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Answers OnStartups is a question and answer site for entrepreneurs looking to start or run a new business. It's 100% free, no registration required.
In what year do payments to subcontactors count, for tax purposes? For example if I don't make the payment until after Jan 1 but the money was earned the previous year, which tax year does that count for?
I'm pretty sure the answer is obvious but just in case.
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1 Answer
up vote 2 down vote accepted
First you need to understand that each country has its own tax laws which vary.
In the United States companies have a choice of using either the cash or accrual basis of accounting. Under the cash basis the revenue counts in the tax year that the payment was actually received (or paid in the case of the company making the payment).
Under the accrual system, the revenue (or cost) is recognized in the year the work was done. Payment could have occurred either before (pre-payment) or after the work.
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From NAS-Central Buffalo - The Linkstation Wiki
Revision as of 08:23, 13 July 2006 by 86.135.152.138 (Talk)
Jump to: navigation, search
Originally by Nick and edited by ...
BurnHard, frontalot, Cathedrow & Ralf from linkstationwiki.org
Installing Apache w/ PHP and MySQL Support.
Contents
Opening Comments
Apache, along with PHP and MySQL, is very straight forward to install on a stock LinkStation 2 with the OpenLink firmware installed. If you have experience with building these packages, or compiling in general, it is a snap. If you have little or no experience in such matter, just follow the guide -- everything is reversible.
If you have not already done so, visit the Openlink section and follow the instructions for installing the telnet enabled firmware. You will also need to download and install the [MIPSel Tools] before continuing.
A Remark on "--prefix"
The prefix argument, which you will see in every section below, allows you to install Unix packages to alternate locations. This is very important is the case of the LinkStation since all three packages take over 75 megs to install. You will not be able to install these packages to your root partition and doing so would be very bad.
I chose to create an "opt" directory under "/mnt/hda" to install each of these packages too, using a separate directory for each. This was done to keep the packages separated and easy to manage in the future. You may, of course, alter your install locations in any way but, if you are new to this, I suggest following my example.
It's also a good idea to create a directory to download stuff when using wget, lets use /mnt/hda/misc
MySQL
Begin with MySQL. If you do not wish to compile MySQL support into your system, please skip to the next section.
cd /mnt/hda/misc
• Download the latest recommended release of MySQL from http://www.mysql.com (4.1.13, at the time of this writing).
wget http://www.mirrorservice.org/sites/ftp.mysql.com/Downloads/MySQL-4.1/mysql-4.1.20.tar.gz
tar -zxvf mysql-xxx' (replacing xxx with your MySQL version number)
cd mysql-xxx' (replacing xxx with your MySQL version number)
groupadd mysql
(Not sure if this is necessary, just following instructions from dev.mysql.com)
• [Ralf] without this MySQL will try to run as root, but you need several special settings for this - better stick to the extra mysql user
useradd -g mysql mysql
./configure --prefix=/mnt/hda/opt/mysql --with-readline
make
make install
cp support-files/my-medium.cnf /etc/my.cnf
• [Ralf] there are more sample configuration files which you can try, e.g. my-small.cfg. Read the beginning of the files for a description
cd /mnt/hda/opt/mysql
bin/mysql_install_db --user=mysql
creates databases
chown -R root .
chown -R mysql var
chgrp -R mysql .
[Ralf] MySQL 5 seems to require the following extra actions:
• Create a MySQL password file:
libexec/mysqlmanager --passwd --user mysql >> /etc/mysqlmanager.passwd
• At the following prompt enter
mysql
You should now have a fully functioning version of MySQL on your LinkStation. Now we can set up the server to start like any other service.
Go back to where you have build MySQL (also see above):
/mnt/hda/misc/mysql-xxx
cp support-files/mysql.server /etc/init.d
chmod 755 /etc/init.d/mysql.server
You can now start your MySQL daemon as follows:
/etc/init.d/mysql.server start
PLEASE REMEMBER TO SET A PASSWORD FOR THE MySQL root USER ! To do so, start the server, then issue the following commands:
/mnt/hda/opt/mysql/bin/mysqladmin -u root password 'new-password'
/mnt/hda/opt/mysql/bin/mysqladmin -u root -h 'servername' password 'new-password'
Start up and shutdown at boot
ln -s /etc/init.d/mysql.server /etc/rc.d/rc2.d/S99mysql.server
ln -s /etc/init.d/mysql.server /etc/rc.d/rc6.d/K92mysql.server
ln -s /etc/init.d/mysql.server /etc/rc.d/rc0.d/K92mysql.server
Important Memory Usage Note: MySQL takes just under 25% of the LinkStation's total available memory when running. This should be taken into serious consideration if you choose to install MySQL support with your web server.
• TODO: Need to get the server running automatically at boot.
[Ralf] Here is how to start MySQL 5 automatically at boot. I guess it works quite similar with MySQL 4.X.
cd /etc/rc.d
ln -s ../init.d/mysql.server rc2.d/S99mysql
ln -s ../init.d/mysql.server rc2.d/K99mysql
Apache 1.3.xx
Apache itself is the next install. If you are not planning on installing PHP, you may ignore the "--enable-module=so" attribute below.
I decided to install Apache 1.3 because that is what my web host uses. Installing Apache 2 would be very similar and the following instructions can be easily adapted by reading the INSTALL document in the Apache 2 tarball.
Download the latest version of Apache 1.3 from http://www.apache.org (1.3.33, at the time of this writing).
wget http://apache.rmplc.co.uk/httpd/apache_1.3.36.tar.gz
tar -zxvf apache-xxx' (replacing xxx with your Apache version number)
cd apache-xxx' (replacing xxx with your Apache version number)
./configure --prefix=/mnt/hda/opt/apache --enable-module=so
make
make install
You will, at the very least, need to change your port to 81 (or some other port).
vi /mnt/hda/opt/apache/conf/httpd.conf
Search for '80' -- change it to '81' (or some other port).
I also suggest changing the root directory to the files to "/mnt/hda/share/www" so you can have easy access to them over the Samba share. Search for 'DocumentRoot' and change the first reference (roughly line 288) to the above path. Search again and you will find another reference to change (around line 313).
Finally, start the server.
/mnt/hda/opt/apache/bin/apachectl start
Copy that start up script to /etc/init.d and include in startup shutdown
cp /mnt/hda/opt/apache/bin/apachectl /etc/init.d
ln -s /etc/init.d/apachectl /etc/rc.d/rc2.d/S99apachectl
ln -s /etc/init.d/apachectl /etc/rc.d/rc6.d/K92apachectl
ln -s /etc/init.d/apachectl /etc/rc.d/rc0.d/K92apachectl
• TODO: Flush out the config file editing instructions.
PHP
Last we will set up PHP. I decided to install the latest version of PHP4 because, again, this is what my web host uses. You may decide to install PHP5, which would requires only 1 slightly different step below.
Pay special attention to the 'configure' (step 6) command below. If you installed the above packages to an alternate location you will need to update the paths in the proper attribute.
1. Download the latest version of PHP4 from http://www.php.net (4.4.0, at the time of this writing).
2. Copy the archive to your LinkStation as you would any other file, into your share folder.
3. Log into your LinkStation and 'cd /mnt/hda/share'
4. Execute 'tar -zxvf php-xxx' (replacing xxx with your PHP version number)
5. Execute 'cd php-xxx' (replacing xxx with your PHP version number)
6. ./configure --prefix=/mnt/hda/opt/php4 --with-mysql=/mnt/hda/opt/mysql --with-apxs=/mnt/hda/opt/apache/bin/apxs --with-config-file-path=/mnt/hda/opt/php4/lib
7. make
8. make install
Copy over the default config file. If you altered the "--with-config-file-path" attribute, in step 6, you will need to change the below command to copy to the appropriate path.
• cp php.ini-dist /mnt/hda/opt/php4/lib
Open up '/mnt/hda/opt/apache/conf/httpd.conf' and verify that the following line is included:
• LoadModule php4_module libexec/libphp4.so (for PHP4)
• LoadModule php4_module libexec/libphp5.so (for PHP5)
If it is not, add it. Also add the following two lines just below the LoadModule command:
1. AddType application/x-httpd-php .php .phtml
2. AddType application/x-httpd-php-source .phps
Restart Apache and PHP should now be working.
• TODO: More information on configuration of PHP
• TODO: Information on adding additional modules to PHP
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From NAS-Central Buffalo - The Linkstation Wiki
Revision as of 16:33, 17 December 2008 by Themel (Talk | contribs)
Jump to: navigation, search
This pages describes how to modify the initrds aka ramdisks of the linkstations/terastations/kuroboxes.
ppc-based boxes
BEWARE: this info is for the original firmimg.bins which were burned to flash. If you flash uboot as a replacement for the stock bootloader you can place the initrd + kernel also to /boot/ instead.
the kernel and the initrd both are inside the firmimg.bin-files which are inside the firmware-update-packages.
so we need to extract both from the firmimg.bin first. some smart japanese guys wrote a tool called firmimgtool.
sourcecode:
http://downloads.nas-central.org/ALL_LS_KB_PPC/DevelopmentTools/Flash/Utilities/firmimgtool.c
here you have all the tools you need compiled for ppc:
http://downloads.nas-central.org/ALL_LS_KB_PPC/DevelopmentTools/Flash/Utilities/flash_dev_tools_ppc.tar.gz
Usage: ./firmimgtool [-icmkr] <firmimg_filename>
-i : show firmimg_file information
-c : cut out from firmimg_file
-m : merge into firmimg_file
-k <filename> : kernel image filename
-r <filename> : ramdisk image filename
-f <filename> : copy headers from file
-h : show this help message
Now we extract kernel.gz and the initrd.gz:
./firmimgtool -c -k kernel.gz -r initrd.gz firmimg.bin
afterwards you should have a kernel.gz and a initrd.gz in the same folder.
unpack initrd.gz
gunzip initrd.gz
and loop mount it
mkdir INITRD
mount -o loop initrd INITRD
now you can change everything you want by changing it in the folder INITRD....if you unmount it all changes are saved.
After applying the changes you need to reassemble the firmimg.bin... this works that way:
umount INITRD
gzip initrd
./firmimgtool -m -k kernel.gz -r initrd.gz firmimg.bin -f firmimg.bin.103
and voila, the new firmimg.bin is ready for flashing.
mipsel-based
the firmimg.bin is encrypted unfortunately. LNI knows how to do this, but he hasn`t published this.
arm9-based boxes
All these boxes feature UBoot as the stock bootloader. The uboot bootloader loads initrd.buffalo from /dev/sda1.
