40 (NP-40) to remove the remaining vegetative cells. After that, the zygotes were collected by centrifugation and resuspended in TEN buffer as previously described.</p>", "<title>Total RNA isolation and mRNA purification</title>", "<p id=\"p0100\">Total RNA was isolated using Trizol (Catalog Nos. 15596026 and 15596018, Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. The mRNA of <italic>Chlamydomonas</italic> was twice purified using a Dynabeads mRNA Purification Kit (Catalog No. 61006, Ambion, Carlsbad, CA) according to the manufacturer’s instruction to remove the ribosomal RNA as much as possible.</p>", "<title>m<sup>6</sup>A dot-blot assay</title>", "<p id=\"p0105\">An m<sup>6</sup>A dot-blot was performed as described previously ##REF##22002720##[41]## with slight modifications. Briefly, the mRNA was serially diluted and loaded as follows: 200 ng, 100 ng, 50 ng, and 25 ng. The mRNA was denatured at 70 °C for 3 min and transferred to a GE Amersham hybond-N<sup>+</sup> membrane (Catalog No. RPN303B, GE Healthcare, Buckinghamshire, UK) using bio-dot apparatus and a vacuum pump. The mRNA was cross-linked under UV light for 3 min, and the membrane was blocked in PBST with 5% skim milk for 1 h. The membrane with mRNA samples was incubated with a diluted anti-m<sup>6</sup>A antibody in PBST with 5% skim milk overnight. The membrane with mRNA samples was washed with PBST three times for 5 min each time, followed by incubating with the diluted goat anti-rabbit secondary antibody in PBST with 5% skim milk for 1 h. After washing with PBST three times, the membrane with mRNA samples was incubated with enhanced chemiluminescence (ECL) prime Western blotting detection reagent (Catalog No. RPN2232, GE Healthcare) for 1 min and was exposed to film. The membrane with mRNA samples was stained with methylene blue to check the loading amounts.</p>", "<title>MeRIP-seq</title>", "<p id=\"p0110\">m<sup>6</sup>A MeRIP-seq was performed following a previously reported protocol ##REF##33510134##[79]##. The 500 ng of purified mRNA was fragmented to a size of about 200 nt using a fragmentation reagent (Catalog No. AM8740, Life Technologies, New York, NY). A total of 30 μl of protein A magnetic beads (Catalog No. 10002D, ThermoFisher Scientific, Waltham, MA) was washed with 1 ml IP buffer [150 mM NaCl, 10 mM Tris-HCl (pH 7.5), 0.1% NP-40 in nuclease-free H<sub>2</sub>O] twice, then resuspended in 500 μl IP buffer with 5 μg anti-m<sup>6</sup>A antibody (Catalog No. ABE572, Millipore, Burlington, MA) mixed in and incubated for at least 6 h at 4 °C with gentle rotation. After two washes with IP buffer [10 mM Tris-HCl (pH 7.4), 150 mM NaCl, and 0.1% NP-40 in DEPC-treated], the mixture of antibodies and beads was resuspended in 500 μl of the IP buffer mixed with 500 ng fragmented mRNA and 5 μl of RNasin plus Rnase inhibitor (Catalog No. N2611, Promega, Madison, WI), which was incubated for 2 h at 4 °C. The beads were then washed twice with 1 ml each of a low-salt IPP buffer [10 mM Tris-HCl (pH 7.5), 50 mM NaCl, 0.1% NP-40 in nuclease-free H<sub>2</sub>O] and a high-salt buffer [10 mM Tris-HCl (pH 7.5), 500 mM NaCl, 0.1% NP-40 in nuclease-free H<sub>2</sub>O] for 10 min at 4 °C. Then, the beads were eluted with 300 μl IPP buffer with 0.5 mg/ml <italic>N</italic><sup>6</sup>-methyladenosine and RNasin with gentle rotation at room temperature for 1 h. The m<sup>6</sup>A-modified RNAs were eluted with 200 μl of RLT buffer supplied in the RNeasy mini kit (Catalog No. 74106, Qiagen, Hilden, Germany) for 2 min at room temperature. The supernatant was collected in a new tube, and 400 μl of absolute ethanol was added. The mixture was then applied to an RNeasy spin column and centrifuged at 13,000 r/min at 4 °C for 30 s. The spin-column was then washed with 500 μl of RPE buffer supplied in the RNeasy mini kit, and then 500 μl of 80% ethanol, before it was centrifuged at full speed for 5 min at 4 °C to dry the column. The m<sup>6</sup>A-modified RNAs were eluted using 10 μl of nuclease-free H<sub>2</sub>O. For the second round of IP, the eluted RNA was re-incubated using new protein A magnetic beads prepared with a new anti-m<sup>6</sup>A antibody, followed by washing, elution, and purification as described above. The purified RNAs were used for library construction using the KAPA standard RNA-Seq kit (Catalog No. KR1139, KAPA, Boston, MA). The libraries were amplified by PCR for 8–12 cycles and size-selected on an 8% TBE gel. Sequencing was carried out by the Illumina Nova 6000 platform.</p>", "<title>Sequencing data analysis</title>", "<p id=\"p0115\">Pair-end reads with a length of 150 bp were generated by MeRIP-seq and RNA-seq. Cutadapt (version 1.16) ##UREF##2##[80]## software and Trimmomatic (version 0.33) ##REF##24695404##[81]## were used to trim adapters and low-quality sequences for raw reads. The remaining reads were aligned to the <italic>Chlamydomonas</italic> genome (version 5.6 for assembly; Phytozome version 12 for gene annotation) using Hisat2 (version 2.0.5) ##REF##25751142##[82]##. Only uniquely mapped reads with mapping quality scores ≥ 20 were used for the subsequent analysis. The number of reads mapped to genes (Phytozome version 12) was counted using the software featureCounts (version 1.6.2) ##REF##24227677##[83]##. The genes with reads per kilobase per million mapped reads (RPKM) &gt; 1 in both replicates as the expressed genes. For MeRIP-seq, the replicates were merged for calling m<sup>6</sup>A peak using R package exomePeak ##REF##24979058##[84]##, with the corresponding input samples serving as control. The software BEDTools’ intersectBed (version 2.28.0) ##REF##20110278##[85]## was used to annotate each m<sup>6</sup>A peak based on the gene annotation information.</p>", "<title>Statistical analysis of DEGs and GO analysis</title>", "<p id=\"p0120\">DEGs among different samples were determined using the R package edgeR ##REF##19910308##[86]##. Transcripts with |log<sub>2</sub> fold change| &gt; 1 and FDR &lt; 0.01 were considered DEGs. GO analysis of a specific gene set was performed using agriGO ##REF##28472432##[87]## (<ext-link ext-link-type=\"uri\" xlink:href=\"https://systemsbiology.cau.edu.cn/agriGOv2/\" id=\"ir010\">https://systemsbiology.cau.edu.cn/agriGOv2/</ext-link>). GO terms with <italic>P</italic> &lt; 0.05 were considered statistically significant.</p>", "<title>Identification of differential m<sup>6</sup>A peaks and motifs within m<sup>6</sup>A peaks</title>", "<p id=\"p0125\">To identify the differential m<sup>6</sup>A peaks, we calculated the fold change of enrichment between different stages and calculated the differential significance using the reads mapped to IP and input from each sample ##REF##26404942##[88]##. The peaks with |log<sub>2</sub> fold change| &gt; log<sub>2</sub> 1.5 and <italic>P</italic> &lt; 0.05 (chi-square test) were considered as differential peaks. HOMER (version 4.7) ##REF##20513432##[89]## was used to identify the motif enriched by m<sup>6</sup>A peaks, and the motif length was limited to 5 nt. The peaks annotated to mRNA were considered target sequences, and the background sequences were constructed by randomly perturbing these peaks using shuffleBed from BEDTools (version 2.28.0) ##REF##20110278##[85]##.</p>", "<title>qRT-PCR analysis</title>", "<p id=\"p0130\">RevertAid first strand cDNA synthesis kit (Catalog No. K1622, ThermoFisher Scientific) was applied to generate cDNA templates by reverse transcription. The TB green premix Ex taq (Catalog No. RR420A, TaKaRa, Kyoto, Japan) was used in the qRT-PCR reaction, and the qRT-PCR was carried out using LightCycler480 (Roche). The <italic>guanine nucleotide-binding protein beta subunit-like</italic> (<italic>CBLP</italic>, Cre06.g278222) gene was used as the internal control. The calculation of relative mRNA expression was performed as described previously ##REF##24034412##[90]##.</p>" ]
[ "<title>Results</title>", "<title>Features of critical periods during the <italic>Chlamydomonas</italic> life cycle</title>", "<p id=\"p0020\">To examine the dynamics of m<sup>6</sup>A modification during sexual reproduction of the <italic>Chlamydomonas</italic> life cycle, six samples from key periods, including mt+ vegetative cells, mt− vegetative cells, mt+ gametes, mt− gametes, zygotes at day 1  (1d zygotes), and zygotes at day 7  (7d zygotes), were collected for MeRIP-seq analysis (##FIG##0##Figure 1##A). During asexual reproduction, cells mainly undertake vegetative growth and mitosis, and the vegetative cells at this stage have classical morphological characteristics: diameters of around 5–7 μm, with two flagella, one cup-shaped chloroplast, an eyespot, a nucleus, and other organelles (##FIG##0##Figure 1##B). The vegetative cells can be induced to form gametes by nitrogen starvation or blue light, which is called gametogenesis ##REF##12223870##[57]##. The gametogenesis of <italic>Chlamydomonas</italic> is presumed to be a stress response, as the gametes show high motility and low photosynthetic activity. It should be noted that gametes are much smaller than vegetative cells (##FIG##0##Figure 1##C). When induced gametes of the opposite mating types are mixed together to form zygotes, the mating responses are triggered rapidly, followed by the adhesion of mating type-specific agglutinins on the surface of flagella ##REF##11950949##[58]##. Compared with the vegetative cells, zygotes without flagella are larger with thicker cell walls (##FIG##0##Figure 1##D and E). After 1 day in the light and 6 days in the dark, the zygote develops into a zygospore, which is more resistant to various stresses. In favorable environments, the zygospores germinate, and meiosis produces haploid vegetative cells.</p>", "<title><bold>m<sup>6</sup>A</bold> modification changes dynamically during the sexual reproduction of <bold><italic>Chlamydomonas</italic></bold></title>", "<p id=\"p0025\">RNA m<sup>6</sup>A modification is critical for the sexual reproduction of mammals and plants ##REF##23177736##[42]##, ##REF##25569111##[47]##, ##REF##29799838##[48]##, ##UREF##1##[49]##, ##REF##18505803##[53]##, ##REF##15047892##[59]##. To examine the levels of m<sup>6</sup>A modification during sexual reproduction in the <italic>Chlamydomonas</italic> life cycle, a dot-blot assay was performed at different stages as described above. The results showed that m<sup>6</sup>A modification was down-regulated during gametogenesis and up-regulated in zygote development, especially in mt+ samples (##FIG##1##Figure 2##A). Based on the presence of predicted RNA adenosine methylase domains (MT-A70) and full-length human METTL3 and METTL14 protein sequences, four candidate <italic>Chlamydomonas</italic> m<sup>6</sup>A methyltransferases were found in the <italic>Chlamydomonas</italic> phytozome (<ext-link ext-link-type=\"uri\" xlink:href=\"https://phytozome-next.jgi.doe.gov/\" id=\"ir005\">https://phytozome-next.jgi.doe.gov/</ext-link>), namely CrMETTL3 (Cre06.g295600), CrMETTL14 (Cre01.g050600), CrMT1 (Cre06.g288100), and CrMT2 (Cre10.g452300) (##FIG##1##Figure 2##B). Among them, CrMT1 and CrMT2 showed lower homology to human METTL3 and METTL14 overall. Quantitative real-time PCR (qRT-PCR) showed that <italic>CrMETTL3</italic> and <italic>CrMETTL14</italic> expression levels consistently declined in gametes with different mating types, increased in 1d zygotes, and then declined again in 7d zygotes (##FIG##1##Figure 2##C), suggesting that m<sup>6</sup>A modification may participate in regulating sexual reproduction and changes dynamically in <italic>Chlamydomonas</italic>.</p>", "<title>Overview of the <bold>m<sup>6</sup></bold>A methylome in <bold><italic>Chlamydomonas</italic></bold></title>", "<p id=\"p0030\">To study the potential role of m<sup>6</sup>A modification in regulating <italic>Chlamydomonas</italic> sexual reproduction, MeRIP-seq was performed on the samples from different stages to compare their transcriptome-wide m<sup>6</sup>A methylomes. Pearson correlation analysis suggested good reproducibility among each group (<xref rid=\"s0115\" ref-type=\"sec\">Figure S1</xref>A and B). Further analysis revealed 24,416, 25,656, 23,288, 23,836, 24,403, and 25,057 m<sup>6</sup>A peaks within 13,255, 13,367, 12,969, 13,313, 13,564, and 13,720 transcripts from mt+ vegetative cells, mt+ gametes, mt− vegetative cells, mt− gametes, 1d zygotes, and 7d zygotes, respectively (##FIG##2##Figure 3##A; <xref rid=\"s0115\" ref-type=\"sec\">Table S1</xref>). The distribution pattern of m<sup>6</sup>A modification along the transcripts was analyzed, and the results of metagene profiles revealed that m<sup>6</sup>A deposition was primarily enriched in the 3′ UTR (##FIG##2##Figure 3##B), which is interestingly consistent with the m<sup>6</sup>A distribution patterns in rice, potato, and maize ##REF##31116744##[55]##, ##REF##34294912##[60]##, ##REF##33016611##[61]##. We then analyzed the distribution of m<sup>6</sup>A peaks within three non-overlapping regions: 5′ UTR, coding sequence (CDS), and 3′ UTR. Among them, m<sup>6</sup>A peaks appeared to be greatly enriched in the 3′ UTR segment (##FIG##2##Figure 3##C), with 73%–76% of the peaks falling into this region. Furthermore, the distribution density plot of m<sup>6</sup>A peaks across the exon length showed that m<sup>6</sup>A peaks tend to occur within exons around 760 bp in length (##FIG##2##Figure 3##D), indicating that the m<sup>6</sup>A modification tends to be catalyzed on long exons while the average length of exons in <italic>Chlamydomonas</italic> is 376.62 bp.</p>", "<p id=\"p0035\">To identify the consensus sequence and enrichment of m<sup>6</sup>A peaks appearing in the transcriptome, HOMER was used to conduct a motif search of high-confidence m<sup>6</sup>A peaks. The DRAC motif (##FIG##2##Figure 3##E), which is a conserved m<sup>6</sup>A motif found in <italic>Arabidopsis</italic>\n##REF##31748418##[50]##, ##REF##25430002##[62]## and other eukaryotes ##REF##22575960##[63]##, was identified in all of the detected stages, including vegetative cells, gametes, and 1d and 7d zygotes. We next compared the transcriptome-wide m<sup>6</sup>A methylome during sexual reproduction. We found that 11,915 m<sup>6</sup>A-modified genes were shared among mt+ vegetative cells, mt+ gametes, and 1d zygotes, and 11,739 m<sup>6</sup>A-modified genes were shared among mt− vegetative cells, mt− gametes, and 1d zygotes (##FIG##2##Figure 3##F and G). Less than 10% of the specific m<sup>6</sup>A-modified genes were detected in all stages. To further analyze the regulatory mechanisms of m<sup>6</sup>A modification during sexual reproduction, we then performed a Gene Ontology (GO) analysis of the genes with m<sup>6</sup>A modifications. The commonly m<sup>6</sup>A-modified genes in mt+ vegetative cells, mt+ gametes, and 1d zygotes were enriched in the primary metabolic process, transmembrane transport, and RNA processing (##FIG##2##Figure 3##H), implying that m<sup>6</sup>A is essential for basic life activities in <italic>Chlamydomonas</italic>. m<sup>6</sup>A modification was also found to be related to the microtubule-based process and photosynthesis, which influence gametogenesis and zygote development during sexual reproduction. Interestingly, the processes enriched by common m<sup>6</sup>A-modified genes in mt− vegetative cells, mt− gametes, and 1d zygotes were similar to the previous findings in mt+ cells (##FIG##2##Figure 3##I). Genes with specific m<sup>6</sup>A methylation at various stages were related to proteolysis and DNA metabolic process (##FIG##2##Figure 3##H and I), indicating that m<sup>6</sup>A methylation generally appears in various stages and is involved in the regulation of important processes during the sexual reproduction of <italic>Chlamydomonas</italic>.</p>", "<title><bold>m<sup>6</sup>A</bold> modification is generally negatively correlated with gene expression level</title>", "<p id=\"p0040\">m<sup>6</sup>A has been proven to regulate the stability of mRNA ##REF##24284625##[29]##, ##REF##27396363##[64]##, ##REF##29180595##[65]##. According to the findings of the m<sup>6</sup>A methylome at different stages, we further examined the gene expression level to investigate the role of m<sup>6</sup>A regulation in mRNA abundance during sexual reproduction. We determined mRNA abundance as previously described and obtained a transcriptome-wide RNA expression map with a strong correlation between biological replicates (##FIG##3##Figure 4##A, Figure <xref rid=\"s0115\" ref-type=\"sec\">S2A</xref>). Briefly, 12,465, 11,043, 13,229, 11,166, 13,241, and 13,347 stably expressed transcripts were obtained from mt+ vegetative cells, mt+ gametes, mt− vegetative cells, mt− gametes, 1d zygotes, and 7d zygotes, respectively (##FIG##3##Figure 4##B; <xref rid=\"s0115\" ref-type=\"sec\">Table S2</xref>). The expression of some stage-specific genes was also determined (<xref rid=\"s0115\" ref-type=\"sec\">Figure S2</xref>B and C), including the well-known <italic>GSP1</italic> (Cre02.g109650) and <italic>GSM1</italic> (Cre08.g375400), which encode transcription factors specifically expressed in mt+ and mt− gametes, respectively, and are involved in the development of zygotes ##REF##9215892##[15]##, ##REF##18487630##[16]##, ##REF##18510927##[17]##. Moreover, early zygote-specific genes were also identified, including <italic>early zygote expressed 9</italic> (<italic>EZY9</italic>, Cre06.g304500), <italic>zygote-specific 2</italic> (<italic>ZYS2/MAW1</italic>, Cre07.g325812), and <italic>early zygote expressed 3</italic> (<italic>EZY3</italic>, Cre11.g482650), in 1d zygotes ##REF##26450704##[24]##.</p>", "<p id=\"p0045\">We next analyzed the differentially expressed genes (DEGs) to investigate the transcriptional changes during sexual reproduction. A total of 7645 and 7640 transcripts were differentially expressed (|log<sub>2</sub> fold change| &gt; 1; FDR &lt; 0.01) between vegetative cells and gametes with mt+ and mt−, respectively (##FIG##3##Figure 4##C; <xref rid=\"s0115\" ref-type=\"sec\">Table S3</xref>), among which 4048 and 4235 genes were down-regulated in mt+ and mt− gametes, respectively. Additionally, we identified 8525 DEGs between mt+ gametes and 1d zygotes, and 8701 genes between mt− gametes and 1d zygotes. Among them, 4675 and 4418 genes exhibited higher expression levels in 1d zygotes than in mt+ and mt− gametes, respectively. We next compared the DEGs between mt+ and mt−. The results (<xref rid=\"s0115\" ref-type=\"sec\">Figure S2</xref>D) showed that more than 60% of DEGs were shared between the mating types during transitions from vegetative cells to gametes and from gametes to zygotes.</p>", "<p id=\"p0050\">To study the relationship between the changes in mRNA abundance and m<sup>6</sup>A methylation, the m<sup>6</sup>A-modified genes were classified into three subgroups: genes with increased methylation levels, decreased methylation levels, and stable methylation levels during the reproduction. In the process of mt+ vegetative cells transitioning to mt+ gametes, genes were divided into three types, including up-m<sup>6</sup>A, down-m<sup>6</sup>A, and stable-m<sup>6</sup>A subgroups, respectively, based on the m<sup>6</sup>A changes in mt+ gametes. The mRNA abundance changes in these three subgroups showed greatly contrasting variability. Compared with stable-m<sup>6</sup>A genes, the mRNA abundance of up-m<sup>6</sup>A genes in mt+ gametes tend to be down-regulated, while down-m<sup>6</sup>A genes generally exhibit significantly higher mRNA abundance (##FIG##3##Figure 4##D, left). These results suggested that mRNA abundance is negatively regulated by m<sup>6</sup>A methylation in the mt+ gametogenesis. The negative correlation between m<sup>6</sup>A and mRNA abundance was also observed in other samples from different stages, including mt− gametogenesis (##FIG##3##Figure 4##E, left), mt+ gametes transitioning to 1d zygotes (##FIG##3##Figure 4##D, right), and mt− gametes transitioning to 1d zygotes (##FIG##3##Figure 4##E, right), suggesting that m<sup>6</sup>A modification negatively regulate mRNA abundance during the sexual reproduction of <italic>Chlamydomonas</italic>.</p>", "<title><bold>m<sup>6</sup>A</bold> is involved in the sexual reproduction by regulating microtubule-based movement</title>", "<p id=\"p0055\">To further explore the role of m<sup>6</sup>A in sexual reproduction, we investigated biological processes related to sexual reproduction and analyzed whether m<sup>6</sup>A could negatively regulate the expression levels of key genes involved. GO analyses showed that most down-regulated genes during mt+ and mt− gametogenesis were enriched in photosynthesis-associated processes (<xref rid=\"s0115\" ref-type=\"sec\">Figure S3</xref>A and C). We speculate that vegetative cells need to reduce photosynthesis in response to nitrogen starvation and undergo gametogenesis. Most up-regulated genes from mt+ vegetative cells transitioning to mt+ gametes were specifically enriched in the microtubule-based process and cilium organization (##FIG##4##Figure 5##A). Previous research has reported that genes associated with microtubule-based processes encode kinesin and dynein proteins, which mediate the intraflagellar transport system, allowing agglutinins to be transported to flagellar membrane surfaces, and are also involved in flagellum assembly to regulate gametogenesis ##REF##11950949##[58]##, ##REF##9585417##[66]##, ##REF##11580207##[67]##. Proteomic analysis of male and female <italic>Plasmodium</italic> gametocytes reveals that kinesin and dynein are proteins expressed in a sex-specific manner ##REF##15935755##[68]##. Among the specifically up-regulated genes related to the microtubule-based process in mt+ gametes (##FIG##4##Figure 5##B), <italic>kinesin motor protein 9-3</italic> (<italic>KIN9-3</italic>, Cre10.g427750), which encodes a kinesin protein, had a significantly lower m<sup>6</sup>A methylation level, indicating that <italic>KIN9-3</italic> is involved in flagellar assembly and associated with sex-specific flagellum formation during mt+ gametogenesis ##REF##31409625##[69]##. In addition, qRT-PCR analysis showed a up-regulated trend of <italic>KIN9-3</italic>, <italic>dynein heavy chain 1</italic> (<italic>DHC1</italic>, Cre12.g484250), and <italic>dynein heavy chain 8</italic> (<italic>DHC8</italic>, Cre16.g685450) (##FIG##4##Figure 5##C).</p>", "<p id=\"p0060\">After the fusion of gametes, a period of light exposure ensures zygote formation and maturation. We detected a global increase in the expression levels of photosynthesis-associated genes in the transition of mt+ and mt− gametes to zygotes, indicating that diploid zygotes may gain energy through photosynthesis (<xref rid=\"s0115\" ref-type=\"sec\">Figure S3</xref>B and C). More interestingly, we found that genes with lower expression in zygotes in both mt+ and mt− gametes participate in the microtubule-based process, movement of cell or cellular component, and cilium assembly, indicating that reduced motility in mature zygotes (##FIG##4##Figure 5##D and E). The identified down-regulated microtubule-related genes with higher m<sup>6</sup>A modification levels are considered candidate genes regulated by m<sup>6</sup>A during the zygotes formation. Among them, <italic>DHC1</italic>, <italic>DHC8, dynein heavy chain 10</italic> (<italic>DHC10</italic>, Cre14.g624950), and <italic>kinesin motor protein 8-1</italic> (<italic>KIN8-1</italic>, Cre13.g602400)<italic>,</italic> as the key genes in the microtubule-based process, were further verified (##FIG##4##Figure 5##F) ##REF##21953912##[70]##. These results suggest that KINs and DHCs are critical for fulfilling sexual reproduction in <italic>Chlamydomonas</italic>.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0065\">As the most prevalent mRNA modification in eukaryotes ##REF##27808276##[71]##, m<sup>6</sup>A modification is involved in many essential biological processes, including cell fate determination ##REF##25569111##[47]##, ##REF##25683224##[72]## and embryo development ##REF##25569111##[47]##, ##REF##28192787##[73]##. In addition, m<sup>6</sup>A modification is important during embryo development and sporogenesis in plants ##REF##18505803##[53]##, ##REF##15047892##[59]##. These findings suggest that m<sup>6</sup>A modulation of mRNA expression may play important roles in the sexual reproduction of both animals and plants. <italic>Chlamydomonas</italic> is an excellent model organism for studying sexual reproduction and life cycle, because it has both characteristics of plants and animals ##REF##17932292##[4]##. However, the role and function of m<sup>6</sup>A during this process in <italic>Chlamydomonas</italic> have remained unclear.</p>", "<p id=\"p0070\">During sexual reproduction and the life cycle of <italic>Chlamydomonas</italic>, the cells undergo the transition from a haploid phase to a diploid phase. The vegetative cells and gametes are haploid, while zygotes are diploid. In this study, we performed MeRIP-seq on six samples with duplicates from different stages of <italic>Chlamydomonas</italic> sexual reproduction and life cycle, and compared their transcriptome-wide m<sup>6</sup>A methylomes. Our analyses reveal that m<sup>6</sup>A peaks are markedly enriched in the 3′ UTR, and the distribution pattern of m<sup>6</sup>A is similar among all of the samples. Interestingly, the most enriched sequence motif identified within m<sup>6</sup>A peaks is DRAC, but not the canonical RNA motif of RRACH ##REF##22575960##[63]##. The DRAC motif is similar to those characterized in <italic>Arabidopsis</italic> and other eukaryotes. Moreover, by combining MeRIP-seq and RNA-seq, we discovered that the m<sup>6</sup>A level is generally negatively influenced by the abundance of the corresponding mRNAs. Collectively, our data reveal the dynamic changes of m<sup>6</sup>A methylation and the negative correlation between methylation levels with stage-specific transcripts during sexual reproduction and the life cycle of <italic>Chlamydomonas</italic>, suggesting a regulatory role of m<sup>6</sup>A in sexual reproduction.</p>", "<p id=\"p0075\">Previous studies have reported that kinesin and dynein are associated with microtubule-based processes and are important sex-specific expressed proteins, which mediate the intraflagellar transport system and are also involved in flagellar assembly to regulate gametogenesis ##REF##11950949##[58]##, ##REF##11580207##[67]##. In our study, the microtubule-based process and cilium organization from the transition of mt+ vegetative cells to gametes are also specifically accumulated. Among the specifically up-regulated genes in mt+ gametes, <italic>KIN9-3</italic>, <italic>DHC6</italic>, and <italic>KIN16-2</italic> show significantly lower m<sup>6</sup>A methylation levels and are closely related to the microtubule-based process during the mt+ gametogenesis. Additionally, the <italic>DHC1</italic>, <italic>DHC8, DHC10,</italic> and <italic>KIN8-1</italic> genes<italic>,</italic> with lower expression and higher m<sup>6</sup>A methylation levels in zygotes, are also involved in the microtubule-based process. These data together suggest that m<sup>6</sup>A modification potentially participates in sexual reproduction and the life cycle by regulating the abundance of transcripts involved in the microtubule-based movement. Microtubules play important roles in maintaining cell morphology, as well as promoting cell division, signal transduction, and material transport. The flagella structure of <italic>Chlamydomonas</italic> is composed of microtubules. <italic>Chlamydomonas</italic> needs to move rapidly after the generation of gametes to increase the chance of mating. The recognition between different mating types requires the participation of proteins and agglutinins. The m<sup>6</sup>A modification may negatively regulate microtubules and promote the movement of flagella, the transport of substances, and the recognition between gametes.</p>", "<p id=\"p0080\">It is noteworthy that the expression levels of photosynthetic-related genes, including those of PSI, PSII assembly and those involved in light-harvesting and the oxidation–reduction cycle, all decrease during gametogenesis (<xref rid=\"s0115\" ref-type=\"sec\">Figure S3</xref>C); this may be related to the nitrogen deficiency treatment to activate gametogenesis program. Similar results have also been observed in a previous study that showed a similar trend in GreenCut2 ##REF##26450704##[24]##, ##REF##21515685##[74]##. Limiting nitrogen leads to decreased photosynthetic activity, carbon assimilation, and chlorophyll biosynthesis in <italic>Chlamydomonas</italic>\n##REF##25515814##[75]##. The limited substrate and energy could be recycled to synthesize macromolecules required for gametogenesis ##REF##25515814##[75]##, ##REF##5088925##[76]##. In contrast, the down-regulated processes such as photosynthesis and carbohydrate metabolism occurring during the transition of vegetative cells to gametes are up-regulated after the formation of the zygotes from the fusion of gametes (<xref rid=\"s0115\" ref-type=\"sec\">Figure S3</xref>B and C). Light plays a key role in the reproductive development of <italic>Chlamydomonas</italic>. Although asexual reproduction may occur in the absence of light, sexual reproduction is entirely dependent on light signals. Photoreceptors regulate the entire process of sexual reproduction in <italic>Chlamydomonas</italic>. For instance, blue light receptors such as Phototropin and Cryptochromes control multiple processes in the sexual reproduction of <italic>Chlamydomonas</italic>. Gametogenesis and zygote germination are regulated by blue and red light, and the occurrence of zygote also requires the presence of blue light receptors ##REF##12716969##[77]##. <italic>Arabidopsis</italic> cryptochrome mediates m<sup>6</sup>A modification of more than 10% of mRNAs in the blue light-regulated transcriptome. Cryptochrome interacts with METTL3/METTL14 and promotes the deposition of m<sup>6</sup>A modifications at target genes by liquid–liquid phase separation ##REF##34650267##[78]##. Whether m<sup>6</sup>A modification during <italic>Chlamydomonas</italic> sexual reproduction is also regulated by photoreceptors and whether these photoreceptors can also regulate the entire sexual reproduction of <italic>Chlamydomonas</italic> by interacting with m<sup>6</sup>A methyltransferases remain to be further explored.</p>", "<p id=\"p0085\">Taken together, we illustrate the first epitranscriptomic RNA m<sup>6</sup>A profile during the sexual reproduction of <italic>Chlamydomonas</italic>, finding that m<sup>6</sup>A exhibits a conservative distribution pattern and is mainly enriched in the 3′ UTR. More importantly, we found a negative correlation between m<sup>6</sup>A methylation level and gene expression, while m<sup>6</sup>A is likely involved in sexual reproduction through regulating microtubule-based movement. Our study provides new insights into epigenetic regulation in the <italic>Chlamydomonas</italic> life cycle and clues for further studies of m<sup>6</sup>A modification in the evolution of animal and plant reproduction.</p>" ]
[]
[ "<p id=\"np010\">Equal contribution.</p>", "<p>The unicellular green alga <italic><bold>Chlamydomonas reinhardtii</bold></italic> (hereafter <italic>Chlamydomonas</italic>) possesses both plant and animal attributes, and it is an ideal model organism for studying fundamental processes such as <bold>photosynthesis</bold>, <bold>sexual reproduction</bold>, and life cycle. <italic><bold>N</bold></italic><sup><bold>6</bold></sup><bold>-methyladenosine</bold> (m<sup>6</sup>A) is the most prevalent mRNA modification, and it plays important roles during sexual reproduction in animals and plants. However, the pattern and function of m<sup>6</sup>A modification during the sexual reproduction of <italic>Chlamydomonas</italic> remain unknown. Here, we performed transcriptome and methylated RNA immunoprecipitation sequencing (MeRIP-seq) analyses on six samples from different stages during sexual reproduction of the <italic>Chlamydomonas</italic> life cycle<italic>.</italic> The results show that m<sup>6</sup>A modification frequently occurs at the main motif of DRAC (D = G/A/U, R = A/G) in <italic>Chlamydomonas</italic> mRNAs. Moreover, m<sup>6</sup>A peaks in <italic>Chlamydomonas</italic> mRNAs are mainly enriched in the 3′ untranslated regions (3′UTRs) and negatively correlated with the abundance of transcripts at each stage. In particular, there is a significant negative correlation between the expression levels and the m<sup>6</sup>A levels of genes involved in the <bold>microtubule-associated pathway</bold>, indicating that m<sup>6</sup>A modification influences the sexual reproduction and the life cycle of <italic>Chlamydomonas</italic> by regulating microtubule-based movement. In summary, our findings are the first to demonstrate the distribution and the functions of m<sup>6</sup>A modification in <italic>Chlamydomonas</italic> mRNAs and provide new evolutionary insights into m<sup>6</sup>A modification in the process of sexual reproduction in other plant organisms.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Jianhua Yang</p>" ]
[ "<title>Data availability</title>", "<p id=\"p0135\">The raw sequence data from RNA-seq and MeRIP-seq have been deposited in the Genome Sequence Archive ##REF##34400360##[91]## at the National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (GSA: CRA005106), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa\" id=\"ir015\">https://ngdc.cncb.ac.cn/gsa</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0140\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0145\"><bold>Ying Lv:</bold> Conceptualization, Methodology, Investigation, Writing – original draft. <bold>Fei Han:</bold> Resources, Investigation, Writing – original draft. <bold>Mengxia Liu:</bold> Software, Data curation, Writing – original draft. <bold>Ting Zhang:</bold> Methodology, Data curation. <bold>Guanshen Cui:</bold> Resources, Investigation. <bold>Jiaojiao Wang:</bold> Software, Validation. <bold>Ying Yang:</bold> Methodology, Writing – review &amp; editing. <bold>Yun-Gui Yang:</bold> Conceptualization, Writing – review &amp; editing. <bold>Wenqiang Yang:</bold> Conceptualization, Writing – review &amp; editing, Supervision. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0160\">The following are the Supplementary data to this article:</p>", "<p id=\"p0165\">\n\n</p>", "<p id=\"p0170\">\n\n</p>", "<p id=\"p0175\">\n\n</p>", "<p id=\"p0180\">\n\n</p>", "<p id=\"p0185\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0150\">This work was supported by the <funding-source id=\"gp005\">National Key R&amp;D Program of China</funding-source> (Grant Nos. 2019YFA0904600, 2018YFA0801200, and 2021YFA0910800) and the <funding-source id=\"gp010\">National Natural Science Foundation of China</funding-source> (Grant Nos. 31870217 and 91940304).</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Sexual life cycle of <italic>Chlamydomonas</italic> and the features of its critical periods</bold></p><p><bold>A</bold><bold>.</bold> Overview of the life cycle of <italic>Chlamydomonas.</italic> Vegetative cells can differentiate into gametes in response to nitrogen deficiency; zygotes can be formed from the mating of gametes with different mating types under light and eventually mature over a few days without light; mature zygotes conversely can germinate to form four daughter cell progenies from the tetrad by the addition of nitrogen and light. Image showing the life cycle at different stages. Vegetative cells (<bold>B</bold>), gametes (<bold>C</bold>), 1d zygotes (<bold>D</bold>), and 7d zygotes (<bold>E</bold>) are shown under a 400× light microscope. “−N” indicates nitrogen deficientcy.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>mRNA m<sup>6</sup>A methylation shows dynamic changes during the life cycle of <italic>Chlamydomonas</italic></bold></p><p><bold>A</bold><bold>.</bold> The overall levels of m<sup>6</sup>A mRNA modification were detected by dot-blot assays using a specific anti-m<sup>6</sup>A antibody (upper panel) and methylene blue staining to show the loading control (lower panel). <bold>B</bold><bold>.</bold> Schematic representations of the putative candidates of m<sup>6</sup>A methyltransferases in <italic>Chlamydomonas</italic>. MT-A70 represents the conserved motif. <bold>C</bold><bold>.</bold> qRT-PCR shows the relative abundance of transcripts of the putative genes encoding m<sup>6</sup>A methyltransferases in <italic>Chlamydomonas</italic>. The <italic>CBLP</italic> gene was used as the internal control. Error bars represent the standard deviation of three biological replicates. Different lowercase letters over the bars show a significant difference via one-way ANOVA followed by Tukey’s post hoc test by SPSS statistics software (<italic>P</italic> &lt; 0.05). Veg (mt+), mating type plus vegetative cell; Veg (mt−), mating type minus vegetative cell; Gam (mt+), mating type plus gamete; Gam (mt−), mating type minus gamete; Zyg (1d), 1d zygote; Zyg (7d), 7d zygote; qRT-PCR, quantitative real-time PCR.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Overview of the m<sup>6</sup>A methylome in <italic>Chlamydomonas</italic></bold></p><p><bold>A</bold><bold>.</bold> Histogram showing the numbers of the detected m<sup>6</sup>A peaks and methylated genes at each stage of the <italic>Chlamydomonas</italic> life cycle. <bold>B</bold><bold>.</bold> Metagene profiles showing the distribution of m<sup>6</sup>A peaks along the transcripts composed of three rescaled non-overlapping segments (5′ UTR, CDS, and 3′ UTR). <bold>C</bold><bold>.</bold> Stacked bar chart showing the percentage of m<sup>6</sup>A peaks within distinct RNA sequence types. <bold>D</bold><bold>.</bold> Density plot showing the distribution of m<sup>6</sup>A peaks across the length of the exon. <bold>E</bold><bold>.</bold> Top sequence motifs identified within m<sup>6</sup>A peaks. <bold>F</bold><bold>.</bold> and <bold>G</bold><bold>.</bold> Venn diagrams showing the overlap of m<sup>6</sup>A-modified genes among the mt+ vegetative cells, mt+ gametes, and 1d zygotes (F) and among the mt− vegetative cells, mt− gametes, and 1d zygotes (H), respectively. <bold>H</bold><bold>.</bold> and <bold>I.</bold> Bar plots showing the GO enrichment of commonly m<sup>6</sup>A-modified genes (left) and specifically m<sup>6</sup>A-modified genes (right) among the mt+ vegetative cells, mt+ gametes, and 1d zygotes (H) and among the mt− vegetative cells, mt− gametes, and 1d zygotes (I), respectively. UTR, untranslated region; CDS, coding sequence; GO, Gene Ontology.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>m<sup>6</sup>A modification is generally negatively correlated with gene expression level</bold></p><p><bold>A</bold><bold>.</bold> Heatmap showing the high correlation among replicates based on the expression matrix. <bold>B</bold><bold>.</bold> Histogram showing the number of genes expressed at each stage of the <italic>Chlamydomonas</italic> life cycle. <bold>C</bold><bold>.</bold> Histogram showing the number of differentially expressed (up-regulated and down-regulated) genes at different stages. <bold>D</bold><bold>.</bold> Cumulative distribution displaying the abundance changes in mRNA classified by m<sup>6</sup>A methylation level during transitions from mt+ vegetative cells to mt+ gametes (left) and from mt+ gametes to 1d zygotes (right). In the left panel, Gam (mt+) &gt; Veg (mt+) means up-m<sup>6</sup>A genes, Gam (mt+) = Veg (mt+) means stable-m<sup>6</sup>A genes, and Gam (mt+) &lt; Veg (mt+) means down-m<sup>6</sup>A genes. In the right panel, Zyg (1d) &gt; Gam (mt+), Zyg (1d) = Gam (mt+), and Zyg (1d) &lt; Gam (mt+) mean up-m<sup>6</sup>A, stable-m<sup>6</sup>A, and down-m<sup>6</sup>A genes, respectively. <bold>E</bold><bold>.</bold> Cumulative distribution displaying the abundance changes in mRNA classified by m<sup>6</sup>A methylation level during transitions from mt− vegetative cells to mt− gametes (left) and from mt− gametes to 1d zygotes (right). In the left panel, Gam (mt−) &gt; Veg (mt−) means up-m<sup>6</sup>A genes, Gam (mt−) = Veg (mt−) means stable-m6A genes, and Gam (mt−) &lt; Veg (mt−) means down-m<sup>6</sup>A genes. In the right panel, Zyg (1d) &gt; Gam (mt−), Zyg (1d) = Gam (mt−), and Zyg (1d) &lt; Gam (mt−) mean up-m<sup>6</sup>A, stable-m<sup>6</sup>A, and down-m<sup>6</sup>A genes, respectively. <italic>P</italic> values were calculated using two-sided Wilcoxon and Mann-Whitney tests. DEG, differentially expressed gene; FC, fold change.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>m<sup>6</sup>A is involved in the life cycle by regulating microtubule-based movement</bold></p><p><bold>A</bold><bold>.</bold> GO enrichment of the up-regulated genes in mt+ gametes during gametogenesis. <bold>B</bold><bold>.</bold> Heatmap of up-regulated genes associated with the microtubule-based process during gametogenesis. <bold>C</bold><bold>.</bold> qRT-PCR analysis showing the expression levels of the target genes regulated by m<sup>6</sup>A during gametogenesis. The <italic>CBLP</italic> gene was used as the internal control. Error bars represent the standard deviation of three biological replicates. n.s., not significant. <bold>D</bold><bold>.</bold> GO enrichment of the down-regulated genes in 1d zygotes during the gamete fusion process. <bold>E</bold><bold>.</bold> Heatmap of down-regulated genes associated with the microtubule-based process during the gamete fusion process. <bold>F</bold><bold>.</bold> qRT-PCR to validate the target genes regulated by m<sup>6</sup>A during gamete fusion. The <italic>CBLP</italic> gene was used as the internal control. Error bars represent the standard deviation of three biological replicates. Different lowercase letters over the bars show a significant difference via one-way ANOVA followed by Tukey’s post hoc test by SPSS statistics software (<italic>P</italic> &lt; 0.05).</p></caption></fig>", "<fig id=\"f0030\" position=\"anchor\"><label>Supplementary figure S1</label><caption><p><bold>Pearson correlation among the independent biological replicates</bold>. Pearson correlation analysis shows the high gene expression correlation among independent biological replicates in RNA-seq (A) and MeRIP-seq (B). MeRIP, methylated RNA immunoprecipitation sequencing.</p></caption></fig>", "<fig id=\"f0035\" position=\"anchor\"><label>Supplementary figure S2</label><caption><p><bold>The profiles of gene expression during the <italic>Chlamydomonas</italic> life cycle</bold>. <bold>A</bold>. PCA based on the gene expression exhibiting the high consistency among replicates. <bold>B</bold>. Heatmap showing the stage-specific expression of some of the differentially expressed genes. <bold>C</bold>. Line chart and box plot of gene expression profiles for reported gamete and zygote specific gene. <bold>D</bold>. Overlap of the upregulated and downregulated expressed genes between mating type minus and plus in the processes of vegetative cells transitioning to gametes (top) and gametes to zygotes (bottom). PCA, principal component analysis; RPKM, reads per kilobase per million mapped.</p></caption></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary figure S3</label><caption><p><bold>Biological pathways related to the Chlamydomonas life cycle. A</bold>. GO enrichment of downregulated genes in both gametes with different mating types (mt+ and mt-) during gametogenesis. <bold>B</bold>. GO enrichment of upregulated genes in 1d zygotes in the transitions of mt+ and mt- gametes to zygotes. <bold>C</bold>. The m6A modification level of photosynthesis is associated with genes during sexual reproduction. GO, gene ontology.</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S1</title><p><bold>The identified m6A peaks at different stages of life cycles</bold>.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S2</title><p><bold>Gene expression reads per kilobase per million mapped reads (RPKM) matrix</bold>.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S3</title><p><bold>The differentially expressed genes at different stages</bold>.</p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e260\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China</p></fn><fn id=\"s0110\" fn-type=\"supplementary-material\"><p id=\"p0155\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.04.004\" id=\"ir020\">https://doi.org/10.1016/j.gpb.2022.04.004</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["10"], "surname": ["Harris"], "given-names": ["E.H."], "italic": ["Chlamydomonas"], "source": ["Annu Rev Plant Phys"], "volume": ["52"], "year": ["2001"], "fpage": ["363"], "lpage": ["406"]}, {"label": ["49"], "surname": ["Fukusumi", "Naruse", "Asano"], "given-names": ["Y.", "C.", "M."], "article-title": ["Wtap is required for differentiation of endoderm and mesoderm in the mouse embryo"], "source": ["Dev Dynam"], "volume": ["237"], "year": ["2008"], "fpage": ["618"], "lpage": ["629"]}, {"label": ["80"], "surname": ["Martin"], "given-names": ["M."], "article-title": ["Cutadapt removes adapter sequences from high-throughput sequencing reads"], "source": ["EMBnet J"], "volume": ["17"], "year": ["2017"], "fpage": ["10"], "lpage": ["12"]}]
{ "acronym": [], "definition": [] }
91
CC BY
no
2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Aug 10; 21(4):756-768
oa_package/91/0d/PMC10787120.tar.gz
PMC10787122
35835441
[ "<title>Introduction</title>", "<p id=\"p0005\">Gene expression and cell growth are not only controlled by genetics but also closely related to epigenetic regulation, such as chemical modifications of RNA. The term “RNA modifications” refers to various forms of modifications that occur on RNA, which are called epitranscriptomic modifications. It is worth mentioning that the term “epitranscriptomics” is still controversial. More than 160 types of post-transcriptional modifications have been found in archaea, bacteria, viruses, and eukaryotes ##REF##32440736##[1]##, and these modifications are widely present on various RNA types, such as messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), microRNA (miRNA), and long non-coding RNA (lncRNA). RNA modifications play important roles in the regulation of RNA processing, are important components of post-transcriptional regulation, and can affect the secondary structure, splicing, stability, and translation of RNA. These modifications further regulate important physiological and pathological processes such as embryo development, tissue and organ differentiation, long-term memory formation, and tumorigenesis ##REF##30262497##[2]##, ##REF##29789545##[3]##, ##REF##24713629##[4]##. Among RNA modifications, <italic>N</italic><sup>6</sup>-methyladenine (m<sup>6</sup>A) is the most widely distributed form of methylation on eukaryotic RNAs ##REF##31100245##[5]##, ##REF##23453015##[6]##, and is also the most thoroughly studied type of RNA modifications. m<sup>6</sup>A was first identified half a century ago as a potential regulator of intracellular mRNA processing. A study conducted in the 1970s discovered that m<sup>6</sup>A also exists on viral transcripts ##REF##166375##[7]##. m<sup>6</sup>A has been identified in a number of viruses, including human immunodeficiency virus (HIV), Rous sarcoma virus, herpes simplex virus 1 (HSV-1), adenovirus, simian virus 40 (SV40), and endogenous retroviruses ##REF##166375##[7]##, ##REF##1086370##[8]##, ##REF##3029112##[9]##, ##REF##3016525##[10]##, ##REF##189800##[11]##, ##REF##170541##[12]##, ##REF##196108##[13]##, ##REF##33401298##[14]##, ##REF##33442060##[15]##, ##REF##1272797##[16]##. In addition to influencing cellular physiological processes, m<sup>6</sup>A plays roles in viral processes, such as the regulation of viral RNA replication and immune processes ##REF##33309325##[17]##, ##REF##33657363##[18]##, ##REF##31070865##[19]##. Here, we summarize the writer, reader, and eraser proteins and describe the mechanism of action of m<sup>6</sup>A during viral infection. For example, we provide an overview of recent studies showing that m<sup>6</sup>A regulates the replication and infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and host interaction processes. We hope that epigenetic modifications will provide new insights into the development of vaccines and antiviral drugs.</p>" ]
[ "<title>Methods for m<bold><sup>6</sup></bold>A detection</title>", "<p id=\"p0060\">To date, a large number of methods for the detection of m<sup>6</sup>A have been reported. Because the methods described in below are mainly based on the strategy of m<sup>6</sup>A-specific antibody enrichment, we briefly introduce these technologies. m<sup>6</sup>A-specific antibodies are a widely used m<sup>6</sup>A detection method; these antibodies can specifically bind to m<sup>6</sup>A-containing RNAs and enrich these RNAs for analysis, which allows m<sup>6</sup>A immunoprecipitation sequencing, <italic>N</italic><sup>6</sup>-methyladenine sequencing (m<sup>6</sup>A-seq) or methylated RNA immunoprecipitation sequencing (MeRIP-seq) (##FIG##0##Figure 1##A) ##REF##22575960##[24]##, ##REF##22608085##[25]##. In MeRIP-seq, mRNA is first cleaved into short fragments ranging from 100 nt to 200 nt, and the transcriptome-wide m<sup>6</sup>A distribution profile can be obtained by specific m<sup>6</sup>A antibody binding, enrichment, and high-throughput sequencing. However, because the resolution of m<sup>6</sup>A peaks obtained with the antibody binding approach is 100–200 nt, the accurate localization of m<sup>6</sup>A marks is impossible, and various strategies have thus been developed to improve the resolution. A novel m<sup>6</sup>A photocrosslinking sequencing method (PA-m<sup>6</sup>A-seq) was developed by introducing the modified base to improve the resolution to 23 nt ##UREF##3##[76]##. Ultraviolet (UV) radiation-induced crosslinking coupled with immunoprecipitation sequencing (CLIP-seq) can reveal interactions between RNA and RNA-binding proteins at the genome-wide level. CLIP-seq and MeRIP-seq were combined to develop a novel m<sup>6</sup>A-specific UV crosslinking immunoprecipitation sequencing technology (miCLIP) (##FIG##0##Figure 1##B) ##REF##26121403##[27]##, which achieves m<sup>6</sup>A sequencing at single-base resolution. This strategy can also provide m<sup>6</sup>A information beyond the conserved RRACH sequence, which compensates for the deficiency of MeRIP-seq. The aforementioned methods cannot be used for the quantitative analysis of m<sup>6</sup>A and the determination of the m<sup>6</sup>A modification level in different transcripts of the same gene. However, m<sup>6</sup>A-level and isoform-characterization sequencing (m<sup>6</sup>A-LAIC-seq) ##REF##27376769##[77]## allows the quantitative analysis of m<sup>6</sup>A levels in specific gene transcripts based on MeRIP-seq. Because m<sup>6</sup>A antibodies can also recognize m<sup>6</sup>Am, the antibody-based methods described above cannot distinguish m<sup>6</sup>A from m<sup>6</sup>Am. <italic>N</italic><sup>6</sup>,2′-<italic>O</italic>-dimethyladenosine-sequencing (m<sup>6</sup>Am-seq) is a recently reported method that effectively distinguishes m<sup>6</sup>A from m<sup>6</sup>Am ##REF##34362929##[78]##. In addition to antibody enrichment, the single-base-resolution detection of m<sup>6</sup>A can be achieved using restriction endonuclease methods ##UREF##4##[79]##, ##REF##31257032##[80]##, but these restriction endonuclease methods have sequence biases. More information about m<sup>6</sup>A can be found in some of the latest reviews ##UREF##5##[81]##, ##REF##33284953##[82]##.</p>" ]
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[ "<p id=\"np010\">Current address: School of Public Health, Wuhan University, Wuhan 430071, China.</p>", "<p><italic>N</italic><sup>6</sup>-methyladenine (<bold>m<sup>6</sup>A</bold>) is the most abundant RNA modification in mammalian messenger RNAs (mRNAs), which participates in and regulates many important biological activities, such as tissue development and stem cell differentiation. Due to an improved understanding of m<sup>6</sup>A, researchers have discovered that the biological function of m<sup>6</sup>A can be linked to many stages of mRNA metabolism and that m<sup>6</sup>A can regulate a variety of complex biological processes. In addition to its location on mammalian mRNAs, m<sup>6</sup>A has been identified on viral transcripts. m<sup>6</sup>A also plays important roles in the life cycle of many viruses and in viral replication in host cells. In this review, we briefly introduce the detection methods of m<sup>6</sup>A, the m<sup>6</sup>A-related proteins, and the functions of m<sup>6</sup>A. We also summarize the effects of m<sup>6</sup>A-related proteins on viral replication and infection. We hope that this review provides researchers with some insights for elucidating the complex mechanisms of the epitranscriptome related to viruses, and provides information for further study of the mechanisms of other modified nucleobases acting on processes such as viral replication. We also anticipate that this review can stimulate collaborative research from different fields, such as chemistry, biology, and medicine, and promote the development of antiviral drugs and vaccines.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Chengqi Yi</p>" ]
[ "<title>Distribution of m<bold><sup>6</sup></bold>A</title>", "<p id=\"p0010\">Since the identification of the first modified base, pseudouridine, a variety of RNA modifications have successively been found, and m<sup>6</sup>A is the most abundant and one of the most thoroughly studied base modifications. In 1974, researchers used isotope labeling to study mRNA methylation in mammalian cells and detected the presence of m<sup>6</sup>A ##REF##4372599##[20]##, ##UREF##0##[21]##. In mammals, m<sup>6</sup>A is found on approximately 0.1%–0.4% of all adenosines in RNA, and each mRNA has approximately three m<sup>6</sup>A sites ##REF##31070865##[19]##, ##REF##25171402##[22]##. m<sup>6</sup>A is mainly concentrated in near-stop codon regions and 3′-untranslated regions (3′-UTRs). Some organisms and organs also contain m<sup>6</sup>A near the 5′-UTR and start codons ##REF##26404942##[23]##, ##REF##22575960##[24]##, ##REF##22608085##[25]##, ##REF##24981863##[26]##. m<sup>6</sup>A is usually found in the conserved DRACH (D = A, G, U; R = G, A; H = A, C, U) sequence ##REF##26121403##[27]##. As m<sup>6</sup>A has gained widespread attention, it has been found in a variety of species, such as mice ##REF##29855379##[28]##, zebrafish ##REF##28869969##[29]##, <italic>Arabidopsis</italic>\n##REF##25430002##[30]##, ##REF##28503769##[31]##, rice, potato ##REF##34294912##[32]##, and viruses ##REF##33309325##[17]##, ##UREF##1##[33]##, ##REF##31711514##[34]##, ##REF##32114429##[35]##. The distribution of m<sup>6</sup>A modifications in different species is highly conserved. For example, approximately half of m<sup>6</sup>A sites are identical between human embryonic stem cells (ESCs) and mouse ESCs ##REF##25456834##[36]##.</p>", "<title>m<sup>6</sup>A writer, eraser, and reader proteins</title>", "<p id=\"p0015\">m<sup>6</sup>A is formed by the addition of a methyl group to the amino group at the 6-position of adenosine by a methyltransferase. The first key methyltransferase, METTL3, was discovered as early as in 1994 ##REF##9409616##[37]##, and subsequently, another protein in the METTL family — METTL14, which also has methyltransferase activity — was also identified as an important component of the methyltransferase complex ##REF##27373337##[38]##, ##REF##24316715##[39]##. METTL3 and METTL14 form a 1:1 stable heterodimer and enhance methyltransferase activity through a synergistic action, in which METTL3 acts as the active catalytic subunit and METTL14 enhances substrate recognition and RNA binding. The knockout of <italic>METTL3</italic> or <italic>METTL14</italic> decreases the m<sup>6</sup>A content ##REF##28914256##[40]##, ##REF##28965759##[41]##, which indicated that METTL3 and METTL14 play a role in the formation of m<sup>6</sup>A. However, other studies have shown that the main function of METTL14 is not to catalyze methyl transfer but to provide an RNA-binding scaffold to activate and enhance the catalytic activity of METTL3 ##REF##27373337##[38]##. WTAP is also an active component of the methyltransferase complex ##REF##24981863##[26]##, ##REF##24316715##[39]##, ##REF##24407421##[42]##, but unlike METTL3, WTAP has no methyltransferase activity. The knockout of <italic>WTAP</italic> decreases the binding of METTL3 to RNA and the m<sup>6</sup>A content ##REF##24407421##[42]##. WTAP can bind to the METTL3–METTL14 complex such that the complex is concentrated in nuclear spots to enhance mRNA methylation. Several other methyltransferases or enzymes with the ability to recruit methyltransferase complexes to target genes have also been identified, and these include METTL5 ##REF##31328227##[43]##, METTL16 ##REF##33930289##[44]##, KIAA1429 ##UREF##2##[45]##, RBM15, RBM15B ##REF##27602518##[46]##, HAKAI, ZC3H13 ##REF##29547716##[47]##, and ZCCHC4 ##REF##30531910##[48]##.</p>", "<p id=\"p0020\">The opposite of methylase activity is demethylase activity. He et al. found that the knockdown and overexpression of <italic>FTO</italic> increases and decreases the m<sup>6</sup>A content, respectively ##REF##22002720##[49]##. FTO, an obesity-related protein and a dioxygenase based on α-ketoglutarate ##REF##18775698##[50]##, has the same conserved functional domain as AlkB, a demethylase family protein ##REF##20376003##[51]##. Written m<sup>6</sup>A is erased by FTO and reverts to adenosine, and this finding provides the first demonstration that m<sup>6</sup>A is dynamically modified and starts a new chapter in the understanding of m<sup>6</sup>A. FTO exhibits demethylase activity not only <italic>in vivo</italic> but also toward single-stranded DNA and RNA <italic>in vitro</italic>. FTO is also involved in tumorigenesis (<italic>e.g.</italic>, by acting as an oncogene in acute myeloid leukaemia ##REF##28017614##[52]##) and can modulate plant growth (<italic>e.g.</italic>, by increasing the rice yield and potato biomass) ##REF##34294912##[32]##. Notably, FTO can also demethylate <italic>N</italic><sup>6</sup>,2′-<italic>O</italic>-dimethyladenosine (m<sup>6</sup>Am) ##REF##28002401##[53]##.</p>", "<p id=\"p0025\">In addition to FTO, ALKBH5 in the AlkB family has the function of erasing methylation ##REF##23177736##[54]##. The knockout and overexpression of <italic>ALKBH5</italic> in cells are accompanied by an increase and a decrease in the m<sup>6</sup>A content, respectively. <italic>ALKBH5</italic> knockdown promotes the transport of mRNA from the nucleus to the cytoplasm and affects the metabolism of RNA and the assembly of mRNA processing factors. In ALKBH5-deficient male mice, the apoptosis of spermatocytes during meiotic metaphase is affected, which leads to impaired fertility. ALKBH5 also functions in the maintenance of tumorigenicity, self-renewal, and tumorigenesis in glioma ##REF##28344040##[55]##, ##REF##28297667##[56]##, promotes the radioresistance and invasion of glioma stem cells ##REF##33375621##[57]##, and suppresses tumor progression ##REF##33431791##[58]##. These results indicate that dynamic changes in m<sup>6</sup>A play an important role in regulating various biological activities.</p>", "<p id=\"p0030\">Following the discovery of the aforementioned m<sup>6</sup>A “writer” and “eraser” proteins, the m<sup>6</sup>A-binding proteins that “read” m<sup>6</sup>A were also discovered. YT521-B homology (YTH) domains can bind to m<sup>6</sup>A-modified RNA ##REF##25389274##[59]##. The knockout of <italic>YTHDF2</italic> increases the expression levels of m<sup>6</sup>A-containing mRNAs, which indicates that YTHDF2 can affect the stability of mRNA by binding to m<sup>6</sup>A ##REF##24284625##[60]##. Another m<sup>6</sup>A reader protein, YTHDF1, promotes protein synthesis by interacting with initiation factors and ribosomes ##REF##26046440##[61]##, and YTHDF3 can cooperate with YTHDF1 to promote protein synthesis. YTHDF1–3 can affect metabolism by binding to m<sup>6</sup>A-containing mRNAs ##REF##28106076##[62]##, ##REF##28106072##[63]##. IGF2BP1–3 have also been identified as m<sup>6</sup>A reader proteins. Unlike recognition by YTHDF2, which reduces the stability of m<sup>6</sup>A-containing mRNAs, the recognition of m<sup>6</sup>A-containing mRNAs by IGF2BP enhances mRNA stability and translation ##REF##29476152##[64]##. The m<sup>6</sup>A-related proteins are summarized in ##TAB##0##Table 1##.</p>", "<title>Functions of m<bold><sup>6</sup></bold>A</title>", "<p id=\"p0035\">High-throughput sequencing and quantitative polymerase chain reaction (qPCR) analysis have revealed that the abundance of m<sup>6</sup>A differs among different types of mRNA. Approximately 46% of mRNAs contain only one m<sup>6</sup>A peak, 37.3% of mRNAs contain two m<sup>6</sup>A peaks, and a few mRNAs contain at least three m<sup>6</sup>A peaks ##REF##22608085##[25]##. The discovery of m<sup>6</sup>A-related proteins has led to the gradual discovery of the related functions of m<sup>6</sup>A and its role in life processes. For example, m<sup>6</sup>A is involved in RNA processing, development, differentiation, metabolism, and fertility. The process of eukaryotic mRNA formation is divided into transcription, splicing, export, translation, and degradation, and studies have shown that m<sup>6</sup>A affects the life cycle of mRNA ##REF##28622506##[65]##.</p>", "<title>mRNA splicing</title>", "<p id=\"p0040\">The processing of a precursor RNA to a mature mRNA requires 5′-capping, 3′-polyadenylation, intron excision, and exon splicing. The precise excision of introns and the splicing of exons are key factors in gene expression that directly affect the diversity of proteins. m<sup>6</sup>A is more abundant in RNA precursors than in mature mRNA ##REF##954080##[66]##. Changes in the expression of WTAP or METTL3 can regulate the expression of related genes and splicing subtypes in transcription and RNA processing, which indicates that writer proteins can affect RNA splicing ##REF##24407421##[42]##. In addition, m<sup>6</sup>A reader proteins can interact with other splicing factors to regulate splicing. Most of the m<sup>6</sup>A-related proteins are located in nuclear spots enriched with splicing factors ##REF##23177736##[54]##, ##REF##25242552##[67]##, which facilitate the connection between m<sup>6</sup>A and RNA splicing. The splicing efficiency is also important for coordinating gene expression, and the deposition of m<sup>6</sup>A on transcripts near the splice junction increases the splicing efficiency ##REF##29924987##[68]##.</p>", "<title>mRNA export from the nucleus</title>", "<p id=\"p0045\">The export of transcribed mRNAs from the nucleus to the cytoplasm is an important process in mRNA translation ##REF##26081607##[69]##. <italic>METTL3</italic> silencing leads to significant nuclear accumulation and delayed transcript processing ##REF##24209618##[70]##. Similarly, the deletion of <italic>YTHDC1</italic> prolongs the retention time of mRNA in the nucleus, which allows the accumulation of transcripts in the nucleus ##REF##28984244##[71]##. In contrast, the deletion of <italic>ALKBH5</italic> induces the nuclear export of mRNA ##REF##23177736##[54]##. Thus, m<sup>6</sup>A can regulate the process of mRNA export from the nucleus to the cytoplasm and further affect the process of gene expression.</p>", "<title>mRNA translation</title>", "<p id=\"p0050\">METTL3 can promote the translation of mRNAs such as the epidermal growth factor receptor and the Hippo pathway effector TAZ. The depletion of METTL3 reduces the translation efficiency, whereas both wild-type and non-methylated METTL3 promote translation. Mechanistic studies have shown that METTL3 enhances mRNA translation through its interaction with the translation initiation machinery independent of its intrinsic activity ##REF##27117702##[72]##. YTHDF1 can not only promote the binding of m<sup>6</sup>A-containing mRNAs to ribosomes but also recruit translation initiation factor complex 3 (eIF3) to promote mRNA translation ##REF##26046440##[61]##. m<sup>6</sup>A can also promote mRNA translation that is resistant to eIF4 inactivation ##REF##29107534##[73]##.</p>", "<title>mRNA stability</title>", "<p id=\"p0055\">The last step in mRNA metabolism is mRNA degradation, and the stability of an mRNA is closely related to its degradation. Specifically, mRNA stability is regulated by m<sup>6</sup>A; for example, the stability of transcripts is increased in METTL3- or METTL14-depleted cells ##REF##24394384##[74]##. YTHDF2 binds to m<sup>6</sup>A-containing mRNA and transports this mRNA to the site of mRNA degradation in the cytoplasm, which accelerates the degradation of mRNA. However, not all m<sup>6</sup>A reader proteins reduce mRNA stability. For example, IGF2BPs can enhance mRNA stability ##REF##29476152##[64]##. ALKBH5 affects the meiotic and haploid stages of spermatogenesis by controlling the splicing and stability of mRNAs ##REF##29279410##[75]##.</p>", "<title>Relationship between m<bold><sup>6</sup></bold>A and viruses</title>", "<p id=\"p0065\">m<sup>6</sup>A is present not only on cellular RNA but also on viral mRNA and regulates the expression levels of viral genes, which are closely related to the viral life cycle. Studies conducted in the 1970s discovered that m<sup>6</sup>A is present on the RNA transcripts of some viruses, such as influenza A virus, SV40, Rous sarcoma virus, and adenovirus. Researchers have speculated that m<sup>6</sup>A plays a role in regulating viral infection, but the exact mechanism and function were unclear. It was not until the 21st century that m<sup>6</sup>A was revealed to have functions such as regulating viral replication. Further research has shown that m<sup>6</sup>A is found in many types of viruses. The effects of m<sup>6</sup>A-related proteins on some viruses are briefly introduced in this section (##TAB##1##Table 2##).</p>", "<title>m<bold><sup>6</sup></bold>A in SV40</title>", "<p id=\"p0070\">SV40, which belongs to the polyomavirus family and is an oncogenic virus found in both humans and monkeys, is the first animal virus whose complete genomic DNA sequence has been determined. The SV40 genome is a circular double-stranded DNA with a size of 5.2 kb. Researchers discovered the presence of m<sup>6</sup>A in SV40 mRNA more than 40 years ago ##REF##223130##[83]##, and subsequent studies revealed that m<sup>6</sup>A in pre-mRNA is very important for the generation of late SV40 mRNAs ##REF##6318439##[84]##. Regulation of the m<sup>6</sup>A content in the cytoplasm of SV40-infected best supportive care-1 (BSC-1) cells revealed that internal m<sup>6</sup>A plays a role in regulating the processing and export of mRNA from the nucleus to the cytoplasm in non-transformed cells. Cullen’s research group revealed that m<sup>6</sup>A can positively regulate SV40 gene expression ##REF##29447282##[85]##. The overexpression of <italic>YTHDF2</italic> in SV40-infected BSC40 cells results in faster viral replication and larger virus plaques. The mutational inactivation of YTHDF2 and METTL3 yields opposite results. Photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) ##REF##20371350##[86]## and PA-m<sup>6</sup>A-seq ##UREF##3##[76]## identified two m<sup>6</sup>A peaks in the early SV40 region and 11 m<sup>6</sup>A peaks in the late transcript. The reduction of m<sup>6</sup>A in late mRNAs slows the replication speed of viral mutants, whereas a decrease in m<sup>6</sup>A in early-stage mRNAs has no effect on infection. The deletion of m<sup>6</sup>A in late mRNAs prevents nuclear processing and reduces the expression of the encoded structural protein VP1, which indicates that m<sup>6</sup>A affects the translation of late mRNAs. The mechanism by which m<sup>6</sup>A affects the nucleation of late mRNAs needs further study.</p>", "<title>m<bold><sup>6</sup></bold>A in hepatitis B virus</title>", "<p id=\"p0075\">The hepatitis B virus (HBV) genome is very small, containing approximately 3200 nucleotides, and HBV completes its life cycle through replicative intermediate pregenomic RNA (pgRNA). Siddiqui et al. revealed how m<sup>6</sup>A regulates HBV gene expression and the reverse transcription of pgRNA ##REF##30104368##[87]##. These researchers first identified the presence of m<sup>6</sup>A on HBV transcripts by MeRIP-seq. The silencing of <italic>METTL3</italic> and <italic>METTL14</italic> (1) decreased the level of m<sup>6</sup>A on HBV pgRNA, (2) reduced the reverse transcription of pgRNA, and (3) increased the expression of HBV protein. MeRIP-seq showed that the typical DRACH motif for m<sup>6</sup>A in the HBV epsilon loop contains m<sup>6</sup>A at the A1907C site. The epsilon loop is located at the end of HBV mRNAs and the 5′ and 3′ ends of pgRNAs. The mutation of m<sup>6</sup>A in the pgRNA 5′ epsilon loop blocks the reverse transcription of pgRNA, and the loss of m<sup>6</sup>A in the 3′ epsilon loop increases the half-life of HBV. These results indicate that m<sup>6</sup>A in the 5′ stem loop positively regulates reverse transcription, whereas m<sup>6</sup>A in the 3′ stem loop negatively regulates RNA stability. These studies show that m<sup>6</sup>A has a dual regulatory function in HBV. m<sup>6</sup>A can more finely tune the events in the HBV life cycle, and this finding improves the understanding of the life cycle of HBV.</p>", "<p id=\"p0080\">Subsequently, Siddiqui et al. reported that m<sup>6</sup>A can regulate host innate immunity to HBV infection ##REF##32719095##[88]##. The depletion of METTL3 and METTL14 increases the retinoic acid-inducible gene I (RIG-I) recognition of viral RNA, which further stimulates the production of type I interferons. The opposite results have been found in <italic>METTL3</italic> and <italic>METTL14</italic> overexpression systems. An increase in the m<sup>6</sup>A content decreases mRNA stability and thus regulates the translation level and abolishes the innate immune response. The binding of YTHDF2 to m<sup>6</sup>A-modified viral RNA blocks the recognition of viral RNA by RIG-I, and thus, HBV can achieve immune evasion through m<sup>6</sup>A.</p>", "<p id=\"p0085\">ISG20 is an exonuclease that binds to and degrades HBV transcripts. Siddiqui et al. found that ISG20 is an interaction partner of YTHDF2, and the resulting complex recognizes m<sup>6</sup>A-containing HBV RNA and performs exonuclease activity ##REF##32059034##[89]##. The silencing of <italic>METTL3</italic> and <italic>METTL14</italic> or <italic>YTHDF2</italic> produces HBV transcripts that are resistant to interferon-α (IFN-α) treatment or ISG20-mediated degradation. Mutation of the m<sup>6</sup>A residue A1907 revealed that this m<sup>6</sup>A site is a key factor in IFN-α-mediated HBV RNA decay, and these results provided the first demonstration of the role of m<sup>6</sup>A in IFN-α-induced viral RNA degradation.</p>", "<title>m<bold><sup>6</sup></bold>A in Kaposi’s sarcoma-associated herpes virus</title>", "<p id=\"p0090\">Kaposi’s sarcoma-associated herpes virus (KSHV) is associated with some malignancies, including primary effusion lymphoma (PEL), Kaposi’s sarcoma (KS), and multicentric Castleman’s disease (MCD) ##REF##21625290##[90]##. The KSHV replication cycle consists of latent and lytic replication phases, which are important for the development of KSHV-related cancers. Nilsen et al. found that KSHV can use m<sup>6</sup>A to regulate its lytic replication ##REF##28592530##[91]##. These researchers first identified m<sup>6</sup>A on most KSHV transcripts through MeRIP-seq. The stimulation of lytic replication increases the level of m<sup>6</sup>A-containing viral mRNA. <italic>FTO</italic> knockdown increases the expression of lytic genes, whereas <italic>METTL3</italic> knockdown decreases the expression of lytic genes. Researchers have used two small-molecule inhibitors and obtained consistent results. Meclofenamic acid can selectively inhibit FTO, and 3-deazaadenosine (DAA) can inhibit the hydrolysis of <italic>S</italic>-adenosylhomocysteine ​​(SAH) to block the formation of m<sup>6</sup>A. Researchers have found that the addition of meclofenamic acid increases the expression of cleavage genes and that the blockade of m<sup>6</sup>A formation by DAA abolishes the expression of cleavage genes. Replication transcription activator (RTA) is an important KSHV cleavage switch protein, and its pre-mRNA contains m<sup>6</sup>A. The blockade of m<sup>6</sup>A formation inhibits splicing of the RTA pre-mRNA and then terminates viral lytic replication. The polyadenylated nucleus (PAN) is a long non-coding transcript involved in the cleavage of KSHV and viral gene expression. Sztuba et al. found that m<sup>6</sup>A on PAN varies dynamically and that modification is increased at the late cleavage stage of KSHV infection ##REF##34187903##[92]##. These studies suggest that m<sup>6</sup>A regulates the replication of KSHV cleavage genes.</p>", "<p id=\"p0095\">Gao et al. also found that most KSHV transcripts are methylated during lytic replication ##REF##29109479##[93]##. The knockdown of <italic>YTHDF2</italic> increases KSHV cleavage replication, and the overexpression of <italic>YTHDF2</italic> reduces the production of virus and the level of viral proteins. These findings are obtained because the binding of YTHDF2 to viral transcripts affects the stability of viral RNA and suggest that YTHDF2 may mediate a host defence mechanism in which the degradation of KSHV is regulated through YTHDF2 and that KSHV cleavage replication is then regulated to inhibit viral replication. Glaunsinger et al. reported that infection with KSHV significantly increases the level of m<sup>6</sup>A in host cells ##REF##29659627##[94]##. Interestingly, m<sup>6</sup>A exerts different proviral and antiviral effects on viral gene expression in different cell types. In some cell types, the knockdown of <italic>METTL3</italic> and <italic>YTHDF2</italic> suppresses the production of virus particles, and m<sup>6</sup>A functions in a proviral manner. The viral lytic transactivator gene <italic>ORF50</italic> contains m<sup>6</sup>A, and this m<sup>6</sup>A positively regulates <italic>ORF50</italic>. In other cell types, the knockdown of <italic>METTL3</italic> and <italic>YTHDF2</italic> exerts antiviral effects. These findings suggest that m<sup>6</sup>A can regulate KSHV gene expression and that this effect can yield significantly different results in different cells.</p>", "<title>m<bold><sup>6</sup></bold>A in HIV-1</title>", "<p id=\"p0100\">HIV-1 can attack the human immune system, particularly the most important CD4<sup>+</sup> T lymphocytes in the human body, and destroying a large number of CD4<sup>+</sup> T cells results in loss of human immune function. Therefore, patients infected with HIV are susceptible to a variety of diseases and malignant tumors and have a higher mortality rate than the general population. Cullen et al. used PA-m<sup>6</sup>A-seq to identify the presence of m<sup>6</sup>A in the HIV-1 genome. The m<sup>6</sup>A sites are concentrated in the 3′-UTR and enhance mRNA expression through the recruitment of YTHDF ##REF##27117054##[95]##. In CD4<sup>+</sup> T cells, <italic>YTHDF</italic> overexpression increases HIV-1 protein expression and viral replication, and the opposite effects are observed in <italic>YTHDF</italic>-knockout cells. This finding shows that m<sup>6</sup>A and YTHDF can positively regulate the expression of HIV-1 mRNA. Researchers have also demonstrated that increased m<sup>6</sup>A levels can enhance HIV-1 replication due to the nuclear m<sup>6</sup>A reader YTHDC1 and the cytoplasmic m<sup>6</sup>A reader YTHDF2 ##REF##34140354##[96]##.</p>", "<p id=\"p0105\">Rana et al. found that the m<sup>6</sup>A content in both the virus and host genomes in HIV-1-infected CD4<sup>+</sup> T cells is increased ##REF##27572442##[97]##. The knockdown of <italic>METTL3</italic> or <italic>METTL14</italic> by short hairpin RNAs (shRNAs) significantly reduces viral replication, and increased reduction is obtained with the knockdown of both <italic>METTL3</italic> and <italic>METTL14</italic>. In contrast, the knockdown of <italic>ALKBH5</italic> significantly increases viral replication. These results indicate that enzymes associated with m<sup>6</sup>A can affect HIV-1 replication. The presence of methylation at A7877 and A7883 in the HIV-1 Rev response element (RRE) RNA stem loop II region was identified by MeRIP-seq, and methylation at these two sites enhances the binding of the HIV-1 Rev protein to the RRE. Mutation of A7883 in the RRE bulge region results in a significant decrease in viral replication and severely affects the nuclear export of viral RNA.</p>", "<p id=\"p0110\">Wu et al. reported that the binding of YTHDF1–3 to m<sup>6</sup>A-modified mRNA reduces HIV-1 reverse transcription and thereby inhibits HIV-1 infection ##REF##27371828##[98]##. This research group found that <italic>YTHDF1–3</italic> overexpression reduces the HIV-1 genomic RNA (gRNA) levels and inhibits early and late reverse transcription of gRNA. Changes in two m<sup>6</sup>A sites on the 5′ leader sequence in gRNA reduces the infectivity of HIV-1; in other words, m<sup>6</sup>A changes the infectivity of the virus. The knockdown of <italic>YTHDF1</italic> or <italic>YTHDF3</italic> increases the infectivity of HIV-1 ##REF##29976753##[99]##. These results suggest a new mechanism by which m<sup>6</sup>A participates in the regulation of HIV-1 replication and viral interaction with the host immune system.</p>", "<title>m<bold><sup>6</sup></bold>A in Flaviviridae</title>", "<p id=\"p0115\">The family Flaviviridae includes a variety of viruses, such as hepatitis C virus (HCV), Zika virus (ZIKV), and dengue virus. Rana et al. found that the m<sup>6</sup>A content of ZIKV RNA is regulated by host methyltransferases and demethylases ##REF##27773536##[100]##. ZIKV infection can change the location of m<sup>6</sup>A on mRNA, the motif of m<sup>6</sup>A, and the target genes of methyltransferases in the host. ZIKV replication increases after <italic>YTHDF</italic> silencing. <italic>METTL3</italic> and <italic>METTL14</italic> knockdown increases ZIKV production, whereas the silencing of <italic>FTO</italic> and <italic>ALKBH5</italic> decreases ZIKV production. The overall effect of m<sup>6</sup>A on viral replication may be due to the regulation of viral RNA metabolism by the binding of YTHDF to m<sup>6</sup>A-containing viral RNA.</p>", "<p id=\"p0120\">Horner et al. demonstrated that m<sup>6</sup>A also regulates HCV infection and that m<sup>6</sup>A-related enzymes affect the HCV life cycle ##REF##27773535##[101]##. Methyltransferase depletion does not affect the replication of HCV RNA but promotes the production of infectious virus particles to increase the HCV infection rate. The depletion of FTO reduces the infection rate of HCV. Unlike the results obtained for other viruses, in which m<sup>6</sup>A regulates viral replication by regulating the stability or translation of other viral RNAs, m<sup>6</sup>A regulates the production of infectious virus particles through the interaction of HCV RNA with host and viral proteins and thereby regulates the HCV infection rate. Researchers have also found that infection with Flaviviridae family members alters the m<sup>6</sup>A content in the transcripts of certain cells. For example, changes in the m<sup>6</sup>A content in these transcripts during viral infection can affect translation or alternative splicing ##REF##31810760##[102]##. These studies lay the foundation for studying the influence of m<sup>6</sup>A on Flaviviridae infection and pathogenesis.</p>", "<title>m<bold><sup>6</sup></bold>A in SARS-CoV-2</title>", "<p id=\"p0125\">SARS-CoV-2 is a positive-sense, single-stranded RNA virus with a genome size of 30 kb ##REF##32015507##[103]##. SARS-CoV-2 has caused a global health emergency since its initial outbreak in 2020. Dozens of RNA modification sites have been identified on the RNA of SARS-CoV-2 by nanopore sequencing ##REF##32330414##[104]##. Yang et al. identified 13 m<sup>6</sup>A peaks on SARS-CoV-2 using MeRIP-seq ##REF##33510134##[105]##. Viral subgenomic mRNA (sgRNA) with a regular 3′-UTR can be methylated by host METTL3, which activates the cellular degradation program to remove the viral RNA. To protect against m<sup>6</sup>A-dependent degradation, the m<sup>6</sup>A-modified RRACH motif is eliminated in SARS-CoV-2 to form a shorter 3′-UTR, and this shorter 3′-UTR prevents viral RNA degradation. Therefore, m<sup>6</sup>A may potentially regulate the abundance of SARS-CoV-2 RNA. These speculations need to be further studied in more complete animal models.</p>", "<p id=\"p0130\">Qin et al. performed the first systematic analysis of the m<sup>6</sup>A profile of the SARS-CoV-2 transcriptome and confirmed that m<sup>6</sup>A in the SARS-CoV-2 genome is dynamically modified in human and monkey cells ##REF##33510385##[106]##. METTL3/14 and ALKBH5 negatively and positively regulate SARS-CoV-2 replication, respectively. SARS-CoV-2 infection also changes the host m<sup>6</sup>A methylome, which indicates that m<sup>6</sup>A is involved in the host–virus interaction. These findings provide ideas for the development of new antiviral drugs based on m<sup>6</sup>A.</p>", "<p id=\"p0135\">Rana et al. showed that m<sup>6</sup>A plays a role in evasion of the host immune response to SARS-CoV-2 infection. The absence of METTL3 increases the binding of RIG-I, which enhances the innate immune signaling pathway and inflammatory gene expression ##UREF##6##[107]##. Through the indirect inhibition of METTL3 to disrupt the viral life cycle and the direct regulation of the level of m<sup>6</sup>A in the viral genome to enhance the comprehensive effect of a timely innate immune response, METTL3 is expected to be used for the treatment of patients with SARS-CoV-2 who have not yet developed cytokine storms. The changes in host factors regulated by the depletion of METTL3 and the specific mechanisms affecting viral replication need to be further studied.</p>", "<p id=\"p0140\">Mohr et al. revealed that METTL3 activity contributes to the early steps of the SARS-CoV-2 replication cycle ##REF##34168039##[108]##. The inhibition of METTL3-mediated catalysis decreases sgRNA synthesis and viral N protein expression. The replication of SARS-CoV-2 can be inhibited by METTL3 depletion, treatment with a highly specific small-molecule inhibitor of METTL3, or YTHDF1/3 depletion. These results indicate that targeting m<sup>6</sup>A to limit SARS-CoV-2 replication may also be a therapeutic strategy.</p>", "<title>m<bold><sup>6</sup></bold>A in severe fever with thrombocytopenia syndrome virus</title>", "<p id=\"p0145\">Severe fever with thrombocytopenia syndrome (SFTS) is an acute infectious disease caused by a new bunyavirus. Due to its high fatality rate and potential for a global pandemic, the World Health Organization declared SFTS as one of the ten top priority infectious diseases. At present, the main clinical treatment for SFTS is the broad-spectrum antiviral drug ribavirin. Zhou et al. performed m<sup>6</sup>A-seq of clinical residual blood samples from patients with SFTS and found that patients infected with severe fever with thrombocytopenia syndrome virus (SFTSV) exhibit significant changes in the abundance of m<sup>6</sup>A compared with healthy individuals ##REF##34561445##[109]##. The genes containing these differential m<sup>6</sup>A peaks are mainly enriched in platelet development, viral transcription, type I interferon signaling, the immune response, and other pathways. Interestingly, m<sup>6</sup>A peaks are also found on the viral genome, which indicates that m<sup>6</sup>A may also exist in SFTSV. RNA sequencing (RNA-seq) was used to analyze the differential gene expression between SFTSV-positive and SFTSV-negative patients, and the results revealed that the <italic>FTO</italic> expression level in positive samples is higher than that in negative samples. As the disease symptoms improves and the viral copy number decreases, the expression of <italic>FTO</italic> decreases slowly. These findings suggest that some immunomodulatory genes may be regulated by m<sup>6</sup>A after SFTSV infection. Future studies, such as experiments with cell models, are needed to explore the relationship between m<sup>6</sup>A and SFTSV.</p>", "<title>Perspectives</title>", "<p id=\"p0150\">As one of the most common modifications of RNA, m<sup>6</sup>A participates in many important biological processes. Although m<sup>6</sup>A was discovered in a variety of viruses more than 40 years ago, the relationship between m<sup>6</sup>A and viruses was unclear. With the development of detection technology, the mechanism by which m<sup>6</sup>A-related proteins regulate viral replication and other processes has been gradually revealed in recent years. For example, host cells actively respond to viral infection by impairing the demethylation activity of ALKBH5 and thereby reprogramming the cellular metabolic state ##REF##31439758##[110]##. By recognizing m<sup>6</sup>A and binding to m<sup>6</sup>A-containing viral RNA, the reader protein YTHDF affects the processing of RNA and then regulates viral activity and infection ##REF##29109479##[93]##. METTL3 interacts with viral RNA-dependent RNA polymerase 3D to enhance the stability and transcription efficiency of 3D protein by increasing the ubiquitination modification level of 3D, which results in the promotion of viral replication ##REF##31070865##[19]##.</p>", "<p id=\"p0155\">m<sup>6</sup>A may exert completely opposite regulatory effects on different viruses. For example, m<sup>6</sup>A may positively regulate SV40 and HIV-1 and negatively regulate HBV, ZIKV, and HCV. The same virus, which may infect different host cell types, may also show opposite results depending on the cell type, <italic>e.g.</italic>, KSHV. In general, m<sup>6</sup>A is neither uniformly antiviral nor proviral but rather regulates viral production by affecting specific RNAs. The reasons for these differences remain unclear, and the current understanding of the regulatory mechanism of m<sup>6</sup>A in viral infections is extremely limited; this question thus needs to be explored in future studies. Methyltransferase inhibitors or demethylase inhibitors can regulate the m<sup>6</sup>A content and thus regulate the life cycle or infection efficiency of a virus, and these agents are expected to be effective antiviral drugs.</p>", "<p id=\"p0160\">We expect that future studies provide a better understanding of the impact of m<sup>6</sup>A on life cycle processes such as viral replication and provide fundamental research support for the development of drugs to treat viral diseases. The mechanism by which m<sup>6</sup>A regulates the stability, shearing, and translation of RNA transcripts needs to be further studied. The development of technology for the detection of m<sup>6</sup>A with a low input is also urgently needed. Some existing viruses, such as SFTSV, cannot currently be treated with a specific drug or prevented by a vaccine, and modified nucleotides play an important role in mRNA vaccines. Whether m<sup>6</sup>A could play a role in vaccine development is also worth exploring.</p>", "<title>Competing interests</title>", "<p id=\"p0165\">Both authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0170\"><bold>Yafen Wang:</bold> Conceptualization, Investigation, Writing – original draft, Visualization. <bold>Xiang Zhou:</bold> Conceptualization, Writing – review &amp; editing. Both authors have read and approved the final manuscript.</p>" ]
[ "<title>Acknowledgments</title>", "<p id=\"p0175\">We gratefully acknowledge the financial support provided by the <funding-source id=\"gp005\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100001809</institution-id><institution>National Natural Science Foundation of China</institution></institution-wrap></funding-source> (Grant No. 21907077 to YW; Grant Nos. 91753201 and 21721005 to XZ), the <funding-source id=\"gp010\">Postdoctoral Innovative Talent Support Program of China</funding-source> (Grant No. BX20180228 to YW), and the <funding-source id=\"gp015\">China Postdoctoral Science Foundation</funding-source> (Grant No. 2019M652691 to YW).</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Schematic diagram of m<sup>6</sup>A detection method</bold></p><p><bold>A.</bold> Schematic diagram of m<sup>6</sup>A-seq ##REF##22575960##[24]##. The fragmented mRNA is enriched with m<sup>6</sup>A-antibody, and non-enriched RNA is used as control. The information containing m<sup>6</sup>A is obtained by comparing the sequenced fragments before and after enrichment with antibody. <bold>B.</bold> Schematic diagram of miCLIP ##REF##26121403##[27]##. After the fragment mRNA was enriched with antibodies, UV cross-linking was carried out, and misincorporation or reverse transcription termination would occur near the cross-linking sites during reverse transcription. m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenine; IP, immunoprecipitation; m<sup>6</sup>A-seq, <italic>N</italic><sup>6</sup>-methyladenine sequencing; MeRIP-seq, methylated RNA immunoprecipitation sequencing; miCLIP, m<sup>6</sup>A individual-nucleotide-resolution cross-linking and immunoprecipitation; UV, ultraviolet.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"t0005\"><label>Table 1</label><caption><p><bold>Roles of m<sup>6</sup>A-related proteins</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Type</bold></th><th>Protein <bold>name</bold></th><th><bold>Function</bold></th></tr></thead><tbody><tr><td>Writer</td><td>METTL3<break/>METTL14<break/>WTAP<break/>KIAA1429<break/>RBM15<break/>RBM15B<break/>HAKAI<break/>ZC3H13<break/>ZCCHC4</td><td>The METTL3–METTL14 complex catalyzes the adenosine methylation of RNA to form m<sup>6</sup>A; other proteins are important components of the complex</td></tr><tr><td>Eraser</td><td>FTO<break/>ALKBH5</td><td>Mediate m<sup>6</sup>A demethylase</td></tr><tr><td>Reader</td><td>YTHDF1<break/>YTHDF2<break/>YTHDF3<break/>IGF2BP1<break/>IGF2BP2<break/>IGF2BP3</td><td>Bind to m<sup>6</sup>A sites; increase or decrease mRNA stability; regulate RNA processing</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0010\"><label>Table 2</label><caption><p><bold>Functions of m<sup>6</sup>A-related proteins in viruses</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Virus</bold></th><th><bold>Gene name</bold></th><th><bold>Expression level</bold></th><th><bold>Consequence</bold></th><th><bold>Ref.</bold></th></tr></thead><tbody><tr><td>SV40</td><td><italic>METTL3</italic></td><td>Down</td><td>Reduced viral replication</td><td>##REF##29447282##[85]##</td></tr><tr><td/><td><italic>YTHDF2</italic></td><td>Up</td><td>Enhanced viral replication; larger viral plaques</td><td/></tr><tr><td/><td><italic>YTHDF2</italic></td><td>Down</td><td>Reduced viral replication</td><td/></tr><tr><td>HBV</td><td><italic>METTL3</italic>, <italic>METTL14</italic></td><td>Down</td><td>Increased HBV protein expression</td><td>##REF##30104368##[87]##</td></tr><tr><td/><td><italic>YTHDF2</italic>, <italic>YTHDF3</italic></td><td>Down</td><td>Increased HBV protein expression</td><td/></tr><tr><td/><td><italic>FTO</italic>, <italic>ALKBH5</italic></td><td>Down</td><td>Decreased HBV protein expression</td><td/></tr><tr><td>KSHV</td><td><italic>METTL3</italic></td><td>Down</td><td>Abolished lytic gene expression (BCBL1 cells)</td><td>##REF##28592530##[91]##</td></tr><tr><td/><td><italic>FTO</italic></td><td>Down</td><td>Enhanced lytic gene expression (BCBL1 cells)</td><td/></tr><tr><td/><td><italic>METTL3</italic></td><td>Down</td><td>Increased protein expression (TREX-BCBL-1 cells); reduced protein levels (iSLK.219 cells)</td><td>##REF##29659627##[94]##</td></tr><tr><td/><td><italic>YTHDF2</italic></td><td>Down</td><td>Increased protein expression (iSLK.BAC16 cells)</td><td/></tr><tr><td/><td><italic>YTHDF2</italic></td><td>Up</td><td>Reduced viral production; decreased levels of viral proteins (endothelial cells)</td><td>##REF##29109479##[93]##</td></tr><tr><td/><td><italic>YTHDF1</italic>, <italic>YTHDC1</italic>, <italic>YTHDC2</italic></td><td>Down</td><td>No significant or consistent effect on viral lytic replication</td><td/></tr><tr><td/><td><italic>YTHDF3</italic></td><td>Down</td><td>Reduced viral lytic replication (endothelial cells)</td><td/></tr><tr><td>HIV-1</td><td><italic>METTL3</italic>, <italic>METTL14</italic></td><td>Down</td><td>Decreased viral replication</td><td>##REF##27572442##[97]##</td></tr><tr><td/><td><italic>ALKBH5</italic></td><td>Down</td><td>Increased viral replication</td><td/></tr><tr><td/><td><italic>YTHDF2</italic></td><td>Up</td><td>Enhanced replication</td><td>##REF##27117054##[95]##</td></tr><tr><td/><td><italic>YTHDF2</italic></td><td>Down</td><td>Reduced replication</td><td/></tr><tr><td/><td><italic>YTHDF1</italic>, <italic>YTHDF2</italic>, <italic>YTHDF3</italic></td><td>Down</td><td>Enhanced infection</td><td/></tr><tr><td/><td><italic>YTHDF1</italic>, <italic>YTHDF2</italic>, <italic>YTHDF3</italic></td><td>Up</td><td>Decreased viral genomic RNA levels</td><td>##REF##29976753##[99]##</td></tr><tr><td/><td><italic>YTHDF1</italic>, <italic>YTHDF2</italic>, <italic>YTHDF3</italic></td><td>Down</td><td>Increased viral infectivity</td><td/></tr><tr><td>ZIKV</td><td><italic>METTL3</italic>, <italic>METTL14</italic></td><td>Up</td><td>Decreased viral titer</td><td>##REF##27773536##[100]##</td></tr><tr><td/><td><italic>METTL3</italic>, <italic>METTL14</italic></td><td>Down</td><td>Increased viral production</td><td/></tr><tr><td/><td><italic>YTHDF1</italic>, <italic>YTHDF2</italic>, <italic>YTHDF3</italic></td><td>Up</td><td>Decreased ZIKV RNA expression</td><td/></tr><tr><td/><td><italic>YTHDF1</italic>, <italic>YTHDF2</italic>, <italic>YTHDF3</italic></td><td>Down</td><td>Increased viral replication</td><td/></tr><tr><td/><td><italic>ALKBH5</italic></td><td>Up</td><td>Increased viral titer</td><td/></tr><tr><td/><td><italic>ALKBH5</italic>, <italic>FTO</italic></td><td>Down</td><td>Decreased viral production</td><td/></tr><tr><td>HCV</td><td><italic>METTL3</italic>, <italic>METTL14</italic></td><td>Down</td><td>Increased infectious HCV particle production</td><td>##REF##27773535##[101]##</td></tr><tr><td/><td><italic>YTHDF1</italic>, <italic>YTHDF2</italic>, <italic>YTHDF3</italic></td><td>Down</td><td>Increased infectious HCV particle production</td><td/></tr><tr><td/><td><italic>FTO</italic></td><td>Down</td><td>Decreased infectious HCV particle production</td><td/></tr><tr><td>SARS-CoV-2</td><td><italic>METTL3</italic>, <italic>METTL14</italic></td><td>Down</td><td>Increased viral replication</td><td>##REF##33510385##[106]##</td></tr><tr><td/><td><italic>YTHDF2</italic></td><td>Down</td><td>Enhanced viral infection and replication</td><td/></tr><tr><td/><td><italic>ALKBH5</italic></td><td>Down</td><td>Decreased viral replication</td><td/></tr></tbody></table></table-wrap>" ]
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[ "<table-wrap-foot><fn><p><italic>Note</italic>: METTL3, methyltransferase-like 3; METTL14, methyltransferase-like 14; WTAP, Wilms’ tumor 1-associating protein; RBM15, RNA binding motif protein 15; RBM15B, RNA binding motif protein 15B; ZC3H13, zinc finger CCCH-type containing 13; ZCCHC4, zinc finger CCHC-type containing 4; FTO, fat mass and obesity-associated protein; ALKBH5, alkB homologue; YTHDF1, YTH domain family protein 1; YTHDF2, YTH domain family protein 2; YTHDF3, YTH domain family protein 3; IGF2BP1, insulin like growth factor 2 mRNA binding protein 1; IGF2BP2, insulin like growth factor 2 mRNA binding protein 2; IGF2BP3, insulin like growth factor 2 mRNA binding protein 3.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p><italic>Note</italic>: SV40, simian virus 40; HBV, hepatitis B virus; KSHV, Kaposi’s sarcoma-associated herpesvirus; HIV-1, human immunodeficiency virus-1; ZIKV, Zika virus; HCV, hepatitis C virus; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"d35e542\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn></fn-group>" ]
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[{"label": ["21"], "surname": ["Perry", "Kelley"], "given-names": ["R.P.", "D.E."], "article-title": ["Existence of methylated messenger RNA in mouse L cells"], "source": ["Cell"], "volume": ["1"], "year": ["1974"], "fpage": ["37"], "lpage": ["42"]}, {"label": ["33"], "surname": ["Kim", "Siddiqui"], "given-names": ["G.W.", "A."], "article-title": ["Hepatitis B virus X protein recruits methyltransferases to affect cotranscriptional "], "italic": ["N"], "sup": ["6"], "source": ["Proc Natl Acad Sci U S A"], "volume": ["118"], "year": ["2021"], "object-id": ["e2019455118"]}, {"label": ["45"], "surname": ["Chen", "Ren", "Ding", "Cai", "Hu", "Zhao"], "given-names": ["X.", "S.", "M.", "Y.", "S.", "Y."], "article-title": ["Identification of m"], "sup": ["6"], "source": ["Blood"], "volume": ["136"], "year": ["2020"], "fpage": ["23"], "lpage": ["24"]}, {"label": ["76"], "surname": ["Chen", "Lu", "Wang", "Fu", "Luo", "Liu"], "given-names": ["K.", "Z.", "X.", "Y.", "G.Z.", "N."], "article-title": ["High-resolution "], "italic": ["N"], "sup": ["6", "6", "6"], "source": ["Angew Chem"], "volume": ["127"], "year": ["2015"], "fpage": ["1607"], "lpage": ["1610"]}, {"label": ["79"], "surname": ["Zhang", "Chen", "Zhao", "Yang", "Roundtree", "Zhang"], "given-names": ["Z.", "L.Q.", "Y.L.", "C.G.", "I.A.", "Z."], "article-title": ["Single-base mapping of m"], "sup": ["6"], "source": ["Sci Adv"], "volume": ["5"], "year": ["2019"], "object-id": ["eaax0250"]}, {"label": ["81"], "surname": ["Zhang", "Qian", "Jia"], "given-names": ["W.", "Y.", "G."], "article-title": ["The detection and functions of RNA modification m"], "sup": ["6", "6"], "source": ["J Biol Chem"], "volume": ["297"], "year": ["2021"], "object-id": ["100973"]}, {"label": ["107"], "surname": ["Li", "Hui", "Bray", "Gonzalez", "Zeller", "Anderson"], "given-names": ["N.", "H.", "B.", "G.M.", "M.", "K.G."], "article-title": ["METTL3 regulates viral m"], "sup": ["6"], "source": ["Cell Rep"], "volume": ["35"], "year": ["2021"], "object-id": ["109091"]}]
{ "acronym": [], "definition": [] }
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2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Aug 11; 21(4):695-706
oa_package/c7/d0/PMC10787122.tar.gz
PMC10787125
36805531
[ "<title>Introduction</title>", "<p id=\"p0020\">Since the circular genomes of plant viroids ##REF##1069269##[1]## and hepatitis delta virus ##REF##2429192##[2]## were discovered, it has become clear that circular RNAs (circRNAs) comprise a large class of covalently closed circular molecules that lack 5′ and 3′ ends. Circular intronic RNAs (ciRNAs) and exonic circRNAs (ecircRNAs) are generated via intron lariat debranching and back-splicing of exons, respectively ##REF##25242744##[3]##, ##REF##24035497##[4]##. Although the existence of circular transcripts has been known for at least 40 years ##REF##1069269##[1]##, their importance has been likely underestimated due to their low abundance ##REF##7684656##[5]##. Recently, more comprehensive investigation of such molecules has resulted from the ability to generate libraries enriched for circRNAs and from the availability of circRNA-specific bioinformatics algorithms ##REF##27350239##[6]##, ##REF##27365365##[7]##.</p>", "<p id=\"p0025\">Back-splicing is much less completely understood compared to canonical splicing. Although most circRNAs in mammals ##REF##25242744##[3]## and <italic>Caenorhabditis elegans</italic>\n##REF##25558066##[8]## are processed from internal exons with long flanking introns containing inverted complementary sequences (ICSs) ##REF##25242744##[3]##, ##REF##27365365##[7]##, ##REF##25281217##[9]##, formation of circRNAs in other species such as <italic>Drosophila melanogaster</italic>\n##REF##25544350##[10]## and <italic>Oryza sativa</italic>\n##REF##26464523##[11]## does not require RNA pairing across flanking introns. In addition to such <italic>cis</italic>-regulation, recent studies have revealed that inhibiting RNA-binding proteins (RBPs) could directly alter circRNA expression ##REF##29174924##[12]##. For instance, RBPs such as interleukin enhancer binding factor 3 (ILF3), nuclear factor 90 (NF90) isoform, DExH-box helicase 9 (DHX9), double-stranded RNA-specific adenosine deaminase (ADAR1), and KH domain containing RNA binding (QKI), regulate the formation of ecircRNAs ##REF##25558066##[8]##, ##REF##25768908##[13]##, ##REF##25921068##[14]##, ##REF##28355180##[15]##, ##REF##28625552##[16]##. Splicing factors such as FUS RNA binding protein (FUS), heterogeneous nuclear ribonucleoprotein L (HNRNPL), and QKI, regulate circRNA expression by binding to the flanking introns of circRNAs ##REF##25768908##[13]##, ##REF##28611215##[17]##. In addition, depleting core spliceosomal components such as SF3A and SF3B caused a marked increase in circRNA levels ##REF##29174924##[12]##. Thus, RBPs have an important role in regulating the biogenesis of circRNAs.</p>", "<p id=\"p0030\">In addition to their biogenesis, the decay of circRNAs directly influences their accumulation levels. Endonuclease RNase L initiates cleavage of circRNAs. Some circRNAs containing microRNA (miRNA) binding sites such as CDR1 antisense RNA (<italic>CDR1as</italic>) may be degraded by AGO2-mediated cleavage ##REF##21964070##[18]##. However, the mechanism of the degradation for most circRNAs remains elusive. Regarding circRNA function, both transcription and splicing of host genes can be modulated by specific circRNAs ##REF##24035497##[4]##, ##REF##25664725##[19]##. For example, <italic>circSEP3</italic> has been proposed to form an RNA:DNA hybrid (R-loop) with its cognate DNA locus in the nucleus; and this R-loop alters exon skipping of linear <italic>SEP3</italic>, which influences floral homeotic phenotypes in <italic>Arabidopsis thaliana</italic>\n##REF##28418376##[20]##.</p>", "<p id=\"p0035\">Thus far, the biogenesis, functions, and decay of circRNAs have not been well understood. In this study, we systematically identified and characterized circRNAs via RNase R-treated RNA sequencing (RNA-seq) libraries from moso bamboo seedlings, with or without gibberellin (GA) and auxin (1-naphthaleneacetic acid, NAA) treatments. Furthermore, we investigated whether circRNAs might regulate the splicing of their corresponding linear RNAs due to R-loop structures. Importantly, we took advantage of a modified protocol for degradome sequencing to detect several miRNA-mediated cleavage events. Finally, we determined that expression of circRNAs could not only be modulated dynamically by GA or NAA hormones but also might affect several hormone-related genes in moso bamboo.</p>" ]
[ "<title>Material and methods</title>", "<title>Plant materials and hormone treatments</title>", "<p id=\"p0190\">After treatment with GA (100 μM), NAA (5 μM), and ddH<sub>2</sub>O for 4 h, 4-week-old whole seedlings of moso bamboo were collected and transferred to liquid nitrogen. Total RNA was isolated with the RNAprep Pure Plant Kit (Catalog No. DP441, Tiangen, Beijing, China), and concentrations and quality were determined using 2% agarose gel analysis and NanoDrop (Catalog No. 840-317400, ThermoFisher Scientific, Waltham, MA) quantification before libraries were constructed and high-throughput sequencing was performed.</p>", "<title>Library preparation and sequencing for circRNAs and linear RNAs</title>", "<p id=\"p0195\">To ensure consistency and comparability of different omics, total RNA was divided into two tubes for circRNA and linear RNA sequencing. For circRNAs, rRNAs were depleted using the Ribo-Zero Magnetic Kit (Catalog No. MRZPL1224, Illumina, San Diego, CA), and then the samples were incubated with 3 U of RNase R (Catalog No. RNR07250, Epicentre, Madison, WI) for 15 min at 37 °C. The other group for conventional RNA-seq was incubated with oligo(T) magnetic beads (Catalog No. Dynabeads 61006, ThermoFisher Scientific, Meridian Rd) to enrich poly(A)+ RNAs. Subsequently, these RNAs were used for library preparation and subjected to sequencing with an Illumina HiSeq 2000 (Illumina).</p>", "<title>Bioinformatics analysis of circRNAs</title>", "<p id=\"p0200\">For each sample, FASTQ reads were first filtered using the HTQC package (v1.92.1) ##REF##23363224##[59]## to remove low-quality reads using default parameters. Clean reads were then mapped to the reference genome ##REF##30202850##[60]## using TopHat (v2.0.11) ##REF##19289445##[61]##. Subsequently, the remaining unmapped reads were aligned to the genome using the TopHat-Fusion algorithm (v2.0.11) for identifying circRNAs with the CIRCexplorer2 annotation program ##REF##27365365##[7]##. Moreover, AS events were detected using CIRCexplorer2 <italic>de novo</italic>\n##REF##27365365##[7]##. MICs were detected by overlapping exons following a previous study ##REF##30835314##[23]##. For evolutionary analysis, circRNAs in <italic>A</italic>. <italic>thaliana</italic> and <italic>O</italic>. <italic>sativa</italic> were also identified by the CIRCexplorer2 annotation program with the same parameters as moso bamboo using publicly available data ##REF##24249833##[27]##, ##REF##27870853##[28]##. Reference sequences and annotation of <italic>A</italic>. <italic>thaliana</italic> (TAIR10) and <italic>O</italic>. <italic>sativa</italic> (MSU6.1) were obtained from The <italic>Arabidopsis</italic> Information Resource (TAIR) and the MSU Rice Genome Annotation Project Database, respectively. We used the bamboo circRNAs as queries against those of <italic>A</italic>. <italic>thaliana</italic> and <italic>O</italic>. <italic>sativa</italic> using BLASTN with an E-value of 0.01, and resulting hits sharing below 50% similar stretches of sequence were removed.</p>", "<p id=\"p0205\">To compare circRNA expression among different samples, we first normalized circRNA abundance with RPM based on reads spanning the back-spliced junction to the total number of mapped reads (units in million). <italic>P</italic> values and false discovery rates (FDRs) were calculated using the DEGseq package ##REF##19855105##[62]##. Differentially expressed circRNAs were detected with fold change ≥ 2, <italic>P</italic> &lt; 0.01, and FDR ≤ 0.01 as cutoff.</p>", "<title>Experimental validation of circRNA</title>", "<p id=\"p0210\">For RNase R treatment and PCR amplification validation, we used the protocols from our previous study ##REF##32735361##[63]##. Briefly, 10× RNase R reaction buffer, RNase R, and diethyl pyrocarbonate (DEPC)-treated water were added and incubated for 15 min at 37 °C for RNase R digestion to take place before adding phenol–chloroform–isoamyl alcohol to stop the exonuclease digestion. The sample was then centrifuged at 13,000 <italic>g</italic> at 4 °C for 5 min, and the supernatant was transferred to a new 1.5-ml RNase-free tube containing LiCl, glycogen, and pre-chilled absolute ethanol (−20 °C) and finally inverted gently and stored at −80 °C for 1 h. Subsequently, RNase R-treated and control samples were reverse-transcribed to form complementary DNA (cDNA) for circRNA amplification with 40 cycles using divergent primers. PCR products with predicted sizes were dissected from a 2% agarose gel and directly sequenced. Divergent primers and convergent primers were designed to detect the candidate circRNA and positive control for linear RNA, and both are listed in Table S10.</p>", "<title>Functional annotation of moso bamboo</title>", "<p id=\"p0215\">Core spliceosomal factor genes, RBP genes (including splicing factor genes), miRNA-related genes, translation-related genes, fast growth-related genes, and hormone-related genes were annotated using Blast2GO ##REF##16081474##[64]## with default options. GO enrichment analysis was performed by BiNGO ##REF##15972284##[65]##. The phylogenetic tree of QKI was prepared with ClustalX1.83 and Interactive Tree Of Life (iTQL) ##REF##30931475##[66]##. The KH domain of QKI was detected by the conserved domain database (CDD) of National Center of Biotechnology Information ##REF##25414356##[67]## and visualized by Gene Structure Display Server (GSDS) 2.0 ##REF##25504850##[68]##.</p>", "<title>Protoplast isolation, plasmid construction, and transfection</title>", "<p id=\"p0220\">Protoplasts of moso bamboo were isolated and transformed as previously described ##UREF##2##[69]##. Briefly, shoots of seedlings were immediately transferred into a culture dish containing enzymatic solution and digested for 3 h at 25 °C with gentle shaking (50 r/min) in the dark. After adding an equal volume of CPW11M [consisting of 50-ml Cell and Protoplast Washing (CPW) buffer and 5.465 g mannitol] to a solution with a pH of 5.7, protoplast pellets were obtained from the miscible solution filtered through two layers of medical gauze and centrifuged for 3 min at 1200 r/min to remove the supernatant. After two additional washing steps using the CPW11M solution, the protoplast pellets were resuspended at a concentration of 1 × 10<sup>5</sup>–1 × 10<sup>6</sup> protoplasts in 1 ml using MES-Mannitol-Mg (MMG) solution.</p>", "<p id=\"p0225\">In this study, pUC22-35s-sGFP was used as the backbone for the construction of the overexpression and RNA interference (RNAi) vectors. To overexpress <italic>circ-DCL4</italic>, <italic>circ-PKL</italic>, <italic>circ-CSLA1</italic>, <italic>circ-BRE1-1</italic>/<italic>circ-BRE1-2</italic>, and the third linear exon of <italic>NRT1</italic>, the endogenous exons were cloned and flanked by 139-bp inverted complementary flanking introns using overlapping PCR ##REF##20569222##[70]##. The two inverted complementary exons (271 bp) from <italic>PedQKI</italic> (PH02Gene29161) were flanked across the intron of <italic>Cunninghamia lanceolata</italic> to construct the vector for <italic>PedQKI</italic> RNAi. <italic>circ-NHLRC2</italic> and <italic>miR166</italic> were amplified and flanked by the promoter (CaMV 35S) and nopaline synthase (NOS) terminator using overlapping PCR. Then, the two resulting products were inserted in the plasmid to enable the co-expression of both <italic>circ-NHLRC2</italic> and <italic>miR166</italic>.</p>", "<p id=\"p0230\">The recombinant plasmids were transfected using the Polyethylene Glycol (PEG)-mediated method. For each sample, 100-μl plasmid, protoplast, and 110-μl PEG solution were mixed and incubated at 25 °C. After incubation, the mixture was added to 5-ml CPW11M solution and centrifuged for 3 min at 1200 r/min. The remaining protoplasts without supernatant were resuspended with 10-ml CPW11M and centrifuged again at 1200 r/min for 3 min. Finally, after adding 10-ml CPW11M solution, the transfected protoplasts were incubated at 25 °C in the dark for 12–20 h. The expression of transcripts including circRNAs, mRNAs, and pre-miRNAs was detected by semi-quantitative RT-PCR using divergent or convergent primers (Table S10).</p>", "<title>Identification of AS events from RNA-seq</title>", "<p id=\"p0235\">Low-quality reads were cleaned with default parameters using the HTQC package (v1.92.1) ##REF##23363224##[59]##, and the remaining reads were mapped to the genome ##REF##30202850##[60]## by TopHat (v2.0.11) ##REF##19289445##[61]##. Aligned reads were used to assemble transcriptome annotation applying Cufflinks (v2.1.1) with default parameters ##REF##22383036##[71]##. Differential expression AS events were detected by rMATS.3.2.2 with the following option “-a 8 -c 0.0001 - analysis U” ##REF##25480548##[72]##. The parameters for “-a” and “-c” represented anchor length and the cutoff splicing difference, respectively. The default anchor length was 8 for RNA-seq splice-aware alignment. The default cutoff splicing difference was 0.0001 for 0.01% difference. To determine whether the frequency of AS events located in the transcribed region of circRNAs was considerably higher than other regions of linear RNA, we randomly selected the same number of transcribed regions without generating circRNAs, and the number of sequences affected by AS was calculated. After repeating the process 1000 times, we determined the mean value and the standard deviation of the simulation data. PCCs between ecircRNAs and four types of AS events were calculated using the expression profiles of ecircRNAs and AS events, which was represented by back-splicing junction reads for ecircRNAs and splicing junction for AS events, respectively. In addition, PCCs between circRNA and linear RNA were calculated based on expression of circRNAs from circRNA sequencing and expression of linear RNA from mRNA sequencing.</p>", "<title>Construction of customized degradome sequencing libraries</title>", "<p id=\"p0240\">The decay of circRNAs lacking the 3′ poly(A) tail of circRNAs cannot be detected by conventional degradome sequencing. A modified degradome library preparation was developed based on 5′ rapid-amplification of cDNA ends (RACE) library preparation. The Dynabeads mRNA Purification Kit (Catalog No. 61006, ThermoFisher Scientific, Carlsbad, CA) was used according to the manufacturer’s instructions to extract total RNA from 4-week-old bamboo seedlings treated with GA, NAA, and H<sub>2</sub>O. Total RNA was then separated into poly(A)− and poly(A)+ groups. Subsequently, rRNAs were removed from the poly(A)− group using the Ribo-Zero Magnetic Kit (Catalog No. MRZPL1224, Illumina). The free 5′ monophosphates of the cleavage transcripts of poly(A)− and poly(A)+ RNA were both ligated to the 5′ RNA adapter. Following reverse transcription with biotinylated random primers, the cDNA library was sequenced using an Illumina HiSeq 2000.</p>", "<title>Bioinformatics analysis for customized degradome sequencing</title>", "<p id=\"p0245\">For customized degradome sequencing, we developed a computational strategy to detect and compare the accumulated decay events termed as degradome peaks with candidate miRNA-mediated cleavage sites in circRNAs. First, degradome sequencing reads were aligned to the genome using Bowtie 2 (v2.2.1) with default parameters ##REF##22388286##[36]##. The mapping reads were calculated at the 5′ end alignment positions and counted as 1/<italic>n</italic> to determine the distribution of reads and the degradome peaks, in which <italic>n</italic> is the total number of mapped reads. The degradome peak was selected by the following cutoff: the percent abundance of cleavage sites was 50% or more in each continuous 21 nt consisting of the 10 nt upstream and downstream of cleavage sites. The <italic>P</italic> value cutoff of cleavage sites calculated by binomial test was determined as 0.05. Then, the 25 upstream and downstream nucleotides of cleavage sites were aligned to mature miRNAs by RNAplex ##REF##18434344##[37]## to identify the target RNA, in which the minimum free energy (MFE) ratio was set as 0.7 or less and the sliced sites were in the ±1 region around cleavage sites. To further detect cleavage sites spanning back-splicing sites, we first extracted the 50 upstream and downstream nucleotides of back-splicing sites from circRNAs including degradome peaks. Then, all reads from the poly(A)− library were aligned to back-splicing junction regions of circRNAs using Bowtie 2 with default parameters ##REF##22388286##[36]##. Finally, the cleavage of circRNAs supported by degradome reads was identified.</p>", "<title>Small RNA sequencing and bioinformatics analysis</title>", "<p id=\"p0250\">To rapidly and effectively obtain high-quality small RNAs for mock and hormone-treated samples, PEG8000 precipitation was utilized to isolate the small RNAs from 5 μg of total RNA for each library and then the 3′ adapter and 5′ adapter were successively ligated to small RNAs before reverse transcription. Finally, the DNA product was enriched using 3.5% polyacrylamide gel electrophoresis (PAGE), and bands of approximately 200 bp were isolated before sequencing using HiSeq 2500.</p>", "<p id=\"p0255\">The raw RNA reads were processed to remove 5′ adapters and 3′ adapters using the fastx-clipper function of the FASTX-Toolkit. The filtered reads were subjected to alignment against the Rfam database ##REF##12520045##[73]## using Bowtie 2 (v2.2.1) ##REF##22388286##[36]## to remove the common RNA families including rRNAs, transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs). The remaining sequences were aligned against the miRBase database (v21) ##REF##24275495##[74]## using the BLAST algorithm to identify miRNAs, allowing for an E-value &lt; 0.05 and three mismatches in total between targets reads and known miRNAs. Completely matched sequences were deemed as conserved miRNAs, and other sequences with no more than three mismatches or gaps were considered as variant miRNAs. RPM mapped reads were used to normalize the expression of miRNA from different libraries.</p>", "<title>Identification and annotation of ORFs from circRNAs</title>", "<p id=\"p0260\">To predict and annotate the cORFs, circRNA sequences excluding introns were multiplied four times for ORF prediction (<xref rid=\"s0145\" ref-type=\"sec\">Figure S5</xref>) applying TransDecoder with lowest length &gt; 10 aa ##REF##23845962##[75]##. Subsequently, three protein databases including Nr ##REF##17130148##[76]##, UniProt, and PsORF ##REF##32333496##[32]## were searched using BLASTP to detect their homologous proteins with known function using the following parameters: identity &gt; 80%, E-value &lt; 0.01, and the length of alignment &gt; 50%. By the same measurement, uORFs and dORFs derived from linear RNAs were predicted and annotated. To detect unique peptides for each of the ORFs in cORFs, uORFs, dORFs, and pORFs, we obtained raw proteome data based on label-free and tandem mass tags approaches ##REF##31330982##[77]##, ##REF##32705116##[78]##. We then performed four independent searches to identify the peptide-matching ORFs using MaxQuant with standard parameters ##REF##27809316##[79]##. Subsequently, we removed the peptides matching more than one ORF, and the ORFs with at least one unique peptide were retained.</p>", "<title>Transformation procedure for six circRNAs</title>", "<p id=\"p0265\">The pCAMBIA1390 vector including six circRNAs and flanking inverted complementary intron sequences were transformed into Kitaake (<italic>O</italic>. <italic>sativa</italic> ssp <italic>japonica</italic>). The mature embryos were used as the material for callus induction and <italic>Agrobacterium</italic>-mediated transformation. The hygromycin-resistant callus was transferred into differentiation medium for regeneration. To validate transformation, genomic DNA from rice leaves was extracted using cetyl trimethylammonium bromide (CTAB) methods, and the expected fragments were amplified using primers of hygromycin genes. Expression levels of the six circRNA transcripts were further detected by RT-PCR using divergent primers (Table S10). All seeds from wild-type and T1 generation plants overexpressing circRNAs were incubated in a petri dish to ensure consistent germination. Germinated seeds were transferred to nutrient soil for seedling growing. Then, plant heights were measured as the height from soil surface to the top leaf. In total, 20 seedlings were selected for each overexpressed circRNA for calculation of above-ground plant height.</p>" ]
[ "<title>Results</title>", "<title>Profile of circRNAs in moso bamboo seedlings</title>", "<p id=\"p0040\">To enrich circRNAs in moso bamboo seedling samples, total RNAs from seedlings treated with double-distilled water (ddH<sub>2</sub>O), NAA, or GA were incubated with RNase R and Ribo-Zero. Sequences were then generated from three biological repeats (##FIG##0##Figure 1##A). In total, we detected 5105, 4461, and 7748 putative circRNAs from ddH<sub>2</sub>O, NAA, and GA treatments, respectively (##FIG##0##Figure 1##B; Table S1). To independently test whether these sequences represent circRNAs, we carried out reverse transcription-polymerase chain reaction (RT-PCR)-based sequence validation with divergent primers for eight randomly selected circRNAs after RNase R treatment. This validation demonstrated that most circRNAs were indeed resistant to exonuclease degradation. The exception was <italic>circ-RAD16</italic>, which was further discovered to include back-spliced junction sites by Sanger sequencing (##FIG##0##Figure 1##C). Thus, we concluded that <italic>circ-RAD16</italic> is an authentic circRNA.</p>", "<p id=\"p0045\">We identified conserved circRNAs by comparing our data with published data of other species ##REF##28315753##[21]##. As shown in ##FIG##0##Figure 1##D, many circRNAs of moso bamboo were homologous to circRNAs of <italic>A</italic>. <italic>thaliana</italic> or <italic>O</italic>. <italic>sativa</italic>. As expected, circRNAs in bamboo exhibited more homology to those of <italic>O</italic>. <italic>sativa</italic> (2843, 19.9% of all circRNAs) than to <italic>A</italic>. <italic>thaliana</italic> (271, 1.9% of all circRNAs). Notably, 193 (1.3% of all circRNAs) were simultaneously detected in all three species, which included <italic>circ-GSL1</italic> (##FIG##0##Figure 1##E<bold>)</bold> generated from the gene encoding callose synthases 1 ##REF##16021399##[22]##. Enriched Gene Ontology (GO) terms for these evolutionarily conserved circRNAs included rhythmic processes, transporter activity and protein-containing complexes (<xref rid=\"s0145\" ref-type=\"sec\">Figure S1</xref>).</p>", "<p id=\"p0050\">The complexity and diversity of circRNAs are further increased by alternative back-splicing ##REF##27350239##[6]##, ##REF##27365365##[7]##, ##REF##30835314##[23]##, which includes the alternative 3′ splice site (A3SS), alternative 5′ splice site (A5SS), exon skipping (ExonS), intron retention (IntronR), alternative 3′ back-splice site (A3BS), and alternative 5′ back-splice site (A5BS), as well as mutually inclusive circRNA (MIC). circRNAs generated by these seven types of alternative back-splicing were identified from all samples by CIRCexplorer2 ##REF##27365365##[7]## (##FIG##0##Figure 1##F). Among the four alternative splicing (AS) types (A3SS, A5SS, ExonS, and IntronR) that generated the different ecircRNA transcripts with same back-splicing sites, IntronR is the most prevalent in linear transcripts of plants, whereas ExonS was the most prevalent from the interior of ecircRNAs. The other three types (A3BS, A5BS, and MIC) generated different ecircRNAs with different back-splicing sites; and A5BA accounted for the largest number of AS events among these three types. Enriched GO terms for these types of ecircRNAs were involved in diverse biological functions, such as chromosome organization, chromatin remodeling, and histone modification (##FIG##0##Figure 1##G).</p>", "<title>The biogenesis of circRNAs is influenced by <italic>cis</italic>- and <italic>trans</italic>-regulation</title>", "<p id=\"p0055\">Although ecircRNA-producing loci in moso bamboo usually had longer flanking introns than control introns (<xref rid=\"s0145\" ref-type=\"sec\">Figure S2</xref>), the ecircRNAs themselves lacked obvious flanking intronic pairing sequences (##FIG##1##Figure 2##A), consistent with previous studies ##REF##25242744##[3]##. However, ecircRNA production can be driven by long artificial flanking inverted complementary introns ##REF##26464523##[11]##. To test the correlation of ICSs with the biogenesis of ecircRNAs, we cloned a 139-bp inverted complementary flanking intron with a representative exon from <italic>CSLA1</italic>, as a representative ecircRNA, and from the third linear exon of <italic>NRT1</italic>, which does not give rise to ecircRNAs (##FIG##1##Figure 2##B). Semi-quantitative RT-PCR revealed that both the circularized exon and the linear exon in the overexpression vectors exhibited much higher circularization efficiency than that in the wild type, suggesting that RNA pairing with ICSs could enhance back-splicing efficiency of ecircRNAs. In particular, the linear exon from <italic>NRT1</italic> also could be induced into ecircRNAs by ICSs as flanking introns. To determine whether interior introns from multiple circularized exons were involved in the biogenesis of ecircRNA, we constructed <italic>circ-PKL1</italic> by including or excluding the interior intron. The presence of the interior intron did not lead to much difference in the rate of ecircRNA production (##FIG##1##Figure 2##C), suggesting that interior introns might not be key regulatory elements for the biogenesis of <italic>circ-PKL1</italic>.</p>", "<p id=\"p0060\">Core spliceosomal components, splicing factors, and some RBPs have been also reported to participate in circRNA regulation ##REF##27365365##[7]##, ##REF##25921068##[14]##, ##REF##24039610##[24]##, ##REF##25543144##[25]##. To further explore the interplay between circRNAs and these proteins, we performed sequence similarity analysis and identified 124 putative core spliceosomal components, 92 splicing factors, and 1132 other RBPs excluding splicing factors and core spliceosomal components in moso bamboo. We also performed RNA-seq to calculate accumulation levels for linear transcripts (##FIG##0##Figure 1##A). Pearson correlation coefficients (PCCs) were calculated based on levels of circRNAs [reads per million (RPM)] from circRNA sequencing and expression of RBP genes from RNA-seq [fragments per kilobase of exon model per million mapped fragments (FPKM)]. The levels of circRNAs were correlated (either positively or negatively; <italic>r</italic> ≥ 0.5 or <italic>r</italic> ≤ −0.5) with the transcript levels for 44, 57, and 497 of core spliceosomal components, splicing factors, and other RBPs, respectively (<xref rid=\"s0145\" ref-type=\"sec\">Figure S3</xref>A and B; Table S2).</p>", "<p id=\"p0065\">We focused on analyzing seven RBPs (SF3A, SF3B, NF90, DHX9, FUS, HNRNPL, and QKI) that have been found to modulate the production of circRNAs in other species ##REF##29174924##[12]##, ##REF##25768908##[13]##, ##REF##25921068##[14]##, ##REF##28355180##[15]##, ##REF##28625552##[16]##, ##REF##28611215##[17]##. SF3A and SF3B, as core spliceosomal components, were encoded by 5 and 13 homologous genes in bamboo, respectively, and showed correlation in levels with 4.68%–46.73% and 11.12%–36.75% of circRNAs (##FIG##1##Figure 2##D). In mammals, NF90 and DHX9 contain double-stranded RNA (dsRNA) binding domains (dsRBDs) and facilitate circRNA formation by directly binding inverted repeated <italic>Alus</italic> (IR<italic>Alus</italic>) ##REF##28355180##[15]##, ##REF##28625552##[16]##. Although the <italic>Alu</italic> element is rare in moso bamboo, NF90 and DHX9 exhibited correlation with 26.78%–32.86% and 20.94%–33.46% of circRNAs, respectively (##FIG##1##Figure 2##D). In addition, the levels of 6.28%–31.77%, 11.52%–41.89%, and 4.98%–49.97% of circRNAs (##FIG##1##Figure 2##D) were strongly correlated with those of transcripts encoding 4, 12, and 34 proteins homologous to splicing factors FUS, HNRNPL, and QKI, respectively. A striking example was <italic>PedQKI</italic> (PH02Gene29161) (<xref rid=\"s0145\" ref-type=\"sec\">Figure S4</xref>), which encodes a conserved KH domain and shows negative or positive correlation with expression of 579 ecircRNAs and 423 ciRNAs (a total of 49.97% of selected circRNAs), respectively. Although expression of <italic>circ-HARBI1</italic> and <italic>circ-ATP2B1</italic> was not markedly altered, knockdown of <italic>PedQKI</italic> decreased the abundance of <italic>circ-ARF17</italic>, <italic>circ-WRKY40</italic>, <italic>circ-VCL1</italic>, and <italic>circ-MTR4</italic> (##FIG##1##Figure 2##E).</p>", "<p id=\"p0070\">Notably, 17 previously unreported proteins, namely, 1 core spliceosomal factor, 2 splicing factors, and 14 other RBPs, were more highly correlated with circRNAs than the above seven RBPs (##FIG##1##Figure 2##F). We further explored the correlation between the expression of these 17 RBPs and of the host genes that generated these circRNAs. We found that the circRNAs and their host genes exhibited distinct correlation patterns (##FIG##1##Figure 2##G). Taken together, these results suggest that core spliceosomal factors, splicing factors, and other RBPs might serve as regulators of the biogenesis of abundant circRNAs. However, this analysis only identified potential RBP regulators by measure of linear dependence/correlation relationships using PCCs between the expression of circRNAs and genes for RBPs. Thus, experimental analysis of RBP–RNA interaction will be required in the future to identify direct regulators of specific circRNA biogenesis by these RBPs.</p>", "<title>circRNA is involved in the regulation of AS by R-loop structures</title>", "<p id=\"p0075\">Our previous study revealed that overexpressing <italic>circ-IRX7</italic> in <italic>Populus trichocarpa</italic> decreased the rate of IntronR in the linear <italic>IRX7</italic> counterpart ##REF##33570252##[26]##. In this study, we used our RNA-seq and published data ##REF##24249833##[27]##, ##REF##27870853##[28]## to identify AS events in bamboo, <italic>A</italic>. <italic>thaliana</italic>, and <italic>O</italic>. <italic>sativa</italic>. We subsequently detected the locations of AS events within ecircRNAs and ciRNAs across the three species (##FIG##2##Figure 3##A and B; Table S3). To further validate if AS preferentially occurred within ecircRNAs, we randomly extracted the same number of messenger RNA (mRNA) segments without producing ecircRNAs and identified locations of AS events within these segments. The AS within the simulated random RNA segments had considerably lower frequencies than that observed within ecircRNAs (##FIG##2##Figure 3##C). This trend was also observed in <italic>A</italic>. <italic>thaliana</italic> and <italic>O</italic>. <italic>sativa</italic> (##FIG##2##Figure 3##C), which demonstrated that the elevated frequency of AS events within ecircRNAs might be conserved in different species. However, AS events located in the ciRNAs did not exhibit this trend (##FIG##2##Figure 3##D).</p>", "<p id=\"p0080\">PCCs between circRNAs and four types of AS events were calculated using their expression profiles according to circRNA sequencing (RPM) and RNA-seq (normalized reads that span splicing junctions), respectively. Approximately 19%–48% of circular transcripts in three species showed positive relationships with AS events (Table S3). To further validate the regulation of splicing by circRNAs, we selected <italic>circ-BRE1-1</italic> and <italic>circ-BRE1-2</italic>, which overlapped with ExonS and IntronR events from <italic>E3 ubiquitin-protein ligase BRE1-like 1</italic>, respectively (##FIG##2##Figure 3##E). Indeed, overexpression of <italic>circ-BRE1-1</italic> and <italic>circ-BRE1-2</italic> considerably changed the number of events in which the long isoforms of IntronR (linear <italic>BRE1-1</italic>) and ExonS (linear <italic>BRE1-2</italic>) were formed (##FIG##2##Figure 3##F), which indicates that circRNAs can modulate the AS events of their linear counterpart.</p>", "<p id=\"p0085\">It has been shown that the presence of <italic>circSEP3</italic> was derived from an exon of <italic>SEP3</italic>, which could result in exon skipping of its linear transcripts via an R-loop structure ##REF##28418376##[20]##. We therefore identified R-loop structures including AS events in transcribed regions of ecircRNAs by integrating circRNA, RNA-seq ##REF##27870853##[28]##, and R-loop data ##REF##28848233##[29]## from <italic>A</italic>. <italic>thaliana</italic>. Notably, transcribed regions of ecircRNAs had a considerably greater frequency of R-loop events compared with random regions (##FIG##2##Figure 3##G). Moreover, R-loop events were considerably more enriched in AS events than in random regions (##FIG##2##Figure 3##G). Camptothecin (CPT) is a TOP1 inhibitor that promotes R-loop accumulation in <italic>A</italic>. <italic>thaliana</italic>\n##REF##28412545##[30]##. We treated seedlings with dimethyl sulfoxide (DMSO) or CPT (10 nM), which revealed that seedlings treated with CPT had enhanced the abundance of <italic>circ-BRF1-1</italic> and long isoforms of IntronR (linear <italic>BRE1-1</italic>) in the transcribed regions of <italic>circ-BRF1-1</italic> (##FIG##2##Figure 3##H). Collectively, these findings indicated that circRNAs could regulate the AS frequency of their precursor transcripts, which may be related to R-loop structure formation by circRNA:DNA hybrids.</p>", "<title>circRNA is involved in the regulation of miRNA/siRNA-related genes</title>", "<p id=\"p0090\"><italic>circAGO2</italic> is generated from <italic>AGO2</italic> and represses AGO2/miRNA-mediated gene silencing ##REF##30341421##[31]##. In total, 163 miRNA-related genes were identified by sequence similarity analysis, and 79 miRNA-related genes, including <italic>AGO1</italic> and <italic>SDN1</italic>, were identified as host genes of circRNAs in moso bamboo (##FIG##3##Figure 4##A; Table S4). We selected <italic>circ-DCL4</italic>, which originates from <italic>DCL4</italic>, for further validation. An RNase R exonuclease experiment revealed the resistance to exonuclease, and sequencing also validated the back-splice sites in <italic>circ-DCL4</italic> (##FIG##3##Figure 4##B). Notably, overexpressing of <italic>circ-DCL4</italic> tended to decrease the expression level of its linear RNA (linear <italic>DCL4</italic>) (##FIG##3##Figure 4##C), which might explain its effect on the biogenesis of miRNAs and small interfering RNAs (siRNAs).</p>", "<title>circRNA is translatable in moso bamboo</title>", "<p id=\"p0095\">In this study, we developed a computational pipeline for detecting translatable open reading frames (ORFs) of circRNAs (cORFs) using proteomics (<xref rid=\"s0145\" ref-type=\"sec\">Figure S5</xref>A). Moreover, we identified upstream ORFs (uORFs) and downstream ORFs (dORFs) of linear transcripts. Annotated coding sequence (CDS) region for each gene was regarded as primary ORF (pORF). As shown in <xref rid=\"s0145\" ref-type=\"sec\">Figure S5</xref>B, a small proportion of cORFs, uORFs, and dORFs showed sequence similarity to entries in Non-Redundant Protein Sequence Database (NR), Database Of Plant Small ORFs (PsORF), and Universal Protein Resource (UniProt). For instance, a conserved cORF derived from <italic>circ-GLO5</italic> was homologous to small ORFs in plants from the PsORF database ##REF##32333496##[32]##, which indicated that these circRNAs might encode functional peptides (<xref rid=\"s0145\" ref-type=\"sec\">Figure S5</xref>C). As the third step, all ORFs were used as a search library for liquid chromatography–mass spectrometry/mass spectrometry (LC–MS/MS)-based proteomics to identify unique peptide evidence for each ORF. In total, 538 cORFs from 536 circRNAs (approximately 7.1% of all 7554 circRNAs) were predicted to be translatable based on proteomics evidence (<xref rid=\"s0145\" ref-type=\"sec\">Figure S5</xref>D; Table S5). For example, <italic>circ-P4H-1</italic> generated a detectable protein with a length of 289 aa spanning the back-splicing site with the evidence of a unique peptide (<xref rid=\"s0145\" ref-type=\"sec\">Figure S5</xref>E).</p>", "<title>miRNA-mediated cleavage of circRNAs</title>", "<p id=\"p0100\">Endonucleases RNase L has been reported to decay circRNAs globally in animals ##REF##31031002##[33]##. Sequence similarity analysis of RNase L from 67 animals revealed a high identity (on average 80.5%) and alignment length (on average 727 aa). By contrast, we did not identify RNase L sequences in 100 plants including moso bamboo (<xref rid=\"s0145\" ref-type=\"sec\">Figure S6</xref>A and B), suggesting that the decay of circRNAs in plants is not mediated by RNase L. Given that miR-671 was identified as a key regulator in the decay of <italic>CDR1as</italic>\n##REF##21964070##[18]##, we hypothesized that miRNAs may also be potential factors contributing to the decay of circRNAs in plants. We began by sequencing nine small RNA libraries constructed from the same material as circRNAs (##FIG##0##Figure 1##A). We detected 823 mature miRNAs including 164 conserved miRNAs and 659 variant miRNAs, which clustered to form 43 miRNA families (<xref rid=\"s0145\" ref-type=\"sec\">Figure S7</xref>A; Table S4). Conventional degradome sequencing ##REF##18542052##[34]## could not detect the cleavage of circular molecules due to the absence of 3′ poly(A) tails of circRNAs. Therefore, we modified the protocol for generating degradome libraries so that we could identify miRNA-mediated cleavage of circRNAs (##FIG##4##Figure 5##A). After poly(A) selection, total RNAs were separated into poly(A)− and poly(A)+ transcripts. Subsequently, the poly(A)− transcripts were subjected to ribosomal RNA (rRNA) depletion followed by immediate ligation to 5′ RNA adapters to enrich the cleavage transcripts of circRNAs including free 5′ monophosphate, whereas the 5′ monophosphate of poly(A)+ transcripts was directly ligated to the 5′ RNA adapter. Finally, these two types of degradome libraries were prepared by reverse transcription and sequenced. As expected, transcript regions including the 5′ untranslated region (5′ UTR), CDS, and 3′ UTR were more enriched with free 5′ monophosphate reads in the poly (A)+ library than in the poly (A)− library (##FIG##4##Figure 5##B). Consistent with previous observations that the cleavage transcripts were biased toward the 3′ end of mRNAs ##REF##18472421##[35]##, the poly(A)+ library also tended to generate more reads including free 5′ monophosphate in the 3′ UTR than in the 5′ UTR. However, the poly(A)− library did not exhibit this tendency (<xref rid=\"s0145\" ref-type=\"sec\">Figure S7</xref>B).</p>", "<p id=\"p0105\">We further developed a computational strategy to identify miRNA cleavage events in circRNAs, termed “degradome peaks in poly(A)− transcripts” (<xref rid=\"s0145\" ref-type=\"sec\">Figure S7</xref>C). In brief, degradome sequencing reads were first aligned to the genome using Bowtie 2 ##REF##22388286##[36]## to detect accumulated cleavage events termed “degradome peaks”. As indicated in ##FIG##4##Figure 5##C, degradome peaks within annotated transcript regions from each poly(A)+ library were considerably higher than those in the poly(A)− library from the same samples. The distribution of degradome peaks was considerably enriched in upstream and downstream regions of circRNAs, regardless of whether the peaks originated from poly(A)+ or poly(A)− libraries (##FIG##4##Figure 5##D, upper). We further compared the distribution of degradome peaks between poly(A)− and poly(A)+ libraries in host genes that generated circRNAs. We observed that the frequency of degradome peaks from the poly(A)− library (approximately 15%) was slightly higher (<italic>P</italic> = 1.49E−12, Fisher’s test) than that from the poly(A)+ library (approximately 13%) in the region of circRNAs (##FIG##4##Figure 5##D, lower).</p>", "<p id=\"p0110\">We calculated the distance from peaks to back-splicing sites to search for the decaying peaks spanning back-splicing sites (##FIG##4##Figure 5##E and F). The degradome reads from these peaks were then aligned to the 50 upstream and downstream nucleotides of back-splicing sites (<xref rid=\"s0145\" ref-type=\"sec\">Figure S7</xref>D). In total, degradome peaks from 118 circRNAs were revealed by degradome reads spanning back-splicing sites (##FIG##4##Figure 5##G). These results collectively suggest that our customized libraries and computational pipeline could effectively identify the decaying sites of poly(A)− transcripts, particularly for circRNAs.</p>", "<p id=\"p0115\">We further identified degradome peaks in the poly(A)− library originating from the miRNA-mediated cleavage of circRNAs. The 25 upstream and downstream nucleotides of specific degradome peaks were aligned to mature miRNAs by RNAplex ##REF##18434344##[37]## to identify candidate miRNA cleavage sites in the ±1-bp region of degradome peaks. Overall, 12 circRNAs and 548 linear RNAs were identified as the cleavage transcripts mediated by 43 and 632 miRNAs, respectively (##FIG##4##Figure 5##H; Table S6). For instance, we observed that <italic>ped-miRNA166</italic> mediated cleavage in <italic>circ-NHLRC2</italic> (##FIG##4##Figure 5##I). For further validation, we overexpressed <italic>circ-NHLRC2</italic> (OV1) and both <italic>circ-NHLRC2</italic> and <italic>miR166</italic> (OV2) (##FIG##4##Figure 5##J<bold>)</bold>. Semi-quantitative RT-PCR revealed that the expression of <italic>circ-NHLRC2</italic> was considerably increased in protoplasts transformed and overexpressing only <italic>circ-NHLRC2</italic> (OV1). By contrast, <italic>circ-NHLRC2</italic> exhibited a decreased tendency in the OV2 vector carrying both <italic>circ-NHLRC2</italic> and <italic>miR166</italic> (##FIG##4##Figure 5##J). Taken together, these observations suggest that miRNAs could contribute to the degradation of circRNAs in moso bamboo.</p>", "<title>circRNA expression is modulated by GA and NAA</title>", "<p id=\"p0120\">The plant hormones GA and NAA are essential for developmental processes in moso bamboo, including root germination and shoot development ##REF##29132316##[38]##, ##REF##29925317##[39]##. However, whether circRNAs respond to hormones has remained unknown. To perform quantitative analyses of circRNAs, we extracted back-splicing junctions relative to normalized circRNA abundance using RPM. Strikingly, the percentage of up-regulated circRNAs upon GA treatment was one-fold more than that of down-regulated circRNAs (27.1% up-regulated and 12.9% down-regulated), whereas substantially fewer were up-regulated than down-regulated upon NAA treatment (3.9% up-regulated and 22.3% down-regulated) (##FIG##5##Figure 6##A and B; Table S7). Furthermore, the expression patterns of seven tested circRNAs were found to be consistent with circRNA sequencing analysis using semi-quantitative RT-PCR (##FIG##5##Figure 6##A and B). For instance, <italic>circ-BRE1-1</italic> from <italic>E3 ubiquitin-protein ligase BRE1-like 1</italic> (PH02Gene28543) displayed much lower levels with GA hormone treatment, whereas NAA treatment resulted in higher levels of <italic>circ-DCL4</italic>. These findings indicate that both GA and NAA treatments induced notable changes and that alteration of circRNA levels was more sensitive to GA than to NAA (##FIG##5##Figure 6##C). Furthermore, transcript levels of 1390 circRNAs were both modulated by GA and NAA, as exemplified by <italic>circ-Q7XPY2</italic> (##FIG##5##Figure 6##C). GO enrichment analysis for differentially expressed circRNAs revealed that intracellular transport and response to external stimulus were highly enriched in response to GA and NAA treatment, respectively (##FIG##5##Figure 6##D).</p>", "<p id=\"p0125\">To further investigate the biological effects of hormone-induced circRNAs, we clustered the expression of circRNAs from different samples. As indicated in <xref rid=\"s0145\" ref-type=\"sec\">Figure S8</xref>A, the host genes for 67 considerably differentially expressed circRNAs were annotated as being related to second messengers, cell inclusion, plant organs, and plant hormones, namely, the abscisic acid and cytokinin pathways. Moreover, circRNAs resulting from rapid growth-related genes, including those related to the cell wall, cellulose, and lignin, were modulated in response to GA and NAA, which is consistent with the phenotype of seedling growth after hormone treatment (##FIG##5##Figure 6##E).</p>", "<p id=\"p0130\">The regulation of concentration gradients for gibberellin and auxin hormones is a key process in plants ##REF##18409210##[40]##, ##REF##29530380##[41]##. In total, 15 GA-related and 87 NAA-related genes were identified as parent genes that could produce circRNAs (Table S7). These circRNAs were likely to mediate biogenesis, function, and transport of gibberellins (<xref rid=\"s0145\" ref-type=\"sec\">Figure S8</xref>B) and auxins (<xref rid=\"s0145\" ref-type=\"sec\">Figure S8</xref>C). For example, <italic>circ-CPS1</italic> and <italic>circ-PhYUC5</italic> were resulted from PH02Gene47426 (<italic>CPS1</italic>) coding ent-copalyl diphosphate synthase 1 and PH02Gene12216 (<italic>PhYUC5</italic>) coding FMO-like, which are involved in gibberellin and auxin biosynthesis, respectively. PCC analysis between circRNAs (RPM) and their linear RNAs (FPKM) indicated that 89 circRNAs correlated in levels with their corresponding linear RNAs (##FIG##5##Figure 6##F). A striking example was <italic>circ-CSLA1</italic>, which is derived from <italic>glucomannan 4-beta-mannosyltransferase 1</italic> (<italic>CSLA1</italic>) and is involved in generating the backbone used for galactomannan synthesis by galactomannan galactosyltransferase ##REF##17307900##[42]##. <italic>circ-CSLA1</italic> was up-regulated in response to GA treatment. Overexpression of <italic>circ-CSLA1</italic> considerably reduced the levels of its linear RNA (##FIG##5##Figure 6##G). Collectively, our results indicated that alteration of circRNA expression in response to GA and NAA might also modulate the expression of host genes.</p>", "<p id=\"p0135\">As stable transformation is difficult in moso bamboo, and both bamboo and <italic>O</italic>. <italic>sativa</italic> are Poaceae family members ##REF##34059654##[43]##, we overexpressed six candidate circRNAs (<italic>circ-SPY</italic>, <italic>circ-MYBS3</italic>, <italic>circ-WRKY4</italic>, <italic>circ-CSLA1</italic>, <italic>circ-AGO1A</italic>, and <italic>circ-GID1</italic>) in rice via <italic>Agrobacterium</italic>-mediated transformation. Stably transformed lines showed successful transgene expression of the six circRNAs (##FIG##5##Figure 6##H). Among these six transformed lines, <italic>circ-AGO1A</italic> and <italic>circ-GID1</italic> increased plant height in three independent lines (##FIG##5##Figure 6##I and J, <xref rid=\"s0145\" ref-type=\"sec\">Figure S9</xref>), demonstrating that circRNAs have biological roles in plants.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0140\">Techniques involving profiling with poly(A)− RNA populations or RNase R enrichment have uncovered global expression of circRNAs ##REF##24039610##[24]##. In this study, our comprehensive sequencing of an RNase R-treated library identified 14,272 circRNAs (##FIG##0##Figure 1##A and B), suggesting that this type of library could enhance the identification of circRNAs. These expanded circRNAs raised the possibility of investigating the expression pattern, evolutionary conservation, and internal structure of circRNAs. Notably, the homologous circRNAs were present in low proportions (##FIG##0##Figure 1##D), which may be explained by the tissue-specific expression. Consistent with previous findings ##REF##27350239##[6]##, ##REF##27365365##[7]##, ##REF##25921068##[14]##, our identified circRNAs harbored alternative back-splicing, AS events, and MICs (##FIG##0##Figure 1##F). In total, over 60% of genes with circRNA AS events from CIRI-AS ##REF##27350239##[6]## overlapped with those from CIRCexplorer2 ##REF##27365365##[7]##, indicating that most of these events could be identified by the different methods.</p>", "<p id=\"p0145\">Emerging studies have revealed that ecircRNA formation is influenced by <italic>cis</italic>-regulatory elements such as ICSs flanking exons ##REF##25242744##[3]## and <italic>trans</italic>-regulatory factors ##REF##27365365##[7]##, ##REF##25921068##[14]##, ##REF##24039610##[24]##, ##REF##25543144##[25]##. Our study strongly indicates that artificial RNA pairing with ICSs could enhance back-splicing efficiency in moso bamboo (##FIG##1##Figure 2##B), although the exons of circular transcripts lack native flanking intronic pairing sequences (##FIG##1##Figure 2##A). Intriguingly, overexpression of ecircRNAs with included or excluded interior introns suggests that interior introns contained within multiple circularized exons may not be a key regulatory element for the biogenesis of circRNAs (##FIG##1##Figure 2##C). However, an extended investigation of the splicing of interior introns in other circRNAs is required to obtain a more comprehensive conclusion.</p>", "<p id=\"p0150\">Several known <italic>trans</italic>-factors reported to participate in circRNA regulation ##REF##27365365##[7]##, ##REF##25921068##[14]##, ##REF##24039610##[24]##, ##REF##25543144##[25]## also exhibited strong associations with circular molecules in our samples (##FIG##1##Figure 2##E). For example, QKI was more closely correlated with 579 ecircRNAs than with 423 ciRNAs. Knockdown analysis further confirmed the alteration in abundance for four selected circRNAs (##FIG##1##Figure 2##E). However, we still do not know whether there is direct regulation of these RPBs on specific motifs or circRNA transcripts due to the lack of RBP–RNA interaction experiment. It will be interesting to investigate these <italic>trans</italic>-regulatory factors for binding motifs around circRNAs using high-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation (CLIP-seq) ##REF##26099751##[44]##.</p>", "<p id=\"p0155\">Combining RNase R-treated circRNA libraries with a common RNA-seq library provided us the opportunity to comprehensively explore the relationship between circRNAs and the AS of their linear counterparts. We identified several potential regulatory circRNAs, such as <italic>circ-BRE1-1</italic> and <italic>circ-BRE1-2</italic>, which like <italic>circSEP3</italic>\n##REF##28418376##[20]##, affected the AS of their precursor transcripts in <italic>Phyllostachys edulis</italic>, <italic>A</italic>. <italic>thaliana</italic>, and <italic>O</italic>. <italic>sativa</italic> (##FIG##2##Figure 3##C–F). Subsequently, we observed that transcribed regions of circRNAs overlapped R-loop events and AS events with considerably greater frequency than random regions (##FIG##2##Figure 3##G). The abundance of long isoforms (linear <italic>BRF1</italic>) was increased after treatment with TOP1 inhibitor, which functions in promoting R-loop accumulation. This result indicated that the R-loop structure could be a potential AS regulator of host genes. Furthermore, <italic>circ-BRF1</italic> also exhibited the identical trend with linear <italic>BRF1</italic>. However, further research is needed to elucidate the relationships between R-loops, AS, and circRNAs, for example, using knockdown analysis of R-loop and a single-strand DNA ligation-based library preparation technique (ssDRIP-seq) ##REF##28848233##[29]##, which should reveal whether R-loop accumulation can influence circRNA abundance and thus promote AS at the genome-wide level.</p>", "<p id=\"p0160\">Our data showed that partial circRNAs could originate from miRNA-related genes. A striking sample was <italic>circ-DCL4</italic>, which was validated by RNase R exonuclease treatment and Sanger sequencing (##FIG##3##Figure 4##B). Overexpression of <italic>circ-DCL4</italic> reduced the expression levels of linear <italic>DCL4</italic> considerably (##FIG##3##Figure 4##C), which suggested that circular transcripts might participate in miRNA biogenesis, activity, and degradation by modulating the level of miRNA-associated genes. The correlation in levels between circRNAs and 823 mature miRNAs provided evidence for this hypothesis (Table S4). In the future, improvement of <italic>Agrobacterium</italic>-mediated transformation efficiency in moso bamboo would allow work to identify how many miRNAs or siRNAs are changed in expression upon overexpressing these specific circRNAs.</p>", "<p id=\"p0165\">We found that plants appear to lack homologs of human RNase L (<xref rid=\"s0145\" ref-type=\"sec\">Figure S6</xref>A and B), which led us to test whether miRNAs contribute to the initiation of degradation of circRNAs, similar to linear RNAs in plants. Degradome sequencing is the gold standard for identifying miRNA-mediated cleavage on a transcriptome-wide scale. However, current efforts have not yet detected miRNA-mediated cleavage of circRNAs using conventional degradome sequencing, largely due to the absence of 3′ poly(A) tail on circRNAs. To overcome this limitation, we modified library preparation for degradome sequencing to enrich the decaying transcripts of circRNA without poly(A) tails (##FIG##4##Figure 5##A) and developed a computational pipeline to identify the cleavage sites in poly(A)− RNA (<xref rid=\"s0145\" ref-type=\"sec\">Figure S7</xref>C). The enrichment and accurate identification of cleavage sites from customized libraries were assessed based on the distribution of degradome reads (##FIG##4##Figure 5##B–D, <xref rid=\"s0145\" ref-type=\"sec\">Figure S7</xref>B) and cleavage transcripts spanning the back-splicing sites (##FIG##4##Figure 5##E–H and 6D). Ultimately, 12 circRNAs were identified as cleavage transcripts mediated by miRNAs (##FIG##4##Figure 5##H). Overexpressing <italic>miR166</italic> down-regulated the expression of <italic>circ-NHLRC2</italic> (##FIG##4##Figure 5##I and J), which provides evidence for miRNA-mediated cleavage of circRNA. However, further investigation is needed to elucidate similarities and differences in miRNA-mediated cleavage mechanisms between circRNAs and linear transcripts, the latter of which involves the major effector endonuclease AGO1 ##REF##18342361##[45]##.</p>", "<p id=\"p0170\">Quantitative analyses allowed us to identify core circRNAs involved in the response to GA and NAA. A total of 1390 circRNAs modulated by both GA and NAA could function as potential mediators of cross-talk between GA and NAA (##FIG##5##Figure 6##C). Further investigation of the biological functions of these hormone-induced circular transcripts indicated that these circRNAs might be involved in processes related to plant hormones, second messengers, cell inclusion bodies, and plant organs (<xref rid=\"s0145\" ref-type=\"sec\">Figure S8</xref>). Notably, genes related to rapid growth, particularly those affecting the cell wall, cellulose, and lignin, also generated considerably differentially expressed circRNAs, which was consistent with the growth-related phenotypes of the hormone-treated seedlings (##FIG##5##Figure 6##E). In addition, circRNAs derived from 15 GA-related and 87 NAA-related genes were likely to mediate biogenesis, function, and transport processes of gibberellin and auxin molecules (<xref rid=\"s0145\" ref-type=\"sec\">Figure S8</xref>B and C). Together, these findings indicate a link between circRNAs and hormones, although further experiments such as the transgenic expression of circRNAs associated with hormone regulation are required to elucidate the underlying mechanisms in bamboo.</p>", "<p id=\"p0175\">In previous studies, genes from moso bamboo were overexpressed in <italic>A</italic>. <italic>thaliana</italic> and <italic>O</italic>. <italic>sativa.</italic> In total, 54 genes from previous studies have been reported to play key roles based on <italic>Agrobacterium</italic>-mediated transformation ##REF##30042769##[46]##, ##REF##32040757##[47]##, ##UREF##0##[48]##, ##REF##30669467##[49]##, ##REF##28916739##[50]##, ##REF##32318830##[51]##, ##REF##31128699##[52]##, ##REF##30176795##[53]##, ##UREF##1##[54]##, ##REF##27021381##[55]##, ##REF##28751687##[56]##, ##REF##28168515##[57]##, ##REF##32333784##[58]##. Among these overexpressed genes, we found 12 genes to generate circRNAs in this study (Table S8). For example, <italic>CWINV4</italic>, encoding cell wall invertase, increased plant height and dry weight in <italic>A</italic>. <italic>thaliana</italic>\n##REF##32333784##[58]## and generated two circRNAs. It will be interesting to investigate the biological role of these circRNAs in bamboo. Here, we overexpressed six candidate circRNAs in rice and observed influences on plant height phenotypes from <italic>circ-AGO1A</italic> and <italic>circ-GID1</italic> (##FIG##5##Figure 6##J), which suggested that some circRNAs have biological roles. The precise roles of these circRNAs could be investigated in the endogenous bamboo system if <italic>Agrobacterium</italic>-mediated transformation efficiency improves in moso bamboo in the future.</p>", "<p id=\"p0180\">Overall, our study not only enhances the view of hormone responses in moso bamboo (##FIG##6##Figure 7##, Module I) but also expands the understanding of circRNAs, including biogenesis (##FIG##6##Figure 7##, Module II), miRNA-mediated degradation (##FIG##6##Figure 7##, Module III), and function (##FIG##6##Figure 7##, Module IV). In particular, our results dissected the interplay between hormones and circRNA metabolism (##FIG##6##Figure 7##; Table S9). First, the expression levels of circRNAs exhibited high correlation with those of 96 splicing factor genes, including five GA-induced factors and two NAA-induced factors (##FIG##6##Figure 7##; Table S9), which was consistent with our findings that alteration of circRNA levels upon GA treatment was more sensitive than that upon NAA treatment (##FIG##6##Figure 7##, Module II: circRNA biogenesis). Second, circRNAs were cleaved by RNA-induced silencing complex (RISC), including three GA-induced RISC and one NAA-induced RISC. We further found that seven circRNAs were subject to miRNA-mediated cleavage in response to hormone treatment, suggesting that hormones might affect the degradation of circRNAs by modulating the expression of RNA silencing complex (RSCs) (##FIG##6##Figure 7##, Module III: circRNA degradation). The steady-state abundance of circRNAs will depend on the balance between these processes of circRNA biogenesis and degradation. Finally, we revealed potential functions of circRNAs, including regulation of AS, translation, and gene expression (##FIG##6##Figure 7##, Module IV: circRNA function). In total, 379 GA-induced circRNAs and 223 NAA-induced circRNAs were positively correlated with AS of their host gene, indicating that these differentially expressed circRNAs might alter AS events in response to hormone signals. Notably, several circRNAs, such as <italic>circ-SF3B2-1</italic>, <italic>circ-EMA1</italic>, and <italic>circ-MYBH</italic>, might be involved in the metabolism of both circRNAs and hormones by affecting the splicing of their linear mRNA counterparts (##FIG##6##Figure 7##).</p>", "<p id=\"p0185\">We further provide evidence that translatable circRNAs might generate functional peptides. We found that translatable circRNAs exhibited dynamic expression upon exposure to hormones. For example, <italic>circ-MYBS</italic> generated a detectable unique peptide, which might play potential roles in regulating hormone metabolism. Moreover, circRNAs could regulate transcription of their parental genes (##FIG##6##Figure 7##, Module IV: circRNA function). A striking example was <italic>circ-DCL4</italic>, originated from miRNA-related genes, which tended to reduce the accumulation level of its linear RNA. The expression of genes related to hormone metabolism might be regulated by several circRNAs, including <italic>circ-CTR1</italic>, <italic>circ-ACL5</italic>, and <italic>circ-IAA7</italic> (##FIG##6##Figure 7##). Taken together, our results highlight the potential interplay between hormone metabolism and circRNA biogenesis, function, and degradation.</p>" ]
[]
[ "<p id=\"np010\">Equal contribution.</p>", "<p><bold>Circular RNAs</bold> (circRNAs) are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GAs) and auxins (1-naphthaleneacetic acid, NAA) remain unknown. Here, we systematically identified and characterized the expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (<bold><italic>Phyllostachys edulis</italic></bold>) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both <italic>cis</italic>- and <italic>trans</italic>-regulation. We explored the function of circRNAs, including their roles in regulating microRNA (miRNA)-related genes and modulating the <bold>alternative splicing</bold> of their linear counterparts. Importantly, we developed a customized <bold>degradome</bold> sequencing approach to detect miRNA-mediated cleavage of circRNAs. Finally, we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and NAA. Collectively, our study provides insights into the biogenesis, function, and miRNA-mediated degradation of circRNAs in moso bamboo.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Xiangfeng Wang</p>" ]
[ "<title>Code availability</title>", "<p id=\"p0275\">The codes have been submitted to BioCode at the National Genomics Data Center (NGDC), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS) / China National Center for Bioinformation (CNCB) (BioCode: BT007322), which are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/biocode/tools/BT007322\" id=\"PC_linknbuQMZDlMg\">https://ngdc.cncb.ac.cn/biocode/tools/BT007322</ext-link>.</p>", "<title>Data availability</title>", "<p id=\"p0270\">Raw sequencing data from mRNA sequencing, circRNA sequencing, degradome sequencing, and small RNA sequencing have been deposited in the Genome Sequence Archive ##REF##34400360##[80]## at the NGDC, BIG, CAS / CNCB (GSA: CRA007877) , and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa\" id=\"ir010\">https://ngdc.cncb.ac.cn/gsa</ext-link>. Raw sequencing data for all the libraries have also been submitted to the NCBI Gene Expression Omnibus (GEO: PRJNA707140).</p>", "<title>Competing interests</title>", "<p id=\"p0280\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0285\"><bold>Yongsheng Wang:</bold> Methodology, Investigation, Software, Validation, Writing – original draft. <bold>Huihui Wang:</bold> Investigation, Validation. <bold>Huiyuan Wang:</bold> Software, Data curation. <bold>Ruifan Zhou:</bold> Investigation, Validation. <bold>Ji Wu:</bold> Validation. <bold>Zekun Zhang:</bold> Software. <bold>Yandong Jin:</bold> Validation. <bold>Tao Li:</bold> Validation. <bold>Markus V. Kohnen:</bold> Software. <bold>Xuqing Liu:</bold> Validation. <bold>Wentao Wei:</bold> Validation. <bold>Kai Chen:</bold> Validation. <bold>Yubang Gao:</bold> Software. <bold>Jiazhi Ding:</bold> Validation. <bold>Hangxiao Zhang:</bold> Software. <bold>Bo Liu:</bold> Conceptualization. <bold>Chentao Lin:</bold> Conceptualization. <bold>Lianfeng Gu:</bold> Conceptualization, Writing – review &amp; editing, Supervision. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0300\">The following are the Supplementary data to this article:</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<p id=\"p0325\">\n\n</p>", "<p id=\"p0330\">\n\n</p>", "<p id=\"p0335\">\n\n</p>", "<p id=\"p0340\">\n\n</p>", "<p id=\"p0345\">\n\n</p>", "<p id=\"p0350\">\n\n</p>", "<p id=\"p0355\">\n\n</p>", "<p id=\"p0360\">\n\n</p>", "<p id=\"p0365\">\n\n</p>", "<p id=\"p0370\">\n\n</p>", "<p id=\"p0375\">\n\n</p>", "<p id=\"p0380\">\n\n</p>", "<p id=\"p0385\">\n\n</p>", "<p id=\"p0390\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0290\">This work was supported by the National Natural Science Foundation of China (Grant Nos. 31971734 and 31800566), the National Key R&amp;D Program of China (Grant No. 2021YFD2200505), the Distinguished Young Scholar Program of Fujian Agriculture and Forestry University (Grant No. xjq202017), the Scientific Research Foundation of Graduate School of Fujian Agriculture and Forestry University (Grant No. 324-1122yb061), and the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University (Grant No. 72202200205), China.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Characterization of circRNAs in moso bamboo</bold></p><p><bold>A.</bold> Flow chart for multi-omics sequencing including mRNA sequencing, circRNA sequencing, degradome sequencing, and small RNA sequencing upon hormone treatment. <bold>B.</bold> Venn diagram showing the number of circRNAs detected in different samples (upper panel). The density plot of back-splicing reads supporting circRNAs (lower panel). <bold>C.</bold> Validation of circRNAs using RT-PCR after RNase R treatment with linear RNA (<italic>NTB</italic>) as control (left panel). Sanger sequencing validated back-splicing junctions of <italic>circ-RAD16</italic>, which was not resistant to RNase R (right panel). <bold>D.</bold> Number (left) and overlap (right) of circRNAs in <italic>Arabidopsis thaliana</italic> and <italic>Oryza sativa</italic> L. that show homology to circRNAs in moso bamboo. <bold>E.</bold> Multiple sequence alignment of conserved <italic>circ-GSL1</italic>. Asterisk symbols indicate highly conservative nucleotides. <bold>F.</bold> Diagrams of different AS types (left panel) and percentage of these circRNAs (right panel). Gray bars and black lines represent exons and introns, respectively. Dotted curves and colored bars indicate AS events. Colored arced lines represent back-splicing (circularization). <bold>G.</bold> GO enrichment analysis of circRNAs with AS events. Darker orange node color indicates more significant <italic>P</italic> values. The circle size is proportional to the number of genes enriched in the terms. The arrows represent hierarchical relations between GO terms. circRNA, circular RNA; AS, alternative splicing; GO, Gene Ontology; A3SS, alternative 3′ splice site; A5SS, alternative 5′ splice site; ExonS, exon skipping; IntronR, intron retention; A3BS, alternative 3′ back-splice site; A5BS, alternative 5′ back-splice site; MIC, mutually inclusive circRNA; mRNA, messenger RNA; RT-PCR, reverse transcription-polymerase chain reaction; GA, gibberellin; NAA, 1-naphthaleneacetic acid.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Biogenesis of circRNAs in moso bamboo</bold></p><p><bold>A.</bold> Distribution of ICSs (brown arrows) in flanking introns of ecircRNAs. Circularized exon and flanking intron are indicated by green bar and gray line, respectively. <bold>B.</bold> Schematic drawings show expression vectors including flanking ICSs (brown arrows), circularized exon (green bar), and linear exon (yellow bar). PCR primers for circRNAs are indicated by black arrows. Semi-quantitative RT-PCR in the lower panel shows circularization efficiency for circularized exon and linear exon, respectively. <bold>C.</bold> Experimental detection of the function of introns in multiple exon circularization of <italic>circ-PKL1</italic>. Schematic drawings of expression vectors including or excluding interior introns. Semi-quantitative RT-PCR in the lower panel shows circularization efficiency of <italic>circ-PKL1</italic> with or without interior intron. <bold>D.</bold> Percentage of circRNAs showing high PCC (<italic>r</italic> ≥ 0.5 or <italic>r</italic> ≤  −0.5) with proteins SF3A, SF3B, FUS, HNRNPL, QKI, NF90, and DHX9. <bold>E.</bold> RNAi knockdown of <italic>PedQKI</italic>. Schematic drawing in the upper panel shows RNAi expression vector to knock down expression of <italic>PedQKI</italic>. The lower panel shows PCR-based validation of the expression of six randomly selected circRNAs in the <italic>QKI</italic> RNAi sample. <italic>ATCB</italic> is a housekeeping gene used as a control.  <bold>F.</bold> PCCs between circRNAs and 17 proteins including 1, 2, and 14 core spliceosomal factors, splicing factors, and other RBPs, respectively. Number in the right panel indicates percentage of circRNAs with high PCC to those proteins. <bold>G.</bold> Distribution of PCCs between ecircRNAs/ciRNAs and linear RNAs generated from the same host genes. ecircRNA, exonic circRNA; ICS, inverted complementary sequence; EV, empty vector; OV, overexpression vector; NOS, nopaline synthase; PCC, Pearson correlation coefficient; RNAi, RNA interference; RBP, RNA-binding protein; ciRNA, circular intronic RNA.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>circRNAs regulate AS in moso bamboo</bold></p><p><bold>A.</bold> Overview of overlapping regions between AS events and ecircRNAs. White bars indicate exons, black bars indicate introns, blue arrows indicate AS events, and colored arced lines indicate back-splicing junctions. <bold>B.</bold> Overview of overlapping regions between AS events and ciRNAs. <bold>C.</bold> The histograms show the number of AS events in the transcribed regions of ecircRNAs (brown bars) and random RNA segments (gray bars) in three species. <bold>D.</bold> The histograms show the number of AS events in the transcribed regions of ciRNAs (light yellow bars) and random RNA segments (gray bars) in three species. <bold>E.</bold> Visualization of IntronR and ExonS events in transcribed regions of <italic>circ-BRE1</italic> and <italic>circ-BRE2</italic>, respectively. <bold>F.</bold> RT-PCR validation of <italic>circ-BRE1-1</italic> and <italic>circ-BRE1-2</italic> and their corresponding AS events, linear <italic>BRE1-1</italic> and linear <italic>BRE1-2</italic>. Divergent arrows represent divergent primers, and convergent arrows represent convergent primers. Linear RNA of <italic>ACTB</italic> was used as a control. <bold>G.</bold> The histogram plot shows the overlap between R-loop and AS events in transcribed regions of ecircRNAs. Black arrow in the left panel indicates the observed number of ecircRNAs located in R-loop regions. <bold>H.</bold> Root phenotype upon DMSO and CPT treatment (left panel). Semi-quantitative RT-PCR shows the expression of <italic>circ-BRE1-1</italic> and linear <italic>BRE1-1</italic> upon CPT treatment (right panel). R-loop, RNA:DNA hybrid; AltA, alternative acceptor; AltD, alternative donor; DMSO, dimethyl sulfoxide; CPT, camptothecin.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>c</bold><bold>ircRNAs regulate miRNA-associated genes in moso bamboo</bold></p><p><bold>A.</bold> The upper panel shows the miRNA-associated genes involved in several major steps in miRNA biogenesis and modes of action in plants. The table in the lower panel shows the number of miRNA-associated genes and their corresponding circRNAs. <bold>B.</bold> RT-PCR and Sanger sequencing for validation of <italic>circ-DCL4</italic> with RNase R treatment. <bold>C.</bold> The left panel shows the vector construction for <italic>circ-DCL4</italic> and linear <italic>DCL4</italic>. RT-PCR validation in the right panel shows the overexpression of <italic>circ-DCL4</italic> and expression of linear <italic>DCL4</italic>. miRNA, microRNA; HEN1, small RNA 2′-<italic>O</italic>-methyltransferase; CDKF, cyclin-dependent kinase F-1; HST, shikimate <italic>O</italic>-hydroxycinnamoyltransferase.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>miRNA-mediated cleavage of circRNAs in moso bamboo</bold></p><p><bold>A.</bold> Flow chart for construction of customized degradome libraries for enriching the decaying circRNA without poly(A) tails. <bold>B.</bold> The box line plot shows the distribution of reads in 5′ UTR, CDS, and 3′ UTR of the gene from poly(A)+ and poly(A)− degradome libraries. <bold>C.</bold> The UpSet plot shows the intersection of cleavage sites among different types of libraries and different hormone treatments. The histogram plot in the upper panel shows the number of cleavage sites shared by different libraries. The histogram plot in the lower panel and the line plot in the right panel show total cleavage sites from each library and the combination of different libraries. <bold>D.</bold> Plot in the upper panel shows the distribution of cleavage sites from two types of libraries in genes divided into three groups: the upstream region of circRNA body, downstream region of circRNA body, and circRNA body. Bar in lower panel shows the percentage of cleavage sites from two types of libraries in transcript regions of circRNAs. <bold>E.</bold> Schematic overview of decaying reads of circRNAs spanning back-splicing sites. Gray bars represent exons, black lines represent introns, black arrows represent cleavage sites, and colored arced lines represent back-splicing. Blue bars and dash arced lines indicate the mapped back-splicing junction reads. <bold>F.</bold> Length distribution between cleavage sites and the 3′ end of transcribed regions of circRNAs. <bold>G.</bold> Venn diagram shows the number of three subgroups. Subgroups 1, 2, and 3 represent the number of circRNAs including cleavage sites based on degradome sequencing, the number of circRNAs with a distance of &lt; 47 nt between cleavage sites and the 3′ end of transcriptional regions of circRNAs, and the number of circRNAs determined by degradome reads spanning back-splicing sites. <bold>H.</bold> Number of circRNAs and linear RNAs including miRNA-mediated cleavage. <bold>I.</bold> Schematic overview of <italic>miR166</italic>-mediated cleavage sites in <italic>circ-NHLRC2</italic>. <bold>J.</bold> The upper panel shows the vector construction for overexpressing <italic>circ-NHLRC2</italic> only (OV1) or both <italic>circ-NHLRC2</italic> and <italic>miR166</italic> (OV2). The lower panel indicates the expression of <italic>circ-NHLRC2</italic> and <italic>miR166</italic> detected by RT-PCR. Divergent and convergent arrows represent divergent and convergent primers, respectively. rRNA, ribosomal RNA; CDS, coding sequence; UTR, untranslated region; TSS, transcription start site; TTS, transcript termination site.</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>Hormone-induced circRNAs in moso bamboo</bold></p><p><bold>A.</bold> The scatterplot in the left panel shows RPMs for H<sub>2</sub>O (X-axis) and GA treatments (Y-axis). Semi-quantitative PCR using divergent primers in the right panel validated the differential expression data of circRNAs in response to GA treatments with linear <italic>ACTB</italic> as internal reference gene using convergent primers. <bold>B.</bold> The scatterplot shows the differential levels of circRNAs in response to NAA, and semi-quantitative PCR shows the validation of the levels of circRNAs based on sequencing. <bold>C.</bold> Venn diagram shows overlapping and unique differential circRNAs in response to GA and NAA. <bold>D.</bold> The histogram plot shows the top 10 GO terms enriched for hormone-induced circRNAs. <bold>E.</bold> Heatmap showing expression levels of circular transcripts related to cell wall, cellulose, and lignin. Red or blue represents high and low abundance of circRNAs, respectively. Image and bar chart in the right panel show the phenotype and height of seedlings upon GA and NAA treatments after 2 weeks. <bold>F.</bold> The PCCs of circRNAs and their host linear RNAs related to fast growth, NAA, and GA. <bold>G.</bold> The vector construction (left panel) and RT-PCR validation (right panel) of <italic>circ-CSLA1</italic> and linear <italic>CSLA1</italic>. Divergent and convergent arrows represent divergent and convergent primers, respectively. <bold>H.</bold> RT-PCR using divergent primers revealed the expression levels of circRNAs in six transformed lines (T1 generation). <bold>I.</bold> The histogram shows the plant height of 24-day-old rice seedlings transformed by <italic>circ-SPY</italic>, <italic>circ-MYBS3</italic>, <italic>circ-WRKY4</italic>, <italic>circ-CSLA1</italic>, <italic>circ-AGO1A</italic>, and <italic>circ-GID1</italic>, respectively. <bold>J.</bold> The phenotypes of plant height of rice seedlings transformed by <italic>circ-AGO1A</italic> and <italic>circ-GID1</italic>. RPM, reads per million; FPKM, fragments per kilobase of exon model per million mapped fragments; WT, wild type; OE, Over expression.</p></caption></fig>", "<fig id=\"f0035\"><label>Figure 7</label><caption><p><bold>The potential interplay between hormone and circRNA metabolism</bold></p><p>Module I: circRNAs originating from hormone-related genes exhibit dynamic expression upon exposure to GA and NAA. Module II: hormones could affect circRNA biogenesis by regulating several splicing factors. Module III: hormones could regulate the degradation of circRNAs though modulating RSC. Module IV: functional circRNAs might regulate hormone metabolism by regulating splicing and transcription of their linear cognates or generating potential proteins from translatable circRNAs. RISC, RNA-induced silencing complex; RSC, RNA silencing complex.</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0095\"><caption><title>Supplementary Figure S1</title><p><bold>GO enrichment analysis for the homologous circRNAs detected in three plants</bold> GO terms on the X-axis are categorized into three types with different colors. The Y-axis indicates the percentage (left Y-axis) and number (right Y-axis) of host genes including homologous circRNAs.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0090\"><caption><title>Supplementary Figure S2</title><p><bold>Length of flanking introns</bold> Cumulative curve and boxplots of the length of upstream and downstream flanking introns of circRNAs in comparison with control introns.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0085\"><caption><title>Supplementary Figure S3</title><p><bold>Distribution of PCCs between circRNAs and RBPs A.</bold> Bar plot of the distribution of PCCs between circRNAs and 24 core spliceosomal components, 92 splicing factors, and 1132 other RBPs excluding splicing factors and core spliceosomal components in bamboo. <bold>B.</bold> Scatterplot of distribution of PCCs between circRNAs and seven RPBs (SF3A, SF3B, NF90, DHX9, FUS, HNRNPL, and QKI) in bamboo.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0080\"><caption><title>Supplementary Figure S4</title><p><bold>Evolutionary trees of human QKI and its 34 homologous proteins in moso bamboo</bold> KH domains are indicated as yellow bars. KH, K homology.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0075\"><caption><title>Supplementary Figure S5</title><p><bold>Translatable circRNAs in moso bamboo A.</bold> Overview of the identification and annotation of the potential cORFs. <bold>B.</bold> The histogram plot shows the percentage of homologous cORFs, uORFs, and dORFs with known protein databases. <bold>C.</bold> Phylogenetic analysis of the cORF of <italic>circ-GLO5</italic> and six homologous cORFs from other species. <bold>D.</bold> Number of the translatable cORFs, uORFs, dORFs, and pORFs based on proteomics. <bold>E.</bold> The MS spectra of cORFs from <italic>circ-P4H-1</italic>. The a, b, and y ions are indicated by red, green, and blue lines, respectively. ORFs, open reading frames; cORFs, ORFs of circRNAs; uORFs, upstream ORFs; dORFs, downstream ORFs; pORFs, primary ORFs; MS, mass spectrometry/mass spectrometry ; m/z, Mass to charge ratio ; Nr, Non-Redundant Protein Sequence Database; PsORF, Database Of Plant Small ORFs; UniProt, Universal Protein Database.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0070\"><caption><title>Supplementary Figure S6</title><p><bold>Homology analysis of RNase L A.</bold> Multiple sequence alignment of RNase L in different species. <bold>B.</bold> The histogram plot shows the number of homologous proteins.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0065\"><caption><title>Supplementary Figure S7</title><p><bold>Construction and analysis of degradome libraries A.</bold> The histogram plot shows the number of miRNAs and top 15 miRNA families. <bold>B.</bold> The boxplot shows the distribution of reads in the 5' UTR, CDSs, and 3' UTR from poly(A)+ and poly(A)− degradome libraries. <bold>C.</bold> A computational pipeline for identifying cleavage sites based on two types of degradome libraries. <bold>D.</bold> A computational pipeline for detecting decaying transcripts of circRNAs spanning back-splicing sites.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Figure S8</title><p><bold>Potential function of hormone-induced circRNAs A.</bold> Heatmap showing expression levels of circular transcripts related to the GO biological process terms plant hormones, second messenger, cell inclusion bodies, and plant organs. <bold>B.</bold> The events in the presence of gibberellin. <bold>C.</bold> The events in the presence of auxin. Red genes indicate host genes that generated circRNAs. The light-green box indicates biosynthesis, light purple indicates transport, and light yellow indicates signaling. Black arrows indicate positive effects, and black dashed lines indicate negative effects.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Figure S9</title><p><bold>The overexpression of six candidate circular RNAs (<italic>circ-SPY</italic>, <italic>circ-MYBS3</italic>, <italic>circ-WRKY4</italic>, <italic>circ-CslA1</italic>, <italic>circ-AGO1A</italic>, and <italic>circ-GID1</italic>) in rice.</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Table S1</title><p><bold>Statistical data for sequencing and circRNAs in seedlings of moso bamboo</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S2</title><p><bold>Core spliceosomal factors, splicing factors, and other RBPs with higher Pearson correlation coefficients</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S3</title><p><bold>Alternative splicing events located in transcribed regions of circRNAs in the three species</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S4</title><p><bold>Identified mature miRNAs and miRNA-related gene in moso bamboo</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S5</title><p><bold>CircRNAs and linear RNAs decayed by miRNAs</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S6</title><p><bold>Translatable circRNAs and translation-related proteins</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S7</title><p><bold>Differentially expressed circRNAs and GA and NAA hormone-related genes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S8</title><p><bold>Genes from bamboo transformed into <italic>Arabidopsis thaliana</italic>, <italic>Oryza sativa</italic>, and <italic>Nicotiana tabacum</italic></bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S9</title><p><bold>Interplay between hormone (GA and NAA) treatment and circRNA metabolism</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S10</title><p><bold>Primers for validation and transformation of circRNAs</bold></p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e276\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0140\" fn-type=\"supplementary-material\"><p id=\"p0295\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2023.01.007\" id=\"ir015\">https://doi.org/10.1016/j.gpb.2023.01.007</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["48"], "surname": ["Cui", "Zhang", "Qi", "Gao", "Chen", "Zhang"], "given-names": ["X.", "Y.", "F.", "J.", "Y.", "C."], "article-title": ["Overexpression of a moso bamboo ("], "italic": ["Phyllostachys edulis", "PheWRKY1", "Arabidopsis thaliana"], "source": ["Botany"], "volume": ["91"], "year": ["2013"], "fpage": ["486"], "lpage": ["494"]}, {"label": ["54"], "surname": ["Wang", "Yang", "Lou", "Wei", "Zhao", "Ren"], "given-names": ["T.", "Y.", "S.", "W.", "Z.", "Y."], "article-title": ["Genome-wide characterization and gene expression analyses of GATA transcription factors in moso bamboo ("], "italic": ["Phyllostachys edulis"], "source": ["Int J Mol Sci"], "volume": ["21"], "year": ["2020"], "fpage": ["14"]}, {"label": ["69"], "surname": ["Chen", "Hu", "Xi", "Wang", "Kohnen", "Gao"], "given-names": ["K.", "K.", "F.", "H.", "M.V.", "P."], "article-title": ["High-efficient and transient transformation of moso bamboo ("], "italic": ["Phyllostachys edulis", "Dendrocalamus latiflorus"], "source": ["J Plant Biol"], "volume": ["66"], "year": ["2021"], "fpage": ["75"], "lpage": ["86"]}]
{ "acronym": [], "definition": [] }
80
CC BY
no
2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Aug 16; 21(4):866-885
oa_package/8f/a6/PMC10787125.tar.gz
PMC10787127
36775055
[ "<title>Introduction</title>", "<p id=\"p0010\">Gene expression includes two major stages, transcription and translation, with the former generating RNAs and the latter generating proteins, which are spatially separated in eukaryote cells. Studies have shown the importance of post-transcriptional activities that occur involving mRNAs, including splicing, editing, capping, poly(A) tailing, and modification ##REF##19742130##[1]##, ##REF##27412912##[2]##, ##REF##25590224##[3]##. Compared with studies on the function of alternative splicing ##REF##30829570##[4]##, ##REF##25922281##[5]## and poly(A) tail of mRNA ##REF##29440281##[6]##, ##REF##32576858##[7]##, ##UREF##0##[8]##, ##REF##29223924##[9]##, ##REF##30503240##[10]##, studies on the base modifications of RNA are still far behind, although they were first discovered more than 60 years ago ##REF##13463012##[11]##. To date, more than 160 RNA base modifications with different biological functions have been detected ##REF##29106616##[12]##, ##REF##28533024##[13]##, ##REF##28216634##[14]##, which are much more abundant than the modifications on DNA. These modifications allow more complexity in gene expression regulation at the post-transcriptional level. Among them, <italic>N</italic><sup>6</sup>-methyladenosine (m<sup>6</sup>A) is one of the most common modifications in the transcriptome of eukaryotes and occurs in nearly all kinds of RNAs ##REF##32850871##[15]##. Studies in humans have identified the proteins involved in the methylation of adenosine, demethylation, and recognition of m<sup>6</sup>A, revealing that m<sup>6</sup>A is essential for gene expression, tumor formation, stem cell fate, animal development, and RNA metabolism ##REF##32850871##[15]##. Moreover, another RNA modification, <italic>N</italic><sup>5</sup>-methylcytosine (m<sup>5</sup>C), is also found to have important biological functions ##REF##28965832##[16]##, ##REF##20007150##[17]##. Undoubtedly, it is of great importance to systematically identify these modifications among transcriptomes.</p>", "<p id=\"p0015\">Several approaches have been developed to detect m<sup>6</sup>A and m<sup>5</sup>C modifications, although some challenges remain. Most of the sequencing methods of m<sup>6</sup>A depend on an m<sup>6</sup>A-specific antibody, whereby methylated RNA immunoprecipitation sequencing (MeRIP-seq) can identify m<sup>6</sup>A peaks ##REF##31154015##[18]##, while photo-crosslinking-assisted m<sup>6</sup>A sequencing (PA-m<sup>6</sup>A-seq), m<sup>6</sup>A cross-linking immunoprecipitation (m<sup>6</sup>A-CLIP), and m<sup>6</sup>A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) can obtain the base resolution of m<sup>6</sup>A ##REF##25491922##[19]##, ##REF##26404942##[20]##, ##REF##26121403##[21]##. The antibody-independent m<sup>6</sup>A sequencing methods, MAZTER-seq and m<sup>6</sup>A-sensitive RNA-endoribonuclease-facilitated sequencing (m<sup>6</sup>A-REF-seq), are based on endoribonuclease ##UREF##1##[22]##, ##REF##31281898##[23]##, and two chemical labeling methods, m<sup>6</sup>A-label-seq and FTO-assisted m<sup>6</sup>A-selective chemical labeling method (m<sup>6</sup>A-SEAL), have also been recently developed ##REF##32341503##[24]##, ##REF##32341502##[25]##. However, the application of these methods may be limited because of the intrinsic bias of antibodies, motif preference of endoribonuclease, and labeling efficiency ##REF##32440736##[26]##. The bisulfite-based sequencing method has a single-base resolution, and it is widely applied to detect m<sup>5</sup>C, although it is insensitive when detecting m<sup>5</sup>C in low abundance ##REF##19059995##[27]##, ##REF##22344696##[28]##. Similar to m<sup>6</sup>A, m<sup>5</sup>C-specific antibodies are also applied to detect m<sup>5</sup>C peaks in transcriptomes ##REF##28965832##[16]##, ##REF##23825970##[29]##. Moreover, methyltransferase-dependent methods of m<sup>5</sup>C, 5-azacytidine-mediated RNA immunoprecipitation (Aza-IP), and miCLIP, are also developed to enrich the m<sup>5</sup>C-modified transcripts ##REF##23604283##[30]##, ##REF##23871666##[31]##. Nonetheless, unconverted cytosines via bisulfite treatment and overexpression of methyltransferase may result in false-positive detection of m<sup>5</sup>C sites ##REF##32440736##[26]##, ##REF##24286375##[32]##, ##REF##27313037##[33]##, ##REF##26541084##[34]##. In addition, parallel control experiments for most of these methods are needed, and unsuitable approaches based on next-generation sequencing (NGS) have been applied to detect more than two different modifications simultaneously.</p>", "<p id=\"p0020\">The direct RNA sequencing (DRS) technique recently developed by Oxford Nanopore Technology (ONT) provides an alternative way to characterize the transcriptome, wherein different ionic currents in nanoscale pores are generated and employed to discriminate nucleosides ##REF##29334379##[35]##, ##REF##27887629##[36]##, ##REF##31740818##[37]##. DRS data have higher correlations with cDNA nanopore data and Illumina datasets, and they tend to cover full transcripts in a strand-specific manner ##REF##29334379##[35]##. Importantly, sequences from DRS retain modification information because reverse transcription and polymerase chain reaction (PCR) amplification are not required, promisingly detecting multiple types of modifications in one experiment. DRS has been successfully applied to quantify transcripts at the isoform level, as well as assess ploy(A) tail length and base modification of m<sup>6</sup>A and m<sup>5</sup>C in human, <italic>Caenorhabditis elegans</italic>, and <italic>Arabidopsis</italic> transcriptome studies ##REF##31740818##[37]##, ##REF##31501426##[38]##, ##REF##31931956##[39]##, ##REF##32024662##[40]##, ##REF##32024661##[41]##, ##REF##32652016##[42]##, displaying its potential power in clarifying the complex transcriptome.</p>", "<p id=\"p0025\">Rice is not only the staple food for more than half of the world’s population, but also a model monocot for molecular genetics studies because of its compact genome among cereals. Its high-quality reference genome has dramatically facilitated functional genomics research ##REF##24280374##[43]##, ##REF##17145706##[44]##, ##REF##18089549##[45]##. A further understanding of the complexity of the rice transcriptome and epitranscriptome might be very helpful in obtaining deeper insights into the mechanism of rice development. Transgenic expression of human RNA demethylase FTO in rice was found to mediate m<sup>6</sup>A demethylation, as well as induce chromatin openness and transcriptional activation, causing an increment in grain yield and biomass ##REF##34294912##[46]##. Rice transgenic lines stimulated root meristem cell proliferation and tiller bud formation, as well as promoted stress tolerance, whereas they did not affect cell size, shoot meristem cell proliferation, root diameter, and plant height ##REF##34294912##[46]##, implying that m<sup>6</sup>A modification differentially regulates the developmental processes. The rice m<sup>6</sup>A methyltransferase OsFIP is indispensable for male gametogenesis, and the <italic>osfip</italic> mutant showed an early degeneration of microspores and abnormal meiosis ##REF##31116744##[47]##, whereas m<sup>6</sup>A-modified genes were considerably different in the callus and leaf of rice ##REF##25483034##[48]##, further indicating the importance of m<sup>6</sup>A in tissue-specific development. Furthermore, an investigation of m<sup>5</sup>C methyltransferase, OsNSUN2, in rice demonstrated that the <italic>osnsnu2</italic> mutant displayed heat-hypersensitivity phenotypes, and heat stress enhanced the m<sup>5</sup>C modification of mRNAs involved in photosynthesis and detoxification ##UREF##2##[49]##. These studies indicate that m<sup>6</sup>A and m<sup>5</sup>C modifications play essential roles in rice. In the present study, DRS was applied to sequence mRNAs from six different developmental tissues to characterize the transcriptome in rice, and the transcripts targeted by m<sup>6</sup>A and m<sup>5</sup>C were simultaneously detected, before clarifying their effects on gene expression and biological function. Our results presented here provide new insights into the post-transcriptional regulation of rice development.</p>" ]