The initrd.buffalo is named initrd.img in the firmware-update-packages. initrd.img is (like the hddrootfs) a password protected zip-file.
just unzip it and supply the right password.
unzip initrd.img
Archive: initrd.img
[initrd.img] initrd.buffalo password:
try one of these (source of passwords)
1NIf_2yUOlRDpYZUVNqboRpMBoZwT4PzoUvOPUp6l
aAhvlM1Yp7_2VSm6BhgkmTOrCN1JyE0C5Q6cB3oBB
YvSInIQopeipx66t_DCdfEvfP47qeVPhNhAuSYmA4
IeY8omJwGlGkIbJm2FH_MV4fLsXE8ieu0gNYwE6Ty
for the LS Pro it is YvSInIQopeipx66t_DCdfEvfP47qeVPhNhAuSYmA4 for example.
the initrd.buffalo still is not the real initrd....as it is booted from uboot is has a 64 byte long header. We use dd to get rid of the header, unzip the resulting image.gz and loop-mount the file
dd if=initrd.buffalo of=initrd.gz ibs=64 skip=1
gunzip initrd.gz
mkdir INITRD
mount -t ext2 -o loop initrd INITRD
there we are...in the folder INITRD you now have loop-mounted the initrd...make your changes as you want.
after making your changes do do this to get the initrd in a bootable condition again:
umount INITRD
rmdir INITRD
mv initrd.buffalo initrd.stock [backup just in case]
gzip initrd
mkimage -A arm -O linux -T ramdisk -C gzip -a 0x0 -e 0x0 -n initrd -d initrd.gz initrd.buffalo
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You are here: Home » Content » Giáo trình môn Viết 1
About: Giáo trình môn Viết 1
Collection type: Course
Course by: GV.Nguyễn Thị Kiều Trang. E-mail the author
View the content: Giáo trình môn Viết 1
Metadata
Name: Giáo trình môn Viết 1
ID: col10772
Language: English (en)
Collection Subtype: Course
Subject: Arts
Keywords: english, viết
License: Creative Commons Attribution License CC-BY 3.0
Authors: GV.Nguyễn Thị Kiều Trang ([email protected])
Copyright Holders: GV.Nguyễn Thị Kiều Trang ([email protected])
Maintainers: vocw ([email protected]), GV.Nguyễn Thị Kiều Trang ([email protected])
Latest version: 1.1 (history)
First publication date: Jul 27, 2009 11:14 am GMT-5
Last revision to collection: Jul 29, 2009 11:32 am GMT-5
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PDF: col10772_1.1.pdf PDF file, for viewing content offline and printing. Learn more.
EPUB: col10772_1.1.epub Electronic book format file, for viewing on mobile devices. Learn more.
Collection Structure XML: col10772_1.1_collection.xml XML that defines the structure of the collection. Cannot be reimported in the editing interface. Learn more.
Source Export ZIP: col10772_1.1_complete.zip The Collection Structure XML, plus the CNXML and included media files for each module in the collection. Cannot be reimported. Learn more.
Offline ZIP: col10772_1.1_offline.zip An offline HTML copy of the content. Also includes XML, included media files, and other support files. Learn more.
Version History
Version: 1.1 Jul 29, 2009 11:32 am GMT-5 by vocw
Changes:
moved from VOCW
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• the title of the work: Giáo trình môn Viết 1
• the Connexions URL where the work can be found: http://cnx.org/content/col10772/1.1/
See the citation section below for examples you can copy.
How to Cite and Attribute This Content
The following citation styles comply with the attribution requirements for the license (CC-BY 3.0) of this work:
American Chemical Society (ACS) Style Guide:
Thị Kiều Trang, G. Giáo trình môn Viết 1, Connexions Web site. http://cnx.org/content/col10772/1.1/, Jul 29, 2009.
American Medical Assocation (AMA) Manual of Style:
Thị Kiều Trang G. Giáo trình môn Viết 1 [Connexions Web site]. July 29, 2009. Available at: http://cnx.org/content/col10772/1.1/.
American Psychological Assocation (APA) Publication Manual:
Thị Kiều Trang, G. (2009, July 29). Giáo trình môn Viết 1. Retrieved from the Connexions Web site: http://cnx.org/content/col10772/1.1/
Chicago Manual of Style (Bibliography):
Thị Kiều Trang, GV.Nguyễn. "Giáo trình môn Viết 1." Connexions. July 29, 2009. http://cnx.org/content/col10772/1.1/.
Chicago Manual of Style (Note):
GV.Nguyễn Thị Kiều Trang, "Giáo trình môn Viết 1," Connexions, July 29, 2009, http://cnx.org/content/col10772/1.1/.
Chicago Manual of Style (Reference, in Author-Date style):
Thị Kiều Trang, G. 2009. Giáo trình môn Viết 1. Connexions, July 29, 2009. http://cnx.org/content/col10772/1.1/.
Modern Languages Association (MLA) Style Manual:
Thị Kiều Trang, GV.Nguyễn. Giáo trình môn Viết 1. Connexions. 29 July 2009 <http://cnx.org/content/col10772/1.1/>. | v0 |
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Info
Search:
Photo by Ivan Kozik
The Australian Collection primarily features trees and shrubs native to Australia. Tall eucalyptus trees, with their distinctive aromatic leaves, dominate the north bank of the creek. With more than 50 species of this native Australian genus, the trees vary from tall and erect specimens to broadly-spreading small trees. Throughout the collection, their characteristic camphor-like fragrance fills the air. A fine collection of bottlebrush, Callistemon, and honey-myrtles, Melaleuca, lines the path near the old bridge. Across the creek, new plantings of showy Australian flowering plants complement older plantings that feature plants from various regions in the world with a Mediterranean climate.
Photo by Mia Ingolia
Photo by Mia Ingolia Photo by Mia Ingolia A gift by Arley Firch Photo by Mia Ingolia Photo by Mia Ingolia Some of the trees from the Australian Collection
This is a Wiki Spot wiki. Wiki Spot is a 501(c)3 non-profit organization that helps communities collaborate via wikis. | v0 |
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Display titleCategory:Categories templates
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Page creatorWmat (Talk | contribs)
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From eLinux.org
Revision as of 14:52, 16 March 2012 by Meltwater (Talk | contribs)
Jump to: navigation, search
Contents
Back to the Hub.
Community Pages:
Tutorials - a list of tutorials. Learn by doing.
Guides - a list of informative guides. Make something useful.
Projects - a list of community projects. Help others out.
Tasks - for advanced users to collaborate on software tasks.
Datasheets - a frambozenier.org documentation project.
Education - a place to share your group's project and find useful learning sites.
Community - links to the community elsewhere on the web.
Games - all kinds of computer games.
Types of Game
HTML5 - Games to play in a web browser.
Game Projects
Coming soon....PyRacer | v0 |
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} | cccc_CC-MAIN-2013-20 | GlobalVoices in Learn more »
Brazilian Family Loses Home to the World Cup
This post also available in:
Español · Río de Janeiro: Elisângela llegó a tiempo para ver caer su casa
Français · Rio de Janeiro: Elisângela est arrivée à temps pour voir sa maison détruite.
Malagasy · Fianakaviana Breziliana Very Trano Noho Ny Fiadiana Ny Ho Tompondakan'ny Baolina Kitra
繁體中文 · 因世界盃而流離失所的巴西家庭
简体中文 · 因世界杯而流离失所的巴西家庭
Português · Rio de Janeiro: Elisângela chegou a tempo de ver sua casa cair
This article, by Andrea Dip, is a part of Agência Pública's special #CopaPública [pt] coverage, and was originally published on June 26, 2012, with the title Elisângela Got Home Just in Time to See it Being Torn Down: Watch the Minidoc [pt]
Elisângela wasn't home when authorities arrived without warning to tear down her house on Pavão-Pavãozinho hill in Rio de Janeiro.
Her 17-year-old daughter answered the door and was told that the property was going to be destroyed at that very moment. Panicking, the girl called her mother:
Tem vários homens da Prefeitura aqui na porta; eles estão dizendo que vão derrubar a nossa casa.
There are many men here from the city at the door; they're saying they are going to tear down our house.
Elisângela ran back home, tried to reason with the men, ask for some time to find another home, but it was no use. In a few hours, all that was left was debris. This happened in early 2011. To this day, Elisângela has not been compensated nor relocated. Her daughter had to go live with her grandmother, while Elisângela still searches for a new home.
Elisângela gazes at the site of her destroyed home. Photo: Agência Pública / Credits: Henrique Zizo
The minidocumentary “We Are the Legacy: the Story of Elisângela” (“O Legado Somos Nós: A História de Elisângela”) is the first in a series of video portraits being produced by the human rights organization Witness, which partnered with the Rio People's World Cup and Olympics Committee (Comitê Popular Rio Copa e Olimpíadas), in an attempt to tell the stories of those affected by forced evictions in Rio de Janeiro, directly or indirectly connected to the 2014 World Cup and the 2016 Olympics. Priscila Neri, from Witness, explains that the idea is to give an alternative to the official narrative, which claims that everything is being done in compliance with the law and through constant dialogue with the communities.
Elisângela at Pavão Pavãozinho. Photo: Agência Pública / Credits: Henrique Zizo
In Elisângela's particular case, the justification provided at the time of the eviction was that her home was in a risk area in Pavão-Pavãozinho, but only some houses were destroyed and, according to the Rio People's World Cup and Olympics Committee, the city hasn't even removed the debris yet. The hill is located between two of Rio's most sought-after neighborhoods: Ipanema and Copacabana.
According to the dossier [pt] published by the Rio People's World Cup and Olympics Committee, the city intends to use the argument of geotechnical or structural risk to evict more than 300 families from the Pavão-Pavãozinho community:
Até o momento a Prefeitura não apresentou o laudo que comprove o risco e nem discutiu com a comunidade a possibilidade de realização de obras para garantir a segurança dos moradores.
Up until now the city hasn't presented any technical report that backs up the risk claim nor has it discussed with the community the possibility of carrying out infrastructural work to ensure the residents’ safety.
Still according to the Rio People's World Cup and Olympics Committee, engineers that have written technical reports about areas like the Pavão-Pavãozinho have pointed out that doing construction work to restrain or strengthen the slope, in order to eliminate the risk of slippage, would cost even less than relocating the families that live in the area.
Watch the minidoc:
The blog #CopaPública [pt] is a citizen journalism initiative that reports how the Brazilian population is being affected by – and mobilizing against – preparations for the 2014 World Cup.
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2024-06-03T21:29:47.544Z | 2013-05-18T08:09:06.000Z | pooxwgknbzzpougaa77hcbag77bmvo2z | {
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} | cccc_CC-MAIN-2013-20 | For the half-year to 30 June 2013, the IPKat's regular team is supplemented by contributions from guest bloggers Stefano Barazza, Matthias Lamping and Jeff John Roberts.
Two of our regular Kats are currently on blogging sabbaticals. They are Birgit Clark and Catherine Lee.
Friday, 17 August 2012
Taking it personally: patents, medicines and genetic markers
Purr-sonalised medicine
The IPKat is all in favour of medicine which, he thinks, can come in really handy -- even when you're unwell. He was therefore fascinated to learn of a recent discussion in Europe of a topic which has already exercised some of the finest minds of his American colleagues: the patenting of inventions relating to personalised medicine. Having heard about this from katfriend Suleman Ali (Holly IP), he is pleased to say that the latter was willingly persuaded to write a short note on the topic for the benefit of readers of this weblog. Here it is:
"Is the EPO changing Its stance on personalised medicine inventions?
Case law is an important means by which we know what is patentable at the European Patent Office (EPO). However, sometimes the EPO’s view of what is patentable in an area changes before the case law does. This can sometimes be detected when Examiners start raising objections they would not have previously done. Clearly, applicants need to know about such changes as soon as possible so that they can revise their filing strategies and re-evaluate their expectations of the claims they are likely obtain. Meetings between the EPO and the epi (the professional institute for EPO attorneys) are very useful forums for obtaining ‘inside information’ about the EPO’s thinking which is not yet apparent from the case law. The June 2012 issue of epi Information provides a report of such a meeting held on 10 November 2011 between the EPO and the biotech committee of the epi. Discussion item 8 is reported as follows:
‘8. Inventions in the area of pharmacogenomics
This concerns cases which are based on a genetic marker to treat a disease, for example methylation profiles. It can involve a new patient group defined by an SNP. The EPO said that often the claims can lack novelty, as one patient will have inevitably been treated with the SNP, even if the art does not explicitly say so.’
The EPO’s comments seem to indicate that it is about to change the way it assesses novelty when looking at medical use claims that refer to treatment of a specific patient group.
To give a little technical background to the EPO’s comments, an SNP is a form of genetic marker which varies between individuals. The idea behind the relatively new field of pharmacogenomics is that, if you know which SNP variants a patient possesses, you can personalise the drugs given to a patient in accordance with his genetic makeup. It is now recognised that the genetic makeup of an individual can be very influential as to whether he responds to a drug, and so one application of pharmacogenomics is to only give those drugs to patients who will respond to them.
Personalised medicines can also be based on non-genetic biomarkers, such as the level of virus the individual has.
Personalised medicines offer the potential to use drugs much more effectively. That is clearly of benefit to patients, but should also help to reduce costs in times when many governments feel increasingly dismayed at the yearly increases needed to health budgets. The sector most likely to benefit in the short time is cancer therapy where most of the work in identifying biomarkers is focussed. However, biomarkers are increasingly being sought for many other diseases.
Presently, suitable biomarkers for personalised medicine are proving difficult to find. So it seems that the sector is going to require a lot of investment -- but in investors in biotech do like to see that strong patent protection is available in the relevant sector.
Personalised medicines, and in fact diagnostics in general, has been thrown into uncertainty in the US after the Supreme Court’s decision in Mayo v Prometheus [on which see earlier Katposts here and here] which found that a claim referring to steps that determined the level of a drug in a patient was directed to a law of nature and was thus not patentable. It would be unfortunate for personalised medicines to be dealt a further blow by the EPO, making the test for novelty stricter in this area.
Claims for personalised medicine inventions can have many different forms, but typically they are along the following lines:
Substance X for use in a method of treating condition Y in an individual with biomarker Z’.
There is an argument here that perhaps applicants only deserve claims to the method of selecting the individual (by detection of the biomarker), and not to treatment of the individual. However there is a lot more money in therapy, with figures being quoted of 6% versus 94% for the money to be made in selection versus therapy. Since personalised medicine results in therapy being more effective, there is an argument that the applicant deserves claims to the therapy step.
The crux of the present issue is whether limiting a medical use claim by specifying that the individual has biomarker Z will confer novelty where the prior art is silent about patients having biomarker Z, but where patients with biomarker Z will inevitably have been treated, i.e. does limiting a medical use claim to a patient group that overlaps with, or is within, the prior art patient group, make the claim novel?
The earliest case to tackle the issue seems to have been T233/96 which gave a strict two-part test for novelty requiring the patient groups to be non-overlapping and for there to be a functional relationship between the biomarker and the therapy, i.e. the patient group could not be an arbitrary group. However, subsequent case law has not followed the test. In T1399/04 the Board cited T233/96, but took a different view, generously allowing claims which covered more than 50% of a prior art patient group. Decisions T836/01 and T1642/06 also allowed claims where patient groups overlapped with the prior art.
Based on the comments at the EPO/epi meeting and from the experiences of attorneys I know who are handling European patent applications in this area, it seems that EPO is taking a stricter view of the issue, and is probably looking for a test case to change the case law. If the EPO decides on a test which is based on the concept of a patient with the relevant biomarker ‘inevitably’ having been treated, presumably this is a prior use test, in which case it would be burdensome for applicants to locate evidence on what actually happened. However if the test is similar to that used in T233/96, i.e. requiring that patient groups do not overlap, then it will have the effect of severely curtailing patent protection for personalised medicines because most drugs are initially given to everyone with the condition.
I hope that the EPO will be wise enough to recognise that making the test for novelty stricter for medical use claims limited by patient group will have a substantial impact on the patent protection that can be obtained in the area of personalised medicines, at a time when this very promising sector needs all the support it can get".
Thanks, Suleman, for this most instructive piece, says the IPKat. Merpel is fascinated by this for quite another reason, though. It reflects a growing trend towards what might be termed "mass personalisation". We have it in branding and marketing, where the use of sophisticated software in reading your emails and online purchases enables a personalised dose of advertising to be specifically targeted at the individual. It also exists in the design and fashion sector, where a combination of interactive software and manufacturing improvements produces the result that a purchaser of, say, sports shoes, can determine the style, size, colour and bolt-on features that characterise it, rather than going into some random shop and putting a tentative foot into a sample shoe that might previously have been tried by someone with sweaty socks and fungal growths between the toes ...
Your own personalised medicine here and here [not for the squeamish]
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} | cccc_CC-MAIN-2013-20 | For the half-year to 30 June 2013, the IPKat's regular team is supplemented by contributions from guest bloggers Stefano Barazza, Matthias Lamping and Jeff John Roberts.
Two of our regular Kats are currently on blogging sabbaticals. They are Birgit Clark and Catherine Lee.
Monday, 27 April 2009
Malicious falsehood case
The IPKat has read with interest Ajinomoto Sweeteners Europe v Asda, a malicious falsehood case.
Ajinomoto is the manufacturer of the artificial sweetener, aspartame. The supermarket, Asda, commenced a campaign which was designed to ensure that, by the end of 2007, none of its 9,000 own-label food and soft-drinks products would contain any artificial colours or flavours or any hydrogenated fat or flavour enhancers. The catch-phrase used was 'NO HIDDEN NASTIES'. One of the statements used in conjunction with the catch-phrase was "No artificial colours or flavours and no aspartame" and "We promise that all good for you products are always low or lower in fat and won't ever contain any hydrogenated fat, artificial flavours, artificial colours or aspartame."
Ajinomoto alleged that the natural and ordinary meaning of the words on the packaging is that aspartame is an especially harmful or unhealthy, or potentially harmful or unhealthy, sweetener and is one which consumers concerned for their own health and that of their families would do well to avoid, either altogether or in the quantities likely to be found in soft drinks and other food products.
In the recent decision, Sir Charles Gray had to decide whether to grant Ajimoto's request for a trial of the preliminary issue "as to the statement(s) of fact contained in or conveyed by the words complained of in paragraphs 4 and 8 of the Particulars of Claim". The alternative would be to hold a single trial incorporating (i) the meaning of the statement; (ii) whether the statement was false and (iii) whether the statement was malicious.
The judge held that in the interests of saving costs, it was right for the preliminary issue to be tried first. If Ajimoto's contention that the meaning of Asda's statements were that aspartame was harmful was rejected then there would be no issue as to falsity, and malice would not be relevant. The judge accepted that the issue of meaning was essentially a "slam dunk" point. Separating the issue of meaning out into a preliminary trial was commonly used in defamation actions and would work here. However, the judge did suggest that the approach might be considered an abuse if it was used as a tactic to 'slice up' the action into three separate trials of meaning, falsity and malice.
The IPKat is all in favour of efficiency and saving costs (except when it comes to kitty treats) and thinks that this looks like a sensible decison.
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} | cccc_CC-MAIN-2013-20 | [maemo-community] The role of the docmaster
From: Murray Cumming murrayc at murrayc.com
Date: Mon May 25 17:30:03 EEST 2009
On Mon, 2009-05-25 at 16:24 +0200, Murray Cumming wrote:
> > 1. Cleanup existing Chinook documentation for Diablo
> > - end result for that was Diablo Reference Manual and example apps in Garge
> > http://maemo.org/maemo_release_documentation/maemo4.1.x/
>
> This is a combination of all the existing documentation, right, as one
> big PDF?
>
> Or does this contain information or modifications that are not in the
> regular API reference. For instance,
> http://maemo.org/api_refs/5.0/beta/hildon/index.html
Sorry. I actually looked now. It's a combination of the
non-api-reference documentation. "Reference Manual" is a bad name for
it.
--
murrayc at murrayc.com
www.murrayc.com
www.openismus.com
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} | cccc_CC-MAIN-2013-20 | Twelve Months of VWXYNot?
As seen everywhere, here are the first sentences of my first post of each month in 2010. Bragging Rights Central, hockey pools, grants, visitors, quizzes, and bears – sounds about right! (But no Winter Olympics posts? That’s hardly representative of the year as a whole!)
January
Congratulations to Massimo for winning the First Annual VWXYNot? Readers’ Choice Comment of the Year Award!
February
Did anyone else see the Canucks-Leafs game on Saturday?!
March
I’m currently (intermittently, half-heartedly) tidying my inbox and desk after the latest round of grant applications.