[ "<title>Materials and methods</title>", "<title>Planting materials and sampling</title>", "<p id=\"p0110\">Rice (<italic>Oryza sativa</italic> L. subsp. <italic>japonica</italic> cultivar Nipponbare) was grown in the field of Hubei University, Wuhan, China. Leaves, stems, and roots from the two-week-old seedlings were collected after germinating and growing in an artificial climate chamber under 28 °C/25 °C, 16-h/8-h light/dark conditions using a 1/2 Murashige and Skoog medium plate. The pistils and stamens were separated and collected from the booting stage in the field, and the embryos were peeled from the mature dry seeds. All tissues were frozen immediately in liquid nitrogen and stored at −80 °C for further use. Each sample was collected in duplicate.</p>", "<title>RNA extraction and isolation</title>", "<p id=\"p0115\">The total RNA of each sample was extracted using Trizol reagent (Catalog No. 15596026, Invitrogen, Gaithersburg, MD) according to the manufacturer’s instructions; it was then precipitated with 2.5 M LiCl, and DNase I (Catalog No. M0303L, New England Biolabs, Ipswich, MA) was added to remove genomic DNA. The quality of RNA was detected using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Qubit 3.0 fluorometer (Life Technologies, Carlsbad, CA). A total of 30 μg of qualified RNA was utilized to enrich poly(A) RNA through the mRNA NEBNext poly(A) mRNA magnetic isolation module (Catalog No. E7490S, New England Biolabs) according to the manufacturer’s specifications.</p>", "<title>Library construction and sequencing</title>", "<p id=\"p0120\">Poly(A) RNA (∼ 500 ng) was used for nanopore DRS. The DRS library was constructed according to the ONT SQK-RNA002 kit protocol, including the optional reverse transcription step recommended by ONT. The library was loaded onto ONT R9.4 flow cells and sequenced on a PromethION sequencer (Oxford Nanopore Technologies, Oxford, UK) for about 48–72 h.</p>", "<p id=\"p0125\">For Illumina sequencing, poly(A) RNA was also used to construct the library using the Illumina TruSeq stranded RNA kit (Catalog No. 20020594, Illumina, San Diego, CA), following the manufacturer’s recommendations. Transcriptome sequencing of the prepared libraries was performed on an Illumina NovaSeq platform with paired-end 150 bp reads (Novogene, Beijing, China).</p>", "<title>Base calling, filtering, and mapping</title>", "<p id=\"p0130\">The raw reads containing continuous current traces from the ONT sequencer were stored in FAST5 format. These reads were base-called on GUPPY (version 3.2.6) software using default RNA parameters and then covered to fastq format using the seqkit tool (version 0.11.0) ##UREF##5##[64]##. The raw fastq reads were filtered by NanoFilt (version 2.6.0) with parameters “-q 7 -l 50” ##REF##29547981##[65]##. The passed reads were firstly corrected by filtering short reads using FMLRC (version 2) ##REF##29426289##[66]## and then aligned with the Nipponbare reference genome (version 7.0) ##REF##24280374##[43]## through minimap2 (version 2.17) ##REF##29750242##[67]## to obtain the consensus and non-redundant sequence using Flair (version 1.4.0) ##REF##32188845##[68]##. StringTie (version 2.1.2) ##REF##31842956##[50]## was applied to combine the aligned sequences, thus producing the novel reference transcript file for the rice genome, and GffCompare ##UREF##3##[51]## was utilized to analyze the novel transcripts derived from ONT DRS. The read coverage along the chromosome was displayed using integrative genomics viewer (IGV) tools ##REF##21221095##[69]##.</p>", "<title>Calculation of DEGs and DEIs from DRS data</title>", "<p id=\"p0135\">The consensus reads obtained by DRS were mapped to novel reference transcripts using minimap2 (version 2.17) with parameters “-a -k14 -uf -x splice --secondary = no” ##REF##29750242##[67]##, and the resulting files were submitted to salmon tools to quantify expression at the gene and transcript levels ##REF##28263959##[52]##. The adjusted <italic>P</italic> values were calculated using the Benjamini–Hochberg method ##UREF##6##[70]## to control the FDR (false discovery rate). The expression levels of the genes and transcripts were expressed as TPM. DEGs and DEIs were defined as |log<sub>2</sub> fold change| &gt; 1 and adjusted <italic>P</italic> &lt; 0.05.</p>", "<title>Expression profiling of Illumina sequencing datasets</title>", "<p id=\"p0140\">All 12 Illumina sequencing datasets were assessed for quality using FastQC (version 0.11.3) and filtered using Trimmomatic (version 0.38) ##REF##24695404##[71]## to obtain clean data. The clean reads were aligned to the Nipponbare reference genome (version 7.0) ##REF##24280374##[43]## using Hisat2 ##REF##31375807##[72]## with default parameters. FeatureCount (version 1.6.4) ##REF##24227677##[73]## in the Rsubread package was used to obtain the read count and TPM value of each expressed gene. A differential expression analysis between pairs of samples was performed using the DESeq2 R package ##REF##25516281##[74]##.</p>", "<title>Poly(A) tail length estimation</title>", "<p id=\"p0145\">The poly(A) tail length of each read was estimated from the raw signal using Nanopolish (version 0.12.5) with parameter polya ##REF##31740818##[37]##. Only the poly(A) length that passed quality control according to nanopolish was further considered for estimation. The median of each transcript from all reads represented the poly(A) tail length.</p>", "<title>RNA base modification detection and analysis</title>", "<p id=\"p0150\">The pass reads of FAST5 files were converted to single-read format using ont_fast5_api (version 3.1.6) with parameter “--recursive”, which were then aligned through default resquiggle in Tombo (version 1.5) ##UREF##4##[53]## with a transcript reference, in which the pipeline of mappy ##REF##29750242##[67]## was applied to align and allocate these reads onto specific isoforms. The modifications of m<sup>5</sup>C and m<sup>6</sup>A in these specific isoforms were further identified. Models of ‘m<sup>5</sup>C’ and ‘<italic>de novo</italic>’ in Tombo were used separately to detect possible modifications in each read. The scores on each site indicated the fraction and coverage of a possible modification on a given site. The sites with fraction &gt; 0.7 and coverage &gt; 10 were selected for further analysis. The nine bases surrounding the modified C were used to analyze the conserved motif through MEME ##REF##19458158##[75]##. For m<sup>6</sup>A detection, MINES tool (cDNA_MINES.py) ##REF##31624092##[76]## with default parameters was implemented to detect m<sup>6</sup>A modification based on the <italic>de novo</italic> model, in which all regions containing a DRACH motif were identified and a new set of regions was generated by extending 10 bp on both sides of the “A” within the DRACH motifs. These regions with coverage &gt; 5 were filtered and subjected to further analysis. The MetaPlotR package ##REF##28158328##[77]## was applied to draw metagene plots of the modification coverage along gene body and UTRs.</p>", "<title>Identification of putative m<sup>6</sup>A methyltransferase in the rice genome</title>", "<p id=\"p0155\">The protein sequences of six m<sup>6</sup>A methyltransferases in <italic>Arabidopsis</italic> (AtMTA, AtMTB, AtMTC, AtFIP37, AtVIR, and AtHAKAI) and five m<sup>6</sup>A methyltransferases in humans (METTL3, METTL14, WTAP, KIAA1429, and HAKAI) ##REF##31070865##[54]## were downloaded from the TAIR database (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.arabidopsis.org/\" id=\"ir020\">https://www.arabidopsis.org/</ext-link>) and the National Center for Biotechnology Information (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ncbi.nlm.nih.gov/\" id=\"ir025\">https://www.ncbi.nlm.nih.gov/</ext-link>), respectively. These proteins were used as queries to blast against the rice protein database through BLASTP, and the proteins with E value &lt; 1E−5 and identity &gt; 40% were screened as candidates. As a result, eight putative m<sup>6</sup>A methyltransferases were identified: OsMETTL14-1 (LOC_Os01g16180, homologous to METTL14), OsMETTL14-2 (LOC_Os03g05420, homologous to METTL14), OsMETTL14-3 (LOC_Os10g31030, homologous to METTL14), OsMETTL3 (LOC_Os02g45110, homologous to METTL3), OsMTC (LOC_Os03g10224, homologous to AtMTC), OsFIP37 (LOC_Os06g27970, homologous to AtFIP37), OsVIR (LOC_Os03g35340, homologous to AtVIR), and OsHAKAI (LOC_Os10g35190, homologous to AtHAKAI).</p>", "<title>Functional enrichment analysis</title>", "<p id=\"p0160\">GO enrichment analyses of m<sup>6</sup>A- and m<sup>5</sup>C-methylated genes were conducted using the agriGO bioinformatics database with hypergeometric test and FDR adjustment ##REF##28472432##[78]##. Terms with FDR &lt; 0.05 were considered significantly enriched.</p>", "<title>RNA base-modified genes and QTL analysis</title>", "<p id=\"p0165\">The data, including physical positions of 8216 rice QTLs, were downloaded from Gramene (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.gramene.org\" id=\"ir030\">https://www.gramene.org</ext-link>), and only QTL intervals of &lt; 2 Mb were selected for further analysis, resulting in 3729 QTLs. The QTL density along the chromosome was calculated in 200-kb windows. The site density of m<sup>6</sup>A and m<sup>5</sup>C modifications was also counted in 200-kb windows. The numbers of sites and corresponding genes in each QTL were analyzed. The distribution of QTLs and modified sites along the chromosome was drawn using R package “RIdeogram” ##UREF##7##[79]##.</p>", "<title>Amplification of novel-identified transcripts</title>", "<p id=\"p0170\">The sequences of the novel-identified transcripts were subjected to designed primers (<xref rid=\"s0140\" ref-type=\"sec\">Table S3</xref>) flanking the overall length for PCR. For novel transcripts that were not from the annotated genes in the rice genome, primers were simultaneously used to amplify cDNA and genomic DNA. For novel transcripts that were from the annotated genes in the rice genome, primers of novel and annotated transcripts were simultaneously used to amplify cDNA. The genomic DNA was extracted from seedling leaves of Nipponbare using modified CTAB methods ##REF##6096873##[80]##, and cDNA was reverse-transcribed from purified mRNA using HiScript II Q RT SuperMix for qPCR (add gDNA wiper) (Catalog No. R233, Vazyme, Nanjing, China). The PCR products were shifted to 0.8% agarose gel. The target bands were recycled using the gel extraction kit (Catalog No. D2500, Omega, Norcross, GA), and the resulting products were inserted into the T-vector according to the TA/Blunt-Zero cloning kit (Catalog No. C601, Vazyme). The clones were sequenced using M13 primer and then further aligned to the reference sequence using CLC sequence viewer (CLC bio LLC, Cambridge, MA).</p>" ]
[ "<title>Results</title>", "<title>Profiling the dynamic transcriptome of rice through DRS</title>", "<p id=\"p0030\">To obtain a dynamic and comprehensive transcriptome of rice, the ONT DRS was applied to analyze different tissues, including the leaf, root, and stem from 2-week-old seedlings, the pistil and stamen from unopened floral buds, and the embryos from mature seeds (<xref rid=\"s0140\" ref-type=\"sec\">Figure S1</xref>). A total of 12 sequence libraries were constructed and loaded onto ONT R9.4 flow cells. Over 70 gigabyte bases and 94 million reads in all libraries were generated, and the read number of each sample ranged from 5.4 to 9.3 million (<xref rid=\"s0140\" ref-type=\"sec\">Table S1</xref>). The high Pearson correlation coefficient (<italic>r</italic>) between the two replicates of each tissue (##FIG##0##Figure 1##A) implied reproducible coverage. The read length distribution of six sequenced tissues was similar (##FIG##0##Figure 1##B), and the average read length for each sample ranged from 619 nt to 1013 nt, with the maximum read length being 15,373 nt and the average read quality score being more than 10 (<xref rid=\"s0140\" ref-type=\"sec\">Table S1</xref>), indicating high-quality DRS data.</p>", "<p id=\"p0035\">Using stringTie ##REF##31842956##[50]## analysis, a total of 45,707 expressed transcripts corresponding to 34,768 genes were identified in the six tissues, with the numbers of expressed genes and transcripts ranging from 21,068 in the embryo to 28,453 in the pistil and from 21,435 in the embryo to 32,633 in the pistil, respectively (##FIG##0##Figure 1##C). Among them, 7257 novel isoforms that were not predicted in the reference genome were detected, and 755 novel genes that were not previously annotated were identified (##FIG##0##Figure 1##C; <xref rid=\"s0140\" ref-type=\"sec\">Table S2</xref>), of which 1756 novel transcripts that belong to intron retained might be immature transcripts. The largest numbers of novel isoforms and genes were identified in the pistil and stamen, respectively, whereas the lowest numbers of novel isoforms and genes were identified in the embryo of mature seed. The novel isoforms were divided into six categories according to GffCompare pipeline ##UREF##3##[51]##, including the following: i, fully contained within a reference intron; j, multi-exon with at least one junction match; m, retained intron(s); o, other same strand overlapping with reference exons; u, none of the above (unknown, intergenic); and  x, exonic overlapping on the opposite strand (##FIG##0##Figure 1##D). Different categories presented different distributions of transcript lengths (##FIG##0##Figure 1##E).</p>", "<p id=\"p0040\">To confirm the existence of the novel transcripts and genes, four novel genes (##FIG##1##Figure 2##A) and five novel isoforms (##FIG##1##Figure 2##B, <xref rid=\"s0140\" ref-type=\"sec\">Figure S2</xref>; <xref rid=\"s0140\" ref-type=\"sec\">Table S</xref>3) were subjected to PCR amplification and sequencing. The PCR band shifts in agarose gel were identical to the predicted length, whereas <italic>novel405</italic>.N2 and LOC_Os12g38051.N1 could not be efficiently amplified because of the low expression levels (##FIG##1##Figure 2##C and D, <xref rid=\"s0140\" ref-type=\"sec\">Figure S3</xref>). Alignment of the sequenced data (<xref rid=\"s0140\" ref-type=\"sec\">Table S</xref>4) with reference sequences also verified the accuracy of the predicted transcripts. These data indicate the reliability of the identified novel transcripts, which could be used for further analyses.</p>", "<title>DRS allowed identifying tissue-specific expression of genes and transcripts</title>", "<p id=\"p0045\">The ONT DRS technique can directly sequence RNA, based on which transcripts with different isoforms can be distinguished, thus facilitating the quantification of mRNAs at the isoform level. Comparison among all the tissues showed that about 48.8% (16,955) of the genes were commonly expressed in all six tissues (<xref rid=\"s0140\" ref-type=\"sec\">Figure S4</xref>), whereas only 37.9% (18,495) of the isoforms were commonly expressed (<xref rid=\"s0140\" ref-type=\"sec\">Figure S5</xref>), indicating the tissue-specific expression of genes and their different isoforms. Further comparison showed that the median of gene expression quantified from short-read sequencing was higher than that from DRS, and the isoform expression level was lower (##FIG##2##Figure 3##A). Pearson correlation analysis was conducted between DRS and Illumina sequencing data to check the reliability of DRS on the quantification of gene expression. The notable correlation in all the six tissues (##FIG##2##Figure 3##B) verified the precision of DRS. The differentially expressed genes (DEGs) and differentially expressed isoforms (DEIs) of the six tissues were further identified using salmon tools at the gene and transcript levels, respectively ##REF##28263959##[52]##, and a large number of DEGs and DEIs were discovered in each comparison (##FIG##2##Figure 3##C). The leaf <italic>vs.</italic> stem comparison revealed the lowest number of DEGs and DEIs, whereas the leaf <italic>vs.</italic> root and stem <italic>vs.</italic> root comparisons revealed the second and third lowest numbers of DEGs and DEIs, respectively (##FIG##2##Figure 3##C). In contrast, the stamen <italic>vs.</italic> root/stem/leaf comparisons revealed the largest numbers of DEGs and DEIs (##FIG##2##Figure 3##C). Generally, more than 95% of the DEIs had their corresponding genes identified as DEGs (##FIG##2##Figure 3##C, <xref rid=\"s0140\" ref-type=\"sec\">Figure S6</xref>). Some genes contained more than one transcript, whereby some were identified as DEIs with no observable changes at the gene expression level, while some genes were identified as DEGs without any of their transcripts being identified as DEIs (<xref rid=\"s0140\" ref-type=\"sec\">Figure S6</xref>), suggesting the existence of tissue-specific genes and transcripts. One gene, LOC_Os01g48990, which displayed tissue-specific expression of its transcripts, was randomly selected to verify these results. The read coverage showed that LOC_Os01g48990.1 was expressed in the leaf, root, and stem, whereas LOC_Os01g48990.2 was expressed in the embryo, pistil, and stamen (##FIG##2##Figure 3##D). Moreover, the number of DEGs from DRS data was lower than in Illumina sequencing, whereas about 85% of DEGs detected in DRS were also identified in Illumina sequencing (<xref rid=\"s0140\" ref-type=\"sec\">Figure S7</xref>).</p>", "<title>High repeatability of m<sup>6</sup>A and m<sup>5</sup>C identification through DRS</title>", "<p id=\"p0050\">As a new technique, DRS has an advantage in identifying modifications ##REF##29334379##[35]##. The development of Tombo software makes it feasible to detect these modified sites ##UREF##4##[53]##. Two modifications, m<sup>6</sup>A and m<sup>5</sup>C, were identified in six tissues with two replicates in the present study. Because of the lower accuracy of DRS compared with NGS, the repeatability of m<sup>6</sup>A and m<sup>5</sup>C identification was evaluated. About 63% to 78% of m<sup>6</sup>A-modified sites were simultaneously detected, and over 90% of m<sup>6</sup>A-modified genes in most tissues were identified in both replicates (<xref rid=\"s0140\" ref-type=\"sec\">Figure S8</xref>A and B), whereas the fraction (frequency of modified sites in the transcript) of overlapping sites in two replicates was significantly highly correlated (<xref rid=\"s0140\" ref-type=\"sec\">Figure S</xref>8C). Similar results were also found in m<sup>5</sup>C-modified sites and genes (<xref rid=\"s0140\" ref-type=\"sec\">Figure S9</xref>), indicating that the sites detected in both replicates have good repeatability, and that independent biological replicates are necessary. The repeatedly detected sites were thus subjected to further analysis. To evaluate the reliability of modifications identified by DRS, the m<sup>6</sup>A MeRIP data from Nipponbare root samples of 15-day-old seedlings ##REF##34294912##[46]## were compared with DRS data of root samples (<xref rid=\"s0140\" ref-type=\"sec\">Figure S10</xref>). The results demonstrated that over 50% of m<sup>6</sup>A-modified genomic regions contained m<sup>6</sup>A sites identified by DRS, and about 70% of m<sup>6</sup>A-modified genes detected by MeRIP were also identified by DRS, implying the reliability of DRS data.</p>", "<title>The m<sup>6</sup>A and m<sup>5</sup>C modifications on transcripts occurred in a common or tissue-specific manner</title>", "<p id=\"p0055\">m<sup>6</sup>A is the most prevalent post-transcriptional modification, and it is necessary for regulating gene expression ##REF##31070865##[54]##. A total of 81,722 m<sup>6</sup>A-modified sites located within 28,059 transcripts were identified in the whole genome, with the number of sites in each tissue ranging from 12,271 in the embryo to 46,535 in the pistil (<xref rid=\"s0140\" ref-type=\"sec\">Table S</xref>5). The site numbers in the root and stem were slightly lower than those in the stem, whereas the site numbers in the leaf and stamen were 2–3-fold greater than those in the embryo, with more than half of these sites having a fraction over 0.5 (##FIG##3##Figure 4##A). The average number of m<sup>6</sup>A sites in each transcript ranged from 1.92 in the embryo to 2.67 in the stem, and the number of genes with m<sup>6</sup>A modification ranged from 5152 in the embryo to 14,051 in the pistil (<xref rid=\"s0140\" ref-type=\"sec\">Table S5</xref>). Most of the transcripts had less than three m<sup>6</sup>A sites, whereas over 25% of isoforms in the stem had more than four m<sup>6</sup>A sites (##FIG##3##Figure 4##B). The fraction of transcripts with more than six modified sites displayed a wide variation (from 0 to 1), but the maximum fraction in these transcripts (median value &gt; 0.92) was significantly higher than that in all modified transcripts (median value &lt; 0.75) (<xref rid=\"s0140\" ref-type=\"sec\">Figure S11</xref>). Considering the variable number of m<sup>6</sup>A modifications among different tissues, the intersection of transcripts with m<sup>6</sup>A modification was analyzed. A small number of transcripts (<italic>n</italic> = 4420) overlapped in all tissues, with 4191 transcripts commonly presented in the leaf, pistil, root, stamen, and stem (##FIG##3##Figure 4##C). Moreover, a proportion of isoforms displayed tissue-specific modification by m<sup>6</sup>A, including 2042 in the pistil, 1894 in the root, 1743 in the stamen, 774 in the stem, 359 in the leaf, and 276 in the embryo (##FIG##3##Figure 4##C). To clarify whether the m<sup>6</sup>A methylase affects the status of m<sup>6</sup>A modification in each tissue, the expression levels of eight putative m<sup>6</sup>A methylase genes were analyzed. Except for <italic>OsMTC</italic>, other genes were expressed in all tissues, with <italic>OsMETTL3</italic>, <italic>OsFIP37</italic>, and <italic>OsHAKAI</italic> showing relatively high expression levels (##FIG##3##Figure 4##D). Consistent with the m<sup>6</sup>A intensity in each tissue, most of these genes had higher expression levels in the pistil, root, and stem, with the lowest expression levels observed in the embryo (##FIG##3##Figure 4##D). These sites were distributed from the 5′-untranslated region (5′-UTRs) to 3′-UTR, mainly around the stop codon of the coding sequence (CDS) (##FIG##3##Figure 4##E). There was an apparent shift of the site distribution toward the 5′-UTR in the stem (##FIG##3##Figure 4##E), in which the largest number of transcripts containing multiple m<sup>6</sup>A modifications was identified. Approximately 40% of m<sup>6</sup>A-modified sites presented the GGACA motif, whereas the other three types of motifs (AGACT, GGACC, and GGACT) also had a considerable ratio (<xref rid=\"s0140\" ref-type=\"sec\">Figure S12</xref>).</p>", "<p id=\"p0060\">m<sup>5</sup>C is another popular internal RNA modification. A total of 338,907 sites with m<sup>5</sup>C modifications located within 25,869 transcripts were identified, with the m<sup>5</sup>C sites in each tissue ranging from 31,339 in the embryo to 163,430 in the root, in which the fraction of most sites was more than 0.8 (##FIG##4##Figure 5##A; <xref rid=\"s0140\" ref-type=\"sec\">Table S</xref>6). The average m<sup>5</sup>C site number per isoform was 6.9 in the embryo and 11.1 in the stem, whereas the other four tissues featured ∼ 8.5 m<sup>5</sup>C sites, exceeding the number recorded for m<sup>6</sup>A modification. Most of the transcripts had more than four m<sup>5</sup>C sites, and over 25% of transcripts in the stem had more than 15 m<sup>5</sup>C sites (##FIG##4##Figure 5##B). Among these transcripts with more than 15 m<sup>5</sup>C sites, the fraction of each site ranged from 0.7 to 1.0, and the maximum fraction in these transcripts was significantly higher than in all the detected transcripts (<xref rid=\"s0140\" ref-type=\"sec\">Figure S13</xref>). The number of m<sup>5</sup>C-modified transcripts commonly identified in the six tissues was 2983 (##FIG##4##Figure 5##C). The peak of m<sup>5</sup>C modification was located around the start codon and stop codon, and the CDS region had the higher proportion of m<sup>5</sup>C sites in all tissues (##FIG##4##Figure 5##D). Similar to m<sup>6</sup>A modification, there was also a shift toward the 5′-UTR in the stem (##FIG##4##Figure 5##E). The expression of eight putative m<sup>5</sup>C methyltransferase genes ##UREF##2##[49]## was also checked. Most had high expression among all six tissues (##FIG##4##Figure 5##F). Specifically, the expression of two genes, <italic>OsNSUN2</italic> and <italic>OsNSUN5</italic>, was much higher in the pistil and root than in the other four tissues (##FIG##4##Figure 5##F). Although the lowest expression of methyltransferase genes was presented in the stamen (##FIG##4##Figure 5##F), the number of m<sup>5</sup>C-modified sites was not the lowest. Nine bases around the modified C were analyzed for conserved elements, with (A/T)GC(T/A) being the most representative element covering 96,434 sites, whereas the other three potential elements were (A/C)(A/T)CAX(C/A)(T/A) (where X = A/T/C/G), TC(A/G/C)(G/A)(G/T), and CAG(A/G)CT (<xref rid=\"s0140\" ref-type=\"sec\">Figure S14</xref>).</p>", "<p id=\"p0065\">Because over half of the expressed transcripts were either m<sup>6</sup>A- or m<sup>5</sup>C-modified, it was necessary to check if the transcript was co-targeted by m<sup>6</sup>A and m<sup>5</sup>C. A comparison of the transcripts modified with m<sup>6</sup>A and m<sup>5</sup>C in each tissue showed that more than half of the m<sup>6</sup>A-modified transcripts were also modified by m<sup>5</sup>C, and over 75% of the m<sup>5</sup>C-modified transcripts were also modified by m<sup>6</sup>A in the rice transcriptome (##FIG##4##Figure 5##G). The number of co-modified transcripts varied in different tissues and ranged from 3389 in the embryo to 14,499 in the root (##FIG##4##Figure 5##G). Moreover, approximately 20% of the transcripts of these modified genes were not modified by m<sup>6</sup>A or m<sup>5</sup>C in each tissue (<xref rid=\"s0140\" ref-type=\"sec\">Figure S15</xref>), implying the isoform-specific patterns of both modifications.</p>", "<title>Both m<sup>6</sup>A and m<sup>5</sup>C modifications were correlated with the expression level and length of poly(A) tail of transcripts</title>", "<p id=\"p0070\">To understand the function of m<sup>6</sup>A and m<sup>5</sup>C, we analyzed the correlation between these two modifications and the expression levels of their targeted transcripts. The results demonstrated that m<sup>6</sup>A- or m<sup>5</sup>C-modified transcripts had significantly higher expression levels than the transcripts with no modification, whereas transcripts with higher fractions of modification sites also had higher expression levels (##FIG##5##Figure 6##A and B). The transcripts with more m<sup>6</sup>A or m<sup>5</sup>C sites tended to have higher expression levels (<xref rid=\"s0140\" ref-type=\"sec\">Figures S16 and S17</xref>), which was apparent for m<sup>5</sup>C. To determine the potential interaction of other factors with transcript expression, we analyzed the relationship between the modifications and poly(A) tail length of the corresponding transcripts. It was found that transcripts with either m<sup>6</sup>A or m<sup>5</sup>C modification had significantly shorter poly(A) tail length than those without modification (##FIG##5##Figure 6##C and D). Although the number of m<sup>6</sup>A modification sites seemed to have no effect on the length of the poly(A) tail (<xref rid=\"s0140\" ref-type=\"sec\">Figure S18</xref>), the number of m<sup>5</sup>C sites had a negative relationship with the length of the poly(A) tail (<xref rid=\"s0140\" ref-type=\"sec\">Figure S19</xref>). To identify any additive effects between m<sup>6</sup>A and m<sup>5</sup>C, the expression of transcripts with both modifications was compared with that with or without either modification. Although transcripts with both modifications had relatively higher expression levels than those with only m<sup>6</sup>A modifications or without modifications (##FIG##5##Figure 6##E), they were similar to those only modified by m<sup>5</sup>C (##FIG##5##Figure 6##E). These results indicate that there is no obviously additive effect on promoting the expression of transcripts, with m<sup>5</sup>C being more effective. Their impact on poly(A) tail length was contrasted with their impact on the expression (##FIG##5##Figure 6##F). According to these results, it seems that poly(A) tail length is negatively correlated with transcript expression. To verify this assumption, the relationship between the poly(A) tail length and the transcript abundance was analyzed. Consistently, the poly(A) tail length was negatively related to the abundance of transcripts in all the tissues (##FIG##5##Figure 6##G).</p>", "<p id=\"p0075\">The proportion of m<sup>6</sup>A- or m<sup>5</sup>C-modified sites located in the 5′-UTR, CDS, and 3′-UTR in each transcript was further calculated, and the correlation between the modification location and the expression level or poly(A) tail length of transcripts was analyzed (<xref rid=\"s0140\" ref-type=\"sec\">Table S</xref>7). The results demonstrated that the m<sup>6</sup>A or m<sup>5</sup>C modification sites located in the 5′-UTR and CDS were weakly positively correlated with the expression level. In contrast, the modifications located in the 3′-UTR were weakly negatively correlated with the expression level. A contrasting tendency was identified in the comparison between m<sup>5</sup>C location and poly(A) tail length, implying that the sites modified by m<sup>6</sup>A or m<sup>5</sup>C in the 5′-UTR and CDS may have been correlated with the expression level and poly(A) tail length of transcripts. To further verify the relationship between the expression level and the numbers of m<sup>5</sup>C and m<sup>6</sup>A sites, eight genes (<italic>OsVAL2</italic>, <italic>OsEBF1</italic>, <italic>FLO2</italic>, <italic>OsPHO2</italic>, <italic>WSL5</italic>, <italic>OsDXR</italic>, <italic>OsPAO</italic>, and <italic>OsPP95</italic>) showing differential modifications among the six tissues were selected to check their expression levels and transcript modification statuses. The results showed that genes with higher expression levels also had more modified m<sup>5</sup>C and m<sup>6</sup>A sites (##FIG##5##Figure 6##H, <xref rid=\"s0140\" ref-type=\"sec\">Figure S20</xref>), implying that m<sup>5</sup>C and m<sup>6</sup>A modifications do correlate with their expression.</p>", "<title>The modified transcripts were involved in central metabolic pathways and exhibited tissue-specific characteristics</title>", "<p id=\"p0080\">Since both modifications could affect the abundance of their target transcripts, we wanted to determine if there were any selections on the target genes, especially in different tissues. Gene Ontology (GO) analysis was conducted on the transcripts modified by m<sup>6</sup>A and/or m<sup>5</sup>C. The transcripts with either m<sup>6</sup>A or m<sup>5</sup>C modifications overlapped in all tissues, and they were mainly involved in translation, different kinds of metabolic processes, gene expression, protein-related processes, and transport (<xref rid=\"s0140\" ref-type=\"sec\">Figure S21</xref>), indicating that both modifications might affect central life activities. GO enrichment analysis also provided some clues on the functions of these tissue-specific transcripts with m<sup>6</sup>A and m<sup>5</sup>C modifications (##FIG##6##Figure 7##). The pistil-specific transcripts with m<sup>6</sup>A modification were mainly involved in RNA metabolism including biosynthesis, splicing, processing, and modification, whereas some of the pistil-specific transcripts with m<sup>5</sup>C modification were enriched in the DNA replication process (##FIG##6##Figure 7##). Root-specific m<sup>6</sup>A- and m<sup>5</sup>C-modified transcripts were mainly involved in protein phosphorylation, phosphorus metabolism, macromolecule modification, cell communication and recognition, and stress and stimulus responses (##FIG##6##Figure 7##). Stamen-specific m<sup>6</sup>A- and m<sup>5</sup>C-modified transcripts were mainly involved in the pH, ion, and chemical homeostatic regulation process, whereas some of the transcripts with m<sup>5</sup>C modification were enriched in cell wall and cytoskeleton organization as well as lipid and carbohydrate metabolism (##FIG##6##Figure 7##). Interestingly, lipid metabolic process-related transcripts with m<sup>6</sup>A and m<sup>5</sup>C were particularly enriched in the stem (##FIG##6##Figure 7##). These results showed that transcripts modified with m<sup>6</sup>A and m<sup>5</sup>C were involved in similar functions, indicating an association between m<sup>6</sup>A and m<sup>5</sup>C modifications. We further analyzed the potential functions of transcripts that were commonly or specifically modified by m<sup>6</sup>A and m<sup>5</sup>C in each tissue. GO analysis of transcripts that were commonly modified by m<sup>6</sup>A and m<sup>5</sup>C revealed enrichment in multiple biological processes such as localization, metabolic, regulation, and transport in all tissues, whereas some GO terms were enriched in specific tissues such as translational initiation and elongation in the embryo, DNA repair and response to DNA damage stimulus in the pistil, cell homeostasis in the leaf, and purine nucleotide-related metabolic processes in the stamen (<xref rid=\"s0140\" ref-type=\"sec\">Figure S22</xref>). A few GO terms were simultaneously enriched in transcripts that were explicitly modified by m<sup>6</sup>A or m<sup>5</sup>C in each tissue, and most GO terms presented tissue and modification specificity (<xref rid=\"s0140\" ref-type=\"sec\">Figure S23</xref>), implying the differential functions of transcripts with m<sup>6</sup>A or m<sup>5</sup>C modifications. These data collectively demonstrate the similar and differential functions of m<sup>6</sup>A- or m<sup>5</sup>C-modified transcripts in a tissue-specific manner.</p>", "<title>Most genes with m<sup>6</sup>A and m<sup>5</sup>C modifications were located within quantitative trait loci</title>", "<p id=\"p0085\">To further characterize whether m<sup>6</sup>A- and m<sup>5</sup>C-modified transcripts could affect any important agronomy traits, we analyzed the distribution of genes encoding the m<sup>6</sup>A- and m<sup>5</sup>C-modified transcripts, and we compared them with previously identified quantitative trait loci (QTLs) along the chromosomes with 200-kb windows. The results showed that m<sup>5</sup>C and m<sup>6</sup>A sites had similar distribution along the chromosome, and the regions with higher QTL density tended to have higher RNA base modifications (##FIG##7##Figure 8##A). Approximately 75% of the sites modified with m<sup>5</sup>C and m<sup>6</sup>A in each tissue were mapped in QTL regions (##FIG##7##Figure 8##B). This result suggests that m<sup>5</sup>C and m<sup>6</sup>A modification might play important roles in regulating the expression of genes located in or close to QTLs. Moreover, over 200 genes modified by m<sup>6</sup>A or m<sup>5</sup>C were located within QTL regions associated with 30 agronomy traits, which involved multiple processes, including development, yield, fertility, flowering, and biotic and abiotic stress (##FIG##7##Figure 8##C), implying that these genes with modified RNA bases may determine the important agronomy traits in the rice genome.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0090\">In the last two decades, noteworthy achievements have been realized in rice genomic research, greatly facilitating genetic and breeding studies. However, it is still elusive how the genome is concordantly expressed to realize its function. Hence, dissecting the dynamic combination of gene expression products or intermediates will be very important to uncover the mechanism of rice development and environmental response. Among relevant methods, transcriptome analysis is a critical approach to dissecting the transcripts, which is highly dependent on high-throughput sequencing techniques ##REF##31341269##[55]##. It has been established that only dissecting the transcripts is not enough to characterize their function. Many post-transcriptional activities involve mRNAs, which might be very important in regulating gene expression ##REF##19742130##[1]##, ##REF##27412912##[2]##, ##REF##25590224##[3]##. However, because of the limitations of the canonical RNA sequencing (RNA-seq) technique, these post-transcriptional activities cannot be finely characterized. The newly developed method DRS has been demonstrated to have an outstanding ability to concurrently identify these activities in humans, yeast, <italic>C. elegans</italic>, and <italic>Arabidopsis</italic>\n##REF##29334379##[35]##, ##REF##31740818##[37]##, ##REF##32024661##[41]##, ##REF##32652016##[42]##. Here, DRS was applied to characterize the transcriptome of six developmental tissues of rice. About 0.2% and 2% of the detected genes and isoforms were identified as novel genes and isoforms, respectively (##FIG##0##Figure 1##C), indicating that DRS could help identify more isoforms. Characterization and verification of the novel genes and isoforms, especially their tissue-specific expression patterns, could help improve the annotation of the rice genome and obtain new information on their functions. However, the DRS data only covered 60%–61% of the isoforms and genes annotated in the reference genome (##FIG##0##Figure 1##C). More than 22% (9776) of expressed genes, especially those with low transcripts per kilobase per million (TPM &lt; 1), detected in RNA-seq could not be detected by DRS. This indicates that DRS may not be powerful enough to detect low-abundance transcripts, which is consistent with its characteristic of not amplifying the targets. It might be necessary to combine DRS and canonical RNA-seq techniques to comprehensively explore the transcriptome complexity, accurately quantify the transcripts, and expand the number of genes and isoforms in a tissue-specific manner.</p>", "<p id=\"p0095\">In addition to the advantages of transcript identification and isoform quantification, DRS can detect the base modifications of RNA, which supposedly play important regulatory roles at the post-transcriptional level. Over 160 types of RNA modifications have been discovered ##REF##29106616##[12]##, among which m<sup>6</sup>A and m<sup>5</sup>C have been verified to play key roles in development and stress response ##REF##31863849##[56]##. Antibody-based high-throughput sequencing techniques have been successfully used for transcriptome-wide mapping of m<sup>6</sup>A and m<sup>5</sup>C modifications of RNA for many eukaryotes such as yeast ##REF##23825970##[29]##, ##REF##24269006##[57]##, <italic>Arabidopsis</italic>\n##REF##28965832##[16]##, ##REF##27396363##[58]##, ##REF##28062751##[59]##, rice ##REF##25483034##[48]##, ##UREF##2##[49]##, and maize ##REF##31409695##[60]##. Accordingly, the dominantly conserved motifs for m<sup>6</sup>A RRACH (R = A/G; H = A/C/U) enriching near the stop codon and 3′-UTR ##REF##29716990##[61]##, and those for m<sup>5</sup>C sites in the CDS and UTR with the conserved motifs HACCR (H = A/U/C; R = A/G) and CTYCTYC(Y = U/C) ##REF##28965832##[16]##, ##REF##28062751##[59]## have been characterized. Because DRS can directly sequence RNA without reverse and amplification processes, it can more accurately detect the base modifications, as proven by recent studies ##REF##31740818##[37]##, ##REF##32024662##[40]##. We globally mapped m<sup>6</sup>A and m<sup>5</sup>C modifications through DRS in developmental rice tissues. The distribution region and conserved motifs for m<sup>6</sup>A in this study were similar to previous reports ##REF##31070865##[54]## (##FIG##3##Figure 4##E and F, <xref rid=\"s0140\" ref-type=\"sec\">Figure S12</xref>). Although the distribution region for m<sup>5</sup>C modification was also consistent with previous results ##REF##28965832##[16]## (##FIG##4##Figure 5##D and E), new conserved motifs were identified in our study (<xref rid=\"s0140\" ref-type=\"sec\">Figure S14</xref>). Thus, further studies on other species are required to determine the species specificity of these findings. Moreover, a high proportion of isoforms with both modifications was detected (##FIG##4##Figure 5##G). However, we did not find any additive effects on the gene expression (##FIG##5##Figure 6##E). It would be interesting to know if isoforms with one of the modifications could facilitate other modifications. Furthermore, m<sup>5</sup>C- or m<sup>6</sup>A-modified genes displayed isoform-specific modifications (<xref rid=\"s0140\" ref-type=\"sec\">Figure S15</xref>), and modification sites located within 5′-UTR, CDS, and 3′-UTR had potentially differential effects on transcript expression (<xref rid=\"s0140\" ref-type=\"sec\">Table S</xref>7). These primary data hint at the importance of sequencing RNA molecules at the transcript level.</p>", "<p id=\"p0100\">The biological importance of m<sup>6</sup>A and m<sup>5</sup>C has been confirmed by previous studies ##REF##32850871##[15]##, ##REF##20007150##[17]##. These modifications can affect the stability or translation efficiency of target mRNAs. Until now, there is still very little direct evidence from any specific mRNAs. In this study, we found that transcripts containing both modifications displayed higher expression levels and shorter poly(A) tails than those without modification (##FIG##5##Figure 6##A and B), and this effect was dependent on the number of modification sites, especially for m<sup>5</sup>C (<xref rid=\"s0140\" ref-type=\"sec\">Figures S16–S19</xref>). Specifically, the m<sup>6</sup>A and m<sup>5</sup>C modification intensities of eight cloned genes were highly associated with their expression levels among different tissues (##FIG##5##Figure 6##E). Moreover, the fraction of m<sup>6</sup>A- or m<sup>5</sup>C-modified sites showed dramatic variations (##FIG##3##Figure 4##A and 5A). In contrast, transcripts with higher fractions tended to display high expression levels (##FIG##5##Figure 6##A and B). The transcripts with m<sup>6</sup>A sites that fell into &gt; 5 categories or with m<sup>5</sup>C sites that fell into &gt; 15 categories presented a significantly higher maximum fraction than all modified transcripts (##FIG##3##Figure 4##B and 5B, <xref rid=\"s0140\" ref-type=\"sec\">Figures S11 and S13</xref>), implying that the effect of modification on transcript expression was also fraction-dependent. These findings indicated that m<sup>6</sup>A and m<sup>5</sup>C might be able to promote the stability of their modified transcripts, with m<sup>5</sup>C being more effective. However, how these modifications correlate with the length of the poly(A) tail is still an open question, which includes the intrinsic factors of modifications and the association of the length of the poly(A) tail with the expression level of transcripts.</p>", "<p id=\"p0105\">GO enrichment analysis showed that the modified transcripts are widely involved in all aspects of biological processes. However, there were some tissue-specific modified groups (##FIG##6##Figure 7##, <xref rid=\"s0140\" ref-type=\"sec\">Figures S21–S23</xref>). The occurrence of modification was seemingly related to a specific biological process or tissue development, which has also been shown in strawberry fruit development ##REF##34078442##[62]## and in the sexual reproduction of <italic>Chlamydomonas reinhardtii</italic>\n##REF##35550876##[63]##. The selection of target genes seems to be a meaningful problem, which was also addressed in this study. Among all the detected transcripts, most of the modified isoforms were found to be located within mapped QTLs controlling important agronomical traits such as yield, flowering, stress, and fertility (##FIG##7##Figure 8##), indicating there might be selectivity toward the targets to be modified. This selection bias might be related to the biological function of modifications.</p>" ]
[]
[ "<p>Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies. However, the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA, which is an important element for the post-transcriptional regulation of gene expression. To comprehensively profile the <italic><bold>N</bold></italic><sup><bold>6</bold></sup><bold>-methyladenosine</bold> (m<sup>6</sup>A) and <italic><bold>N</bold></italic><sup><bold>5</bold></sup><bold>-methylcytosine</bold> (m<sup>5</sup>C) modifications on RNA, <bold>direct RNA sequencing</bold> (DRS) using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in <bold>rice</bold>. Approximately 94 million reads were generated, with an average length ranging from 619 nt to 1013 nt, and a total of 45,707 transcripts across 34,763 genes were detected. Expression profiles of transcripts at the isoform level were quantified among tissues. Transcriptome-wide mapping of m<sup>6</sup>A and m<sup>5</sup>C demonstrated that both modifications exhibited tissue-specific characteristics. The transcripts with m<sup>6</sup>A modifications tended to be modified by m<sup>5</sup>C, and the transcripts with modifications presented higher expression levels along with shorter poly(A) tails than transcripts without modifications, suggesting the complexity of gene expression regulation. Gene Ontology analysis demonstrated that m<sup>6</sup>A- and m<sup>5</sup>C-modified transcripts were involved in central metabolic pathways related to the life cycle, with modifications on the target genes selected in a tissue-specific manner. Furthermore, most modified sites were located within quantitative trait loci that control important agronomic traits, highlighting the value of cloning functional loci. The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome, improving our understanding of the rice genome.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Chengqi Yi</p>" ]
[ "<title>Data availability</title>", "<p id=\"p0175\">The raw FAST5 data have been deposited in the Genome Sequence Archive ##REF##34400360##[81]## at the National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (GSA: CRA007279), which are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa\" id=\"PC_linknJFWVNwFcS\">https://ngdc.cncb.ac.cn/gsa</ext-link>. The long read data of each sample have been deposited in the Sequence Read Archive at the National Center for Biotechnology Information (SRA: PRJNA752930).</p>", "<title>Competing interests</title>", "<p id=\"p0180\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0185\"><bold>Feng Yu:</bold> Conceptualization, Methodology, Software, Writing – original draft. <bold>Huanhuan Qi:</bold> Visualization, Software, Data curation. <bold>Li Gao:</bold> Visualization, Investigation. <bold>Sen Luo:</bold> Investigation. <bold>Rebecca Njeri Damaris:</bold> Writing – review &amp; editing. <bold>Yinggen Ke:</bold> Investigation, Writing – original draft. <bold>Wenhua Wu:</bold> Resources, Supervision. <bold>Pingfang Yang:</bold> Conceptualization, Project administration, Funding acquisition, Writing – review &amp; editing. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0200\">The following are the Supplementary data to this article:</p>", "<p id=\"p0205\">\n\n</p>", "<p id=\"p0210\">\n\n</p>", "<p id=\"p0215\">\n\n</p>", "<p id=\"p0220\">\n\n</p>", "<p id=\"p0225\">\n\n</p>", "<p id=\"p0230\">\n\n</p>", "<p id=\"p0235\">\n\n</p>", "<p id=\"p0240\">\n\n</p>", "<p id=\"p0245\">\n\n</p>", "<p id=\"p0250\">\n\n</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<p id=\"p0270\">\n\n</p>", "<p id=\"p0275\">\n\n</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<p id=\"p0325\">\n\n</p>", "<p id=\"p0330\">\n\n</p>", "<p id=\"p0335\">\n\n</p>", "<p id=\"p0340\">\n\n</p>", "<p id=\"p0345\">\n\n</p>", "<p id=\"p0005\">\n \n \n</p>", "<title>Acknowledgments</title>", "<p id=\"p0190\">This work was supported by the National Natural Science Foundation of China (Grant No. 31671775). We thank Benagen Tech Solutions Company Limited (Wuhan, China) for technical assistance.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Summary of DRS data for different rice tissues</bold></p><p><bold>A.</bold> Pearson correlation analysis between replicates of sequenced libraries in six rice tissues. <italic>r</italic> indicates the Pearson correlation coefficient. <bold>B.</bold> The length of transcripts detected by DRS in different tissues. <bold>C.</bold> The number of genes and isoforms identified by DRS and its comparison with the data in the reference genome (MSU7.0, <ext-link ext-link-type=\"uri\" xlink:href=\"https://rice.plantbiology.msu.edu/\" id=\"ir005\">https://rice.plantbiology.msu.edu/</ext-link>). <bold>D.</bold> The number of different types of novel transcripts identified by DRS through GffCompare pipeline analysis. Transcript type indicates the different types of novel transcripts: i, fully contained within a reference intron; j, multi-exon with at least one junction match; m, retained intron(s); o, other same strand overlapping with reference exons; u, none of the above (unknown, intergenic); x, exonic overlapping on the opposite strand. <bold>E.</bold> The length distribution of different types of novel transcripts. DRS, direct RNA sequencing.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Verification of the novel genes and transcripts identified by DRS</bold></p><p><bold>A.</bold> Novel genes that were not annotated in the reference genome. The read coverage of <italic>novel405</italic> and <italic>novel547</italic> was from the stem tissue, and the read coverage of <italic>novel655</italic> and <italic>novel689</italic> was from the pistil tissue. R1 and R2 represent the read coverage of independent biological replicates, and N1 and N2 represent the newly annotated transcripts. The arrows represent the location of primers. <bold>B.</bold> Novel transcripts that were different from the annotated genes in the reference genome. The blue color represents the annotated transcripts in the reference genome, and the red color represents the novel transcripts. Ref1 and Ref2 indicate different transcripts annotated in the reference genome. <bold>C.</bold> Verification of novel genes through RT-PCR. The same primer was used to amplify genomic DNA and cDNA. The cDNA template for <italic>novel405</italic>, <italic>novel547</italic>, <italic>novel655</italic>, and <italic>novel689</italic> was from the stem, stem, pistil, and pistil tissues, respectively. G represents the band amplified from genomic DNA; M represents marker bands. <bold>D.</bold> Verification of the novel isoforms through RT-PCR. The specific primer for each transcript was designed, and the cDNA template for LOC_Os01g64090, LOC_Os02g03440, LOC_Os02g32814, LOC_Os03g48626, and LOC_Os12g38051 was from the root, pistil, stem, stem, and root tissues, respectively. RT-PCR, reverse transcription-polymerase chain reaction.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Analysis of the expression of genes and isoforms detected in six tissues</bold></p><p><bold>A.</bold> The mRNA expression at gene and isoform levels. Gene indicates the expression at the gene level from the DRS data; isoform indicates the expression at the isoform level; short indicates the expression at the gene level from the short-read sequencing data of the cDNA library using Illumina platform. <bold>B.</bold> Pearson correlation analysis of expression at the gene level in six tissues determined by DRS and short-read sequencing from the cDNA library using Illumina platform. <bold>C.</bold> Analysis of the DEGs and DEIs among tissues. Overlapping represents the number of genes overpping between DEGs and genes presenting DEIs. <bold>D.</bold> The expression of LOC_Os01g48990 in an isoform-specific manner in the six tissues. The read coverage was displayed through IGV software. R1 and R2 represent two different replicates. TPM, transcripts per kilobase per million; DEG, differentially expressed gene; DEI, differentially expressed isoform; IGV, integrative genomics viewer.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Profiling of m<sup>6</sup>A modification in the transcripts of rice tissues</bold></p><p><bold>A.</bold> The number of m<sup>6</sup>A-modified sites. Each site was classified into different categories on the basis of its fraction. <bold>B.</bold> The ratio of transcripts with a different number of m<sup>6</sup>A-modified sites. <bold>C.</bold> The number of commonly-detected and tissue-specific m<sup>6</sup>A-modified transcripts. <bold>D.</bold> The expression levels of possible m<sup>6</sup>A writer genes. <italic>OsMETTL14-1</italic>, <italic>OsMETTL14-2</italic>, and <italic>OsMETTL14-3</italic> are homologs of human <italic>METTL14</italic>; <italic>OsMETTL3</italic> is a homolog of human <italic>METTL3</italic>; <italic>OsFIP37</italic> is a homolog of <italic>AtFIP37</italic>; <italic>OsVIR</italic> is a homolog of <italic>AtVIR</italic>; <italic>OsHAKAI</italic> is a homolog of <italic>AtHAKAI</italic>. <bold>E.</bold> The density of m<sup>6</sup>A-modified bases along the gene body in six tissues. The position of each modified site along the gene body was normalized by the length of the transcript using R pipeline MetaPlotR. <bold>F.</bold> The ratio of m<sup>6</sup>A-modified sites distributed in the 5′-UTR, CDS, and 3′-UTR. m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenosine; UTR, untranslated region; CDS, coding sequence.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Profiling of m<sup>5</sup>C modification in the transcripts of rice tissues</bold></p><p><bold>A.</bold> The number of m<sup>5</sup>C-modified sites in different tissues. Each site was classified into different categories on the basis of its fraction. <bold>B.</bold> The ratio of transcripts with a different number of m<sup>5</sup>C-modified sites. <bold>C.</bold> The number of commonly-detected and tissue-specific m<sup>5</sup>C-modified transcripts. <bold>D.</bold> The density of m<sup>5</sup>C-modified bases along the gene body. The position of each modified site along the gene body was normalized by the length of the transcript using R pipeline MetaPlotR. <bold>E.</bold> The ratio of m<sup>5</sup>C-modified sites distributed in the 5′-UTR, CDS, and 3′-UTR in the six tissues. <bold>F.</bold> The expression levels of possible m<sup>5</sup>C methyltransferase genes. <italic>OsNSUN1</italic>–<italic>OsNSUN8</italic> correspond to LOC_Os08g0484400, LOC_Os09g0471900, LOC_Os02g0320100, LOC_Os02g0724600, LOC_Os09g0551300, LOC_Os08g0365900, LOC_Os02g0217800, and LOC_Os09g0477900, respectively. <bold>G.</bold> The comparison of m<sup>5</sup>C- and m<sup>6</sup>A-modified transcripts in each tissue. m<sup>5</sup>C, 5-methylcytosine.</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>Relationship of m<sup>6</sup>A and m<sup>5</sup>C with transcript expression level and poly(A) tail length</bold></p><p><bold>A.</bold> Comparison of the expression level of transcripts with and without m<sup>6</sup>A modification in each tissue. High indicates the transcripts with the maximum fraction ranging from 0.5 to 1.0; low indicates the transcripts with the maximum fraction ranging from 0.0 to 0.5; no indicates the transcripts without m<sup>6</sup>A modification. <bold>B.</bold> Comparison of the expression level of transcripts with and without m<sup>5</sup>C modification in each tissue. High indicates the transcripts with the maximum fraction ranging from 0.9 to 1.0; low indicates the transcripts with the maximum fraction ranging from 0.7 to 0.9; no indicates the transcripts without m<sup>5</sup>C modification. <bold>C</bold><bold>.</bold> Comparison of poly(A) tail length of transcripts with and without m<sup>6</sup>A modification in each tissue. m<sup>6</sup>A indicates the transcripts modified by m<sup>6</sup>A; no indicates the transcripts not modified by m<sup>6</sup>A. <bold>D.</bold> Comparison of poly(A) tail length of transcripts with and without m<sup>5</sup>C modification in each tissue. m<sup>5</sup>C indicates the transcripts modified by m<sup>5</sup>C; no indicates the transcripts not modified by m<sup>5</sup>C. <bold>E.</bold> The expression level of transcripts with different modifications. Both indicates the transcripts modified by both m<sup>6</sup>A and m<sup>5</sup>C; m<sup>6</sup>A indicates the transcripts modified by m<sup>6</sup>A only; m<sup>5</sup>C indicates the transcripts modified by m<sup>5</sup>C only; no indicates the transcripts without m<sup>6</sup>A and m<sup>5</sup>C modifications. <bold>F.</bold> The poly(A) tail length of transcripts with different modifications. <bold>G.</bold> Pearson correlation analysis between poly(A) tail length and expression level of isoforms. <bold>H.</bold> Comparison of expression level with the numbers of m<sup>6</sup>A and m<sup>5</sup>C sites among six tissues in eight cloned genes: <italic>OsVAL2</italic> (LOC_Os07g48200.1), <italic>OsEBF1</italic> (LOC_Os06g40360.1), <italic>FLO2</italic> (LOC_Os04g55230.1), <italic>OsPHO2</italic> (LOC_Os05g48390.1), <italic>WSL5</italic> (LOC_Os03g04660.1), <italic>OsDXR</italic> (LOC_Os01g01710.1), <italic>OsPAO</italic> (LOC_Os03g05310.1), and <italic>OsPP95</italic> (LOC_Os07g32380.1). ***, <italic>P</italic> &lt; 0.001 for each comparison.</p></caption></fig>", "<fig id=\"f0035\"><label>Figure 7</label><caption><p><bold>GO analysis of tissue-specific transcripts with m</bold><sup><bold>6</bold></sup><bold>A and m</bold><sup><bold>5</bold></sup><bold>C modifications in each tissue through agriGO</bold></p><p>The left panel shows the enriched GO terms of tissue-specific transcripts modified by m<sup>6</sup>A in each tissue, and the right panel shows the enriched GO terms of tissue-specific transcripts modified by m<sup>5</sup>C in each tissue. The enriched GO terms were selected according to FDR &lt; 0.05. GO, Gene Ontology; FDR, false discovery rate.</p></caption></fig>", "<fig id=\"f0040\"><label>Figure 8</label><caption><p><bold>Comparison</bold><bold>of</bold><bold>RNA base-modified regions with</bold><bold>previously mapped QTL</bold><bold>s</bold></p><p><bold>A.</bold> The distribution of QTLs, m<sup>5</sup>C sites, and m<sup>6</sup>A sites along the chromosome with a 200-kb window size. The QTL information was downloaded from Gramene (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.gramene.org\" id=\"ir010\">https://www.gramene.org</ext-link>), and QTL intervals no more than 2 Mb were selected for further analysis. The display was drawn using the R package “RIdeogram”. <bold>B.</bold> The ratio of m<sup>5</sup>C- and m<sup>6</sup>A-modified sites localized within QTL regions. <bold>C.</bold> Heatmap showing the number of RNA base-modified genes localized within the QTL regions. The top 30 traits are shown. QTL, quantitative trait locus.</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0150\"><caption><title>Supplementary Figure S1</title><p><bold>The pictures of six tissues that were subjected to direct RNA sequencing</bold> Leaves, stems, and roots from the two-week-old seedlings, pistil and stamen from the booting stage, and embryo from the mature dry seeds were collected. Red rectangular box and arrow indicate the sampled tissues.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0145\"><caption><title>Supplementary Figure S2</title><p><bold>The reads coverage of newly identified isoforms in Figure 2 showing by IGV software</bold> The reads coverage of <italic>LOC_Os01g64090</italic> in root, <italic>LOC_Os03g48626</italic> in stem, <italic>LOC_Os02g32814</italic> in stem, <italic>LOC_Os02g03440</italic> in pistil, and <italic>LOC_Os12g38051</italic> in root were displayed. R1 and R2 represent two independent replicates. Red color indicates novel isoforms. IGV, integrative genomics viewer.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0140\"><caption><title>Supplementary Figure S3</title><p><bold>The negative controls of amplified products in Figure 2</bold> RNA indicated that the no reversely transcribed RNA was treated as a template, cDNA was the template reversely transcribed from RNA, and DNA was the genome DNA of Nipponbare. All of the primers except actin were from Figure 2, and the primer of actin was designed from rice gene <italic>LOC_Os03g50885.1.</italic> S, stem; P, pistil; R, root<italic>.</italic></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0135\"><caption><title>Supplementary Figure S4</title><p><bold>The upset plot displayed the number of expressed genes in six tissues through direct RNA sequencing</bold> The number of expressed genes in root, stem, stamen, pistil, leaf, and embryo were shown through upset plot.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0130\"><caption><title>Supplementary Figure S5</title><p><bold>The upset plot displayed the number of expressed isoforms in six tissues through direct RNA sequencing</bold> The number of expressed isoforms in root, stem, stamen, pistil, leaf, and embryo were shown through upset plot.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0125\"><caption><title>Supplementary Figure S6</title><p><bold>Veen diagram showing the overlapped number of DEIs and DEGs in each comparison</bold> The number of differentially expressed isoforms and genes were compared among six tissues of root, stem, stamen, pistil, leaf, and embryo. DEIs, differentially expressed isoforms; DEGs, differentially expressed genes.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0120\"><caption><title>Supplementary Figure S7</title><p><bold>Comparison of the differentially expressed genes identified by DRS and NGS</bold> The differentially expressed genes that detected by DRS and NGS in comparison of embryo with leaf, root, embryo, stamen, and stem, leaf with stamen, and root with stamen were displayed. DRS, direct RNA sequencing; NGS, next-generation sequencing (Illumina).</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0115\"><caption><title>Supplementary Figure S8</title><p><bold>Comparison of the repeatability of m6A identification in six tissues A.</bold> Comparison of the m6A sites between two replications. <bold>B.</bold> Comparison of the genes modified by m6A between two replications. <bold>C.</bold> Correlation analysis for the fraction of the overlapped sites in two replications. Rep 1, replicate 1; Rep 2, replicate 2.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0110\"><caption><title>Supplementary Figure S9</title><p><bold>Comparison of the repeatability of m<sup>5</sup>C identification in six tissues A.</bold> Comparison of the m<sup>5</sup>C sites between two replications. <bold>B.</bold> Comparison of the genes modified by m<sup>5</sup>C between two replications. <bold>C.</bold> Correlation analysis for the fraction of the overlapped sites in two replications. Rep1, replicate 1; Rep2, replicate 2.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0105\"><caption><title>Supplementary Figure S10</title><p><bold>Comparison of the m<sup>6</sup>A modification identified by DRS with previous identification through MeRIP in the root A.</bold> Comparison of the m<sup>6</sup>A-modified sites in DRS data with genomic regions identified by MeRIP. <bold>B.</bold> Comparison of the m<sup>6</sup>A-modified genes in DRS data with modified genes detected by MeRIP. The sites and genes that overlapped in two replications were used; Rep1, replicate 1; Rep2, replicate 2; MeRIP, methylated RNA immunoprecipitation sequencing.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0100\"><caption><title>Supplementary Figure S11</title><p><bold>Comparing the fraction of modified sites in all transcripts with these falling into &gt; 5 categories in Figure 4B</bold> The fraction of m<sup>6</sup>A-modified sites in each transcript was calculated, and the maximum fraction in each transcript was counted.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0095\"><caption><title>Supplementary Figure S12</title><p><bold>The percentage of m6A-modified motifs in the six tissues</bold> The percentage of four conserved motifs surrounding the modified base A in root, stem, stamen, pistil, leaf, and embryo was calculated, respectively.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0090\"><caption><title>Supplementary Figure S13</title><p><bold>Comparison of the fraction of modified sites in all transcripts with those falling into &gt; 15 categories in Figure 5B</bold> The fraction of m<sup>5</sup>C-modified sites in each transcript was calculated, and the maximum fraction in each transcript was counted.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0085\"><caption><title>Supplementary Figure S14</title><p><bold>The significantly enriched motif around the modified base C through MEME analysis</bold> Four conserved motifs surrounding the modified base C were identified and the corresponding site number wal calculated.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0080\"><caption><title>Supplementary Figure S15</title><p><bold>The proportion of modified and non-modified transcripts of modified genes</bold> The ratio of m<sup>6</sup>A and m<sup>5</sup>C modified transcripts in modified genes in tissue of root, stem, stamen, pistil, leaf, and embryo was shown, respectively.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0075\"><caption><title>Supplementary Figure S16</title><p><bold>The expression level of transcripts with different sites of m6A modification</bold> The m<sup>6</sup>A modified transcripts were divided into three categories based on modified site number, and the expression level of each category in root, stem, stamen, pistil, leaf, and embryo was calculated, respectively. TPM, transcripts per kilobase per million.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0070\"><caption><title>Supplementary Figure S17</title><p><bold>The expression level of transcripts with different sites of m<sup>5</sup>C modification</bold> The m<sup>5</sup>C modified transcripts were divided into six categories based on modified site number, and the expression level of each category in root, stem, stamen, pistil, leaf, and embryo was calculated, respectively. TPM, transcripts per kilobase per million.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0065\"><caption><title>Supplementary Figure S18</title><p><bold>The poly(A) tail length of transcripts with the different number of m<sup>6</sup>A modification sites</bold> The m<sup>6</sup>A modified transcripts were divided into three categories based on modified site number, and the polyA tail length of each category in root, stem, stamen, pistil, leaf, and embryo was calculated, respectively.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Figure S19</title><p><bold>The poly(A) tail length of transcripts with the different number of m<sup>5</sup>C modification sites</bold> The m<sup>5</sup>C modified transcripts were divided into six categories based on modified site number, and the polyA tail length of each category in root, stem, stamen, pistil, leaf, and embryo was calculated, respectively.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Figure S20</title><p><bold>The distribution of modification sites in transcript <italic>LOC_Os06g40360.1</italic> A.</bold> The m<sup>6</sup>A and m<sup>5</sup>C modified sites in each tissue distributed within <italic>LOC_Os06g40360.1</italic>. <bold>B.</bold> Ionic current signal of each nucleoside in transcript <italic>LOC_Os06g40360.1</italic>. The position indicated the transcript length from 2645 to 2669, m indicated the methylated A or C, red color indicated the nucleoside signal, and black color indicated the model.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Figure S21</title><p><bold>The GO analysis of commonly modified transcripts in all six tissues through AgriGO</bold> The left panel showed GO terms of 4420 transcripts that were commonly modified by m<sup>6</sup>A, and the right panel showed GO terms of 2983 transcripts that were commonly modified by m<sup>5</sup>C. The significant GO terms were selected by FDR &lt; 0.05. GO, gene ontology; FDR, false discovery rate.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Figure S22</title><p><bold>The GO analysis of commonly modified transcripts by m<sup>6</sup>A and m<sup>5</sup>C in six tissues in Figure 5G through AgriGO</bold> The transcripts that commonly modified by m<sup>6</sup>A and m<sup>5</sup>C in root, stem, stamen, pistil, leaf, and embryo were subjected to enrich the GO terms, respectively. The significant GO terms were selected by FDR &lt; 1E–05.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Figure S23</title><p><bold>The GO analysis of specifically modified transcripts by m<sup>6</sup>A and m<sup>5</sup>C in each tissue in Figure 5G through AgriGO</bold> The transcripts that specifically modified by m<sup>6</sup>A and m<sup>5</sup>C in root, stem, stamen, pistil, leaf, and embryo were subjected to enrich the GO terms, respectively. The significant GO terms were selected by FDR &lt; 1E–04.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S1</title><p><bold>Statistical information of Nanopore native RNA clean reads in all sequenced samples</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S2</title><p><bold>The information of novel identified transcripts through stringTie</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S3</title><p><bold>The sequence information for amplifying the novel transcripts identified by direct RNA sequencing</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S4</title><p><bold>The sequence of newly identified transcripts that were sequenced by Sanger technique</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S5</title><p><bold>The detailed information of detected m<sup>6</sup>A sites in six tissues</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S6</title><p><bold>The detailed information of detected m<sup>5</sup>C sites in six tissues</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S7</title><p><bold>The correlation between expression level or poly(A) tail length of transcripts and the location of modified sites</bold></p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e389\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0135\" fn-type=\"supplementary-material\"><p id=\"p0195\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2023.02.002\" id=\"ir035\">https://doi.org/10.1016/j.gpb.2023.02.002</ext-link>.</p></fn></fn-group>" ]
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{ "acronym": [], "definition": [] }
81
CC BY
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2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Aug 11; 21(4):788-804
oa_package/cb/b6/PMC10787127.tar.gz
PMC10787128
36791953
[ "<title>Introduction</title>", "<p id=\"p0010\">As the predominant internal modification in eukaryotic mRNAs, <italic>N</italic><sup>6</sup>-methyladenosine (m<sup>6</sup>A) is a critical transcriptional regulator in a novel molecular mechanism that profoundly affects various biological processes by modulating multiple aspects of mRNA processing and metabolism ##REF##32321323##[1]##, including mRNA abundance ##REF##24713629##[2]##, ##REF##24662220##[3]##, stabilization ##REF##24284625##[4]##, and splicing ##UREF##0##[5]##. Along with the well-studied epigenetic regulation via modifications to DNA and histones, the dynamic and reversible m<sup>6</sup>A modification is mediated by m<sup>6</sup>A methyltransferases (writers) and demethylases (erasers). In addition to these two crucial components, m<sup>6</sup>A readers are responsible for the localization and recognition of m<sup>6</sup>A-containing RNA sequences, which are necessary for the implementation of the biological effects of m<sup>6</sup>A modifications. Consequently, m<sup>6</sup>A writers, erasers, and readers collaboratively orchestrate a complex regulatory network that governs m<sup>6</sup>A modifications. Although there has been considerable progress in the research conducted to clarify the potential functions of m<sup>6</sup>A modifications in animals, the effects of the m<sup>6</sup>A regulatory mechanism in the plant kingdom are just beginning to be determined. The m<sup>6</sup>A-mediated regulatory mechanism reportedly influences the normal growth of <italic>Arabidopsis thaliana</italic> roots and shoots ##REF##27396363##[6]##, ##REF##31110512##[7]##. Furthermore, there is growing evidence that m<sup>6</sup>A modifications are also involved in regulating responses to diverse environmental stresses, including drought ##REF##29618631##[8]##, cold ##REF##34149789##[9]##, and ultraviolet (UV) radiation ##REF##22575960##[10]##. More recently, a few studies have started to precisely functionally characterize the m<sup>6</sup>A regulatory mechanism or m<sup>6</sup>A regulatory genes in the plant kingdom ##REF##31387610##[11]##, ##REF##32842619##[12]##, ##REF##34078442##[13]##, ##REF##34211493##[14]##. Compared with model plants, there has been relatively little research on the regulatory mechanisms as well as the functions of m<sup>6</sup>A modifications in horticultural crops.</p>", "<p id=\"p0015\">Tea (<italic>Camellia sinensis</italic>) is an important and traditional economically valuable crop cultivated on a large scale in many developing and developed countries. Its tender buds and leaves are mostly used to produce highly consumed and popular beverages. Oolong tea, which is one of the six tea types in China, is famous for its elegant floral and fruity aroma, as well as its unique brisk-smooth and mellow taste. The development of the flavor and sensory characteristics of oolong tea largely depends on the postharvest manufacturing process ##UREF##1##[15]##. During the manufacturing of oolong tea, withering is the first essential stage affecting the palatability and commercial value of the final product. The harvested leaves are still in a live state and continue to be exposed to various environmental stresses during the withering stage, in which there are obvious changes to multiple tastes and aroma compounds, as well as endogenous phytohormones, which directly or indirectly endow oolong tea with its characteristic flavor and health benefits ##REF##30100425##[16]##, ##REF##30277806##[17]##, ##REF##28450026##[18]##. Among these taste compounds in tea plants, flavonoids are a large group of secondary metabolites that are closely associated with tea palatability. More specifically, catechins are the dominant flavonoid components and comprise 12%–24% of the dry weight in tea leaves ##REF##33719437##[19]##. Flavonoids and catechins are the major contributors to the astringency and bitterness of tea ##UREF##2##[20]##. Moreover, catechins can be further oxidized to high-molecular-weight polymeric compounds (<italic>i.e.</italic>, theaflavins) that provide tea with beneficial health-promoting properties and a characteristic mellow taste ##REF##20014758##[21]##. As the most representative aroma compounds in oolong tea, volatile terpenoids are critical components of high-quality oolong tea because of their contributions to the pleasant floral and fruity fragrance. Decades of studies have demonstrated that multiple environmental stresses caused by withering treatments induce several multidimensional responses (<italic>e.g.</italic>, at the genetic and metabolic levels) that further modulate the formation of the oolong tea flavor ##REF##30309549##[22]##, ##UREF##3##[23]##. However, information regarding the upstream mechanism regulating the flavor-related genes and relevant metabolites remains limited.</p>", "<p id=\"p0020\">Previous research has indicated that solar-withering, which is a conventional method for producing tea, may be used to improve the flavor of high-quality oolong tea ##REF##31929782##[24]##, ##REF##33112139##[25]##. Light serves as an energy source and signaling molecule required for the metabolic changes that occur during solar-withering. Typically, light quality and intensity are crucial parameters that determine the effects of solar-withering on tea quality. Earlier studies largely focused on the mechanism underlying the effects of light quality on the tea flavor ##REF##28416872##[26]##, ##UREF##4##[27]##. Few researchers have investigated the effects of different shading rates on the metabolism of tea flavor compounds and the formation of tea flavors during the solar-withering stage. The establishment of traditional solar-withering methods relies heavily on the subjective experiences of tea producers and random trials, leading to fluctuations in tea quality. To overcome this limitation, characterizing the metabolic pathways that affect flavor formation as well as the regulatory mechanisms under different shading rates during the solar-withering stage is vital for optimizing the shading rate to produce high-quality oolong tea efficiently. There has recently been accumulating evidence that epigenetic changes, including DNA methylation and histone modifications, are crucial for the biosynthesis of secondary metabolites and tea aroma formation ##REF##33773659##[28]##, ##REF##33464046##[29]##. Unfortunately, the effects of RNA methylation, which is another epigenetic modification, and the precise regulatory mechanisms underlying the m<sup>6</sup>A-mediated flavor formation in the tea-withering stage remain largely unknown. The availability of a chromosome-level tea genome has laid a solid foundation for investigations on m<sup>6</sup>A modifications in tea plants ##REF##32353625##[30]##.</p>", "<p id=\"p0025\">In the present study, an integrated RNA methylome and transcriptome analysis was conducted to elucidate the effects of m<sup>6</sup>A modifications on the formation of flavor-related compounds in tea leaves in response to different shading rates during the solar-withering stage. We systematically identified the differentially methylated peak (DMP)-associated genes and revealed that the changes to m<sup>6</sup>A in many DMP-associated genes are inextricably associated with the solar-withering conditions, especially the shading rate. We further demonstrated that CsALKBH4<italic>-</italic>mediated RNA demethylation alters the extent of the m<sup>6</sup>A modifications within the 3′ untranslated region (3′ UTR) and near the stop codon and regulates the expression levels of m<sup>6</sup>A-modified RNAs, thereby affecting the accumulation of flavor metabolites and tea palatability. The effects of the m<sup>6</sup>A-mediated alternative splicing (AS) regulatory mechanism during the solar-withering stage were also explored. These findings described herein provide important insights into the regulatory effects of m<sup>6</sup>A modifications on tea plants and the contribution of the m<sup>6</sup>A-mediated regulatory mechanism to the development of high-quality oolong tea via a solar-withering method.</p>" ]
[ "<title>Materials and methods</title>", "<title>Plant materials and solar-withering treatments</title>", "<p id=\"p0135\">Fresh tea buds with the first three leaves were collected from <italic>C. sinensis</italic> cv. Tieguanyin plants cultivated in a tea plantation at Fujian Agriculture and Forestry University, Fuzhou, China (E 119°14′, N 26°05′). The harvested tea leaves were evenly divided into five groups. The first group (<italic>i.e.</italic>, FL) was untreated and analyzed immediately. The other four groups were laid out on bamboo sieves for the solar-withering treatments with different shading rates. Briefly, black nylon sunshade nets were positioned 0.2 m above the bamboo sieves. The solar-withering treatments were as follows: SW1 (high shading rate provided by a sunshade net with 1500 meshes; 10,000 ± 400 lx); SW2 (moderate shading rate provided by a sunshade net with 1000 meshes; 20,000 ± 800 lx); SW3 (low shading rate provided by a sunshade net with 500 meshes; 40,000 ± 1200 lx); and SW4 (no sunshade net; 80,000 ± 2000 lx). The duration of the solar-withering treatment was 45 min. The other environmental parameters were consistent with those used in our previous study ##REF##31929782##[24]##. Three independent biological replicates were included in each solar-withering treatment. The light intensity and spectrum were measured using a spectral irradiance colorimeter (Catalog No. SPIC-300, Everfine Corporation, Hangzhou, China), whereas the UV intensity was recorded using a UV radiometer (Catalog No. UV340B, Sanpometer Corporation, Shenzhen, China). After the solar-withering treatments, the samples were collected, frozen immediately in liquid nitrogen, and stored at −80 °C.</p>", "<title>Quantitative analysis of the m<sup>6</sup>A/A ratio</title>", "<p id=\"p0140\">The global m<sup>6</sup>A/A ratio for the tea leaves was determined as previously described ##REF##33843075##[59]##. Briefly, RNA was extracted from each sample using the TransZol UP reagent (Catalog No. ET111, TransGen, Beijing, China). Then, the quantitative analysis of the global m<sup>6</sup>A/A ratio was performed using the EpiQuik m<sup>6</sup>A RNA methylation quantification kit (Catalog No. P-9005, Epigentek, Farmingdale, NY).</p>", "<title>MeRIP-seq and data analysis</title>", "<p id=\"p0145\">For MeRIP-seq, total RNA was extracted from each sample using the TransZol UP reagent (Catalog No. ET111, TransGen). The integrity and quantity of the obtained RNA were assessed by RNase-free agarose gel electrophoresis and the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples passed the quality checks, and there were no signs of RNA degradation (<xref rid=\"s0140\" ref-type=\"sec\">Figure S14</xref>). Next, poly(A) mRNA was isolated from the total RNA samples using the Dynabeads mRNA purification kit (Catalog No. 61,006, ThermoFisher Scientific, Waltham, CA). The enrichment of m<sup>6</sup>A was examined using the Magna MeRIP m<sup>6</sup>A kit (Catalog No. 17-10,499, Millipore, Billerica, MA). Briefly, the mRNA was fragmented into approximately 100-nt fragments using the fragmentation buffer. The fragmented RNA was divided into two groups, one of which was mixed with m<sup>6</sup>A-specific antibodies in the IP buffer. The other group of RNA was used as the input control. The m<sup>6</sup>A-containing fragments and non-IP fragments were used for constructing strand-specific libraries using the NEBNext Ultra II RNA library prep kit (Catalog No. E7770, New England Biolabs, Ipswich, MA). The average fragment size in each paired-end library was 100 ± 50 bp. Finally, m<sup>6</sup>A MeRIP-seq was performed using the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA). Three independent biological replicates were sequenced for each sample.</p>", "<p id=\"p0150\">The raw reads containing adapter sequences and undetermined bases were removed using the Trimmomatic tool ##REF##24695404##[60]##, after which the high-quality reads were mapped to the chromosome-level tea genome using the HISAT software ##REF##25751142##[61]##. The R-package exomePeak ##REF##24979058##[62]## was used to identify the m<sup>6</sup>A peaks in each m<sup>6</sup>A-IP sample, with the corresponding non-IP sample serving as the background. In all three independent biological replicates, peaks with an overlap of at least 50% of their length and <italic>P</italic> &lt; 0.05 were designated as high-confidence m<sup>6</sup>A peaks. The m<sup>6</sup>A peaks were visualized using the integrative genomics viewer software ##REF##22517427##[63]##. According to the genomic location information, the distribution of peaks in the non-overlapping mRNA regions, including the 5′ UTR, CDS, and 3′ UTR, was determined using BEDTools ##REF##20110278##[64]##. The MEME suite ##REF##19458158##[32]## and HOMER tool ##REF##20513432##[33]## were used to search for motifs within the m<sup>6</sup>A peaks. The DMPs between groups were identified using the DiffBind software ##UREF##6##[65]##, with |FC| ≥ 2 and <italic>P</italic> &lt; 0.05 set as the thresholds. The FPKM values were calculated to represent the mRNA expression levels in the input libraries using the StringTie software ##REF##25690850##[66]##. Differentially expressed genes were identified (|FC| ≥ 2 and <italic>P</italic> &lt; 0.05) using the R package DESeq2 ##REF##25516281##[67]##. The expression profiles of candidate genes (standardized FPKM values) were visualized using the TBtools software ##REF##32585190##[68]##. The rMATS program ##REF##25480548##[69]## was used to detect AS events, which were considered significant if the false discovery rate was less than 0.05. The AS transcripts were validated by reverse transcription-polymerase chain reaction (RT-PCR) assays involving specific primers (<xref rid=\"s0140\" ref-type=\"sec\">Table S12</xref>) as previously described ##REF##28744294##[70]##. The PCR products were monitored by agarose gel electrophoresis. Differentially expressed genes associated with AS events were defined as DAGs according to previously described criteria ##REF##31959105##[58]##. The KEGG enrichment analysis of DMP-associated genes and DAGs was performed using a published method ##REF##33112139##[25]##.</p>", "<title>m<sup>6</sup>A-IP-qPCR and qRT-PCR analyses</title>", "<p id=\"p0155\">The m<sup>6</sup>A-IP-qPCR analysis was performed according to an established procedure ##REF##31387610##[11]##, with minor modifications. Briefly, the RNA samples used for the m<sup>6</sup>A MeRIP-seq analysis were fragmented into approximately 300-nt segments using the aforementioned fragmentation buffer. Some of the fragmented RNA samples were used for m<sup>6</sup>A-IP, which was completed using m<sup>6</sup>A-specific antibodies. The non-IP RNA was used as the input control. The m<sup>6</sup>A-containing RNA and non-IP RNA samples were reverse transcribed into cDNA using the TransScript first-strand cDNA synthesis SuperMix kit (Catalog No. AT301, TransGen). The m<sup>6</sup>A enrichment of specific mRNA regions was detected using the LightCycler 480 platform (Roche, Basel, Switzerland). The m<sup>6</sup>A abundance was quantified according to the 2<sup>−ΔΔC<sub>T</sub></sup> method ##REF##11846609##[71]##. The relative abundance of specific mRNA regions in the m<sup>6</sup>A-IP sample was first normalized against that of <italic>CsActin</italic> (GenBank: HQ420251), which has no obvious m<sup>6</sup>A-modified peak and served as an internal control, and then normalized against that for the non-IP sample.</p>", "<p id=\"p0160\">The qRT-PCR analysis was conducted using the LightCycler 480 platform as previously described ##REF##31929782##[24]##. The non-fragmented RNA samples were reverse transcribed into cDNA as described above. <italic>CsActin</italic> was used to normalize the mRNA expression levels. Relative mRNA levels were calculated using the 2<sup>−ΔΔC<sub>T</sub></sup> method. The analysis was completed using three independent biological replicates. Details regarding the primers used for the m<sup>6</sup>A-IP-qPCR and qRT-PCR assays are provided in <xref rid=\"s0140\" ref-type=\"sec\">Table S12</xref>.</p>", "<title>Analysis of volatiles by GC<bold>–</bold>MS</title>", "<p id=\"p0165\">The volatile compounds in tea samples were extracted and analyzed as previously described ##REF##33866239##[72]##. The Agilent model 7890B gas chromatograph and the 7000D mass spectrometer (Agilent Technologies) were used to detect the volatile compounds. Each assay was conducted using three replicates. The detected volatiles were identified according to the retention time and mass spectra data in the National Institute of Standards and Technology Mass Spectral Library (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.nist.gov/srd/nist-standard-reference-database-1a\" id=\"PC_link6utBQhbKFn\">https://www.nist.gov/srd/nist-standard-reference-database-1a</ext-link>/). The relative abundance of individual volatile compounds was determined on the basis of the chromatogram peak area.</p>", "<title>Analysis of the metabolome by LC–MS</title>", "<p id=\"p0170\">Metabolites were extracted and analyzed essentially as previously described ##REF##33149146##[73]##. Briefly, freeze-dried tea samples were ground into a powder using a tissue grinder (Catalog No. JXFSTPRP-24, Jingxin Company, Shanghai, China), after which 800 μl 70% methanol and 250 µl 2′,7′-dichlorofluorescein were added to the powdered material. After centrifuging the extracts at 14,000 <italic>g</italic> for 15 min, the supernatants were passed through a 0.22-µm polyvinylidene fluoride filter and analyzed using the ACQUITY two-dimensional ultra-performance liquid chromatography platform (Waters, Milford, MA) connected to a Q-Exactive quadrupole-orbitrap mass spectrometer (ThermoFisher Scientific). The compounds were separated in the Hypersil GOLD aQ column (100 mm × 2.1 mm, 1.9 μm, ThermoFisher Scientific), with 0.1% formic acid in pure water (v/v; solvent A) and 0.1% formic acid in acetonitrile (v/v; solvent B) used at a flow rate of 0.3 ml/min. The gradient elution was completed as follows: 5% solvent B for 2 min, linear increase to 95% solvent B over 22 min, 95% solvent B for 5 min, and then return to the initial condition (5% solvent B) within 3 min. The column temperature was set at 40 °C. Peaks were detected and the retention time was corrected using the compound discoverer software (version 3.1; ThermoFisher Scientific). The detected metabolites were identified by comparing their molecular mass, retention time, and mass spectrometry fragmentation patterns with those of the authentic standards, mzCloud (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.mzcloud.org/\" id=\"ir015\">https://www.mzcloud.org/</ext-link>), and mzVault (<ext-link ext-link-type=\"uri\" xlink:href=\"https://mytracefinder.com/tag/mzvault/\" id=\"ir020\">https://mytracefinder.com/tag/mzvault/</ext-link>) databases. The relative abundance of each metabolite was calculated using the metaX tool ##REF##28327092##[74]##. The total flavonoid content of tea leaves was measured according to the aluminum chloride colorimetric method ##REF##31929782##[24]##. Three independent biological replicates were included in each experiment.</p>", "<title>Gene suppression and mRNA stability assays</title>", "<p id=\"p0175\">The gene suppression assay was performed as previously described ##REF##34211493##[14]##. The freshly detached tea bud and the first leaf from tea plants grown under natural conditions were added to 1.5-ml microcentrifuge tubes containing 1 ml 20 μM siRNA solution or negative control siRNA (siRNA-NC) solution. After incubating for 12 h and 24 h, the tea bud and first leaf were collected for a qRT-PCR analysis. Specific siRNAs were obtained from GenePharma (Shanghai, China). Details regarding the siRNA and siRNA-NC solutions are listed in <xref rid=\"s0140\" ref-type=\"sec\">Table S12</xref>. The overall m<sup>6</sup>A abundance and metabolite content in the gene-silenced leaves and the NC-leaves were examined as described above.</p>", "<p id=\"p0180\">To assess mRNA stability, leaf discs were obtained from the gene-silenced tea leaves and then immersed in sterile water that was supplemented with 10 μg/ml actinomycin D (Catalog No. A1410, Sigma, St Louis, MO). Tea leaves immersed in sterile water were used as the controls. Total RNA was isolated from the leaves sampled at 6 h and 12 h, respectively. The mRNA stability was determined using a previously described qRT-PCR method ##REF##33843075##[59]## and specific primers (<xref rid=\"s0140\" ref-type=\"sec\">Table S12</xref>).</p>", "<title>Statistical analysis</title>", "<p id=\"p0185\">The correlations among the full-length transcripts, AS transcripts, and flavor metabolites were determined using the Pearson’s correlation coefficient. The differences among various groups were assessed by conducting a one-way analysis of variance (ANOVA) and Tukey’s <italic>post hoc</italic> test, with <italic>P</italic> &lt; 0.05 set as the threshold for significance. Data are herein presented as the mean ± standard deviation (SD). The raw data for the qRT-PCR analysis are provided in <xref rid=\"s0140\" ref-type=\"sec\">Table S11</xref>.</p>" ]
[ "<title>Results</title>", "<title>Significant changes in global abundance and distribution of m<sup>6</sup>A modifications in tea leaves in response to solar-withering treatments</title>", "<p id=\"p0030\">The light intensity, spectrum, and UV intensity of solar-withering treatments with different shading rates were monitored (<xref rid=\"s0140\" ref-type=\"sec\">Figure S1</xref>). The withering treatments were performed as follows: solar-withering with a high shading rate (SW1), solar-withering with a moderate shading rate (SW2), solar-withering with a low shading rate (SW3), and solar-withering with natural sunlight (SW4). Notably, the light intensity and UV intensity under the sunshade net decreased as the shading rate increased. However, the use of the sunshade net had little effect on the spectral composition, light quality, and wavelength. There were considerable differences in the UV intensity between the solar-withering with and without the shading net. The shading treatment substantially decreased the UV intensity. From SW1 to SW3, the different shading rates had relatively little effect on the UV intensity. The external characteristics of fresh leaves (FLs) and the solar-withered leaves produced using different shading rates were recorded (##FIG##0##Figure 1##A). FLs were straight, glossy, and jade green. Decreases in the shading rate during the solar-withering treatments resulted in increasingly shrunken, deformed, and darker-colored withered leaves. We then calculated the global m<sup>6</sup>A/A ratio of these tea leaves (##FIG##0##Figure 1##B). The solar-withering treatments with different shading rates decreased the global m<sup>6</sup>A level. The comparison of the various leaves detected a gradually decreasing trend in the overall m<sup>6</sup>A level from FLs to the SW3 leaves, but the m<sup>6</sup>A level rebounded following the SW4 treatment.</p>", "<title>Overview of the m<sup>6</sup>A MeRIP-seq</title>", "<p id=\"p0035\">To ascertain the effects of m<sup>6</sup>A-mediated regulatory mechanisms under solar-withering conditions, we performed an m<sup>6</sup>A methylated RNA immunoprecipitation sequencing (MeRIP-seq) experiment to analyze the m<sup>6</sup>A modifications at the mRNA level in tea leaves that underwent solar-withering with different shading rates (<xref rid=\"s0140\" ref-type=\"sec\">Figure S2</xref>). A total of 34–50 and 63–76 million high-quality clean reads were obtained for the immunoprecipitated (IP) libraries and input libraries, respectively, among which 28–41 and 55–67 million reads were mapped to the tea genome (<xref rid=\"s0140\" ref-type=\"sec\">Table S1</xref>). The base quality score of 20 (Q20) and base quality score of 30 (Q30) indices for each library exceeded 93% and 88%, respectively. Only the m<sup>6</sup>A peaks in all biological replicates with high-confidence coefficients were selected for further analyses. A total of 3570, 3249, 2966, 2809, and 2883 high-confidence m<sup>6</sup>A peaks were identified for the FL, SW1, SW2, SW3, and SW4 samples, respectively (<xref rid=\"s0140\" ref-type=\"sec\">Figure S3</xref>). Among these m<sup>6</sup>A peaks, 4605 were newly generated after the solar-withering treatment. Additionally, 31,720, 31,958, 32,146, 32,215, and 31,988 transcripts were obtained from the FL, SW1, SW2, SW3, and SW4 samples, respectively. Next, we identified 5277 high-confidence m<sup>6</sup>A peaks in 4289 transcripts. A total of 1988 m<sup>6</sup>A-marked genes were present in all samples (<xref rid=\"s0140\" ref-type=\"sec\">Figure S4</xref>). The solar-withering treatment induced the production of 843 new m<sup>6</sup>A-marked genes. The changes in the number of m<sup>6</sup>A-marked genes in response to solar-withering with different shading rates were consistent with the total m<sup>6</sup>A abundance dynamics. These observations suggest that the m<sup>6</sup>A abundance is closely related to these changes in the number of m<sup>6</sup>A-marked genes, which is in accordance with the findings of a previous study on tomato ##REF##31387610##[11]##. The number of m<sup>6</sup>A-marked genes gradually decreased from FLs to the SW3 leaves, whereas there were more m<sup>6</sup>A-marked genes in the SW4 leaves than in the SW3 leaves. In addition, most of the m<sup>6</sup>A-marked genes (2229 genes) were common to the FL <italic>vs.</italic> SW2 and FL <italic>vs.</italic> SW4 comparisons, whereas 219 and 216 m<sup>6</sup>A-marked genes were unique to the FL <italic>vs.</italic> SW2 and FL <italic>vs.</italic> SW4 comparisons, respectively. These results imply that the m<sup>6</sup>A-marked genes did not differ significantly between these two comparisons, with most m<sup>6</sup>A-marked genes common to both comparisons. Most of the 4289 m<sup>6</sup>A-marked genes in the five samples (average of 96.90%) contained a single m<sup>6</sup>A peak, with only a few containing more than three m<sup>6</sup>A peaks (<xref rid=\"s0140\" ref-type=\"sec\">Table S2</xref>). The distribution of m<sup>6</sup>A peaks in the tea leaves during the solar-withering treatment was then investigated. Major m<sup>6</sup>A modifications within transcripts were primarily near the stop codon and 3′ UTR (##FIG##0##Figure 1##C). Only 1.46%–2.13% of the m<sup>6</sup>A modifications were located in the coding sequence (CDS) and 5′ UTR or near the start codon (##FIG##0##Figure 1##D). From FLs to the SW3 leaves, the proportion of m<sup>6</sup>A modifications increased in the 3′ UTR and near the stop codon, but decreased in the 5′ UTR and CDS and near the start codon. Surprisingly, the proportion of m<sup>6</sup>A modifications in the 3′ UTR and around the stop codon was lower in the SW4 leaves than that in the SW3 leaves, whereas the opposite trend was observed for the m<sup>6</sup>A peaks in the 5′ UTR and CDS and near the start codon. Next, the m<sup>6</sup>A peaks were normalized by the enrichment algorithm ##REF##25430002##[31]##. The results revealed that m<sup>6</sup>A modifications accumulated preferentially in the 3′ UTR and around the stop codon (<xref rid=\"s0140\" ref-type=\"sec\">Figure S5</xref>). Overall, the distribution of m<sup>6</sup>A peaks in tea leaves during the solar-withering treatment changed slightly.</p>", "<p id=\"p0040\">To identify the enriched motifs within the m<sup>6</sup>A peaks in tea plants, all of the m<sup>6</sup>A peaks were scanned using the MEME suite ##REF##19458158##[32]## and HOMER tool ##REF##20513432##[33]##. As expected, the canonical motif RRACH (R = G/A and H = A/U/C) was enriched in most of the m<sup>6</sup>A peaks (<xref rid=\"s0140\" ref-type=\"sec\">Figure S6</xref>). Moreover, another enriched motif, UGUAY (Y = C/U), was similar to the plant-specific motif URUAY, which can be recognized by m<sup>6</sup>A readers ##REF##29716990##[34]##. Although the UGUAY motif is relatively common in the m<sup>6</sup>A peaks of tomato ##REF##31387610##[11]##, it has not been detected in other plant species. Hence, the enriched motifs at m<sup>6</sup>A-modified sites were relatively conserved in two horticultural plant species (<italic>i.e.</italic>, tea and tomato).</p>", "<title>Analysis of DMP-associated genes</title>", "<p id=\"p0045\">To clarify the potential effects of m<sup>6</sup>A modifications during the solar-withering stage, we first searched for DMPs in the m<sup>6</sup>A methylome. The DMPs were identified according to the following criteria: |fold change (FC)| ≥ 2 and <italic>P</italic> &lt; 0.05. A total of 265 DMPs were detected in the FL <italic>vs.</italic> SW1 comparison, of which 203 and 62 were hypermethylated and hypomethylated peaks, respectively (<xref rid=\"s0140\" ref-type=\"sec\">Table S3</xref>). The 215 DMPs identified in the FL <italic>vs.</italic> SW4 comparison were similar to the number of DMPs detected in the FL <italic>vs.</italic> SW2 comparison (<italic>i.e.</italic>, 217), but more than the 183 DMPs identified in the FL <italic>vs.</italic> SW3 comparison. These results reflected the apparent changes in the global m<sup>6</sup>A status in the withered leaves following the solar-withering treatments with different shading rates. The number of detected DMPs decreased from the FL <italic>vs.</italic> SW1 comparison to the FL <italic>vs.</italic> SW3 comparison, whereas it increased substantially in the FL <italic>vs.</italic> SW4 comparison. Intriguingly, the change in the number of DMPs under solar-withering conditions was in accordance with the overall change in the total m<sup>6</sup>A level. Hence, the m<sup>6</sup>A modifications in tea leaves were tightly associated with the solar-withering treatment conditions, especially the shading rate.</p>", "<p id=\"p0050\">To evaluate the overall correlation between m<sup>6</sup>A modifications and gene expression levels in response to solar-withering treatments, 1137 DMP-associated genes with varying expression levels between samples were selected (<xref rid=\"s0140\" ref-type=\"sec\">Figure S7</xref>). The results showed that 74.9% of the DMP-associated genes in the FL <italic>vs.</italic> SW1 comparison, 79.6% of the DMP-associated genes in the FL <italic>vs.</italic> SW2 comparison, 83.2% of the DMP-associated genes in the FL <italic>vs.</italic> SW3 comparison, and 79.6% of the DMP-associated genes in the FL <italic>vs.</italic> SW4 comparison with increased or decreased m<sup>6</sup>A levels displayed negatively regulated gene expression. In contrast, only 25.1% of the DMP-associated genes in the FL <italic>vs.</italic> SW1 comparison, 20.4% of the DMP-associated genes in the FL <italic>vs.</italic> SW2 comparison, 16.8% of the DMP-associated genes in the FL <italic>vs.</italic> SW3 comparison, and 20.4% of the DMP-associated genes in the FL <italic>vs.</italic> SW4 comparison with increased or decreased m<sup>6</sup>A levels displayed positively regulated gene expression. Thus, the m<sup>6</sup>A modifications in most DMP-associated genes were negatively correlated with gene expression levels during the solar-withering treatment. Interestingly, combined with the increasing proportion of m<sup>6</sup>A modifications in the 3′ UTR and near the stop codon from FLs to the SW3 leaves, m<sup>6</sup>A modifications within these regions tended to decrease the mRNA abundance. Furthermore, the proportion of m<sup>6</sup>A modifications within the 3′ UTR and around the stop codon was lower in the SW4 leaves than that in the SW3 leaves, which was consistent with the obvious decrease in the proportion of DMP-associated genes with expression levels that were negatively correlated with m<sup>6</sup>A abundance. The m<sup>6</sup>A peaks distributed within the 3′ UTR and around the stop codon were negatively correlated with the mRNA abundance, whereas the m<sup>6</sup>A peaks located in the 5′ UTR and CDS and near the start codon tended to be positively correlated with gene expression. Therefore, the multifaceted effects of m<sup>6</sup>A modifications on mRNA expression may depend on the position of the m<sup>6</sup>A peaks. The specific distribution of m<sup>6</sup>A peaks is closely related to gene expression in tea leaves as well as in several other important crops, including rice ##REF##34167554##[35]##, strawberry ##REF##34078442##[13]##, and apple ##REF##34679252##[36]##.</p>", "<p id=\"p0055\">Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to decipher the biological functions of the identified DMP-associated genes. Consistent with the fact that withering affects the formation of flavor compounds in tea, the enriched KEGG pathways among the m<sup>6</sup>A-labeled genes were associated with genetic information processing (##FIG##1##Figure 2##A). More than half of the DMP-associated genes were assigned to the ribosome, RNA transport, and spliceosome pathways. Moreover, several DMP-associated genes were associated with three metabolism-related pathways. Among these pathways, the rich factor was highest for the terpenoid backbone biosynthesis pathway, which is closely related to the formation of the oolong tea aroma. We focused on the ribosome, RNA transport, spliceosome, and terpenoid backbone biosynthesis pathways in the subsequent analyses.</p>", "<title>Negative correlation between the m<sup>6</sup>A abundances and the expression levels of most DMP-associated genes under solar-withering conditions</title>", "<p id=\"p0060\">The m<sup>6</sup>A-seq analysis showed that the m<sup>6</sup>A abundances and the expression levels of several core genes involved in the four aforementioned KEGG pathways were significantly altered during the solar-withering process (<xref rid=\"s0140\" ref-type=\"sec\">Figure S8</xref>A and B). In the ribosome pathway, the m<sup>6</sup>A abundances of 34 ribosomal protein-encoding (RP) genes were affected by the solar-withering treatment (<xref rid=\"s0140\" ref-type=\"sec\">Table S4</xref>). These RP genes are indispensable for ribosome formation and protein biosynthesis and have important roles in the transcription–translation process. We also determined that 20 and 16 DMP-associated genes are involved in RNA transport and spliceosome pathways, respectively (<xref rid=\"s0140\" ref-type=\"sec\">Tables S5 and S6</xref>). RNA transport is functionally linked to several steps in the RNA processing stage, including RNA splicing, 3′-end formation, and transcription–translation processes, which are critical for various biological functions ##REF##30972423##[37]##. AS is a pivotal post-transcriptional event that diversifies the generated transcripts and the corresponding proteins, making it a critical molecular mechanism that regulates transcriptional abundance in the plant kingdom. Interestingly, significant changes in the m<sup>6</sup>A levels were detected for eight terpenoid biosynthesis-related genes in response to the solar-withering treatment (<xref rid=\"s0140\" ref-type=\"sec\">Table S7</xref>).</p>", "<p id=\"p0065\">For each of the four aforementioned pathways, we selected one DMP-associated gene in which there was a dynamic change in the m<sup>6</sup>A level following the solar-withering treatments with different shading rates. The four genes encode the large subunit ribosomal protein L10e (RB-L10e), eukaryotic translation initiation factor 4A (EIF4A), core spliceosomal Sm protein (Sm), and 1-deoxy-D-xylulose-5-phosphate synthase (DXS), respectively. The m<sup>6</sup>A peaks in their mRNA sequences were mainly distributed in the 3′ UTR and around the stop codon (##FIG##1##Figure 2##B). Our m<sup>6</sup>A-seq datasets revealed significant changes in the m<sup>6</sup>A levels of these four genes (<xref rid=\"s0140\" ref-type=\"sec\">Figure S9</xref>A). We then performed an m<sup>6</sup>A-immunoprecipitation-quantitative polymerase chain reaction (m<sup>6</sup>A-IP-qPCR) analysis to further validate the m<sup>6</sup>A levels of the four aforementioned genes. As expected, the m<sup>6</sup>A levels in <italic>CsRB-L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic> decreased sharply from FLs to the SW3 leaves, but increased from the SW3 leaves to the SW4 leaves (##FIG##1##Figure 2##C). The expression levels of these four genes increased from FLs to the SW3 leaves, but then decreased in the SW4 leaves, as revealed by both transcriptome datasets (<xref rid=\"s0140\" ref-type=\"sec\">Figure S9</xref>B) and the quantitative real-time polymerase chain reaction (qRT-PCR) data (##FIG##1##Figure 2##D). These results indicate that the m<sup>6</sup>A modifications in these mRNAs were negatively correlated with their corresponding expression levels, which is in agreement with the findings of a previous study that demonstrated that mRNAs with low m<sup>6</sup>A levels tend to be highly expressed in tomato ##REF##31387610##[11]##. We detected obvious changes in the contents of seven monoterpenoids and one apocarotenoid using gas chromatography–mass spectrometry (GC–MS) (##FIG##1##Figure 2##E). Specifically, the abundances of all eight volatiles increased markedly from FLs to the SW3 leaves before decreasing significantly in the SW4 leaves. We also determined that the accumulation of eight volatile terpenoids was positively correlated with the <italic>CsDXS</italic> expression level, but negatively correlated with the m<sup>6</sup>A level of <italic>CsDXS</italic> and the overall m<sup>6</sup>A level under solar-withering conditions.</p>", "<title>Expression profiles of m<sup>6</sup>A regulatory genes in response to solar-withering</title>", "<p id=\"p0070\">The effects of RNA methylation are tightly associated with the transcript levels of RNA methyltransferase, demethylase, and reader genes ##REF##32411708##[38]##. Thus, we speculated that the m<sup>6</sup>A levels of these mRNAs are coordinately governed by m<sup>6</sup>A regulatory genes. Based on our recent report ##REF##34211493##[14]##, 34 m<sup>6</sup>A regulatory genes were identified in the tea reference genome. We initially analyzed the expression profiles of m<sup>6</sup>A regulatory genes under solar-withering conditions (##FIG##2##Figure 3##A). The m<sup>6</sup>A regulatory genes with |FC| ≥ 2 and <italic>P</italic> &lt; 0.05 were considered to be differentially expressed between samples. The transcript levels of all m<sup>6</sup>A writer and reader genes were not obviously altered by the solar-withering conditions. Among the 16 m<sup>6</sup>A eraser genes, only <italic>CsALKBH4A</italic> and <italic>CsALKBH4B</italic> had significant changes in their transcript levels after the solar-withering treatments. We also noticed that <italic>CsALKBH6</italic> transcription was significantly induced only following the SW3 treatment. These results indicate that dynamic changes in m<sup>6</sup>A modifications may be mainly controlled by m<sup>6</sup>A eraser genes, with <italic>CsALKBH6</italic> playing a particularly important role in the regulation of m<sup>6</sup>A levels in response to SW3. Next, a qRT-PCR analysis confirmed the expression patterns of m<sup>6</sup>A regulatory genes revealed by the transcriptome data, and demonstrated that the <italic>CsALKBH4A</italic> and <italic>CsALKBH4B</italic> expression levels increased continuously from FLs to the SW3 leaves, but then clearly decreased in the SW4 leaves (##FIG##2##Figure 3##B). This trend was in accordance with the expression patterns of <italic>CsRB-L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic>, but was inversely correlated with the m<sup>6</sup>A abundances of these four genes and the global m<sup>6</sup>A level under solar-withering conditions. Moreover, the <italic>CsALKBH6</italic> expression level increased significantly only following the SW3 treatment, whereas the expression of the m<sup>6</sup>A writer and reader genes was unaffected by the solar-withering treatments. These observations imply that the m<sup>6</sup>A eraser-mediated removal of m<sup>6</sup>A marks on mRNAs is closely linked with variations in m<sup>6</sup>A levels and the expression of DMP-associated genes.</p>", "<title>CsALKBH4-mediated RNA demethylation may activate terpenoid biosynthesis</title>", "<p id=\"p0075\">To further functionally characterize <italic>CsALKBH4A</italic> and <italic>CsALKBH4B</italic> during the solar-withering process, we transiently suppressed the expression of these two genes via an siRNA-mediated gene silencing strategy (##FIG##3##Figure 4##A). As anticipated, the expression of both <italic>CsALKBH4A</italic> and <italic>CsALKBH4B</italic> was significantly down-regulated in the gene-silenced leaves, whereas the transcription of these two genes was not substantially altered by treatments with the corresponding negative control (NC) (##FIG##3##Figure 4##B and C). The inhibited expression of <italic>CsALKBH4A</italic> and <italic>CsALKBH4B</italic> led to a marked increase in the overall m<sup>6</sup>A level in the gene-silenced tea leaves (##FIG##3##Figure 4##B and C), which occurred concomitantly with an obvious increase in the m<sup>6</sup>A levels of <italic>CsRB-L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic> (<xref rid=\"s0140\" ref-type=\"sec\">Figure S10</xref>A) (compared with the respective NC). Conversely, the <italic>CsRB-L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic> mRNA levels were markedly lower in the gene-silenced leaves than in the NC-treated leaves (<xref rid=\"s0140\" ref-type=\"sec\">Figure S10</xref>B). Accordingly, the diminished expression of these four genes may be mainly attributed to the suppression of CsALKBH4-mediated RNA demethylation. To further investigate how m<sup>6</sup>A demethylation influences the transcription of <italic>CsRB-L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic>, we explored whether CsALKBH4-mediated RNA demethylation modulates the stability of the transcripts of these four genes by monitoring mRNA decay rates after an actinomycin D treatment (##FIG##3##Figure 4##B and C). We observed that the <italic>CsRB</italic>-<italic>L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic> mRNAs degraded more rapidly in the <italic>CsALKBH4A</italic>- and <italic>CsALKBH4B</italic>-silenced leaves than in the NC-treated leaves. Notably, for <italic>CsRB</italic>-<italic>L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic>, their mRNA decay rates were negatively correlated with their expression levels and positively correlated with their m<sup>6</sup>A levels. These results suggest that excessive m<sup>6</sup>A modifications in the <italic>CsRB</italic>-<italic>L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic> mRNAs have a destabilizing effect, which results in a clear decrease in transcript levels. To assess the effects of RNA demethylation on the accumulation of volatile terpenoids, the terpenoid contents in <italic>CsALKBH4A</italic>- and <italic>CsALKBH4B</italic>-silenced leaves were measured. The transcriptional repression of these two genes resulted in a substantial decrease in the contents of the eight volatile terpenoids (##FIG##4##Figure 5##A and B), suggesting that CsALKBH4-mediated RNA demethylation may directly activate terpenoid biosynthesis by removing m<sup>6</sup>A marks and enhancing the stability of the corresponding mRNAs.</p>", "<title>RNA demethylation modulates AS events by influencing m<sup>6</sup>A modifications and the expression of spliceosome-related genes</title>", "<p id=\"p0080\">The spliceosome pathway was one of the main enriched KEGG pathways among the DMP-associated genes. The m<sup>6</sup>A modifications of the core genes <italic>Sm</italic>, <italic>Prp18</italic> (encoding pre-mRNA-splicing factor 18), and <italic>Prp31</italic> (encoding pre-mRNA-splicing factor 31) in the spliceosome pathway were significantly altered by the solar-withering treatment, which was consistent with the obvious expression changes detected for these genes. Thus, we hypothesized that RNA demethylation might contribute to the regulation of AS events by controlling the m<sup>6</sup>A levels and the expression levels of spliceosome-related genes. To test this hypothesis, we first investigated the AS events during the solar-withering treatments with different shading rates. A total of 18,188 AS events were detected in 13,606 genes in five tea samples. There were substantially more AS events in the solar-withered leaves than in FLs, suggesting that solar-withering conditions may influence the occurrence of AS events (<xref rid=\"s0140\" ref-type=\"sec\">Table S8</xref>). Within a certain shading rate range (<italic>i.e.</italic>, SW1–SW3), the frequency of AS events was closely correlated with the decreases in the shading rate. In contrast, solar-withering without shading substantially decreased the number of AS events. In the examined samples, the predominant AS events resulted in retained introns. This observation is in accordance with the results of earlier investigations on maize ##REF##27339440##[39]##, cotton ##REF##28892169##[40]##, and tea ##REF##34154536##[41]##. We next comprehensively identified the differentially expressed alternative splicing genes (DAGs) among the solar-withering treatments with different shading rates. There were more DAGs in the FL <italic>vs.</italic> SW3 comparison than in the FL <italic>vs.</italic> SW1 and FL <italic>vs.</italic> SW2 comparisons, implying that increasing the light intensity of the solar-withering treatment may promote the differential expression of AS genes (<xref rid=\"s0140\" ref-type=\"sec\">Table S9</xref>). However, there were fewer DAGs in the FL <italic>vs.</italic> SW4 comparison than in the FL <italic>vs.</italic> SW3 comparison. These findings indicate that the shading rate during the solar-withering treatment affects the number of AS events, possibly by modulating the expression of AS genes.</p>", "<title>Association between flavonoid, catechin, and theaflavin contents and the AS gene transcript levels under solar-withering conditions</title>", "<p id=\"p0085\">To further explore the putative effects of DAGs under solar-withering conditions, we performed a KEGG analysis of all identified DAGs. Metabolic pathways were the most enriched pathways among the DAGs, followed by the flavonoid biosynthesis pathway (##FIG##5##Figure 6##A). Therefore, structural genes involved in flavonoid biosynthesis may be affected by the m<sup>6</sup>A-mediated AS regulatory mechanism (<xref rid=\"s0140\" ref-type=\"sec\">Figure S11</xref>; <xref rid=\"s0140\" ref-type=\"sec\">Table S10</xref>). We selected <italic>4CL</italic> (encoding 4-coumarate CoA ligase) and <italic>F3′H</italic> (encoding flavonoid 3′-hydroxylase) as two flavonoid biosynthesis-related DAGs for further analyses. AS events generated two and three splicing variants for <italic>4CL</italic> and <italic>F3′H</italic>, respectively. On the basis of the fragments per kilobase per million mapped reads (FPKM) values obtained from the transcriptome datasets, the expression profiles of these AS transcripts under solar-withering conditions were analyzed (##FIG##5##Figure 6##B). The expression of the full-length <italic>Cs4CL</italic> transcript decreased substantially from FLs to the SW3 leaves, but then obviously increased in the SW4 leaves. The expression profile of the AS transcript <italic>Cs4CL-a</italic> was similar to that of the full-length transcript after the solar-withering treatment, whereas the <italic>Cs4CL-a</italic> transcript abundance was lower than that of <italic>Cs4CL</italic> following the same solar-withering treatment. Solar-withering also strongly inhibited the transcription of <italic>CsF3′H-a</italic>. Because of the high cycle threshold value &gt; 35 for <italic>CsF3′H</italic> and <italic>CsF3′H-b</italic> in the qRT-PCR assay (<xref rid=\"s0140\" ref-type=\"sec\">Table S11</xref>), the expression levels for these two transcripts were extremely low in FLs and the solar-withered leaves. Hence, <italic>CsF3′H-a</italic> may be the predominant transcript involved in flavonoid biosynthesis. The qRT-PCR analysis confirmed the transcriptome datasets were reliable (##FIG##5##Figure 6##C). To identify the AS transcripts related to the biosynthesis of flavonoids and catechins during solar-withering with different shading rates, the flavonoid and catechin contents in all five samples were compared (<xref rid=\"s0140\" ref-type=\"sec\">Figure S12</xref>A). There was a sharp decrease in the total flavonoid content from FLs to the SW3 leaves, but there was a distinct rebound from SW3 to SW4.</p>", "<p id=\"p0090\">Excessive and insufficient amounts of catechins have detrimental effects on tea flavor and the health benefits of tea. In this study, we examined whether the solar-withering process increases the palatability of oolong tea, while also decreasing the health benefits of tea. Intriguingly, AS events were detected for <italic>APX1</italic> (encoding ascorbate peroxidase 1) and <italic>GPX3</italic> (encoding glutathione peroxidase 3), which are involved in metabolic pathways. These two genes are reportedly responsible for the conversion of catechins into theaflavins ##REF##33233254##[42]##, ##REF##32129069##[43]##. We hypothesized that the solar-withering treatments strongly inhibited catechin biosynthesis, resulting in an obvious increase in the theaflavin content. To assess this hypothesis, the total theaflavin content and the contents of four theaflavin components were measured using liquid chromatography–mass spectrometry (LC–MS). As expected, the solar-withering treatments caused the individual theaflavin contents and the total theaflavin content to increase substantially (<xref rid=\"s0140\" ref-type=\"sec\">Figure S12</xref>A). Additionally, the theaflavin contents were inversely correlated with the catechin contents under solar-withering conditions. Next, we observed that the <italic>CsGPX3</italic>, <italic>CsAPX1</italic>, and <italic>CsAPX1</italic>-<italic>a</italic> expression levels increased dramatically from FLs to the SW3 leaves, but then clearly decreased in the SW4 leaves. One AS transcript (<italic>CsGPX3</italic>-<italic>a</italic>) was unaffected by the solar-withering treatments. We then detected a premature stop codon (PTC) in the <italic>CsGPX3</italic>-<italic>a</italic> mRNA (##FIG##5##Figure 6##D).</p>", "<p id=\"p0095\">To further elucidate the possible effects of AS transcripts on the accumulation of flavonoids, catechins, and theaflavins, the relationships between the abundances of flavonoid-related AS transcripts and metabolites were evaluated via Pearson’s correlation analysis (<xref rid=\"s0140\" ref-type=\"sec\">Figure S12</xref>B). Three transcripts (<italic>CsF3′H</italic>, <italic>CsF3′H-b</italic>, and <italic>CsGPX3</italic>-<italic>a</italic>) were excluded from this analysis because they were not expressed in FLs and the solar-withered leaves. The expression levels of the full-length <italic>Cs4CL</italic> transcript and the <italic>Cs4CL</italic>-<italic>a</italic> AS transcript were positively correlated with the total flavonoid, total catechin, and eight individual catechin contents. Positive correlations were also detected between the expression level of the <italic>CsF3′H</italic>-<italic>a</italic> AS transcript and the abundances of the aforementioned metabolites. Moreover, we observed that the accumulation of four individual theaflavin components and the total theaflavin content were positively correlated with the expression of <italic>CsGPX3</italic>, <italic>CsAPX1</italic>, and <italic>CsAPX1</italic>-<italic>a</italic>. We also examined the effects of AS transcripts (<italic>Cs4CL-a</italic>, <italic>CsF3′H-a</italic>, and <italic>CsAPX1-a</italic>) on the accumulation of the associated metabolites (<xref rid=\"s0140\" ref-type=\"sec\">Figure S13</xref>A). As expected, the <italic>Cs4CL-a</italic>, <italic>CsF3′H-a</italic>, and <italic>CsAPX1-a</italic> transcript levels were considerably down-regulated in the gene-silenced leaves, whereas they were not obviously altered by the corresponding NC treatments. Next, the flavonoid, catechin, and theaflavin contents in the gene-silenced leaves were analyzed (<xref rid=\"s0140\" ref-type=\"sec\">Figure S13</xref>B). The total flavonoid and total catechin contents as well as the accumulation of eight individual catechins decreased sharply following the silencing of <italic>Cs4CL-a</italic> or <italic>CsF3′H-a</italic>, which was in contrast to the lack of any significant changes to the total theaflavin content and the abundances of four individual theaflavins. The transcriptional repression of <italic>CsAPX1-a</italic> did not affect the flavonoid and catechin contents in the gene-silenced leaves, but it inhibited the accumulation of theaflavins. These observations imply that some AS transcripts are likely critical for the accumulation of flavonoids, catechins, and theaflavins.</p>" ]
[ "<title>Discussion</title>", "<title>Dynamic changes in global m<sup>6</sup>A level in tea leaves are mainly controlled by m<sup>6</sup>A erasers under solar-withering conditions</title>", "<p id=\"p0100\">In the past few decades, several studies on the environmental stresses during tea manufacturing (<italic>e.g.</italic>, withering stage) have clarified the molecular basis of specific metabolic activities related to tea flavor formation ##UREF##1##[15]##, ##REF##30277806##[17]##. Recent research confirmed epigenetic modifications, such as DNA methylation and histone modifications, influence the production of tea flavor-related substances ##REF##33773659##[28]##, ##REF##33464046##[29]##. However, it remains unclear whether RNA methylation (epitranscriptome-level changes) also regulates flavor-related metabolic pathways and tea flavor formation.</p>", "<p id=\"p0105\">In the present study, we observed that m<sup>6</sup>A modifications are widely distributed among mRNAs in tea plants, with dynamic changes in the m<sup>6</sup>A levels induced by solar-withering treatments. More specifically, in response to solar-withering conditions, the overall m<sup>6</sup>A level decreased dramatically. From FLs to the SW3 leaves, the overall m<sup>6</sup>A level gradually decreased, but the m<sup>6</sup>A level increased in the SW4 leaves. Thus, solar-withering treatments significantly decreased the m<sup>6</sup>A levels. Moreover, there was a positive correlation between the shading rate and the global m<sup>6</sup>A abundance within a certain range. According to earlier investigations ##REF##33730390##[44]##, ##REF##30256509##[45]##, the overall DNA methylation level is mediated by DNA methyltransferases and demethylases. In addition, the corresponding RNA methyltransferases and demethylases have been identified in tea plants ##REF##34211493##[14]##. Therefore, we speculated that the overall m<sup>6</sup>A level may be controlled by RNA methyltransferases and demethylases under solar-withering conditions. To evaluate this hypothesis, we comprehensively examined the expression profiles of m<sup>6</sup>A regulatory genes following solar-withering treatments. Notably, obvious transcript-level changes were detected in two m<sup>6</sup>A eraser genes (<italic>CsALKBH4A</italic> and <italic>CsALKBH4B</italic>) during the solar-withering treatments with different shading rates, whereas the expression levels of other m<sup>6</sup>A eraser and reader genes were only slightly affected by solar-withering. These findings are consistent with the reported phenomena in <italic>A. thaliana</italic>\n##REF##20351290##[46]## and tomato ##REF##31387610##[11]##. Similarly, during the solar-withering stage, tea leaves are subjected to multiple environmental stresses, including UV radiation ##UREF##1##[15]##. Thus, our results imply that the removal of m<sup>6</sup>A marks, rather than the addition and decoding of these marks, may be vital for tea plant responses to multiple stresses during the tea-withering stage. The inclusion of sunshade nets in solar-withering treatments prevents the excessive UV irradiation of tea leaves, thereby minimizing the damages to the living tea leaves. The <italic>CsALKBH4A</italic> and <italic>CsALKBH4B</italic> transcription levels increased continuously as the shading rate increased (from FLs to the SW3 leaves). Furthermore, the global m<sup>6</sup>A level was negatively correlated with the expression of these two m<sup>6</sup>A eraser genes. Additionally, the overall m<sup>6</sup>A level increased in the <italic>CsALKBH4</italic>-silenced leaves. These observations suggest that m<sup>6</sup>A demethylation is primarily responsible for the decrease in the global m<sup>6</sup>A level from FLs to the SW3 leaves. However, tea leaves were exposed to high UV doses during the solar-withering without the sunshade net (SW4). Exposures to high UV doses may lead to irreversible damages to the osmotic regulatory activities of plasma membranes ##REF##34739246##[47]##, ##REF##18256053##[48]##, ##REF##32194607##[49]##, ultimately leading to ruptured cells and further disruptions to the normal expression of the nuclear-localized genes <italic>CsALKBH4A</italic> and <italic>CsALKBH4B</italic>\n##REF##34211493##[14]##. In the current study, low UV doses induced <italic>CsALKBH4</italic> expression within a certain range during the solar-withering treatments with the sunshade net, whereas high UV doses strongly inhibited <italic>CsALKBH4</italic> expression when the solar-withering treatment was completed without a sunshade net. The down-regulated expression of <italic>CsALKBH4</italic> in response to the SW4 treatment may have impaired the ability of m<sup>6</sup>A erasers to remove m<sup>6</sup>A modifications, which may help to explain the observed increase in the overall m<sup>6</sup>A level from SW3 to SW4. Collectively, these results indicate that the dynamic changes in global m<sup>6</sup>A level in tea leaves undergoing solar-withering treatments with different shading rates are mainly controlled by m<sup>6</sup>A erasers. In addition, CsALKBH4-mediated RNA demethylation likely affects critical processes during the tea-withering stage.</p>", "<title>RNA demethylation directly contributes to the accumulation of volatile terpenoids and the formation of tea aromas</title>", "<p id=\"p0110\">Environmental stresses can considerably affect the accumulation of specialized metabolites in tea leaves, thereby affecting tea quality ##UREF##5##[50]##. During postharvest processing, tea leaves are exposed to various environmental stresses, which induce obvious alterations to many flavor-related compounds, leading to the production of teas with unique flavors ##REF##30277806##[17]##. Although the effects of specific metabolites on tea flavor formation have been investigated at the transcriptional, translational, and metabolic levels, the functional roles of epigenetic modifications, especially RNA methylation, and the regulatory mechanisms underlying the m<sup>6</sup>A-mediated flavor formation in the tea-withering stage remain unclear.</p>", "<p id=\"p0115\">In the current study, an integrated RNA methylome and transcriptome analysis revealed that the variations in the number of DMPs in response to solar-withering with different shading rates were in accordance with the changes in the total m<sup>6</sup>A level. The number of DMPs decreased between the FL <italic>vs.</italic> SW1 and FL <italic>vs.</italic> SW3 comparisons, but it increased in the FL <italic>vs.</italic> SW4 comparison. This increase may be associated with the inhibition of <italic>CsALKBH4</italic> expression due to high UV doses during solar-withering without a sunshade net. The down-regulated expression of <italic>CsALKBH4</italic> in the SW4 leaves hindered RNA demethylation, thereby increasing the differences in the m<sup>6</sup>A levels between the SW4 leaves and the leaves that underwent the other treatments and finally leading to an increase in the number of DMPs. A total of 1137 genes with DMPs under solar-withering conditions were functionally characterized. The KEGG pathway analysis showed that the identified DMP-associated genes were mainly associated with the terpenoid biosynthesis pathway. Volatile terpenoids are major quality-related compounds in oolong tea. Specifically, they significantly influence the formation of floral and honey-like aromas in high-quality oolong tea because of their low odor thresholds ##UREF##1##[15]##. Moreover, several lines of evidence suggest that environmental stresses can alter the m<sup>6</sup>A levels of transcripts ##REF##32842619##[12]##, ##REF##32933187##[51]##. In our study, the expression levels of seven terpenoid biosynthesis-related genes increased significantly under solar-withering conditions, which may be related to the observed considerable accumulation of volatile terpenoids. The positive correlations between the expression levels of these structural genes related to terpenoid biosynthesis and terpenoid contents imply that multiple stresses induced by solar-withering promote terpenoid accumulation by up-regulating the expression of terpenoid biosynthesis-related genes. This is in accordance with the results of another study ##REF##28450026##[18]##. In addition, the m<sup>6</sup>A levels in these terpenoid biosynthesis-related genes were negatively correlated with the corresponding expression levels. Similarly, an earlier investigation has demonstrated that the expression of genes with low m<sup>6</sup>A levels tends to be up-regulated ##REF##34178005##[52]##. These results suggest that the expression levels of m<sup>6</sup>A-containing genes may be governed by RNA methylation. According to recent reports, knocking out m<sup>6</sup>A writer genes can dramatically decrease the m<sup>6</sup>A levels of m<sup>6</sup>A-modified genes, which results in marked increases in gene expression levels ##REF##27396363##[6]##, ##REF##31116744##[53]##. In an earlier study, the overaccumulation of m<sup>6</sup>A marks on mRNAs adversely affected gene expression in the <italic>AtALKBH10B</italic> mutant line, suggesting that m<sup>6</sup>A modifications may negatively affect mRNA expression ##REF##29180595##[54]##. In our study, the suppression of <italic>CsALKBH4A</italic> and <italic>CsALKBH4B</italic> expression resulted in a significant decrease in the stability of <italic>CsDXS</italic> mRNA and the transcripts of three DMP-associated genes. Furthermore, the abundances of eight volatile terpenoids decreased in the <italic>CsALKBH4A</italic>- or <italic>CsALKBH4B</italic>-silenced leaves. These findings along with the CsALKBH4-mediated RNA demethylation mentioned above suggest that RNA demethylation may regulate the overall m<sup>6</sup>A level by modulating the expression of m<sup>6</sup>A eraser genes, while also stabilizing the mRNAs of DMP-associated genes, thereby increasing their expression. However, some reports indicate that mRNA abundance is positively correlated with m<sup>6</sup>A modifications ##REF##34078442##[13]##, ##REF##33568300##[55]##, which is inconsistent with our data. Therefore, the mechanism underlying the regulatory effects of m<sup>6</sup>A modifications on mRNAs in the solar-withering stage will need to be more thoroughly characterized. A recent study concluded that abiotic stress can alter the location of m<sup>6</sup>A peaks in transcripts ##REF##34149789##[9]##. The data generated in the present study showed that m<sup>6</sup>A peaks in <italic>CsDXS</italic> and three other DMP-associated genes were distributed within the 3′ UTR and around the stop codon under solar-withering conditions, indicating that solar-withering can affect the m<sup>6</sup>A levels in these DMP-associated genes, but it cannot induce the redistribution of m<sup>6</sup>A marks. Upon reviewing the reports that m<sup>6</sup>A modifications positively affect mRNA abundance, we noted that these m<sup>6</sup>A marks are mainly concentrated in the CDS region. This observation along with our other findings indicates that m<sup>6</sup>A modifications may have distinct regulatory effects on mRNA expression depending on their distribution in the transcript structure. Considered together, these findings suggest that CsALKBH4-mediated RNA demethylation promotes the expression of DMP-associated genes involved in terpenoid biosynthesis and the accumulation of aroma-related terpenoids by enhancing mRNA stability. Additionally, the shading rate was negatively correlated with the expression of terpenoid biosynthesis-related genes and terpenoid contents from FLs to the SW3 leaves, implying that within a certain range, moderate shading promotes terpenoid biosynthesis and the formation of a high-quality aroma in oolong tea. Inadequate shading during the SW4 treatment inhibited CsALKBH4-mediated RNA demethylation, with the detrimental effects on the expression of terpenoid biosynthesis-related genes ultimately leading to a significant decrease in the terpenoid content. This is consistent with the beneficial effects of moderate shading on flavor formation during the production of teas. Hence, solar-withering treatments of tea leaves may be optimized by controlling the shading rate, which is critical for enhancing tea aromas.</p>", "<title>RNA modifications indirectly affect the contents of flavonoid, catechin, and theaflavin by triggering the AS regulatory mechanism</title>", "<p id=\"p0120\">The AS regulatory mechanism is a crucial component of plant responses to diverse environmental stimuli ##REF##32589747##[56]##. The generation of many AS transcripts leads to the expression of various proteins that alleviate the adverse effects of multiple stresses. Although many AS events related to secondary metabolism have been detected, the specific mechanisms regulating AS events associated with flavor-related genes and tea flavor formation during the tea manufacturing process are still unclear. Recent research found that m<sup>6</sup>A modifications have important regulatory effects on RNA splicing ##REF##32411708##[38]##. Likewise, we observed that CsALKBH4-mediated RNA demethylation influences <italic>CsSm</italic> mRNA abundance in the spliceosome pathway by enhancing its stability. According to previous research, <italic>Sm</italic> encodes a crucial spliceosome component ##REF##29856907##[57]## that interacts with several small nuclear RNAs (snRNAs) and then binds to a series of additional proteins to form small nuclear ribonucleoprotein particles. Within the spliceosome, snRNAs contribute to the catalysis and recognition of splice sites during pre-mRNA splicing. Intriguingly, both the frequency of AS events and the number of DAGs were closely associated with <italic>CsSm</italic> expression. Therefore, RNA demethylation might regulate AS events by modulating the m<sup>6</sup>A abundance and the expression of spliceosome-related genes.</p>", "<p id=\"p0125\">To further investigate AS-mediated regulatory effects under solar-withering conditions, we performed a KEGG pathway enrichment analysis of all identified DAGs. Most of the DAGs were assigned to metabolic pathways and the flavonoid biosynthesis pathway. The subsequent analysis of the expression of four DAGs involved in these pathways revealed that the AS transcripts with the PTC (<italic>CsF3′H</italic>-<italic>b</italic> and <italic>CsGPX3</italic>-<italic>a</italic>) were expressed at almost undetectable levels under solar-withering conditions. This phenomenon may reflect the introduction of PTC into the gene structure, leading to the production of loss-of-function truncated proteins, which may be degraded via the nonsense-mediated decay pathway. This possibility is supported by the results of the analysis of the correlation between metabolite accumulation and the expression of AS transcripts, which revealed a lack of correlation between <italic>CsF3′H</italic>-<italic>b</italic> expression and the accumulation of flavonoids and catechins. Additionally, <italic>CsGPX3</italic>-<italic>a</italic> expression was only marginally correlated with the theaflavin level. Notably, the expression patterns of two non-PTC-type AS transcripts (<italic>Cs4CL-a</italic> and <italic>CsF3′H-a</italic>) were consistent with those of the corresponding full-length transcripts under solar-withering conditions. Meanwhile, <italic>Cs4CL-a</italic> and <italic>CsF3′H-a</italic> were more highly expressed than their full-length transcripts regardless of the shading rate during the solar-withering treatment. These findings imply that these two AS transcripts are the predominant transcripts in the flavonoid biosynthesis pathway. Similarly, <italic>CsbHLH-2</italic>, which is an AS transcript, is commonly formed in response to exposure to cold stress, during which it enhances stress tolerance by positively regulating certain signaling pathways ##REF##31959105##[58]##. Another AS transcript (<italic>CsAPX1</italic>-<italic>a</italic>) and its full-length transcript may participate in the coordinated regulation of theaflavin biosynthesis. The AS-mediated regulation of flavor metabolites was supported by our analysis of the correlation between AS transcripts and metabolites under solar-withering conditions, which revealed that <italic>Cs4CL-a</italic> and <italic>CsF3′H-a</italic> are positively correlated with the accumulation of flavonoids and catechins. A positive correlation was also detected between the AS transcript <italic>CsAPX1</italic>-<italic>a</italic> and the theaflavin content. We propose that the accumulation of flavonoids, catechins, and theaflavins is mediated by the canonical full-length transcripts as well as by particular AS transcripts, which may be important for the post-transcriptional regulation induced by solar-withering. Therefore, the down-regulated expression of <italic>Cs4CL</italic>, <italic>Cs4CL</italic>-<italic>a</italic>, and <italic>CsF3′H</italic>-<italic>a</italic> as well as the up-regulated expression of <italic>CsGPX3</italic>, <italic>CsAPX1</italic>, and <italic>CsAPX1-a</italic> in solar-withered leaves synergistically modulates flavonoid biosynthesis and flavonoid catabolism to promote the conversion of compounds associated with bitterness and astringency (<italic>e.g.</italic>, flavonoids and catechins) into theaflavins, which provide tea with a mellow taste. Compared with the other treatments, SW3 resulted in the lowest catechin content and the highest theaflavin content, suggesting that a moderate shading rate is ideal for decreasing bitterness and astringency and enhancing the mellow taste of tea infusions. Hence, RNA demethylation indirectly affects the accumulation of flavonoids, catechins, and theaflavins by triggering the AS-mediated regulatory mechanism, thereby improving the palatability of oolong tea.</p>", "<p id=\"p0130\">In conclusion, our integrated RNA methylome and transcriptome analysis reveal that the m<sup>6</sup>A-mediated regulatory mechanism coordinates the accumulation of specialized metabolites in tea leaves during the solar-withering stage. Moreover, the dynamic changes in global m<sup>6</sup>A level that occur in tea leaves in response to different shading rates during the solar-withering step are mainly controlled by m<sup>6</sup>A erasers. Furthermore, CsALKBH4-driven RNA demethylation directly affects the accumulation of volatile terpenoids and tea aroma formation by mediating the stability and abundance of terpenoid biosynthesis-related transcripts, while also indirectly regulating the contents of flavonoid, catechin, and theaflavin as well as the formation of tea taste-related substances by activating the AS-mediated regulatory mechanism. These findings have elucidated the effects of epigenetic modifications on the transcription of genes in the tea flavor-related metabolic pathways. They also indicate that the m<sup>6</sup>A-mediated regulatory mechanism may be targeted to enhance the high-quality flavor and palatability of oolong tea (##FIG##6##Figure 7##). Our work provides a solid foundation for future attempts at deciphering the functional effects of m<sup>6</sup>A modifications in tea plants, and it has also broadened our understanding of the regulatory mechanisms underlying m<sup>6</sup>A-mediated flavor formation during the solar-withering stage of the tea manufacturing process.</p>" ]
[]
[ "<p>The epitranscriptomic mark <italic>N</italic><sup>6</sup>-methyladenosine (m<sup>6</sup>A), which is the predominant internal modification in RNA, is important for plant responses to diverse stresses. Multiple environmental stresses caused by the tea-<bold>withering</bold> process can greatly influence the accumulation of specialized metabolites and the formation of tea flavor. However, the effects of the m<sup>6</sup>A-mediated regulatory mechanism on flavor-related metabolic pathways in tea leaves remain relatively uncharacterized. We performed an integrated RNA methylome and transcriptome analysis to explore the m<sup>6</sup>A-mediated regulatory mechanism and its effects on flavonoid and terpenoid metabolism in tea (<italic>Camellia sinensis</italic>) leaves under solar-withering conditions. Dynamic changes in global m<sup>6</sup>A level in tea leaves were mainly controlled by two m<sup>6</sup>A erasers (CsALKBH4A and CsALKBH4B) during solar-withering treatments. Differentially methylated peak-associated genes following solar-withering treatments with different shading rates were assigned to terpenoid biosynthesis and spliceosome pathways. Further analyses indicated that CsALKBH4-driven RNA demethylation can directly affect the accumulation of volatile terpenoids by mediating the stability and abundance of terpenoid biosynthesis-related transcripts and also indirectly influence the flavonoid, catechin, and theaflavin contents by triggering alternative splicing-mediated regulation. Our findings revealed a novel layer of epitranscriptomic gene regulation in tea flavor-related metabolic pathways and established a link between the m<sup>6</sup>A-mediated regulatory mechanism and the formation of tea flavor under solar-withering conditions.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Jianhua Yang</p>" ]
[ "<title>Data availability</title>", "<p id=\"p0190\">The raw sequencing data have been deposited in the Genome Sequence Archive ##REF##34400360##[75]## at the National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (GSA: CRA006400), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/\" id=\"ir455\">https://ngdc.cncb.ac.cn/</ext-link>.</p>", "<title>Conmpeting interests</title>", "<p id=\"p0195\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0200\"><bold>Chen Zhu:</bold> Methodology, Validation, Formal analysis, Investigation, Writing – original draft, Writing – review &amp; editing. <bold>Shuting Zhang:</bold> Software, Formal analysis, Data curation, Writing – original draft. <bold>Chengzhe Zhou:</bold> Validation, Investigation. <bold>Caiyun Tian:</bold> Validation, Investigation. <bold>Biying Shi:</bold> Software, Data curation. <bold>Kai Xu:</bold> Validation, Investigation. <bold>Linjie Huang:</bold> Validation, Investigation. <bold>Yun Sun:</bold> Software, Data curation. <bold>Yuling Lin:</bold> Conceptualization, Formal analysis. <bold>Zhongxiong Lai:</bold> Conceptualization, Formal analysis, Writing – review &amp; editing, Funding acquisition, Project administration. <bold>Yuqiong Guo:</bold> Conceptualization, Methodology, Formal analysis, Investigation, Writing – review &amp; editing, Project administration. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0215\">The following are the Supplementary data to this article:</p>", "<p id=\"p0220\">\n\n</p>", "<p id=\"p0225\">\n\n</p>", "<p id=\"p0230\">\n\n</p>", "<p id=\"p0235\">\n\n</p>", "<p id=\"p0240\">\n\n</p>", "<p id=\"p0245\">\n\n</p>", "<p id=\"p0250\">\n\n</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<p id=\"p0270\">\n\n</p>", "<p id=\"p0275\">\n\n</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<p id=\"p0325\">\n\n</p>", "<p id=\"p0330\">\n\n</p>", "<p id=\"p0335\">\n\n</p>", "<p id=\"p0340\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0205\">This work was supported by the Earmarked Fund for China Agriculture Research System of Ministry of Finance and Ministry of Agriculture and Rural Affairs (Grant No. CARS-19), the Scientific Research Foundation of Graduate School of Fujian Agriculture and Forestry University (Grant No. 324-1122yb070), the Scientific Research Foundation of Horticulture College of Fujian Agriculture and Forestry University (Grant No. 2019B01), the Rural Revitalization Tea Industry Technical Service Project of Fujian Agriculture and Forestry University (Grant No. 11899170145), the “Double first-class” scientific and technological innovation capacity and enhancement cultivation plan of Fujian Agriculture and Forestry University (Grant No. KSYLP004), the 6.18 Tea Industry Technology Branch of Collaborative Innovation Institute (Grant No. K1520001A), the Fujian Agriculture and Forestry University Construction Project for Technological Innovation and Service System of Tea Industry Chain (Grant No. K1520005A01), the Construction of Plateau Discipline of Fujian Province (Grant No. 102/71201801101), the Tea Industry Branch of Collaborative Innovation Institute of Fujian Agriculture and Forestry University (Grant No. K1521015A), and the Special Fund for Science and Technology Innovation of Fujian Zhang Tianfu Tea Development Foundation (Grant No. FJZTF01), China. We are grateful to Liwen Bianji (Edanz) (www.liwenbianji.cn) for its linguistic assistance.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Global abundance and</bold><bold>distribution</bold><bold>of m<sup>6</sup>A modifications</bold><bold>in tea leaves under solar-withering with different shading rates</bold></p><p><bold>A.</bold> The external phenotypes of withered leaves before and after solar-withering with different shading rates. <bold>B.</bold> Dynamics of global m<sup>6</sup>A level in tea leaves under solar-withering with different shading rates. Data are presented as mean ± SD. Different lowercase letters over the error bars indicate significantly different groups via one-way ANOVA and Tukey’s <italic>post hoc</italic> test (<italic>P</italic> &lt; 0.05). <bold>C.</bold> Metagenomic profiles of m<sup>6</sup>A distribution along transcripts. <bold>D.</bold> Pie charts showing the fractions of m<sup>6</sup>A peaks falling into five transcript segments (5′ UTR, start codon, CDS, stop codon, and 3′ UTR). m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenosine; IP, immunoprecipitation; FL, fresh leaf; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight; 5′ UTR, 5′ untranslated region; CDS, coding sequence; 3′ UTR, 3′ untranslated region; SD, standard deviation; ANOVA, analysis of variance.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>m<sup>6</sup>A abundances of representative DMP-associated genes were</bold><bold>negatively correlated with their expression levels</bold><bold>as well as</bold><bold>the accumulation of volatile terpenoids under solar-withering with different shading rates</bold></p><p><bold>A.</bold> KEGG enrichment analysis of DMP-associated genes. From the outside to the inside, the first circle indicates enriched KEGG pathways and the number of genes corresponds to the outer circle. The second circle indicates the number of genes in the genome background and the <italic>P</italic> value for the enrichment of the genes in the specified KEGG pathway. The third circle indicates the number of DMP-associated genes. The fourth circle indicates the enrichment factor of each KEGG pathway. <bold>B.</bold> The distribution of m<sup>6</sup>A reads in <italic>CsRB-L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic>. Exons and introns in the gene structures are represented by thick boxes and lines, respectively. <bold>C.</bold> Relative m<sup>6</sup>A enrichment of <italic>CsRB-L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic> under solar-withering with different shading rates determined by m<sup>6</sup>A-IP-qPCR. <bold>D.</bold> Relative expression levels of <italic>CsRB-L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic> under solar-withering with different shading rates determined by qRT-PCR. <bold>E.</bold> Relative contents of volatile terpenoids under solar-withering with different shading rates determined by GC–MS. Data are presented as mean ± SD. Different lowercase letters over the error bars indicate significantly different groups via one-way ANOVA and Tukey’s <italic>post hoc</italic> test (<italic>P</italic> &lt; 0.05). DMP, differentially methylated peak; KEGG, Kyoto Encyclopedia of Genes and Genomes; m<sup>6</sup>A-IP-qPCR, m<sup>6</sup>A-immunoprecipitation-quantitative polymerase chain reaction; qRT-PCR, quantitative real-time polymerase chain reaction; GC–MS, gas chromatography–mass spectrometry.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Expression profiles of m<sup>6</sup>A regulatory genes under solar-withering with different shading rates</bold></p><p><bold>A.</bold> The heatmap of m<sup>6</sup>A regulatory genes under solar-withering with different shading rates based on the transcriptome datasets. The expression values of m<sup>6</sup>A regulatory genes were normalized using <italic>z</italic>-score formula. The number in the box indicates the original FPKM value. <bold>B.</bold> Expression patterns of four m<sup>6</sup>A writer genes, five m<sup>6</sup>A eraser genes, and three m<sup>6</sup>A reader genes under solar-withering with different shading rates determined by qRT-PCR. Data are presented as mean ± SD. Different lowercase letters over the error bars indicate significantly different groups via one-way ANOVA and Tukey’s <italic>post hoc</italic> test (<italic>P</italic> &lt; 0.05). FPKM, fragments per kilobase per million mapped reads.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>CsALKBH4-mediated RNA demethylation contributes to the accumulation of volatile terpenoids by removing the m<sup>6</sup>A marks and enhancing the stability of corresponding mRNAs</bold></p><p><bold>A.</bold> Diagram of <italic>CsALKBH4A-</italic> and <italic>CsALKBH4B</italic>-silenced assay in tea leaves via an siRNA-mediated gene silencing strategy. The freshly detached tea bud and first leaf from naturally grown tea plants were incubated in 1.5-ml microcentrifuge tubes that contained 1 ml of 20 μM siRNA or siRNA-NC solution. After incubation for 12 h and 24 h, the tea bud and first leaf were harvested and then used for qRT-PCR and metabolite detection. <bold>B.</bold> Gene expression, global m<sup>6</sup>A level, and mRNA stability in <italic>CsALKBH4A-</italic>silenced tea leaves. <bold>C.</bold> Gene expression, global m<sup>6</sup>A level, and mRNA stability in <italic>CsALKBH4B-</italic>silenced tea leaves. To evaluate the mRNA stability, the leaf discs were collected from gene-silenced tea leaves and incubated in sterile water that contained 10 μg/ml actinomycin D solution. Tea leaves incubated in sterile water were used as controls. Total RNA was isolated from the leaves sampled at 6 h and 12 h, respectively. The mRNA levels of <italic>CsRB-L10e</italic>, <italic>CsEIF4A</italic>, <italic>CsSm</italic>, and <italic>CsDXS</italic> were examined by qRT-PCR. Data are presented as mean ± SD. The differences among various groups were assessed by conducting a one-way ANOVA and Tukey’s <italic>post hoc</italic> test. *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01. siRNA-NC, negative control siRNA.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Relative contents of volatile terpenoids in</bold><italic><bold>CsALKBH4A</bold></italic><bold>/</bold><italic><bold>CsALKBH4B</bold></italic><bold><italic>-</italic>silenced tea leaves determined by GC–MS</bold></p><p><bold>A.</bold> Relative contents of volatile terpenoids in <italic>CsALKBH4A-</italic>silenced tea leaves. <bold>B.</bold> Relative contents of volatile terpenoids in <italic>CsALKBH4B-</italic>silenced tea leaves. Data are presented as mean ± SD. The differences among various groups were assessed by conducting a one-way ANOVA and Tukey’s <italic>post hoc</italic> test. *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01.</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>AS-mediated regulatory mechanism influences the accumulation of flavor-related metabolites</bold></p><p><bold>A.</bold> KEGG enrichment analysis of DAGs. From the outside to the inside, the first circle indicates enriched KEGG pathways and the number of genes corresponds to the outer circle. The second circle indicates the number of genes in the genome background and the <italic>P</italic> value for the enrichment of the genes in the specified KEGG pathway. The third circle indicates the number of DAGs. The fourth circle indicates the enrichment factor of each KEGG pathway. <bold>B.</bold> The heatmap of DAGs and their AS transcripts under solar-withering with different shading rates based on the transcriptome datasets. The expression values of DAGs and their AS transcripts were normalized using the <italic>z</italic>-score formula. The number in the box indicates the original FPKM value. <bold>C.</bold> Expression patterns of <italic>Cs4CL</italic>, <italic>CsF3′H</italic>, <italic>CsGPX3</italic>, and <italic>CsAPX1</italic> as well as their AS transcripts under solar-withering with different shading rates determined by qRT-PCR. Data are presented as mean ± SD. Different lowercase letters over the error bars indicate significantly different groups via one-way ANOVA and Tukey’s <italic>post hoc</italic> test (<italic>P</italic> &lt; 0.05). <bold>D.</bold> RT-PCR validation and gene structure of the full-length transcripts and AS transcripts. M indicates the lane with DNA size markers. The full-length transcripts and AS transcripts on the gel images are denoted with black and red triangles, respectively. AS, alternative splicing; DAG, differentially expressed alternative splicing gene; RT-PCR, reverse transcription-polymerase chain reaction.</p></caption></fig>", "<fig id=\"f0035\"><label>Figure 7</label><caption><p><bold>Schematic model for the effects of m<sup>6</sup>A-mediated regulatory mechanism on the accumulation of flavor metabolites in tea (<italic>Camellia sinensis</italic>) leaves under solar-withering</bold></p><p>CsALKBH4-driven RNA demethylation can not only directly affect the accumulation of volatile terpenoids and the tea aroma formation by mediating the stability and abundance of terpenoid biosynthesis-related genes, but also indirectly regulate the contents of flavonoids, catechins, and theaflavins, as well as the tea taste formation via triggering the AS-mediated regulatory mechanism. These findings uncover a novel layer of epitranscriptomic gene regulation in tea flavor-related metabolic pathways and establish a strong link between m<sup>6</sup>A-mediated regulatory mechanism and the improvement of high-quality flavor and palatability in oolong tea. Solid arrows indicate direct regulation, and dashed arrows indicate indirect regulation. PTC, premature stop codon.</p></caption></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary Figure S1</label><caption><p><bold>The light intensity, spectrum, and UV intensity of solar-withering with different shading rates</bold> SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight; UV, ultraviolet.</p></caption></fig>", "<fig id=\"f0045\" position=\"anchor\"><label>Supplementary Figure S2</label><caption><p><bold>Brief workflow for MeRIP-seq</bold> The fragmented RNA was divided into two portions, one of which was enriched with an m<sup>6</sup>A-specific antibody in IP buffer. The other RNA without IP treatment was used as the input control. Finally, the two portions of RNA were sequenced using an Illumina NovaSeq 6000 platform. IP, immunoprecipitation; m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenosine; MeRIP, m<sup>6</sup>A methylated RNA immunoprecipitation.</p></caption></fig>", "<fig id=\"f0050\" position=\"anchor\"><label>Supplementary Figure S3</label><caption><p><bold>Venn diagrams showing the overlap of m<sup>6</sup>A peaks identified from fresh leaves and four solar-withered leaves with different shading rates</bold> FL, fresh leaves; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight.</p></caption></fig>", "<fig id=\"f0055\" position=\"anchor\"><label>Supplementary Figure S4</label><caption><p><bold>Venn diagrams showing the overlap of m<sup>6</sup>A-marked genes identified from fresh leaves and four solar-withered leaves with different shading rates</bold> FL, fresh leaves; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight.</p></caption></fig>", "<fig id=\"f0060\" position=\"anchor\"><label>Supplementary Figure S5</label><caption><p><bold>Enrichment score of m<sup>6</sup>A peaks in five transcript segments</bold> 5′ UTR, 5′ untranslated region; CDS, coding sequence; 3′ UTR, 3′ untranslated region; FL, fresh leaves; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight.</p></caption></fig>", "<fig id=\"f0065\" position=\"anchor\"><label>Supplementary Figure S6</label><caption><p><bold>Top sequence motifs identified within m<sup>6</sup>A peaks in tea leaves under solar-withering with different shading rates</bold> m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenosine.</p></caption></fig>", "<fig id=\"f0070\" position=\"anchor\"><label>Supplementary Figure S7</label><caption><p><bold>Correlation between m<sup>6</sup>A modification and expression levels of the DMP-associated genes under solar-withering with different shading rates</bold> DMP-associated genes, differentially methylated peak-associated genes; m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenosine; FL, fresh leaves; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight.</p></caption></fig>", "<fig id=\"f0075\" position=\"anchor\"><label>Supplementary Figure S8</label><caption><p><bold>m<sup>6</sup>A abundance and expression levels of DMP-associated genes under solar-withering with different shading rates based on RNA methylome and transcriptome datasets A.</bold> m<sup>6</sup>A abundance of DMP-associated genes under solar-withering with different shading rates. <bold>B.</bold> Expression levels of DMP-associated genes under solar-withering with different shading rates. The m<sup>6</sup>A abundance and expression levels of DMP-associated genes were normalized using the <italic>z</italic>-score formula, respectively. FPKM, fragments per kilobase per million mapped reads; KEGG, kyoto encyclopedia of genes and genomes; m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenosine; FL, fresh leaves; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight.</p></caption></fig>", "<fig id=\"f0080\" position=\"anchor\"><label>Supplementary Figure S9</label><caption><p><bold>m<sup>6</sup>A abundance and expression levels of <italic>CsRB-L10e, CsEIF4A, CsSm</italic>, and <italic>CsDXS</italic> under solar-withering with different shading rates based on RNA methylome and transcriptome datasets A.</bold> m<sup>6</sup>A abundance of <italic>CsRB-L10e, CsEIF4A, CsSm,</italic> and <italic>CsDXS</italic> under solar-withering with different shading rates. <bold>B.</bold> Expression levels of <italic>CsRB-L10e, CsEIF4A, CsSm</italic>, and <italic>CsDXS</italic> under solar-withering with different shading rates. Data are presented as mean ± standard deviation. Different lowercase letters over the error bars indicate significantly different groups via one-way analysis of variance and Tukey’s <italic>post hoc</italic> test (<italic>P</italic> &lt; 0.05). m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenosine; FPKM, fragments per kilobase per million mapped reads; FL, fresh leaves; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight.</p></caption></fig>", "<fig id=\"f0085\" position=\"anchor\"><label>Supplementary Figure S10</label><caption><p><bold>Relative m<sup>6</sup>A enrichment and relative expression levels of <italic>CsRB-L10e, CsEIF4A, CsSm</italic>, and <italic>CsDXS</italic> in <italic>CsALKBH4A-</italic> or <italic>CsALKBH4B</italic>-silenced leaves A.</bold> Relative m<sup>6</sup>A enrichment of <italic>CsRB-L10e, CsEIF4A, CsSm</italic>, and <italic>CsDXS</italic> in <italic>CsALKBH4A</italic>- or <italic>CsALKBH4B</italic>-silenced leaves determined by m<sup>6</sup>A-IP-qPCR. <bold>B.</bold> Relative expression levels of <italic>CsRB-L10e, CsEIF4A, CsSm,</italic> and <italic>CsDXS</italic> in <italic>CsALKBH4A</italic>- or <italic>CsALKBH4B</italic>-silenced leaves determined by qRT-PCR. Data are presented as mean ± standard deviation. The differences among various groups were assessed by conducting a one-way analysis of variance and Tukey’s <italic>post hoc</italic> test. *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenosine; m<sup>6</sup>A-IP-qPCR, m<sup>6</sup>A-immunoprecipitation-quantitative polymerase chain reaction; qRT-PCR, quantitative real-time polymerase chain reaction.</p></caption></fig>", "<fig id=\"f0090\" position=\"anchor\"><label>Supplementary Figure S11</label><caption><p><bold>Expression levels of DAGs and their AS transcripts involved in flavonoid biosynthesis pathway under solar-withering with different shading rates based on transcriptome datasets</bold> Expression values of DAGs and their AS transcripts were normalized using the <italic>z</italic>-score formula. DAGs, differentially expressed alternative splicing genes; AS, alternative splicing; FL, fresh leaves; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight.</p></caption></fig>", "<fig id=\"f0095\" position=\"anchor\"><label>Supplementary Figure S12</label><caption><p><bold>Relative contents of flavor-related metabolites and correlation analyses of full-length transcripts, AS transcripts, and flavor metabolites A.</bold> Relative contents of flavonoids, catechins, and theaflavins under solar-withering with different shading rates determined by LC-MS. Data are presented as mean ± standard deviation. Different lowercase letters over the error bars indicate significantly different groups via one-way analysis of variance and Tukey’s <italic>post hoc</italic> test (<italic>P</italic> &lt; 0.05). <bold>B.</bold> Correlation analyses of full-length transcripts, AS transcripts, and flavor metabolites. The correlation analyses were performed based on Pearson’s correlation coefficient. The number below the circle indicates the corresponding Pearson’s correlation coefficient. A correlation coefficient greater than 0 indicates a positive correlation, while a correlation coefficient less than 0 indicates a negative correlation. LC-MS, liquid chromatography-mass spectrometry; FL, fresh leaves; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight; C, catechin; CG, catechin gallate; EC, epicatechin; ECG, epicatechin gallate; EGC, epigallocatechin; EGCG, epigallocatechin gallate; GC, gallocatechin; GCG, gallocatechin gallate; TF1, theaflavin; TF2A, theaflavin-3-gallate; TF2B, theaflavin-3′-gallate; TF3, theaflavin-3,3′-digallate; KEGG, kyoto encyclopedia of genes and genomes.</p></caption></fig>", "<fig id=\"f0100\" position=\"anchor\"><label>Supplementary Figure S13</label><caption><p><bold>Relative expression levels of <italic>Cs4CL-a, CsF3'H-a,</italic> and <italic>CsAPX1-a</italic>, as well as the contents of flavor metabolites in AS transcript-silenced leaves A.</bold> Relative expression levels of <italic>Cs4CL-a, CsF3'H-a</italic>, and <italic>CsAPX1-a</italic> in AS transcript-silenced leaves determined by qRT-PCR. <bold>B.</bold> The contents of flavor metabolites in AS transcript-silenced leaves were determined by LC-MS. Data are presented as mean ± standard deviation. The differences among various groups were assessed by conducting a one-way analysis of variance and Tukey’s <italic>post hoc</italic> test. *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; C, catechin; CG, catechin gallate; EC, epicatechin; ECG, epicatechin gallate; EGC, epigallocatechin; EGCG, epigallocatechin gallate; GC, gallocatechin; GCG, gallocatechin gallate; TF1, theaflavin; TF2A, theaflavin-3-gallate; TF2B, theaflavin-3′-gallate; TF3, theaflavin-3,3′-digallate.</p></caption></fig>", "<fig id=\"f0105\" position=\"anchor\"><label>Supplementary Figure S14</label><caption><p><bold>RNA quality of fresh leaves and four solar-withered leaves with different shading rates</bold> Three independent biological replicates were performed for each sample. FL, fresh leaves; SW1, solar-withering with a high shading rate; SW2, solar-withering with a middle shading rate; SW3, solar-withering with a low shading rate; SW4, solar-withering with natural sunlight.</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Table S1</title><p><bold>A summary of m<sup>6</sup>A-seq reads in tea leaves under solar-withering with different shading rates</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Table S2</title><p><bold>The number of m<sup>6</sup>A peaks detected in m6A-marked genes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Table S3</title><p><bold>Statistics of DMPs under solar-withering with different shading rates</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S4</title><p><bold>DMP-associated genes involved in ribosome pathway</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S5</title><p><bold>DMP-associated genes involved in RNA transport pathway</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S6</title><p><bold>DMP-associated genes involved in spliceosome pathway</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S7</title><p><bold>DMP-associated genes involved in the terpenoid biosynthesis pathway</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S8</title><p><bold>Statistics of AS events under solar-withering with different shading rates</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S9</title><p><bold>Statistics of DAGs under solar-withering with different shading rates</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S10</title><p><bold>DAGs involved in the flavonoid biosynthesis pathway</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S11</title><p><bold>Raw data for qRT-PCR</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S12</title><p><bold>Primers used in this study</bold></p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e290\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0135\" fn-type=\"supplementary-material\"><p id=\"p0210\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2023.02.003\" id=\"ir025\">https://doi.org/10.1016/j.gpb.2023.02.003</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["5"], "surname": ["Pendleton", "Chen", "Liu", "Hunter", "Xie", "Tu"], "given-names": ["K.E.", "B.B.", "K.Q.", "O.V.", "Y.", "B.P."], "article-title": ["The U6 snRNA m"], "sup": ["6"], "source": ["Cell"], "volume": ["169"], "year": ["2017"], "object-id": ["824\u201335.e14"]}, {"label": ["15"], "surname": ["Zeng", "Zhou", "Su", "Yang"], "given-names": ["L.T.", "X.C.", "X.G.", "Z.Y."], "article-title": ["Chinese oolong tea: an aromatic beverage produced under multiple stresses"], "source": ["Trends Food Sci Tech"], "volume": ["106"], "year": ["2020"], "fpage": ["242"], "lpage": ["253"]}, {"label": ["20"], "surname": ["Zhang", "Cao", "Granato", "Xu", "Ho"], "given-names": ["L.", "Q.Q.", "D.", "Y.Q.", "C.T."], "article-title": ["Association between chemistry and taste of tea: a review"], "source": ["Trends Food Sci Tech"], "volume": ["101"], "year": ["2020"], "fpage": ["139"], "lpage": ["149"]}, {"label": ["23"], "surname": ["Ni", "Xu", "Wei", "Li", "Jin", "Deng"], "given-names": ["T.C.", "S.S.", "Y.M.", "T.H.", "G.", "W.W."], "article-title": ["Understanding the promotion of withering treatment on quality of postharvest tea leaves using UHPLC-orbitrap-MS metabolomics integrated with TMT-based proteomics"], "source": ["LWT"], "volume": ["147"], "year": ["2021"], "fpage": ["111614"]}, {"label": ["27"], "surname": ["Li", "He", "Yu", "Zhou", "Ran", "Chen"], "given-names": ["Y.C.", "C.", "X.L.", "J.T.", "W.", "Y.Q."], "article-title": ["Effects of red-light withering on the taste of black tea as revealed by non-targeted metabolomics and transcriptomics analysis"], "source": ["LWT"], "volume": ["147"], "year": ["2021"], "fpage": ["111620"]}, {"label": ["50"], "surname": ["Shao", "Zhang", "Lv", "Shen"], "given-names": ["C.Y.", "C.Y.", "Z.D.", "C.W."], "article-title": ["Pre- and post-harvest exposure to stress influence quality-related metabolites in fresh tea leaves ("], "italic": ["Camellia sinensis"], "source": ["Sci Hortic"], "volume": ["281"], "year": ["2021"], "fpage": ["109984"]}, {"label": ["65"], "surname": ["Stark", "Brown"], "given-names": ["R.", "G."], "article-title": ["DiffBind: differential binding analysis of ChIP-seq peak data"], "source": ["Bioconductor"], "year": ["2011"], "pub-id": ["10.18129/B9.bioc.DiffBind"]}]
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2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Aug 14; 21(4):769-787
oa_package/a7/3d/PMC10787128.tar.gz
PMC10787129
0
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[ "<title>Conclusion</title>", "<p>Admittedly, since the COVID-19 pandemic declaration, the global macroeconomic environment has not been spared its negative consequences. Although devastating, evidence from this study shows signs of recovery a year on. This study proposes strict targeted policies aimed at sustaining the recovery in addition to addressing the internal and external macroeconomic risks. If this is unattended to, many developing countries may experience one of the worst socio-eco-political crises ever.</p>" ]
[ "<p>A year after the World Health Organization´s declaration of the novel COVID-19 as a pandemic, the global macro-economic landscape has experienced severe shocks. As a result, developed and developing countries have been saddled with intense economic uncertainties. In this study, we discuss the global macro-economic environment during the pandemic declaration period and juxtapose it with the one-year post-pandemic declaration. The evidence shows significant negative impacts on macro-economic variables in the year of the declaration. However, signs of recovery are evident a year on, albeit slowly. To sustain and accelerate the recovery gains, we suggest that strategic macro-management policies are designed and strictly implemented. Anything short of this will see especially fragile countries plunged into an “economic abyss” with severe sociopolitical implications.</p>" ]
[ "<title>Commentary</title>", "<p>The COVID-19 disease, also known as the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), is alleged to have started in the city of Wuhan in China. It was not until March 2020 that the World Health Organisation (WHO) declared it a global pandemic. This declaration was occasioned by a 13-fold and a threefold increase in the number of cases and the number of countries with cases, respectively. The economic shock associated with the pandemic led to certain responses in the global macroeconomic environment in the short and medium-term [##UREF##0##1##,##UREF##1##2##]. Therefore, this study examines the macroeconomic impact a year after the COVID-19 pandemic declaration by the WHO. That is, how has the macroeconomic environment changed a year after the declaration of COVID-19 as a pandemic?</p>", "<p><bold>Gross domestic product (GDP):</bold> undoubtedly, COVID-19 has had an adverse effect on the global economy. Production suffered severely in many countries across the world, with supply-value chains disrupted globally. According to the World Bank, global gross output fell by an estimated 3.4% in 2020, with declining growth rates recorded in many regions across the globe. Sub-Saharan Africa´s regional economy (GDP) declined by 2.2% in 2020; Latin America and the Caribbean´s economy declined by 6.4%, Middle East and North Africa´s declined by 4.0%; and South Asia´s economy declined by 5.2% in 2020 [##UREF##2##3##]. In the East Asia and Pacific region, however, the economy grew by 1.2% in 2020 [##UREF##2##3##], which is a paltry rate of growth given the region´s high pre-pandemic growth rates. The economic decline recorded globally could be linked to border closures and domestic restrictions on mobility and production, thus disrupting supply value chains globally and, consequently, global output. Due to border closures in many parts of the world, industries suffered huge hits, with the aviation, hospitality and tourism industries being massively affected worldwide. Local restrictions, including lockdowns, also affected much of production in several countries. Even in countries where restrictions were not nationwide, they were imposed in local administrative areas with high population and high levels of business activity, thus severely hampering economic production. Additionally, the sheer number of people who got critically ill from COVID-19 infections also meant that critical labour was unavailable to work. While some industries were able to eventually shift part or all of their production online where workers who were not critically ill nor isolated could work remotely, it took some time for workers to adapt to that mode of work, thus losing crucial man hours. As a result, the GDP growth of many economies failed to meet anticipated pre-COVID levels. The economic situation was worse for developing countries because those countries have hardly automated work systems, and remote working was not the norm in these countries. Indeed, developing countries are set to suffer more from economic downturns resulting from COVID-19 due to inadequate resources and buffers. The United Nations Development Programme (UNDP) has, for instance, projected that at least $220 billion worth of income will be lost in developing countries as a result of COVID-19 . The consequence is an increase in the number of people who will be pushed into extreme poverty in these countries, with its associated inequalities. For example, since the outbreak of the pandemic, inter- and intra-country inequalities have worsened [##REF##34511653##4##]. The foregoing provides evidence of the damning effect COVID-19 has had on production and the potential effects particularly for developing countries going into the future. A year later, signs of economic recovery are evident at the global level. Thus, the global economy picked up in the year 2021, with growth increasing to an estimated 5.5% [##UREF##2##3##]. This was largely due to the lifting of COVID-19 related restrictions and the restoration of global supply chains, driving production close to pre-pandemic levels. Sustaining this level of growth would be possible if there were no new waves of infections that might necessitate a re-introduction of COVID-19 related restrictions. To forestall an occurrence of new waves and the dire effects particularly for developing countries, easy access to vaccines is needed to ramp up vaccinations among larger sections of their populations. This way, new infections would be kept in check, and economic activities could continue without interruptions with associated wellbeing implications.</p>", "<p><bold>Unemployment and labor:</bold> labour and labour mobility in almost every country were affected by the COVID-19 pandemic. As explained in the previous section, due to reduced production, firms were forced to lay off workers during the period, especially if their operations made remote working impossible or non-feasible. As a result, unemployment increased in many countries, further worsening the plight of lower-income earners. The International Labour Organization (ILO) reports that 8.8% of global working hours were lost in 2020 [##UREF##3##5##]. This is the equivalent of 255 million full-time jobs, with regions such as Latin America and the Caribbean, Southern Asia and Southern Europe the hardest hit. Among those who stayed employed during the pandemic, working hours reduced, thus leading to lower incomes for them. Indeed, global income (not accounting for income support) declined by an estimated 8.3% in 2020, which is the equivalent of 4.4% of global GDP [##UREF##3##5##]. Given the fact that GDP growth suffered in many countries, economies shrank, and the prospects for new job openings going forward are even more limited. Furthermore, since the COVID-19 pandemic opened some firms to the possibility of remote working and the potential to achieve targets with limited physical infrastructure, such as office space, previous work requirements and conditions may likely not return for some of these firms. They may opt for operating with skeletal staff working remotely and may thus not need to employ peripheral staff such as office keepers, office security, front desk staff among others. This implies that high unemployment, particularly among low skilled personnel, is set to exacerbate. The International monetary fund [##UREF##4##6##] projected that losses in working hours would continue in the year 2021, with an average loss of 3.0% in global working hours which is the equivalent of 90 million full-time jobs. This was despite the economic recovery that was expected in the year 2021 and is testament to the fact that while production might return to pre-pandemic levels or close to that, it may not be accompanied by the full restoration of jobs that existed before the pandemic. In other words, employment recovery is set to lag behind output recovery, and this raises concerns for the future of work globally but more critically, in developing countries where relatively larger proportions of unskilled labor exist. A good starting point to restoring employment and work is to ensure mass vaccinations across countries. This will reduce the likelihood of infections among the labor force thus making them healthy with regards to COVID-19. This is a first step to making sure that labor is able to take up job openings should they become available. Furthermore, job creation should form a central part of the economic recovery policies across the globe. Such recovery policies ought to be robust and pay attention to production activities that can yield more jobs, especially for youth. Furthermore, low skilled workers who are trainable ought to be re-trained to be able to take up the jobs that may become available but require different set of skills than what they currently possess.</p>", "<p><bold>Global trade:</bold> following historical evidence of global shocks, the onset of the COVID-19 meant that there would be disruptions in global trade. Eventually, in 2020, commerce and output volumes fell to their lowest levels since World War II. In the first half of 2020, global industrial production and goods trade declined at a rate comparable to that seen during the depths of the Global financial crisis. However, they appeared and vanished more rapidly, indicating a stronger V-shaped recovery in 2020. The trends in global merchandise trade for 2020 and 2021 are presented in ##FIG##0##Figure 1##. Generally, the effects of trade and production on specific items, services, and trading partners were highly variable. In fact, while the rest of the world suffered disruptions in trade, face masks were China's most exported product in May 2020. Exports in China fell sharply in February 2020, but soon rebounded and returned to normal by March 2020. However, shipments from the United States and Germany fell in April, recovering very slowly [##UREF##5##7##]. In addition, oil exports in African countries like Nigeria and Algeria fell by more than half while merchandise trade in many non-oil producing African countries changed marginally. Nonetheless, commerce in travel and tourism services also fell precipitously, while trade in digitally supplied services, such as telecommunications and information technology services, grew rapidly. It is estimated that in 2020, the value of goods exports reduced by 8.2% compared to the value of services exports, which declined by 16.7 percent [##UREF##6##8##]. By August of 2021, services and goods trade had recovered somewhat compared to the start of the epidemic, but new lockdowns and restrictive measures had caused more slumping. Recent trends in global trade point to some short to medium-term risk to global trade. This gives a bleak forecast for global trade in 2022. The invasion of Ukraine by Russia, new lockdowns in Shanghai and other parts of China over COVID-19 concerns make it difficult for suppliers to supply global demand for goods and services. Given that exports from Russia, China and Ukraine influence trade in other regions of the world, it is imperative that a solution is found to end the Russia-Ukraine war. Also, a cure for COVID-19 that is more robust might help end the uncertainties around jobs and help get economies working the way they were before the onset of the pandemic.</p>", "<p><bold>Inflation:</bold> in theory, one would expect the general price levels to rise in the face of sustained supply restrictions. These restrictions have adversely affected trade due to the rising cost of production which consequently forced general price levels to rise. Therefore, it is not surprising that there is inflation in food commodities globally. International food prices peaked in 2007-2008 and 2010-11. From ##FIG##1##Figure 2##, it is obvious that food prices rose again in January-March 2022. The increase has sparked fears of a new global food crisis, resulting in increased hunger among the world's poor and, possibly, social upheaval. The increase in food prices is also observed in the ##FIG##1##Figure 2##, which shows trends in the global market prices for commodities like rice, maize and sugar. Given the trajectory of the Food and Agriculture Organization (FAO) food price index and trend in global commodity prices from January 2022, it is reasonable to assume that prices for products will continue to rise. This is actually observed in the data on global prices of staples like rice, maize and sugar. A number of factors are probably driving inflation globally at this point in time. First, even though COVID-19 incidences have decreased significantly, the invasion of Ukraine by Russia has brought abruptions to global trade and caused supply shortages in countries that buy certain food commodities from either country. Both countries play an important role in the commerce of important foods like wheat, barley, corn, petroleum and other petroleum products. This makes it imperative that world policymakers find a solution to the impasse between these two countries and eliminate any associated supply chain disruptions. Secondly, according to harsh weather (hurricanes or drought) has produced shortages in oil supplies, coffee supply and microchip chips utilized in other smart technology. Because of Brexit and America´s tariffs on American imports, they argue, supplies to consumers in these countries and those elsewhere who rely on such commodities are being affected [##UREF##7##9##]. Finally, a number of countries have withdrawn the aid given to protect businesses and employment from the pandemic. It is possible that additional taxes will be implemented in order for governments to recoup their finances and promote fixed capital creation in the short- to medium-term, as a result. It is imperative that these triggers are addressed carefully in order to avoid a food crisis. The global economy will be better off without any subsequent crises.</p>", "<p><bold>Financial markets:</bold> the effects of the pandemic did not spare the world´s financial sector especially the fragile markets in developing countries. This has also, to a large extent, made the situation of poor households worse, as access to credit is anticipated to be tighter because of the pandemic and other related shocks. For example, the growth in domestic credit to the private sector as percentage of GDP for the world stood at 12.05 percent in the year 2020. In the absence of data, we used a five-year moving average to forecast estimates for 2021 and realise a 6.01 percent decline in domestic credit to the private sector. The reason is not farfetched. At the peak of the COVID -19 pandemic and the associated shutdowns of businesses, governments around the world had to support the private sector with special credit facilities to turn around businesses considering the critical nature of the private sector to growth and by extension economic wellbeing of the citizenry. As many economies around the world opened to businesses due to the easing of restrictions, the government credit support is expected to be reduced hence the decline. Similarly, on the capital market, the stock traded to GDP recorded a predicted growth of 24.61 percent, in the year 2020; this is expected to increase by 10.96 percent in the year 2021. The predicted growth could be attributed to GDP contractions in 2020, hence the stock value of stock traded assumed a large proportion of GDP. The predicted estimate for 2021 is plausible because most economies are on a rebound; hence, the value of stock traded would not weigh as high as that of the year 2020 relative to the predicted GDP growth. Using the market capitalisation to GDP measure, the ratio of the market capitalization of listed companies to GDP was 23.72 percent for the world in the year 2020, this is expected to decline sharply by 10.49 percent in the year 2021, possibly because many listed companies are recovering from the shocks of COVID-19 and are yet to record pre-pandemic year´s financial performance which would trigger investor buying sentiments. In addition, the rebound support to especially developing economies is expected to cause growth in world gross debt level by 13.59; this forecast is based on the International Monetary fund fiscal monitor [##UREF##4##6##].</p>" ]
[ "<title>Competing interests</title>", "<p>The authors declare no competing interests.</p>", "<title>Authors' contributions</title>", "<p>Each author has equal weight and is listed in alphabetical order. All the authors read and approved the final version of the manuscript.</p>" ]
[ "<fig position=\"float\" id=\"F1\"><label>Figure 1</label><caption><p>monthly world food [rice, sugar and maize] prices (Jan 2020-Mar 2022) source: United Nations Conference on trade and development</p></caption></fig>", "<fig position=\"float\" id=\"F2\"><label>Figure 2</label><caption><p>quarterly growth rate of global merchandise trade (Q1 2019-Q4 2021) source: United Nations Conference on trade and development</p></caption></fig>" ]
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[ "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Kwame Adjei-Mantey et al. COVID-19 pandemic and the global economic situation: a year on. Pan African Medical Journal. 2023;46(56). 10.11604/pamj.2023.46.56.35920</p></fn></fn-group>" ]
[ "<graphic xlink:href=\"PAMJ-46-56-g001\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-56-g002\" position=\"float\"/>" ]
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[{"label": ["1"], "surname": ["Amoah", "Amoah"], "given-names": ["A", "B"], "article-title": ["The COVID-19 pandemic lockdown: a buzz of negativity with a silver lining of social connectedness"], "source": ["JEAS"], "year": ["2022"], "volume": ["38"], "issue": ["1"], "fpage": ["178"], "lpage": ["197"]}, {"label": ["2"], "surname": ["Kugbey", "Amoah", "Dotse", "Amoako-Asiedu", "Delalorm", "Nyarko-Sampson"], "given-names": ["N", "A", "S", "E", "C", "E"], "article-title": ["The angel within the devil: COVID-19 silver linings"], "source": ["Pan Afr Med J"], "year": ["2021"], "month": ["Dec"], "day": ["21"], "fpage": ["40"], "lpage": ["251"]}, {"label": ["3"], "collab": ["World Bank"], "article-title": ["Global economic prospects"], "year": ["2022"], "publisher-loc": ["Washington DC"], "publisher-name": ["World Bank"]}, {"label": ["5"], "collab": ["International Labour Organization's"], "article-title": ["Monitor: COVID-19 and the world of work"], "source": ["ILO"], "year": ["2020"], "month": ["Apr"], "day": ["29"], "fpage": ["27"]}, {"label": ["6"], "collab": ["International Monetary Fund"], "article-title": ["World Economic Outlook"], "source": ["IMF"], "year": ["2020"], "publisher-loc": ["Washington DC"]}, {"label": ["7"], "surname": ["Hidalgo"], "given-names": ["CA"], "article-title": ["How COVID-19 has affected trade, in eight charts"], "comment": ["Accessed May 1, 2022"]}, {"label": ["8"], "collab": ["Organisation for Economic Co-operation and Development"], "article-title": ["International trade during the COVID-19 pandemic: big shifts and uncertainty"], "comment": ["Accessed May 1, 2022"]}, {"label": ["9"], "surname": ["Timmins", "Thomas"], "given-names": ["B", "D"], "article-title": ["Inflation: seven reasons the cost of living is going up around the world"], "comment": ["Accessed May 1 2022"]}]
{ "acronym": [], "definition": [] }
9
CC BY
no
2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 17; 46:56
oa_package/80/a2/PMC10787129.tar.gz
PMC10787130
0
[ "<title>Introduction</title>", "<p>In order to achieve the joint United Nations program on HIV/AIDS (UNAIDS) 95-95-95 goals, widespread access TO VIRAL LOAD (VL) testing and early infant diagnosis (EID) is necessary [##UREF##0##1##,##REF##35925943##2##]. Laboratory services are essential to effective diagnosis, treatment and monitoring of patients infected with HIV and other infectious diseases. In Kenya, VL and EID services are provided by a network of high throughput reference laboratories [##REF##35747559##3##]. Since the laboratories test a large number of samples, the potential risk of systematic errors is high and can undermine confidence in these services.</p>", "<p>High-quality laboratory testing is critical for patient care, disease prevention, and surveillance [##REF##20716795##4##]. Provision of quality services can be partially guaranteed through setting up quality management systems (QMS), a set of policies, processes and procedures that direct and control an organization with regard to quality [##UREF##1##5##]. Quality management systems (QMS) is composed of twelve essential interconnected building blocks that ensure processes are carried out in a systematic manner to allow for continuous improvement, meet regulatory requirements, and achieve customer satisfaction [##REF##28643484##6##]. International Organization for Standardization (ISO) 15189 assesses the competence of QMS within the laboratory, providing a framework for increased analytical quality and verifying that laboratories are not deviating from quality and competency standards [##REF##20855635##7##].</p>", "<p>Achievement of ISO 15189 accreditation demonstrates competency in providing quality services and technical competency in conducting testing [##REF##28643484##6##]. The importance of establishing QMS and achieving accreditation cannot be understated. However, it is a costly undertaking especially in developing countries where laboratory infrastructure and personnel are already affected by lack of resources and prioritization. Accreditation requires leadership, time, attention, resources and continuous commitment to evaluation and improvement [##REF##35937765##8##]. Fulfilling the requirements of international and/or regional laboratory accreditation schemes has proven a challenge within the sub-Saharan region due to the financial implications on an already burdened system [##UREF##2##9##].</p>", "<p>Implementation of quality systems and successful accreditation of laboratories in low and middle countries has been achieved through combining the Strengthening Laboratory Management Towards Accreditation (SLMTA) task-based program and the WHO Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA), which is a stepwise accreditation preparedness program [##REF##35811751##10##]. SLMTA is a hands-on training program aimed at effecting tangible laboratory improvements in developing countries [##UREF##3##11##]. It includes a series of three workshops that are supplemented by assigned improvement projects and supportive site visits or mentoring [##UREF##4##12##]. Laboratory performance is evaluated using the WHO Regional Office for Africa (WHO/AFRO) SLIPTA checklist which checks a laboratory´s compliance with ISO 15189 on a five-star score scale [##REF##35937766##13##].</p>", "<p>In 2010, Kenya adopted the SLMTA program to improve overall quality of laboratory services. The EID/VL network in Kenya has 10 reference laboratories, out of which three were already accredited by 2010 [##REF##26753130##14##]. It was determined that the remaining seven laboratories should begin the process of achieving accreditation status. The Clinical and Laboratory Standards Institute (CLSI) was contracted to offer supplementary training and focused mentorship to these 6 laboratories. The HIV Laboratory, Alupe is one of the laboratories at the Kenya Medical Research Institute (KEMRI). It was established in 2010 to provide HIV laboratory diagnostic and monitoring services and is part of the EID/VL network. By 2015, the laboratory was not accredited; however, like the rest of KEMRI, it had adopted ISO 9001: 2005 and ISO 15189: 2012 guidelines to setup policies and procedures. Quality performance was monitored using the quality indicators which included enrolment in external quality assurance (EQA), laboratory turnaround time and sample rejections. However, the QMS were insufficiently robust to assure quality laboratory services.</p>", "<p>In this paper, we describe the experiences, challenges faced and lessons learned by the KEMRI HIV laboratory, Alupe during its journey to set up QMS and obtain accreditation.</p>", "<p><bold>Objective:</bold> to outline the progress towards accreditation through implementation of the SLMTA-SLIPTA approach at KEMRI HIV Laboratory, Alupe.</p>" ]
[ "<title>Methods</title>", "<p><bold>Study design:</bold> this was an implementation science study; qualitative data was collected through longitudinal observation.</p>", "<p><bold>Study setting:</bold> the KEMRI HIV Laboratory, Alupe is located in Western Kenya, Busia County along Malaba Road. It supports research studies and also provides diagnostic services in support of the national HIV program. The accreditation process began in September 2015 and was concluded in March 2017. The study obtained data from patient samples collected at comprehensive care clinics in various health facilities in Western Kenya networked to KEMRI HIV Laboratory, Alupe for routine VL and EID testing. This data covered the September 2015-March 2017 period when mentorship was ongoing.</p>", "<p><bold>Participants:</bold> the study was implemented by laboratory scientists and technicians.</p>", "<p><bold>Variables:</bold> variables collected were Internal audit scores, turnaround time, EQA performance, rejection rates, and corrective actions.</p>", "<p><bold>Data sources/measurement:</bold> data was collected by observation. Turnaround time and rejection rates were calculated using the laboratory information management system (LIMS). Audits were assessed using the SLIPTA scoring system based on weighted marks out of a total of 258 points and the star rating was as follows: 0-142 points: 0 stars, 143-165 points: 1 star, 166-191 points: 2 stars, 192-217 points: 3 stars, 218-243 points: 4 stars and 244-258 points: 5 stars. EQA performance was collected from EQA reports and corrective actions were collated from audit reports and corrective action forms.</p>", "<p><bold>Bias:</bold> samples of borderline quality were rejected or accepted subjectively. This may have led to bias in the rejection rates.</p>", "<p><bold>Study size:</bold> this study involves a performance matrix for just one laboratory.</p>", "<p><bold>Quantitative variables:</bold> turnaround time, rejection rates, and EQA results.</p>", "<p><bold>Statistical methods:</bold> simple descriptive statistics were used to calculate turnaround time and rejection rates. Data was presented in graphs and tables.</p>", "<p><bold>Inception and planning:</bold> in a meeting held in August 2015, SLMTA in-country mentors from CLSI and the laboratory management jointly agreed to initiate steps towards accreditation, using the SLMTA program approach and the WHO SLIPTA checklist. The proposed mentorship included three workshops spaced throughout the mentorship sessions and improvement projects to effect immediate and measurable laboratory improvements. Regular supervisory visits and on-site training were proposed. The training was focused on targeting each Quality system essential (QSE) and undertaking improvement projects aimed at addressing gaps.</p>", "<p><bold>Internal audits:</bold> it was agreed in the planning meeting that audits would be carried out in three phases, baseline audit in September 2015, mid-term audit in January 2016, and exit audit in July 2016. These were conducted using the SLIPTA checklist to assess strengths, weaknesses, and progress made. The checklist scoring system was based on weighted marks out of a total of 258 points and the star rating was as follows: 0-142 points: 0 stars, 143-165 points: 1 star, 166-191 points: 2 stars, 192-217 points: 3 stars, 218-243 points: 4 stars and 244-258 points: 5 stars.</p>", "<p>Ten mentorship sessions were conducted between September 2015 and July 2016. Each session was planned to run over a period of two weeks. Various activities were proposed for the mentorship and internal audit process. First, a baseline audit was conducted to establish the status of the laboratory in terms of QMS implementation. This would then be followed by a two-week mentorship session to address the existing gaps. Over the next two weeks, an action plan was developed, and implementation was conducted over a two-week period. These steps were repeated for a period of 5 sessions prior to a mid-term audit.</p>", "<p>The mid-term audit was planned to measure the overall progress from the mentorship sessions where QSE targets would be reviewed and an action plan generated. Following this audit, a series of targeted sessions, workshops, and trainings were planned to address the gaps identified in the audit. The next five sessions focused on further QMS implementation culminating in an exit audit.</p>", "<p><bold>Performance of quality indicators:</bold> quality performance was monitored using quality indicators including turnaround time (TAT), external quality assurance, sample rejection rates, and corrective actions.</p>", "<p><bold>Turnaround time (TAT):</bold> using the national guidelines of turnaround time (TAT) of 5 days for EID and 10 days for VL, the laboratory monitored the number of samples that had attained this requirement over a period of one year (September 2015 to August 2016). The percentage of the number of samples that had met the national TAT requirements was calculated as a total number of samples meeting TAT against samples received. Using the laboratory set guidelines that required at least 80% of the samples to meet TAT, the calculated percentage was compared against this set threshold.</p>", "<p><bold>External quality assurance (EQA):</bold> the laboratory receives external quality assurance (EQA) panels from the Global AIDS Program (GAP)-Centers for Disease Control and Prevention (CDC) proficiency testing program for both VL and EID in two cycles. Cycle 1 panels were received within the first quarter of the year and cycle 2 panels within the third quarter of the year. The acceptable performance was defined by any EQA panel scoring at least 80% in each cycle.</p>", "<p><bold>Sample rejection rates:</bold> rejections were monitored on a monthly basis for a period of 21 months. Rejection criteria for viral load plasma samples included hemolysis, sample identification (ID) mismatch, sample clots, use of expired sample collection tubes, wrong sample type, compromised temperature during transportation, missing request form, and insufficient sample volume. Rejection criteria for EID samples included missing request forms, sample clots, improper packaging, and insufficient samples. The rejection rate was calculated as a percentage of the total samples rejected over the total samples received. A 2% acceptable sample rejection limit was set.</p>", "<p><bold>Corrective actions:</bold> corrective actions were evaluated based on corrective action forms and audit reports. The baseline audit was performed in September 2015, a midterm audit was conducted in January 2016, and the exit audit in July 2016. The laboratory was assessed based on the 12 quality essentials and this involved evaluating the requirements of the twelve quality essentials based on ISO 15189: 2012.</p>", "<p><bold>External audits:</bold> accreditation covers QMS set-up and implementation and the technical competence to carry out diagnostics within the scope of the accreditation. The Kenya National Accreditation Service (KENAS), which is the national body mandated to oversee the accreditation of laboratories to the ISO 15189 standard, was contracted by KEMRI to provide audit services at a cost. An assessment was performed between September 2016 and November 2016 to evaluate the compliance of the laboratory to ISO 15189: 2012 using KENAS checklist.</p>" ]
[ "<title>Results</title>", "<p><bold>Participants:</bold> a total of 15 laboratory scientists and technicians were involved in this study.</p>", "<p><bold>Descriptive data:</bold> data on internal audits, turnaround time, rejection rates, EQA performance, and corrective actions was collected and described.</p>", "<p><bold>Outcome Data:</bold> the primary outcome was laboratory accreditation. Secondary outcomes included scores in audits and improvements in quality indicators.</p>", "<title>Main results</title>", "<p><bold>Inception and planning:</bold> we commenced this process successfully in September 2015 beginning with targeted training on the 12 QSE conducted on-site facilitated by SLMTA-trained mentors. Each intervention was geared towards aligning the laboratory processes to the ISO 15189 standard and establishing a robust QMS system. A comprehensive list of QSE, mentorship-based interventions, and outcomes are presented in ##TAB##0##Table 1##.</p>", "<p><bold>Internal audits:</bold> the lab scored zero stars (47%) at the baseline audit conducted in October 2015, three stars (75%) at the midterm in January 2016, and four stars (94%) at the exit in July 2016 (##FIG##0##Figure 1##).</p>", "<p>The gaps that were identified, improvement projects, monitoring indicators, outcomes, and time of closure are all presented in ##TAB##1##Table 2##.</p>", "<p><bold>Performance in external quality assurance:</bold> qualitative testing (EID) and quantitative testing (VL) were the two parameters chosen during the objective setting for external quality assurance (EQA). The lab scored 100% in EID EQA throughout the 6 cycles between 2014 and 2016. For VL EQA, the lab scored 60% in cycle A in 2014, 60% in cycle B in 2014, 80% in cycle A in 2015, 60% in cycle B in 2015, and 100% in cycle A in 2016, 80% in cycle B in 2016. These results are presented in ##FIG##1##Figure 2##.</p>", "<p><bold>Performance in laboratory turnaround time:</bold> for EID, turnaround time (TAT) scored between 80% and 100%, whereas viral load TAT scored between 70% and 100% (##FIG##2##Figure 3##).</p>", "<p><bold>Laboratory rejection rates:</bold> the lab maintained a rejection rate below 2% for all the tests for the duration of the exercise. This data is shown in ##FIG##3##Figure 4##.</p>", "<p><bold>Corrective actions:</bold> corrective actions were evaluated and the results outlined correspond to pre-analytical, analytical, and post-analytical phases (##FIG##4##Figure 5##).</p>", "<p><bold>External audits and subsequent accreditation:</bold> a KENAS audit was successfully conducted in September 2016 and 12 non-conformities were identified; all were closed within 30 days. During the final assessment conducted in November 2016 after the submission of corrective actions from the September audit, the lab scored 96% and was deemed suitable for accreditation. Accreditation was awarded in March 2017.</p>" ]
[ "<title>Discussion</title>", "<p>At the baseline audit, performed in September 2015, the KEMRI HIV Laboratory, Alupe was rated at zero stars. This was despite the fact that in the year before the accreditation process started in August 2015, the laboratory had attempted to put a quality management system in place. The laboratory has been in existence since 2010, and has several performance indicators in place including EQA, TAT monitoring, and sample rejection monitoring. Worldwide, using the SLMTA approach, 84% of all laboratories scored at least 1 star [##UREF##3##11##]. The baseline survey for the KEMRI HIV Laboratory, Alupe not only indicated glaring gaps in quality system essentials but also implied that just having good intentions and an idea about QMS is not enough to provide quality services. Through the SLMTA-SLIPTA approach, and working with CLSI, the laboratory successfully developed an effective quality management system. This particular approach has also been successfully used in other countries such as Tanzania, Ethiopia [##REF##33240798##15##]. At the end of the accreditation process, the laboratory scored 94% in key metrics, with a four-star rating. This score is higher than the global average of 64%, with only 13.6% of laboratories enrolled in SLIPTA reaching four and five stars by exit audit [##UREF##3##11##]. We think that strong support from the mentoring partner, as well as committed, motivated, and skilled staff, were the key ingredients in this success. Staff motivation is corroborated as a factor of success by other studies.</p>", "<p>Sequential evaluation of the corrective actions was significant in determining the progress of QMS implementation and adherence to the ISO 15189: 2012. Corrective actions were analyzed from audit reports generated from baseline, midterm, and exit audits. The corrective actions were divided into pre-analytical, analytical, and post-analytical phases. Generally, the variation in the number of corrective actions identified across the four types of audits was contributed by the goal and the nature of each audit. At baseline, the auditors focused on the major gaps existing within the laboratory, and therefore a smaller number of corrective actions were addressed compared to the midterm audit. Besides, some areas in the SLIPTA checklist had not been established at the time of baseline audit and therefore there were fewer corrective actions raised in these particular areas, unlike the midterm audit where all the parameters of the checklist had been established by the laboratory and were assessed. The exit audit recorded a lower number of corrective actions as most of those that had been raised during the mid-term audit had been closed.</p>", "<p>Whereas EQA for EID consistently returned excellent outcomes, the performance of VL fluctuated from cycle to cycle. This could be attributed to equipment downtime, faulty backups, and VL EQA panel limitations. VL EQA panels are delivered in small volumes that are insufficient for retesting after failure due to equipment downtime. Other studies evaluated their EQA performance before and after accreditation and noted significant improvement in performance after accreditation [##REF##30016273##16##]. Viral load (VL) turnaround time, from sample reception in the lab to release of results, showed remarkable improvement from 60% in August 2015 to 100% in 2016. The poor performance in 2015 could be attributed to a surge in the number of samples being received in the laboratory without a proportional increase in human resources, stock outs of consumables and reagents, and machine breakdown. This is a common challenge in high throughput labs and requires close collaboration between the laboratory and key stakeholders. Similar findings regarding improvement in TAT were seen in a number of studies with some studies having TAT percentages at 92% [##REF##30167386##17##].</p>", "<p>Throughout the mentorship period, rejection rates did not exceed the set limit of 2%. This excellent rate was attributed to the development of the sample collection manual and its distribution to facilities served by the laboratory. Introduction of facility training also played a role in this reduction. However, the laboratory had no direct control of the quality of the samples received from the field and could not sustain targeted training due to resource limitations. Sample rejection rate therefore looks like an imperfect quality indicator in resource-limited laboratories. It may be much more appropriate in reference laboratories that are able to institute and maintain sample collection training for the health facilities they serve. Rejection rates have been shown in similar studies to significantly reduce after accreditation [##REF##26753130##14##,##REF##30167386##17##].</p>", "<p>Fulfilling the requirements of international and/or regional laboratory accreditation schemes has proven to be a challenge due to the high costs of closing gaps [##REF##29043195##18##]. Most existing gaps required only a little investment in resources and were therefore easily closed by the midterm audit. Other gaps were harder to close, requiring significant investment. For instance, the laboratory initially could not show evidence of client training. Client training required financial resources the laboratory did not have; these were eventually provided by partners.</p>", "<p>The laboratory was not an independent legal identity, rather, it is part of a legal entity. The audit tools are designed for institutions with legal identities. This lack of individual identity was considered a gap and took significant time and effort to be resolved.</p>", "<p>Gaps identified under equipment QSE included inadequate equipment installation and placement records, and lack of instrument calibration. The placement of machines is under the control of the ministry of health (MOH); this lack of control by the laboratory causes significant challenges with procurement and maintenance. Even the selection, purchasing, and verification of LIMS is under MOH. The tools used by auditors need to be customized to cater to such peculiarities, especially within public laboratories. Inadequate waste management and lack of evidence of space evaluation were the main gaps identified in facilities and safety QSE. The former required the installation of an incinerator while the latter needed several interventions including infrastructural changes. All these required management support and significant resources.</p>", "<p>Achieving and maintaining accreditation has significant monetary implications and for that reason, laboratories in Africa that have received accreditation have tended to be privately funded or partner-supported [##REF##24838322##19##, ####REF##32727444##20##, ##REF##36246699##21####36246699##21##]. A major contributor to that cost was external audits, which turned out to be even more costly than many budget items for service delivery. On further analysis, it was realized that KENAS provides auditors from a central location, and all expenses are met by the laboratories. This expensive and inefficient model, can cause public laboratories pecuniary embarrassment, and they can benefit from decentralization of audit services.</p>", "<p><bold>Lessons learned:</bold> from the foregoing, it is clear that laboratories ought to enroll and participate in established QMS systems. Even then, not all that do so achieve excellence. In our experience, it was essential to have resources, trained and motivated staff, accreditation champions, and buy-in from top-level management. Many of the gaps in the quality system essentials were attributed to a lack of resources. The gaps were addressed through the provision of financial resources either by the mentoring partner or very rarely, by KEMRI. The reluctance of the parent institution to invest in accreditation might have arisen from a lack of political buy-in and strategic planning from the outset. The laboratory team found it especially difficult to convince top-level management that investing in accreditation can lead to significant cost-savings, particularly when such discussions are initiated midway through the process. Public laboratories, which are particularly vulnerable, would do well to introduce accreditation within the key results areas of institutional strategic plans.</p>", "<p>A second lesson learned is that to obtain accreditation in a public laboratory, staff must be willing to provide creative solutions and to work extra hard including outside of office hours. Staff motivation and management involvement are critical for success in accreditation.</p>", "<p><bold>Limitations:</bold> the single most important limitation in this study was that the laboratory is a public asset managed through government bureaucratic systems. In this environment, activities that involve finances or procurement are often slow and sometimes fail. This makes our findings hard to generalize across all laboratories. Secondly, we were unable to quantify the costs associated with implementing the SLMTA-SLIPTA approach. This was because the laboratory was a public facility and several costs were invisible to the implementing team.</p>" ]
[ "<title>Conclusion</title>", "<p>The SLMTA-SLIPTA approach is suitable in the accreditation of resource-limited laboratories. It is recommended that the approach is modified to be relevant to laboratories that are only part of a legal entity. The auditor´s responsibilities of identifying areas of non-conformity and providing onsite technical assistance are a “game-changer” unique to this approach. However, the annual subscription fees exceed the ability of many facilities and this is a key reason accreditation is a pipe dream for most resource-limited laboratories. With sustained input from the management, laboratory staff, mentors, and collaborators, using the stepwise improvement process, any laboratory can improve on its quality systems and implement QMS that is compliant with the standards of ISO 15189: 2012.</p>", "<title>\nWhat is known about this topic\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p>\n<italic>Accreditation is the most effective approach to assure quality of all laboratory services;</italic>\n</p></list-item><list-item><p><italic>Getting accreditation is especially difficult for poorly resourced laboratories and only 13.6% of laboratories enrolled in SLIPTA reach four and five stars by exit audit</italic>.</p></list-item></list>\n</p>", "<title>\nWhat this study adds\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p><italic>In this study, our findings suggest that the SLMTA-SLIPTA approach needs to be modified to be relevant to laboratories that are only part of a legal entity, or that are public assets managed through government bureaucratic systems</italic>.</p></list-item></list>\n</p>" ]
[ "<title>Introduction</title>", "<p>accreditation is the most effective approach to ensure the quality of services. Laboratory performance can be evaluated using the World Health Organization (WHO)-SLIPTA checklist, which checks a laboratory´s compliance with ISO 15189 on a five-star score scale and improved using the SLMTA approach. Compliance is assessed by an external body and can result in accreditation. In this paper, we describe the steps taken by the Kenya Medical Research Institute (KEMRI) HIV Laboratory, Alupe, a resource-limited public entity, towards accreditation, and discuss the lessons learned.</p>", "<title>Methods</title>", "<p>the laboratory adopted a SLMTA-SLIPTA approach that included targeted mentorship, on-site workshops, and training. Mentorship-based interventions were used to establish a robust quality management system. Targeted mentorship, on-site workshops, and training were conducted between September 2015 and July 2016. Audits used the SLIPTA checklist to detect gaps in 12 quality system essentials. Performance indicators including turnaround time, external quality assurance, sample rejection rates, and corrective actions were tracked. An external assessment by the national accreditation body was conducted between September 2016 and November 2016.</p>", "<title>Results</title>", "<p>training and mentorship-based interventions were successfully conducted. Quality management systems aligned with ISO 15189 were established. Baseline, midterm, and exit audits yielded scores of 47%, 75%, and 94% respectively. Early infant diagnosis external quality assurance scores were 100% in 2014-2016, while average viral load scores were at 60%, 70% and 90% during the same period. Turnaround time from September 2015 surpassed the 80% target. Accreditation was awarded in March 2017.</p>", "<title>Conclusion</title>", "<p>the SLMTA-SLIPTA approach is suitable for quality improvement in resource-limited laboratories.</p>" ]
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[ "<title>Acknowledgments</title>", "<p>We wish to acknowledge KEMRI management and the CLSI mentors all whom contributed to the success of KEMRI Alupe HIV Laboratory. We wish to thank Joshua Ageng´o, Catherine Syeunda, Maureen Adhiambo, Samuel Ochieng´ and Kibet Yegon for technical support. We acknowledge the Kenya MOH for support in the EID and VL testing services.</p>", "<title>Competing interests</title>", "<p>The authors declare no competing interests.</p>", "<title>Authors' contributions</title>", "<p>Matilu Mwau was responsible for the conceptualization of the concept, funding acquisition, data curation, acquiring resources, and overall supervision; Joy Mwende Ndunda, James Sitati, and Rebecca Loraine Achieng were responsible for data curation, formal analysis, methodology, writing and revising the original draft; Laurie Kennedy was involved with data curation, writing of the original draft and methodology; Janepher Achieng was instrumental in visualization; James Sitati assisted with formal analysis, visualization, writing the original and review of the final draft; Mary Inziani, Videlis Nduba, Carolyne Ndila, Cynthia Kademba, and Agnes Wanjiru were involved in visualization, analysis and editing. All the authors read and approved the final version of this manuscript.</p>" ]
[ "<fig position=\"float\" id=\"F1\"><label>Figure 1</label><caption><p>WHO Regional Office for Africa (WHO/AFRO) SLIPTA scores and star rating, KEMRI Alupe Laboratory</p></caption></fig>", "<fig position=\"float\" id=\"F2\"><label>Figure 2</label><caption><p>performance in early infant diagnosis (EID) and viral load (VL) external quality assurance (EQA) Indicators</p></caption></fig>", "<fig position=\"float\" id=\"F3\"><label>Figure 3</label><caption><p>turnaround time for both early infant diagnosis (EID) and viral load (VL) tests</p></caption></fig>", "<fig position=\"float\" id=\"F4\"><label>Figure 4</label><caption><p>early infant diagnosis (EID) and viral load (VL) sample rejection rates</p></caption></fig>", "<fig position=\"float\" id=\"F5\"><label>Figure 5</label><caption><p>summary of corrective actions identified during baseline, midterm and exit audits</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"T1\"><label>Table 1</label><caption><p>quality systems essentials (QSE) based-mentorship interventions and outcomes used in quality management systems (QMS) implementation and monitoring at KEMRI HIV Laboratory, Alupe, 2015-2016</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">QSE</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mentorship interventions</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Outcomes</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Documents and records</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Generation of all documents aligning with the ISO 15189 standard</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Standard operating procedures, manuals, forms</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Management review meeting</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Review of management responsibilities for laboratory quality management system, on relationship between laboratory audits, customer satisfaction, quality indicators, corrective actions, and feedback loops</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Generating management review schedules and incorporating them into quality plans</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Organization and personnel</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Training on laboratory organization, staffing matrix, continuous education, competency assessments, appraisals, and communication for quality services</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Generating staff personnel files and initiating competency assessments</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Client and customer care management</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Initiating customer surveys, complaint registers and communication networks to get feedback from clients</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Collecting data from customer surveys, complaints, and overall client feedback</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Equipment</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mentorship on maintenance of equipment files, method validation and verification, routine equipment maintenance</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Drafting service contract agreements with machine manufacturers and maintaining an equipment inventory and maintenance log</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Evaluation and audits</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Training on conducting internal audits using SLIPTA checklist</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Drafting an annual audit schedule</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Purchasing and inventory</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Initiating inventory controls to track supplies received at the laboratory</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Introducing reorder levels, inventory logs</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Process control</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Review of external quality assessments and internal quality control procedures, identification of barriers, outcomes, root cause analysis, and corrective actions for unacceptable external quality assessment results</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Documenting trends in EQA, and internal quality controls</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Information management</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Refresher on reporting of validated laboratory results and use of verified laboratory information system to manage laboratory reports</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Developing procedures on information management system verification</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Identification of non-conformities, corrective action, and preventive action</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Mentorship on how to conduct internal audits, investigating the root cause, and appropriate corrective actions</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Documenting trends in non-conforming events, developing documents for recording non-conformities and their corrective and preventive actions</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Occurrence management and process improvement</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Training on quality indicator monitoring and implementation of the tools</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Identify and track quality indicators at different time intervals</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Facilities and biosafety</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Guiding laboratory staff on safety requirements and various safety training</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Track any adverse events within the laboratory, development of manuals and procedures, adoption of national waste management policies</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T2\"><label>Table 2</label><caption><p>quality systems essentials (QSE) Gaps, improvement projects and outcomes during quality management systems (QMS) implementation using SLMTA-SLIPTA approach at KEMRI HIV Laboratory Alupe, 2015-2016</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Quality essential</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Gap identified</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Improvement project</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Monitoring indicator</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Outcome</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Time of closure</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Documents and records</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No legal entity, no quality manual</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Follow up with KEMRI through the PI; develop quality policy manual</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Availability of gazette KEMRI ACT; quality policy manual in place</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Obtained the Legal entity Implementation of approved Quality policy</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Exit Midterm</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Management reviews and management responsibilities</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No management review meetings and schedules in place</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Develop a quality plan/schedule</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Reports of MRM on file</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Implementation of developed quality plan</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Midterm</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Organization and personnel</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No designated QA officers</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">QA officer appointed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Appointment letter issued and JD specified</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Active QA office</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Midterm</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Client management and customer service</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No evidence of client training by qualified staff; no customer satisfaction surveys</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Develop the laboratory handbook and training schedule for clients; develop a quality plan/schedule</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Client training logs filed; file completed survey tools</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Trained clients Satisfied customers</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Exit Midterm</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Equipment</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Inadequate equipment installation and placement records; no evidence of QC checks after equipment repair</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Develop equipment management procedure; performing QC checks after equipment repair</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Filing of equipment installation and placement records; copies of QC Checks are attached to repair record and filed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Updated record for all equipment; efficient equipment operation</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Exit; midterm</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Evaluation and audits</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No risk management plan</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Develop a quality plan and risk assessment tool</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Records of identified and action taken filed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Proper identification and management of risks</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Exit</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Purchasing and inventory</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Inadequate environmental monitoring of storage areas</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Develop environmental monitoring tools</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Completed Environmental monitoring tools filed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Environmental monitoring of the storage area done</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Midterm</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Process control</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No records of the selection and evaluation of referral laboratories</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Develop procedure for selection and evaluation of referral laboratories</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Completed referral checklist and referral laboratories list filed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Reduced service delay/ backlogs</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Midterm</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Information management</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No evidence of LIMs selection</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Follow up on LIMs selection report</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">LIMs selection report in the file</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Accessible LIMs selection report in the laboratory</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Exit</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Identification of non-conformities, corrective and preventive action</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No NC registers</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Develop NC, CA, and PA management procedure</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Completed NCs register</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Updated RCA and CA</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Midterm</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Occurrence management and process improvement</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No clearly defined quality indicators</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Develop a quality indicator monitoring tool</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Quality Indicators reports filed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Periodic QI monitoring</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Midterm</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Facilities and biosafety</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">No safety officer</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Appoint safety officer</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">An appointment letter issued and JD defined</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Competent safety office</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Midterm</td></tr></tbody></table></table-wrap>" ]
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[ "<table-wrap-foot><fn id=\"TF1-1\"><p>EQA: external quality assurance; HIV: human immunodeficiency virus; ISO: International Organization for Standardization; KEMRI: Kenya Medical Research Institute; SLIPTA: Stepwise Laboratory Quality Improvement Process Towards Accreditation; QMS: quality management systems; QSE: quality systems essentials</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF2-1\"><p>CA: corrective action; EQA: external quality assurance; HIV: human immunodeficiency virus; ISO: International Organization for Standardization; JD: job description; KEMRI: Kenya Medical Research Institute; LIMS: laboratory information management systems; MRM: management review meeting; PA: preventive action; PI: principal investigator; SLIPTA: Stepwise Laboratory Quality Improvement Process Towards Accreditation; SLMTA: Strengthening Laboratory Management Towards Accreditation; QA: quality assurance; QC: quality control; NC: non conformity; QMS: quality management systems; QSE: quality systems essentials</p></fn></table-wrap-foot>", "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Joy Mwende Ndunda et al. Accreditation of a molecular HIV diagnostic laboratory following the Strengthening Laboratory Management Towards Accreditation (SLMTA)-Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) approach in Kenya: an implementation science study. Pan African Medical Journal. 2023;46(60). 10.11604/pamj.2023.46.60.39549</p></fn></fn-group>" ]
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[{"label": ["1"], "collab": ["World Health Organization (WHO)"], "article-title": ["Updated recommendations on HIV prevention, infant diagnosis, antiretroviral initiation and monitoring"], "year": ["2021"], "publisher-loc": ["Geneva"], "publisher-name": ["World Health Organization"]}, {"label": ["5"], "surname": ["Pereira"], "given-names": ["P"], "article-title": ["ISO 15189: 2012 Medical laboratories-Requirements for quality and competence"], "year": ["2020"], "publisher-loc": ["Westgard QC"], "publisher-name": ["Madison, WI, USA"]}, {"label": ["9"], "surname": ["Makokha", "Mwalili", "Basiye", "Zeh", "Emonyi", "Langat"], "given-names": ["EP", "S", "FL", "C", "WI", "R"], "etal": ["et al"], "article-title": ["Using standard and institutional mentorship models to implement SLMTA in Kenya"], "source": ["African journal of laboratory medicine"], "year": ["2016"], "month": ["Jan"], "day": ["1"], "volume": ["5"], "issue": ["2"], "fpage": ["1"], "lpage": ["8"]}, {"label": ["11"], "surname": ["Yao", "Maruta", "Luman", "Nkengasong"], "given-names": ["K", "T", "ET", "JN"], "article-title": ["The SLMTA programme: Transforming the laboratory landscape in developing countries"], "source": ["Afr J Lab Med"], "year": ["2016"], "month": ["Jan"], "day": ["1"], "volume": ["5"], "issue": ["2"], "fpage": ["1"], "lpage": ["8"]}, {"label": ["12"], "surname": ["Nwaokorie", "Ojo"], "given-names": ["FO", "EA"], "article-title": ["Overview of the implementation of quality management system in Nigerian medical laboratories"], "source": ["University of Lagos Journal of Basic Medical Sciences"], "year": ["2021"], "volume": ["6"], "issue": ["1 & 2"]}]
{ "acronym": [], "definition": [] }
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2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 17; 46:60
oa_package/2c/82/PMC10787130.tar.gz
PMC10787131
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[ "<title>Image in medicine</title>", "<p>A 51-year-old female presented to us with complaints of breathlessness, cough with expectoration, left-sided chest and back pain with general tiredness for the past 1 month. She was a farmer by profession, with no significant past history. All routine investigations were done. Contrast computed tomography thorax showed a large heterogeneously enhancing soft tissue mass occupying the left hemithorax and single precarinal necrotic node. Bronchoscopy followed by CT-guided lung biopsy was done, which showed a neuroendocrine tumour with high mitotic activity and extensive necrosis suggestive of large cell neuroendocrine carcinoma. Immunohisto chemical staining for neuroendocrine markers was done, which was positive for chromogranin A and synaptophysin. She was then shifted to the oncology department for surgery followed by chemotherapy. Lung neuroendocrine tumours are rare tumours accounting for about 20% of all lung tumours, 1-2 % of all tumours and 25% of all neuroendocrine tumours. Lung tumours comprise 75-80%, neuroendocrine tumours (NETs), 1-2 % carcinoid tumours (typical and atypical carcinoid), 3% large cell neuroendocrine carcinoma of the lung (LCNEC) and 15-20% small cell lung cancer (SCLC). Immunohistochemical examination is the most important criterion for lung neuroendocrine tumours (LNET). The classical symptoms of carcinoid tumours are cough, dyspnoea, recurrent respiratory tract infection and haemoptysis. For patients with high surgical risk, interventional bronchoscopy and endobronchial resection may be done. For advanced SCLC, chemotherapy with cisplatin and etoposide is the standard treatment.</p>" ]
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[ "<fig position=\"float\" id=\"F1\"><label>Figure 1</label><caption><p>chest X-ray showing left opaque hemithorax with trachea pushed to the right side and a blue arrow showing left bronchus cut-off sign</p></caption></fig>" ]
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[ "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Ashwin Karnan et al. A rare neuroendocrine tumor of the lung. Pan African Medical Journal. 2023;46(54). 10.11604/pamj.2023.46.54.41283</p></fn></fn-group>" ]
[ "<graphic xlink:href=\"PAMJ-46-54-g001\" position=\"float\"/>" ]
[]
[]
{ "acronym": [], "definition": [] }
0
CC BY
no
2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 13; 46:54
oa_package/c2/22/PMC10787131.tar.gz
PMC10787132
0
[ "<title>Introduction</title>", "<p>Chronic recurrent multifocal osteomyelitis (CRMO) is a rare non-microbial inflammatory bone affection [##REF##23263195##1##]. It occurs preferentially in children and young adults [##UREF##0##2##]. Autoimmune is the most suggested etiopathogenesis [##REF##16122996##3##]. It usually manifests by multifocal bone pain with insidious onset and recurrent evolution. Osteolytic lesions are usually observed in affected bones on radiographs. It often constitutes an exclusion diagnosis after eliminating malignant tumors and bone infections. This case aimed to highlight diagnosis difficulties in such a rare location in which bone biopsy was contributive.</p>" ]
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[ "<title>Discussion</title>", "<p>Chronic recurrent multifocal osteomyelitis (CRMO) is a chronic non-microbial osteomyelitis. It's a rare disease with a prevalence of 1 to 2/10<sup>6</sup> [##REF##27730289##4##]. This disorder affects children and adolescents, more often females [##REF##27730289##4##]. It belongs to the juvenile form of synovitis, acne, palmoplantar pustulosis, hyperostosis, and osteitis (SAHPO) group syndrome. Manifestations could be unique or multifocal. Typical locations are long bones metaphysis (74%), pelvis (38%), spine (46%), clavicle (25%), mandible (18%), sternum (8%), and ribs (8%) [##UREF##0##2##]. Isolated involvement of the clavicle presented in our case is typical of what has been described as Friedrich's disease [##REF##1776913##5##]. Chronic recurrent multifocal osteomyelitis pathogenesis is still unclear and may be related to the imbalance between pro-inflammatory cytokines (IL-6, IL-1, TNF α) and anti-inflammatory cytokines (IL-10). These cytokines are involved in bone resumption and remodeling through osteoblasts and osteoclasts activation [##REF##26404542##6##].</p>", "<p>Clinical presentation often involves bone pain, swelling, inflammatory joint signs as in our case, and sometimes fever [##REF##23263195##1##]. A mildly elevated ESR is the only abnormality that can be observed in patients with CRMO. Some patients may have higher white blood cell count or elevated CRP [##REF##28401420##7##]. Radiologic signs are various and non-specific remains often normal in the early stage of the disease. In the later stage osteolytic and hyperostosis bone reaction could be noted as in our child after one month of spontaneous evolution. Scintigraphy shows in addition to bone isotope uptake in painful areas other sites in multifocal form. MRI remains sensitive but not specific for CRMO diagnosis (inflammatory bone signal) with enhancement after gadolinium injection. Whole-body MRI, non-radiating imaging, is more sensitive than bone scintigraphy in detecting clinically asymptomatic lesions [##REF##22284608##8##]. Biopsy is still controversial because histological features are not specific (inflammatory infiltrates with neutrophils, lymphocytes, plasma cells, and histiocytes as well as osteolysis, and sclerosis [##REF##23263195##1##]) but it helps to exclude infectious osteomyelitis, and malignant bone tumors, especially in a single bone lesion as in our patient. Mycobacterial detection is consistently negative [##REF##22284608##8##]. Chronic recurrent multifocal osteomyelitis diagnosis is challenging and can be based on major and minor clinical imaging, and histopathology criteria established by Jansson <italic>et al</italic>. [##REF##19840301##9##,##REF##16782988##10##]. Diagnosis could be retained if there are two major criteria or one major and three minor criteria [##REF##16782988##10##]. Our case associates two major and two minor criteria.</p>", "<p>There are no consensus recommendations for CROM treatment. Non-steroidal anti-inflammatory drugs are given as the first intention in therapeutic management to control pain and prevent bone damage. Corticosteroids are used in patients who are resistant to NSAIDs. Methotrexate represents a second-line treatment. Sulfasalazine is generally used in patients with associated inflammatory bowel disease [##REF##28401420##7##].</p>" ]
[ "<title>Conclusion</title>", "<p>Chronic recurrent multifocal osteomyelitis (CRMO) of the clavicle in a 9-year-old child with delayed diagnosis in this unusual location. Clinical and imaging signs were not specific miming bone tumors and infection with osteolytic bone lesion. Bone biopsy was helpful by excluding sarcoma. Non-steroidal anti-inflammatory drug treatment was effective and can be sufficient for recovery and remains the first recommended treatment.</p>" ]
[ "<p>Chronic recurrent multifocal osteomyelitis (CRMO) is a rare disease. It is a non-microbial inflammatory bone affection that occurs more often in children with insidious onset and non specific presentation making diagnosis challenging. This study reports a case of CRMO with an unusual location. A 9-year-old child had a painful swelling over the medial side of clavicle with fixed mass. Radiographs showed osteolytic lesion on the medial part of clavicle extending to the acromioclavicular joint with soft tissue edema in magnetic resonance imaging (MRI). No inflammatory markers in biological exam. Needle biopsy, initially performed, suspected bone infection but children didn´t recover after 2 weeks of antibiotics. Surgical biopsy, histology sections were compatible with CRMO diagnosis. Children received a non steroid inflammatory drug with positive response, pain relief and decreasing of the clavicle swelling. CRMO should be suspected and biopsy is some time helpful in such unusual location.</p>" ]
[ "<title>Patient and observation</title>", "<p><bold>Patient information:</bold> a 9-year-old girl with no previous medical history was seen in the outpatient department for a painful swelling over the left clavicle that had been evolving over a month with no history of trauma.</p>", "<p><bold>Clinical findings:</bold> physical exams found a girl with good general condition and with no fever. A swelling above the proximal quarter of the clavicle was noted, which was firm, painful, and fixed to the deep plane with skin redness (##FIG##0##Figure 1##). Shoulder motion was limited by pain.</p>", "<p><bold>Timeline of current episode:</bold> in April 2022 child presented swelling and pain over her left clavicle. X-ray, ultrasound, and MRI were performed in addition of biological markers. First needle biopsy then surgical biopsy in May 2022 with histology section, immunohistochemical study. The patient was referred to the rheumatology department. Bone scintigraphy searching for other locations. Non-steroidal anti-inflammatory drug (NSAID) treatment, July 2022 decreasing of clavicle swelling and pain relief.</p>", "<p><bold>Diagnostic assessment:</bold> an osteolytic lesion on the medial part of the left clavicle with cortical disruption was noted on a shoulder X-ray (##FIG##1##Figure 2##). inflammatory markers were negative (white blood cells count was 9250 cells per mm<sup>3</sup>, creatinine reactive protein (CRP) was 8 mg/L, and the erythrocyte sedimentation rate (ESR) was 12 mm first hour). Wright serology was negative. Ultrasonography revealed a sleeve around the medial end of the left clavicle with irregularities in the bone cortex. MRI showed an extensive lesion measuring 9 x 2 x 2 cm located at the medial end of the left clavicle and extending to the acromioclavicular joint (##FIG##2##Figure 3##). A needle biopsy was initially performed, suspected bone infection and the child received antibiotics with no recovery and appearance of important periosteal apposition on radiographs (##FIG##3##Figure 4##). Ewing's sarcoma was still suspected and a second open biopsy was performed two weeks later as well as the culture of mycobacteria and the polymerase chain reaction (PCR) for the Koch bacillus.</p>", "<p>Histology study reveals no tumor cells but a fibroblastic component filling the intertrabecular spaces. An inflammatory neutrophils and osteoclasts cells infiltration was observed (##FIG##4##Figure 5##). CD1a was negative in the immunohistochemical study, which eliminated Langerhansian histiocytosis. Bone scintigraphy was performed and showed increased uptake on the inner part of the left clavicle with no other locations (##FIG##5##Figure 6##).</p>", "<p><bold>Diagnosis:</bold> chronic recurrent multifocal osteomyelitis diagnosis was sustained based on osteolytic bone lesion, normal blood count, good general health state and bone biopsy excluded sarcoma and showed no specific osteitis.</p>", "<p><bold>Therapeutic interventions:</bold> the child received a non-steroidal anti-inflammatory drug (NSAID): naproxen at a dose of 5 mg/Kg for three months.</p>", "<p><bold>Follow-up and outcome of interventions:</bold> spectacular improvement of pain after two weeks of NSAID and resumption of normal sports activities. The swelling of the clavicle disappeared after 10 weeks. The child remains asymptomatic and in excellent clinical condition, with no reported recurrence.</p>", "<p><bold>Patient perspective:</bold> “<italic>I can now play basketball at school with my friends</italic>”.</p>", "<p><bold>Informed consent:</bold> the patient’s parents gave informed consent for using the data file for scientific publication. Authors certified that their child couldn´t be recognized in the clinical photo.</p>" ]
[ "<title>Competing interests</title>", "<p>The authors declare no competing interests.</p>", "<title>Authors' contributions</title>", "<p>Patient management: Wajdi Arfa, Malek Ben Chaalia, and Mourad Jenzri; data collection: Khaled Kamoun, Wajih Oueslati, and Leila Abid; manuscript drafting: Khaled Kamoun; manuscript revision: Khaled Kamoun, Mourad Jenzri. All the authors read and approved the final version of this manuscript.</p>" ]
[ "<fig position=\"float\" id=\"F1\"><label>Figure 1</label><caption><p>clinical image of shoulders: swelling above the left clavicle with skin redness</p></caption></fig>", "<fig position=\"float\" id=\"F2\"><label>Figure 2</label><caption><p>anteroposterior shoulders X-ray: osteolytic bone lesion with cortical disruption involving proximal part of left clavicle</p></caption></fig>", "<fig position=\"float\" id=\"F3\"><label>Figure 3</label><caption><p>A,B,C) clavicle magnetic resonance imaging: axial section; low intense lesion in T1-weighted images and high intense in T2-weighted, heterogeneously enhancing, edematous signal of the surrounding soft</p></caption></fig>", "<fig position=\"float\" id=\"F4\"><label>Figure 4</label><caption><p>anteroposterior control shoulder X-ray: periosteal clavicle apposition with “onion bulb” shape lesion</p></caption></fig>", "<fig position=\"float\" id=\"F5\"><label>Figure 5</label><caption><p>A) hematoxylin-Eosin staining x200: Trabecular architecture of bone; B) hematoxylin-Eosin staining x400: inflammatory cell infiltration mainly including neutrophils</p></caption></fig>", "<fig position=\"float\" id=\"F6\"><label>Figure 6</label><caption><p>bone scintigraphy: isolated isotop uptaking on the inner part of the left clavicle with no other location</p></caption></fig>" ]
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[ "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Khaled Kamoun et al. Chronic recurrent multifocal osteomyelitis of clavicle: a rare isolated location (a case report). Pan African Medical Journal. 2023;46(53). 10.11604/pamj.2023.46.53.39452</p></fn></fn-group>" ]
[ "<graphic xlink:href=\"PAMJ-46-53-g001\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-53-g002\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-53-g003\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-53-g004\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-53-g005\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-53-g006\" position=\"float\"/>" ]
[]
[{"label": ["2"], "surname": ["Majeed", "El-Shanti", "Al-Rimawi", "Al-Masri"], "given-names": ["HA", "H", "H", "N"], "article-title": ["On mice and men: An autosomal recessive syndrome of chronic recurrent multifocal osteomyelitis and congenital dyserythropoietic anemia"], "source": ["J Pediatr"], "year": ["2000"], "volume": ["137"], "issue": ["3"], "fpage": ["441"], "lpage": ["2"]}]
{ "acronym": [], "definition": [] }
10
CC BY
no
2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 12; 46:53
oa_package/68/81/PMC10787132.tar.gz
PMC10787133
0
[ "<title>Introduction</title>", "<p>Syphilis prevalence is still high, especially among the key populations in the world, such as the male-sex-male group. The key population also becomes an important cofactor of human immunodeficiency virus (HIV) transmission [##UREF##0##1##]. Cutaneous manifestations presenting as EM-like eruption in secondary syphilis are very uncommon, thus making the diagnosis challenging. Furthermore, HIV coinfection often makes syphilis manifestations more atypical [##UREF##1##2##]. We describe an atypical case of a 34-year-old male-sex-male patient with secondary syphilis and HIV coinfection resembling erythema multiforme clinically and histologically who showed significant improvement with a single dose of benzathine penicillin injection of 2,4 million IU therapy.</p>" ]
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[ "<title>Discussion</title>", "<p>The presence of erythematous plaques resembling a target lesion with a necrotic area in the center and a history of coronavirus disease 2019 (COVID-19) vaccination, in this case, led to suspicion of erythema multiforme (EM) due to vaccination as the initial assessment after eliminating herpes simplex virus (HSV) infection and medications as the common trigger factors of EM. Secondary syphilis is suspected as a differential due to the history of being MSM and the presence of erythematous lesions on the palms and soles which are typical for secondary syphilis lesions. Syphilis diagnosis needs a combination of a thorough medical history (including sexual history), clinical symptoms, and additional examinations. Two laboratory serologic tests are necessary for a presumptive diagnosis of syphilis: a nontreponemal test, such as the Venereal Disease Research Laboratory (VDRL), and a treponemal test, such as the <italic>Treponema pallidum</italic> hemagglutination assay (TPHA). Examination using a dark field microscope as the definitive method can detect <italic>T. pallidum</italic> directly from exudates or tissue, but it is usually limited because of unavailability in each healthcare facility and the lesions on keratinized skin (palmoplantar lesions and maculopapular rash on the body) typically do not contain enough treponemes to give a positive result [##UREF##0##1##,##UREF##1##2##].</p>", "<p>Erythema multiforme (EM) is a rare, immune-mediated disease of cutaneous or mucocutaneous eruption characterized by “target” lesions that typically affect the face and extremities, but can also affect palms and soles and induce burning or itching symptoms [##UREF##2##3##,##UREF##3##4##]. The course of EM is often acute, mild, and self-limited, but carries a risk of relapse and may be persistent in some cases. The precipitating event relates to infection in 90% of cases, while less than 10% are caused by medications. The most commonly identified etiology is HSV type 1, while it has also been linked to HSV-2 and other infections. Vaccines have also been linked to EM, which is probably an epiphenomenon of immunogenicity to viral antigens, but the incidence is low [##REF##31305041##5##]. The majority of erythema multiforme cases don't need any additional diagnostic procedures, however, histopathological analysis may be helpful to confirm the diagnosis as well as to differentiate between EM and other diagnoses [##REF##31305041##5##,##REF##29352387##6##]. Histopathology examination of EM exhibits a significant dermal inflammatory infiltration, liquefactive necrosis, degeneration, and dyskeratotic keratinocytes in the epidermis that lies above. The dermo-epidermal interface is obscured by a lichenoid reaction pattern, which is characterized by a mild to moderate infiltrate of lymphocytes, some of which migrate into the basal layer. Additionally, there is some epidermal spongiosis and basal vacuolar alteration [##UREF##2##3##]. The location of the skin biopsy, as well as the time point of the biopsy during the disease course, affect the histological characteristics of EM [##REF##29352387##6##].</p>", "<p>Meanwhile, the histological pattern of secondary syphilis varies greatly, with neutrophils in the stratum corneum, irregular/psoriasiform acanthosis, effacement of the rete ridges/elongated rete ridges, vacuolar interface with vacuolar predominance/with equal numbers of lymphocytes and vacuoles, endothelial swelling, presence of plasma cells, lymphocytes with ample cytoplasm, and interstitial inflammation [##UREF##4##7##]. Although most of the studies found that plasma cells are the most common finding in secondary syphilis, up to one-third of all biopsies may have scant or absent plasma cells, and the vascular changes may not be prominent. The histopathologic examination for secondary syphilis has low specificity and low sensitivity since the features can also be seen in conditions clinically mimicking secondary syphilis maculopapular lesions [##UREF##4##7##,##UREF##5##8##]. The Warthin-Starry technique or the Steiner variant of the Dieterle technique are the two most used methods for finding spirochetes in tissue sections of secondary syphilis lesions. The organisms were primarily found near the dermal-epidermal junction [##REF##15330990##9##]. Immunohistochemistry is superior for detecting spirochetes compared with silver stains, however, it may not always be routinely available at many healthcare facilities. There are still certain cases where both immunohistochemistry and silver stains are unable to detect organisms [##UREF##4##7##].</p>", "<p>The histological finding, in this case, revealed basal cell vacuolar degeneration of the epidermis and lymphocytic infiltrates along the dermal-epidermal junction and superficial dermis. It did not show any plasma cells and spirochetes. Silver stain or immunohistochemistry examination could not be performed due to unavailability in the hospital. Secondary syphilis diagnosis was then made based on history taking, clinical manifestations, and syphilis serologic results. The patient showed rapid clinical resolution after a single dose of benzathine penicillin 2,4-million-unit intramuscular injection. Patient achieved serological cure by the decline of VDRL titer more than four-fold to 1: 4 after 3 months of follow-up and 1: 1 after 6 months of follow-up. It is important to raise suspicion of secondary syphilis in patients with sexual risk behavior. The key to early identification and treatment of secondary syphilis is the combination of clinical pathologic correlation and serologic testing. Accurate diagnosis can lead to proper treatment and prevent complications.</p>" ]
[ "<title>Conclusion</title>", "<p>This case highlights that the dermatological manifestations of secondary syphilis are highly variable, earning it the name of “The Great Imitator”. Erythema multiforme (EM)-like lesions are an uncommon presenting sign of secondary syphilis. Coinfection with HIV may play a part in the atypical presentation of the lesions. Even though rare in occurrence, syphilis should be considered in the differential diagnosis of HIV patients presenting with targetoid lesions. A single dose of benzathine penicillin 2.4-million-unit intramuscular injection is sufficient to achieve a serological cure for early syphilis with HIV coinfection like in this case as indicated by a decrease in the nontreponemal titer more than 4-fold after 6 months of follow-up. Accurate diagnosis will lead to appropriate management of the patient.</p>" ]
[ "<p>Secondary syphilis is known as “The Great Imitator”. It can mimic numerous diseases clinically and histologically, including erythema multiforme (EM). Coinfection with HIV often makes its manifestations more atypical leading to delays in diagnosis and therapy. A 34-year-old male-sex-male patient who had received coronavirus disease 2019 (COVID-19) vaccine 1 week earlier presented with complaints of slightly pruritic scaly erythematous targetoid plaques and erythematous macules on the trunk and extremities for 6 weeks. Histopathology examination showed basal cell vacuolar degeneration of the epidermis and lymphocytic infiltrates along the dermal-epidermal junction and superficial dermis, consistent with EM. Upon further investigation, syphilis and HIV serology were reactive (VDRL 1: 128, TPHA 1: 40960, CD4+ 461 cells/µl). Lesions improved significantly after a single dose of 2,4-million units of benzathine penicillin intramuscular injection. Secondary syphilis presenting as erythema multiforme (EM)-like eruptions is very rare. Physicians should be aware of this unusual presentation to prevent complications.</p>" ]
[ "<title>Patient and observation</title>", "<p><bold>Patient information:</bold> a 34-year-old male-sex-male patient with a history of receiving 1<sup>st</sup> dose of coronavirus disease 2019 (COVID-19) vaccine 1 week earlier presented with complaints of slightly pruritic red skin patches on his trunk and extremities, including his palms and soles, for 6 weeks. No history of fever, cough, running nose, sore throat, mouth ulcers, weight loss, hair loss, genital ulcers, or mouth ulcers. There was also no history of taking medicines and food supplements, smoking, drinking alcohol, and a blood transfusion before. No history of the same complaints in his family.</p>", "<p><bold>Clinical Findings:</bold> the patient was well-oriented and had normal vital signs. The physical examination showed multiple sharply demarcated erythematous annular scaly plaques with a necrotic area in the center which looked like targetoid lesions with a diameter between 3-6 cm on his lower extremities (##FIG##0##Figure 1##). There were also multiple erythematous macules and plaques on his trunk and upper extremities, some lesions were scaly and confluences. Palms and soles are also affected (##FIG##1##Figure 2##). No lymphadenopathy or lesions were found.</p>", "<p><bold>Diagnostic assessment:</bold> the potassium hydroxide examination was negative. The IgM and IgG anti-herpes simplex virus (HSV)-1 and anti-HSV-2 serology examinations were non-reactive. The histopathology examination revealed basal cell vacuolar degeneration in the epidermal layer and the dermal layer showed lymphocytic infiltrates along the dermal-epidermal junction and the superficial dermis, consistent with EM (##FIG##2##Figure 3##). The dark field microscope examination showed negative results for spirochetes. The blood test results were reactive for venereal disease research laboratory (VDRL) with a titer of 1: 128 and <italic>Treponema pallidum</italic> hemagglutination assay (TPHA) with a titer of 1: 40960, while the HIV serology was reactive with a cluster of differentiation-4 (CD4)+ value of 461 cells/µl. Complete blood count examination showed normal Hb 13,5 g/dl, thrombocytes 46.000/µl, white blood cells 8.500/µl, eosinophil 3%, basophil 1%, neutrophil 69%, monocytes 11%, lymphocytes 16%. Immunohistochemistry and the Warthin-Starry technique for finding spirochetes in tissue sections of secondary syphilis lesions couldn´t be performed due to unavailability in our hospital. Polymerase chain reaction (PCR) examination for treponema also could not be done due to unavailability.</p>", "<p><bold>Diagnosis:</bold> secondary syphilis with HIV-coinfection.</p>", "<p><bold>Therapeutic interventions:</bold> the patient received 2,4 million IU of single-dose benzathine penicillin along with antiretroviral therapy.</p>", "<p><bold>Follow-up and outcome of interventions</bold>: the lesions showed significant improvement with a decline of syphilis serological titer after 3 months follow-up became VDRL 1: 4 and TPHA 1: 640, and after 6 months follow-up became VDRL 1: 1 and TPHA 1: 320.</p>", "<p><bold>Patient perspective:</bold> “I was shocked when I found out that I got syphilis and HIV positive, but I feel more relieved because I can get the proper treatment and some of the red patches have disappeared. Hopefully, I can get treatment more regularly and my condition will be improved.”</p>", "<p><bold>Informed consent:</bold> it has been signed by the patient.</p>" ]
[ "<title>Competing interests</title>", "<p>The authors declare no competing interest.</p>", "<title>Authors' contributions</title>", "<p>Patient management: Dwi Murtiastutik and Afif Nurul Hidayati. Data collection: Amira Suryani Rahmatika, Astindari, Maylita Sari, and Linda Astari. Manuscript drafting: Regitta Indira Agusni. Manuscript revision: Amira Suryani Rahmatika, Astindari, Maylita Sari, and Linda Astari. All authors read and approved final version of the manuscript.</p>" ]
[ "<fig position=\"float\" id=\"F1\"><label>Figure 1</label><caption><p>targetoid lesions on the lower extremities</p></caption></fig>", "<fig position=\"float\" id=\"F2\"><label>Figure 2</label><caption><p>the clinical manifestations on the trunk and extremities</p></caption></fig>", "<fig position=\"float\" id=\"F3\"><label>Figure 3</label><caption><p>the histopathology examination; A) the histopathology examination revealed the epidermis with basal cell vacuolar degeneration and the dermis layer showed a lymphocytic infiltrate along the dermal-epidermal junction and the superficial dermis layer which was compatible with erythema multiforme (20x magnification); B) histopathology of the same lesion with 400x magnification</p></caption></fig>" ]
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[ "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Amira Suryani Rahmatika et al. Unusual presentation of secondary syphilis mimicking erythema multiforme in HIV positive patient: a case report. Pan African Medical Journal. 2023;46(55). 10.11604/pamj.2023.46.55.41497</p></fn></fn-group>" ]
[ "<graphic xlink:href=\"PAMJ-46-55-g001\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-55-g002\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-55-g003\" position=\"float\"/>" ]
[]
[{"label": ["1"], "surname": ["Tuddenham", "Zenilman"], "given-names": ["SA", "JM"], "article-title": ["Syphilis Fitzpatrick\u00b4s Dermatology"], "year": ["2019"], "publisher-loc": ["New York"], "publisher-name": ["McGraw Hill Education"]}, {"label": ["2"], "surname": ["Workowski", "Bachmann", "Chan", "Johnston", "Muzny", "Park"], "given-names": ["KA", "LH", "PA", "CM", "CA", "I"], "etal": ["et al"], "collab": ["Syphilis"], "article-title": ["Sexually Transmitted Infections Treatment Guidelines 2021 centers for Disease Control and Prevention (CDC) MMWR Recommendations and Reports"], "source": ["MMWR Recomm Rep"], "year": ["2021"], "month": ["Jul"], "day": ["23"], "volume": ["70"], "issue": ["4"], "fpage": ["1"], "lpage": ["187"]}, {"label": ["3"], "surname": ["Cartron", "Blaszczak", "Kaffenberger", "Trinidad"], "given-names": ["AM", "A", "BH", "JCL"], "article-title": ["Approaching target and targetoid Eruptions in Inpatient Dermatology"], "source": ["Curr Dermatol Rep"], "year": ["2020"], "volume": ["9"], "issue": ["4"], "fpage": ["210"], "lpage": ["9"]}, {"label": ["4"], "surname": ["Bhandari", "Khullar"], "given-names": ["M", "G"], "article-title": ["Target and targetoid lesions in dermatology"], "source": ["Indian J Dermatol Venereol Leprol"], "year": ["2021"], "month": ["Jul"], "day": ["29"], "volume": ["88"], "issue": ["4"], "fpage": ["430"]}, {"label": ["7"], "surname": ["Trovato", "Tognetti", "Campoli", "Cinotti"], "given-names": ["E", "L", "M", "E"], "article-title": ["Syphilis Diagnosis and Treatment?"], "source": ["State of The Art"], "year": ["2021"], "issue": ["March"]}, {"label": ["8"], "surname": ["Patterson"], "given-names": ["J"], "article-title": ["Spirochetal infections"], "source": ["Weedon\u00b4s Skin Pathology"], "year": ["2021"], "edition": ["5th ed"], "publisher-loc": ["China"], "publisher-name": ["Elsevier"], "fpage": ["573"], "lpage": ["80"]}]
{ "acronym": [], "definition": [] }
9
CC BY
no
2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 16; 46:55
oa_package/fb/6d/PMC10787133.tar.gz
PMC10787134
0
[ "<title>Introduction</title>", "<p>Evidence has shown that by 2025, the number of overweight/obese children aged 5 -17 years globally will increase to 335 million [##REF##27684716##1##]. Also, there has been growing evidence on the increasing prevalence of childhood overweight/obesity in the developing and industrialized nations [##REF##33292679##2##, ####UREF##0##3##, ##REF##17902211##4##, ##REF##24880830##5##, ##REF##29029897##6####29029897##6##]. This has been attributed to rapid urbanization, high rates of sedentary lifestyle and unhealthy eating habits [##REF##21270205##7##]. Obesity in children is defined as the accumulation of excess body fat with a body mass index (BMI) of ≥ 95<sup>th</sup>percentile for age and gender [##REF##27653184##8##] Recent reports in Cameroon indicated that the highest prevalence of overweight/obesity was observed among children in the grass field area including the North West Region [##UREF##0##3##,##REF##26636970##9##] with a higher prevalence in the urban (23%) compared to the semi-urban area (1.9%) [##REF##34152698##10##]. Moreover, central obesity in children have been found to positively correlate with dyslipidemia, hypertension and alterations in the metabolism of blood glucose and T2DM [##REF##16123512##11##]. The persistent rise in the global prevalence of obesity in the pediatric population due to the nutrition and epidemiological transition is becoming worrisome given it is a major risk factor for metabolic syndrome in this vulnerable group [##REF##35051409##12##,##REF##31263167##13##]. Thus, early detection through screening will help in reducing adverse cardiovascular outcomes in early life. For instance, a report in the Center Region of Cameroon indicated that the prevalence of hypertension among primary school pupils in 2019 was 1.6% [##REF##31993352##14##]. Another report in 2021 in children (3 to 19 years) in the Center and West Regions of Cameroon showed a hypertension prevalence of 8.6% and 12.0% in the urban and semi-urban areas respectively [##REF##26636970##9##]. Moreover, a recent systematic review by Noubiap <italic>et al</italic>. [##REF##35051409##12##] reported an elevated BP prevalence of 5.5% among sub-Saharan African children and adolescents with overweight and obesity being a major risk factor for elevated BP among the children. In addition, a systematic review [##REF##18559702##15##] as well as a meta-analysis [##REF##19839954##16##] have shown that childhood BP levels persist into adulthood, with pubertal hypertension being a strong predictor of hypertension in later life [##REF##22108410##17##]. The prevalence of hypertension among obese children and adolescents has been found to be based on the degree of excess weight [##REF##34783422##18##]. Also, evidence has demonstrated that elevated BP in the pediatric population, is associated with pathological changes such as atherosclerosis, left ventricular hypertrophy and an increase in the carotid intima-media thickness [##REF##16735644##19##], with a greater carotid artery intima-media thickness in obese children [##REF##35544586##20##,##REF##22275742##21##] compared to their non-obese counterparts. Studies in children and adolescents have demonstrated the relationship between obesity and using BMI as a proxy [##REF##17627321##22##], WC [##REF##31166521##23##] and WHtR [##REF##35016145##24##] with hypertension. While some reports have found WC measurements [##REF##31263167##13##,##REF##31166521##23##] as the best tool in predicting cardiometabolic risk in children, others have found WHtR [##REF##34692623##25##,##REF##16432546##26##]. However, Millar <italic>et al</italic>. [##UREF##1##27##] did not find any superiority of the central adiposity indices over BMI in predicting cardio metabolic risk. Despite evidence of childhood obesity rise in Cameroon with a six-fold risk of developing hypertension in an obese child [##REF##22108410##17##,##REF##29435442##28##], the association between WC, WHtR and BMI with hypertension in children and adolescents in our setting has not been adequately explored. This study therefore set out to determine the proportion of secondary school adolescents with elevated BP and high blood pressure in relation to some measures of adiposity (BMI, WC, WHtR) and to examine the association between blood pressure and the adiposity indices among these children in the Bamenda municipality of the North West Region of Cameroon.</p>" ]
[ "<title>Methods</title>", "<p><bold>Study participants:</bold> this study made use of an institution-based data collected between March 2022 to June 2022, involving children and adolescents aged 10 -19 years attending some secondary schools in the North West Region (NWR) of Cameroon selected through a 2-stage sampling technique. The first stage of the recruitment process was a random selection of 4 secondary schools (2 public and 2 private) from the list of 66 secondary schools which was obtained from the Regional Delegation of Secondary Education of the NWR of Cameroon and asked to take part in our study. During the second stage, a quota sampling technique was used to select a total of 602 children and adolescents from the different levels of study in secondary education. However, 68 of the children and adolescents were excluded from the study during data analysis given that they were underweight and had incomplete data giving a final dataset of 534 children and adolescents (168 boys and 366 girls) with mean age 15.1 ± 2.3 years. Using a prevalence of 21.6% obtained from a study by Srirama and Subramanian in India, amongst school children and a level of significance (ɑ) of 5%, a minimum sample size of 328 children and adolescents was obtained using the Cochran's formula [##REF##24049221##29##].</p>", "<title>Data collection</title>", "<p><bold>Anthropometric measurements:</bold> all anthro pometric measurements (weight, height and waist circumference) were taken by well-trained nurses during school hours (9.00am and 1.00pm) on the school campuses ensuring all standard protocols were respected. Height was measured without shoes using a portable stadiometer (Seca 213, Germany), to the nearest 0.1cm. Body weight was measured to the nearest 0.1kg using a digital scale (Omron BF511, Japan). The BMI (body mass index) for each child was calculated by dividing weight (kg) by height (cm) squared [##REF##10797032##30##]. Waist circumference was measured to the nearest 0.5cm using an inelastic and flexible ergonomic circumference tape (Seca 201, USA), according to the protocol by McCarthy <italic>et al</italic>. [##REF##11593353##31##]. Waist-to-height ratio was also used to assess central obesity. The WHtR was calculated by dividing the WC (cm) by height (cm) and all the children were classified as ´low risk´ and ´high risk´ of developing cardiovascular diseases when the WHtR was &lt; 0.5 and ≥ 0.5 respectively [##REF##16432546##26##].</p>", "<p><bold>Blood pressure:</bold> systolic and diastolic blood pressure of the children were measured using an automated blood pressure device (SANITAS SBM21, Hamburg, Germany). Blood pressure was measured with the children sitting in a relaxed position with the arm resting and the palm facing upwards on the same day, three times within a 3-minute interval. The average of the three (3) measurements was recorded. Elevated BP and hypertension were defined as three elevated systolic or diastolic BP readings of ≥ 90<sup>th</sup> percentile to &lt;95<sup>th</sup> percentile and ≥ 95<sup>th</sup> percentile (for the child's age, sex and height) respectively [##REF##32520365##32##].</p>", "<p><bold>Statistical analysis:</bold> IBM-SPSS for Windows version 23 statistical package was used for data analysis. Normality of all continuous variables was checked using the Kolmogorov-Smirnov (K-S) test. Weight, height, BMI and WC were adjusted for age and gender (z scores) using the WHO LMS Growth software [##UREF##2##33##]. This package has different growth reference data including WHO (2006), WHO (2007), UK-CDC (2000) and the British (1990) growth reference data for children and adolescents. The study participants were classified as being overweight (&gt;1 z-score) and obese (&gt; 2 z-score) with respect to BMI. Also, a WC z-score of 1.33 was used to classify participants as overweight/obese [##REF##16143968##34##]. In addition, a WHtR of ≥ 0.5 was used to define participants at high cardiometabolic risk (“high risk”) [##REF##16432546##26##]. The prevalence of elevated BP and hypertension for the different adiposity indices (BMI, WC and WHtR) were then calculated. The association between categorical variables was assessed using Chi-square test and proportions presented with their respective 95% confidence intervals. In addition, the means of continuous variables was assessed using an independent student t-test and ANOVA as appropriate. Pearson correlation was used to assess the association between the measures of adiposity with blood pressure (SBP and DBP). Finally, linear regression models (unadjusted and adjusted for age, gender and school type) were used to assess the relationship between the adiposity indices (BMI, WC, WHtR) with blood pressure (SBP and DBP). A p-value of &lt; 0.05 was set as cut off for statistical significance.</p>", "<p><bold>Ethical considerations:</bold> the approval for this study was obtained from The University of Bamenda`s Institutional Review Board (IRB) (Ref: 2022/0421H/UBa/IRB). Administrative authorization was obtained from the Regional Delegation of Public Health of the North West Region and Regional Delegation for Basic Education of the North West Region (Ref. No. G649/1188/MINSEC/RDSE/NW/SDGA of 13 Jan 2022). In addition, all the principals/parents/guardians gave written informed consent was given by all the children/adolescents before any data collection procedure was carried out.</p>" ]
[ "<title>Results</title>", "<p><bold>Descriptive characteristics of the study population:</bold>\n##TAB##0##Table 1## is a description of the study population by gender. On average males were significantly (p &lt;0.001) older and taller than females. Also, we observed that 68.7% of females were BMI-obese compared to 13.3% of males and this difference was significant (p= 0.001). In addition, females had a higher mean diastolic BP (68.3mmHg) compared to males (64.5 mmHg) and this difference was significant (p= 0.001). However, there was no significant difference (p &gt;0.05) in the mean body weight, WHtR, WC and systolic BP between males and females. In addition, a higher proportion of females (23.2%) were BMI-overweight/obese compared to males (11.3%) and the difference was significant (X<sup>2</sup>=10.403, p= 0.001). With respect to WC, it was observed that a significantly (p &lt;0.001) higher proportion of girls (36.1%) were centrally overweight/obese (WC) compared to boys (4.2%). While, the proportion of females with WHtR ≥ 0.5 was higher (3.8%) compared to males (1.8%). However, it was not significant (X<sup>2</sup>=1.721, p =0.291).</p>", "<p><bold>Prevalence of elevated blood pressure and hypertension:</bold> the overall prevalence of elevated BP and hypertension in this study was 39.2% (with 8.6% and 7.9% of the hypertensive children in stage I and stage II respectively) (##TAB##1##Table 2##, ##TAB##2##Table 3##). With respect to gender, there was a non-significant difference (X<sup>2</sup>=0.474, p =0.765) in the proportion of females with elevated BP and high BP compared to males (39.9% vs 37.5%). However, more hypertensive females (8.5%) were in Stage II compared to males (6.5%). ##FIG##0##Figure 1##, ##FIG##1##Figure 2## and ##FIG##2##Figure 3## shows the prevalence of elevated BP and hypertension by BMI, WC and WHtR amongst the study participants. A higher proportion of the BMI overweight/obese children had elevated BP (56.1%) and high blood pressure (53.5%) compared to their healthy weight counterparts (20.2% and 15.1%) respectively. However, the difference was not significant (X<sup>2</sup>= 6.818, p =0.146). Also, it was observed that a higher proportion of the centrally overweight/obese children (WC) had elevated BP (25.9%) and hypertension (25.2%) compared to children with normal WC (21.5% and 14.3%) respectively and the difference was significant (X<sup>2</sup>= 15.452, p &lt;0.001). In addition, there was a significant difference (X<sup>2</sup>= 9.585, p = 0.002) in the proportion of ‘high-risk´ children (WHtR ≥ 0.5) with elevated BP (29.4%) and hypertension (41.2%) compared to the “low-risk” (WHtR &lt; 0.5) children (22.4% and 15.4%) respectively.</p>", "<p><bold>Mean blood pressure profile of study participants according to weight status:</bold>\n##TAB##3##Table 4## shows the mean blood pressure profile of study participants according to weight status. Considering the whole sample, there was on average a 17.1mmHg and 9.4mmHg significant (p &lt; 0.05) differences in the mean SBP and DBP observed amongst the BMI-obese children and the healthy weight children respectively. Similarly, there was a 13.9mmHg and 4.6mmHg significant (p &lt;0.05) differences in the mean SBP and DBP between children who were centrally overweight/obese (WC) and those with normal WC respectively. Additionally, we observed a significant (p &lt;0.05) difference in the mean SBP and DBP amongst children whose WHtR was ≥ 0.5 and &lt; 0.5 respectively. With respect to gender, we observed a 19.1mmHg and 9.8mmHg significant (p &lt; 0.05) mean differences in SBP and DBP between the BMI-obese females and the BMI healthy weight females respectively. Similarly, a 15.8mmHg and 9.5mmHg significant (p &lt; 0.05) differences were also seen in the mean SBP and DBP between the centrally overweight/obese (WC) females and the normal weight females respectively. Furthermore, there was a significantly (p =0.007) higher mean SBP (136.2mmHg) amongst the WHtR “high risk” females compared to their “low risk” counterparts (115.9mmHg). On the contrary, there was a 9.5mmHg non-significant ((p = 0.051) difference in the mean DBP between the WHtR “high risk” females compared to the “low risk” group. ##TAB##4##Table 5## shows the Pearson correlation coefficients between the different measures of adiposity with blood pressure (SBP and DBP). In this present study, we found a significant positive weak correlation (p&lt;0.001) between BMI (r= 0.169), WC (r= 0.329) and WHtR (r= 0.237) with systolic BP. Similarly, a significant positive weak association (p &lt; 0.05) was observed between the BMI (r = 0.089), WC (r= 0.118) and WHtR (r= 0.095) with diastolic BP.</p>", "<p><bold>Association between the measures of adiposity and blood pressure (SBP and DBP):</bold>\n##TAB##5##Table 6## shows the linear regression (unadjusted and adjusted for age, gender and school type) for the association between BMI, WC, WHtR and blood pressure amongst the study participants. There was a significant positive association (p &lt;0.001) between waist circumference (β= 0.75; 95% CI= 0.57, 0.92), BMI (β= 0.88; 95% CI= 0.49, 1.25) and WHtR (β= 67.08; 95% CI= 45.64, 88.51) with systolic blood pressure for the unadjusted analysis. After adjusting for age, gender and school type, only waist circumference (β= 0.66; 95% CI = (0.43, 0.89) was significantly associated positively (p&lt;0.001) with systolic blood pressure. Similarly, there was a significant positive association (p &lt;0.003) between waist circumference (β= 0.24; 95% CI= 0.10, 0.38), BMI (β= 0.44; 95% CI= 0.15, 0.73) and WHtR (β= 25.19; 95% CI= 8.54, 41.86) with diastolic blood pressure for the unadjusted analysis. However, after adjusting for age, gender and school type, there was no significant association (p &gt;0.05) between the measures of adiposity (BMI, WC and WHtR) with diastolic blood pressure.</p>" ]
[ "<title>Discussion</title>", "<p>Measures of adiposity such as BMI, WC and WHtR have been shown to be associated with high BP in children and adolescents. However, very little attention has been focused on the influence of these different anthropometric indices of obesity on blood pressure in the paediatric population in spite of the fact that these measures increase the risk of high BP even in BMI-healthy weight children [##REF##24157679##35##,##REF##33022021##36##]. Early routine diagnosis, management and control of high BP through the periodic evaluation of anthropometric indices in children and adolescents especially in normal weight children is essential for the prevention of childhood obesity-related cardiovascular outcomes. This study set out to determine the proportion of secondary school adolescents with elevated BP and high blood pressure in relation to some measures of obesity (BMI, WC, WHtR) and to examine the association between blood pressure and the obesity indices (BMI, WC, WHtR) among these children in the Bamenda municipality of the North West Region of Cameroon. This study found that the prevalence of elevated BP and hypertension amongst the study participants was high for the BMI-obese, WC overweight/obese children and the “high risk” (WHtR ≥ 0.5) children and adolescents respectively. In addition, this study found that BMI, WC and WHtR were positively associated with blood pressure with waist circumference being an independent predictor for blood pressure in the children and adolescents in our setting. This study found that the overall prevalence of elevated BP and hypertension amongst the children was 39.2% (with 8.6% and 7.9% of the hypertensive children in Stage I and Stage II respectively). In Cameroon, there is limited population data on paediatric hypertension and adiposity. The findings of our study are higher than those reported by Noubiap <italic>et al</italic>. [##REF##35051409##12##] in a systematic review in sub-Saharan Africa, where they reported an overall prevalence of 5.5% for elevated BP amongst children and adolescents. The findings are also higher than those reported in the Centre region of Cameroon by Chelo <italic>et al</italic>. [##REF##31993352##14##] who found a prevalence of 1.6%.</p>", "<p>However, the study in the Centre region was carried out on primary school children aged 5-17 years. Again, in Malaysia [##UREF##3##37##] amongst secondary school children aged 13 -15 years, the prevalence of elevated BP and hypertension were 13.2% and 17.0% respectively, lower than the values reported in our study. Similarly in Nigeria a survey by Okpokowuruk and colleagues [##REF##29854068##38##] in a semi-urban environment reported a hypertension prevalence of 2.6%, lower than that reported in our study. However, the findings in our study are similar to those reported in Dar-es-Salaam in Tanzania by Muhihi <italic>et al</italic>. [##REF##29433455##39##] who reported a hypertension prevalence of 15.2% in primary school children 5- 17 years and 19.2% in Pakistan [##REF##32509482##40##] where a hypertension prevalence of 19.2% was reported. However, the Pakistani study was carried out on children 4-12 years old who had not attained puberty. Methodological differences, including the variations in statistical methods may explain the discrepancies in the prevalence of hypertension in our study with that observed in the other studies. Moreover, there has been evidence of an overweight/obesity and nutrition transition in school-aged children in sub-Saharan Africa and the changes in dietary and lifestyle patterns differs across the countries in the African region as such may explain the differences in the prevalence of hypertension amongst school going children and adolescents between our study and that of other studies observed across the continent. In addition, considering the whole sample, we found that the prevalence of hypertension was 53.6%, 25.2% and 41.2% amongst the BMI overweight/obese, centrally overweight/obese (WC) and the children with an increased cardiometabolic risk (WHtR ≥ 0.5) respectively. These findings are higher than those reported in Brazil [##REF##32489800##41##] and China [##REF##33579239##42##] where the prevalence of elevated BP using central overweight/obesity (WC) was 18.0% and 13.2% but similar to those obtained in Tanzania [##REF##29433455##39##] and Pakistan [##REF##32509482##40##] where a prevalence of 15.2% and 19.2% were reported respectively. These findings highlight the necessity for cost-effective strategies for creating awareness tailored to our context, early diagnosis, control and proper management of children with elevated BP in order to prevent in order to reduce the complications resulting from hypertension early in childhood and in later life.</p>", "<p>The high prevalence of hypertension from the different adiposity indices in our study participants might be attributed to the obesity epidemic combined with the fact that adolescence is a period of independence with less parental control compounded with lifestyle challenges such as low levels of physical activity, unhealthy diet and socio-cultural factors, all of which increase the risk of hypertension. In addition, the higher proportion in girls compared to boys might be due to hormonal changes and psychosocial factors resulting from the rapid biological changes associated with puberty onset in this age group. Our findings highlight the need for periodic screening of secondary school children and adolescents including those with BMI-healthy weight using all the adiposity indices for the early identification of incident HTN in this vulnerable population thereby preventing adverse cardiovascular outcomes in early life. Evidence suggest that obese children and adolescents have an increased carotid artery intima-media thickness than their non-obese participants [##REF##22275742##21##]. Our study found that 19.5% of the investigated children were BMI-overweight/obese, 26% were centrally overweight/obese (WC) and 3.2% were at “high risk” (WHtR ≥ 0.5). These findings are in higher than those reported amongst secondary school children in China [##REF##33579239##42##] and Malaysia [##UREF##3##37##] where the prevalence of overweight/ obesity was 18.3% and 24.3% respectively. The differences in the prevalence of central overweight/obesity might be attributed to the small sample size in our study compared to the Chinese and Malaysian studies which involved 29,516 and 2,461 secondary school children and adolescents respectively. Evidence has proven that in the children and adolescents, the risk of developing hypertension in an overweight/obese child is six-times higher compared to a child with normal BMI [##REF##35051409##12##]. Also, it has been shown that children and adolescents at “high risk” (WHtR ≥ 0.5) have an increased risk of developing high BP levels [##REF##29280649##43##]. Our study found that the BMI-obese, centrally overweight/obese (WC) and “high risk” (WHtR ≥ 0.5) children had a significantly higher mean systolic BP and diastolic BP compared to their normal weight counterparts. In addition, the BMI-obese, centrally overweight/obese (WC) and “high risk” (WHtR ≥ 0.5) girls had a significantly higher mean systolic BP and diastolic BP compared to their normal weight or “low risk” counterparts, a finding which was not observed in males.</p>", "<p>These findings are in contrast to those obtained in children and adolescents in Lithuania [##REF##31263167##13##] and China [##REF##33579239##42##] who found that boys had a significantly higher mean SBP and DBP compared to girls. The differences in blood pressure by gender can be attributed to sex hormones which have been found to be strongly involved in the developmental differences in blood pressure between men and women with BP progressing more rapidly in women than in men beginning early in life [##REF##31940010##44##]. Again, this study revealed that BMI, WC and WHtR which are all measures of obesity were significantly and positively correlated with systolic BP and diastolic BP. These findings are similar to those reported by Kuciene <italic>et al</italic>. [##REF##31263167##13##] amongst Lithuanian children and adolescents where they also reported a positive correlation between BMI, WC and WHtR with systolic and diastolic BP. Similarly, studies amongst Malaysian [##REF##23979777##45##] and Brazilian [##UREF##4##46##] secondary school children and adolescents also found that BMI, WC and WHtR were significantly associated with hypertension in the paediatric population and could be used as indicators for children and adolescents at risk of hypertension. Visceral fat measured using waist circumference has been found to be strongly correlated with blood pressure [##REF##23979777##45##]. This present study found WC as an independent predictor for children and adolescents at risk of hypertension. This finding is in line with findings in other countries where WC has also been found to be significantly associated with high BP in the paediatric population [##UREF##4##46##,##REF##29023455##47##]. This finding suggests that amongst children and adolescents in our setting, WC can be used as a screening tool for children and adolescent at risk of hypertension. This finding highlights the necessity for more efforts on health promotion in schools by encouraging regular physical activity, healthy nutrition and weight control in the paediatric population as a primary prevention method for elevated BP in this vulnerable group.</p>", "<p>The limitations to this study worth mentioning include: firstly, the tanner staging to assess the level of puberty in the children and adolescents was not done and this could have affected the relationship between WC, BMI and WHtR with blood pressure especially in females. Also, the influence of genetics on BMI cannot be completely ruled out given that family history of hypertension and obesity were not assessed in this present study. In addition, given that malaria can result in an enlarged spleen, the spleen size of the children was not measured in this present study as such it might have influenced the WC values. Finally, this study was carried out only in one municipality in one region of the country as such the findings might not truly be representative of the blood pressure profile of all secondary school adolescents in the country. Despite the limitations of this study, the study is innovative in that it is the first study in Cameroon to the best of our knowledge describing the association between three measures of obesity (BMI, WC and WHtR) with blood pressure amongst secondary school adolescents in the North West Region of Cameroon.</p>" ]
[ "<title>Conclusion</title>", "<p>This study conducted among secondary school adolescents in Cameroon found that the overall prevalence of elevated BP and hypertension amongst the study participants was high (39.2%). In addition, the study has demonstrated that WC is positively associated with high BP in children and adolescents. Therefore, WC can be used in predicting children and adolescents at high risk of hypertension in early life in our setting, given that centrally overweight/obese children at risk of hypertension might be missed if BMI is the only measure for adiposity. Further research needs to be conducted in other regions of the country to assess the relationship between WC and a positive family history with other risk factors for cardiovascular diseases in children and adolescents in order to reduce the risk of cardiovascular diseases in later life.</p>", "<title>\nWhat is known about this topic\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p>\n<italic>Overweight and obesity using body mass index as a proxy for overweight and obesity is linked with pediatric hypertension;</italic>\n</p></list-item><list-item><p>\n<italic>Pubertal hypertension is a strong predictor for adult hypertension or hypertension in later life 3;</italic>\n</p></list-item><list-item><p><italic>Height has been positively associated with childhood hypertension</italic>.</p></list-item></list>\n</p>", "<title>\nWhat this study adds\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p>\n<italic>The prevalence of elevated blood pressure and hypertension amongst the children was high;</italic>\n</p></list-item><list-item><p>\n<italic>Body mass index, waist circumference (WC) and waist-to-height ratio (WHtR were positively correlated with blood pressure in this study and it’s the first in Cameroon to use three indices of adiposity amongst secondary school BMI- healthy weight adolescents to assess its relationship with hypertension;</italic>\n</p></list-item><list-item><p><italic>Waist circumference was found to be an independent predictor for hypertension in our setting</italic>.</p></list-item></list>\n</p>" ]
[ "<title>Introduction</title>", "<p>measures of obesity such as body mass index (BMI), waist circumference (WC) and waist-to-height ratio (WHtR) have been shown to be associated with high blood pressure (BP) in children and adolescents. The purpose of this study was to determine the proportion of secondary school adolescents with elevated BP and high BP in relation to some measures of adiposity (BMI, WC, WHtR) and to examine the association between BP and adiposity indices amongst the children.</p>", "<title>Methods</title>", "<p>the study was an institutional-based cross-sectional study involving 534 adolescents (mean age 15.1 ± 2.3 years) attending 4 secondary schools (2 public and 2 private) in the Bamenda municipality of the North West Region of Cameroon. Anthropometric and BP measurements were carried out following standard procedures. Diagnosis of hypertension in the children was done by obtaining three elevated systolic or diastolic BP readings (BP ≥ 95<sup>th</sup> percentile for the child's age, sex and height). Linear regression was used to determine the relationship between BP and some measures of adiposity (BMI, WC, WHtR) amongst the children</p>", "<title>Results</title>", "<p>the prevalence of elevated BP and hypertension amongst the study participants was 33.3% and 33.3% in the BMI-obese children, 25.9% and 25.2% in the WC overweight/obese children and 29.4% and 41.2% in the “high risk” (WHtR ≥ 0.5) children respectively. Body mass index-obese, WC overweight/obese and “high risk” (WHtR ≥ 0.5) children had a significantly (p &lt;0.05) higher mean SBP and DBP compared to their healthy weight counterparts. Linear regression indicated a significant association (p &lt;0.001) between WC (β=0.75; 95% CI = 0.57, 0.92), BMI (β=0.88; 95% CI = 0.49, 1.25) and WHtR (β= 67.08; 95% CI = 45.64, 88.51) with systolic BP for the unadjusted analysis. After adjusting for age, gender and school type, only WC (β= 0.66; 95% CI = (0.43, 0.89) showed a positive significant (p &lt;0.001) relationship with systolic BP.</p>", "<title>Conclusion</title>", "<p>this study has demonstrated that WC is positively associated with high BP in children and adolescents. Thus, WC can be used in predicting children and adolescents with a high risk of developing high BP in our setting.</p>" ]
[]
[ "<title>Acknowledgments</title>", "<p>The authors are grateful to all the children and adolescents from all the schools that participated in our study as well as the school nurses who assisted in data collection and to all the school administrators who granted us access to their schools.</p>", "<title>Competing interests</title>", "<p>The authors declare no competing interests.</p>", "<title>Authors’ contributions</title>", "<p>Conception and study design, data collection, data analysis and interpretation, manuscript drafting, manuscript revision: Loveline Lum Niba, Lifoter Kenneth Navti and Ahmadou Jingi Musa. Guarantor of the study: Loveline Lum Niba. All the authors have read and agreed to the final version of the manuscript.</p>" ]
[ "<fig position=\"float\" id=\"F1\"><label>Figure 1</label><caption><p>prevalence of elevated blood pressure and hypertension in the study population with respect to Body mass index (BMI)</p></caption></fig>", "<fig position=\"float\" id=\"F2\"><label>Figure 2</label><caption><p>prevalence of elevated blood pressure and hypertension in the study population with respect to waist circumference (WC)</p></caption></fig>", "<fig position=\"float\" id=\"F3\"><label>Figure 3</label><caption><p>prevalence of elevated blood pressure and hypertension in the study population with respect to waist-to-height ratio (WHtR)</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"T1\"><label>Table 1</label><caption><p>characteristics of the study participants by gender</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"2\" colspan=\"1\">Variable</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Whole sample n=534</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Males (n=168)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Females (n=366)</th><th align=\"left\" rowspan=\"2\" colspan=\"1\">P-value</th></tr><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mean (SD)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mean (SD)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mean (SD)</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Age (years)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">15.1 (2.3)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">15.7 (2.3)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">14.9(2.2)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Height (cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">159.3 (11.0)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">163.7 (13.3)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">157.3(9.2)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Height z-score+</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">-0.37 (1.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">-0.61 (1.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">-0.26(1.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.011</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Weight (kg)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">58.4 (10.2)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">59.6(10.7)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">57.9(10.2)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.087</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Weight z-score+</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.57 (0.95)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.21(0.92)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.73(0.93)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI (kg/m<sup>2</sup>)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">22.9 (3.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">22.2 (3.6)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">23.3(3.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.002</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI z-score+</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.87 (0.83)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.62 (0.84)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.98(0.81)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WHtR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.37 (0.06)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.37(0.05)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.37(0.06)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.258</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Waist circumference (cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">69.9 (7.2)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">69.2(6.6)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">70.3(7.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.092</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WC z-score+</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.56(1.2)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">-0.10(0.86)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.87(1.1)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Systolic BP (mmHg)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">116.4(15.7)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.6(15.0)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">116.7(16.0)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.416</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Diastolic BP (mmHg)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">67.1(11.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">64.5(12.7)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">68.3(11.3)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.001</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T2\"><label>Table 2</label><caption><p>prevalence of elevated blood pressure and HTN amongst the study participants</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"2\" colspan=\"1\">Blood pressure status</th><th align=\"left\" rowspan=\"2\" colspan=\"1\">N</th><th align=\"left\" colspan=\"2\" rowspan=\"1\">Frequency</th></tr><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">%</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">(95% CI)</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Normal blood pressure</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">325</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">60.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(56.6 - 64.9)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Elevated blood pressure</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">121</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">22.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(19.3 - 26.4)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Hypertension</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Stage I</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">46</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">8.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(6.5 -11.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Stage II</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">42</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">7.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(5.8 - 10.5)</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T3\"><label>Table 3</label><caption><p>prevalence of elevated blood pressure and HTN amongst the study participants by gender</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Variable</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">All the children (N=534)</th><th align=\"left\" colspan=\"2\" rowspan=\"1\">Males (N= 168)</th><th align=\"left\" colspan=\"2\" rowspan=\"1\">Females (N=366)</th><th align=\"left\" rowspan=\"2\" colspan=\"1\">p-value</th></tr><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\"/><th align=\"left\" rowspan=\"1\" colspan=\"1\">n (%)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">n (%)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">(95% CI)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">n (%)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">(95% CI)</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Blood pressure status</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.765</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Normotensive</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">325 (60.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">105(62.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(56.9 - 67.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">220(60.1)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(55.0 - 65.0)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Elevated BP</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">121(22.7)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">35(20.8)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(15.4 - 27.6)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">86(23.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(19.4 - 28.1)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Hypertensive</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">88(16.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">28(16.7)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(13.4 - 26.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">60(16.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(12.9 -20.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T4\"><label>Table 4</label><caption><p>mean blood pressure profile of study participants according to weight status</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"3\" colspan=\"1\">Variables</th><th align=\"left\" rowspan=\"1\" colspan=\"1\"/><th align=\"left\" colspan=\"5\" rowspan=\"1\">Blood pressure status</th><th align=\"left\" rowspan=\"3\" colspan=\"1\">p-value</th></tr><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\"/><th align=\"left\" colspan=\"2\" rowspan=\"1\">SBP (mmHg)</th><th align=\"left\" rowspan=\"2\" colspan=\"1\">p-value</th><th align=\"left\" colspan=\"2\" rowspan=\"1\">DBP (mmHg)</th></tr><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">N</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mean</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">(95% CI)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mean</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">(95% CI)</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Whole sample</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI category (kg/m<sup>2</sup>)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001*</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.004*</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Healthy weight</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">430</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(113.9 -116.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td><td align=\"left\" rowspan=\"1\" colspan=\"1\">66.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(65.3 - 67.6)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Overweight</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">89</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">118.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(115.1-121.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">68.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(66.5 - 70.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Obese</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">15</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">132.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(119.6 -145.3)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td><td align=\"left\" rowspan=\"1\" colspan=\"1\">75.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(66.7 - 84.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Waist circumference(cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001**</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.022**</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Normal weight</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">495</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(114.1-116.7)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">66.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(65.7 - 67.7)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Central overweight/obesity</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">39</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">129.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(123.5- 135.1)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">71.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(67.1 - 75.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WHtR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.004**</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.038**</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Low risk (&lt; 0.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">517</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(114.5- 117.1)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">66.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(65.8 - 67.8)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">High risk (≥ 0.05)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">133.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(122.4 -145.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">75.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(67.4 - 83.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Males</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI category (kg/m<sup>2</sup>)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.711*</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.986*</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Healthy weight</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">149</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(112.7 -117.8)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">64.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(62.4 -66.6)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Overweight</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">118.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(113.5 -122.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">64.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(59.1 - 70.0)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Obese</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">118.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(102.4 -162.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">66.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(62.6 - 66.4)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Waist circumference (cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Normal</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">158</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(112.7 -117.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.081*</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">64.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(62.6 - 66.6)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.702**</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Central overweight/obesity</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">123.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">114.2 -133.0)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">63.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(56.1 - 69.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WHtR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.367 **</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.836**</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Low risk (&lt; 0.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">165</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(113.1-117.7)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">64.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(66.8 - 69.0)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">High risk (≥ 0.05)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">123.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(100.7-145.7)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">66.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(67.9 - 86.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Females</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI category (kg/m<sup>2</sup>)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001*</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.004*</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Healthy weight</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">281</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(113.8-117.3)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">67.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(66.2 -68.8)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Overweight</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">72</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">118.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(114.5 –121.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">69.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(67.3 - 72.1)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Obese</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">13</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">134.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(119.9 –149.3)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">77.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(58.2 - 94.8)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Waist circumference (cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001**</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.004**</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Normal</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">337</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(113.9 -117.1)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">67.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(66.6 - 68.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Central overweight/obesity</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">29</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">131.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(124.0 -138.6)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">74.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(69.2 --79.0)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WHtR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.007 **</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.051**</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Low risk (&lt; 0.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">352</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">115.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(114.3- 117.5)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">67.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(66.8 - 69.0)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">High risk (≥ 0.05)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">14</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">136.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(122.4 -149.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">77.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(67.9 - 86.9)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T5\"><label>Table 5</label><caption><p>Pearson correlation between blood pressure and measures of adiposity</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Measures of adiposity</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Pearson’s coefficient (r)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">p-value</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Systolic blood pressure</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI (kg/m<sup>2</sup>)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.169</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WC (cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.329</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WHtR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.237</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Diastolic blood pressure</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI (kg/m<sup>2</sup>)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.089</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.040</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WC (cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.118</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.007</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">WHtR</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.095</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.029</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T6\"><label>Table 6</label><caption><p>linear regression analysis (unadjusted and adjusted) for the association between the measures of adiposity and blood pressure among participants</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"2\" colspan=\"1\">Exposure</th><th align=\"left\" colspan=\"3\" rowspan=\"1\">Unadjusted</th><th align=\"left\" colspan=\"3\" rowspan=\"1\">Adjusted for age, gender and school type</th></tr><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Estimate (β)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">(95% CI)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">p-value</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Estimate (β)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">(95% CI)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">p-value</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Systolic blood pressure (mmHg)</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Waist circumference (cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.75</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(0.57, 0.92)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.66</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(0.43, 0.89)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>&lt;0.001</bold>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI (kg/m<sup>2</sup>)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.88</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(0.49, 1.25)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 0.34</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(-0.97, 0.29)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.293</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Waist-to-height (WHtR) ratio</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">67.08</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(45.64, 88.51)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt;0.001</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">34.25</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(-6.88, 54.75)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.102</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Diastolic blood pressure (mmHg)</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Waist circumference (cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.24</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(0.10, 0.38)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.001</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.16</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(-0.02, 0.34)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.081</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI (kg/m<sup>2</sup>)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.44</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(0.15, 0.73)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.003</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.11</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(-0.39, 0.61)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.662</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Waist-to-height (WHtR) ratio</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">25.19</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(8.54, 41.86)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.003</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.04</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">(-29.48, 35.56)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.854</td></tr></tbody></table></table-wrap>" ]
[]
[]
[]
[]
[]
[]
[ "<table-wrap-foot><fn id=\"TF1-1\"><p>+Based on WHO 2007 reference data; BMI: body mass index; WHtR:waist-to-height ratio; BP: blood pressure;WC:waist circumference</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF2-1\"><p>HTN: hypertension; CI:confidence interval</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF3-1\"><p>BP: blood pressure; HTN: hypertension</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF4-1\"><label>*</label><p>Calculated using one way analysis of variance (ANOVA); ** Calculated using student t-test; WHtR: Waist to Height; SBP: systolic blood pressure; DBP: diastolic blood pressure;WC: waist circumference</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF5-1\"><p>BMI: body mass index;WC: waist circumference WHtR: waist-to-height ratio</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF6-1\"><p>BMI: body mass index</p></fn></table-wrap-foot>", "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Loveline Lum Niba et al. Relationship between measures of adiposity and hypertension amongst secondary school adolescents in an urban setting in Cameroon. Pan African Medical Journal. 2023;46(57). 10.11604/pamj.2023.46.57.41547</p></fn></fn-group>" ]
[ "<graphic xlink:href=\"PAMJ-46-57-g001\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-57-g002\" position=\"float\"/>", "<graphic xlink:href=\"PAMJ-46-57-g003\" position=\"float\"/>" ]
[]
[{"label": ["3"], "surname": ["Navti", "Foudjo"], "given-names": ["LK", "BUS"], "article-title": ["10-Year changes in adiposity in Cameroon school-age children: Evidence for increasing central adiposity and higher adiposity levels in tallest-for-age children"], "source": ["J Obes"], "year": ["2021"], "month": ["Oct"], "day": ["15"], "fpage": ["2021"], "comment": ["6866911"]}, {"label": ["27"], "surname": ["Millar", "Perry", "Phillips"], "given-names": ["SR", "IJ", "CM"], "article-title": ["Surrogate measures of adiposity and cardiometabolic risk-Why the uncertainty? A Review of recent meta-analytic studies"], "source": ["J Diabetes Metab"], "year": ["2013"], "volume": ["S11"], "fpage": ["004"]}, {"label": ["33"], "surname": ["Pan", "Cole"], "given-names": ["H", "TJ"], "article-title": ["LMSgrowth, a Microsoft Excel add-in to access growth references based on the LMS method"], "year": ["2022"], "comment": ["Version 2.77"]}, {"label": ["37"], "surname": ["Lian", "Thon", "Hazmi", "Feng"], "given-names": ["CW", "CC", "H", "GKW"], "article-title": ["Rural-urban comparison in prevalence of hypertension and its factors among adolescents of Sarawak, Malaysia: A cross-sectional study"], "year": ["2020"], "month": ["Apr"], "day": ["4"], "volume": ["18"], "issue": ["1"], "fpage": ["26"], "lpage": ["38"]}, {"label": ["46"], "surname": ["Cheah", "Chang", "Hazmi", "Kho"], "given-names": ["WL", "CT", "H", "GWF"], "article-title": ["Using anthropometric indicator to identify hypertension in adolescents: a study in Sarawak, Malaysia"], "source": ["Int J Hypertens"], "year": ["2018"], "month": ["Aug"], "day": ["1"], "fpage": ["2018"], "comment": ["6736251"]}]
{ "acronym": [], "definition": [] }
47
CC BY
no
2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 17; 46:57
oa_package/9a/24/PMC10787134.tar.gz
PMC10787135
0
[ "<title>Introduction</title>", "<p>Antimicrobial resistance (AMR) is a growing problem worldwide due to improper antimicrobial prescription and use, particularly in low- and middle-income countries (LMIC) [##UREF##0##1##, ####REF##32331515##2##, ##REF##30149777##3##, ##REF##26199723##4####26199723##4##]. Children younger than 5 years account for up to 80% of those treated with antibiotics for upper respiratory tract infections (URTI), despite evidence showing that a significant number of children with URTI do not need antimicrobial agents [##REF##23133703##5##,##REF##31086618##6##]. In LMIC, there is still an assumption that antibiotics are effective for treating every child with URTI [##UREF##1##7##, ####REF##33761948##8##, ##REF##29388610##9####29388610##9##]. This could be due to poor understanding of the effects of antibiotics, and poor antimicrobial stewardship [##REF##31086618##6##,##UREF##2##10##,##REF##31200888##11##]. Parental knowledge of antibiotics and their use in the treatment of URTI and pharyngotonsillitis in children is precarious and undetermined in Tanzania, and data regarding this topic are scarce in both Tanzania and other LMIC.</p>", "<p>Infections of adenoids and tonsils, alone or as part of upper respiratory infection, are the main reason for children seeking medical attention in most LMICs. It is estimated that nearly all children receive a course of antibiotics, regardless of the clinical presentation or, if done, laboratory microbiological results [##UREF##0##1##,##REF##31086618##6##,##REF##36160279##12##]. The majority of caretakers and parents tend to present their children for medical attention due to sore throat and sleep apnoea [##REF##31815643##13##]. However, acute tonsillopharyngitis, being the most common cause of sore throat, is often viral, and a bacterial etiology is only responsible for a small percentage of cases [##UREF##3##14##,##REF##34859224##15##]. Of those bacterial pathogens, group A β-haemolytic streptococcus (GABHS) is a common cause of tonsillopharyngitis. In children, the incidence ranges between 15-30% [##UREF##3##14##,##UREF##4##16##,##UREF##5##17##]. Studies have shown that the rate of prescribing antibiotics for GABHS is unnecessarily high [##REF##31220878##18##, ####REF##19582348##19##, ##REF##26882912##20####26882912##20##].</p>", "<p>Although it is sometimes difficult to differentiate between viral and bacterial etiologies of tonsillopharyngitis, appropriate history taking together with physical and laboratory findings might be helpful [##REF##30149777##3##,##UREF##6##21##,##REF##29879264##22##]. Clinical presentation of adenotonsillitis amongst other respiratory diseases has provided a mechanism for antimicrobial misprescription in many parts of the developing world.</p>", "<p>Several guidelines, such as those by the UK´s National Institute for Health and Care Excellence (NICE), Dutch, German, and American Centers for Disease Control and Prevention (CDC), recommend against the unnecessary use of antimicrobial agents in pharyngotonsillitis as well as other upper respiratory tract infections [##REF##31220878##18##,##REF##26882912##20##,##UREF##7##23##, ####REF##16461445##24##, ##UREF##8##25####8##25##]. These guidelines recommend antibiotics only in cases of severe infection or strongly suspected GABHS infection [##REF##26882912##20##,##UREF##7##23##, ####REF##16461445##24##, ##UREF##8##25####8##25##]. However, this is contrary to the Tanzanian National Standards Treatment Guideline (STG) that advocates antibiotics regardless of clinical and laboratory arguments [##UREF##3##14##,##REF##16461445##24##, ####UREF##8##25##, ##UREF##9##26####9##26##]. It is estimated that there is a major underreporting of antibiotic misuse both from healthcare providers and consumers. Following the introduction of Accredited Drug Dispensing Outlets (ADDO) 20 years ago, Tanzanians have increased and easy access to antibiotics. ADDO are certified stores and have aided in increasing access to essential drugs in rural and peri-urban areas. Due to their profit making practice, poor adherence to policy, and lack of timely inspection and supervision ADDOs have been a major source of unprescribed antibiotics, and as such they have been contributing to AMR [##UREF##0##1##,##REF##26199723##4##,##REF##23133703##5##,##REF##33761948##8##,##REF##31220878##18##].</p>", "<p>A hospital-based survey was conducted to study the usage of antibiotics and parental knowledge on antibiotic use among children with recurrent chronic tonsillitis and/or tonsillar hypertrophy who are scheduled for (adeno) tonsillectomy ((A)TE) at a tertiary-level academic hospital.</p>" ]
[ "<title>Methods</title>", "<p><bold>Study design:</bold> a cross-sectional survey was conducted.</p>", "<p><bold>Setting:</bold> this study was conducted at a tertiary academic hospital (Kilimanjaro Christian Medical Centre (KCMC)) that serves approximately 6 million people in Northern Tanzania, between March and October 2022.</p>", "<p><bold>Participants:</bold> parents who brought their children to the Ear, Nose and Throat (ENT) outpatient clinic to see one of the authors (DK and/or JL) and who met the study inclusion criteria.</p>", "<p><bold>Variables:</bold> demographic data were collected from both the child and parents. The number of throat infections/URTI as well as the use of antibiotics during the 12 months prior to visiting the hospital were collected. The number of antibiotic courses taken, type of antibiotic(s), and how the antibiotic(s) were obtained was registered.</p>", "<p><bold>Data sources/measurement:</bold> a modified and well-structured questionnaire, which was adapted from a WHO questionnaire that was used in a multi-country awareness survey, was used to assess the parents´ knowledge of antibiotics and antibiotic use [##REF##31086618##6##,##UREF##10##27##]. Parents who gave written consent were asked to complete the printed study questionnaire with 20 questions (<ext-link xlink:href=\"https://www.panafrican-med-journal.com/content/article/46/59/full/annex1.pdf\" ext-link-type=\"uri\">Annex 1</ext-link>) [##UREF##11##28##].</p>", "<p><bold>Bias:</bold> our study was based on self-reported data, that may be subject to courtesy and recall biases.</p>", "<p><bold>Study size:</bold> a total of 173 children who attended our outpatient clinic were enrolled in this study of which, 157 were included after meeting inclusion criteria and consented to participate.</p>", "<p><bold>Inclusion and exclusion criteria:</bold> ages between 1 and 18 years scheduled for (A)TE due to (obstructive) sleep-disordered breathing as a result of adenotonsillar hypertrophy and/or recurrent chronic tonsillitis without known immunodeficiency syndrome(s) were included.</p>", "<p><bold>Quantitative variables:</bold> descriptive statistics were used to summarize the data. Continuous variables were expressed as means and standard deviations, while categorical variables were expressed as frequencies and percentages.</p>", "<p><bold>Statistical methods:</bold> statistical analyses were performed using R (version 4.2.0; R Foundation for Statistical Computing, Vienna, Austria).</p>", "<p><bold>Ethical consideration:</bold> ethical approval secured from hospital's ethical committee. This study was reported according to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement.</p>" ]
[ "<title>Results</title>", "<p><bold>Participants:</bold> one hundred and fifty-seven parents consented to participate in the survey.</p>", "<p><bold>Descriptive data:</bold>\n##TAB##0##Table 1## provides the demographic characteristics of the children in the study. More than half (54%) of the children were below the age of 5 years.</p>", "<p><bold>Outcome data:</bold> about 90% of children reported to have health insurance coverage, with the majority covered by the national insurance scheme National Health Insurance Fund (NHIF). About 40% of fathers and 30% of mothers reported to have attended college, and more than 50% of both parents were employed in the formal sector (i.e. employed by parastatal/private/government organizations) while 29% and 39% of fathers and mothers were in informal employments (i.e. self-employed as entrepreneur/driver/tailor/ crafts (wo) man/seller), respectively.</p>", "<p><bold>Main results:</bold> over a twelve-month period, children reported a median number of 4.00 (IQR 3.00 - 5.00) episodes of throat/upper respiratory tract infections prior to visiting the hospital. In total 88% of the children used at least one antibiotic course during that year. A total of 232 courses were used, resulting in a median number of 1.00 (IQR 1.00 - 2.00) antibiotics per child over the last twelve months (##TAB##1##Table 2##). About 43% of the children who participated were prescribed at least two doses of antibiotics before visiting an ENT practitioner, some were prescribed even broad-spectrum antibiotics. Amoxicillin/clavulanic acid was the most commonly used antibiotic, followed by azithromycin. Other antibiotics taken are described in ##TAB##2##Table 3##. Although most antibiotics were prescribed by a clinician (92%), about 5% were leftovers from a previous prescription(s), while others were either borrowed, shared from a friend/colleague/family member, or bought over the counter without proper prescription. Most parents (88%) ensured that their children finished the prescribed antibiotic. However, about 8% believed it was okay to obtain the same course of antibiotics without visiting the clinician if their child showed similar signs and symptoms in the future.</p>" ]
[ "<title>Discussion</title>", "<p>The aim of this study was to investigate the usage of antibiotics and the level of knowledge regarding antibiotic use among parents of children who were scheduled to undergo (A)TE. The use of antibiotics, including broad-spectrum antibiotics, was found to be high in our study group. The majority of study participants were children of employed parents or those under the voluntary national health insurance fund, which costs approximately 18 US dollars per year [##REF##35933731##29##,##UREF##12##30##]. These participants had access to medical and surgical services at this tertiary academic hospital at no additional cost. However, other medical centers do not accept these insurances for A(TE) purposes as they are underpaid by the insurer. In such cases, the insured has to either subside the difference or pay the whole amount [##UREF##12##30##, ####REF##22388500##31##, ##REF##30689879##32####30689879##32##]. Reports show that only 32% of Tanzanian people have health insurance [##REF##35933731##29##,##REF##22388500##31##,##UREF##13##33##,##UREF##14##34##]. Therefore, the group of children without insurance is underrepresented in this survey. Therefore, our findings should be interpreted with caution.</p>", "<p>Reports show that about 28.6% and 7.8% of the general population enroll in secondary school and tertiary education respectively [##UREF##15##35##]. In our current study, most parents had finished tertiary education. Most of those parents were aware that antibiotics must be prescribed by doctors and that the full course of medication should be finished. This knowledge may probably be attributed to their level of education, hence influencing their knowledge towards antibiotic use. Their relatively high level of education and employment also may explain the high percentage of health insurance [##REF##34859224##15##,##UREF##12##30##,##REF##27684066##36##]. Nevertheless, this study shows that antibiotics are still being over-prescribed in children in Northern Tanzania for conditions such as sore throat and/or URTI, including the prescription of even broader antimicrobials, such as third line cephalosporins [##REF##29388610##9##,##REF##30462700##37##].</p>", "<p>There are several reasons why improper practices regarding antibiotic prescription and use continue to occur. Among the reasons, are the insufficient evidence-based national treatment guidelines that advocates the use of antibiotic without thorough clinical and microbiological bases [##REF##29388610##9##,##UREF##9##26##,##UREF##16##38##]. Other East African countries guidelines advocate a more strict policy towards the use of antibiotics for URTI and pharyngotonsillitis [##UREF##17##39##, ####REF##34781920##40##, ##UREF##18##41##, ##REF##25646259##42####25646259##42##]. Reports show that even the availability of effective guidelines does not seem to be the single factor to significantly affects trends towards proper antibiotic prescription. That is why other factors should be considered in taking measures on antimicrobial stewardship [##REF##32959738##43##]. Many practitioners in Tanzania adhere well to STG that emphasizes on prescription of antibiotic in acute and chronic tonsilitis and URTI [##REF##23133703##5##,##REF##26882912##20##,##REF##30462700##37##]. We strongly believe that the STG is outdated and lacks clarity towards antibiotic prescription in the treatment of throat and/or URTI. Poor antimicrobial stewardship strategies which have enabled easy prescription, access, and dispensing of antibiotics, also contribute to misprescription. The use of leftover and sharing antibiotics is also practiced by some parents. This may be due to limited knowledge of antimicrobial use especially in rural areas, being attributed to poor health-seeking behavior among people with financial constraints and lower levels of education. Understanding the cost implication and hazards of AMR particularly in children, strict measures should be taken by the government of Tanzania through its regulatory authorities [##REF##26199723##4##,##REF##27684066##36##].</p>", "<p>It is worth noting that our study has limitations. Our study was based on self-reported data, that may be subject to courtesy and recall biases. Additionally, the survey was performed at a tertiary referral academic hospital that is affordable for mostly insured patients and only a few patients paying out of pocket, which may limit the generalizability of the findings to the rest of the Tanzanian population. Nonetheless, having a properly updated national treatment guideline will aid in antibiotic stewardship. Further education on proper antibiotic use will also greatly contribute to combating AMR.</p>", "<p><bold>Funding and role of the funding source:</bold> all costs are mainly covered by a grant from the Radboudumc Revolving Research Fund (R3Fund). Funder of the study had no role in trial design, data collection, data analysis, data interpretation, or writing of the report.</p>" ]
[ "<title>Conclusion</title>", "<p>The use of antibiotics, including broad-spectrum antibiotics, was found to be high in our study group. Although parents demonstrate a relatively good understanding of antibiotic usage, it is plausible to speculate that a higher prevalence of non-insured, unemployed, and less educated parents may lead to an increased incidence of misuse and misinterpretation of antibiotics. Considering the potential influence of socio-economic factors, educational programs should be directed towards this specific group to enhance understanding of appropriate antibiotic use, without leaving behind prescribing clinicians and dispensing personnel. Updating STG in Tanzania and adhering to evidence-based antibiotic prescribing principles offer a promising strategy for effectively managing URTI and tonsillitis, while simultaneously curbing unnecessary antibiotic prescriptions. A comprehensive approach involving healthcare professionals, policymakers, and the community is crucial in promoting judicious antibiotic use and safeguarding public health.</p>", "<title>\nWhat is known about this topic\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p>\n<italic>Upper respiratory tract infections (URTIs) primarily involve viral infections affecting the nose, throat, sinuses, and upper airways;</italic>\n</p></list-item><list-item><p>\n<italic>Antibiotics are frequently overprescribed for URTIs and pharyngotonsillitis, even when viral causes are likely;</italic>\n</p></list-item><list-item><p><italic>Antibiotic overuse/misuse can lead to antibiotic resistance, a global health concern; proper diagnosis of bacterial infections before prescribing antibiotics is crucial</italic>.</p></list-item></list>\n</p>", "<title>\nWhat this study adds\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p>\n<italic>High use of antibiotics, including broad-spectrum antibiotics, in URTI and tonsillitis treatment among children;</italic>\n</p></list-item><list-item><p>\n<italic>Parents demonstrate good antibiotic understanding, but higher misuse is associated with non-insured, unemployed, and less educated parents;</italic>\n</p></list-item><list-item><p><italic>Educational programs targeting socio-economically disadvantaged groups can improve appropriate antibiotic use; updating STG and adhering to evidence-based prescribing principles are promising strategies</italic>.</p></list-item></list>\n</p>" ]
[ "<title>Introduction</title>", "<p>Antimicrobial Resistance (AMR) is a growing concern globally, mostly being contributed by a limited understanding of antibiotic utilization as a result of inappropriate acquisition and prescription. Parental awareness is essential in optimizing their usage and preserving the effectiveness of these crucial medications. The current study investigates the usage and parental knowledge of antibiotics in children undergoing (adeno) tonsillectomy ((A)TE) in Northern Tanzania.</p>", "<title>Methods</title>", "<p>a cross-sectional survey was conducted among parents/caregivers of children who underwent (A)TE in Northern Tanzania. A modified and well-structured questionnaire, which was adapted from a World Health Organization (WHO) questionnaire and used to assess the parents´ knowledge of antibiotics and antibiotic use.</p>", "<title>Results</title>", "<p>the study included 157 participants. About 54% of the children under the age of 5 years. As of 88% of children had already received antibiotics prior to surgery, 92% of the used antibiotics were prescribed by a clinician, and 5% of parents to used leftovers antibiotics for their children. While 88% of the parents reported adhering to prescriptions, 8% of reported buying the same antibiotic (as prescribed before) without consulting a clinician again when their children are sick.</p>", "<title>Conclusion</title>", "<p>the use of antibiotics, including broad-spectrum antibiotics, was found to be high in our study group. Parents demonstrate a relatively good understanding of antibiotic usage. It is plausible to speculate that a higher prevalence of non-insured, unemployed, and less educated parents may lead to an increased incidence of misuse and misinterpretation of antibiotics.</p>" ]
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[ "<title>Competing interests</title>", "<p>The authors declare no competing interests.</p>", "<title>Authors' contributions</title>", "<p>Denis Robert Katundu, Maroeska Rovers, and Niels van Heerbeek designed the study and drafted the manuscript; Gerjon Hannink analysed the data; all authors verified the data and analysis; Denis Robert Katundu and Jesca Godlisten Lyimo performed inclusion, collected all study data, and follow-up of all patients, and participated in surgical procedures. All the authors read and approved the final version of this manuscript.</p>", "<title>Annex</title>", "<p><ext-link xlink:href=\"https://www.panafrican-med-journal.com/content/article/46/59/full/annex1.pdf\" ext-link-type=\"uri\"><bold>Annex 1</bold></ext-link>: questionnaire for study assessing antibiotic use in pediatric pre (a)te patients (PDF - 99 Kb)</p>" ]
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[ "<table-wrap position=\"float\" id=\"T1\"><label>Table 1</label><caption><p>demographic characteristics of study participants, recruited from the Ear Nose and Throat (ENT) Department of Kilimanjaro Christian Medical Centre (Tanzania), from March to October 2022 (N=157)</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Age (group)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">N (%)</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1-5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">85 (54.1)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">6-11</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">65 (41.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">12-18</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">7 (4.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Sex</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Female</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">79 (50.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Male</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">78 (49.7)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Weight (kg) (mean (SD))</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">20.18 (8.27)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Level of education</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Pre-school</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">122 (77.7)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Primary</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">31 (19.7)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Secondary</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">4 (2.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Health/medical insurance status</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Yes</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">141 (89.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">No</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">16 (10.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Marital status of parents (%)</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Married</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">141 (89.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Divorced</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2 (1.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Single parenthood</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">14 (8.9)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Highest level of education father</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">University</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">62 (39.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">College</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">49 (31.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Secondary</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">36 (22.9)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Primary</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">6 (3.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Pre-school</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2 (1.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">No-formal education</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2 (1.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Employment status, father</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Employed by parastatal/private/government organization</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">104 (66.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Self-employed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">46 (29.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Unemployed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">7 (4.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Highest level of education, mother</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">University</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">31 (19.7)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">College</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">63 (40.1)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Secondary</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">55 (35.0)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Primary</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">6 (3.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Pre-school</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">1 (0.6)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">No-formal education</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">1 (0.6)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Employment status mother</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Employed by parastatal/private/government</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">82 (52.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Self-employed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">62 (39.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Unemployed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">13 (8.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Scheduled surgery</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Tonsillectomy</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">20 (12.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Adenotonsillectomy</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">137 (87.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>BMI category by WHO (%)</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Underweight</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">49 (31.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Normal weight</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">43 (27.4)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Pre-obesity</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">37 (23.6)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Obesity class I</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">25 (15.9)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Obesity class II</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3 (1.9)</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T2\"><label>Table 2</label><caption><p>antibiotic prescribing practices and parental knowledge of antibiotic use among 157 children with throat and upper respiratory tract infections, recruited from the Ear Nose and Throat (ENT) Department of Kilimanjaro Christian Medical Centre (Tanzania), from March to October 2022 (N=157)</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Characteristics</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">n (%)</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Antibiotics prescribed?</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Yes</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">139 (88.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">No</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">18 (11.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Number of throat infections/URTI in the previous year per child</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">4 (2.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">4 (2.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17 (10.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">38 (24.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">28 (17.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">30 (19.1)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">19 (12.1)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">10 (6.4)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2 (1.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0 (0)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">10</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">1 (0.6)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">11</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">4 (2.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Number of antibiotic courses per child</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17 (10.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">71 (45.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">49 (31.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17 (10.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3 (1.9)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>How were antibiotics obtained?</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Prescribed by doctor/clinician</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">145 (92.4)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Used the previous “leftover”</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">8 (5.1)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Bought over the counter</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3 (1.9)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Borrowed/shared from friend/colleague/family member</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">1 (0.6)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>When to stop antibiotics?</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">When you finish the dose as directed</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">139 (88.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">When you feel better</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">18 (11.5)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Is it okay to use antibiotics given to someone else?</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">No</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">157 (96.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Yes</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">5 (3.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Is it okay to use the same antibiotic as before without consulting a clinician again?</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">  </td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">No</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">144 (91.7)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Yes</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">13 (8.3)</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T3\"><label>Table 3</label><caption><p>antibiotic use among 157 children with throat and upper respiratory tract infections during the 12 months preceding (adeno) tonsillectomy recruited from the Ear Nose and Throat (ENT) Department of Kilimanjaro Christian Medical Centre (Tanzania), from March to October 2022 (N=157)</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Antibiotic</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">n (%)</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Amoxicillin/clavulanic acid</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">86 (37.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Azithromycin</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">60 (26.4)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ampicillin</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">31 (.3)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ampicillin/cloxacillin</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">21 (9.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Amoxicillin/flucloxacillin</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17 (7.4)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Amoxicillin</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">14 (6.1)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Ceftriaxone</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">13 (5.7)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Penicillin V</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">4 (1.7)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cephalexin</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2 (0.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Penicillin</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2 (0.8)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Do not remember</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">5 (2.2)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Total</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">227 (100)</td></tr></tbody></table></table-wrap>" ]
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[ "<table-wrap-foot><fn id=\"TF1-1\"><p>BMI: body mass index; WHO: World Health Organization</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF2-1\"><p>URTI: upper respiratory tract infections; SD: standard deviation</p></fn></table-wrap-foot>", "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Denis Robert Katundu et al. Usage and parental knowledge of antibiotics in children undergoing (adeno) tonsillectomy in northern Tanzania. Pan African Medical Journal. 2023;46(59). 10.11604/pamj.2023.46.59.41190</p></fn></fn-group>" ]
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[{"label": ["1"], "surname": ["Do", "Vu", "Nguyen", "Punpuing", "Khan", "Gyapong"], "given-names": ["NTT", "HTL", "CTK", "S", "WA", "M"], "etal": ["et al"], "article-title": ["Community-based antibiotic access and use in six low-income and middle-income countries: a mixed-method approach"], "source": ["Lancet Glob Heal"], "year": ["2021"], "volume": ["9"], "issue": ["5"], "fpage": ["e610"], "lpage": ["e619"]}, {"label": ["7"], "surname": ["Bochkaeva"], "given-names": ["ZV"], "article-title": ["Antibiotic Knowledge, Attitude and Practice of Use Among Early Years Medical and Non-medical Students in Tanzania"], "source": ["Acta Medica"], "year": ["2020"], "volume": ["51"], "issue": ["3"], "fpage": ["1"], "lpage": ["8"]}, {"label": ["10"], "surname": ["Islam", "Charani", "Holmes"], "given-names": ["MS", "E", "AH"], "article-title": ["The AWaRe point prevalence study index: simplifying surveillance of antibiotic use in paediatrics"], "source": ["Lancet Glob Heal"], "year": ["2019"], "volume": ["7"], "issue": ["7"], "fpage": ["e811"], "lpage": ["e812"]}, {"label": ["14"], "surname": ["Alasmari", "Bamashmous", "Alshuwaykan", "Alahmari", "Alshahrani", "Alqarni"], "given-names": ["NS", "RO", "RM", "MA", "AA", "SA"], "etal": ["et al"], "article-title": ["Causes and Treatment of Tonsillitis"], "source": ["Egypt J Hosp Med"], "year": ["2017"], "volume": ["69"], "issue": ["8"], "fpage": ["2975"], "lpage": ["80"]}, {"label": ["16"], "surname": ["Mahakit", "Moungthong", "Sombulna", "Chantaratchada"], "given-names": ["P", "G", "T", "S"], "article-title": ["The correlation of micro-organisms between tonsillar crypt culture and tonsillar core culture in chronic tonsillitis"], "source": ["J Med Assoc Thai"], "year": ["2005"], "volume": ["88"], "issue": ["Suppl 3"], "fpage": ["S82"], "lpage": ["8"]}, {"label": ["17"], "surname": ["Angeli", "Fukuda", "Gallegos", "Ladue", "Miniti", "Suarez"], "given-names": ["G", "J", "GB", "L", "A", "S"], "etal": ["et al"], "article-title": ["Efficacy of lincomycin versus penicillin and clarithromycin in patients with acute pharyngitis/tonsillitis caused by group A beta-hemolytic streptococci and a clinical history of recurrence"], "source": ["Curr Ther Res-Clin Exp"], "year": ["1997"], "volume": ["58"], "issue": ["12"], "fpage": ["917"], "lpage": ["29"]}, {"label": ["21"], "surname": ["Hammouda", "Abdel-Khalek", "Awad", "Abdel-Aziz", "Fathy"], "given-names": ["M", "Z", "S", "M", "M"], "article-title": ["Chronic tonsillitis bacteriology in Egyptian children including antimicrobial susceptibility"], "source": ["Aust J Basic Appl Sci"], "year": ["2009"], "volume": ["3"], "fpage": ["1948"], "lpage": ["53"]}, {"label": ["23"], "collab": ["National Institute for Health and Care Excellence (NICE)"], "article-title": ["Sore throat (acute): antimicrobial prescribing"], "source": ["NICE Guidel"], "year": ["2018"], "fpage": ["1"], "lpage": ["18"]}, {"label": ["25"], "collab": ["Centers for Disease Control"], "article-title": ["Pediatric Outpatient Treatment Recommendations"], "source": ["Last Reviewed: February 1, 2017"], "comment": ["Accessed 16"], "sup": ["th"]}, {"label": ["26"], "collab": ["National Medicines and Therapeutic Committee"], "article-title": ["Standard Treatment Guidelines and National Essential Medicines List Tanzania Mainland"], "year": ["2001"], "volume": ["93"], "fpage": ["799"], "lpage": ["801"], "comment": ["Accessed on 24"], "sup": ["th"]}, {"label": ["27"], "collab": ["World Health Organization"], "article-title": ["World Health Report 1995: summary"], "year": ["2021"], "comment": ["Accessed on 24"], "sup": ["th"]}, {"label": ["28"], "surname": ["Thomas", "Bomar"], "given-names": ["M", "P"], "article-title": ["Upper Respiratory Tract Infection - StatPearls - NCBI Bookshelf"], "source": ["National Center for Biotechnology Information (NCBI)"], "year": ["2022"]}, {"label": ["30"], "surname": ["Chomi", "Mujinja", "Enemark", "Hansen", "Kiwara"], "given-names": ["EN", "PG", "U", "K", "AD"], "article-title": ["Health care seeking behaviour and utilisation in a multiple health insurance system: does insurance affiliation matter?"], "source": ["Int J Equity Heal"], "year": ["2014"], "month": ["Mar"], "day": ["19"], "fpage": ["13"], "lpage": ["25"]}, {"label": ["33"], "article-title": ["Medic East Africa 2019, Healthcare Market Insights: Tanzania"], "year": ["2019"], "comment": ["Accessed on 24"], "sup": ["th"]}, {"label": ["34"], "collab": ["The International Trade Administration. 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{ "acronym": [], "definition": [] }
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2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 17; 46:59
oa_package/2c/4d/PMC10787135.tar.gz
PMC10787136
0
[ "<title>Introduction</title>", "<p>Informal sector carpenters in Douala, Cameroon, face potential risks to their respiratory health due to their daily exposure to fine particles and wood dust in their work environment [##UREF##0##1##,##REF##24086847##2##]. These precarious working conditions expose them to chronic respiratory problems, including asthma and bronchitis, which can impair their quality of life and ability to perform their trade [##REF##18678700##3##,##REF##1549828##4##]. In this context, the use of respiratory protective masks, such as FFP3 masks, has become a common practice in the industry. The informal carpentry sector presents inherent risks to the respiratory health of artisans, who are exposed daily to fine particles and aerosols during tasks such as cutting, sanding, and machine use. These work conditions can lead to persistent respiratory issues, indicating reduced lung function and general well-being. To assess whether preventive use of respiratory masks could improve their respiratory health, participants underwent spirometry measurements before and after the intervention, while continuing their carpentry activities. This before-after study, conducted over a period of five months from December 2019 to May 2020, aims to demonstrate the importance of preventing respiratory problems in informal sector carpenters through regular use of FFP3 respiratory masks. The study holds crucial significance in highlighting the beneficial effect of regular FFP3 mask-wearing for the prevention of respiratory problems among informal sector carpenters. The findings can further raise awareness about the importance of respiratory safety in this occupational domain and encourage the widespread adoption of similar preventive measures. By demonstrating the substantial advantages of using respiratory protective masks, this study aspires to enhance the health and well-being of these artisans while underscoring the paramount significance of prevention in preserving their long-term respiratory health. The research's scientific background and rationale lie in the need to address the occupational hazards faced by informal sector carpenters and evaluate the potential benefits of using FFP3 masks to safeguard their respiratory health. The study seeks to contribute valuable insights into the effectiveness of preventive measures in improving the lung function of this specific workforce and provide evidence-based support for respiratory protection in the informal sector. Objectives: i) To assess the impact of regular FFP3 respiratory mask usage on spirometric parameters, including forced vital capacity (FVC), forced expiratory volume in one second (FEV1), Tiffeneau index, and peak expiratory flow (PEF), among informal sector carpenters in Douala; ii) to compare the spirometric measurements before and after the five-month intervention period to evaluate any significant changes in respiratory function. Hypotheses: i) H0 (Null hypothesis): there will be no significant difference in spirometric parameters before and after the intervention, indicating that FFP3 mask usage has no impact on the respiratory functions of informal sector carpenters. ii) H1 (Alternative hypothesis): there will be a significant improvement in spirometric parameters after the five-month FFP3 mask intervention, indicating that regular mask usage positively influences the respiratory health of informal sector carpenters.</p>" ]
[ "<title>Methods</title>", "<p><bold>Study design:</bold> the study design is a before-after study, also known as a pre-post intervention study. It involves assessing the respiratory functions of informal sector carpenters before and after a five-month intervention period during which they wear FFP3 respiratory masks while performing their professional activities. Spirometry measurements will be taken at two time points: before the intervention (baseline) and after the five-month intervention.</p>", "<p><bold>Setting:</bold> the study was conducted in Douala, Cameroon, which is a major city with a significant informal carpentry sector. Douala is known for its high levels of air pollution and occupational hazards related to woodworking activities. The locations of data collection include various carpentry workshops and sites within the city.</p>", "<p><bold>Relevant dates:</bold> the study was carried out over a period of five months, from December 2019 to May 2020. The recruitment of participants and baseline spirometry measurements took place in December 2019, before the intervention started. The intervention, which involved the regular usage of FFP3 masks, began in January 2020 and continued until May 2020. The follow-up spirometry measurements were conducted in May 2020, after the five-month intervention period was completed.</p>", "<title>Periods of recruitment, exposure, follow-up, and data collection</title>", "<p><bold>Recruitment:</bold> participants were recruited in December 2019. Informal sector carpenters in Douala who met the inclusion criteria were invited to participate in the study. The inclusion criteria involved being active carpenters, aged between 18 and 65 years, and having a minimum of one year of work experience in carpentry.</p>", "<p><bold>Exposure:</bold> the exposure period involved the five months from January 2020 to May 2020, during which the participants used FFP3 respiratory masks regularly while performing their carpentry tasks. They were provided with the masks and instructed to wear them throughout their working hours.</p>", "<p><bold>Follow-up:</bold> the follow-up period took place in May 2020, after the intervention ended. At this time, the participants underwent spirometry measurements again to evaluate any changes in their respiratory functions.</p>", "<p><bold>Data collection:</bold> data collection for spirometry measurements was conducted at two time points: baseline (December 2019) and follow-up (May 2020). The spirometry tests were performed by trained healthcare professionals following standardized procedures to ensure accurate and reliable results.</p>", "<p><bold>Participants:</bold> in this particular study, the participants are informal sector carpenters in Douala, Cameroon. The inclusion criteria involve being active carpenters, aged between 18 and 65 years, and having a minimum of one year of work experience in carpentry. The study does not involve comparing the outcomes of different groups; instead, it assesses changes in individual participants' respiratory functions before and after the five-month intervention period of using FFP3 respiratory masks. Each participant's baseline spirometry measurements were taken before the intervention (pre-intervention), and follow-up spirometry measurements were taken after the five-month intervention period (post-intervention). By comparing these measurements within each participant, the study evaluates the impact of regular FFP3 mask usage on their respiratory functions over time.</p>", "<p><bold>Outcomes:</bold> spirometric parameters: the primary outcomes of interest are spirometric parameters, including forced vital capacity (FVC), forced expiratory volume in one second (FEV1), Tiffeneau index (FEV1/FVC ratio), and peak expiratory flow (PEF). These measurements provide insights into the participants' respiratory function and lung health.</p>", "<p><bold>Exposure:</bold> filtering face pieces (FFP3) respiratory m usage: the main exposure of interest is the regular usage of FFP3 respiratory masks by the informal sector carpenters during their professional activities. The participants were provided with FFP3 masks and instructed to wear them throughout their working hours during the intervention period.</p>", "<p><bold>Predictors:</bold> duration of FFP3 mask usage: the duration of FFP3 mask usage, measured in months, is a predictor variable of interest. This variable represents the period of time the participants consistently wore the masks during their carpentry activities.</p>", "<title>Potential confounders</title>", "<p><bold>Age:</bold> age is a potential confounding factor as it can influence the participants' baseline respiratory functions and the effect of mask usage on lung health.</p>", "<p><bold>Smoking status:</bold> smoking status may affect the participants' respiratory health independently of the intervention and should be considered as a potential confounder.</p>", "<p><bold>Previous respiratory conditions:</bold> participants with pre-existing respiratory conditions may have different baseline respiratory functions, and their conditions could confound the impact of mask usage on lung health.</p>", "<p><bold>Occupational exposure to other respiratory hazards:</bold> the participants' exposure to other occupational respiratory hazards, apart from woodworking dust, may influence their respiratory health.</p>", "<title>Effect modifiers</title>", "<p><bold>Gender:</bold> gender may act as an effect modifier, as there might be differences in the impact of FFP3 mask usage on respiratory functions between males and females. Years of professional experience: The number of years the participants have worked as carpenters could potentially modify the effect of mask usage on their lung function.</p>", "<p><bold>Diagnostic criteria:</bold> there are no specific diagnostic criteria for the outcomes of spirometric parameters in this study. Spirometry is a standard procedure used to assess respiratory function, and the measurements are interpreted using reference values based on age, height, and gender to identify any abnormalities or changes in lung function. The pre-intervention spirometry measurements serve as baseline values for each participant, and the post-intervention measurements are used to compare changes in respiratory function over the study period. By clearly defining the outcomes, exposure, predictors, potential confounders, and effect modifiers, the study aims to conduct a comprehensive analysis to evaluate the impact of FFP3 mask usage on the respiratory functions of informal sector carpenters in Douala. This approach allows for accurate interpretation of the study's findings and minimizes bias to draw meaningful conclusions about the intervention's effectiveness. The data sources and measurement methods provided remain accurate for this before-after study design. The spirometric parameters, FFP3 mask usage, and potential confounders and effect modifiers were collected for each participant at two time points, ensuring internal comparability within the study population.</p>", "<title>Bias</title>", "<p>\n<bold>Efforts to address potential sources of bias</bold>\n</p>", "<p><bold>Selection bias:</bold> to minimize selection bias, a systematic approach was used to recruit participants from the informal carpentry sector in Douala. Inclusion criteria, such as being active carpenters aged between 18 and 65 years with at least one year of work experience, were defined to ensure the study population represents the target group accurately. Moreover, efforts were made to include a diverse sample of carpenters from different workshops and sites to enhance the generalizability of the findings.</p>", "<p><bold>Information bias:</bold> to reduce information bias, spirometry measurements and other data were collected by trained healthcare professionals following standardized protocols. This helps ensure accurate and consistent data collection, reducing the likelihood of measurement errors or misclassification of exposure and outcome variables. Participants were also given clear instructions on self-reporting FFP3 mask usage to minimize reporting bias.</p>", "<p><bold>Confounding:</bold> in our study, we did not specifically address potential confounding effects, as the spirometer used already accounted for relevant covariates such as age and gender in its measurements. Additionally, with a sample size of 37, dividing participants into groups for further analysis could introduce bias in the statistical analysis. Furthermore, our study design involved comparing individuals to themselves before and after using the FFP3 mask, which mitigates the impact of confounding factors on the observed spirometric outcomes.</p>", "<p><bold>Study size:</bold> the study size was determined to ensure adequate statistical power to detect meaningful changes in spirometric parameters before and after the intervention. A sample size calculation was performed based on factors such as expected effect size, variability in spirometric measurements, significance level, and desired statistical power [##UREF##1##5##,##REF##2161310##6##]. The calculated sample size required for the paired design was initially 31 subjects, but a target sample size of 310 subjects was chosen to account for potential “no-shows” and ensure sufficient participants for paired measurements. The larger sample size enhances the study's ability to detect significant differences and increases the generalizability of the findings to the target population, ensuring the study's statistical validity and meaningful conclusions.</p>", "<p><bold>Quantitative variables handling in the analyses:</bold> in our before-after study, the main quantitative variables of interest are the spirometric parameters, such as forced vital capacity (FVC), forced expiratory volume in one second (FEV1), Tiffeneau index (FEV1/FVC ratio), and peak expiratory flow (PEF). These quantitative variables were handled as follows in the analyses.</p>", "<p><bold>Pre-intervention and post-intervention measurements:</bold> for each participant, spirometry measurements were taken at two time points: before the intervention (baseline) and after the five-month intervention period (follow-up). The raw numerical values of FVC, FEV1, Tiffeneau index, and PEF were recorded for both time points.</p>", "<p><bold>Comparison within participants:</bold> as a before-after study, the primary analysis focused on comparing spirometric parameters within each participant. The change in spirometric measurements from baseline to follow-up was calculated for each participant. This was done by subtracting the baseline values from the follow-up values to obtain the change scores.</p>", "<p><bold>Statistical analysis:</bold> the change scores for each spirometric parameter were used as the outcome variables in the statistical analysis. Paired t-test was used to compare the mean changes in spirometric parameters before and after the intervention. This test allowed for the assessment of the significance of the changes and whether the regular usage of FFP3 masks had a significant impact on respiratory functions.</p>", "<p><bold>Subgroup analyses:</bold> we did not subdivide our sample for the reason above mentioned.</p>", "<p><bold>Adjusting for confounding variables:</bold> with this number, we didn´t adjust for potential confounding variables identified like age and smoking status as above mentioned. No regression models.</p>", "<p><bold>Groupings of quantitative variables:</bold> in our before-after study, there are no separate groups to compare; each participant serves as their own control. The primary analysis involves comparing the individual changes in spirometric parameters before and after the intervention for each participant. Therefore, there are no specific groupings chosen for quantitative variables in this study design. Instead, the focus is on assessing changes within each participant over time. By handling quantitative variables in this manner, the study can evaluate the impact of regular FFP3 mask usage on the respiratory functions of informal sector carpenters in Douala, providing valuable insights into the intervention's effectiveness in improving their lung health.</p>", "<p><bold>Statistical methods for before-after study:</bold> we used paired t-tests to compare the mean differences in the outcome variable (spirometric parameters) between the two time points within each participant. Paired t-tests are appropriate for normally distributed data and are commonly used in before-after studies to assess the intervention's impact.</p>", "<p><bold>Descriptive statistics:</bold> we used descriptive statistics to summarize the baseline characteristics of the study participants and the changes in the outcome variables after the intervention.</p>", "<p><bold>Confidence intervals:</bold> confidence intervals are calculated around the mean differences in the outcome variables before and after the intervention. These intervals provide a range within which the true population parameter is likely to lie with a certain level of confidence. In this before-after study design, the primary focus is on analyzing changes in outcomes within each participant, using paired t-tests to determine if the intervention had a significant effect on the respiratory functions of informal sector carpenters in Douala. Descriptive statistics, effect size calculations, and confidence intervals further provide valuable insights into the magnitude and significance of the observed changes.</p>", "<p><bold>Sampling approach:</bold> this study employed a combination of cluster sampling and convenience sampling to select participants from the city of Douala, which is divided into 6 administrative districts: Douala I, Douala II, Douala III, Douala IV, Douala V, and Douala VI. All six districts were selected for inclusion in the study.</p>", "<p><bold>Sample size calculation:</bold> the sample size was initially calculated to achieve a statistical power of 80%, a 95% confidence level, and a 5% significance level for a paired two-sample design. Based on the expected improvement in spirometric parameters (PEF, FVC, Tiffeneau index, and FEV1) from an average of 95% to 100% of their own expected values, the calculated sample size required for this study was 31 subjects based on the sample size formula for paired tests [##UREF##1##5##,##REF##2161310##6##]. However, to account for potential “no-shows” due to the COVID crisis and ensure sufficient participants for the paired measurements, a tenfold margin was applied, leading to a target sample size of 310 subjects.</p>", "<p><bold>Portable spirometer use:</bold> the use of the portable spirometer in this study is justified due to its comparable results to a spirometer used in a specialized pulmonary center when used correctly [##REF##26440676##7##]. It is crucial to ensure that the spirometer is operated accurately to obtain reliable and consistent data. The fact that both types of spirometers yield similar variations in results suggests that any discrepancies are more likely attributed to user error or subject cooperation rather than the method's reliability [##REF##7271065##8##,##REF##18364054##9##]. Moreover, the portable spirometer aligns better with the actual working conditions of the carpenters, as it is the device commonly used for regular health monitoring in a professional setting [##REF##24735032##10##]. This choice reflects the real-life scenario and provides a more realistic assessment of the respiratory health of the workers during their daily activities, contributing to the validity and practicality of the study's findings [##REF##24735032##10##].</p>", "<p><bold>Statistical analysis:</bold> the primary analysis involved calculating the mean differences in spirometric parameters before and after the intervention [##UREF##1##5##]. Paired t-tests were used to determine the statistical significance of the observed changes. The confidence interval was set at 95% to estimate the precision of the effect size. We used SPSS 26.0 for statistical processing.</p>", "<p><bold>Ethical considerations:</bold> our protocol was submitted to the National GP Ethics Committee, and the recruitment started after obtaining ethical clearance as well as oral consent from each participant. Strict confidentiality measures were implemented to protect their privacy.</p>" ]