April
One of my best friends from the UK should be landing in Vancouver in a couple of minutes, with her lovely hubby and adorable two year old son!
May
My parents are here!
June
As you may remember from an old post, since I moved to Canada in 2002 I’ve spent much, much more time worrying about bears than actually encountering them.
July
My boss is a very busy man whose trainees sometimes have a hard time getting his attention.
August
I’m back from my trip with more photos than I can reasonably fit into a blog post, so please bear with me while I attempt to cull the collection!
September
Yes folks, it’s time for another fun quiz from my puzzle-a-day desk calendar!
October
New archive post!
November
First of all, many thanks to Chall and ScientistMother for hosting the last two updates!
December
Spotted on a whiteboard in a PI’s office, written in massive letters (colours as in original):
Book chapters and reviews are for people with no data - NEVER SAY YES
(actually, this was the entire post).
Right, now let’s see your versions!
About Cath@VWXYNot?
"one of the sillier science bloggers [...] I thought I should give a warning to the more staid members of the community." - Bob O'Hara, December 2010
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} | cccc_CC-MAIN-2013-20 | Talk:20.109(F12) Pre-Proposal: Engineering Viral Magnetic Nanoparticles for Magnetic Hyperthermic Cancer Therapy
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This is a brainstorming page.
You are very welcome to write any crazy / non-crazy / inventive / conventional / knowledgeable ideas or information you may have about our project.
Some key words: Magnetic Nanoparticles (MNP), Viruses, Magnetic Hyperthermia, Bioengineering
Contents
What is Magnetic Hyperthermia?
Definition
How it works?
Under an alternating magnetic field, MNP releases heat due to relaxation of magnetic moments (hysteresis). This can cause an increase in temperature to the range of 41C to 47C. Since tumor cells are more heat sensitive than normal cells, they will be killed by this thermal dissipation.
Here is an interesting tidbit from a paper I was reading: "In addition to the expected tumor cell death, hyperthermia treatment has also induced unexpected biological responses, such as tumor-specific immune responses as a result of heat-shock protein expression. These results suggest that hyperthermia is able to kill not only local tumors exposed to heat treatment, but also tumors at distant sites, including metastatic cancer cells." (Kobayashi)
Current Research
• Clinical trials in prostate cancer
• Shows promising results when coupled with irradiation on breast cancer (mouse)
Current Limitations (This information will help us shape and define the problem.)
(1) To achieve the necessary rise in temperature with minimal dose of MNP.
In other words, this means:
• High specific loss power / specific absorption rate (SLP) of the MNP.
• why is higher applied dosage bad? > leads to unnecessary heat dissipation
(2) Lack of knowledge about the metabolism, clearance, and toxicity of MNP.
Biomedical potentials of MNP
• Could be used as early detection for the following using MRI:
• Inflammation
• Cancer
• Diabetes
• Atherosclerosis
• Drug Delivery
• Cellular labeling and tissue targeting
• Purifying and separating cells and DNAs
• Hyperthermia
• Transfection by magnetic nanoparticles
• Tissue repair
• Magnetic resonance imaging (MRI)
Types of Relevant Viruses
1. Tobacco Mosaic Virus (TMV)
• 18nmx300nm, helical
• Can withstand high temperatures up to 50C for 30mins (conventional hyperthermia involves heating up to 50C from an external source
• Safe for human consumption
• Mann group has active research on it
• 2130 molecules of coat protein
2. M13 Bacteriophage
• 6.6nmx880nm, helical (Length is too long - pose an issue in targeting cells)
• Lots of research done by the Belcher group, including attaching MNPs to M13 for imaging purposes
• We are familiar with the system
3. Cowpea chlorotic mottle virus (CCMV)
• 26nm, icosahedral
4. Cowpea mosaic virus (CPMV)
• 27nm, icosahedral
5. Brome mosaic virus (BMV)
• 28nm, icosahedral
6. Turnip yellow mosaic virus (TYMV)
• 30nm, icosahedral
Current Work in Viral MNP Attachment
Attachment of MNPs to M13 phage for in vivo imaging of prostate cancer
What we propose to do
See flowchart sketch.
Specific Aims
1. Identifying / Screening for appropriate virus vehicles and tumor-specific anchoring sequencse
2. Developing / Engineering viral MNPs
3. in vivo testing for efficacy of engineered vMNPs in mouse tumor cells.
We will start with using ferritin (Fe3O4) as the MNP.
Steps Stage 1: Virus Hunt
We need to investigate how the selected virus (likely one of the following: TMV, M13, CCMV, CPMV, BMV or TPMV) interacts with mammalian cells in vivo.
Stage 2: Screening for MNP binding site on virus
We will start by using Fe3O4 as our MNP of interest. With this, a protein coat screen of the selected virus for a protein coat that can bind with our MNP is necessary.
Stage 3: Screening for tumor-specific sequence binding site on virus
We need to do a protein coat or RNA screen of the virus for a region that can bind with a tumor-specific peptide sequence. If necessary, we might need to screen tumors for unique short sequences on their cell surfaces.
Stage 4: Virus engineering
We can now engineer wild-type viruses using specific protein coats or RNA regions isolated in Stage 2 and 3 to produce the viral MNP of interest.
Stage 5: in vivo testing
Perform an in vivo experiment by injecting the engineered viral MNPs into the circulatory system of mice that have developed tumors. By subjecting these mice to an alternating magnetic field under standard hyperthermia conditions and measuring the change in tumor size, we will be able to quantify the efficacy of using viral MNPs in magnetic hyperthermia.
Future directions:
• Experimenting with double layer MNP to increase response
• Target other cancerous cells
• Experiment with other types of viruses
Quantitative Goals (We can quantify with IC50 value)
• Currently, with the aid of 10Gy radiation, the hyperthermia treatment successfully accumulated less than 0.3mg Fe/g tissue. Dosage: 0.2mg Fe per gram of mouse. Say mouse is 25g, so 5mg total dosage injected. so 1% efficiency with the aid of radiation. (MNP sizes used: 70nm and 120nm; murine flank breast tumors were 150mm3)
Calculations:
From http://manalis-lab.mit.edu/publications/grover%20PNAS%202011.pdf, we estimated that a typical cell has an average density of 1.1g/mL. Since the murine flank breast tumors were 150mm3, and 0.25mg Fe/g of tumor was detected in the tumors, we can calculate that only a total of 0.0495mg of Fe is accumulated in the tumors. This gives a % efficacy of 1%.
• South Korean experiment: 75ug of MNPs were injected.
• From Belcher lab's paper, what is the % efficacy of using M13?
Potential Issues
• "The actual rotations of the nanoparticles are disordered because the microviscosity of the local environment in cancer cells is not constant, and effective elasticity depends on the binding conditions between nanoparticles and membranes."
but this is actually present because when treatment is done with individual MNPs, one side of the MNP is always bound to the targeted cell, so direction is never constant!
Future Directions
Useful Resources
1. Gupta AK, Naregalkar RR, Vaidya VD, and Gupta M. Recent advances on surface engineering of magnetic iron oxide nanoparticles and their biomedical applications. Future Medicine. 2007. 2(1), 23-39.
2. Bakoglidis KD, Simeonidis K, Sakellari D, G. Stefanou, and Angelakeris M. Size-Dependent Mechanisms in AC Magnetic Hyperthermia Response of Iron-Oxide Nanoparticles. IEEE Transactions on Magnetics. 2012. 48:1320-1323.
3. Great layman's way of explaining magnetic hyperthermia http://trialx.com/curetalk/2012/11/cancer-treatment-multifunctional-magnetic-nanoparticles-for-molecular-imaging-and-hyperthermia/
4. A.J. Giustini, A.A. Petryk, S.M. Cassim, J.A. Tate, I. Baker, P.J. Hoopes. Magnetic nanoparticle hyperthermia in cancer treatment. Nano LIFE 2010; 01: 17.
5. D. Ghosh, Y. Lee, S. Thomas, A. G. Kohli, D. S. Yun, A. M. Belcher, K. A. Kelly. M13-templated magnetic nanoparticles for targeted in vivo imaging of prostate cancer. Nat. Nanotechnol. 2012; 7 (10): 677–82.
6. Add more references as deem appropriate
Feedback
11/29 from Professor Angela Belcher:
1. Look at Nature Nano Belcher lab paper
2. Need to do very good characterization of materials using TEM, elemental analysis, etc.
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Why not add this quote to your bookmarks?
There can be no forced inspiration. Stojanovic, Dejan
This quote is about inspiration · Search on Google Books to find all references and sources for this quotation.
A bit about Stojanovic, Dejan ...
Dejan Stojanoviæ was born in Pec, Kosovo (the former Yugoslavia), in 1959. Although a lawyer by education, he has never practiced law and instead became a journalist. He is a poet, essayist, philosopher, and businessman and published six critically acclaimed books of poetry in Serbia: "Circling," "The Sun Watches the Sun," "The Sign and Its Children," "The Shape," "The Creator," and "Dance of Time." In 1986, as a young writer, he was recognized among 200 writers at the Bor (former Yugoslavia) Literary Festival. He also received the prestigious "Rastko Petrovic" Award from the Society of Serbian Writers for his book of interviews with major European and American artists and writers. In addition to poetry and prose, he has worked as a correspondent for the Serbian weekly magazine "Pogledi" ("Views"). His book of interviews from 1990 to 1992 in Europe and America, entitled Conversations, included interviews with several major American writers, including Nobel Laureate Saul Bellow, Charles Simic, and Steve Tesic. He has been living in Chicago since 1990.
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Life should be as colorful as the rainbow. Please remember, you are your own painter always....... Mak Kazeronnie
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To do nothing at all is the most difficult thing in the world, the most difficult and the most intellectual. Wilde, Oscar
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212 - The Extra Degree
The one extra degree makes the difference. This simple analogy reflects the ultimate definition of excellence. Because it's the one extra degree of effort, in business and life, that can separate the good from the great. This powerful book by S.L. Parker and Mac Anderson gives great examples, great quotes and great stories to illustrate the 212° concept. A warning - once you read it, it will be hard to forget. Your company will have a target for everything you do ... 212°
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"A dream is a scripture, and many scriptures are nothing but dreams."
Eco, Umberto on dream
"The ideology of this America wants to establish reassurance through Imitation. But profit defeats ideology, because the consumers want to be thrilled not only by the guarantee of the Good but also by the shudder of the Bad."
Eco, Umberto on america
"The comic is the perception of the opposite; humor is the feeling of it."