[ "<title>Results</title>", "<p>The objective was to assess the impact of FFP3 respiratory mask usage on the respiratory functions of informal sector carpenters in Douala.</p>", "<p><bold>Key results:</bold> improved spirometric parameters: the study found significant improvements in spirometric parameters after the five-month intervention period. Forced vital capacity (FVC) increased from 89.6% to 93.7% (p &lt; 0.000), forced expiratory volume in one second (FEV1) increased from 88.1% to 95.0% (p &lt; 0.000), Tiffeneau index (FEV1/FVC ratio) increased from 82.4% to 84.9% (p &lt; 0.000), and Peak expiratory flow (PEF) increased from 6.7 l/s to 7.9 l/s (p&lt; 0.000).</p>", "<p><bold>Positive impact on lung function:</bold> the regular use of FFP3 masks had a positive effect on the respiratory health of informal sector carpenters. The improvements in spirometric parameters indicated enhanced lung function and reduced airway obstruction.</p>", "<p><bold>Significance of preventive measures:</bold> the study highlights the importance of preventive measures, such as using FFP3 masks, in safeguarding the respiratory well-being of carpenters exposed to occupational hazards. The key results demonstrate that the consistent use of FFP3 respiratory masks significantly enhanced the respiratory functions of informal sector carpenters in Douala. The findings underscore the importance of implementing preventive measures to protect the respiratory health of this specific workforce and highlight the potential benefits of respiratory protective equipment in occupational settings.</p>", "<p><bold>General characteristics of the population:</bold>\n##TAB##0##Table 1## outlines the general characteristics of the population, with the total sample size being n=310. The proportions and corresponding 95% confidence intervals (CIs) are presented for each parameter. In terms of marital status, the majority were married, accounting for 70.7% (95% CI: 69.1- 72.3). Singles represented 29.0% (95% CI: 27.4 - 30.6), while divorced individuals constituted a small percentage of 0.3% (95% CI: 0.28 - 0.32). Regarding educational levels, 0.6% (95% CI: 0.6 - 0.7) had no formal education, 28.3% (95% CI: 26.7 - 29.8) had primary education, 64.5% (95% CI: 62.7 - 66.3) had secondary education, and 6.5% (95% CI: 6.0 - 7.0) had attained a university level education. In terms of years of professional experience, 41.7% (95% CI: 39.8 - 43.6) had less than 10 years, 32.1% (95% CI: 30.4 - 34.8) had 10 to 19 years, and 26.2% (95% CI: 24.7 - 27.1) had 20 years or more of experience. Interestingly, more than a quarter of the carpenters reported having over 20 years of working experience. It's worth noting that only a very small percentage had achieved a university level of education (##TAB##0##Table 1##).</p>", "<p><bold>General anthropological parameters, medical history, and clinical symptoms of the study population:</bold> we adopted a conventional occupational medicine approach in our study population, involving a survey, measurement of anthropological parameters, and examination of medical histories. The average age of our population was 38 years, with a mean body mass index (BMI) at the threshold of overweight. The systolic and diastolic blood pressures were within normal ranges on average. We observed a small proportion of self-reported asthmatics, but a significant percentage of smokers. One-tenth of the population reported drug allergies, and half engaged in physical exercise. One-quarter of the population experienced coughing, and one-fifth had nasal discharge. About one in twenty had ocular irritations or dyspnea, and nearly one-tenth reported chest pain (##TAB##1##Table 2##).</p>", "<p><bold>Spirometric characteristics before the use of masks:</bold>\n##TAB##2##Table 3## provides an overview of spirometric characteristics observed before mask usage. The table includes the mean and standard deviation (sd) values for various parameters, namely FVC (% predicted), FVC (liters), FEV1 (% predicted), FEV1 (liters), FEV1/FVC (% predicted), MEF25-75 (liters per second), and PEF (liters per second). Additionally, the table presents the corresponding minimum and maximum values, as well as the 95% confidence intervals (CIs) for each parameter. The distribution of certain parameters based on percentage ranges is also displayed. For FVC (% predicted), 12.8% measured below 80%, while 87.2% measured equal to or above 80%. In terms of FEV1 (% predicted), 84.1% registered below 80%, and 15.9% measured equal to or above 80%. For FEV1/FVC (% predicted), 8.4% had values below 70%, and 91.6% had values equal to or above 70%. Moreover, the prevalence of obstructive syndrome was found to be 7.8%, and the prevalence of restrictive syndrome was 12.0%, with corresponding 95% CIs of 7.2 - 8.4 and 11.2 - 12.8, respectively (##TAB##3##Table 4##).</p>", "<p><bold>Parameters associated with spirometric impairment:</bold>\n##TAB##3##Table 4## examines other parameters linked with spirometric impairment. The table compares mean age and mean years of professional experience for specific subgroups based on FVC (% predicted), FEV1 (% predicted), and FEV1/FVC (% predicted). For each subgroup, the mean age is presented with its respective 95% confidence interval (CI) and the associated p-value. In the case of FVC (% predicted), individuals with FVC values below 80% had a mean age of 41.3 years (95% CI: 41.1 - 41.4), while those with FVC values equal to or above 80% had a mean age of 37.5 years (95% CI: 37.4 - 37.6), with a p-value of 0.046. Concerning mean years of professional experience, the respective values were 15.3 years (95% CI: 15.26 - 15.34) for FVC &lt; 80% and 13.4 years (95% CI: 13.36 - 13.44) for FVC &gt;= 80%, with a p-value of 0.218. Similarly, for FEV1 (% predicted), the mean age was 37.5 years (95% CI: 37.46 - 37.54) for FEV1 &lt; 80% and 40.6 years (95% CI: 40.56 - 40.64) for FEV1 &gt;= 80%, with a p-value of 0.057. The mean years of professional experience were 13.2 years (95% CI: 13.16 - 13.24) for FEV1 &lt; 80% and 16.0 years (95% CI: 15.96 - 16.04) for FEV1 &gt;= 80%, with a p-value of 0.051. Regarding FEV1/FVC (% predicted), the mean age for FEV1/FVC &lt; 70% was 46.6 years (95% CI: 46.56 - 46.64), while for FEV1/FVC &gt;= 70% it was 37.2 years (95% CI: 37.16 - 37.24), with a p-value of 0.000. The mean years of professional experience were 17.9 years (95% CI: 17.86 - 17.94) for FEV1/FVC &lt; 70% and 13.2 years (95% CI: 13.16 - 13.24) for FEV1/FVC &gt;= 70%, with a p-value of 0.015 (##TAB##3##Table 4##).</p>", "<p><bold>Comparative anthropological, clinical, and spirometric characteristics before and after mask usage:</bold>\n##TAB##4##Table 5## presents a comparison of anthropological, clinical, and spirometric characteristics before and after the usage of FFP3 masks. The table outlines the values before and after mask usage, along with the confidence interval (CI) of the difference and the associated p-value (significance level). For BMI, there was negligible change as the values before and after mask usage were very close (24.21 and 24.20 respectively), with a CI of -0.2 to +0.2, resulting in a p-value of 0.91 (NS) indicating no significant difference. In terms of blood pressure, SBP (mmHg) showed a decrease from 125.5 to 121.9 after mask usage, with a CI of 1.2 to 6.0 and a significant p-value of 0.005. Regarding DBP (mmHg), there was minimal change from 80.7 to 80.0 after mask usage, with a CI of -0.4 to +2.1 and a p-value of 0.2 (NS), suggesting no significant difference. Moving to spirometric parameters, significant improvements were observed after mask usage. FVC (% predicted) increased from 89.6 to 93.7, with a CI of -6.0 to -2.3 and a highly significant p-value of 0.000. FVC (liter) increased from 3.7 to 3.9, with a CI of -0.3 to -0.1 and a p-value of 0.000. Similarly, FEV1 (% predicted) increased from 88.1 to 95.0, with a CI of -9.1 to -4.7 and a p-value of 0.000. FEV1 (liter) increased from 3.1 to 3.3, with a CI of -0.3 to -0.2 and a p-value of 0.000. FEV1/FVC (% predicted) increased from 82.4 to 84.9, with a CI of -3.3 to -1.2 and a p-value of 0.000. FEV1/FVC increased from 0.82 to 0.85, with a CI of -0.03 to -0.02 and a p-value of 0.000. MEF25-75 (l/sec) increased from 3.3 to 3.6, with a CI of -0.8 to -0.5 and a p-value of 0.000. PEF (l/sec) increased from 6.7 to 7.9, with a CI of -1.7 to -0.2 and a p-value of 0.000 (##TAB##4##Table 5##).</p>" ]
[ "<title>Discussion</title>", "<p>The respiratory health of individuals working in the informal carpentry sector is often at risk due to prolonged exposure to wood dust and other airborne pollutants [##UREF##0##1##,##UREF##2##11##]. Such exposure has been linked to various respiratory issues, including asthma and other allergic conditions, which can significantly impact the quality of life for these workers. In light of these concerns, the present study aimed to investigate the potential benefits of using FFP3 respiratory protective masks among informal sector carpenters in Douala. This chapter discusses the impact of FFP3 mask usage on the respiratory functions of these carpenters, with a particular focus on Peak Expiratory Flow (PEF), Forced Vital Capacity (FVC) and Tiffeneau Index measurements. These parameters serve as valuable indicators of lung function. The results obtained from a five-month before-after study highlight the positive effects of FFP3 mask intervention, emphasizing the importance of adopting appropriate respiratory protective measures to safeguard the respiratory health of informal sector carpenters in occupational settings. Longitudinal spirometry studies contribute to our understanding of the natural progression and risk factors associated with various respiratory diseases [##REF##24315469##12##,##REF##21915065##13##].</p>", "<p><bold>Forced vital capacity:</bold> the results of our study revealed a significant improvement in forced vital capacity (FVC) among informal sector carpenters in Douala following regular use of FFP3 masks. This increase in FVC indicates enhanced air volume that the subjects can forcefully exhale after a maximal inhalation. Increased FVC suggests improved overall lung function and reduced airway obstruction. These observations are consistent with findings from other similar studies [##REF##18678700##3##,##REF##3201190##14##], reinforcing the idea that wearing respiratory protective masks can play a crucial role in preserving and enhancing the respiratory health of workers exposed to fine particles and harmful aerosols [##UREF##3##15##].</p>", "<p><bold>Forced expiratory volume in one second (FEV1):</bold> our study also demonstrated a significant improvement in forced expiratory volume in one second (FEV1) among carpenters after the intervention with FFP3 masks. Forced expiratory volume in one second is a key indicator of airway ability to expel air from the lungs during a forced expiration [##REF##18678700##3##,##REF##36549709##16##]. The increase in FEV1 suggests enhanced lung function and reduced bronchial obstruction. These results align with previous research that highlighted the positive impact of wearing respiratory protective masks on the FEV1 of workers exposed to respiratory health hazards in their professional environment [##REF##11584114##17##].</p>", "<p><bold>Tiffeneau index:</bold> the ratio of FEV1 to FVC, is another crucial parameter to assess the respiratory health of individuals. Our results showed a clear improvement in the Tiffeneau index among informal sector carpenters after using 10FFP3 masks. An increase in this index indicates reduced airway obstruction, suggesting an overall improved respiratory function in the subjects [##REF##11584114##17##,##UREF##4##18##]. Decreased value of Tiffeneau index is common in works exposed to respiratory hazards. These findings are consistent with previous studies, providing additional evidence that regular use of respiratory protective masks can help prevent and alleviate respiratory problems among workers exposed to high respiratory risk factors.</p>", "<p>Peak expiratory flow (PEF): peak expiratory flow (PEF) measures the maximum speed at which an individual can exhale air during a forced expiration. Our results demonstrated a significant improvement in PEF among carpenters following the intervention with FFP3 masks. An increase in PEF indicates improved airflow in the airways and suggests enhanced lung function [##REF##35139866##19##]. These results align with other studies that have also highlighted the positive effects of wearing respiratory protective masks on PEF in workers exposed to polluted occupational environments [##REF##35139866##19##]. In a study of Greek furniture workers, the authors found no difference when comparing office workers to exposed workers. They did not conduct a before-after study, but rather compared workers exposed to chemicals. Their sample size was lower in each of the compared groups [##REF##31619088##20##]. The improvement in PEF among carpenters underscores the importance of prevention of respiratory problems through the regular use of suitable respiratory protective masks[##REF##18678700##3##]. On the other hand, the greater the exposure to hazards, the worse the value of the PEF [##REF##24086847##2##,##UREF##4##18##,##REF##15852759##21##, ####REF##16749338##22##, ##REF##15683157##23####15683157##23##]. Overall, our study provides strong evidence that the regular use of FFP3 masks has a positive impact on the respiratory health of informal sector carpenters in Douala. The significant improvements in forced vital capacity (FVC), forced expiratory olume in one second (FEV1), Tiffeneau index, and peak expiratory flow (PEF) indicate enhanced lung function and reduced airway obstruction. These findings are consistent with previous research, highlighting the crucial role of respiratory protective masks in preserving and enhancing the respiratory well-being of workers exposed to fine particles and harmful aerosols [##UREF##5##24##]. Implementing preventive measures such as mask-wearing and in some instance playing some sport are essential to safeguard the respiratory health of workers in the informal sector and improve overall occupational health outcomes in similar settings [##REF##23914626##25##].</p>", "<p><bold>Generalizability:</bold> while the study's findings provide valuable insights into the impact of FFP3 mask usage on the respiratory functions of informal sector carpenters in Douala, it is crucial to exercise caution when extrapolating these results to other populations or settings. The external validity of the study depends on the context and relevance of the study population and intervention to the target population of interest. For more robust generalizability, replication of the study in diverse populations and settings is necessary.</p>", "<title>Limitation</title>", "<p><bold>Selection bias:</bold> the study's sample consisted of informal sector carpenters in Douala who voluntarily participated. This could introduce selection bias if those who chose to participate were more health-conscious or had better respiratory health than those who opted not to participate (healthy worker effect). As a result, the observed improvements in spirometric parameters might be overestimated if healthier individuals were more likely to be included in the study.</p>", "<p><bold>Compliance bias:</bold> the study relied on self-reported compliance with FFP3 mask usage. Participants may overestimate their adherence to wearing masks consistently, leading to compliance bias. If some participants were less diligent in using masks than reported, the actual impact of FFP3 masks on respiratory functions could be less pronounced than observed.</p>", "<p><bold>Generalizability:</bold> the study was conducted in a specific region (Douala, Cameroon) and among informal sector carpenters. Therefore, the generalizability of the findings to other occupational groups or regions with different working conditions may be limited.</p>", "<p><bold>Confounding factors:</bold> although the study attempted to control for potential confounders (e.g. age, smoking status) in the analysis, there may still be unmeasured or residual confounding that influences the observed results. Factors such as other occupational exposures or pre-existing respiratory conditions could potentially bias the findings.</p>", "<p><bold>Lack of control group:</bold> as a before-after study without a control group, there is no direct comparison to a group not using FFP3 masks. Without a control group, it is challenging to determine if the observed improvements are solely due to the intervention or if other factors could have contributed to the changes in spirometric parameters.</p>", "<p><bold>Duration of intervention:</bold> the five-month intervention period might not be sufficient to capture the long-term impact of FFP3 mask usage on respiratory health. Longer follow-up periods would provide a more comprehensive understanding of the sustained effects of the intervention.</p>", "<p><bold>Self-reported data:</bold> the study relied on self-reported data for certain variables, such as occupational exposure and previous respiratory conditions. Self-reported data may be subject to recall bias and may not be as accurate as data collected through objective measures.</p>", "<p><bold>Sample size:</bold> while efforts were made to achieve an adequate sample size, the study's final sample may still be relatively small, which could limit the precision of the estimated effects.</p>", "<p>Considering these limitations, it is essential to interpret the study's findings cautiously. While the results suggest a positive impact of FFP3 mask usage on respiratory functions in informal sector carpenters, the potential biases and uncertainties should be taken into account when drawing conclusions and considering the implications of the study. Further research with larger and more diverse samples, longer follow-up periods, and objective measurements of mask usage would help strengthen the evidence on the effectiveness of FFP3 masks in occupational settings.</p>", "<p><bold>Funding:</bold> the present study on the impact of FFP3 respiratory mask usage on the respiratory functions of informal sector carpenters in Douala was personally funded by the main researcher using personal funds. No external funding was received from any institution or other entity for this research. As the sole founder and main researcher, I personally financed the study, which ensures independence and eliminates any potential conflicts of interest related to funding sources.</p>" ]
[ "<title>Conclusion</title>", "<p>This before-after study conducted among informal sector carpenters in Douala over a five-month period provides compelling evidence for the importance of preventing respiratory problems through regular use of FFP3 respiratory masks. Significant improvements in spirometric parameters, including forced vital capacity (FVC), forced expiratory volume in one second (FEV1), Tiffeneau index, and peak expiratory flow (PEF), were observed among participants who wore the masks during their professional activities. These findings support the beneficial effects of respiratory protective masks on lung function and respiratory health in workers exposed to hazardous occupational environments. Implementing preventive measures, such as wearing FFP3 masks, is crucial to preserve the respiratory health of informal sector carpenters. Increased awareness of occupational risks and collaboration among stakeholders are essential in safeguarding the respiratory well-being of artisans. In conclusion, regular use of FFP3 masks is an effective preventive measure for respiratory problems among informal sector carpenters, reinforcing the need for safe work practices and promoting respiratory health in their profession. These findings contribute to the existing scientific knowledge and strengthen the argument for adopting safe work practices to protect the respiratory health of workers. It is crucial for regulatory authorities, and occupational health authorities to collaborate in promoting the prevention of respiratory problems and enhancing the quality of life for artisans exposed to respiratory hazards in their profession.</p>", "<title>\nWhat is known about this topic\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p>\n<italic>Negative impact of occupational risks on the respiratory health of informal sector workers;</italic>\n</p></list-item><list-item><p>\n<italic>Potential for improvement in spirometric parameters through preventive measures;</italic>\n</p></list-item><list-item><p><italic>Occupational health disparities in informal sector workers; existing literature has highlighted the disparities in occupational health protection and access to preventive measures among informal sector workers</italic>.</p></list-item></list>\n</p>", "<title>\nWhat this study adds\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p>\n<italic>Novel intervention assessment in an understudied population; this study represents a pioneering effort in evaluating the impact of FFP3 mask usage on the spirometric parameters of informal sector workers, specifically carpenters in Douala;</italic>\n</p></list-item><list-item><p>\n<italic>Evidence-based support for respiratory health interventions; with the absence of prior studies investigating the use of FFP3 masks on carpenters' respiratory health, this research provides evidence-based support for the adoption of preventive measures in the informal sector;</italic>\n</p></list-item><list-item><p><italic>Policy implications for respiratory protection in informal sectors: by demonstrating the positive impact of FFP3 mask usage on the respiratory functions of carpenters, this study adds weight to the argument for implementing policies that mandate the use of appropriate respiratory protective equipment in the informal sector</italic>.</p></list-item></list>\n</p>" ]
[ "<title>Introduction</title>", "<p>informal sector carpenters in Douala, Cameroon, face potential risks to their respiratory health due to daily exposure to fine particles and wood dust. The study aims to demonstrate the importance of preventing respiratory problems in this population through regular use of filtering face pieces (FFP3) respiratory masks.</p>", "<title>Methods</title>", "<p>the before-after study involved 37 carpenters who wore FFP3 masks during their professional activities for five months. Spirometry measurements were taken before and after the intervention to assess changes in respiratory function.</p>", "<title>Results</title>", "<p>significant improvements were observed in forced vital capacity (FVC) 89.6 % to 95.0 % (p&lt;0.000), forced expiratory volume in one second (FEV1) 88.1 % to 95.0 % (p&lt;0.000), Tiffeneau index 82.4 to 84.9 (p&lt;0.000), and peak expiratory flow (PEF) 6.7 l/s to 7.9 l/s (p&lt;0.000) after mask usage, indicating enhanced lung function.</p>", "<title>Conclusion</title>", "<p>the regular use of FFP3 masks had a positive impact on the respiratory health of informal sector carpenters in Douala, enhancing lung function and reducing airway obstruction. The study highlights the importance of preventive measures to safeguard the respiratory well-being of workers exposed to occupational hazards. Spell out Greek characters (i.e: alpha, beta).</p>" ]
[]
[ "<title>Competing interests</title>", "<p>The authors declare no competing interest.</p>", "<title>Authors' contributions</title>", "<p>Catherine Bouland, Jean Junior Eye Ngoa, Jules Nebo and Joseph Francis Nde Djiele made substantial contributions to the work and manuscript preparation; Catherine Bouland suggested the interventional study; Jean Junior Eye Ngoa, and Joseph Francis Nde Djiele critically reviewed the manuscript, providing valuable corrections and enhancing its overall writing style; Jean Junior Eye Ngoa and Jules Nebo played a crucial role in supervising the field survey teams, ensuring data collection was carried out effectively; additionally, Jean Junior Eye Ngoa completed the data encoding process and Jules Nebo hosted the research center; Joseph Francis Nde Djiele led the study's design, overseeing all aspects of data processing, including data cleaning and analysis. Furthermore, Joseph Francis Nde Djiele took the lead in writing the article and was responsible for its submission. All the authors have read and agreed to the final manuscript.</p>" ]
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[ "<table-wrap position=\"float\" id=\"T1\"><label>Table 1</label><caption><p>general characteristics of the population</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Parameter (n=310)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Proportion (%)</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">IC 95%</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Marital status</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Married</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">70.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">69.1 – 72.3</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Single</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">29.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">27.4-30.6</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Divorced</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.28-0.32</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Educational level</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">None</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.6 – 0.7</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Primary</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">28.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">26.7 – 29.8</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Secondary</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">64.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">62.7 – 66.3</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">University</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">6.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">6.0 – 7.0</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Years of professional experience</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Less than 10 years</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">41.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">39.8 – 43.6</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">10 to 19 years</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">32.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">30.4 – 34.8</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">20 years and above</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">26.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">24.7 – 27.1</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T2\"><label>Table 2</label><caption><p>anthropological parameters of the study population</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Anthropological parameters</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mean</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Sd</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Min</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Max</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">95% CI</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Age (years)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">38.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">11.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">18.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">63.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">36.8 – 39.2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Weight (Kg)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">75.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">11.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">50.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">130.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">74.5 – 77.1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Height (cm)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">171.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">8.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">146.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">200.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">170.4 – 172.2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">26.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">5.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">90.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">25.4 – 26.6</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">SBP (mmHg)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">127.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">11.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">100.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">180.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">126.5 – 128.9</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">DBP (mmHg)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">82.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">8.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">56.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">110.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">82.2 – 84.2</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T3\"><label>Table 3</label><caption><p>spirometric characteristics before mask usage</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Parameters</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mean</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">sd</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Min</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Max</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">95% CI</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FVC (% predicted)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">97.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">25.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">161.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">96.6 – 98.6</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FVC (liters)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">1.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">7.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.8 – 4.8</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1 (% predicted)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">95.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">30</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">153</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">94.9 – 96.9</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1 (liters)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">5.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.2 – 4.2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1/FVC (% predicted)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">82.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">8.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">44.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">100.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">81.1 – 83.1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">MEF25-75 (liters per second)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">1.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">7.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.4 – 3.6</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PEF (liters per second)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">7.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">1.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">14.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">7.4 - 7.7</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Parameters</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>Percentage (%)</bold>\n</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">\n<bold>95% CI</bold>\n</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FVC (% predicted)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt; 80%</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">12.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">11.9 – 13.7</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">≧ 80%</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">87.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">86.3 - 88.1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1 (% predicted)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt; 80%</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">84.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">83.1 - 85.1</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">≧80%</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">15.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">14.7 - 16.9</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1/FVC (% predicted)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">&lt; 70%</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">8.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">7.0- 8.9</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">≧ 70%</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">91.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">90.0 - 92.2</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Obstructive syndrome</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">7.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\">7.2 - 8.4</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Restrictive syndrome</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">12.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">11.2 - 12.8</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T4\"><label>Table 4</label><caption><p>other parameters associated with spirometric impairment</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Parameter</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mean age</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">95% CI</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">P</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Mean years of professional experience</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">95% CI</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">P</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FVC (% predicted) &lt; 80% ≧ 80%</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">41.3 37.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">41.1- 41.4 37.4-37.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.046</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">15.3 13.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">15.26-15.34 13.36-13.44</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.218</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1 (% predicted) &lt; 80% ≧ 80%</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">37.5 40.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">37.46- 37.54 40.56- 40.64</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.057</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">13.2 16.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">13.16 -13.24 15.96 - 16.04</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.051</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1/FVC (% predicted) &lt; 70% ≧ 70%</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">46.6 37.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">46.56- 46.64 37.16 -37.24</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.000</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17.9 13.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">17.86- 17.94 13.16 -13.24</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.015</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T5\"><label>Table 5</label><caption><p>comparative anthropological, clinical, and spirometric characteristics before and after mask usage</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Parameter</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Before FFP3 mask usage</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">After FFP3 mask usage</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">CI of the difference</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">P (Sig)</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">BMI</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">24.21</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">24.20</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 0.2 ± 0.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.91 (NS)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">SBP (mmHg)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">125.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">121.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">1.2 - 6.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.005 (sig)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">DBP (mmHg)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">80.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">80.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 0.4 ± 2.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.2 (NS)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FVC (% predicted)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">89.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">93.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 6.0 – - 2.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.000 (Sig)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FVC (litre)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 0.3 – - 0.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.000 (Sig)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1 (% predicted)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">88.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">95.0</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 9.1 – - 4.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.000 (Sig)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1 (litre)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.1</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 0.3 – - 0.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.000 (Sig)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1/FVC (% predicted)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">82.4</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">84.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 3.3 – - 1.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.000 (Sig)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">FEV1/FVC</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.82</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.85</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 0.03 – - 0.02</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.000 (Sig)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">MEF25-75 (l/sec)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.3</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">3.6</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 0.8 – - 0.5</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.000 (Sig)</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">PEF (l/sec)</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">6.7</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">7.9</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">- 1.7 – - 0.2</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">0.000 (Sig)</td></tr></tbody></table></table-wrap>" ]
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[ "<table-wrap-foot><fn id=\"TF1-1\"><p>More than a quarter of the carpenters had more than 20 years of working experience; only a very few had reached university level education</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF2-1\"><p>The examination of anthropological parameters, encompassing age, weight, height, body mass index (BMI), Systolic blood pressure (SBP), and diastolic blood pressure (DBP) within the study population, reveals that the average values are generally within normal ranges, indicating no significant abnormalities</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF3-1\"><p>the table provides an overview of spirometric characteristics before mask usage and offers insights into the distribution of these parameters within the studied population; less than a tenth of the carpenters exhibited an obstructive syndrome, while only 12% presented a restrictive syndrome; forced vital capacity (FVC); forced expiratory volume in one second (FEV1); pulsed electric fields (PEF); maximal expiratory flow (MEF)</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF4-1\"><p>The findings indicate that increased exposure to wood dust was associated with worse spirometry parameters; forced vital capacity (FVC); forced expiratory volume in one second (FEV1);</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"TF5-1\"><p>Overall, the results demonstrate improvements in spirometric parameters after the carpenters started using FFP3 masks; these improvements are particularly noticeable considering the matched nature of the data, as the carpenters were compared to themselves; forced expiratory volume in one second (FEV1); forced vital capacity (FVC); body mass index (BMI), Systolic blood pressure (SBP), and diastolic blood pressure (DBP); pulsed electric fields (PEF); maximal expiratory flow (MEF); filtering face pieces (FFP3)</p></fn></table-wrap-foot>", "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Catherine Bouland et al. Impact of filtering face pieces (FFP3) respiratory protective mask usage on the respiratory functions of informal sector carpenters in Douala: a five-month before-after study. Pan African Medical Journal. 2023;46(52). 10.11604/pamj.2023.46.52.41225</p></fn></fn-group>" ]
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[{"label": ["1"], "surname": ["Nde Djiele", "Wangata Shadi", "De"], "given-names": ["J", "J", "Brouwer"], "article-title": ["Formal and informal sector workers care in Cameroon: need for equitable protection approach based on rational assessment of risks and exposures through carpenters respiratory system assessment"], "source": ["Journal of Asthma and Bronchitis"], "year": ["2015"]}, {"label": ["5"], "surname": ["Gayatri"], "given-names": ["Vishwakarma"], "article-title": ["Sample size and power calculation"], "source": ["CBS Publishers and Distributors"], "year": ["2020"]}, {"label": ["11"], "surname": ["Surber", "Guberan", "Girard"], "given-names": ["R", "M", "JP"], "article-title": ["Allergies respiratoires aux poussi\u00e8res de bois: Cas cliniques et \u00e9tudes \u00e9pid\u00e9miologiques"], "source": ["Revue Fran\u00e7aise d\u00b4Allergologie et d\u00b4Immunologie Clinique"], "year": ["1977"], "month": ["Sep"], "day": ["1"], "volume": ["17"], "issue": ["4"], "fpage": ["193"], "lpage": ["8"]}, {"label": ["15"], "surname": ["Solanki", "Barot", "Chaudhari"], "given-names": ["V", "K", "P"], "article-title": ["Pulmonary Function Impairment among Stone Cutting Workers in North Gujarat"], "source": ["Int J Health Sci Res 10"], "year": ["2021"], "volume": ["11"], "fpage": ["39"], "lpage": ["46"]}, {"label": ["18"], "surname": ["Johncy", "Ajay", "Dhanyakumar", "Raj", "Samuel"], "given-names": ["SS", "KT", "G", "NP", "TV"], "article-title": ["Dust Exposure and Lung Function Impairment in Construction Workers"], "source": ["JPBS"], "year": ["2011"], "volume": ["24"], "issue": ["1"], "fpage": ["9"], "lpage": ["13"]}, {"label": ["24"], "surname": ["Shadab", "Agrawal", "Aslam", "Islam", "Ahmad"], "given-names": ["M", "DK", "M", "N", "Z"], "article-title": ["Occupational Health Hazards among Sewage Workers: Oxidative Stress and Deranged Lung Functions"], "source": ["J Clin Diagn Res"], "year": ["2014"], "month": ["Apr"], "volume": ["8"], "issue": ["4"], "fpage": ["BC11"], "lpage": ["2"]}]
{ "acronym": [], "definition": [] }
25
CC BY
no
2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 9; 46:52
oa_package/15/cd/PMC10787136.tar.gz
PMC10787137
0
[ "<title>Introduction</title>", "<p>Early detection of an ST-segment Elevation Myocardial Infarction (STEMI) is crucial, but there are rare cases where STEMI mimics can mislead to its diagnosis [##REF##18958255##1##]. The “spiked helmet sign” is an electrocardiogram marker associated with severe non-coronary causes [##REF##22134944##2##]. Littmann and colleagues first described this sign in 2011 [##REF##22134944##2##]. It manifested as a dome-shaped ST-segment elevation, where the upward shift occurs before the onset of the QRS complex [##REF##22134944##2##]. Reported cases observed this sign of intrathoracic diseases such as pneumothorax, intrabdominal surgical pathologies such as bowel perforations [##REF##32628916##3##], subarachnoid hemorrhage, sepsis, and severe metabolic disturbance [##REF##32568589##4##]. A delay in early and prompt management of these underlying causes can result in fatal outcomes. The spiked helmet sign was high-risk mortality in the case series (around 75%) [##REF##22134944##2##]. Despite its recognition, the exact underlying pathophysiology remains unclear [##REF##32568589##4##]. We report an original case of a 60-year-old patient admitted for erysipelas. During hospitalization, her electrocardiogram showed a spiked helmet sign.</p>" ]
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[ "<title>Discussion</title>", "<p>The spiked helmet sign is an electrocardiogram pattern, STEMI mimics that Littmann and colleagues first described in 2011 in a series of 8 patients with severe extracardiac pathologies; 6 of whom died within 10 days of the spiked helmet sign diagnosis [##REF##22134944##2##]. Therefore, it has been hypothesized as a marker of high-risk mortality [##REF##22134944##2##]. The spiked helmet sign is characterized by a dome-shaped ST-segment elevation preceded by an upward shift of the baseline preceding the onset of the QRS complex [##REF##22134944##2##], and is often associated with a prolonged QT interval and invisible p waves [##REF##34505073##5##] (##FIG##2##Figure 3##). While This electrocardiogram pattern was first described as occurring in the inferior leads DII, DIII, and AVF [##REF##22134944##2##], however, other cases reported antero-septal and lateral lead presentations [##REF##32838962##6##]. The spiked helmet sign was associated with a variety of severe pathologies including sepsis, gastro-intestinal perforation, hypoxemic pneumonia, viral myocarditis [##REF##32838962##6##], subarachnoid hemorrhage, and anoxic-ischemic axonal lesions [##REF##34505073##5##]. Cases of intrathoracic hyperpressure in patients on invasive ventilation or with pneumothorax [##REF##34505073##5##] are also reported, as well as concomitant severe ionic disorders such as hypomagnesemia [##UREF##0##7##]. This sign was also described in a patient with Takotsubo syndrome [##UREF##1##8##]. Notably coronary angiography in these patients often showed normal coronary arteries and markers of myocardial necrosis were negative.</p>", "<p>The underlying pathophysiology of the spiked helmet sign remains unknown. However, several hypotheses have been proposed. One suggests that this electrocardiogram pattern was an artifact due to synchronization between the diaphragmatic contractions and the ventricular systoles. This phenomenon has been observed through spirography [##REF##21353235##9##]. This synchronization was due to muscular hyperexcitability secondary to ionic disorders, and to direct mechanical stimulation of the diaphragm by the lower wall of the heart or by the phrenic nerve [##REF##22134944##2##]. Another hypothesis was based on the QT interval prolongation associated with very wide negative t waves. It suggests an adrenergic hyperstimulation in response to stressful situations like sepsis and subarachnoid hemorrhage [##REF##31048224##10##]. Lastly, some authors have proposed that it could be an electrocardiogram artifact secondary to epidermal distension, as seen in cases of intrathoracic or intra-abdominal hypertension [##REF##22134944##2##].</p>", "<p>On one hand, several explanations can be considered in our patient for the spiked helmet sign, firstly the presence of hypokalemia could support the hypothesis of QT interval prolongation, however, the “spiked helmet sign” persisted after the correction of the patient´s electrolyte disorders. Suggesting that hypokalemia alone cannot fully explain this electrocardiogram pattern. Secondly, the associated state of severe sepsis could support the hypothesis of adrenergic hyperstimulation, particularly given that the spiked helmet sign regressed after the control of the infection. On the other hand, several arguments did not support the ischemic origin of ST-segment elevation. Notably, the coronary lesions observed on angiography were not consistent with the extent of cardiac repolarization abnormalities observed on the electrocardiogram. Furthermore, the ST segment elevation persisted for 48 hours and then regressed without electrical sequelae of myocardial necrosis. Finally, there were no concomitant echocardiographic wall motion abnormalities on transthoracic echocardiography.</p>", "<p>First, the originality of our case consists in the diffuse character of the “spiked helmet sign” in almost all electrocardiogram leads, then despite the poor prognosis associated with this electrocardiogram entity the patient´s outcome was favorable.</p>" ]
[ "<title>Conclusion</title>", "<p>The value of the “spiked helmet sign” as a marker of high-risk mortality has yet to be established. A precise interpretation of the electrocardiogram particularly the baseline, is essential to accurately identify this STEMI mimic. The early recognition of the pattern helped in the early and intensive management of the patient´s sepsis and electrolyte disturbance and led to a favorable outcome.</p>" ]
[ "<p>Early diagnosis of the spiked helmet sign is challenging. This ST-elevation myocardial infarction mimic was first described in 2011 by Littmann and colleagues and was linked to severe non-coronary pathologies, with a high risk of mortality. We present a case of a 60-year-old female patient who developed severe erysipelas with sepsis associated with severe hypokalemia. She had a spiked helmet sign on her routine electrocardiogram at hospital admission. We performed a coronary angiogram that showed no culprit artery. She developed afterward an ischemic stroke. Through intensive management of the patient’s sepsis and electrolyte disturbance, she had a favorable outcome.</p>" ]
[ "<title>Patient and observation</title>", "<p><bold>Patient information:</bold> a 60-year-old female with a previous history of hypertension, who had discontinued her treatment, was initially admitted to a rural hospital's medical department to treat erysipelas in her right leg. The patient's medical history did not include any reports of chest pain.</p>", "<p><bold>Clinical findings:</bold> on physical examination, the patient had a Glasgow coma scale of 15, a temperature measuring 39.2°C, and her cardiorespiratory assessment revealed normal findings. She had an erysipelas in her right leg without any necrotic lesions.</p>", "<p><bold>Timeline of the current episode:</bold> the main steps from the patient´s admission to management are summarized in (##FIG##0##Figure 1##).</p>", "<p><bold>Diagnostic assessment:</bold> upon admission, a routine electrocardiogram revealed a diffuse ST-segment elevation and a prolonged QT interval [corrected QT (Bazett) = 516 milliseconds] (##FIG##1##Figure 2## and ##FIG##2##Figure 3##). Initially, we diagnosed a circumferential STEMI leading to the administration of a loading dose of antithrombotic therapy. The patient was subsequently transferred to our cardiac catheterization room for immediate coronary angiography and potential primary percutaneous coronary intervention. The invasive exploration showed a normal-sized left main coronary artery with mild calcification and no significant lesion. The left anterior descending coronary artery showed multiple staged intermediate lesions. A significant stenosis involved the ostial and proximal circumflex artery (##FIG##3##Figure 4##). However, we were unable to visualize the right coronary artery. Following coronary angiography, she presented a predominantly brachio-facial right hemiparesis, with ipsilateral central facial paralysis, associated with Broca's aphasia, and swallowing disorders. Cerebral and supra-aortic trunk computed tomography scans showed normal results, confirming a diagnosis of left superficial sylvian ischemic stroke. The patient was transferred to our cardiovascular intensive care unit and she remained clinically stable. The follow-up electrocardiograms showed the same aspect. A transthoracic echocardiogram performed did not reveal any abnormal findings. Initial blood tests revealed hypokalemia: 2.3 mmol/l, hypocalcemia: 2.02 mmol/l, active inflammatory signs C-reactive protein: 373 mg/L and leukocytosis, white blood cells: 20,900cells/mm<sup>3</sup>. Additionally, the complete blood count showed hypochromic microcytic anemia: 11.3 g/dl, with mean corpuscular volume: 76 femtoliters (fl) post-coronary angiography. The ultrasensitive troponin level was at 7700ng/l. Creatine-phosphokinase at 4400 IU/l, lactate dehydrogenase at 484 UI/l, and liver transaminases Aspartate Transaminase, and Alanine Transaminase respectively at 239 and 56 IU/l.</p>", "<p><bold>Diagnosis:</bold> the patient presented a STEMI mimic, the “Spiked helmet sign” concomitant with a right leg erysipelas, sepsis, and severe hypokalemia. This was followed by the occurrence of a left superficial sylvian ischemic stroke.</p>", "<p><bold>Therapeutic interventions:</bold> we initiated an anti-ischemic treatment in conjunction with appropriate antibiotic therapy and correction of electrolyte disorders.</p>", "<p><bold>Follow-up and outcome of interventions:</bold> within three days of initiating antibiotic therapy the patient became apyrexial and presented a regression of local signs of erysipelas. During the course of treatment, the ST-segment elevation persisted for 48 hours, followed by a gradual regression. After four days, we observed a complete resolution, and there were no lasting sequelae of myocardial necrosis.</p>", "<p><bold>Informed consent:</bold> we could not reach the patient after her discharge to obtain her consent. However, we did not describe any information enabling her identification, ensuring the protection of the patient´s privacy.</p>" ]
[ "<title>Competing interests</title>", "<p>The authors declare no competing interests.</p>", "<title>Authors' contributions</title>", "<p>Patient management: Salihou Fall, Sameh Ben Farhat, Ahmed Chelly, Ahmed Mohamed El Hedi, Saeb ben Saad, Mehdi Slim, Houssem Thabet, Sami Ouanness, Aymen Elhraiech, Rym Gribaa, Neffati Elyes. data collection: Salihou Fall, Ahmed Chelly, Hella Kaddour, Sameh Ben Farhat. Manuscript drafting: Salihou Fall, Sameh Ben Farhat, Saeb Ben Saad, Ahmed Chelly. All the authors have read and agreed to the final manuscript.</p>" ]
[ "<fig position=\"float\" id=\"F1\"><label>Figure 1</label><caption><p>timeline of the current episode from admission to management</p></caption></fig>", "<fig position=\"float\" id=\"F2\"><label>Figure 2</label><caption><p>patient’s 18-leads electrocardiogram: a regular sinus rhythm with an upward shift of the TP segment, with thin QRS complex and a dome-shaped ST-segment elevation in leads: DI DII DIII AVF V2 V3 V4 V5 V6 V7 V8 V9, and ST segment depression in AVR and V1; with a prolonged QT interval corrected QT (Bazett) at 516 milliseconds</p></caption></fig>", "<fig position=\"float\" id=\"F3\"><label>Figure 3</label><caption><p>enlargement of the electrocardiogram showing the resemblance of the electrocardiogram pattern to the German spiked helmet from the 19<sup>th</sup> century known as “Picklehauben”</p></caption></fig>", "<fig position=\"float\" id=\"F4\"><label>Figure 4</label><caption><p>patient’s coronary angiogram: normal-sized left main coronary artery with mild calcification and no significant lesion; the left anterior descending coronary artery presented multiple staged intermediate lesions and significant stenosis involving the ostial and proximal segments of the circumflex artery</p></caption></fig>" ]
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[ "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Salihou Fall et al. The spiked helmet sign in a patient with erysipelas: an alarming electrocardiogram sign (a case report). Pan African Medical Journal. 2023;46(58). 10.11604/pamj.2023.46.58.40438</p></fn></fn-group>" ]
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[{"label": ["7"], "surname": ["Raja Najar"], "given-names": ["R"], "article-title": ["Spiked Helmet Sign in Electrocardiogram, Sign of Hypomagnesaemia: A Case Study"], "source": ["IJSRP"], "year": ["2020"], "volume": ["10"], "issue": ["11"], "fpage": ["995"], "lpage": ["998"]}, {"label": ["8"], "surname": ["Samadov", "Gasimov", "Aliyev", "Isayev"], "given-names": ["F", "E", "F", "E"], "article-title": ["The \u00b4Spiked Helmet\u00b4 sign-A potential relationship to Takotsubo cardiomyopathy"], "source": ["Am J Emerg Med"], "year": ["2018"], "month": ["Feb"], "volume": ["36"], "issue": ["2"], "fpage": ["345.e5"], "lpage": ["345.e7"]}]
{ "acronym": [], "definition": [] }
10
CC BY
no
2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 17; 46:58
oa_package/7b/91/PMC10787137.tar.gz
PMC10787138
0
[ "<title>Introduction</title>", "<p>Le diverticule sous urétral est une pathologie rare. Son incidence dans la population féminine est estimée entre 0,6% et 6%. Il est exceptionnellement rapporté chez l´homme et l´enfant [##REF##31258943##1##]. Il s´agit d´une hernie de la muqueuse urétrale à travers les fibres musculaires lisses. Le sac herniaire communique avec la lumière urétrale par un collet et fait protrusion au niveau du septum inter urétro-vaginal [##REF##18094307##2##]. Son etiopathogénie est mal connue. Il peut être congénital ou acquis [##REF##34978545##3##]. A côté des formes asymptomatiques, la survenue de symptômes du bas appareil urinaire, surtout obstructif, est le principal mode de révélation [##REF##35931432##4##]. Le diagnostic est clinique [##REF##18094307##2##]. La cure chirurgicale du diverticule ou diverticulectomie est le traitement de référence [##REF##36427974##5##]. Le cadre scientifique de notre étude vise à comprendre l´incidence et les caractéristiques du diverticule sous urétral chez les femmes de notre population locale. Nous souhaitons identifier les facteurs de risque associés à sa survenue, évaluer les manifestations cliniques et étudier les options de prise en charge appropriées. Nos hypothèses préalables sont que l´incidence du diverticule sous urétral dans notre population féminine locale est similaire aux estimations internationales, certains facteurs comme l´âge ou les antécédents obstétricaux peuvent accroître le risque, les symptômes obstructifs du bas appareil urinaire seront plus fréquents chez les femmes atteintes de diverticules sous urétraux et la diverticulectomie améliorera les symptômes urinaires et réduira les récidives.</p>" ]
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[ "<title>Discussion</title>", "<p>Le diverticule sous-urétral de la femme est rare, son incidence varie de 0,6 à 6% [##REF##31258943##1##]. Il survient souvent entre 30 et 50 ans [##REF##18094307##2##], en concordance avec les données de notre série. L´ethiopathogénie est mal connue, avec une origine probablement multifactorielle. Une incidence accrue allant jusqu´à 6 % dans les populations afro-américaines suggère l´implication de facteurs génétiques héréditaires [##REF##34978545##3##]. L´existence de diverticules sous urétraux chez le nouveau-né sous-tend une origine congénitale. Le diverticule est alors soit isolé soit associé à un syndrome polymalformatif de l´appareil urogénital: reliquats mésonéphrotiques (canal de Gardner), anomalies d´accolement des bourgeons embryonnaires primitifs (union défectueuse des plis primaires), kystes de la paroi vaginale d´origine müllérienne ou dilatation congénitale des glandes para-urétrales [##REF##18094307##2##]. L´origine acquise reste la plus fréquente [##REF##35931432##4##]. Plusieurs facteurs de risque sont décrits: multiparité, traumatisme obstétrical (forceps) ou sténoses urétrales [##REF##34978545##3##]. Il existe une corrélation étroite entre infections urogénitales et diverticules sous urétraux, le diverticule étant parfois un abcès des glandes peri-urétrales fistulisées dans l´urètre [##REF##18094307##2##]. Plusieurs de ces facteurs sont largement retrouvés dans notre série. La symptomatologie est polymorphe. Il s´agit le plus souvent de la tétrade des “4D”: douleur urétrale violente (souvent en fin de miction), dribbling, dyspareunie et dysurie [##REF##35931432##4##], tous retrouvés dans notre série. L´issue de pus ou urine par l´urètre lors de rapports sexuels et les infections urinaires récidivantes sont également très évocateurs [##REF##34978545##3##]. L´association à incontinence urinaire d´effort est inconstamment retrouvée de 5 à 71% des cas [##REF##36427974##5##].</p>", "<p>L´urétrorragie et la rétention aiguë d´urine sont plus rarement retrouvées [##REF##35931432##4##]. Dix (10) à 20% des diverticules restent asymptomatiques. L´examen clinique sous valve pose le diagnostic [##REF##18094307##2##], révélant une tuméfaction molle des deux tiers distaux de l´urètre, postéro-latéral, rarement en antérieure [##REF##34978545##3##]. La présentation est hétérogène: diamètre variant de quelques millimètres à plusieurs centimètre, unique ou multiple, collet diverticulaire punctiforme ou centimètrique [##REF##31258943##1##]. L´écoulement de liquide par le méat urétral à la pression douce est caractéristique, rapporté par 45% de nos patientes, en concordance avec la littérature [##REF##35931432##4##]. Une induration diverticulaire oriente vers des calculs ou une tumeur intradiverticulaire [##REF##35931432##4##]. L´urétrocystographie rétrograde et mictionelle est un examen de référence. Sa sensibilité est de 85% [##REF##19001648##6##]. Il montre typiquement une opacité arrondie retro-urétrale et objective l´éventuel caractère rétentioniste du diverticule [##REF##19001648##6##]. Dans les cas douteux, l´urétrographie à pression positive avec sonde urétral à double ballon double la sensibilité de l´examen [##REF##10569571##7##]. La diverticulographie par ponction directe est décrite [##REF##34978545##3##]. L´échographie est plus sensible mais moins spécifique. Elle étudie au mieux les diverticules non opacifiés. Plusieurs techniques sont décrites: sus-pubienne, trans-périnéale et trans-labiale, endo-vaginale ou endo-uretrale. L´echographie dynamique du plancher pelvien supplante actuellement l´uretrocystographie [##REF##32448559##8##]. L´IRM pelvienne avec injection de Gadolinium a une sensibilité proche de 100%, même en cas de petit diverticules. Elle est réservée aux cas douteux [##REF##19001648##6##]. L´utilisation de la cystographie rétrograde et mictionelle avec acquisition par tomodensitométrie ou 16-MDCT <italic>(Multiple Detector Computed Tomography cystoscopy)</italic> est rapporté [##REF##15855122##9##].</p>", "<p>L´urètro-cystoscopie recherche le collet diverticulaire et une tumeur intra-diverticulaire. Jusqu´à 30% des cystoscopies échouent à retrouver l´orifice diverticulaire [##REF##36427974##5##]. Les diagnostics différentiels sont résumés dans le ##TAB##0##Tableau 1## [##REF##31258943##1##]. Les complications infectieuses du diverticule sont très fréquentes, jusqu´à 60%, allant des infections urinaires à répétitions aux suppurations intra-diverticulaires et fistulisation intra-vaginale [##REF##18094307##2##]. La présence de calculs intra-diverticulaires est variable, de 1,5 à 34% des cas [##REF##31258943##1##]. Un cas est retrouvé dans notre série. Moins de 100 cas de tumeur maligne intradiverticulaire sont rapportés: adénocarcinome (60%), carcinome urothéliaux (28%) et carcinome épidermoïde (12%). Quinze (15) cas d´adénome néphrogénique bénin sont retrouvés [##REF##36605685##10##]. Le traitement de référence est chirurgicale: la diverticulectomie transvaginale [##REF##35931432##4##]. L´application préalable d´œstrogène locaux semble améliorer la trophicité des tissus. La position genu-pectorale est la plus fréquente. Le décubitus ventral est possible [##REF##18094307##2##]. La distension préalable du diverticule facilite la dissection: sonde urétérale enroulée dans le diverticule, sonde de Fogarty ou injection de sillicone [##REF##35931432##4##]. La préservation du fascia péri-urétral améliore les résultats à long terme. L´interposition d´un lambeau graisseux des grandes lèvres entre le facia péri-urétrale et la paroi vaginale est possible en cas de tissus péri-urétraux de mauvaise qualité [##REF##32797263##11##]. L´utilisation de la laparoscopie robot assistée est décrite, sans supériorité vis-à-vis de la voie transvaginale classique [##REF##36129481##12##]. En cas d´impossibilité de la diverticulectomie, des techniques alternatives existent. Elles améliorent uniquement le drainage du diverticule. Il s´agira de faire communiquer le diverticule et le vagin <italic>(marsupialisation vaginal de Spence et Duckett)</italic> [##REF##36963669##13##] ou d´inciser endoscopiquement le collet diverticulaire (<italic>technique de Lapides</italic>) [##REF##33598843##14##].</p>", "<p>D´autres méthodes sont décrites: éléctrocoagulation trans-urétrale, comblement par compresses de cellulose , excision partielle du diverticule ou injection intradiverticulaire de Téflon [##REF##35931432##4##]. L´incidence des complications de la diverticulectomie varie de 8 à 20%. Elles sont résumées dans le ##TAB##1##Tableau 2## [##REF##31258943##1##].</p>", "<p>La diverticulectomie donne le meilleur taux de succès: 89 à 96% contre 78% pour la marsupialisation vaginale [##REF##35313135##15##]. Nous avons réalisé une diverticulectomie pour toutes nos patientes.</p>", "<p><bold>Limites:</bold> l´étude présente certaines limites: a) la population de 39 patientes limite la généralisation des résultats; b) la nature rétrospective induit de possible biais de sélection et des limitations dans la collecte et l´analyse des données; c) les données utilisées ont été extraites des dossiers médicaux, avec de possible lacunes dans les informations disponibles.</p>" ]
[ "<title>Conclusion</title>", "<p>Le diverticule sous-urétral de la femme est une affection rare chez les femmes d´âge moyen. Il est à l´origine de nombreuses manifestations urogénitales polymorphes. Il doit être systématiquement recherché en cas d´infections urinaires récidivantes. Le diagnostic est clinique, confirmé par l´échographie ou l´urétrographie rétrograde, voire l´IRM dans les cas difficiles. La diverticulectomie par voie vaginale est la technique de choix, offrant d´excellents résultats à long terme.</p>", "<title>\nEtat des connaissances sur le sujet\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p>\n<italic>Le diverticule sous-urétral est une affection rare chez les femmes d´âge moyen, pouvant entraîner divers symptômes urogénitaux;</italic>\n</p></list-item><list-item><p>\n<italic>Le diagnostic repose principalement sur l´examen clinique, complété par des examens d´imagerie tels que l´échographie ou l´urétrocystographie rétrograde;</italic>\n</p></list-item><list-item><p><italic>La diverticulectomie par voie vaginale est la méthode de traitement privilégiée, offrant de bons résultats à long terme</italic>.</p></list-item></list>\n</p>", "<title>\nContribution de notre étude à la connaissance\n</title>", "<p>\n<list list-type=\"bullet\"><list-item><p>\n<italic>Une meilleure compréhension des caractéristiques cliniques et épidémiologiques du diverticule sous-urétral chez les femmes, permettant d´affiner le diagnostic précoce et d´identifier les facteurs de risque spécifiques;</italic>\n</p></list-item><list-item><p>\n<italic>Une confirmation de l´importance du diagnostic clinique, mettant en évidence l´importance de l´examen physique et des antécédents médicaux pour orienter les investigations et les décisions thérapeutiques;</italic>\n</p></list-item><list-item><p><italic>Des données sur les résultats à long terme de la diverticulectomie transvaginale, soutenant son efficacité comme traitement de référence et fournissant des informations sur les taux de réussite, les complications postopératoires et la qualité de vie des patientes</italic>.</p></list-item></list>\n</p>" ]
[ "<p>Nous rapportons l´analyse rétrospective de 30 années d´expérience concernant 39 femmes atteintes de diverticule sous-urétral. L´âge moyen est de 37 ans (24-56 ans). La parité moyenne est de 2 (1-7). Soixante-cinq pourcent (65%) soient 25 des accouchements sont dystociques, avec utilisation de forceps dans 43% (17) des cas. Des antécédents infectieux urologiques ou gynécologiques sont présents chez toutes les patientes. Les symptômes révélateurs sont hétérogènes et sont principalement les infections urinaires récidivantes (26 cas), la pollakiurie (23 cas), l´écoulement urétral post-mictionnel (21 cas), la douleur vaginale (17 cas) et une sensation de boule vaginale (15 cas). Le bilan radiologique est variable: urographie intra-veineuse, urétrocystographie rétrograde et mictionnelle, échographie ou IRM. La diverticulectomie par voie transvaginale est le traitement pour toutes les patientes, sans complication per-opératoire rapportée. A 4 ans les résultats sont satisfaisants. Nous déplorons 4 récidives diverticulaires. Ces données fournissent des informations importantes sur les caractéristiques cliniques, les résultats diagnostiques et les résultats à long terme de la diverticulectomie transvaginale, permettant ainsi une meilleure prise en charge de cette affection rare.</p>", "<p>We here report a retrospective analysis of 30 years´ experience with 39 female patients suffering from suburethral diverticula. The average age of patients was 37 years of age (24-56 years). The average parity was 2 (1-7); 65% of deliveries were complicated by dystocia, with forceps used in 43% of cases. All patients had a history of urological or gynaecological infections. The revealing symptoms were heterogeneous but recurrent urinary tract infections (26 cases), pollakiuria (23 cases), post-micturition urethral discharge (21 cases), vaginal pain (17 cases) and a sensation of vaginal bulge (15 cases) were mostly reported. Radiological assessment were performed, including intravenous urography, retrograde and micturition urethrography, ultrasound, or MRI. Transvaginal diverticulectomy was the treatment of choice for all patients, with no reported intraoperative complications. At 4 years of follow up outcome was satisfactory. Four patients developed recurrence of diverticulitis. These data provide important information about clinical features, diagnostic results and long-term outcomes of transvaginal diverticulectomy, enabling better management of this rare condition.</p>" ]
[ "<title>Méthodes</title>", "<p><bold>Cadre de l´étude:</bold> il s´agit d´une étude rétrospective descriptive des dossiers médicaux de 39 patientes prises en charge dans notre service pour un diverticule de l´urètre entre janvier 1986 à décembre 2022. Il s´agit d´une étude exhaustive regroupant tous les cas pris en charge dans notre formation.</p>", "<p><bold>Type d´étude:</bold> il s´agit d´une série de cas.</p>", "<p><bold>Participants à l´étude:</bold> nous avons recruté nos patientes selon les critères d´inclusion suivants: patiente de sexe féminin, porteuse d´un diverticule sous urétral confirmé et prise en charge dans le service d´Urologie A du CHU Ibn Sina de Rabat durant la période 1986-2022.</p>", "<p><bold>Conception de l´étude:</bold> nous avons collecté et exploité les différentes données épidémiologiques, cliniques, anatomopathologiques et thérapeutiques de nos patientes à partir de leurs dossiers médicaux, puis nous avons comparé ces données à la littérature en utilisant les bases de recherches de PubMed, Scopus et Google Scholar.</p>", "<p><bold>Analyse des données:</bold> les données présentées dans le texte sont principalement observationnelles avec des informations descriptives. Il n´a pas été utilisé de méthodes statistiques formelles.</p>", "<p><bold>Consentement éclairé:</bold> nous avons obtenu le consentement éclairé de toutes les participantes que nous avons pu contacter, conformément aux normes éthiques et réglementaires. Le processus de consentement a été expliqué en détail, garantissant ainsi la participation volontaire et informée de chaque individu. La nature rétrospective de nos données a parfois rendu difficile la joignabilité de certains patients.</p>", "<title>Résultats</title>", "<p><bold>Caractéristique des patientes:</bold> l´âge moyen est de 37 ans (24-56 ans) quatre patientes sont nullipares. La parité moyenne est de 2(1-7). 65% des accouchements ont été au moins une fois dystocique et 43% ont nécessité l´utilisation de forceps. Dans tous les cas des antécédents infectieux urologique ou gynécologiques sont retrouvés. Dans 87% des cas il s´agit de cervicovaginite ou de salpingite. Le délai moyen de consultation est de 20 mois (2 mois-7 ans).</p>", "<p><bold>La symptomatologie révélatrice est hétérogène:</bold> infections urinaires récidivantes (26 cas), pollakiurie (23 cas), écoulement urétral post mictionnel (21 cas), douleur vaginal (17 cas), perception d´une voussure vaginale (15 cas), dysurie (10%), dyspareunies (2 cas), rétention aigue des urines (2 cas) et hématurie intermitante terminale (2 cas). Dans tous les cas l´examen clinique met en évidence une masse vaginale antérieure de consistance molle, avec émission d´urines purulentes à la pression (20 cas) ##FIG##0##Figure 1##. Le diverticule est majoritairement unique (34 cas).</p>", "<p><bold>L´imagerie:</bold> l´urographie intra-veineuse UIV (8 cas), montre dans 5 cas une opacité arrondie de la région sous-vésicale sur le cliché post-mictionel. Une urétrocystographie rétrograde et mictionelle UCRM (26 cas), montre à chaque fois une opacité arrondi siégeant derrière l´urètre (##FIG##1##Figure 2##). Une échographie transpérinéale (15 cas), montre à chaque fois une image arrondie hypoechogène, parfois hétérogène avec un sédiment urinaire (##FIG##2##Figure 3##). L ´imagerie par résonnance magnétique pelvienne IRM est faite dans un cas douteux (##FIG##3##Figure 4##). L´urétro-cystoscopie (18 cas) retrouve dans 15 cas le collet diverticulaire. L´examen cytobactériologique des urines est systématique. Il est positif dans 34 cas: <italic>Escherichia Coli</italic> (16 cas), <italic>Klebsiella</italic>.</p>", "<p><bold>Le traitement est chirurgical dans tous les cas:</bold> diverticulectomie par voie trans-vaginale, sous rachianesthesie, en position genu-pectorale, avec incision vaginale antérieure longitudinale (27 cas) ou en U inversé (12 cas) (##FIG##4##Figure 5##).</p>", "<p><bold>Complication et suivie:</bold> aucune complication per-opératoire n’est rapportée, l´ablation de la sonde urétrale est faite vers le 4<sup>e</sup> jour en moyenne. L´étude anatomopathologique du sac herniaire est systématique et à chaque fois sans particularité. Le suivi médian est de 4 ans, avec des résultats satisfaisant et disparitions des signes cliniques (35 cas). Dans 4 cas il y a une récidive du diverticule.</p>" ]
[ "<title>Conflits d´intérêts</title>", "<p>Les auteurs ne déclarent aucun conflit d´intérêts.</p>", "<title>Contributions des auteurs</title>", "<p>Salim Lachkar, Imad Boualaoui et Ibrahimi Ahmed: collecte des données, rédaction et participation à la prise en charge thérapeutique. Hachem El Sayegh, Yassine Nouini: relecture, correction et participation à la prise en charge. Tous les auteurs ont lu et approuvé la version finale du manuscrit</p>" ]
[ "<fig position=\"float\" id=\"F1\"><label>Figure 1</label><caption><p>vue pré-opératoire d´un diverticule sous urétral</p></caption></fig>", "<fig position=\"float\" id=\"F2\"><label>Figure 2</label><caption><p>résultat d´une uretrocytographie rétrograde pour diverticule</p></caption></fig>", "<fig position=\"float\" id=\"F3\"><label>Figure 3</label><caption><p>résultat d´une échographie pour diverticule UB-vessie, D-diverticule</p></caption></fig>", "<fig position=\"float\" id=\"F4\"><label>Figure 4</label><caption><p>résultat d´une IRM pour diverticule</p></caption></fig>", "<fig position=\"float\" id=\"F5\"><label>Figure 5</label><caption><p>vue post-opératoire immédiate</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"T1\"><label>Tableau 1</label><caption><p>diagnostiques différentiels des diverticules sous urétraux de la femme [##REF##31258943##1##]</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Abcès des glandes de Skène</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Néoplasie urètrale</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Hémangiome</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Kyste du canal de Gardner</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Néoplasie vaginale antérieure</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Varices urétrales</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Kyste mullérien</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Urétérocèle ectopique</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fibromyome péri urétral</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Endométriose urétrale</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Urétrocèle</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fibromyome vaginal</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Cystocèle vaginal</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Kyste de la paroi vaginale</td><td align=\"left\" rowspan=\"1\" colspan=\"1\"/><td align=\"left\" rowspan=\"1\" colspan=\"1\"/></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"T2\"><label>Tableau 2</label><caption><p>complications des diverticules sous urétraux de la femme [##REF##31258943##1##]</p></caption><table frame=\"border\" rules=\"all\"><thead valign=\"top\"><tr><th align=\"left\" rowspan=\"1\" colspan=\"1\">Complication</th><th align=\"left\" rowspan=\"1\" colspan=\"1\">Pourcentage (%)</th></tr></thead><tbody valign=\"top\"><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fistules urétro-vaginales</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">6</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Récidive du diverticule</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">15</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Incontinence urinaire</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">11</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Fistules cervico-vaginales</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">rare</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Sténoses urétréales</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">rare</td></tr><tr><td align=\"left\" rowspan=\"1\" colspan=\"1\">Infection urinaire</td><td align=\"left\" rowspan=\"1\" colspan=\"1\">2</td></tr></tbody></table></table-wrap>" ]
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[ "<fn-group><fn id=\"fn1\"><p><bold>Cite this article:</bold> Salim Lachkar et al. A propos de 39 cas de diverticules sous-urétraux de la femme: expérience monocentrique sur 30 ans. Pan African Medical Journal. 2023;46(51). 10.11604/pamj.2023.46.51.41246</p></fn></fn-group>" ]
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{ "acronym": [], "definition": [] }
15
CC BY
no
2024-01-14 23:41:58
Pan Afr Med J. 2023 Oct 6; 46:51
oa_package/74/4c/PMC10787138.tar.gz
PMC10787145
0
[ "<title>Introduction</title>", "<p>Spinal epidural abscess (SEA) is a rare diagnosis with an incidence of approximately 0.2-2 cases per 10,000 hospital admissions [##UREF##0##1##]. Risk factors for SEA include diabetes mellitus, trauma, intravenous catheters, drug use, and alcoholism [##REF##24937797##2##]. It is uncommon for these abscesses to occur in patients without comorbidities. The condition predominantly affects males and occurs in the middle age. The most common infectious agent is Staphylococcus aureus (S. aureus) (50-90%), followed by Gram-negative bacilli (10-17%) and Streptococcus (8-17%), while 5-10% of SEA are polymicrobial in origin [##REF##7969230##3##]. Hematogenous spread accounts for a significant proportion of SEA cases, and they are generally bacterial in etiology, with S. aureus being the most commonly cultured species [##REF##24937797##2##]. Typically, at the time of diagnosis, the abscess spans multiple segments, with the majority situated in the posterior region. Abscesses found anteriorly are generally associated with vertebral osteomyelitis [##REF##21185728##4##].</p>", "<p>SEA, a nosological entity, commonly affects the thoracic spine and presents with fever and paraparesis. Symptoms typically evolve over hours to days [##REF##11346365##5##]. However, the classic clinical triad of back pain, fever, and neurological deficit manifests in only a minority of patients [##REF##17093252##6##]. The development of SEA can be categorized into four stages: stage I involves back and/or neck pain at the level of the affected vertebral column, along with fever; stage II is characterized by radicular pain radiating from the affected part of the spinal cord; stage III exhibits neurological deficits such as hypoesthesia, motor weakness, and bowel or bladder dysfunction; and stage IV involves progression to paralysis [##REF##11346365##5##].</p>", "<p>MRI is the gold standard for diagnosing myelitis and spinal cord abscesses. There is hypointensity in T1 and hyperintensity in T2 due to edema, while the infected area shows slightly less hyperintensity in T2 than the edema in a non-vascular distribution [##REF##25952173##7##]. The preferred treatment approach typically involves prompt surgical debridement along with intravenous antibiotics [##UREF##1##8##].</p>" ]
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[ "<title>Discussion</title>", "<p>SEA is an infection of the epidural space characterized by the accumulation of granulation tissue and/or pus between the dura mater and the vertebral periosteum [##UREF##0##1##]. The assessment of risk factors, including advanced age, lack of insurance, liver disease, alcoholism, HIV, and renal insufficiency, has shown high sensitivity and negative predictive value [##REF##11346365##5##]. Diabetes mellitus, intravenous drug use, and local/systemic infections (e.g., respiratory, urinary, soft tissue) are the other significant sources of spinal epidural empyema. However, a substantial portion of cases has been found to have no identifiable cause of infection [##REF##24937797##2##].</p>", "<p>These abscesses occur within the epidural space between the dura mater and the vertebral periosteum, leading to direct mechanical compression or indirect ischemia of the spinal cord secondary to thrombophlebitis [##REF##17093252##6##]. The most frequently identified pathogen is methicillin-sensitive Staphylococcus aureus (40%), both in blood cultures and surgical samples, followed by methicillin-resistant Staphylococcus aureus (30%) [##REF##11346365##5##]. Bacteria enter the epidural space either through contiguous spread (in around one-third of the cases) or hematogenous dissemination (in approximately half of the cases), with the infection source remaining unidentified in the remaining cases. Abscesses are more likely to develop in larger epidural spaces containing fat, which is susceptible to infection [##REF##17093252##6##].</p>", "<p>A meta-analysis of thoracic SEA cases by Howie et al. reported that the most common symptoms are neurological deficits (68%), back pain (64%), and fever (24%); however, the triad of these findings is not specific to SEA [##UREF##2##9##]. Acute transverse myelitis is clinically characterized by symptoms and signs of acute or subacute development of neurological dysfunction in motor, sensory, and autonomic nerves, as well as spinal cord tracts [##REF##17982180##10##]. Our patient presented over a week with motor and sensory dysfunction, paraplegia, anesthesia, and autonomic dysfunction characterized by constipation and acute urinary retention.</p>", "<p>A well-established classification system outlines the progression of physical findings: in the initial stage, there is localized pain in the back at the level of the affected vertebral column; subsequently, there is radicular pain extending from the affected segment of the spinal cord, followed by impaired motor function, sensory loss, and dysfunction in bladder and bowel control. In the second stage, individuals with cervical or lumbar abscesses typically report neck pain radiating to the arms or lower back pain radiating to the legs. However, in the case of thoracic abscesses in the second stage, the presentation can be more elusive, manifesting as chest or abdominal pain [##REF##24007734##11##], leading to diagnostic delays. The various stages of clinical presentation of SEA are outlined in Table ##TAB##0##1##.</p>", "<p>In bacterial myelitis or spinal cord abscess, its origin has been postulated from a contiguous focus in the vertebral column, hematogenous spread, or secondary to bacteremia derived from a distant source. White blood cell count increases in only 13-60% of cases, that too moderately. While not crucial for diagnosis, white blood cell count can provide general guidance in assessing treatment response [##REF##19389491##12##]. Bacteremia resulting from or originating from SEAs is identified in around 60% of patients, particularly in those with S. aureus infection compared to other organisms [##REF##16523124##13##]. C-reactive protein (CRP) measurement can help differentiate serious causes of back pain, such as infections, cancer, and fractures, from mundane chronic back pain due to degenerative disease [##REF##18756836##14##]. Measurement of CRP levels in blood has been found to help accelerate the diagnosis for patients with spinal column infections, including SEAs [##REF##31021957##15##]. Lumbar puncture plays a less important role in diagnosing SEA and should not be routinely performed [##REF##21185728##4##]. Typically, Gram staining of cerebrospinal fluid (CSF) yields negative results, and cultures of CSF are positive in less than 25% of patients undergoing microbiological evaluation of their CSF [##REF##17093252##6##].</p>", "<p>Gadolinium-enhanced MRI and myelography followed by CT of the spine exhibit high sensitivity (exceeding 90%) in detecting SEAs. Nevertheless, MRI is the preferred imaging modality due to its less invasive nature, ability to outline both the longitudinal and para-spinal extension of the abscess (crucial for surgical planning), and the capacity to differentiate between infection and cancer based on the appearance and intensity of the image signal [##REF##17093252##6##]. In the case of SEA, two main patterns can be observed on MRI. One is the phlegmonous stage of the infection, which appears as a homogeneous enhancement of the affected area correlating with granulomatous tissue, microabscess, and pus accumulation. The other stage is the abscess surrounded by inflammatory tissue, showing a heterogeneous degree of peripheral enhancement with gadolinium. In this latter stage, the collection appears with a high T2 signal, with a generally low T1 signal surrounded by an enhancing rim. Diffusion-weighted imaging/apparent diffusion coefficient commonly demonstrates restricted diffusion of abscess content (Table ##TAB##1##2##) [##REF##8316663##16##].</p>", "<p>The treatment of choice is generally urgent surgical debridement combined with intravenous antibiotics [##REF##11346365##5##]. Once the pathogen is identified, antibiotic therapy can be adjusted according to the susceptibility profile, and a switch to oral formulations (if sensitivity permits) can be considered after at least three weeks of intravenous administration. The usual duration of antibiotic treatment is 4-12 weeks [##REF##9703173##17##]. In our case, targeted antimicrobial therapy was chosen based on the susceptibility profile. The preferred surgical procedure is laminectomy with debridement of infected tissues, as it represents a true neurosurgical emergency and should be performed as soon as possible [##REF##19013810##18##]. It has been demonstrated in adults that there is a risk of deterioration with non-surgical management, even in patients for whom treatment is initiated in the absence of neurological deficits [##REF##30797918##19##].</p>", "<p>Medical management is only considered in neurologically intact patients for whom surgery is contraindicated due to comorbidities or in cases with high-risk surgery (infection with holocord distribution or anterior location of the abscess), or patients already neurologically compromised (&gt;48 hours of paraplegia). If a conservative approach is chosen, monitoring of neurological status, inflammatory markers, and repeated MRI is mandatory [##REF##32291492##20##].</p>" ]
[ "<title>Conclusions</title>", "<p>SEA is a rare condition, and hence a high index of clinical suspicion is required to detect it. Although various risk factors have been associated with this condition, it can manifest in patients without any of these factors, as described in our case. Medical personnel must identify early clinical signs, such as pain and motor or sensory deficits, and accurately interpret the results of blood tests and imaging studies to promptly initiate medical treatment with antibiotics and surgical intervention. The surgical approach involves posterior laminectomies at the affected spinal segments and abscess drainage. The goal is to prevent the persistence of neurological deficits in potentially salvageable patients with appropriate diagnostic and therapeutic interventions.</p>" ]
[ "<p>A spinal epidural abscess (SEA) is a rare infection characterized by pus formation in the spinal epidural space, associated with various degrees of motor, sensory, or combined deficits. It is linked to several risk factors and predominantly impacts middle-aged men. This report discusses an atypical case of a patient without any predisposing factors who developed a cervicothoracic SEA associated with significant transverse myelitis. A targeted literature search was conducted on PubMed, Scopus, and SpringerLink, employing terms such as \"spinal epidural abscess, subdural empyema, and transverse myelitis.\" While there are numerous studies on this topic with a multidisciplinary approach, reports of cryptogenic SEA associated with the extensive involvement of cervical and thoracic spinal segments are rare. SEA is a very uncommon condition. Hence, a comprehensive understanding of its clinical presentation is crucial for adopting an appropriate diagnostic approach and delivering timely treatment.</p>" ]
[ "<title>Case presentation</title>", "<p>A 19-year-old male, with no significant personal medical history or reported intravenous drug use, presented in good overall health. One week before the admission, he had complained of right-sided chest pain and an unspecified fever. Subsequently, he had developed symptoms such as constipation, abdominal distension, urinary retention, paresthesias, and muscle weakness in the lower extremities, resulting in impaired mobility. Upon admission to the emergency room, he was afebrile, with a heart rate of 78 beats per minute, a respiratory rate of 18 breaths per minute, and a blood pressure of 110/70 mmHg. Neurological examination revealed areflexic paraparesis and anesthesia from the T4 dermatome. The echocardiogram showed no abnormalities in mobility, thrombi, vegetations, or shunts, with a left ventricular ejection fraction (LVEF) of 55%. Electromyography of all four limbs, including F-waves and somatosensory potentials, indicated a conduction block at the spinal level but produced inconclusive results. MRI revealed a posterior extra-axial spinal lesion extending from C6 to L1, appearing hypointense in T1 and hyperintense in T2. The lesion did not enhance with gadolinium but caused compression and displacement of the spinal cord towards the anterior region. Hyperintensity in T2 was observed, suggestive of myelitis from T4 to T11 (Figures ##FIG##0##1##-##FIG##3##4##).</p>", "<p>During the neurosurgical procedure, an abscess was observed in the left paravertebral muscle at the T4-T5 level, with a fistulous tract entering the epidural cavity between the laminae of T4 and T5 through a spontaneous dural hole (Figure ##FIG##4##5##). Purulent secretion was present in the intradural spinal canal with a thick, yellowish appearance. The surgical intervention involved resection of the spinous process and bilateral laminectomy of T5, bilateral hemilaminectomy of T6, and surgical cleaning with drainage of 12 cc of purulent fluid, which was sent for microbiological analysis. Culture and antibiogram of the purulent fluid from the spinal epidural space revealed methicillin-sensitive Staphylococcus aureus.</p>", "<p>The postoperative course was characterized by a progressive decrease in leukocytes; however, the patient continued to have paraparesis and anesthesia in the limbs without functional improvement. On the third day, a suprapubic cystostomy was performed due to acute urinary retention. The patient was discharged and, in the following days, developed spastic paralysis in both lower limbs, remaining under outpatient surveillance with follow-up by the Neurosurgery and Infectious Disease services. Two months later, he was readmitted due to grade III sacral ulcers requiring surgical debridement, and no functional improvement in the lower limbs was reported.</p>" ]
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[ "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG1\"><label>Figure 1</label><caption><title>Axial T2-weighted MRI</title><p>The image demonstrates an intradural-extradural spinal epidural abscess in the dorsal region at the T1 level, with ventral displacement of the spinal cord (arrows)</p><p>MRI: magnetic resonance imaging</p></caption></fig>", "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG2\"><label>Figure 2</label><caption><title>Sagittal T1-weighted MRI</title><p>The image demonstrates a poorly defined and heterogeneous cervicothoracic spinal epidural abscess at C6-T10. There are hypointense and isointense images in the posterior region of the spinal canal</p><p>MRI: magnetic resonance imaging</p></caption></fig>", "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG3\"><label>Figure 3</label><caption><title>Sagittal T2-weighted MRI</title><p>The image showing a cervicothoracic spinal epidural abscess at C6-T10 and hyperintense intramedullary images corresponding to areas of myelitis</p><p>MRI: magnetic resonance imaging</p></caption></fig>", "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG4\"><label>Figure 4</label><caption><title>Sagittal T1-weighted MRI with gadolinium administration</title><p>The image shows a heterogenous cervicothoracic spinal epidural abscess at C6-T10 with hypointense and isointense images in the posterior region of the spinal canal and hyperintense linear enhancement, predominantly in the ventral region (arrows)</p><p>MRI: magnetic resonance imaging</p></caption></fig>", "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG5\"><label>Figure 5</label><caption><title>Transsurgical photo</title><p>The image shows purulent material in the left paravertebral muscle at the T4-T5 level, with a fistulous tract entering the epidural space between the laminae of T4 and T5 through a spontaneous dural orifice</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"TAB1\"><label>Table 1</label><caption><title>Stages of clinical presentation of spinal epidural abscess</title></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Stages</td><td rowspan=\"1\" colspan=\"1\">Clinical manifestations</td></tr><tr><td rowspan=\"1\" colspan=\"1\">I</td><td rowspan=\"1\" colspan=\"1\">Non-specific pain and fever</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">II</td><td rowspan=\"1\" colspan=\"1\">Pain radiating to the segment of affected nerve roots</td></tr><tr><td rowspan=\"1\" colspan=\"1\">III</td><td rowspan=\"1\" colspan=\"1\">Motor deficit, sensory deficit, bladder, and bowel dysfunction</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">IV</td><td rowspan=\"1\" colspan=\"1\">Paralysis</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"TAB2\"><label>Table 2</label><caption><title>Stages of spinal epidural abscess on MRI</title><p>MRI: magnetic resonance imaging</p></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Stages</td><td rowspan=\"1\" colspan=\"1\">MRI characteristics</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Phlegmonous stage</td><td rowspan=\"1\" colspan=\"1\">T1 hypointense, T2 hyperintense, poorly defined lesion</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Inflammatory stage</td><td rowspan=\"1\" colspan=\"1\">T1 isointense or hyperintense, T2 hyperintense, poorly defined lesion</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Capsular stage</td><td rowspan=\"1\" colspan=\"1\">T1 hyperintense, T2 hyperintense, well-defined lesion</td></tr></tbody></table></table-wrap>" ]
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[ "<fn-group content-type=\"other\"><title>Author Contributions</title><fn fn-type=\"other\"><p><bold>Concept and design:</bold>  Harvey Misael Aguilar Mora</p><p><bold>Acquisition, analysis, or interpretation of data:</bold>  Harvey Misael Aguilar Mora, Julio Cesar Soto Barraza</p><p><bold>Drafting of the manuscript:</bold>  Harvey Misael Aguilar Mora</p><p><bold>Critical review of the manuscript for important intellectual content:</bold>  Harvey Misael Aguilar Mora, Julio Cesar Soto Barraza</p><p><bold>Supervision:</bold>  Harvey Misael Aguilar Mora, Julio Cesar Soto Barraza</p></fn></fn-group>", "<fn-group content-type=\"other\"><title>Human Ethics</title><fn fn-type=\"other\"><p>Consent was obtained or waived by all participants in this study</p></fn></fn-group>", "<fn-group content-type=\"competing-interests\"><fn fn-type=\"COI-statement\"><p>The authors have declared that no competing interests exist.</p></fn></fn-group>" ]
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[{"label": ["1"], "article-title": ["The indications and timing for operative management of spinal epidural abscess: literature review and treatment algorithm"], "source": ["Neurosurg Focus"], "person-group": ["\n"], "surname": ["Tuchman", "Pham", "Hsieh"], "given-names": ["A", "M", "PC"], "fpage": ["0"], "volume": ["37"], "year": ["2014"]}, {"label": ["8"], "article-title": ["Spinal epidural abscess: an analysis of 24 cases"], "source": ["Surg Neurol"], "person-group": ["\n"], "surname": ["Pereira", "Lynch"], "given-names": ["CE", "JC"], "fpage": ["0"], "lpage": ["9"], "volume": ["63"], "year": ["2005"]}, {"label": ["9"], "article-title": ["Vertebral osteomyelitis and spinal epidural abscess: an evidence-based review"], "source": ["J Spinal Disord Tech"], "person-group": ["\n"], "surname": ["Boody", "Jenkins", "Maslak", "Hsu", "Patel"], "given-names": ["BS", "TJ", "J", "WK", "AA"], "fpage": ["0"], "lpage": ["27"], "volume": ["28"], "year": ["2015"]}]
{ "acronym": [], "definition": [] }
20
CC BY
no
2024-01-14 23:41:58
Cureus.; 16(1):e52189
oa_package/bd/a0/PMC10787145.tar.gz
PMC10787148
0
[ "<title>Introduction</title>", "<p id=\"p0010\">With the growing burden of atrial fibrillation (AF), AF ablation volume is increasing.##REF##32716709##1## Catheter ablation for AF has emerged as the standard approach for invasive management of AF and is the most common catheter-directed ablation procedure performed today.##REF##28506916##2## However, catheter ablation carries a risk for serious complications, including cerebrovascular events. Minimizing the risk of these events through strict intraprocedural anticoagulation is essential.##REF##37225362##3##</p>", "<p id=\"p0015\">Catheter ablation requires transseptal puncture and placement of 1 or 2 sheaths in the left atrium that remain across the interatrial septum for the duration of the ablation procedure. This procedure exposes patients to periprocedural bleeding and cerebral thromboembolic events, necessitating optimal anticoagulation management before, during, and after the procedure.##REF##15145112##4##, ##REF##15946349##5##, ##REF##20516376##6##, ##REF##30354610##7## To reduce these risks, data support continuing uninterrupted anticoagulation with warfarin or non–vitamin K antagonist oral anticoagulants (NOACs), administration of intravenous unfractionated heparin prior to transseptal puncture, and maintenance of intraprocedural activated clotting times (ACT) &gt;300 seconds.##REF##18568395##8##, ##REF##24607716##9##, ##REF##30460702##10##, ##REF##27004444##11##</p>", "<p id=\"p0020\">Recent reports have demonstrated unpredictable and highly variable initial levels of anticoagulation using NOACs.##REF##28506916##2##<sup>,</sup>##REF##29532536##12##<sup>,</sup>##REF##28800176##13## At the University of Wisconsin, an academic center in Madison, Wisconsin, with 5 electrophysiologists performing catheter ablation during the study period, heparin dosing was inconsistent between providers and required frequent nurse-physician interactions for dosing decisions. Others have reported on similar knowledge gaps in catheter ablation for AF: (1) difficulty achieving therapeutic ACT, especially with NOACs; (2) practice variation among individual providers; and (3) lack of protocols to deliver intraprocedural anticoagulation.##REF##31230179##14##, ##REF##30390125##15##, ##REF##33476459##16##, ##REF##33749350##17## The protocols described in these prior reports did not include a computer-based clinical decision support system (CDSS).</p>", "<p id=\"p0025\">A well-designed computer-based CDSS can improve patient care.##REF##15767266##18## At the University of Wisconsin, a computer-based CDSS has significantly improved patient blood management.##REF##29717482##19## The electrophysiology team at the University of Wisconsin hypothesized that a similar system could improve intraprocedural anticoagulation. Here, we report the results of a retrospective evaluation of that computerized, adaptive, rule-based heparin dosing algorithm to determine the impact on time to goal ACT and the number of procedures with out-of-range ACTs during AF catheter ablation compared to historical controls.</p>" ]
[ "<title>Methods</title>", "<p id=\"p0030\">The Digital Intern® (Integrated Vital Medical Dynamics [iVMD], Madison, WI) is a collection of computer algorithms developed to support clinical care. A Digital Intern module contributed to guideline-based standardization of red blood cell transfusion at the University of Wisconsin.##REF##29717482##19## The Digital Intern procedure–based heparin dosing calculator supports heparin dosing for patients during interventional cardiology and neuroendovascular procedures. This algorithm was modified and evaluated to support heparin dosing during electrophysiologic procedures from January 2021 through October 2021 as part of a quality improvement effort. Here, we retrospectively evaluated the impact of this modified module, ie, “dosing algorithm,” on maintenance of guideline-based therapeutic ACT during AF ablation. This retrospective review received approval from the University of Wisconsin School of Medicine and Public Health Institutional Review Board (IRB 2022-0312).</p>", "<title>Dosing algorithm development</title>", "<p id=\"p0035\">The dosing algorithm is a rule-based, deterministic system that mathematically generates recommendations based on the distance of the current ACT to the goal ACT (##FIG##1##Figure 1##). These rules are represented in a mathematical function and use individual patient response to previous recommendations to refine future recommendations. An initial bolus is calculated based on patient weight, baseline ACT, oral anticoagulant, and goal ACT. At specified times, staff obtain additional ACTs. An infusion rate is calculated after obtaining the first postbolus ACT. Each bolus dose and infusion rate change paired with subsequent ACT measurements continues to refine the coefficients in the function that generates each recommendation to meet the needs of a specific patient. Those coefficients are adjusted until steady state is achieved. The specific mathematical function and coefficients that produce the adaptive adjustments are proprietary and not specified here. A Q-submission (a request for feedback and meetings prior to medical device submission) was prepared by iVMD and reviewed by the US Food &amp; Drug Administration (FDA). As the product provides recommendations supported by medical literature and reviewed by medical personnel, the FDA ruled that no regulation of this product was required.</p>", "<p id=\"p0040\">Modification of the product for the electrophysiology lab occurred in 3 phases (##FIG##1##Figure 1##). Based on prior institutional experience and published data, initial heparin bolus and infusion rates were selected (120 units/kg in patients anticoagulated on an uninterrupted direct oral anticoagulant, 75 units/kg in patients anticoagulated with warfarin, and 100 units/kg in patients on no anticoagulation).##REF##28506916##2##<sup>,</sup>##REF##27004444##11##<sup>,</sup>##REF##29579168##20## To initiate the protocol, an ACT was drawn (ACT+ assay; Hemochron Signature Elite ACT machine; Werfen, Bedford, MA). The standard bolus amount was adjusted downward proportionate to the proximity of the baseline ACT to the goal ACT. In all patients, the initial infusion was 18 units/kg for NOACs and 15 units/kg for warfarin.</p>", "<p id=\"p0045\">The second phase added an adjustment for variable responses to the initial heparin bolus. In the first month of development, approximately 50% of patients reached an ACT &gt;300 seconds after the initial bolus (<xref rid=\"appsec1\" ref-type=\"sec\">Supplemental Table 1</xref>). This observation led to the addition of an adaptive module, which modified subsequent boluses and the heparin infusion rate, scaling up subsequent recommendations if the first ACT post bolus was less than goal.</p>", "<p id=\"p0050\">In the third phase, infusion rates were increased based on the final rates observed (<xref rid=\"appsec1\" ref-type=\"sec\">Supplemental Table 2</xref>), and the bolus amount for dabigatran was decreased. Dabigatran data were limited, but the postbolus ACT was consistently &gt;400 seconds using a bolus amount of 120 units/kg. Final baseline bolus and infusion rates were as follows: apixaban, bolus = 120 units/kg, infusion 27 units/kg; rivaroxaban, bolus = 120 units/kg, infusion 25 units/kg; dabigatran, bolus 90 units/kg, infusion 18 units/kg; warfarin, bolus 75 units/kg, infusion 24 units/kg; no anticoagulation, bolus = 120 units/kg, infusion 24 units/kg.</p>", "<title>Catheter ablation and intraprocedural anticoagulation management</title>", "<p id=\"p0055\">Catheter ablation was performed using standard techniques.##REF##28506916##2## Patients presented in the fasted state and were placed under general anesthesia. Anticoagulation was uninterrupted. Ablations were completed with 1 or 2 transseptal sheaths with heparin infusions flowing through those sheaths. Bolus heparin was given by anesthesia (1000 units/mL concentration), first administered following venous sheath insertion, and the heparin infusion was initiated after the first post-bolus ACT, prior to transseptal puncture.</p>", "<p id=\"p0060\">Nurses interacted with the dosing algorithm through a web-based application programming interface accessed through the electronic medical record (EMR) (##FIG##2##Figure 2##). Inputs included anticoagulant, goal ACT (300–350 s for all left atrial ablations), hours since last dose of medication, sex, weight, creatinine, AST, ALT, total bilirubin, and a baseline ACT. No patient identifiers are entered into the interface. The dosing algorithm calculations are performed on an Amazon Web Services instance managed by iVMD. As shown in ##FIG##2##Figure 2##, the dosing algorithm recommendations are then returned to the staff through the same interface. Staff input the bolus and infusion rates chosen and resulting ACTs. Nursing staff drew ACTs every 10–15 minutes initially based on suggestions from the dosing algorithm. If 3 consecutive ACTs were stable at goal ACT, duration was extended to 30 minutes. Importantly, nurses provided oversight of the ACTs. The ACT+ coefficient of variation is reported at ≤10%.##UREF##0##21## If any ACT seemed inaccurate, it was redrawn for confirmation.</p>", "<title>Study design</title>", "<p id=\"p0065\">Outcomes related to intraprocedural heparin dosing in 50 consecutive historical controls (September 2020 through December 2020) were compared to outcomes in 139 cases performed using the dosing algorithm (October 2021 through February 2022). Primary outcomes included time to ACT &gt;300 seconds, number of patients with any ACT &gt;400 seconds, and number of patients with any ACT &lt;300 seconds while operating in the left atrium. Nurses using the algorithm completed the 100-point System Usability Scale (SUS) assessment and provided qualitative assessments. The SUS provides a widely used, “quick and dirty” tool for measuring reliability of hardware, software, mobile devices, websites, and applications.##UREF##1##22## For dosing algorithm cases, predictors of the total heparin bolus amount required to achieve an ACT &gt;300 seconds and the final heparin infusion rate were modeled.</p>", "<title>Data collection</title>", "<p id=\"p0070\">Data entered into the dosing algorithm and recommendations were stored in an Amazon Web Services database accessible by iVMD and available to the University of Wisconsin team (no patient identifiers present in these data). All ACT readings, bolus amounts, and infusions were also stored in the University of Wisconsin EMR as part of the clinical record. Under IRB approval, EMR data were accessed for patients included in the study and datasets were developed through chart review by the University of Wisconsin team (M.M.). Deidentified datasets developed through chart review were used for analysis (F.O.) and are available for review upon request. Only cardiology staff from the University of Wisconsin had access to both datasets and the outcomes.</p>", "<title>Statistical analysis</title>", "<p id=\"p0075\">We used descriptive analysis to summarize the study data, including frequencies and counts for categorical data and mean and standard deviation for continuous demographics and outcomes. Categorical variables were compared using χ<sup>2</sup> tests and Fisher exact tests. We checked for skewness and normality in continuous variables using histogram plots and Bartlett’s tests. We used a Student <italic>t</italic> test for all numerical comparisons, as all data were found to be normally distributed. The outcomes shown in ##FIG##3##Figure 3## and <xref rid=\"appsec1\" ref-type=\"sec\">Supplemental Table 3</xref> were analyzed using linear and logistic regression models to obtain coefficients and odds ratios.</p>", "<p id=\"p0080\">To find predictors of heparin bolus amount to achieve ACT &gt;300 seconds and final heparin infusion rate, we used a generalized linear model to report beta coefficients and 95% confidence intervals. We first conducted a univariate analysis to determine univariate significance and then we included significant predictors from the univariate analysis into a multivariate analysis, adjusting for each factor. Candidate variables included in the univariate analysis were selected based on factors that may influence NOAC dosing (age, weight, renal function, and liver function) and other commonly available variables that may be relevant (baseline ACT, platelets, sex, and body mass index [BMI]). We assessed for multicollinearity between the independent factors using a variance inflation factor. All variables that had a variance inflation factor of 10 or greater were excluded from the adjusted model. Since BMI and weight were directly related, we included only the weight variable to avoid multicollinear estimates. All <italic>P</italic> values that were less than or equal to .05 were considered significant. We conducted our analysis using SAS 9.4 (SAS Institute Inc 2013. SAS/ACCESS® 9.4 Interface to ADABAS: Reference. Cary, NC: SAS Institute Inc).</p>" ]
[ "<title>Results</title>", "<title>Clinical characteristics</title>", "<p id=\"p0085\">##TAB##0##Table 1## includes the characteristics of the 50 historical controls and 139 patients with intraprocedural heparin dosing performed using the dosing. All patients were on uninterrupted thromboembolic prophylaxis at the time of the procedure. There were no significant differences between the groups. The total heparin bolus amount (mean) used per patient was also very similar between historical controls and dosing algorithm cases.</p>", "<title>Dosing algorithm compared to historical controls</title>", "<p id=\"p0090\">Results comparing dosing algorithm performance to historical controls are shown in ##FIG##3##Figure 3## and <xref rid=\"appsec1\" ref-type=\"sec\">Supplemental Table 3</xref>. Using the dosing algorithm, the time to reach goal ACT dropped from 33.3 ± 23.6 minutes to 17.6 ± 11.1 minutes, a statistically significantly change (beta coefficient for linear regression -15.8, confidence interval [CI]: -20.8 to -10.8, <italic>P</italic> &lt; .001). There were also statistically significant reductions in patients experiencing ACT &lt;300 seconds while operating in the left atrium (odds ratio [OR] 0.20, CI: 010–0.39, <italic>P</italic> &lt; .001) or ACT &gt;400 seconds at any point during the procedure (OR 0.21, CI: 0.07–0.59, <italic>P</italic> = .003). In historical controls, 54% of patients (27/50) experienced an ACT &lt;300 seconds while operating in the left atrium compared to 19% (26/139) for the dosing algorithm and 20% (10/50) experienced an ACT &gt;400 seconds compared to 5% (7/139) for the dosing algorithm. When the ACT did drop below 300 seconds while operating in the left atrium, time spent with ACT below goal using the dosing algorithm did decrease, but this was not statistically significant. A high percentage of the dosing recommendations were followed without modification: 98.8% of bolus recommendations and 96.2% of infusion recommendations.</p>", "<title>Qualitative outcomes</title>", "<p id=\"p0095\">Nurses using the algorithm completed the SUS. This 10-item questionnaire is an industry standard for classifying the ease of use of websites and applications. A SUS score above 68 is considered average and a score &gt;80.3 is considered excellent; the dosing algorithm scored 96 (standard deviation 5, n = 7). Nurses and electrophysiologists also provided quotes regarding the dosing algorithm. Positive comments from electrophysiologists included “Fewer distractions during difficult cases, less delay to therapeutic ACT” and “More reliably achieving ACTs, less mental burden on operator.” However, there was some caution expressed as well: “The team just needs to be vocal when an ACT does not increase as expected post heparin so that troubleshooting can occur.” The nurses using the dosing algorithm reported “More autonomy in my practice. Less interruptions for the physician” and “Love the nurse autonomy and consistency.”</p>", "<title>Predictors of heparin doses</title>", "<p id=\"p0100\">For the 139 dosing algorithm cases, regression modeling was performed to determine predictors of the total heparin bolus amount to achieve ACT &gt;300 seconds and the final heparin infusion rate. Using a generalized linear model, warfarin for thromboembolic prophylaxis, age, sex, weight, BMI, estimated glomerular filtration rate (eGFR), and baseline ACT were univariate predictors of total bolus amount to achieve ACT &gt;300 seconds (##TAB##1##Table 2##). Being on warfarin, weight, and baseline ACT remained statistically significant after multivariate analysis, with eGFR nearly reaching statistical significance. Statistically significant univariate predictors of final infusion rate included being on warfarin (compared to being on apixaban), age, sex, weight, BMI, and eGFR (##TAB##2##Table 3##). Being on warfarin, sex, and weight remained statistically significant after a multivariate analysis.</p>", "<title>Complications</title>", "<p id=\"p0105\">Complications included in the American Heart Association Get With the Guidelines AF Ablation registry are documented locally. There was a single reported complication in each arm: a pericardial effusion in the historical controls and a pseudoaneurysm requiring thrombin injection in the dosing algorithm arm.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0110\">The current work describes the development of a computerized, adaptive, rule-based heparin dosing algorithm to maintain therapeutic intraprocedural ACT during catheter ablation of AF. The dosing algorithm demonstrated benefits on the speed of reaching goal ACT and maintaining therapeutic anticoagulation compared to historical controls at the University of Wisconsin. The frequency at which the ACT dropped below the therapeutic range and rose into a supratherapeutic range was significantly reduced using our algorithm. Given the infrequent nature of clinically evident stroke / transient ischemic attack in recent reports (pooled incidence of 0.17%), it is difficult to demonstrate a hard outcome benefit with such a small study.##REF##37225362##3## However, Di Biase and colleagues##REF##24607716##9## did demonstrate silent cerebral injury was more frequent in a cohort of 428 patients when they did not have strict adherence to guideline-directed intraprocedural anticoagulation. This finding suggests that protocols that improve maintenance of therapeutic ACTs during AF ablation, like the one presented here, are important interventions to avoid significant procedural-related cerebral injury.</p>", "<p id=\"p0115\">The present study also showed workflow improvements based on the usability score and subjective feedback provided by physicians and nurses. Staff and providers noted the benefits gained by removing the need for physician intervention for each heparin decision. These are very important findings. Gilmartin and colleagues##REF##35297037##23## demonstrated that Veterans Affairs cardiac catheterization laboratories that harnessed data to develop reliability enhancing work practices had higher staff job satisfaction, lower burnout, lower intent to leave, lower staff turnover, and higher perceived safety climate. Implementation of the present dosing algorithm represents one such attempt to create a reliability-enhancing practice that improved satisfaction in the University of Wisconsin electrophysiology laboratory.</p>", "<p id=\"p0120\">Other centers have reported on the difficulty achieving therapeutic ACTs during catheter ablation for AF in patients on NOACs and have developed protocols to make improvements. Kishima and colleagues##REF##30390125##15## examined a retrospective cohort of 190 patients on NOACs and found that only 42% of patients reached an ACT &gt;300 seconds at 30 minutes. After adjusting the protocol to include a higher initial bolus (100 U/kg + 5000 U) in patients with preablation ACT &lt;130 seconds, this metric increased to 81%. In 89 patients on NOACs, Payne and colleagues##REF##31230179##14## found that 29% of ACTs were therapeutic when using an initial bolus of 120 U/kg and increased to 49% when the initial bolus was increased to 150 U/kg. Bradley and colleagues##REF##33476459##16## reported that a protocol-guided approach that accounted for preprocedure oral anticoagulant and weight-based dosing did increase the proportion of therapeutic ACT on first draw to 76.6%, from 57.7%, and decreased the average time to therapeutic ACT to 30 minutes; however, supratherapeutic ACT on first draw (&gt;400 seconds) increased from 6.4% to 18.2%. Safani and colleagues##REF##33749350##17## reported impressive results using a comprehensive weight-adjusted, weight-based protocol that demonstrated a time to ACT &gt;300 seconds of 14.6 minutes in 99 patients on NOACs. The authors used an adjusted weight with an initial bolus of 200 units/kg and infusion rate of 35 units/kg. In this study, all patients were on NOACs but over 75% of the patients were receiving dabigatran. While 90.8% of readings were ≥300 seconds, over 25% of all ACTs were more than 400 seconds.</p>", "<p id=\"p0125\">The current study is notable for several reasons. The algorithm described here achieved time to goal ACT comparable to that shown by Safani and colleagues (17.6 min compared to 14.6 min) while reducing the frequency of ACT &gt;400 seconds. The modeling suggests a path forward to improve initial heparin bolus and infusion amounts, possibly by including sex and eGFR in addition to baseline ACT, weight, and anticoagulant type. A larger retrospective model derivation and validation study is required prior to making these additions. Although the assessments of usability were unblinded and subjective, the user satisfaction reported is unique to this study and important to consider, given the findings from Gilmartin and colleagues.</p>", "<p id=\"p0130\">Finally, the use of computerized CDSS accessible through the EMR is novel. As described by Sutton and colleagues,##REF##32047862##24## a computerized CDSS consists of the following: (1) a base—here, a set of rules and a mathematical function; (2) an interface engine, in this case a web-based interface opened through the EMR to input necessary clinical data; and (3) a communication mechanism: recommendations are communicated through the web-based interface. In the age of the EMR, attempts to develop effective CDSS are important to support the delivery of quality care. To date, many CDSS have targeted order sets, documentation templates, and patient-specific alerts.##REF##32479177##25## However, a task like heparin dosing in the electrophysiology lab lends itself to a computer-based CDSS, as most published guidance and protocols require repeated measurements and calculations that take into account specific patient characteristics like weight and anticoagulant type.##REF##28506916##2##<sup>,</sup>##REF##30390125##15##, ##REF##33476459##16##, ##REF##33749350##17## The work here demonstrates a beginning, but there are limitations to be addressed and future work to be done to refine the tool.</p>", "<title>Limitations</title>", "<p id=\"p0135\">This is a small, observational quality improvement study that describes the first implementation of this heparin dosing algorithm. The sample size is similar to other published reports but does limit the results.##REF##31230179##14##, ##REF##30390125##15##, ##REF##33476459##16##, ##REF##33749350##17## The number of patients on each of the 4 preprocedural oral anticoagulants studied here is small—especially dabigatran—making the results less generalizable. When the ACT did drop below goal, the time below goal did decrease using the algorithm, but it was not a statistically significant decrease. The study was likely underpowered to establish this finding. The dosing algorithm requires initialization with a bolus amount and infusion rate. A larger sample size will allow for more refined derivation and validation of models to predict these values.</p>", "<p id=\"p0140\">The lack of external validation limits generalizability and reproducibility. To mitigate potential bias, retrospective data collection (M.M.) and statistical analysis (F.O.) were performed by personnel outside of the electrophysiology team using the algorithm or the iVMD team that developed the dosing algorithm. However, those personnel were not blinded to the nature of the cases when doing analysis (control vs algorithm). To address these concerns, a multicenter randomized controlled trial with blinded analysis should be performed to confirm the findings of this study.</p>", "<p id=\"p0145\">A future study should include objective measures of workflow improvement. The workflow improvements are key findings and require substantiation. Potential measures to include are time required for a decision regarding dosing, frequency of intraprocedural provider distractions, and the number of intraprocedural ACTs. Finally, it is critical to point out that this algorithm does require human oversight. The “fundamental theorem” of biomedical informatics states that persons supported by information technology will be better than the same person who is unassisted—not replaced by the information technology.##REF##19074294##26## That is especially true in this case, as errors in ACT measurement can be introduced owing to sample collection. Staff running ACT measurements using this algorithm will continue to review results and rerun samples if results are unexpected.</p>", "<title>Future directions</title>", "<p id=\"p0150\">The current work is a starting point and represents 1 cycle in a continuous learning process (see Graphical Abstract).##REF##33269600##27## As has been described previously, there is individual variability in response to heparin that we do not fully understand.##REF##29532536##12## As shown in ##TAB##1##Tables 2## and ##TAB##2##3##, using the 139 dosing algorithm cases, we are beginning to understand factors that may contribute to this variability. A next step based on the modeling shown here will be to use a larger dataset to derive and test models for initial bolus and infusion rates that take into account sex and renal function in addition to anticoagulation type, weight, and baseline ACT.</p>", "<p id=\"p0155\">Moving forward, it is also important to consider what the higher doses of heparin required for apixaban and rivaroxaban represent. A recent study by Martin and colleagues##REF##32012701##28## performed ex vivo testing using samples from patients on warfarin, patients on NOACs, or untreated patients. The authors argued that differences in ACT values observed for the different anticoagulants following a fixed dose of anticoagulant did not reflect a true difference in anticoagulant activity based on antithrombin concentrations (although those data were not shown) and that the higher doses of heparin may cause harm. This is an important discussion to continue within the electrophysiology community, and the result of that discussion could lead to a different target for intraprocedural anticoagulation.</p>", "<p id=\"p0160\">No matter what the ultimate target is for anticoagulation, we feel that a heparin dosing algorithm delivered in a computer-based CDSS will have the potential to meet that target consistently while providing benefits to the workflow within the electrophysiology laboratory. After refining the initial heparin bolus and infusion amounts based on the modeling work described above, we look forward to a multi-institutional randomized controlled trial to address the limitations in the current report. A rigorous study done in a separate institution or multiple institutions that better defines how the dosing algorithm impacts workflows will be a critical step to better understand the effectiveness of the dosing algorithm.##REF##32047862##24##<sup>,</sup>##REF##32479177##25##</p>" ]
[ "<title>Conclusion</title>", "<p id=\"p0165\">The use of a deterministic, adaptive, rule-based dosing algorithm to dose intraprocedural heparin during AF ablation delivered as a computerized CDSS improved maintenance of therapeutic anticoagulation during AF ablation and provided subjective improvement in procedural workflows in this small, single-institution implementation.</p>" ]
[ "<title>Background</title>", "<p>Cerebral thromboembolism during atrial fibrillation (AF) ablation is an infrequent (0.17%) complication in part owing to strict adherence to intraprocedural anticoagulation. Failure to maintain therapeutic anticoagulation can lead to an increase in events, including silent cerebral ischemia.</p>", "<title>Objective</title>", "<p>To evaluate a computerized, clinical decision support system (CDSS) to dose intraprocedural anticoagulation and determine if it leads to improved intraprocedural anticoagulation outcomes during AF ablation.</p>", "<title>Methods</title>", "<p>The Digital Intern dosing algorithm is an adaptive, rule-based CDSS for heparin dosing. The initial dose is calculated from the patient’s weight, baseline activated clotting time (ACT), and outpatient anticoagulant. Subsequent recommendations adapt based on individual patient ACT changes. Outcomes from 50 cases prior to algorithm introduction were compared to 139 cases using the algorithm.</p>", "<title>Results</title>", "<p>Procedures using the dosing algorithm reached goal ACT (over 300 seconds) faster (17.6 ± 11.1 minutes vs 33.3 ± 23.6 minutes pre-algorithm, <italic>P</italic> &lt; .001). ACTs fell below goal while in the LA (odds ratio 0.20 [0.10–0.39], <italic>P</italic> &lt; .001) and rose above 400 seconds less frequently (odds ratio 0.21 [0.07–0.59], <italic>P</italic> = .003). System Usability Scale scores were excellent (96 ± 5, n = 7, score &gt;80.3 excellent). Preprocedure anticoagulant, weight, baseline ACT, age, sex, and renal function were potential predictors of heparin dose to achieve ACT &gt;300 seconds and final infusion rate.</p>", "<title>Conclusion</title>", "<p>A heparin dosing CDSS based on rules and adaptation to individual patient response improved maintenance of therapeutic ACT during AF ablation and was rated highly by nurses for usability.</p>", "<title>Graphical abstract</title>", "<title>Keywords</title>" ]
[]
[ "<title>Supplementary data</title>", "<p id=\"p0200\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0170\">This work would not have been possible without the dedication and support of the nurses and technicians in our electrophysiology laboratory. We are particularly grateful for the work of Angela Dinkela, RN, and Rebecca Schoonhoven, RN, who were critical to our transition to this heparin dosing algorithm.</p>", "<title>Funding Sources</title>", "<p id=\"p0175\">This quality improvement study did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.</p>", "<title>Disclosures</title>", "<p id=\"p0180\">Drs Kalscheur, Martini, Modaff, Fleeman, Kipp, and Wright and Ms Osman have no pertinent disclosures. Mr Mahnke is an employee of Integrated Vital Medical Dynamics, LLC. Dr Medow is CEO/CTO of Integrated Vital Medical Dynamics, LLC.</p>", "<title>Authorship</title>", "<p id=\"p0185\">All authors attest they meet the current ICMJE criteria for authorship.</p>", "<title>Patient Consent</title>", "<p id=\"p0190\">This project was reviewed using the University of Wisconsin-Madison Health Sciences QI / Program Evaluation Self-Certification Tool and was deemed to be Quality Improvement. Therefore, individual patient consent was not required for implementation.</p>", "<title>Ethics Statement</title>", "<p id=\"p0195\">This quality improvement study aimed to improve maintenance of guideline-directed intraprocedural anticoagulation during AF ablation. The project was approved as quality improvement using the University of Wisconsin-Madison Health Sciences QI / Program Evaluation tool in consultation with staff from our local IRB. The retrospective review of data was approved by the University of Wisconsin School of Medicine and Public Health Institutional Review Board (IRB 2022-0312), and patient privacy was protected by using only deidentified data for analyses. During development and implementation, the project team carefully monitored results to ensure that outcomes were no worse than historic care. The project team reported results honestly and transparently, and acknowledged any limitations and biases as described above.</p>" ]
[ "<fig id=\"undfig1\" position=\"anchor\"></fig>", "<fig id=\"fig1\"><label>Figure 1</label><caption><p>Description and development of the heparin dosing algorithm. <bold>A:</bold> The Digital Intern (Integrated Vital Medical Dynamics, Madison, WI) procedure–based heparin dosing calculator, ie, “dosing algorithm,” is an adaptive, rule-based system that mathematically generates recommendations based on the distance from current activated clotting time (ACT) to the central target. To initiate the algorithm, initial bolus and infusion recommendations are required. Bolus<sub>1</sub> is determined based on patient weight, type of anticoagulant, and distance from goal ACT to ACT<sub>0</sub>. The individual patient response to Bolus<sub>1</sub> scales the coefficients that generate all future bolus and infusion recommendations. From ACT<sub>2</sub> onward, the previous bolus, change in infusion rate, (Goal ACT - ACT<sub>n</sub>), and (ACT<sub>n</sub>−ACT<sub>n</sub><sub>−</sub><sub>1</sub>) continue to refine the coefficients until steady state is achieved. Text in black boxes represent initial user inputs, those in circles are subsequent user inputs, and text in rhombi represent actions of the dosing algorithm. <bold>B:</bold> The algorithm was developed in 3 phases. Baseline performance was established using recommendations from consensus documents and institutional experience to initiate the algorithm (<italic>blue boxes</italic>). Next, a module was added to account for significant variation in response to the initial bolus (<italic>green boxes</italic>). Finally, adjustments were made in the initial bolus amount and infusion rate (<italic>red boxes</italic>).</p></caption></fig>", "<fig id=\"fig2\"><label>Figure 2</label><caption><p>Heparin dosing algorithm initiation and use. <bold>A:</bold> The heparin dosing algorithm was opened by staff directly from the electronic medical record. <bold>B.</bold> Staff then input required data. Patient characteristics input by staff and used in the algorithm calculations included medication used for thromboembolic prophylaxis, weight, and baseline ACT (highlighted in figure). Additional characteristics input included time since last dose of anticoagulant, sex, creatinine, AST, ALT, and total bilirubin. An initial bolus dose was then suggested. Staff entered subsequent activated clotting time results and received recommendations on bolus and infusion rates. Actual doses delivered were tabulated.</p></caption></fig>", "<fig id=\"fig3\"><label>Figure 3</label><caption><p>Intraprocedural anticoagulation outcomes improved with the dosing algorithm. <bold>A:</bold> The time to reach goal activated clotting time (ACT) dropped from 33.3 ± 23.6 minutes to 17.6 ± 11.1 minutes, beta coefficient for linear regression -15.8, confidence interval (CI): -20.8 to -10.8, <italic>P</italic> &lt; .001. In this box plot, the box covers the interquartile range while the whiskers are restricted to 1.5 times the interquartile range; outliers are defined as greater than 1.5 times the interquartile range. <bold>B:</bold> The percentage of patients experiencing ACT &lt;300 seconds while operating in the left atrium dropped from 54% (27/50 historical controls) to 19% (26/139 dosing algorithm), odds ratio (OR) 0.20, CI: 0.10–0.39, <italic>P</italic> &lt; .001. <bold>C:</bold> The percentage of patients with any ACT &gt;400 seconds decreased from 20% (10/50 historical controls) to 5% (7/139 dosing algorithm), OR 0.21, CI: 0.07–0.59, <italic>P</italic> = .003.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"tbl1\"><label>Table 1</label><caption><p>Characteristics of the study sample</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th>Variable</th><th>Historical control (N = 50)</th><th>Dosing algorithm (N = 139)</th><th><italic>P</italic> value</th></tr></thead><tbody><tr><td>Anticoagulation, n (%)</td><td/><td/><td/></tr><tr><td> Warfarin</td><td align=\"char\">5 (10.0)</td><td align=\"char\">16 (11.5)</td><td align=\"char\">.38</td></tr><tr><td> Apixaban</td><td align=\"char\">34 (68.0)</td><td align=\"char\">106 (76.3)</td><td/></tr><tr><td> Rivaroxaban</td><td align=\"char\">9 (18.0)</td><td align=\"char\">15 (10.8)</td><td/></tr><tr><td> Dabigatran</td><td align=\"char\">2 (4.0)</td><td align=\"char\">2 (1.4)</td><td/></tr><tr><td>INR (if on warfarin), mean (SD)</td><td align=\"char\">2.3 (0.29)</td><td align=\"char\">2.4 (0.42)</td><td align=\"char\">.12</td></tr><tr><td>Age, mean (SD)</td><td align=\"char\">62.1 (10.9)</td><td align=\"char\">64.4 (9.8)</td><td align=\"char\">.17</td></tr><tr><td>Sex, n (%)</td><td/><td/><td/></tr><tr><td> Male</td><td align=\"char\">28 (56.0)</td><td align=\"char\">87 (62.6)</td><td align=\"char\" rowspan=\"2\">.41</td></tr><tr><td> Female</td><td align=\"char\">22 (44.0)</td><td align=\"char\">52 (37.4)</td></tr><tr><td>Weight (kg), mean (SD)</td><td align=\"char\">94.5 (20.0)</td><td align=\"char\">98.6 (24.9)</td><td align=\"char\">.30</td></tr><tr><td>BMI, mean (SD)</td><td align=\"char\">31.2 (7.0)</td><td align=\"char\">31.8 (6.9)</td><td align=\"char\">.60</td></tr><tr><td>Creatinine, mean (SD)</td><td align=\"char\">0.98 (0.24)</td><td align=\"char\">1.02 (0.32)</td><td align=\"char\">.42</td></tr><tr><td>eGFR, mean (SD)</td><td align=\"char\">75.6 (17.2)</td><td align=\"char\">74.9 (20.4)</td><td align=\"char\">.83</td></tr><tr><td>AST, mean (SD)</td><td align=\"char\">26.5 (15.2)</td><td align=\"char\">25.7 (11.6)</td><td align=\"char\">.70</td></tr><tr><td>ALT, mean (SD)</td><td align=\"char\">30.8 (23.7)</td><td align=\"char\">26.8 (16.8)</td><td align=\"char\">.20</td></tr><tr><td>Tbili, mean (SD)</td><td align=\"char\">0.71 (0.37)</td><td align=\"char\">0.74 (0.35)</td><td align=\"char\">.61</td></tr><tr><td>Platelets, mean (SD)</td><td align=\"char\">212.7 (35.3)</td><td align=\"char\">220.9 (63.6)</td><td align=\"char\">.39</td></tr><tr><td>Total bolus doses of heparin, mean (SD)</td><td align=\"char\">12,430.0 (4844.5)</td><td align=\"char\">12,417.3 (4227.1)</td><td align=\"char\">.99</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tbl2\"><label>Table 2</label><caption><p>Predictors of heparin bolus amount to achieve activated clotting time &gt;300 seconds</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"2\">Variable</th><th colspan=\"3\">Univariate<hr/></th><th colspan=\"3\">Multivariate<hr/></th></tr><tr><th>β</th><th>95% CI</th><th><italic>P</italic> value</th><th>β</th><th>95% CI</th><th><italic>P</italic> value</th></tr></thead><tbody><tr><td>Anticoagulation</td><td/><td/><td/><td/><td/><td/></tr><tr><td> Apixaban</td><td>Ref</td><td>Ref</td><td>Ref</td><td>Ref</td><td>Ref</td><td>Ref</td></tr><tr><td> Warfarin</td><td align=\"char\">-4475.2</td><td align=\"char\">-6598.6, -2351.9</td><td align=\"char\">&lt;.001∗</td><td align=\"char\">-2693.7</td><td align=\"char\">-4197.1, -1190.4</td><td align=\"char\">.001∗</td></tr><tr><td> Rivaroxaban</td><td align=\"char\">-437.7</td><td align=\"char\">-2621.7, 1746.3</td><td align=\"char\">.69</td><td align=\"char\">1210.8</td><td align=\"char\">-484.6, 2906.3</td><td align=\"char\">.16</td></tr><tr><td> Dabigatran</td><td align=\"char\">-4037.7</td><td align=\"char\">-9688.4, 1612.9</td><td align=\"char\">.16</td><td align=\"char\">-1387.3</td><td align=\"char\">-5166.9, 2392.2</td><td align=\"char\">.47</td></tr><tr><td>INR (if on warfarin)</td><td align=\"char\">-5616.2</td><td align=\"char\">-9723.8, -1508.7</td><td/><td/><td/><td/></tr><tr><td>Time since last AC dose (h)</td><td align=\"char\">2.3</td><td align=\"char\">-1.1, 5.6</td><td align=\"char\">.19</td><td/><td/><td/></tr><tr><td>Age</td><td align=\"char\">-125.7</td><td align=\"char\">-195.3, -56.2</td><td align=\"char\">&lt;.001∗</td><td align=\"char\">-12.6</td><td align=\"char\">-68.4, 43.3</td><td align=\"char\">.66</td></tr><tr><td>Sex = male</td><td align=\"char\">2848.1</td><td align=\"char\">1458.6, 4237.7</td><td align=\"char\">&lt;.001∗</td><td align=\"char\">769.9</td><td align=\"char\">-255.2, 1795.2</td><td align=\"char\">.14</td></tr><tr><td>Weight (kg)</td><td align=\"char\">97.4</td><td align=\"char\">74.1, 120.8</td><td align=\"char\">&lt;.001∗</td><td align=\"char\">86.8</td><td align=\"char\">66.7, 106.9</td><td align=\"char\">&lt;.001∗</td></tr><tr><td>BMI</td><td align=\"char\">274.2</td><td align=\"char\">182.3, 366.1</td><td align=\"char\">&lt;.001∗</td><td/><td/><td/></tr><tr><td>Creatinine</td><td align=\"char\">-1570.1</td><td align=\"char\">-3766.1, 626.4</td><td align=\"char\">.16</td><td/><td/><td/></tr><tr><td>eGFR</td><td align=\"char\">65.1</td><td align=\"char\">31.5, 98.7</td><td align=\"char\">&lt;.001∗</td><td align=\"char\">26.8</td><td align=\"char\">-0.63, 54.3</td><td align=\"char\">.06</td></tr><tr><td>AST</td><td align=\"char\">-48.7</td><td align=\"char\">-126.7, 29.3</td><td align=\"char\">.22</td><td/><td/><td/></tr><tr><td>ALT</td><td align=\"char\">10.8</td><td align=\"char\">-40.7, 62.4</td><td align=\"char\">.68</td><td/><td/><td/></tr><tr><td>Tbili</td><td align=\"char\">-2423.2</td><td align=\"char\">-5195.9, 349.6</td><td align=\"char\">.09</td><td/><td/><td/></tr><tr><td>Platelets</td><td align=\"char\">1.9</td><td align=\"char\">-9.4, 13.1</td><td align=\"char\">.74</td><td/><td/><td/></tr><tr><td>Baseline ACT</td><td align=\"char\">-79.9</td><td align=\"char\">-106.9, -52.8</td><td align=\"char\">&lt;.001∗</td><td align=\"char\">-74.0</td><td align=\"char\">6902.2, 19,931.9</td><td align=\"char\">&lt;.001∗</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tbl3\"><label>Table 3</label><caption><p>Predictors of final heparin infusion rate</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"2\">Variable</th><th colspan=\"3\">Univariate<hr/></th><th colspan=\"3\">Multivariate<hr/></th></tr><tr><th>β</th><th>95% CI</th><th><italic>P</italic> value</th><th>β</th><th>95% CI</th><th><italic>P</italic> value</th></tr></thead><tbody><tr><td>Anticoagulation</td><td/><td/><td/><td/><td/><td/></tr><tr><td> Apixaban</td><td>Ref</td><td>Ref</td><td>Ref</td><td>Ref</td><td>Ref</td><td>Ref</td></tr><tr><td> Warfarin</td><td align=\"char\">-883.2</td><td align=\"char\">-1525.6, -240.7</td><td align=\"char\">.007∗</td><td align=\"char\">-875.8</td><td align=\"char\">-1326.8, -424.8</td><td align=\"char\">&lt;.001∗</td></tr><tr><td> Rivaroxaban</td><td align=\"char\">107.7</td><td align=\"char\">-553.1, 768.4</td><td align=\"char\">.75</td><td align=\"char\">-142.3</td><td align=\"char\">-615.6, 330.9</td><td align=\"char\">.55</td></tr><tr><td> Dabigatran</td><td align=\"char\">-1070.7</td><td align=\"char\">-2780.2, 638.9</td><td align=\"char\">.22</td><td align=\"char\">-476.1</td><td align=\"char\">-1678.6, 726.4</td><td align=\"char\">.43</td></tr><tr><td>INR (if on warfarin)</td><td align=\"char\">-514.5</td><td align=\"char\">-2245.4, 1216.4</td><td align=\"char\">.53</td><td/><td/><td/></tr><tr><td>Time since last AC dose to start</td><td align=\"char\">-0.2</td><td align=\"char\">-1.2, 0.9</td><td align=\"char\">.72</td><td/><td/><td/></tr><tr><td>Age</td><td align=\"char\">-31.8</td><td align=\"char\">-52.4, -11.2</td><td align=\"char\">.003∗</td><td align=\"char\">-7.28</td><td align=\"char\">-25.0, 10.5</td><td align=\"char\">.42</td></tr><tr><td>Sex = male</td><td align=\"char\">1170.3</td><td align=\"char\">787.8, 1552.9</td><td align=\"char\">&lt;.001∗</td><td align=\"char\">580.3</td><td align=\"char\">253.6, 906.9</td><td align=\"char\">.001∗</td></tr><tr><td>Weight (kg)</td><td align=\"char\">33.0</td><td align=\"char\">26.8, 39.3</td><td align=\"char\">&lt;.001∗</td><td align=\"char\">27.6</td><td align=\"char\">21.2, 33.9</td><td align=\"char\">&lt;.001∗</td></tr><tr><td>BMI</td><td align=\"char\">81.2</td><td align=\"char\">54.4, 108.1</td><td align=\"char\">&lt;.001∗</td><td/><td/><td/></tr><tr><td>Creatinine</td><td align=\"char\">-77.2</td><td align=\"char\">-724.9, 570.5</td><td align=\"char\">.81</td><td/><td/><td/></tr><tr><td>eGFR</td><td align=\"char\">13.6</td><td align=\"char\">3.5, 23.7</td><td align=\"char\">.009∗</td><td align=\"char\">3.77</td><td align=\"char\">-4.9, 12.4</td><td align=\"char\">.39</td></tr><tr><td>AST</td><td align=\"char\">-9.1</td><td align=\"char\">-31.8, 13.6</td><td align=\"char\">.43</td><td/><td/><td/></tr><tr><td>ALT</td><td align=\"char\">3.12</td><td align=\"char\">-11.9, 18.2</td><td align=\"char\">.68</td><td/><td/><td/></tr><tr><td>Tbili</td><td align=\"char\">-569.9</td><td align=\"char\">-1366.0, 226.1</td><td align=\"char\">.16</td><td/><td/><td/></tr><tr><td>Platelets</td><td align=\"char\">0.8</td><td align=\"char\">-2.5, 4.1</td><td align=\"char\">.64</td><td/><td/><td/></tr><tr><td>Baseline ACT</td><td align=\"char\">-7.8</td><td align=\"char\">-16.6, 0.91</td><td align=\"char\">.08</td><td/><td/><td/></tr></tbody></table></table-wrap>" ]
[]
[]
[]
[]
[]
[ "<supplementary-material content-type=\"local-data\" id=\"mmc1\"><caption><title>Supplemental Tables 1–6</title></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p>ALT = alanine transaminase; AST = aspartate aminotransferase; BMI = body mass index; eGFR = estimated glomerular filtration rate; INR = international normalized ratio; SD = standard deviation; Tbili = total bilirubin.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"tspara0025\"><p>β = beta coefficient; AC = anticoagulant; ACT = activated clotting time; ALT = alanine transaminase; AST = aspartate aminotransferase; BMI = body mass index; eGFR = estimated glomerular filtration rate; Tbili = total bilirubin.</p></fn><fn id=\"tspara0030\"><p>Example interpretation: a 1-unit increase in eGFR denotes a heparin bolus increase of 65.1 units.</p></fn><fn id=\"tspara0035\"><p>Asterisk (∗) indicates statistically significant at <italic>P</italic> ≤ .05.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn id=\"tspara0045\"><p>β = beta coefficient; AC = anticoagulant; ACT = activated clotting time; ALT = alanine transaminase; AST = aspartate aminotransferase; BMI = body mass index; eGFR = estimated glomerular filtration rate; Tbili = total bilirubin.</p></fn><fn id=\"tspara0050\"><p>Example interpretation: a 1-unit increase in eGFR denotes a heparin infusion increase of 13.6 units.</p></fn><fn id=\"tspara0055\"><p>Asterisk (∗) indicates statistically significant at <italic>P</italic> ≤ .05.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"appsec2\" fn-type=\"supplementary-material\"><label>Appendix</label><p id=\"p0205\">Supplementary data associated with this article can be found in the online version at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.cvdhj.2023.11.001\" id=\"intref0010\">https://doi.org/10.1016/j.cvdhj.2023.11.001</ext-link>.</p></fn></fn-group>" ]
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[ "<media xlink:href=\"mmc1.docx\"/>" ]
[{"label": ["21"], "mixed-citation": ["Accriva Diagnostics I. Hemochron Signature Elite Operator\u2019s Manual. Bedford, MA."]}, {"label": ["22"], "surname": ["Brooke"], "given-names": ["J.S.U.S."], "article-title": ["a quick and dirty usability scale"], "source": ["Usability Eval Ind"], "year": ["1995"], "fpage": ["189"]}]
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28
CC BY
no
2024-01-14 23:41:58
Cardiovasc Digit Health J. 2023 Nov 14; 4(6):173-182
oa_package/a4/29/PMC10787148.tar.gz
PMC10787149
0
[ "<title>Introduction</title>", "<p id=\"p0010\">Cardiovascular disease is one of the leading causes of mortality globally##REF##33309175##1## and cardiovascular healthcare accounts for a large portion of global healthcare costs and expenses. Early detection and prevention will decrease the burden of cardiovascular disease and will therefore decrease mortality, morbidity, and costs. Cardiovascular monitoring using big data from wearables and machine learning can drastically increase the availability and efficiency of cardiovascular healthcare globally, at the fraction of the costs of conventional medical-grade devices.</p>", "<p id=\"p0015\">Electrocardiogram (ECG) monitoring, such as Holters or implantable loop recorders, are the gold standard for monitoring of outpatients with known or suspected arrhythmias. However, they are burdensome, can only be used for a limited period of time, and are expensive. Implantable loop recorders are invasive and have to be manually activated and analyzed in the hospital. This severely limits the use of these devices for long-term home monitoring of patients, and they have suboptimal patient comfort. For patients with chronic cardiovascular diseases, such as atrial fibrillation and heart failure, this implies frequent hospital visits and sometimes even hospital admissions (associated with higher mortality) that can be prevented by continuous and adequate home monitoring.</p>", "<p id=\"p0020\">With the widespread availability of reliable, consumer-grade wearables such as smartwatches, continuous monitoring of, for example, heart rate with photoplethysmography and step counting with accelerometers is possible. This monitoring is easy, patient friendly, and cost effective. Combining the power of large amounts of data (big data) and novel machine learning techniques, these time series can be used to detect and perhaps even predict cardiovascular disease, therefore improving patient care. There are some caveats, however, as not all wearables have the same characteristics and quality. Consequently, they have been used with moderate success.##REF##29562087##2##<sup>,</sup>##UREF##0##3## They also provide less informative diagnostic signals as compared to, for example, electrocardiography or other commonly used cardiologic diagnostic modalities. The challenge but also the strength of machine learning models is that they learn by example and therefore large amounts of data are needed for which the cardiovascular outcome (class label) has been determined. Typically, supervised learning is used, where each observation of the data has a class label. This must be done with ECGs, since photoplethysmography or derived signals are difficult to interpret by a clinician. This so-called labeling or annotating of signals by physicians is infeasible for the large amounts of (continuous) data required, and therefore semi-automated##UREF##1##4##<sup>,</sup>##REF##36148649##5## and fully automated##REF##29562087##2##<sup>,</sup>##UREF##0##3## ECG labeling systems##UREF##2##6## have been developed. However, these still require a lot of manual labor from continuously monitored users.</p>", "<p id=\"p0025\">Therefore, the objective of the ME-TIME is (early) detection and prevention of heart disease by leveraging time series data from smartwatches, a cloud-based infrastructure, and machine learning algorithms specifically designed to function effectively with minimal labeling efforts.</p>" ]
[ "<title>Methods</title>", "<title>Study design and data collection</title>", "<p id=\"p0030\">ME-TIME (registered at <ext-link ext-link-type=\"uri\" xlink:href=\"http://ClinicalTrials.gov\" id=\"intref0010\">ClinicalTrials.gov</ext-link>; ID: <ext-link ext-link-type=\"ClinicalTrials.gov\" xlink:href=\"NCT05802563\" id=\"intref0015\">NCT05802563</ext-link>) is designed as an observational cohort study consisting of 3 data subject groups, as depicted in ##FIG##0##Figure 1##. The first group consists of patients with systolic heart failure (HF group); the second group consists of patients with documented atrial fibrillation (AF group); and the third group, serving as a reference, consists of healthy volunteers. The rationale for creating distinct AF and HF groups comes from their unique pathophysiological characteristics. Consequently, heart rate patterns that are indicative of these diseases might also be different. The HF group consists of 50 study participants with systolic heart failure, defined as a left ventricular ejection fraction &lt;35% without documented atrial fibrillation. The AF group consists of 50 patients with documented atrial fibrillation (paroxysmal, persistent, or permanent) without systolic heart failure. Ejection fractions will be assessed from echocardiograms that are made within 1 year of inclusion, and if this is not available an echocardiogram will be performed. The reference group consists of 100 participants without any prior medical history and without medication use. Potential study subjects that meet any of the following criteria will be excluded from participation in this study: age &lt;18 years, age &gt;85 years, recent pulmonary venous antrum isolation (&lt;1 year), kidney or liver failure, known systemic active inflammatory disease, impaired mental state, inability to use a fitness tracker or mobile phone, impaired cognition, and inability to understand the study protocol.</p>", "<p id=\"p0035\">Patients will be asked by their treating physician if they may be approached by an investigator to inform them about the study and potential participation. Healthy participants are recruited through local advertising. Anyone that is interested will then receive an information brochure and informed consent form. At least 2 days after the patient’s receipt of the brochure, the research team will call the patient to schedule an appointment. During this visit, the patient submits the signed consent form and will undergo an ECG and blood pressure measurement that will be analyzed by an experienced cardiologist (I.B.). Participants can use their own Fitbit and are otherwise provided with a Fitbit Inspire 2 or Fitbit Charge 5 smartwatch. The device type is assigned to a participant at random to prevent device sampling bias. This will also help to investigate the effect of device type on the performance of the final model. A Fitbit account will be created for all participants which will be connected to a custom-built data platform using the Google Cloud Platform. Our platform features a data portal for research staff to easily register or deregister participants by authorizing a connection to their Fitbit data. Data are extracted daily from Fitbits until the observation period ends and can be analyzed either in the cloud or locally.</p>", "<p id=\"p0040\">All participants will be asked to fill out a survey regarding their health. All participants are monitored for a period of 3 months. After written consent from the 200 subjects, heart rate, step counter, and sleep time series data are extracted from the data platform. Clinical metadata such as age, height, weight, blood pressure at baseline, health survey, and medication use are saved in the Castor (Ciwit BV, Amsterdam, The Netherlands) electronic database.</p>", "<title>Data privacy</title>", "<p id=\"p0045\">After performing a thorough data protection impact assessment, the local hospital security information and privacy officers granted permission to perform the study. This was also validated by the ethics review board. The data protection impact assessment describes a data management plan conforming to the European General Data Protection Regulation. To protect the data privacy of the participants, all data are pseudonymized. Only the researchers have access to the sensor data, and only the Principal Investigator has access to personal information of participants (ie, names, contact information, etc). They have all signed processing agreements. Second, the Google servers storing the data are only located within the Netherlands; hence the data does not leave the country, therefore conforming to Dutch law. This is done to have a clear data infrastructure both legally and technically to explain to participants.</p>", "<title>Data characteristics and preparation</title>", "<p id=\"p0050\">The data first undergoes a process involving resampling and artifact removal. In our experience with Fitbit smartwatches, the heart rate is nonuniformly sampled, with a prevalent rate of 0.2 Hz. Therefore, the heart rate is resampled to once per 5 seconds. The step counter is sampled once per minute.</p>", "<p id=\"p0055\">Artifacts involving samples with numerous consecutive constant values are removed, if more than 12 consecutive constant values (equivalent to 1 minute of heart rate samples) are detected. This 1-minute threshold was chosen based on visual inspection, which revealed that heart rate patterns typically occur in the order of minutes, often spanning 10–20 minutes. For sequences with fewer than 12 consecutive missing values, linear interpolation is applied. From the cleaned time series, smaller segments, denoted as windows, are extracted and employed as input for a machine learning model. This process involves a sliding window and windows containing time gaps are excluded. Windows have 2 design considerations: the window size, which determines the number of samples within a window and defines its dimensionality, and the stride, which establishes the step size dictating the shift between windows.</p>", "<p id=\"p0060\">Although the cardiovascular condition of each subject is known, it is unknown in which specific windows these conditions manifest themselves. This is owing to the paroxysmal nature of atrial fibrillation and the variable symptoms of heart failure, which can be influenced by factors like medication adjustments, dietary changes, and the disease’s progressive course. In other words, the subject label is known, but the individual window labels are unknown. This is visually represented in ##FIG##1##Figure 2##a, where the subject label is depicted by the blue/red colors and the unknown window labels are indicated by black dotted lines.</p>", "<title>Planned machine learning approach</title>", "<p id=\"p0065\">Our planned machine learning approach is tailored to operate in this setting through a 2-stage process. To learn informative patterns/features directly from the input data, despite the lack of labeled windows, the first stage involves using self-supervised learning. A commonly used self-supervised learning technique involves compressing the input windows to a lower-dimensional representation and then reconstructing the original input from this compact representation, as depicted in ##FIG##1##Figure 2##b.##REF##32964139##7##<sup>,</sup>##UREF##3##8## Instead of reconstruction, another technique is to forecast future time points of the input data.##UREF##4##9## The second stage involves multiple-instance learning (MIL). MIL, depicted in ##FIG##2##Figure 3## and more elaborately explained in ##BOX##0##Box 1##, is suitable for data where a single prediction is made collectively on a group of samples (known as a “bag”) instead of predicting on individual samples (known as “instances”). MIL techniques align well with our time series data, where during the training phase only 1 label related to the subject (bag label) is known while the individual labels of the compressed windows (instance labels) remain unknown. In the testing phase the primary objective is to predict 1 clinical outcome for each subject. The key concept in MIL is that each bag of instances is labeled as positive (heart disease) if it contains a certain amount of positive instances and negative (healthy) if it contains no positive instances (only negative instances). Although traditional MIL approaches often classify a bag as positive even with just 1 positive instance, we aim to minimize false-positives by setting a threshold on the number of positive instances required to label a bag as positive. This threshold will be determined through hyperparameter tuning. Thus, instead of learning a model that predicts the cardiovascular outcome of individual instances, we are learning a model that predicts the outcome of a bag of instances.</p>", "<p id=\"p0070\">\n\n</p>", "<title>Algorithm validation</title>", "<p id=\"p0095\">In our specific setting where the model encounters data from previously unseen subjects without any prior knowledge, we use leave-p-subjects-out cross-validation (LPSOCV). This approach, shown in ##FIG##3##Figure 4##, ensures a more accurate reflection of real-world situations. LPSOCV involves multiple iterations, or folds, during which data from distinct subjects are used for training and validation purposes (ie, the model is validated on data from subjects that the model is not trained on), mitigating observation bias.</p>", "<p id=\"p0100\">Machine learning models are sensitive to the distribution of classes. To mitigate potential bias owing to different class distributions in each fold, we incorporate stratification during the cross-validation process. This ensures that the ratio of nonarrhythmic, atrial fibrillation, and heart failure subjects remains approximately consistent and that the influence of inconsistent class distribution across different folds is minimized.</p>", "<p id=\"p0105\">However, Fitbit time series data exhibit inter-subject variability resulting from individuals’ distinct physical attributes,##UREF##5##10## making the development of a universally effective model for “new” subjects challenging. In order to examine the effect of inter-subject variability, we will assess the model on 2 distinct test sets. The first is an external test set that consists of subjects not previously encountered, randomly selected to make up 20% of the total subjects, with an equal number from each class. This allows us to evaluate the model’s generalization capabilities. The second test set is an internal one, encompassing the final 20% of data from subjects previously encountered by the model. This segment of data was excluded during the cross-validation phase and serves as a baseline, as it minimizes the influence of inter-subject variability, providing a reliable reference for comparison.</p>", "<p id=\"p0110\">Parameters not directly learned by the machine learning model, such as window parameters, are termed hyperparameters. Since optimal values are typically unknown in advance, multiple options are examined during LPSOCV, and the best-performing one, with the best average performance over all folds, is chosen for the final model; a process known as hyperparameter tuning.</p>" ]
[ "<title>Results</title>", "<p id=\"p0115\">Preliminary findings are discussed in the following sections.</p>", "<title>Study characteristics</title>", "<p id=\"p0120\">So far, 62 of the 200 envisioned subjects have been included and data from 22 subjects (15 healthy, 7 AF) have been extracted successfully from the data platform for preliminary analysis (##TAB##0##Table 1##).</p>", "<title>Data show large inter-subject variability</title>", "<p id=\"p0125\">Nonoverlapping 1-hour windows are used to segment heart rate and step counter time series data from 6 subjects. To visualize this high-dimensional data, UMAP##UREF##6##11## is employed to reduce the data to 2 dimensions while maintaining as much structure as possible. The resulting embedding is displayed in ##FIG##4##Figure 5##, where the distribution of the 2-dimensional UMAP samples are illustrated per subject.</p>", "<p id=\"p0130\">When there is little overlap between subjects, finding a shared pattern among them becomes challenging, making it difficult for a model to learn. As a result, the performance of a machine learning model could be impacted as, during testing, a subject can significantly deviate from the subjects on which the model was trained.</p>", "<title>Heart rate peak alignment in acceleration-deceleration curves indicate difference between 7 AF patients and 15 healthy controls</title>", "<p id=\"p0135\">Next, we explored the heart rate recovery curves after activity (acceleration-deceleration curves).##REF##19837772##12## First a peak is detected, whereafter the start (onset) and end (recovery) points associated to that peak are determined by the minimum heart rate value 5 minutes before and 15 minutes after the peak. The curves are preprocessed by aligning the peaks on the time axis. Additionally, for every subject, the amplitude of the curves is rescaled by the average peak value across all curves for that individual. ##FIG##5##Figure 6## shows the curves for light activity, defined by a maximum of 20 steps in the 5 minutes preceding the peak and fewer than 10 steps in the 15 minutes after the peak. There are 2 noticeable differences in heart rate patterns between persistent AF patients (in red) and healthy participants (in blue). The standard deviation for AF patients is considerably smaller than that of healthy individuals, and their heart rate recovery is slower, as observed at the 6-minute mark. These distinctions could potentially serve as clinical indicators for atrial fibrillation.</p>", "<title>MIL can detect healthy cardiovascular outcomes</title>", "<p id=\"p0140\">The peak aligned acceleration-deceleration curves are concatenated with their corresponding step counter data and grouped per week to form bags. The MILES (Multiple-Instance Learning via Embedded Instance Selection) model is then used to classify every week as healthy or AF. The results in ##TAB##1##Table 2## show that even though the sensitivity is low, the specificity is decent. This shows potential in avoiding unnecessary visits to a cardiologist for patients who have symptoms that are wrongly suspected to be related to heart problems.</p>", "<title>Step counter and heart rate are correlated with a time delay</title>", "<p id=\"p0145\">Next, we examined whether the cross-correlation function between the heart rate window and its corresponding step counter window is indicative of heart disease. To calculate the correlation, we consider varying window sizes and time differences (lags) between heart rate and steps. The computed cross-correlation matrix for the healthy group, along with the AF and HF patient groups, as shown in ##FIG##6##Figure 7##, shows that the heart rate is correlated with the step counter with 1-minute delay.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0150\">By building a suitable infrastructure with Cloud technology, big data acquired in the study is used to develop data-efficient models using methods from multiple instance and self-supervised learning.</p>", "<p id=\"p0155\">We aim to examine the influence of inter-subject variability on predicting cardiovascular disease and will explore potential methods to mitigate these variabilities.##REF##31494539##13##<sup>,</sup>##UREF##7##14## We expect that patterns indicative of cardiovascular disease become apparent within a timeframe of minutes, hours, or more, considering that consumer-grade wearables have a slower sampling rate compared to the gold standard. We have shown 1 example of such a pattern: the acceleration-deceleration curve. Preselecting windows based on such patterns furthermore mitigates searching through substantial amounts of data that may not provide much information about cardiovascular disease. Inspecting the cross-correlation for several combinations of window size and lag show a different profile for healthy and AF group individuals, showing that it is meaningful to analyze step counter and heart rate together. Big data for heart disease detection requires substantial labeling efforts from physicians.</p>", "<p id=\"p0160\">Using self-supervised learning and MIL, a model can be trained with much fewer labels. Our findings demonstrate this by employing MILES to achieve high specificity, which can aid in ruling out heart disease in individuals experiencing symptoms similar to heart disease but without the condition (ie, false-positives).</p>" ]
[ "<title>Conclusion</title>", "<p id=\"p0165\">The ongoing ME-TIME study is a longitudinal observational study that uses machine learning with time series data from consumer-grade smartwatches to detect atrial fibrillation and heart failure. This will contribute to cost-effective cardiovascular monitoring of outpatients, thereby reducing exacerbation of cardiovascular disease and effectively increasing capacity of global cardiovascular healthcare.</p>" ]
[ "<title>Background</title>", "<p>Smartwatches enable continuous and noninvasive time series monitoring of cardiovascular biomarkers like heart rate (from photoplethysmograms), step counter, skin temperature, et cetera; as such, they have promise in assisting in early detection and prevention of cardiovascular disease. Although these biomarkers may not be directly useful to physicians, a machine learning (ML) model could find clinically relevant patterns. Unfortunately, ML models typically need supervised (ie, annotated) data, and labeling of large amounts of continuous data is very labor intensive. Therefore, ML methods that are data efficient, ie, needing a low number of labels, are required to detect potential clinical value in patterns found in wearable data.</p>", "<title>Objective</title>", "<p>The primary study objective of the ME-TIME (Machine Learning Enabled Time Series Analysis in Medicine) study is to design an ML model that can detect atrial fibrillation (AF) and heart failure (HF) from wearable data in a data-efficient manner. To achieve this, self-supervised and weakly supervised learning techniques are used.</p>", "<title>Methods</title>", "<p>Two hundred subjects (100 reference, 50 AF, and 50 HF) are being invited to participate in wearing a Fitbit fitness tracker for 3 months. Interested volunteers are sent a questionnaire to determine their health, in particular cardiovascular health. Volunteers without any (history of) serious illness are assigned to the reference group. Participants with AF and HF are recruited in the Haga teaching hospital in The Hague, The Netherlands.</p>", "<title>Results</title>", "<p>Enrollment commenced on May 1, 2022, and as of the time of this report, 62 subjects have been included in the study. Preliminary analysis of the data reveals significant inter-subject variability. Notably, we identified heart rate recovery curves and time-delayed correlations between heart rate and step count as potential strong indicators for heart disease.</p>", "<title>Conclusion</title>", "<p>Using self-supervised and multiple-instance learning techniques, we hypothesize that patterns specific to AF and HF can be found in continuous data obtained from smartwatches.</p>", "<title>Keywords</title>" ]
[ "<title>Declaration of generative AI and AI-assisted technologies in the writing process</title>", "<p id=\"p0170\">During the preparation of this work the first author used chatGPT in order to correct spelling and grammar and to improve sentence clarity. After using this tool/service, the authors reviewed and edited the content as needed and take full responsibility for the content of the publication.</p>" ]
[ "<title>Funding Sources</title>", "<p id=\"p0175\">This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.</p>", "<title>Disclosures</title>", "<p id=\"p0180\">The authors declare no conflict of interest.</p>", "<title>Authorship</title>", "<p id=\"p0185\">All authors attest they meet the current ICMJE criteria for authorship.</p>", "<title>Patient Consent</title>", "<p id=\"p0190\">Informed consent was obtained from all subjects involved in the study.</p>", "<title>Institutional Review Board Statement</title>", "<p id=\"p0195\">The study was conducted in accordance with the Declaration of Helsinki, and approved by the Institutional Review Board (or Ethics Committee) of METC-LDD (protocol code NL73708.058.20) for studies involving humans.</p>" ]
[ "<fig id=\"fig1\"><label>Figure 1</label><caption><p>Data analysis pipeline for the ME-TIME study. Included participants (image 1) are given a smartwatch (image 2), which is connected to our data acquisition and storage platform (image 3). The resulting data are then preprocessed (image 4) and put into the data-efficient machine learning model (image 5). AF = atrial fibrillation group; HF = heart failure group; Ref = reference group.</p></caption></fig>", "<fig id=\"fig2\"><label>Figure 2</label><caption><p>Pipeline for the study’s proposed approach. <bold>a:</bold> Segmentation of the time series of each subject (1 healthy and 2 atrial fibrillation) using a sliding window. Only the label of the entire subject is available, instead of each individual window. <bold>b:</bold> The windows are inputs to an autoencoder and are compressed to a smaller (2-dimensional for illustrative purposes) representation. <bold>c:</bold> The compressed representation is used to train a multiple-instance classifier that can distinguish between healthy, atrial fibrillation, or heart failure). AF = atrial fibrillation.</p></caption></fig>", "<fig id=\"fig3\"><label>Figure 3</label><caption><p>Illustration of multiple-instance learning. The red and blue lines indicate bags of heart disease patients and reference subjects. Even though the labels for each instance are not known, for the sake of this example, the plus and minus signs depict time windows where heart disease is present or absent, respectively. The decision boundary is depicted by a dotted circle, where instances within the circle are classified as heart disease, and instances outside the circle are classified as healthy.</p></caption></fig>", "<fig id=\"fig4\"><label>Figure 4</label><caption><p>Our leave-p-subjects-out cross-validation strategy consists of the following: On the left, cross-validation folds are illustrated using 3 subjects with corresponding subject number. Green and blue represent training and validation subjects, respectively. On the right, a single fold is expanded and additionally illustrates the internal and external test sets. Each row corresponds to a subject, and the dotted squares within each row represent windows. The yellow external test block encompasses entire subjects and their corresponding data points that have not been encountered by the model. Meanwhile, the dark yellow internal test block consists of unobserved data points, representing the final 20% measurements of the time series from subjects already encountered during model development.</p></caption></fig>", "<fig id=\"fig5\"><label>Figure 5</label><caption><p>Visualization of heart rate windows (upper image) and step windows (lower image) of 6 subjects. Each window has data of 1 hour (720 time points for heart rate, 60 for steps, respectively). Each high-dimensional window is mapped to a 2-dimensional (2D) location using UMAP.##UREF##6##11## The contour curves illustrate the distribution of the 2D UMAP samples for each subject, with each color representing 1 of the 6 subjects.</p></caption></fig>", "<fig id=\"fig6\"><label>Figure 6</label><caption><p>Acceleration-deceleration curves during light activity. Red and blue represent data from subjects with persistent atrial fibrillation (n=7) and no heart disease (n=15), respectively. The mean and standard deviation are shown per time point (5 second intervals) for both groups.</p></caption></fig>", "<fig id=\"fig7\"><label>Figure 7</label><caption><p>Cross-correlation matrices between windowed heart rate data and number of steps for healthy and the persistent atrial fibrillation (AF) group. Rows are window sizes and columns lag between heart rate and step counter.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"tbl1\"><label>Table 1</label><caption><p>Characteristics of preliminary study participants as of May 2022</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th>Characteristic</th><th>Ref</th><th>HF</th><th>AF</th></tr></thead><tbody><tr><td>Participants, n</td><td align=\"char\">25</td><td align=\"char\">15</td><td align=\"char\">22</td></tr><tr><td>Age, y</td><td/><td/><td/></tr><tr><td> 18–39</td><td align=\"char\">16</td><td align=\"char\">1</td><td align=\"char\">0</td></tr><tr><td> 40–54</td><td align=\"char\">3</td><td align=\"char\">3</td><td align=\"char\">2</td></tr><tr><td> 55–64</td><td align=\"char\">5</td><td align=\"char\">5</td><td align=\"char\">3</td></tr><tr><td> 65+</td><td align=\"char\">1</td><td align=\"char\">6</td><td align=\"char\">17</td></tr><tr><td>Sex</td><td/><td/><td/></tr><tr><td> Male</td><td align=\"char\">12</td><td align=\"char\">12</td><td align=\"char\">15</td></tr><tr><td> Female</td><td align=\"char\">13</td><td align=\"char\">3</td><td align=\"char\">7</td></tr><tr><td>BMI</td><td/><td/><td/></tr><tr><td> 18.5–24.9</td><td align=\"char\">14</td><td align=\"char\">3</td><td align=\"char\">7</td></tr><tr><td> 25–29.9</td><td align=\"char\">6</td><td align=\"char\">6</td><td align=\"char\">8</td></tr><tr><td> 30+</td><td align=\"char\">5</td><td align=\"char\">6</td><td align=\"char\">7</td></tr><tr><td>Diabetes</td><td/><td/><td/></tr><tr><td> Yes</td><td align=\"char\">0</td><td align=\"char\">5</td><td align=\"char\">4</td></tr><tr><td> No</td><td align=\"char\">25</td><td align=\"char\">10</td><td align=\"char\">18</td></tr><tr><td>Smoking</td><td/><td/><td/></tr><tr><td> Yes</td><td align=\"char\">0</td><td align=\"char\">6</td><td align=\"char\">5</td></tr><tr><td> No</td><td align=\"char\">25</td><td align=\"char\">9</td><td align=\"char\">17</td></tr><tr><td>Hypertension</td><td/><td/><td/></tr><tr><td> Yes</td><td align=\"char\">2</td><td align=\"char\">8</td><td align=\"char\">15</td></tr><tr><td> No</td><td align=\"char\">23</td><td align=\"char\">7</td><td align=\"char\">7</td></tr><tr><td>Device</td><td/><td/><td/></tr><tr><td> Charge 5</td><td align=\"char\">23</td><td align=\"char\">8</td><td align=\"char\">12</td></tr><tr><td> Inspire 2</td><td align=\"char\">2</td><td align=\"char\">7</td><td align=\"char\">10</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"tbl2\"><label>Table 2</label><caption><p>Confusion matrix of per-week healthy vs atrial fibrillation classification of the MILES model with peak aligned curves concatenated with step counter data, with true and predicted labels shown vertically and horizontally, respectively</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th>True/Predicted label</th><th>AF</th><th>Healthy</th></tr></thead><tbody><tr><td>AF</td><td align=\"char\">11</td><td align=\"char\">14</td></tr><tr><td>Healthy</td><td align=\"char\">7</td><td align=\"char\">33</td></tr></tbody></table></table-wrap>" ]
[]
[ "<boxed-text id=\"dtbox1\"><sec id=\"dtbox1sec1\"><title>Box 1. A simple multiple-instance learning example</title><p id=\"p0075\">MIL is elaborated with an example in 3 steps.</p><p id=\"p0080\"><bold>Initial setup</bold> Under traditional supervised learning, each window must be annotated to train a machine learning model. However, in our MIL setting (##FIG##2##Figure 3##), only the bag label is known for the entire set of windows related to a subject. A bag label is considered negative if none of the subject’s individual samples are associated with heart disease, indicating that the subject is not affected by it. Conversely, a bag label is positive if a certain amount of the subject’s samples is linked to heart disease.</p><p id=\"p0085\"><bold>Learning</bold> The algorithm then learns a model based on the bag-level labels only. The goal of the MIL algorithm is to learn a model that can correctly predict the bag-level labels given the instances in each bag. By training on the bag-level labels, the MIL algorithm can capture patterns and relationships within the data that help identify the presence or absence of heart disease. Note that the decision boundary produced by the model in ##FIG##2##Figure 3## is not ideally suited for classifying individual windows, which is expected, as it did not use this information. However, if a sufficient number of windows are classified accurately, the correct bag label can still be predicted. This is accomplished during training by aggregating these accurate classifications using methods like majority voting, or by setting a threshold for the minimum number of positively predicted windows needed to assign a positive bag label.</p><p id=\"p0090\"><bold>Prediction</bold> Once the model is trained, it can predict the label of a new bag by examining the instances in the bag. If the model predicts that a certain percentage of instances in the bag are positive defined by the threshold, the bag is classified as positive (heart disease) and negative (healthy) otherwise. By analyzing the presence or absence of positive instances within the bag, the MIL algorithm can make predictions on a bag level, providing insights into the subject’s condition.</p></sec></boxed-text>" ]
[]
[]
[]
[]
[ "<table-wrap-foot><fn><p>AF = atrial fibrillation group; BMI = body mass index; HF = heart failure group; Ref = reference group.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p>AF = atrial fibrillation.</p></fn></table-wrap-foot>" ]
[ "<graphic xlink:href=\"gr1\"/>", "<graphic xlink:href=\"gr2\"/>", "<graphic xlink:href=\"gr3\"/>", "<graphic xlink:href=\"gr4\"/>", "<graphic xlink:href=\"gr5\"/>", "<graphic xlink:href=\"gr6\"/>", "<graphic xlink:href=\"gr7\"/>" ]
[]