Eco, Umberto on humor
"I would define the poetic effect as the capacity that a text displays for continuing to generate different readings, without ever being completely consumed."
Eco, Umberto on poetry and poets
"Fear prophets and those prepared to die for the truth, for as a rule they make many others die with them, often before them, at times instead of them."
Eco, Umberto on prophecy
"The good of a book lies in its being read. A book is made up of signs that speak of other signs, which in their turn speak of things. Without an eye to read them, a book contains signs that produce no concepts; therefore it is dumb."
Eco, Umberto on books - reading
"Nothing gives a fearful man more courage than another's fear."
Eco, Umberto on courage
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"The pleasures of love are pains that become desirable, where sweetness and torment blend, and so love is voluntary insanity, infernal paradise, and celestial hell -- in short, harmony of opposite yearnings, sorrowful laughter, soft diamond."
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Photo Gallery: Celtics-Hawks G5
This first pic sums-up last night's loss. The rest of the pics & top play GIFs after the jump… [...]
May 9, 2012 KWAPT Post Game Galleries, Uncategorized Comments Off
Hawks shake up lineup for Game 5
Larry Drew is moving Kirk Hinrich and Jason Collins to the bench. I expected Al Horford to start. Even if he's still rusty, Horford is a better option than Collins. Marvin Williams is shooting 21% in this series. I'm guessing Drew wants him to defend Paul Pierce? This switch will put either Rajon Rondo or [...]
May 8, 2012 Chuck - Red's Army Uncategorized 1
Josh Smith is not limping
Here's an update on Hawks forward Josh Smith. I'll use my deductive reasoning abilities to say no limp = will play. If Smith can't go, Marvin Williams and Tracy McGrady will see time at power forward, reports CBS Sports. The real reason I'm posting this tweet is to poke fun at James Winfro, a delusional [...]
May 3, 2012 Chuck - Red's Army Uncategorized Comments Off
Update: Josh Smith doubtful for Game 3 with sprained ligament
The Hawk announced today via Twitter that Josh Smith, who left with 4:20 left in the 4th quarter last night, has a sprained ligament in his left knee. Atlanta's Josh Smith has a strained left tendon and his status is day-to-day. If Smith is unavailable for Game 3, then we'll see a lot of more [...]
May 2, 2012 John - Red's Army Uncategorized 3 | v0 |
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From Sugar Labs
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Founder, Earth Treasury, an NGO to link schools around the world for education and business. See Plans and Essays.
NEW PROJECT: Replacing Textbooks XOs and other netbooks cost much less than printed textbooks, so as soon as we replace enough of the textbooks with Open Education Resources, we can explain that OLPC + Sugar delivers better education while saving money. Mokurai has received permission to set up a server for this purpose at Sugar Labs, and is also raising funds to support it.
CrowdRise Fundraiser donations
Mokurai volunteers at OLPC and Sugar Labs as a volunteer coordinator, localization administrator (Khmer and Kreyòl), and general knoker (an especially Yiddish know-all, the kind who did math homework in pen), based on
• his training as a mathematician, classroom teacher, amateur musician and linguist, philosopher, and Buddhist priest
• plus his lifetime of encyclopedic reading, many years in high-tech market research and technical writing, and work in Unicode and Free Software.
Contents
Vision
End Poverty at a Profit all around by educating children to collaborate and not be helpless.
Quotes
• Epictetus - "Only the educated are free."
• Aristotle - "All men by nature desire to know. An indication of this is the delight we take in our senses."
More quotes
Mission
The mission is whatever planning, funding, research, development, and deployment is needed to make that happen, with a focus on Management by Exception in order to keep on top of what is needed in changing circumstances and make sure that nothing gets missed that we must have.
Sugar Labs has the Sugar software as its main focus, but needs to work with others on the rest of the mission. We should raise substantial funding to support these substantive projects, up to the point at which they can become self-sustaining, in the manner of the Grameen Group of companies.
These are the principal elements of the mission today. More will appear.
• Extend the OLPC and Sugar Labs work with evidence-based education research, curriculum development, and the redesign of textbooks, taking maximum advantage of software on the XO, and of the best research that we can find or carry out on how children learn, and what is of greatest value for them to learn.
• Engineer appropriate solutions for electricity and Internet connections in even the poorest and most remote villages in every target environment, in collaboration with university Schools of Engineering, Engineers Without Borders, and others, in order to maximize the usefulness of XOs to children everywhere.
• Work with microfinance organizations to place these electricity and Internet solutions along with XOs. The intention is to jump-start local economies by selling modest amounts of surplus power and bandwidth, and thereby raise the money to pay off the original loans and make further investments.
• Create an R&D consortium to further all of these goals and whatever else turns out to be necessary. We know that issues of economics, governance, social attitudes, and sustainability are important. What do we need to know, and how can we come to know it? What can we learn from the children themselves, and from teachers, parents, and others?
• Tap into Barack Obama's plans to increase global development aid by $25 billion annually, including a $2 billion Global Education Fund; into the UN Millennium Development Goals program; Make Poverty History; and all of the other initiatives that share our vision, even if they don't know it yet.
• Save as many languages and cultures as possible from extinction by teaching the children how to record them.
• Link children, schools, and communities together around the world in a safe manner for collaborative development.
• Teach children how to create sustainable international businesses together using their new knowledge and skills.
Current Projects and Partners
OLPC and Sugar Labs, of course, within the scope of their own missions to provide hardware, software, content, and teacher training materials. In each case, the intention is to expand to a comprehensive, integrated program including infrastructure, education, community development, and economic opportunity. Volunteers, donors, and partners welcome.
By country
• Ghana
• Nana's House (school and orphanage), computers, Internet, and accessories for students and teachers
• Winneba Linux Users Group, Linux+Sugar Installfests
• Catch IT Young youth computer training
• University of Education, Winneba, research, curriculum, teaching materials, localization
• OneVillage Foundation Ghana, Winneba wireless broadband project
• Nigeria
• Fantsuam Foundation microfinance project and Cisco Network Academy
• Kenya
• Asante Foundation Maasai schools and cultural preservation
• Uganda
• Bunabumali Good Shepherd Orphanage and School, computers, accessories, electricity, Internet
• Mt. Elgon coffee growers co-operative equipment and training
• School programs and the rest
• Tanzania
• Mt. Kilimanjaro coffee growers co-operative equipment and training
• School programs and the rest
Components
• Interactive digital textbooks, with Lots of partners.
• Free computers for schools, two per pupil: one at school, one at home. Possibly Computers4Africa
• Flash drives for carrying software and work, so that students can use them on any computer
• Electricity generation and storage, Engineers Without Borders
• Broadband Internet, OVF Ghana
• Microfinance, Fantsuam Foundation
• Economic opportunity, education program to be developed at EduForge, social entrepreneurial investors welcome.
Analysis
The following is as much a prediction as a set of goals. Much of this will happen regardless of us. We can make those parts happen sooner, and more effectively. The other parts have to do with the new ideas that we are discovering and shaping together, particularly integrated development that includes the economy, the social structure of society, and spiritual growth. The only project that I know of that currently does this is the Sarvodaya Shramadana Movement in Sri Lanka, which I commend to your study and, if possible, participation.
Preliminary
For several years I have been seeing a gradual coming together of many strands in development toward the possibility of an integrated strategy that can be replicated worldwide. After the initial stage, it should all become self-sustaining in the manner of the Grameen Bank, Grameen Phone, and the like, and thus independent of the usual sources of non-profit funding. Here are the leading strands.
• ICT4D, including newly powerful mobile phones, computers, and Internet at prices that make sense in even the poorest and most remote villages, given the promise of economic growth to enable paying back costs.
• One Laptop Per Child, for many reasons, including a rethinking of curricula, textbook content, and publishing models. Scarcity of information is no longer the limiting factor in education. Electronic publications still take effort and time to write, but the reproduction cost on the Internet is nearly nil. Governments will soon realize that they don't have to buy textbooks. They can contract for writing textbooks and other materials with the proviso that the government, or we should say the public, owns the copyright. We can take advantage of Free Software and Open Access publishing throughout this process, and of a century of discoveries in how children really learn. Currently XOs are $198 each, with $75 versions promised for 2010. GiveOneGetOne is to start up again in November.
• WiMax and other broadband technologies that can provide Internet to whole countries (90-95% coverage) for $10 per person installed.
• Fiber optic cables for every country in Africa. There is one installed on the West Coast, two being laid on the East Coast, and four more promised. Rwanda and the other dozen landlocked countries in Africa are making deals with their neighbors for overland links. Some regions in Central Asia may take a little longer.
• New satellite launches that promise both to break the current cartel pricing in Africa, and to link Africa directly to South America, the Middle East, and Asia, not just by multihop through Europe.
• African banks that are now in a position to start creating a continent-wide network and to roll out electronic banking.
• Global GIS initiatives dealing with mapping critical poverty issues: environment, water, agriculture, climate, health, and much more.
• More than 100,000 of the million and more NGOs of the world now connected with each other through Wiser Earth.
• Barack Obama's plan to double US Foreign Aid, and redirect it to much more efficient methods (toward helping the poor, not just subsidizing US agriculture, manufacturing, and consulting). This includes a $2 billion annual Global Education Fund.
• The microfinance movement's casting about for the next big challenge. I predict village electricity and Internet along with school computers, and I am working on alliances toward that end.
Sugar Labs has taken over software development for the OLPC XO. Walter Bender of Sugar Labs is putting together a research consortium to tackle problems in education, and I am assisting in recruiting, and in problem definition. My program is not of the usual kind, where we know what subjects we mean to tackle.
My version of the mission is: Whatever turns out to be needed. My self-appointed task is to find the holes in current programs, and fill them, first with my own efforts and second by recruiting others to do the work, research further solutions, and plan where we might go next. Among the critical tasks are village electricity and Internet, redesigning curricula and textbooks, and bringing all of this together into target communities with microfinance, with a flexible, integrated business plan for whole societies to advance societal infrastructure (education, health, clean water, and other essentials), and the private sector (sole proprietorships, sustainable international companies, producer and consumer co-operatives), and shared values.
It is no longer practical to impose the illusion of shared values on a society. They must grow out of the situation. The report on OLPC's early effects in Ethiopia gives a glimpse into where we are going. Within a few months, in a highly traditional society that has valued teaching politeness and obedience over subject matter in schools, and where asking questions of a teacher was considered insulting, the XO and its software have opened up a new, collaborative relationship between teachers and students. This is in no small part attributable to the collaborative nature of the XO's Sugar and other software. Access to the information riches of the Internet is another important factor. See Academic Papers on the OLPC Wiki for this and other recent reports.