[{"label": ["3"], "surname": ["Wasserlauf", "You", "Patel", "Valys", "Albert", "Passman"], "given-names": ["J.", "C.", "R.", "A.", "D.", "R."], "article-title": ["Smartwatch performance for the detection and quantification of atrial fibrillation"], "source": ["Circ Arrhythm Electrophysiol"], "volume": ["12"], "year": ["2019"], "object-id": ["e006834"]}, {"label": ["4"], "surname": ["Zhu", "Nathan", "Kuang"], "given-names": ["L.", "V.", "J."], "article-title": ["Atrial fibrillation detection and atrial fibrillation burden estimation via wearables"], "source": ["IEEE J Biomed Health Inform"], "volume": ["26"], "year": ["2021"], "fpage": ["2063"], "lpage": ["2074"]}, {"label": ["6"], "surname": ["Hall", "Mitchell", "Wood", "Holland"], "given-names": ["A.", "A.R.J.", "L.", "C."], "article-title": ["Effectiveness of a single lead AliveCor electrocardiogram application for the screening of atrial fibrillation: a systematic review"], "source": ["Medicine (Baltimore)"], "volume": ["99"], "year": ["2020"], "object-id": ["e21388"]}, {"label": ["8"], "surname": ["Mienye", "Sun", "Wang"], "given-names": ["I.D.", "Y.", "Z."], "article-title": ["Improved sparse autoencoder based artificial neural network approach for prediction of heart disease"], "source": ["Informatics in Medicine Unlocked"], "volume": ["18"], "year": ["2020"], "object-id": ["100307"]}, {"label": ["9"], "surname": ["Spathis", "Perez-Pozuelo", "Brage", "Wareham", "Mascolo"], "given-names": ["D.", "I.", "S.", "N.J.", "C."], "part-title": ["Self-supervised transfer learning of physiological representations from free-living wearable data"], "source": ["Proceedings of the Conference on Health"], "year": ["2021"], "publisher-name": ["Inference, and Learning"], "fpage": ["69"], "lpage": ["78"]}, {"label": ["10"], "surname": ["Quer", "Gouda", "Galarnyk", "Topol", "Steinhubl"], "given-names": ["G.", "P.", "M.", "E.J.", "S.R."], "article-title": ["Inter-and intraindividual variability in daily resting heart rate and its associations with age, sex, sleep, BMI, and time of year: retrospective, longitudinal cohort study of 92,457 adults"], "source": ["PLoS One"], "volume": ["15"], "year": ["2020"], "object-id": ["e0227709"]}, {"label": ["11"], "mixed-citation": ["McInnes L, Healy J, Melville J. Umap: Uniform manifold approximation and projection for dimension reduction. arXiv preprint arXiv:1802.03426\u00a02018."]}, {"label": ["14"], "surname": ["Lan", "Ng", "Hong", "Feng"], "given-names": ["X.", "D.", "S.", "M."], "article-title": ["Intra-inter subject self-supervised learning for multivariate cardiac signals"], "source": ["Proceedings of the AAAI Conference on Artificial Intelligence"], "volume": ["36"], "year": ["2022"], "fpage": ["4532"], "lpage": ["4540"]}]
{ "acronym": [], "definition": [] }
14
CC BY
no
2024-01-14 23:41:58
Cardiovasc Digit Health J. 2023 Oct 4; 4(6):165-172
oa_package/df/67/PMC10787149.tar.gz
PMC10787169
0
[ "<title>Introduction</title>", "<p>Preeclampsia (PE) is a multisystem disorder that causes high blood pressure and often comes with new organ dysfunction or proteinuria. It is linked to a number of issues that put women and their unborn babies at a higher risk for more complications and problems that will last a lifetime [##REF##15733721##1##]. PE has been significantly prevalent in developing countries and constitutes a leading cause of maternal mortality in low-income countries [##UREF##0##2##]. Women with PE in developing countries have a higher risk of mortality than those in developed countries, and hypertension is one of the leading causes of maternal mortality in PE [##REF##23403779##3##]. Currently, PE is generally classified into early-onset PE (EOP) and late-onset PE (LOP), which exhibit different clinical manifestations and pathogenesis. EOP is associated with placental insufficiency and defective vascular remodeling, whereas LOP is most likely caused by maternal factors, particularly vascular maladaptation [##REF##25561694##4##,##REF##18824660##5##].</p>", "<p>PE has been linked to long-term damage to the kidneys, such as a higher risk of albuminuria [##REF##24034653##6##], chronic kidney disease (CKD) [##UREF##1##7##], and end-stage kidney disease (ESKD) [##REF##31352975##8##]. Some studies report that kidney dysfunction can resolve in most women with a history of PE [##REF##29289477##9##,##REF##27491315##10##]. However, some women with PE may experience persistently decreased glomerular filtration rate (GFR) and/or proteinuria and/or an increased risk of CKD [##REF##27939480##11##,##REF##20346562##12##]. Only a few data points were presented about its long-term effects on kidney function later in life, mostly in EOP and LOP. EOP and LOP are linked to various outcomes, biochemical markers, and clinical features in both the mother and the fetus. Because of this, it is believed that EOP is a major risk for both the mother and the fetus, while LOP may have milder symptoms [##REF##31637053##13##]. It has been suggested that EOP and LOP have different risks of developing renal impairment in women with PE. Unfortunately, to our knowledge, there is no data or international publication on the risk of CKD following PE in a developing country. Thus, this study intends to explore the risk of renal failure in EOP and LOP five years after PE in Indonesia, one of low middle income country in Southeast Asia. This article was previously posted to the Research Square preprint server on January 23, 2023.</p>" ]
[ "<title>Materials and methods</title>", "<p>This was a retrospective cohort study of women who had previously been diagnosed with severe PE or eclampsia and delivered at Dr. Soetomo General Academic Hospital, one of the largest tertiary referral hospitals in East Indonesia, between January 2013 and June 2014. Using the medical records, we identified all patients who met our criteria and included them in the exposed group, whereas women who recorded having an uncomplicated pregnancy constituted the control group. All exposed cases who lived in Surabaya and were willing to engage in this study were then enrolled. However, women with pre-existing comorbidities such as chronic hypertension, kidney disease, diabetes, autoimmune disease, and cardiac disease at the time of their pregnancy, women who had twins or multiple fetuses, and patients who died over the course of this study were excluded. All samples were contacted and/or visited at their residences before being invited to the hospital for a medical examination and blood sampling test.</p>", "<p>PE or eclampsia was defined according to revised International Society for the Study of Hypertension in Pregnancy (ISSHP) criteria: the presence of hypertension (systolic blood pressure &gt;140mmHg and/or diastolic blood pressure &gt;90mmHg), which developed after 20 weeks of pregnancy, and the coexistence of one or more of the following new-onset conditions: proteinuria (spot urine protein/creatinine ratio 430mg/mmol or 4,300 mg protein/24 h or at least ‘‘2+’’ on dipstick testing), and/or other maternal organ dysfunction and/or suspected intrauterine growth restriction (IUGR). Depending on time, EOP was defined as PE that develops before 34 weeks of gestation, whereas LOP was defined as PE that develops at or after 34 weeks of gestation [##UREF##2##14##]. An uncomplicated pregnancy history was defined as a woman who gave birth between 37 and 42 weeks of gestation, had normal blood pressure, and was without IUGR.</p>", "<p>Patients who met the inclusion criteria and did not meet the inclusion criteria were contacted by telephone or made home visits, and subjects willing to participate in the study were asked to come to the hospital to have their blood pressure and kidney function checked. Blood pressure checks are carried out in the hospital using an electronic blood pressure monitor after the patient has rested for 30 minutes.</p>", "<p>The primary outcome of the study was the risk of CKD defined according to Kidney Disease Improvement Global Outcomes (KDIGO) 2012 definitions for the classification of CKD based on renal function measured by GFR. Renal function was measured using serum creatinine (Cr) values determined by the Jaffe method and calibrated using isotope dilution mass spectrometry (IDMS) method. Estimated Glomerular Filtration Rate (eGFR) was calculated using the modified Cockcroft and Gault: GFR = (((l40 - age (year)) x weight (kg))/(72 x serum creatinine (mg/dL))) x 0.85. Proteinuria was measured using urinalysis examination. According to these criteria, risk of CKD classified into low risk if the eGFR &gt;60 mL/min/1.73m<sup>2</sup> and proteinuria &lt;30 mg/g, whereas high risk if the eGFR 30-44 mL/min/1.73m<sup>2</sup> and proteinuria &lt;30mg/g or the eGFR &gt;60 mL/min/1.73m<sup>2</sup> and proteinuria &gt;300 mg/g [##UREF##3##15##].</p>", "<p>Basic characteristics data were presented for women with priorly diagnosed EOP or LOP compared to those healthy pregnant women. Categorical data was presented as frequencies (percentage), while continuous variables was presented either as mean (standard deviation/SD) or median (interquartile range/IQR). Differences were analyzed using Kruskal Wallis and the Fisher exact test was applied as an alternative test. Differences in values between groups considered statistically significant if the P-value was &lt;0.05. Odds ratios for the primary outcomes were calculated using logistic regression with 95% confidence intervals (CI). All statistical analysis were performed using SPSS 21 software (IBM Corp., Armonk, NY). The Human Research and Ethics Committee for Basic Science and Clinical Research of Dr. Soetomo General Academic Hospital approved the research protocol (Ref. No: 0842/KEPK/XII/2018). Informed consent was obtained from all participants before the initiation of the study.</p>" ]
[ "<title>Results</title>", "<p>During periods of study, 673 women who were previously diagnosed with PE between January 2013 and June 2014 were listed in their medical records. At the beginning, all patients were assessed for eligibility criteria, of whom 235 met inclusion and exclusion criteria and were enrolled in this study. After excluding some patients due to some reasons, we finally included 62 exposed women with prior PE history, consisting of 27 with EOP and 35 with LOP. We also recruited 30 healthy pregnant women to participate in this study as a control group. Details regarding the study selection are documented in Figure ##FIG##0##1##.</p>", "<p>The basic characteristics and laboratory outcomes of the included participants when first diagnosed with PE are presented in Table ##TAB##0##1##. Our study found that women with prior PE tend to have a higher mean maternal age compared to the control group with normotensive blood pressure at the time of delivery. The LOP group was dominated by multiparity, whereas the EOP group was dominated by nulliparity. Our results also showed that women with EOP had a significantly higher mean body mass index (BMI) compared to women with LOP and the control group (p = 0.019) and were more likely to have chronic hypertension, kidney disease, and diabetes. However, those with chronic hypertension or CKD at baseline were excluded from further analysis. As expected, the mean systolic blood pressure of women with prior EOP and LOP was significantly higher compared to the control group (p = 0.001), as well as diastolic blood pressure (p = 0.001). Our study also found that gestational age at delivery significantly differed between groups (p = 0.001). Moreover, there was no statistically significant difference in eGFR between the EOP, LOP, and control groups (p = 0.577).</p>", "<p>After five years from being first diagnosed with severe PE, the mean systolic and diastolic blood pressure showed significantly higher result in EOP group compared to all groups (p = 0.001). We obtained those women with EOP also had higher mean of BMI (30.23 ± 4.94 kg/m<sup>2</sup>) compared to LOP and control group (27.07 ± 4.51 kg/m<sup>2</sup> and 28.27 ± 4.07 kg/m<sup>2</sup>, respectively), although failed to show significant difference (p = 0.084). All parameters in renal function showed statistically significant difference between groups, except for the number of positive proteinuria and abnormal protein-to-creatinine ratio between LOP compared to control group (p &gt; 0.05). Additionally, our analysis obtained those women with prior EOP history showed a significant decrease of eGFR compared to all groups (p = 0.001), indicating that the group with prior history of EOP may pose worse renal outcome compared to other groups. Detailed information regarding other characteristics is documented in Table ##TAB##1##2##.</p>", "<p>Further analysis regarding the incidence of persistent hypertension among women with prior history of PE were varied from 66.7% and 25.7% in EOP and LOP groups respectively. According to the logistic regression analysis, RR of developing persistent hypertension is significantly higher among women with prior history of EOP (RR 5.778; P-value = 0.002; 95% CI 1.919-17.395), as well as the risk of developing CKD (RR 6.75; P-value = 0.001; 95% CI 2.194-20.764) compared to women with prior history of LOP (Table ##TAB##2##3##). Likewise, according to KDIQO 2012 classification, women with prior severe PE history had significantly higher risk of further developing CKD (RR 20.94; P-value = 0.004; 95% CI 2.679-163.723) compared to normotensive control group.</p>" ]
[ "<title>Discussion</title>", "<p>This study revealed that five years after delivery, women with a history of PE were at risk for persistent hypertension. EOP and LOP cases had higher blood pressure than normal pregnant women. Results from prior studies indicated that roughly 20% and 8% of women with a history of PE still had hypertension and proteinuria six months postpartum, respectively [##REF##29783931##16##]. The study by Berks et al. showed 39% and 14% of women with a prior history of PE remained with high blood pressure and proteinuria three months postpartum, while 18% and 8% remained with hypertension and proteinuria two years afterward [##REF##19935034##17##].</p>", "<p>Our study found that women with EOP have higher blood pressure than LOP. Women with EOP have a risk of developing persistent hypertension 5.7 times higher than LOP. A study by Veerbeek et al. observed that nearly half of women with a history of EOP developed persistent postpartum hypertension. Moreover, the blood pressure of women with an EOP history and pregnancy-induced hypertension was considerably greater than that of women with a LOP history [##REF##25561694##4##]. Comparing EOP and LOP, the maternal vascular response and remodeling pattern revealed distinct vascular adaptations. Therefore, increased vascular resistance can contribute to systolic and diastolic dysfunction and could be a driving force behind the development of chronic hypertension in women with EOP [##REF##18824660##5##]. Consequently, our findings support the idea that cardiovascular risk during pregnancy is predictive of cardiovascular risk later in life, particularly the risk of persistent hypertension [##REF##17975257##18##,##REF##26203257##19##].</p>", "<p>Our study indicated that women with a history of severe PE had a greater risk of CKD than the normotensive group. The risk of developing CKD at five years after delivery in severe PE patients is 20 times higher than in normal pregnancies. Patients with a previous history of PE presented lower eGFR and had more cases of persistent protein urine than normal pregnant women. Moreover, eGFR was the lowest in the EOP group. A previous report, including a large cohort study, found hypertensive disorders of pregnancy are associated with an increased risk of subsequent CKD. Renal impairment was also found earlier in women with GH and PE than in normotensive women [##REF##27491315##10##]. Another study also reported a close association between PE and gestational hypertension with the risk of renal disorder in the future [##UREF##1##7##,##REF##18716297##20##, ####REF##8534622##21##, ##REF##11533780##22####11533780##22##].</p>", "<p>The risk of CKD in EOP and LOP differed significantly in this study. EOP had a higher risk of developing CKD than LOP. The large cohort study by Vikse et al., with a sample of 570,433 women, showed that PE was a risk factor for the development of end-stage renal disease (ESRD). The risk is higher in PE patients who give birth to premature babies or children with low birth weight, which indicates EOP cases [##REF##18716297##20##]. Irreversible vascular damage due to more severe endothelial damage and inflammatory stress in EOP than in LOP cannot be disregarded [##UREF##4##23##]. Renal histology of postpartum biopsies on PE patients showed glomerular endotheliosis and vascular injury as classic pathologies features [##REF##7242320##24##] support this finding. PE is suggested to develop kidney disease by causing acute renal impairment, endothelial damage, and podocyte loss [##REF##7242320##24##].</p>", "<p>Endothelial dysfunction induced by PE persists after PE in many patients [##REF##15738035##25##]. The remaining endothelial dysfunction is unknown; It could be assumed that endothelial cell disturbance enhances by a high level of Soluble vascular endothelial growth factor receptor-1 (sFlt-1) in women with a history of PE and also due to epigenetic changes induced by PE [##UREF##5##26##].</p>", "<p>Increased levels of sFlt-1 have been found in formerly preeclamptic women [##REF##15579783##27##,##REF##18231881##28##]. This persistence of elevated levels of sFlt-1 in women with a history of PE is expected due to an extra-placental source such as endothelial cells and monocytes. This increased sFlt-1 may lead to changes in the vascular endothelium, increasing the risk of renovascular diseases in later life. Interestingly, increasing sFlt-1 was also found in CKD patients without a history of PE, which positively correlates with proteinuria [##REF##19608702##29##].</p>", "<p> This fact follows EOP. The combination of insufficient immune tolerance to the fetus and poor placentation resulted in the elevation of serum sFlt-1 and decreasing of Placental growth factor (PlGF) level, thus causing vascular endothelial dysfunction, which led to PE manifestation by 34 weeks gestation [##UREF##6##30##]. It may explain that the risk of developing CKD was higher in EOP than in LOP.</p>", "<p>The strengths of this study are mostly related to our hospital (Dr. Soetomo General Academic Hospital), a level 3 and top referral center hospital in eastern Indonesia. At level 3, we have many cases of PE, and almost all cases of EOP and all conservative management are referred to our hospital. Therefore, we have a large number of EOP and LOP cases.</p>", "<p>As the limitation of the study, we have to consider that this was a retrospective cohort study. Thus, some information may be missed, like no assessment of renal anatomic abnormalities before pregnancy or when the patient was diagnosed with severe PE, as it is not a standard procedure for initial examination before pregnancy or at the time of diagnosis in our hospital. The high mobility of the population makes this research even more challenging. Since most of the patients in this study were seasonal residents who moved frequently, it was difficult to ascertain their whereabouts, reducing the number of participating patients. However, these limitations do not invalidate our conclusion that EOP is associated with a higher risk of CKD than LOP.</p>", "<p>Awareness that severe PE may be associated with a higher risk of persistent hypertension and CKD means that PE patients should follow up regarding this risk. It is necessary to regularly evaluate blood pressure and kidney function to assess the possibility of CKD.</p>" ]
[ "<title>Conclusions</title>", "<p>In women with a history of PE, the outcome of persistent hypertension and/or proteinuria may have renal repercussions. It was found that both systolic and diastolic blood pressures were strongly linked to a history of PE. This has an impact on future kidney problems in both the EOP and LOP groups. In a five-year follow-up, women with severe PE had a higher risk of developing CKD than normotensive women. In addition, women with a history of EOP are more likely to develop persistent hypertension and CKD than women with a prior LOP history.</p>" ]
[ "<p>Background and objective: Preeclampsia (PE) has been disproportionately prevalent in developing countries and constitutes a leading cause of maternal mortality, and also has long-term impacts, including renal consequences. This study aimed to explore the risk of persistent hypertension and kidney failure in early-onset PE (EOP) and late-onset PE (LOP) in the five years after delivery.</p>", "<p>Methods: This retrospective cohort study included women with a prior history of severe PE or normotensive pregnancy admitted to tertiary hospitals in Indonesia. The blood pressure, body mass index (BMI), urea, creatinine serum, and protein urine were analyzed, and the risk of chronic kidney disease (CKD) after five years was performed using the Kidney Disease Improvement Global Outcomes (KDIGO) classification.</p>", "<p>Results: Twenty-seven EOP, 35 LOP, and 30 normotensive cases were included. Mean blood pressure after five years was recorded as 115.6 ± 14.25 mmHg in the normotensive group, 131.82 ± 19.34 mmHg in the LOP group, and 154.96 ± 23.48 mmHg in the EOP group. According to the KDIGO classification, the normotensive group had an average 10% risk of CKD, but severe PE had a risk of CKD greater than 90%. In the severe PE group, the risk of CKD was 20.94 times higher compared to normotensive women (OR 20.94; 95% CI 2.67-163.72, p = 0.004). The risk of CKD in the EOP group was 6.75 times higher than in the LOP group (OR 6.75; 95% CI 2.19-20.76, p = 0.001), whereas persistent hypertension in the EOP group was 5.78 times higher than in the LOP group (OR 5.78; 95% CI 1.91-17.395, p = 0.002).</p>", "<p>Conclusions: PE women have a higher risk of CKD than normotensive women. Women with a history of EOP are more likely to develop persistent hypertension and CKD than women with a prior LOP history.</p>" ]
[]
[]
[ "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG1\"><label>Figure 1</label><caption><title>Study flowchart.</title><p>PE, pre-eclampsia; EOP, early-onset pre-eclampsia; LOP, late-onset pre-eclampsia.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"TAB1\"><label>Table 1</label><caption><title>Baseline characteristics of the sample at delivery</title><p> *P-value from Kruskal-Wallis test for three groups, while Fisher exact test for each two groups; C, control group; EOP, early-onset severe preeclampsia; LOP, late-onset severe preeclampsia; SD, standard deviation; BMI, body mass index; BUN, blood urea nitrogen; Cr, serum creatinine; eGFR, estimated glomerular filtration rate.</p></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"2\" colspan=\"1\">Characteristics</td><td rowspan=\"2\" colspan=\"1\">Control (n = 30)</td><td colspan=\"2\" rowspan=\"1\">Pre-eclampsia</td><td colspan=\"3\" rowspan=\"1\">P-value</td></tr><tr><td rowspan=\"1\" colspan=\"1\">LOP (n = 35)</td><td rowspan=\"1\" colspan=\"1\">EOP (n = 27)</td><td rowspan=\"1\" colspan=\"1\">C -LOP</td><td rowspan=\"1\" colspan=\"1\">C-EOP</td><td rowspan=\"1\" colspan=\"1\">LOP-EOP</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Age, mean (SD), years</td><td rowspan=\"1\" colspan=\"1\">30.1 ± 6.06</td><td rowspan=\"1\" colspan=\"1\">34.46 ± 7.38</td><td rowspan=\"1\" colspan=\"1\">33.07 ± 7.01</td><td colspan=\"3\" rowspan=\"1\">                     0.058</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Parity, n (%)</td><td rowspan=\"1\" colspan=\"1\"> </td><td colspan=\"5\" rowspan=\"1\"> </td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Nullipara</td><td rowspan=\"1\" colspan=\"1\">11 (36.6)</td><td rowspan=\"1\" colspan=\"1\">14 (40)</td><td rowspan=\"1\" colspan=\"1\">20 (74.1)</td><td rowspan=\"1\" colspan=\"1\">0.785</td><td rowspan=\"1\" colspan=\"1\">0.005*</td><td rowspan=\"1\" colspan=\"1\">0.006*</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Multipara</td><td rowspan=\"1\" colspan=\"1\">19 (63.4)</td><td rowspan=\"1\" colspan=\"1\">21 (60)</td><td rowspan=\"1\" colspan=\"1\">7 (25.9)</td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\"> </td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">BMI, mean (SD), (kg/m<sup>2</sup>)</td><td rowspan=\"1\" colspan=\"1\">28.27 ± 4.07</td><td rowspan=\"1\" colspan=\"1\">27.07 ± 4.51</td><td rowspan=\"1\" colspan=\"1\">30.23 ± 4.94</td><td colspan=\"3\" rowspan=\"1\">                       0.019*</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Gestational age at delivery, mean (SD), (weeks)</td><td rowspan=\"1\" colspan=\"1\">38.89 ± 1.38</td><td rowspan=\"1\" colspan=\"1\">37.20 ± 2.86</td><td rowspan=\"1\" colspan=\"1\">33.3 ± 3.01</td><td colspan=\"3\" rowspan=\"1\">                       0.001*</td></tr><tr style=\"background-color:#ccc\"><td colspan=\"2\" rowspan=\"1\">Blood pressure at admission mean (SD), (mmHg)</td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\"> </td><td colspan=\"3\" rowspan=\"1\"> </td></tr><tr><td rowspan=\"1\" colspan=\"1\">Systolic</td><td rowspan=\"1\" colspan=\"1\">111.66 ± 12.05</td><td rowspan=\"1\" colspan=\"1\">160.34 ± 18.22</td><td rowspan=\"1\" colspan=\"1\">168.88 ± 15.63</td><td colspan=\"3\" rowspan=\"1\">                        0.001*</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Diastolic</td><td rowspan=\"1\" colspan=\"1\">70.66 ± 9.07</td><td rowspan=\"1\" colspan=\"1\">102.11 ± 8.20</td><td rowspan=\"1\" colspan=\"1\">90.00 ± 16.40</td><td colspan=\"3\" rowspan=\"1\">                        0.001*</td></tr><tr><td colspan=\"2\" rowspan=\"1\">Renal function test at admission</td><td colspan=\"5\" rowspan=\"1\"> </td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">BUN, n (%)        BUN &gt; 21 mg/dL</td><td rowspan=\"1\" colspan=\"1\">0 (0)</td><td rowspan=\"1\" colspan=\"1\">2 (5.7)</td><td rowspan=\"1\" colspan=\"1\">5 (18.5)</td><td rowspan=\"1\" colspan=\"1\">0.187</td><td rowspan=\"1\" colspan=\"1\">0.014*</td><td rowspan=\"1\" colspan=\"1\">1.117</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Serum creatinine, n (%)       Cr &gt; 1.1 mg/dL</td><td rowspan=\"1\" colspan=\"1\">1 (3.3)</td><td rowspan=\"1\" colspan=\"1\">0 (0)</td><td rowspan=\"1\" colspan=\"1\">2 (7.4)</td><td rowspan=\"1\" colspan=\"1\">0.280</td><td rowspan=\"1\" colspan=\"1\">0.495</td><td rowspan=\"1\" colspan=\"1\">0.104</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">eGFR, mean (SD) (ml/min/1.73m<sup>2</sup>)</td><td rowspan=\"1\" colspan=\"1\">194.93 ± 33.03</td><td rowspan=\"1\" colspan=\"1\">171.37 ± 50.86</td><td rowspan=\"1\" colspan=\"1\">163.79 ± 57.78</td><td colspan=\"3\" rowspan=\"1\">                   0.577</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Proteinuria (+), n (%)</td><td rowspan=\"1\" colspan=\"1\">0 (0)</td><td rowspan=\"1\" colspan=\"1\">35 (100)</td><td rowspan=\"1\" colspan=\"1\">27 (100)</td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\"> </td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"TAB2\"><label>Table 2</label><caption><title>Characteristics of the sample five years after delivery</title><p>*P-value from Kruskal-Wallis test for three groups, while Fisher exact test for each two groups; C, control group; EOP, early-onset severe preeclampsia; LOP, late-onset severe preeclampsia; SD, standard deviation; BMI, body mass index; BUN, blood urea nitrogen; Cr, serum creatinine; eGFR, estimated glomerular filtration rate.</p></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"2\" colspan=\"1\">Characteristics</td><td rowspan=\"2\" colspan=\"1\">Control (n = 30)</td><td colspan=\"2\" rowspan=\"1\">Pre-eclampsia</td><td colspan=\"3\" rowspan=\"1\">P-value</td></tr><tr><td rowspan=\"1\" colspan=\"1\">LOP (n = 35)</td><td rowspan=\"1\" colspan=\"1\">EOP (n = 27)</td><td rowspan=\"1\" colspan=\"1\">C-         LOP</td><td rowspan=\"1\" colspan=\"1\">C- EOP</td><td rowspan=\"1\" colspan=\"1\">LOP EOP</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">BMI, mean (SD), (kg/m<sup>2</sup>)</td><td rowspan=\"1\" colspan=\"1\">28.27 ± 4.07</td><td rowspan=\"1\" colspan=\"1\">27.07 ± 4.51</td><td rowspan=\"1\" colspan=\"1\">30.23 ± 4.94</td><td colspan=\"3\" rowspan=\"1\">                     0.084</td></tr><tr><td colspan=\"2\" rowspan=\"1\">Blood pressure at admission mean (SD), (mmHg)</td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\"> </td><td colspan=\"3\" rowspan=\"1\"> </td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">    Systolic</td><td rowspan=\"1\" colspan=\"1\">115.6 ± 14.25</td><td rowspan=\"1\" colspan=\"1\">131.82 ± 19.34</td><td rowspan=\"1\" colspan=\"1\">154.96 ± 23.48</td><td colspan=\"3\" rowspan=\"1\">                     0.001*</td></tr><tr><td rowspan=\"1\" colspan=\"1\">    Diastolic</td><td rowspan=\"1\" colspan=\"1\">66.53 ± 11.41</td><td rowspan=\"1\" colspan=\"1\">81.74 ± 14.49</td><td rowspan=\"1\" colspan=\"1\">96.00 ± 16.16</td><td colspan=\"3\" rowspan=\"1\">                     0.001*</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">    Persistent hypertension, n (%)</td><td rowspan=\"1\" colspan=\"1\">0 (0)</td><td rowspan=\"1\" colspan=\"1\">9 (25.7)</td><td rowspan=\"1\" colspan=\"1\">18 (66.7)</td><td rowspan=\"1\" colspan=\"1\">0.003*</td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\">0.001*</td></tr><tr><td colspan=\"2\" rowspan=\"1\">Renal function test, mean (SD)</td><td colspan=\"5\" rowspan=\"1\"> </td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">BUN, n (%)        BUN &gt; 21 mg/dL</td><td rowspan=\"1\" colspan=\"1\">0 (0)</td><td rowspan=\"1\" colspan=\"1\">0 (0)</td><td rowspan=\"1\" colspan=\"1\">10 (37.1)</td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\">0.001*</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Serum creatinine, n (%)       Cr &gt; 1.1 mg/dL</td><td rowspan=\"1\" colspan=\"1\">0 (0)</td><td rowspan=\"1\" colspan=\"1\">0 (0)</td><td rowspan=\"1\" colspan=\"1\">10 (37.1)</td><td rowspan=\"1\" colspan=\"1\"> </td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\">0.001*</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">eGFR, mean (SD) (ml/min/1.73m<sup>2</sup>)</td><td rowspan=\"1\" colspan=\"1\">143.67 ± 33.77</td><td rowspan=\"1\" colspan=\"1\">120.80 ± 42.81</td><td rowspan=\"1\" colspan=\"1\">97.22 ± 28.71</td><td colspan=\"3\" rowspan=\"1\">                               0.001*</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Proteinuria (+), n (%)</td><td rowspan=\"1\" colspan=\"1\">4 (13.3)</td><td rowspan=\"1\" colspan=\"1\">11 (31.4)</td><td rowspan=\"1\" colspan=\"1\">18 (66.7)</td><td rowspan=\"1\" colspan=\"1\">0.087</td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\">0.006*</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Abnormal albumine-to-cratinine ratio, n (%)</td><td rowspan=\"1\" colspan=\"1\">4 (13.3)</td><td rowspan=\"1\" colspan=\"1\">13 (37.1)</td><td rowspan=\"1\" colspan=\"1\">19 (70.4)</td><td rowspan=\"1\" colspan=\"1\">0.031*</td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\">0.010*</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Abnormal protein-to-creatinine ratio, n (%)</td><td rowspan=\"1\" colspan=\"1\">6 (20)</td><td rowspan=\"1\" colspan=\"1\">9 (25.7)</td><td rowspan=\"1\" colspan=\"1\">18 (66.7)</td><td rowspan=\"1\" colspan=\"1\">0.589</td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\">0.001*</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Persistent proteinuria, n (%)</td><td rowspan=\"1\" colspan=\"1\">0 (0)</td><td rowspan=\"1\" colspan=\"1\">11 (31.4)</td><td rowspan=\"1\" colspan=\"1\">18 (66.7)</td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\">0.001*</td><td rowspan=\"1\" colspan=\"1\">0.006*</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"TAB3\"><label>Table 3</label><caption><title>The association between the type of PE with the incidence of persistent hypertension and the risk of developing CKD 5 years after diagnosis.</title><p>*P-value from Kruskal-Wallis test for three groups; PE, pre-eclampsia; EOP, early-onset pre-eclampsia; LOP, late-onset pre-eclampsia; CKD, chronic kidney disease; RR, relative risk; CI, confidence interval.</p></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"2\" colspan=\"1\">\nVariables\n</td><td colspan=\"2\" rowspan=\"1\">\nType of PE\n</td><td rowspan=\"2\" colspan=\"1\">\nTotal\n</td><td rowspan=\"2\" colspan=\"1\">\nP-value\n</td><td rowspan=\"2\" colspan=\"1\">\nRR\n(95%CI)\n</td></tr><tr><td rowspan=\"1\" colspan=\"1\">\nLOP\n</td><td rowspan=\"1\" colspan=\"1\">\nEOP\n</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">\nPersistent Hypertension\n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td></tr><tr><td rowspan=\"1\" colspan=\"1\">\n     Yes\n</td><td rowspan=\"1\" colspan=\"1\">\n9 (25.7%)\n</td><td rowspan=\"1\" colspan=\"1\">\n18 (66.7%)\n</td><td rowspan=\"1\" colspan=\"1\">\n27\n</td><td rowspan=\"2\" colspan=\"1\">\n0.002*\n</td><td rowspan=\"2\" colspan=\"1\">\n5.778 (1.919 – 17.395)\n</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">\n     No\n</td><td rowspan=\"1\" colspan=\"1\">\n26 (74.3%)\n</td><td rowspan=\"1\" colspan=\"1\">\n9 (33.3%)\n</td><td rowspan=\"1\" colspan=\"1\">\n35\n</td></tr><tr><td rowspan=\"1\" colspan=\"1\">\nRisk of CKD\n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td><td rowspan=\"1\" colspan=\"1\">\n \n</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">\n     High\n</td><td rowspan=\"1\" colspan=\"1\">\n8 (22.9%)\n</td><td rowspan=\"1\" colspan=\"1\">\n18 (66.7%)\n</td><td rowspan=\"1\" colspan=\"1\">\n26\n</td><td rowspan=\"2\" colspan=\"1\">\n0.001*\n \n</td><td rowspan=\"2\" colspan=\"1\">\n6.75 (2.194 – 20.764)\n</td></tr><tr><td rowspan=\"1\" colspan=\"1\">\n     Low\n</td><td rowspan=\"1\" colspan=\"1\">\n27(77.1%)\n</td><td rowspan=\"1\" colspan=\"1\">\n9 (33.3%)\n</td><td rowspan=\"1\" colspan=\"1\">\n36\n</td></tr></tbody></table></table-wrap>" ]
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[ "<fn-group content-type=\"other\"><title>Author Contributions</title><fn fn-type=\"other\"><p><bold>Concept and design:</bold>  Ernawati Ernawati, Aditiawarman Aditiawarman, Erry Gumilar Dachlan</p><p><bold>Acquisition, analysis, or interpretation of data:</bold>  Ernawati Ernawati, Aditiawarman Aditiawarman, Agus Sulistyono, Kamalia Hasanah, Salsabilah N. Ridfah, M Ilham A. Akbar, Erry Gumilar Dachlan</p><p><bold>Drafting of the manuscript:</bold>  Ernawati Ernawati, Aditiawarman Aditiawarman, Agus Sulistyono, Kamalia Hasanah, Salsabilah N. Ridfah, M Ilham A. Akbar</p><p><bold>Critical review of the manuscript for important intellectual content:</bold>  Ernawati Ernawati, Kamalia Hasanah, Salsabilah N. Ridfah, Erry Gumilar Dachlan</p><p><bold>Supervision:</bold>  Ernawati Ernawati, Erry Gumilar Dachlan</p></fn></fn-group>", "<fn-group content-type=\"other\"><title>Human Ethics</title><fn fn-type=\"other\"><p>Consent was obtained or waived by all participants in this study. Ethics Committee of Dr. Soetomo General Academic Hospital issued approval Ref. No: 0842/KEPK/XII/2018</p></fn></fn-group>", "<fn-group content-type=\"other\"><title>Animal Ethics</title><fn fn-type=\"other\"><p><bold>Animal subjects:</bold> All authors have confirmed that this study did not involve animal subjects or tissue.</p></fn></fn-group>", "<fn-group content-type=\"competing-interests\"><fn fn-type=\"COI-statement\"><p>The authors have declared that no competing interests exist.</p></fn></fn-group>" ]
[ "<graphic xlink:href=\"cureus-0015-00000050488-i01\" position=\"float\"/>" ]
[]
[{"label": ["2"], "article-title": ["OS018. Maternal mortality and its mainly possible cause pre-eclampsia/eclampsia in developing country (Surabaya-Indonesia as the model)"], "source": ["Pregnancy Hypertens"], "person-group": ["\n"], "surname": ["Akbar", "Wicaksono", "Dachlan"], "given-names": ["A", "B", "EG"], "fpage": ["184"], "volume": ["2"], "year": ["2012"]}, {"label": ["7"], "article-title": ["Pre-eclampsia and risk of later kidney disease: nationwide cohort study"], "source": ["BMJ"], "person-group": ["\n"], "surname": ["Kristensen", "Basit", "Wohlfahrt", "Damholt", "Boyd"], "given-names": ["JH", "S", "J", "MB", "HA"], "fpage": ["0"], "volume": ["365"], "year": ["2019"]}, {"label": ["14"], "article-title": ["Early and late-onset pre-eclampsia"], "source": ["Pregnancy Hypertens"], "person-group": ["\n"], "surname": ["Tranquilli"], "given-names": ["AL"], "fpage": ["241"], "volume": ["4"], "year": ["2014"]}, {"label": ["15"], "article-title": ["KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease Vol. 3"], "source": ["Kidney Int Suppl"], "person-group": ["\n"], "surname": ["KDIGO CKD Work"], "given-names": ["Group"], "fpage": ["1"], "lpage": ["150"], "volume": ["3"], "year": ["2013"], "uri": ["https://kdigo.org/wp-content/uploads/2017/02/KDIGO_2012_CKD_GL.pdf"]}, {"label": ["23"], "article-title": ["Review: preeclampsia, acute atherosis of the spiral arteries and future cardiovascular disease: two new hypotheses"], "source": ["Placenta"], "person-group": ["\n"], "surname": ["Staff", "Dechend", "Redman"], "given-names": ["AC", "R", "CW"], "fpage": ["0"], "lpage": ["8"], "volume": ["34 Suppl"], "year": ["2013"]}, {"label": ["26"], "article-title": ["From preeclampsia to renal disease: a role of angiogenic factors and the renin-angiotensin aldosterone system?"], "source": ["Nephrol Dial Transplant"], "person-group": ["\n"], "surname": ["van der Graaf", "Toering", "Faas", "Lely"], "given-names": ["AM", "TJ", "MM", "AT"], "fpage": ["0"], "lpage": ["7"], "volume": ["27 Suppl 3"], "year": ["2012"]}, {"label": ["30"], "article-title": ["Progress in the understanding of the pathophysiology of immunologic maladaptation related to early-onset preeclampsia and metabolic syndrome related to late-onset preeclampsia"], "source": ["Am J Obstet Gynecol"], "person-group": ["\n"], "surname": ["Robillard", "Dekker", "Scioscia", "Saito"], "given-names": ["PY", "G", "M", "S"], "fpage": ["0"], "lpage": ["75"], "volume": ["226"], "year": ["2022"]}]
{ "acronym": [], "definition": [] }
30
CC BY
no
2024-01-14 23:41:58
Cureus.; 15(12):e50488
oa_package/93/aa/PMC10787169.tar.gz
PMC10787170
0
[ "<title>Introduction</title>", "<p>Since their first description in 1891, total hip replacements (THR) have undergone significant evolution over the last 100 years. They are regarded as one of the most successful orthopaedic interventions [##UREF##0##1##]. McKee and Watson-Farrar first described the use of uncemented THRs in the 1950s when they implanted a cementless acetabular and femoral system into patients with reasonable results [##REF##5937593##2##]. It was not, however, until the 1980s that the mechanical engineering of the materials used improved [##REF##19337818##3##]. Uncemented implants rely primarily on a tight fit of the implant within the bone. Long-term survivorship depends on the biological anchoring of the implant to the bone [##REF##25802848##4##]. This is achieved through osseointegration, which histologically can be defined as direct contact between the implant surface and host bone without intervening fibrous tissue [##REF##29345170##5##]. Extensive research into porous coatings paved the way for the widespread use of hydroxyapatite (HA), a coating chosen for its biocompatible and osteoconductive properties. It has been used successfully for over 30 years, improving the stability and osseointegration of uncemented implants [##REF##25802848##4##].</p>", "<p>The use of uncemented implants has risen in the UK, particularly amongst younger patients [##REF##29345170##5##]. The National Joint Registry’s (NJR) 19th annual report showed that 35.4% of THRs performed in 2021 were uncemented, rising steadily since 2004 (18.3%) [##UREF##1##6##]. Uncemented fixation is the most popular fixation method of choice in Canada, Australia, and the United States [##UREF##2##7##,##UREF##3##8##].</p>", "<p>There is debate regarding the use of cemented versus uncemented THRs [##REF##19337818##3##,##REF##29345170##5##,##UREF##2##7##, ####UREF##3##8##, ##REF##26403875##9####26403875##9##]. The majority of literature supports the use of cemented THRs, with evidence from various joint registry databases supporting improved patient-reported outcomes with cemented implants [##REF##19337818##3##,##UREF##2##7##,##REF##30203412##10##, ####REF##31584416##11####31584416##11##] and lower revision rates in older patients [##REF##30203412##10##,##REF##24081667##12##, ####REF##31934332##13##, ##REF##34145801##14####34145801##14##]. A concern with using cementless implants in the elderly population is osteoporosis, where failure of osseointegration and loosening of implants pose a higher risk of peri-prosthetic fracture [##REF##24771260##15##].</p>", "<p>Cementless systems offer several key benefits by negating the use of bone cement. Cement causes fragmentation and wear debris, leading to osteolysis and peri-prosthetic loosening. Cement is neither osteoconductive nor inductive and cannot remodel [##REF##24081667##12##,##REF##34145801##14##,##REF##24771260##15##]. A rare, but potentially fatal, problem of using cement is the risk of bone cement implantation syndrome. This condition can cause severe arrhythmias and even cardiac arrest [##REF##24081667##12##,##REF##23539124##16##], leading to a 16-fold increase in 30-day mortality (intraoperative mortality rate up to 4.3%) [##UREF##4##17##,##REF##32734511##18##, ####REF##8363862##19##, ##REF##16906119##20##, ##UREF##5##21##, ##REF##7797866##22##, ##UREF##6##23####6##23##]. In addition to removing the use of cement, cementless systems offer a shorter duration of surgery and less intraoperative blood loss [##REF##23539124##16##].</p>", "<p>Others have demonstrated good results in terms of survivorship and revision rates with the use of cementless systems within the ortho-geriatric population [##REF##29345170##5##,##REF##24081667##12##, ####REF##31934332##13##, ##REF##34145801##14####34145801##14##,##REF##20814676##24##]. Although there is a rise in the popularity of uncemented THRs, the current guidelines by the NJR and Getting It Right First Time (GIRFT) recommend cemented or hybrid fixation in patients over 70 [##UREF##1##6##,##UREF##4##17##].</p>", "<p>The majority of the literature focuses on patient-reported outcomes and complication rates, with relatively few papers focusing on the radiographic assessment of uncemented THRs in different age groups. The purpose of this study was to assess the radiographic stability of uncemented total hip replacements conducted in a trauma and orthopaedic unit in the UK among two specific age groups (above and below age 69). The study aimed to determine whether there was a discernible radiographic distinction in implant stability determined by measurable lucency around the implants between these age groups.</p>", "<p>Our primary aim was to see if there was any statistically significant difference in the rates of implant radiographic lucency at two years between the two groups, those above 69 and those under 69 years of age. Our secondary aims were to compare loosening rates between collared and non-collared stems and femoral type (Dorr classification). We also collected data on any complications or revisions required.</p>" ]
[ "<title>Materials and methods</title>", "<p>Materials</p>", "<p>This was a retrospective study aiming to evaluate the radiographic outcomes of the uncemented THRs. The analysis was conducted on 123 patients of all ages who underwent an elective procedure under one surgeon at one unit in the UK (Bedfordshire NHS Foundation Trust, UK) between January 2017 and April 2018 and had a minimum radiographic follow-up period of two years.</p>", "<p>All patients had the same approach (anterolateral) and implant used Corail stem (CORAIL® Total Hip System, De Puy Synthes, Warsaw, Indiana, USA) and Pinnacle cup (PINNACLE® Hip Solutions, De Puy Synthes, Warsaw, Indiana, USA).</p>", "<p>We collected information on the age of the patient, gender, implant used (collared or non-collared), Dorr classification for femur type [##REF##8363862##19##], and revision rates. A radiographic analysis of the biologic fixation of both the femoral stem and acetabular component was performed for the immediate postoperative, six-month, one-year, and two-year follow-up radiographs of all the patients.</p>", "<p>Methods</p>", "<p>At each of the follow-ups (post-operative, six-month, one-year and two-year), the femoral stem's Gruen zones [##REF##16906119##20##] (Figure ##FIG##0##1##) and the acetabular component's DeLee and Charnley zones [##UREF##5##21##] were evaluated. We measured several radiographic parameters.</p>", "<p>For the femoral component, signs of lucency, stem subsidence, and proximal femoral stress shielding were measured. A lucency was defined as &gt;2 mm evident on the radiographs within a zone (Figure ##FIG##1##2##). Stem subsidence was defined as sinking of the stem greater than 5 mm.</p>", "<p>For the acetabular component, signs of lucency and migration were measured. A lucency in this region was again defined as greater than 2 mm, and migration was defined as greater than 2 mm. Three orthopaedic surgeons, each with a minimum of five years of orthopaedic experience, performed the evaluation.</p>", "<p>Following the collection of the data, descriptive analysis was performed, and then statistical analysis was employed (the chi-square test) to determine if there was any significant difference between the two age groups, collared versus non-collared stems, and types of femur. Descriptive analysis was performed for complications and revisions.</p>" ]
[ "<title>Results</title>", "<p>The overall mean age of the 123 patients was 69.3±8.6 years old. There were 58 males and 65 females. Fifty-three collared stems (43.08%) and 70 non-collared stems (56.91%) were used. Based on the Dorr classification [##REF##8363862##19##], there were 31 type A, 84 type B, and 8 type C femurs.</p>", "<p>The demographic distribution between the two groups revealed that there were 53 patients in the under-69 group with a mean age of 58.1 years and 70 patients in the over-69 group with a mean age of 76.8 years.</p>", "<p>Primary outcome results</p>", "<p>We noted overall femur lucency in 16 cases (13%), with 11 cases in zone 1, 9 cases in zone 2, 2 cases in zone 6, and 8 cases in zone 7. We did not observe any stem subsidence in any of the groups at two years. The results are summarised in Table ##TAB##0##1##.</p>", "<p>There was no statistically significant difference in the rate of femoral lucency between the two age groups (p = 0.62). In the under-69-year-old group, eight cases of femur lucency were noted (15%), and in the above-69 group, eight cases of femur lucency were also noted (11.4%) (chi-square p = 0.5). The highest incidence of radiolucent lines was noted on the one-year follow-up radiographs. Evidence of lucency was absent in immediate post-operative radiographs, with only a small incidence (3.25%) at six months. There was no further progression after two years. The results are illustrated in Figure ##FIG##1##2##. Cup lucency was noted in 12 cases (9.75%). Seven cases are in zone 1, 10 cases in zone 2, and 2 cases in zone 3. There was no evidence of cup migration. The results are summarised in Table ##TAB##1##2##.</p>", "<p>There was a statistically significant difference in the rates of acetabular cup lucency between the two age groups (p = 0.018), with higher rates noted in the under-69 group. Among the 53 patients in the under-69-year-old age group, loosening of the cup radiographically was confirmed in nine cases (16.9%) preliminary in zones 1 and 2 (Charnley zones), whereas in the above-69-year-old group, only in three cases (4.28%).</p>", "<p>Secondary outcome results</p>", "<p>There was no statistically significant difference in lucency between collared and non-collared stems. When comparing the collared versus non-collared groups, there were five cases of femur loosening in the collared group (9.43%) and eight cases in the non-collared group (11.45%) (chi-square p = 0.72). No cases of subsidence were noted (Table ##TAB##2##3##).</p>", "<p>Further statistical analysis was performed among the different femoral type groups (Dorr A, B, and C types) to determine if the femoral type was predisposed to radiographic lucency. Radiographic lucency was noted in six cases among the type A femurs, nine cases in the type B group, and one case among the type C femurs on the one-year post-operative radiograph, with no statistical significance among the groups (p = 0.47).</p>", "<p>There were no noted revisions. There was one peri-prosthetic fracture, in the under-69 year age group, of the greater trochanter (Vancouver A type) around a well-fixed, non-collared, uncemented Corail stem, which was addressed using a trochanteric plate and fixed in situ.</p>" ]
[ "<title>Discussion</title>", "<p>This is a retrospective study comparing short-term differences in radiographic features observed with the use of the uncemented Corail/Pinnacle THA system between two age groups. Our study found there was no statistically significant difference in rates of radiographic lucency after two years with regard to the femoral component. There was, however, a statistically significant difference in rates of radiographic lucency of the acetabular cup between the age groups (p = 0.018), with higher rates actually observed in the under-69-year-old age group. There was no statistically significant difference based on the use of collared versus non-collared stems or femoral type. Additionally, there were no revision rates, and only one peri-prosthetic fracture was observed during this time. From these results, the authors conclude that there is no increased risk of loosening when using the Corail/Pinnacle system in the short term in patients over 69 years old.</p>", "<p>After almost 40 years since the first human implantation of HA-coated implants [##REF##20814676##24##], there is evidence in the recent literature supporting the use of uncemented THR implants in the elderly population [##REF##20814676##24##, ####REF##33940937##25##, ##UREF##7##26####7##26##]. While, worldwide, the number of uncemented THRs is rising [##UREF##2##7##], in the UK, the GIRFT recommendation for the elderly population is the use of cemented or hybrid implants, mainly over concerns of peri-prosthetic fractures, revision rates, poor bone osseointegration and the risk of loosening [##REF##31571579##27##,##REF##30995903##28##].</p>", "<p>Osseointegration seems to be the key element in the survivorship of the implant and is a continuous process, occurring at any stage, in any case, regardless of the underlying bone quality and the age group of the patient [##UREF##6##23##,##REF##20814676##24##]. The principle that in the elderly population with osteoporosis, the osseointegration process is restricted seems to have fallen out of favour, with studies indicating similar results between young and active and older osteoporotic patients [##REF##33940937##25##].</p>", "<p>From our study, there was no statistically significant difference in the short-term radiographic assessment of biologic fixation of the femoral stem. Interestingly, the radiographic analysis of the uncemented cup revealed a higher rate of radiolucencies in the younger age group in comparison to the elderly group, indicating that, in our cohort of patients, the age of the patient did not predict the osseointegration of the implant in the short-term follow-up.</p>", "<p>To this note, while registered studies attribute an excellent long-term outcome to cemented implants, the number of studies supporting good mid-term results of uncemented implants in the elderly is rising [##REF##33940937##25##,##REF##30995903##28##,##UREF##8##29##], with our study showing similar results. The discrepancy between the registries and the evidence from the uncemented implant studies could possibly be explained by the individual type of uncemented implant used rather than the uncemented THR concept [##UREF##8##29##]. Specifically, the uncemented CORAIL stem relies on an impaction broaching system rather than an extraction system, which is frequently used by other uncemented stems. This technical difference in the broaching system, along with the biomechanics of a fully HA-coated stem, might possibly explain the excellent survivorship of the Corail/Pinnacle system with more than 20 years of long-term results [##UREF##9##30##]. When considering data published based on NJR performance, a report analysing the use of 102,823 patients receiving the collared CORAIL hip and PINNACLE cementless cup (mean age 66.5 years) had a 29% lower risk of revision when compared to all other cementless systems on the registry across all age groups [##UREF##9##30##].</p>", "<p>Our results, in addition to those of other multiple studies [##REF##33940937##25##,##REF##30995903##28##,##UREF##8##29##], support the safe use of uncemented THR constructs in the elderly population. A summary of some of the key papers that support the use of uncemented THA in the elderly population is summarised in Table ##TAB##2##3##.</p>", "<p>The advantages of such systems (reduced risk of bone cement implantation syndrome, shorter hospital duration, intraoperative time, and blood loss) can improve peri-operative care in such a cohort of patients. It is, however, important for the surgeon considering the use of a cementless construct to use a system that has evidence of good survivorship in the elderly group. Further long-term studies comparing the use of different uncemented broaching systems (impaction vs. extraction) may prove useful in helping determine if the difference in technique has a significant contribution to outcomes in the age group.</p>", "<p>The authors recognise that there are limitations to this study. One main limitation is the follow-up time. Our results have only been able to generate conclusions based on a short-term follow-up (two years); further studies would be required to see if there are any medium- or long-term differences in radiographic outcomes.</p>", "<p>Another limitation is possible inter-observer bias. Three authors collected the data, and therefore there is a possible risk of discrepancy. This was minimised by ensuring all authors were aware of the zones of measurement and the definitions of lucency/subsidence prior to data collection. The radiographic images were reviewed on the hospital Picture Archiving and Communication System (PACS) using its measuring system to allow for objective measurements to be made.</p>" ]
[ "<title>Conclusions</title>", "<p>Our study found there was no statistically significant difference in rates of loosening of the femoral component based on age or the use of collared versus non-collared stems. Despite the statistically significant higher incidence of radiographic lucency of the acetabular cup in the under-69-year-old age group (p = 0.018), no clinical correlation was noted. Additionally, there were no revision rates, and only one peri-prosthetic fracture was observed during this time. Our results suggest that there is no correlation between age and radiographic loosening rates in the short-term follow-up.</p>", "<p>The uncemented Pinnacle/Corail construct seems to perform equally well in all age groups at short-term follow-up. The age of the patient does not seem to predict the osseointegration of the implant during the short-term follow-up.</p>" ]
[ "<p>Introduction</p>", "<p>The idea of an uncemented, fully coated hydroxyapatite (HA) stem was introduced almost 40 years ago, aiming to achieve a solid biological fixation by preserving natural bone activity. While many studies underline the longevity of uncemented total hip replacement (THR), NHS England’s Best Practice Tariff (BPT) recommends using cemented implants in patients over the age of 69, with financial penalties when this policy is not met. At the same time, the ‘paradox’ of increased use of uncemented implants worldwide has been well described, with many surgeons using them regardless of the age group of the patient.</p>", "<p>Materials and methods</p>", "<p>This study focuses on the radiographic evaluation of the uncemented Pinnacle/Corail total hip replacement construct in 123 patients of all age groups who underwent an elective procedure, with a minimum radiographic follow-up of two years. Implant information (collared or non-collared stem), femur type (Dorr classification), age, gender, and revision rate were collected and radiographic analysis of the femoral stem and acetabular component was performed for the immediate post-operative, six-month, one- to two-year follow-up radiograph of all patients. We conducted a statistical analysis, dividing the patients into two groups based on age: those above or below 69 years old.</p>", "<p>Results</p>", "<p>There was no statistically significant difference in rates of radiographic lucency after two years with regard to the femoral component. Both collared and non-collared stems seem to perform equally well, with no significant difference detected. However, a statistically significant difference in rates of radiographic lucency of the acetabular cup was noted between the two age groups (p=0.018), with higher rates detected in the under-69-year-old age group.</p>", "<p>Conclusion</p>", "<p>This study demonstrates that, radiographically, the uncemented Pinnacle/Corail construct performs equally well in all age groups. In our cohort of patients, the age of the patient did not predict the osseointegration of the implant in the short-term follow-up.</p>" ]
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[ "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG1\"><label>Figure 1</label><caption><title>Incidence of radiographic lucency (&gt;2 mm) around the Gruen zones of the femur.</title></caption></fig>", "<fig position=\"anchor\" fig-type=\"figure\" id=\"FIG2\"><label>Figure 2</label><caption><title>Example of uncemented collared pinnacle/corail THR, with &gt;2 mm lucency in zone 1 of the femoral stem (12 months post-operative radiograph).</title></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"TAB1\"><label>Table 1</label><caption><title>Radiographic evaluation of the femoral stem.</title></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Radiographic evaluation of the femoral stem</td><td rowspan=\"1\" colspan=\"1\">Post-operative radiograph</td><td rowspan=\"1\" colspan=\"1\">6-month post-operative</td><td rowspan=\"1\" colspan=\"1\">1-year post-operative radiograph</td><td rowspan=\"1\" colspan=\"1\">2-year post-operative radiograph</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Radiolucent lines (&gt;2 mm)</td><td rowspan=\"1\" colspan=\"1\">0%</td><td rowspan=\"1\" colspan=\"1\">3.25% (4 cases)</td><td rowspan=\"1\" colspan=\"1\">13% (16 cases)</td><td rowspan=\"1\" colspan=\"1\">13% (16 cases)</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Subsidence (&gt;5 mm)</td><td rowspan=\"1\" colspan=\"1\">0%</td><td rowspan=\"1\" colspan=\"1\">0%</td><td rowspan=\"1\" colspan=\"1\">0%</td><td rowspan=\"1\" colspan=\"1\">0%</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Stress shielding the proximal femur</td><td rowspan=\"1\" colspan=\"1\">0%</td><td rowspan=\"1\" colspan=\"1\">0.81% (1 case)</td><td rowspan=\"1\" colspan=\"1\">6.5% (8 cases)</td><td rowspan=\"1\" colspan=\"1\">7.31% (9 cases)</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"TAB2\"><label>Table 2</label><caption><title>Radiographic evaluation of the acetabular component.</title></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Radiographic evaluation of the cup (123 cases)</td><td rowspan=\"1\" colspan=\"1\">Post-operative radiograph (123 cases)</td><td rowspan=\"1\" colspan=\"1\">6-month post-operative (123 cases)</td><td rowspan=\"1\" colspan=\"1\">1-year post-operative (123 cases)</td><td rowspan=\"1\" colspan=\"1\">2-year post-operative (123 cases)</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Radiolucent lines (&gt;2 mm)</td><td rowspan=\"1\" colspan=\"1\">0%</td><td rowspan=\"1\" colspan=\"1\">2.43% (3 cases)</td><td rowspan=\"1\" colspan=\"1\">9.75% (12 cases)</td><td rowspan=\"1\" colspan=\"1\">9.75% (12 cases)</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Migration (&gt;2 mm)</td><td rowspan=\"1\" colspan=\"1\">0%</td><td rowspan=\"1\" colspan=\"1\">0%</td><td rowspan=\"1\" colspan=\"1\">0%</td><td rowspan=\"1\" colspan=\"1\">0%</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"TAB3\"><label>Table 3</label><caption><title>Secondary outcome results.</title></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">\nRadiographic evaluation of the femoral stem\n</td><td rowspan=\"1\" colspan=\"1\">\nNumber of cases\n</td><td rowspan=\"1\" colspan=\"1\">\nNumber of cases with radiographic lucency\n</td><td rowspan=\"1\" colspan=\"1\">\nSubsidence (&gt;5 mm)\n</td></tr><tr><td rowspan=\"1\" colspan=\"1\">\nCollared stem\n</td><td rowspan=\"1\" colspan=\"1\">\n53\n</td><td rowspan=\"1\" colspan=\"1\">\n5 cases (9.43%)\n</td><td rowspan=\"1\" colspan=\"1\">\n0%\n</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">\nNon-collared stem\n</td><td rowspan=\"1\" colspan=\"1\">\n70\n</td><td rowspan=\"1\" colspan=\"1\">\n8 cases (11.45%)\n</td><td rowspan=\"1\" colspan=\"1\">\n0%\n</td></tr><tr><td rowspan=\"1\" colspan=\"1\">\nP-value\n</td><td rowspan=\"1\" colspan=\"1\">\n-\n</td><td rowspan=\"1\" colspan=\"1\">\n0.72\n</td><td rowspan=\"1\" colspan=\"1\"> </td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"TAB4\"><label>Table 4</label><caption><title>Highlighting key papers and findings which support the use of uncemented THA in elderly population.</title><p>PROMS: patient-reported outcome measures.</p></caption><table frame=\"hsides\" rules=\"groups\"><tbody><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Paper</td><td rowspan=\"1\" colspan=\"1\">Method</td><td rowspan=\"1\" colspan=\"1\">Results/conclusion</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Lewis et al. [##REF##33940937##25##]</td><td rowspan=\"1\" colspan=\"1\">Prospectively collected data from a single-surgeon database of over 1000 uncemented THA’s (Corail/Pinnacle) performed with a mean follow-up of 5 years. Compared two groups, under 65 vs. over 65 and under 70 vs. over 70.</td><td rowspan=\"1\" colspan=\"1\">No significant difference in the number of revisions. PROMS were overall better than the national comparison. Those over 65/69 maintained a meaningful improvement in the Oxford Hip Score compared to younger group.</td></tr><tr style=\"background-color:#ccc\"><td rowspan=\"1\" colspan=\"1\">Gkagkalis et al. [##REF##30995903##28##]</td><td rowspan=\"1\" colspan=\"1\">A prospective multicenter observational study comparing the young (under 60) and geriatric population (over 75) with mean follow up of 49.2 months with uncemented calcar guided short stem THA.</td><td rowspan=\"1\" colspan=\"1\">No difference in the VAS score between rest pain, load pain and satisfaction. Improved Harris Hip Score in younger patients. No difference in radiological parameters. Higher risk of periprosthetic fracture in older group. Conclusion – advanced age alone should not be a contra-indication, but those with markedly reduced bone quality and Dorr C femur are at high risk of fracture. Should therefore be reserved for Dorr A and B with good bone quality.</td></tr><tr><td rowspan=\"1\" colspan=\"1\">Zimmerer et al. [##UREF##8##29##]</td><td rowspan=\"1\" colspan=\"1\">Retrospectively evaluated 107 uncemented THAs in patients over 75 with mean follow up of 6.4 years.</td><td rowspan=\"1\" colspan=\"1\">6.3 year survivor rate of 98% with good clinical outcomes. Survivor rate is similar in literature to that of younger patients. Cementless stem showed low revision rate even in patients over 75 in mid-term. Periprosthetic fracture was not a relevant failure mechanism.</td></tr></tbody></table></table-wrap>" ]
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[ "<fn-group content-type=\"other\"><title>Author Contributions</title><fn fn-type=\"other\"><p><bold>Concept and design:</bold>  Georgios Saraglis, Joe Muscat , Yadu Shankarappa, Mohammad Sameh Mohammad Elgeweny, Mohamed Moustafa Mohamed Hussein</p><p><bold>Acquisition, analysis, or interpretation of data:</bold>  Georgios Saraglis, Joe Muscat , Yadu Shankarappa, Mohammad Sameh Mohammad Elgeweny, Mohamed Moustafa Mohamed Hussein</p><p><bold>Drafting of the manuscript:</bold>  Georgios Saraglis, Joe Muscat , Yadu Shankarappa, Mohammad Sameh Mohammad Elgeweny, Mohamed Moustafa Mohamed Hussein</p><p><bold>Critical review of the manuscript for important intellectual content:</bold>  Georgios Saraglis, Yadu Shankarappa, Mohammad Sameh Mohammad Elgeweny, Mohamed Moustafa Mohamed Hussein</p><p><bold>Supervision:</bold>  Georgios Saraglis, Joe Muscat , Yadu Shankarappa, Mohammad Sameh Mohammad Elgeweny, Mohamed Moustafa Mohamed Hussein</p></fn></fn-group>", "<fn-group content-type=\"other\"><title>Human Ethics</title><fn fn-type=\"other\"><p>Consent was obtained or waived by all participants in this study</p></fn></fn-group>", "<fn-group content-type=\"other\"><title>Animal Ethics</title><fn fn-type=\"other\"><p><bold>Animal subjects:</bold> All authors have confirmed that this study did not involve animal subjects or tissue.</p></fn></fn-group>", "<fn-group content-type=\"competing-interests\"><fn fn-type=\"COI-statement\"><p>The authors have declared that no competing interests exist.</p></fn></fn-group>" ]
[ "<graphic xlink:href=\"cureus-0015-00000050487-i01\" position=\"float\"/>", "<graphic xlink:href=\"cureus-0015-00000050487-i02\" position=\"float\"/>" ]
[]
[{"label": ["1"], "article-title": ["Total hip arthroplasty - over 100 years of operative history"], "source": ["Orthop Rev (Pavia)"], "person-group": ["\n"], "surname": ["Knight", "Aujla", "Biswas"], "given-names": ["SR", "R", "SP"], "fpage": ["0"], "volume": ["3"], "year": ["2011"]}, {"label": ["6"], "article-title": ["The National Joint Registry 18th Annual Report 2022"], "source": ["The National Joint Registry 19th Annual Report"], "person-group": ["\n"], "surname": ["Ben-Shlomo", "Blom", "Boulton"], "given-names": ["Y", "A", "C"], "publisher-loc": ["London"], "publisher-name": ["National Joint Registry"], "year": ["2022"], "uri": ["https://www.ncbi.nlm.nih.gov/books/NBK587525/"]}, {"label": ["7"], "article-title": ["Cemented or cementless fixation for primary hip arthroplasty\u2014evidence from The International Joint Replacement Registries"], "source": ["Ann Joint"], "person-group": ["\n"], "surname": ["Zhang", "Yan", "Zhang"], "given-names": ["C", "CH", "W"], "fpage": ["57"], "volume": ["2"], "year": ["2017"]}, {"label": ["8"], "article-title": ["Cemented versus uncemented fixation in total hip replacement: a systematic review and meta-analysis of randomized controlled trials"], "source": ["Orthop Rev (Pavia)"], "person-group": ["\n"], "surname": ["Abdulkarim", "Ellanti", "Motterlini", "Fahey", "O'Byrne"], "given-names": ["A", "P", "N", "T", "JM"], "fpage": ["0"], "volume": ["5"], "year": ["2013"]}, {"label": ["17"], "article-title": ["GIRFT hip and knee replacement pathway"], "date-in-citation": ["\n"], "month": ["12"], "year": ["2023", "2020"], "uri": ["https://gettingitrightfirsttime.co.uk/wp-content/uploads/2020/08/GIRFT-Hip-and-Knee-replacement-pathway-May-2020-003.pdf"]}, {"label": ["21"], "article-title": ["Radiological demarcation of cemented sockets in total hip replacement"], "source": ["Clin Orthop Relat Res"], "person-group": ["\n"], "surname": ["DeLee", "Charnley"], "given-names": ["JG", "J"], "fpage": ["20"], "lpage": ["32"], "volume": ["121"], "year": ["1976"], "uri": ["https://pubmed.ncbi.nlm.nih.gov/991504/"]}, {"label": ["23"], "article-title": ["Corail Stem Long-Term Results Based Upon the 15-Year"], "source": ["Springer"], "person-group": ["\n"], "surname": ["Vidalain"], "given-names": ["JP"], "publisher-loc": ["London"], "publisher-name": ["Springer"], "year": ["2004"]}, {"label": ["26"], "article-title": ["Minimum 10-year results of a tapered, titanium, hydroxyapatite-coated hip stem: an independent review"], "source": ["J Arthroplasty"], "person-group": ["\n"], "surname": ["Froimson", "Garino", "Machenaud", "Vidalain"], "given-names": ["MI", "J", "A", "JP"], "fpage": ["1"], "lpage": ["7"], "volume": ["22"], "year": ["2007"]}, {"label": ["29"], "article-title": ["Midterm survivorship of an uncemented hydroxyapatite-coated titanium femoral component and clinically meaningful outcomes in patients older than 75 years"], "source": ["J Clin Med"], "person-group": ["\n"], "surname": ["Zimmerer", "Navas", "Kinkel", "Weiss", "Hauschild", "Streit"], "given-names": ["A", "L", "S", "S", "M", "M"], "volume": ["10"], "year": ["2021"]}, {"label": ["30"], "article-title": ["Analysis of collared and collarless total hip replacement using the Cementless Corail\u00ae total hip system"], "date-in-citation": ["\n"], "month": ["3"], "year": ["2023", "2023"], "publisher-name": ["14th Annual report "], "uri": ["http://14th Annual report"]}]
{ "acronym": [], "definition": [] }
30
CC BY
no
2024-01-14 23:41:58
Cureus.; 15(12):e50487
oa_package/a7/e8/PMC10787170.tar.gz
PMC10787173
0
[ "<title>Introduction</title>", "<p id=\"p0040\">Neglected tropical diseases (NTD) are a diverse group of communicable diseases that occur in tropical and subtropical regions and affect more than one billion people globally (##UREF##2##CDC, 2021##). Leishmaniasis is classified as an NTD, caused by parasites of the genus <italic>Leishmania</italic> (pathogens), which are transmitted to humans and animals (hosts) through infected female phlebotomine sand flies (vectors). The Eastern Mediterranean Region accounts for 80% of the cutaneous leishmaniasis cases worldwide (##UREF##16##WHO, 2021##). The most serious form and often fatal, also called kala-azar, is attributed to vector species of the genus of <italic>Phlebotomus</italic> in the Old World, and of <italic>Lutzomyia</italic> in the New World. The main foci of Old World leishmaniasis are located in China, India, Central Asia, East Africa, the Mediterranean basin, and Brazil (##UREF##3##Dedet, 2010##).</p>", "<p id=\"p0045\">Environmental changes such as deforestation, building of dams, irrigation schemes, and urbanization have been directly linked to leishmaniasis infections (##UREF##16##WHO, 2021##). Global warming is among the most important drivers of the potential expansion of leishmaniases, while tourism and trade could facilitate the transportation of its vectors and pathogens all over the globe (##REF##18598618##Dujardin et al., 2008##). Although <italic>Phlebotomus</italic> sand flies are unable to actively disperse over distant areas (##REF##10887662##Léger et al., 2000b##), environmental changes may provide suitable conditions for their survival and reproduction and promote their geographical expansion (##REF##24820558##Medlock et al., 2014##).</p>", "<p id=\"p0050\">Cyprus, an island between Southeast Europe, North Africa, and West Asia, is prone to the transmission of leishmaniasis due to a list of factors, including urbanization, extensive agriculture, changing environmental conditions, and population movement from countries where the disease is endemic (##REF##18156082##Antoniou et al., 2008##). <italic>Phlebotomus</italic> sand flies are widespread in Cyprus, and there is evidence of pathogenicity among Cypriot patients (##UREF##1##Alwassouf et al., 2016##; ##REF##31346541##Billioud et al., 2019##). Although the visceral and cutaneous forms of leishmaniasis were nearly eradicated by 1996, recent evidence suggests an increase in frequency among the population due to the active circulation of the parasites transmitted by autochthonous sand fly species and a set of favourable conditions potentially leading to their geographical spread (##REF##20207870##Mazeris et al., 2010##). Cyprus is the only area in Europe where cases of anthroponotic visceral leishmaniasis have been reported and attributed to <italic>Leishmania donovani</italic>, which is related to <italic>Leishmania infantum</italic>, while an <italic>L. infantum/L. donovani</italic> hybrid has been reported in <italic>Phlebotomus tobbi</italic> (##REF##18156082##Antoniou et al., 2008##; ##REF##26608249##Seblova et al., 2015##).</p>", "<p id=\"p0055\">Field inventories and geodatabases of vector species are essential tools for public health planning. A comprehensive account of vector fauna, however, is often a challenge as individual studies can each cover small parts of a region. Here, we sampled and compiled the data about sand fly fauna across Cyprus and investigated the potential distributions of a selected subset - selected for species importance in disease transmission. We employed remote sensing datasets and weather-driven population dynamics modelling to bridge the gaps and derive high-resolution geospatial and seasonal activity. Applications as such demonstrate the use of predictive mathematical modelling in studying leishmaniasis epidemiology and hold the promise of identifying long-term changes in geographical patterns due to climate change.</p>" ]
[ "<title>Materials and methods</title>", "<title>Geographical distribution of sand fly species in Cyprus</title>", "<p id=\"p0060\">Sand fly sampling was performed intermittently between 2013 and 2020 through the collaboration of three institutions: The University of Crete, the Joint Services Health Unitʼs Vector Ecology and Applied Entomology Laboratory, and Ege University. Adult specimens were collected from 8 villages, located in the southwest and central areas of the island, with CDC miniature light traps equipped with a fine net cage, and morphologically identified using published keys (##UREF##9##Lewis, 1987##).</p>", "<p id=\"p0065\">The list of sand fly species was complemented with peer-reviewed literature on sand fly ecology in Cyprus. The terms “sand flies”, “phlebotomine”, “leishmaniasis”, and “Cyprus” were screened in English, Greek, Turkish, and French using Google Scholar, the University of Illinois Library, and Scopus. References mentioned within the relevant publications were also examined; however, studies reporting pathogens or leishmaniasis infections were excluded.</p>", "<p id=\"p0070\">Geographical coordinates, where available, or the city/village of the sampling locations were mapped using the publicly available QGIS 3.14 software.</p>", "<title>Land cover preferences of the species of medical importance</title>", "<p id=\"p0075\">Land cover preference was assessed for two sand fly species, <italic>Phlebotomus papatasi</italic> and <italic>P. tobbi</italic>, based on expert opinion retrieved from ##UREF##5##ECDC (2019)##. The preference scale is based on CORINE Land Cover (CLC) classification and employs 3 levels: (i) primary land type (land classes providing the most suitable habitat for a species and providing the likelihood of the greatest vector numbers); (ii) secondary land type (land classes where a species may still be found but less likely and in much lower numbers than above); and (iii) unsuitable land type (land classes where a species is unlikely to be found except in exceptional circumstances). The CLC classification for 2018 was retrieved from the Copernicus Land Monitoring Service and used for preference mapping (##UREF##8##Kosztra et al., 2019##).</p>", "<title>Generation of high-resolution meteorological covariates</title>", "<p id=\"p0080\">Meteorological data were generated over Cyprus for the year 2015 using the open-source, community-based, state-of-the-art Weather Research and Forecasting (WRF-ARW) Model (##UREF##14##Skamarock et al., 2008##). The model was configured according to the operational numerical weather forecasts of the Cyprus Department of Meteorology. The model set-up has been extensively validated and proven highly accurate for the Eastern Mediterranean and Cyprus (##UREF##6##Georgiou et al., 2018##). The meteorological fields, generated with a nested configuration setup, were at an ultra-fine spatiotemporal resolution (i.e. 2 km horizontal grid spacing and 1-h temporal frequency).</p>", "<title>Spatiotemporal modelling of sand fly abundance</title>", "<p id=\"p0085\">The expected population size of <italic>P. papatasi</italic> in Cyprus in 2015 was simulated using the stochastic climate-driven population dynamics model of the species presented in ##REF##30792449##Erguler et al. (2019)##. The model was simulated with air temperature and relative humidity obtained from the meteorological model. Two sets of parameters, labelled Combined A for Steni and Combined A for Geri - each with 1000 alternative configurations - were used to simulate the average number of adult females per day per trap (a proxy to expected population size). Model output implies that the system is observed similarly - the sampling design is identical - throughout the island and is the same as in the original publication. The first three months of 2015 were discarded as the transient phase of the simulations.</p>", "<p id=\"p0090\">The two parameter sets, inferred for the Steni and Geri villages, are identical in physiological traits and environmental dependencies except for initial conditions and the fraction Ψ<sub>B</sub>. The fraction represents the impact of breeding site conditions on fecundity, gonotrophic cycle, and larva and pupa development. As evident from the land type classification and the original publication, observations were made mainly on the primary land type in Steni and on the secondary land type in Geri. Thus, population size was simulated over the island by switching between the two sets for each land type.</p>", "<p id=\"p0095\">We present in <xref rid=\"appsec1\" ref-type=\"sec\">Supplementary Text S1</xref> a Python code to perform the spatiotemporal simulations described.</p>" ]
[ "<title>Results and discussion</title>", "<title>Exploring the boundaries of the rich sand fly fauna in Cyprus</title>", "<p id=\"p0100\">We compiled a dataset of sand fly presence in Cyprus with 18 species of phlebotomine sand flies from 2 genera and 6 subgenera. A list of all species is given in ##TAB##0##Table 1## and maps for species with known geolocations are provided in <xref rid=\"appsec1\" ref-type=\"sec\">Supplementary Figs. S1–S3</xref>. We found that <italic>P. papatasi</italic>, <italic>P. tobbi</italic>, <italic>P. sergenti</italic>, and <italic>P. galilaeus</italic> are among the most frequently reported and widely distributed species; their locations are mapped in ##FIG##1##Fig. 1##. While <italic>P. papatasi</italic> was found in almost all sampling locations, <italic>P. tobbi</italic> exhibited a slightly narrower range (not recorded in the south-eastern peninsula). On the contrary, <italic>P. mascittii</italic> (3 locations), <italic>P. kyreniae</italic> (5 locations), and <italic>P. killicki</italic> (1 location) have been seldom encountered. We note that, due to the morphological similarity within the subgenus <italic>Transphlebotomus</italic>, the presence of <italic>P. mascittii</italic> on the island has been found suspicious and in need of further molecular confirmation (##REF##26006062##Kasap et al., 2015##).</p>", "<p id=\"p0105\">Through our survey, we confirmed the presence of 7 species of <italic>Phlebotomus</italic> and 3 species of <italic>Sergentomya</italic> (<xref rid=\"appsec1\" ref-type=\"sec\">Supplementary Table S1</xref> and <xref rid=\"appsec1\" ref-type=\"sec\">Supplementary Figs. S1–S3</xref>). As expected, <italic>P. papatasi</italic> was the dominant species, in all of the locations, followed by <italic>P. tobbi</italic> and <italic>P. galilaeus</italic>, albeit fewer in numbers. In addition, we detected <italic>S. minuta</italic> in large numbers in Aigoi Trimithias, which suggests that the village is a novel hotspot for this species. We did not detect certain species, such as <italic>P. kyreniae</italic> and <italic>P. economidesi</italic>, which exhibited restricted geographical ranges. Our dataset suggests that the number of species identified largely depends on the geographical extent of the study design. For instance, the surveys reported by ##UREF##4##Demir et al. (2010)##, ##REF##10887662##Léger et al. (2000b)##, and ##UREF##15##Töz et al. (2013)##, differ largely from those by ##REF##27609635##Dokianakis et al. (2016##, ##REF##29454363##2018)## and ##REF##30792449##Erguler et al. (2019)##, with respect to the area covered and the number of species reported.</p>", "<p id=\"p0110\">We note that while the earlier reports, including the comprehensive assessments of ##REF##21015625##Adler (1946)## and ##UREF##11##Minter and Eitrem (1989)##, employed morphological identification methods; contemporary reports employed genetic and serology techniques more often as a result of the recent developments in biochemical and molecular analysis (##REF##10380101##Field et al., 1999##; ##REF##25499083##Ergunay et al., 2014##; ##REF##27609635##Dokianakis et al., 2016##, ##REF##29454363##2018##). In addition to the improved accuracy in identification, molecular methods enable establishing phylogenetic relationships between populations at different locations.</p>", "<p id=\"p0115\"><italic>Phlebotomus papatasi</italic> and <italic>P. perfiliewi</italic> are common vectors of sand fly fever viruses and likely causes of phlebovirus circulation in the Cypriot population (##UREF##1##Alwassouf et al., 2016##; ##REF##31346541##Billioud et al., 2019##). <italic>Phlebotomus tobbi</italic> has been related to infections with cutaneous and visceral leishmaniasis in the Middle East and the Eastern Mediterranean basin (##REF##26608249##Seblova et al., 2015##). Likewise, <italic>P. papatasi</italic> and <italic>P. sergenti</italic> have been identified as vectors of <italic>Leishmania major</italic> and <italic>L. tropica</italic>, respectively (##REF##17207663##Volf and Myskova, 2007##). Due to suitable rodent reservoirs for the parasite, <italic>L. major</italic> has long been acknowledged as endemic in the Jordan Valley even though it is currently missing from Europe (##REF##30412694##Özbilgin et al., 2019##). In the last few decades, however, cases caused by <italic>L. major</italic> were reported outside its endemic range, such as in the southern region of Israel, i.e. Negev highlands, the western Negev, the Arava (##REF##30412694##Özbilgin et al., 2019##), and south-eastern Turkey, i.e. Adana Province (##REF##25279543##Saroufim et al., 2014##).</p>", "<title>Risk assessment: Mapping sand fly abundance in space and time</title>", "<p id=\"p0120\">To bridge the gap between observations, we used expert assessment on habitat preferences applied on satellite-derived high-resolution land cover data (##UREF##8##Kosztra et al., 2019##). The key for suitable habitat types, i.e. primary, secondary, and unsuitable habitat types, is published in the recent technical report of ECDC for a range of vector species (##UREF##5##ECDC, 2019##). We used this key to map the habitat preferences of <italic>P. papatasi</italic> and <italic>P. tobbi</italic>, two of the most abundant and medically important sand fly species, in Cyprus (##FIG##2##Fig. 2##).</p>", "<p id=\"p0125\">We found that the primary habitats of <italic>P. papatasi</italic> are urban and suburban areas while <italic>P. tobbi</italic> is well-adjusted to Mediterranean sclerophyllous vegetation - a secondary habitat for <italic>P. papatasi</italic>. Rural locations of Cyprus typically include low scrublands/phrygana and maqui vegetation, which can affect sand fly diversity and thus infection risk. In previous studies, the broad-leaved forest was emphasized as a suitable habitat for sand flies (##UREF##10##Martinez et al., 2007##); however, this kind of habitat only makes up a small portion of the island.</p>", "<p id=\"p0130\">The widespread distribution of <italic>P. papatasi</italic>, predicted by its habitat preference, is highly consistent with the observations and is a result of its strong ecological adaptability. This species has been observed in high densities in damaged ecosystems and has been collected from a variety of biotopes (##REF##14651661##Wasserberg et al., 2003##; ##REF##19769053##Guernaoui and Boumezzough, 2009##). It also adapts well to artificial environments (##REF##1841221##Kamhawi et al., 1991##).</p>", "<p id=\"p0135\">In addition to the availability of appropriate breeding grounds, we employed expected population size, estimated by climate-sensitive mathematical modelling, as a proxy to disease risk due to <italic>P. papatasi</italic>. We simulated the average number of adult females (see <xref rid=\"sec2.4\" ref-type=\"sec\">Section 2.4</xref>) from April to December (##FIG##3##Fig. 3##C), and found that it matches the observed distribution of the species on the island (##FIG##1##Fig. 1##). In particular, <italic>P. papatasi</italic> is absent from areas of high altitude and maintains high numbers in densely populated urban and suburban areas with high levels of recorded temperature and relative humidity. The highest abundance was predicted along the southern coastline and the Mesaoria Plain, including the capital of the island, Nicosia.</p>", "<p id=\"p0140\">We identified multiple peaks of activity throughout the year starting in May and ending in September, when the population gradually declines (##FIG##3##Fig. 3##A). Two distinct periods of activity emerged and corresponded to two main generations of sand flies. The first generation appears in May and slowly disappears in June, from when the second, more sustained generation follows. We note that the second generation appears not in isolation but is a combination of two or three overlapping generations maintained by the suitability of ambient temperature and near-surface relative humidity.</p>", "<p id=\"p0145\">We found that <italic>P. papatasi</italic> population size increases approximately uniformly across the island, except around the Troodos Mountain, until it peaks in July-September (##FIG##3##Fig. 3##A). The peak season is displaced with relatively lower and more clustered abundance in October-December (##FIG##3##Fig. 3##A), where high population size is maintained in certain areas, “hotspots”, such as Avdimou, Limassol, Larnaca, Nicosia, and the northern section of the Mesaoria Plain.</p>", "<p id=\"p0150\">The spatiotemporal dynamics agrees well with the surveillance reports from counties with similar climates, such as Greece (##REF##29458398##Tsirigotakis et al., 2018##) and Israel (##UREF##12##Müller et al., 2011##). In Israel, many sand fly species concentrate in humid areas during dry summers and reach their peak numbers at the end of the summer period, similar to the July-September period identified in Cyprus. In April and May, when vegetation is thick and relative humidity is high, many species tend to distribute evenly throughout their habitats (##UREF##12##Müller et al., 2011##), similar to the April-June period identified in Cyprus.</p>", "<p id=\"p0155\">Here, we included a range of biotic, e.g. population structure and climate-sensitive physiology, and abiotic factors, e.g. temperature, relative humidity, and land cover, to predict the dynamics of <italic>P. papatasi</italic>. In addition, we note that socioeconomic factors, the population of stray dogs, certain types of land cover (e.g. dump sites, quarries, green urban areas, and vineyards), and altitude are also important factors for sand fly populations and leishmaniasis spread (##REF##29097638##Artun and Kavur, 2017##; ##UREF##7##Iliopoulou et al., 2018##).</p>", "<p id=\"p0160\">Although the population of stray dogs is directly linked with canine leishmaniasis infections, the possibility of human infections typically increases with the number of infected dogs in an area (##REF##20207870##Mazeris et al., 2010##). We plan to incorporate these additional factors, as well as the dynamics of pathogen reservoirs and disease transmission, in future studies for a more in-depth assessment of risk.</p>", "<p id=\"p0165\">We established a direct link between a meteorological model and a population dynamics model, predicting the dynamics of <italic>P. papatasi</italic> across the island on a daily basis. Although we concluded our analysis in a calendar year, our setup enables executing the WRF model in forecasting mode and extending predictions into the future for short-term operational risk assessment.</p>" ]
[ "<title>Results and discussion</title>", "<title>Exploring the boundaries of the rich sand fly fauna in Cyprus</title>", "<p id=\"p0100\">We compiled a dataset of sand fly presence in Cyprus with 18 species of phlebotomine sand flies from 2 genera and 6 subgenera. A list of all species is given in ##TAB##0##Table 1## and maps for species with known geolocations are provided in <xref rid=\"appsec1\" ref-type=\"sec\">Supplementary Figs. S1–S3</xref>. We found that <italic>P. papatasi</italic>, <italic>P. tobbi</italic>, <italic>P. sergenti</italic>, and <italic>P. galilaeus</italic> are among the most frequently reported and widely distributed species; their locations are mapped in ##FIG##1##Fig. 1##. While <italic>P. papatasi</italic> was found in almost all sampling locations, <italic>P. tobbi</italic> exhibited a slightly narrower range (not recorded in the south-eastern peninsula). On the contrary, <italic>P. mascittii</italic> (3 locations), <italic>P. kyreniae</italic> (5 locations), and <italic>P. killicki</italic> (1 location) have been seldom encountered. We note that, due to the morphological similarity within the subgenus <italic>Transphlebotomus</italic>, the presence of <italic>P. mascittii</italic> on the island has been found suspicious and in need of further molecular confirmation (##REF##26006062##Kasap et al., 2015##).</p>", "<p id=\"p0105\">Through our survey, we confirmed the presence of 7 species of <italic>Phlebotomus</italic> and 3 species of <italic>Sergentomya</italic> (<xref rid=\"appsec1\" ref-type=\"sec\">Supplementary Table S1</xref> and <xref rid=\"appsec1\" ref-type=\"sec\">Supplementary Figs. S1–S3</xref>). As expected, <italic>P. papatasi</italic> was the dominant species, in all of the locations, followed by <italic>P. tobbi</italic> and <italic>P. galilaeus</italic>, albeit fewer in numbers. In addition, we detected <italic>S. minuta</italic> in large numbers in Aigoi Trimithias, which suggests that the village is a novel hotspot for this species. We did not detect certain species, such as <italic>P. kyreniae</italic> and <italic>P. economidesi</italic>, which exhibited restricted geographical ranges. Our dataset suggests that the number of species identified largely depends on the geographical extent of the study design. For instance, the surveys reported by ##UREF##4##Demir et al. (2010)##, ##REF##10887662##Léger et al. (2000b)##, and ##UREF##15##Töz et al. (2013)##, differ largely from those by ##REF##27609635##Dokianakis et al. (2016##, ##REF##29454363##2018)## and ##REF##30792449##Erguler et al. (2019)##, with respect to the area covered and the number of species reported.</p>", "<p id=\"p0110\">We note that while the earlier reports, including the comprehensive assessments of ##REF##21015625##Adler (1946)## and ##UREF##11##Minter and Eitrem (1989)##, employed morphological identification methods; contemporary reports employed genetic and serology techniques more often as a result of the recent developments in biochemical and molecular analysis (##REF##10380101##Field et al., 1999##; ##REF##25499083##Ergunay et al., 2014##; ##REF##27609635##Dokianakis et al., 2016##, ##REF##29454363##2018##). In addition to the improved accuracy in identification, molecular methods enable establishing phylogenetic relationships between populations at different locations.</p>", "<p id=\"p0115\"><italic>Phlebotomus papatasi</italic> and <italic>P. perfiliewi</italic> are common vectors of sand fly fever viruses and likely causes of phlebovirus circulation in the Cypriot population (##UREF##1##Alwassouf et al., 2016##; ##REF##31346541##Billioud et al., 2019##). <italic>Phlebotomus tobbi</italic> has been related to infections with cutaneous and visceral leishmaniasis in the Middle East and the Eastern Mediterranean basin (##REF##26608249##Seblova et al., 2015##). Likewise, <italic>P. papatasi</italic> and <italic>P. sergenti</italic> have been identified as vectors of <italic>Leishmania major</italic> and <italic>L. tropica</italic>, respectively (##REF##17207663##Volf and Myskova, 2007##). Due to suitable rodent reservoirs for the parasite, <italic>L. major</italic> has long been acknowledged as endemic in the Jordan Valley even though it is currently missing from Europe (##REF##30412694##Özbilgin et al., 2019##). In the last few decades, however, cases caused by <italic>L. major</italic> were reported outside its endemic range, such as in the southern region of Israel, i.e. Negev highlands, the western Negev, the Arava (##REF##30412694##Özbilgin et al., 2019##), and south-eastern Turkey, i.e. Adana Province (##REF##25279543##Saroufim et al., 2014##).</p>", "<title>Risk assessment: Mapping sand fly abundance in space and time</title>", "<p id=\"p0120\">To bridge the gap between observations, we used expert assessment on habitat preferences applied on satellite-derived high-resolution land cover data (##UREF##8##Kosztra et al., 2019##). The key for suitable habitat types, i.e. primary, secondary, and unsuitable habitat types, is published in the recent technical report of ECDC for a range of vector species (##UREF##5##ECDC, 2019##). We used this key to map the habitat preferences of <italic>P. papatasi</italic> and <italic>P. tobbi</italic>, two of the most abundant and medically important sand fly species, in Cyprus (##FIG##2##Fig. 2##).</p>", "<p id=\"p0125\">We found that the primary habitats of <italic>P. papatasi</italic> are urban and suburban areas while <italic>P. tobbi</italic> is well-adjusted to Mediterranean sclerophyllous vegetation - a secondary habitat for <italic>P. papatasi</italic>. Rural locations of Cyprus typically include low scrublands/phrygana and maqui vegetation, which can affect sand fly diversity and thus infection risk. In previous studies, the broad-leaved forest was emphasized as a suitable habitat for sand flies (##UREF##10##Martinez et al., 2007##); however, this kind of habitat only makes up a small portion of the island.</p>", "<p id=\"p0130\">The widespread distribution of <italic>P. papatasi</italic>, predicted by its habitat preference, is highly consistent with the observations and is a result of its strong ecological adaptability. This species has been observed in high densities in damaged ecosystems and has been collected from a variety of biotopes (##REF##14651661##Wasserberg et al., 2003##; ##REF##19769053##Guernaoui and Boumezzough, 2009##). It also adapts well to artificial environments (##REF##1841221##Kamhawi et al., 1991##).</p>", "<p id=\"p0135\">In addition to the availability of appropriate breeding grounds, we employed expected population size, estimated by climate-sensitive mathematical modelling, as a proxy to disease risk due to <italic>P. papatasi</italic>. We simulated the average number of adult females (see <xref rid=\"sec2.4\" ref-type=\"sec\">Section 2.4</xref>) from April to December (##FIG##3##Fig. 3##C), and found that it matches the observed distribution of the species on the island (##FIG##1##Fig. 1##). In particular, <italic>P. papatasi</italic> is absent from areas of high altitude and maintains high numbers in densely populated urban and suburban areas with high levels of recorded temperature and relative humidity. The highest abundance was predicted along the southern coastline and the Mesaoria Plain, including the capital of the island, Nicosia.</p>", "<p id=\"p0140\">We identified multiple peaks of activity throughout the year starting in May and ending in September, when the population gradually declines (##FIG##3##Fig. 3##A). Two distinct periods of activity emerged and corresponded to two main generations of sand flies. The first generation appears in May and slowly disappears in June, from when the second, more sustained generation follows. We note that the second generation appears not in isolation but is a combination of two or three overlapping generations maintained by the suitability of ambient temperature and near-surface relative humidity.</p>", "<p id=\"p0145\">We found that <italic>P. papatasi</italic> population size increases approximately uniformly across the island, except around the Troodos Mountain, until it peaks in July-September (##FIG##3##Fig. 3##A). The peak season is displaced with relatively lower and more clustered abundance in October-December (##FIG##3##Fig. 3##A), where high population size is maintained in certain areas, “hotspots”, such as Avdimou, Limassol, Larnaca, Nicosia, and the northern section of the Mesaoria Plain.</p>", "<p id=\"p0150\">The spatiotemporal dynamics agrees well with the surveillance reports from counties with similar climates, such as Greece (##REF##29458398##Tsirigotakis et al., 2018##) and Israel (##UREF##12##Müller et al., 2011##). In Israel, many sand fly species concentrate in humid areas during dry summers and reach their peak numbers at the end of the summer period, similar to the July-September period identified in Cyprus. In April and May, when vegetation is thick and relative humidity is high, many species tend to distribute evenly throughout their habitats (##UREF##12##Müller et al., 2011##), similar to the April-June period identified in Cyprus.</p>", "<p id=\"p0155\">Here, we included a range of biotic, e.g. population structure and climate-sensitive physiology, and abiotic factors, e.g. temperature, relative humidity, and land cover, to predict the dynamics of <italic>P. papatasi</italic>. In addition, we note that socioeconomic factors, the population of stray dogs, certain types of land cover (e.g. dump sites, quarries, green urban areas, and vineyards), and altitude are also important factors for sand fly populations and leishmaniasis spread (##REF##29097638##Artun and Kavur, 2017##; ##UREF##7##Iliopoulou et al., 2018##).</p>", "<p id=\"p0160\">Although the population of stray dogs is directly linked with canine leishmaniasis infections, the possibility of human infections typically increases with the number of infected dogs in an area (##REF##20207870##Mazeris et al., 2010##). We plan to incorporate these additional factors, as well as the dynamics of pathogen reservoirs and disease transmission, in future studies for a more in-depth assessment of risk.</p>", "<p id=\"p0165\">We established a direct link between a meteorological model and a population dynamics model, predicting the dynamics of <italic>P. papatasi</italic> across the island on a daily basis. Although we concluded our analysis in a calendar year, our setup enables executing the WRF model in forecasting mode and extending predictions into the future for short-term operational risk assessment.</p>" ]
[ "<title>Conclusions</title>", "<p id=\"p0170\">Leishmaniasis is a climate-sensitive disease; temperature, land cover, and relative humidity have profound impacts on the ecology of its vector, phlebotomine sand flies, and thus the intensity of the vector-host-parasite interactions. Cyprus hosts a rich sand fly fauna and an active circulation of <italic>Leishmania</italic> parasites, which pose both veterinary and public health concerns. The island-wide distribution patterns, composed for several species, naturally exhibit gaps and observational biases. Here, we showed that climate-sensitive mathematical modelling, assimilated with satellite imagery and meteorological models, augments observations to improve our understanding of the spatiotemporal dynamics of selected species. Model-based risk assessment can indicate potential breeding habitats and times of peak activity, informing public health policies for developing optimum intervention strategies. The risk of sand fly-borne disease outbreaks can thus be reduced by employing site-specific measures rather than using area-wide applications of pesticides, therefore, minimising the environmental impact of vector control.</p>" ]
[ "<p>Visceral and cutaneous leishmaniases are important public health concerns in Cyprus. Although the diseases, historically prevalent on the island, were nearly eradicated by 1996, an increase in frequency and geographical spread has recently been recorded. Upward trends in leishmaniasis prevalence have largely been attributed to environmental changes that amplify the abundance and activity of its vector, the phlebotomine sand flies. Here, we performed an extensive field study across the island to map the sand fly fauna and compared the presence and distribution of the species found with historical records. We mapped the habitat preferences of <italic>Phlebotomus papatasi</italic> and <italic>P. tobbi</italic>, two medically important species, and predicted the seasonal abundance of <italic>P. papatasi</italic> at unprecedented spatiotemporal resolution using a climate-sensitive population dynamics model driven by high-resolution meteorological forecasting. Our compendium holds a record of 18 species and the locations of a subset, including those of potential public and veterinary health concern. We confirmed that <italic>P. papatasi</italic> is widespread, especially in densely urbanized areas, and predicted that its abundance uniformly peaks across the island at the end of summer. We identified potential hotspots of <italic>P. papatasi</italic> activity even after this peak. Our results form a foundation to inform public health planning and contribute to the development of effective, efficient, and environmentally sensitive strategies to control sand fly populations and prevent sand fly-borne diseases.</p>", "<title>Graphical abstract</title>", "<p></p>", "<title>Highlights</title>", "<p><list list-type=\"simple\" id=\"ulist0010\"><list-item id=\"u0010\"><label>•</label><p id=\"p0010\">The first georeferenced database of sand fly species in Cyprus.</p></list-item><list-item id=\"u0015\"><label>•</label><p id=\"p0015\">The first model-based island-wide seasonal profiling of <italic>Phlebotomus papatasi.</italic></p></list-item><list-item id=\"u0020\"><label>•</label><p id=\"p0020\">Links meteorological covariates and land type with sand fly physiology.</p></list-item><list-item id=\"u0025\"><label>•</label><p id=\"p0025\">Sand fly activity occurs in multiple peaks but almost uniformly across the island.</p></list-item><list-item id=\"u0030\"><label>•</label><p id=\"p0030\">Highlights hotspots and times for planning sand fly control.</p></list-item></list></p>", "<title>Keywords</title>" ]
[ "<title>Funding</title>", "<p id=\"p0175\">This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. This research was performed within the framework of the <funding-source id=\"gs3\">EMME-CARE</funding-source> project, which received funding from the European Unionʼs <funding-source id=\"gs1\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/100010661</institution-id><institution>Horizon 2020 Research and Innovation Programme</institution></institution-wrap></funding-source> under grant agreement No. 856612 and the <funding-source id=\"gs2\">Cyprus Government</funding-source>. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.</p>", "<title>Ethical approval</title>", "<p id=\"p0180\">Not applicable.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0185\"><bold>Maria Christou:</bold> Conceptualization, Formal analysis, Investigation, Data curation, Visualization, Writing – original draft, Writing – review &amp; editing. <bold>Behich Koyutourk:</bold> Investigation, Data curation, Visualization, Writing – review &amp; editing. <bold>Kardelen Yetismis:</bold> Investigation, Writing – review &amp; editing. <bold>Angeliki F. Martinou:</bold> Investigation, Resources, Writing – review &amp; editing. <bold>Vasiliki Christodoulou:</bold> Investigation, Writing – review &amp; editing. <bold>Maria Koliou:</bold> Supervision, Writing – review &amp; editing. <bold>Maria Antoniou:</bold> Resources, Supervision, Writing – review &amp; editing. <bold>Christoforos Pavlou:</bold> Investigation, Writing – review &amp; editing. <bold>Yusuf Ozbel:</bold> Resources, Supervision, Writing – review &amp; editing. <bold>Ozge Erisoz Kasap:</bold> Data curation, Writing – review &amp; editing. <bold>Bulent Alten:</bold> Resources, Supervision, Writing – review &amp; editing. <bold>Pantelis Georgiades:</bold> Investigation, Writing – review &amp; editing. <bold>George K. Georgiou:</bold> Investigation, Writing – review &amp; editing. <bold>Theodoros Christoudias:</bold> Investigation, Supervision, Writing – review &amp; editing. <bold>Yiannis Proestos:</bold> Investigation, Writing – review &amp; editing. <bold>Jos Lelieveld:</bold> Resources, Supervision, Writing – review &amp; editing. <bold>Kamil Erguler:</bold> Conceptualization, Methodology, Software, Formal analysis, Visualization, Project administration, Supervision, Writing – review &amp; editing, All authors have read and approved the final version of the manuscript.</p>", "<title>Declaration of competing interests</title>", "<p id=\"p0190\">The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.</p>" ]
[ "<title>Supplementary data</title>", "<p id=\"p0200\">The following is/are the supplementary data to this article.</p>", "<title>Data availability</title>", "<p id=\"p0035\">The data supporting the conclusions of this article are included within the article and its supplementary files. The entomological surveillance data are available in Table 1 and Supplementary Table S1. Python code to perform the spatiotemporal simulations described is provided in Supplementary Text S1. The meteorological covariates are available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.5281/zenodo.8413232\" id=\"PC_linkkAabkli3Ec\">https://doi.org/10.5281/zenodo.8413232</ext-link>, and the spatiotemporal simulation outputs are available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.5281/zenodo.8413593\" id=\"PC_linkxEzg0LOfcE\">https://doi.org/10.5281/zenodo.8413593</ext-link>.</p>", "<title>Acknowledgements</title>", "<p id=\"p0195\">The authors would like to thank Florence Dubart for helping with the translation of French literature that made accessible valuable information on phlebotomine sand flies.</p>" ]
[ "<fig id=\"undfig1\" position=\"anchor\"><alt-text id=\"alttext0010\">Image 1</alt-text></fig>", "<fig id=\"fig1\"><label>Fig. 1</label><caption><p>The distribution of the four common sand fly species in Cyprus. The marks represent the locations of the centroids of the administrative regions where the species were detected.</p></caption><alt-text id=\"alttext0030\">Fig. 1</alt-text></fig>", "<fig id=\"fig2\"><label>Fig. 2</label><caption><p>Land type preference for <italic>P. papatasi</italic> and <italic>P. tobbi</italic>.</p></caption><alt-text id=\"alttext0035\">Fig. 2</alt-text></fig>", "<fig id=\"fig3\"><label>Fig. 3</label><caption><p>The expected population size of <italic>P. papatasi</italic> estimated by climate-sensitive mathematical modelling. Geospatial distribution of abundance is shown in panel <bold>A</bold> for three time periods (April-June, July–September, and October-December), and matches the temporal dynamics (<bold>B</bold>). The temporal dynamics of average number of females is given for both primary (<italic>black line</italic>) and secondary (<italic>green line</italic>) habitats. The average geospatial distribution of population size is given in panel <bold>C</bold>, where abundance corresponds to the average number of females per day per trap (see <xref rid=\"sec2.4\" ref-type=\"sec\">Section 2.4</xref>).</p></caption><alt-text id=\"alttext0040\">Fig. 3</alt-text></fig>" ]
[ "<table-wrap position=\"float\" id=\"tbl1\"><label>Table 1</label><caption><p>The compendium of the sand fly species of Cyprus, 1946–2023.</p></caption><alt-text id=\"alttext0045\">Table 1</alt-text><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"2\">Subgenus</th><th rowspan=\"2\">Species</th><th colspan=\"16\">References<hr/></th></tr><tr><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th><th>8</th><th>9</th><th>10</th><th>11</th><th>12</th><th>13</th><th>14</th><th>15</th><th>16</th></tr></thead><tbody><tr><td align=\"left\"><italic>Phlebotomus</italic></td><td align=\"left\"><italic>Phlebotomus papatasi</italic></td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td></tr><tr><td align=\"left\"><italic>Artemievus</italic></td><td align=\"left\"><italic>Phlebotomus alexandri</italic></td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td align=\"left\">✓</td></tr><tr><td rowspan=\"2\" align=\"left\"><italic>Paraphlebotomus</italic></td><td align=\"left\"><italic>Phlebotomus sergenti</italic></td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td/><td/><td/><td align=\"left\">✓</td></tr><tr><td align=\"left\"><italic>Phlebotomus jacusieli</italic></td><td/><td/><td/><td/><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td align=\"left\">✓</td><td/><td/><td/><td/><td/></tr><tr><td rowspan=\"5\" align=\"left\"><italic>Larroussius</italic></td><td align=\"left\"><italic>Phlebotomus perfiliewi</italic></td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td/><td/><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td/><td/><td align=\"left\">✓</td></tr><tr><td align=\"left\"><italic>Phlebotomus tobbi</italic></td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td></tr><tr><td align=\"left\"><italic>Phlebotomus galilaeus</italic></td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td/><td/><td/><td align=\"left\">✓</td></tr><tr><td align=\"left\"><italic>Phlebotomus neglectus</italic></td><td/><td/><td/><td/><td/><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td/><td align=\"left\">✓</td><td/><td/><td/><td align=\"left\">✓</td></tr><tr><td align=\"left\"><italic>Larroussius</italic> sp.</td><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td align=\"left\">✓</td><td/><td/><td/><td/><td/></tr><tr><td rowspan=\"2\" align=\"left\"><italic>Adlerius</italic></td><td align=\"left\"><italic>Phlebotomus halepensis</italic></td><td/><td/><td/><td/><td/><td/><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td/><td/><td/><td/></tr><tr><td align=\"left\"><italic>Phlebotomus kyreniae</italic></td><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td/></tr><tr><td rowspan=\"3\" align=\"left\"><italic>Transphlebotomus</italic></td><td align=\"left\"><italic>Phlebotomus killicki</italic></td><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td align=\"left\">✓</td><td/><td/></tr><tr><td align=\"left\"><italic>Phlebotomus economidesi</italic></td><td/><td/><td/><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td/><td/></tr><tr><td align=\"left\"><italic>Phlebotomus mascittii</italic></td><td align=\"left\">✓</td><td/><td/><td/><td align=\"left\">✓</td><td/><td/><td/><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td/><td/></tr><tr><td rowspan=\"6\" align=\"left\"><italic>Sergentomyia</italic></td><td align=\"left\"><italic>Sergentomyia minuta</italic></td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td align=\"left\">✓</td><td/><td align=\"left\">✓</td></tr><tr><td align=\"left\"><italic>Sergentomyia azizi</italic></td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td/><td/><td/></tr><tr><td align=\"left\"><italic>Sergentomyia fallax</italic></td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td align=\"left\">✓</td></tr><tr><td align=\"left\"><italic>Sergentomyia dentata</italic></td><td/><td/><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td align=\"left\">✓</td><td/><td align=\"left\">✓</td></tr><tr><td align=\"left\"><italic>Sergentomyia antennata</italic></td><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/></tr><tr><td align=\"left\"><italic>Sergentomyia</italic> sp.</td><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td align=\"left\">✓</td><td align=\"left\">✓</td><td/><td/><td/><td align=\"left\">✓</td></tr><tr><td/><td align=\"left\">Unidentified species</td><td/><td/><td align=\"left\">✓</td><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td/><td align=\"left\">✓</td></tr></tbody></table></table-wrap>" ]
[]
[]
[]
[]
[]
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[ "<table-wrap-foot><fn><p><italic>References</italic>: 1, ##REF##21015625##Adler (1946)##; 2, ##UREF##11##Minter and Eitrem (1989)##; 3, ##REF##10380101##Field et al. (1999)##; 4, ##REF##10887661##Léger et al. (2000a)##; 5, ##REF##10887662##Léger et al. (2000b)##; 6, ##REF##11304945##Depaquit et al. (2001)##; 7, ##UREF##13##Rastgeldi et al. (2005)##; 8, ##UREF##4##Demir et al. (2010)##; 9, ##REF##20207870##Mazeris et al. (2010)##; 10, ##UREF##15##Töz et al. (2013)##; 11, ##REF##25499083##Ergunay et al. (2014)##; 12, ##UREF##0##Alten et al. (2016)##; 13, ##REF##27609635##Dokianakis et al. (2016)##; 14, ##REF##29454363##Dokianakis et al. (2018)##; 15, ##REF##30792449##Erguler et al. (2019)##; 16, Present study.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"appsec2\" fn-type=\"supplementary-material\"><label>Appendix A</label><p id=\"p0205\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.crpvbd.2023.100152\" id=\"intref0010\">https://doi.org/10.1016/j.crpvbd.2023.100152</ext-link>.</p></fn></fn-group>" ]
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[ "<media xlink:href=\"mmc1.pdf\"><alt-text>Multimedia component 1</alt-text></media>", "<media xlink:href=\"mmc2.pdf\"><alt-text>Multimedia component 2</alt-text></media>", "<media xlink:href=\"mmc3.pdf\"><alt-text>Multimedia component 3</alt-text></media>" ]
[{"surname": ["Alten", "Maia", "Afonso", "Campino", "Jim\u00e9nez", "Gonz\u00e1lez"], "given-names": ["B.", "C.", "M.O.", "L.", "M.", "E."], "article-title": ["Seasonal dynamics of phlebotomine sand fly species proven vectors of Mediterranean leishmaniasis caused by "], "italic": ["Leishmania infantum"], "source": ["PLoS Negl. Trop. Dis."], "volume": ["10"], "year": ["2016"], "object-id": ["e0004458"]}, {"surname": ["Alwassouf", "Christodoulou", "Bichaud", "Ntais", "Mazeris", "Antoniou", "Charrel"], "given-names": ["S.", "V.", "L.", "P.", "A.", "M.", "R.N."], "article-title": ["Seroprevalence of sandfly\u2010borne phleboviruses belonging to three serocomplexes (Sandfly fever Naples, Sandfly fever Sicilian and Salehabad) in dogs from Greece and Cyprus using neutralization test"], "source": ["PLoS Negl. Trop. Dis."], "volume": ["10"], "year": ["2016"], "object-id": ["e0005063"]}, {"collab": ["CDC"], "part-title": ["Leishmaniasis"], "year": ["2021"], "publisher-name": ["Centers for Disease Control and Prevention"], "publisher-loc": ["Atlanta"], "ext-link": ["https://www.cdc.gov/parasites/leishmaniasis/index.html"]}, {"surname": ["Dedet", "Hamer", "Griffiths", "Maguire", "Heggenhougen", "Quah"], "given-names": ["J.P.", "D.H.", "J.K.", "J.H.", "H.K.", "S.R."], "part-title": ["Protozoan diseases: Leishmaniasis"], "source": ["Public Health and Infectious Diseases"], "year": ["2010"], "publisher-name": ["Elsevier"], "comment": ["280 pp"]}, {"surname": ["Demir", "Gocmen", "Ozbel"], "given-names": ["Y.", "S.", "B."], "article-title": ["Faunistic study of sand flies in Northern Cyprus"], "source": ["N. West. J. Zool."], "volume": ["6"], "year": ["2010"], "fpage": ["149"], "lpage": ["161"]}, {"collab": ["ECDC"], "part-title": ["Technical Report: A spatial modelling method for vector surveillance"], "year": ["2019"], "publisher-name": ["European Centre for Disease Prevention and Control"], "publisher-loc": ["Stockholm"], "ext-link": ["https://www.ecdc.europa.eu/en/publications-data/spatial-modelling-method-vector-surveillance"]}, {"surname": ["Georgiou", "Christoudias", "Proestos", "Kushta", "Hadjinicolaou", "Lelieveld"], "given-names": ["G.K.", "T.", "Y.", "J.", "P.", "J."], "article-title": ["Air quality modelling in the summer over the eastern Mediterranean using WRF-Chem: Chemistry and aerosol mechanism intercomparison"], "source": ["Atmos. Chem. 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NATO ASI Series"], "volume": ["vol. 171"], "year": ["1989"], "publisher-name": ["Springer"], "publisher-loc": ["Boston, MA"], "fpage": ["207"], "lpage": ["216"], "pub-id": ["10.1007/978-1-4613-1575-9_26"]}, {"surname": ["M\u00fcller", "Kravchenko", "Rybalov", "Schlein"], "given-names": ["Y.", "G.C.", "V.D.", "L."], "article-title": ["Characteristics of resting and breeding habitats of adult sand flies in the Judean Desert"], "source": ["J. Vector Ecol."], "volume": ["36"], "year": ["2011"], "fpage": ["195"], "lpage": ["205"]}, {"surname": ["Rastgeldi", "\u00d6zbel", "\u00d6zensoy", "Ertabaklar", "G\u00f6cmen"], "given-names": ["S.", "Y.", "T.S.", "H.", "H."], "article-title": ["Phlebotominae sand flies (Diptera: Psychodidae) of the northern part of Cyprus island"], "source": ["Arch. Inst. Pasteur. Tunis"], "volume": ["82"], "year": ["2005"], "fpage": ["121"]}, {"surname": ["Skamarock", "Klemp", "Dudhia", "Gill", "Barker", "Duda"], "given-names": ["W.C.", "J.B.", "J.", "D.O.", "D.M.", "M.G."], "part-title": ["A description of the advanced research WRF version 3"], "year": ["2008"], "publisher-name": ["University Corporation for Atmospheric Research NCAR Technical Note 475"], "fpage": ["113 pp"], "pub-id": ["10.5065/D68S4MVH"]}, {"surname": ["T\u00f6z", "Ertabaklar", "G\u00f6\u00e7men", "Demir", "Karakus", "Arserim"], "given-names": ["S.\u00d6.", "H.", "B.", "S.", "M.", "S.K."], "article-title": ["An epidemiological study on canine leishmaniasis (CanL) and sand flies in Northern Cyprus"], "source": ["Turk. Parazitoloji Derg."], "volume": ["37"], "year": ["2013"], "fpage": ["107"]}, {"collab": ["WHO"], "part-title": ["Leishmaniasis"], "year": ["2021"], "publisher-name": ["World Health Organization"], "publisher-loc": ["Geneva"], "ext-link": ["https://www.who.int/data/gho/data/themes/topics/topic-details/GHO/leishmaniasis"]}]
{ "acronym": [], "definition": [] }
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Curr Res Parasitol Vector Borne Dis. 2023 Nov 6; 4:100152
oa_package/bc/7b/PMC10787173.tar.gz
PMC10787174
36494035
[ "<title>Introduction</title>", "<p id=\"p0005\">To answer the key question of how new traits arise during the macroevolutionary process, biologists have long realized the necessity to understand the gene regulation in development responsible for morphological diversity, <italic>i.e.</italic>, which genes are expressed, what regulatory element changes are involved, and how regulatory element changes affect development ##REF##18614008##[1]##. Only recently have the field of large-scale omics and the accumulation of data matured sufficiently to explore these theoretical concepts in detail. Here, we investigate the ruminant multi-chambered stomach, a key mammalian organ innovation and a cornerstone of evolutionary theory, as an example to illustrate a novel framework for integrating multi-omics data to address the fundamental question of organ innovation.</p>", "<p id=\"p0010\">The rumen hosts a diverse ecosystem of microorganisms and facilitates efficient plant fiber digestion and short-chain fatty acid uptake, which significantly promotes the expansion and diversification of ruminant animals by providing a unique evolutionary advantage relative to non-ruminants ##REF##33165812##[2]##. This remarkable morphological innovation raises the fundamental question of how the genetic toolkit generates functional complexity through development and evolution ##REF##18614008##[1]##, ##REF##29358652##[3]##, ##REF##15630479##[4]##. By comparing 51 ruminants with 12 mammalian outgroup species genomes, we previously identified 221,166 ruminant-specific conserved non-coding elements (RSCNEs), which span approximately 0.61% of the genome (16.5 Mb in total) ##REF##31221828##[5]##. These RSCNEs are potential regulatory elements of proximal or distal genes for transcriptional regulation in the development of morphological and physiological traits ##REF##17304246##[6]##. In addition, we previously sequenced two representative ruminants (sheep and roe deer) for gene expression across 50 tissues. Comparative transcriptome analysis revealed 656 rumen-specific expressed genes (RSEGs) and implied that the anatomical predecessor of the rumen is the esophagus by the most similar expression profile ##REF##31221828##[5]##, ##REF##26989612##[7]##. There is a pressing need to understand how RSCNEs lead to changes in the expression of RSEGs.</p>", "<p id=\"p0015\">One major bottleneck is that the cellular context, target genes (TGs), and mode of gene regulation of RSCNEs are largely unknown. First, the regulatory role of RSCNEs could be spatiotemporally dynamic and highly context-specific. Second, some RSCNEs were located distant (<italic>e.g</italic>., more than 500 kb) from any gene and therefore could not be associated with any TGs using standard the closest transcription start site (TSS) approaches, such as GREAT ##REF##20436461##[8]##. This problem is emphasized by a recent finding that a non-coding region associated with a human craniofacial disorder causally affects the expression of <italic>SOX9</italic> at a distance of up to 1.45 Mb during a restricted time window of facial progenitor development ##UREF##0##[9]##. This example motivated us to interpret the function of RSCNEs by uncovering gene regulatory networks (GRNs) with distal regulations from multi-omics data integration at different developmental time points and in different tissue types.</p>", "<p id=\"p0020\">To tackle the aforementioned challenges, we generated time series of paired gene expression and chromatin accessibility data during rumen and esophagus development in sheep to reconstruct a developmental GRN. Our previous efforts showed that jointly modeling multi-omics data allows us to infer high-quality tissue-specific regulatory networks ##REF##28576882##[10]##, which can be used to identify key transcription factors (TFs) during differentiation ##UREF##1##[11]##, reveal causal regulations ##REF##32188700##[12]##, and interpret functionally important genetic variants ##REF##33004791##[13]##. Taken together, we aim to integrate multi-omics data to reconstruct a genome-wide GRN during different stages of development in an apomorphic organ. Specifically, this allows us to understand how TFs bind to functional RSCNEs to coordinate cell type-specific gene expression of RSEGs and hence to gain further insights into the evolutionary development of new traits.</p>" ]
[ "<title>Materials and methods</title>", "<title>CNEReg infers developmental regulatory network to interpret CNEs</title>", "<p id=\"p0135\">CNEReg aims to systematically fill the gap between CNEs and their significantly impacted morphology in evolution. This is done by reconstructing a developmental regulatory network by paired time series of paired gene expression and chromatin accessibility data. Particularly in sheep, CNEs are RSCNEs, and morphology is the innovation of the rumen organ, which is further denoted by the set of rumen-specific genes. We reconstructed a gene regulatory network during rumen development to systematically understand how TFs regulate genes via batteries of RSCNEs, which over development led to the cell type-specific activation of RSEGs.</p>", "<p id=\"p0140\">The main idea of CNEReg is to define those TTFs as major players in evo-devo and to study how those TFs are regulated by RSCNEs and how they utilize RSCNEs to regulate RSEGs. CNEReg models the expression of TGs conditional on the chromatin accessibility of RSCNEs and the expression of TFs. CNEReg is composed of three steps, as shown in ##FIG##2##Figure 3##, and uses three equations to model (1) the expression of TTFs, (2) the expression of RSEGs, and (3) the functional influence of RSCNEs (##FIG##2##Figure 3##; ##TAB##0##Table 1##).</p>", "<title>Defining and identifying TTFs</title>", "<p id=\"p0145\">We identified TTFs by their nearby evolutionally conserved CREs in the genome, expression patterns across tissues, and expression levels in developmental stages. TTFs should satisfy-four conditions: (1) TFs should be rumen-specifically expressed genes (37 TFs in the 656 RSEGs); (2) there should be active-RSCNEs around TFs (±1 Mb, 35 TFs remain); (3) TFs should be expressed (FPKM &gt; 1) at least one time point during rumen development (30 TFs remain); and (4) these TFs should have additional tissue specificity. TFs were ranked by our tissue specificity JMS (see “Defining tissue specificity score” section)<italic>,</italic> and only the TFs for the top 50 specificities in at least one tissue were selected (18 TFs remain). Finally, 18 TFs were identified as TTFs and are listed in <xref rid=\"s0165\" ref-type=\"sec\">Table S5</xref>. These TFs played a leading role in rumen development (<xref rid=\"s0165\" ref-type=\"sec\">Table S5</xref>) and served as the main component to construct the rumen developmental regulatory network.</p>", "<title>Modeling expression of TTFs</title>", "<p id=\"p0150\">We modeled how TTFs are regulated from paired gene expression and chromatin accessibility data to reconstruct the upstream regulatory network of TTFs. We established a linear regression model as follows to reveal the upstream regulators of the 18 TTFs (schematic illustration in ##FIG##2##Figure 3## and mathematical notations in ##TAB##0##Table 1##).where is the expression of the <italic>l</italic>-th TTF; is the set of TFs with significant motif match in the <italic>i</italic>-th active-RSCNE; and is the expression of the <italic>m</italic>-th candidate TF with a binding motif to regulate the <italic>l</italic>-th TTF. The Spearman correlation coefficient between and is greater than 0.6 [false discovery rate (FDR) <italic>Q</italic> value &lt; 0.01] to ensure the potential regulatory relationship; represents the chromatin accessibility score of the <italic>i</italic>-th active-RSCNE within 2 Mb around the <italic>l</italic>-th TTF. is the parameter to be estimated. If is statistically significant non-zero in the regression analysis, the <italic>i</italic>-th active-RSCNE and its TFs in will be contained in the upstream regulatory network of the -th TTF.</p>", "<title>Modeling expression of RSEGs</title>", "<p id=\"p0155\">We modeled how the RSEGs are regulated by TTFs and their active-RSCNEs from paired gene expression and chromatin accessibility data, <italic>i.e</italic>., to reconstruct the downstream network regulated by TTFs. We established the linear regression model as follows (schematic illustration in ##FIG##2##Figure 3## and mathematical notations in ##TAB##0##Table 1##):where is the expression of the <italic>l</italic>-th TTF; represents the chromatin accessibility score of the <italic>k</italic>-th active-RSCNE with binding sites of the -th TTF; and is the expression of the <italic>n</italic>-th RSEG with the <italic>k-</italic>th active-RSCNE within approximately 2 Mb. In practice, we determine the downstream regulation relationship with Spearman correlation that can eliminate the outlier values to simplify the calculation. When the Spearman correlation coefficient between and is greater than 0.7 (FDR <italic>Q</italic> value &lt; 0.01), the <italic>n</italic>-th RSEG is likely to be regulated by the <italic>l</italic>-th TTF through binding to the <italic>k</italic>-th active-RSCNE. The extracted TTF, active-RSCNEs, and RSEG triplets are formed the TTF’s downstream regulatory network.</p>", "<title>Quantifying the functional influence of active-RSCNEs</title>", "<p id=\"p0160\">We quantified the functional influence of active-RSCNEs, ranked the active-RSCNEs, and selected the top active-RSCNEs as experimental candidates. This task can be done by integrating the RSCNE’s conservation score in comparative genomics analysis with its regulatory potential in our developmental regulatory network.</p>", "<p id=\"p0165\">We first collected conservation scores of active-RSCNEs from a comparative genomics study ##REF##31221828##[5]##. RSCNEs were classified into two types by their conservation patterns across species. Type I RSCNEs had no outgroup sequence aligned, and type II RSCNEs had orthologous sequences in one or more outgroups but were only conserved in ruminants. For the -th active-RSCNE, the conservation score was calculated by the PhastCons score (type I) or PhyloP score (type II).</p>", "<p id=\"p0170\">We then estimated the regulatory strength of active-RSCNEs in the upstream and downstream regulatory networks of TTFs. An active-RSCNE played a regulatory role in the regulatory network if four conditions were satisfied: (1) this active-RSCNE should be a chromatin-accessible peak; (2) TTFs should bind to this active-RSCNE; (3) RSEGs regulated by this active-RSCNE with TTF binding should be expressed; and (4) the expression of binding TTFs and the accessibility of this active-RSCNE should be correlated with the expression of regulated RSEGs. By combining these four factors, we defined the regulatory strength of the -th active-RSCNE at time point in the regulatory network as follows:where is the chromatin accessibility score of the -th active-RSCNE at time point in the rumen; is the motif binding strength of the -th TTF on the -th active-RSCNE (computed by HOMER); is the expression of the -th TTF at time point in the rumen; is the expression of the -th RSEG at time point in the rumen; and is the Spearman correlation coefficient between and from the regulatory network. Then, the regulatory strength of the -th active-RSCNE was defined as the maximum value across all time points in rumen samples as follows:</p>", "<p id=\"p0175\">The regulatory strength is from the multi-omics data in development, and the conservation score is from multi-genome data across species. The two measures are at the regulation level and genome sequence level, respectively. They can be naturally assumed to be independent of each other. In practice, we found that the regulatory strength and the conservation score were quite complementary to each other (<xref rid=\"s0165\" ref-type=\"sec\">Figures S4 and S5</xref>) for active-RSCNEs. Hence, we defined the functional influence of the -th active-RSCNE as the geometric mean of the regulatory strength and the conservation score as follows:</p>", "<p id=\"p0180\">This functional influence score allows us to prioritize active-RSCNEs by approximating their importance in rumen innovation.</p>", "<title>Defining tissue specificity score</title>", "<p id=\"p0185\">Specificity illustrates the property that genes are functional in one particular biological context compared with other contexts. For our transcriptomics data across 50 tissues in sheep, genes highly expressed in only one or several tissues but not expressed in other tissues were defined as tissue specific. Our gene expression matrix had 23,126 rows (the number of expressed genes) and 830 columns (the number of samples sequenced in 50 sheep tissues with each tissue having several biological replicates; <xref rid=\"s0165\" ref-type=\"sec\">Table S10</xref>).</p>", "<p id=\"p0190\">To quantify the tissue specificity, we proposed a Jensen–Shannon Median expression Score (JMS) for a gene in certain tissues to combine the gene expression level with a Jensen–Shannon divergence (JSD) value as follows:where represents the gene’s median expression in a certain tissue across biological replicates. can guarantee that the numerator and denominator are of the same magnitude. JSD is the Jensen–Shannon divergence to evaluate the gene’s expression specificity introduced in ##UREF##7##[44]##. It adopts an entropy-based measure to assess the similarity between two probability distribution statistics as follows:where and are two probability distributions constructed from our gene expression values across tissues. <italic>n</italic> is the number of samples. Given each row of our gene expression matrix, we normalized the gene expression vector, <italic>i.e.</italic>, each element in this vector was divided by the sum of all elements. For a given gene, is its corresponding normalized row vector. Given the tissue we are interested, is constructed as a control vector whose components are in the given tissue with replicates and 0 in other tissues. Finally, the JSD will be calculated as the divergence between <italic>P</italic> and <italic>Q</italic> for a certain gene in certain tissue. The smaller the JSD value was, the more specific this gene was in this tissue.</p>", "<p id=\"p0195\">In summary, our JMS provided a relative specificity score by a nonlinear measure of divergence by emphasizing significantly highly expressed genes in certain tissues to enhance specificity. This JMS allows us to better explore the TTF expression patterns and recruitment of genes based on tissue specificity.</p>", "<title>Differential regulatory network construction between rumen and esophagus</title>", "<p id=\"p0200\">We constructed a differential regulatory network between rumen and esophagus by extracting differential RSEGs, differential TTFs, and active-RSCNEs associated sub-network from the regulatory network of TTFs. The differential RSEGs and differential TTFs are defined as follows.</p>", "<title>Differential RSEGs between rumen and esophagus</title>", "<p id=\"p0205\">We used the R packages “<italic>limma</italic>” and “edgeR” to extract differential genes at four developmental time points (E60/D1/D7/D28) with thresholds of FDR &lt; 0.05 and log<sub>2</sub> fold change (FC) &gt; 1 (FC of FPKM in the rumen relative to that in the esophagus). It was noted that at time point Y1, we had only one biological replicate for RNA-seq data in the rumen and esophagus separately, and we could not perform an F test on these two samples. Instead, we identified genes with FPKM &gt; 2 in the rumen and FC &gt; 2 as differential genes. Then, we combined differential genes at five time points to obtain differential gene sets between rumen and esophagus. Differential RSEGs between rumen and esophagus were the intersection of the differential gene set and the RSEG set in the regulatory network of TTFs.</p>", "<title>Differential accessible peaks between rumen and esophagus</title>", "<p id=\"p0210\">We implemented the R packages “<italic>limma</italic>” and “edgeR” to obtain differential accessible peaks between rumen and esophagus at five developmental time points (E60/D1/D7/D28/Y1) with thresholds of FDR &lt; 0.05 and |log<sub>2</sub> FC| &gt; 1.</p>", "<title>Differential TTFs between rumen and esophagus</title>", "<p id=\"p0215\">We first collected 1027 TFs of sheep from animalTFDB3.0 (<ext-link ext-link-type=\"uri\" xlink:href=\"http://bioinfo.life.hust.edu.cn/AnimalTFDB/\" id=\"ir045\">http://bioinfo.life.hust.edu.cn/AnimalTFDB/#!/</ext-link>). The 15,835 expressed genes in the rumen and esophagus were intersected with these 1027 TFs to obtain 768 TFs for the following analysis. We used HOMER to find TFs binding to the differential accessible peaks with threshold of −log<sub>10</sub>\n<italic>P</italic> value &gt; 6 at each time point. Then, we used the R packages “<italic>limma</italic>” and “edgeR” to obtain differentially expressed TFs at four time points (E60/D1/D7/D28) with thresholds of FDR &lt; 0.05 and log<sub>2</sub> FC &gt; 1. We identified differentially expressed TFs at time point Y1 with threshold FPKM &gt; 2 in the rumen and FC &gt; 2. The differential TF set was defined as the intersection of TFs binding to differential accessible peaks and differentially expressed TFs. Differential TTFs between the rumen and esophagus were the intersection of the differential TF set and TTF set in the regulatory network of TTFs.</p>", "<title>Hierarchical clustering and PCA</title>", "<p id=\"p0220\">We performed hierarchical clustering on the gene expression and peak chromatin accessibility profiles in 14 rumen samples at five time points (E60/D1/D7/D28/Y1). Heatmap was plotted by the R package “pheatmap” with “correlation” as the distance measure and “complete” as the clustering method. Then, we performed dimensional reduction by PCA with the R function “prcomp”. The gene expression and chromatin accessibility value were log-transformed as log<sub>2</sub> (FPKM+1) and log<sub>2</sub> (openness+1) as input. The openness score was calculated for each peak under each condition as the FC of read number per base pair ##REF##28576882##[10]##. The first two principal components are shown in ##FIG##0##Figure 1##D and E.</p>", "<title>Collecting samples for ATAC-seq and RNA-seq</title>", "<p id=\"p0225\">We collected a total of 37 samples of the rumen, esophagus epithelium tissues, and liver tissues from 14 Hu sheep, including five time points (E60/D1/D7/D28/Y1) from XiLaiYuan Ecological Agriculture Co., Ltd. (Taizhou, China). All samples were rinsed with PBS and soaked in cold 1× PBS supplemented with penicillin–streptomycin (Catalog No. 15140122, Gibco, Grand Island, NY). All animals were slaughtered under the guidelines of the Northwest A&amp;F University Animal Care Committee.</p>", "<title>ATAC-seq library preparation, sequencing, and analysis</title>", "<p id=\"p0230\">All the protocols for ATAC-seq used in this study have been described previously ##REF##33165812##[2]##. Hence, we described the experimental procedures and approaches here briefly. The ruminal and esophageal epithelial cells were separated manually from the muscular layer. Then, 0.25% trypsin pre-warmed in 37 °C water bath was used to digest the ruminal and esophageal epithelial cells. Dulbecco’s modified eagle medium (DMEM) solution was added to the cell suspension to adjust the cell density to 1 × 10<sup>6</sup> cells/ml. To prepare nuclei, the cells were lysed using cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl<sub>2</sub>, and 0.1% NP40). Subsequently, the transposition reaction was conducted using the TruePrep DNA library prep kit v2 for Illumina (Catalog No. TD501-01/02, Vazyme, Nanjing, China). The samples were immediately purified using a Qiagen MinElute kit. PCR was performed to amplify the library for 14 cycles according to the manufacturer’s recommendations (Catalog No. TD501-01/02, Vazyme).</p>", "<p id=\"p0235\">Sequencing reads must undergo QC and adapter trimming to optimize the alignment process. FastQC (version 0.11.5) ##UREF##8##[45]## was used to assess overall quality. Reads were trimmed for quality as well as the presence of adapter sequences using the Trim Galore Wrapper script ##UREF##9##[46]## with default parameters. Raw ATAC-seq reads of sheep were mapped to the sheep reference genome [National Center for Biotechnology Information (NCBI) assembly Oar_v4.0] using Bowtie2 (version 2.2.8) ##REF##22388286##[47]## with default parameters. Duplicated reads were removed using the default parameters in Picard (version 2.1.1). Reads mapping to mitochondrial DNA were excluded from the analysis together with low-quality reads [Mapping Quality (MAPQ) &lt; 20]. Then, accessible regions and narrow peaks were identified using MACS ##REF##18798982##[48]##. Open accessible peaks were identified in their biological replicates of each tissue using “bedtools intersect” parameter, and the consensus peak matrix with openness scores of each peak in each sample was constructed by merging these regions and calculating with the R package “Diffbind” (version 2.10.0) ##UREF##10##[49]##. Finally, the genomic distributions of peaks were annotated using the R packages “GenomicFeatures”, “ChIPseeker”, and “AnnotationHub”.</p>", "<title>RNA-seq library preparation and sequencing</title>", "<p id=\"p0240\">We prepared directional RNA-seq libraries from cells of the same samples used for ATAC-seq. One milliliter of TRIzol (Catalog No. 15596026, Invitrogen, Carlsbad, CA) was added to each sample and frozen at −80 °C until utilization. In all tissue samples collected for this study, total RNA was isolated from a frozen sample according to the TRIzol protocol (Catalog No. 15596026, Invitrogen). Sequencing libraries were generated using a NEBNext ultra RNA library prep kit for Illumina (Catalog No. E7760S, New England Biolabs, Ipswich, MA) according to the manufacturer’s recommendations. All prepared libraries were sequenced by the Illumina HiSeq X Ten platform, and paired-end reads with a length of 150 bp were generated. All sequencing procedures were performed by Novogene Technology (Beijing, China).</p>", "<p id=\"p0245\">We obtained high-quality reads by removing adaptor sequences and filtering low-quality reads from raw reads using Trimmomatic (version 0.36) ##REF##24695404##[50]##. High-quality reads were all aligned to the NCBI assembly Oar_v4.0 reference sheep genome ##REF##24904168##[51]## by STAR (version 2.5.1) ##REF##23104886##[52]##. To improve the mapping rate, the unmapped reads of each sample were extracted by SAMtools (version 1.3) ##REF##19505943##[53]## for further mapping by HISAT2 (version 2.0.3-beta) ##REF##25751142##[54]##. We computed FPKM values for the genes in each sample using StringTie (version 1.3.4) ##REF##27560171##[55]##.</p>", "<p id=\"p0250\">As the samples were prepared and sequenced in three known distinct batches (see <xref rid=\"s0165\" ref-type=\"sec\">Table S1</xref>), we used the <italic>removeBatchEffect()</italic> function from the R <italic>limma</italic> package to build a linear model with the batch information and the cell types on log<sub>2</sub> (FPKM + 1), and we regressed out the batch variable.</p>", "<title>Regulatory activity experiments</title>", "<p id=\"p0255\">We selected fibroblast cells of ruminants for <italic>in vitro</italic> regulatory activity experiments. Sheep and goat fibroblast cells were provided by Guangxi University and were cultured in DMEM containing 10% fetal bovine serum (FBS; Catalog No. 10099141C, Gibco). All cell lines used in this study were maintained in the specified medium supplemented with 1× penicillin–streptomycin (Catalog No.15140122, Gibco) and incubated in 5% CO<sub>2</sub> at 37 °C.</p>", "<p id=\"p0260\">Firstly, sequences of candidate RSCNEs identified were cloned into pGL3-promoter vector (Catalog No. E1761, Promega, Madison, WI), which was digested by <italic>Bam</italic>HI and <italic>Sal</italic>I in the luciferase gene downstream. All constructs were further confirmed by sanger sequencing. Then, all reporter plasmid constructs were transfected using TurboFect (Catalog No. R0531, ThermoFisher Scientific, Waltham, MA), and renilla luciferase pRL-TK-Rluc (Catalog No. P1232, Promega) was used as control. Subsequently, luciferase expression was monitored with the dual luciferase assay (Catalog No. E1910, Promega) after 24-h transfection. Each assay was monitored at least five times, independently. The <italic>t</italic>-test was applied to calculate the significance of the regulatory activity using GraphPad Prism 7.0 software (Prism, San Diego, CA). Statistically significant differences need to meet the criterion of <italic>P</italic> &lt; 0.05.</p>" ]
[ "<title>Results</title>", "<title>The landscapes of accessible chromatin regions and gene expression during rumen development</title>", "<p id=\"p0025\">We resolved high-resolution chromatin accessibility and gene expression landscapes during rumen development by collecting ruminal epithelial cells, esophageal epithelial cells, and hepatocyte cells at five stages [embryonic day 60 (E60), postnatal day 1 (D1), postnatal day 7 (D7), postnatal day 28 (D28), and adult 1 year (Y1)] from 14 sheep (##FIG##0##Figure 1##A). Our experimental design covers the major stages of ruminal epithelium differentiation and development ##REF##6225353##[14]##, ##UREF##2##[15]## and ensures an exact matching of tissues used for RNA sequencing (RNA-seq) and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) libraries. In total, 37 ATAC-seq and 34 RNA-seq datasets, including biological and technical replicates, showed high quality (see Materials and methods; <xref rid=\"s0165\" ref-type=\"sec\">Tables S1 and S2</xref>). The ATAC-seq samples have an average of 115 Mb post-quality control (QC) uniquely mapped fragments to the sheep Oar_4.0 genome (<xref rid=\"s0165\" ref-type=\"sec\">Table S1</xref>; <xref rid=\"s0165\" ref-type=\"sec\">Figure S1</xref>A), which are highly enriched at TSSs (<xref rid=\"s0165\" ref-type=\"sec\">Figure S1</xref>B) and show a nucleosome structure consistent distribution (<xref rid=\"s0165\" ref-type=\"sec\">Figure S1</xref>C). We obtained 178,651 open chromatin regions (OCRs) across all samples (in average 46,872 peaks per sample) (<xref rid=\"s0165\" ref-type=\"sec\">Table S1</xref>).</p>", "<p id=\"p0030\">Hierarchical clustering of gene expression and chromatin accessibility showed that rumen development is a multi-stage biological process (##FIG##0##Figure 1##B and C). Stages E60 and D1 clustered in one group, and D7, D28, and Y1 clustered in another group by gene expression. Chromatin accessibility patterns further distinguished stages E60 and D1. Principal component analysis (PCA) for 14,637 expressed genes and 178,651 OCRs corroborated this multi-stage pattern (##FIG##0##Figure 1##D and E). Early developmental stages E60 and D1 showed larger replicate variation than D7, D28, and Y1 at both chromatin accessibility and gene expression levels (##FIG##0##Figure 1##D and E). In addition, chromatin accessibility showed a smoother trajectory than gene expression during rumen development (##FIG##0##Figure 1##C).</p>", "<p id=\"p0035\">The esophagus showed very similar multi-stage development (<xref rid=\"s0165\" ref-type=\"sec\">Figure S2</xref>A and B). PCA indicated a larger variance in developmental stages (PC1 32%) and a smaller variance among tissue types (PC2 25%) (<xref rid=\"s0165\" ref-type=\"sec\">Figure S2</xref>C and D). This pattern is consistent with a previous study showing that gene expression divergence between tissues/cell types increases as development progresses ##REF##25468934##[16]##. Importantly, our chromatin accessibility data mirror this pattern, <italic>i.e.</italic>, the similarity in chromatin accessibility distribution between the two tissues declines as development progresses.</p>", "<title>Active-RSCNEs serve as enhancers in the process of rumen development and evolution</title>", "<p id=\"p0040\">We obtained 159,837 reproducible OCRs by intersecting peaks from three replicates for the rumen and esophagus at four developmental stages. The number of reproducible OCRs was the largest at stage E60 (approximately 40%) and decreased along the developmental stages (##FIG##1##Figure 2##A), which is consistent with the observation of higher amounts of accessible chromatin at the embryonic stage ##REF##31243369##[17]##. Most reproducible OCRs were located at distal intergenic (39.42%), intron (32.61%), and promoter (±3 kb from TSS; 21.46%) regions (##FIG##1##Figure 2##B). After overlapping the OCRs with 221,166 RSCNEs from ruminant comparative genomics analysis ##REF##31221828##[5]##, we identified 1601 active-RSCNEs with an average length of 82 bp (<xref rid=\"s0165\" ref-type=\"sec\">Table S3</xref>). Again, the number of active-RSCNEs decreased during the developmental stages in both the rumen and esophagus (##FIG##1##Figure 2##C). They were mainly located in distal intergenic (48.95%), intron (42.40%), and promoter (4.96%) regions (##FIG##1##Figure 2##D). Compared with all reproducible OCRs, active-RSCNEs were less abundant in promoter regions by 15% (<xref rid=\"s0165\" ref-type=\"sec\">Figure S3</xref>A), and the esophagus showed a consistent trend (<xref rid=\"s0165\" ref-type=\"sec\">Figure S3</xref>B). This suggests that active-RSCNEs tend to function as distal elements during development. In addition, our observation that most active-RSCNEs are found in early developmental stages (&gt; 90% in E60, D1, and D7) emphasizes the importance of early developmental cellular context for interpreting the regulatory role of conserved non-coding elements (CNEs).</p>", "<p id=\"p0045\">We next associated the 1601 active-RSCNEs with their 1796 genes nearby. Gene Ontology (GO) analysis of these genes showed enrichment in terms such as “primary metabolic process”, “catalytic activity”, and “regulation of signaling” (<xref rid=\"s0165\" ref-type=\"sec\">Figure S3</xref>C). Moreover, TFs were significantly enriched in these 1796 genes (<xref rid=\"s0165\" ref-type=\"sec\">Figure S3</xref>D; Fisher’s exact test, <italic>P</italic> = 4.20E−4). These 1796 genes overlapped with 656 RSEGs by 85 genes (##FIG##1##Figure 2##E; Fisher’s exact test, <italic>P</italic> value = 5.50E−11) that were enriched in “cardiac muscle cell apoptotic process”, “tongue development”, and “keratinization” (##FIG##1##Figure 2##F).</p>", "<p id=\"p0050\">The 1601 active-RSCNEs are composed of 414 type I and 1187 type II RSCNEs (##FIG##1##Figure 2##G; <xref rid=\"s0165\" ref-type=\"sec\">Table S3</xref>). Type I RSCNEs have no known orthologs in non-ruminant outgroups, and type II orthologs exhibit significantly higher substitution rates among outgroups ##REF##31221828##[5]##. The ratio between type I and type II active-RSCNEs is ∼ 0.35, which is 4-fold lower than that of all RSCNEs (a type I/type II ratio of ∼ 1.77) (##FIG##1##Figure 2##G). This surprising fact suggests that type II RSCNEs tend to be more activated in the developmental stage than type I RSCNEs. Because of the deeper evolutionary origin of type II RSCNEs, they are more likely to function by altering existing regulatory elements. Furthermore, we found that active-RSCNEs are enriched for binding motifs of transcriptional regulators known to play a vital role in rumen development (AP-1, PITX1, TP63, KLF, GRHL, TEAD, OTX, and HOX; 128 motifs with Benjamini <italic>Q</italic> value &lt; 1E−3 are listed in <xref rid=\"s0165\" ref-type=\"sec\">Table S4</xref>), suggesting that some active-RSCNEs may act as rumen developmental enhancers.</p>", "<p id=\"p0055\">To assess whether the RSCNEs are likely to play an enhancer role, we next compared our 1601 active-RSCNEs with the 523,159 developmental regions of transposase-accessible chromatin (d-TACs) from mice ##REF##32728240##[18]## and 926,535 human enhancers from Encyclopedia of DNA Elements (ENCODE) phase III ##REF##32728249##[19]##. Approximately 24% of the active-RSCNEs can be found in these datasets (##FIG##1##Figure 2##H), and 11 active-RSCNEs show <italic>in vivo</italic> reporter activity according to the VISTA database ##REF##17130149##[20]## (##FIG##1##Figure 2##H). To validate the potential regulatory activity, 10 active-RSCNEs of length ∼ 300 bp were randomly selected and assessed for enhancer activity detection in both sheep and goat fibroblasts <italic>in vitro</italic>. Nine of them showed significantly higher luciferase transcriptional activation than the pGL3-promoter control (<italic>t</italic>-test, <italic>P</italic> &lt; 0.05; ##FIG##1##Figure 2##I). Collectively, these results suggest that active-RSCNEs potentially serve as enhancers in the process of rumen development and evolution.</p>", "<title>CNE interpretation method by GRN</title>", "<p id=\"p0060\">After finding that active-RSCNEs may function as enhancers and hence have significant impacts on morphological evolution ##REF##32181886##[21]##, we next developed the CNE interpretation method to integrate multi-omics data into gene regulatory network (CNEReg) as an evolutionarily conserved non-coding element interpretation method. The method works by modeling the paired gene expression and chromatin accessibility data during rumen and esophagus development and consolidating them into a GRN. A GRN helps to understand in detail the process of TF binding to active-RSCNEs and how this leads to the cell type-specific activation of RSEGs during different stages of development. CNEReg takes as input a set of paired time-series gene expression and chromatin accessibility data, ruminant comparative genomes, and comparative transcriptomes and outputs the developmental regulatory network of the active-RSCNEs. The three major steps of CNEReg include multi-omics data integration, model component identification, and developmental regulatory network inference (##FIG##2##Figure 3##A and B; see Materials and methods). The major steps and results of developmental regulatory network reconstruction are illustrated in the following sections.</p>", "<title>Identifying TTFs during rumen development and evolution</title>", "<p id=\"p0065\">We proposed toolkit transcription factors (TTFs) as the core concept of CNEReg and developed a computational pipeline to define and discover the developmental genetic TTFs in evo-devo that may control development, pattern formulation and identity of body parts, and recruit novel function (details in Materials and methods). We first separated 37 TFs from 619 non-TF TGs in 656 RSEGs. These 37 TFs were further filtered by a more stringent expression specificity Jensen–Shannon Median expression Score (JMS) and were required to have nearby active-RSCNEs 1 Mb upstream or downstream of the TSS (see Materials and methods). Finally, 18 TTFs were defined (<xref rid=\"s0165\" ref-type=\"sec\">Table S5</xref>). Their expression profile phylogeny well recovered the tissue lineage system (##FIG##3##Figure 4##A). Rumen was clustered the closest to the reticulum, omasum, esophagus, and then skin and other keratin tissues, which is consistent with the basic stratified epithelium shared in the rumen with skin. These 18 TTFs also well represented the major functions of the rumen associated with other tissue systems, including the gastrointestinal system, integumentary system, reproductive system, muscular system, nervous system, and endocrine system (##FIG##3##Figure 4##B).</p>", "<p id=\"p0070\">We observed that the rumen recruited TTFs from multiple tissues to drive gene expression. More TTFs were expressed from the gastrointestinal system than from other systems. For example, paired box protein 9 (PAX9) is a known key TF during esophagus differentiation that may play an important role in the origin of rumen from the esophagus ##REF##15454262##[22]##. The homeobox family TFs HOXC8 and HOXC4, together with PITX1, are key developmental regulators of specific positional identities on the anterior-posterior axis ##REF##7579525##[23]##, ##REF##10235263##[24]##. The other four TTFs, OVOL1, SOX21, TFAP2A, and TP63, are from the integumentary system and serve as master regulators in the regulation of epithelial development and differentiation ##REF##16636146##[25]##, ##REF##14729569##[26]##, ##REF##1716766##[27]##, ##UREF##3##[28]##.</p>", "<p id=\"p0075\">We classified 18 TTFs into two types according to their dynamic gene expression pattern during rumen development. PITX1, BARX2, SOX2, GRHL1, GRHL3, TFAP2A, OTX1, DMRT2, and TWIST2 are early-development TTFs showing the highest expression at E60 or D1 (##FIG##3##Figure 4##C). In contrast, PAX9, TP63, HOXC4, SOX21, HOXC8, OVOL1, PPARG, POU2F3, and TEAD4 were late-development TTFs and were highly expressed at D7, D28, or Y1 (##FIG##3##Figure 4##C). We further associated those TTFs with 6 cell types by scRNA-seq data in the skin organoid culture system ##REF##32494013##[29]##, and they showed specific expression levels at single-cell resolution in a complex skin organ model by reprogramming pluripotent stem cells. For example, TWIST2 is specifically expressed in fibroblast (##FIG##3##Figure 4##C). TWIST2 remodels chromatin accessibility to regulate the maturation of fibroblasts ##UREF##4##[30]## and is required for epithelial–mesenchymal transition ##UREF##5##[31]##. Its high expression at the early developmental stage of the rumen may relate to the ruminal epithelial development. Totally, our results indicated these identified TTFs act important regulatory roles in diverse cell types of the rumen.</p>", "<title>Constructing upstream and downstream regulations of rumen TTFs</title>", "<p id=\"p0080\">To explore how TTFs are regulated and recruited, we scanned the active-RSCNEs near TTFs for sequence-specific TF motif binding by HOMER ##REF##20513432##[32]##, retained those TFs correlating well with TTFs (Spearman’s correlation coefficient &gt; 0.6 across RNA-seq samples), and fitted a linear regression model integrating our paired expression and chromatin accessibility data to reveal upstream regulators of 18 rumen TTFs (##FIG##2##Figure 3##B; see Materials and methods). The resulting upstream regulatory network of TTFs (##FIG##3##Figure 4##D) identified 39 active-RSCNEs (15 type I and 24 type II) bound by 113 TFs for 18 TTFs (<xref rid=\"s0165\" ref-type=\"sec\">Table S6</xref>). GRHL1, an important regulator of keratin expression ##REF##18288204##[33]##, is regulated by 31 TFs via 6 active-RSCNEs, suggesting its potential roles in rumen development.</p>", "<p id=\"p0085\">To explore the regulatory roles of these 18 TTFs, we first scanned 1440 active-RSCNEs located 1 Mb upstream or downstream around 512 RSEGs [fragments per kilobase per million mapped reads (FPKM) &gt; 1 in at least one development stage] by HOMER ##REF##20513432##[32]## for binding sites of the 18 rumen TTFs. Then, a linear regression model quantitatively associated the accessibility of active-RSCNEs with the expression of TTFs and RSEGs (##FIG##2##Figure 3##B; see Materials and methods). The resulting downstream regulatory network of TTFs linked 139 active-RSCNEs (26 type I and 113 type II) with 14 TTFs and 93 RSEGs (##FIG##4##Figure 5##A; <xref rid=\"s0165\" ref-type=\"sec\">Table S7</xref>). RSEGs were categorized into seven different tissue systems by their expression specificity ##REF##31221828##[5]##, ##REF##26989612##[7]##. The gastrointestinal and integumentary systems both have 28 RSEGs that are functionally enriched in the hair/molting cycle process (Fisher’s exact test, adjusted <italic>P</italic> = 1.50E−2) and regulation of antimicrobial peptide production (Fisher’s exact test, adjusted <italic>P</italic> = 3.58E−6). This is consistent with our previous finding that the rumen evolved several important antibacterial functions specifically managing the microbiome composition ##REF##33165812##[2]##. The <italic>SLC14A1</italic> gene was specifically highly expressed in the rumen and hypothesized to be recruited from the urinary system (##FIG##4##Figure 5##A). CNEReg identified four active-RSCNEs bound by three TTFs, OTX1, PPARG, and SOX21, to regulate <italic>SLC14A1</italic> (##FIG##4##Figure 5##B).</p>", "<p id=\"p0090\">CNEReg designed a functional influence score by integrating regulation and conservation in evolution (##FIG##2##Figure 3##B; see Materials and methods) and ranked the active-RSCNEs in TTF upstream (<xref rid=\"s0165\" ref-type=\"sec\">Figure S4</xref>; <xref rid=\"s0165\" ref-type=\"sec\">Table S6</xref>) and downstream networks (<xref rid=\"s0165\" ref-type=\"sec\">Figure S5</xref>; <xref rid=\"s0165\" ref-type=\"sec\">Table S7</xref>). Then, we selected the top 10 active-RSCNEs for enhancer activity detection in sheep fibroblasts <italic>in vitro</italic>. Nine of ten showed significantly higher luciferase transcriptional activation than the pGL3-promoter control (<italic>t</italic>-test, <italic>P</italic> &lt; 0.05) (<xref rid=\"s0165\" ref-type=\"sec\">Figure S6</xref>). Collectively, CNEReg provides a high-quality developmental regulatory network to study rumen evolution.</p>", "<title>Regulatory sub-network underlying the rumen and esophagus divergence</title>", "<p id=\"p0095\">We previously hypothesized that the anatomical predecessor of the rumen is the esophagus based on their similar expression profile compared with 49 other tissues ##REF##31221828##[5]##, ##REF##26989612##[7]##. It is therefore of interest to identify the gene regulatory network underlying the differentiation between the rumen and esophagus. We first identified differentially expressed genes (4, 258, 577, and 2372 for E60, D1, D7, and Y1, respectively, in <xref rid=\"s0165\" ref-type=\"sec\">Figure S7</xref>A) and differentially accessible regions (9436, 10,004, 3984, 3566, and 26 for E60, D1, D7, D28, and Y1, respectively, in <xref rid=\"s0165\" ref-type=\"sec\">Figure S7</xref>B) between the rumen and esophagus at each developmental stage. Then, we identified six TTFs (PPARG, SOX21, TP63, OTX1, SOX2, and HOXC8) showing both significant differences in expression and in motifs enriched within the rumen OCRs (##FIG##5##Figure 6##A; see Materials and methods). HOXC8 showed the largest difference at the earliest developmental stage, both in expression level and motif enrichment, and SOX21, SOX2, OTX1, and PPARG showed similar trends. TP63 differentiates from D7, in which the gene expression level and motif enrichment decline quickly in the esophagus but not in the rumen.</p>", "<p id=\"p0100\">We extracted the six differential TTFs from the TTF downstream regulatory network to form a regulatory sub-network that also included 24 differentially expressed RSEGs and 38 active-RSCNEs (##FIG##5##Figure 6##B; <xref rid=\"s0165\" ref-type=\"sec\">Table S8</xref>). The 24 differentially expressed RSEGs were classified into gastrointestinal, integumentary, reproductive, nervous, muscular, immune, and urinary systems, and 10 of 24 non-TF RSEGs were classified into integumentary systems. Seven non-TF RSEGs (<italic>KRT17</italic>, <italic>KRT36</italic>, LOC101118712, <italic>ATP6V1C2</italic>, <italic>KLK10</italic>, <italic>SPINK9</italic>, and <italic>IRX</italic>) were regulated by SOX21. A previous study revealed that SOX21 could determine the fate of ectodermal organs and control epithelial differentiation ##UREF##3##[28]##. We observed that SOX21 binds to RSCNE with genomic coordinates “chr11:40325877-150” to regulate the expression of KRT17, KRT36, and LOC101118712. The functional influence of RSCNE with genomic coordinates “chr11:40325877-150” was ranked at the top of all type II active-RSCNEs in the differentially regulatory sub-network (<xref rid=\"s0165\" ref-type=\"sec\">Table S8</xref>). These RSEGs were enriched in epidermal development, formation of anatomical boundaries, and urea transmembrane transport biological processes (<xref rid=\"s0165\" ref-type=\"sec\">Table S9</xref>), which are consistent with the functional differences between the rumen and esophagus. The 38 active-RSCNEs may imply the potential genetic basis of rumen origin and evolution from the esophagus.</p>", "<title>Transposable elements may rewire the GRN through active-RSCNEs</title>", "<p id=\"p0105\">After interpreting active-RSCNEs as important regulators of TTFs and RSEGs in rumen development, we next addressed the genomic origin of the active-RSCNEs. Transposable elements (TEs) are known to constitute a high proportion of taxonomy-specific CNEs, play a central role in rewiring gene regulatory networks, and facilitate the novel or rapid evolution of ecologically relevant traits ##REF##21946353##[34]##, ##REF##1379564##[35]##. Hence, we estimated the percentage of active-RSCNEs may be derived from TEs. Among 39 and 139 active-RSCNEs in the TTF upstream and downstream networks, we identified 6 (15.38%) and 12 (8.6%) TEs, respectively. This gives a 1.8-fold enrichment of TEs in active-RSCNEs associated with TTFs relative to non-TTF RSEGs. At the gene level, 6 of 18 TTFs (33.33%) and 12 of 93 RSEGs (12.90%) are regulated by TEs via active-RSCNEs. This gives a 2.58-fold enrichment of TEs associated with TTFs relative to RSEGs. If we associated the TEs with RSEGs by their proximity in genome coordinates, there were 85 TEs around all 656 RSEGs (±200 kb), <italic>i.e.</italic>, 13% of RSEGs are associated with TEs in average. However, 33.3% TTFs are associated with TEs, and this is 1.56-fold higher than RSEGs. Together, our data suggest that TEs may recruit TTFs and rewire the regulatory network to give rise to trait novelties.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0110\">The evolution of new traits is driven by several types of genetic reprogramming, including mutations in protein-coding genes and post-transcriptional mechanisms, the transformation of regulatory elements, such as promoters and enhancers, and the recruitment of gene expression from other organs ##UREF##6##[36]##, ##REF##28812655##[37]##. Mutations in non-coding regulatory regions are believed to selectively perturb TG expression in a specific tissue context and thereby circumvent any pleiotropic effects from protein-coding mutations ##REF##21852499##[38]##. Recent advances in comparative genomics, along with the increased availability of whole genome sequences, have led to the identification of many CNEs, which are assumed to have regulatory functions ##REF##18614008##[1]##, ##REF##17304246##[6]##, ##REF##15131266##[39]##. Therefore, the time is ripe for an analytical framework to investigate the regulatory role of such CNEs.</p>", "<p id=\"p0115\">Biologically, we propose a model of gene expression recruitment by CNEs. Our results show how CNEs can regulate gene expression as either <italic>trans</italic>-regulatory elements (TTFs in this study) or <italic>cis</italic>-regulatory elements (CREs; active-RSCNEs in this study) of TGs (RSEGs). Methodologically, CNEReg provides a framework to integrate comparative genomics, comparative transcriptomic, and multi-omics data to interpret CNEs by GRN. On the one hand, GRN identifies TTFs and active-RSCNEs as hypotheses, which need to be pursued by <italic>in vitro</italic> and <italic>in vivo</italic> functional studies. On the other hand, GRN presents the global picture of how the rumen recruits gene expression from other tissues by activating RSCNEs to achieve many traits. This allows us to explore many biological hypotheses and rank candidates for further functional study. As an example, we reconstructed a sub-network underlying rumen and esophagus divergence, which could further interpret the differences between the rumen and its ancestral organ. The identified TTFs and active-RSCNEs in the sub-network may account for the origin and evolution of the rumen. For example, as one of the genes in Hox gene family, <italic>HOXC8</italic> has been implicated in the divergence of axial morphology ##REF##9482889##[40]##. The proper expression of Hox genes is essential for the precise patterning of the body plan. <italic>HOXC8</italic> shows differences in gene expression and motif enrichment between the rumen and esophagus during development. These results indicate that the rumen employed a different gene regulatory program when differentiating from the esophagus.</p>", "<p id=\"p0120\">Our method for systematically interpreting conserved <italic>cis</italic>-regulatory sequences in non-coding regions by integrating developmental multi-omics data will have a broad interest in other applications. For example, the Zoonomia project describes a whole-genome alignment of 240 species comprising representatives from more than 80% of mammalian families ##REF##33177664##[41]##. The bird 10,000 Genomes Project provides a comparative genome dataset for 363 genomes from 92.4% of bird families ##REF##33177665##[42]##. Recently, 6.9 million CNEs from many vertebrate genomes have been collected into the dbCNS and await interpretation ##REF##33196844##[43]##.</p>", "<p id=\"p0125\">Our work is limited in several aspects. CNEReg infers gene regulation as the interaction of TFs with accessible DNA regions in development and relies on the correlation of gene expression and chromatin accessibility across samples. A much deeper understanding can be revealed by ChIP-seq data and 3D chromatin interaction data to provide physical enhancer-promoter interactions. In addition, time course regulatory analysis of omics data measured at shorter and closer developmental stages will help us to infer more accurate regulatory network ##REF##32188700##[12]##. Furthermore, developmental samples are known as a heterogeneous mixture of many cell types, and it will be fruitful to infer the GRNs of the underlying cell types based on scATAC-seq and scRNA-seq data ##REF##28576882##[10]##.</p>", "<p id=\"p0130\">In conclusion, CNEReg is demonstrated as a systematic approach to understanding the large-scale maps of CNEs by modeling omics data over development for its act on gene regulation. We see the potential that CNEReg can be generalized to understand the complex traits or the origin and evolution of vertebrate organs with multi-omics data generated in proper time and space. Our method allows evo-devo thinking in how gene regulation could evolve and shape animal evolution.</p>" ]
[]
[ "<p id=\"np010\">Equal contribution.</p>", "<p>The genetic information coded in DNA leads to <bold>trait innovation</bold> via a <bold>gene regulatory network</bold> (GRN) in development. Here, we developed a <bold>conserved non-coding element</bold> interpretation method to integrate multi-omics data into gene r<underline>eg</underline>ulatory network (CNEReg) to investigate the <bold>ruminant</bold> multi-chambered stomach innovation. We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep, and revealed 1601 active ruminant-specific conserved non-coding elements (active-RSCNEs). To interpret the function of these active-RSCNEs, we defined <bold>toolkit transcription factors</bold> (TTFs) and modeled their regulation on rumen-specific genes via batteries of active-RSCNEs during development. Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules. Notably, 6 TTFs (OTX1, SOX21, HOXC8, SOX2, TP63, and PPARG), as well as 16 active-RSCNEs, functionally distinguished the rumen from the esophagus. Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Ge Gao</p>" ]
[ "<title>Ethical statement</title>", "<p id=\"p0265\">This study was carried out under the guidelines and approval of the Northwest A&amp;F University Animal Care Committee (Approval No. NWAFAC1008).</p>", "<title>Code availability</title>", "<p id=\"p0275\">All source codes are available freely for academic usage at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/biocode/tools/BT007284\" id=\"ir060\">https://ngdc.cncb.ac.cn/biocode/tools/BT007284</ext-link>.</p>", "<title>Data availability</title>", "<p id=\"p0270\">Raw data from this study have been deposited in the NCBI (NCBI: PRJNA485657), which are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ncbi.nlm.nih.gov/\" id=\"ir050\">https://www.ncbi.nlm.nih.gov/</ext-link>, and also in the Genome Sequence Archive ##REF##34400360##[56]## at the National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (GSA: CRA005494), which are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa\" id=\"ir055\">https://ngdc.cncb.ac.cn/gsa</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0280\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0285\"><bold>Xiangyu Pan:</bold> Conceptualization, Methodology, Software, Formal analysis, Investigation, Resources, Data curation, Writing – original draft, Visualization. <bold>Zhaoxia Ma:</bold> Methodology, Software, Formal analysis, Investigation, Writing – original draft, Visualization. <bold>Xinqi Sun:</bold> Methodology, Software, Formal analysis, Writing – original draft, Visualization. <bold>Hui Li:</bold> Validation, Resources. <bold>Tingting Zhang:</bold> Validation, Resources. <bold>Chen Zhao:</bold> Visualization. <bold>Nini Wang:</bold> Visualization. <bold>Rasmus Heller:</bold> Writing – review &amp; editing. <bold>Wing Hung Wong:</bold> Supervision. <bold>Wen Wang:</bold> Conceptualization, Investigation, Supervision. <bold>Yu Jiang:</bold> Conceptualization, Investigation, Writing – review &amp; editing, Supervision, Resources. <bold>Yong Wang:</bold> Conceptualization, Methodology, Investigation, Writing – review &amp; editing, Supervision. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0300\">The following are the Supplementary material to this article:</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<p id=\"p0325\">\n\n</p>", "<p id=\"p0330\">\n\n</p>", "<p id=\"p0335\">\n\n</p>", "<p id=\"p0340\">\n\n</p>", "<p id=\"p0345\">\n\n</p>", "<p id=\"p0350\">\n\n</p>", "<p id=\"p0355\">\n\n</p>", "<p id=\"p0360\">\n\n</p>", "<p id=\"p0365\">\n\n</p>", "<p id=\"p0370\">\n\n</p>", "<p id=\"p0375\">\n\n</p>", "<p id=\"p0380\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0290\">This work was supported by the <funding-source id=\"gp005\">National Key R&amp;D Program of China</funding-source> (Grant No. 2020YFA0712402), the <funding-source id=\"gp010\">Strategic Priority Research Program of the Chinese Academy of Sciences</funding-source> (Grant No. XDPB17), the <funding-source id=\"gp015\">CAS Project for Young Scientists in Basic Research</funding-source> (Grant No. YSBR-077), the <funding-source id=\"gp020\">National Natural Science Foundation of China</funding-source> (Grant Nos. 12025107, 11871463, 11688101, and 61621003), the <funding-source id=\"gp025\">National Thousand Youth Talents Plan, and the CAS “Light of West China” Program</funding-source> (Grant No. xbzg-zdsys-201913), China. We thank <funding-source id=\"gp030\">High-Performance Computing (HPC) of Northwest A&amp;F University (NWAFU)</funding-source> for providing computing resources.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>T</bold><bold>ime</bold><bold>-</bold><bold>series data</bold><bold>of paired expression and chromatin accessibility</bold><bold>reveal the regulatory landscape for rumen development</bold></p><p><bold>A</bold><bold>.</bold> Experimental design diagram for multi-replicate, multi-tissue, and multi-level omics data profiling during sheep development from E60 to postnatal stages (D1, D7, and D28) to Y1. Hierarchical clustering of gene expression for 14,637 genes (<bold>B</bold>) and chromatin accessibility for 178,651 OCRs (<bold>C</bold>). Unsupervised PCA of rumen gene expression (<bold>D</bold>) and chromatin accessibility (<bold>E</bold>). ATAC-seq, Assay for Transposase-Accessible Chromatin with high-throughput sequencing; RNA-seq, RNA sequencing; E60, embryonic day 60; D1, postnatal day 1; D7, postnatal day 7; D28, postnatal day 28; Y1, adult 1 year; OCR, open chromatin region; PCA, principal component analysis; PC, principal component.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Characterization of active-RSCNEs as developmental enhancers</bold></p><p><bold>A.</bold> Number of reproducible peaks at each developmental stage in the rumen and esophagus. <bold>B.</bold> Annotating reproducible peaks by location in different genomic regions. <bold>C.</bold> Number of active-RSCNEs at each developmental stage in the rumen and esophagus. <bold>D.</bold> Annotating active-RSCNEs by location in different genomic regions. <bold>E.</bold> The genes nearest to active-RSCNEs are enriched in RSEGs. <italic>P</italic> value is calculated by Fisher’s exact test. <bold>F.</bold> GO enrichment analysis for genes near the active-RSCNEs. <bold>G.</bold> Number of type I and type II RSCNEs in total RSCNEs and active-RSCNEs. <bold>H.</bold> The intersections among active-RSCNEs with enhancers from d-TACs, cCREs, and VISTA. <bold>I.</bold> Luciferase activity assay of 10 active-RSCNEs randomly chosen from 1601 active-RSCNEs. RSCNE, ruminant-specific conserved non-coding element; RSEG, rumen-specific expressed gene; GO, Gene Ontology; UTR, untranslated region; d-TAC, developmental region of transposase-accessible chromatin; cCRE, candidate <italic>cis</italic>-regulatory element.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>CNEReg interprets RSCNEs by reconstructing the developmental regulatory network</bold></p><p><bold>A.</bold> CNEReg inputs paired time-series gene expression and chromatin accessibility data, ruminant comparative genomes, and comparative transcriptomes, and outputs the developmental regulatory network of active-RSCNEs. Three major steps of CNEReg include multi-omics data integration, model component identification, and developmental regulatory network inference. <bold>B.</bold> The developmental regulatory network reconstruction is further illustrated in three steps. Step 1: inferring the upstream regulation of rumen TTFs. Step 2: inferring the downstream regulation of TTFs to TGs via active-RSCNEs. Step 3: deriving active-RSCNE’s functional influence score by integrating regulatory strength in the network and evolutionary conservation score. The model components and notations of CNEReg are detailed in ##TAB##0##Table 1##. TG, target gene; TF, transcription factor; TTF, toolkit transcription factor; CNEReg, conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network; RSCNE, ruminant-specific conserved non-coding element.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>18 rumen TTFs and their upstream regulations</bold></p><p><bold>A.</bold> Phylogeny of 50 tissues from sheep based on the expression of 18 rumen TTFs groups the samples well by different lineages and biological systems. <bold>B.</bold> Biological functions of 18 rumen TTFs (marked in green) and the tissue with high expression (marked in blue). Tissues are grouped and colored by their lineages. <bold>C.</bold> 18 rumen TTFs are grouped into early-development (cold-colored) and late-development (warm-colored) by their dynamic expression patterns during the developmental stages. In addition, 18 rumen TTFs associated with specific cell type names were visualized by a uniform manifold approximation and projection plot in skin organoid scRNA-seq data. <bold>D.</bold> The upstream gene regulatory network of rumen TTFs shows the candidate TFs with statistical significance. Nodes are colored by early- and late-development TTFs. Blue edges highlight the regulatory relationship among TTFs.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Downstream regulatory network of rumen TTFs</bold></p><p><bold>A.</bold> Downstream regulatory network with 14 rumen TTFs regulating 93 TGs via 139 active-RSCNEs. TTFs are colored by the tissue they are highly expressed, and TGs are annotated and colored by their biological system. <bold>B.</bold> An example from the regulatory network shows that <italic>SLC14A1</italic> is regulated by four active-RSCNEs with TTF motifs. The expression and chromatin accessibility tracks are derived from rumen ATAC-seq (D1 or D7) and RNA-seq data (Y1).</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>Regulatory network sheds light on the difference between the rumen and esophagus in the development</bold></p><p><bold>A.</bold> Dynamics across stages for the six differential TTFs between the rumen and esophagus by integrating motif enrichment in differential ATAC-seq peaks and gene expression levels. <bold>B.</bold> Downstream regulatory sub-network of six differential rumen TTFs. FPKM, fragments per kilobase of exon per million mapped fragments.</p></caption></fig>", "<fig id=\"f0035\" position=\"anchor\"><label>Supplementary Figure S1</label><caption><p>Data quality check for the ATAC-seq samples by their sequence depth, fragment distribution, and QC score A. The number of raw reads and percentile of uniquely aligned reads. The number of raw reads ranges from 110 to 330 million for each ATAC-seq sample, and the percentiles of uniquely aligned reads across all samples is 59% on average. B. QC scores of all ATAC-seq samples. The QC score is defined as the ratio of the total read count at the TSS centered up- and downstream 2 Kbp windows to the randomly selected background [-3 K, -2 K] among all genes. Higher QC score indicates that ATAC-seq signals are enriched in open chromatin regions such as promoters. All the samples were required to reach the standard score of 4, <italic>i.e.</italic>, the fold change was larger than 1. C. Insert size distribution of one example esophagus-0-1. The other 29 samples show a similar pattern. This fragment length distribution reveals a sharp peak at less than 100 bp regions for nucleosome-free fragments, and the second largest peak is within 200 bp for the mono nucleosome fragment. Again, this indicates good data quality. ATAC-seq, Assay for Transposase-Accessible Chromatin with high-throughput sequencing; QC, Quality Control; TSS, Transcription Start Site.</p></caption></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary Figure S2</label><caption><p>Paired expression and chromatin accessibility time series data reveal the regulatory landscape for rumen and esophagus development. Hierarchical clustering of gene expression (A) and chromatin accessibility (B) of all samples, including biological and technical replicates. PCAof 14,637 genes (C) and 178,651 open chromatin regions (D). The rumen and esophagus show consistent developmental patterns at both gene expression and chromatin accessibility levels. The variation between the rumen and esophagus is less than the variation among developmental stages. PCA, Principal component analysis.</p></caption></fig>", "<fig id=\"f0045\" position=\"anchor\"><label>Supplementary Figure S3</label><caption><p>Further characterization of active-RSCNEs A. The percentage of location in distal intergenic and promoter for reproducible peaks and active-RSCNEs. B. The percentage of location in distal intergenic regions and promoters for active-RSCNEs at each developmental stage of the rumen and esophagus. C. GO enrichment analysis of 1796 genes near active-RSCNEs. D. Fisher’s exact test shows that 1796 genes near active-RSCNEs are enriched in TFs (<italic>P</italic> value = 4.20E−5) but not non-TF genes (<italic>P</italic> value = 1.00, no significance). TF, Transcription Factor; TG, Target Gene; GO, Gene Ontology.</p></caption></fig>", "<fig id=\"f0050\" position=\"anchor\"><label>Supplementary Figure S4</label><caption><p>Relationships between the regulatory strength and the conservation score of the TTF upstream network Scatter diagrams show the regulatory strength (y-axis), conservation score (x-axis), and functional influence score (node color) of type I (A) and type II (B) active-RSCNEs with regulated genes in the network shown in Figure 4.</p></caption></fig>", "<fig id=\"f0055\" position=\"anchor\"><label>Supplementary Figure S5</label><caption><p>Relationships between the regulatory strength and the conservation score of the TTF downstream network Scatter diagrams show the regulatory strength (y-axis), conservation score (x-axis), and functional influence score (node color) of type I (A) and type II (B) active-RSCNEs with regulated genes from the network in Figure 5.</p></caption></fig>", "<fig id=\"f0060\" position=\"anchor\"><label>Supplementary Figure S6</label><caption><p>Luciferase activity assays of 10 active-RSCNEs with the top functional influence score Nine of 10 showed significant regulatory activity in the PGL-3 promoter (one-sided <italic>t</italic>-test, *, <italic>P</italic> &lt; 0.05, **, <italic>P</italic> &lt; 0.01, ***, <italic>P</italic> &lt; 0.001).</p></caption></fig>", "<fig id=\"f0065\" position=\"anchor\"><label>Supplementary Figure S7</label><caption><p>Differentially expressed genes and differentially accessible peaks between the rumen and esophagus at each stage A. Barplots showing the number of differentially expressed genes between the rumen and esophagus at each stage. B. Barplots showing the number of differentially accessible peaks between the rumen and esophagus at each stage. DEG, Differentially Expressed Gene.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"t0005\"><label>Table 1</label><caption><p>Components and notations of the CNEReg model</p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Data and variable</bold></th><th><bold>Notation</bold></th><th><bold>Example</bold></th></tr></thead><tbody><tr><td>Expression of TTFs</td><td> = expression of the <italic>l</italic>-th TTF on <italic>t</italic>-th time point</td><td> = 25.48 on D7 in rumen</td></tr><tr><td>Expression of TFs</td><td> = expression of the <italic>m-</italic>th TF</td><td> = 1035.79 on D7 in rumen</td></tr><tr><td>Expression of RSEGs</td><td> = expression of the <italic>n</italic>-th RSEG on <italic>t</italic>-th time point</td><td> = 42.34 on D7 in rumen</td></tr><tr><td>Accessibility of active-RSCNEs</td><td> = openness of the <italic>k</italic>-th active-RSCNE on <italic>t</italic>-th time point</td><td> = 18.83 on D7 in rumen</td></tr><tr><td>TFs with motif match in an active-RSCNE</td><td> = the set of TFs with significant motif match in <italic>i</italic>-th active-RSCNE</td><td>HOXC8 has motif match at active-RSCNE Chr1:196579342–242</td></tr><tr><td>Motif matching strength of TFs on RSCNEs</td><td> = sum of −log <italic>P</italic> value of <italic>l</italic>-th TF’s motif on <italic>i</italic>-th active-RSCNE</td><td> = 4.28486</td></tr></tbody></table></table-wrap>" ]
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width=\"0.333333em\"/><mml:mo>+</mml:mo><mml:msub><mml:mi>γ</mml:mi><mml:mrow><mml:mi>l</mml:mi><mml:mo>,</mml:mo><mml:mi>n</mml:mi><mml:mo>,</mml:mo><mml:mi>k</mml:mi></mml:mrow></mml:msub><mml:msup><mml:mfenced><mml:mrow><mml:msub><mml:mi mathvariant=\"italic\">TTF</mml:mi><mml:mi>l</mml:mi></mml:msub><mml:mo>∙</mml:mo><mml:msub><mml:mi>O</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:mrow></mml:mfenced><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:msup><mml:mo>+</mml:mo><mml:msub><mml:mi>ε</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>,</mml:mo><mml:mspace width=\"1em\"/><mml:msub><mml:mi>ε</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>∼</mml:mo><mml:mspace width=\"3.33333pt\"/><mml:mi>N</mml:mi><mml:mrow><mml:mo>(</mml:mo><mml:mn>0</mml:mn><mml:mo>,</mml:mo><mml:msubsup><mml:mi>σ</mml:mi><mml:mi>n</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>)</mml:mo></mml:mrow></mml:math></disp-formula>", "<inline-formula><mml:math id=\"M24\" altimg=\"si13.svg\"><mml:msub><mml:mrow><mml:mi mathvariant=\"italic\">TTF</mml:mi></mml:mrow><mml:mi>l</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M25\" altimg=\"si21.svg\"><mml:msub><mml:mi>O</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M26\" altimg=\"si19.svg\"><mml:mi>l</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M27\" altimg=\"si22.svg\"><mml:msub><mml:mrow><mml:mi mathvariant=\"italic\">RSEG</mml:mi></mml:mrow><mml:mi>n</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M28\" altimg=\"si23.svg\"><mml:msub><mml:mi>γ</mml:mi><mml:mrow><mml:mi>l</mml:mi><mml:mo>,</mml:mo><mml:mi>n</mml:mi><mml:mo>,</mml:mo><mml:mi>k</mml:mi></mml:mrow></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M29\" altimg=\"si22.svg\"><mml:msub><mml:mrow><mml:mi mathvariant=\"italic\">RSEG</mml:mi></mml:mrow><mml:mi>n</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M30\" altimg=\"si24.svg\"><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mrow><mml:mi mathvariant=\"italic\">TTF</mml:mi></mml:mrow><mml:mi>l</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msub><mml:mi>O</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:msup></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M31\" altimg=\"si25.svg\"><mml:mi>k</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M32\" altimg=\"si26.svg\"><mml:msub><mml:mi>C</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M33\" altimg=\"si27.svg\"><mml:msub><mml:mi>R</mml:mi><mml:mrow><mml:mi>k</mml:mi><mml:mo>,</mml:mo><mml:mi>t</mml:mi></mml:mrow></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M34\" altimg=\"si25.svg\"><mml:mi>k</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M35\" altimg=\"si28.svg\"><mml:mi>t</mml:mi></mml:math></inline-formula>", "<disp-formula id=\"e0015\"><label>(3)</label><mml:math id=\"M36\" altimg=\"si29.svg\"><mml:msub><mml:mi>R</mml:mi><mml:mrow><mml:mi>k</mml:mi><mml:mo>,</mml:mo><mml:mi>t</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:msub><mml:mo>∑</mml:mo><mml:mrow><mml:mi>l</mml:mi><mml:mo>,</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:msub><mml:mfenced><mml:mrow><mml:msub><mml:mi>O</mml:mi><mml:mrow><mml:mi>k</mml:mi><mml:mo>,</mml:mo><mml:mi>t</mml:mi></mml:mrow></mml:msub><mml:mo>∙</mml:mo><mml:msub><mml:mi>B</mml:mi><mml:mrow><mml:mi>k</mml:mi><mml:mo>,</mml:mo><mml:mi>l</mml:mi></mml:mrow></mml:msub><mml:mo>∙</mml:mo><mml:msqrt><mml:msub><mml:mi mathvariant=\"italic\">TTF</mml:mi><mml:mrow><mml:mi>l</mml:mi><mml:mo>,</mml:mo><mml:mi>t</mml:mi></mml:mrow></mml:msub><mml:mo>∙</mml:mo><mml:msub><mml:mi mathvariant=\"italic\">RSEG</mml:mi><mml:mrow><mml:mi>n</mml:mi><mml:mo>,</mml:mo><mml:mi>t</mml:mi></mml:mrow></mml:msub></mml:msqrt><mml:mo>∙</mml:mo><mml:msup><mml:mn>2</mml:mn><mml:msub><mml:mi>γ</mml:mi><mml:mrow><mml:mi>l</mml:mi><mml:mo>,</mml:mo><mml:mi>n</mml:mi><mml:mo>,</mml:mo><mml:mi>k</mml:mi></mml:mrow></mml:msub></mml:msup></mml:mrow></mml:mfenced></mml:math></disp-formula>", "<inline-formula><mml:math id=\"M37\" altimg=\"si7.svg\"><mml:msub><mml:mi>O</mml:mi><mml:mrow><mml:mi>k</mml:mi><mml:mo>,</mml:mo><mml:mi>t</mml:mi></mml:mrow></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M38\" altimg=\"si25.svg\"><mml:mi>k</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M39\" altimg=\"si28.svg\"><mml:mi>t</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M40\" altimg=\"si30.svg\"><mml:msub><mml:mi>B</mml:mi><mml:mrow><mml:mi>k</mml:mi><mml:mo>,</mml:mo><mml:mi>l</mml:mi></mml:mrow></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M41\" altimg=\"si19.svg\"><mml:mi>l</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M42\" altimg=\"si25.svg\"><mml:mi>k</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M43\" altimg=\"si31.svg\"><mml:msub><mml:mrow><mml:mi mathvariant=\"italic\">TTF</mml:mi></mml:mrow><mml:mrow><mml:mi>l</mml:mi><mml:mo>,</mml:mo><mml:mi>t</mml:mi></mml:mrow></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M44\" altimg=\"si19.svg\"><mml:mi>l</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M45\" altimg=\"si28.svg\"><mml:mi>t</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M46\" altimg=\"si32.svg\"><mml:msub><mml:mrow><mml:mi mathvariant=\"italic\">RSEG</mml:mi></mml:mrow><mml:mrow><mml:mi>n</mml:mi><mml:mo>,</mml:mo><mml:mi>t</mml:mi></mml:mrow></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M47\" altimg=\"si33.svg\"><mml:mi>n</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M48\" altimg=\"si28.svg\"><mml:mi>t</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M49\" altimg=\"si23.svg\"><mml:msub><mml:mi>γ</mml:mi><mml:mrow><mml:mi>l</mml:mi><mml:mo>,</mml:mo><mml:mi>n</mml:mi><mml:mo>,</mml:mo><mml:mi>k</mml:mi></mml:mrow></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M50\" altimg=\"si22.svg\"><mml:msub><mml:mrow><mml:mi mathvariant=\"italic\">RSEG</mml:mi></mml:mrow><mml:mi>n</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M51\" altimg=\"si24.svg\"><mml:msup><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mrow><mml:mi mathvariant=\"italic\">TTF</mml:mi></mml:mrow><mml:mi>l</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msub><mml:mi>O</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:msup></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M52\" altimg=\"si34.svg\"><mml:msub><mml:mi>R</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M53\" altimg=\"si25.svg\"><mml:mi>k</mml:mi></mml:math></inline-formula>", "<disp-formula id=\"e0020\"><label>(4)</label><mml:math id=\"M54\" altimg=\"si35.svg\"><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:munder><mml:mi mathvariant=\"normal\">max</mml:mi><mml:mi>t</mml:mi></mml:munder><mml:msub><mml:mi>R</mml:mi><mml:mrow><mml:mi>k</mml:mi><mml:mo>,</mml:mo><mml:mi>t</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></disp-formula>", "<inline-formula><mml:math id=\"M55\" altimg=\"si34.svg\"><mml:msub><mml:mi>R</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M56\" altimg=\"si26.svg\"><mml:msub><mml:mi>C</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M57\" altimg=\"si36.svg\"><mml:msub><mml:mi>W</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M58\" altimg=\"si25.svg\"><mml:mi>k</mml:mi></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M59\" altimg=\"si34.svg\"><mml:msub><mml:mi>R</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M60\" altimg=\"si26.svg\"><mml:msub><mml:mi>C</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:math></inline-formula>", "<disp-formula id=\"e0025\"><label>(5)</label><mml:math id=\"M61\" altimg=\"si37.svg\"><mml:mrow><mml:msub><mml:mi>W</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:msqrt><mml:mrow><mml:msub><mml:mi>R</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>·</mml:mo><mml:msub><mml:mi>C</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:mrow></mml:msqrt></mml:mrow></mml:math></disp-formula>", "<disp-formula id=\"e0030\"><label>(6)</label><mml:math id=\"M62\" altimg=\"si38.svg\"><mml:mrow><mml:mi mathvariant=\"italic\">JMS</mml:mi><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mfrac><mml:mroot><mml:mrow><mml:mi mathvariant=\"italic\">med</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>3</mml:mn></mml:mroot><mml:mrow><mml:mi mathvariant=\"italic\">JSD</mml:mi></mml:mrow></mml:mfrac></mml:mrow></mml:math></disp-formula>", "<inline-formula><mml:math id=\"M63\" altimg=\"si39.svg\"><mml:mrow><mml:mi mathvariant=\"italic\">med</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M64\" altimg=\"si40.svg\"><mml:mroot><mml:mrow><mml:mi mathvariant=\"italic\">med</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>G</mml:mi><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow><mml:mn>3</mml:mn></mml:mroot></mml:math></inline-formula>", "<disp-formula id=\"e0035\"><label>(7)</label><mml:math id=\"M65\" altimg=\"si41.svg\"><mml:mrow><mml:mi mathvariant=\"italic\">JSD</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>P</mml:mi><mml:mo stretchy=\"false\">|</mml:mo><mml:mfenced open=\"|\" close=\")\"><mml:mrow><mml:mi>Q</mml:mi></mml:mrow></mml:mfenced><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>k</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:munderover><mml:msub><mml:mi>x</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mi>l</mml:mi><mml:mi>o</mml:mi><mml:mi>g</mml:mi><mml:mfrac><mml:mrow><mml:mn>2</mml:mn><mml:msub><mml:mi>x</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:mrow></mml:mfrac><mml:mo>+</mml:mo><mml:munderover><mml:mo>∑</mml:mo><mml:mrow><mml:mi>k</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>n</mml:mi></mml:munderover><mml:msub><mml:mi>y</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mi>l</mml:mi><mml:mi>o</mml:mi><mml:mi>g</mml:mi><mml:mfrac><mml:mrow><mml:mn>2</mml:mn><mml:msub><mml:mi>y</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mi>x</mml:mi><mml:mi>k</mml:mi></mml:msub><mml:mo>+</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>k</mml:mi></mml:msub></mml:mrow></mml:mfrac><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:mrow></mml:math></disp-formula>", "<inline-formula><mml:math id=\"M66\" altimg=\"si42.svg\"><mml:mi>P</mml:mi><mml:mo>=</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mo>⋯</mml:mo><mml:mo>,</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M67\" altimg=\"si43.svg\"><mml:mi>Q</mml:mi><mml:mo>=</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mo>⋯</mml:mo><mml:mo>,</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M68\" altimg=\"si43.svg\"><mml:mi>Q</mml:mi><mml:mo>=</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mo>⋯</mml:mo><mml:mo>,</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M69\" altimg=\"si42.svg\"><mml:mi>P</mml:mi><mml:mo>=</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo>,</mml:mo><mml:mo>⋯</mml:mo><mml:mo>,</mml:mo><mml:msub><mml:mi>x</mml:mi><mml:mi>n</mml:mi></mml:msub><mml:mo>)</mml:mo></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M70\" altimg=\"si44.svg\"><mml:mfrac><mml:mn>1</mml:mn><mml:mi>m</mml:mi></mml:mfrac></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M71\" altimg=\"si45.svg\"><mml:mi>m</mml:mi></mml:math></inline-formula>" ]
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[]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Table S1</title><p>Statistics of ATAC-seq data used in this study</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Table S2</title><p>Statistics of RNA-seq data used in our study</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S3</title><p>Identification of 1601 active-RSCNEs</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S4</title><p>Motif binding enrichment results of 1601 active-RSCNEs</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S5</title><p>Gene expression profile of 18 rumen TTFs during rumen and esophagus development</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S6</title><p>Upstream regulatory relationship of 18 rumen TTFs</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S7</title><p>Downstream regulatory relationship of 18 rumen TTFs</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S8</title><p>Differential regulatory sub-network between the rumen and esophagus</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S9</title><p>GO enrichment analysis of 52 TGs in the differential regulatory sub-network between the rumen and esophagus</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S10</title><p>Gene expression profile of 655 RSEGs represented by the FPKM value</p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p><italic>Note</italic>: CNEReg, conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network; TTF, toolkit transcription factor; TF, transcription factor; RSEG, rumen-specific expressed gene; RSCNE, ruminant-specific conserved non-coding element.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"d35e305\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0160\" fn-type=\"supplementary-material\"><p id=\"p0295\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.11.007\" id=\"ir065\">https://doi.org/10.1016/j.gpb.2022.11.007</ext-link>.</p></fn></fn-group>" ]
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56
CC BY
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2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Jun 7; 21(3):632-648
oa_package/73/c7/PMC10787174.tar.gz
PMC10787175
36669641
[ "<title>Introduction</title>", "<p id=\"p0005\">Messenger RNA (mRNA) polyadenylation is a critical mRNA processing event that occurs toward the completion of transcription and involves two tightly coupled steps: cleavage at the nascent transcript followed by the addition of an untemplated poly(A) tail to its 3′ end ##REF##27677860##[1]##, ##REF##31267064##[2]##. Over 70% of mammalian genes possess more than one poly(A) site, suggesting the possibility of the modulated use of selective poly(A) sites through alternative polyadenylation (APA) ##REF##27677860##[1]##, ##REF##31267064##[2]##. APA contributes substantially to the complexity of the transcriptome and proteome by generating isoforms of the same gene with distinct 3′ untranslated regions (UTRs) or coding regions. APA is dynamically regulated in various cellular processes and diseases, including cell activation, proliferation, differentiation, neurodegenerative disorders, and cancer ##REF##21925375##[3]##, ##REF##25544561##[4]##, ##REF##25601023##[5]##, ##REF##25896326##[6]##, ##REF##25892335##[7]##, ##REF##25409906##[8]##, ##REF##24993033##[9]##, ##REF##24569168##[10]##, ##REF##25413384##[11]##, ##REF##23632313##[12]##. Studies using bulk 3′ end sequencing (3′-seq) ##REF##31267064##[2]##, ##REF##24695098##[13]##, ##REF##31267126##[14]## and/or RNA sequencing (RNA-seq) ##REF##31267126##[14]##, ##REF##34649612##[15]## revealed extensive 3′ UTR lengthening or shortening events in various processes. For example, 3′ UTRs generally shorten in proliferating cells, whereas 3′ UTRs lengthen during embryonic differentiation ##REF##19372383##[16]## and animal neurogenesis ##REF##23520388##[17]##, ##REF##16356263##[18]##.</p>", "<p id=\"p0010\">In contrast to bulk methodologies, single-cell RNA sequencing (scRNA-seq) protocols characterize the transcriptional landscape in individual cells, with many protocols utilizing 3′ selection or enrichment in library construction, such as Drop-seq ##REF##26000488##[19]##, CEL-Seq ##REF##22939981##[20]##, and 10X Genomics ##REF##28091601##[21]##. Although most scRNA-seq studies initially focus only on gene expression profiling, these scRNA-seq technologies inherently capture a notable amount of information on isoform usage, providing substantial potential to profile APA events at the single-cell level. Computational tools, including scDAPA ##UREF##0##[22]##, scAPA ##REF##31501864##[23]##, Sierra ##REF##32641141##[24]##, scAPAtrap ##REF##33142319##[25]##, and scDaPars ##REF##34035046##[26]##, have been proposed to identify APA sites in single cells and/or profile differential APA isoform usage among cell types using scRNA-seq. Particularly, single-cell APA profile compiled from scRNA-seq enables the discovery of hidden subpopulations of cells that are unrecognizable in conventional gene expression analysis ##REF##33142319##[25]##, ##REF##34035046##[26]##, revealing the possibility of discerning cell identities with the APA layer independent of gene expression.</p>", "<p id=\"p0015\">Even though scRNA-seq is powerful in profiling the transcriptome of individual cells, the spatial information of cells is not preserved because of tissue dissociation prior to sequencing. The characterization of the spatial organization and molecular features of cells is essential to understanding cellular interactions and organization in the tissue microenvironment ##REF##34145435##[27]##. Several strategies for spatial transcriptomics (ST), including MERFISH ##REF##25858977##[28]##, seqFISH ##REF##24681720##[29]##, and ST through spatial barcoding ##REF##27365449##[30]##, have been established to measure spatially resolved gene expression, and they provide opportunities to decipher the spatial context of the transcriptomic landscape within single cells and/or across tissue sections. The identification of spatially variable (SV) genes is usually the first critical step in analyzing ST data to spatially resolve the transcriptomic landscape across tissues. Recently, a few computational approaches have been proposed to explore spatial gene expression trends, including SpatialDE ##REF##29553579##[31]##, Trendsceek ##REF##29553578##[32]##, SPARK ##REF##31988518##[33]##, and SPARK-X ##REF##34154649##[34]##. Continuous gradients or spatial gene expression patterns can be identified by these tools, and this contributes to disclosing significant biological discoveries that otherwise cannot be revealed using scRNA-seq alone. Although most spatially resolved transcriptomic studies have restricted analysis at the gene level, these studies, particularly the ST method of spatial barcoding, may provide additional information on transcript isoforms, enabling multiple layers of transcriptome information to be obtained from ST experiments without changing the experimental methods. Recently, dynamic alternative splicing and brain region-specific isoform expression have been observed using single-cell isoform RNA sequencing technology ##REF##33469025##[35]##. These pioneering studies have implicated potential SV genes and/or splice isoforms. However, the pattern of APA usage in spatial contexts remains unclear.</p>", "<p id=\"p0020\">In this study, we developed a toolkit referred to as stAPAminer for mining spatial patterns of APA from spatially barcoded ST data. First, poly(A) sites were identified from ST data, and then APA site usages of genes in individual spots were quantified. In particular, an imputation model based on k-nearest neighbors (KNN) was designed to recover APA signals obtained from the ST data by borrowing information from the spatial gene expression profile, and this can effectively mitigate the noise and bias caused by the dropout phenomenon. Based on the profile of imputed APA usage, APA genes with differential APA usage between morphological layers and genes with global spatial trends in APA usage variation were identified. By analyzing well-established mouse olfactory bulb (MOB) ST data, we presented a detailed view of spatial APA usage across MOB regions with stAPAminer. We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial APA patterns that represent APA dynamics in different morphological layers. These genes were enriched in Gene Ontology (GO) terms directly associated with olfactory bulb development, highlighting the benefits of spatial APA analysis using stAPAminer. By extending the analysis to two additional replicates of the MOB ST data, we observed that the spatial APA patterns of several genes were reproducible among replicates, thus demonstrating the robustness and effectiveness of stAPAminer in spatial APA analysis. stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution variation, establishing an additional layer of gene expression at isoform resolution.</p>" ]
[ "<title>Materials and methods</title>", "<title>Data</title>", "<p id=\"p0115\">The input of stAPAminer is a poly(A) site matrix, with each row being a poly(A) site and each column being a spot. Currently, there are several ST strategies such as MERFISH ##REF##25858977##[28]##, seqFISH ##REF##24681720##[29]##, and ST through spatial barcoding ##REF##27365449##[30]##, among which APA sites can only be identified from the spatially barcoded ST data using existing scRNA-seq tools such as scAPAtrap or Sierra. However, if APA sites could be identified from other types of ST data in the future, stAPAminer would also be applicable to ST data. In this study, the spatially barcoded ST data of MOB ##REF##27365449##[30]## were used. We downloaded the gene expression measurements of the MOB data from Spatial Transcriptomics Research (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.spatialresearch.org/\" id=\"ir020\">https://www.spatialresearch.org/</ext-link>), which were collected from spatial locations known as spots. Corresponding array oligonucleotides with positional barcodes were also obtained. Following the studies of SpatialDE ##REF##29553579##[31]## and SPARK ##REF##31988518##[33]##, the MOB Replicate 11 file was primarily used, which consisted of 16,218 genes measured on 262 spots. We retained spots with ten or more read counts, resulting in 260 spots. Two additional replicates of MOB (Replicate 5 and Replicate 12) were used for validation. Raw sequencing data were downloaded from Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) (SRA: SRR3382373), which are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ncbi.nlm.nih.gov/sra\" id=\"ir025\">https://www.ncbi.nlm.nih.gov/sra</ext-link>. The lengths of barcodes and unique molecular identifiers (UMIs) were 18 nt and 9 nt, respectively. The genome assembly (version GRCm38) and latest genome annotation of mice were downloaded from Ensembl (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.ensembl.org\" id=\"ir030\">https://www.ensembl.org</ext-link>).</p>", "<title>Identification and quantification of APA sites from ST data</title>", "<p id=\"p0120\">The process of extracting APA sites from ST data was similar to that of scRNA-seq data. The raw ST data were double-stranded, including read 1 and read 2. First, barcodes and UMIs were extracted from read 1, and umi_tools ##REF##28100584##[63]## was adopted to append the barcode and UMI information to the sequence header of read 2 to generate a new read 2 FASTQ file. Reads from the read 2 file were aligned to the reference genome using STAR ##REF##23104886##[64]##, and only uniquely mapped reads were retained. After mapping, PCR duplicates were removed using the dedup function in umi_tools, and one read per UMI for each genomic coordinate remained. scAPAtrap ##REF##33142319##[25]## was used to identify poly(A) sites from these mapped reads. Poly(A) sites were annotated with information, such as genomic regions and genes, with the movAPA package ##REF##33258917##[65]## using the R annotation package “TxDb.Mmusculus.UCSC.mm10.knownGene”. Similar to previous studies ##REF##18411206##[66]##, ##REF##21746925##[67]##, ##REF##24626288##[68]##, ##REF##25048171##[69]##, the 3′ UTRs of annotated genes were extended by 1000 bp to recruit intergenic poly(A) sites, which may originate from authentic 3′ UTRs.</p>", "<title>Quantification and imputation of spatial APA usage</title>", "<p id=\"p0125\">We calculated the RUD for each 3′ UTR APA gene from the ST data using the movAPAindex function in movAPA ##REF##33258917##[65]##. Briefly, only 3′ UTR APA genes that contained at least two poly(A) sites in the 3′ UTR were retained. The distal poly(A) site is the one that is farthest from the start codon among all the 3′ UTR sites. The RUD score of each gene is the ratio of the expression level of the distal poly(A) site to the sum of the expression levels of all poly(A) sites located in the 3′ UTR. The RUD value ranged between 0 and 1. A larger RUD value of a gene in a spot indicated higher usage of the distal poly(A) site of this gene in this spot (<italic>i.e.</italic>, 3′ UTR lengthening). If no poly(A) site was expressed in a gene for a given spot, then the respective RUD value was called a dropout. Finally, an RUD matrix was obtained for the ST dataset, where each row denoted a gene and each column denoted a spot.</p>", "<p id=\"p0130\">To explore the spatial patterns of intronic APA, we filtered poly(A) sites that were supported by at least three reads and present in at least three spots, and retained genes with multiple poly(A) sites and at least one intronic poly(A) site. We calculated the ratio for each intronic poly(A) site as the expression level of the respective site to the sum of the expression levels of all the sites in the same gene. The highest ratio of intronic poly(A) site(s) was considered the intronic APA usage of a gene. This ratio was also between 0 and 1. A larger ratio of a gene in a spot indicated higher usage of the intronic poly(A) site of the gene in this spot.</p>", "<p id=\"p0135\">Owing to the inherent technical issues of spatial RNA-seq and lower expression at the APA isoform level than at the gene level, the APA usage matrix (RUD or ratio) is substantially sparser than the gene–spot expression matrix. Although the APA usage matrix contains usage information at the APA isoform level and has a higher resolution than the gene expression matrix, it was obtained from APA genes alone; consequently, it does not store as many genes as the gene–spot expression matrix. To mitigate the high sparsity of the APA usage matrix, we designed a KNN-based imputation model and introduced the gene–spot expression matrix to obtain the correlation between spots to better impute the APA usage matrix. Given a gene–spot matrix <italic>G</italic> with genes and spots, the matrix was first scaled (including data centering and standardization). Next, the Euclidean distance between the two spots was calculated to obtain a spot–spot distance matrix [Equation ##FORMU##5##(1)##]. Subsequently, a ranking matrix could be obtained, which was a spot–spot matrix that stored the spot indexes for each spot in descending order according to the distance between all other spots and the respective spot. represents the spot index of the <italic>j</italic>-th spot closest to the <italic>i</italic>-th spot.</p>", "<p id=\"p0140\">Here, is the scaled gene expression level of gene in spot .</p>", "<p id=\"p0145\">Given an APA usage matrix with genes and spots, first, the values for those genes not expressed in the gene–spot matrix were set to 0. Next, for each spot, the nearest spots (default ) were selected according to the ranking matrix . The nearest spots for any spot (<italic>i.e.</italic>, the <italic>i</italic>-th row in ) are the first columns of the <italic>i</italic>-th row in the ranking matrix. Then, for a gene with missing APA usage in the matrix , the average APA usage of this gene in these spots is calculated for the imputation [Equation ##FORMU##22##(2)##]. Notably, only spots with non-zero APA usage for the gene were counted.</p>", "<p id=\"p0150\">Here, is the imputed APA usage for gene in spot ; denotes the set of nearest spots with APA usage for the respective gene; is the number of spots in .</p>", "<p id=\"p0155\">After the first round of imputation, a small part of the APA usage values remained missing when the respective genes were not expressed in any of the nearest spots. Subsequently, we repeated the imputation step [Equation ##FORMU##22##(2)##] and performed multiple iterations until there were no missing entries or no additional missing entries could be filled. In each iteration, the average value of the APA usage of neighboring spots was calculated according to the newly imputed APA usage matrix. In addition, in the stAPAminer package, users can set the maximum number of iterations, which stops when the number of iterations reaches the set value. If there are still missing entries after the entire iteration process, we can directly set their values to 0.</p>", "<p id=\"p0160\">Several performance indicators were adopted to evaluate the KNN-based imputation model. First, we manually obtained the true layer where each spot was located by combining the spatial information of each layer with the hematoxylin &amp; eosin-stained bright field image of MOB slices. The true labels of the layers were used as references. To examine whether the imputed APA usage matrix better reflects the true relationship between spots than the raw APA usage matrix, we first adopted the FindClusters function (resolution = 5) in Seurat ##REF##31178118##[70]## to cluster spots based on the APA usage matrix and used the following four metrics to evaluate the performance in the context of clustering: ARI, Jaccard, Purity, and NMI. The ARI score ranged from −1 to 1, and the scores of Jaccard, Purity, and NMI ranged from 0 to 1, with higher values reflecting better performance. In addition, four internal validation metrics, namely DBI ##REF##21868852##[38]##, CH ##UREF##1##[39]##, SC ##UREF##2##[40]##, and Dunn index ##UREF##3##[41]##, were employed to quantitatively assess the consistency of a clustering structure, which was independent of clustering methods or prior knowledge of true labels. A smaller DBI score or higher CH, SC, or Dunn score indicated better separation among clusters. Moreover, we calculated Pearson’s correlation coefficient between each pair of spots under the same layer to examine whether the correlation of spots on the same layer after imputation was higher than that before imputation.</p>", "<p id=\"p0165\">The most important parameter in our KNN-based imputation model was the <italic>k</italic> value. We proposed a strategy to determine the optimal <italic>k</italic> value based on a comprehensive index. Briefly, given a set of <italic>k</italic> values, the APA usage matrix is imputed for each <italic>k</italic>. Clustering was then performed on the imputed matrix to obtain eight clustering index values, including four internal validation metrics (DBI, SC, CH, and Dunn) and four external metrics (ARI, Jaccard, NMI, and Purity). Next, the Z-score was calculated for each index, and the sum of all Z-score values was considered the comprehensive index. Finally, the <italic>k</italic> value with the highest comprehensive index score was regarded as the optimal <italic>k</italic>.</p>", "<title>Identification of genes with spatial patterns of APA usage</title>", "<p id=\"p0170\">To fully explore the spatial patterns of APA usage, we identified three types of APA genes, namely DEAPA, LSAPA, and SVAPA. DEAPA genes exhibit differential APA usage between the two layers and are similar to DEGs in conventional gene expression studies. LSAPA genes exhibit layer-specific APA usage. SVAPA genes exhibit distinct spatial APA usage patterns in the global spatial context, which are similar to SV genes in conventional ST studies. We followed the Seurat tutorial ##REF##31178118##[70]## to cluster spots based on the APA usage matrix and obtained five spot clusters (equal to the number of layers). These clusters were annotated as GCL, MCL, OPL, GL, and ONL according to the hematoxylin &amp; eosin staining image. To identify DEAPA genes, we used the FindMarkers function in Seurat with the APA usage matrix as input. This function identifies DEAPA genes between two groups of spots using the Wilcoxon Rank Sum test. Genes with an adjusted <italic>P</italic> value &lt; 0.05 and log<sub>2</sub> fold change &gt; 0.5 were considered DEAPA genes. We also identified LSAPA genes using FindMarkers by comparing spots in one layer to all spots in the remaining layers.</p>", "<p id=\"p0175\">In addition, we detected genes with SV APA usages, <italic>i.e.</italic>, SVAPA genes. In contrast to DEAPA genes that show differential APA usage between the two groups of spots, SVAPA genes have distinct spatial APA usage patterns in the global spatial context. Currently, there is no tool available for identifying global spatial patterns from ratio-type data, but there are several tools for identifying SV genes, which can be applied to the APA usage matrix. SPARK ##REF##34154649##[34]## utilize a non-parametric method to effectively detect spatially expressed genes from large ST data, which controls type I errors and produces high power. SPARK is identified to be ten times more powerful than other existing methods ##REF##34154649##[34]##. Considering that SPARK is designed for count data, we transformed the APA usage values, which are between 0 and 1, into count data by taking 10 as the base (for 3′ UTR APA) or by log<sub>2</sub> conversion (for intronic APA). This transformation made the data approximately conform to the Poisson distribution required by SPARK. The transformed APA usage matrix was then used as the input for SPARK, and genes with adjusted <italic>P</italic> value &lt; 0.05 were considered genes with spatial APA usage patterns. Moreover, we implemented a unified interface in stAPAminer to import SVAPA results, which facilitates the incorporation of results from other tools upon the availability of more dedicated tools in the future.</p>", "<p id=\"p0180\">After obtaining the DEAPA, LSAPA, and SVAPA genes, we combined these three sets of genes without redundancy to compile a unique gene set with dynamic APA usage in a spatial context. We then adopted k-means to cluster these genes into ten groups based on their APA usage profile, using the kmeans function of the R package stats with arguments “iter.max = 1e+9, nstart = 1000”. Next, the mean APA usage profile for each group of genes was calculated for each spot; each group was considered one spatial APA pattern. We selected five groups with the most distinguished spatial APA usage patterns. Moreover, we calculated Pearson’s correlation to measure the similarity between the APA usage profile of each gene in a group and the average profile of the group, and selected genes with Pearson’s correlation &gt; 0.5 and <italic>P</italic> &lt; 0.05, as representative genes with spatial APA patterns.</p>" ]
[ "<title>Results</title>", "<title>stAPAminer facilitates the analysis of spatial APA dynamics from ST data</title>", "<p id=\"p0025\">We developed an R package, stAPAminer, to explore spatial APA dynamics from ST data (##FIG##0##Figure 1##). First, poly(A) sites from ST data were identified and quantified using existing tools such as scAPAtrap (##FIG##0##Figure 1##A). Subsequently, a poly(A) site expression matrix was obtained, and this was similar to the conventional gene–cell expression matrix obtained from scRNA-seq, except that each row denotes one poly(A) site rather than a gene and each column denotes a spot. Next, a matrix of 3′ UTR or intronic APA usage was obtained from the poly(A) site expression matrix (##FIG##0##Figure 1##B). Genes with at least two 3′ UTR poly(A) sites were extracted for 3′ UTR APA analysis, and the APA usage of each gene was represented by the relative usage of the distal poly(A) site (RUD). For intronic APA analysis, APA genes with at least one intronic poly(A) site were extracted, and the APA usage of each gene was represented by the ratio of the intronic site (see Materials and methods). The APA usage matrix was even sparser than the gene–spot expression matrix. Therefore, we proposed a KNN-based imputation model for recovering APA signals in the APA usage matrix. This model leverages the gene expression profile to infer the spot–spot distance and then imputes the sparse APA usage matrix by borrowing information on APA usage from neighboring spots. The <italic>k</italic> value is the most critical parameter in the KNN-based imputation model, which can be determined using a strategy based on a comprehensive index (see Materials and methods). After the imputation, benchmarking analyses were conducted to investigate the performance of the imputation model. The imputed APA usage matrix was used to explore spatial APA dynamics (##FIG##0##Figure 1##C) to detect genes with differential APA usages between layers (DEAPA), layer-specific DEAPA (LSAPA), and SV APA usages (SVAPA). These three APA genes reflect the spatial characteristics of APA from different aspects, establishing the full landscape of spatial APA dynamics. Moreover, representative spatial APA patterns can be obtained by clustering these APA genes based on their APA usage profiles. stAPAminer was implemented as an open-source R package available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/BMILAB/stAPAminer\" id=\"ir015\">https://github.com/BMILAB/stAPAminer</ext-link>.</p>", "<title>Genome-wide poly(A) sites were identified from MOB ST data</title>", "<p id=\"p0030\">We applied stAPAminer to analyze a spatially barcoded ST dataset of MOB ##REF##27365449##[30]##. Following other studies ##REF##29553579##[31]##, ##REF##31988518##[33]##, we primarily used the MOB Replicate 11 file for analysis, which consists of 11,274 genes on 260 spots after filtration (hereafter referred to as ST-MOB). A total of 47,886 poly(A) sites were extracted using the scAPAtrap pipeline (##FIG##1##Figure 2##A), with an average of 14,436 poly(A) sites per spot (<xref rid=\"s0100\" ref-type=\"sec\">Table S1</xref>). The majority of the poly(A) sites were located in 3′ UTRs/extended 3′ UTRs (21,671) or introns (17,645), and this is consistent with previous observations in scRNA-seq ##REF##32641141##[24]##, ##REF##33142319##[25]##. The base composition surrounding the 3′ UTR poly(A) sites from ST-MOB resembled the general profile of annotated poly(A) sites (##FIG##1##Figure 2##B). A high frequency of core poly(A) hexamers was observed in the upstream poly(A) site region, including AAUAAA, AUUAAA, and GU-rich hexamers (<xref rid=\"s0100\" ref-type=\"sec\">Figure S1</xref>). Next, we used the poly(A) sites identified from MOB scRNA-seq data (hereafter referred to as SC-MOB) ##REF##30517858##[36]## and annotated poly(A) sites of bulk 3′-seq from PolyASite 2.0 ##REF##31617559##[37]## to validate the poly(A) sites identified from ST-MOB. Up to 16,433 poly(A) sites and 28,290 poly(A) sites from ST-MOB were detected in SC-MOB and PolyASite 2.0, respectively. In contrast, 24,891 poly(A) sites were exclusively observed in ST-MOB, which may represent potential novel polyadenylation events in the ST data that cannot be detected using scRNA-seq or bulk 3′-seq. Poly(A) sites from ST-MOB were close to the annotated poly(A) sites or sites from SC-MOB (##FIG##1##Figure 2##C). Additionally, the poly(A) site expression profile of ST-MOB was highly correlated with that of SC-MOB (Pearson’s correlation = 0.7) (##FIG##1##Figure 2##D) and neural-related samples from bulk 3′-seq (Pearson’s correlation = 0.69) (<xref rid=\"s0100\" ref-type=\"sec\">Figure S2</xref>). These observations demonstrate the authenticity of the poly(A) sites identified from ST-MOB data.</p>", "<title>stAPAminer effectively recovers highly sparse APA signals obtained from ST-MOB</title>", "<p id=\"p0035\">After identifying poly(A) sites from ST-MOB, the expression level of each poly(A) site was quantified by counting the effective reads of the respective poly(A) site region (<italic>i.e.</italic>, peak). Here, we analyzed the 3′ UTR APA genes. For genes with multiple poly(A) sites in the 3′ UTR, RUD score (between 0 and 1) was used to measure the global trend of the 3′ UTR length change. An RUD matrix was generated from ST-MOB data, with rows representing genes and columns representing spots. To mitigate the impact of the high dropout rate, we proposed a KNN-based imputation method implemented in our stAPAminer package to recover the RUD matrix. First, we examined the clustering performance based on the comprehensive index for different <italic>k</italic> values from 2 to 100 and determined that the optimal <italic>k</italic> value for the KNN model was 10 (##FIG##2##Figure 3##A). After imputation with the KNN model (<italic>k</italic> = 10), we examined whether stAPAminer could efficiently recover the profile of APA usages. We applied Uniform Manifold Approximation and Projection (UMAP) visualization to the raw and imputed RUD matrices to show the differences between MOB layers. The 2-dimensional embeddings showed that the different layers became considerably distinguishable after the imputation (##FIG##2##Figure 3##B). The inferred layer labels of spots based on the imputed RUD matrix were more consistent with the reference labels than those inferred from the raw RUD matrix [<italic>e.g.</italic>, adjusted rand index (ARI): imputed = 0.643; raw = 0.547] (##FIG##2##Figure 3##C). Similar results were obtained using three other metrics, namely Jaccard, normalized mutual information (NMI), and Purity. Four additional metrics without relying on the reference labels, namely the Davies and Bouldin index (DBI) ##REF##21868852##[38]##, Calinski–Harabasz (CH) ##UREF##1##[39]##, silhouette coefficient (SC) ##UREF##2##[40]##, and Dunn index ##UREF##3##[41]##, were used to quantitatively assess spot separation. According to these metrics, the imputed RUD matrix improved spot separation by recovering the true signals of APA usage (##FIG##2##Figure 3##C). We further compared the spot–spot correlation in the same layer of the tissue section using the imputed and raw RUD matrices. The median Pearson’s correlation of spot pairs in the same layer was only 0.311 to 0.501 using the raw RUD matrix, whereas stAPAminer substantially increased the spot–spot correlation of all five layers (from 0.525 to 0.622) (##FIG##2##Figure 3##D). Previously, scDaPars ##REF##34035046##[26]## was proposed to identify and quantify APA events from scRNA-seq data. It first identifies APA events from scRNA-seq using DaPars ##REF##25409906##[8]##, a tool for identifying APA events from bulk RNA-seq, and then utilizes a regression model to impute the missing values in the APA usage matrix obtained from scRNA-seq. Although the underlying strategies differ, both stAPAminer and scDaPars can impute sparse APA signals. Here, we used scDaPars to impute raw APA signals obtained from ST-MOB and then compared the performances of scDaPars and stAPAminer. Regardless of the performance indicators used, stAPAminer outperformed scDaPars (##FIG##2##Figure 3##E and F), further demonstrating its superiority in imputing highly sparse APA signals.</p>", "<p id=\"p0040\">Next, we examined whether stAPAminer could reveal spatial APA usage patterns. We used SPARK ##REF##31988518##[33]## to identify genes with SVAPA (see Materials and methods). For genes with strong SVAPA (<italic>e.g.</italic>, the well-known layer-specific marker genes <italic>Grm4</italic>\n##REF##30954358##[42]##, <italic>Chl1</italic>\n##REF##12391163##[43]##, and <italic>Mobp</italic>\n##REF##12203392##[44]##), the pattern from imputed data was concordant with that from the raw data (##FIG##2##Figure 3##G). Notably, the patterns of these genes were considerably more distinguishable according to the APA profile (either RUD or imputed RUD) than according to the raw gene spot expression profile. In particular, we also observed cases wherein the raw RUD matrix exhibited a substantially weak signal that was enhanced in the imputed data (<italic>e.g.</italic>, <italic>St8sia5</italic>, <italic>Myef2</italic>, and <italic>Per1</italic>) (##FIG##2##Figure 3##G). For example, <italic>St8sia5</italic> was highly expressed in all layers, whereas no pattern was observed according to either the gene expression profile or the raw RUD profile. In contrast, after imputation, a distinct pattern was observed for this gene, with much higher RUD scores (<italic>i.e.</italic>, longer 3′ UTR) on the mitral cell layer (MCL) or outer plexiform layer (OPL) than on the other layers. Two 3′ UTR poly(A) sites were identified in ST-MOB for <italic>St8sia5</italic> (Table S1), both of which were supported by annotated poly(A) sites from PolyA_DB 3 ##REF##29069441##[45]##. <italic>St8sia5</italic> has been reported to induce ganglioside GQ1b expression and enhance neuronal differentiation via the MAP kinase pathway ##REF##22189683##[46]##. Another gene, <italic>Myef2</italic>, is a transcriptional repressor of the myelin basic protein gene, the expression of which is usually up-regulated in nerve sheath myxomas and schwannomas ##REF##21997683##[47]##. In addition, gene has two 3′ UTR poly(A) sites identified from ST-MOB, both of which were annotated in PolyA_DB 3. <italic>Myef2</italic> has a unique pattern according to the imputed RUD profile, with a longer 3′ UTR on the granular cell layer (GCL) than on the other layers. A similar case was observed for <italic>Per1</italic>, which contributes to phasing molecular and electrical circadian rhythms in suprachiasmatic nucleus neurons to increase the robustness of cellular timekeeping ##REF##27602274##[48]##. These results show that the imputation strategy in stAPAminer can effectively mitigate the noise caused by the dropout phenomenon and help detect genes with distinct patterns of APA usage from highly sparse and noisy ST data.</p>", "<title>stAPAminer reveals spatial dynamics of 3′ UTR APA usages from ST-MOB</title>", "<p id=\"p0045\">Based on the imputed gene–spot RUD matrix, we explored APA usage profiles in spatially defined domains within the olfactory bulb. The RUD profile clearly separated the different morphological layers (##FIG##3##Figure 4##A). We detected 905 genes (403 non-redundant genes) with differential APA usage (<italic>i.e.</italic>, DEAPA genes) between each pair of morphological layers (<xref rid=\"s0100\" ref-type=\"sec\">Table S2</xref>). For comparison, we also identified 1146 differentially expressed genes (DEGs) using only the gene–spot expression matrix (<xref rid=\"s0100\" ref-type=\"sec\">Table S3</xref>). Although the numbers of DEAPA genes and DEGs were comparable, the overlap between the two gene sets was substantially limited, and a considerable number of genes were exclusively present in the DEAPA gene list. For example, between the GCL and MCL, only one common gene was observed among 78 DEGs and 54 DEAPA genes (##FIG##3##Figure 4##B). A similar case was observed in the GCL and olfactory nerve layer (ONL). These DEAPA genes were not recognizable by conventional gene expression analysis but represented genes with differential APA usage between layers. Among the 905 DEAPA genes, 111 were not present in the conventional gene–spot expression matrix. This may be because the scAPAtrap that we used was highly sensitive in capturing poly(A) sites, even for minimally expressed genes, whereas these genes may not be detected in conventional gene expression analysis pipelines. ##FIG##3##Figure 4##C shows two representative example genes, which showed clear spatial APA usage patterns but no gene expression patterns. <italic>Adarb2</italic> (also known as <italic>ADAR3</italic>) was extremely low and loosely expressed in GCL or ONL according to the gene expression profile, and no pattern was observed between these two layers. In contrast, it has two 3′ UTR poly(A) sites exclusively identified from ST-MOB (Table S1), showing differential APA usage between GCL and ONL. <italic>Adarb2</italic> encodes a catalytically inactive protein that is primarily expressed in the brain, thalamus, and amygdala, and may be associated with disorders such as amyotrophic lateral sclerosis ##REF##21310295##[49]##. <italic>Mapk8ip3</italic> encodes a protein that functions as a motor in brain neurons, moving items along the axons ##REF##30945334##[50]##. <italic>Mapk8ip3</italic> was moderately expressed in both OPL and ONL without differential gene expression. Two 3′ UTR poly(A) sites were identified for this gene (Table S1), and differential APA usage was observed between OPL and ONL. Therefore, the APA profile potentially encodes complementary information that is absent or insignificant in the conventional gene–spot expression profile, which contributes to distinguishing the morphological layers. Next, we examined the presence of these DEAPA genes among known biologically important genes in the olfactory system. We compiled representative genes in the olfactory system presented in previous studies and public resources (<xref rid=\"s0100\" ref-type=\"sec\">Table S4</xref>), including marker genes highlighted in the original study ##REF##27365449##[30]##, cell type-specific marker genes provided in a recent scRNA-seq study on MOB ##REF##30517858##[36]##, and genes related to the olfactory system from the Harmonizome database ##REF##27374120##[51]##. A moderate number of DEAPA genes (71 out of 403 non-redundant genes) were present in the representative gene list, suggesting the potential biological function of these APA genes. Indeed, the overlap is relatively limited; however, this is not unexpected as these DEAPA genes were identified based on spatial APA profiles independent of gene expression, whereas the compiled representative gene list is based on gene expression profiles.</p>", "<p id=\"p0050\">Furthermore, we detected 784 LSAPA genes by comparing the RUD profile of one layer to all other layers (Table S5). The majority of these LSAPA genes (69%) were detected in the GCL and ONL (##FIG##3##Figure 4##D). ##FIG##3##Figure 4##E shows some representative LSAPA genes that demonstrated clear spatial APA usage patterns but no gene expression patterns. For example, <italic>Snrnp27</italic> and <italic>St8sia5</italic> are constitutively expressed across all layers; however, they show distinct spatial APA usage patterns on GCL and MCL, respectively. <italic>Snrnp27</italic> has two poly(A) sites identified from ST-MOB (<xref rid=\"s0100\" ref-type=\"sec\">Table S1</xref>), and a previous microarray study identified altered expression of this gene during the progression of Alzheimer’s disease ##REF##23637700##[52]##. Additionally, <italic>Fibcd1</italic>, a known chitin-binding receptor of the innate immune system, shows glomerular layer (GL) specificity according to the gene expression and APA profiles. However, the layer-specific pattern obtained from the APA profile was more distinguishable. <italic>Fibcd1</italic> has recently been recognized as an evolutionarily conserved component of the brain extracellular matrix that is associated with a complex neurodevelopmental disorder ##UREF##4##[53]##. Notably, two other genes, <italic>Dhdh</italic> and <italic>Cep126</italic>, were not detected in the gene–spot expression profile; however, they demonstrated layer-specific APA usage in OPL and ONL, respectively. <italic>Cep126</italic> is a regulator of microtubule organization at the centrosome and has been identified to be associated with diseases such as monomelic amyotrophy ##REF##24867236##[54]##. Notably, even though the gene is not expressed in any spot, its poly(A) sites could be detected. This is probably because of the different tools or strategies used to quantify genes and poly(A) sites. Here, the gene expression profile was obtained using a conventional gene expression analysis pipeline, and the poly(A) site expression profile was obtained using scAPAtrap. scAPAtrap is considerably sensitive and can detect poly(A) sites for genes with low expression ##REF##33142319##[25]##, whereas such genes may be undetectable using tools such as Cell Ranger. Owing to the fact that the sum of the expression levels of poly(A) sites in a gene can also be considered as the gene expression, we also summarized the read counts of all poly(A) sites in these two genes to represent their gene expression; however, no spatial pattern was observed for these two genes (<xref rid=\"s0100\" ref-type=\"sec\">Figure S3</xref>). These results indicate that the profile of APA usage encodes an additional layer of spatial information with high resolution that is invisible in the gene expression profile.</p>", "<p id=\"p0055\">Next, we used SPARK to identify SVAPA genes. Using the imputed RUD matrix as the input, 133 genes with adjusted <italic>P</italic> value &lt; 0.05 were considered SVAPA genes (<xref rid=\"s0100\" ref-type=\"sec\">Table S6</xref>). Similarly, we identified 772 SV genes with SPARK, using the gene–spot expression matrix as the input (<xref rid=\"s0100\" ref-type=\"sec\">Table S7</xref>). A considerably limited overlap was observed between these SVAPA and SV genes. Only 16 genes were detected as both SVAPA and SV genes (<xref rid=\"s0100\" ref-type=\"sec\">Figure S4</xref>), possibly because SVAPA and SV genes were detected based on APA and gene expression profiles, respectively. These two independent groups of genes possess spatial patterns at the gene and APA isoform levels.</p>", "<p id=\"p0060\">By combining DEAPA, LSAPA, and SVAPA genes, we obtained a comprehensive list of 654 non-redundant genes with spatial APA usage patterns (##FIG##4##Figure 5##A). A limited number of genes (101) were common to all three gene sets, indicating that these three gene sets are complementary in reflecting the full landscape of spatial APA dynamics. We performed clustering on the combined gene set and obtained the following five major spatial expression patterns (##FIG##4##Figure 5##B): pattern I representing ONL, pattern II representing the combination of GL and MCL; pattern III representing the combination of GL, ONL, and OPL; pattern IV representing GCL; and pattern V representing layers other than ONL. All five patterns were clearly visualized using five representative genes, namely <italic>Thg1l</italic>, <italic>Zfp983</italic>, <italic>Zfp974</italic>, <italic>Srnp27</italic>, and <italic>Srcap</italic> (##FIG##4##Figure 5##C). For example, <italic>Thg1l</italic>, encoding a tRNA-histidine guanylyltransferase 1-like protein associated with autosomal recessive ataxia with abnormal neurodevelopment ##REF##33682303##[55]##, generally showed high RUD scores (<italic>e.g.</italic>, longer 3′ UTR) on ONL. In contrast, <italic>Srcap</italic>, encoding a <italic>Snf2</italic>-related CREBBP activator protein associated with diseases such as musculoskeletal defects and behavioral abnormalities, displayed higher RUD scores in multiple layers, except for ONL. Next, we performed functional enrichment analyses of the combined gene list of 654 genes. A total of 66 GO terms were enriched in these genes at a false discovery rate (FDR) of 5% (<xref rid=\"s0100\" ref-type=\"sec\">Table S8</xref>). Several enriched GO terms were directly associated with functions related to olfactory bulb development, such as synapse organization, neuron differentiation, and nervous system development. These APA genes and GO terms highlight the benefits of spatial APA analysis using stAPAminer.</p>", "<title>Spatial 3′ UTR APA patterns explored from additional replicates of ST-MOB demonstrate the robustness of stAPAminer</title>", "<p id=\"p0065\">Next, we explored the spatial APA patterns from two additional replicates of ST-MOB to evaluate the robustness of stAPAminer. We extracted poly(A) sites from two adjacent tissue sections (Replicate 5 and Replicate 12) of ST-MOB for the analysis of spatial APA dynamics. The profile of poly(A) site expression of ST-MOB (Replicate 11) was highly similar to both replicates (Pearson’s correlation = 0.87 and 0.86 for Replicate 5 and Replicate 12, respectively) (<xref rid=\"s0100\" ref-type=\"sec\">Figure S5</xref>). Moreover, when repeating the imputation procedure on Replicate 5 (<xref rid=\"s0100\" ref-type=\"sec\">Figure S6</xref>) and Replicate 12 (<xref rid=\"s0100\" ref-type=\"sec\">Figure S7</xref>), we observed that our results were highly reproducible. For both replicates, different layers became more distinguishable after imputation (<xref rid=\"s0100\" ref-type=\"sec\">Figures S6</xref>A and S7A), and imputation improved spot separation or spot clustering (<xref rid=\"s0100\" ref-type=\"sec\">Figures S6</xref>B and S7B). These results demonstrate the robustness of the imputation method for stAPAminer. We also compiled DEAPA, SVAPA, and LSAPA genes for both replicates, resulting in 695 non-redundant genes for Replicate 5 (<xref rid=\"s0100\" ref-type=\"sec\">Table S9</xref>) and 556 non-redundant genes for Replicate 12 (<xref rid=\"s0100\" ref-type=\"sec\">Table S10</xref>). For all three replicates, considerably more LSAPA or DEAPA genes were identified than SVAPA genes (##FIG##4##Figure 5##A, <xref rid=\"s0100\" ref-type=\"sec\">Figure S8</xref>). This may be because different strategies were used to characterize spatial APA dynamics, <italic>i.e.</italic>, LSAPA or DEAPA genes were identified by comparing between layers, whereas SVAPA genes were identified by inferring the spatial trend globally.</p>", "<p id=\"p0070\">Although the number of genes with spatial APA patterns was comparable among the three replicates, a limited number of consensus genes (364) were identified from two or more replicates, and a considerable number of genes were exclusively identified in one replicate (##FIG##5##Figure 6##A). The primary reason may be attributed to the inherent nature of the high sparsity and noise of the ST data, as well as the biological variance suffered from different replicates. Nevertheless, we observed several notable and reproducible results (##FIG##5##Figures 6##B, <xref rid=\"s0100\" ref-type=\"sec\">Figure S9</xref>). For example, DEAPA between GCL and ONL was observed for <italic>Adarb2</italic> in Replicate 11 (##FIG##3##Figure 4##C), and a similar pattern was also observed in Replicate 12 (##FIG##5##Figure 6##B), whereas this gene was not detected in Replicate 5. Notably, this gene also seemed to display a weak spatial gene expression pattern according to the tissue image; however, the pattern could not be detected by spatial expression analysis (<italic>i.e.</italic>, the gene is not present in Table S7). Similarly, <italic>Mpp2</italic>, enconding a postsynaptic MAGUK scaffold protein ##REF##27756895##[56]##, showed a higher expression level or RUD score on GCL than other layers, and the pattern of APA usage was substantially more distinguishable than that of gene expression (<xref rid=\"s0100\" ref-type=\"sec\">Figure S9</xref>). <italic>Mpp2</italic> was also detected as an SV gene by spatial expression analysis (Table S7). In particular, the spatial pattern of APA usage was not observed because of the high dropout rate in Replicate 11, whereas the pattern was recovered after APA imputation and was highly consistent with that of Replicate 5. It is probable that some weak gene expression patterns may originate from noise, or some genes may possess both patterns of spatial gene expression and APA usage, but with varying strengths. We also observed some genes whose gene expression was not detected in the gene–spot matrix, although poly(A) sites and spatial APA patterns were detected in the imputed APA profile (<italic>e.g.</italic>, <italic>Dnal1</italic> and <italic>Tmem268</italic>) (<xref rid=\"s0100\" ref-type=\"sec\">Figure S9</xref>). This revealed the high sensitivity of stAPAminer in identifying and imputing APA profiles for genes that may be missed by conventional gene expression pipelines. These results demonstrate the ability and robustness of stAPAminer to identify spatial APA patterns.</p>", "<title>stAPAminer reveals extensive spatial dynamics of intronic APA usages from ST-MOB</title>", "<p id=\"p0075\">Having demonstrated the spatial dynamics of 3′ UTR APA, we next sought to explore the spatial patterns of intronic APA from ST-MOB. First, we obtained a matrix of intronic APA usage (see Materials and methods), containing 4011 genes present in 260 spots. The matrix was then imputed using the KNN model in stAPAminer (<italic>k</italic> = 10). The layer clustering result based on the imputed intronic APA signals was similar to that based on the 3′ UTR APA signal (ARI: intronic APA = 0.605, 3′ UTR APA = 0.643) (##FIG##2##Figure 3##B and ##FIG##6##Figure 7##A). Based on the imputed intronic APA signal matrix, we further identified 601 non-redundant DEAPA genes (<xref rid=\"s0100\" ref-type=\"sec\">Table S11</xref>), 386 LSAPA genes (<xref rid=\"s0100\" ref-type=\"sec\">Table S12</xref>), and 226 SVAPA genes (adjusted <italic>P</italic> value &lt; 0.05) (<xref rid=\"s0100\" ref-type=\"sec\">Table S13</xref>). Combining these three sets of genes, 669 non-redundant genes with spatial APA usage patterns were obtained, among which 130 genes showed spatial 3′ UTR APA patterns as well (##FIG##6##Figure 7##B). Next, we clustered these genes based on their intronic APA profiles and obtained the following five major spatial APA patterns (##FIG##6##Figure 7##C): pattern I representing ONL; pattern II representing the combination of GL and MCL; pattern III representing the combination of GL, ONL, and OPL; pattern IV representing GCL; and pattern V representing layers other than ONL. These five patterns were clearly visualized using five representative genes, namely <italic>Adgrg6</italic>, <italic>Mia3</italic>, <italic>P3h2</italic>, <italic>Sema3c</italic>, and <italic>Rapgef2</italic> (##FIG##6##Figure 7##D). <italic>Adgrg6</italic> is a protein-coding gene essential for the normal differentiation of promyelinating Schwann cells and normal myelination of axons ##REF##24227709##[57]##. <italic>Mia3</italic> is involved in cell migration related to sprouting angiogenesis ##REF##27138255##[58]##. <italic>P3h2</italic> encodes an enzyme catalyzing the post-translational formation of 3-hydroxyproline in collagens ##REF##18487197##[59]##. <italic>Sema3c</italic> encodes a protein which acts as an attractant for growing axons and thus plays a critical role in axonal outgrowth and guidance ##REF##33856648##[60]##. <italic>Rapgef2</italic> is involved in cAMP-induced Ras and Erk1/2 signaling, leading to sustained inhibition of long-term melanogenesis by reducing dendritic elongation and melanin synthesis ##REF##11359771##[61]##. Functional enrichment analysis of the combined gene list revealed that these genes were associated with the olfactory system, and most were directly related to the structure and regulation of synaptic organization (<xref rid=\"s0100\" ref-type=\"sec\">Table S14</xref>). In contrast, although genes with spatial 3′ UTR APA patterns were also associated with olfactory bulb development, they were enriched in synaptic organization, neuronal differentiation, and nervous system development (Table S8). These results indicate extensive spatial dynamics of intronic APA usage, even though genes with spatial intronic APA patterns are distinct from those with spatial 3′ UTR APA patterns.</p>", "<title>The KNN-based imputation model in stAPAminer is robust to data with different dropout rates and spot sizes</title>", "<p id=\"p0080\">The KNN-based imputation method was embedded in our stAPAminer package to recover the sparse APA usage matrix; and the most critical parameter in the model was the <italic>k</italic> value. Here, we evaluated the influence of the spot size of the RUD matrix on the choice of the <italic>k</italic> value. First, we examined the influence of the number of dropout spots on the <italic>k</italic> value. We set the percentage of dropout spots in ST-MOB from 10% to 90% by masking all genes in randomly selected spots, while keeping the spot number among layers unchanged. Subsequently, the clustering performance based on the comprehensive index was evaluated under different <italic>k</italic> values at each dropout rate. In general, the larger the dropout rate, the larger the optimal <italic>k</italic> value (##FIG##7##Figure 8##A). This may be because when the dropout rate increases, more adjacent spots are needed to obtain sufficient information to achieve comparable clustering performance. However, even with an extremely high dropout rate (<italic>e.g.</italic>, &gt; 50%), a <italic>k</italic> value within 20 can yield moderately high performance. Next, to evaluate the influence of the spot size on the <italic>k</italic> value, we randomly sampled 20% to 90% of spots from a total of 260 spots, while keeping the proportion of spot numbers among layers unchanged, and then tested the performance at different <italic>k</italic> values. Regardless of the spot size, the optimal <italic>k</italic> value was approximately 10 (##FIG##7##Figure 8##B). After reaching the optimal <italic>k</italic> value, the performance decreases gradually with the increase in <italic>k</italic> value, which may be because a large <italic>k</italic> value may result in increased biases by introducing the information of spots from other layers. In general, our model is robust to different <italic>k</italic> values. It is recommended to use a smaller <italic>k</italic> value with an equally high comprehensive index score to ensure high performance and avoid introducing biased information on spots from other layers owing to a large <italic>k</italic> value.</p>", "<p id=\"p0085\">Next, we examined whether the KNN model in stAPAminer may be overfitted and evaluated the sensitivity of stAPAminer in recovering spatial APA patterns. To the best of our knowledge, this is the first study on the analysis of spatial APA patterns, and there is no gold standard for genes with spatial APA patterns; thus, it is difficult to validate whether an identified spatial APA pattern is true. Alternatively, we compiled a silver standard dataset containing genes with reproducible spatial APA patterns. Briefly, we first identified genes with spatial APA patterns in each of the three ST-MOB replicates (Replicate 5, Replicate 11, and Replicate 12) and established a list of 401 genes with spatial APA patterns present in at least two replicates. These genes were considered authentic instances and were used as true references for further evaluation. Assuming that our KNN-based imputation model is potentially overfitted, the accuracy of the spatial APA patterns identified from the RUD matrix with a higher dropout rate after imputation would be lower than that of the raw RUD matrix. Accordingly, we mimicked data with higher sparsity to verify whether the KNN-based imputation model is overfitted. We increased the dropout rate of the already sparse raw RUD matrix by 10%–30% by randomly masking the values in the matrix. We then used the KNN-based model to recover the extremely sparse RUD matrix. We identified spatial APA patterns from the RUD matrix before and after imputation and calculated the sensitivity according to the compiled silver standard. Regardless of the sparsity of the data, the sensitivity of pattern recognition on the imputed data was considerably higher than that before imputation (##FIG##7##Figure 8##C). Notably, the silver standard data that we constructed only represents true instances, whereas spatial APA patterns that are not in the silver standard are not necessarily false. Considering that there is no gold standard for false instances, only true positives (TP) and false negatives (FN), rather than false positives (FP) or true negatives (TN), can be calculated. Therefore, we calculated only the sensitivity to evaluate the results. Moreover, we used Moran’s I ##UREF##5##[62]## value to measure the significance of the identified spatial patterns and observed that the spatial autocorrelation of the patterns obtained after imputation was significantly improved (##FIG##7##Figure 8##D). These results are substantially strong, even for highly sparse data, suggesting that our KNN-based imputation model is unlikely to be overfitted and can effectively enhance or recover the RUD signal, thereby considerably improving the sensitivity of spatial pattern recognition.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0090\">ST technologies have the advantage of revealing an unbiased map of transcripts in complex tissues and cell cultures. Established spatially resolved approaches can detect genes with localized expression patterns at a single-cell resolution. However, these approaches have primarily focused on gene-level analysis rather than isoform-level analysis. Consequently, these studies could neither measure isoform usage in a spatially defined tissue region nor detect significant spatial isoform usage in a spatial context. Therefore, it is essential to develop new methods for exploring isoform usage from ST data. The rich data generated by ST experiments promises isoform-level analysis, which complements conventional gene-level studies using ST data. In this study, we presented stAPAminer, a novel method for analyzing spatial APA dynamics in spatially resolved transcriptomic studies. The method allows to anchor the APA isoform usage in a spatial view and reveals crucial spatial expression patterns at isoform resolution. The integration of APA isoform usage and gene expression in a spatial context promises to establish spatial maps of APA dynamics. Our study further defines an atlas of APA events with distinct spatial APA usage patterns, which supplements SV genes to capture the spatial complexity of MOB subregions. We verified the identified genes with significant spatial APA usage in various ways and demonstrated the improvement of layer classification by integrating spatial APA information.</p>", "<p id=\"p0095\">Limited by the sequencing depth, the gene expression profile obtained from ST data is usually sparse, with ubiquitous low counts and zeros. Moreover, the obtained APA profile is sparser than the already sparse gene expression profile, and this presents a huge computational challenge for studying the spatial patterns of APA isoform usage. The stAPAminer pipeline incorporates a KNN-based imputation model for recovering APA signals, thus mitigating the sparsity of the APA isoform matrix and yielding stronger spatial patterns. Evidence for APA isoform addition to cellular diversity has been bolstered by APA signal imputation (##FIG##2##Figure 3##). After imputation, the signals of genes with a spatial pattern of APA usage were retained or considerably enhanced (##FIG##2##Figure 3##F). Additional analyses using data with varied spot sizes and different numbers of dropout spots and genes demonstrated that the KNN model is robust to different <italic>k</italic> values and can substantially improve the sensitivity of spatial pattern recognition (##FIG##7##Figure 8##). stAPAminer has several desirable features for mitigating the high sparsity of APA profiles. First, the scAPAtrap ##REF##33142319##[25]## used in our pipeline can accurately identify all potential poly(A) sites, including those with low read coverage, by incorporating the strategies of peak identification and poly(A) read anchoring. Second, the KNN-based imputation model in stAPAminer can efficiently impute missing values by clustering spots based on gene signatures rather than the APA profile alone. This promises the inference of associations between ST spots by borrowing information from the gene expression profile of the ST data, thus avoiding the lack of information or overfitting when using the APA data alone. Third, the multiple rounds of iterations performed during the imputation process enable the gradual inclusion of newly imputed information. However, despite the effectiveness of stAPAminer in exploring spatial APA dynamics, it can be further improved in two aspects in the future. First, it is crucial to determine whether an entry into the APA ratio matrix is truly missing before imputation. Second, to identify global spatial patterns of APA, the APA ratio matrix is transformed into a count matrix to meet the input requirement of SPARK; such a transformation may not be theoretically reasonable or fully meet the model’s assumption. Additional work is required to develop more sophisticated approaches to address these issues.</p>", "<p id=\"p0100\">Using stAPAminer, we identified three types of genes with spatial APA dynamics, namely DEAPA, LSAPA, and SVAPA genes. Moreover, we explored the spatial patterns of both the 3′ UTR APA and intronic APA. A total of 654 non-redundant 3′ UTR APA genes from the combined list of DEAPA, LSAPA, and SVAPA genes were obtained from the ST-MOB data (##FIG##4##Figure 5##A), representing five major spatial expression patterns (##FIG##4##Figure 5##B). Similarly, 601 intronic APA genes with spatial patterns were obtained; however, these genes were distinct from those with spatial 3′ UTR APA patterns (##FIG##6##Figure 7##). We provided several lines of evidence to validate these genes with spatial APA dynamics. First, the poly(A) sites identified from the ST-MOB data had high confidence, were supported by annotated poly(A) sites, and possessed typical poly(A) signals (##FIG##1##Figure 2##). Second, we examined the presence of these genes in the list of representative biologically important genes in the olfactory system from several previous studies ##REF##27365449##[30]##, ##REF##30517858##[36]## (Table S4). Third, the enriched GO terms of these APA genes were directly associated with functions related to olfactory bulb development (Table S8). Fourth, when overlaying the APA signal of an APA gene on the tissue images, well-defined spatial patterns were revealed (##FIG##2##Figure 3##, ##FIG##3##Figure 4##, ##FIG##4##Figure 5##). Fifth, the spatial APA patterns of many genes were reproducible among the replicates (##FIG##5##Figure 6##, <xref rid=\"s0100\" ref-type=\"sec\">Figure S9</xref>). Notably, genes with spatial APA dynamics identified using stAPAminer are not necessarily present in genes obtained from conventional gene expression studies; however, these lines of evidence provide significant clues to the functional importance of the identified APA genes.</p>", "<p id=\"p0105\">Compared with spatial patterns obtained using spatial expression analysis, we observed several notable cases of spatial APA patterns using stAPAminer. We identified some highly expressed genes with distinguishable spatial APA patterns but without any spatial gene expression patterns (<italic>e.g.</italic>, <italic>St8sia5</italic>, <italic>Myef2</italic>, and <italic>Per1</italic>) (##FIG##2##Figure 3##F). In addition, some genes presented detectable spatial APA and gene expression patterns, with the APA pattern being more distinguishable (<italic>e.g.</italic>, <italic>Mpp2</italic>) (<xref rid=\"s0100\" ref-type=\"sec\">Figure S9</xref>). Some genes, which seem to have spatial gene expression patterns but were not computationally detected using existing tools, demonstrated apparent spatial APA patterns (<italic>e.g.</italic>, <italic>Adarb2</italic>) (##FIG##5##Figure 6##B). These different groups of genes suggest the presence of SV patterns at the APA isoform level independent of the gene expression profile. In particular, some genes were not observed in the gene–spot matrix, whereas their spatial APA patterns were detected (<italic>e.g.</italic>, <italic>Dnal1</italic> and <italic>Tmem268</italic>) (<xref rid=\"s0100\" ref-type=\"sec\">Figure S9</xref>). This result is unlikely to be due to noise or random bias because we observed the same pattern in at least two replicates. The primary reason may be the different pipelines used to obtain the gene–spot expression matrix and the gene–spot RUD matrix. The scAPAtrap tool ##REF##33142319##[25]## used in this study has been proven to be highly sensitive and can identify poly(A) sites in extremely low-expressed genes that may not be detected in conventional gene expression analysis pipelines. Moreover, the APA signals are amplified through the imputation process of the stAPAminer, which further contributes to the successful identification of spatial APA patterns. These results demonstrate the effectiveness and robustness of stAPAminer in identifying different spatial APA patterns. In the future, it will be necessary to benchmark different methods for obtaining gene expression matrices and/or RUD matrices, as well as to propose methods that can mitigate discrepancies among replicates to identify more reproducible spatial patterns.</p>", "<p id=\"p0110\">In summary, we present a detailed view of spatial APA usage across MOB regions using our proposed stAPAminer toolkit. To the best of our knowledge, our stAPAminer approach is one of the first computational approaches to explore the transcriptional atlas of spatial APA patterns with spatial resolution. stAPAminer employs the power of ST to explore genome-wide spatial patterns of APA usage variation at isoform resolution, establishing an additional layer of gene expression. The combination of spatial maps of gene expression and APA usage will allow us to deduce a more comprehensive set of genes summarizing spatial and cellular information and redefine the overall transcriptome complexity of a tissue.</p>" ]
[]
[ "<p><bold>Alternative polyadenylation</bold> (APA) contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases. <bold>Single-cell RNA sequencing</bold> (scRNA-seq) has enabled the profiling of APA at the single-cell level; however, the spatial information of cells is not preserved in scRNA-seq. Alternatively, <bold>spatial transcriptomics</bold> (ST) technologies provide opportunities to decipher the spatial context of the transcriptomic landscape. Pioneering studies have revealed potential spatially variable genes and/or splice isoforms; however, the pattern of APA usage in spatial contexts remains unappreciated. In this study, we developed a toolkit called stAPAminer for mining <bold>spatial patterns</bold> of APA from spatially barcoded ST data. APA sites were identified and quantified from the ST data. In particular, an <bold>imputation</bold> model based on the k-nearest neighbors algorithm was designed to recover APA signals, and then APA genes with spatial patterns of APA usage variation were identified. By analyzing well-established ST data of the mouse olfactory bulb (MOB), we presented a detailed view of spatial APA usage across morphological layers of the MOB. We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers. By extending this analysis to two additional replicates of the MOB ST data, we observed that the spatial APA patterns of several genes were reproducible among replicates. stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution. This toolkit is available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/BMILAB/stAPAminer\" id=\"ir005\">https://github.com/BMILAB/stAPAminer</ext-link> and <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/biocode/tools/BT007320\" id=\"ir010\">https://ngdc.cncb.ac.cn/biocode/tools/BT007320</ext-link>.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Yi Xing</p>" ]
[ "<title>Code availability</title>", "<p id=\"p0185\">Our implementation of stAPAminer is available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/BMILAB/stAPAminer\" id=\"ir035\">https://github.com/BMILAB/stAPAminer</ext-link> and <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/biocode/tools/BT007320\" id=\"ir040\">https://ngdc.cncb.ac.cn/biocode/tools/BT007320</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0190\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0195\"><bold>Guoli Ji:</bold> Investigation, Methodology, Data curation, Writing – review &amp; editing. <bold>Qi Tang:</bold> Data curation, Software, Visualization, Writing – review &amp; editing. <bold>Sheng Zhu:</bold> Data curation, Software, Visualization. <bold>Junyi Zhu:</bold> Data curation, Formal analysis. <bold>Pengchao Ye:</bold> Formal analysis. <bold>Shuting Xia:</bold> Formal analysis. <bold>Xiaohui Wu:</bold> Conceptualization, Writing – original draft, Writing – review &amp; editing, Supervision, Project administration, Funding acquisition. All authors have read and approved the final manuscript. All authors read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0210\">The following are the Supplementary data to this article:</p>", "<p id=\"p0215\">\n\n</p>", "<p id=\"p0220\">\n\n</p>", "<p id=\"p0225\">\n\n</p>", "<p id=\"p0230\">\n\n</p>", "<p id=\"p0235\">\n\n</p>", "<p id=\"p0240\">\n\n</p>", "<p id=\"p0245\">\n\n</p>", "<p id=\"p0250\">\n\n</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<p id=\"p0270\">\n\n</p>", "<p id=\"p0275\">\n\n</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0200\">This work was supported by the National Natural Science Foundation of China (Grant Nos. T2222007 to Xiaohui Wu, 61573296 to Guoli Ji, and 81901287 to Shuting Xia) and the Suzhou City People’s Livelihood Science and Technology Project, China (Grant No. SYS2020086 to Shuting Xia).</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Schema of stAPAminer</bold></p><p><bold>A.</bold> Identification of poly(A) sites from ST data using scAPAtrap. <bold>B.</bold> Quantification and imputation of APA usages. The sparse gene–spot matrix of APA usages is imputed by the KNN-based imputation model embedded in stAPAminer and the optimal <italic>k</italic> value is determined using a comprehensive index. <bold>C.</bold> Analysis of spatial APA dynamics with stAPAminer. stAPAminer can be used to detect SVAPA, DEAPA, and LSAPA. SVAPA, spatially variable APA usage; DEAPA, differential APA usage between layers; LSAPA, layer-specific DEAPA; mRNA, messenger RNA; RNA-seq, RNA sequencing; ST, spatial transcriptomics; UMI, unique molecular identifier; BC, barcode; UTR, untranslated region; GCL, granular cell layer; MCL, mitral cell layer; OPL, outer plexiform layer; ONL, olfactory nerve layer; GL, glomerular layer; ARI, adjusted rand index; NMI, normalized mutual information; UMAP, Uniform Manifold Approximation and Projection; BAM, Binary Alignment/Map; GFF, General Feature Format; APA, alternative polyadenylation; FC, fold change; KNN, <italic>k</italic>-nearest neighbors.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Validation of poly(A) sites identified from the ST-MOB data</bold></p><p><bold>A.</bold> Distribution of poly(A) sites from ST-MOB in different genomic regions. <bold>B.</bold> Nucleotide compositions of the sequences surrounding 3′ UTR poly(A) sites from ST-MOB. Y-axis denotes the fractional nucleotide content at each position. On the X-axis, “0” denotes the poly(A) site. <bold>C.</bold> Comparison of the ST-MOB poly(A) sites with the annotated poly(A) sites in the PolyASite 2.0 database and the poly(A) sites identified from SC-MOB. The curves show the distance from ST-MOB poly(A) sites to annotated poly(A) sites and SC-MOB poly(A) sites. <bold>D.</bold> Scatter plot showing the correlation of poly(A) site expression profiles obtained from ST-MOB and SC-MOB. Each dot is one poly(A) site and the axis is log<sub>2</sub> scaled. Pearson’s correlation is indicated in (D). CDS, coding sequence; MOB, mouse olfactory bulb; scRNA-seq, single-cell RNA sequencing; SC-MOB, scRNA-seq data of MOB.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Validation of stAPAminer in imputing APA signals</bold></p><p><bold>A.</bold> The comprehensive index score with the increase in the <italic>k</italic> value. The vertical dotted line marks the optimal <italic>k</italic> value (<italic>k</italic> = 10), corresponding to the maximum comprehensive index score. <bold>B.</bold> Visualization of ST spots on the tissue image before (raw) and after (imputed) imputation. <bold>C.</bold> Evaluation of the performance of the imputation model. Four metrics were used for evaluating the performance in the context of clustering, including ARI, Jaccard, NMI, and Purity, and four internal validation metrics without relying on the reference labels were also used, including DBI, CH, SC, and Dunn. <bold>D.</bold> Boxplot showing Pearson’s correlations between spot pairs in each layer estimated using imputed and the raw RUD scores. For each layer, correlations of all pairwise spots were calculated. <bold>E.</bold> Evaluation of the performance of stAPAminer and scDaPars. <bold>F.</bold> Boxplot showing Pearson’s correlations between spot pairs in each layer estimated between stAPAminer and scDaPars. <bold>G.</bold> Spatial patterns of APA usages for representative genes using raw (middle) and imputed (bottom) RUD matrices. The top row shows the tissue image based on the scaled gene expression level of the respective gene. Color represents RUD scores or scaled gene expression levels (yellow, high; blue, low). RUD, relative usage of the distal poly(A) site; DBI, Davies and Bouldin index; CH, Calinski–Harabasz; SC, silhouette coefficient.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Application of stAPAminer to ST-MOB data for identification and analysis of genes with spatial APA pattern</bold></p><p><bold>A.</bold> UMAP plot showing the 2-dimensional embeddings of spots on the five layers. <bold>B.</bold> Venn diagrams showing the overlap between DEAPA genes and DEGs by comparing GCL and MCL (top) as well as GCL and ONL (bottom). <bold>C.</bold> Two representative genes showing clear spatial APA usage patterns but no gene expression patterns. <italic>Adarb2</italic> is a DEAPA gene between GCL and ONL; <italic>Mapk8ip3</italic> is a DEAPA gene between OPL and ONL. Gene expression levels and RUD scores of spots on the respective layers are shown, and spots on other layers are colored as gray. <bold>D.</bold> Number of LSAPA genes on each layer. <bold>E.</bold> Representative LSAPA genes on the five layers, which showed clear spatial APA usage patterns but no gene expression patterns. DEG, differentially expressed gene.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Combined analysis of genes with spatial APA usage pattern</bold></p><p><bold>A.</bold> Upset plot showing overlap of DEAPA genes, LSAPA genes, and SVAPA genes. <bold>B.</bold> Five major spatial APA patterns by clustering on the combined gene set. <bold>C.</bold> Representative tissue images of the five patterns (top) and the corresponding example genes for individual patterns (bottom). The tissue image for each pattern was generated by averaging RUD scores on each spot for all genes with the respective pattern.</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>Analysis of spatial APA dynamics from additional two replicates of ST-MOB with stAPAminer</bold></p><p><bold>A.</bold> Upset plot showing the overlap of genes with spatial APA pattern among the three replicates (Replicate 5, Replicate 11, and Replicate 12). <bold>B.</bold> An example gene (<italic>Adarb2</italic>) with differential APA usage between GCL and ONL. Tissue images based on the scaled gene expression level (top), raw RUD scores (middle), and imputed (bottom) RUD matrices were shown. Color represents RUD scores or scaled gene expression levels (yellow, high; blue, low).</p></caption></fig>", "<fig id=\"f0035\"><label>Figure 7</label><caption><p><bold>Analysis of spatial patterns of intronic APA from ST-MOB</bold></p><p><bold>A.</bold> Visualization of ST spots on the tissue image after intronic APA imputation. <bold>B.</bold> Venn diagram showing the overlap of 3′ UTR APA genes and intronic APA genes with spatial APA patterns. <bold>C.</bold> Five major spatial APA patterns by clustering on the combined gene set. <bold>D.</bold> Representative tissue images of the five patterns (top) and the corresponding example genes for individual patterns (bottom). The tissue image for each pattern was generated by averaging intronic ratio scores on each spot for all genes with the respective pattern.</p></caption></fig>", "<fig id=\"f0040\"><label>Figure 8</label><caption><p><bold>Evaluation of the KNN-based imputation model using RUD matrix with varied spot sizes and dropout rates</bold></p><p><bold>A.</bold> The value of the comprehensive index with the increase in the <italic>k</italic> value under different number of dropout spots. The percentages of dropout spots were set from 10% to 90% by masking all genes in randomly selected spots, while keeping the spot number among layers unchanged. <bold>B.</bold> The value of the comprehensive index with the increase in the <italic>k</italic> value under different number of sampled spots. 20% to 90% spots were randomly sampled, while keeping the proportion of spot number among layers unchanged. <bold>C.</bold> Sensitivity of the KNN-based imputation model under RUD matrices with different dropout rates. The dropout rate of the raw RUD matrix was increased by 10%–30% through randomly masking values in the matrix. Genes with spatial APA pattern present in at least two replicates of Replicate 5, Replicate 11, and Replicate 12 were used as the true reference. Spatial APA patterns from the RUD matrix before and after imputation were identified to obtain sensitivity, respectively. <bold>D.</bold> Moran’s I value of spatial APA patterns identified from RUD matrices with different dropout rates. The RUD matrix was processed as in (C). For all plots in this figure, the RUD matrix of MOB Replicate 11 was used, which contained a total of 260 spots.</p></caption></fig>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0115\"><caption><title>Supplementary Figure S1</title><p><bold>Motifs identified in the upstream 50 nt region of the poly(A) site</bold> Motifs were identified by MEME for 3′ UTR poly(A) sites. Top ten motifs, each with three most significant hexamers, were shown.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0110\"><caption><title>Supplementary Figure S2</title><p><bold>Scatter plot showing the correlation of poly(A) site expression profiles obtained from ST-MOB and bulk 3′ end sequencing (3′-seq)</bold> Each dot is one poly(A) site and both axes are natural-log scaled. The Pearson’s correlation is indicated in the plot. Here the bulk 3'-seq data contains a total of 32 neural-related samples from the PolyASite 2.0 database.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0105\"><caption><title>Supplementary Figure S3</title><p><bold>Two representative genes showing clear spatial APA usage patterns but no gene expression pattern</bold> The “Gene” row is the average gene expression level of the respective gene in all spots which represented by the sum of expression levels of poly(A) sites in the gene. The “RUD” row is the average RUD score of the gene in all spots.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0100\"><caption><title>Supplementary Figure S4</title><p><bold>Overlap between SVAPA genes and SV genes</bold> The 16 overlapped genes are <italic>Sft2d2</italic>, <italic>Runx1t1</italic>, <italic>Epha5</italic>, <italic>Gabrb2</italic>, <italic>Gja1</italic>, <italic>Igfbp4</italic>, <italic>Tmem132b</italic>, <italic>Fam149a</italic>, <italic>Camk1d</italic>, <italic>Ak5</italic>, <italic>Pde5a</italic>, <italic>Rbfox1</italic>, <italic>Crtc1</italic>, <italic>Grasp</italic>, <italic>Magt1</italic>, <italic>and Fibcd1</italic>. SV, spatially variable.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0095\"><caption><title>Supplementary Figure S5</title><p><bold>Scatter plots showing expression levels of poly(A) sites between replicates A.</bold> Correlation between Replicate 5 and Replicate 11. <bold>B.</bold> Correlation between Replicate 5 and Replicate 12. Each dot is one poly(A) site and both axes are log2 scaled.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0090\"><caption><title>Supplementary Figure S6</title><p><bold>Validation of stAPAminer in imputing APA signals using Replicate 5 of ST-MOB A.</bold> Visualization of ST spots on the tissue image before (Raw) and after (Imputed) imputation. <bold>B.</bold> Evaluation of the performance of the imputation model. Four metrics were used for evaluating the performance in the context of clustering, including ARI, Jaccard, NMI, and Purity, and four internal validation metrics without relying on the reference labels were also used, including DBI, CH, SC, and Dunn. <bold>C.</bold> Boxplot showing Pearson’s correlations between spot pairs in each layer estimated using imputed and the raw RUD scores. For each layer, correlations of all pairwise spots were calculated.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0085\"><caption><title>Supplementary Figure S7</title><p><bold>Validation of stAPAminer in imputing APA signals using Replicate 12 of ST-MOB A.</bold> Visualization of ST spots on the tissue image before (Raw) and after (Imputed) imputation. <bold>B.</bold> Evaluation of the performance of the imputation model. Four metrics were used for evaluating the performance in the context of clustering, including ARI, Jaccard, NMI, and Purity, and four internal validation metrics without relying on the reference labels were also used, including DBI, CH, SC, and Dunn. <bold>C.</bold> Boxplot showing Pearson’s correlations between spot pairs in each layer estimated using imputed and the raw RUD scores. For each layer, correlations of all pairwise spots were calculated.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0080\"><caption><title>Supplementary Figure S8</title><p><bold>Upset plot showing the overlap of DEAPA, LSAPA, and SVAPA genes A.</bold> The result for Replicate 5. <bold>B.</bold> The result for Replicate 12.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0075\"><caption><title>Supplementary Figure S9</title><p><bold>Representative genes with spatial APA dynamics detected from the three replicates of ST-MOB</bold> Tissue images of the respective gene based on the scaled gene expression level (top), raw RUD scores (middle) and imputed (bottom) RUD matrices were shown. Color represents RUD scores or scaled gene expression levels (yellow, high; blue, low).</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0070\"><caption><title>Supplementary Table S1</title><p><bold>Poly(A) sites identified from ST-MOB using scAPAtrap</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0065\"><caption><title>Supplementary Table S2</title><p><bold>DEAPA genes between each pair of morphological layers</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Table S3</title><p><bold>Differentially expressed genes identified using the gene–spot expression matrix</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Table S4</title><p><bold>List of representative genes in the olfactory system presented in previous studies or public resources</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Table S5</title><p><bold>LSAPA genes by comparing the RUD profile of a layer to all other layers</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S6</title><p><bold>SVAPA genes identified by SPARK</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S7</title><p><bold>SV genes identified by SPARK</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S8</title><p><bold>GO terms enriched in the combined list of DEAPA, LSAPA, and SVAPA genes</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S9</title><p><bold>DEAPA, LSAPA, and SVAPA genes identified for Replicate 5 of ST-MOB</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S10</title><p><bold>DEAPA, LSAPA, and SVAPA genes identified for Replicate 12 of ST-MOB</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S11</title><p><bold>DEAPA genes of intronic APA between each pair of morphological layers</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S12</title><p><bold>LSAPA genes of intronic APA by comparing the intronic ratio profile of a layer to all other layers</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S13</title><p><bold>SVAPA genes that display spatial intronic APA patterns identified by SPARK</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S14</title><p><bold>Top 10 GO terms enriched in the combined gene list of DEAPA, LSAPA, and SVAPA genes with intronic APA</bold></p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e156\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0095\" fn-type=\"supplementary-material\"><p id=\"p0205\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2023.01.003\" id=\"ir045\">https://doi.org/10.1016/j.gpb.2023.01.003</ext-link>.</p></fn></fn-group>" ]
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{ "acronym": [], "definition": [] }
70
CC BY
no
2024-01-14 23:41:58
Genomics Proteomics Bioinformatics. 2023 Jun 18; 21(3):601-618
oa_package/cd/bb/PMC10787175.tar.gz
PMC10787176
36031057
[ "<title>Introduction</title>", "<p id=\"p0005\">The therian X and Y chromosomes originated from a pair of ancestral autosomes about 190–166 million years ago (MYA) ##REF##26616198##[1]##. Evolutionary degeneration of the Y chromosome caused dose reduction of X-linked genes ##REF##31768022##[2]##, ##REF##32559446##[3]##. The dosage compensation of sex chromosome and its underlying mechanisms attracted long-term attention in molecular evolution ##REF##25189265##[4]##. Susumu Ohno proposed that the expression of X-linked genes should be doubled to compensate the dose reduction of X chromosome in males (XY), and that one X chromosome in females (XX) should be inactivated to avoid X-tetrasomy formation in females and to balance gene expression level between sexes ##REF##16847345##[5]##. Ohno’s hypothesis lays the theoretical foundation for the evolution of sex chromosome dosage compensation ##REF##26616198##[1]##, ##UREF##0##[6]##.</p>", "<p id=\"p0010\">Several previous studies have reported the up-regulation of X-linked genes in some certain mammalian tissues (X:AA ratio ≈ 1) by microarray ##REF##16341221##[7]##, ##REF##18076287##[8]##, ##REF##22120049##[9]##, RNA sequencing (RNA-seq) ##REF##35388014##[10]##, ##REF##22019781##[11]##, ##REF##22120048##[12]##, ##REF##31582851##[13]##, ##REF##26370379##[14]##, and recently used ribosome sequencing (Ribo-seq) ##REF##33177713##[15]##, but Ohno’s hypothesis has also been challenged ##REF##30642250##[16]##, ##REF##27593371##[17]##. Due to the unavailability of the ancestral proto-X (<underline>X</underline>), the aforementioned tests of Ohno’s hypothesis depended on indirect calculation of the expression ratio of the current X to autosomes (X:AA). An innovative study directly compared the human X-linked genes with their orthologs in chickens ##REF##22753487##[18]##, an outgroup species diverged from therians (∼ 310 MYA) prior to the origin of the X chromosome, but its inclusion of unexpressed genes in the evaluation of dosage compensation is disputable ##REF##22019781##[11]##. In addition, the existing studies have only investigated specific tissues and developmental stages, which might not be representative ##REF##28566535##[19]##, ##REF##26786896##[20]##. Fortunately, the emergence of developmental transcriptome data covering multiple tissues, developmental stages, and species enables us to perform a comprehensive analysis of the regulation and evolution of dosage compensation ##REF##31243369##[21]##, ##REF##32669715##[22]##. We thus took advantage of the multi-omics datasets and comprehensively analyzed the X:AA ratios and X:<underline>XX</underline> ratios to test Ohno’s hypothesis. Our analysis reveals per-allele up-regulation of X-linked genes at the transcriptome, translatome, and proteome levels across tissues and developmental stages in mammalian species, systematically validating Ohno’s hypothesis of dosage compensation in mammals.</p>" ]
[ "<title>Materials and methods</title>", "<title>Expression analysis</title>", "<p id=\"p0110\">Developmental transcriptome data of humans, mice, and chickens were downloaded from European Bioinformatics Institute (EBI) ArrayExpress: E-MTAB-6814, E-MTAB-6798, and E-MTAB-6769, respectively. The datasets covered the developmental stages from organogenesis to adulthood across seven major tissues (brain, cerebellum, heart, kidney, liver, ovary, and testis) ##REF##31243369##[21]##. RNA-seq and sample-matched Ribo-seq data used for cross-species comparison in ##FIG##2##Figure 3## were obtained from the article by Wang et al. ##REF##33177713##[15]##, including three organs (brain, liver, and testis) in humans, opossums, platypuses, and chickens. We used snakePipes (v1.3.0) ##REF##31134269##[52]##, a workflow package, for processing high-throughput data, to estimate the gene expression level across tissues in the three species. In RNA-seq analysis, we used snakePipes to integrate STAR (v2.6.1) and featureCounts (v2.0.0) for mapping reads and for quantifying uniquely mapped reads, respectively. The reference genome version of humans, mice, and chickens was hg38, mm10, and GRCg6a, respectively. We measured gene expression with FPKM based on read counts with only protein-coding genes considered. There were 19,694 and 21,297 protein-coding genes in humans and mice, respectively. Detailed information and resource for public data used in this study are presented in <xref rid=\"s0105\" ref-type=\"sec\">Table S2</xref>. We directly downloaded the gene expression matrix of rhesus, rats, rabbits, and opossums from EBI ArrayExpress: E-MTAB-6813, E-MTAB-6811, E-MTAB-6782, and E-MTAB-6833, respectively. To examine the tissue distribution of genes, we assigned a gene to a tissue in which this gene showed maximum expression level or protein abundance. The HKGs were identified by Eisenberg and Levanon ##REF##23810203##[53]## based on RNA-seq data, including 5701 AHKGs and 191 XHKGs. Considering the current proteomic coverage and resolution, X-linked genes and autosomal genes were separately divided into 100 bins in terms of normalized intensity-based absolute quantification (iBAQ), and only the first 25 X and autosomal bins were investigated.</p>", "<title>Tissue specificity and developmental-stage specificity</title>", "<p id=\"p0115\">A tau value was used to measure the tissue specificity of genes ##REF##15388519##[54]##. For gene A, we defined its mean FPKM value throughout all developmental stages in a certain tissue as gene A’s expression level in this tissue.</p>", "<p id=\"p0120\">The genes with FPKM values of 0 in all tissues were excluded in the analysis. The tau value was calculated in the following formula:where <italic>x<sub>i</sub></italic> means the expression level of gene <italic>x</italic> in tissue <italic>i</italic>. The tau value ranges from 0 to 1, and 0 indicates “broadly expressed”, and 1 represents “highly specific”. The same formula was applied to calculating the developmental-stage specificity of all genes in each tissue. It should be noted that because the different tissues covered different numbers of sampling stage, the tissue specificity (tau) was not suitable for across-tissue comparison.</p>", "<title>Calculation of the X:AA ratio</title>", "<p id=\"p0125\">The ratio of mean expression level of X-linked genes to that of autosomal genes (X:AA ratio) was calculated, and only genes with FPKM &gt; 1 were considered. For expression with error, we randomly sampled the genes size-matched with those of the X chromosome from autosomes 1000 times, and calculated the expression ratio of X to sampled A. The error bar represented 90% confidence interval.</p>", "<title>Identification of stage-correlated genes</title>", "<p id=\"p0130\">In each tissue, a gene had a series of expression values corresponding to different development stages. We computed Spearman’s rank correlation coefficient between gene expression values and development stages (from young to old), as previously reported ##REF##32669715##[22]##. Stage-positively- or negatively-correlated genes represent the genes which show increased or decreased expression throughout development stages in a certain tissue, respectively. GO analysis was conducted using clusterProfiler ##REF##22455463##[55]##.</p>", "<title>Atlas of X:AA ratios in mammals</title>", "<p id=\"p0135\">We combined RNA-seq data of 32 human adult tissues with GTEx data ##REF##30777892##[23]##. If there were both RNA-seq data and GTEx data for a certain tissue, the mean value of these two data was defined as the X:AA ratio of this tissue. We integrated RNA-seq data of 17 mouse tissues into ENCODE data to calculate the X:AA ratio. We used developmental transcriptome data to estimate the X:AA ratio in rhesus, rats, and rabbits. The visualization was realized using R package gganatogram ##REF##30467523##[56]##.</p>", "<title>Expression ratio between X and <underline>XX</underline></title>", "<p id=\"p0140\">We defined the expression ratio of human X-linked genes to outgroup species (chickens, platypuses, and opossums) orthologous genes as the X:<underline>XX</underline> ratio, and that of human autosomal genes to outgroup species orthologous genes as the AA:<underline>AA</underline> ratio. The orthologous gene information was downloaded from Ensembl bioMart ##REF##31598706##[57]##. Because chicken chromosomes 1 and 4 are orthologous to the human X chromosome ##REF##15592404##[58]##, 325 human X-linked genes whose orthologous genes were located on chicken chromosome 1 or 4 were investigated when the X:<underline>XX</underline> ratio was calculated. Then, 11,070 human autosomal genes whose orthologous genes were not located on chicken chromosome Z or W were investigated when the AA:<underline>AA</underline> ratio was calculated. Because there were more unexpressed genes on the human X chromosome than on the human AA, chicken <underline>XX</underline>, and chicken <underline>AA</underline> in a given tissue, we analyzed only the genes whose FPKM &gt; 1 for a really fair comparison, and applied a scaling procedure for appropriate across-species comparison. Briefly, we scaled the expression levels to make the median of orthologous gene expression levels equal between species. After normalizing the median of AA:<underline>AA</underline> ratios into 1, we computed X:<underline>XX</underline> ratios. The X:<underline>XX</underline> ratio median of 0.5 indicated the evolutionarily reduced expression of human X-linked genes and no dosage compensation, whereas the X:<underline>XX</underline> ratio median of 1 indicated evolutionary maintenance of the human X-linked gene expression and dosage compensation existence. The opossum chromosomes 4, 7, and X were orthologous to the human X chromosome ##REF##17495919##[59]##. One previous study reported the double up-regulation of opossum X-linked genes in both males and females at the single-cell level ##REF##32814901##[60]##. Therefore, the opossum X chromosome was treated as a pair of autosomes in this study, and we repeated the same analysis in opossums as in chickens. A total of 375 and 12,592 gene pairs were used to compute the human:opossum X:<underline>XX</underline> ratio and AA:<underline>AA</underline> ratio, respectively. A total of 415 and 10,740 gene pairs were utilized to calculate the human:platypus X:<underline>XX</underline> ratio and AA:<underline>AA</underline> ratio, respectively.</p>", "<title>Epigenomic analysis of human genomes</title>", "<p id=\"p0145\">Epigenetic data were downloaded from Roadmap Epigenomics Project (<ext-link ext-link-type=\"uri\" xlink:href=\"https://egg2.wustl.edu/roadmap/\" id=\"ir005\">https://egg2.wustl.edu/roadmap/</ext-link>; <xref rid=\"s0105\" ref-type=\"sec\">Table S2</xref>). In this study, all consolidated epigenomes were included (<italic>n</italic> = 127). Detailed information on 15-state chromHMM model and matched colors was presented in the original Roadmap paper (<ext-link ext-link-type=\"uri\" xlink:href=\"https://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html\" id=\"ir010\">https://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html#core_15state</ext-link>) except that the 15_Quies state was colored with gray. In the 50-state model, epigenetic states with only hg19-based coordinate were provided, and thus we used University of California, Santa Cruz (UCSC) genome browser liftover to convert it to hg38-based coordinate ##REF##31691824##[61]##. We defined upstream 2-kb and downstream 1-kb regions of TSS as promoter regions. BEDTools intersect ##REF##20110278##[62]## was utilized to obtain the epigenetic states overlapped with promoters. A promoter which had any overlap (≥ 1 bp) with a state was regarded as annotated by this state.</p>" ]
[ "<title>Results</title>", "<title>Tissue-dependent X:AA expression ratios in mammals</title>", "<p id=\"p0015\">The recently published RNA-seq data across the tissues of multiple mammalian species make possible a comprehensive test of Ohno’s hypothesis (X:AA ratio). We used public RNA-seq data of 32 main healthy adult human tissues ##REF##30777892##[23]## and only analyzed protein-coding genes on the X chromosome and autosomes to allow the comparison between our results with previous studies. We found tissue-dependent X:AA ratios, ranging from 0.12 (pancreas) to 1.4 (cerebral cortex) (##FIG##0##Figure 1##A). Most X:AA ratios of our investigated tissues fitted Ohno’s hypothesis with X:AA ≈ 1, except for pancreas (0.12), saliva-secreting gland (0.45), skeletal muscle tissue (0.51), and liver (0.51). Because <italic>Xist</italic> is necessary for silencing one copy of the X chromosomes in females ##REF##32445708##[24]##, we showed its expression pattern across adult tissues (<xref rid=\"s0105\" ref-type=\"sec\">Figure S1</xref>). We also used Genotype Tissue Expression (GTEx) to validate the results ##REF##32913098##[25]##. The lowest X:AA ratio (0.24) and the highest ratio (1.27) were still observed in human pancreas and neural tissues, respectively (<xref rid=\"s0105\" ref-type=\"sec\">Figure S2</xref>), indicating great consistency between different datasets. We further estimated tissue-wide X:AA ratios in other mammals, including rhesus (<italic>Macaca mulatta</italic>), mice (<italic>Mus musculus</italic>), rats (<italic>Rattus norvegicus</italic>), and rabbits (<italic>Oryctolagus cuniculus</italic>) (##FIG##0##Figure 1##B, <xref rid=\"s0105\" ref-type=\"sec\">Figure S3</xref>; see Materials and methods) ##REF##31243369##[21]##, ##REF##32669715##[22]##, ##REF##32913098##[25]##, ##REF##25582907##[26]##. Among the investigated tissues shared by these five species, we observed the consistent pattern that the highest ratio existed in the brain, and the lowest ratio existed in the liver, demonstrating tissue-dependent X:AA ratios at the transcriptome level.</p>", "<p id=\"p0020\">Given that protein-coding genes were frequently regulated at multiple levels after transcription ##REF##33177713##[15]##, ##REF##30777893##[27]##, ##REF##24870543##[28]##, transcriptome might offer an incomplete picture of gene activity. Therefore, the protein abundance would represent the dosage compensation better than transcriptome, and the X:AA ratio might be closer to the actual ratio at the translatome level than at the transcriptome level. To achieve a precise evaluation of X:AA ratio, we took advantage of Ribo-seq data ##REF##33177713##[15]##, which allowed the direct measurement of translation ##REF##26465719##[29]##. Because only the liver samples were from males and females, we first analyzed the X:AA ratio in the liver in males and females separately and observed that X-linked genes greatly resembled autosomal genes at the translatome level in both males and females (<xref rid=\"s0105\" ref-type=\"sec\">Figure S4</xref>) (<italic>P</italic> &gt; 0.05, Wilcoxon test). We then mixed liver samples from males and females, and found similar patterns in the brain (X:AA = 1.13), testis (X:AA = 0.88), and liver (X:AA = 0.97) (##FIG##0##Figure 1##C, <xref rid=\"s0105\" ref-type=\"sec\">Figure S5</xref>). Notably, in the liver, no up-regulation of X-linked genes has been detected at the transcriptome level using multiple RNA-seq datasets in humans and mice (##FIG##0##Figure 1##A). We speculated that the X:AA ratio in a certain tissue that deviated from 1 at the transcriptome level could be restored to 1 at other gene regulatory levels due to extensive buffering at different expression levels ##REF##33177713##[15]##, ##REF##24318729##[30]##, ##REF##33310749##[31]##, and <italic>vice versa</italic>.</p>", "<p id=\"p0025\">We further incorporated mass spectrometry proteome data across 29 tissues, which would allow a more direct measurement of protein abundance, to verify the results from Ribo-seq data ##REF##30777892##[23]##. The X:AA ratio of protein concentrations between matched bins (see Materials and methods) were approximately 0.75 across all tissues and reached 1 in the brain, endometrium, placenta, and testis (##FIG##0##Figure 1##D, <xref rid=\"s0105\" ref-type=\"sec\">Figure S6</xref>). Interestingly, we also noticed that in the pancreas, the X:AA ratio was about 1 at the proteome level, whereas the lowest X:AA ratio was observed at the transcriptome level from different datasets, and such inconsistency might be attributed to poor correlation between transcriptome and proteome data ##REF##30777892##[23]##. Most of the tissues (55%) showed X:AA ≈ 1 at the proteome level (including adrenal gland, appendix, brain, colon, endometrium, esophagus, fallopian tube, heart, lung, pancreas, placenta, prostate, smooth muscle, spleen, testis, and thyroid), despite incomplete up-regulation in some tissues, which reconfirmed the up-regulated expression of X chromosome.</p>", "<title>Dynamic developmental X:AA ratios in mammals</title>", "<p id=\"p0030\">To determine whether X:AA ratio was dependent on development stages, we measured X:AA ratio in different development stages from early organogenesis to adulthood across seven major tissues (brain, cerebellum, heart, kidney, liver, ovary, and testis) in humans and mice using the recently published RNA-seq dataset ##REF##31243369##[21]##. To avoid possible biased evaluation of the X:AA ratio because “filter-by-expression” strategy was only limited to complete dosage compensation model ##REF##33579636##[32]##, we selected a series of expression cutoffs from 0 to 1 based on fragments per kilobase million (FPKM) with an additional group retaining all genes as the control. The “zero” cutoff (FPKM, 0) means that only the genes with FPKM &gt; 0 were retained for further analysis. Interestingly, the X:AA ratio showed developmental dynamics in a tissue-specific manner in both humans and mice. In neural tissues (brain and cerebellum), we found a noticeable positive correlation between the X:AA ratio and development stage (rho = 0.86, <italic>P</italic> = 2.49 × 10<sup>−7</sup>) (##FIG##1##Figure 2##A, <xref rid=\"s0105\" ref-type=\"sec\">Figures S7 and S8</xref>). This correlation was insensitive to different expression thresholds. Conversely, in the remaining tissues, the X:AA ratio was negatively correlated with development stage (##FIG##1##Figure 2##B and C). In addition, in the liver, the X:AA ratio was close to 1 at early development stage and decreased to 0.5 with development in humans (rho = −0.51, <italic>P</italic> = 0.012) and mice (rho = −0.96, <italic>P</italic> = 0) (##FIG##1##Figure 2##B, <xref rid=\"s0105\" ref-type=\"sec\">Figure S8</xref>D). As for reproductive tissues, the human ovary samples only spanned the developmental stages from 4 weeks post-conception (wpc) to 18 wpc. During these stages, the X:AA ratio in the testis and ovary was similar, ranging from 1 to 1.5 (##FIG##1##Figure 2##C and D, <xref rid=\"s0105\" ref-type=\"sec\">Figure S8</xref>F and G), whereas the X:AA ratio dropped to 0.5 after reproductive maturity, presumably due to the low expression of X-linked genes in numerous germ cells after meiotic sex chromosome inactivation. Consistently, one previous study has reported that a low X:AA ratio might be essential for male sperm cell development ##REF##29756331##[33]##. In mice, the X:AA ratio in the testis was comparable to that in ovary (about 1) before 2 weeks post-born (wpb) and dropped to 0.5 at 4 wpb and 9 wpb, whereas the X:AA ratio was still near 1 in ovary at 4 wpb and 9 wpb. One previous work observed an up-regulation of X-linked genes in a specific cell type such as mouse oocytes before reproductive maturity ##REF##26370379##[14]##, which showed a developmental stage-dependent X:AA ratio. The ovary tissue contained many cell types, including germ cells, immune-related cells, and other somatic cells ##REF##32123174##[34]##. The oocytes harbored two active X chromosomes and exhibited a low X:AA ratio (&lt; 1) at mature stage ##REF##26370379##[14]##. Meanwhile, the X:AA ratio in the mature ovary, which reflected the mean value of all types of ovary cells rather than that of oocytes alone, was near 1 in our data. Because the testis is different from other tissues including the ovary in multiple aspects such as cell composition and chromatin state, the developmental pattern of the X:AA ratio in the testis could not be identical to that in any other tissues.</p>", "<p id=\"p0035\">The separate analysis of the male somatic tissue samples and female ones indicated a similar dynamic pattern of the X:AA ratio between males and females (<xref rid=\"s0105\" ref-type=\"sec\">Figure S9</xref>). Because female tissue samples (92, 36%) were much less than male samples (162, 64%), the correlation between the X:AA ratio and development stage was not significant in females (Spearman correlation, <italic>P</italic> &gt; 0.05). We also examined the expression dynamics of <italic>Xist</italic> during development and observed no clear pattern (<xref rid=\"s0105\" ref-type=\"sec\">Figure S10</xref>).</p>", "<p id=\"p0040\">In this study, we also found that the X chromosome was doubly up-regulated (X:AA ratio = 1) at an early stage across all tissues, suggesting a high similarity in development regulation at the earliest stage (4 wpc) and increasing molecular and morphological differences across different tissues during development ##REF##31243369##[21]##, ##REF##31243368##[35]##. Considering the effects of development stages, they should be taken into account when we examined the expression of X-linked genes.</p>", "<p id=\"p0045\">To reveal the reason for the dynamics of the X:AA ratio, we identified the genes (autosomal and X-linked genes) whose expression was correlated with development stage (Spearman correlation, rho &gt; 0 for positive correlation, rho &lt; 0 for negative correlation) using a previously described method ##REF##32669715##[22]##. The expression levels of stage-positively-correlated genes (rho &gt; 0.8, <italic>P</italic> &lt; 0.05) and stage-negatively-correlated genes (rho &lt; −0.8, <italic>P</italic> &lt; 0.05) in the brain, liver, and testis are presented in ##FIG##1##Figure 2##E–J. Gene Ontology (GO) analysis showed that these stage-correlated genes were involved in biological processes of corresponding tissues. In the brain, the stage-positively-correlated genes were enriched in vesicle-mediated neurotransmitter transport and synapse signal release pathways; in the liver, they were enriched in fatty acid and organic acid metabolic pathways; and in the testis, they were enriched in spermatid development, differentiation, and fertilization pathways (<xref rid=\"s0105\" ref-type=\"sec\">Table S1</xref>), suggesting that the function demand and expression timing during development led to the dynamic X:AA ratio. We also used other correlation thresholds (from 0.5 to 0.9) to screen stage-correlated genes. In the brain, as the thresholds became more stringent, more X-linked stage-positively-correlated genes were found than autosomal stage-positively-correlated genes, but stage-negatively-correlated genes exhibited an opposite pattern (##FIG##1##Figure 2##K), suggesting that more X-linked stage-positively-correlated genes and less stage-negatively-correlated genes might result in a higher X:AA ratio during development. The aforementioned speculation was confirmed by our data that the less stage-positively-correlated genes and more stage-negatively-correlated genes were enriched on the X chromosome in the liver and testis (##FIG##1##Figure 2##L and M). Our results revealed that development stage-correlated genes contributed to the dynamics of the X:AA ratio.</p>", "<p id=\"p0050\">To further analyze the expression dynamics of X-linked genes, we calculated the expression ratio of X-linked genes to autosomal housekeeping genes (AHKGs). <xref rid=\"s0105\" ref-type=\"sec\">Figure S11</xref> shows a stable expression level of housekeeping genes (HKGs) during development. Because the HKGs were constitutively and steadily expressed, the expression ratio of X-linked genes to AHKGs would follow the expression pattern of X-linked genes. As expected, the ratio of X-linked genes to AHKGs (X:AHKG ratio) in the brain was still positively correlated with development stages (##FIG##1##Figure 2##N), suggesting the increased expression level of X-linked genes during development. Further, we observed that the ratio of X-linked housekeeping gene (XHKGs) to AHKGs (XHKG:AHKG ratio) remained unchanged during development, instead of dynamic (##FIG##1##Figure 2##O), confirming again that the aforementioned pattern was attributed to stage-correlated genes.</p>", "<title>Expression maintenance of X-linked genes in mammalian evolution</title>", "<p id=\"p0055\">As Ohno has stressed, the expression of the current X chromosome should be doubled (X:<underline>XX</underline> ≈ 1) to maintain the same expression level as ancestral autosomes evolved into sex chromosomes (proto-X/Y, proto-X hereafter marked as <underline>XX</underline>). Ohno’s hypothesis of X:<underline>XX</underline> ≈ 1 would be equivalent to X:AA ≈ 1 under two assumptions: ##FORMU##0##(1)## gene expression on the current autosomes (AA) is comparable to that on the proto-autosomes (<underline>AA</underline>) (AA:<underline>AA</underline> ≈ 1); (2) gene expression on the proto-X is comparable to that on the proto-autosomes (<underline>XX</underline>:<underline>AA</underline> ≈ 1) ##REF##22753487##[18]##. To directly test dosage compensation and determine whether the dynamic X:AA ratio was responsible for the dynamic dosage compensation, we investigated the expression ratio of X-linked genes in humans (X) to the autosomal orthologous genes (<underline>XX</underline>, 1:1 orthologs) in opossums, platypuses, and chickens (X:<underline>XX</underline>) (##FIG##2##Figure 3##A; see Materials and methods) ##REF##22753487##[18]##. The phylogenetic distance of the three species from humans was as follows: opossums &lt; platypuses &lt; chickens. The expression level of opossum <underline>XX</underline> (<italic>R</italic> = 0.50–0.67 at the transcriptome level, and <italic>R</italic> = 0.30–0.67 at the translatome level) was more similar to that of human X than platypuses (<italic>R</italic> = 0.45–0.53 at the transcriptome level, and <italic>R</italic> = 0.30–0.71 at the translatome level) and chickens (<italic>R</italic> = 0.11–0.46 at the transcriptome level, and <italic>R</italic> = 0.17–0.46 at the translatome level) (<xref rid=\"s0105\" ref-type=\"sec\">Figures S12 and S13</xref>), suggesting that the expression of autosomal orthologs on the closer relatives could better represent that of human X-linked genes. At the transcriptome level, the X:<underline>XX</underline> ratio was 0.57 for humans:chickens on average (0.66 in the brain, 0.57 in the liver, and 0.49 in the testis), and 0.62 for humans:platypuses (0.61 in the brain, 0.74 in the liver, 0.5 in the testis), and 0.78 for humans:opossums (0.82 in the brain, 0.77 in the liver, 0.75 in the testis) (##FIG##2##Figure 3##B–D). The comparison of humans with opossums (the closest relative of humans among the three species) resulted in the X:<underline>XX</underline> ratio closest to 1. For all the three species, X:<underline>XX</underline> ratio was closer to 1 at the translatome level than at the transcriptome level across all the three tissues (Chickens, 0.83, 0.78, and 0.85; Platypuses, 0.82, 0.77, and 0.90; Opossums, 0.92, 0.86, and 0.92, in the brain, liver, and testis, respectively) (##FIG##2##Figure 3##E–G). These observations indicated that the current X chromosome was up-regulated about two folds to compensate the decay of Y chromosome in a tissue-independent manner, and that the dynamic X:AA ratios across tissues was not due to dosage compensation.</p>", "<p id=\"p0060\">Using chicken and opossum <underline>XX</underline> as control, we further addressed whether the developmental dynamics of current X chromosome was conferred by dosage compensation based on the X:<underline>XX</underline> ratio at the Carnegie-matched stages ##REF##31243369##[21]##. Unlike the X:AA ratio, the X:<underline>XX</underline> ratio was not stage-related (##FIG##2##Figure 3##H–K, <xref rid=\"s0105\" ref-type=\"sec\">Figure S14</xref>), confirming that the dynamic X:AA ratios across developmental stages did not result from dosage compensation.</p>", "<title>High tissue and stage specificity of gene expression on the X chromosome may be responsible for dynamics of X:AA ratios</title>", "<p id=\"p0065\">The inconsistency in change trend between the X:<underline>XX</underline> ratio (stable) and X:AA ratio (dynamic) could have resulted from the different gene contents and expression preferences of the X chromosome due to its monosomy ##REF##18929654##[36]##, ##REF##21301475##[37]##, ##REF##14739461##[38]##. We compared the expression patterns of X-linked and autosomal genes in mammals using RNA-seq data across seven tissues (brain, cerebellum, heart, kidney, liver, ovary, and testis) from early organogenesis to adulthood ##REF##31243369##[21]##. We found that about 34% of all X-linked genes showed a higher expression level in the testis than in other tissues in humans and mice, followed by brain and cerebellum (##FIG##3##Figure 4##A), which was consistent with previous findings ##REF##24733023##[39]##, ##REF##33171144##[40]##. Such tendency was robust when the extended 32 tissues were investigated, and the X chromosome favored testis with 26.4% genes significantly enriched (Fisher’s exact test, <italic>P</italic> = 6 × 10<sup>−7</sup>) (##FIG##3##Figure 4##B). These RNA-seq results were in accordance with those from mass spectrometry (<xref rid=\"s0105\" ref-type=\"sec\">Figure S15</xref>A). The expression of X-linked genes exhibited higher tissue and developmental-stage specificity than that of autosomal genes across all tissues in humans and mice (##FIG##3##Figure 4##C and D, <xref rid=\"s0105\" ref-type=\"sec\">Figure S15</xref>B and C). A similar phenomenon was also observed in rhesus, rabbits, rats, and opossums (<xref rid=\"s0105\" ref-type=\"sec\">Figure S16</xref>), demonstrating the preference of dynamic expression of the X chromosome in mammals.</p>", "<p id=\"p0070\">To explain the high tissue and developmental-stage specificity of X-linked genes, we quantitatively investigated the epigenetic modifications contributing to selective expression of genes across human tissues based on Roadmap Epigenomics Project data ##REF##31822674##[41]##, ##REF##31501771##[42]##. We analyzed the dynamics of each promoter to obtain their epigenetic profile. The results indicated that the median number of epigenetic states displayed by X-linked genes was 11 across all epigenomes, which was higher than that by autosomal ones (with median of 10) (Wilcoxon test, <italic>P</italic> &lt; 0.05), supporting that X chromosome acquires variable gene regulation (##FIG##3##Figure 4##E). We further calculated the total proportion of promoters annotated with each epigenetic state across all Roadmap epigenomics. Half of X-linked gene promoters were in the quiescent state (15_Quies) (##FIG##3##Figure 4##F, <xref rid=\"s0105\" ref-type=\"sec\">Figure S17</xref>), which represents the lack of five constituent histone modifications (H3K4me3, H3K4me1, H3K36me3, H3K9me3, and H3K27me3), followed by active transcription start site (TSS) state and regulatory chromHMM state (1_TssA, 2_TssAFlnk, 3_TxFlnk, 6_EnhG, and 7_Enh). More X-linked genes in the quiescent state than autosomal ones suggested an enrichment of more unexpressed genes. As expected, X chromosome had a significantly higher percentage of unexpressed genes (FPKM &lt; 1) than autosomes in humans (∼ 1.22-fold, <italic>P</italic> &lt; 2.22 × 10<sup>−16</sup>) and mice (∼ 1.26-fold, <italic>P</italic> &lt; 2.22 × 10<sup>−16</sup>) (##FIG##3##Figure 4##G, <xref rid=\"s0105\" ref-type=\"sec\">Figure S18</xref>A). The higher percentage of unexpressed genes was enriched on the X chromosome than on autosomes when a less strict cutoff (FPKM = 0) was used in humans (∼ 1.7-fold) and mice (∼ 1.58-fold) (<xref rid=\"s0105\" ref-type=\"sec\">Figure S18</xref>B and C). Moreover, we observed the higher percentage of unexpressed genes on the X chromosome than that on autosomes in different tissues (<xref rid=\"s0105\" ref-type=\"sec\">Figures S19–S22</xref>). Specifically, the X chromosome exhibited the highest percentage of unexpressed genes in the liver (58% in humans, 64% in mice). The lowest percentage of unexpressed genes was found in the gonad and brain, which was in line with the previous reports on the brain and testis preference of the X chromosome ##REF##14739461##[38]##, ##REF##24733023##[39]##. We also noted that the percentage of unexpressed genes was as low in the ovary as in the testis, which agreed with previous results that the genes related to spermatogenesis and oogenesis were enriched on the X chromosome ##REF##29756331##[33]##, ##REF##29544636##[43]##. Because only the expressed genes need to be compensated, these genes with high tissue and stage specificity were paid special attention to when we tested Ohno’s hypothesis.</p>", "<p id=\"p0075\">We further determined whether the dynamic X:AA ratio resulted from the different tissue/stage specificity of the gene expression on the X chromosome and autosomes. As mentioned above, 32 human tissues showed the varied X:AA ratios. We identified approximately 290 (in pancreas) to 4180 (in testis) tissue-specific genes from 32 human tissues (see Materials and methods). The X:AA ratio in a certain tissue was positively correlated with the percentage of X-linked tissue-specific genes in the corresponding tissue (##FIG##3##Figure 4##H). After further dividing the tissues into the X:AA ≈ 0.5 group (pancreas, saliva secreting gland, liver, and skeletal muscle tissue) and the X:AA ≈ 1 group (the rest 28 tissues from 32 tissues), we found that tissues in the X:AA ≈ 1 group had more tissue-specific genes (<xref rid=\"s0105\" ref-type=\"sec\">Figure S23</xref>), thus validating that X-linked tissue-specific genes contributed to the X:AA ratio in the corresponding tissue.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0080\">As Ohno hypothesized, therian X-linked genes could be up-regulated two folds to counteract the degeneration of Y homologs and to reach the same expression levels of ancestral X-linked genes ##UREF##0##[6]##. Because of the unavailability of ancestral X chromosome, Ohno’s hypothesis is often indirectly tested by comparing the gene expression level between X and AA under the assumption that the gene expression levels are comparable among <underline>XX</underline>, <underline>AA</underline>, and AA. Since the first empirical test was conducted, however, there has been an ongoing debate on the validity of Ohno’s hypothesis for fifteen years ##REF##16341221##[7]##, ##REF##22120049##[9]##, ##REF##22120048##[12]##, ##REF##31582851##[13]##, ##REF##26370379##[14]##, ##REF##33177713##[15]##, ##REF##30642250##[16]##, ##REF##27593371##[17]##, ##REF##22753487##[18]##, ##REF##25697342##[44]##, ##REF##21102464##[45]##, ##REF##22615540##[46]##. These previous studies tended to be limited to RNA-seq or only focus on a subset of tissue expression data. In this study, in combination with GTEx and the encyclopedia of DNA elements (ENCODE) project data ##REF##32913098##[25]##, ##REF##25582907##[26]##, we dramatically expanded the sequencing datasets ##REF##30777892##[23]## and provided a comprehensive profile of the X:AA ratio across tissues, developmental stages, and species. Moreover, despite the random errors of RNA-seq and the poor correlation between mRNA concentration and protein abundance ##REF##30777892##[23]##, we still found the comparable gene expression levels between the X chromosome and autosomes at the translatome and proteome levels, suggesting the up-regulation of the current X chromosome at three expression levels. It should be noted that previous studies did not detect dosage compensation at the proteome level ##REF##22753487##[18]##, ##REF##25697342##[44]##, which might be due to the limited resolution of mass spectrometry ##REF##33177713##[15]## and the difference in cell biology between cell line and tissue.</p>", "<p id=\"p0085\">Another limitation of previous works lies in that merely high-throughput data of adult tissues have been investigated, whereas the data of adult even aged tissues alone could not provide a full picture of X:AA ratio across the entire life span. Additionally, because all tissues are developed from a single zygote, it is hard to determine when and how different X:AA ratios are produced in these adult tissues. To fill this gap, we applied the published developmental transcriptome data ranging from early organogenesis to adulthood, and focused on seven tissues representing three levels: liver (endoderm); kidney, heart, ovary, and testis (mesoderm); and brain and cerebellum (ectoderm) in humans and mice. Our results revealed a dynamic X:AA ratio during development, and the difference in chromosomal distribution of stage-correlated genes contributed to the diverse dynamics of the X:AA ratio among three germ layers. We also noted that the X chromosome was fully up-regulated at the earliest development stage across seven tissues, but the X:AA ratio gradually differed during development, demonstrating the high similarity of expression programs at the early stage and increasing discrepancy during development ##REF##31243369##[21]##.</p>", "<p id=\"p0090\">One limitation of this study is that only bulk RNA-seq data were used for testing Ohno’s hypothesis. Recently emerging single-cell technology will provide a new insight into the transcriptional status at single-cell resolution ##REF##32033589##[47]##. Therefore, future studies are suggested to investigate the up-regulation of X-linked genes and the heterogeneity of the X:AA ratio at the single-cell level.</p>", "<p id=\"p0095\">The aforementioned tests of Ohno’s hypothesis based on the X:AA ratio are indirect. To directly examine dosage compensation, we calculated the X:<underline>XX</underline> ratio at the transcriptome and translatome levels. Due to the extensive buffering between the expression levels, the expression difference between species is smaller at the translatome level than at the transcriptome level ##REF##33177713##[15]##, thus resulting in a more robust evaluation of dosage compensation. Furthermore, the Carnegie-matched stage comparison of humans and chickens or opossums showed a constant X:<underline>XX</underline> ratio value close to 1, in contrast with the dynamic pattern of the X:AA ratio. These observations in combination with the expression preference of X-linked tissue-specific genes (##FIG##3##Figure 4##) suggest that dynamic changes of the X:AA ratio might be attributed to the expression of certain tissue-specific genes in specific tissues, finally resulting in a deviation of the X:AA ratio from 1.</p>", "<p id=\"p0100\">One previous study claimed that gene expression of the X chromosome was halved, thereby refuting Ohno’s hypothesis ##REF##22753487##[18]##. Repeating their analysis using the same data ##REF##22012392##[48]##, we found that the human X chromosome harbored more unexpressed genes than human autosomes, chicken <underline>XX</underline>, and chicken <underline>AA</underline>, whereas no difference was observed between chicken <underline>XX</underline> and chicken <underline>AA</underline> (<xref rid=\"s0105\" ref-type=\"sec\">Figure S24</xref>). When extremely weakly expressed genes (the genes with FPKM &lt; 0.01) or even unexpressed genes were taken into account, the expression level of the human X chromosome was significantly and specifically underestimated, thus resulting in the decreased X:<underline>XX</underline> ratio. This also aroused another debate over whether all the genes or merely the expressed genes should be investigated. In this study, we revealed that compared with autosomal genes, X-linked genes exhibited higher tissue and developmental-stage specificity and were enriched in quiescent states (##FIG##3##Figure 4##), which resulted in more unexpressed X-linked genes in a certain tissue at a certain development stage. We suggest that the expressed genes under a frequently used threshold (FPKM &gt; 1) should be considered for a “fair comparison”, because only expressed genes need to be compensated. It should be noted that abundant non-coding RNAs exist in mammalian tissues, especially in the brain and testis, and they exert important regulatory functions ##REF##29887379##[49]##, ##REF##33649327##[50]##, ##REF##24463510##[51]##. Considering the high expression variability and number discrepancy of the non-coding RNAs in the different datasets, we only used protein-coding genes to assess X:AA and X:<underline>XX</underline> ratios, as described in previous studies ##REF##16341221##[7]##, ##REF##22019781##[11]##, ##REF##31582851##[13]##, ##REF##27593371##[17]##, ##REF##22753487##[18]##, ##REF##33579636##[32]##, which makes it easier to compare our results with previous reports. The improvement of non-coding RNA annotation in humans and other species and the increase in the knowledge of their functions will further promote the test of Ohno’s hypothesis in the future.</p>" ]
[ "<title>Conclusion</title>", "<p id=\"p0105\">In summary, we systematically tested dosage compensation in five mammalian species and confirmed the up-regulation of X-linked genes at three expression levels across multiple tissues. Based on developmental transcriptome data, we found a dynamic spatial-temporal X:AA ratio and a stable dosage compensation (X:<underline>XX</underline> ratio). Finally, we revealed the differences in the tissue/stage specificity and the epigenetic regulation between X-linked and autosomal genes, and it was these differences that resulted in the discrepancy of these two expression ratios. Overall, our work supports Ohno’s hypothesis and reveals gene expression balance within a genome.</p>" ]
[ "<p>In the evolutionary model of <bold>dosage compensation</bold>, per-allele expression level of the <bold>X chromosome</bold> has been proposed to have twofold up-regulation to compensate its dose reduction in males (XY) compared to females (XX). However, the expression regulation of X-linked genes is still controversial, and comprehensive evaluations are still lacking. By integrating multi-omics datasets in <bold>mammals</bold>, we investigated the expression ratios including X to autosomes (X:AA ratio) and X to orthologs (X:<underline>XX</underline> ratio) at the transcriptome, translatome, and proteome levels. We revealed a dynamic spatial-temporal X:AA ratio during development in humans and mice. Meanwhile, by tracing the <bold>evolution</bold> of orthologous gene expression in chickens, platypuses, and opossums, we found a stable expression ratio of X-linked genes in humans to their autosomal orthologs in other species (X:<underline>XX</underline> ≈ 1) across tissues and developmental stages, demonstrating stable dosage compensation in mammals. We also found that different epigenetic regulations contributed to the high tissue specificity and stage specificity of X-linked gene expression, thus affecting X:AA ratios. It could be concluded that the dynamics of X:AA ratios were attributed to the different gene contents and expression preferences of the X chromosome, rather than the stable dosage compensation.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Zhongming Zhao</p>" ]
[ "<title>Code availability</title>", "<p id=\"p0150\">All custom computer scripts used in this study are available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/biocode/tools/BT007244/releases/1.0\" id=\"ir015\">https://ngdc.cncb.ac.cn/biocode/tools/BT007244/releases/1.0</ext-link> and <ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/Shengqian95/DosageCompensation\" id=\"ir020\">https://github.com/Shengqian95/DosageCompensation</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0155\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0160\"><bold>Sheng Hu Qian:</bold> Investigation, Data curation, Formal analysis, Validation, Visualization, Writing – original draft, Writing – review &amp; editing. <bold>Yu-Li Xiong:</bold> Investigation, Visualization. <bold>Lu Chen:</bold> Methodology. <bold>Ying-Jie Geng:</bold> Visualization. <bold>Xiao-Man Tang:</bold> Data curation. <bold>Zhen-Xia Chen:</bold> Conceptualization, Resources, Writing – original draft, Writing – review &amp; editing, Supervision, Funding acquisition. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0175\">The following are the Supplementary material to this article:</p>", "<p id=\"p0180\">\n\n</p>", "<p id=\"p0185\">\n\n</p>", "<p id=\"p0190\">\n\n</p>", "<p id=\"p0195\">\n\n</p>", "<p id=\"p0200\">\n\n</p>", "<p id=\"p0205\">\n\n</p>", "<p id=\"p0210\">\n\n</p>", "<p id=\"p0215\">\n\n</p>", "<p id=\"p0220\">\n\n</p>", "<p id=\"p0225\">\n\n</p>", "<p id=\"p0230\">\n\n</p>", "<p id=\"p0235\">\n\n</p>", "<p id=\"p0240\">\n\n</p>", "<p id=\"p0245\">\n\n</p>", "<p id=\"p0250\">\n\n</p>", "<p id=\"p0255\">\n\n</p>", "<p id=\"p0260\">\n\n</p>", "<p id=\"p0265\">\n\n</p>", "<p id=\"p0270\">\n\n</p>", "<p id=\"p0275\">\n\n</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0165\">We thank Asifa Akhtar and Yidan Sun from Max Planck Institute of Immunobiology and Epigenetics for valuable comments. We also thank all members in our laboratory for their helpful discussions. Great gratitude goes to Ping Liu from Huazhong Agriculture University for her work at English editing. This work was supported by the <funding-source id=\"gp005\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100001809</institution-id><institution>National Natural Science Foundation of China</institution></institution-wrap></funding-source> (Grant No. 31871305), the <funding-source id=\"gp010\">Opening Foundation of State Key Laboratory of Freshwater Ecology and Biotechnology, China</funding-source> (Grant No. 2020FB08), the <funding-source id=\"gp015\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100012226</institution-id><institution>Fundamental Research Funds for the Central Universities, China</institution></institution-wrap></funding-source> (Grant Nos. 2662018PY021 and 2662019PY003), and the <funding-source id=\"gp020\">Huazhong Agricultural University Scientific &amp; Technological Self-innovation Foundation, China</funding-source> (Grant No. 2016RC011).</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Expression ratio of X:AA across mammalian anatomies</bold></p><p><bold>A.</bold> X:AA ratios across 32 adult human tissues. Black points indicate mean value and error bars represent 90% confidence interval. Public RNA-seq data are obtained from the article by Wang and his colleagues ##REF##30777892##[23]##. Appendix, esophagus, gallbladder, prostate, rectum, small intestine, testis, and urinary bladder are from male donors. Adrenal gland, brain, duodenum, endometrium, fallopian tube, fat, heart, lymph node, ovary, pancreas, salivary gland, smooth muscle, spleen, and thyroid are from female donors. The genders of donors of remaining tissues are unknown. <bold>B.</bold> X:AA ratios in humans (50 tissues), rhesus (<italic>Macaca mulatta</italic>, 7 tissues), mice (<italic>Mus musculus</italic>, 22 tissues), rats (<italic>Rattus norvegicus</italic>, 7 tissues), and rabbits (<italic>Oryctolagus cuniculus</italic>, 7 tissues). Human female reproductive tissues, including ovary, endometrium, vagina, fallopian tube, uterus, uterine cervix, and ectocervix, are attached. Data are integrated from GTEx ##REF##32913098##[25]##, ENCODE ##REF##25582907##[26]##, and the article by Cardoso-Moreira and his colleagues ##REF##31243369##[21]##. <bold>C.</bold> Expression distributions of X-linked and autosomal genes in human brain, liver, and testis at the translatome level. Ribo-seq data are obtained from the article by Wang and his colleagues ##REF##33177713##[15]##, including three organs (brain, liver, and testis) in humans. <bold>D.</bold> Comparison of protein abundances between X-linked genes and autosomal genes in human brain, liver, and testis. The protein abundances of X-linked and autosomal genes are separately divided into 100 expression bins, and top 25 bins are used for analysis. Human proteome data are obtained from the article by Wang and his colleagues ##REF##30777892##[23]##. Sample sizes of the brain, liver, and testis are 1, 4, and 1, respectively. Diamonds represent the X:AA ratio in each bin. n.s., no significant difference (Wilcoxon test). X, X chromosome; A, autosome; AA, a pair of autosomes; X:AA ratio, the expression ratio of X to autosomes; RNA-seq, RNA sequencing; Ribo-seq, ribosome sequencing; GTEx, Genotype Tissue Expression; ENCODE, the encyclopedia of DNA elements; FPKM, fragments per kilobase million; iBAQ, intensity-based absolute quantification.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Dynamics of X:AA ratio during development</bold></p><p><bold>A.–D.</bold> X:AA ratios in the brain (A), liver (B), testis (C), and ovary (D) in humans. The “zero” cutoff (FPKM, 0) means that only the genes with FPKM &gt; 0 are retained for further analysis. <bold>E.–G.</bold> Expression profile of stage-positively-correlated genes (rho &gt; 0.8) in the brain (E), liver (F), and testis (G). <bold>H.–J.</bold> Expression profile of stage-negatively-correlated genes (rho &lt; −0.8) in the brain (H), liver (I), and testis (J). All genes (autosomal and X-linked genes) are used to identify stage-correlated genes. <bold>K.–M.</bold> Percentage of X-linked stage-correlated (positive and negative) genes under different correlation thresholds in the brain (K), liver (L), and testis (M). R &gt; 0.5 indicates that the absolute Spearman correlation coefficients (rho) are higher than 0.5. The gray dotted line indicates the average proportion of X-linked genes. Red color represents stage-positively-correlated genes, whereas blue color denotes stage-negatively-correlated genes. <bold>N.</bold> Expression ratio of X-linked genes to HKGs in the brain. Developmental transcriptome data are obtained from the article by Cardoso-Moreira and his colleagues ##REF##31243369##[21]##. The HKGs are identified by Eisenberg and Levanon ##REF##23810203##[53]## based on RNA-seq data, including 5701 AHKGs and 191 XHKGs. <bold>O.</bold> Expression ratio of XHKGs to AHKGs in the brain. wpc, weeks post-conception; dpb, days post-born; mpb, months post-born; ypb, years post-born; HKG, housekeeping gene; AHKG, autosomal housekeeping gene; XHKG, X-linked housekeeping gene.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Comparison of expression levels of orthologous genes between humans and outgroup species (chickens, platypuses, and opossums)</bold></p><p><bold>A.</bold> Origin and evolution of mammalian X chromosome. The genes on the human X chromosome are located on autosomes in chickens (birds, on chromosome 1 and 4) and platypuses (monotremes, on chromosome 6, 15, and 18). The X chromosome of opossums (marsupials) stands for the most ancient segment of the mammalian X chromosome (shown in red). <bold>B.</bold> Human X:chicken <underline>XX</underline> ratios in the brain, liver, and testis after the median of human AA:chicken <underline>AA</underline> ratios is normalized to 1 at the transcriptome level. <bold>C.</bold> Same as in (B) with platypuses as outgroup species. <bold>D.</bold> Same as in (B) with opossums as outgroup species. <bold>E.</bold> X:<underline>XX</underline> ratio at the translatome level with chickens as outgroup species. <bold>F.</bold> Same as in (E) with platypuses as outgroup species. <bold>G.</bold> Same as in (E) with opossums as outgroup species. RNA-seq and Ribo-seq data used are from the article by Wang and his colleagues ##REF##33177713##[15]##. <bold>H.</bold> Human X:chicken <underline>XX</underline> ratios at Carnegie-matched stages at the transcriptome level in the brain. <bold>I</bold><bold>.</bold> Human X:opossum <underline>XX</underline> ratios at Carnegie-matched stages at the transcriptome level in the brain. <bold>J.</bold> Human X:chicken <underline>XX</underline> ratios at Carnegie-matched stages at the transcriptome level in the liver. <bold>K.</bold> Human X:opossum <underline>XX</underline> ratios at Carnegie-matched stages at the transcriptome level in the liver. Developmental transcriptome data are obtained from the article by Cardoso-Moreira and his colleagues ##REF##31243369##[21]##. <underline>AA</underline>, genes in other species that are one-to-one orthologous to human autosomal genes; <underline>XX</underline>, genes in other species that are one-to-one orthologous to human X-linked genes; MYA, million years ago.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Expression pattern of the X chromosome and autosomes</bold></p><p><bold>A.</bold> Tissue distribution in which genes showed maximum expression at the transcriptome level. <bold>B.</bold> Same as in (A) with 32 extended tissues used (data from the article by Wang and his colleagues ##REF##30777892##[23]##). <bold>C.</bold> Tissue specificity of genes across all chromosomes. A theoretical box line (blue) generated by averaging tau values of autosomal genes. <bold>D.</bold> Developmental-stage specificity of gene expression. Developmental-stage specificity indicates the expression specificity of genes during development, and high specificity refers to the situation in which genes are only expressed at specific stages, low specificity refers to the case in which genes are broadly expressed at all development stages. <bold>E.</bold> Number of epigenetic states within each gene. ChromHmm data are obtained from Roadmap Epigenomics Project ##REF##31501771##[42]##, including 127 consolidated epigenomes. <bold>F.</bold> Percentage of bases within genes on each chromosome annotated with each epigenetic state, summed of all epigenomes. <bold>G.</bold> Percentage of unexpressed genes under the expression cutoff of FPKM = 1 in humans. The genes with FPKM ≤ cutoff are defined as unexpressed. Each dot represents the corresponding percentage of unexpressed genes on the autosomes or X chromosome. The two dots linked by one line are from the same tissue. <bold>H.</bold> Correlation between the X:AA ratio and the percentage of X-linked tissue-specific genes. A point indicates a tissue. A total of 32 tissues are used. *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; ***, <italic>P</italic> &lt; 0.001; n.s., no significant difference (Wilcoxon test).</p></caption></fig>" ]
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[ "<disp-formula id=\"e0005\"><label>(1)</label><mml:math id=\"M1\" altimg=\"si1.svg\"><mml:mrow><mml:mi mathvariant=\"italic\">tau</mml:mi><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:msubsup><mml:mrow><mml:mo>∑</mml:mo></mml:mrow><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mrow><mml:mi>n</mml:mi></mml:mrow></mml:msubsup><mml:mrow><mml:mo>(</mml:mo><mml:mn>1</mml:mn><mml:mo>-</mml:mo><mml:msub><mml:mrow><mml:mi>a</mml:mi></mml:mrow><mml:mrow><mml:mi>i</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:mrow><mml:mrow><mml:mi>n</mml:mi><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:mfrac><mml:mo>;</mml:mo><mml:msub><mml:mrow><mml:mi>a</mml:mi></mml:mrow><mml:mrow><mml:mi>i</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:msub><mml:mrow><mml:mi>x</mml:mi></mml:mrow><mml:mrow><mml:mi>i</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:munder><mml:mrow><mml:mi>max</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mo>≤</mml:mo><mml:mi>i</mml:mi><mml:mo>≤</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:munder><mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mi>x</mml:mi></mml:mrow><mml:mrow><mml:mi>i</mml:mi></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:mfrac></mml:mrow></mml:math></disp-formula>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0130\"><caption><title>Supplementary Figure S1</title><p><bold>Expression level of Xist across human tissues</bold>. The classification of these tissues follows that in previous study ##REF##30777892##[23]##.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0125\"><caption><title>Supplementary Figure S2</title><p><bold>X:AA ratio across human tissues using GTEx RNA-seq data</bold> Error bar indicated 90% confidence interval. The type of human tissues (anatomy) follows GTEx project ##REF##32913098##[25]##.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0120\"><caption><title>Supplementary Figure S3</title><p><bold>X:AA ratio across mouse tissues using ENCODE RNA-seq data</bold> Error bar indicated 90% confidence interval. The type of mouse tissues follows ENCODE project ##REF##25582907##[26]##.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0115\"><caption><title>Supplementary Figure S4</title><p><bold>Expression level of genes at the translatome level in human males and females</bold> A. Expression distributions of X-linked genes and autosomal genes at the translatome level in human males and females. <bold>B.</bold> Cumulative frequencies of X-linked genes and autosomal genes in human males and females. A theoretical curve (dashed red line) is generated by doubling the expression level of X-linked genes. Wilcoxon test; n.s., no significant difference.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0110\"><caption><title>Supplementary Figure S5</title><p><bold>Cumulative frequencies of genes at the translatome level A.</bold> Cumulative frequencies of X-linked genes and autosomal genes in humans. A theoretical curve (dashed red line) is generated by doubling the expression level of X-linked genes. <bold>B.</bold> Expression distributions of X-linked genes and autosomal genes in mice. <bold>C.</bold> Cumulative frequencies of X-linked genes and autosomal genes in mice. Wilcoxon test; ***, <italic>P</italic> &lt; 0.001; n.s., no significant difference.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0105\"><caption><title>Supplementary Figure S6</title><p><bold>Comparison of protein abundance between X-linked genes and autosomal genes across human tissues</bold> The protein abundances of X-linked and autosomal genes are separately divided into 100 expression bins, and top 25 bins are used for analysis.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0100\"><caption><title>Supplementary Figure S7</title><p><bold>Dynamics of X:AA expression ratio during human development</bold> X:AA ratio in the human cerebellum <bold>(A)</bold>, heart <bold>(B)</bold>, and kidney <bold>(C)</bold> under various thresholds.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0095\"><caption><title>Supplementary Figure S8</title><p><bold>Dynamics of X:AA expression ratio during mouse development X:AA ratio in the mouse brain</bold><bold>(A)</bold>, cerebellum <bold>(B)</bold>, heart <bold>(C)</bold>, liver <bold>(D)</bold>, kidney <bold>(E)</bold>, testis <bold>(F)</bold>, and ovary <bold>(G)</bold>. The classification of these tissues follows that in previous study ##REF##31243369##[21]##. “e” means embryo, for example, e10 represents embryonic day 10.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0090\"><caption><title>Supplementary Figure S9</title><p><bold>Dynamics of X:AA expression ratio during human male and female development</bold> X:AA ratio in the human brain in males <bold>(A)</bold> and females <bold>(B)</bold> under various thresholds. X:AA ratio in the human cerebellum in males <bold>(C)</bold> and females <bold>(D)</bold> under various thresholds. X:AA ratio in the human heart in males <bold>(E)</bold> and females <bold>(F)</bold> under various thresholds. X:AA ratio in the human kidney in males <bold>(G)</bold> and females <bold>(H)</bold> under various thresholds. X:AA ratio in the human liver in males <bold>(I)</bold> and females <bold>(J)</bold> under various thresholds.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0085\"><caption><title>Supplementary Figure S10</title><p><bold>Expression dynamics of <italic>Xist</italic> during human development Expression level of <italic>Xist</italic> in the human brain</bold><bold>(A)</bold>, cerebellum <bold>(B)</bold>, heart <bold>(C)</bold>, liver <bold>(D)</bold>, kidney <bold>(E)</bold>, and ovary <bold>(F)</bold> during development.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0080\"><caption><title>Supplementary Figure S11</title><p><bold>Expression level of HKGs during human development</bold> Expression level of HKGs in the human brain <bold>(A)</bold>, cerebellum <bold>(B)</bold>, heart <bold>(C)</bold>, liver <bold>(D)</bold>, kidney <bold>(E)</bold>, testis <bold>(F)</bold>, and ovary <bold>(G)</bold> during development.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0075\"><caption><title>Supplementary Figure S12</title><p><bold>Expression correlation of one-to-one orthologous genes between humans and outgroup species at the transcriptome level</bold> Expression correlation of orthologous genes in the brain between humans and chickens <bold>(A)</bold>, between humans and platypuses <bold>(B)</bold>, and between humans and opossums <bold>(C)</bold>. Expression correlation of orthologous genes in the liver between humans and chickens <bold>(D)</bold>, between humans and platypuses <bold>(E)</bold>, and between humans and opossums <bold>(F)</bold>. Expression correlation of orthologous genes in the testis between humans and chickens <bold>(G)</bold>, between humans and platypuses <bold>(H)</bold>, and between humans and opossums <bold>(I)</bold>.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0070\"><caption><title>Supplementary Figure S13</title><p><bold>Expression correlation of one-to-one orthologous genes between humans and outgroup species at the translatome level</bold> Expression correlation of orthologous genes in the brain between humans and chickens <bold>(A)</bold>, between humans and platypuses <bold>(B)</bold>, and between humans and opossums <bold>(C)</bold>. Expression correlation of orthologous genes in the liver between humans and chickens <bold>(D)</bold>, between humans and platypuses <bold>(E)</bold>, and between humans and opossums <bold>(F)</bold>. Expression correlation of orthologous genes in the testis between humans and chickens <bold>(G)</bold>, between humans and platypuses <bold>(H)</bold>, and between humans and opossums <bold>(I)</bold>.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0065\"><caption><title>Supplementary Figure S14</title><p><bold>Comparison of humans X with outgroup species XX across testis development A.</bold> Comparison of human X with chicken XX in the testis. <bold>B.</bold> Comparison of human X with opossum XX in the testis.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Figure S15</title><p><bold>Expression pattern of the X chromosome and autosomes A.</bold> Tissue distribution in which genes showed maximum expression at proteome level using the extended 32 tissues. <bold>B.</bold> Tissue specificity of genes across all chromosomes. A theoretical box line (blue) generated by averaging tau values of autosomal genes. <bold>C.</bold> Developmental stage-specificity of genes expression. Developmental stage-specificity indicates the expression specificity of genes during development, and high specificity refers to the situation in which genes are only expressed at specific stages, low specificity refers to the case in which genes are broadly expressed at all development stages. Wilcoxon test; *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; ***, <italic>P</italic> &lt; 0.001; n.s., no significant difference.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Figure S16</title><p><bold>Tissue specificity and stage specificity across chromosomes A.</bold> Tissue specificity of genes across all chromosomes in rhesus. A theoretical box line (blue) generated by averaging tau values of autosomal genes. <bold>B.</bold> Developmental stage-specificity of genes expression in rhesus. Developmental stage-specificity indicates the expression specificity of genes during development, and high specificity refers to the situation in which genes are only expressed at specific stages, low specificity refers to the case in which genes are broadly expressed at all development stages. <bold>C.</bold> same as in A in rats. <bold>D.</bold> same as in B in rats. <bold>E.</bold> same as in A in rabbits. <bold>F.</bold> same as in B in rabbits. <bold>G.</bold> same as in A in opossums. <bold>H.</bold> same as in B in opossums. Wilcoxon test; *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; ***, <italic>P</italic> &lt; 0.001; n.s., no significant difference.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Figure S17</title><p><bold>Epigenetic chromHMM state across chromosomes A.</bold> Number of bases within promoters annotated with each chromHMM state, summed across all 127 epigenomes. <bold>B.</bold> Percentage of state overlapped with promoter of genes on the X and autosomes. <bold>C.</bold> Proportion of state annotated overlapped with promoter of genes on each chromosome annotated with each epigenetic state, summed across all epigenomes. The color legend is shared between the panels.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Figure S18</title><p><bold>Percentage of unexpressed genes under different expression cutoffs A.</bold> Percentage of unexpressed genes under the expression cutoff of FPKM = 1 in mice. <bold>B.</bold> Percentage of unexpressed genes under the expression cutoff of FPKM = 0 in humans. <bold>C.</bold> Percentage of unexpressed genes under the expression cutoff of FPKM = 0 in mice. The genes with FPKM = cutoff are defined as unexpressed. Each dot represents corresponding percentage of unexpressed genes on the autosomes or X chromosome. The two dots linked by one line are from the same tissue.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Figure S19</title><p><bold>Percentage of unexpressed genes under the expression cutoff of FPKM = 1 across human tissues</bold> Same as in Figure 4G but each tissue is shown individually. The genes with FPKM ≤ cutoff are defined as unexpressed. Each dot represents corresponding percentage of unexpressed genes on the autosomes or X chromosome. The two dots linked by one line are from the same tissue.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Figure S20</title><p><bold>Percentage of unexpressed genes under the expression cutoff of FPKM = 1 across</bold><bold>mouse tissues</bold> Same as in Figure S13A but each tissue is shown individually. The genes with FPKM ≤ cutoff are defined as unexpressed. Each dot represents corresponding percentage of unexpressed genes on the autosomes or X chromosome. The two dots linked by one line are from the same tissue.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Figure S21</title><p><bold>Percentage of unexpressed genes under the expression cutoff of FPKM = 0 across human tissues</bold> Same as in Figure S13B but each tissue is shown individually. The genes with FPKM = cutoff are defined as unexpressed. Each dot represents corresponding percentage of unexpressed genes on the autosomes or X chromosome. The two dots linked by one line are from the same tissue.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Figure S22</title><p><bold>Percentage of unexpressed genes under the expression cutoff of FPKM = 0 across</bold><bold>mouse tissues</bold> Same as in Figure S13C but each tissue is shown individually. The genes with FPKM = cutoff are defined as unexpressed. Each dot represents corresponding percentage of unexpressed genes on the autosomes or X chromosome. The two dots linked by one line are from the same tissue.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Figure S23</title><p><bold>Number of X-linked tissue-specific genes in X:AA ∼ 0.5 group and X:AA ∼ 1 group</bold> The Pancreas, saliva secreting gland, liver, and skeletal muscle are divided into X:AA ∼ 0.5 group, and the remaining tissues (shown in Figure 1A) are divided into X:AA ∼ 1 group. Wilcoxon test; **, <italic>P</italic> &lt; 0.01.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Figure S24</title><p><bold>Comparison of unexpressed genes between humans and chickens A.</bold> Percentage of unexpressed genes of human X, human AA, chicken XX, and chicken AA under the expression cutoff of FPKM = 1. The genes with FPKM ≤ cutoff are defined as unexpressed. <bold>B.</bold> Percentage of unexpressed genes of human X, human AA, chicken XX, and chicken AA under the expression cutoff of FPKM = 0. The three lines of significance analysis from top to bottom represent the comparison between human X and human AA, between chicken XX and chicken AA, and between human X and chicken XX, respectively. Fisher’s exact test; *, <italic>P</italic> &lt; 0.05; **, <italic>P</italic> &lt; 0.01; ***, <italic>P</italic> &lt; 0.001; n.s., no significant difference. The classification of these tissues follows that in previous study ##REF##22012392##[48]##.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S1</title><p><bold>GO analysis of stage-positively-correlated (rho &gt; 0.8) and stage- negatively-correlated (rho &lt; −0.8) genes in the brain, liver, and testis</bold>.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S2</title><p><bold>Information and resource of public data used in this study.</bold></p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e174\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0100\" fn-type=\"supplementary-material\"><p id=\"p0170\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.08.003\" id=\"ir025\">https://doi.org/10.1016/j.gpb.2022.08.003</ext-link>.</p></fn></fn-group>" ]
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[{"label": ["6"], "surname": ["Ohno"], "given-names": ["S."], "part-title": ["Sex chromosomes and sex-linked genes"], "year": ["1967"], "publisher-name": ["Springer"], "publisher-loc": ["Berlin"]}]
{ "acronym": [], "definition": [] }
62
CC BY
no
2024-01-14 23:41:59
Genomics Proteomics Bioinformatics. 2023 Jun 27; 21(3):589-600
oa_package/23/90/PMC10787176.tar.gz
PMC10787177
36183975
[ "<title>Introduction</title>", "<p id=\"p0005\">Cellular functions depend on myriads of protein–protein interaction (PPI) networks acting in consort and understanding cellular mechanisms on a large scale will require a relatively exhaustive catalog of PPIs. Hence, there have been major efforts to perform high-throughput experimental mapping of physical interactions between human proteins ##REF##28284537##[1]##. The methodologies involve binary interaction mapping using yeast 2-hybrid ##REF##25416956##[2]##, biochemical fractionation of soluble complexes combined with mass spectrometry (MS) ##REF##26344197##[3]##, and affinity purification mass spectrometry (AP-MS) ##REF##26186194##[4]##, ##REF##28514442##[5]##, ##REF##29568061##[6]##.</p>", "<p id=\"p0010\">In parallel to these experimental initiatives, computational tools were developed to help complete the human interactome ##REF##27074302##[7]##. Such tools are particularly useful for the identification of transient, cell type, or environmentally dependent interactions that escape current typical experimental protocols. Computational methods that can be used at large scales are created and/or validated using PPIs previously obtained experimentally ##REF##27074302##[7]##, ##REF##30886144##[8]##. Thus, although computational tools complement experimental approaches, the experimental detection of PPIs is key to building a comprehensive catalog of interactomes.</p>", "<p id=\"p0015\">The BioPlex network is the largest human proteome-scale interactome; initially, BioPlex 1.0 reporting 23,744 interactions among 7668 proteins was followed by BioPlex 2.0, which forms the basis of the current study, with 56,553 interactions reported involving 10,961 proteins. Recent pre-print BioPlex 3.0 reached 118,162 interactions among 14,586 proteins in HEK293T cells ##REF##26186194##[4]##, ##REF##28514442##[5]##, ##REF##33961781##[9]##. The enrichment of interactors of roughly half of currently annotated (or reference) human proteins allowed the authors to functionally contextualize poorly characterized proteins, identify communities of tight interconnectivity, and find associations between disease phenotypes and these protein groups. Here, a community represents a group of nodes in the network that are more closely associated with themselves than with any other nodes in the network as identified with an unsupervised clustering algorithm. In addition, pre-print BioPlex now provides a first draft of the interactome in HCT116 cells ##REF##33961781##[9]##.</p>", "<p id=\"p0020\">The experimental strategy behind BioPlex is based on the expression of each protein-coding open reading frame (ORF) present in the human ORFeome with an epitope tag, the affinity purification of the corresponding protein, and the confident identification of its specific protein interactors by MS. The identification of peptides and proteins in each protein complex is performed using the UniProt database. Hence, only proteins and alternative splicing-derived protein isoforms annotated in the UniProt database can be detected. Using this common approach, the human interactome is necessarily made up of proteins already annotated in the UniProt database, precluding the detection of novel unannotated proteins. Yet, beyond isoform-derived proteomic diversity, multiple recent discoveries point to a general phenomenon of translation events of non-canonical ORFs in both eukaryotes and prokaryotes, including small ORFs and alternative ORFs (altORFs) ##UREF##0##[10]##, ##REF##31504789##[11]##, ##REF##29140531##[12]##. Typically, small ORFs are between 10 and 100 codons, whereas altORFs can be larger than 100 codons. Here, we use the term altORFs for non-canonical ORFs independently of their size. On average, altORFs are ten times shorter than conventional annotated ORFs, but several thousands are longer than 100 codons ##REF##29083303##[13]##. altORFs encode alternative proteins (altProts) and are found both upstream (<italic>i.e.</italic>, 5′ UTR) and downstream (<italic>i.e.</italic>, 3′ UTR) of the reference coding sequence (CDS) as well as overlapping the reference CDS in a shifted reading frame within mRNAs (##FIG##0##Figure 1##A and B). Additionally, RNAs transcribed from long non-coding RNA genes and pseudogenes are systematically annotated as non-coding RNAs (ncRNAs); yet, they may also harbor altORFs and encode altProts ##REF##29083303##[13]##. Consequently, the fraction of multi-coding or polycistronic human genes and of protein-coding “pseudogenes” may have been largely underestimated. altORFs translation events are experimentally detected by ribosome profiling ##REF##31504789##[11]##, a method that detects initiating and/or elongating ribosomes at the transcriptome wide level ##UREF##1##[14]##. Alternatively, large-scale MS detection of altProts requires first the annotation of altORFs and then <italic>in silico</italic> translation of these altORFs to generate customized protein databases containing the sequences of the corresponding proteins ##REF##28627015##[15]##. This integrative approach, termed proteogenomics, has emerged as a new research field essential to better capture the coding potential and the diversity of the proteome ##REF##25357241##[16]##, ##REF##28456751##[17]##.</p>", "<p id=\"p0025\">The translation of altORFs genuinely expands the proteome, and proteogenomics approaches using customized protein databases allows for routine MS-based detection of altProts ##UREF##2##[18]##, ##REF##32780568##[19]##. In order to uncover altProts otherwise undetectable using the UniProt database we re-analyzed the raw MS data from the BioPlex 2.0 interactome with our OpenProt proteogenomics database.</p>", "<p id=\"p0030\">OpenProt contains the sequences of proteins predicted to be encoded by all ORFs larger than 30 codons in the human transcriptome. This large ORFeome includes ORFs encoding proteins annotated by NCBI RefSeq, Ensembl, and UniProt, termed here reference proteins (refProts). It also includes still unannotated ORFs that encode novel isoforms sharing a high degree of similarity with refProts from the same gene. Finally, the third category of ORFs, termed altORFs, potentially encode altProts and share no significant sequence similarity with a refProt from the same gene (##TAB##0##Table 1##). OpenProt is not limited by the three main assumptions that shape current annotations: (1) a single functional ORF in each mRNA, typically the longest ORF; (2) RNAs with ORFs shorter than 100 codons are typically annotated as ncRNAs; and (3) RNAs transcribed from genes annotated as pseudogenes are automatically annotated as ncRNAs. Thus, in addition to proteins present in NCBI RefSeq, Ensembl, and UniProt, OpenProt also contains the sequence for novel proteins, including novel isoforms and altProts ##REF##30299502##[20]##, ##REF##33179748##[21]##. Using OpenProt, we were able to detect and map altProts within complexes of known proteins which increased protein diversity by including a higher number of small proteins. In addition, the data confirmed the significant contribution of pseudogenes to protein networks with 117 out of 261 altProts encoded by genes annotated as pseudogenes. We also detected many interacting proteins encoded either by the same gene or by a pseudogene and its corresponding parental gene. In sum, this work improves our knowledge of both the coding potential of the human transcriptome and the composition of protein communities by bringing diversity (<italic>i.e.</italic>, small proteins) and inclusivity (<italic>i.e.</italic>, proteins encoded in RNAs incorrectly annotated as ncRNAs) into the largest human PPI network to date.</p>" ]
[ "<title>Materials and methods</title>", "<title>Classification of proteins, transcripts, and genes</title>", "<p id=\"p0225\">refProts are known proteins annotated in NCBI RefSeq, Ensembl, and/or UniProt. Novel isoforms are unannotated proteins with a significant sequence identity to a refProt from the same gene; for these isoforms, BLAST search yields a bit score over 40 for an overlap over 50% of the queried reference sequence. altProts are unannotated proteins with no significant identity to a refProt from the same gene.</p>", "<p id=\"p0230\">altORFs correspond to unannotated ORFs predicted to encode proteins with no significant identity to any other annotated protein.</p>", "<p id=\"p0235\">We classify RNA transcripts as dual coding or bicistronic based on the relative position of the ORFs on the transcript. If they are overlapping (<italic>i.e.</italic>, if they share nucleotides) we classify the transcript as dual coding, if they are sequential (<italic>i.e.</italic>, if they share no nucleotides) we classify it as bicistronic. Gene classification with this respect is inherited from the classification of transcript that it produces. Note that transcripts and genes can hold both dual coding and bicistronic classifications.</p>", "<title>Re-analysis of AP-MS data</title>", "<p id=\"p0240\">Files obtained from the authors of the BioPlex 2.0 contained the results of 8364 AP-MS experiments using 3033 bait proteins (tagged with GFP) in two technical replicates or more barring missing replicates and corrupted files ##REF##26186194##[4]##, ##REF##28514442##[5]##. Files were converted from RAW to MGF format using ProteoWizard 3.0 and searched with SearchGUI 2.9.0 using an ensemble of search engines (Comet, OMSSA, X!Tandem, and MS-GF+). Search parameters were set to a precursor ion tolerance of 4.5 ppm and fragment ion tolerance of 20 ppm, trypsin digestion with a maximum of two missed cleavages, and variable modifications including oxidation of methionine and acetylation of N termini. The minimum and maximum length for peptides were 8 and 30 aa, respectively. Search results were aggregated using PeptideShaker 1.13.4 with a 0.001% protein-level FDR as described previously ##REF##30299502##[20]##. In addition to already annotated proteins, the OpenProt database includes all predicted altProts and novel isoforms. Because large databases result in a large increase of false positive rates ##REF##25357241##[16]##, ##UREF##5##[69]##, this effect is balanced using an FDR of 0.001% at protein level (1% at peptide level) as previously described ##UREF##2##[18]##, ##REF##32780568##[19]##. The protein library contained a non-redundant list of all refProts (134,477 proteins) from UniProt (release 2019_03_01), Ensembl (GRCh38.95), and RefSeq (GRCh38.p12), in addition to all altProts (488,956 proteins) and novel isoforms (68,612 proteins) predicted from OpenProt 1.6. altProt identifiers throughout the current article are accessions from OpenProt starting with “IP_”. The library was concatenated with reversed sequences for the target decoy approach to spectrum matching.</p>", "<title>Validation of altProt identifications</title>", "<p id=\"p0245\">Novel protein identifications were supported by unique peptides. A minimum of one unique peptide detected in two technical replicas (two injections of the same purifications) was necessary to identify an altProt. A minimum of two unique peptides detected in two technical replica was necessary for the identification of refProts. Because altProts are on average 6 times smaller than refProts (##FIG##0##Figure 1##D) and thus present less probability of unique peptide detection, a threshold of one unique peptide for altProt identification was deemed necessary. All peptides assigned to altProts are unique matches to the altProt sequence, no non-unique peptides were assigned to altProts. Peptide assignment rules are different for altProts and refProts because more stringent criteria are necessary to confidently identify novel proteins. Unambiguous unique peptides are required for the identification of non-canonical proteins ##REF##25357241##[16]##.</p>", "<p id=\"p0250\">An additional peptide-centric approach was used to both enforce a significant <italic>P</italic> value on the PSM and validate that spectra supporting such peptides could not be better explained by peptides from refProts with post-translational modifications. PepQuery allows the search of specific peptides in spectra databases using an unrestricted modification search option ##REF##30610011##[22]##. All possible peptide modifications from UniMod artifact and post-translational modifications were considered when ensuring unicity of spectral matches (downloaded March 2020) ##REF##15174123##[70]##.</p>", "<p id=\"p0255\">Because the OpenProt library is derived from the transcriptome as described by annotation of the reference genome, it is possible that genetic variations specific to the cell line used in the BioPlex study (HEK293T) affect the sequences of translated proteins. The sequenced genome of HEK293T ##REF##25182477##[71]## was screened to ensure that peptides mapped to altProts did not present single amino acid variations (SAAVs). No variants were found in the regions corresponding to the peptides identifying altProts.</p>", "<p id=\"p0260\">AltProt sequences with peptides validated with PepQuery have been submitted to the UniProt Knowledgebase. All annotated spectra matched to altProt peptides are available in mzIdentML and MGF formats in <xref rid=\"s0175\" ref-type=\"sec\">File S1</xref>.</p>", "<title>Synthetic peptide MS/MS analysis</title>", "<p id=\"p0265\">To validate the fragmentation pattern of peptides assigned to altProts in the BioPlex dataset, a set of 100 tryptic peptides from 72 different altProts encoded by transcripts of various biotypes were synthesized (&gt; 50% purity; Biomatik, Ontario, Canada) and subjected to LC-MS/MS analysis.</p>", "<p id=\"p0270\">Two injections were prepared: one containing all synthetic peptides and the other containing a selection of 16 peptides from the first run that were undetected or only resulted in spectra of poor quality. First, the powder was resuspended in a solution of 1% formic acid and 50% acetonitrile. Then, the suspension was diluted to 20 nM in 1% formic acid and 5% acetonitrile prior to injection for the shotgun method (with the same parameters as those in the “MS analysis of in-house affinity purifications” section below) or injection for paired reaction monitoring (PRM) method (as published in ##REF##32161257##[36]##). Briefly, peptides were loaded and separated onto a nano high performance liquid chromatography (nanoHPLC) system (Catalog No. Dionex Ultimate 3000, ThermoFisher Scientific, Mississauga, Canada) with a constant flow of 4 μl/min onto a trap column [Acclaim PepMap100 C18 column (0.3 mm id × 5 mm), Dionex Corporation, Sunnyvale, CA]. Peptides were then eluted off toward an analytical column heated to 40 °C [PepMap C18 nano column (75 μm × 25 cm)] with a linear gradient of 5%–45% of solvent B (80% acetonitrile with 0.1% formic acid) over a 42-min gradient at a constant flow (450 nl/min).</p>", "<p id=\"p0275\">Peptides were analyzed on an OrbiTrap Q Exactive (ThermoFisher Scientific) spectrometer using the PRM method. An inclusion list containing the <italic>m/z</italic> values corresponding to the monoisotopic form of the peptides was generated. The collision energy was set at 28% and resolution for the MS/MS was set at 35,000 for 200,000 ions with maximum filling time of 110 ms with an isolation window of 2.0. Data acquisition was conducted with Xcalibur version 4.3.73.11.</p>", "<p id=\"p0280\">PSM was conducted using SearchGUI (version 3.3.17) and PeptideShaker (version 1.16.42) against the Swiss-Prot library (October 1, 2020) of proteins concatenated with the sequences of the 72 altProts (20,431 sequences) with FDR controlled at 1%. PSMs of synthetic peptides were then compared with PSMs observed in the BioPlex dataset using a spectral correlation measure as described by Toprak and his colleagues ##REF##24623587##[72]##. An example spectrum comparison (generated with the Universal Spectrum Explorer ##REF##33970638##[73]##) as well as an overall summary is available in <xref rid=\"s0175\" ref-type=\"sec\">Figure S2</xref>. All synthetic and BioPlex spectral comparisons are provided in <xref rid=\"s0175\" ref-type=\"sec\">Table S2</xref>.</p>", "<title>Obtaining spectral counts</title>", "<p id=\"p0285\">Because altProts are smaller than refProts, they have a lower number of uniquely identifying peptides. For this reason, altProts with at least one unique peptide across multiple replicates were considered, but only refProts identified with at least two unique peptides across multiple replicates were retained for downstream analysis. Spectra shared among refProts were counted in the total spectral count of each protein. Spectra assigned to altProts were counted only if unique to the protein or shared with another altProt. Spectra shared between an altProt and at least one refProt were given to the refProt. refProt spectral counts were combined by gene following the methodology of the original study; however, it was necessary to keep altProts separate as many are encoded by genes that already contain a refProt or other altProts.</p>", "<title>Interaction scoring</title>", "<p id=\"p0290\">Following protein identifications, HCIPs were identified following the method outlined in the original study ##REF##26186194##[4]##. Briefly, the CompPASS R package was first used to compute statistical metrics (weighted D-score, Z-score, and entropy) of prey identification based on PSM counts. The results from CompPASS were then used to build a vector of nine features (as described by Huttlin and his colleagues ##REF##26186194##[4]##) for each candidate bait–prey pair which were passed to a Naive Bayes classifier (CompPASS Plus) tasked with the discrimination of HCIPs from background identifications. The original study also included a class for wrong identification, but because decoy information was unavailable and because our approach employs a FDR three orders of magnitudes lower in the identification step, a third class was not deemed necessary. The classifier was trained in cross-validation fashion using 96 well plate batches as splits and PPIs from the original study as target labels for true interactors.</p>", "<p id=\"p0295\">Threshold selection was implemented considering the Jaccard overlap (<italic>J</italic>), precision, recall, and F1 score metrics [see Equations ##FORMU##0##(1)##, ##FORMU##1##(2)##, ##FORMU##2##(3)##, ##FORMU##3##(4)##] between networks resulting from the re-analysis and the original study. The main differences between the OpenProt-derived re-analysis and BioPlex 2.0 lie in the total spectral counts resulting from the use of different search algorithms and more stringent FDR. It was thus important to tune model threshold selection to maximally reproduce results from the original study (<xref rid=\"s0175\" ref-type=\"sec\">Figure S1</xref>A). A threshold of 0.045 was selected as it compromised well between optimal Jaccard overlap, F score, and precision (<xref rid=\"s0175\" ref-type=\"sec\">Figure S1</xref>B). A summary of protein and interaction counts is shown in <xref rid=\"s0175\" ref-type=\"sec\">Figure S1</xref>D.where <italic>A</italic> represents the set of OpenProt-derived PPIs and <italic>B</italic> represents the set of BioPlex 2.0 PPIs.</p>", "<title>Network assembly and structural analysis</title>", "<p id=\"p0310\">Bait–prey pairs classified as HCIPs were combined into an undirected network using genes to represent refProt nodes and OpenProt protein accessions to represent altProt nodes. The NetworkX 2.5 Python package was used for network assembly and all network metrics calculations.</p>", "<p id=\"p0315\">The power law fit to the degree distribution was computed with the discreet maximum likelihood estimator described by Clauset and his colleagues ##UREF##6##[74]##.</p>", "<p id=\"p0320\">A list of known protein complexes from CORUM 3.0 ##REF##30357367##[75]## (core complexes, downloaded March 2020) was mapped onto the resulting network to assess the validity of identified interactions (<xref rid=\"s0175\" ref-type=\"sec\">Table S5</xref>). Only complexes in which at least two subunits corresponded to baits present in the network were selected for downstream analyses. The portion of subunits identified in the direct neighbourhood of baits was computed for each complex.</p>", "<title>Patterns of interactions involving altProts and refProts</title>", "<p id=\"p0325\">We aimed to assess the relationship between pseudogene-derived altProts and their corresponding refProts from parental genes, in terms of their sequence similarity and their degrees of separation in the network. Parental genes of pseudogenes were selected via the psiCube resource ##REF##25157146##[76]## combined with manual curation using Ensembl. Needleman–Wunch global alignment algorithm (with BLOSUM62 matrix) as implemented by the sciki-bio Python package (version 0.5.5) was used as a similarity measure between protein sequences.</p>", "<p id=\"p0330\">To assess degrees of separation, shortest path lengths were computed both for altProt–refProt pairs of pseudogene–parental gene and altProt–refProt pairs encoded by the same gene. For the former, when the refProt was not present in the network, or when no path could be computed between nodes, the shortest path length was computed using a mapping of either the BioPlex 2.0 or BioGRID networks ##REF##16381927##[77]##.</p>", "<title>Community detection via clustering</title>", "<p id=\"p0335\">A Python implementation of the Markov clustering algorithm (<ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/GuyAllard/markov_clustering\" id=\"ir010\">https://github.com/GuyAllard/markov_clustering</ext-link>) was used to partition the network into clusters of proteins ##REF##11917018##[41]##. Various values of the inflation parameter between 1.5 and 2.5 were attempted and, similarly to the original study, a value of 2.0 was selected as it compared favorably with known protein complexes. Only clusters of three proteins or higher were retained yielding a total of 1054 clusters. Connections between clusters were determined by calculating enrichment of links between proteins in pairs of clusters using a hypergeometric test with alpha value set to &lt; 0.05 and a Benjamini–Hochberg corrected FDR of 1%. A total of 266 pairs of clusters were found to be significantly connected.</p>", "<title>Disease association analysis</title>", "<p id=\"p0340\">A list of 32,375 disease–gene associations curated by DisGeNET (downloaded March 2020) was mapped onto the network of 1054 protein communities. A disease was associated with a cluster when it was deemed enriched in genes associated with the disease as calculated by hypergeometric testing, with alpha value set to &lt; 0.01 and Benjamini–Hochberg corrected FDR of 1%.</p>", "<title>GO enrichment analysis</title>", "<p id=\"p0345\">GO term enrichments for both altProt second neighborhoods and protein clusters were computed using the GOATOOLS Python package (version 1.0.2). Count propagation to parental terms was set to true, with alpha value to 0.05 and a Benjamini–Hochberg corrected FDR of 1%. The set of all nodes in the network was used as background.</p>", "<title>Cloning and antibodies</title>", "<p id=\"p0350\">All nucleotide sequences were generated by the Bio Basic Gene Synthesis service, except for pcDNA3-FLAG-FADD which was gifted by Jaewhan Song (Catalog No. 78802, Addgene plasmid; <ext-link ext-link-type=\"uri\" xlink:href=\"https://n2t.net/addgene%3a78802\" id=\"ir015\">https://n2t.net/addgene:78802</ext-link>). IP_117582, IP_624363, and IP_762813 were all tagged with 2× FLAG (DYKDDDDKDYKDDDDK) at their C-termini. IP_198808 was tagged with eGFP at its C-terminus. All altProt CDSs were subcloned into a pcDNA3.1 plasmid. The CDSs of RPL18, eEF1A1, and PHB were derived from their canonical transcripts (NM_000979.3, NM_001402.6, and NM_001281496.1, respectively). RPL18 and PHB were tagged with eGFP at their C-termini and eEF1A1 was tagged with eGFP at its N-terminus. All refProt CDSs were subcloned into a pcDNA3.1 plasmid.</p>", "<title>Cell culture, transfection, and immunofluorescence assay</title>", "<p id=\"p0355\">HEK293 and HeLa cultured cells were routinely tested negative for mycoplasma contamination using Universal Mycoplasma Detection Kit (Catalog No. 30–1012K, ATCC, Manassas, VA). Transfection, immunofluorescence, and confocal analyses were carried out as previously described ##REF##33226175##[67]##. Transfection was carried out with jetPRIME (Catalog No. CA89129-924, VWR, Toronto, Canada) according to the manufacturer’s protocol unless otherwise stated. For Co-IP assays, a total of 6 µg of DNA per 100-mm dish was transfected consisting of 3 µg of each construct, except for pEGFP, which was transfected under the following conditions: 0.1 µg when co-transfected with IP_117582-Flag and Flag-FADD, 0.3 µg when co-transfected with IP_762813-Flag, and 0.6 µg when co-transfected with IP_624363-Flag to compensate for its higher transfection and expression efficiency. For immunofluorescence assay, cells were fixed in 4% paraformaldehyde for 20 min at 4 °C, solubilized in 1% Triton for 5 min, and incubated in blocking solution (10% Normal Goat Serum in PBS) for 20 min. Primary anti-Flag antibodies (Catalog No. F1804, Millipore Sigma, Etobicoke, Canada) were diluted as 1:1000 in the blocking solution. Secondary anti-mouse Alexa Fluor 647 antibodies (Catalog No. 4410S, Cell Signaling Technology, New England Biolabs, Whitby, Canada) were diluted at 1:1000 in the blocking solution. All images were taken on a Leica TCS SP8 STED 3X confocal microscope.</p>", "<title>Affinity purification and Western blotting</title>", "<p id=\"p0360\">Co-IP experiments via ChromoTek GFP-Trap (Proteintech, Rosemont, IL) were carried out as previously described ##REF##29083303##[13]##, whereas experiments via Anti-FLAG M2 Magnetic Beads (Catalog No. M8823, Millipore Sigma) were conducted according to the manufacturer’s protocol with minor modifications. Briefly, HEK293 cells were lysed in the lysis buffer (150 mM NaCl, 50 mM Tris pH 7.5, 1% Triton, and 1× EDTA-free Roche protease inhibitors) and incubated on ice for 30 min prior to a double sonication at 12% amplitude for 3 s each (1 min on ice between sonications). The cell lysates were centrifuged, the supernatant was isolated, and the protein content was assessed using BCA assay (Catalog No. PI23223, ThermoFisher Scientific). Anti-FLAG beads were conditioned with the lysis buffer. Then, 20 µl of beads were added to 1 mg of proteins at a final concentration of 1 mg/ml and incubated overnight at 4 °C. Then, the beads were washed four times with the lysis buffer (twice with 800 µl and twice with 500 µl) prior to elution in 45 µl of Laemmli buffer and boiled at 95 °C for 5 min. For Co-IP of PHB1-GFP and RPL18-GFP, stringent wash was done with modified lysis buffer [250 mM NaCl with 20 µg/ml peptide FLAG (Catalog No. F3290, Millipore Sigma)] prior to elution with 200 µg/ml peptide FLAG. Eluates were loaded onto 12% SDS-PAGE gels for Western blotting of GFP- and FLAG-tagged proteins. 40 µg of input lysates were loaded into gels as inputs. Western blotting was carried out as previously described ##REF##33226175##[67]##. The primary antibodies were diluted as follows: anti-Flag (1:1000; Catalog No. F7425, Millipore Sigma) and anti-GFP (1:8000; Catalog No. sc-9996, Santa Cruz, Dallas, TX). The secondary antibodies were diluted as follows: anti-mouse HRP (1:10000; Catalog No. sc-516102, Santa Cruz) and anti-rabbit HRP (1:10000; Catalog No. 7074S, Cell Signaling Technology).</p>", "<title>Affinity purification of nuclear extracts</title>", "<p id=\"p0365\">For Co-IP with GFP beads of Flag-FADD and IP_198808-GFP, nuclear extracts were used instead of cells lysate because the interaction was exclusively observed in the nucleus by confocal microscopy. Nuclear extracts were prepared as previously described ##REF##11340173##[78]##. Briefly, HEK293a cells were lysed in Buffer A (10 mM HEPES pH 7.9, 10 mM KCl, 1.5 mM MgCl<sub>2</sub>, 0.34 M sucrose, 10% glycerol, 1 mM DTT, 0.1% Triton, and 1× EDTA-free Roche protease inhibitors) and incubated on ice for 8 min before centrifugation at 1300 <italic>g</italic> for 5 min to remove cytoplasmic soluble proteins (supernatant). The pellet was resuspended with Buffer B (3 mM EDTA, 0.2 mM EGTA, and 1× EDTA-free Roche protease inhibitors) and incubated for 30 min on ice prior to centrifuge at 1700 <italic>g</italic> for 5 min. The supernatant containing nuclear proteins was used for Co-IP. 1/50 volume was kept for input and the remaining was used with anti-FLAG conditioned beads and incubated for 2 h at 4 °C with agitation. The volume was adjusted to 1 ml with lysis buffer (see the “Affinity purification and Western blotting” section). Then, the beads were washed four times with lysis buffer (twice with 800 µl and twice with 500 µl) prior to elution with 30 µl of glycine (0.1 M pH 3.0), 10 min agitation, and stopped with 6 µl Tris (1 M pH 8.0). Eluates were loaded onto 12% SDS-PAGE gels for Western blotting (see the “Affinity purification and Western blotting” section for details).</p>", "<title>AP-MS</title>", "<p id=\"p0370\">For interactome analysis by MS, HEK293 cells at a 70% confluence were transfected with GFP-tagged PHB or with FLAG-tagged PHBP19 (IP_762813). After 24 h of transfection, cells were rinsed twice with PBS, and lysed in the AP lysis buffer (150 mM NaCl, 50 mM Tris-HCl, and 1% Triton). Protein concentration was evaluated with a BCA dosage and 1 mg of total protein was incubated at 4 °C for 4 h with agarose ChromoTek GFP beads (Proteintech) for PHB-GFP or with magnetic FLAG beads (Catalog No. M8823, Millipore Sigma) for IP_762813-Flag. The beads were pre-conditioned with the AP lysis buffer. The beads were then washed twice with 1 ml of AP lysis buffer, and 5 times with 5 ml of 20 mM NH<sub>4</sub>HCO<sub>3</sub> (ABC) (Catalog No. A6141, Millipore Sigma). Proteins were eluted and reduced from the beads using 10 mM DTT with 15 min at 55 °C, and then treated with 20 mM IAA for 1 h at room temperature in the dark. Proteins were digested overnight by adding 1 μg of trypsin (Promega, Madison, WI) in 100 μl ABC at 37 °C overnight. Digestion was quenched using 1% formic acid and the supernatant was collected. Beads were washed once with acetonitrile/water/formic acid (1/1/0.01 v/v) and pooled with supernatant. Peptides were dried with a speedvac, desalted using a C18 Zip-Tip (Millipore Sigma), and resuspended into 30 μl of 1% formic acid in water prior to MS analysis.</p>", "<title>MS analysis of in-house affinity purifications</title>", "<p id=\"p0375\">Peptides were separated in a PepMap C18 Nano Column (75 μm × 50 cm; ThermoFisher Scientific). The setup used a 0%–35% gradient (0–215 min) of 90% acetonitrile, 0.1% formic acid at a flow rate of 200 nl/min followed by acetonitrile wash and column re-equilibration for a total gradient duration of 4 h with a Ultimate 3000 RSLC (ThermoFisher Scientific). Peptides were sprayed using an EASY-Spray Source (ThermoFisher Scientific) at 2 kV coupled to a quadrupole-Orbitrap (Q Exactive, ThermoFisher Scientific) mass spectrometer. Full-MS spectra within a <italic>m/z</italic> 350–1600 mass range at 70,000 resolution were acquired with an automatic gain control (AGC) target of 1E6 and a maximum accumulation time (maximum IT) of 20 ms. Fragmentation (MS/MS) of the top ten ions detected in the Full-MS scan at 17,500 resolution, AGC target of 5E5, and a maximum IT of 60 ms with a fixed first mass of 50 within a 3 <italic>m/z</italic> isolation window at a normalized collision energy (NCE) of 25. Dynamic exclusion was set to 40 s. MS RAW files were searched with the Andromeda search engine implemented in MaxQuant 1.6.9.0. The digestion mode was set at Trypsin/P with a maximum of two missed cleavages per peptides. Oxidation of methionine and acetylation of N-terminal were set as variable modifications, and carbamidomethylation of cysteine was set as fixed modification. Precursor and fragment tolerances were set at 4.5 and 20 ppm, respectively. Files were searched using a target-decoy approach against UniProt Knowledgebase (<italic>Homo sapiens</italic>, Swiss-Prot, released in October 2020) with the addition of IP_762813 sequence for a total of 20,360 entries. The FDR was set at 1% for PSM, peptide, and protein levels. Only proteins identified with at least two unique peptides were kept for downstream analyses.</p>", "<title>HCIP scoring of in-house affinity purifications</title>", "<p id=\"p0380\">Protein interactions were scored using the SAINT algorithm ##REF##21131968##[79]##. For each AP-MS, experimental controls were used: GFP alone-transfected cells for PHB-GFP AP and mock-transfected cells for IP_762813-2F AP. For the PHB-GFP AP, controls from the CRAPome repository ##REF##23921808##[80]## corresponding to transient GFP-tag expression in HEK293 cells, pulled using camel agarose beads were used. These controls are: CC42, CC44, CC45, CC46, CC47, and CC48. For the IP_762813-Flag AP, controls from the CRAPome repository ##REF##23921808##[80]## corresponding to transient FLAG-tag expression in HEK293 cells, pulled using M2-magnetic beads were used. These controls are: CC55, CC56, CC57, CC58, CC59, CC60, and CC61. The fold-change over the experimental controls (FC_A), over the CRAPome controls (FC_B), and the SAINT probability scores were calculated as follows. The FC_A was evaluated using the geometric mean of replicates and a stringent background estimation. The FC_B was evaluated using the geometric mean of replicates and a stringent background estimation. The SAINT score was calculated by SAINTexpress using experimental controls and default parameters. Proteins with a SAINT score above 0.8, a FC_A and a FC_B above 1.5 were considered HCIPs.</p>", "<title>Network visualization of in-house affinity purifications</title>", "<p id=\"p0385\">The network was built using Python scripts (version 3.7.3) and the NetworkX package (version 2.4). The interactions from the STRING database were retrieved from their protein links downloadable file. Only interactions with a combined score above 750 were kept.</p>" ]