There is more, but that will do to begin with.
General Consequences
• We are looking at the possibility of ending poverty as we know it within a generation, except in the most repressive countries (Burma and North Korea are the most likely, but a few others might possibly regress).
• We are doing this by means that promise far freer markets, with
• Market access for all, at least for electronic markets, including easy entry and exit
• General availability of essential economic information, including the price of almost anything right up to the moment
• General availability of production technologies, except where embargoes linger (Cuba, Burma, Syria, Iran, North Korea and a few others)
In short, these and a few other points add up to the closest approximation to the economic ideal of Perfect Competition ever seen, worldwide. We can confidently predict the largest explosion of productivity and prosperity ever seen, and at some point the end of the continual search for ever-more-benighted denizens of ever-poorer countries to ship jobs off to. The existence of wage differentials between countries is conclusive proof that their market relations are not free.
• A complete communications network, in which every person will have the means to connect with any other person who answers the phone.
• Directories and social network sites that enable everybody to find the right people to do business with and make alliances with for any economic, social, spiritual, or political purpose.
• We can confidently predict an explosive growth of civil society organizations worldwide, among other things.
AKA
• Edward Mokurai Cherlin/Czerwin
• גרשון בן יסעף
• Эдуард Георгеевич Черлын
• 장영구/張永久
• 法雲默雷/धर्ममेघशब्दगर्ज
Contact
Background
Mokurai has extensive experience in every aspect of computers, as a tech writer, editor, and publisher, global market analyst, and software developer. Previous work includes math software and textbooks, Computer Science papers, Free Software for voting, Unicode support on the XO, fighting spam around the world, and earlier anti-poverty projects. He can sometimes get people to stop talking past each other and answer the real questions (though not necessarily Nicholas %-[ ). See, for example,the IETF discussions on multilingual URIs.
When I wrote a guide for new Internet users at Newbie.Net, there were three questions I couldn't answer:
I'm contributing information on countries and languages on the OLPC Wiki, including writing systems, fonts, keyboard layouts, sources of literature, and other items of interest, and administering localization projects. I will be adding material on education and on the other impacts of the Laptop. It will have major effects in social development, health, economic opportunity, politics, and other important areas.
Contributions
I started to work on OLPC documentation, but then I discovered that even more pressing needs were being ignored. So now I have appointed myself Shadow Chairman & CEO of OLPC. Don't tell Nicholas.
Social Networks
I'm on too many of these networks. If you want to connect with me, please use LinkedIn, Wiser Earth, or Flickr for photos.
Wikis
There are too many of these, too.
Generalist
Buddhist priest, software developer, market researcher, technical writer, Peace Corps volunteer, cook, goatherd, music teacher...
I edited the Geode processor manuals for National Semiconductor, before they sold the product line to AMD. (The Laptop contains an AMD Geode processor.)
Languages: Hebrew, German, Latin, Russian, French, Swahili, Korean, Japanese Chinese, Sanskrit, Pali, Classical Greek, Lojban, Klingon
Programming languages: APL, LISP/Scheme, FORTH, SNOBOL, FORTRAN, COBOL, Algol, Java, C, C++, Pascal, Smalltalk, Python, scripting languages. And I'm learning Squeak.
Unicode
Free/Open Source Software: I-APL, Open Voting Consortium, others
Math
Science Check out Astronomy Picture of the Day and the world's biggest telescopes, for neutrinos and gravity waves.
Co-founder of global anti-spam organization, The Coalition Against UCE (Unsolicited Commercial E-mail)
Music: Yale Concert Band and Marching Band, clarinet; First Prize, Classical, in first-ever Foreigner's Korean Music contest of the Korea Herald on gayageum; Slavyanka Russian Chorus; Music Around the World pre-school multilingual music program; banjo, recorders, spoons, piano, harpsichord, dumbek
Simputer: Simple, inexpensive, multilingual computer for poor people
Village telemedicine over wireless
Science Fiction: John Brunner would have loved the OLPC project if he had lived to see it. Check out Stand on Zanzibar (includes national development projects in fictional countries), The Shockwave Rider (integrated disaster recovery and sustainable communities), The Sheep Look Up (environmental catastrophe), and The Stone that Never Come Down (What if people couldn't ignore information they have?).
Geek code GAT d-- s+:+ a+++ C++ UL++ P+ L+++ E- W++ N+++@ o+ K++ M+ b+++ e+++ h---- r+++ w--- APL++++ House, MD+++
Basic level in Korean, Chinese, Swahili, Japanese, Spanish, German
Intermediate level in Russian, French
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East Norway
From Wikitravel
Scandinavia : Norway : East Norway
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East Norway (actually southeast) is the region surrounding the capital Oslo, where the largest number of people live.
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[edit] Understand
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[edit] Get in
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Oslo totally dominates this region. Oslo and its airport at Gardermoen is the transport hub for East Norway. Roads and railway lines has Oslo as their focal points. All railway lines, including the airport express train, terminate at Oslo Central Station ("Oslo S"). Main roads E6, E18, E16 and Road 4 meet at or near Oslo S. Regional as well as long distance buses depart from the bus station next door to Oslo S. Oslo Subway (T-banen) has a main station underground next to the train station.
[edit] By plane
• Fagernes Airport (Leirin - operated by DOT), (10 minutes from Fagernes), [1]. edit The local airport with daily connections to Oslo (30 minutes)
[edit] By bus
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Difference between revisions of "Meran"
From Wikitravel
Burgraviate : Meran
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(added listing Bar Rossini)
(added listing Sketch Clublounge)
Line 88: Line 88:
*<drink name="Café Forum" alt="" address="Via Leonardo da Vinci 11 (Postgasse)" directions="" phone="" url="" hours="" price="" lat="" long="">A fine Cocktails and Wine Bar.</drink>
*<drink name="Café Forum" alt="" address="Via Leonardo da Vinci 11 (Postgasse)" directions="" phone="" url="" hours="" price="" lat="" long="">A fine Cocktails and Wine Bar.</drink>
*<drink name="Bar Rossini" alt="" address="Corso della libertà 19" directions="" phone="" url="www.rossini-bar.it" hours="" price="" lat="" long=""></drink>
*<drink name="Bar Rossini" alt="" address="Corso della libertà 19" directions="" phone="" url="www.rossini-bar.it" hours="" price="" lat="" long=""></drink>
+
*<drink name="Sketch Clublounge" alt="" address="Passegiata lungo Passirio 40" directions="" phone="" url="www.sketch.bz" hours="" price="" lat="" long=""></drink>
Revision as of 19:16, 26 February 2009
Meran (Italian: Merano) [1] is the second largest town in South Tyrol with a population of about 35,000 (63,000 including the metropolitan area). A slight majority (51.5%) of the population is German-speaking, while the others are Italian-speaking. It's an old spa town with very charming promenades and interesting highlights.
Contents
Get in
Meran is located outside of the Brenner line and whether you want to reach the town by plane, by train, by bus or by car you have likely to reach before Bolzano and from this point Meran. Meran is located 33 km (20 miles) north-west from Bolzano.
By plane
The Airport Bolzano Dolomites is nearest airport, which is located in Bolzano.
Getting to/from the airport
Many hotels offer a transfer from Bolzano airport, especially if you book through a travel agency (in this case you probably have the possibility to have a transfer from other major airports). In the airport you will find some rent-a-car agencies. http://www.taxidriver-tirol.at/
By train
In order to get in Meran by train you have to arrive in Bolzano first and from here you can take the train to Meran (every 30 minutes). When you buy the ticket at the departure station you can have the ticket from Bolzano to Meran included, saying that your destination is Meran. The Meran Central Rail Station is closed to the town centre.
By bus
Some German, Austrian and Swiss travel agencies offer direct bus connection to Meran. Normally international bus lines stop in Bolzano and from here you can take the bus Bolzano-Meran (bus line 201) at the Bolzano Bus Station or other stops inside Bolzano (like Dominikanerplatz). Buses are run by SASA [2], which uses the same orange buses you can find inside cities, and SAD's [3], with grey-coloured buses (they operate on the same line). There is a departure every hour. A fare from Bolzano to Merano costs EUR 4 (only 2.61 with value card).
By car
You have to exit at Bolzano South on motorway A22 and taking the modern freeway. In Meran there are three exits: Sinich/Meran Süd, Meran Zentrum and Algund (freeway end). If you are coming from Landeck in Austria or Engadin, Switzerland, you can follow the signs along the road. 90.152.220.34 15:49, 28 October 2008 (EDT)
Get around
The best way in order to discover Meran is by foot, but it's covered by an excellent public transport system, which is composed by buses and a chair lift to the village of Tirol.
By Bus
In Meran there are 9 bus lines (generally 6 am - 9 pm) run by SASA [4] and 1 of this have also a night service (9 pm - 1 am). Buses pass frequently (every 15-25 minutes). Buses run always on time.
Stamp your ticket at the start of its first use (there are green - on new buses yellow - stamping machines). You have to buy another ticket if you stop and you catch a bus after 45 minutes after the printing (only with single trip ticket or spent value card). Payment is by the honor system and inspectors check for valid tickets. If you don't have one, it's an instant EUR 25 fine (plus the fare you were supposed to have paid). All timetables and bus maps you can find free in the tourist offices or in the bus station.
All urban buses stops are request stops (exept end of the line): If you want to get off press the red (in some blue) button, while if you want to get on a bus you have to wave your hand.
Chair lift
Meran is connected with the village of Tirol - located on a hill above the town - by a chair lift, which is in service between April and November.
By Taxi
Taxis are only on call available. Meran's taxi service is powered by Radio Taxi 24h24 calling 0473 21 20 13.
By bike
Meran has a good bike trail system - but not so developed as in Bolzano, though - but around the town it's excellent. Maps are available in tourist offices and online [5].
Rentals are available in the following places:
• Rail Station
• Spa Building
• Tennis Centre
The service is available from April until mid of October (M-Sa 9AM-7PM) and it's free. You only have to pay a EUR 5 bail - which is returned if the bike has not been damaged.
By car
The public transportation or your own feet should be enough in order to travel inside Meran. Finding a parking in the town centre can be complicated.
In winter (from November to March) the whole city is forbidden for the EURO 0 cars in order to prevent from air pollution. In cases of high concentration of polluted substances the streets are forbidden also for EURO 1 cars.