[ "<title>Results</title>", "<title>Re-analysis of BioPlex 2.0 MS data and identification of preyed altProts</title>", "<p id=\"p0035\">We employed the OpenProt proteogenomic library in the re-analysis of high-throughput AP-MS experiments from the BioPlex 2.0 network. Given the size of the OpenProt database (##FIG##0##Figure 1##C), the false discovery rate (FDR) for protein identification was adjusted from 1% down to 0.001% to mitigate against spurious identifications ##REF##30299502##[20]##. Such stringent FDR settings inevitably lead to fewer prey proteins identified; thus, our highly conservative methodology is likely to leave behind many false negatives. The BioPlex 2.0 network is built in a gene-centric manner to simplify the analysis by making abstraction of protein isoforms. In the current analysis, all refProts and their isoforms are also grouped under their respective gene, but results concerning altProts are necessarily given at the protein level.</p>", "<p id=\"p0040\">In total, 426 unannotated proteins from 414 genes and 8972 refProts were identified in the re-analysis of raw MS data from the pull-down of 3033 refProts (baits), using a combination of multiple identification algorithms (##FIG##0##Figure 1##C). Because these identifications resulted from the re-analysis of raw MS data from BioPlex 2.0 with the OpenProt MS pipeline, we sought to determine the overlap between total sets of genes identified. refProts from 6546 genes (or 84% of total re-analysis results) were found in both BioPlex 2.0 and in the present work (<xref rid=\"s0175\" ref-type=\"sec\">Figure S1</xref>A), indicating that the re-analysis could reliably reproduce BioPlex results.</p>", "<p id=\"p0045\">Although peptide spectrum match (PSM) scores of altProt peptides tended to be slightly lower than those of refProt on average, the overall distributions were similar (<xref rid=\"s0175\" ref-type=\"sec\">Figure S2</xref>A). For this reason, our stringent approach in the identification of altProts included the use of PepQuery to validate protein detection using a peptide-centric approach ##REF##30610011##[22]##. This tool includes a step which verified that altProt-derived peptides were supported by experimental spectra that could not be better explained by peptides from refProts with any post-translational modification. In addition, peptides were screened for isobaric substitutions in order to reject dubious peptides that could match refProts ##REF##28929764##[23]##. A total of 278 altProt identifications were validated with PepQuery including 136 altProts encoded by pseudogenes (##FIG##0##Figure 1##C, <xref rid=\"s0175\" ref-type=\"sec\">Figure S1</xref>; <xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>).</p>", "<p id=\"p0050\">The observed fragmentation pattern of peptides was validated through MS/MS analysis of 100 synthetic peptides from 72 altProts encoded by transcripts of various biotypes. The spectral correlation coefficient was computed between spectra observed in BioPlex and those of synthetic peptides and 74 of these showed coefficients higher than 0.6 (<xref rid=\"s0175\" ref-type=\"sec\">Figure S2</xref>B; <xref rid=\"s0175\" ref-type=\"sec\">Table S2</xref>). An example comparison of spectra with correlation coefficient of 0.66 is shown in <xref rid=\"s0175\" ref-type=\"sec\">Figure S2</xref>C (median correlation coefficient across comparisons of 0.78). These results confirmed that spectra assigned to altProt peptides were representative of the fragmentation pattern obtained from corresponding synthetic peptides.</p>", "<p id=\"p0055\">MS-based identification of short proteins with a minimum of 2 unique suitable tryptic peptides remains an important challenge and most of short proteins are typically detected with a single unique peptide ##REF##23160002##[24]##, ##REF##24490786##[25]##. Of the 278 altProts validated by PepQuery (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>), 68 complied with the Human Proteome Project PE1 level for proteins with strong protein-level evidence, Guidelines v3.0 ##REF##31599596##[26]##. Apart from their detection in the BioPlex dataset, 156 were also detected in other MS datasets and 18 showed evidence of translation via ribosome profiling (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>). In addition, 27 of detected altProts were reported by the SmProt resource and 5 were present in the sORFs library (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>) ##REF##29140531##[12]##, ##REF##28137767##[27]##.</p>", "<p id=\"p0060\">As expected, detected altProts were much shorter than refProts with a median size of 77 aa <italic>versus</italic> 472 aa (##FIG##0##Figure 1##D; <xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>). It is well known that small proteins suffer from less sequence coverage in MS/MS analysis ##REF##33760615##[28]##, ##REF##20803007##[29]## and this was also observed in the current study. The average detected sequence coverage was 41% for refProts and 23% for altProts. This is only considering peptides that are unique to altProts. If peptides matching both a refProt and an altProt were detected, they were not considered as evidence for the expression of the altProt and so were excluded from the coverage calculation. Pseudogene products particularly are usually identified with a small number of peptides (sometimes only one), because other peptides are shared with the protein from the parental gene.</p>", "<p id=\"p0065\">altORFs encoding the 278 detected and PepQuery-validated altProts were distributed among 971 transcripts (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>), and in addition to the 117 pseudogene-derived altProts, 43 were exclusively encoded by genes of non-coding biotypes (##FIG##0##Figure 1##E). A third were found in transcripts already encoding a refProt (##FIG##0##Figure 1##E), indicating that the corresponding genes are in fact either bicistronic (two non-overlapping ORFs) or dual-coding (two overlapping ORFs) (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>). Of the altProts encoded by transcripts from genes of protein-coding biotype, most were encoded by a frame-shifted altORF overlapping the annotated CDS or downstream of the annotated CDS in the 3′ UTR (##FIG##0##Figure 1##F). The remaining altORFs were encoded by 5′ UTRs or by transcripts annotated as non-coding but transcribed from those genes of protein-coding biotype. From the localization of altORFs relative to the canonical CDS in the mRNA from protein-coding genes, we conclude that 70 of those genes are in fact bicistronic and 56 are dual-coding (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>). In addition, transcripts from three pseudogenes have been found to encode two altProts suggesting that they are in fact bicistronic (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>).</p>", "<p id=\"p0070\">We collected protein orthology relationships from 10 species computed by OpenProt (##FIG##0##Figure 1##G). Although 100 altProts were specific to humans, a large number had orthologs in the mouse and chimpanzee, and 28 were even conserved through evolution because 116 yeast altProts displayed at least one functional domain signature (InterProScan, version 5.14–53.0, ##REF##30398656##[30]##), further supporting their functionality (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>).</p>", "<title>Assembling PPIs into a network</title>", "<p id=\"p0075\">After identification of prey proteins, CompPASS was used to compute semi-quantitative statistics based on PSM across technical replicates ##REF##19615732##[31]##. These metrics allow filtration of background and spurious interactions from the raw identifications of prey proteins to obtain high-confidence interacting proteins (HCIPs). To mitigate against the otherwise noisy nature of fast-paced high-throughput approaches and to filter prey identifications down to the most confident interactions, we applied a Naïve Bayes classifier similar to CompPASS Plus ##REF##26186194##[4]##. The classifier used representations of bait–prey pairs computed from detection statistics and assembled into a vector of 9 features as described by Huttlin and his colleagues ##REF##26186194##[4]##. High confidence interactions reported by BioPlex 2.0 served as target labels. HCIP classification resulted in the retention of 3.2% of the starting set of bait–prey pairs identified (<xref rid=\"s0175\" ref-type=\"sec\">Figure S1</xref>C). Notably, 694 baits from the original dataset were excluded after filtration because no confident interaction could be distinguished from background.</p>", "<p id=\"p0080\">Following protein identifications and background filtration, the network was assembled by integrating all bait–prey interactions into one network (##FIG##1##Figure 2##A). All refProts and their isoforms were grouped under their respective gene, similar to the BioPlex analysis, but separate nodes are shown for altProts. In total, the re-analysis with OpenProt found 6301 prey proteins from the purification of 2311 bait proteins altogether engaged in 19,968 interactions, 51% of which were also reported by BioPlex 2.0 (##FIG##1##Figure 2##B). The average number of interactions per bait was 9.7. Among prey proteins, 261 altProts were found engaged in 316 interactions with 292 bait proteins.</p>", "<p id=\"p0085\">Compared with BioPlex 2.0, a smaller total number of protein identification was expected because the OpenProt MS analysis pipeline is more stringent with a tolerance of 20 ppm on peak positions rather than 50 ppm and a 0.001% protein FDR as opposed to 1%. Indeed, we identified 19,968 interactions in our re-analysis, compared with 56,553 interactions reported by BioPlex 2.0 (##FIG##1##Figure 2##B). Among the 19,968 interactions, 10,017 (51%) were also reported by BioPlex 2.0, and 9700 (49%) were reported in the recently released BioPlex 3.0 (##FIG##1##Figure 2##B). Interestingly, 11,329 interactions (20%) from BioPlex 2.0 were not confirmed in BioPlex 3.0 using a larger number of protein baits, although the same experimental and computational methodologies were used (##FIG##1##Figure 2##B). This observation illustrates the challenge in the identification of PPIs with large-scale data given the relatively low signal to noise ratio in AP-MS data.</p>", "<title>Network structural features and altProt integration</title>", "<p id=\"p0090\">Network theoretic analysis confirmed that the OpenProt-derived network displayed the expected characteristics of natural networks. Variability in the number of interacting partners of a given protein in a network (node degree) is typically very wide and the degree distribution that characterizes this variation follows a power law ##REF##11415319##[32]##. Similar to other protein networks, the degree distribution of the OpenProt-derived network also fitted a power law, an indication that most of the proteins have few connections and a minor fraction is highly connected (also called hubs) (##FIG##1##Figure 2##C). The degree of connectivity of altProts varied between 1 and 5 whereas that of refProt was between 1 and 179. On the one hand, because long and multidomain proteins are over-represented among hub proteins ##REF##16780599##[33]##, this difference may be explained by the fact that altProts in the network were on average 6 times shorter than refProts (##FIG##0##Figure 1##D). On the other hand, none of the altProts were used as baits which also explains their lower observed connectivity because average degree was 1.2 for preys but 5.3 for baits.</p>", "<p id=\"p0095\">The mean degrees of separation between any two proteins in the OpenProt-derived network was 5 (##FIG##1##Figure 2##D), in agreement with the small-world effect that characterizes biological networks ##REF##11522199##[34]##.</p>", "<p id=\"p0100\">Centrality analysis allows sorting proteins according to their relative influence on network behavior in which the most central proteins tend to be involved in the most essential cellular processes ##REF##11333967##[35]##. Here, the eigenvector centrality (EVC) measure indicates that altProts are found both at the network periphery connected to refProts of lesser influence as well as connected to central refProts of high influence (##FIG##1##Figure 2##E). Because no altProts were used as baits, they are likely artificially pushed toward the edges of the network. Known complexes from the CORUM database were mapped onto the network to assess the portion of complex subunits identified in the re-analysis (<xref rid=\"s0175\" ref-type=\"sec\">Table S3</xref>). In most cases a majority were recovered (75% of complexes showed ≥ 50% recovery) (##FIG##1##Figure 2##F). We observed 33 altProts in the neighborhood of CORUM complex subunits that served as bait, <italic>i.e.</italic>, directly interacting with the CORUM complex. Here multiple interesting patterns of altProt interactions were already noticeable: (1) altProts detected in the interactome of their respective refProts (##FIG##1##Figure 2##G, i), (2) altProts originating from pseudogenes and detected in the interactome of refProts encoded by the parental gene (##FIG##1##Figure 2##G, ii), and (3) altProts from protein-coding genes or pseudogenes detected in network regions outside the immediate neighborhood of the related protein/gene (##FIG##1##Figure 2##G, iii–vi).</p>", "<p id=\"p0105\">The OpenProt-derived PPI network displayed with a degree sorted circle layout showed that preyed altProts generally had a lower degree of connectivity compared with refProts (##FIG##2##Figure 3##A). This might be expected in part because no altProts were used as baits in the network, but also based on the limited range of binding capacity due to their smaller size. In order to investigate the local neighborhood of altProts, subnetworks were extracted by taking nodes within shortest path length of 2 and all edges between these for each altProt (here called second neighborhood). The most connected altProt is a product of a tubulin pseudogene (##FIG##2##Figure 3##A, i). Other notable altProts with high degree include OpenProt accessions IP_711679, encoded in a transcript of the <italic>SLC38A10</italic> gene currently annotated as a ncRNA (##FIG##2##Figure 3##A, ii), and IP_117582, a novel protein encoded by an altORF overlapping the reference CDS in the <italic>BEND4</italic> gene (##FIG##2##Figure 3##A, iii). Although these two altProts would not qualify as hub proteins per say, they seem to participate in the bridging of hubs from otherwise relatively isolated regions. Several other examples of altProts encoded by a lncRNA gene (##FIG##2##Figure 3##A, iv), in pseudogenes (##FIG##2##Figure 3##A, v–viii), and in protein-coding genes (##FIG##2##Figure 3##A, iv and ix) integrate the network with a variety of topologies. One of these subnetworks features IP_710744, a recently discovered altProt and polyubiquitin precursor with three ubiquitin variants, was encoded in the <italic>UBBP4</italic> pseudogene ##REF##32161257##[36]##. The ubiquitin variant Ubbp4<sup>A2</sup> differs from canonical ubiquitin by one amino acid (T55S) and can be attached to target proteins ##REF##32161257##[36]##. Before network assembly this variant was identified reproducibly (across technical replicates) in the purification of 11 baits. Following HCIP identifications, only three interactions remained (##FIG##2##Figure 3##A, v), likely because widespread identifications lead the Naïve Bayes classifier to assume non-specificity for those showing lower abundance. The three interactors include two ubiquitin ligases, <italic>UBE2E2</italic> (Q96LR5) and <italic>UBE2E3</italic> (Q969T4), and <italic>USP48</italic> (Q86UV5), a peptidase involved in the processing of ubiquitin precursors.</p>", "<p id=\"p0110\">After observing second neighborhoods of altProts we sought to evaluate the effect of altProt inclusion into local neighborhoods of refProts. To do so, we computed the EVC of each refProt within their own second neighborhood extracted from the assembled network with and without altProts. This analysis highlighted <italic>LDHC</italic> which undergoes a marked increase in EVC in its second neighborhood (1.0 <italic>versus</italic> 0.5) when the altProts IP_556449 and IP_564999 (both pseudogenes of the LDH family) are included (##FIG##2##Figure 3##B, i and ii). This shows that node influence in this region of the network is impacted by the presence of altORF products.</p>", "<p id=\"p0115\">In total, 39 pseudogene-encoded altProts were uncovered in the direct interactome of refProts from their respective parental genes (<xref rid=\"s0175\" ref-type=\"sec\">Table S4</xref>, shortest path length of 1), of which two more examples are illustrated with more details in ##FIG##2##Figure 3##C.</p>", "<p id=\"p0120\"><italic>GAPDH</italic> is known to have a large number of pseudogenes ##REF##19835609##[37]##. Yet protein products originating from seven <italic>GAPDH</italic> pseudogenes were confidently identified in the purification of the canonical GAPDH protein (##FIG##2##Figure 3##C, i). Because the glycolytic active form of this enzyme is a tetramer, we conjecture that GAPDH tetramers may assemble from a heterogenous mixture of protein products from the parental gene and many of its pseudogenes. GAPDH is a multifunctional protein ##REF##20727968##[38]##; although different posttranslational modifications may explain in part how this protein switches function ##REF##19779498##[39]##, it is possible that heterologous and homologous complexes contribute to GAPDH functional diversity. This is supported by the fact that 4 of the smallest protein products from <italic>GAPDH</italic> pseudogenes only contain the GAPDH NAD binding domain (IPR020828; IP_735797, IP_761275, IP_735800, IP_591881); the protein encoded by <italic>GAPDHP1</italic> only contains the GAPDH catalytic domain (IPR020829; IP_560713); whereas the largest proteins from <italic>GAPDH</italic> pseudogenes contain both domains (IP_557819, IP_672168, IP_3422225, IP_755869) (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>). The <italic>PHB1</italic> subnetwork highlights an interaction between <italic>PHB1</italic> and <italic>PHBP19</italic>, one of the 21 <italic>PHB</italic> pseudogenes (##FIG##2##Figure 3##B, ii). <italic>PHB1</italic> and <italic>PHB2</italic> are paralogs and the proteins they encode, PHB1 and PHB2, heterodimerize; similar to GAPDH, the PHB1/PHB2 complex is multifunctional ##REF##19889967##[40]##, and the dimerization of PHB1 or PHB2 with <italic>PHBP19</italic>-derived IP_762813, which also contains a prohibitin domain (IPR000163), may regulate the various activities of the complex. Each GAPDH pseudogene identification is supported by a unique peptide (<xref rid=\"s0175\" ref-type=\"sec\">Figure S3</xref>A). Whereas most peptides differ by one or two amino acids with the canonical sequence, the spectrum in <xref rid=\"s0175\" ref-type=\"sec\">Figure S3</xref>B clearly shows the presence of co-eluding peptides of GAPDH and GAPDHP1 and was likely assigned to the refProt in the BioPlex analysis, but received a better score with the pseudogene in the OpenProt-derived analysis.</p>", "<p id=\"p0125\">We reasoned that pseudogene-derived altProts directly interacting with their parental gene-derived refProts (parental protein) may result from the generally high degree of sequence similarity, particularly for refProts known to multimerize. However, although a slight reduction of alignment scores was observed with an increase in degrees of separation, the 39 altProts directly interacting with parental protein display a large variety of sequence alignment scores (##FIG##2##Figure 3##D). This suggests that direct interactions between pseudogene-derived altProts and their respective parental refProts involve other mechanisms in addition to sequence identity. Because 37 of the 39 altProts share between 1 and 6 InterPro entries with their respective parental proteins (<xref rid=\"s0175\" ref-type=\"sec\">Table S1</xref>), protein domains may be an important mechanism driving these interactions.</p>", "<p id=\"p0130\">The mean degrees of separation between a refProt and an altProt encoded in the same gene reveals two types of relationships (##FIG##2##Figure 3##E). 19% (14) of altProt–refProt pairs have a degree of separation of 1, that is to say these altProts were found in the direct interactome of the corresponding refProt from the same gene (<xref rid=\"s0175\" ref-type=\"sec\">Table S4</xref>). Hence, these protein pairs encoded by the same genes are clearly involved in the same function through direct or indirect physical contacts. Interestingly, 12 of these 14 altProts are encoded by dual-coding genes, <italic>i.e.</italic>, with altORFs overlapping annotated CDSs. The remaining altProt–refProt pairs follow a distribution of degrees of separation similar to the whole network (compare ##FIG##2##Figures 3##E and ##FIG##1##2##D). This suggests that they are not more closely related than any random pair of proteins in the network despite shared transcriptional regulation.</p>", "<title>Cluster detection reveals altProts as new participants in known protein communities</title>", "<p id=\"p0135\">Biological networks are organized in a hierarchy of interconnected subnetworks called clusters or communities. To identify these communities, unsupervised Markov clustering ##REF##11917018##[41]## was used similarly to methodology applied to BioPlex 2.0 ##REF##28514442##[5]##. Partitioning of the network resulted in 1054 protein clusters, 160 of which contained at least one altProt (##FIG##3##Figure 4##A). The size of altProts in these communities varied between 29 to 269 aa indicating that protein length may not be a limiting factor in their involvement in functional groups. Links between clusters were drawn in which the number of connections between members of cluster pairs was higher than expected (detailed in Materials and methods).</p>", "<p id=\"p0140\">In order to assign biological function to these clusters, and therefore generate testable hypotheses about the function of altProts detected among them, enrichment of Gene Ontology (GO) terms was computed for each community against the background of all human genes. Several communities of different sizes showing significant GO term enrichment are detailed in ##FIG##3##Figure 4##B.</p>", "<p id=\"p0145\">About 50% of identified clusters showed GO term enrichment. The same analysis with the original BioPlex network showed 57% of clusters with GO term enrichment; possibly because a higher number of protein identifications yielded a larger network and therefore a higher probability of significant enrichment.</p>", "<p id=\"p0150\">The altProt IP_293201 from the gene <italic>RNF215</italic> was identified as a novel interactor of three subunits of the RNA exosome multisubunit complex (cluster #27), suggesting a possible role in RNA homeostasis. Clusters #42 and #369 included protein communities with essential activities: the large eukaryotic initiation factor EIF3 and the recently discovered KICSTOR complex, a lysosome-associated negative regulator of mTORC1 signaling ##REF##28199306##[42]##. At least one pseudogene encoded altProt was detected in each of these clusters. Intriguingly, altProts IP_790907 (cluster #42) and IP_602155 (cluster #369) interact with the parental proteins EIF3E and ITFG2, respectively. These altProts may either compete with the parental proteins to change the activity of the complexes, or function as additional subunits because each contains a relevant functional domain (initiation factor domain IPR019382 and ITFG2 domain PF15907, respectively). Several subunits of the spliceosome are present in cluster #8, a protein community that includes IP_637160, a novel interactor of SNRPA1, which contains a U2A'/phosphoprotein 32 family A domain (IPR003603) where U2A' is a protein required for the spliceosome assembly ##REF##9799242##[43]##. Cluster #56 contains the two regulatory subunits of PKA, PRKAR1B, and PRKAR2B, which form a dimer, and several A-kinase scaffold proteins that anchor this dimer to different subcellular compartments ##REF##18757829##[44]##. Two altProts interacting with PRKAR2B are also present in this cluster. Interestingly, altProt IP_156019 is encoded by an altORF overlapping the canonical PRKAR2B CDS; hence, <italic>PRKAR2B</italic> is a dual-coding gene with both proteins, the refProt and the altProt, interacting with each other. The discovery of new altProts in known protein communities demonstrates a potential for the increase in our knowledge of biological complexes. We compiled the results of the clustering and GO enrichment into an interactive web application available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://seb-leb.github.io/altprot-ppi\" id=\"ir005\">https://seb-leb.github.io/altprot-ppi</ext-link>.</p>", "<title>Disease association</title>", "<p id=\"p0155\">The curated list of disease–gene associations published by DisGeNET relates 6970 genes with 8141 diseases in 32,375 associations ##REF##31680165##[45]##. After mapping this disease–gene association network onto our network of protein communities, 687 clusters of which 93 contained at least one altProt were found in association with 2612 diseases (##FIG##4##Figure 5##A). The 116 disease–cluster associations involving at least one altProt were distributed among 21 disease classes (##FIG##4##Figure 5##B). The distribution of disease–cluster associations involving altProts among the disease classes was similar to those involving refProts. Thus, no preferential association of altProts with certain disease classes could be observed.</p>", "<p id=\"p0160\">A selection of subnetworks illustrates how altProts associate with different diseases (##FIG##4##Figure 5##C). <italic>ADAM10</italic> encodes a transmembrane refProt with metalloproteinase activity. Among protein substrates that are cleaved by ADAM10 and shed from cells, some act on receptors and activate signaling pathways important in normal cell physiology ##REF##19049889##[46]##. Overexpression of this protease or increased shedding of tumorigenic proteoforms results in overactivation of signaling pathways and tumorigenesis ##REF##19005493##[47]##, ##REF##32265938##[48]##. IP_233890 is an altProt expressed from bicistronic <italic>ADAM10</italic> and its association with a subnetwork of transcription factors involved in tumorigenesis may further clarify the role of that gene in cancer (##FIG##4##Figure 5##C, i). Cluster #165 illustrates the association of a pair of refProt/altProt expressed from the same dual-coding gene, <italic>ZNF408</italic>, with three different diseases (##FIG##4##Figure 5##C, ii). The implication of pseudogene-derived altProts is emphasized by the association of three of them with acute myelocytic leukemia through their interaction with <italic>ANXA2</italic> (cluster #508; ##FIG##4##Figure 5##C, iii). Two of these interactions occur between a refProt from the parental gene and altProts encoded by two of its pseudogenes.</p>", "<p id=\"p0165\">Cluster #43 relates proteins that are key regulators of entry into and progression of cell cycle, including at the level of DNA replication and check point control to preserve the integrity of the genome in dividing cells ##REF##25383541##[49]##, ##REF##30531861##[50]##. Through its association with this cluster (##FIG##4##Figure 5##C, iv), AltProt IP_236856 is likely involved in cell cycle progression and DNA integrity, and characterization of its molecular activity may yield mechanistic insight surrounding associated pathologies.</p>", "<title>Functional validation of PPIs involving an altProt</title>", "<p id=\"p0170\">Interactions representative of the three following classes of complexes involving altProts were selected for further experimental validation: an altProt encoded by a dual-coding gene and interacting with the respective refProt, an altProt expressed from a pseudogene and interacting with the refProt encoded by the parental gene, and an altProt interacting with a refProt coded by a different gene.</p>", "<p id=\"p0175\">The dual-coding <italic>FADD</italic> gene expresses altProt IP_198808 in addition to the conventional FADD protein, and both proteins interact within the DISC complex (##FIG##1##Figure 2##G, i). We took advantage of a previous study aiming at the identification of the FADD interactome to test whether this altProt may also have been missed in this analysis because the protein database used did not contain altProt sequences ##REF##27122307##[51]##. In this work, the authors developed a new method called Virotrap to isolate native protein complexes within extracellular virus-like particles to avoid artifacts of cell lysis in AP-MS. Among the baits under study FADD was selected to isolate the native FADD complex. First, we used the peptide-centric search engine PepQuery to directly test for the presence or the absence of IP_198808-derived specific peptides in the FADD complex datasets. Rather than interpreting all MS/MS spectra, this approach tests specifically for the presence of the queried peptides ##REF##26217018##[52]##. Indeed, two unique peptides from IP_198808 were detected in each of the replicates of that study via PepQuery (<xref rid=\"s0175\" ref-type=\"sec\">Figure S4</xref>A, peptides i and v). Second, we used a conventional spectrum-centric and database search analysis with the UniProt database to which was added the sequence of IP_198808. The altProt was identified in the FADD interactome (<xref rid=\"s0175\" ref-type=\"sec\">Figure S4</xref>B) with 4 unique peptides (<xref rid=\"s0175\" ref-type=\"sec\">Figure S4</xref>A, peptides i and iii–v). In cells co-transfected with Flag-FADD and IP_198808-GFP, FADD formed large filaments (##FIG##5##Figure 6##A, right), previously labeled death effector filaments ##REF##9606215##[53]##. IP_198808 co-localized in the same filaments in the nucleus, whereas the cytosolic filaments contained FADD only. Finally, this interaction was validated by reciprocal co-immunoprecipitation (Co-IP) (##FIG##5##Figure 6##A, left; <xref rid=\"s0175\" ref-type=\"sec\">Figure S5</xref>A). These proteomic, microscopic, and biochemical approaches confirmed the interaction between the two proteins encoded in dual-coding <italic>FADD</italic>.</p>", "<p id=\"p0180\">Next, we selected two pairs of interactions of an altProt expressed from a pseudogene with a refProt expressed from the corresponding parental gene. The interaction between altProt IP_624363 encoded in the <italic>EEF1AP24</italic> pseudogene and EEF1A1 (##FIG##2##Figure 3##A, vi) was confirmed by reciprocal Co-IP from cell lysate from cells co-transfected with GFP-eEF1A1 and IP_624363 (##FIG##5##Figure 6##B, left; <xref rid=\"s0175\" ref-type=\"sec\">Figure S5</xref>B). Both proteins also displayed strong co-localization signals (##FIG##5##Figure 6##B, right). In order to validate the interaction between <italic>PHBP19</italic>-encoded IP_762813 and PHB1, we performed two experiments. First, PHB1 co-immunoprecipitated with IP_762813 using cell lysates from cells co-transfected with PHB1-GFP and IP_762813-Flag (##FIG##5##Figure 6##C, left) and the reversed Co-IP was also confirmed (<xref rid=\"s0175\" ref-type=\"sec\">Figure S5</xref>C). Second, we performed independent AP-MS experiments for both IP_762813 and PHB1 in HEK293 cells. We confirmed the presence of PHB1 in the interactome of IP_762813 and the presence of IP_762813 in the interactome of PHB1 (##FIG##5##Figure 6##C, right; <xref rid=\"s0175\" ref-type=\"sec\">Figure S4</xref>C and D). Interestingly, we observed shared interactors between IP_762813 and PHB1 [IRS4 (O14654), ATP1A1 (P05023), and XPO1 (O14980)], as well as interactors specific to each. Prey–prey interactions from STRING also showed a certain interconnectivity of both interactomes, whereas each retained unique interactors (##FIG##5##Figure 6##C, right; <xref rid=\"s0175\" ref-type=\"sec\">Figure S4</xref>C). The altProt IP_117582 encoded in the <italic>BEND4</italic> gene is one of the most detected altProt with PSM in seven different pull-downs and three of these interactions were deemed high confidence by the model and integrated our network (##FIG##2##Figure 3##A, iii). The interaction with RPL18 was tested and confirmed by reciprocal Co-IP in cells co-transfected with RPL18-GFP and IP_117582-Flag (##FIG##5##Figure 6##D, left; <xref rid=\"s0175\" ref-type=\"sec\">Figure S5</xref>D), and their co-localization was also confirmed by immunofluorescence (##FIG##5##Figure 6##D, right).</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0185\">The discovery of unannotated altProts encoded by ORFs localized in “non-coding” regions of the transcriptome raises the question of the function of these proteins. The translation of altProts may result from biological translational noise producing non-bioactive molecules. Alternatively, altProts may play important biological roles ##REF##31504789##[11]##. Here, we addressed the issue of the functionality of altProts by testing their implication in PPIs. We have re-analyzed the BioPlex 2.0 proteo-interactomics data using the proteogenomics resource OpenProt which provides customized databases for all ORFs larger than 30 codons in 10 species ##REF##30299502##[20]##, ##REF##33179748##[21]##. Under stringent conditions, a total of 278 prey altProts were detected, of which 261 could be confidently mapped in the network of 254 bait refProts. Among them, 117 altProts are expressed from pseudogenes; 118 are expressed from dual-coding and bicistronic genes; and 43 are expressed from transcripts which were annotated as ncRNAs but should in fact be protein-coding. In addition to revealing new members of protein communities, this study lends definitive support to the functionality of hundreds of altProts and provides avenues to investigate their function.</p>", "<p id=\"p0190\">The detection of 278 altProts under stringent conditions confirms the hindrance introduced by three assumptions of conventional annotations: (1) eukaryotic protein-coding genes are monocistronic; (2) RNAs transcribed from genes annotated as pseudogenes are ncRNAs; and (3) ncRNAs are annotated as such based on non-experimental criteria, including the largely used 100 codons minimal length ##REF##19043537##[54]##. The persistence of these assumptions in conventional genomic annotations limits the repertoire of proteins encoded by eukaryotic genomes ##REF##29626081##[55]##. It remains possible that functional altORFs in regions of the transcriptome annotated as non-coding are exceptions and that a large fraction of genes and RNAs comply with current assumptions. However, an ever-increasing number of proteogenomics studies demonstrate that thousands of altORFs and their corresponding proteins are translated ##REF##29083303##[13]##, ##REF##32139545##[56]##.</p>", "<p id=\"p0195\">Conventional annotations introduce some confusion by opting to create a new gene entry within a previously annotated gene where a novel protein product has been reported or where novel transcripts have been mapped, rather than annotate a second ORF in the initial gene. The result is that some genomic regions have been assigned a second gene in the same orientation, nested within a previously annotated gene. This is the case for the pseudogene <italic>ENO1P1</italic> [Ensembl: ENSG00000244457; genomic location: chr1:236,483,165–236,484,468 (GRCh38.p13)] which overlaps with the protein-coding gene <italic>EDARADD</italic> [Ensembl: ENSG00000186197; genomic location: chr1:236,348,257–236,502,915 (GRCh38.p13)] which also encodes altProt IP_079312. Thus, as a result of this annotation, a pseudogene (<italic>ENO1P1</italic>) is nested within a protein-coding gene (<italic>EDARADD</italic>). Similarly, a second protein-coding gene termed <italic>AL022312.1</italic> [Ensembl: ENSG00000285025; genomic location: chr22:39,504,231–39,504,443 (GRCh38.p13)] was added within the protein-coding gene <italic>MIEF1</italic> [Ensembl: ENSG00000100335; genomic location: chr22:39,499,432–39,518,132 (GRCh38.p13)] to annotate the recently discovered altORF upstream of the <italic>MIEF1</italic> CDS ##REF##29083303##[13]##, ##REF##23950983##[57]##. We suggest that recognizing the polycistronic nature of some human genes to be able to annotate multiple protein-coding sequences in the same gene is more straightforward than annotating additional small genes nested in longer genes in order to comply with monocistronic annotations.</p>", "<p id=\"p0200\">The involvement of 261 altProts in 316 of the 19,968 PPIs in the current network represents a sizable number of previously missing nodes and edges and contributes to the understanding of network topology. The impact of altProt inclusion on network structure is revealed by the bridging role many seem to play between interconnected regions (##FIG##2##Figure 3##A, i–ix). This linkage of otherwise independent complexes introduces major changes to network structure shown to be related to biological system state (<italic>e.g.</italic>, cell type) ##REF##33961781##[9]##. Results from the current analysis are thus anticipated to yield insight regarding molecular function and mechanisms of protein complexes in the contexts of cell type and other suborganismally defined states ##REF##33961781##[9]##. Indeed, the presence of altProts in protein communities associated with known function and/or diseases makes it possible to generate testable hypotheses regarding their role in physiological and pathological mechanisms ##REF##33133425##[58]##.</p>", "<p id=\"p0205\">An important observation stemming from the current study is that many pseudogenes encode one altProt in the network, including some encoding two altProts. Strikingly, several altProts expressed from pseudogenes interact with their respective parental protein (more likely to interact compared with any pair of proteins in the network with 45 pairs of pseudogene–parental gene directly interacting out of 107 pairs <italic>vs.</italic> 39,936 direct PPIs of 56,115,693 possible pairs in the networks). This suggests that pseudogene-encoded altProts are functional paralogs and that their incorporation into homomeric protein complexes of the parental protein could modulate or change the activity of the parental complex. Such function would be reminiscent of the role of homomers and heteromers of paralogs in the evolution of protein complexes in yeast, allowing structural and functional diversity ##REF##31454312##[59]##, ##REF##17411433##[60]##. The GAPDH subnetwork with its seven pseudogene-encoded altProts is particularly striking. Besides its canonical function in glycolysis, GAPDH displays a variety of different functions in different subcellular locations, including apoptosis, DNA repair, regulation of RNA stability, transcription, membrane fusion, and cytoskeleton dynamics ##REF##20727968##[38]##, ##REF##19779498##[39]##, ##REF##22388977##[61]##. We propose that the incorporation of different paralog subunits in this multimeric complex results in the assembly of different heteromeric complexes and may at least in part entail such functional and localization diversity. This hypothesis is in agreement with the speculation that the diversity of functions associated with GAPDH correlates with the remarkable number of GAPDH pseudogenes ##REF##19835609##[37]##.</p>", "<p id=\"p0210\">Among the genes encoding the 261 altProts inserted in the network, 14 encode refProt/altProt pairs that specifically interact with each other, which implies that these pairs are involved in the same function. Such functional cooperation between a refProt and an altProt expressed from the same eukaryotic gene confirms previous observations in humans ##REF##29083303##[13]##, ##REF##32139545##[56]##, ##REF##23760502##[62]##, ##REF##11447126##[63]##. Dual-coding genes are common in viruses ##REF##20610432##[64]## and proteins expressed from viral overlapping ORFs often interact ##REF##30339683##[65]##. The general tendency of physical or functional interaction between two proteins expressed from the same gene should help decipher the role of newly discovered proteins provided that functional characterization of the known protein is available. Molecular mechanisms behind the functional cooperation of such protein pairs remain to be explored.</p>", "<p id=\"p0215\">Furthermore, several pairs of proteins encoded by the same gene but acting in distant parts of the network have also been identified. Could these altProts be a source of cross talk between functional modules under the same regulation at the genetic level, but multiplexed at the protein function level?</p>", "<p id=\"p0220\">The current study shows that the 261 altProts incorporated in the network differ from refProts by their size (6 times smaller in average), but do not form a particular class of gene products; rather they are members of common communities present throughout the proteomic landscape. Initial serendipitous detection of altProts subsequently called for proteogenomics approaches which widened discoveries via systematic and large-scale detection ##UREF##3##[66]##, ##REF##33226175##[67]##. System resilience and biodiversity have long been linked in the ecology literature ##UREF##4##[68]##; by analogy the increased proteomic diversity due to altProts could be a contributing factor to this effect in cellular systems. To find out the extent to which altProts play widespread and important biological functions will require more studies in functional genomics.</p>" ]
[]
[ "<p>Recent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions [<italic>i.e.</italic>, untranslated regions (UTRs), open reading frames overlapping annotated coding sequences in a different reading frame, and non-coding RNAs] frequently encode proteins, termed <bold>alternative proteins</bold> (<bold>altProts</bold>). This suggests that previously identified protein–protein interaction (PPI) networks are partially incomplete because altProts are not present in conventional protein databases. Here, we used the proteogenomic resource OpenProt and a combined spectrum- and peptide-centric analysis for the re-analysis of a high-throughput human network proteomics dataset, thereby revealing the presence of 261 altProts in the network. We found 19 genes encoding both an annotated (reference) and an alternative protein interacting with each other. Of the 117 altProts encoded by <bold>pseudogenes</bold>, 38 are direct interactors of reference proteins encoded by their respective parental genes. Finally, we experimentally validate several interactions involving altProts. These data improve the blueprints of the human PPI network and suggest functional roles for hundreds of altProts.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Minjia Tan</p>" ]
[ "<title>Code availability</title>", "<p id=\"p0395\">The Python scripts and notebooks containing the analyses are available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/Seb-Leb/altProts_in_communities\" id=\"ir025\">https://github.com/Seb-Leb/altProts_in_communities</ext-link>.</p>", "<title>Data availability</title>", "<p id=\"p0390\">The protein interaction AP-MS data for both IP_762813 and PHB1 in HEK293 cells are deposited to the ProteomeXchange Consortium via the PRIDE ##REF##26545397##[81]## partner repository (ProteomeXchange: PXD02249), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD02249\" id=\"ir020\">http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD02249</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0400\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0405\"><bold>Sébastien Leblanc:</bold> Conceptualization, Investigation, Visualization, Data curation, Formal analysis, Writing – original draft, Writing – review &amp; editing. <bold>Marie A. Brunet:</bold> Conceptualization, Investigation, Writing – review &amp; editing. <bold>Jean-François Jacques:</bold> Investigation, Writing – review &amp; editing. <bold>Amina M. Lekehal:</bold> Investigation. <bold>Andréa Duclos:</bold> Investigation. <bold>Alexia Tremblay:</bold> Investigation. <bold>Alexis Bruggeman-Gascon:</bold> Investigation. <bold>Sondos Samandi:</bold> Project administration, Supervision, Writing – review &amp; editing. <bold>Mylène Brunelle:</bold> Project administration, Supervision. <bold>Alan A. Cohen:</bold> Formal analysis, Writing – review &amp; editing. <bold>Michelle S. Scott:</bold> Formal analysis, Writing – review &amp; editing. <bold>Xavier Roucou:</bold> Conceptualization, Resources, Funding acquisition, Project administration, Supervision, Writing – original draft, Writing – review &amp; editing. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0420\">The following are the Supplementary material to this article:</p>", "<p id=\"p0425\">\n\n</p>", "<p id=\"p0430\">\n\n</p>", "<p id=\"p0435\">\n\n</p>", "<p id=\"p0440\">\n\n</p>", "<p id=\"p0445\">\n\n</p>", "<p id=\"p0450\">\n\n</p>", "<p id=\"p0455\">\n\n</p>", "<p id=\"p0460\">\n\n</p>", "<p id=\"p0465\">\n\n</p>", "<p id=\"p0470\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0410\">We thank the Gygi lab for providing MS datasets and particularly Ed Huttlin for helpful email exchanges. Xavier Roucou, Michelle S. Scott, and Alan A. Cohen are members of the Fonds de Recherche du Québec Santé (FRQS)-supported Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke. This research was supported by the Canadian Institutes for Health Research (CIHR) (Grant No. PJT-175322), and by a Canada Research Chair in Functional Proteomics and Discovery of Novel Proteins to Xavier Roucou. We thank the team at Calcul Québec and Compute Canada for their support with the use of the supercomputer mp2 from Université de Sherbrooke. We thank Darel Hunting for critically reviewing the manuscript.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Analysis overview and identification of altProts in the human interactome</bold></p><p><bold>A.</bold> and <bold>B.</bold> The classical model of RNA transcript CDS annotation includes only one refORF on mRNAs encoding a refProt and no functional ORF within ncRNAs (A), whereas the alternative translation model considers multiple proteins encoded in different reading frames in the same transcript including refProts and altProts (B). <bold>C.</bold> Our re-analysis pipeline of high-throughput AP-MS experiments from BioPlex 2.0 employs stringent criteria to ensure confident identification of both protein detection and interaction detection. Of the 426 altProts initially identified in the dataset, 261 joined the network of protein interactions after filtration. <bold>D.</bold> altProts are in general shorter than refProts. Boxes represent the inter quartile range marked at the median and the whiskers are set at 1.5 times inter quartile range over and under the 25th and 75th percentiles. <bold>E.</bold> Identified altProts (278) were encoded by transcripts of a variety of biotypes. 118 of identified altProts are encoded by transcripts of protein-coding biotype, 117 by transcripts of pseudogenes, and 43 exclusively by transcripts of non-coding biotype. <bold>F.</bold> altORFs found to be encoded by transcripts from genes of protein-coding biotype are most often overlapping the canonical CDS or localized downstream in the 3′ UTR. A significant fraction of altORFs also localize in ncRNAs of protein-coding genes. <bold>G.</bold> Orthology data across 10 species from OpenProt 1.6 for detected altProts. altProt, alternative protein; ORF, open reading frame; refProt, reference protein; altORF, alternative ORF; refORF, reference ORF; AP-MS, affinity purification mass spectrometry; ncRNA, non-coding RNA; CDS, coding sequence; UTR, untranslated region; FDR, false discovery rate; HCIP, high-confidence interacting protein.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Interaction mapping and network features of</bold><bold>PPI</bold><bold>s</bold></p><p><bold>A.</bold> The largest component of the network assembled from the OpenProt-based re-analysis of high-throughput AP-MS data from BioPlex 2.0. <bold>B.</bold> A venn diagram of bait–prey interactions identified with the OpenProt-derived re-analysis, BioPlex 2.0, and BioPlex 3.0 shows a significant overlap despite the smaller overall size of the re-analysis results (due to stringent filtration). It should also be noted that altProts were not present in the BioPlex 2.0 analytical pipeline which accounts for part of the gap in overlap. <bold>C.</bold> The degree distribution (distribution of node connectivity) follows a power law as demonstrated by a discrete maximum likelihood estimator fit. Most of the proteins have a small number of connections, whereas a few are highly connected (often called hubs). <bold>D.</bold> The distribution of degrees of separation between all protein pairs (<italic>i.e.</italic>, the length of the shortest path between all pairs of proteins) indicates that the network fits small-world characteristics. <bold>E.</bold> altProts were found diffusely throughout the network and across the spectrum of EVC (dark lines). EVC is a relative score that indicates the degree of influence of nodes on the network; here, altProts display involvement in both influential and peripheral regions. <bold>F.</bold> Known protein complexes from the CORUM 3.0 resource (Giurgiu et al. ##REF##30357367##[75]##) were mapped onto the network. Subunit recovery rate confirms the overall validity of the interactions confidently identified by the pipeline. All CORUM core complexes for which at least two subunits appear as baits in the network were considered. <bold>G.</bold> Selected CORUM complexes are shown with the addition of altProts found in the interaction network of baited subunits. Black edges indicate detection in the re-analysis, and gray edges indicate those only reported by CORUM. PPI, protein–protein interaction; EVC, eigenvector centrality.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Specific features of</bold><bold>PPI</bold><bold>s involving preyed altProts</bold></p><p><bold>A.</bold> Degree-sorted circular layout of the OpenProt-derived full network separated by bait and preys. Direct neighbors and neighbors of neighbors (here called second neighborhood) were extracted for each altProt. Second neighborhoods of altProts display a variety of topologies with some acting as bridges (iv, v, vii, and ix) and others embedded in interconnected regions (i–iii and vi). Larger nodes represent the proteins for which the second neighborhood was extracted. <bold>B.</bold> Second neighborhood of the refProt LDHC extracted from the network assembled without altProts (i) and with altProts (ii). Inclusion of altProts in the network revealed that LDHC second degree network contains two proteins encoded by pseudogenes of the LDH family. Larger nodes represent the proteins for which the second neighborhood was extracted. <bold>C.</bold> Detailed second neighborhood of two pseudogene-encoded altProts. (i) GAPDH refProt shows 9 altProt interactors encoded by pseudogenes of GAPDH. (ii) AltProt encoded by <italic>PHBP19</italic> seen in the neighborhood of the PHB refProt. Larger nodes represent the proteins for which the second neighborhood was extracted. <bold>D.</bold> altProt found in the direct interactome of corresponding refProt from parental genes display a wide array of sequence similarity to the refProt. Pairs of altProt–refProt from pairs of pseudogene–parental gene are slightly closer in the network if their NW protein sequence global alignment score is higher. <bold>E.</bold> The distribution of degrees of separation between altProt–refProt pairs of the same gene is bimodal with a sub-population (75%) following a distribution similar to the full network (see ##FIG##1##Figure 2##D), and the other placing altProts in the direct neighborhood of refProts from the same gene. NW, Needleman–Wunch.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Protein communities obtained via unsupervised community detection reveal new members</bold></p><p><bold>A.</bold> Protein communities identified via the Markov clustering algorithm (Enright et al. ##REF##11917018##[41]##). A total of 1054 clusters and 266 connections between them were identified; however, here are shown only components of three clusters or more for brevity. Nodes represent protein clusters sized relative to the number of proteins. Connections between clusters were determined by calculating enrichment of links between proteins in pairs of clusters using a hypergeometric test with maximal alpha value of 0.05 and correction for multiple testing was applied with 1% FDR. <bold>B.</bold> Focus on selected clusters showing significant enrichment of GO terms. Enrichment was computed against background of whole genome with alpha value set to &lt; 0.05 and Benjamini–Hochberg corrected FDR of 1%. GO, Gene Ontology; BP, biological process; MF, molecular function; CC; cellular compartment.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Communities of proteins with altProt members are associated</bold><bold>with</bold><bold>disease phenotypes</bold></p><p><bold>A.</bold> Network of associations between protein clusters (blue and red nodes) and diseases (yellow nodes) from DisGenNet. Gene–disease enrichment was computed for each pair of disease–cluster, and associations were deemed significant after hypergeometric test with alpha set to 0.01 and multiple testing correction set at maximum 1% FDR. <bold>B.</bold> Disease–cluster associations counted by disease classification (altProt-containing clusters as red bars, and refProt-only clusters as blue bars) and sorted by portion of associations involving a cluster with altProts (dark red bars). <bold>C.</bold> Focus on clusters with significant disease associations showing involvement of altProts. <italic>ADAM10</italic> is a gene associated with tumorigenesis and produces an altProt here detected as part of a cluster associated to neoplastic processes (i). Other disease–cluster associations include genetic connective tissue diseases involving a pair of proteins encoded by the same gene (ii) and a cluster comprising pseudogene-derived altProts and parental gene refProt in association with another oncological pathology (iii). Cluster #43 highlights associations of a cluster to both rare and common diseases with a community of proteins located at the membrane (iv).</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>Experimental validation of refProt–altProt interactions</bold></p><p><bold>A.</bold> Validation of FADD and IP_198808 protein interaction encoded by a bicistronic gene. Left panel: immunoblot of Co-IP with GFP-trap Sepharose beads performed on HEK293 lysates co-expressing Flag-FADD and IP_198808-GFP or GFP only. Right panel: confocal microscopy of HeLa cells co-expressing IP_198808-GFP (green channel) and Flag-FADD (immunostained with anti-Flag; red channel). r = Pearson’s correlation. The associated Manders’ Overlap Coefficients are M1 = 0.639 and M2 = 0.931, respectively. <bold>B.</bold> Validation of eEF1A1 and IP_624363 protein interaction encoded by a pseudogene/parental gene couple. Left panel: immunoblot of Co-IP with Anti-FLAG magnetic beads performed on HEK293 lysates co-expressing GFP-eEF1A1 and IP_624363-Flag or pcDNA3.1 empty vector. Right panel: confocal microscopy of HeLa cells co-expressing GFP-eEF1A1 (green channel) and IP_624363-Flag (immunostained with anti-Flag; red channel). r = Pearson’s correlation. The associated Manders’ Overlap Coefficients are M1 = 0.814 and M2 = 0.954, respectively. <bold>C.</bold> Validation of PHB1 and IP_762813 protein interaction encoded by a pseudogene/parental gene couple. Left panel: immunoblot of Co-IP with Anti-FLAG magnetic beads performed on HEK293 lysates co-expressing PHB1-GFP and IP_762813-Flag or pcDNA3.1 empty vector. Right panel: comparison of the interaction networks of IP_762813-Flag (purple) and PHB1-GFP (blue) from independent AP-MS experiments of both proteins. Three independent AP-MS datasets for each protein. <bold>D.</bold> Validation of RPL18 and IP_117582 protein interaction. Left panel: immunoblot of Co-IP with Anti-FLAG magnetic beads performed on HEK293 lysates co-expressing RPL18-GFP and IP_117582-Flag or pcDNA3.1 empty vector. Right panel: confocal microscopy of HeLa cells co-expressing RPL18-GFP (green channel) and IP_117582-Flag (immunostained with anti-Flag; red channel). r = Pearson’s correlation. The associated Manders’ Overlap Coefficients are M1 = 0.993 and M2 = 0.972, respectively. All Western blots and confocal images are representative of at least three independent experiments. GFP, green fluorescent protein; IP, immunoprecipitation; Co-IP, co-immunoprecipitation.</p></caption></fig>", "<fig id=\"f0035\" position=\"anchor\"><label>Supplementary Figure S1</label><caption><p><bold>Network assembly details A.</bold> Overlap of total proteins (nodes) in BioPlex 2.0 and OpenProt derived networks. <bold>B.</bold> Classifier performance across thresholds. Scores were computed using the BioPlex 2.0 network as ground truth. <bold>C.</bold> The overlap of unfiltered interactions between BioPlex 2.0 and the result of OpenProt 1.6 derived re-analysis was considerable (92% of re-analysis candidate PPIs) (i). Upon filtration the overlap is still significant despite the marked smaller size of the OpenProt derived network (59% of re-analysis PPIs). <bold>D.</bold> Detailed counts of protein and interaction identifications.</p></caption></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary Figure S2</label><caption><p><bold>PSM score distributions and validation of novel peptide fragmentation A.</bold> Distribution of PSM scores involving peptides of refProts (blue) and altProts (red). The histogram shows the distribution of scores for those below 100%. PSM scoring is a combination of scores from all search algorithms via SearchGUI and is outputted as a confidence level. <bold>B.</bold> Distribution of Pearson correlation scores indicating the degree to which spectra obtained from synthetic peptides were found contained in spectra observed in the BioPlex data. 100 peptides from altProts were synthesized and analyzed under an MS/MS regime similar to BioPlex to validate the fragmentation pattern of observed spectra (see Methods). 98 synthetic peptides produced spectra correlating with the spectra of the corresponding peptides observed in the BioPlex data. 2 synthetic peptides were not detected in the analysis and were excluded from the comparisons. <bold>C.</bold> Top: spectrum observed in the BioPlex data (spectrum title: j6218.11202.11202.2) assigned to peptide APSGPTALGLGAAYER uniquely mapping to the altProt IP_250569 encoded by the long non-coding RNA gene AC004706.3. Bottom: spectrum obtained from MS/MS analysis of the synthetic peptide APSGPTALGLGAAYER. The two spectra have a PCC of 0.66 which places the comparison near the median for all peptides. The majority of comparisons between observed and synthetic spectra is therefore of equal or better quality to that of APSGPTALGLGAAYER. alt, alternative; ref, reference; PSM, peptide spectrum match; PCC, Pearson correlation coefficient.</p></caption></fig>", "<fig id=\"f0045\" position=\"anchor\"><label>Supplementary Figure S3</label><caption><p><bold>GAPDH pseudogenes identified with unique peptides A.</bold> Alignement of GAPDH refProt sequence with the altProt sequences derived from pseudogenes of GAPDH. Blue color represents the level of identity between sequences per amino acid. Boxed subsequences show the peptides detected in the BioPlex 2.0 raw data. Amino acids colored in red highlight the differences with the refProt sequence. A spectrum associated to the peptide boxed in blue is shown in panel B. <bold>B.</bold> Mass spectrum from the BioPlex 2.0 (file name: j6172.raw, spectrum title: j6172.8294.8294.2) shows the presence of two similar peptides. All four spectrum matching algorithms assigned the spectrum to the pseudogene derived altProt but shifted peaks of y fragment ions suggested the presence of a similar peptide from the refProt with a single amino acid difference (T&gt;A). Peak annotations in green correspond to the y ions of the refProt peptide.</p></caption></fig>", "<fig id=\"f0050\" position=\"anchor\"><label>Supplementary Figure S4</label><caption><p><bold>Validation details A.</bold> Validation of interaction between proteins FADD and IP_198808 encoded by the same mRNA. IP_198808 peptides iii, iv, and v were detected in re-analyses of both ViroTrap and BioPlex 2.0 AP-MS of FADD. Peptides i and ii were exclusively identified in ViroTrap and BioPlex 2.0 re-analyses, respectively. PSMs for i and v from the ViroTrap dataset were validated against unrestricted modifications of refProts using PepQuery. <bold>B.</bold> FADD network after re-analysis of ViroTrap MS data including IP_198808 sequence in the database. <bold>C.</bold> Detailed view of the combined network from AP-MS experiments of PHB refProt and PHBP19 altProt. <bold>D.</bold> Alignment of IP_762813 altProt encoded by pseudogene PHBP19 and PHB1 refProt sequences based on amino acids using Clustalω with default settings. Blue shading indicates amino acid similarity. Unique peptides detected are underlined red.</p></caption></fig>", "<fig id=\"f0055\" position=\"anchor\"><label>Supplementary Figure S5</label><caption><p><bold>Complementary co-IP immunoblot validatio</bold>n <bold>A.</bold> Validation of FADD and IP_198808 protein interaction encoded by a bicistronic gene. Immunoblot of co-IP with Anti-FLAG magnetic beads performed on HEK293 nuclear extract co-expressing Flag-FADD and IP_198808-GFP or pcDNA3.1 empty vector with IP_198808-GFP. <bold>B.</bold> Validation of eEF1A1 and IP_624363 protein interaction encoded from a pseudogene/parental gene couple. Immunoblot of co-IP with GFP-trap sepharose beads performed on HEK293 lysates co-expressing GFP-eEF1A1 and IP_624363-Flag or GFP with IP_624363-Flag constructs. <bold>C.</bold> Validation of PHB1 and IP_762813 protein interaction encoded by a pseudogene/parental gene couple. Immunoblot of co-IP with GFP-trap sepharose beads performed on HEK293 lysates co-expressing PHB1-GFP and IP_762813-Flag or GFP with IP_762813-Flag constructs. <bold>D.</bold> Validation of RPL18 and IP_117582 protein interaction. Immunoblot of co-IP with GFP-trap sepharose beads performed on HEK293 lysates co-expressing RPL18-GFP and IP_117582-Flag or GFP with IP_117582-Flag constructs. All western blots and confocal images are representative of at least 3 independent experiments.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"t0005\"><label>Table 1</label><caption><p><bold>Terminology definitions</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Terminology</bold></th><th><bold>Definition</bold></th></tr></thead><tbody><tr><td>ORF</td><td>Sequence of nucleotides bounded by start and stop codons potentially translated into protein by ribosomes</td></tr><tr><td>refORF</td><td>Annotated ORF producing a known protein</td></tr><tr><td>altORF</td><td>Unannotated ORF producing an unknown/unannotated protein; altORFs can be found on mRNAs overlapping refORFs or in untranslated regions, or on ncRNAs</td></tr><tr><td>refProt</td><td>Annotated protein product resulting from the translation of a refORF</td></tr><tr><td>altProt</td><td>Unannotated protein product resulting from the translation of an altORF with no significant homology with any refProt from the same gene</td></tr><tr><td>Novel isoform</td><td>Unannotated protein product resulting from the translation of an altORF with high homology to a refProt from the same gene</td></tr></tbody></table></table-wrap>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary File S1</title><p><bold>BioPlex altProt spectra</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S1</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S2</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S3</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S4</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S5</title></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p><italic>Note</italic>: ORF, open reading frame; refORF, reference ORF; altORF, alternative ORF; refProt, reference protein; altProt, alternative protein; ncRNA, non-coding RNA.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"d35e182\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0170\" fn-type=\"supplementary-material\"><p id=\"p0415\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.09.008\" id=\"ir030\">https://doi.org/10.1016/j.gpb.2022.09.008</ext-link>.</p></fn></fn-group>" ]
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2024-01-14 23:41:59
Genomics Proteomics Bioinformatics. 2023 Jun 30; 21(3):515-534
oa_package/e3/cc/PMC10787177.tar.gz
PMC10787190
0
[ "<title>Introduction</title>", "<p>Photodynamic therapy (PDT) is an evolving treatment modality that has gained approval from the U.S. Food and Drug Administration for the treatment of various cancers, including microinvasive lung cancer, obstructing esophageal cancer, and non-small cell lung cancer. It is also utilized for premalignant conditions, such as Barrett’s esophagus, and non-oncologic conditions, such as age-related macular degeneration.##REF##15896084##1##<named-content content-type=\"online\"></named-content><named-content content-type=\"print\"><sup>–</sup></named-content>##REF##17030646##4## PDT offers valuable advantages, such as minimal invasion, low systemic toxicity, versatility, and repeatability. However, the optimal clinical outcomes of PDT have been hindered by the lack of a reliable dosimetry metric that accurately quantifies the effective treatment dose, which is essential for predicting and guiding PDT.##REF##27552311##5## The challenges in achieving accurate dosimetry for PDT stem from its dynamic and complex nature, involving intricate interactions between light, the photosensitizer (PS), and tissue oxygen ().##REF##8310013##6## In a typical PDT process, the PS is excited by specific wavelengths of treatment light, causing it to transition from its ground state to the excited singlet state. Subsequently, the PS undergoes intersystem crossing, leading to its transition to the triplet state. Type II PDT, the most clinically relevant process, occurs when the triplet state transfers energy to ground-state oxygen, , generating singlet oxygen, . This singlet oxygen induces photodamage in the photosensitized area.##UREF##0##7##<named-content content-type=\"online\"></named-content><named-content content-type=\"print\"><sup>–</sup></named-content>##REF##28084040##11##</p>", "<p>Conventional PDT dosimetry relies on a prescribed administered drug dose and the total light fluence, which represents the energy per unit area delivered by the end of treatment. Although these basic dosimetry metrics can be accurately and easily monitored, they often prove insufficient due to significant inter- and intra-patient variability in PS localization and the tumor microenvironment.##UREF##1##12##<named-content content-type=\"online\"></named-content><named-content content-type=\"print\"><sup>–</sup></named-content>##UREF##2##14## Thus, the improvement of dosimetry methods is crucial for advancing the application of PDT. The PDT dose, defined as the temporal integral of the product of <italic>in vivo</italic> PS concentration and light fluence in the target tissue, has been demonstrated in several preclinical studies as a more effective dosimetric quantity than light fluence or PS concentration alone, particularly under well-oxygenated conditions.##REF##27552311##5##<sup>,</sup>##UREF##3##15##<named-content content-type=\"online\"></named-content><named-content content-type=\"print\"><sup>–</sup></named-content>##REF##28083883##17##</p>", "<p>Our research group has developed a dosimeter that enables the simultaneous measurement of light fluence rate and PS fluorescence during treatment. This dosimeter has been successfully employed in clinical measurements as part of an ongoing phase II/III clinical trial of Photofrin-mediated PDT for pleural mesothelioma.##REF##27825687##18##<named-content content-type=\"online\"></named-content><named-content content-type=\"print\"><sup>–</sup></named-content>##UREF##4##20## The measured PS fluorescence at the tissue surface allows for the calculation of PS concentration. Together with the measured light fluence, this information facilitates the determination of the PDT dose delivered to the superficial tissue of the pleural cavity. We have observed spatial heterogeneities in the delivered PDT dose on the cavity surface due to complex pharmacokinetics and tissue conditions.##UREF##2##14## Consequently, it is crucial for the dosimetry system to cover the entire cavity surface rather than focusing on a single isolated point. To address this, the newly developed dosimetry system features eight dual-function channels, enabling the monitoring of eight different locations. The primary aim of this study is to provide updated information on PDT dose variations within the context of our pleural PDT clinical trial. Notably, the study expands its scope by increasing the number of patients from 8 to 20 and the inclusion of sites from 22 to 78.##UREF##2##14##<sup>,</sup>##UREF##5##21## Furthermore, our research involves a thorough and detailed examination of the obtained data. This includes a comprehensive reanalysis of fluorescence data to derive PS uptake, a thorough reevaluation of tissue optical properties through Diffuse Reflectance Spectroscopy (DRS) data, and a complete reassessment of optical property correction factors for determining PS uptake in both patients and phantoms. Through these efforts, we address previously existing gaps in the literature, providing a more comprehensive and updated understanding of the subject matter. In addition, we aim to incorporate an optical infrared (IR) navigation system to provide comprehensive dosimetry guidance throughout the pleural PDT procedure. Although existing real-time dosimetry methods primarily focus on <italic>in-vivo</italic> light fluence measurements, the use of innovative instruments makes real-time PDT dose evaluation feasible. This study provides a summary of the current state of the art in multichannel PDT dose measurements for clinical applications and explores the various potentials of this versatile dosimetry system.</p>" ]
[ "<title>Materials and Methods</title>", "<title>Clinical Trial and Concurrent Measurements</title>", "<p>Patients with pleural mesothelioma were enrolled in a phase II/III randomized clinical trial at the Hospital of the University of Pennsylvania after providing informed consent. A subset of patients underwent lung-sparing surgical resection combined with interoperative Photofrin-mediated PDT, and the remaining patients received surgery alone. Further details regarding the PDT technique and treatment protocol can be found elsewhere.##REF##25995987##22## For patients receiving PDT, Photofrin (Pinnacle Biologics, Chicago, Illinois) was administered intravenously at a dose of 2 mg per kg of body weight, 24 h prior to PDT. PDT was performed immediately following surgery using a KTP-pumped dye laser (model 630 XP, Laserscope, Inc., San Jose, California) with 632 nm light. The prescribed total light fluence was set at . The instantaneous light fluence rate was measured using eight isotropic detectors (Medlight SA, Ecublens, Switzerland) sutured at the apex, posterior chest wall (PCW), anterior chest wall (ACW), posterior sulcus (PS), anterior sulcus (AS), posterior mediastinum (PM), pericardium (Peri), and diaphragm (Diaph)##REF##32053799##23## on the pleural cavity surface (see ##FIG##0##Fig. 1##). The cumulative light fluence was simultaneously calculated until the prescribed light dose was achieved at all locations. In addition to the light fluence rate, the Photofrin fluorescence excited by the treatment light was monitored using the same eight isotropic detectors. The light was delivered via a bare optical fiber embedded in a modified endotracheal tube. To facilitate light scattering, the treatment tube and pleural cavity were filled with 0.1% Intralipid. The physician sequentially moved the light source along the inner surface of the cavity during PDT until the prescribed light dose was reached.##UREF##6##24##</p>", "<p>Accurately quantifying fluorescence emission <italic>in vivo</italic> is challenging due to the varying optical properties of the surrounding tissue. To mitigate this effect, diffuse reflectance measurements were obtained on the inner surface of the pleural cavity before and after PDT treatment for optical property correction. A custom-made fiber optic-based contact probe (FiberOptic Systems, Inc., Simi Valley, California) was employed, consisting of one source fiber connected to an air-cooled quartz-tungsten-halogen lamp (Avalight HAL-S, Avantes, Inc., Louisville, Colorado) and nine detection fibers spaced at distances ranging from 1.4 to 8.7 mm from the source fiber. The detection fibers captured the diffuse reflected light, which was then directed to a spectrograph and recorded on a charge-coupled device (CCD)-based camera sensor (InSpectrum 150, Roper Scientific, Princeton, New Jersey) for radially resolved diffuse reflectance measurement. Background signals were concurrently measured for subsequent subtraction. The acquired spectra were fitted using a nonlinear fitting algorithm implemented in the MATLAB programming environment (The MathWorks, Natick, Massachusetts) to extract the tissue optical properties at each measured location. Further information regarding the probe design and fitting algorithm can be found elsewhere.##UREF##5##21##<sup>,</sup>##UREF##7##25##</p>", "<title>PDT Dose Dosimeter Instrumentation</title>", "<p>The comprehensive multichannel dosimetry system incorporated the use of eight isotropic detectors that were sutured onto the interior pleural surface. These detectors were connected to individual channels within the dosimetry system. ##FIG##1##Figure 2## provides a front view of the multichannel dosimetry system and a schematic diagram of its internal setup. The system enclosure contained a total of 16 channels [##FIG##1##Fig. 2(a)##]. The internal structure of the equipment is shown in ##FIG##1##Fig. 2(b)##. The bottom row was comprised of channels 1 to 8, with each channel split into two fibers through 1-to-2 bifurcated fibers (Ocean Optics, Dunedin, Florida) internally inside the box. The bifurcated fibers of each channel were connected to the photodiodes and one spectrometer (Exemplar, B&amp;W Tek, Inc., Newark, Delaware) for the simultaneous monitoring of the fluence rate of the treatment light and Photofrin fluorescence. To block the treatment light, a long-pass filter was installed for each channel in conjunction with the spectrometer. Due to space constraints, the remaining channels (channels 9 to 16) do not have the bifurcations, so they cannot measure the PS uptake and were solely connected to the dosimetry system. The PDT dose dosimetry instrument always had 16 channels for light dosimetry and was incrementally expanded to 8 channels to measure the PS uptake and light fluence rate simultaneously.</p>", "<p>The spectrometers were utilized for measuring the Photofrin fluorescence, and the photodiodes served as monitors for the fluence rate of the treatment light. Recently, the dual-function channels were expanded from four to eight, allowing for a more comprehensive measurement of the entire cavity. The spectrometer had a wavelength range of 200 to 1050 nm and a resolution of 0.42 nm using a diode array with dimensions of elements and an element size of . The achieved spectral resolution was 0.47 nm. The isotropic detector directly measured the light fluence rate at the surface of the cavity. However, it should be noted that this measurement might differ from the intra-tissue light fluence rate due to variations in tissue optical properties. To ensure the accurate measurement of the transmitted fluorescence (signal after 633 nm), long pass filters (Semrock, Inc., Rochester, New York) were employed to block the treatment light. No filtration was required for the treatment-light signal prior to reaching the photodiodes.##REF##29106380##26## In this study, all eight isotropic detectors were utilized and connected to channels 1 to 8 to simultaneously measure the fluence rate of the treatment light and Photofrin fluorescence throughout the pleural cavity.</p>", "<title>Spectroscopy</title>", "<p>Fluorescence spectra were collected for eight strategic locations within the pleural cavity wall, as described in Sec. <xref rid=\"sec2.1\" ref-type=\"sec\">2.1</xref> and shown in ##FIG##0##Fig. 1##, using eight single-channel CCD spectrometers. To evaluate the concentration of Photofrin, the raw fluorescence spectra obtained during PDT were corrected for the spectral response of each spectrometer. Subsequently, a single value decomposition (SVD) fitting algorithm was applied to analyze the spectra using a basis spectrum [##FIG##2##Fig. 3(a)##].##REF##11202366##27## The basis spectrum consisted of a laser component and a Photofrin fluorescence component, which were established through extensive phantom studies. The laser component served as a reference for the excitation light intensity. Background spectra were measured and subtracted. In the SVD algorithm, a 21-term Fourier series was incorporated to account for any unknown spectroscopic components, such as ambient room light. However, its weight in the fitting routine was lower than that of the measured fluorescence emission components.</p>", "<p>##FIG##2##Figure 3(b)## presents an example of representative raw fluorescence spectra measured from the eight channels of patient #53. Throughout the treatment, each channel captured hundreds of fluorescence spectra, which were individually fitted using the SVD algorithm. The peaks observed around 675 nm corresponded to the fluorescence signal of Photofrin detected by the isotropic detectors. Slight shifts in the peak wavelengths were observed across different channels, attributed to the distinct long-pass filter characteristics of each channel. To accommodate this, during SVD fitting, adjustments were made to the basis spectrum to align with the shifted peaks for different channels. By fitting the raw measured spectra with the basic components, unitless SVD amplitudes were obtained. The laser components enabled the elimination of variations in the excitation light, allowing for the quantification of the local Photofrin concentration. A linear relationship was found between the SVD amplitudes and the local Photofrin concentration, enabling the quantification by multiplying with a constant. The determination of this constant was demonstrated in a previous study.##REF##29106380##26## The SVD fitting method utilized a large number of fluorescence spectra measured throughout the treatment at each location, leading to a significant reduction in uncertainties. The SVD fitting results were later adjusted to accommodate distortions arising from variations in optical properties, as elaborated in detail in Sec. <xref rid=\"sec2.4\" ref-type=\"sec\">2.4</xref>.</p>", "<title>Optical Property Correction</title>", "<p>Accurately quantifying the Photofrin concentration using raw fluorescence spectra captured by the spectrometer has proven challenging due to the complexity of the surrounding tissues.##REF##34692191##28##<named-content content-type=\"online\"></named-content><named-content content-type=\"print\"><sup>–</sup></named-content>##REF##25911633##31## To account for the influence of different optical properties on the detected fluorescence signal, a correction factor based on absorption coefficient () and scattering coefficient () was introduced.##UREF##6##24##<sup>,</sup>##UREF##8##32## This correction factor, CF, was determined using a series of tissue-simulating phantoms with varying optical properties ( to and to ) while keeping the Photofrin concentration constant at . Intralipid (Fresenius Kabi, Germany) was used as a light scatterer, and ink (Parker<sup>®</sup> Quink<sup>®</sup>) served as the light absorber in the phantoms. The values of and represent the absorption and reduced scattering coefficients, respectively, at the emission wavelength of 630 nm, corresponding to the Photofrin fluorescence. The fluorescence signals from these phantoms were measured using the 8-channel PDT dosimeter. The raw fluorescence spectra obtained were then fitted using the SVD fitting algorithm described in the previous section, yielding an SVD amplitude () for each phantom, as shown in ##FIG##2##Fig. 3(c)##. An empirical formula fitting the experimental data was employed to calculate the optical property correction factor, <italic>CF</italic>, from a given tissue optical properties to that of the reference tissue optical properties ( and ): where parameters , , , and , were determined from fitting by Origin Pro 2023b (OriginLab Corp., Northampton, Massachusetts). The SVD amplitude obtained from the fluoresce spectrum is corrected by the calculated CF: </p>", "<p>Monte Carlo calculations were conducted to determine the fitting function and its parameters.##REF##29106380##26##<sup>,</sup>##UREF##9##33## A different set of tissue-simulating phantoms, featuring varied Photofrin concentrations ranging from 0 to , was employed to create a calibration curve for the and the absolute Photofrin concentrations. The resulting calibration curve is shown in ##FIG##2##Fig. 3(d)##. This calibration curve enables the determination of absolute Photofrin concentrations by utilizing the optical property correction factor ().</p>", "<title>Real-Time Scanning and Navigation System</title>", "<p>To enhance the prediction and efficacy of PDT, our research group has developed a comprehensive real-time scanning and navigation system, in addition to the light dosimetry system. This system consists of a commercial optical infrared (IR) camera (Polaris, NDI, Waterloo, Canada), trackable wands, and a 3D scanner, as shown in ##FIG##3##Fig. 4##. The hand-held 3D scanner (Structure Core, Occipital, Boulder, Colorado) is utilized for rapid and precise capture and reconstruction of the pleural cavity, enabling the identification of the target surface for real-time calculation of light fluence distribution during PDT.##UREF##10##34## The IR navigation system comprises stereo cameras, a modulated laser source (wavelength 850 nm), and a treatment wand equipped with the PDT light source and nine passive markers. The cameras track the position of the light source in real time by detecting the light reflected from the markers on the wand at a rate of 20 to 60 Hz. This navigation system has been successfully employed in clinical trials for both HPPH- and Photofrin-mediated pleural PDT. The collected data from these trials have been utilized for post-treatment analysis, providing valuable insights into the treatment process and facilitating outcome prediction.##UREF##11##35## By incorporating this innovative scanning and navigation system alongside the dosimetry system, we can provide more comprehensive real-time guidance for PDT, leading to improved treatment efficiency.</p>", "<p>To provide real-time feedback on the light fluence distribution across the entire inner surface of the cavity, a newly developed graphical user interface (GUI) was implemented.##UREF##12##36##<sup>,</sup>##REF##35996976##37## This GUI enables the visualization of the light fluence distribution in real time. Simultaneously, the light dosimetry system was utilized to measure the light fluence for verification purposes. It should be noted that the light fluence at each point of interest on the inner surface of the cavity is the sum of both the primary component and the scattered component of the treatment light.##REF##25995987##22## The GUI provides a comprehensive and real-time representation of the light distribution, allowing for enhanced monitoring and optimization of the PDT procedure. The primary component of the light fluence rate () is calculated as where is the source power (mW) and is the distance (mm) between the point light source and the cavity surface. For more accurate calculation, scatter light fluence rate is included; it is calculated as where is an empirical constant.##REF##32053799##23##<sup>,</sup>##REF##35996976##37## The ultimate goal is to integrate this innovative system with the newly developed 8-channel dosimetry system, enabling the provision of real-time PDT dose information for the pleural cavity during PDT.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Tissue Optical Properties and Correction Factors</title>", "<p>In this study, <italic>in vivo</italic> diffuse reflectance measurements were conducted at 52 sites within the pleural cavities of 11 patients. Initially, the PDT dose dosimetry system had four channels capable of simultaneously measuring light fluence rate and fluorescence. However, for the latest two patients, the system was expanded to eight channels, covering all eight predetermined locations within the pleural cavity for each patient. In this paper, the presented data for the four-channel system differ from previously reported results obtained using the same system. All raw data underwent thorough validation and were re-analyzed specifically for this study. ##TAB##0##Table 1## summarizes the tissue absorption and reduced scattering coefficients ( and ) at the excitation wavelength of 630 nm for all measurement sites where diffuse reflectance spectra were obtained, along with the corresponding correction factors. Significant heterogeneity in both absorption and reduced scattering coefficients can be observed both within and among patients.</p>", "<p>The maximum variation of and is 8 times and 2.8 times, respectively, among all sites with a mean (SD) of (0.13) and (2.4) , respectively. The variations in tissue optical properties can be attributed to factors such as thermal damage to the surrounding tissue induced by electrosurgery during tumor resection and the diverse characteristics of cellular content and chromophores throughout the tissues.##REF##32003006##38## These factors are uncontrollable during the treatments, necessitating post-treatment correction. To provide a comprehensive understanding and address the influence of optical properties, correction factors derived from measurements taken at 78 sites across 20 patients at the treatment wavelength are illustrated in ##FIG##4##Fig. 5##. This includes data from earlier cases using 2- or 4- channel PDT dose dosimetry systems. CFs were computed for individual sites using Eq. (1) to adjust the measured fluorescence for distortions arising from variable optical properties at different sites and among different patients. This correction is essential for ensuring the accurate quantification of PS concentration. The CFs range from 0.54 to 2.57 across the 78 sites. The mean CF value is 1.0 (indicated by the dashed line), and the median CF value is 1.08. The values for each site are presented in ##TAB##0##Table 1##. The maximum variation among all sites is 4.7 times, and the maximum variation among sites within individual patients is 1.8 times.</p>", "<title>Temporal and Spatial Distribution of Photofrin and PDT Dose</title>", "<p>##FIG##5##Figure 6## shows the temporal changes in local Photofrin concentrations for 16 sites in the most recent two cases, in which all eight dual-function channels were utilized. The discrete data points in the graph were obtained from measured fluorescence spectra using the SVD fitting method described earlier. It is worth noting that some data points exhibit larger variations, which can be attributed to the fluctuations in the incident treatment light fluence rate (ranging from 0 to ). This variation stems from the movement of the light source during PDT, which introduces errors in the measurement of Photofrin fluorescence excited by the treatment light.</p>", "<p>To facilitate a clearer observation of the trend of Photofrin variation during the treatment, the fitted data points for each channel were smoothed by calculating the average of all data points every 10 min of treatment time. The smoothed results are depicted by the solid curves in the graph. The relatively small temporal fluctuations in Photofrin concentration throughout the treatment for each site suggest that, despite the significant variations observed between different locations, the changes in Photofrin uptake over time within each site remain relatively stable. This phenomenon suggests that the uptake of Photofrin is not significantly influenced by the treatment itself but exhibits variation across different locations. The observed differences in optical properties ( and , tabulated in ##TAB##0##Table 1## for each patient) at these locations can be attributed to the inherent complexity of the tissue environment. This observation aligns with the substantial variation in CFs (see ##FIG##4##Fig. 5##), calculated based on the tissue optical properties at the sites, as described in Sec. <xref rid=\"sec3.1\" ref-type=\"sec\">3.1</xref>. Importantly, there is no significant photobleaching of Photofrin during PDT, corroborating findings from previous studies.##REF##29106380##26##</p>", "<p>The mean Photofrin concentrations (shown on the left axis) and PDT doses (shown on the right axis) obtained from all 78 sites in the pleural cavities of 20 patients are shown in ##FIG##6##Fig. 7##. The average (SD) and median Photofrin concentrations for all 78 sites are 4.98 (2.38) and , respectively. The PDT dose delivered to each site is defined as the product of the local Photofrin concentration ([PS], in ) and the delivered light dose. The treatment for each site was halted when the measured total light fluence of was reached, ensuring a consistent total fluence across all subjects: </p>", "<p>The differences in effective PDT doses delivered to different sites were influenced by the heterogeneities in Photofrin uptakes along the pleural cavities. The delivered PDT doses for each site are shown on the same plot (##FIG##5##Fig. 6##) with a secondary vertical axis on the right to indicate the corresponding values. The average (SD) and median PDT doses for all 78 sites are 493 (236) and , respectively. The maximum variation among all sites is 9.8 times, indicating significant differences in the delivered PDT doses across the pleural cavities. Similarly, the maximum variation among sites within each patient is 3.1 times, highlighting the variability in PDT doses within individual patients.</p>", "<p>The substantial variations observed within and among patients align with previous studies and underscore the importance of considering both Photofrin concentration and PDT dose in the development of an effective dosimetry system. Traditional approaches that solely rely on monitoring light fluence may not provide comprehensive information to ensure uniform PDT doses across all treatment sites. One potential limitation in real-time monitoring of Photofrin concentration is the time-consuming post-treatment fitting and analysis of measured fluorescence spectra. However, this study demonstrates relatively stable Photofrin concentrations throughout the time course of PDT, enabling the utilization of data acquired at the beginning of treatment for comprehensive real-time guidance throughout the rest of the procedure. Therefore, the innovative 8-channel PDT dose dosimeter holds the potential to assist physicians in delivering more uniform PDT doses to all sites, ultimately improving the outcomes of pleural PDT treatment.</p>", "<title>Real-Time Navigation System</title>", "<p>The preliminary results for light delivery efficiency with and without real-time guidance using the scanning and navigation system are depicted in ##FIG##7##Fig. 8##. A pleural phantom (see ##FIG##0##Fig. 1##), created using a 3D printing technique and based on a CT scan of an actual human pleural cavity, was utilized in our real-time navigation study. To simulate clinical conditions more accurately, six isotropic detectors were placed at predetermined locations on the inner surface of the pleural phantom (Apex, PCW, ACW, PS, PM, Peri) and connected to the light dosimetry system. The positions “Diaph” and “AS” were not included due to the positioning of the opening on the phantom, which allowed the scanner and treatment light source access. By comparing the results, it can be observed that employing the scanning and navigation system leads to a more uniform overall light distribution compared with PDT treatment using detectors alone. Although the prescribed light doses are accurately achieved at the crucial positions where the isotropic detectors are fixed, there are some remaining “cold spots” with lower light fluence. The innovative real-time navigation system effectively addresses this issue and enables the achievement of uniform light fluence distribution by the end of the treatment. The infrared (IR) navigation system has been utilized in previous clinical pleural PDT trials to track the motion of the light source during PDT and evaluate the uniformity of light fluence distribution across the entire pleural cavity after treatment. This serves as a baseline for the application of the updated navigation system, which incorporates rapid scanning and real-time feedback capabilities. The integration of these advancements can further enhance the accuracy and effectiveness of pleural PDT procedures.##REF##31556122##39##</p>", "<p>The real-time light fluence calculation of the novel system was validated by comparing the calculation with the data measured by all six detectors used in the phantom studies with different optical properties. To account for the general scattering inside the cavity and reduce the percentage error, a constant “” was introduced based on previous studies. In this study, the scatter component was applied after treatment. The percentage error from the measured light dose at the end of treatment with real-time calculated light fluence using the primary component only [Eq. (1)] and the primary and scattering component together [Eq. (2)], along with the respective “” values used, are summarized in ##TAB##1##Table 2##. The variation in “” values was found to be small among previous clinical cases, and this study confirms the same observation. After applying the scatter component, the range of the percentage error in light fluences is between 0.9% and 12.8%, which is comparable to the findings of previous studies (ranging from 0.7% to 15.4%).##REF##32053799##23## This study demonstrates the improvement in light delivery efficiency achieved by utilizing the real-time navigation system, and the algorithm employed is validated. The validation process affirms the accuracy and reliability of the real-time light fluence calculation, establishing its suitability for application in pleural PDT procedures. This establishes a foundation for the development of a comprehensive real-time guidance system, integrating the 8-channel dosimetry system with the navigation system. Through the combination of real-time calculated light fluence data for the pleural cavity and simultaneously measured PS concentrations at eight crucial sites, our objective is to furnish physicians with real-time PDT dose information. This information serves as a guidance tool for optimizing light delivery during PDT, with the overarching goal of further advancing treatment efficiency.</p>" ]
[ "<title>Results and Discussion</title>", "<title>Tissue Optical Properties and Correction Factors</title>", "<p>In this study, <italic>in vivo</italic> diffuse reflectance measurements were conducted at 52 sites within the pleural cavities of 11 patients. Initially, the PDT dose dosimetry system had four channels capable of simultaneously measuring light fluence rate and fluorescence. However, for the latest two patients, the system was expanded to eight channels, covering all eight predetermined locations within the pleural cavity for each patient. In this paper, the presented data for the four-channel system differ from previously reported results obtained using the same system. All raw data underwent thorough validation and were re-analyzed specifically for this study. ##TAB##0##Table 1## summarizes the tissue absorption and reduced scattering coefficients ( and ) at the excitation wavelength of 630 nm for all measurement sites where diffuse reflectance spectra were obtained, along with the corresponding correction factors. Significant heterogeneity in both absorption and reduced scattering coefficients can be observed both within and among patients.</p>", "<p>The maximum variation of and is 8 times and 2.8 times, respectively, among all sites with a mean (SD) of (0.13) and (2.4) , respectively. The variations in tissue optical properties can be attributed to factors such as thermal damage to the surrounding tissue induced by electrosurgery during tumor resection and the diverse characteristics of cellular content and chromophores throughout the tissues.##REF##32003006##38## These factors are uncontrollable during the treatments, necessitating post-treatment correction. To provide a comprehensive understanding and address the influence of optical properties, correction factors derived from measurements taken at 78 sites across 20 patients at the treatment wavelength are illustrated in ##FIG##4##Fig. 5##. This includes data from earlier cases using 2- or 4- channel PDT dose dosimetry systems. CFs were computed for individual sites using Eq. (1) to adjust the measured fluorescence for distortions arising from variable optical properties at different sites and among different patients. This correction is essential for ensuring the accurate quantification of PS concentration. The CFs range from 0.54 to 2.57 across the 78 sites. The mean CF value is 1.0 (indicated by the dashed line), and the median CF value is 1.08. The values for each site are presented in ##TAB##0##Table 1##. The maximum variation among all sites is 4.7 times, and the maximum variation among sites within individual patients is 1.8 times.</p>", "<title>Temporal and Spatial Distribution of Photofrin and PDT Dose</title>", "<p>##FIG##5##Figure 6## shows the temporal changes in local Photofrin concentrations for 16 sites in the most recent two cases, in which all eight dual-function channels were utilized. The discrete data points in the graph were obtained from measured fluorescence spectra using the SVD fitting method described earlier. It is worth noting that some data points exhibit larger variations, which can be attributed to the fluctuations in the incident treatment light fluence rate (ranging from 0 to ). This variation stems from the movement of the light source during PDT, which introduces errors in the measurement of Photofrin fluorescence excited by the treatment light.</p>", "<p>To facilitate a clearer observation of the trend of Photofrin variation during the treatment, the fitted data points for each channel were smoothed by calculating the average of all data points every 10 min of treatment time. The smoothed results are depicted by the solid curves in the graph. The relatively small temporal fluctuations in Photofrin concentration throughout the treatment for each site suggest that, despite the significant variations observed between different locations, the changes in Photofrin uptake over time within each site remain relatively stable. This phenomenon suggests that the uptake of Photofrin is not significantly influenced by the treatment itself but exhibits variation across different locations. The observed differences in optical properties ( and , tabulated in ##TAB##0##Table 1## for each patient) at these locations can be attributed to the inherent complexity of the tissue environment. This observation aligns with the substantial variation in CFs (see ##FIG##4##Fig. 5##), calculated based on the tissue optical properties at the sites, as described in Sec. <xref rid=\"sec3.1\" ref-type=\"sec\">3.1</xref>. Importantly, there is no significant photobleaching of Photofrin during PDT, corroborating findings from previous studies.##REF##29106380##26##</p>", "<p>The mean Photofrin concentrations (shown on the left axis) and PDT doses (shown on the right axis) obtained from all 78 sites in the pleural cavities of 20 patients are shown in ##FIG##6##Fig. 7##. The average (SD) and median Photofrin concentrations for all 78 sites are 4.98 (2.38) and , respectively. The PDT dose delivered to each site is defined as the product of the local Photofrin concentration ([PS], in ) and the delivered light dose. The treatment for each site was halted when the measured total light fluence of was reached, ensuring a consistent total fluence across all subjects: </p>", "<p>The differences in effective PDT doses delivered to different sites were influenced by the heterogeneities in Photofrin uptakes along the pleural cavities. The delivered PDT doses for each site are shown on the same plot (##FIG##5##Fig. 6##) with a secondary vertical axis on the right to indicate the corresponding values. The average (SD) and median PDT doses for all 78 sites are 493 (236) and , respectively. The maximum variation among all sites is 9.8 times, indicating significant differences in the delivered PDT doses across the pleural cavities. Similarly, the maximum variation among sites within each patient is 3.1 times, highlighting the variability in PDT doses within individual patients.</p>", "<p>The substantial variations observed within and among patients align with previous studies and underscore the importance of considering both Photofrin concentration and PDT dose in the development of an effective dosimetry system. Traditional approaches that solely rely on monitoring light fluence may not provide comprehensive information to ensure uniform PDT doses across all treatment sites. One potential limitation in real-time monitoring of Photofrin concentration is the time-consuming post-treatment fitting and analysis of measured fluorescence spectra. However, this study demonstrates relatively stable Photofrin concentrations throughout the time course of PDT, enabling the utilization of data acquired at the beginning of treatment for comprehensive real-time guidance throughout the rest of the procedure. Therefore, the innovative 8-channel PDT dose dosimeter holds the potential to assist physicians in delivering more uniform PDT doses to all sites, ultimately improving the outcomes of pleural PDT treatment.</p>", "<title>Real-Time Navigation System</title>", "<p>The preliminary results for light delivery efficiency with and without real-time guidance using the scanning and navigation system are depicted in ##FIG##7##Fig. 8##. A pleural phantom (see ##FIG##0##Fig. 1##), created using a 3D printing technique and based on a CT scan of an actual human pleural cavity, was utilized in our real-time navigation study. To simulate clinical conditions more accurately, six isotropic detectors were placed at predetermined locations on the inner surface of the pleural phantom (Apex, PCW, ACW, PS, PM, Peri) and connected to the light dosimetry system. The positions “Diaph” and “AS” were not included due to the positioning of the opening on the phantom, which allowed the scanner and treatment light source access. By comparing the results, it can be observed that employing the scanning and navigation system leads to a more uniform overall light distribution compared with PDT treatment using detectors alone. Although the prescribed light doses are accurately achieved at the crucial positions where the isotropic detectors are fixed, there are some remaining “cold spots” with lower light fluence. The innovative real-time navigation system effectively addresses this issue and enables the achievement of uniform light fluence distribution by the end of the treatment. The infrared (IR) navigation system has been utilized in previous clinical pleural PDT trials to track the motion of the light source during PDT and evaluate the uniformity of light fluence distribution across the entire pleural cavity after treatment. This serves as a baseline for the application of the updated navigation system, which incorporates rapid scanning and real-time feedback capabilities. The integration of these advancements can further enhance the accuracy and effectiveness of pleural PDT procedures.##REF##31556122##39##</p>", "<p>The real-time light fluence calculation of the novel system was validated by comparing the calculation with the data measured by all six detectors used in the phantom studies with different optical properties. To account for the general scattering inside the cavity and reduce the percentage error, a constant “” was introduced based on previous studies. In this study, the scatter component was applied after treatment. The percentage error from the measured light dose at the end of treatment with real-time calculated light fluence using the primary component only [Eq. (1)] and the primary and scattering component together [Eq. (2)], along with the respective “” values used, are summarized in ##TAB##1##Table 2##. The variation in “” values was found to be small among previous clinical cases, and this study confirms the same observation. After applying the scatter component, the range of the percentage error in light fluences is between 0.9% and 12.8%, which is comparable to the findings of previous studies (ranging from 0.7% to 15.4%).##REF##32053799##23## This study demonstrates the improvement in light delivery efficiency achieved by utilizing the real-time navigation system, and the algorithm employed is validated. The validation process affirms the accuracy and reliability of the real-time light fluence calculation, establishing its suitability for application in pleural PDT procedures. This establishes a foundation for the development of a comprehensive real-time guidance system, integrating the 8-channel dosimetry system with the navigation system. Through the combination of real-time calculated light fluence data for the pleural cavity and simultaneously measured PS concentrations at eight crucial sites, our objective is to furnish physicians with real-time PDT dose information. This information serves as a guidance tool for optimizing light delivery during PDT, with the overarching goal of further advancing treatment efficiency.</p>" ]
[ "<title>Conclusions</title>", "<p>In this study, a real-time 8-channel PDT dose dosimeter was developed and utilized for Photofrin-mediated pleural PDT. The mean PDT dose among the 20 patients included in the study was found to be . However, it was observed that, with the same administered Photofrin dose and total light dose, PDT doses could vary significantly, ranging up to 980% among different patients and 310% within the same patient. This variability implies that, relying solely on light fluence as the treatment guidance during PDT leads to a non-uniform distribution of PDT dose throughout the pleural cavity, potentially impacting the overall treatment outcome. Recognizing PDT dose as a crucial dosimetry parameter, it can serve as a superior guiding tool for physicians during PDT. To address this issue and improve the consistency of PDT doses, the 8-channel dose dosimeter was developed, providing a means to initiate PDT dose-mediated pleural PDT. The system incorporated commercial tracking and scanning tools along with customized software to enable real-time feedback and monitoring. The scanning and navigation system efficiently identified the target surface and facilitated quick registration for real-time light fluence distribution calculation during PDT. The developed system has been successfully applied in phantom studies, demonstrating its ability to provide reliable real-time feedback on the light source position and 2D light fluence distribution.</p>", "<p>The significance of the 8-channel system lies in its potential to provide informative real-time guidance at all sites currently used in the clinical trial. By addressing variations in PDT doses and ensuring uniform dose distribution, the system offers a promising avenue for starting a new clinical trial utilizing PDT dose as dosimetry metrics. Future development will prioritize the integration of the 8-channel dosimetry system with the scanning and navigation system to guide light delivery during PDT. This integration aims to guarantee the consistent distribution of PDT dose, thereby further elevating the effectiveness of cancer treatment outcomes.</p>" ]
[ "<title>Abstract.</title>", "<title>Significance</title>", "<p>Photodynamic therapy (PDT) is an established cancer treatment utilizing light-activated photosensitizers (PS). Effective treatment hinges on the PDT dose-dependent on PS concentration and light fluence-delivered over time. We introduce an innovative eight-channel PDT dose dosimetry system capable of concurrently measuring light fluence and PS concentration during treatment.</p>", "<title>Aim</title>", "<p>We aim to develop and evaluate an eight-channel PDT dose dosimetry system for simultaneous measurement of light fluence and PS concentration. By addressing uncertainties due to tissue variations, the system enhances accurate PDT dosimetry for improved treatment outcomes.</p>", "<title>Approach</title>", "<p>The study positions eight isotropic detectors strategically within the pleural cavity before PDT. These detectors are linked to bifurcated fibers, distributing signals to both a photodiode and a spectrometer. Calibration techniques are applied to counter tissue-related variations and improve measurement accuracy. The fluorescence signal is normalized using the measured light fluence, compensating for variations in tissue properties. Measurements were taken in 78 sites in the pleural cavities of 20 patients.</p>", "<title>Results</title>", "<p>Observations reveal minimal Photofrin concentration variation during PDT at each site, juxtaposed with significant intra- and inter-patient heterogeneities. Across 78 treated sites in 20 patients, the average Photofrin concentration for all 78 sites is , with a median concentration of . The average PDT dose for all 78 sites is , with a median dose of . A significant variation in PDT doses is observed, with a maximum difference of 3.1 times among all sites within one patient and a maximum difference of 9.8 times across all patients.</p>", "<title>Conclusions</title>", "<p>The introduced eight-channel PDT dose dosimetry system serves as a valuable real-time monitoring tool for light fluence and PS concentration during PDT. Its ability to mitigate uncertainties arising from tissue properties enhances dosimetry accuracy, thus optimizing treatment outcomes and bolstering the effectiveness of PDT in cancer therapy.</p>", "<title>Keywords:</title>" ]
[]
[ "<title>Acknowledgments</title>", "<p>This work was supported by grants from the National Institutes of Health (NIH) (Grant Nos. R01 EB028778, R01 EB032821, and P01 CA87971). D.S. was supported by the NIH National Institute of Dental &amp; Craniofacial Research (NIDCR) (Grant No. T90DE030854) and the Center for Innovation &amp; Precision Dentistry (CiPD) at the University of Pennsylvania. The 3D-printed object was printed courtesy of the University of Pennsylvania Libraries’ Holman Biotech Commons with design consultation.</p>", "<p><bold>Dennis Sourvanos</bold>, DDS DScD, is a periodontal surgeon and currently an NIH NIDCR T-90 postdoctoral fellow with the Center for Innovation and Precision Dentistry (CiPD). This is a dual appointment through the Schools of Dental Medicine and Engineering at the University of Pennsylvania. As a training clinician scientist with an emphasis on translational research, his focus is on gaining expertise in the translational science of hard and soft tissue regeneration. He is presently engaged with a multidisciplinary collaboration of researchers within the greater University of Pennsylvania ecosystem. Their primary focus is on developing novel biotherapeutics and photobiomodulation protocols toward the innovation of hard tissue (bone) regenerative therapies within the surgical arena.</p>", "<p><bold>Theresa M. Busch</bold>, PhD, is a professor and associate director of the Division of Research, Department of Radiation Oncology at the University of Pennsylvania. Her research interests encompass the study of tumor microenvironment as it relates to radiation therapy, including ionizing radiation as well as nonionizing radiation in the form of PDT. She is involved in national and international societies on photomedical research and is currently treasurer for the American Society for Photobiology. She serves as a vice chair for inclusion, diversity, and equity in the Department of Radiation Oncology.</p>", "<p><bold>Sunil Singhal</bold>, MD, FACS, is a professor of thoracic surgery at the University of Pennsylvania Perelman School of Medicine. He has a research focus on preventing recurrences after cancer surgery. To that end, his laboratory studies molecular imaging to identify sources of local recurrences and tumor immunology to modulate suppressive immune populations. His work has largely focused on developing targeted fluorophores for <italic>in vivo</italic> surgical margin detection.</p>", "<p><bold>Timothy C. Zhu</bold>, PhD, is an ABR and ABMP board certified medical physicist and professor of radiation oncology at the University of Pennsylvania. His research interests include photodynamic therapy (PDT) dosimetry, reactive oxygen species dosimetry, radiation transport, and image guided interventions. He is the associate director of PDT physics, in charge of all PDT related physics aspect of PDT clinical protocols. </p>", "<p>Biographies of the authors are not available.</p>", "<title>Disclosures</title>", "<p>Theresa M. Busch received support from Simphotek and personal fees from Lumeda and IBA outside the submitted work. Keith A. Cengel received support from Simphotek. All other authors declare no commercial conflicts of interest related to this article.</p>", "<title>Code and Data Availability</title>", "<p>Data underlying the results presented in this paper may be obtained from the authors upon reasonable request.</p>" ]
[ "<fig position=\"float\" id=\"f1\"><label>Fig. 1</label><caption><p>Point cloud data of a reconstructed pleural cavity, with isotropic locations marked, were generated using our scanning system.</p></caption></fig>", "<fig position=\"float\" id=\"f2\"><label>Fig. 2</label><caption><p>(a) The front view of the 8-channel PDT dose dosimetry instrument and (b) the schematic diagram of the system setup. The bifurcated fibers are connected to channels 1–8 internally, enabling the simultaneous measurement of light fluence and PS uptake. A long-pass filter is employed for each channel, leading to a slight variance in the peak wavelength of the measured spectrum. To ensure independent functionality, distinct long-pass filters are employed for each channel.</p></caption></fig>", "<fig position=\"float\" id=\"f3\"><label>Fig. 3</label><caption><p>(a) The basis spectrum consists of a laser component, a Photofrin fluorescence component, and a Fourier component; (b) example of measured raw fluorescence spectra from 8 channels of patient #53. The peaks at 675 nm arise from fluorescence of the isotropic detector. Slight shifts in the peak wavelength occur as a result of using different long-pass filters for each channel. (c) Fluorescence SVD amplitudes for Photofrin in tissue-simulating phantom experiments with different optical properties ( and to ) with a constant Photofrin concentration of , measured in phantoms using 8-channel PDT dosimeter (solid lines) and fits using Eq. (2) (dashed lines). The correction factor (CF) and the corrected Photofrin SVD amplitudes were obtained using Eqs. (1) and (2). (d) Photofrin concentration calibration curve.</p></caption></fig>", "<fig position=\"float\" id=\"f4\"><label>Fig. 4</label><caption><p>Instruments consist of the newly developed real-time navigation system. The optical infrared (IR) navigation system is made up of (a) an IR camera and (b) a treatment wand with a laser fiber inserted. The novel scanning system is made up of (c) a 3D scanning device for capturing the pleural surface.</p></caption></fig>", "<fig position=\"float\" id=\"f5\"><label>Fig. 5</label><caption><p>CF at 78 different sites in the pleural cavities of 20 patients. (a) Patient #07 to #29. (b) Patient #32 to #52. The mean value is represented by the dashed line.</p></caption></fig>", "<fig position=\"float\" id=\"f6\"><label>Fig. 6</label><caption><p>Temporal changes of Photofrin concentrations measured from 16 sites in the pleural cavity of the 2 most recent patients (#052 and #053) during the PDT treatments. To convert from to , can be used.</p></caption></fig>", "<fig position=\"float\" id=\"f7\"><label>Fig. 7</label><caption><p>Mean Photofrin concentrations and PDT dose delivered to 78 different sites in the pleural cavities of 20 patients. (a) Patient #07 to #29. (b) Patient #32 to #52. The mean value is represented by the dashed line.</p></caption></fig>", "<fig position=\"float\" id=\"f8\"><label>Fig. 8</label><caption><p>Comparison of light fluence map at the end of treatment with six detector positions labeled. (a) Without real-time fluence map guidance. (b) With real-time fluence map guidance. The overall light fluence distribution presented for the whole surface area was calculated based on the navigation system and Eqs. (3) and (4). Light fluence data were measured by the isotropic detectors at the locations marked with “X” to verify the calculations.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"t001\"><label>Table 1</label><caption><p>Summary of absorption coefficients, scattering coefficients, and correction factors for 20 patients. The light fluence on the surface is the same at for all patients. Information about patients 07, 08, 12, 14, 16, 17, 18, and 20 can be found elsewhere and were reprocessed in this study.##REF##29106380##26##</p></caption><!--OASIS TABLE HERE--><table frame=\"hsides\" rules=\"groups\"><colgroup><col align=\"center\"/><col align=\"left\"/><col align=\"center\"/><col align=\"center\"/><col align=\"center\"/><col align=\"left\"/><col align=\"left\"/><col align=\"center\"/><col align=\"center\"/><col align=\"center\"/></colgroup><thead><tr><th rowspan=\"2\" align=\"center\">Patient</th><th rowspan=\"2\" align=\"left\">Site<xref rid=\"t001fn1\" ref-type=\"table-fn\">*</xref></th><th colspan=\"2\" align=\"center\">Optical properties<hr/></th><th rowspan=\"2\" align=\"center\">CF</th><th rowspan=\"2\" align=\"left\">Patient</th><th rowspan=\"2\" align=\"left\">Site<xref rid=\"t001fn1\" ref-type=\"table-fn\">*</xref></th><th colspan=\"3\" align=\"center\">Optical properties<hr/></th></tr><tr><th align=\"center\"> ()</th><th align=\"center\"> ()</th><th align=\"center\" valign=\"top\"> ()</th><th align=\"center\" valign=\"top\"> ()</th><th align=\"center\">CF</th></tr></thead><tbody><tr><td rowspan=\"2\" align=\"center\">#007</td><td align=\"left\">AS</td><td align=\"center\">0.24</td><td align=\"center\">11.6</td><td align=\"center\">0.80</td><td rowspan=\"4\" align=\"left\">#038</td><td align=\"left\">PM</td><td align=\"center\">0.23</td><td align=\"center\">6.8</td><td align=\"center\">1.06</td></tr><tr><td align=\"left\">PS</td><td align=\"center\">0.37</td><td align=\"center\">16.6</td><td align=\"center\">0.81</td><td align=\"left\">PS</td><td align=\"center\">0.32</td><td align=\"center\">12.3</td><td align=\"center\">0.89</td></tr><tr><td rowspan=\"2\" align=\"center\">#008</td><td align=\"left\">Apex</td><td align=\"center\">0.32</td><td align=\"center\">7.7</td><td align=\"center\">1.19</td><td align=\"left\">Apex</td><td align=\"center\">0.38</td><td align=\"center\">8.4</td><td align=\"center\">1.24</td></tr><tr><td align=\"left\">PCW</td><td align=\"center\">0.16</td><td align=\"center\">9.1</td><td align=\"center\">0.75</td><td align=\"left\">ACW</td><td align=\"center\">0.19</td><td align=\"center\">12.5</td><td align=\"center\">0.69</td></tr><tr><td rowspan=\"2\" align=\"center\">#012</td><td align=\"left\">Apex</td><td align=\"center\">0.12</td><td align=\"center\">14.7</td><td align=\"center\">0.55</td><td rowspan=\"4\" align=\"left\">#040</td><td align=\"left\">PM</td><td align=\"center\">0.25</td><td align=\"center\">10.2</td><td align=\"center\">0.87</td></tr><tr><td align=\"left\">PM</td><td align=\"center\">0.24</td><td align=\"center\">13.1</td><td align=\"center\">0.75</td><td align=\"left\">AS</td><td align=\"center\">0.35</td><td align=\"center\">11.2</td><td align=\"center\">0.98</td></tr><tr><td rowspan=\"2\" align=\"center\">#014</td><td align=\"left\">PS</td><td align=\"center\">0.15</td><td align=\"center\">13.4</td><td align=\"center\">0.61</td><td align=\"left\">Diaph</td><td align=\"center\">0.41</td><td align=\"center\">12.5</td><td align=\"center\">1.00</td></tr><tr><td align=\"left\">Peri</td><td align=\"center\">0.09</td><td align=\"center\">12.5</td><td align=\"center\">0.53</td><td align=\"left\">Peri</td><td align=\"center\">0.42</td><td align=\"center\">9.1</td><td align=\"center\">1.25</td></tr><tr><td rowspan=\"2\" align=\"center\">#016</td><td align=\"left\">Apex</td><td align=\"center\">0.08</td><td align=\"center\">7.1</td><td align=\"center\">0.63</td><td rowspan=\"4\" align=\"left\">#047</td><td align=\"left\">Peri</td><td align=\"center\">0.23</td><td align=\"center\">12.6</td><td align=\"center\">0.75</td></tr><tr><td align=\"left\">PCW</td><td align=\"center\">0.09</td><td align=\"center\">11.9</td><td align=\"center\">0.54</td><td align=\"left\">PM</td><td align=\"center\">0.32</td><td align=\"center\">9.5</td><td align=\"center\">1.04</td></tr><tr><td rowspan=\"4\" align=\"center\">#017</td><td align=\"left\">Apex</td><td align=\"center\">0.42</td><td align=\"center\">9.0</td><td align=\"center\">1.26</td><td align=\"left\">PS</td><td align=\"center\">0.24</td><td align=\"center\">10.8</td><td align=\"center\">0.83</td></tr><tr><td align=\"left\">PCW</td><td align=\"center\">0.26</td><td align=\"center\">8.8</td><td align=\"center\">0.97</td><td align=\"left\">AS</td><td align=\"center\">0.26</td><td align=\"center\">9.9</td><td align=\"center\">0.90</td></tr><tr><td align=\"left\">PM</td><td align=\"center\">0.24</td><td align=\"center\">10.9</td><td align=\"center\">0.82</td><td rowspan=\"4\" align=\"left\">#049</td><td align=\"left\">Peri</td><td align=\"center\">0.52</td><td align=\"center\">7.9</td><td align=\"center\">1.58</td></tr><tr><td align=\"left\">ACW</td><td align=\"center\">0.33</td><td align=\"center\">12.4</td><td align=\"center\">0.90</td><td align=\"left\">Apex</td><td align=\"center\">0.34</td><td align=\"center\">8.8</td><td align=\"center\">1.13</td></tr><tr><td rowspan=\"4\" align=\"center\">#018</td><td align=\"left\">PS</td><td align=\"center\">0.44</td><td align=\"center\">5.9</td><td align=\"center\">1.76</td><td align=\"left\">ACW</td><td align=\"center\">0.52</td><td align=\"center\">10.2</td><td align=\"center\">1.32</td></tr><tr><td align=\"left\">Apex</td><td align=\"center\">0.44</td><td align=\"center\">5.8</td><td align=\"center\">1.79</td><td align=\"left\">PCW</td><td align=\"center\">0.34</td><td align=\"center\">9.9</td><td align=\"center\">1.04</td></tr><tr><td align=\"left\">PCW</td><td align=\"center\">0.70</td><td align=\"center\">7.4</td><td align=\"center\">2.04</td><td rowspan=\"4\" align=\"left\">#050</td><td align=\"left\">ACW</td><td align=\"center\">0.27</td><td align=\"center\">9.4</td><td align=\"center\">0.95</td></tr><tr><td align=\"left\">ACW</td><td align=\"center\">0.72</td><td align=\"center\">5.9</td><td align=\"center\">2.50</td><td align=\"left\">PM</td><td align=\"center\">0.32</td><td align=\"center\">10.9</td><td align=\"center\">0.95</td></tr><tr><td rowspan=\"4\" align=\"center\">#020</td><td align=\"left\">PS</td><td align=\"center\">0.57</td><td align=\"center\">9.0</td><td align=\"center\">1.53</td><td align=\"left\">Apex</td><td align=\"center\">0.47</td><td align=\"center\">9.3</td><td align=\"center\">1.32</td></tr><tr><td align=\"left\">Apex</td><td align=\"center\">0.27</td><td align=\"center\">9.0</td><td align=\"center\">0.98</td><td align=\"left\">Peri</td><td align=\"center\">0.22</td><td align=\"center\">12.3</td><td align=\"center\">0.74</td></tr><tr><td align=\"left\">PCW</td><td align=\"center\">0.32</td><td align=\"center\">10.9</td><td align=\"center\">0.95</td><td rowspan=\"8\" align=\"left\">#052</td><td align=\"left\">PM</td><td align=\"center\">0.25</td><td align=\"center\">13.06</td><td align=\"center\">0.76</td></tr><tr><td align=\"left\">PM</td><td align=\"center\">0.42</td><td align=\"center\">10.3</td><td align=\"center\">1.15</td><td align=\"left\">AS</td><td align=\"center\">0.47</td><td align=\"center\">13.17</td><td align=\"center\">1.05</td></tr><tr><td rowspan=\"4\" align=\"center\">#027</td><td align=\"left\">ACW</td><td align=\"center\">0.32</td><td align=\"center\">8.9</td><td align=\"center\">1.08</td><td align=\"left\">Diaph</td><td align=\"center\">0.35</td><td align=\"center\">10.23</td><td align=\"center\">1.04</td></tr><tr><td align=\"left\">PM</td><td align=\"center\">0.26</td><td align=\"center\">11.9</td><td align=\"center\">0.81</td><td align=\"left\">ACW</td><td align=\"center\">0.39</td><td align=\"center\">13.45</td><td align=\"center\">0.93</td></tr><tr><td align=\"left\">Apex</td><td align=\"center\">0.23</td><td align=\"center\">9.5</td><td align=\"center\">0.87</td><td align=\"left\">Apex</td><td align=\"center\">0.36</td><td align=\"center\">11.22</td><td align=\"center\">1.00</td></tr><tr><td align=\"left\">Peri</td><td align=\"center\">0.26</td><td align=\"center\">9.8</td><td align=\"center\">0.91</td><td align=\"left\">PCW</td><td align=\"center\">0.27</td><td align=\"center\">10.86</td><td align=\"center\">0.87</td></tr><tr><td rowspan=\"4\" align=\"center\">#029</td><td align=\"left\">ACW</td><td align=\"center\">0.38</td><td align=\"center\">9.6</td><td align=\"center\">1.14</td><td align=\"left\">Peri</td><td align=\"center\">0.34</td><td align=\"center\">12.17</td><td align=\"center\">0.92</td></tr><tr><td align=\"left\">PCW</td><td align=\"center\">0.65</td><td align=\"center\">5.2</td><td align=\"center\">2.57</td><td align=\"left\">PS</td><td align=\"center\">0.29</td><td align=\"center\">13.18</td><td align=\"center\">0.81</td></tr><tr><td align=\"left\">Diaph</td><td align=\"center\">0.14</td><td align=\"center\">13.2</td><td align=\"center\">0.60</td><td rowspan=\"8\" align=\"left\">#053</td><td align=\"left\">PM</td><td align=\"center\">0.38</td><td align=\"center\">10.89</td><td align=\"center\">1.05</td></tr><tr><td align=\"left\">Apex</td><td align=\"center\">0.28</td><td align=\"center\">10.3</td><td align=\"center\">0.92</td><td align=\"left\">PCW</td><td align=\"center\">0.31</td><td align=\"center\">10.80</td><td align=\"center\">0.94</td></tr><tr><td rowspan=\"4\" align=\"center\">#032</td><td align=\"left\">Apex</td><td align=\"center\">0.21</td><td align=\"center\">6.43</td><td align=\"center\">1.04</td><td align=\"left\">ACW</td><td align=\"center\">0.27</td><td align=\"center\">10.69</td><td align=\"center\">0.88</td></tr><tr><td align=\"left\">PCW</td><td align=\"center\">0.17</td><td align=\"center\">4.97</td><td align=\"center\">1.09</td><td align=\"left\">Apex</td><td align=\"center\">0.35</td><td align=\"center\">6.91</td><td align=\"center\">1.35</td></tr><tr><td align=\"left\">PM</td><td align=\"center\">0.18</td><td align=\"center\">6.33</td><td align=\"center\">0.97</td><td align=\"left\">Peri</td><td align=\"center\">0.33</td><td align=\"center\">8.59</td><td align=\"center\">1.12</td></tr><tr><td align=\"left\">ACW</td><td align=\"center\">0.18</td><td align=\"center\">4.95</td><td align=\"center\">1.13</td><td align=\"left\">PS</td><td align=\"center\">0.32</td><td align=\"center\">7.92</td><td align=\"center\">1.17</td></tr><tr><td rowspan=\"4\" align=\"center\">#035</td><td align=\"left\">AS</td><td align=\"center\">0.38</td><td align=\"center\">9.1</td><td align=\"center\">1.18</td><td align=\"left\">AS</td><td align=\"center\">0.22</td><td align=\"center\">9.15</td><td align=\"center\">0.87</td></tr><tr><td align=\"left\">PM</td><td align=\"center\">0.48</td><td align=\"center\">9.2</td><td align=\"center\">1.35</td><td align=\"left\">Diaph</td><td align=\"center\">0.28</td><td align=\"center\">9.12</td><td align=\"center\">0.99</td></tr><tr><td align=\"left\">Peri</td><td align=\"center\">0.25</td><td align=\"center\">10.2</td><td align=\"center\">0.87</td><td rowspan=\"6\" colspan=\"2\" align=\"center\">mean ± SD</td><td rowspan=\"6\" align=\"center\">0.31 ± 0.13</td><td rowspan=\"6\" align=\"center\">9.9 ± 2.4</td><td rowspan=\"6\" align=\"center\">1.03 ± 0.36</td></tr><tr><td align=\"left\">Diaph</td><td align=\"center\">0.22</td><td align=\"center\">8.1</td><td align=\"center\">0.93</td></tr><tr><td rowspan=\"4\" align=\"center\">#037</td><td align=\"left\">PM</td><td align=\"center\">0.17</td><td align=\"center\">9.9</td><td align=\"center\">0.74</td></tr><tr><td align=\"left\">Apex</td><td align=\"center\">0.22</td><td align=\"center\">9.3</td><td align=\"center\">0.86</td></tr><tr><td align=\"left\">ACW</td><td align=\"center\">0.33</td><td align=\"center\">9.8</td><td align=\"center\">1.03</td></tr><tr><td align=\"left\">PCW</td><td align=\"center\">0.26</td><td align=\"center\">9.5</td><td align=\"center\">0.93</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t002\"><label>Table 2</label><caption><p>Percent error from measured light dose at the end of treatment with the calculated light fluence using (a) the primary component only and (b) the primary plus scattering component. Here, the study 1, 2, and 3 refer to liquid phantoms with different optical properties, i.e., , (0.5, 10), and (1, 20) .</p></caption><!--OASIS TABLE HERE--><table frame=\"hsides\" rules=\"groups\"><colgroup><col align=\"left\"/><col align=\"center\"/><col align=\"center\"/><col align=\"center\"/><col align=\"center\"/><col align=\"center\"/><col align=\"center\"/><col align=\"center\"/><col align=\"center\"/></colgroup><thead><tr><th colspan=\"2\" align=\"left\" valign=\"top\">Study</th><th align=\"center\" valign=\"top\">Peri (%)</th><th align=\"center\" valign=\"top\">PM (%)</th><th align=\"center\" valign=\"top\">ACW (%)</th><th align=\"center\" valign=\"top\">PCW (%)</th><th align=\"center\" valign=\"top\">PS (%)</th><th align=\"center\" valign=\"top\">Apex (%)</th><th align=\"center\" valign=\"top\"> ()</th></tr></thead><tbody><tr><td rowspan=\"3\" align=\"left\">(a)</td><td align=\"center\">1</td><td align=\"center\">33.7</td><td align=\"center\">33.5</td><td align=\"center\">32.8</td><td align=\"center\">15.2</td><td align=\"center\">26.7</td><td align=\"center\">14.2</td><td align=\"center\">NA</td></tr><tr><td align=\"center\">2</td><td align=\"center\">22.7</td><td align=\"center\">33.1</td><td align=\"center\">35.0</td><td align=\"center\">24.7</td><td align=\"center\">15.3</td><td align=\"center\">24.9</td><td align=\"center\">NA</td></tr><tr><td align=\"center\">3</td><td align=\"center\">31.6</td><td align=\"center\">31.5</td><td align=\"center\">21.9</td><td align=\"center\">15.6</td><td align=\"center\">28.9</td><td align=\"center\">17.4</td><td align=\"center\">NA</td></tr><tr><td rowspan=\"3\" align=\"left\">(b)</td><td align=\"center\">1</td><td align=\"center\">3.3</td><td align=\"center\">5.3</td><td align=\"center\">12.8</td><td align=\"center\">4.2</td><td align=\"center\">7.1</td><td align=\"center\">1.4</td><td align=\"center\">6.5</td></tr><tr><td align=\"center\">2</td><td align=\"center\">7.1</td><td align=\"center\">3.0</td><td align=\"center\">5.3</td><td align=\"center\">0.9</td><td align=\"center\">4.8</td><td align=\"center\">3.1</td><td align=\"center\">6.8</td></tr><tr><td align=\"center\">3</td><td align=\"center\">1.3</td><td align=\"center\">3.9</td><td align=\"center\">9.2</td><td align=\"center\">17.9</td><td align=\"center\">2.9</td><td align=\"center\">7.6</td><td align=\"center\">6.5</td></tr></tbody></table></table-wrap>" ]
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overflow=\"scroll\"><mml:mrow><mml:msub><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>a</mml:mi><mml:mo>,</mml:mo><mml:mi>ref</mml:mi></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>0.32</mml:mn><mml:mtext>  </mml:mtext><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math28\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi><mml:mo>,</mml:mo><mml:mi>ref</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup><mml:mo>=</mml:mo><mml:mn>10</mml:mn><mml:mtext>  </mml:mtext><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<disp-formula id=\"e001\"><mml:math id=\"math29\" display=\"block\" overflow=\"scroll\"><mml:mrow><mml:mi>CF</mml:mi><mml:mo>=</mml:mo><mml:msub><mml:mrow><mml:mi>C</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn></mml:mrow></mml:msub><mml:mo stretchy=\"false\">(</mml:mo><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>a</mml:mi></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi>b</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msubsup><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo><mml:msub><mml:mrow><mml:mi mathvariant=\"normal\">b</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:msubsup><mml:mo>+</mml:mo><mml:msub><mml:mrow><mml:mi>C</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>,</mml:mo></mml:mrow></mml:math><label>(1)</label></disp-formula>", "<inline-formula><mml:math id=\"math30\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mrow><mml:mi>C</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>15.30</mml:mn><mml:mo>±</mml:mo><mml:mn>0.52</mml:mn></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math31\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mi>C</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mn>0.023</mml:mn><mml:mo>±</mml:mo><mml:mn>0.013</mml:mn></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math32\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mrow><mml:mi>b</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mn>0.85</mml:mn><mml:mo>±</mml:mo><mml:mn>0.15</mml:mn></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math33\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mi>b</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mo>=</mml:mo><mml:mo>−</mml:mo><mml:mn>0.95</mml:mn><mml:mo>±</mml:mo><mml:mn>0.09</mml:mn></mml:mrow></mml:math></inline-formula>", "<disp-formula id=\"e002\"><mml:math id=\"math34\" display=\"block\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mrow><mml:mi>A</mml:mi></mml:mrow><mml:mrow><mml:mi>corr</mml:mi></mml:mrow></mml:msub><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>a</mml:mi><mml:mo>,</mml:mo><mml:mi>ref</mml:mi></mml:mrow></mml:msub><mml:mo>,</mml:mo><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi><mml:mo>,</mml:mo><mml:mi>ref</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>=</mml:mo><mml:mi>C</mml:mi><mml:mi>F</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>a</mml:mi></mml:mrow></mml:msub><mml:mo>,</mml:mo><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>·</mml:mo><mml:mi>A</mml:mi><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>a</mml:mi></mml:mrow></mml:msub><mml:mo>,</mml:mo><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>.</mml:mo></mml:mrow></mml:math><label>(2)</label></disp-formula>", "<inline-formula><mml:math id=\"math35\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mn>5</mml:mn><mml:mtext>  </mml:mtext><mml:mi>mg</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>kg</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math36\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mrow><mml:mi>A</mml:mi></mml:mrow><mml:mrow><mml:mi>cor</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math37\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mrow><mml:mi>A</mml:mi></mml:mrow><mml:mrow><mml:mi>cor</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math38\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>φ</mml:mi></mml:mrow></mml:math></inline-formula>", "<disp-formula id=\"e003\"><mml:math id=\"math39\" display=\"block\" overflow=\"scroll\"><mml:mrow><mml:mi>ϕ</mml:mi><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>S</mml:mi></mml:mrow><mml:mrow><mml:mn>4</mml:mn><mml:mi>π</mml:mi><mml:msup><mml:mrow><mml:mi>r</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:mfrac><mml:mo>,</mml:mo></mml:mrow></mml:math><label>(3)</label></disp-formula>", "<inline-formula><mml:math id=\"math40\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>S</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math41\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>r</mml:mi></mml:mrow></mml:math></inline-formula>", "<disp-formula id=\"e004\"><mml:math id=\"math42\" display=\"block\" overflow=\"scroll\"><mml:mrow><mml:mi>ϕ</mml:mi><mml:mo>=</mml:mo><mml:mfrac><mml:mi>S</mml:mi><mml:mrow><mml:mn>4</mml:mn><mml:mi>π</mml:mi><mml:msup><mml:mi>r</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:mfrac><mml:mo>+</mml:mo><mml:mi>b</mml:mi><mml:mo>,</mml:mo></mml:mrow></mml:math><label>(4)</label></disp-formula>", "<inline-formula><mml:math id=\"math43\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>b</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math44\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math45\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math46\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mn>60</mml:mn><mml:mtext>  </mml:mtext><mml:msup><mml:mrow><mml:mi>Jcm</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math47\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math48\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math49\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math50\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math51\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math52\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math53\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math54\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math55\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math56\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math57\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>a</mml:mi></mml:msub><mml:mo>=</mml:mo><mml:mn>0.31</mml:mn></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math58\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup><mml:mo>=</mml:mo><mml:mn>9.9</mml:mn></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math59\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msup><mml:mi>cm</mml:mi><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math60\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mn>1200</mml:mn><mml:mtext>  </mml:mtext><mml:msup><mml:mrow><mml:mi>mW</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:mi>cm</mml:mi></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math61\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msup><mml:mrow><mml:mi>mg</mml:mi><mml:mtext> </mml:mtext><mml:mi>kg</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math62\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>μ</mml:mi><mml:mi mathvariant=\"normal\">M</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math63\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mn>1</mml:mn><mml:mtext>  </mml:mtext><mml:msup><mml:mrow><mml:mi>mg</mml:mi><mml:mtext> </mml:mtext><mml:mi>kg</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup><mml:mo>=</mml:mo><mml:mn>1.65</mml:mn><mml:mtext>  </mml:mtext><mml:mi>μ</mml:mi><mml:mi mathvariant=\"normal\">M</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math64\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msub><mml:mi>μ</mml:mi><mml:mi>a</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math65\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math66\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>μ</mml:mi><mml:mi mathvariant=\"normal\">M</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math67\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mn>4.47</mml:mn><mml:mtext>  </mml:mtext><mml:mi>μ</mml:mi><mml:mi mathvariant=\"normal\">M</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math68\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>μ</mml:mi><mml:mi mathvariant=\"normal\">M</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math69\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mn>60</mml:mn><mml:mtext>  </mml:mtext><mml:mi mathvariant=\"normal\">J</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<disp-formula id=\"e005\"><mml:math id=\"math70\" display=\"block\" overflow=\"scroll\"><mml:mrow><mml:mi>PDT</mml:mi><mml:mtext> dose </mml:mtext><mml:mo>(</mml:mo><mml:mfrac><mml:mrow><mml:mi>μ</mml:mi><mml:mi>MJ</mml:mi></mml:mrow><mml:mrow><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:mfrac><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mo stretchy=\"false\">[</mml:mo><mml:mi>PS</mml:mi><mml:mo stretchy=\"false\">]</mml:mo><mml:mo stretchy=\"false\">(</mml:mo><mml:mi>μ</mml:mi><mml:mi mathvariant=\"normal\">M</mml:mi><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>·</mml:mo><mml:mn>60</mml:mn><mml:mtext> </mml:mtext><mml:mo>(</mml:mo><mml:mfrac><mml:mrow><mml:mi mathvariant=\"normal\">J</mml:mi></mml:mrow><mml:mrow><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:mfrac><mml:mo>)</mml:mo><mml:mo>.</mml:mo></mml:mrow></mml:math><label>(5)</label></disp-formula>", "<inline-formula><mml:math id=\"math71\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>μ</mml:mi><mml:mi>MJ</mml:mi><mml:mo>/</mml:mo><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math72\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mn>442.79</mml:mn><mml:mtext>  </mml:mtext><mml:mi>μ</mml:mi><mml:mi>MJ</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math73\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>b</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math74\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>b</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math75\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>b</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math76\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mo stretchy=\"false\">(</mml:mo><mml:msub><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>a</mml:mi></mml:mrow></mml:msub><mml:mo>,</mml:mo><mml:msubsup><mml:mrow><mml:mi>μ</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mo>′</mml:mo></mml:mrow></mml:msubsup><mml:mo stretchy=\"false\">)</mml:mo><mml:mo>=</mml:mo><mml:mtext> </mml:mtext><mml:mo stretchy=\"false\">(</mml:mo><mml:mn>0.1</mml:mn><mml:mo>,</mml:mo><mml:mn>2</mml:mn><mml:mo stretchy=\"false\">)</mml:mo></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math77\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math78\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mi>B</mml:mi></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math79\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:msup><mml:mrow><mml:mi>mWcm</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"math80\" display=\"inline\" overflow=\"scroll\"><mml:mrow><mml:mn>493.17</mml:mn><mml:mtext>  </mml:mtext><mml:mi>μ</mml:mi><mml:mi>MJ</mml:mi><mml:mo stretchy=\"false\">/</mml:mo><mml:msup><mml:mrow><mml:mi>cm</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>" ]
[]
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[ "<table-wrap-foot><fn id=\"t001fn1\"><label>*</label><p>See Sec. <xref rid=\"sec2.1\" ref-type=\"sec\">2.1</xref> and ##FIG##0##Fig. 1## for detailed description of sites.</p></fn></table-wrap-foot>" ]
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{ "acronym": [], "definition": [] }
39
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2024-01-14 23:41:59
J Biomed Opt. 2024 Jan 13; 29(1):018001
oa_package/c9/d1/PMC10787190.tar.gz
PMC10787192
36775056
[ "<title>Introduction</title>", "<p id=\"p0010\">Cancer is one of the deadliest public health problems worldwide, and cases are still rapidly growing. In 2020, it is estimated that around 10 million people have died of cancer ##REF##33538338##[1]##. Individualized medicine is a promising concept, which aims to improve the prognosis of patients by adapting the patient’s treatment to their unique clinical and molecular characteristics. One of the main goals of individualized medicine is the prediction of the response of patients to different treatments, and identification of biomarkers that enable such prediction. High-throughput sequencing technologies along with major initiatives such as The Cancer Genome Atlas (TCGA) ##REF##24071849##[2]## have provided a unique opportunity for machine learning (ML) algorithms to address these challenges. However, ML models and particularly deep learning (DL) approaches require a large number of samples with known drug response to train generalizable models. However, data on clinical drug response (CDR) of cancer patients, even in large databases such as TCGA, are usually small for most drugs and do not lend themselves to the training of DL models.</p>", "<p id=\"p0015\">On the other hand, large databases of molecular profiles of hundreds of <italic>in vitro</italic> cancer cell lines (CCLs) and their response to hundreds of drugs ##REF##23180760##[3]##, ##REF##22460905##[4]##, ##REF##23993102##[5]## have enabled development of various ML algorithms for prediction of drug response ##REF##24880487##[6]##, ##REF##31342013##[7]##, ##REF##30304378##[8]##. Unfortunately, these models, even though accurate in predicting the drug response of held-out CCLs, usually do not generalize well to predicting the CDR of real tumors from cancer patients, and their prediction performance significantly deteriorates due to the major biological and statistical differences between CCLs and tumors ##REF##31967990##[9]##.</p>", "<p id=\"p0020\">Recognizing these issues, some studies have adopted to utilize tumor samples with known CDR in the training of their models, either by fully training their models on data corresponding to tumor samples ##REF##27354694##[10]##, ##REF##33734318##[11]##, ##REF##33761889##[12]##, or using them in addition to CCLs (<italic>e.g.</italic>, using transfer learning ##REF##32657371##[13]##). However, as a result of this strategy, these studies have only been able to develop models on very few drugs due to the small sample sizes of patient cohort data with known drug response. Another strategy is to train ML models completely on preclinical CCLs but use computational approaches to overcome the statistical differences between CCLs and tumors. For example, multiple approaches ##REF##31967990##[9]##, ##REF##24580837##[14]## have used batch removal methods such as ComBat ##REF##16632515##[15]## to reduce the discrepancy between the training CCLs and test tumors. One limitation of these methods is that ComBat is used as a preprocessing step such that the gene expression (GEx) profiles of both CCLs (training set) and tumors (test set) are adjusted. As a result, prediction of CDR of new cancer patients requires retraining of the model.</p>", "<p id=\"p0025\">In this study, our goal was to develop a DL computational pipeline, fully trained on the GEx profile and drug response of preclinical CCLs, to (1) predict the CDR of cancer patients and (2) identify biomarkers of drug response for a variety of cancer drugs. Motivated by Huang et al. ##REF##31967990##[9]##, who showed that carefully incorporating information on the tissue (or cancer) types of the test samples can improve the predictive power of computational models, we developed a DL pipeline with tissue-informed normalization (TINDL) to achieve these goals. Unlike methods mentioned above, TINDL requires normalization of only test samples, and as a result retraining of the model is not necessary for new test samples.</p>", "<p id=\"p0030\">The TINDL pipeline includes two phases. The first phase is responsible for prediction of CDR of cancer patients, and the second phase makes these predictions interpretable by identifying a small number of genes that considerably contribute to the predictive ability of the model. Focusing on drugs shared between the Genomics of Drug Sensitivity in Cancer (GDSC) ##REF##23180760##[3]## and TCGA ##REF##24071849##[2]##, we showed that TINDL can distinguish between the sensitive and resistant patients for 10 (out of 14) drugs, considerably improving the performance of other methods, including our previous work, tissue-guided least absolute shrinkage and selection operator (TG-LASSO) ##REF##31967990##[9]##. TINDL utilizes a simple, yet effective, tissue-informed normalization to reduce the statistical discrepancies between the GEx profiles of the training and test samples. We showed that TINDL outperforms other DL-based models that try to explicitly remove these discrepancies using other techniques such as ComBat or domain adaptation ##UREF##0##[16]##, ##UREF##1##[17]##.</p>", "<p id=\"p0035\">Focusing on tamoxifen, for which TINDL performed best, we showed that only a small panel of genes identified by TINDL can be used to predict the CDR of cancer patients. Moreover, using small interfering RNA (siRNA) gene knockdown of 10 genes identified by TINDL in two breast CCLs (MCF7 and T47D), we showed that the knockdown of any of these genes significantly changed the response to tamoxifen in MCF7 and the knockdown of 7 of them significantly changed the response to this drug in T47D. These <italic>in vitro</italic> experiments further validated the TINDL pipeline and its ability to identify biomarkers of drug response.</p>" ]
[ "<title>Materials and methods</title>", "<title>Datasets</title>", "<p id=\"p0170\">We used the publicly available data from GDSC and TCGA for training and testing, respectively. For training data, we used the robust multi-array analysis (RMA)-normalized GEx data in GDSC, which contains 958 unique cell lines. For the test data, we used RNA sequencing [in fragments per kilobase million (FPKM)] from primary tumors in TCGA. For both datasets, we filtered out genes with missing values. We also removed genes that were not expressed (FPKM &lt; 1) for at least 90% of all the TCGA samples, and transformed the remaining genes using log<sub>2</sub> (FPKM + 0.1). Only genes that were present in both datasets were included, which summed up to 15,650 genes. We used z-score to normalize the GDSC GEx data (gene-wise) as well as the ln IC50 values (drug-wise). We obtained CDR of cancer patients from the <xref rid=\"s0145\" ref-type=\"sec\">supplementary file</xref> of Ding and his colleagues ##REF##27354694##[10]##. Because the number of samples with known drug response in TCGA is relatively small, in our analysis we also included samples that have received multiple drugs in their course of treatment. We only focused on drugs which are common to both datasets and have at least 20 samples with known CDR in TCGA. We used a tissue-informed normalization, which is detailed below. Furthermore, we recategorized the CDRs to sensitive (corresponding to complete and partial responses) and resistant (corresponding to stable disease and clinically progressive disease). Details on sample counts and tissue types per drug are in Table S1.</p>", "<title>Tissue-informed normalization</title>", "<p id=\"p0175\">TINDL trained a separate model for each drug. Each model performed a separate normalization on the GEx profiles of test samples from TCGA to account for the cancer types and tissues of origin of the samples. First, for each drug , the set of tissues/cancer types to which this drug was administered in the TCGA samples was identified (referred to as ). All samples corresponding to (excluding those used in the test set) were collected from TCGA, forming the unlabeled dataset. Then, the gene-wise mean () and standard deviation () of these unlabeled samples were calculated and used to normalize labeled test samples corresponding to drug . More specifically, for a gene of an arbitrary sample in the test set, the normalized value would be:where   is the log-transformed expression for gene of that sample. The test samples were then used as input to the trained model to predict the normalized ln IC50 values, which were compared with the actual CDR categories for evaluation.</p>", "<title>Architecture of TINDL, hyperparameter selection, and training</title>", "<p id=\"p0180\">We used grid-search and 5-fold cross validation to select the number of epochs, batch size, and learning rate of all our DL-based models (including TINDL). We only used the training data corresponding to CCLs (from GDSC) to perform the hyperparameter search, in which the set of hyperparameters with the highest average Pearson correlation coefficient on the validation set across the five folds were chosen. Specific hyperparameters chosen using this procedure for TINDL are provided in Table S9. In addition to the input layer (which contained one node for each gene), we used three hidden layers with dense connections, each with 512, 256, and 128 hidden nodes, in the order of their distance to the input layer. We used a rectified linear units (ReLU) activation function and added a dropout layer with 0.2 probability of dropping out prior to the output layer.</p>", "<p id=\"p0185\">Models were trained using mean squared error (MSE) as the loss function, and the normalized ln IC50 values as the labels. During hyperparameter tuning, models were allowed to train up to a maximum of 1000 epochs, but early stopping was applied when the loss of model did not decrease after 30 epochs. After hyperparameter tuning, we retrained a final model using all the labeled CCL samples. We used 10 different random initializations (<italic>i.e.</italic>, seeds) and ensembled the models by averaging their predictions to ensure robustness of the results. Note that individual models were trained independently. Loss curves for hyperparameter tuning and final training are shown in <xref rid=\"s0145\" ref-type=\"sec\">Figures S12 and S13</xref>. A similar technique was used for ADDA-DL, DANN-DL, ComBat-DL, TrainNorm-DL, and TestNorm-DL.</p>", "<title>Calculation of contribution scores of genes</title>", "<p id=\"p0190\">In the second phase of TINDL (##FIG##0##Figure 1##B), we used CXPlain ##UREF##2##[18]## as the explainer to assign a contribution score to each gene in each sample. CXPlain is a method that attempts to provide causal explanations of predictions of a trained model. This is achieved by training a separate model (called “explainer”) using the outputs of the trained model (called “predictor”). This method utilizes Granger causality ##UREF##8##[80]## to evaluate the contribution of a single feature (gene in our case) by zeroing out features one by one and calculating the normalized difference of the predictor’s original error and its error when the feature is zeroed out. In our case, we defined error as , where is the true value and  is the output of the predictor for sample , being the number of features. Note that our predictor was an ensemble, and is the average of the outputs of the individual models. Prior to training the explainer, the real contribution vectors, , are calculated for each training sample as follows:where . Here, denotes the predictor’s error when given but with feature zeroed out. The explainer has an architecture such that the dimensions of the input vector and the output vector are the same. Each of the outputs correspond to the predicted contribution for the corresponding feature. The explainer is trained by minimizing the Kullback–Leibler (KL) divergence of the real contributions and predicted contributions of the training set.</p>", "<p id=\"p0200\">We used a neural network with two layers and 512 hidden units for the explainer, and used the ensemble mode, which trained 10 independent explainers and reported their median as the final contribution values. We modified the code of CXPlain library to fit our application, which we also included in our published code. Once trained, we predicted the contribution values of each genes in each of the samples in the testing set. To obtain drug-specific gene contribution scores, we calculated the mean contribution score of each gene across all the labeled test samples for that drug and normalized it such that the largest contribution score of a drug equals 1.</p>", "<title>Identification of genes with highest contribution scores</title>", "<p id=\"p0205\">After obtaining contribution scores to each gene for a drug, we sought to identify the top genes that substantially affect the predictions our model. We sorted the genes according to their final test contribution scores and plotted a curve (<xref rid=\"s0145\" ref-type=\"sec\">Figure S7</xref>), where the X-axis is the rank of the gene and the Y-axis is the drug-specific contribution score   of gene . We used the kneedle algorithm ##UREF##5##[24]## to identify the point of maximum curvature, called “knee”, which we then treated as the cutoff for the top genes. Kneedle relies on the idea that if one forms a line from (1, ) to () and rotate the curve around the point (), the “knee” can be approximated by the set of points in the local maxima. Among these points, the point that is farthest from the line is then identified as the knee.</p>", "<title>Knowledge-guided pathway enrichment analysis</title>", "<p id=\"p0210\">We identified pathways associated with the top identified genes using KnowEng’s GSC pipeline ##REF##31971940##[47]##. We used the network-guided mode, which incorporates knowledge in the form of gene–gene interactions to augment the analysis. For the knowledge network, we selected the experimentally verified protein–protein interactions within the STRING database ##REF##30476243##[81]##. We then proceeded with the default 50% network smoothing parameter and used the “Enrichr” pathway collection. This pipeline does not provide a <italic>P</italic> value, but rather uses a score called “Difference Score” to implicate top pathways. Any pathway above the 0.5 threshold is considered associated with the input query set. A value above this threshold shows that the pathway has a high relevance score to the input query set (using a random walk with restarts algorithm), compared with the background ##REF##31971940##[47]##.</p>", "<title>Precision at <italic>k</italic>-th percentile</title>", "<p id=\"p0215\">For each drug, we used TINDL’s predictions of ln IC50 of the tumor samples, and identified the <italic>k</italic>-th percentiles of the distribution (<italic>k</italic> ≤ 50), which we denoted as . We stratified the predictions such that all predictions below was predicted as positives (<italic>i.e.</italic>, sensitive). We then calculated the precision at <italic>k</italic>-th percentile as , where and are the true positives and false positives at <italic>k</italic>-th percentile, respectively.</p>", "<title>Baseline models</title>", "<p id=\"p0220\">SVR, random forests, and LASSO regression were all implemented using scikit-learn. Geeleher’s method ##REF##24580837##[14]## was reimplemented using scikit-learn and pyComBat, a python implementation of ComBat ##REF##16632515##[15]##. We used the available implementation of TG-LASSO ##REF##31967990##[9]##. All hyperparameters were tuned as described in the previous subsections except for TG-LASSO, which has its built-in hyperparameter tuning.</p>", "<p id=\"p0225\">To ensure a fair comparison, all DL-based baseline models used a similar architecture to TINDL. Additionally, the hyperparameter tuning and training procedure was also similar to the one described above for TINDL. Below, we describe model-specific considerations. For ComBat-DL we used ComBat ##REF##16632515##[15]## for removing the discrepancy between TCGA and GDSC datasets. Similar to TINDL, we used both labeled and unlabeled samples of TCGA for this purpose.</p>", "<p id=\"p0230\">ADDA-DL utilizes ADDA ##UREF##1##[17]##, to remove the discrepancy between TCGA and GDSC datasets. ADDA is a unidirectional domain adaptation technique, which takes a pretrained neural network and attempts to adapt the network to the target dataset by forcing the latent feature space of the target dataset (TCGA) to be similar to that of the source dataset (GDSC). We used the TINDL model as the pretrained network, which we adapt through the adversarial losses of ADDA. We used the unlabeled tumor samples from the drugs target tissues during training. Details are provided in File S1.</p>", "<p id=\"p0235\">DANN-DL utilizes DANN ##UREF##0##[16]## to remove the discrepancy between TCGA and GDSC datasets. DANN utilizes the shared latent feature space to allow the model to be used on the target dataset despite only being trained using the labels of source dataset. This is done by incorporating a gradient-reversed discriminative loss function such that a discriminator cannot tell whether the given embedding came from the source (GDSC) or target (TCGA) datasets. Similar to ADDA-DL, we used the unlabeled tumor samples from the drugs target tissues for training of the discriminator.</p>", "<p id=\"p0240\">TrainNorm-DL and TestNorm-DL are two default workflows when domain discrepancies are not an important problem. In the TrainNorm-DL, we used the training set’s mean and standard deviation to normalize both the training set and the test set. This is analogous to assuming that the training set and test set belong to the same domain. The TestNorm-DL uses a per dataset normalization technique, in which the test set is normalized using its own mean and standard deviation, whereas the training set also uses its own summary statistics. The same model as TINDL was used for these baselines because the difference in normalization only affects the test set.</p>", "<p id=\"p0245\">GCN ##UREF##3##[22]## and GAT ##UREF##4##[23]## are two types of graph neural networks. For both architectures, the STRING co-expression graph ##REF##30476243##[81]## was used as the input structure. Only genes that existed in both STRING and the transcriptomic dataset were utilized. Each node in the graph is a gene, represented by the concatenation of a unique trainable embedding vector (gene-specific, shared across samples) and the expression value of gene (sample-specific). The purpose of gene-specific vectors is to allow GCN and GAT to distinguish differences between genes, which would normally be ignored because of the permutation invariance properties of architectures. The complete model is similar to that of TINDL, but with the first two layers replaced with GCN or GAT, corresponding to two-hop message passing in the graph.</p>", "<p id=\"p0250\">LSTM is a type of recurrent neural network, which are typically used for sequential data. We used the gene indices of our input file as the artificially induced ordering, and split the features into ten windows. Only the embedding coming from the last window (10th pass to the LSTM) was fed to the subsequent fully-connected layers. Only one LSTM layer was used because the parameters of one layer of LSTM are more comparable to two layers of a fully-connected network. The complete model resembles TINDL, but with the first layer replaced with an LSTM layer.</p>", "<title>Measurement of distance of clinical and preclinical samples in the latent space of DL-based models</title>", "<p id=\"p0255\">To assess the ability of each DL-based model in removing discrepancy between preclinical and clinical samples, we used pairwise Euclidean distance of samples based on their representation learned by the encoder of the DL models. Because these representations are used by the decoder to make predictions, comparing these latent representations is more meaningful than comparing input feature representations. We used Ward’s method ##UREF##9##[82]## to assess the distance of preclinical samples and clinical samples, which is one of the most popular methods in assessing the distance of two groups of samples. This method, which is widely used in hierarchical clustering, has the advantage that not only analyzes the Euclidean distances of the data points, but also incorporates their variance in determining the distance of two groups of samples.</p>", "<title>Chemicals and reagents</title>", "<p id=\"p0260\">Dulbecco’s Modified Eagle’s medium (DMEM; Catalog No. 11-965-092) was purchased from ThermoFisher Scientific (Carlsbad, CA). Fetal bovine serum (FBS; Catalog No. 10-437-028) and charcoal-stripped FBS (Catalog No. 12-676-029) were from Invitrogen (Carlsbad, CA). On-Target Plus SMARTpool siRNAs targeting <italic>RPP25</italic>, <italic>EMP1</italic>, <italic>EXTL3</italic>, <italic>EXOC2</italic>, <italic>NUP37</italic>, <italic>RPL13</italic>, <italic>WBP2NL</italic>, <italic>RPS6</italic>, <italic>GBP1</italic>, and <italic>JAK2</italic> as well as negative siRNA controls were purchased from Dharmacon (Horizon Discovery, Lafayette, CO). Reagents and primers for quantitative real-time polymerase chain reaction (qRT-PCR) were purchased from QIAGEN (Valencia, CA) and Integrated DNA Technologies (Coralville, IA). 17β-estradiol (E2; Catalog No. E2758) and 4-hydroxytamoxifen (OH-TAM; Catalog No. 579002) were purchased from Sigma Aldrich (Saint Louis, MO).</p>", "<title>Cell lines</title>", "<p id=\"p0265\">MCF7 and T47D cell lines were obtained from American Type Culture Collection (ATCC; Manassus, VA) in 2014, and the identities of all cell lines were confirmed by the medical genome facility at Mayo Clinic (Rochester, MN) using short tandem repeat profiling upon receipt. MCF7 cells were cultured in DMEM containing 10% FBS. T47D cells were cultured in RPMI-1640 containing 10% FBS.</p>", "<title>Transfection and gene silencing</title>", "<p id=\"p0270\">Specific siRNAs that targeted <italic>RPP25</italic>, <italic>EMP1</italic>, <italic>EXTL3</italic>, <italic>EXOC2</italic>, <italic>NUP37</italic>, <italic>RPL13</italic>, <italic>WBP2NL</italic>, <italic>RPS6</italic>, <italic>GBP1</italic>, <italic>JAK2</italic>, and negative siRNA controls (Horizon Discovery) were transfected into MCF7 and T47D cells in 96-well plates using Lipofectamine RNAiMAX Transfection Reagent (Catalog No. 13778500, ThermoFisher Scientific, Waltham, MA) according to the vendor’s protocol ##UREF##7##[67]##, ##REF##34048027##[83]##. Total RNA was extracted 48 h after transfection for RNA quantification. Specific siGENOME siRNA SMARTpool Reagents (Catalog Nos. M-020782-01-0005 for <italic>RPP25</italic>, M-010507-00-0005 for <italic>EMP1</italic>, M-012578-00-0005 for <italic>EXTL3</italic>, M-017357-01-0005 for <italic>EXOC2</italic>, M-014282-00-0005 for <italic>NUP37</italic>, M-013714-00-0005 for <italic>RPL13</italic>, M-017184-00-0005 for <italic>WBP2NL</italic>, M-003024-01-0005 for <italic>RPS6</italic>, M-005153-02-0005 for <italic>GBP1</italic>, and M-003146-02-0005 for <italic>JAK2</italic>) against a given gene as well as a negative control, siGENOME Non-Targeting siRNA (Catalog No. D-001206-13-20), were purchased from Horizon Discovery. For the purpose of drug tamoxifen response assay, cells were plated in base medium supplemented with 5% charcoal stripped FBS for 24 h, and then cultured in FBS-free DMEM media for another 24 h before transfection. Different treatments were started 24 h after transfection.</p>", "<title>qRT-PCR</title>", "<p id=\"p0275\">qRT-PCR assays were performed for measuring GEx using Power SYBR Green RNA-to-CT 1-Step Kit (Catalog No. 4389986, ThermoFisher Scientific, Grand Island, NY) and PrimeTime (Integrated DNA Technologies, Coralville, IA) pre-designed quantitative polymerase chain reaction (qPCR) primers. RNA was extracted using the QIAGEN RNeasy Kit (Catalog No. 74104, QIAGEN, Germantown, MD). RNA was measured by NanoDrops3000 (ThermoFisher Scientific, Rockford, IL). qRT-PCR reactions were prepared as per the manufacturer’s protocol. Samples were run using StepOnePlus Real-Time PCR System (ThermoFisher Scientific, Carlsbad, CA). For the experiments, we used three technical replicates. GEx was normalized to the negative siRNA control. Table S8 shows the knockdown efficiency of each gene and corresponding statistical analysis.</p>", "<title>Tamoxifen sensitivity assay</title>", "<p id=\"p0280\">Drugs were dissolved in dimethyl sulfoxide (DMSO), and aliquots of stock solutions were frozen at −80 °C. Cytotoxicity assays were performed in triplicate at each drug concentration. Specifically, 4000 breast cancer cells were seeded in 96-well plates, cultured in base media containing 5% (v/v) charcoal-stripped FBS for 24 h, and subsequently cultured in FBS-free base media for another 24 h. Cells were then transfected with either control siRNA or siRNA targeting a specific gene. After 24-h transfection, the media were replaced with fresh FBS-free base media, and the cells were treated with 10 μl of tamoxifen at final concentrations of 0, 0.1875, 0.375, 0.75, 1.5, 3, 6, 12, 24, and 48 μM ##REF##28968398##[84]##. After incubation for an additional 72 h, cytotoxicity was determined by quantification of DNA content using CyQUANT assay (Catalog No. C35012, Invitrogen, Carlsbad, CA) following the manufacturer’s instructions ##REF##29335246##[85]##, ##REF##32701512##[86]##, ##REF##30944027##[87]##. 100 μl of CyQUANT assay solution was added, and plates were incubated at 37 °C for 1 h and then read in a Safire2 Microplate Reader with filters appropriate for 480-nm excitation and 520-nm emission.</p>" ]