See
Museums, Galleries, and Memorials
• Touriseum - South Tyrol Museum of Tourism with Botanical Garden [6] - admission €9.80 (students/handicapped people €7.50, over 65 €8.50, after 6PM €5.00, children up to 6 years free) It's a very interesting highlight. The Museum hosted at Trauttmansdorff Castle reports the long history of tourist tradition in South Tyrol. The ticket includes the visit to the well-kept and quite wide Botanical Garden. The Museum is open only from the first half of March to the first half of September, considering that the Botanical Garden is closed during the cold season.
• City Museum - admission €2.00 (reduced €1.50) It's located in a former hotel, it shows interesting archaeological and historical founds.
• Princely Castle Museum - admission €2.00 (reduced €1.50) de, it Building from the 15th century located in the old town with an interesting exhibition for lovers of medieval history.
• Jewish Museum - free entry. The small museum located at the only South Tyrol's Synogogue reports the history and documentation about the Jewish community in South Tyrol.
• Women's Museum Evelyn Ortner - [7] - free entry. Unique museum about women specialized in culture of women's everyday life.
• Meran Art - City Gallery - [8] - free entry. Exhibitions of contemporary art, literature and architecture and other interesting features.
• Monument of Empress Elisabeth - is a statue situated at the Summer Promenade's entrance, which was modeled with white marble after Sissi's assasination in Geneva in 1898. The Empress of Austria visited Meran four times - the last time being one year before her death. During the fascist dictatorship it was deplaced, cutting off the statue's head. After WWII the statue was replaced and the head re-modeled. It shows an interesting parallel with the Monument of Walther von der Vogelweide in Bolzano.
Churches
• Main Parish Church Gothic bulding with Baroque features in the old town built in different periods between 1302 and the 18th century. Its bell tower is one of the highest in South Tyrol (83 metres) and it shows 7 clocks.
• Holy Spirit's Church Gothic building built between the 14th and 15th century beyond the Passer river. A building built by Fascist Italy in rationalist style hides the church, because the Gothic style was considered to be a symbol of the German-speaking countries.
• Holy Mary's Church Located in the district of Untermais it's an interesting Romanic building built in the 12th century.
Buy
Eat
• Restaurant Kallmünz, Piazza Rena 12.
• Restaurant Sissi - Andrea Fenoglio, Via G. Galilei 44, [9].
Drink
• Café Forum, Via Leonardo da Vinci 11 (Postgasse). A fine Cocktails and Wine Bar.
• Bar Rossini, Corso della libertà 19, [10].
• Sketch Clublounge, Passegiata lungo Passirio 40, [11].
Sleep
• Hotel Palace Merano - Espace Henri Chenot, Via Cavour 2, [12].
• Hotel Aurora, Passegiata lungo Passirio 38, [13].
Contact
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Valparaíso
From Wikitravel
Chile : Central Chile : Valparaíso
Revision as of 12:32, 26 January 2013 by 201.214.125.238 (Talk)
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For other places with the same name, see Valparaíso (disambiguation).
Valparaíso is a city of around 300,000 on the Pacific coast of Central Chile. Frequently referred to as simply Valpo, it is located approximately 120km west of the capital, Santiago de Chile. The city is widely known for its bohemian culture, brightly colored houses, and beautiful seaside views.
View from downtown Valparaiso (Chile) to one of the hills.
Valparaiso (Chile), focusing on one of the escalators (Ascensores) connecting the harbour area to the hills.
Understand
• The city's main economic activities are shipping, petroleum refining, and tourism.
• Valparaiso was designated a UNESCO World Heritage Site in 2003.
• Visiting Valparaiso has less to do with touring specific sites than it is about roaming the chaotic, hilly streets, and taking in the views and ambiance. There is also an active nightlife and a constantly changing variety of artistic events.
Get in
By plane
Valparaiso does not have its own airport. The closest airport with commercial service is Arturo Merino Benitez International Airport (SCL) in Santiago, 115km from Valparaiso, which offers extensive domestic and international service.
To to get to Valparaíso from Santiago's airport, you will catch a bus heading to Pajaritos outside of the airport terminal. This will drop you off at the North side of "Pajaritos" a bus/subway station on the outskirts of Santiago, cross to the South side of the Subway station to get to the Bus Platform. From here, buses leave frequently for Valparaiso and other destinations; you may also take the subway into downtown Santiago. It is generally not necessary to have a bus ticket before arriving at Pajaritos.
Alternately, there are many transfer service companies at the airport, a van for max 8 people is around 85.000CLP.
Also, there are many rent-a-car companies at the airport. By car from the airport to Valparaíso is only 1 hour.
By train
The Metro Valparaíso or Merval runs between Valparaiso and Viña del Mar, as well as surrounding communities.[1] It runs from 6.00am to 11.30pm, and is new, clean and fast. Adult fares range from Ch$204 to Ch$1080 depending on the time of day and the distance travelled, but value cards of a minimum of Ch$1200 must be used; single tickets are not sold.
By car
While Valparaiso itself can be a bit of a difficult city in which to drive, the area's highway system is generally of good quality. Note that there are often tolls on highways.
By bus
Buses from a wide variety of destinations within Chile have scheduled service to Valparaiso, in addition to service to the Argentine city of Mendoza. The bus terminal is located close to the National Congress building.
Approximate bus travel times to/from Valparaiso:
• 1.5 hours: Santiago de Chile (many times every hour)
• 7 hours: La Serena (every other hour)
• 12 hours: Mendoza, Argentina (the road may be closed in winter due to bad weather)
Local buses also ply between Viña del Mar and Valparaiso, taking about 15 minutes each way. Fares range from Ch$350 to Ch$380.
By boat
Some cruise ships dock in Valparaiso, mostly as part of a long South American itinerary. Also possible is a Freighter Cruise from Mexico, taking two weeks and making several stops along the way.
Get around
The city micros are run by Transporte Metropolitano Valparaíso.[2] Exact routes and fares can be found under "Empresas" on the website, and single journeys cost about Ch$250 for local routes and Ch$300 for routes running between El Plan and the hills.
Colectivos are taxis painted in black with yellow roofs that run fixed routes, and are a very common mode of transport between (and within) Valparaiso, Viña del Mar, and other surrounding areas. The cost of the trip, while more expensive than the bus or metro, depends upon the distance being traveled following a system of zones. There are also regular taxis that do custom rides, but they are less common and more expensive. This type of taxis often congregate in the area around the Plaza Anibal Pinto.
The recently completed light-rail system, Metro Valparaíso or Merval, runs along the coast. It starts at Valparaiso's port and heads into Viña del Mar and other more rural locales. The metro provides quick access to major places of interest, and is only slightly more expensive than taking public buses. Adult fares range from Ch$204 to Ch$1080 depending on the time of day and the distance travelled, but value cards of a minimum of Ch$1200 must be used; single tickets are not sold.
Ascensores, funiculars, ply between El Plan, or the coastal strip, with the cerros, or hillside communitiies. They are for the most part old and creaky, but generally reliable. The fare may sometimes differ between going up and going down, but cost about Ch$300 each way. The ascensors are a unique mode of transportation in Valparaiso, and offer gorgeous views of the cityscape, port, and the Pacific Ocean.
See
• Cerros Alegre and Concepción
• Plaza Echaurren – Serrano Street
• Cerro Bellavista: residential area & artistic hill with colorful murals
• Museo a cielo abierto: 20 murals spread out over cerro Bellavista
• Ascensor & cerro Polanco: unique vertical funicular on Polanco hill with plenty of nice paintings
• Cerro Cordillera
• Banking area - Prat Street
• Paseo 21 de Mayo (Cerro Artilleria)
• La Matriz Church and surroundings
• Ascensores (inclines)
• La Sebastiana, one of three homes of poet Pablo Neruda (cerro Bellavista)
• Ex Cárcel, a former jail turned cultural center and concert venue
• Museo Naval y Maritimo (Naval and Maritime Museum), Paseo 21 de Mayo 45, at top of Ascensor Artillería, 56 32 2437651, [3]. Tuesday to Sunday, 10.00am to 6.00pm. This museum is dedicated to military naval exploits and battles, and puts a large focus on the Chilean victory against Peru and Bolivia in the War of the Pacific.
Do
Going to Valparaiso and not going on the ascensores (inclines) is like going to Venice and not taking a ride on a Gondola, only that the ascensores cost as little as 100 Chilean Pesos (around 20 US cents). They are also of practical use as they help many local people get to the higher parts of town, saving them from having to walk otherwise long and steep pedestrian routes.
During the last week in the year, Valparaiso holds an annual carnival that everyone should experience at least once in their lives. Each year the festival centers around a different country, from which performers and artists are invited to come and represent their culture and their work in theater, music, and the performance arts. Most activities are free and are held outdoors. The celebration culminates with a New Year firework display that within five of the most beautiful in the planet. Oops, but get ready in time because the city's population triples on those dates. I recommend visiting the Mirador del Cerro Artillery, panoramic view of the city of Vina del Mar, Reñaca, Con Con and more ... It reaches through the "lift" Artillery, in operation since 1893 (ask for Customs plaza area), its current value is 250 Chilean pesos, on the first floor is the Mirador "Walk May 21," (delivered to the community in the year 1911) in which impossible not to enjoy the restaurant "Calaufquen", typical dishes of fresh seafood, with a fair value. We are here with a Craft Fair in which they can buy from winter clothing (ponchos, Ruan, scarves, socks, gloves, wool hats), souvenir of the most varied models and prices, up figures and jewelry from lapis lazuli (blue stone semi-precious which is only in Chile and Afghanistan), by price and quality of the stone, I recommend the last local. Also visit the Naval Museum "(500 Chilean pesos) whose income is in the midst of the Paseo.
• The German Pirate (myvalparaiso.cl), [4]. Amazing tour by a German man who's lived in Valparaiso for years. He seems to know everything and everyone about the place. He speaks Spanish, English and German. Discounts for groups. You're unlikely to find a more immersive tour of Valparaiso.
Learn
The universities of Valparaiso are:
• 'University Federico Santamaria' [5]
• 'University of Valparaiso' [6]
• 'University of Playa Ancha' [7]
• 'Pontifical Catholic University of Valparaiso'[8]
Many international students study at the Catholic University and the University of Valparaiso.