[ "<title>Results</title>", "<title>Prediction of CDR and identification of biomarkers of drug response using cell line data</title>", "<p id=\"p0040\">We developed TINDL to (1) predict the CDR of cancer patients (test set) and (2) identify predictive biomarkers of drug response based on models completely trained on preclinical cell line data (training set). The pipeline has two major phases: the modeling phase and the gene identification phase. In the modeling phase (##FIG##0##Figure 1##A), a neural network is trained using the GEx profiles of CCLs and their response to a drug [<italic>i.e.</italic>, normalized ln IC50 values in this study, where IC50 stands for half-maximal inhibitory concentration]. The trained model was then used to predict the drug response of cancer patients based on the carefully normalized GEx profiles of their primary tumors. Details of the DL architecture are provided in Materials and methods.</p>", "<p id=\"p0045\">We designed the normalization step of GEx profiles of patient tumors to address two important issues. First, we required this approach to remove the discrepancy between the statistical properties of GEx of CCLs and patient tumors, originating from the technical differences in protocols for measuring the data and the biological differences between preclinical CCLs and clinical tumors. Second, we required this approach to incorporate information on the tissues of origin (or cancer types) of tumors in the prediction task. In a previous study ##REF##31967990##[9]##, we showed that information on the tissues of origin of samples plays an important role in improving prediction performance; however, most commonly used methods for this task are not capable of appropriately incorporating this information. For this purpose and given a drug, we first identified the set of tissues (henceforth referred to as “target tissues”) of the clinical samples to which the drug was administered. Then, we collected additional GEx profile of samples from the same target tissues, independent of what drug was used for their treatment. The GEx profile of each test sample was then normalized against this additional set of “unlabeled” data (see Materials and methods for details).</p>", "<p id=\"p0050\">This simple, yet effective, normalization approach used in our pipeline removes the statistical discrepancy between the test and training datasets by mapping the expression of each gene in each dataset to a distribution with unit variance and zero mean. However, because the test samples are normalized while considering the GEx of a much larger unlabeled set of samples, this normalization will not be negatively affected if the size of the test set is small (<italic>e.g.</italic>, if we want to predict the drug response of a single sample), which is superior compared with methods that perform the normalization using only the test samples. In addition, because the normalization is done independently for the training and test sets, one does not need to retrain the DL model every time in which the drug response of a new test sample is to be predicted (a shortcoming of our previous approach ##REF##31967990##[9]##).</p>", "<p id=\"p0055\">The second phase of the pipeline seeks to assign a contribution score to each gene based on its contribution to the trained predictive model to enable interpretability of the model (##FIG##0##Figure 1##B). In this phase, we first used CXPlain ##UREF##2##[18]## to assign a sample-specific score to each gene. These scores were then averaged over all samples (separately for each gene) and normalized to provide a final contribution score. Additionally, we used the distribution of these scores to systematically identify the critical point that the contribution of the genes diminishes, enabling us to narrow down the top ranked list of genes for follow-up analysis (pathway enrichment analysis, gene knockdown experiments, <italic>etc</italic>.). The details of this phase are provided in Materials and methods.</p>", "<title>TINDL distinguishes between sensitive and resistant patients for the majority of the evaluated drugs</title>", "<p id=\"p0060\">In order to assess the performance of TINDL in predicting CDR of cancer patients, we obtained GEx profiles of primary cancer tumors from the TCGA database ##REF##24071849##[2]##. We used the data corresponding to Response Evaluation Criteria in Solid Tumors (RECIST) CDR of TCGA patients, collected and processed in a previous study ##REF##27354694##[10]##, and identified 14 drugs that satisfied two conditions: (1) there were at least 20 patients with known CDR values for each drug in TCGA database and (2) the ln IC50 drug response values of these drugs were measured in the GDSC database. Similar to previous studies ##REF##31967990##[9]##, ##REF##24580837##[14]##, we transformed the CDR of these tumors into a Boolean label in which “resistant” referred to patients with CDR of “stable disease” or “progressive disease” and “sensitive” referred to patients with CDR of “complete response” or “partial response”. These CDR values were used to evaluate the predicted drug response values using TINDL and other algorithms but were not used for training them. The list of these 14 drugs, number of TCGA patients, and their cancer types are provided in Table S1. Similarly, we obtained GEx profiles and ln IC50 drug response values of CCLs from different lineages from the GDSC database ##REF##23180760##[3]##, corresponding to the 14 drugs mentioned above (see Table S1 for the number of training samples for each drug).</p>", "<p id=\"p0065\">Following previous work in this area ##REF##31967990##[9]##, ##REF##24580837##[14]##, we used a one-sided Mann–Whitney <italic>U</italic> test to determine if the predicted ln IC50 values of resistant patients for a drug are significantly higher than those of sensitive patients. ##TAB##0##Table 1##, <xref rid=\"s0145\" ref-type=\"sec\">Table S2</xref>, and <xref rid=\"s0145\" ref-type=\"sec\">Figures S1 and S2</xref> show the performance of TINDL in the prediction of CDR of TCGA samples using preclinical GDSC samples for different drugs. TINDL is capable of distinguishing between resistant and sensitive patients for 10 (out of 14) drugs (<italic>P</italic> &lt; 0.05, one-sided Mann–Whitney <italic>U</italic> test) with a combined <italic>P</italic> value of 2.77E–10 (Fisher’s method).</p>", "<p id=\"p0070\">Next, we defined a measure called precision at <italic>k</italic>-th percentile to determine whether patients whose predicted ln IC50 is within the lower tail of the distribution correspond to sensitive patients (<italic>i.e.</italic>, responders to the drug). For different values of <italic>k</italic>, tumors with predicted ln IC50 in the bottom <italic>k</italic>% were predicted as sensitive, and their count was used to calculate precision. ##FIG##1##Figure 2##A and Table S3 show precision at <italic>k</italic>-th percentile of TINDL for different values of <italic>k</italic>. These results suggest that for six drugs (tamoxifen, etoposide, vinorelbine, cyclophosphamide, bleomycin, and cisplatin), TINDL can identify responders with a precision at <italic>k</italic>-th percentile above 84% for any choice of <italic>k</italic>. The distribution of predicted CDR values for sensitive and resistant patients for these drugs are shown in ##FIG##1##Figure 2##B.</p>", "<title>TINDL outperforms alternative methods in prediction of CDR</title>", "<p id=\"p0075\">Next, we sought to determine how TINDL performs against alternative computational models. For this purpose, we considered multiple traditional and state-of-the-art ML models ##REF##31967990##[9]##, ##REF##24580837##[14]## for predicting CDR of cancer patients from preclinical CCLs. The detailed performance measures for each drug and each model are provided in Table S2 and <xref rid=\"s0145\" ref-type=\"sec\">Figures S1 and S2</xref>, and the summary of the results are provided in ##TAB##1##Table 2##. In this table, we used the combined <italic>P</italic> value of 14 drugs to summarize the performance of different methods (Fisher’s method). As shown in ##TAB##1##Table 2##, TINDL can distinguish between sensitive and resistant patients for 10 (out of 14) drugs (with a combined <italic>P</italic> value of 2.77E−10 for all drugs), whereas the second-best method in this table can only distinguish between sensitive and resistant patients for 7 drugs. Similar to our previous study ##REF##31967990##[9]##, we also observed that regression with least absolute shrinkage and selection operator (LASSO) and its variation, TG-LASSO, performed reasonably well (when considering all drugs), whereas support vector regression (SVR) and random forests did not perform as well.</p>", "<p id=\"p0080\">As discussed earlier, one of the major challenges in predicting the CDR of cancer patients based on ML models trained on preclinical CCLs is the statistical differences between these samples. To assess the performance of TINDL against other DL models that explicitly try to remove these statistical differences, we considered three alternative methods, as well as two baselines that could be considered “default workflows”, had we not foreseen the dire impact of these statistical differences. The first method (referred to as ComBat-DL) utilizes ComBat ##REF##16632515##[15]## as a preprocessing step to remove the statistical discrepancy between CCLs and tumor samples. ComBat ##REF##16632515##[15]## is a popular method for removing batch effects in GEx datasets and has been widely used for drug response prediction ##REF##31967990##[9]##, ##REF##24580837##[14]##, ##REF##26121976##[19]## and other applications ##REF##27549193##[20]##, ##REF##29608179##[21]##. The ComBat-transformed GEx profiles are then used in a DL architecture similar to TINDL for a fair comparison. The second and third methods are based on Domain Adaptive Neural Network (DANN) ##UREF##0##[16]## and Adversarial Discriminative Domain Adaptation (ADDA) ##UREF##1##[17]##, two domain adaptation techniques that were originally developed for image processing, so here we called them DANN-DL and ADDA-DL, respectively. Instead of adapting the GEx input features, these methods adjust the latent feature representations learned by the encoder. DANN uses adversarial neural networks to create a shared latent feature space between the datasets. ADDA, on the other hand, is a unidirectional domain adaptation approach that builds over a pretrained predictor and tries to adapt the first few layers of the neural network such that the latent feature representation of target dataset aligns with that of the source dataset.</p>", "<p id=\"p0085\">Although the three approaches mentioned above actively try to reduce the discrepancy between the training set and test set, two default workflows (TrainNorm-DL and TestNorm-DL) actively ignore this challenge. In particular, TrainNorm-DL assumes that the test set (tumors) comes from the same distribution as the training set (CCLs), and therefore uses the mean and standard deviation of the training set to normalize all of the data. This is essentially the default workflow for most ML tasks in order to prevent data leakage during normalization. The TestNorm-DL normalizes the test set and training set separately (<italic>i.e.</italic>, it uses the mean and standard deviation of the test set to normalize itself). One should note that TestNorm-DL is not an ideal approach in practice, because it requires a large number of test samples to be present and is not recommended when predicting the response of a small number of samples.</p>", "<p id=\"p0090\">We trained models of these methods with a similar architecture to that of TINDL, with the exception of the discriminators, which are specific to ADDA and DANN and are used for domain adaptation. The details of these methods, including their architecture and training procedure, are provided in Materials and methods and File S1. ##TAB##2##Table 3## and Table S2 show the performance of these DL-based approaches. These results showed that in all three cases of explicit discrepancy removal, only for 7 (out of 14) drugs the predicted normalized ln IC50 of sensitive patients was significantly smaller than those of resistant patients. As expected, TrainNorm-DL did not perform as well (6 out of 14) as the others DL approaches. TestNorm-DL was able to segregate sensitive patients in 8 drugs, which surprisingly came second to TINDL, but this method is not well suited for applications in which only very few samples exist in the test set.</p>", "<p id=\"p0095\">To assess the superior performance of TINDL compared with the first three DL-based models above, we assessed their ability in removing the discrepancy between preclinical and clinical samples. We did not include the default workflows in this analysis, because they ignore this discrepancy. For this purpose, we assessed the distance of clinical samples and preclinical samples for each method and each drug (see Materials and methods for details of calculating distances). Because methods that use domain adaptation do not modify the input features, but rather seek to remove the domain discrepancies in the latent space (the output of the encoder), we used the learned representation of each sample in the latent space for all methods. Using a one-sided Wilcoxon signed-rank test, we observed that the learned representations of TINDL for clinical samples have a significantly smaller average distance to preclinical samples compared with ComBat-DL (<italic>P</italic> = 6.10E−5), ADDA-DL (<italic>P</italic> = 4.27E−4), and DANN-DL (<italic>P</italic> = 6.10E−5), for all drugs (##FIG##2##Figure 3##A). The effectiveness of tissue-informed normalization of TINDL in removing the statistical discrepancy between the preclinical and clinical embeddings can also be visually observed using principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) plots of the representations learned by each method (##FIG##2##Figure 3##B, <xref rid=\"s0145\" ref-type=\"sec\">Figures S3–S6</xref>).</p>", "<p id=\"p0100\">Next, we sought to determine whether the latent space representation similarity has an influence on drug response prediction performance of TINDL across different drugs. We observed a negative Spearman rank correlation (r =  −0.17, <italic>P</italic> = 3.93E−2) between the aforementioned distances and the area under the receiver operating characteristic curve (AUROC) of prediction for different drugs. In particular, tamoxifen that had the highest AUROC (Table S2, AUROC = 0.92) also had the smallest average distance between clinical and preclinical representations of its samples among all drugs in TINDL. These results further support the conclusion that reducing the discrepancy between the statistical characteristics of clinical and preclinical samples plays an important role in the success of TINDL in the prediction of CDR.</p>", "<title>More complex neural network architectures do not show improvement</title>", "<p id=\"p0105\">We also assessed the performance of different neural network architectures when used as the feature extractor, instead of fully-connected (FC) networks that were used in the previous section. Specifically, we used long short-term memory (LSTM), graph convolutional network (GCN) ##UREF##3##[22]##, and graph attention network (GAT) ##UREF##4##[23]## for the first few layers of the model (see Materials and methods for details). All models were subjected to the same protocol and evaluation techniques as the other DL methods based of FC networks. A summary of the results are provided in ##TAB##3##Table 4##, and more detailed evaluation metrics are provided in Table S2. Although in theory GCN and GAT may hold some advantage compared with a FC architecture because the features (GEx) are not independent, these architectures did not show an improvement over FC networks. LSTM was expected not to perform well because the data are not sequential. Nevertheless, it is interesting that for some of the drugs, the LSTM is able to separate the sensitive and resistant patients.</p>", "<title>TINDL identifies biomarkers of drug response</title>", "<p id=\"p0110\">We used TINDL (##FIG##0##Figure 1##B) to assign a score to the contribution of each gene in the trained model (see Material and methods for details). <xref rid=\"s0145\" ref-type=\"sec\">Figure S7</xref> shows the distribution of these scores for each drug. To identify the threshold below which the contribution of the genes to the predictive model is small, we used a method called kneedle ##UREF##5##[24]##, which systematically determines this threshold for each drug based on the distribution of the scores. This method identified between 64 (for pemetrexed) to 243 (for bleomycin) genes, depending on the drugs. The ranked list of genes identified by TINDL using this drug-specific threshold is provided in Table S4.</p>", "<p id=\"p0115\">Next, we sought to determine whether the identified genes are drug specific. To this end, we calculated the Jaccard similarity coefficient of drug pairs (<xref rid=\"s0145\" ref-type=\"sec\">Figure S8</xref>A). The results revealed a high degree of drug specificity with the average Jaccard similarity coefficient for all drugs equal to only 0.027. However, some genes were implicated for multiple drugs (<xref rid=\"s0145\" ref-type=\"sec\">Figure S8</xref>B; Table S5). Previous studies have shown that these genes are involved in several cancers and are associated with sensitivity to multiple drugs ##UREF##6##[25]##, ##REF##34043102##[26]##, ##REF##28060381##[27]##, ##REF##33271565##[28]##, ##REF##34272396##[29]##, ##REF##34966587##[30]##, ##REF##31800589##[31]##. Multidrug resistance (MDR) is one of the reasons for reduced effectiveness of many cancer therapeutic agents ##REF##27057637##[32]##. MDR is defined as the insensitivity to therapeutic substances that are not associated by structure or mechanism of action ##REF##25685543##[33]##. The classical mechanism of MDR is associated with the overexpression of the ATP-binding cassette (ABC) transporter genes (<italic>ABCB1</italic>, <italic>ABCD1</italic>, <italic>etc</italic>.), which contribute to the reduction of the effective drug concentration transporting the drug out of the cells ##REF##19725928##[34]##. In addition to the classical MDR mechanism associated with the overexpression of ABC genes, there are atypical mechanisms ##REF##31603457##[35]##, ##REF##34546840##[36]##, ##REF##29516570##[37]##. Examples of these atypical mechanisms include escaping adaptive immune responses ##REF##31603457##[35]##. Dysregulation of many genes, <italic>e.g.</italic>, <italic>APOBEC3A</italic>, promote evolution and progression of cancers, escape adaptive immune responses, and lead to development of drug resistance in multiple cancers ##REF##28655787##[38]##, ##REF##35859169##[39]##. Other atypical mechanisms include dysregulation of genes, such as <italic>CRYAB</italic>, related to macrophage infiltration and polarization ##REF##34546840##[36]##, and dysregulation of genes that regulate drug-induced apoptosis by activating the survival pathways such as MEK/ERK signaling and inhibiting the mitochondrial apoptosis pathway in cervical cancer cells ##REF##29516570##[37]##. In particular, Schlafen family member 11 (SLFN11) was implicated for nine drugs and was the top contributor for bleomycin, cisplatin, doxorubicin, etoposide, gemcitabine, and irinotecan, and the top third contributor for oxaliplatin. SLFN11 is a putative DNA/RNA helicase that is recruited to the stressed replication fork and inhibits DNA replication. DNA replication is one of the fundamental biological processes in which dysregulation can cause genome instability ##REF##23446422##[40]##. This instability is one of the hallmarks of cancer and confers genetic diversity during tumorigenesis ##REF##21376230##[41]##. Various studies have shown that the expression of this gene sensitizes cancer cells to many chemotherapeutic agents including cisplatin, oxaliplatin, irinotecan, gemcitabine, doxorubicin, and etoposide ##REF##31128155##[42]##, ##REF##26525741##[43]##, ##REF##33339894##[44]##. Epigenetically mediated suppression of SLFN11 via EZH2 contributes to acquired chemotherapy resistance, one that can be prevented and/or actively remodeled through targeting EZH2 ##REF##28196596##[45]##. Several potent and selective EZH2 inhibitors are now in different stages of clinical development with promising safety profile, including phase II (Epizyme) and phase I (Constellation, GSK) trials in multiple solid tumor and hematological indications. Our data support the notion that the combination of down-regulating SLFN11 via EZH2 inhibitor with chemotherapeutic reagents should be considered in multiple cancer types ##REF##25629630##[46]##.</p>", "<p id=\"p0120\">To better understand the functional characteristics of genes implicated by TINDL for multiple drugs, we used KnowEnG’s gene set characterization (GSC) pipeline ##REF##31971940##[47]## to identify pathways associated with 29 genes identified by TINDL for at least 4 drugs (<xref rid=\"s0145\" ref-type=\"sec\">Figure S8</xref>B). This pipeline enables identification of associated pathways while incorporating interactions among genes and their protein products through network-guided analysis. The results (Table S5) implicated five pathways, including “regulation of toll-like receptor signaling pathway”, “alpha-synuclein signaling”, “Arf6 trafficking events”, “insulin pathway”, and “RalA downstream regulated genes”. Innate immune receptors such as toll-like receptors (TLRs) are responsible for recognizing molecular patterns associated with pathogens and provide critical molecular links between innate cells and adaptive immune responses. Engagement of TLRs on dendritic cells (DCs) promotes cross-talk between the innate and the adoptive immune system, maturation and migration of DCs into lymph nodes leading to activation, and proliferation and survival of tumor antigen-specific naïve CD4<sup>+</sup> and CD8<sup>+</sup> T cells ##REF##15128790##[48]##. Tumor cells themselves do not express molecules which would induce DC maturation, so application of TLR agonists is an important element of immunotherapy protocols aiming T cell activation ##REF##11607032##[49]##. In addition, TLR agonists have been proposed as adjuvants for cancer vaccines ##REF##28921471##[50]##. TLR3 agonist as an adjuvant with conventional chemotherapy can break tolerogenic or immunosuppressive effects generated by the tumor and drive T cell responses and tumor rejection ##REF##12907622##[51]##, ##REF##19052556##[52]##.</p>", "<p id=\"p0125\">Alpha-synuclein (α-syn) is a neuronal protein responsible for regulating synaptic vesicle trafficking. α-syn is frequently expressed in various brain tumors and melanoma ##REF##10672322##[53]##, and its up-regulation has been linked to aggressive phenotypes of meningiomas ##REF##27895530##[54]##. Moreover, loss of α-syn results in dysregulation of iron metabolism and suppression of melanoma tumor growth ##REF##33664298##[55]##. Oncogenic activation of synuclein contributes to the cancer development by promoting tumor cell survival via activation of JNK/caspase apoptosis pathway and ERK, and by providing resistance to certain chemotherapeutic drugs ##REF##9665134##[56]##, suggesting synuclein as a new therapeutic target for future treatment to overcome resistance to certain chemotherapeutic. ADP-ribosylation factor 6 (ARF6) governs the trafficking of bioactive cargos to tumor-derived microvesicles (TMVs) which comprise a class of extracellular vesicles released from tumor cells that facilitate communication between the tumor and the surrounding microenvironment ##REF##31235936##[57]##. Invasive tumor cells shed TMVs containing bioactive cargo and utilize TMVs to degrade extracellular matrix during cell invasion ##REF##30397076##[58]##. Indeed, several studies have suggested a correlation between ARF6 expression and invasion and metastasis of multiple cancers ##REF##28625359##[59]##, ##REF##23747719##[60]##, suggesting that antagonistic ARF6 signaling can dictate TMV shedding and the overall mode of invasion. Insulin, a signaling molecule that controls systemic metabolic homeostasis, can be seen as enabling tumor development by providing a mechanism for PI3K activation and enhanced glucose uptake ##REF##30051890##[61]##, ##REF##32493414##[62]##, and plays a role in cytotoxic therapy response ##REF##31719636##[63]##. RAS-related protein RalA is a member of the Ral family, and the RalA pathway contributes to anchorage independent growth, tumorigenicity, migration, and metastasis ##REF##18219307##[64]##, ##REF##21779498##[65]##. In conclusion, the link between genes implicated for multiple drugs and the pathways mentioned above that play different roles in cancer may point to shared mechanisms of action among different anti-cancer drugs. We also performed a similar pathway enrichment analysis for genes implicated for each drug separately and the results are provided in Table S6.</p>", "<title>Functional validation confirms the role of TINDL-identified genes in response to tamoxifen</title>", "<p id=\"p0130\">We sought to evaluate the drug response-predictive ability of top identified genes by TINDL, both computationally and experimentally. We focused on tamoxifen due to the good prediction performance of TINDL for this drug (AUROC = 0.92, <italic>P</italic> = 1.14E−3 for Mann–Whitney <italic>U</italic> test). First, using only top implicated genes for this drug (<italic>n</italic> = 136 based on the threshold identified by kneedle), we observed a consistently high value of AUROC and a significant Mann–Whitney <italic>U</italic> test <italic>P</italic> value (##FIG##3##Figure 4##A, AUROC = 0.89, <italic>P</italic> = 2.32E−3). Next, we reduced the number of genes for the model to only top 20 and observed that AUROC remains high even with this small number of genes (##FIG##3##Figure 4##A, AUROC = 0.90, <italic>P</italic> = 1.65E−3). This shows that even a small panel of 20 genes can be used to predict the CDR of this drug, suggesting potential clinical applications in precision medicine for these small panels of genes.</p>", "<p id=\"p0135\">Next, we set out to determine whether genes identified by TINDL as predictive of tamoxifen response could be associated <italic>in vitro</italic> with relevant changes in drug sensitivity. We selected 10 genes identified by TINDL, which included the top 9 ranked genes (<italic>RPP25</italic>, <italic>EMP1</italic>, <italic>EXTL3</italic>, <italic>EXOC2</italic>, <italic>NUP37</italic>, <italic>RPL13</italic>, <italic>WBP2NL</italic>, <italic>RPS6</italic>, and <italic>GBP1</italic>) as well as the gene ranked as 19 (<italic>JAK2</italic>), due to its involvement with the type II interferon signaling pathway, an important pathway in cancer ##REF##34155388##[66]##. We used estrogen receptor positive breast CCLs, MCF7 and T47D, because tamoxifen has most often been used as the treatment for estrogen receptor positive breast cancer patients in general and 85% of patients in our test dataset for this drug corresponded to breast cancer. We measured the dose–response values of tamoxifen in these two cell lines for these ten genes using CyQUANT assay, which provides an accurate measure of cell numbers based on DNA content ##UREF##7##[67]##. We defined “significance” as a gene knockdown with a significant change in apparent IC50 in comparison with a negative control siRNA. Knockdown of all ten genes with specific siRNAs had a significant effect on tamoxifen sensitivity in MCF7 cell line (<italic>P</italic> &lt; 0.0001, extra sum-of-squares F test), validating 100% of tested genes in this cell line (##FIG##3##Figure 4##B, <xref rid=\"s0145\" ref-type=\"sec\">Figure S9</xref>; Table S7). Similarly, our experiments confirmed seven of these genes in T47D cell line (##FIG##3##Figure 4##C, <xref rid=\"s0145\" ref-type=\"sec\">Figure S10</xref>; Table S7). Taken together, through the functional validation in estrogen receptor positive breast cancer cells, we found that the expression of seven genes, <italic>RPP25</italic>, <italic>EXOC2</italic>, <italic>NUP37</italic>, <italic>RPL13</italic>, <italic>RPS6</italic>, <italic>GBP1</italic>, and <italic>JAK2</italic>, were involved in tamoxifen-induced response in both cell lines, and three genes, <italic>EMP1</italic>, <italic>EXTL3</italic>, and <italic>WBP2NL</italic> were involved in tamoxifen-induced response in MCF7. The percentage of variation in the IC50 of breast cancer cells that was explained by the variation of expression of these ten genes is provided in Table S7, whereas Table S8 shows the efficiency of knockdown for each gene.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0140\">Predicting the response of an individual to cancer treatments and identification of predictive biomarkers of drug response are two major goals of individualized medicine. Computational models that can achieve these goals based on preclinical <italic>in vitro</italic> data can make a considerable impact, due to the significant ease of preclinical data generation and data collection compared with clinical samples. This is particularly important for newly developed or newly approved drugs, for which clinical samples may be very limited or non-existent. However, the biological and statistical differences between CCLs and patient tumors make this task challenging. In a recent study ##REF##31967990##[9]##, we assessed the ability of a wide range of ML models trained on preclinical CCLs, including those that incorporate auxiliary information such as gene interaction networks, in predicting the CDR of cancer patients. Our analysis confirmed the difficulty of this task and emphasized the importance of carefully designing advanced computational techniques.</p>", "<p id=\"p0145\">In this study, we developed TINDL, and showed its substantial improvement compared with the state-of-the-art ML models (based on both traditional and DL techniques) (##FIG##0##Figure 1##). Our results showed the importance of removing the statistical discrepancies between preclinical and clinical samples, as well as incorporating the cancer types and tissues of origin of the tumor samples. TINDL is not simply a drug response predictor, but rather allows identification of the most predictive biomarkers for each drug. The biomarkers identified by multiple drugs (<xref rid=\"s0145\" ref-type=\"sec\">Figure S8</xref>B) suggested important genes and signaling pathways that may play important roles in the mechanism of action of different drugs in cancer. Many genes identified during our study have been reported to have altered levels of expression in response to a given drug, especially <italic>SLFN11</italic> for multiple chemotherapies ##REF##31128155##[42]##, ##REF##26525741##[43]##, ##REF##33339894##[44]##, ##REF##33328609##[68]##, ##REF##31092045##[69]##, <italic>SALL4</italic> for cisplatin ##REF##33975879##[70]##, <italic>ABCB1</italic> for taxane and doxorubicin ##REF##32536602##[71]##, ##REF##33753859##[72]##, <italic>PIGB</italic> for gemcitabine ##REF##24483146##[73]##, and <italic>BAX</italic> to oxaliplatin ##REF##23329644##[74]##. These results suggest that our preclinical-to-clinical model could generate biologically relevant candidate genes and pathways for understanding mechanisms underlying drug resistance, and may offer additional combinational therapeutic strategies to overcome certain drug resistance.</p>", "<p id=\"p0150\">Focusing on tamoxifen, we were able to show that only a small panel of 20 genes can preserve the predictive performance of TINDL for this drug (##FIG##3##Figure 4##A). Moreover, functional validation of 10 of these genes identified by TINDL using siRNA knockdown performed with MCF7 and T47D estrogen receptor positive breast cancer cells, confirmed the direct role of these genes in response to tamoxifen (##FIG##3##Figure 4##B and C, <xref rid=\"s0145\" ref-type=\"sec\">Figures S9 and S10</xref>). These results suggest that, like many complex traits, response to tamoxifen also involves multiple genes in different pathways. In addition, these results provide us with new insights into novel mechanisms in tamoxifen response. For example, among these genes, <italic>RPS6</italic> is the canonical substrate of S6 kinase (S6K), which is activated by integrin engagement and inactivated by detachment. Abnormal expression of <italic>RPS6</italic> has been indicated as a critical trigger for detachment-induced keratinization related to breast cancer development ##REF##24658685##[75]##. Indeed, the prognostic value of <italic>RPS6</italic> was assessed by Kaplan–Meier plotter analysis of GEx data from estrogen receptor positive/HER2 negative breast tumor samples of 686 patients. High expression of <italic>RPS6</italic> was associated with better relapse-free survival (RFS) in this cohort of patients (<xref rid=\"s0145\" ref-type=\"sec\">Figure S11</xref>A). Decreased phosphorylation of <italic>RPS6</italic> was previously observed in tamoxifen-resistant breast cancer cells compared with parental cells ##REF##20234184##[76]##. However, to the best of our knowledge, no previous study has linked <italic>RPS6</italic> to tamoxifen sensitivity. The fact that we found that <italic>RPS6</italic> expression can predict tamoxifen sensitivity and that knockdown of <italic>RPS6</italic> desensitized breast cancer cells to tamoxifen exposure by two folds suggests a potential role for <italic>RPS6</italic> in the estrogen response pathway, in addition to its role as a protein synthesis regulator. In addition to its prognostic value, further analysis revealed that high messenger RNA (mRNA) expression of <italic>RPS6</italic> was also remarkably associated with prolonged RFS in tamoxifen-treated patients (<xref rid=\"s0145\" ref-type=\"sec\">Figure S11</xref>B). This hypothesis will need to be tested further in future experiments. The second gene that influenced tamoxifen response the most was <italic>RPL13</italic>, also known as “Ribosomal Protein L13”. <italic>RPL13</italic> encodes a component of the 60S ribosomal subunit that is expressed at significantly higher levels in benign breast lesions than in breast carcinomas ##REF##9854818##[77]##. Similarly, to the best of our knowledge, no previous study has linked <italic>RPL13</italic> to estrogen signaling or tamoxifen response. Kaplan–Meier Plotter analysis revealed that patients with high expression of <italic>RPL13</italic> had a significantly longer RFS than those with low <italic>RPL13</italic> expression (<xref rid=\"s0145\" ref-type=\"sec\">Figure S11</xref>C). Our observations here suggest an important role of <italic>RPL13</italic> expression level in predicting tamoxifen sensitivity, and could help identify additional drug targets or treatment options to overcome tamoxifen resistance.</p>", "<p id=\"p0155\">Our analysis suggests that TINDL performs better than other approaches (in terms of the number of drugs for which it can distinguish between resistant and sensitive tumors). Although its superior performance compared with traditional ML models can be attributed to higher capacity of DL approaches in modeling complex and nonlinear relationships, its superior performance compared with DL-based domain adaptation techniques reveals its ability to remove the discrepancies between the preclinical and clinical samples. In this study, we performed additional analyses on the embedding space, which confirmed the hypothesis above both visually and quantitatively. When inspecting the principal components and the UMAPs of the samples in the embedding space from the two datasets (##FIG##2##Figure 3##B, <xref rid=\"s0145\" ref-type=\"sec\">Figures S3–S6</xref>), it was clearly visible that the distributions of GDSC and TCGA samples were quite distinct from each other when using domain adaptation models or ComBat. However, embeddings learned by TINDL showed a mixing of the GDSC and TCGA samples, which can be interpreted as a better reduction of the domain discrepancy. We quantified this observation by calculating the average inter-domain distance of the samples in the latent space (smaller value is better). As shown in ##FIG##2##Figure 3##A, TINDL had a significantly lower average distance compared with the existing approaches. One possible reason for this observation is that the other approaches do not incorporate prior information about the target domain. Tissues have distinct GEx profiles, which was leveraged by TINDL. Another reason is the difficulty of assessing the level of adaptation in domain adaptation models because vector representations of GEx (unlike images) cannot be visually verified. Furthermore, domain adaptation methods can suffer from a “mode collapse” problem in which all samples are mapped in a small subspace in the latent space such that the discriminator is confused, which is erroneously equated to having a sufficient adaptation. We would like to point out that in spite of the shortcomings of current domain adaptation techniques, we posit that novel domain adaptation methods can be developed to improve the results. However, such methods need to be carefully designed for the analysis of GEx data and must take into account biological factors that influence the response of cancer patients to different drugs. In addition, including information on the cancer type or even subtype of each cancer may be necessary to achieve better results.</p>", "<p id=\"p0160\">Another important consideration is that due to the limitation of CCLs in mimicking patient tumors (<italic>e.g.</italic>, their growth in 2D environment, being more homogenous than tumors, and not being able to capture the effect of tumor microenvironment), computational models trained on CCLs are limited in their ability to predict CDR of cancer patients, even if they remove the statistical discrepancies of the training and test sets. As a result, availability of large datasets, pertaining to better models of cancer (such as patient-derived organoids or xenografts), plays an important role in improving the predictive ability of computational models.</p>", "<p id=\"p0165\">In this study, our focus was models trained only on GEx profiles of samples, because previous studies have shown this data modality to be most informative regarding drug response ##REF##24880487##[6]##. However, a multi-omics approach that incorporates different molecular characteristics of samples may provide a more complete understanding of the mechanisms of drug response in cancer. Nevertheless, such models need to be carefully designed to avoid over-fitting due to the additional number of features, which can cause severe performance deterioration. Another limitation of this study was that all the computational models were trained on CCLs and their response to single drugs. However, some of the patients in the TCGA dataset have received multiple drugs in the course of their treatment, which we had to include in the analysis due to the small number of samples with known CDR. In such cases, any computational models trained on single drugs can only provide an approximation. To improve the prediction performance in such cases, a computational model must also consider the synergistic and antagonistic effects of the drugs. Recent large publicly available datasets such as DrugComb ##REF##31066443##[78]## and DrugCombDB ##REF##31665429##[79]## that contain response of different cell lines to pairs of drugs provide an opportunity for developing such methods, a direction that we will pursue in the future.</p>" ]
[]
[ "<p>Prediction of the response of <bold>cancer</bold> patients to different treatments and identification of biomarkers of <bold>drug response</bold> are two major goals of individualized medicine. Here, we developed a <bold>deep learning</bold> framework called TINDL, completely trained on preclinical cancer cell lines (CCLs), to predict the response of cancer patients to different treatments. TINDL utilizes a tissue-informed normalization to account for the tissue type and cancer type of the tumors and to reduce the statistical discrepancies between CCLs and patient tumors. Moreover, by making the deep learning black box interpretable, this model identifies a small set of genes whose expression levels are predictive of drug response in the trained model, enabling identification of biomarkers of drug response. Using data from two large databases of CCLs and cancer tumors, we showed that this model can distinguish between sensitive and resistant tumors for 10 (out of 14) drugs, outperforming various other machine learning models. In addition, our small interfering RNA (siRNA) knockdown experiments on 10 genes identified by this model for one of the drugs (tamoxifen) confirmed that tamoxifen sensitivity is substantially influenced by all of these genes in MCF7 cells, and seven of these genes in T47D cells. Furthermore, genes implicated for multiple drugs pointed to shared mechanism of action among drugs and suggested several important signaling pathways. In summary, this study provides a powerful deep learning framework for prediction of drug response and identification of biomarkers of drug response in cancer. The code can be accessed at <ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/ddhostallero/tindl\" id=\"ir005\">https://github.com/ddhostallero/tindl</ext-link>.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Xin Gao</p>" ]
[ "<title>Code availability</title>", "<p id=\"p0285\">An implementation of TINDL in Python, with appropriate documentation, is available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://github.com/ddhostallero/tindl\" id=\"PC_linkev28qq2NSl\">https://github.com/ddhostallero/tindl</ext-link>. Preprocessed input data and trained models are also linked in the code repository.</p>", "<title>Competing interests</title>", "<p id=\"p0290\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0295\"><bold>David Earl Hostallero:</bold> Methodology, Software, Formal analysis, Visualization, Data curation, Writing – original draft, Writing – review &amp; editing. <bold>Lixuan Wei:</bold> Investigation, Visualization, Writing – review &amp; editing. <bold>Liewei Wang:</bold> Investigation, Writing – review &amp; editing. <bold>Junmei Cairns:</bold> Conceptualization, Supervision, Funding acquisition, Writing – review &amp; editing. <bold>Amin Emad:</bold> Conceptualization, Methodology, Formal analysis, Supervision, Funding acquisition, Writing – original draft, Writing – review &amp; editing. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0310\">The following are the Supplementary data to this article:</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<p id=\"p0325\">\n\n</p>", "<p id=\"p0330\">\n\n</p>", "<p id=\"p0335\">\n\n</p>", "<p id=\"p0340\">\n\n</p>", "<p id=\"p0345\">\n\n</p>", "<p id=\"p0350\">\n\n</p>", "<p id=\"p0355\">\n\n</p>", "<p id=\"p0360\">\n\n</p>", "<p id=\"p0365\">\n\n</p>", "<p id=\"p0370\">\n\n</p>", "<p id=\"p0375\">\n\n</p>", "<p id=\"p0380\">\n\n</p>", "<p id=\"p0385\">\n\n</p>", "<p id=\"p0390\">\n\n</p>", "<p id=\"p0395\">\n\n</p>", "<p id=\"p0400\">\n\n</p>", "<p id=\"p0405\">\n\n</p>", "<p id=\"p0410\">\n\n</p>", "<p id=\"p0415\">\n\n</p>", "<p id=\"p0420\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0300\">This work was supported by the New Frontiers in Research Fund (NFRF) of Government of Canada (Grant No. NFRFE-2019-01290 to Amin Emad and Junmei Cairns), the Natural Sciences and Engineering Research Council of Canada (NSERC) (Grant No. RGPIN-2019-04460 to Amin Emad), and the McGill Initiative in Computational Medicine (MiCM) to Amin Emad. This work was also funded by Génome Québec, the Ministère de l'Économie et de l'Innovation du Québec, Institut de Valorisation des Données (IVADO), the Canada First Research Excellence Fund, and Oncopole, which receives funding from Merck Canada Inc., and the Fonds de Recherche du Québec – Santé to Amin Emad. This research was enabled in part by support provided by Calcul Québec (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.calculquebec.ca\" id=\"ir015\">https://www.calculquebec.ca</ext-link>) and Compute Canada (<ext-link ext-link-type=\"uri\" xlink:href=\"https://www.computecanada.ca\" id=\"ir020\">https://www.computecanada.ca</ext-link>) to Amin Emad.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>The pipeline used for prediction of drug responses and identification of important genes</bold></p><p><bold>A.</bold> In phase 1, the gene expression data of the CCLs and ln IC50 values were both z-score normalized, whereas the tumor gene expression data (test data) were normalized using the tissue-informed normalizer. We then used this model to train a CDR predictor using the CCL data. After training, the model predicted the drug response value for the tumors. <bold>B.</bold> In phase 2, the trained CDR predictor was used to train a neural network explainer using the same training data. We used the trained explainer to give gene contribution scores for each genes of the test samples. We aggregated the scores across samples and then selected the top genes by estimating the point of maximum curvature. CCL, cancer cell line; CDR, cancer drug response; IC50, half-maximal inhibitory concentration.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Performance metrics for a subset of the drugs</bold></p><p>To prevent the figure from becoming cluttered, the results corresponding to only six drugs are shown (see Tables S2 and S3 for performance metrics of all drugs). <bold>A.</bold> Precision at <italic>k</italic>-th percentile for identification of sensitive patients. <bold>B.</bold> Distribution of predicted drug response for sensitive and resistant patients. The <italic>P</italic> values are calculated using a one-sided Mann<bold>–</bold>Whitney <italic>U</italic> test.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Evaluation of the embeddings of</bold><bold>DL</bold><bold>models</bold></p><p><bold>A.</bold> Scatter plots comparing the distance between preclinical and clinical samples in the embedding space for each drug. Each point in the scatter plot corresponds to a different drug. The <italic>P</italic> values are calculated using a one-sided Wilcoxon signed-rank test. The error bars show the 95% confidence intervals and are calculated based on ten runs of each method with random initializations. <bold>B.</bold> PCA of the embeddings used by each method to predict the response to etoposide. Visually, the TCGA samples are better mixed (<italic>i.e.</italic>, are not easily separable) with GDSC samples in TINDL compared with other methods. TINDL, deep learning pipeline with tissue-informed normalization; PCA, principal component analysis; PC, principal component; TCGA, The Cancer Genome Atlas; GDSC, Genomics of Drug Sensitivity in Cancer; DL, deep learning; DANN, Domain Adaptive Neural Network; ADDA, Adversarial Discriminative Domain Adaptation.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Top genes identified for tamoxifen</bold><bold>response</bold><bold>and their functional validation</bold></p><p><bold>A.</bold> The ROC curves for tamoxifen when different number of genes were used for CDR prediction. TINDL utilized the GEx values of all genes (AUROC = 0.92), whereas TINDL-top20 (AUROC = 0.90) and TINDL-kneedle (AUROC = 0.83) assigned a value of 0 to all genes except for top 20 and top genes identified by kneedle, respectively. <bold>B.</bold> Tamoxifen dose–response curves corresponding to the siRNA knockdown of <italic>RPS6</italic> and <italic>RPL13</italic> in MCF7 cells. Cytotoxicity assays were performed using technical triplicate experiments with three wells per drug concentration. Knockdown efficiency was assessed by qRT-PCR using three technical replicates (Table S8). The dose–response curves for all genes are provided in Figure S9. <bold>C.</bold> Tamoxifen dose–response curves corresponding to the siRNA knockdown of <italic>RPS6</italic> and <italic>RPL13</italic> in T47D cells. Cytotoxicity assays were performed using technical triplicate experiments with three wells per drug concentration. Knockdown efficiency was assessed by qRT-PCR using three technical replicates (Table S8). The dose–response curves for all genes are provided in Figure S10. All <italic>P</italic> values are calculated using an extra sum-of-squares F test. ROC, receiver operating characteristic; AUROC, area under the receiver operating characteristic curve; GEx, gene expression; qRT-PCR, quantitative real-time polymerase chain reaction; NC, negative control; mRNA, messenger RNA; siRNA, small interfering RNA.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"t0005\"><label>Table 1</label><caption><p><bold>The number of TCGA samples and the performance of TINDL in predicting their CDR for 14 drugs</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Drug</bold></th><th><bold>Number of clinical samples</bold></th><th><bold>Number of sensitive samples</bold></th><th><bold>Number of resistant samples</bold></th><th><bold><italic>P</italic> value</bold></th></tr></thead><tbody><tr><td>Cisplatin</td><td>303</td><td>237</td><td>66</td><td>6.36E−4</td></tr><tr><td>Tamoxifen</td><td>20</td><td>14</td><td>6</td><td>1.14E−3</td></tr><tr><td>Etoposide</td><td>84</td><td>73</td><td>11</td><td>4.00E−3</td></tr><tr><td>Doxorubicin</td><td>100</td><td>68</td><td>32</td><td>1.42E−2</td></tr><tr><td>Paclitaxel</td><td>158</td><td>111</td><td>47</td><td>2.29E−2</td></tr><tr><td>Vinorelbine</td><td>30</td><td>23</td><td>7</td><td>2.41E−2</td></tr><tr><td>Oxaliplatin</td><td>54</td><td>33</td><td>21</td><td>2.41E−2</td></tr><tr><td>Temozolomide</td><td>95</td><td>11</td><td>84</td><td>2.94E−2</td></tr><tr><td>Bleomycin</td><td>52</td><td>46</td><td>6</td><td>3.41E−2</td></tr><tr><td>Gemcitabine</td><td>157</td><td>75</td><td>82</td><td>4.57E−2</td></tr><tr><td>Cyclophosphamide</td><td>101</td><td>96</td><td>5</td><td>5.60E−2</td></tr><tr><td>Pemetrexed</td><td>38</td><td>18</td><td>20</td><td>2.86E−1</td></tr><tr><td>Irinotecan</td><td>23</td><td>6</td><td>17</td><td>3.04E−1</td></tr><tr><td>Docetaxel</td><td>102</td><td>67</td><td>35</td><td>7.04E−1</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0010\"><label>Table 2</label><caption><p><bold>The performance of different computational models in predicting CDR of TCGA samples using models completely trained on preclinical GDSC CCLs</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Algorithm</bold></th><th><bold>Number of drugs with <italic>P</italic> &lt; 0.05</bold><bold>(one-sided Mann–Whitney <italic>U</italic> test)</bold></th><th><bold>Total number of evaluated drugs</bold></th><th><bold>Combined <italic>P</italic> value (Fisher)</bold></th></tr></thead><tbody><tr><td>TINDL</td><td>10</td><td>14</td><td>2.77E−10</td></tr><tr><td>LASSO</td><td>7</td><td>14</td><td>7.47E−7</td></tr><tr><td>TG-LASSO ##REF##31967990##[9]##</td><td>6</td><td>14</td><td>8.32E−7</td></tr><tr><td>SVR (RBF kernel)</td><td>5</td><td>14</td><td>1.89E−6</td></tr><tr><td>Geeleher, et al. ##REF##24580837##[14]##</td><td>4</td><td>14</td><td>5.63E−3</td></tr><tr><td>Random forests</td><td>4</td><td>14</td><td>3.12E−3</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0015\"><label>Table 3</label><caption><p><bold>The performance of DL-based methods that explicitly try to remove discrepancy between preclinical training and clinical test datasets</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Algorithm</bold></th><th><bold>Number of drugs with</bold><bold><italic>P</italic></bold> <bold>&lt; 0.05 (a one-sided Mann–Whitney</bold> <bold><italic>U</italic></bold> <bold>test)</bold></th><th><bold>Tatol number of evaluated drugs</bold></th><th><bold>Combined</bold><italic><bold>P</bold></italic><bold>value (Fisher)</bold></th></tr></thead><tbody><tr><td>ComBat-DL</td><td>7</td><td>14</td><td>6.73E−10</td></tr><tr><td>ADDA-DL</td><td>7</td><td>14</td><td>2.16E−7</td></tr><tr><td>DANN-DL</td><td>7</td><td>14</td><td>1.66E−6</td></tr><tr><td>TrainNorm-DL</td><td>6</td><td>14</td><td>4.68E−7</td></tr><tr><td>TestNorm-DL</td><td>8</td><td>14</td><td>1.80E−9</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0020\"><label>Table 4</label><caption><p><bold>The performance of different neural network architectures when used as feature extractors</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th><bold>Architecture</bold></th><th><bold>Number of drugs with</bold><bold><italic>P</italic></bold> <bold>&lt; 0.05 (a one-sided Mann–Whitney</bold> <bold><italic>U</italic></bold> <bold>test)</bold></th><th><bold>Total number of evalutated drugs</bold></th><th><bold>Combined <italic>P</italic> value (Fisher)</bold></th></tr></thead><tbody><tr><td>GAT</td><td>7</td><td>14</td><td>2.75E−11</td></tr><tr><td>GCN</td><td>6</td><td>14</td><td>2.85E−7</td></tr><tr><td>LSTM</td><td>6</td><td>14</td><td>1.86E−5</td></tr></tbody></table></table-wrap>" ]
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[ "<supplementary-material content-type=\"local-data\" id=\"m0115\"><caption><title>Supplementary File S1</title><p><bold>Supplementary methods</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0110\"><caption><title>Supplementary Figure S1</title><p><bold>ROC curves of TINDL and baseline approaches in different drugs</bold> LASSO, least absolute shrinkage and selection operator; SVR, support vector regression; RF, random forest; TG-LASSO, tissue guided LASSO</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0105\"><caption><title>Supplementary Figure S2</title><p><bold>Precision–recall curves of TINDL and baseline approaches in different drugs</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0100\"><caption><title>Supplementary Figure S3</title><p><bold>UMAP and PCA plots of the learned latent features of different drugs by TINDL</bold> Purple points indicate cell line samples (GDSC) and orange points indicate tumor samples (TCGA). UMAP, Uniform Manifold Approximation and Projection.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0095\"><caption><title>Supplementary Figure S4</title><p><bold>UMAP and PCA plots of the learned latent features of different drugs by Combat-DL</bold> Purple points indicate cell line samples (GDSC) and orange points indicate tumor samples (TCGA).</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0090\"><caption><title>Supplementary Figure S5</title><p><bold>UMAP and PCA plots of the learned latent features of different drugs by ADDA-DL</bold> Purple points indicate cell line samples (GDSC) and orange points indicate tumor samples (TCGA).</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0085\"><caption><title>Supplementary Figure S6</title><p><bold>UMAP and PCA plots of the learned latent features of different drugs by DANN-DL</bold> Purple points indicate cell line samples (GDSC) and orange points indicate tumor samples (TCGA).</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0080\"><caption><title>Supplementary Figure S7</title><p><bold>Contribution scores of genes in the trained model of TINDL</bold> The Y-axis shows the contribution score, and the X-axis shows genes in a descending order of their score. Orange points indicate the “knees” found by kneedle algorithm, representing the threshold below which the contribution of genes to the trained model is small. The numbers in the brackets show number of genes above threshold and threshold.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0075\"><caption><title>Supplementary Figure S8</title><p><bold>Genes identified by TINDL for different drugs A.</bold> Heatmap of the Jaccard similarity of the selected top genes in the 14 drugs. <bold>B.</bold> Number of drugs in which the genes were identified as a top gene. Only genes that were present in the top genes of at least four drugs are included.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0070\"><caption><title>Supplementary Figure S9</title><p><bold>Tamoxifen dose–response curves corresponding to the siRNA knockdown of 10 genes identified by TINDL in MCF7 cells</bold> Knockdown efficiency was assessed by qRT-PCR using three technical replicates (Table S8). Gene expression was normalized to siRNA negative control. Table S8 shows the knockdown efficiency of each gene and corresponding statistical analysis.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0065\"><caption><title>Supplementary Figure S10</title><p><bold>Tamoxifen dose–response curves corresponding to the siRNA knockdown of 10 genes identified by TINDL in T47D cells</bold> Knockdown efficiency was assessed by qRT-PCR using three technical replicates (Table S8). Gene expression was normalized to siRNA negative control. Table S8 shows the knockdown efficiency of each gene and corresponding statistical analysis.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0060\"><caption><title>Supplementary Figure S11</title><p><bold>Kaplan–Meier survival analysis of <italic>RPS6</italic> and <italic>RPL13</italic> gene expression in estrogen receptor positive/HER2 negative breast cancer patients using Kaplan–Meier Plotter A.</bold> RFS of <italic>RPS6</italic> in systemically untreated patients. <bold>B.</bold> RFS of <italic>RPS6</italic> in tamoxifen treated patients. <bold>C.</bold> RFS of <italic>RPL13</italic> in tamoxifen treated patients. RFS, relapse free survival; HR, hazard ratio.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0055\"><caption><title>Supplementary Figure S12</title><p><bold>MSE curves of different hyperparameters during grid-search</bold> To reduce cluttering, only the average value across the five folds were plotted. The shaded regions are the 90% confidence intervals. The chosen number of epochs is denoted as a vertical line, while the purple curves represent the training and validation curves of the chosen set of hyperparameters. MSE, mean squared error.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0050\"><caption><title>Supplementary Figure S13</title><p><bold>Training MSE curves of the 10 different initializations during the final training</bold> Individual models are denoted as the gray curves while their average is denoted by the purple curve. The final training uses all the labeled cell lines as the training set so there are no validation curves.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0045\"><caption><title>Supplementary Table S1</title><p><bold>Information regarding the samples used in both training and testing sets</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0040\"><caption><title>Supplementary Table S2</title><p><bold>Performance of different models in predicting CDR</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Table S3</title><p><bold>Precision at k<sup>th</sup> percentile of TINDL</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Table S4</title><p><bold>List of top genes identified by our pipeline</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S5</title><p><bold>Genes and pathways associated with multiple drugs</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S6</title><p><bold>Pathways associated with genes implicated for each drug by TINDL</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S7</title><p><bold>The result of siRNA gene knockdown experiments in MCF7 and T47D cell lines for 10 genes identified by TINDL for tamoxifen</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S8</title><p><bold>Efficiency of knockdown experiments</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S9</title><p><bold>Learning rates, and batch sizes, and number of epochs used in the final models</bold></p></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p><italic>Note</italic>: <italic>P</italic> values were calculated by a one-sided Mann–Whitney <italic>U</italic> test to determine if TINDL can distinguish between sensitive and resistant patients. To ensure the results are not biased by the initialization of the parameters of model, TINDL was trained using ten random initializations, and the mean aggregate of its prediction was used to calculate the <italic>P</italic> values. Drugs were sorted based on their associated <italic>P</italic> values. TINDL, deep learning pipeline with tissue-informed normalization; TCGA, The Cancer Genome Atlas; CDR, cancer drug response.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p><italic>Note</italic>: The combined <italic>P</italic> value combined over all 14 drugs using Fisher’s method. CCL, cancer cell line; GDSC, Genomics of Drug Sensitivity in Cancer; LASSO, least absolute shrinkage and selection operator; SVR, support vector regression; TG-LASSO, tissue-guided LASSO.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p><italic>Note</italic>: The combined <italic>P</italic> value combined over all 14 drugs using Fisher’s method. To ensure a fair comparison, a similar architecture to TINDL was used for all these methods. Additionally, each model was trained using ten random initializations, and the mean aggregate of these predictions was used for calculating the <italic>P</italic> values. DL, deep learning; DANN, Domain Adaptive Neural Network; ADDA, Adversarial Discriminative Domain Adaptation.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p><italic>Note</italic>: The combined <italic>P</italic> value combined over all 14 drugs using Fisher’s method. To ensure a fair comparison, a similar architecture to TINDL was used for all these methods. Additionally, each model was trained using ten random initializations, and the mean aggregate of these predictions was used for calculating the <italic>P</italic> values. GAT, graph attention network; GCN, graph convolutional network; LSTM, long short-term memory.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"d35e528\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0140\" fn-type=\"supplementary-material\"><p id=\"p0305\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2023.01.006\" id=\"ir025\">https://doi.org/10.1016/j.gpb.2023.01.006</ext-link>.</p></fn></fn-group>" ]
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{ "acronym": [], "definition": [] }
87
CC BY
no
2024-01-14 23:41:59
Genomics Proteomics Bioinformatics. 2023 Jun 11; 21(3):535-550
oa_package/8f/d0/PMC10787192.tar.gz
PMC10787194
36096444
[ "<title>Introduction</title>", "<p id=\"p0005\">Among the more than 150 distinct chemical modifications naturally decorating cellular RNAs ##REF##29106616##[1]##, <italic>N</italic><sup>6</sup>-methyladenosine (m<sup>6</sup>A) is the most pervasive marker on mRNAs and long non-coding RNAs (lncRNAs), and has been associated with a number of essential biological functions and processes ##REF##28759256##[2]##, ##REF##23453015##[3]##, including mRNA stability ##REF##24284625##[4]##, splicing ##REF##33930289##[5]##, translation ##REF##30232453##[6]##, ##REF##29186125##[7]##, heat shock ##REF##26458103##[8]##, DNA damage ##REF##28297716##[9]##, and embryonic development ##REF##18505803##[10]##. Increasing evidence has indicated a critical role of m<sup>6</sup>A dysregulation in various human diseases, especially multiple cancers, such as breast cancer ##REF##26896799##[11]##, ##REF##27590511##[12]## and prostate cancer ##REF##20976066##[13]##. For example, inhibition of an m<sup>6</sup>A methyltransferase (METTL13) could be used as a potential therapeutic strategy against acute myeloid leukemia ##REF##33902106##[14]##.</p>", "<p id=\"p0010\">Developed in 2012, m<sup>6</sup>A-seq (methylated RNA immunoprecipitation sequencing; MeRIP-seq) was the first whole transcriptome m<sup>6</sup>A profiling approach ##REF##22575960##[15]##, ##REF##22608085##[16]##. It relies on antibody-based enrichment of the m<sup>6</sup>A signals, enabling the identification of m<sup>6</sup>A-containing regions with a resolution of around 100 nt. Currently, m<sup>6</sup>A-seq is still the most popular m<sup>6</sup>A profiling approach and has been applied in more than 30 different organisms. Besides m<sup>6</sup>A-seq, recent advances in integration of ultraviolet cross-linking, enzymatic activity, and domain fusion have offered improved even base-resolution m<sup>6</sup>A detection through techniques such as, miCLIP/m<sup>6</sup>A-CLIP-seq ##REF##26121403##[17]##, ##REF##28637692##[18]##, m<sup>6</sup>A-REF-seq ##REF##31281898##[19]##, and DART-seq ##REF##31548708##[20]##. However, compared with m<sup>6</sup>A-seq, these approaches require more complicated experimental procedures and have therefore been applied in fewer biological contexts.</p>", "<p id=\"p0015\">To date, more than 120 computational approaches have been developed for the computational identification of RNA modifications ##REF##32670500##[21]##, ##REF##31714956##[22]## from the primary RNA sequences. These include the iRNA toolkits ##REF##28641529##[23]##, ##REF##30113871##[24]##, ##UREF##0##[25]##, ##REF##26314792##[26]##, ##REF##28476023##[27]##, ##REF##31581049##[28]##, ##REF##31581051##[29]##, ##REF##30590059##[30]##, ##REF##28427142##[31]##, MultiRM ##REF##34188054##[32]##, DeepPromise ##REF##31714956##[22]##, RNAm5CPred ##REF##31726390##[33]##, SRAMP ##REF##26896799##[11]##, Gene2vec ##REF##30425123##[34]##, PEA ##REF##29850798##[35]##, PPUS ##REF##26076723##[36]##, WHISTLE ##REF##30993345##[37]##, m5UPred ##REF##33230471##[38]##, WeakRM frameworks ##REF##34252943##[39]##, ##REF##34843978##[40]##, m6ABoost ##REF##34157120##[41]##, PULSE ##REF##33631424##[42]##, m6AmPred ##REF##33660783##[43]##, BERMP ##REF##30416381##[44]##, and MASS ##REF##33744973##[45]##. Together, these efforts have greatly advanced our understanding of multiple RNA modifications in different RNA regions and in various species (see recent reviews ##REF##31714956##[22]##, ##REF##31609411##[46]##, ##UREF##1##[47]##, ##REF##29165544##[48]##). A number of epitranscriptome databases have been constructed. MODOMICS collects the pathways related to more than 150 different RNA modifications ##REF##29106616##[1]##. RMBase ##REF##29040692##[49]##, m<sup>5</sup>C-Atlas ##REF##34986603##[50]##, and m<sup>6</sup>A-Atlas ##UREF##2##[51]## assembled millions of experimentally validated m<sup>6</sup>A and m<sup>5</sup>C sites. REPIC has been established as a comprehensive atlas for exploring the association between m<sup>6</sup>A RNA methylation and chromatin modifications ##REF##32345346##[52]##. ConsRM provides the conservation score of individual m<sup>6</sup>A sites at the base resolution, which can be used to differentiate the functionally important and ‘passenger’ m<sup>6</sup>A sites ##REF##33401308##[53]##. m6A2Target compiles the target molecules of m<sup>6</sup>A methyltransferases, demethylases, and binding proteins ##UREF##3##[54]##. This work has extended our knowledge of the functional epitranscriptome, and greatly facilitated relevant research. Special efforts have also been made to explore the effects of genetic variants on RNA modifications and their association with various diseases. m6AVar ##REF##29036329##[55]## was the first database that focused on the genetic factors related to epitranscriptome disturbance. It documented more than 400,000 m<sup>6</sup>A-affecting genetic variants, which were further labeled with disease and phenotype associations identified from genome-wide association study (GWAS) analysis. This prediction framework was improved and later applied to eight other RNA modifications (m<sup>5</sup>C, m<sup>1</sup>A, m<sup>5</sup>U, Ψ, m<sup>6</sup>Am, m<sup>7</sup>G, and 2′-O-Me, and A-to-I) by RMVar ##REF##33021671##[56]## and RMDisease ##UREF##4##[57]##. These aforementioned databases systematically revealed the general association between epitranscriptome layer dysregulation and various diseases (see a recent review ##REF##33705860##[58]##).</p>", "<p id=\"p0020\">Existing computational approaches for epitranscriptome analysis have been quite successful in providing a large quantity of useful information; however, most of them failed to consider the tissue specificity of m<sup>6</sup>A epi-transcriptome ##REF##32375858##[59]##, ##REF##32406913##[60]##. Indeed, a recent study by Liu et al<italic>.</italic> unveiled distinct tissue-specific signatures of the m<sup>6</sup>A epitranscriptome in human and mouse ##REF##31676230##[61]##, which are induced by context-specific expression of m<sup>6</sup>A regulators [methyltransferases, demethylases, and RNA-binding proteins (RBPs)] ##REF##31912146##[62]## and genetic drivers ##REF##33414547##[63]##. Nevertheless, most existing approaches for RNA modification site prediction completely ignore the context specificity of the epitranscriptome and simply assume a single model for different tissues, undermining their accuracy and applicability. To the best of our knowledge, the only three approaches that clearly support the identification of tissue-specific m<sup>6</sup>A methylation are im6A-TS-CNN ##REF##32858457##[64]##, iRNA-m6A ##REF##32435427##[65]##, and TS-m6A-DL ##REF##34471503##[66]##, all covering only three human tissue types (brain, liver, and heart). Similarly, when screening for the genetic variants that can affect RNA modifications, previous work assumes a consistent influence in different tissues (see <xref rid=\"s0130\" ref-type=\"sec\">Table S1</xref> for a detailed description and comparison). However, because different epitranscriptome patterns were observed among different tissues, genetic mutations that can alter m<sup>6</sup>A methylation in one tissue may not necessarily function similarly in a different tissue. Likewise, there are significant differences in incidence, mortality, and molecular signatures across cancer originating from different tissues ##REF##33879792##[67]##, ##REF##21994229##[68]##. It is therefore highly desirable to develop approaches that could take full advantage of the tissue-specific RNA methylation profiles so as to make more reliable predictions with respect to a specific tissue type ##REF##34048560##[69]##. This is particularly critical for studying the epitranscriptome circuits of diseases that are explicitly associated with a specific tissue, such as, cancers.</p>", "<p id=\"p0025\">To address this issue, we present here a comprehensive online platform m6A-TSHub for unveiling the context-specific m<sup>6</sup>A methylation and m<sup>6</sup>A-affecting mutations in 23 human tissues. m6A-TSHub consists of four core components: (1) m6A-TSDB, a database for 184,554 experimentally validated m<sup>6</sup>A-containing peaks (m<sup>6</sup>A sites) derived from 23 distinct human normal tissues and 499,369 m<sup>6</sup>A-containing peaks (m<sup>6</sup>A sites) from 25 matched tumor conditions, extracted from 233 m<sup>6</sup>A-seq samples, respectively; (2) m6A-TSFinder, an integrated online server for the prediction of tissue-specific m<sup>6</sup>A modifications in 23 human tissues, built upon a gated attention-based multi-instance deep neural network; (3) m6A-TSVar, a web server for systemically assessing the tissue-specific impact of genetic variants on m<sup>6</sup>A RNA modification in 23 human tissues; (4) m6A-CAVar, a database of 587,983 The Cancer Genome Atlas (TCGA) cancer mutations (derived from 27 cancer types) that may lead to the gain or loss of m<sup>6</sup>A sites in the corresponding cancer-originating tissues.</p>", "<p id=\"p0030\">In addition, the m<sup>6</sup>A-associated variants were also annotated with their potential post-transcriptional regulatory roles, including RBP binding regions, microRNA (miRNA) targets, and splicing sites, along with their known disease and phenotype linkage integrated from GWAS catalog ##UREF##5##[70]## and ClinVar databases ##REF##26582918##[71]##. The m6A-TSHub is freely accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.xjtlu.edu.cn/biologicalsciences/m6ats\" id=\"PC_linkVmxCdZjAJh\">www.xjtlu.edu.cn/biologicalsciences/m6ats</ext-link>, and should be a useful resource for studying the m<sup>6</sup>A methylome and genetic basis of epitranscriptome disturbance with respect to a specific cancer type or tissue. The overall design of m6A-TSHub is shown in ##FIG##0##Figure 1##.</p>" ]
[]
[]
[ "<title>Discussion and perspectives</title>", "<p id=\"p0145\">The context-specific expression and functions of m<sup>6</sup>A regulations have been repeatedly reported in existing studies ##REF##32375858##[59]##, ##REF##32406913##[60]##, ##REF##31676230##[61]##, ##REF##31912146##[62]##, ##REF##33414547##[63]##, suggesting the involvement of the tissue-specific m<sup>6</sup>A methylome in essential biological processes and multiple disease mechanisms. Besides, the associations between RNA methylation levels and the activities of RNA methylation regulators were clearly unveiled, reporting that there exist some condition-specific RNA co-methylation patterns (a group of RNA m<sup>6</sup>A methylation sites whose methylation levels go up and down together) ##REF##25370990##[108]##, ##REF##34122508##[109]##, ##REF##33400655##[110]##. These co-methylation patterns are enriched by the substrate targets of m<sup>6</sup>A regulators and thus are probably regulated by specific m<sup>6</sup>A methyltransferase or demethylase.</p>", "<p id=\"p0150\">Here, we present m6A-TSHub, a comprehensive online platform for unveiling the context-specific m<sup>6</sup>A methylation and m<sup>6</sup>A-affecting mutations in 23 human tissues and 25 tumor conditions. In m6A-TSHub, a total of 184,554 and 499,369 m<sup>6</sup>A sites derived from 23 normal human tissues and 25 matched tumor samples were collected (m6A-TSDB), from which some potential patterns for the tissue-specific m<sup>6</sup>A modification sites were revealed (<italic>e.g.</italic>, heart-enriched genes <italic>RYR2</italic> and <italic>PXDNL</italic>; <xref rid=\"s0130\" ref-type=\"sec\">Figure S2</xref>). Based on these collected data, 23 distinct m<sup>6</sup>A prediction models were built at the tissue level using deep neural networks (m6A-TSFinder). In addition, to elucidate the genetic factor of epitranscriptome dysregulation, m6A-CAVar identified a total of 587,983 cancer somatic mutations that may alter the m<sup>6</sup>A status in corresponding cancer originating tissues and annotated them with various functional annotations, including features relating to post-transcriptional regulations (RBP binding regions, miRNA targets, and splicing sites), disease and phenotype associations, as well as other useful genomic information (transcript structure, phastCons, and deleterious level) to provide a more comprehensive overview. We also provide a web server m6A-TSVar for assessing the effect of genetic variants on m<sup>6</sup>A methylation in a specific tissue.</p>", "<p id=\"p0155\">Although most of the existing approaches for RNA modification site prediction ignore the tissue-specific signatures of m<sup>6</sup>A methylation, by taking advantage of existing tissue-specific epitranscriptome data, our method can predict the m<sup>6</sup>A methylation within a specific tissue. Compared with existing approaches for tissue-specific m<sup>6</sup>A methylation site prediction ##REF##32858457##[64]##, ##REF##32435427##[65]##, ##REF##34471503##[66]##, our approach m6A-TSFinder achieved a higher prediction performance (##TAB##1##Table 2##) and hugely expanded the number of supported tissue types from 3 to 23 (##TAB##0##Table 1##).</p>", "<p id=\"p0160\">Compared with existing approaches for decoding the epitranscriptome impact of genetic variants, m6A-CAVar has the following two major advantages. First, m6A-CAVar relies on a finer prediction model (m6A-TSFinder) that appreciates the specific pattern of RNA methylomes across different tissues. By directly learning from the epitranscriptome profiles in 23 healthy human tissues, m6A-CAVar is able to evaluate the tissue-specific impact of cancer somatic variants on m<sup>6</sup>A modification in their originating tissue, providing a more detailed picture of the genome–epitranscriptome association. This improves on existing approaches that ignore the distinct signatures of RNA methylation across different tissues and thus fail to address tissue-specific effects. Second, the predicted m<sup>6</sup>A dynamics in m6A-CAVar were systematically validated using available epitranscriptome datasets from the matched healthy and cancerous samples, providing another layer of quality assurance from real omic datasets. In contrast, existing approaches use those datasets only to provide the m<sup>6</sup>A site information without searching for potential evidence of m<sup>6</sup>A status switching.</p>", "<p id=\"p0165\">To date, epitranscriptome data are still rather scarce. Due to the limited availability of datasets, matched healthy tissue and cancer m<sup>6</sup>A profiling samples are only available for 14 out of the total 27 cancer types, prohibiting a more thorough validation of the predicted results. Furthermore, a substantial discrepancy has been observed among different RNA modification profiling approaches due to technical biases ##REF##30414851##[111]##, ##REF##26968262##[112]##, ##REF##24286375##[113]##, ##REF##32508872##[114]##, which can produce additional inaccuracy. Currently, context-specific epitranscriptome prediction is only possible for a small number of conditions (cell line, tissue type, and treatment) with data ##REF##32858457##[64]##, ##REF##32435427##[65]##, ##REF##34471503##[66]##. However, the m6A-TSHub framework will be further expanded when epitranscriptome datasets are more abundantly available for more comprehensive and less biased screening of context-specific m<sup>6</sup>A-variants, along with linking the tissue-specific epitranscriptome patterns with other important cancer-associated factors such as human aging ##REF##33879792##[67]##, ##REF##31560156##[115]##. Besides, the current version of m6A-TSHub was built on human genome assemble hg19. A LiftOver file from hg19 to hg38 was provided on the ‘download’ page, and the next version of the database will be updated based on the latest genome assembly. Particularly promising is the recent development in Nanopore direct RNA sequencing technology that enables simultaneous identification of multiple RNA modifications with simplified sample preparation procedures ##REF##33413586##[116]##, ##REF##32907883##[117]##, ##REF##31439691##[118]##, ##REF##33986546##[119]##, ##REF##31501426##[120]##, ##REF##30718479##[121]##, ##REF##33243990##[122]##, ##REF##34293115##[123]##, ##REF##34282325##[124]##.</p>" ]
[]
[ "<p>As the most pervasive epigenetic marker present on mRNAs and long non-coding RNAs (lncRNAs), <bold><italic>N</italic><sup>6</sup>-methyladenosine</bold> (m<sup>6</sup>A) RNA methylation has been shown to participate in essential biological processes. Recent studies have revealed the distinct patterns of m<sup>6</sup>A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m<sup>6</sup>A methylation. We present here a comprehensive online platform, m6A-TSHub, for unveiling the context-specific m<sup>6</sup>A methylation and genetic mutations that potentially regulate m<sup>6</sup>A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB, a comprehensive database of 184,554 functionally annotated m<sup>6</sup>A sites derived from 23 human tissues and 499,369 m<sup>6</sup>A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder, a web server for high-accuracy prediction of m<sup>6</sup>A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar, a web server for assessing the impact of genetic variants on tissue-specific m<sup>6</sup>A RNA modifications; and (4) m6A-CAVar, a database of 587,983 The Cancer Genome Atlas (TCGA) <bold>cancer mutations</bold> (derived from 27 cancer types) that were predicted to affect m<sup>6</sup>A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m<sup>6</sup>A methylome and the genetic factors of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.xjtlu.edu.cn/biologicalsciences/m6ats\" id=\"PC_linkSZ6DS3Exyn\">www.xjtlu.edu.cn/biologicalsciences/m6ats</ext-link>.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Jianhua Yang</p>" ]
[ "<title>Data collection and processing</title>", "<title>Data resource — m6A-TSDB</title>", "<p id=\"p0035\">We collected the epitranscriptome profiles of 23 healthy human tissues, from which the tissue-specific RNA methylation patterns were learned using deep neural networks. Specifically, the raw sequencing data of 78 m<sup>6</sup>A-seq samples were downloaded directly from Gene Expression Omnibus (GEO) repository of National Center for Biotechnology Information (NCBI) ##UREF##6##[72]## and National Genomics Data Center (NGDC) ##REF##33175170##[73]## (<xref rid=\"s0130\" ref-type=\"sec\">Table S2</xref>). Adaptors and low-quality nucleotides were removed by Trim Galore ##UREF##7##[74]##, followed by quality control using FastQC. The processed reads were then aligned to the reference genome GRCh37/hg19 by HISAT2 ##REF##31375807##[75]##. The m<sup>6</sup>A-enriched regions (peaks) located on transcripts were detected by exomePeak2 ##REF##24979058##[76]## using its default setting with GC contents corrected. In total, m<sup>6</sup>A profiling samples from 23 healthy human tissues (184,554 m<sup>6</sup>A-containing peaks) were processed. We filtered all obtained m<sup>6</sup>A-enriched regions to retain peaks with at least one DRACH consensus motif and used these peak regions containing tissue-specific m<sup>6</sup>A signals as positive data. Negative data were randomly collected from non-peak regions located on the same transcript of the corresponding positive data, and cropped to balance the length and number between positive and negative regions (with a positive-to-negative ratio of 1:1). The genomic sequences of both positive and negative regions were then extracted for developing the tissue-specific m<sup>6</sup>A prediction model.</p>", "<p id=\"p0040\">To evaluate the effect of cancer somatic variants on m<sup>6</sup>A methylation in their originating tissues, a total of 2,587,191 cancer somatic variants from 27 different cancer types were obtained from TCGA (release version v27.0-fix) ##UREF##8##[77]## (<xref rid=\"s0130\" ref-type=\"sec\">Table S3</xref>). Meanwhile, 155 m<sup>6</sup>A-seq samples profiling the epitranscriptome (499,369 m<sup>6</sup>A-containing peaks) of 25 cancer cell lines (corresponding to 17 tissue types) were also obtained using the same data processing pipeline (<xref rid=\"s0130\" ref-type=\"sec\">Table S2</xref>), which were used for the validation of the predicted effects on m<sup>6</sup>A methylation of the variants (detailed in the following).</p>", "<title>Learning tissue-specific m<sup>6</sup>A methylation with deep neural networks <bold>—</bold> m6A-TSFinder</title>", "<p id=\"p0045\">The purpose of weakly supervised learning is to develop predictive models by learning from weakly labeled data, such as m<sup>6</sup>A peaks of low resolution detected by the m<sup>6</sup>A-seq (or MeRIP-seq) technique ##REF##22575960##[15]##, ##REF##22608085##[16]##. Unlike supervised learning based on single-nucleotide resolution data, it works for the case in which only coarse-grained labels (indicating whether a genome bin contains an m<sup>6</sup>A site) are available for these peaks of various lengths. We previously proposed a general weakly supervised learning framework WeakRM ##REF##34252943##[78]##, which takes labels at the sequence level (rather than a nucleotide level) as input and predicts the sub-regions that are most likely to contain the RNA modification. As a simplified illustration shown in ##FIG##1##Figure 2##, the m6A-TSFinder framework is divided into several sub-sections. Firstly, multi-instance learning treats each entire RNA sequence as a ‘bag’, with multiple ‘instances’ within the ‘bag’ determined by a fixed-length sliding window. Previous studies have shown that a 40–50-nt context region is sufficient for modification predictions. Therefore, in m6A-TSFinder, a sliding window of 50 nt was used, which was also helpful in improving the prediction resolution. Secondly, the RNA instances were fed into the m6A-TSFinder model using one-hot encoding, which is widely used in deep learning-based models. The extracted instances pass through the same feature extraction module (the weights of the network are shared in this module) and output instance-level features. The network architecture of the feature extraction section used in m6A-TSFinder includes the first convolutional layer to capture motifs, a max-pooling layer to remove weak features and enlarge the receptive field, a dropout layer that prevents overfitting in training, and a second convolutional layer which learns local dependencies among motifs. In order to further improve the performance of the model, in m6A-TSFinder, we use a long short-term memory (LSTM) layer to replace the second convolutional layer, so that the model can learn the long-range dependence of the motif while maintaining local dependence. Lastly, gated attention was used as the score function to obtain bag-level probabilities from multiple instance-level features. The gated attention module consists of three fully connected layers. The first two layers learn hidden representations from the instance features using tanh and sigmoid activation functions. Their element-wise multiplication is then sent to the third fully connected layer, which learns the similarity between the product and a context feature vector and outputs an attention score for each instance. The score is further normalized using the softmax function, so that the weights of all instances add up to 1. The weighted summation of instance features is treated as the bag-level feature and used to output the final probability score. Together, our model can be trained end-to-end using the binary cross-entropy loss calculated by the bag-level label. Our model was trained using the Adam optimizer under the Tensorflow framework. The learning rate was initially set to 1E−4, and gradually decayed to 1E−5 during the training process of 20 epochs. It is worth mentioning that when the number of instances is consistently set to 1, the weight of the instance is always 1, and the label becomes the instance level. In that case, the gated attention module is degraded, and the network becomes a strong supervised learning framework with two feature extraction layers.</p>", "<title>Decoding the tissue-specific effect of variants on m<sup>6</sup>A methylation — m6A-TSVar &amp; m6A-CAVar</title>", "<p id=\"p0050\">Similar to previous studies ##REF##29036329##[55]##, ##REF##33021671##[56]##, ##REF##32163126##[79]##, ##REF##26464443##[80]##, a cancer somatic variant is defined as a tissue-specific m<sup>6</sup>A variant if it could lead to the gain or loss of m<sup>6</sup>A methylation in a specific tissue. The tissue-specific inference was made possible by our deep neural network model m6A-TSFinder. Specifically, the predicted tissue-specific m<sup>6</sup>A variants were further classified into three confidence levels — low, medium, and high (##FIG##2##Figure 3##).</p>", "<title>Low confidence level</title>", "<p id=\"p0055\">An m<sup>6</sup>A-associated variant with a low confidence level was defined directly by the tissue-specific prediction model. For example, a synonymous somatic variant (Chr5:92929473, positive strand, C &gt; T, TCGA barcode: TCGA-49-6742-01A-11D-1855-08) was extracted from The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) project, which was then predicted to eliminate the methylation of an experimentally validated m<sup>6</sup>A-containing region (Chr5:92929314-92929786, positive strand) originally detected in human lung tissue ##REF##31676230##[61]##.</p>", "<title>Medium confidence level</title>", "<p id=\"p0060\">The m<sup>6</sup>A variants with a medium confidence level are those that can be verified on available epitranscriptome data from cancer samples originating from the matched tissue. After the low confidence level mentioned above, by checking the m<sup>6</sup>A-containing regions reported in lung adenocarcinoma cancer cell lines A549 ##REF##24981863##[81]## and H1299 ##REF##27117702##[82]##, we confirmed that no m<sup>6</sup>A peaks were further observed in A549 and H1299 for the variant-affected region (Chr5:112176059-112176334, positive strand). Consequently, this LUAD somatic variant was upgraded to a ‘medium’ confidence level in the m6A-CAVar database. It is worth noting that the predicted m<sup>6</sup>A dynamics in m6A-CAVar were systematically validated using available epitranscriptome datasets from the matched healthy and cancer samples, providing another layer of quality assurance from real omic datasets: existing approaches only use those datasets to provide the m<sup>6</sup>A site information without searching for potential evidence of m<sup>6</sup>A status switching.</p>", "<title>High confidence level</title>", "<p id=\"p0065\">Only a very small number of variants have been clearly associated with diseases and phenotypes unveiled by GWAS analysis, and are known as disease-TagSNPs. These variants exhibited their clinical significance and are very likely to be functionally important. Thus, m<sup>6</sup>A variants of ‘high’ confidence level were defined as the validated m<sup>6</sup>A variants that can also be mapped to disease-TagSNPs extracted from ClinVar ##REF##26582918##[71]## and GWAS catalog ##UREF##5##[70]##, while those not validated were referred to as ‘critical’.</p>", "<p id=\"p0070\">Additionally, the association level (AL) between an SNP and m<sup>6</sup>A RNA modification was defined as follows:where and represent the probability of m<sup>6</sup>A RNA modification for the wild-type and mutated sequences, respectively. The AL ranges from 0 to 1, with 1 indicating the maximum impact on m<sup>6</sup>A methylation. The statistical significance was assessed by comparing the ALs of all mutations, with which the upper bound of the <italic>P</italic> value can be calculated from its absolute ranking. The m<sup>6</sup>A-associated variants with AL &gt; 0.4 and <italic>P</italic> &lt; 0.1 were retained. We also considered the possibility of a variant destroying a part of (but not an entire) m<sup>6</sup>A peaks. For peaks wider than 500 nt, the impacts were also evaluated on the 200-nt flanking regions of the variant.</p>", "<p id=\"p0075\">The predicted m<sup>6</sup>A variants were then validated on the epitranscriptome datasets from the matched healthy and cancer samples. We consider a prediction validated by omic data if the matched dynamics of m<sup>6</sup>A sites were observed under the healthy tissue and the cancer samples with the same tissue origin. It may be worth noting that, omic data were only used to inform the prediction of m<sup>6</sup>A sites in previous studies ##REF##29036329##[55]##, ##REF##33021671##[56]##, ##REF##32163126##[79]##, ##REF##26464443##[80]##; however, our analysis also relies on it to confirm the predicted disturbance of m<sup>6</sup>A status between the healthy and cancer conditions. This extra layer of confirmation directly from available omic datasets should effectively enhance the reliability of our database.</p>", "<title>Functional annotation</title>", "<p id=\"p0080\">The identified m<sup>6</sup>A variants were annotated with various information, including transcript region [coding sequence, 3′ untranslated region (UTR), 5′ UTR, start codon, and stop codon], gene annotation (gene symbol, gene type, and Ensembl gene ID), evolutionary conservation (phastCons 60-way), deleterious level by SIFT ##REF##19561590##[83]##, PolyPhen2 HVAR ##REF##20354512##[84]##, PolyPhen2HDIV ##REF##20354512##[84]##, LRT ##REF##19602639##[85]## and FATHMM ##REF##23033316##[86]## using the ANNOVAR package ##REF##20601685##[87]##, absolute ranking by comparing with the ALs of all mutations (top 1% and top 5%), and TCGA sample information (TCGA case ID, TCGA barcode, TCGA sample count, and sample total variant number). A total of 177,998 high-confidence m<sup>6</sup>A sites detected using base-resolution technology previously were collected and used to pinpoint the precise location of the mediated m<sup>6</sup>A sites within the variant-affected regions (<xref rid=\"s0130\" ref-type=\"sec\">Table S4</xref>). In addition, aspects of the post-transcriptional machinery that can be mediated by m<sup>6</sup>A methylation were also annotated, including RBP binding regions from POSTAR2 ##UREF##9##[88]##, miRNA–RNA interaction from miRanda ##REF##26267216##[89]## and starBase2 ##REF##24297251##[90]##, and splicing sites from UCSC ##REF##23950696##[91]## annotation with GT-AG role. Furthermore, to unveil potentially related pathogenesis, any association between disease and m<sup>6</sup>A variants was extracted from the GWAS catalog ##UREF##5##[70]## and ClinVar ##REF##26582918##[71]## databases.</p>", "<title>Database and web interface implementation</title>", "<p id=\"p0085\">Hypertext markup language (HTML), cascading style sheets (CSS), and hypertext preprocessor (PHP) were applied to construct the m6A-TSHub web interface. All metadata were stored using MySQL tables. Besides, ECharts was exploited to present statistical diagrams, and the Jbrowse genome browser ##REF##27072794##[92]## was included for interactive exploration and visualization of relevant records for genome regions of interest.</p>", "<title>Database content and usage</title>", "<title>Collection of m<sup>6</sup>A sites from 23 normal human tissues and 25 cancer cell lines in m6A-TSDB</title>", "<p id=\"p0090\">In m6A-TSDB, a total of 184,554 and 499,369 m<sup>6</sup>A-containing peaks were collected from 23 normal human tissues and 25 cancer samples, respectively. Among them, 17 out of 25 tumor samples have the m<sup>6</sup>A profiles of their matched primary tissues. The m<sup>6</sup>A-enriched peaks were called using exomePeak2 ##REF##24979058##[76]## with GC-correction function after mapping the processed reads to human reference genome version hg19. It is worth mentioning that, for a more complete m<sup>6</sup>A epitranscriptome landscape view, a total of 177,998 base-resolution m<sup>6</sup>A sites collected from 27 datasets using six different m<sup>6</sup>A profiling techniques were integrated and used to pinpoint the precise location of the mediated m<sup>6</sup>A sites within all tissue-specific m<sup>6</sup>A peaks (<xref rid=\"s0130\" ref-type=\"sec\">Table S4</xref>). In addition, all m<sup>6</sup>A-containing peaks were labeled with information showing whether these sites were affected by cancer somatic variants and potential involved post-transcriptional regulations. All data collected in the m6A-TSDB can be freely downloaded or shared.</p>", "<title>Performance evaluation and model interpretation of tissue-specific m<sup>6</sup>A site prediction by m6A-TSFinder</title>", "<p id=\"p0095\">The performance of tissue-specific m<sup>6</sup>A site predictors was evaluated using 10-fold cross-validation and independent testing. For each distinct human tissue, we randomly selected 15% of experimentally validated m<sup>6</sup>A sites and used them as an independent testing dataset. For 10-fold cross-validation, the training data were randomly divided into 10 groups with the same number of positive and negative peaks. The prediction performance of each tissue-specific predictor is shown in ##TAB##0##Table 1##. In general, the prediction accuracy for most tissues (20 out of the total 23 tissues) is in line with conventional approaches for m<sup>6</sup>A site prediction under strong supervision with base-resolution datasets, which typically reported a prediction performance between 0.8 and 0.85 in terms of the area under receiver operating characteristic (ROC) curve (AUROC) ##REF##31714956##[22]##, ##REF##34136099##[93]##. The performance for kidney (AUROC = 0.718), bone marrow (AUROC = 0.757), and brainstem (AUROC = 0.789) was somewhat worse, but the reasons are not very clear. In addition, in order to find the recurring sequence patterns preferred by each tissue-specific m<sup>6</sup>A prediction model, we further divided the peaks into instances of length (l = 50) and extracted the consensus motifs from instances with predicted values higher than 0.5 using integrated gradient and TF-Modisco, under each tissue model, respectively. By trimming the overall letter frequencies with three gaps and two mismatches allowed, we identified one consistence motif under all tissue models (<xref rid=\"s0130\" ref-type=\"sec\">Figure S1</xref>), which was matched to the known m<sup>6</sup>A consensus motif DRACH. Please refer to <xref rid=\"s0130\" ref-type=\"sec\">Figure S1</xref> for details.</p>", "<title>Performance compared with existing approaches</title>", "<p id=\"p0100\">We further compared the performance of the proposed m6A-TSFinder with existing m<sup>6</sup>A predictors specifically targeted at the tissue level. Dao et al. previously developed a Support Vector Machine (SVM)-based model (iRNA-m6A) for m<sup>6</sup>A identification in the human brain, liver, and kidney ##REF##32435427##[65]##. Later, im6A-TS-CNN ##REF##32858457##[64]## and TS-m6A-DL ##REF##34471503##[66]## further improved prediction performance by applying a convolutional neural network (CNN), using the same training and testing datasets provided in Dao’s work. It is worth mentioning that the training and testing datasets used in their work contain positive and negative sequences fixed to 41-nt length with m<sup>6</sup>A sites or unmethylated adenosines in the center. These models learn to capture discriminative sequence patterns at positions with a fixed distance from the target adenosine. When making predictions, the well-trained models take the centered adenosine and its surrounding sequences and return the probability that the central adenosine is methylated. When only low-resolution data are available, sequence lengths vary from 100 nt to hundreds, and methylation is not fixed at the center of the sequence. Therefore, the pre-set requirements of these base-resolution models (TS-m6A-DL, im6A-TS-CNN, and iRNA-m6A) cannot be fulfilled, making it difficult to fairly evaluate their performance on low-resolution data. Furthermore, the only three tissue-specific base-resolution datasets originate from m6A-REF-seq, which can only detect m<sup>6</sup>A in NNACA, whereas the 23 low-resolution considered in this work contain m<sup>6</sup>A from broader sequence contexts. Inconsistencies between data further limit direct comparisons between models. Nevertheless, we apply m6A-TSFinder to the same training and testing datasets of the three base-resolution models to show performance and fair comparisons when base-resolution data are available. Specifically, as described in the “Data collection and processing” section, the prediction of m<sup>6</sup>A from fixed-length sequences centered at the target site can be considered a special case of m6A-TSFinder, in which each input sequence is treated as a single instance. As shown in ##TAB##1##Table 2##, when tested on the independent dataset, m6A-TSFinder outperformed the three competing methods in two of the three tissues tested (brain and liver) and achieved the best average performance (AUROC = 0.8593). The improvement may be due to the application of the LSTM layer after the convolutional layer, which enables the model to learn the long-range dependencies between the motifs. In addition, by learning from the low-resolution datasets, we expanded the human tissues supported from 3 to 23, which could significantly facilitate future research focusing on the dynamics of m<sup>6</sup>A methylome across different tissues.</p>", "<title>Assessing the impact of genetic variants on tissue-specific m<sup>6</sup>A sites by m6A-TSVar</title>", "<p id=\"p0105\">The m6A-TSVar web server was designed to assess the impact of genetic variants on tissue-specific m<sup>6</sup>A RNA methylation using deep neural networks. The collected experimentally validated m<sup>6</sup>A peaks from 23 human tissues were integrated. The changes in the probability of m<sup>6</sup>A methylation affected by mutations were calculated, with the returned value of AL indicating how extreme the impact on m<sup>6</sup>A methylation was. To our best knowledge, the m6A-TSVar is the first web server for exploring m<sup>6</sup>A-affecting variants within a specific tissue by integrating the tissue-specific m<sup>6</sup>A patterns.</p>", "<title>Screening for cancer variants that affect m<sup>6</sup>A in their primary tissues in m6A-CAVar</title>", "<p id=\"p0110\">In m6A-CAVar, the cancer somatic variants from 27 TCGA projects were extracted. Their impacts on m<sup>6</sup>A RNA modifications in the corresponding 23 healthy human tissues were evaluated and then systematically validated using 17 paired normal and tumor samples. A total of 587,983 cancer somatic variants were predicted to affect the m<sup>6</sup>A methylation status in their originating tissues (the “low-confidence level” group). Among them, the dynamic m<sup>6</sup>A status induced by 122,473 variants was observed on the available epitranscriptome profiles (the “medium-confidence level” group), and 1718 confirmed m<sup>6</sup>A-variants were known to be associated with diseases and other phenotypes from GWAS analysis (the “high-confidence level” group) (##TAB##2##Table 3##). Please refer to “Data collection and processing” section for more details related to the definition of different confidence groups.</p>", "<title>Deciphering the tissue specificity of cancer m<sup>6</sup>A variants</title>", "<p id=\"p0115\">Of interest is whether m<sup>6</sup>A variants function in different cancer-originating tissues. For this purpose, we calculated the proportion of m<sup>6</sup>A variants that function in different numbers of tissues, and the results suggested that most m<sup>6</sup>A-associated cancer variants are tissue- and cancer-specific (93.25%), whereas only around 1.17% are functional in the originating tissues of more than three types of cancers (##FIG##3##Figure 4##A). The consistency is much higher at the gene level. Only around 16.59% of m<sup>6</sup>A variant-carrying genes are associated with a single tissue. More than 60.29% were shared in more than three tissue types (##FIG##3##Figure 4##B), suggesting some common epitranscriptome layer circuitry at the gene level in different cancers. We further examined the proportion of shared m<sup>6</sup>A variant-carrying genes between two different tissues. As shown in ##FIG##3##Figure 4##C, most tissues, <italic>e.g.</italic>, skin and stomach, strongly correlated with each other. However, tissues like the heart, testis, and thyroid showed a rather weak association with other tissues, which may suggest more tissue-specific epitranscriptome circuitry for cancers originating in those tissues.</p>", "<p id=\"p0120\">We finally identified the m<sup>6</sup>A variant-carrying genes that are associated with the most TCGA cancer types. Only experimentally validated m<sup>6</sup>A variants (medium confidence level and above) were considered here for a more reliable analysis. Top of the list was <italic>CENPF,</italic> in which variants may change its m<sup>6</sup>A methylation status in the primary tissue of 15 cancer types, followed by <italic>DST</italic>, <italic>MKI67</italic>, and <italic>PLEC</italic>, which were all related to 14 cancer types (detailed in <xref rid=\"s0130\" ref-type=\"sec\">Table S5</xref>). Among them, the roles in epitranscriptome regulation of <italic>CENPF</italic>, <italic>MKI67</italic>, and <italic>PLEC</italic> have been indicated previously in glioblastoma ##REF##28344040##[94]##, breast cancer ##REF##21524841##[95]##, and pancreatic cancer ##REF##32355831##[96]##, respectively.</p>", "<title>Enhanced web interface and application</title>", "<p id=\"p0125\">The m6A-TSHub features a user-friendly web interface with multiple useful functions, including databases and online servers, which enable users to fast query databases, upload their own custom jobs, and download all m<sup>6</sup>A-related information at the tissue level. The collected functional m<sup>6</sup>A-affecting variants can be queried by a human body diagram according to their primary tissues (##FIG##4##Figure 5##A), as well as by different cancer types along with further filters (<italic>e.g.</italic>, gene type, m<sup>6</sup>A status, confidence level, and disease association; ##FIG##4##Figure 5##B). The query function also returns several categories of useful information, including TCGA project names ##UREF##8##[77]##, tumor-growth tissues, genes, chromosome regions, COSMIC ID ##REF##30371878##[97]##, and disease phenotypes (##FIG##4##Figure 5##C). The details of tissue-specific m<sup>6</sup>A peaks collected in m6A-TSDB (##FIG##4##Figure 5##D) and cancer m<sup>6</sup>A-associated variants in m6A-CAVar (##FIG##4##Figure 5##E) can be viewed by clicking the site or variant ID, along with annotated disease-association regulations (##FIG##4##Figure 5##F). Furthermore, online servers allow for the identification of m<sup>6</sup>A sites and m<sup>6</sup>A-associated variants within user-defined regions, with 23 types of human tissues to be selected (##FIG##4##Figure 5##G and H). A genome browser is available for interactive exploration of the genome regions of interest, including the human gene annotation track, 23 normal tissue tracks, 25 cancer cell line tracks, single-base m<sup>6</sup>A epitranscriptome landscape track, and post-transcriptional regulation tracks. All metadata provided in the m6A-TSHub can be freely downloaded, along with server scripts provided to run the prediction tools locally (required language: R and Python). Users can refer to the ‘help’ and ‘download’ page for more detailed guidance and instructions.</p>", "<title>Case study 1: <italic>PIK3CA</italic> variant in colon cancer</title>", "<p id=\"p0130\">Previous studies have reported that m<sup>6</sup>A RNA modification plays an important role in colon cancer ##REF##31676230##[61]##, ##REF##31823961##[98]##, ##REF##32993738##[99]##, ##REF##32913527##[100]##. The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) project ##UREF##8##[77]## presented a large number of somatic variants identified from various colon adenocarcinoma samples. However, it is still unclear which single genetic variant may lead to m<sup>6</sup>A dysregulation. In m6A-CAVar, a somatic variant at Chr3:178952085 (A &gt; T) on <italic>PIK3CA</italic> identified from TCGA-COAD project (TCGA barcode: TCGA-AA3821-01A-01W-0995-10) was predicted to erase the m<sup>6</sup>A methylation of a region (Chr3:178951888-178952363, positive strand). The m<sup>6</sup>A methylation was observed in healthy human colon, but disappeared in the colon adenocarcinoma cancer cell line HCT116 ##REF##31619268##[101]##. This somatic variant is also recorded in the COSMIC database from colon tumor samples under the legacy identifier of COSM776, and reported to be associated with 27 submitted interpretations and evidence in the ClinVar database ##REF##26582918##[71]##, including PIK3CA-related overgrowth spectrum (ClinVar accession: RCV000201235.1), breast adenocarcinoma (ClinVar accession: RCV000014629.5), and pancreatic adenocarcinoma (ClinVar accession: RCV000417557.1). Taken together, these observations strongly support the functional importance of this variant. Additionally, the m<sup>6</sup>A-associated variant falls within the binding regions of two RBPs (TARDBP and NUDT21), whose interaction may be regulated by the loss of m<sup>6</sup>A methylation in the cancer condition, providing some putative downstream regulatory consequences of the variant.</p>", "<title>Case study 2: <italic>PLEC</italic> variant in glioblastoma</title>", "<p id=\"p0135\">Glioblastoma (GBM) is the most aggressive type of brain tumor and is associated with rising mortality. The roles of m<sup>6</sup>A regulators in this disease have been previously indicated ##UREF##10##[102]##, ##REF##26461092##[103]##, ##REF##22014570##[104]##, ##REF##22409458##[105]##. A somatic cancer variant on <italic>PLEC</italic> was identified from the The Cancer Genome Atlas Glioblastoma Multiforme (TCGA-GBM) project (TCGA barcode: TCGA-06-5416-01A-01D-1486-08) at Chr8:144991388 (C &gt; T). This cancer variant was predicted to lead to a gain of an m<sup>6</sup>A site on a previously unmethylated region in a healthy human cerebrum. Indeed, an m<sup>6</sup>A site was detected in this region from malignant GBM tumor cell line U-251. This mutation has a record in ClinVar database (ClinVar accession: RCV000177727.1). Screening for potential post-transcriptional regulations revealed that the cancer variant falls within the target binding regions of six RBPs, including the m<sup>6</sup>A reader YTHDF1, which is known to bind m<sup>6</sup>A-containing RNAs and promote cancer stem cell properties of GBM cells ##REF##31908598##[106]##. It should be of immediate interest to ask whether the methylation of <italic>PLEC</italic> regulates its interaction with YTHDF1 and other RBPs, and what the functional consequences are.</p>", "<title>Case study 3: <italic>EGFR</italic> variant in lung cancer</title>", "<p id=\"p0140\">The associations between m<sup>6</sup>A RNA modifications and human lung cancers have been well studied. The m<sup>6</sup>A eraser FTO may be a prognostic factor in The Cancer Genome Atlas Lung Squamous Cell Carcinoma (TCGA-LUSC) ##REF##29842885##[107]##, and the m<sup>6</sup>A writer METTL3 regulates <italic>EGFR</italic> expression to promote cell invasion of human lung cancer cells ##REF##27117702##[82]##. The m6A-CAVar database can be used to explore the role of m<sup>6</sup>A variants of <italic>EGFR</italic> in lung cancers. We first search by gene name ‘<italic>EGFR</italic>’ on the front page of the m6A-CAVar database, then filter the results and keep only records related to lung tissue, which retains a total of 10 cancer m<sup>6</sup>A-associated variants from two lung cancer types (##FIG##5##Figure 6##A and B). Alternatively, the users can query all recorded m<sup>6</sup>A-associated variants that function in lung tissue by simply clicking the relevant part from the human body diagram (##FIG##5##Figure 6##C). More details can be accessed by clicking the variant ID. For example, if we check further details of an m<sup>6</sup>A-gain variant from the TCGA-LUAD project at Chr7:55259515 (T &gt; G), we can see that this variant is recorded in the ClinVar database and is relevant to eight disease conditions, including lung cancers (##FIG##5##Figure 6##D), which may suggest potential cancer pathogenesis originates in the epitranscriptome layer.</p>", "<title>Data availability</title>", "<p id=\"p0170\">The data underlying this article are available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.xjtlu.edu.cn/biologicalsciences/m6ats\" id=\"PC_linkfls9fG6ULY\">www.xjtlu.edu.cn/biologicalsciences/m6ats</ext-link>. The online versions of the m6A-TSFinder and m6A-TSVar web server are available at <ext-link ext-link-type=\"uri\" xlink:href=\"https://www.xjtlu.edu.cn/biologicalsciences/m6ats\" id=\"PC_linkj8xfPncso6\">www.xjtlu.edu.cn/biologicalsciences/m6ats</ext-link> by clicking the ‘tool’ section. The local version and project codes can be accessed on the ‘download’ page.</p>", "<title>Competing interests</title>", "<p id=\"p0175\">The authors declare that they have no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p01769\"><bold>Bowen Song:</bold> Methodology, Data curation, Software, Visualization, Writing – original draft. <bold>Daiyun Huang:</bold> Software, Supervision. <bold>Yuxin Zhang:</bold> Visualization. <bold>Zhen Wei:</bold> Resources. <bold>Jionglong Su:</bold> Visualization. <bold>João Pedro de Magalhães:</bold> Visualization. <bold>Daniel J. Rigden:</bold> Writing – review &amp; editing. <bold>Jia Meng:</bold> Conceptualization, Supervision, Writing – review &amp; editing, Funding acquisition. <bold>Kunqi Chen:</bold> Conceptualization, Resources, Writing – review &amp; editing, Funding acquisition. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0190\">The following are the Supplementary material to this article:</p>", "<p id=\"p0195\">\n\n</p>", "<p id=\"p0200\">\n\n</p>", "<p id=\"p0205\">\n\n</p>", "<p id=\"p0210\">\n\n</p>", "<p id=\"p0215\">\n\n</p>", "<p id=\"p0220\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0180\">This work was supported by the <funding-source id=\"gp005\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100001809</institution-id><institution>National Natural Science Foundation of China</institution></institution-wrap></funding-source> (Grant Nos. 32100519 and 31671373), the <funding-source id=\"gp010\">Scientific Research Foundation for Advanced Talents of Fujian Medical University</funding-source> (Grant No. XRCZX2021019), and the <funding-source id=\"gp015\">XJTLU Key Program Special Fund</funding-source> (Grant Nos. KSF-T-01, KSF-E-51, and KSF-P-02), China. The authors also acknowledge the researcher of the various resources mentioned in the manuscript to share their data, especially for tissue-specific m<sup>6</sup>A sequencing data.</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>The overall design of m6A-TSHub</bold></p><p>By integrating 184,554 m<sup>6</sup>A sites detected from 23 different healthy human tissues (m6A-TSDB), a deep learning framework that learns tissue-specific RNA methylation patterns was developed (m6A-TSFinder). The effect of genetic variants on tissue-specific m<sup>6</sup>A sites was then evaluated (m6A-TSVar). A total of 587,983 cancer somatic mutations were predicted to be able to affect m<sup>6</sup>A methylation of RNA in their corresponding cancer-originating tissues. The predicted m<sup>6</sup>A-affecting SNPs were then systematically validated using available cancer epitranscriptome datasets, and then functionally annotated with disease and phenotype associations from GWAS, along with features relating to the post-transcriptional machinery (miRNA target sites, splicing sites, and RBP binding sites) that are potentially mediated by m<sup>6</sup>A modification (m6A-CAVar). A web interface was constructed to enable the exploration, query, online analysis, and download of relevant results and data. m<sup>6</sup>A, <italic>N</italic><sup>6</sup>-methyladenosine; TCGA, The Cancer Genome Atlas; GWAS, genome-wide association study; RBP, RNA-binding protein; miRNA, microRNA.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>A simplified graphic illustration of the proposed m6A-TSFinder framework</bold></p><p>RNA-seq, RNA sequencing; MeRIP-seq, methylated RNA immunoprecipitation sequencing; CNN, convolutional neural network; LSTM, long short-term memory.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Workflow of how to determine the confidence level of m<sup>6</sup>A variants</bold></p><p>Three types of confidence levels were applied. The cancer-driving somatic variants were extracted from TCGA projects, and mapped to the m<sup>6</sup>A profiling samples derived from corresponding tumor-growth tissues. A tissue-specific weakly supervised model was then applied to obtain m<sup>6</sup>A-associated variants classified into the low-confidence level group. m<sup>6</sup>A profiling samples from tumor-growth tissues were then used for validation of the prediction results, and the validated portion was classified into the medium-confidence level group. Lastly, all variants with a medium confidence level were annotated with disease information from ClinVar and GWAS, and then classified into the high-confidence level group. Lung tissue, healthy and cancerous, is used as an example here. The same protocol was followed for all 23 tissues. GWAS, genome-wide association study.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>Tissue</bold><bold>specificity of cancer m<sup>6</sup>A variants</bold></p><p><bold>A.</bold> The proportion of m<sup>6</sup>A variants that are shared among different tissues. Most m<sup>6</sup>A-associated variants (93.25%) were identified in only 1 tissue, with 3.86%, 1.70%, and 1.17% identified in 2, 3, and more than 3 tissues, respectively. <bold>B.</bold> The proportion of m<sup>6</sup>A variant-carrying genes shared among tissues. The consistency is much higher at the gene level. Most m<sup>6</sup>A variants-carrying genes are shared among multiple tissues, with only 16.59% associated to one tissue type. <bold>C.</bold> The pairwise association of tissues in terms of proportion of shared m<sup>6</sup>A variant-carrying genes. Most tissues are significantly correlated. The exceptions are heart, adrenal gland, lymph nodes, bone marrow, testis, and thyroid.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>Enhanced web interface</bold></p><p><bold>A.</bold> A human body diagram is available for querying cancer somatic m<sup>6</sup>A-associated variants in their originating tissues. <bold>B.</bold> Users can query the associated variants by cancer type. <bold>C.</bold> Users can also query the variant-associated disease, region, gene symbol, COSMIC, and Rs ID, and further filter the returned results. <bold>D.</bold> Details of tissue-specific m<sup>6</sup>A peaks collected in m6A-TSDB. <bold>E.</bold> Details of cancer-related m<sup>6</sup>A-associated variants. <bold>F.</bold> Details of disease annotation involved. <bold>G.</bold> The online tools provided for analysis of user-uploaded files, including assessing m<sup>6</sup>A-associated variants in tissues (m6A-TSVar). <bold>H.</bold> The online tool for identifying tissue-specific m<sup>6</sup>A sites (m6A-TSFinder).</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>Case study on</bold><bold>the</bold><bold><italic>EGFR</italic></bold><bold>gene</bold></p><p><bold>A.</bold> Searching for the gene <italic>‘EGFR’</italic> in m6A-CAVar database returns a total of 10 m<sup>6</sup>A variants identified in two lung cancer types. The details of which can be viewed by clicking the m6A-CAVar ID. <bold>B.</bold> Users can further filter the search results in specific cancer types. <bold>C.</bold> A human body map provided on the front page of m6A-CAVar website. It enables quick positioning of cancer m<sup>6</sup>A-associated variants functioning at a specific tissue. <bold>D.</bold> The disease and phenotype associations of recorded m<sup>6</sup>A variant.</p></caption></fig>" ]
[ "<table-wrap position=\"float\" id=\"t0005\"><label>Table 1</label><caption><p><bold>Performance evaluation of tissue-specific m<sup>6</sup>A model</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"2\"><bold>Tissue type</bold></th><th colspan=\"4\"><bold>10-fold cross-validation</bold><hr/></th><th colspan=\"4\"><bold>Independent testing</bold><hr/></th></tr><tr><th><bold>Accuracy</bold></th><th><bold>Precision</bold></th><th><bold>MCC</bold></th><th><bold>AUROC</bold></th><th><bold>Accuracy</bold></th><th><bold>Precision</bold></th><th><bold>MCC</bold></th><th><bold>AUROC</bold></th></tr></thead><tbody><tr><td>Lung</td><td align=\"center\">0.764</td><td align=\"center\">0.835</td><td align=\"center\">0.536</td><td align=\"center\">0.843</td><td align=\"center\">0.775</td><td align=\"center\">0.761</td><td align=\"center\">0.55</td><td align=\"center\">0.853</td></tr><tr><td>Bladder</td><td align=\"center\">0.758</td><td align=\"center\">0.760</td><td align=\"center\">0.517</td><td align=\"center\">0.836</td><td align=\"center\">0.766</td><td align=\"center\">0.750</td><td align=\"center\">0.532</td><td align=\"center\">0.848</td></tr><tr><td>Colon</td><td align=\"center\">0.740</td><td align=\"center\">0.770</td><td align=\"center\">0.482</td><td align=\"center\">0.810</td><td align=\"center\">0.744</td><td align=\"center\">0.730</td><td align=\"center\">0.490</td><td align=\"center\">0.810</td></tr><tr><td>Lymph node</td><td align=\"center\">0.771</td><td align=\"center\">0.797</td><td align=\"center\">0.544</td><td align=\"center\">0.844</td><td align=\"center\">0.78</td><td align=\"center\">0.735</td><td align=\"center\">0.570</td><td align=\"center\">0.844</td></tr><tr><td>Cerebrum</td><td align=\"center\">0.745</td><td align=\"center\">0.799</td><td align=\"center\">0.495</td><td align=\"center\">0.827</td><td align=\"center\">0.758</td><td align=\"center\">0.768</td><td align=\"center\">0.515</td><td align=\"center\">0.834</td></tr><tr><td>Cerebellum</td><td align=\"center\">0.715</td><td align=\"center\">0.718</td><td align=\"center\">0.432</td><td align=\"center\">0.798</td><td align=\"center\">0.72</td><td align=\"center\">0.731</td><td align=\"center\">0.441</td><td align=\"center\">0.801</td></tr><tr><td>Hypothalamus</td><td align=\"center\">0.733</td><td align=\"center\">0.724</td><td align=\"center\">0.467</td><td align=\"center\">0.799</td><td align=\"center\">0.746</td><td align=\"center\">0.74</td><td align=\"center\">0.493</td><td align=\"center\">0.811</td></tr><tr><td>Brainstem</td><td align=\"center\">0.727</td><td align=\"center\">0.742</td><td align=\"center\">0.454</td><td align=\"center\">0.764</td><td align=\"center\">0.721</td><td align=\"center\">0.713</td><td align=\"center\">0.443</td><td align=\"center\">0.789</td></tr><tr><td>Kidney</td><td align=\"center\">0.685</td><td align=\"center\">0.694</td><td align=\"center\">0.369</td><td align=\"center\">0.755</td><td align=\"center\">0.647</td><td align=\"center\">0.628</td><td align=\"center\">0.297</td><td align=\"center\">0.718</td></tr><tr><td>Bone marrow</td><td align=\"center\">0.694</td><td align=\"center\">0.634</td><td align=\"center\">0.391</td><td align=\"center\">0.757</td><td align=\"center\">0.698</td><td align=\"center\">0.721</td><td align=\"center\">0.397</td><td align=\"center\">0.757</td></tr><tr><td>Liver</td><td align=\"center\">0.742</td><td align=\"center\">0.747</td><td align=\"center\">0.484</td><td align=\"center\">0.805</td><td align=\"center\">0.737</td><td align=\"center\">0.717</td><td align=\"center\">0.476</td><td align=\"center\">0.803</td></tr><tr><td>Ovary</td><td align=\"center\">0.730</td><td align=\"center\">0.710</td><td align=\"center\">0.464</td><td align=\"center\">0.814</td><td align=\"center\">0.726</td><td align=\"center\">0.722</td><td align=\"center\">0.453</td><td align=\"center\">0.812</td></tr><tr><td>Prostate</td><td align=\"center\">0.752</td><td align=\"center\">0.779</td><td align=\"center\">0.507</td><td align=\"center\">0.819</td><td align=\"center\">0.759</td><td align=\"center\">0.736</td><td align=\"center\">0.521</td><td align=\"center\">0.830</td></tr><tr><td>Soft tissue</td><td align=\"center\">0.766</td><td align=\"center\">0.855</td><td align=\"center\">0.544</td><td align=\"center\">0.855</td><td align=\"center\">0.771</td><td align=\"center\">0.775</td><td align=\"center\">0.543</td><td align=\"center\">0.858</td></tr><tr><td>Skin</td><td align=\"center\">0.750</td><td align=\"center\">0.850</td><td align=\"center\">0.511</td><td align=\"center\">0.835</td><td align=\"center\">0.773</td><td align=\"center\">0.753</td><td align=\"center\">0.547</td><td align=\"center\">0.857</td></tr><tr><td>Stomach</td><td align=\"center\">0.772</td><td align=\"center\">0.820</td><td align=\"center\">0.549</td><td align=\"center\">0.852</td><td align=\"center\">0.77</td><td align=\"center\">0.764</td><td align=\"center\">0.539</td><td align=\"center\">0.848</td></tr><tr><td>Corpus uterus</td><td align=\"center\">0.722</td><td align=\"center\">0.656</td><td align=\"center\">0.452</td><td align=\"center\">0.813</td><td align=\"center\">0.734</td><td align=\"center\">0.715</td><td align=\"center\">0.470</td><td align=\"center\">0.822</td></tr><tr><td>Adrenal gland</td><td align=\"center\">0.737</td><td align=\"center\">0.771</td><td align=\"center\">0.474</td><td align=\"center\">0.804</td><td align=\"center\">0.741</td><td align=\"center\">0.716</td><td align=\"center\">0.485</td><td align=\"center\">0.817</td></tr><tr><td>Heart</td><td align=\"center\">0.778</td><td align=\"center\">0.824</td><td align=\"center\">0.558</td><td align=\"center\">0.854</td><td align=\"center\">0.772</td><td align=\"center\">0.759</td><td align=\"center\">0.546</td><td align=\"center\">0.846</td></tr><tr><td>Rectum</td><td align=\"center\">0.747</td><td align=\"center\">0.725</td><td align=\"center\">0.496</td><td align=\"center\">0.826</td><td align=\"center\">0.767</td><td align=\"center\">0.747</td><td align=\"center\">0.536</td><td align=\"center\">0.828</td></tr><tr><td>Testis</td><td align=\"center\">0.743</td><td align=\"center\">0.770</td><td align=\"center\">0.489</td><td align=\"center\">0.810</td><td align=\"center\">0.731</td><td align=\"center\">0.734</td><td align=\"center\">0.463</td><td align=\"center\">0.804</td></tr><tr><td>Thyroid gland</td><td align=\"center\">0.765</td><td align=\"center\">0.805</td><td align=\"center\">0.533</td><td align=\"center\">0.845</td><td align=\"center\">0.753</td><td align=\"center\">0.733</td><td align=\"center\">0.509</td><td align=\"center\">0.830</td></tr><tr><td>Pancreas</td><td align=\"center\">0.761</td><td align=\"center\">0.770</td><td align=\"center\">0.523</td><td align=\"center\">0.838</td><td align=\"center\">0.751</td><td align=\"center\">0.739</td><td align=\"center\">0.502</td><td align=\"center\">0.834</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0010\"><label>Table 2</label><caption><p><bold>Performance comparison between m6A-TSFinder and competing approaches on independent dataset</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"2\"><bold>Tissue type</bold></th><th colspan=\"4\"><bold>Performance on independent dataset</bold><bold>(AUROC)</bold><hr/></th></tr><tr><th><bold>m6A-TSFinder</bold></th><th><bold>TS-m6A-DL</bold></th><th>im6A<bold>-TS-CNN</bold></th><th><bold>iRNA-</bold>m6A</th></tr></thead><tbody><tr><td>Brain</td><td align=\"center\">0.8132</td><td align=\"center\">0.8097</td><td align=\"center\">0.8056</td><td align=\"center\">0.7845</td></tr><tr><td>Liver</td><td align=\"center\">0.8850</td><td align=\"center\">0.8784</td><td align=\"center\">0.8805</td><td align=\"center\">0.8681</td></tr><tr><td>Kidney</td><td align=\"center\">0.8796</td><td align=\"center\">0.8802</td><td align=\"center\">0.8727</td><td align=\"center\">0.8565</td></tr><tr><td>Average</td><td align=\"center\">0.8593</td><td align=\"center\">0.8561</td><td align=\"center\">0.8529</td><td align=\"center\">0.8364</td></tr></tbody></table></table-wrap>", "<table-wrap position=\"float\" id=\"t0015\"><label>Table 3</label><caption><p><bold>Tissue-specific m<sup>6</sup>A cancer variants collected in m6A-CAVar</bold></p></caption><table frame=\"hsides\" rules=\"groups\"><thead><tr><th rowspan=\"2\"><bold>Cancer type</bold></th><th rowspan=\"2\"><bold>Primary tissue</bold></th><th rowspan=\"2\"><bold>Matched cancer cell line</bold></th><th rowspan=\"2\"><bold>Variant type</bold></th><th colspan=\"3\" align=\"center\"><bold>Classification</bold><hr/></th><th rowspan=\"2\"><bold>Total</bold></th></tr><tr><th><bold>Low</bold></th><th>Medium</th><th><bold>High</bold></th></tr></thead><tbody><tr><td rowspan=\"2\"><break/>TCGA-LUAD</td><td rowspan=\"2\">Lung</td><td rowspan=\"2\">A549, H1299</td><td>Gain</td><td>27,845</td><td>6526</td><td>30</td><td>34,401</td></tr><tr><td>Loss</td><td>1233</td><td>1391</td><td>2</td><td>2626</td></tr><tr><td rowspan=\"2\">TCGA-BLCA</td><td rowspan=\"2\">Urinary bladder</td><td rowspan=\"2\">BCa5637</td><td>Gain</td><td>25,508</td><td>3702</td><td>13</td><td>29,223</td></tr><tr><td>Loss</td><td>3079</td><td>1691</td><td>6</td><td>4776</td></tr><tr><td rowspan=\"2\"><break/>TCGA-COAD</td><td rowspan=\"2\">Colon</td><td rowspan=\"2\">HT29, HCT116</td><td>Gain</td><td>30,540</td><td>8391</td><td>82</td><td>39,013</td></tr><tr><td>Loss</td><td>6</td><td>8284</td><td>74</td><td>8364</td></tr><tr><td rowspan=\"2\">TCGA-DLBC</td><td rowspan=\"2\">B lymphocyte cell lines</td><td rowspan=\"2\">OCI-Ly1</td><td>Gain</td><td>1189</td><td>82</td><td>2</td><td>1273</td></tr><tr><td>Loss</td><td>74</td><td>69</td><td>0</td><td>143</td></tr><tr><td rowspan=\"8\"><break/>TCGA-GBM</td><td rowspan=\"2\">Cerebrum</td><td rowspan=\"8\">U251, GOS-3, PBT003</td><td>Gain</td><td>8509</td><td>3648</td><td>47</td><td>12,204</td></tr><tr><td>Loss</td><td>1453</td><td>1181</td><td>12</td><td>2646</td></tr><tr><td rowspan=\"2\">Cerebellum</td><td>Gain</td><td>8319</td><td>3659</td><td>38</td><td>12,016</td></tr><tr><td>Loss</td><td>1928</td><td>1271</td><td>4</td><td>3203</td></tr><tr><td rowspan=\"2\">Hypothalamus</td><td>Gain</td><td>6723</td><td>3414</td><td>27</td><td>10,164</td></tr><tr><td>Loss</td><td>1522</td><td>1482</td><td>18</td><td>3022</td></tr><tr><td rowspan=\"2\">Brainstem</td><td>Gain</td><td>7559</td><td>3168</td><td>40</td><td>10,767</td></tr><tr><td>Loss</td><td>1374</td><td>1451</td><td>8</td><td>2833</td></tr><tr><td rowspan=\"2\">TCGA-KIRC</td><td rowspan=\"2\">Kidney</td><td rowspan=\"2\">iSLK.219</td><td>Gain</td><td>3844</td><td>227</td><td>4</td><td>4075</td></tr><tr><td>Loss</td><td>54</td><td>33</td><td>0</td><td>87</td></tr><tr><td rowspan=\"2\">TCGA-LAML</td><td rowspan=\"2\">HSCs</td><td rowspan=\"2\">MOLM13, THP1, NOMO-1, MONO-MAC-6, MA9.3ITD</td><td>Gain</td><td>448</td><td>274</td><td>0</td><td>722</td></tr><tr><td>Loss</td><td>3</td><td>35</td><td>3</td><td>41</td></tr><tr><td rowspan=\"2\">TCGA-LIHC</td><td rowspan=\"2\">Liver</td><td rowspan=\"2\">HepG2, Huh7, SMMC7721, HCCLM3</td><td>Gain</td><td>7416</td><td>2511</td><td>2</td><td>9929</td></tr><tr><td>Loss</td><td>18</td><td>1765</td><td>4</td><td>1787</td></tr><tr><td rowspan=\"2\">TCGA-OV</td><td rowspan=\"2\">Ovary</td><td rowspan=\"2\">PEO1</td><td>Gain</td><td>7022</td><td>531</td><td>0</td><td>7553</td></tr><tr><td>Loss</td><td>1350</td><td>1090</td><td>6</td><td>2446</td></tr><tr><td rowspan=\"2\">TCGA-PRAD</td><td rowspan=\"2\">Prostate gland</td><td rowspan=\"2\">Cd-RWPE-1</td><td>Gain</td><td>3825</td><td>636</td><td>6</td><td>4467</td></tr><tr><td>Loss</td><td>550</td><td>288</td><td>2</td><td>840</td></tr><tr><td rowspan=\"2\">TCGA-SARC</td><td rowspan=\"2\">Soft tissues</td><td rowspan=\"2\">U20S</td><td>Gain</td><td>3592</td><td>1324</td><td>4</td><td>4920</td></tr><tr><td>Loss</td><td>373</td><td>28</td><td>0</td><td>401</td></tr><tr><td rowspan=\"2\">TCGA-SKCM</td><td rowspan=\"2\">Skin</td><td rowspan=\"2\">Mel624</td><td>Gain</td><td>79,470</td><td>17,177</td><td>118</td><td>96,765</td></tr><tr><td>Loss</td><td>6472</td><td>1559</td><td>2</td><td>8033</td></tr><tr><td rowspan=\"2\">TCGA-STAD</td><td rowspan=\"2\">Stomach</td><td rowspan=\"2\">BGC823</td><td>Gain</td><td>35,438</td><td>2202</td><td>34</td><td>37,674</td></tr><tr><td>Loss</td><td>1103</td><td>3313</td><td>27</td><td>4443</td></tr><tr><td rowspan=\"2\">TCGA-UCEC</td><td rowspan=\"2\">Corpus uteri</td><td rowspan=\"2\">HEC-1-A</td><td>Gain</td><td>80,712</td><td>38,242</td><td>266</td><td>119,220</td></tr><tr><td>Loss</td><td>7813</td><td>1828</td><td>22</td><td>9663</td></tr><tr><td rowspan=\"2\">TCGA-LUSC</td><td rowspan=\"2\">Lung</td><td rowspan=\"2\">–</td><td>Gain</td><td>31,106</td><td>–</td><td>118</td><td>31,224</td></tr><tr><td>Loss</td><td>2328</td><td>–</td><td>2</td><td>2330</td></tr><tr><td rowspan=\"4\">TCGA-MESO</td><td rowspan=\"2\">Lung</td><td rowspan=\"2\">–</td><td>Gain</td><td>595</td><td>–</td><td>4</td><td>599</td></tr><tr><td>Loss</td><td>57</td><td>–</td><td>0</td><td>57</td></tr><tr><td rowspan=\"2\">Heart</td><td rowspan=\"2\">–</td><td>Gain</td><td>674</td><td>–</td><td>5</td><td>679</td></tr><tr><td>Loss</td><td>102</td><td>–</td><td>0</td><td>102</td></tr><tr><td rowspan=\"8\">TCGA-LGG</td><td rowspan=\"2\">Cerebrum</td><td rowspan=\"2\">–</td><td>Gain</td><td>6714</td><td>–</td><td>92</td><td>6806</td></tr><tr><td>Loss</td><td>1423</td><td>–</td><td>19</td><td>1442</td></tr><tr><td rowspan=\"2\">Cerebellum</td><td rowspan=\"2\">–</td><td>Gain</td><td>6601</td><td>–</td><td>109</td><td>6710</td></tr><tr><td>Loss</td><td>1745</td><td>–</td><td>16</td><td>1761</td></tr><tr><td rowspan=\"2\">Hypothalamus</td><td rowspan=\"2\">–</td><td>Gain</td><td>5010</td><td>–</td><td>77</td><td>5087</td></tr><tr><td>Loss</td><td>1698</td><td>–</td><td>11</td><td>1709</td></tr><tr><td rowspan=\"2\">Brainstem</td><td rowspan=\"2\">–</td><td>Gain</td><td>5740</td><td>–</td><td>114</td><td>5854</td></tr><tr><td>Loss</td><td>1528</td><td>–</td><td>13</td><td>1541</td></tr><tr><td rowspan=\"2\"><break/>TCGA-KICH</td><td rowspan=\"2\">Kidney</td><td rowspan=\"2\">–</td><td>Gain</td><td>484</td><td>–</td><td>9</td><td>493</td></tr><tr><td>Loss</td><td>9</td><td>–</td><td>0</td><td>9</td></tr><tr><td rowspan=\"2\">TCGA-KIRP</td><td rowspan=\"2\">Kidney</td><td rowspan=\"2\">–</td><td>Gain</td><td>4028</td><td>–</td><td>17</td><td>4045</td></tr><tr><td>Loss</td><td>118</td><td>–</td><td>0</td><td>118</td></tr><tr><td rowspan=\"2\"><break/>TCGA-CHOL</td><td rowspan=\"2\">Liver</td><td rowspan=\"2\">–</td><td>Gain</td><td>728</td><td>–</td><td>2</td><td>730</td></tr><tr><td>Loss</td><td>166</td><td>–</td><td>2</td><td>168</td></tr><tr><td rowspan=\"2\">TCGA-ACC</td><td rowspan=\"2\">Adrenal gland</td><td rowspan=\"2\">–</td><td>Gain</td><td>2285</td><td>–</td><td>21</td><td>2306</td></tr><tr><td>Loss</td><td>385</td><td>–</td><td>3</td><td>388</td></tr><tr><td rowspan=\"2\">TCGA-PCPG</td><td rowspan=\"2\">Adrenal gland</td><td rowspan=\"2\">–</td><td>Gain</td><td>345</td><td>–</td><td>1</td><td>346</td></tr><tr><td>Loss</td><td>57</td><td>–</td><td>0</td><td>57</td></tr><tr><td rowspan=\"2\">TCGA-READ</td><td rowspan=\"2\">Rectum</td><td rowspan=\"2\">–</td><td>Gain</td><td>12,433</td><td>–</td><td>100</td><td>12,533</td></tr><tr><td>Loss</td><td>1098</td><td>–</td><td>4</td><td>1102</td></tr><tr><td rowspan=\"2\">TCGA-THYM</td><td rowspan=\"2\">Heart</td><td rowspan=\"2\">–</td><td>Gain</td><td>520</td><td>–</td><td>7</td><td>527</td></tr><tr><td>Loss</td><td>80</td><td>–</td><td>2</td><td>82</td></tr><tr><td rowspan=\"2\">TCGA-TGCT</td><td rowspan=\"2\">Testis</td><td rowspan=\"2\">–</td><td>Gain</td><td>405</td><td>–</td><td>3</td><td>408</td></tr><tr><td>Loss</td><td>109</td><td>–</td><td>0</td><td>109</td></tr><tr><td rowspan=\"2\"><break/>TCGA-THCA</td><td rowspan=\"2\">Thyroid gland</td><td rowspan=\"2\">–</td><td>Gain</td><td>992</td><td>–</td><td>6</td><td>998</td></tr><tr><td>Loss</td><td>156</td><td>–</td><td>0</td><td>156</td></tr><tr><td rowspan=\"2\">TCGA-PAAD</td><td rowspan=\"2\">Pancreas</td><td rowspan=\"2\">–</td><td>Gain</td><td>6473</td><td>–</td><td>55</td><td>6528</td></tr><tr><td>Loss</td><td>1236</td><td>–</td><td>3</td><td>1239</td></tr><tr><td>Total</td><td>–</td><td>–</td><td>–</td><td>463,792</td><td>122,473</td><td>1718</td><td>587,983</td></tr></tbody></table></table-wrap>" ]
[ "<disp-formula id=\"e0005\"><label>(1)</label><mml:math id=\"M1\" altimg=\"si1.svg\"><mml:mrow><mml:mtext>AL</mml:mtext><mml:mo linebreak=\"goodbreak\">=</mml:mo><mml:mrow><mml:mfenced open=\"{\"><mml:mrow><mml:mrow><mml:mtable><mml:mtr><mml:mtd><mml:mrow><mml:mtext>2</mml:mtext><mml:msub><mml:mi>P</mml:mi><mml:mrow><mml:mi mathvariant=\"italic\">SNP</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:mn>2</mml:mn><mml:mi>max</mml:mi><mml:mrow><mml:mfenced open=\"(\" close=\")\"><mml:mrow><mml:mrow><mml:mn>0.5</mml:mn><mml:mo>,</mml:mo><mml:msub><mml:mi>P</mml:mi><mml:mrow><mml:mi mathvariant=\"italic\">WT</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:mtd><mml:mtd><mml:mrow><mml:mtext>for gain</mml:mtext></mml:mrow></mml:mtd></mml:mtr><mml:mtr><mml:mtd><mml:mrow><mml:mrow><mml:mn>2</mml:mn><mml:msub><mml:mi>P</mml:mi><mml:mrow><mml:mi mathvariant=\"italic\">WT</mml:mi></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:mn>2</mml:mn><mml:mi>max</mml:mi><mml:mrow><mml:mfenced open=\"(\" close=\")\"><mml:mrow><mml:mrow><mml:mn>0.5</mml:mn><mml:mo>,</mml:mo><mml:msub><mml:mi>P</mml:mi><mml:mrow><mml:mi mathvariant=\"italic\">SNP</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:mrow></mml:mtd><mml:mtd><mml:mrow><mml:mtext>for loss</mml:mtext></mml:mrow></mml:mtd></mml:mtr></mml:mtable></mml:mrow></mml:mrow></mml:mfenced></mml:mrow></mml:mrow></mml:math></disp-formula>", "<inline-formula><mml:math id=\"M2\" altimg=\"si2.svg\"><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mrow><mml:mi mathvariant=\"italic\">WT</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>", "<inline-formula><mml:math id=\"M3\" altimg=\"si3.svg\"><mml:mrow><mml:msub><mml:mi>P</mml:mi><mml:mrow><mml:mi mathvariant=\"italic\">SNP</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>" ]
[]
[]
[]
[]
[ "<supplementary-material content-type=\"local-data\" id=\"m0035\"><caption><title>Supplementary Figure S1</title><p><bold>Motif captured under each tissue-specific m6A prediction model</bold> The consensus motifs from instances with higher than average weights were extracted using TF-MoDISco, under each tissue model, respectively. To sum up, we identified one consistence motif GGACU under all tissue models, which was matched to the known m6A consensus motif DRACH.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0030\"><caption><title>Supplementary Figure S2</title><p><bold>m6A patterns captured under specific human gene A.</bold> human gene <italic>RYR2</italic> encodes a ryanodine receptor found in cardiac muscle sarcoplasmic reticulum, this gene was biased expressed in heart and brain. We found three m6A sites located on gene <italic>RYR2</italic> from heart samples, compared with two m6A sites from brain, one from liver, one from ovary, and one from uterus, respectively. <bold>B.</bold> for human gene <italic>PXDNL</italic> (biased expression in heart), we observed only one tissue-specific m6A sites from heart sample. <bold>C.</bold> and <bold>D.</bold> human gene <italic>HMGCS2</italic> and <italic>C6</italic> were both reported to be biased expressed in liver. We found one m6A peak located on gene <italic>HMGCS2</italic> and gene <italic>C6</italic>, respectively, identified from human liver sample.</p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0025\"><caption><title>Supplementary Table S1</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0020\"><caption><title>Supplementary Table S2</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0015\"><caption><title>Supplementary Table S3</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S4</title></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S5</title></caption></supplementary-material>" ]
[ "<table-wrap-foot><fn><p><italic>Note</italic>: MCC, Matthew’s correlation coefficient; AUROC, the area under receiver operating characteristic curve.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p><italic>Note</italic>: For a fair comparison, the m6A-TSFinder was rebuilt for human brain, liver, and kidney, using the same training and testing datasets applied in the three previous studies. The 41-nt sequences were considered as one instance and fed into m6A-TSFinder.</p></fn></table-wrap-foot>", "<table-wrap-foot><fn><p><italic>Note</italic>: TCGA-LUAD, The Cancer Genome Atlas Lung Adenocarcinoma; TCGA-BLCA, The Cancer Genome Atlas Bladder Urothelial Carcinoma; TCGA-COAD, The Cancer Genome Atlas Colon Adenocarcinoma; TCGA-DLBC, The Cancer Genome Atlas Lymphoid Neoplasm Diffuse Large B-cell Lymphoma; TCGA-GBM, The Cancer Genome Atlas Glioblastoma Multiforme; TCGA-KIRC, The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma; TCGA-LAML, The Cancer Genome Atlas Acute Myeloid Leukemia; TCGA-LIHC, The Cancer Genome Atlas Liver Hepatocellular Carcinoma; TCGA-OV, The Cancer Genome Atlas Ovarian Serous Cystadenocarcinoma; TCGA-PRAD, The Cancer Genome Atlas Prostate Adenocarcinoma; TCGA-SARC, The Cancer Genome Atlas Sarcoma; TCGA-SKCM, The Cancer Genome Atlas Skin Cutaneous Melanoma; TCGA-STAD, The Cancer Genome Atlas Stomach Adenocarcinoma; TCGA-UCEC, The Cancer Genome Atlas Uterine Corpus Endometrial Carcinoma; TCGA-LUSC, The Cancer Genome Atlas Lung Squamous Cell Carcinoma; TCGA-MESO, The Cancer Genome Atlas Mesothelioma; TCGA-LGG, The Cancer Genome Atlas Brain Lower Grade Glioma; TCGA-KICH, The Cancer Genome Atlas Kidney Chromophobe; TCGA-KIRP, The Cancer Genome Atlas Kidney Renal Papillary Cell Carcinoma; TCGA-CHOL, The Cancer Genome Atlas Cholangiocarcinoma; TCGA-ACC, The Cancer Genome Atlas Adrenocortical Carcinoma; TCGA-PCPG, The Cancer Genome Atlas Pheochromocytoma And Paraganglioma; TCGA-READ, The Cancer Genome Atlas Rectum Adenocarcinoma; TCGA-THYM, The Cancer Genome Atlas Thymoma; TCGA-TGCT, The Cancer Genome Atlas Testicular Germ Cell Tumors; TCGA-THCA, The Cancer Genome Atlas Thyroid carcinoma; TCGA-PAAD, The Cancer Genome Atlas Pancreatic Adenocarcinoma; HSC, hematopoietic stem cell.</p></fn></table-wrap-foot>", "<fn-group><fn id=\"d35e1747\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0125\" fn-type=\"supplementary-material\"><p id=\"p0185\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.09.001\" id=\"ir025\">https://doi.org/10.1016/j.gpb.2022.09.001</ext-link>.</p></fn></fn-group>" ]
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{ "acronym": [], "definition": [] }
124
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2024-01-14 23:41:59
Genomics Proteomics Bioinformatics. 2023 Aug 9; 21(4):678-694
oa_package/fe/e7/PMC10787194.tar.gz
PMC10787195
35952936
[ "<title>Introduction</title>", "<p id=\"p0005\">The genetic information is transmitted from DNA to RNA, and then to proteins. However, the correlation between mRNA abundance and protein expression level is far from linear, suggesting that the translation process plays an indispensable role in determining the output of proteins ##REF##21593866##[1]##. During protein synthesis, tRNAs decode the mRNA templates via codon–anticodon pairing and deliver the amino acids to the corresponding polypeptide chain in the ribosomes ##REF##21428957##[2]##. tRNAs are small non-coding RNAs, 70–90 nt in length, transcribed by RNA polymerase III (RNAPIII), and constitute 4%–10% of the total RNA in a cell ##REF##25534324##[3]##. Although there are only 20 amino acids and 64 codons, about 400 nuclear-derived tRNAs have been annotated in mammals (<italic>e.g.</italic>, 429 and 401 annotated tRNA genes in human and mouse genomes, respectively) in addition to 22 mitochondrial tRNAs (mt-tRNAs) ##REF##26673694##[4]##. tRNA transcripts that carry the same anticodons but different sequences are termed isodecoders ##REF##17088292##[5]##, while different tRNA species accepting the same amino acids are termed isoacceptors ##REF##25534324##[3]##. There are 49 and 47 isoacceptors annotated in human and mouse genomes, respectively ##REF##18984615##[6]##, ##REF##21873999##[7]##.</p>", "<p id=\"p0010\">In bacteria and yeast, the tRNA abundance correlates well with the codon usage of highly translated genes (HTGs) ##REF##10570992##[8]##, ##REF##8709146##[9]##, ##REF##3916708##[10]##. In mammals, the relationship between them is still in debate. Several studies have reported correlations between the tRNA abundance and codon usage. For example, Dittmar et al<italic>.</italic> reported that the tRNA abundance is significantly correlated with the codon usage of tissue-specific and highly expressed genes ##REF##17194224##[11]##. Gingold et al<italic>.</italic> found that tRNAs induced in proliferative cells or differentiated cells often decode codons enriched in mRNAs related to cell autonomy and multicellularity ##REF##25215487##[12]##. Waldman et al<italic>.</italic> reported better adaptation of tissue-specific genes with the tRNA pool when compared with non-specific genes ##REF##20097653##[13]##. Hernandez-Alias et al<italic>.</italic> reported that the tissue-specific tRNA pools determine the translational efficiency (TE) of proliferation-related genes ##REF##32149479##[14]##. Najafabadi et al<italic>.</italic> reported that the codon usage correlates with the TE of genes involved in adaptation to environmental and physiological changes ##REF##19773421##[15]##. However, other studies have reported that the correlations are poor. Sémon et al<italic>.</italic> reported that the significant differences in synonymous codon usages between tissues are not due to translational selection ##REF##16280544##[16]##. Kanaya et al<italic>.</italic> reported that the ribosome genes and histone genes show no difference in codon usage, implying no translational regulation through tRNAs ##REF##11675589##[17]##. Thus, it is unclear how tRNA expression profiles are correlated to the TE of specific transcripts.</p>", "<p id=\"p0015\">To address this issue, quantitative tRNA expression evaluation is desirable. However, due to the stable structure and diverse post-transcriptional modifications of tRNAs which interfere with reverse transcription efficiency and adaptor ligation, it has been difficult for standard sequencing methods to detect tRNA pools efficiently and quantitatively. Most studies have utilized microarrays or RNAPIII chromatin immunoprecipitation followed by sequencing (ChIP-seq) to identify tRNA transcriptomes. In recent years, more next-generation sequencing methods have been developed to measure the abundance of tRNAs ##REF##31486704##[18]##, ##REF##33859402##[19]##, ##REF##35032425##[20]##, ##REF##32796835##[21]##, ##REF##33581077##[22]##. However, none of these studies have compared the tRNA abundance with matched translatome data. Therefore, whether the dynamics of tRNA expression contribute to the establishment of tissue-specific translatomes in mammals has not been well addressed.</p>", "<p id=\"p0020\">Although still largely elusive, the regulation of tRNA expression can be possibly mediated by transcriptional and post-transcriptional mechanisms. On the one hand, the occupancy of RNAPIII as considered at the isoacceptor family level was invariant in multiple mammalian tissues ##REF##21873999##[7]##. On the other hand, the RNA modification and structure of tRNAs can regulate the ribonuclease-catalyzed degradation of tRNAs ##REF##33658722##[23]##, ##REF##32900285##[24]##, ##REF##28875994##[25]##. It was also reported that multiple tRNAs were degraded when histidine or leucine becomes limited, suggesting that the tRNA expression was also under post-transcriptional regulation ##REF##27903898##[26]##.</p>", "<p id=\"p0025\">In this study, to overcome the difficulty of measuring tRNA expression, we applied the demethylase-tRNA sequencing (DM-tRNA-seq) method developed by Zheng et al. ##REF##26214130##[27]## to evaluate the diversity of tRNA pools in three mouse tissues (brain, heart, and testis). The DM-tRNA-seq utilizes engineered demethylase AlkB to remove base methylation on tRNAs and can measure the tRNA transcriptome efficiently and quantitatively ##REF##26214130##[27]##. Meanwhile, we applied ribosome-tagging sequencing (RiboTag-seq) to capture the ribosome-associated mRNAs in the same mouse tissues ##REF##19666516##[28]##. We found various degrees of variations of tRNA expression at the isodecoder, isoacceptor, and amino acid isotype levels among different mouse tissues, suggesting the dynamic expression of tRNAs. We then found that the tRNA adaptation index (tAI) was significantly correlated with TE intra- but not inter-tissues. Our study suggests that the differential tRNA expression between tissues is not likely to contribute to tissue-specific translatomes, but may result from post-transcriptional regulation of tRNAs.</p>" ]
[ "<title>Materials and methods</title>", "<title>Animals</title>", "<p id=\"p0130\">Mice were maintained on a 12-h light/12-h dark cycle. The <italic>RiboTag</italic> mice (Stock No. 011029, Jackson Laboratory, Bar Harbor, ME) and <italic>CMV-Cre</italic> mice (Stock No. 006054, Jackson Laboratory, Bar Harbor, ME) were purchased from Jackson Laboratory. The <italic>RiboTag</italic> mice were bred to the <italic>CMV-Cre</italic> mice to obtain homozygous mice constitutively expressing <italic>Rpl22-HA</italic>. Once the model of <italic>Rpl22-HA</italic>-expressing homozygous mice was built successfully, we maintained the colony as a separate mouse line.</p>", "<title>Tissue sample preparation and RNA isolation</title>", "<p id=\"p0135\">All mouse tissue samples were isolated from adult male <italic>CMV-Cre:RiboTag</italic> mice using procedures approved by the Animal Research Committee of the First Affiliated Hospital, Sun Yat-sen University, China. Samples were rapidly frozen in liquid nitrogen and stored at −80 °C until use. Then, 1 ml of TRIzol (Catalog No. 15596026, Invitrogen, Carlsbad, CA) was added per 100 mg of dissected whole tissue, and samples were homogenized in TRIzol buffer with a homogenizer (Catalog No. 2010, Jingxin, Shanghai, China) until the suspension was completely homogeneous. Cell debris was removed by a high-speed centrifugation procedure. RNA was isolated according to the manufacturer’s instructions of TRIzol reagent, resuspended in nuclease-free water, and stored at −80 °C until DM-tRNA-seq.</p>", "<title>Recombinant protein purification</title>", "<p id=\"p0140\">Recombinant wild-type and D135S AlkB proteins were purified as previously described ##REF##31619810##[51]##. pET30a-AlkB and pET30a-AlkB-D135S were transformed into BL21 bacteria for induced expression of recombinant proteins. Bacteria were inoculated and cultured on lysogeny brothmedium (LB; Catalog No. ST156, Beyotime Biotechnology, Shanghai, China) at 37 °C. The expression of recombinant wild-type and D135S AlkB proteins was induced in BL21 bacteria (OD<sub>600</sub> = 0.6–0.7) using 0.5 mM isopropyl β-D-thiogalactoside (IPTG; Catalog No. I5502, Sigma, St. Louis, MO) at 20 °C overnight. Then the bacteria were collected and lysed by sonication, centrifuged at 15,000 r/min at 4 °C for 60 min. The supernatant was collected for the purification of recombinant proteins using Ni-NTA Agarose (Catalog No. 30210, Qiagen, Alameda, CA) following the manufacturer’s instructions and stored at −80 °C.</p>", "<title>DM-tRNA-seq</title>", "<p id=\"p0145\">DM-tRNA-seq was performed following the previously reported protocol ##REF##26214130##[27]##, ##REF##24831542##[47]## with some modifications. Small RNAs (&lt; 200 nt) were first purified using the Quick-RNA Microprep kit (Catalog No. R1050, Zymo Research, Orange, CA). Isolated small RNAs were treated with recombinant wild-type and D135S AlkB proteins to remove the dominant methylations on RNAs. Then, demethylated RNAs were purified with Oligo Clean &amp; Concentrator kit (Catalog No. D4060, Zymo Research). After that, AlkB-treated RNA libraries were constructed with NEBNext Small RNA Library Prep Set (Catalog No. E7330S, New England Biolabs, Ipswich, MA). The cDNA libraries were sequenced on Illumina HiSeq X10 with paired-end 2 × 150 bp read length.</p>", "<title>Western blot</title>", "<p id=\"p0150\">Tissue-specific lysates were extracted with radioimmunoprecipitation assay (RIPA) buffer by a homogenizer. Western blot assays were performed as described previously ##REF##30171794##[52]##. Nitrocellulose membranes were blocked using 5% Blotting Grade Blocker Non-Fat Dry Milk (Catalog No. 1706404XTU, Bio-Rad, Hercules, CA) and were then incubated with primary antibody at 4 °C overnight. For primary antibodies used were as follows: anti-HA tag (Catalog No. ab9110, Abcam, Cambridge, UK), anti-IgG (Catalog No. B900620, Proteintech, Wuhan, China), and anti-tubulin (Catalog No. 11224-1-AP, Proteintech). The blots were then incubated with horseradish peroxidase-conjugated secondary antibody (Catalog No. 7074, Cell Signaling Technology, Berkeley, CA) at room temperature for 1 h, and the proteins were then detected using the electrogenerated chemiluminescence (ECL) chemiluminescence system (Catalog No. 4600, Tanon, Shanghai, China).</p>", "<title>Polysome immunoprecipitation</title>", "<p id=\"p0155\">RiboTag immunoprecipitation was performed as previously described ##REF##31216392##[31]## with some modifications. Tissue samples were extracted from <italic>CMV-Cre:RiboTag</italic> mice, flash-frozen in liquid nitrogen, and stored at −80 °C until use. Tissues were homogenized in ice-cold homogenization buffer [50 mM Tris-HCl pH 7.4, 1% NP-40, 100 mM KCl, 12 mM MgCl<sub>2</sub>, 100 μg/ml cycloheximide (Catalog No. 66819, Sigma), 1:100 protease inhibitor cocktail (Catalog No. 4693116001, Roche, Mannheim, Germany), 1 mg/ml Heparin, 1 mM dithiothreitol (DTT), 200 U/ml RNasin (Catalog No. N2111, Promega, Madison, WI) in RNase-free water] with a homogenizer until the suspension was completely homogeneous. To remove cell debris, the homogenate was transferred to a microcentrifuge tube and centrifuged at 13,000 <italic>g</italic> at 4 °C for 15 min. Supernatants were transferred to a fresh microcentrifuge tube on ice, and then 70 μl was removed for input fraction analysis and 8 μl (8 µg) of anti-HA antibody was added to the supernatant, followed by 4 h of incubation with slow rotation in a cold room at 4 °C. Meanwhile, Pierce Protein A/G Magnetic Beads (Catalog No. 88803, ThermoFisher Scientific, Waltham, MA), 80 μl per sample, were equilibrated to homogenization buffer by washing three times. At the end of 4 h of incubation with antibody, beads were added to each sample, followed by incubation overnight at 4 °C. The following day, samples were placed in a magnet on ice, and supernatants were recovered before washing the pellets three times for 10 min in high salt buffer (50 mM Tris-HCl pH 7.4, 1% NP-40, 300 mM KCl, 12 mM MgCl<sub>2</sub>, 100 μg/ml cycloheximide, 1 mM DTT). At the end of the washes, beads were magnetized and excess buffer was removed. To prepare total RNA, 5 volumes of Qiagen RLT buffer (Catalog No. 79216, Qiagen) were added to the remaining pellets or the input samples. Total RNA was prepared according to the manufacturer’s instructions using RNeasy Mini Kit (Catalog No. 74104, Qiagen), quantified with a NanoDrop 2000 spectrophotometer (Catalog No. ND2000USCAN, ThermoFisher Scientific), and taken for RNA sequencing (RNA-seq). For high-throughput sequencing, both input and IP samples were used for library construction with the SMARTer Stranded Total RNA-seq Kit v2 (Catalog No. 635005, Takara, Dalian, China), and single-end 50-base reads were generated on the BGISEQ500 platform.</p>", "<title>Processing of high-throughput sequencing data</title>", "<p id=\"p0160\">The nuclear tRNA and mt-tRNA reference sequences were downloaded from GtRNAdb ##REF##26673694##[4]## and mt-RNA database mitotRNAdb ##REF##18957446##[29]##, respectively. Nuclear tRNAs and mt-tRNAs with unique sequences generated by collapsing the identical tRNAs were merged and used as the reference for downstream mapping. DM-tRNA-seq raw reads were first processed using Cutadapt (v1.18) to remove adaptor sequences and 3′-CCA sequences, and to discard reads shorter than 25 nt. Then, Bowtie2 (v2.3.5) ##REF##22388286##[53]## was used to align the adaptor-trimmed and filtered reads to the tRNA reference sequences of the mouse genome (mm10) with the parameters: --min-score G,1,8 --local -D 20 -R 3 -N 1 -L 10 -I S,1,0.5. Only reads with unique hits and mapping quality &gt; 10 were considered for further analysis. The RPMs of isodecoders were calculated by multiplying the number of reads mapped to the gene by 1 × 10<sup>6</sup> and dividing it by the total number of mapped reads. The anticodon-level or amino acid-level counts were calculated by summing up the counts of isodecoders with the same anticodons or encoding the same amino acids. tRNA-seq read count tables at both the anticodon level and isodecoder level were used to perform differential tRNA expression analysis between each two of the three mouse tissues using the DESeq2 ##REF##20979621##[30]##. Differentially expressed tRNAs were determined by requiring FDR &lt; 0.05 between any two tissues. The same pipeline was also applied to the public data of PANDORA-seq ##REF##33820973##[49]## and CPA-seq ##REF##33867522##[50]## to calculate the total RPM of tsRNA derived from each tRNA isodecoder.</p>", "<p id=\"p0165\">RiboTag-seq raw reads were first mapped to rRNA reference sequences using Bowtie2 (v2.3.5). Reads that were mapped to rRNAs were discarded. The remaining reads were then mapped to the mouse genome (mm10) using STAR (v2.7.5). Only uniquely mapped reads were considered for further analysis. Gene expression was calculated using StringTie v1.3.5.</p>", "<title>Metric definition</title>", "<p id=\"p0170\">Codon index was defined to measure the usage of the <italic>i-</italic>th codon and calculated as follows:</p>", "<p id=\"p0175\">Here, <italic>x<sub>ij</sub></italic> denotes the number of occurrences of the <italic>i-</italic>th codon in the <italic>j-</italic>th gene, <italic>IP FPKM<sub>j</sub></italic> denotes the FPKM value of the <italic>j-</italic>th gene in IP of RiboTag-seq, <italic>n</italic> denotes the number of codons, and <italic>m</italic> denotes the number of genes.</p>", "<p id=\"p0180\">RSCU was defined by modifying the previously defined RSCU by Sharp et al. ##REF##3526280##[32]## with IP FPKM as the weight of each gene. It was calculated for the <italic>j-</italic>th codon for the <italic>i-</italic>th amino acid as follows:</p>", "<p id=\"p0185\">Here, <italic>n<sub>i</sub></italic> denotes the number of the synonymous codon for the <italic>i-</italic>th amino acid, <italic>x<sub>ijk</sub></italic> denotes the number of occurrences of the <italic>j-</italic>th codon for the <italic>i-</italic>th amino acid in the <italic>k-</italic>th gene, <italic>m</italic> denotes the number of genes, and <italic>IP FPKM<sub>k</sub></italic> denotes the FPKM value of the <italic>k-</italic>th gene in IP of RiboTag-seq.</p>", "<p id=\"p0190\">RSAU was calculated for the <italic>j-</italic>th anticodon for the <italic>i-</italic>th amino acid as follows:</p>", "<p id=\"p0195\">Here, <italic>n<sub>i</sub></italic> denotes the number of the anticodon for the <italic>i-</italic>th amino acid, and <italic>x<sub>ij</sub></italic> denotes the RPM of the <italic>j-</italic>th anticodon for the <italic>i-</italic>th amino acid.</p>", "<p id=\"p0200\">RSIU was calculated for the <italic>j-</italic>th isodecoder for the <italic>i-</italic>th anticodon as follows:</p>", "<p id=\"p0205\">Here, <italic>n<sub>i</sub></italic> denotes the number of the isodecoders for the <italic>i</italic>-th anticodon, and <italic>x<sub>ij</sub></italic> denotes the RPM of the <italic>j</italic>-th isodecoder for the <italic>i-</italic>th anticodon.</p>", "<p id=\"p0210\">Amino acid composition was calculated for the <italic>i-</italic>th amino acid as follows:</p>", "<p id=\"p0215\">Here, <italic>n<sub>i</sub></italic> denotes the number of codons encoding the <italic>i-</italic>th amino acid for the <italic>j-</italic>th gene, <italic>IP FPKM<sub>j</sub></italic> denotes the FPKM value of the <italic>j-</italic>th gene in IP of RiboTag-seq, and <italic>m</italic> denotes the number of genes used in the calculation.</p>", "<title>tRNA and translatome analyses</title>", "<p id=\"p0220\">Permutation was performed by randomly switching the anticodons of the isodecoders and regrouping them into anticodons according to the permutated anticodons. We compared the mean CVs of anticodon expression, RSAU values, and tRNA isotype expression with 10,000 times of permutations. The <italic>P</italic> values of permutation analyses were determined by calculating the fraction of the RSAU values of permutations greater (isoacceptor expression, isotype expression) or less (RSAU) than the observed data.</p>", "<p id=\"p0225\">TEs were calculated as the ratios between the FPKMs of IPs and the inputs of RiboTag-seq. Only the genes with FPKM &gt; 1 in both input and IP samples were used in the downstream analyses. RSCU values were calculated as previously described by Sharp et al<italic>.</italic>\n##REF##3526280##[32]## based on the top 5% HTGs. The coding region of the longest coding isoform of each gene was used for codon analyses. For comparison, RSCU values based on randomly sampled 5% genes with FPKM &gt; 1 in both input and IP samples were also calculated. Significance was determined by Wilcoxon signed-rank test.</p>", "<p id=\"p0230\">tAI was calculated by R package tAI ##REF##15448185##[36]##. tAIs using different tRNA pools were calculated for genes with the top 5%, medium 5%, and bottom 5% of TEs. The significance between them was based on Wilcoxon signed-rank test. Data visualization and plotting were performed using ggplot2, ggrepel, and ggforce R packages.</p>", "<p id=\"p0235\">The correlation analyses between isoacceptor abundances and the codon compositions of the top 5% HTGs of each tissue were based on the general codon–anticodon recognition rules for tRNA genes ##REF##15448185##[36]##. Codons recognized by multiple anticodons as well as anticodons that recognize multiple codons were repeated to form one-to-one codon–anticodon pairs.</p>" ]
[ "<title>Results</title>", "<title>Dynamic expression of tRNA isodecoders among different mouse tissues</title>", "<p id=\"p0030\">In order to systematically elucidate the tissue specificity of tRNA expression, we obtained total RNA samples from three tissues (brain, heart, and testis) of adult male <italic>CMV-Cre:RiboTag</italic> mice, and generated tRNA libraries for DM-tRNA-seq with two biological replicates (##FIG##0##Figure 1##A). The reads per million mapped reads (RPM) was calculated for each tRNA annotated in genomic tRNA database GtRNAdb ##REF##26673694##[4]## and mt-tRNA database mitotRNAdb ##REF##18957446##[29]## (<xref rid=\"s0125\" ref-type=\"sec\">Figure S1</xref>; <xref rid=\"s0125\" ref-type=\"sec\">Table S1</xref>). As shown in ##FIG##0##Figure 1##B, the biological replicates of the same tissues were highly similar to each other and clustered together, suggesting tissue-specific expression of tRNAs. We noted that the tRNA expression pattern of the brain tissue is less reproducible than that of the heart and testis, possibly reflecting the higher cell heterogeneity of the brain. In addition, we found that mt-tRNAs accounted for 11.1% of the total detected tRNAs in the testis but 64.4% in the heart and 38.9% in the brain, which is consistent with the orders of energy demands in these tissues (##FIG##0##Figure 1##C). Since the dynamics of mt-tRNA contents are more likely to reflect the dynamics of the number of mitochondria in the cells, we focused on the dynamics of cytosolic tRNAs (ct-tRNAs), which may relate to the translational regulation of nuclear-derived genes.</p>", "<p id=\"p0035\">Differential expression analysis of tRNA isodecoders was performed on three tissues using DESeq2 ##REF##20979621##[30]##. Among the 224 detected tRNA isodecoders with unique sequences, 131 (58%) of them had significantly differential expression [false discovery rate (FDR) &lt; 0.05] across the three tissues (##FIG##0##Figure 1##D). To further elucidate the potential role of expression regulation of tRNA isodecoders on translation, we defined a metric, relative synonymous isodecoder usage (RSIU), to analyze the usage bias of synonymous isodecoders with the same anticodons (details in Materials and methods). As shown in ##FIG##0##Figure 1##E, we observed remarkable differences in the RSIU values among the tissues, and 36 of the 224 isodecoders showed more than 2-fold higher RSIU values in one tissue than those in the other two tissues. For example, the RSIU value of isodecoder Gly-CCC-4-1 in the testis was 6.9 and 4.5 folds of that in the heart and brain, respectively.</p>", "<title>Tissue-specific expression of isodecoders results in tissue-specific expression rather than tissue-specific usage bias of anticodons</title>", "<p id=\"p0040\">To assess tRNA expression at the anticodon level, the 224 ct-tRNAs identified by DM-tRNA-seq were separated into 51 groups, including 47 isoacceptors with unique anticodons as well as 4 special tRNA groups (tRNA-SeC-TCA, tRNA-Sup-TTA, tRNA-Sup-TCA, and tRNA-iMet-CAT). The expression heatmap of these 51 tRNA groups demonstrated the differential expression across the three tissues (##FIG##1##Figure 2##A). We found that the samples of the same tissues were clustered together according to the expression of the 51 tRNA groups, suggesting tissue-specific expression of anticodons (##FIG##1##Figure 2##A and B). Of note, we realized that the coefficient of variations (CVs) of the expression of the 47 isoacceptors among tissues were significantly smaller than those of isodecoders (##FIG##1##Figure 2##C), consistent with the recent study reporting a milder difference in isoacceptor expression among tissues ##REF##32796835##[21]##. To validate our results, we also compared the CVs of isoacceptors and isodecoders using one published tRNA dataset examined by a different technology QuantM-tRNA seq ##REF##32796835##[21]##. Similarly, we observed greatly reduced CVs of the expression of isoacceptors than isodecoders (<xref rid=\"s0125\" ref-type=\"sec\">Figure S2</xref>A). To test whether the relatively small variations of isoacceptor expression were due to genuinely tissue-specific expression of anticodons, we calculated the expression of isoacceptors using QuantM-tRNA seq data. Based on the heatmap of <italic>Z</italic>-score transformed expression of isoacceptors, we found reproducible tissue-specific isoacceptor expression, although different regions of brain were not largely distinct from each other (<xref rid=\"s0125\" ref-type=\"sec\">Figure S2</xref>B), which is consistent with our results using DM-tRNA-seq, suggesting the tissue-specific expression of isoacceptors.</p>", "<p id=\"p0045\">Then we asked why the CVs of isoacceptors were smaller than isodecoders. We suspected that averaging the subgroups of isodecoders would reduce variations due to statistical principles. We therefore asked whether the reduced variations of isoacceptors among tissues were simply statistically due to the random combinations of isodecoders. For this purpose, we performed permutation analyses by randomly permutating anticodon of the isodecoders and regrouped them into isoacceptors according to the permutated anticodon. We found that the observed mean CV of the isoacceptors among tissues was greater than 86% of 10,000 permutations, indicating a non-significant difference (##FIG##1##Figure 2##D). The results suggest that the dynamic expression of isoacceptors is simply a reflection of the dynamic expression of isodecoders. In other words, although not so remarkable, the dynamic expression of isoacceptors is genuine.</p>", "<p id=\"p0050\">We then turned to uncover the relationships among the expression levels of the isodecoders. We calculated the Pearson correlation coefficient (PCC) of any two isodecoders across all six samples (##FIG##1##Figure 2##E). The PCCs of isodecoder pairs encoding different amino acids, which are the most unrelated isodecoders, were around 0, suggesting that the unrelated isodecoders are independently regulated. Interestingly, we found that the PCCs between the isodecoder pairs with different anticodons but encoding the same amino acids were significantly greater than those of isodecoder pairs encoding different amino acids. In addition, the isodecoder pairs with the same anticodons turned out to have the highest PCCs. To confirm, we performed the same analyses using the published dataset of tRNA expression in multiple mouse tissues based on a different tRNA sequencing technology QuantM-tRNA seq ##REF##32796835##[21]##. We observed similar results that the isodecoder pairs with the same anticodons and the pairs with different anticodons but encoding the same amino acids were almost equal and both had significantly greater PCCs than the unrelated pairs (<xref rid=\"s0125\" ref-type=\"sec\">Figure S2</xref>C). These results suggest that functionally related isoacceptors do not randomly fluctuate among different tissues but are associated and possibly co-regulated across different tissues, especially at the amino acid level.</p>", "<p id=\"p0055\">Nevertheless, it is an interesting question whether the tissue-specific expression of isoacceptors results in tissue-specific usage bias of tRNA anticodons encoding the same amino acids, which would subsequently lead to differential TEs in different tissues. To address this question, we calculated the relative synonymous anticodon usage (RSAU) values according to the expression of anticodons in the three tissues, respectively (details in Materials and methods). We found that the overall variations of RSAU values across tissues were much lower than RSIU values (##FIG##0##Figures 1##E and ##FIG##1##2##F). We further found that the CVs of RSAU values among three tissues were significantly smaller than random permutations (##FIG##1##Figure 2##G). The mean CVs of permutated RSAU values greater than the mean of observed CV could be obtained 9957 times out of 10,000 permutations, suggesting that the variations of RSAU values among different tissues are prohibited. The aforementioned results demonstrate that the distinctive expression of tRNA isoacceptors does not play a vital role in selecting specific synonymous anticodons or determining the TEs in different tissues.</p>", "<p id=\"p0060\">Because the isodecoders encoding the same amino acids tend to be co-regulated, we speculated that the diversity of tRNA pools is most likely to match the amino acid composition within specific physiological states during the translation process. We then tested whether the tRNA isotype expression at amino acid level also had tissue specificity by combing the tRNAs encoding the same amino acids. As shown in ##FIG##2##Figure 3##A and B, there is obvious tissue-specific tRNA isotype expression. In addition, the mean CV of isotype expression across these three tissues is greater than all 10,000 permutations, suggesting that there is genuine tissue-specific isotype expression (##FIG##2##Figure 3##C and D). These results together with the aforementioned results imply that the dynamic regulation of tRNAs among tissues is more likely a reflection of tissue-specific needs of tRNAs encoding specific amino acids rather than optimizing the codon usages for efficient translation.</p>", "<title>RiboTag-seq analysis of translatomes in multiple mouse tissues</title>", "<p id=\"p0065\">To further elucidate whether dynamic tRNA expression contributes to the establishment of tissue-specific translatomes, we performed RiboTag-seq in the same samples that were applied to DM-tRNA-seq. The RiboTag-seq technology takes advantage of RPL22, a component of the 60S subunit of ribosome, to capture the actively translating ribosomes (##FIG##3##Figure 4##A). The expression of RPL22-HA protein can be activated by Cre recombinase-mediated replacement of exon 4 with an HA-tagged exon 4 of <italic>Rpl22</italic>\n##REF##31216392##[31]##. To create a line of mice constitutively expressing RPL22-HA protein in multiple tissues, <italic>RiboTag</italic> mice were mated with <italic>CMV-Cre</italic> mice (##FIG##3##Figure 4##B). We validated the heterozygous <italic>CMV-Cre</italic> and homozygous <italic>Rpl22-HA</italic> alleles in the genomes of offspring, and confirmed the expression of RPL22-HA protein in homogenate of multiple tissues, followed by efficient immunoprecipitating (##FIG##3##Figure 4##C, <xref rid=\"s0125\" ref-type=\"sec\">Figure S3</xref>A–C).</p>", "<p id=\"p0070\">Since RiboTag-seq only sequenced the RNAs bound by the translation factor RPL22, we calculated the translation levels, which were represented by the gene expression levels of immunoprecipitation RNAs (IP), as well as TEs, which were the translation levels normalized by the expression of input RNAs (<xref rid=\"s0125\" ref-type=\"sec\">Figure S1</xref>; <xref rid=\"s0125\" ref-type=\"sec\">Table S2</xref>). Strong tissue-specific gene expression as well as TEs were observed (##FIG##3##Figure 4##D and E). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the HTGs (top 5%) revealed enrichment for tissue development or tissue physiology-related processes and pathways (<xref rid=\"s0125\" ref-type=\"sec\">Figure S4</xref>A–C). We then asked whether the composition of codons was different among these tissues. For this purpose, we defined a metric of codon index (details in Materials and methods), which is the proportion of specific codons in all of the top 5% HTGs weighted by the translation level of each gene. As shown in ##FIG##3##Figure 4##F, there are distinctive codon indexes among the three tissues, suggesting that it might be necessary for tissue-specific tRNA pools. To test whether the usage biases of synonymous codons also differ among tissues, for each codon, we modified the previously defined metric relative synonymous codon usage (RSCU) ##REF##3526280##[32]## by adding IP fragments per kilobase per million mapped of fragments (FPKM) as the weight of each gene, which is the observed IP FPKM weighted frequency of specific codon divided by the frequency expected under the assumption of equal usage of the synonymous codons. Based on the top 5% HTGs of each tissue, we found moderate differences among the brain, heart, and testis (##FIG##3##Figure 4##G). However, the CVs of RSCU values among the three tissues based on the top 5% HTGs were still significantly higher than the CVs based on randomly sampled 5% genes, suggesting that codon usage biases of HTGs are truly differential among tissues (##FIG##3##Figure 4##H).</p>", "<title>tRNA pools adapt better to HTGs in the same tissues but not to tissue-specifically translated genes</title>", "<p id=\"p0075\">The more accurate interaction analysis between mRNAs and cognate tRNAs will provide a pivotal way for evaluating effective and accurate translation ##REF##30451861##[33]##, ##REF##25921436##[34]##. To further elucidate the intrinsic relationship between tRNA expression and mRNA translation, we integrated the data of tissue-specific DM-tRNA-seq and RiboTag-seq to comprehensively uncover the correlation between tRNA pools and codon usage bias in HTGs. The adaptation of a specific gene to a specific tRNA pool in terms of codon usage bias can be well evaluated using a widely used metric tAI ##REF##3547335##[35]##, ##REF##15448185##[36]##. We found that the HTGs had significantly higher tAI values than the moderately translated genes (MTGs) and lowly translated genes (LTGs) in all the three tissues based on the tRNA pools of the corresponding tissues (##FIG##4##Figure 5##A), suggesting the role of tRNAs in regulating translation in the same tissues. However, when we tested the tAI values of HTGs with the tRNA pools from other tissues, we found that the HTGs did not show the highest tAI values based on the tRNA pools of the same tissues. Instead, the tRNA pool of heart had the best adaptation with the HTGs of all tissues (##FIG##4##Figure 5##B). In addition, we performed the correlation analysis between isoacceptor abundances and the codon compositions of the top 5% HTGs of each tissue based on the general codon–anticodon recognition rules for tRNA genes ##REF##15448185##[36]##. Similar to the tAI analyses, we found significant correlations in both the heart and testis but not between tissues (<xref rid=\"s0125\" ref-type=\"sec\">Figure S5</xref>A and B). The aforementioned results suggest that although HTGs require more optimal tRNA pools in each tissue, the tissue-specific regulation of tRNA expression is not for the purpose of better adapting the tissue-specific usage biases of synonymous codons. In other words, mammals are not likely to regulate tissue-specific translation of certain genes through regulating the compositions of tRNA pools, which is consistent with the observation that the usage biases of anticodons do not show significant differences among different tissues (##FIG##1##Figure 2##G).</p>", "<title>tRNA expression correlates with amino acid composition in the same tissues but not between tissues</title>", "<p id=\"p0080\">The analyses of tRNA expression across diverse tissues revealed that isodecoders encoding the same amino acids are likely co-regulated, suggesting that the dynamics of tRNA expression in different tissues might be related with different amino acid compositions of peptides in different tissues. To test this hypothesis, we first tested whether the amino acid compositions are different across the translatomes of different tissues. We calculated each amino acid composition by summing up the number of codons encoding the amino acid of the top 5% HTGs weighted by the translation level (FPKM of IP). As shown in ##FIG##5##Figure 6##A, we observed reproducible tissue-specific amino acid compositions, which is consistent with our observations that the tRNA isotype expression is tissue-specific (##FIG##2##Figure 3##A). We also found a positive correlation between the amino acid composition and the tRNA isotype expression in heart (<italic>P</italic> = 0.023), and trends of positive correlations in brain (<italic>P</italic> = 0.067) and testis (<italic>P</italic> = 0.11), respectively (##FIG##5##Figure 6##B). To further address whether the tissue-specific tRNA expression is related to the tissue-specific amino acid compositions of peptides, we tested the correlation of amino acid compositions subtracted by the means with the <italic>Z</italic>-scores of tRNA isotype expression among the three tissues. We observed a non-significant correlation between them (##FIG##5##Figure 6##C). Non-significant correlations were also observed when we compared the differences of amino acid compositions and the differences of tRNA isotype expression between any two tissues (<xref rid=\"s0125\" ref-type=\"sec\">Figure S6</xref>A and B).</p>", "<p id=\"p0085\">We found that the isodecoders encoding the same amino acid were co-regulated across different tissues (##FIG##1##Figure 2##E). Based on the aforementioned results, this co-regulation is not likely due to active regulatory mechanisms to control the translatomes in a tissue-specific manner. On the contrary, it might be due to post-transcriptional regulation of tRNAs, such as tRNA modifications and aminoacylation, the attachment of amino acids to tRNAs.</p>" ]
[ "<title>Discussion</title>", "<p id=\"p0090\">Although it is well known that tRNAs play a vital role in the synthesis of protein, whether the tRNA pool correlates well with TE is obscure. Here, based on multiple measurements of tRNAs and translatomes in multiple mouse tissues, we confirmed genuinely dynamic expression of tRNA isodecoder pools as well as isoacceptors among three mouse tissues. Meanwhile, the tRNA pools are significantly correlated with TEs and amino acid compositions of the HTGs in the same tissues but not between tissues. We finally propose that the tissue-specific expression of tRNA may be due to post-transcriptional regulation.</p>", "<p id=\"p0095\">Interestingly, tRNA expression is significantly correlated with TE in the same tissues but not between different tissues. Consistently, several studies have reported that tRNA–codon bias co-adaptation is not tissue-specific but globally driven ##REF##20097653##[13]##, ##REF##16418745##[37]##. These results together suggest the organisms may not regulate the translation of specific genes tissue-specifically through regulating tRNA expression, probably due to the difficulty of achieving precise adjustment through the regulation of tRNA expression. Nevertheless, we cannot rule out that there may be a weak correlation to be revealed and more accurate detection methods need to be developed in the future.</p>", "<p id=\"p0100\">It has advantages of using RiboTag-seq to measure the TEs in this study. In contrast to ribosome profiling (Ribo-seq), which measures the translation through obtaining the mRNA fragments protected by ribosomes ##REF##19213877##[38]##, the RiboTag-seq takes advantage of RPL22, a component of the 60S subunit of the ribosome, to pull down the mRNAs involved in translation elongation. In principle, Ribo-seq has difficulty in distinguishing the large and small ribosome subunits, and thus cannot distinguish translation initiation and elongation. In contrast, RiboTag-seq captures full-length mRNAs bound by actively translating polysomes, thus providing a more specific measurement of translation elongation. Since translation initiation and elongation may relate to TE in different manners ##REF##32821926##[39]##, RiboTag-seq overcomes the drawback of Ribo-seq. In addition, considering that we have found a significant correlation between tAI and TE, the RiboTag-seq technology used in this study is reliable in representing the translatome ##REF##19666516##[28]##.</p>", "<p id=\"p0105\">In this study, we hypothesize that the difference of tRNA between tissues is due to passive post-transcriptional regulation during the process of tRNA maturation. First, we found that the isodecoders encoding the same amino acid are co-regulated. Second, there is no difference of RNAPIII binding on tRNA genes at the isoacceptor level among tissues ##REF##21873999##[7]##, suggesting that differences in tRNA may be related to post-transcriptional regulation. In addition, it was reported that in <italic>Escherichia coli</italic>, tRNA can be destabilized and degraded in the case of amino acid starvation and upon the demand for protein synthesis decreases, suggesting that the content of tRNA is related to the concentration of the free amino acids ##REF##27903898##[26]##. Meanwhile, several groups have found that certain amino acids such as cysteine ##REF##12456664##[40]##, glycine ##REF##32859890##[41]##, serine ##REF##29390138##[42]##, and threonyl ##REF##28272317##[43]## have key impacts on the modifications of tRNAs, and some modifications of tRNA will further affect tRNA abundances ##REF##16387656##[44]##, ##REF##20459084##[45]##. Therefore, post-transcriptional regulation of tRNAs may also contribute to the tissue-specific expression of tRNAs and translatomes. This manner of tRNA regulation passively fine-tunes the tRNA expression in a tissue-specific manner but not for the purpose of regulating the translatomes.</p>", "<p id=\"p0110\">One possible post-transcriptional regulation that may result in tRNA differences between tissues is through the aminoacylation process, which might be regulated by free amino acid concentrations and the activities of aminoacyl-tRNA synthetases (aaRSs). The activities of aaRSs are dynamic ##REF##30588513##[46]##. Mammals have 20 cytosolic aaRSs, which are the enzymes that attach amino acids to tRNAs and thus allow tRNA molecules to act as adaptors to decode mRNAs. Individual tRNA isotype is aminoacylated by a specific aaRS. The aminoacylated tRNA is captured by a translation elongation factor and it is delivered to the ribosome for protein synthesis. The expression of tRNA isotypes and free amino acid concentrations may affect the levels of aminoacyl-tRNAs, which in turn may have positive or negative feedback on the early processing steps of tRNAs or affect the stability of tRNAs in a tissue-specific manner, thus leading to the observed dynamic expression of tRNAs.</p>", "<p id=\"p0115\">Another post-transcriptional regulation that may result in tRNA differences between tissues is through tRNA modification. tRNAs are the most generally modified RNA species in cells. Eukaryotic tRNAs contain an average of 13 modified bases per molecule. Modifications occurring in the anticodon loop are essential to regulate mRNA decoding, while modifications outside of the anticodon loop are vital to regulate tRNA stability, tRNA localization, and tRNA folding ##REF##33658722##[23]##. Dynamic variations at the levels of tRNA modifications play important roles in regulating the TEs and translation accuracies of particular genes that rely on the codon usages. However, the profiling of tissue-specific tRNA modification is still lacking. In the future, the development of novel large-scale methods to reveal the tRNA modification level can point the light way to understand the diverse function of tRNAs during translation process.</p>", "<p id=\"p0120\">Since it is known that DM-tRNA-seq can also generate a large fraction of incomplete tRNA reads due to the incomplete erasure of the modifications on tRNAs ##REF##33581077##[22]##, the difference of tRNA read length also reflects the differences of modifications. According to the percent of reads with length &gt; 40 bp, we found the proportions are quite similar between different tissues but the proportion of mt-tRNAs is larger than ct-tRNAs (<xref rid=\"s0125\" ref-type=\"sec\">Figure S7</xref>). This result is consistent with the previous report that ct-tRNAs and mt-tRNAs are modified differently. mt-tRNAs of higher eukaryotes have smaller and shorter stem and loop regions than those of ct-tRNAs ##REF##33658722##[23]##. Modifications in mt-tRNAs are less diverse comparing with ct-tRNAs ##REF##32859890##[41]##, ##REF##24831542##[47]##. m<sup>1</sup>A9 and m<sup>2</sup>G10 are considerably abundant modifications identified in mt-tRNA species ##REF##32859890##[41]##, which can be removed by AlkB demethylases ##REF##26214130##[27]## and result in longer mt-tRNAs reads in DM-tRNA-seq.</p>", "<p id=\"p0125\">In addition, tRNA modifications also contribute to different biogenesis of tRNA-derived small RNAs (tsRNAs), which are known to regulate translation in versatile ways ##REF##34053843##[48]##. Based on the expression of tsRNAs in the brain, heart, and testis examined by the PANDORA-seq ##REF##33820973##[49]## and CPA-seq ##REF##33867522##[50]##, we found the expression of tsRNAs was significantly and positively correlated with the expression of tRNAs in the same tissues and between different tissues (<xref rid=\"s0125\" ref-type=\"sec\">Figure S8</xref>A and B). The results suggest that tissue-specific expression of tRNA might be related to tsRNAs. It is possible that there might be unknown mechanisms that dynamically regulate the expression of tRNAs in different tissues in order to dynamically generate tsRNA in different tissues.</p>" ]
[]
[ "<p id=\"np010\">Equal contribution.</p>", "<p>Although the function of tRNAs in the translational process is well established, it remains controversial whether tRNA abundance is tightly associated with <bold>translational efficiency</bold> (TE) in mammals. Moreover, how critically the expression of tRNAs contributes to the establishment of <bold>tissue-specific</bold> proteomes in mammals has not been well addressed. Here, we measured both <bold>tRNA expression</bold> using demethylase-tRNA sequencing (DM-tRNA-seq) and TE of mRNAs using ribosome-tagging sequencing (RiboTag-seq) in the brain, heart, and testis of mice. Remarkable variation in the expression of tRNA isodecoders was observed among different tissues. When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons, we observed an expected reduction in the variation of anticodon expression across all samples, an unexpected smaller variation of anticodon usage bias, and an unexpected larger variation of tRNA isotype expression at amino acid level. Regardless of whether or not they share the same anticodons, the isodecoders encoding the same amino acids are co-expressed across different tissues. Based on the expression of tRNAs and the TE of mRNAs, we find that the tRNA adaptation index (tAI) and TE are significantly correlated in the same tissues but not between tissues; and tRNA expression and the <bold>amino acid composition</bold> of translating peptides are positively correlated in the same tissues but not between tissues. We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms. This study provides a resource for tRNA and translation studies, as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.</p>", "<title>Keywords</title>", "<p id=\"ms005\">Handled by Chengqi Yi</p>" ]
[ "<title>Ethical statement</title>", "<p id=\"p0240\">Animal experiments were licensed with the Approval No. SYSU-IACUC-2021-000089 and performed in agreement with the guidelines of the Animal Research Committee of the First Affiliated Hospital, Sun Yat-sen University, China.</p>", "<title>Code availability</title>", "<p id=\"p0245\">Source codes used for processing and analyzing the DM-tRNA-seq and RiboTag-seq data have been submitted to BioCode at the National Genomics Data Center (NGDC), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS) / China National Center for Bioinformation (CNCB) (BioCode: BT007304), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/biocode/tools/BT007304\" id=\"ir005\">https://ngdc.cncb.ac.cn/biocode/tools/BT007304</ext-link>.</p>", "<title>Data availability</title>", "<p id=\"p0250\">The raw sequencing data of DM-tRNA-seq and RiboTag-seq in this study have been deposited in the Genome Sequence Archive ##REF##34400360##[54]## at the NGDC, BIG, CAS / CNCB (GSA: CRA005907), and are publicly accessible at <ext-link ext-link-type=\"uri\" xlink:href=\"https://ngdc.cncb.ac.cn/gsa\" id=\"ir010\">https://ngdc.cncb.ac.cn/gsa</ext-link>.</p>", "<title>Competing interests</title>", "<p id=\"p0255\">The authors have declared no competing interests.</p>", "<title>CRediT authorship contribution statement</title>", "<p id=\"p0260\"><bold>Peng Yu:</bold> Methodology, Validation, Visualization, Writing – original draft. <bold>Siting Zhou:</bold> Software, Formal analysis, Visualization, Writing – original draft. <bold>Yan Gao:</bold> Investigation, Funding acquisition. <bold>Yu Liang:</bold> Investigation. <bold>Wenbing Guo:</bold> Formal analysis. <bold>Dan Ohtan Wang:</bold> Writing – review &amp; editing. <bold>Shuaiwen Ding:</bold> Writing – review &amp; editing. <bold>Shuibin Lin:</bold> Conceptualization, Writing – review &amp; editing, Supervision, Project administration, Funding acquisition. <bold>Jinkai Wang:</bold> Conceptualization, Writing – review &amp; editing, Supervision, Project administration, Funding acquisition. <bold>Yixian Cun:</bold> Conceptualization, Writing – review &amp; editing, Supervision, Project administration. All authors have read and approved the final manuscript.</p>" ]
[ "<title>Supplementary material</title>", "<p id=\"p0275\">The following are the Supplementary material to this article:</p>", "<p id=\"p0280\">\n\n</p>", "<p id=\"p0285\">\n\n</p>", "<p id=\"p0290\">\n\n</p>", "<p id=\"p0295\">\n\n</p>", "<p id=\"p0300\">\n\n</p>", "<p id=\"p0305\">\n\n</p>", "<p id=\"p0310\">\n\n</p>", "<p id=\"p0315\">\n\n</p>", "<p id=\"p0320\">\n\n</p>", "<title>Acknowledgments</title>", "<p id=\"p0265\">We are grateful to Prof. Jianrong Yang for his constructive discussion and comments. This work was supported by the <funding-source id=\"gp005\">National Key R&amp;D Program of China</funding-source> (Grant No. 2018YFA0107200 to Jinkai Wang), the <funding-source id=\"gp010\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100001809</institution-id><institution>National Natural Science Foundation of China</institution></institution-wrap></funding-source> (Grant Nos. 31970594 and 31771446 to Jinkai Wang; Grant Nos. 81922052 and 81974435 to Shuibin Lin; Grant No. 31971335 to Dan Ohtan Wang), the <funding-source id=\"gp015\">Natural Science Foundation of Guangdong, China</funding-source> (Grant No. 2019B151502011 to Shuibin Lin; Grant No. 2021A1515110650 to Yan Gao), and the <funding-source id=\"gp020\"><institution-wrap><institution-id institution-id-type=\"doi\">10.13039/501100002858</institution-id><institution>China Postdoctoral Science Foundation</institution></institution-wrap></funding-source> (Grant No. 2021M703755 to Yan Gao).</p>" ]
[ "<fig id=\"f0005\"><label>Figure 1</label><caption><p><bold>Dynamic expression of tRNA isodecoders among different mouse tissues</bold></p><p><bold>A.</bold> Schematic representation of DM-tRNA-seq based on AlkB demethylation. <bold>B.</bold> Heatmap of pairwise PCCs of tRNA isodecoder expression among the six samples of the three mouse tissues. <bold>C.</bold> Stacked bar plot depicting the percentages of ct-tRNA reads and mt-tRNA reads in three mouse tissues. <bold>D.</bold> Heatmap showing the expression of tRNA isodecoders (<italic>Z</italic>-score) in the six samples of the three mouse tissues. <bold>E.</bold> Line chart comparing the strength of isodecoders’ usage bias in different tissues as measured by RSIU. The representative isodecoders with high tissue specificity are indicated. PCR, polymerase chain reaction; PCC, Pearson correlation coefficient; ct-tRNA, cytosolic tRNA; mt-tRNA, mitochondrial tRNA; RPM, reads per million mapped reads; RSIU, relative synonymous isodecoder usage.</p></caption></fig>", "<fig id=\"f0010\"><label>Figure 2</label><caption><p><bold>Tissue-specific expression of isodecoders results</bold><bold>in tissue-specific expression</bold><bold>rather than tissue-specific</bold><bold>usage bias of anticodons</bold></p><p><bold>A.</bold> Heatmap showing the <italic>Z</italic>-scores of tRNA isoacceptor expression in the six samples of the three mouse tissues. <bold>B.</bold> MDS plot displaying the clustering of the six samples of the three mouse tissues according to the tRNA expression profiles. <bold>C.</bold> Box plot comparing the CVs of isodecoders and isoacceptors among the six samples of the three mouse tissues. <italic>P</italic> value was calculated by two-tailed Wilcoxon test. <bold>D.</bold> Density plot showing the distribution of mean CVs of isoacceptor expression across the six samples for 10,000 permutations as well as the observed as indicated by red dot and arrow. <italic>P</italic> value was calculated as the proportion of permutations with greater X-axis values than the observed. <bold>E.</bold> Box plot comparing the pairwise PCCs of three groups of isodecoders: same anticodon, same AA but different anticodons, and different AA, according to the corresponding anticodons and amino acids of the pairs of two isodecoders. <italic>P</italic> values were calculated by two-tailed Wilcoxon test. <bold>F.</bold> Line chart comparing the strength of anticodon usage bias based on DM-tRNA-seq in three tissues as measured by RSAU. <bold>G.</bold> Density plot showing the distribution of mean CVs of RSAU values across the six samples for 10,000 permutations as well as the observed as indicated by red dot and arrow. <italic>P</italic> value was calculated as the proportion of permutations with smaller X-axis values than the observed. MDS, multidimensional scaling; CV, coefficient of variation; AA, amino acid; RSAU, relative synonymous anticodon usage.</p></caption></fig>", "<fig id=\"f0015\"><label>Figure 3</label><caption><p><bold>Tissue</bold>-<bold>specific tRNA isotype expression at amino acid level</bold></p><p><bold>A.</bold> Heatmap showing the <italic>Z</italic>-scores of tRNA isotype expression in the six samples of three mouse tissues. <bold>B.</bold> Heatmap showing the log<sub>2</sub>-transformed FCs of tRNA isotype expression for the pairwise comparisons of the three tissues. <bold>C.</bold> Box plot comparing the CVs of tRNA isotype expression across six samples (observed) with five random permutations. <italic>P</italic> values were calculated by two-tailed Wilcoxon test. <bold>D.</bold> Density plot showing the distribution of mean CVs of tRNA isotype expression across the six samples for 10,000 permutations as well as the observed as indicated by red dot and arrow. <italic>P</italic> value was calculated as the proportion of permutations with greater X-axis values than the observed. FC, fold change.</p></caption></fig>", "<fig id=\"f0020\"><label>Figure 4</label><caption><p><bold>RiboTag-seq analysis of translatomes in multiple mouse tissues</bold></p><p><bold>A.</bold> Overview of RiboTag-seq technology. <bold>B.</bold> Diagram depicting the <italic>RiboTag</italic> mouse systems. <bold>C.</bold> Western blot analysis of RPL22-HA in different tissues of <italic>CMV-Cre:RiboTag</italic> mouse. <bold>D.</bold> Heatmap showing pairwise PCCs among the six mouse samples in three tissues based on the FPKMs of genes in input samples of RiboTag-seq. <bold>E.</bold> Heatmap showing the <italic>Z</italic>-scores of TEs in six samples of three mouse tissues. <bold>F.</bold> Heatmap showing the <italic>Z</italic>-scores of codon indexes of top 5% HTGs in six samples of three mouse tissues. <bold>G.</bold> Line chart comparing the strength of codon usage bias in different tissues as measured by RSCU. <bold>H</bold>. Box plot comparing the CVs of RSCU values of the top 5% HTGs (observed) across six samples with four random permutations. <italic>P</italic> values were calculated by two-tailed Wilcoxon test. HA, hemagglutinin; 7MeG, <italic>N</italic><sup>7</sup>-methylated guanosine; wt, wild-type; FPKM, fragments per kilobase per million mapped of fragments; TE, translational efficiency; HTG, highly translated gene; RSCU, relative synonymous codon usage.</p></caption></fig>", "<fig id=\"f0025\"><label>Figure 5</label><caption><p><bold>tRNA pools adapt better to HTGs in the same tissues but not to tissue</bold>-<bold>specifically translated genes</bold></p><p><bold>A.</bold> Box plots comparing the tAI of genes with different TE levels based on the tRNA pools of the same tissues in the three tissues, respectively. <bold>B.</bold> Box plots showing the tAI values of the top 5% HTGs in the brain (left panel), heart (middle panel), and testis (right panel) calculated based on the tRNA pools of the three tissues, respectively. <italic>P</italic> values were calculated by two-tailed Wilcoxon test. tAI, tRNA adaptation index; MTG, moderately translated gene; LTG, lowly translated gene.</p></caption></fig>", "<fig id=\"f0030\"><label>Figure 6</label><caption><p><bold>tRNA expression correlates with amino acid composition in the same tissues but not between tissues</bold></p><p><bold>A.</bold> Heatmap showing the <italic>Z</italic>-scores of amino acid compositions of the top 5% HTGs in the six samples of three mouse tissues. <bold>B.</bold> Scatter plots showing the correlation of amino acid compositions of the top 5% HTGs with the tRNA isotype expression in the brain (left panel), heart (middle panel), and testis (right panel). Blue lines indicate fitted linear models and PCCs are shown. <bold>C.</bold> Scatter plot showing non-significant linear correlation of amino acid compositions subtracted by means with the <italic>Z</italic>-scores of tRNA isotype expression in all three tissues.</p></caption></fig>", "<fig id=\"f0035\" position=\"anchor\"><label>Supplementary Figure S1</label><caption><p><bold>The bioinformatics analysis flow chart</bold> The left flow chart shows the bioinformatic analysis steps of DM-tRNA-seq data; and the right flow chart shows the bioinformatic analysis steps of RiboTag-seq data.</p></caption></fig>", "<fig id=\"f0040\" position=\"anchor\"><label>Supplementary Figure S2</label><caption><p><bold>Dynamic expression of anticodons using published QuantM-tRNA seq data A.</bold> Comparison of the CVs of isodecoders and isoacceptors among seven tissues. <italic>P</italic> values of two-tailed Wilcoxon tests are indicated. <bold>B.</bold> Heatmap representing the Z-scores of tRNA reads which collapsed by known isoacceptor groups in seven tissues. Two outliers were removed from the analysis (Cortex_1 and Tibialis_1). <bold>C.</bold> Box plot comparing the pairwise PCCs of three groups of isodecoders: “same anticodon”, “same amino acid but different anticodons”, and “different amino acids” according to the corresponding anticodons and amino acids of the pairs of two isodecoders.</p></caption></fig>", "<fig id=\"f0045\" position=\"anchor\"><label>Supplementary Figure S3</label><caption><p><bold>RiboTag-seq analysis of translatomes in multiple mouse tissues reveals tissue-specific translational efficiency and codon usage biases A.</bold> PCR products using primers that amplify CMV-Cre recombinase and the loxP-containing intron sequence of the <italic>Rpl22</italic> gene. The PCR product of <italic>Rpl22</italic> gene activated by CMV-Cre recombinase is 260 bp, and the non-activated PCR product is 290 bp. <bold>B.</bold> Western blots using an anti-HA antibody demonstrate the presence of RPL22-HA specifically in anti-HA pellets versus supernatant. <bold>C.</bold> Agilent Technologies 2100 Bioanalyzer (Catalog No. G2939BA, Agilent Technologies, Palo Alto, Calif.) electropherogram analysis of total RNAs from brain, heart, and testis immunoprecipitates. WT, wild type; IP, immunoprecipitation.</p></caption></fig>", "<fig id=\"f0050\" position=\"anchor\"><label>Supplementary Figure S4</label><caption><p><bold>Metascape enrichment analysis of HTGs in different tissues A.</bold> Metascape enrichment analysis of top 5% HTGs in brain. <bold>B.</bold> Metascape enrichment analysis of top 5% HTGs in heart. <bold>C.</bold> Metascape enrichment analysis of top 5% HTGs in testis.</p></caption></fig>", "<fig id=\"f0055\" position=\"anchor\"><label>Supplementary Figure S5</label><caption><p><bold>Pairwise correlation analyses of isoacceptor abundances and the codon compositions among the three tissues A.</bold> Correlation analysis between isoacceptor abundances and the codon compositions. <bold>B.</bold> Correlation analysis between the FCs of isoacceptor abundances and the FC of codon compositions between two tissues.</p></caption></fig>", "<fig id=\"f0060\" position=\"anchor\"><label>Supplementary Figure S6</label><caption><p><bold>Pairwise correlation analyses of tRNA isotype expression and amino acid compositions among the three tissues A.</bold> Pairwise correlation analyses of the three tissues between delta amino acid compositions and the FCs of tRNA isotype expression of all genes. <bold>B.</bold> Pairwise correlation analyses of the three tissues between delta amino acid compositions and the FCs of tRNA isotype expression of HTGs.</p></caption></fig>", "<fig id=\"f0065\" position=\"anchor\"><label>Supplementary Figure S7</label><caption><p><bold>Comparison of the percentages of reads with lengths greater than 40 bp between ct-tRNAs and mt-tRNAs</bold></p></caption></fig>", "<fig id=\"f0070\" position=\"anchor\"><label>Supplementary Figure S8</label><caption><p><bold>Correlation analyses of the expression of tRNAs and tsRNAs among the three tissues A.</bold> Correlation analysis of the isodecoder RPMs between tsRNA and tRNA. <bold>B.</bold> Correlation analysis between the FCs of tsRNA and the FCs of tRNA.</p></caption></fig>" ]
[]
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[]
[]
[]
[]
[ "<supplementary-material content-type=\"local-data\" id=\"m0010\"><caption><title>Supplementary Table S1</title><p><bold>The counts and expression of tRNAs</bold></p></caption></supplementary-material>", "<supplementary-material content-type=\"local-data\" id=\"m0005\"><caption><title>Supplementary Table S2</title><p><bold>The gene FPKMs of IP and input of RiboTag-seq</bold></p></caption></supplementary-material>" ]
[ "<fn-group><fn id=\"d35e163\"><p id=\"np005\">Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China.</p></fn><fn id=\"s0120\" fn-type=\"supplementary-material\"><p id=\"p0270\">Supplementary data to this article can be found online at <ext-link ext-link-type=\"uri\" xlink:href=\"https://doi.org/10.1016/j.gpb.2022.07.006\" id=\"ir015\">https://doi.org/10.1016/j.gpb.2022.07.006</ext-link>.</p></fn></fn-group>" ]
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54
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2024-01-14 23:41:59
Genomics Proteomics Bioinformatics. 2023 Aug 8; 21(4):834-849
oa_package/9d/df/PMC10787195.tar.gz