Work
Buy
Valparaiso, to its charm, is not a city of malls and department stores. While several large grocery stores are present, most other shopping is done in smaller, non-chain stores tucked in along crowded city streets, or with street vendors; larger chain stores (and more upscale goods) are more commonly found in nearby Viña del Mar. A large shopping center, however, is found on the eastern end of Avenida Brasil.
Eat
The most traditional food in Valparaiso is the Chorrillana, a heaping mound of french fries topped with steak, onion, and eggs. You can eat this in the traditional restaurant J Cruz. Fresh seafood is readily available in many small restaurants around the city, especially around the muelle (wharf) areas, and is considered a must for any seafood lover. Neighboring Viña del Mar features a much larger (and more expensive) variety of international cuisines, including Thai, Mexican, and Argentine.
There are also some restaurants which specialize in different seafood dishes near Mercado Puerto, which is near the last metro station. The more the customers dining inside the restaurants, the better the dishes you'll be likely to get.
Bakeries are located on nearly every block, and produce quite delicious breads that can be had warm and right out of the oven at almost any time throughout the day. They are best enjoyed smothered with palta, which are grown en masse in Chile (palta is the Chilean word for avocado, known in most other Spanish-speaking countries as aguacate). In addition to the many types of bread, another widely available snack to keep you settled as you walk the streets are empanadas, a flaky pastry, almost like a croissant, filled with meat or cheese.
Budget
On the second floor of the Mercado Cardonal (cnr Ave Brasil and Uruguay) there are a few excellent, cheap and midrange restaurants serving lunch.
• Chile - Suecia, Calle Bellavista (Just off the square). Open even on Sundays. Good sandwiches, hot dogs and set menus at $2500.
• El Valenciano, Avenida Colon 3110, +56 32 225 1619. Delicious chicken, good sandwiches and good value meals.
• Estación Cielo Amierto, Ferrari 68 (Cerro Bellavista). A cute cafe on the Cerro Bellavista which has juices, smoothies, and sandwiches.
• Los Portenos II, (at the corner of Valdivia and Cochrane), 225 19 15. Delicious seafood dishes and many local people choose this restaurant at weekends.
• Cafe del Poeta, Plaza Anibal Pinto (Opposite the statue of A. Pinto). Good place for a sweat treat. Try the truffa de chocolate.
Mid-range
• Bijoux (Bijoux Restobar), Abtao 561-A, Cerro Concepcion, 56 9 9548 2321 (). Beautiful little Restaurant in the heart of Cerro Concepciòn. Instead of a menu card, the chef and owner comes to you and according to the daily market specialities and your wishes he creates an individual menu just for you.The food is always fresh, delicious and offers an unique experience in Chile. cl$7900.
• Le Filou Montpellier Almte Montt 382. Great French-run restaurant in Cerro Concepciòn.
• Epif Calle Dr. Grossi 268, Cerro Alegre. Tastey vegetarian food and drinks at reasonable prices. Cozy cafe environment with great music and service.
• Delicatessen Emporio, Urriola 383, C. Concepcion (Head north (and up) from the Armada main buiding - two blocks), +56-32-2339373, [9]. Beautiful food in a small, romantic setting. Carpaccio with oysters was exquisite, Garbanzo soup was flavorful (read: spicey), fresh and probably the best I've ever had. 7,500 for a full lunch.
• La Concepción Papudo 541, Cerro Concepción.[10] Voted best restaurant in Valparaiso in many magazines and on TripAdvisor. They serve everything from daily fresh fish to classic Chilean dishes with a modern presentation.[11]
Splurge
Cafe Turri Paseo Gervasoni (by the ascensor conception) great views and good food
Drink
On weekends, the time to go out for a drink (Chilean people call it "salir de carrete") starts no earlier than midnight, though somewhat earlier during the week. The pubs and clubs close at 5 AM on weekends, and 4 AM on weekdays.
Drinking alcohol in the streets is not allowed and 18 years is the minimum age for drinking alcohol, though enforcement of these rules is somewhat lax. If you are under 18, you may not be allowed entry into some pubs.
Chile is a major wine-producing country, and bottles of fairly tasty wines can be had for slightly more than US$1.
Nightlife
• La Torre - offers inexpensive drinks, and is frequented by university students
• Balmaceda
• Barcelona
• La Piedra Feliz - a more expensive and touristy club that often features salsa dancing, mosty for the older crowds
• Club El Cielo
• Club Stockolmo
• Club El Huevo - one of the largest dance clubs in Valparaiso which usually features a young crowd [12]
• Bar La Playa
• Mascara - caters to an artsy and gay/lesbian crowd
Many clubs and bars are also found in Viña del Mar. Public transportation and taxis continue to run throughout the night, making it entirely feasible to have accommodations in one city while going out for the night in the other.
Coffee
• Puro Cafe, Calle Edwards, 301, Valparaiso, + 56 9 96380239. One of the very few places in Chile to have real espresso, not instant coffee. The cafe has beautiful and comfortable furniture, making probably the best place in Valparaiso for coffee.
Sleep
Budget
• Hostel Casa Verde Limón [13] Cumming 198, (56) (32) 2121699, nice living room where you can meet people, very helpful staff, dorms from $5500
• Hostal Pilcomayo, Pilcomayo #491 (Cerro Concepción), 032-2251075 ([email protected]). Basic rooms, very friendly atmosphere. The large living rooms makes it a good meeting place. Free internet.Dorm room 6000 per person.www.hostalpilcomayo.cl
• Angel Hostal [14] Cumming 160 Cerro Carcel, (56)(32) 2126940. Dorm room 7000 per person. Double room 8000 per person, matrimonial and single beds. Good breakfast, decent rooms, friendly helpful staff, good place to meet people, free internet and some tickets to nightlife bohemian experience.
• Hostal Girasoles [15] Almirante Montt 167, (56)(32) 2331024. Dorm room 8000 per person. Double room 15000 per person with breakfast, WiFi. They have sinlges as well. Clean rooms and bathroom and a central location close to Plaza Anibal Pinto. From the bus terminal you can catch a colectivo towards Anibal Pinto for 200 pesos, Almirante Montt is one of the streets off the plaza uphill.
Mid-range
• APARTMENTS: Valparaiso Experience, Pasaje Santa Margarita, Cerro BELLAVISTA, Valparaíso, Chile (Strategic central location on residential and artistic hill Bellavista, boasting great views over The Pacific ocean and coastline), (+56 9) 88308764, [16]. Valparaiso Experience offers fuly furnished ocean view apartments on residential cerro (hill) Bellavista. A remodeled building from 1904 with 3 apartments: Queen Mary Duplex - 4 bedrooms/2 bathrooms/large living-kitchen and 2 deck terraces with panoramic views - sleeps max. 8, Pablo Neruda Apartment - 3 bedrooms/1 bathroom/living/kitchen/patio sleeps 5-6, Bellavista Cottage - 2 bedrooms/1 bathroom/kitchen-living/garden with deck terrace and a couple of generous peach trees. A new building on the same central location with 4 luxury ECCO duplex apartments, each provided with solar panels/double glazing windows/central heating/2 bedrooms/2 bathrooms/full kitchen/bright living/ample deck terraces with panoramic ocean views.
• The Mirador Bed and Breakfast, 251 Levarte, [17]. A very comfortable hospedaje in the Playa Ancha sector of the city, with several rooms, small apartments, and a balcony with a great view of the city and port. Internet and Wi-Fi. A nice kitchen to use. Parking. Marisol, the owner, is wonderful and very helpful.
• The Yellow House, Capitán Muñoz Gamero 91, Cerro Artillería, Valparaíso, Chile (The Yellow House is easily reached by using the Ascensor Artilleria, on foot, by public transport or by car.), (56) 32 2339435, [18]. The Yellow House has 7 comfortable guest rooms. Most rooms as well as the homes two galleries, living and dining areas offer wonderful views of the port and harbour and on a clear day extend as far as the AndesMountains separating Chile and Argentina. The Yellow House also has a book exchange, WiFi, cable TV and a selection of board games. The house was built in the late 1800s and has been fully restored. The "Ocean View" room, as the name indicates, has the best view and is really worth it.
• Residencia en El Cerro, Pasaje Pierre Lotti 51, Conceptione, Valparaíso, Chile (Pierre Lotti 51 is easily reached by using the Ascensor Concepcion.). For absolute quietness, except for the creaking floors, try Residencia en El Cerro, Pasaje Pierre Lotti 51. Next door at 43 there is also accommodation. This Hostal is on an alley where no traffic get and the gardens add a little attractive colour. A twin room costs 30,000 a night. Breakfast is just OK with coffee/tea, bread, butter and jam. The place is in its original 1880`s decor - maybe. Wi-fi, TV.
Stay safe
In the context of Chile being a relatively safe country, Valparaiso is amongst its more dangerous locales, like many harbour cities around the world. Mainly, watch out for pickpockets, for instance avoid hanging your purse or bag in the back of your chair when seated, because it may get stolen. Violent crime is very uncommon, but normal precautionary measures should be taken; while in the street, do not display expensive jewelry. The port area (called "Puerto") is generally considered to be dangerous even during the day.
Contact
Cope
• There is a laundry in the mall of Hotel Prat. 5kg $3700.
Consulates
Get out
• Viña del Mar - The beachtown Viña del Mar is only ten minutes by train from Valparaíso, and slightly longer by bus. If you take bus 612 from Plaza Echaurren you will get a full tour of the Valpo hills, and you can jump off at La Sebastiana.
• The idyllic village Quintay is 45 minutes to the south by car. Take a colectivo from Calle 12 de Feberero, behind the bus terminal, 'they leave as soon as they fill up. $1400.
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This publication is the final issue in this series. In future, statistics on housing finance provided by savings and trading banks will be shown in two other ABS publications as follows:
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: Well, whaddaya know. The rubric problem was on my end after all. You can get your rubrics here. And please, send me your ideas for additional rubrics. Eight is not enough.
I'm gradually going through all the Crummy articles and changing them from evil Microsoft-created files into friendly Linux files. I'm taking the opportunity to do some minor updates and change links. Eventually all the Crummy links will work. Help me out by sending me dead links.
If you have to send me mail on Saturday, send it to [email protected]. The UCLA mailserver is going down for maintenance on that day, and I won't be able to get mail from [email protected] until Sunday [Sunday Sunday!] or Monday.
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Category: Organizations > Habitat Conservation > Wilderness Areas
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Global Response members (all ages) collaborate with communities worldwide to stop environmental destruction through effective citizen letter campaigns.
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GLOBAL RESPONSE is an international letter-writing network of environmental activists. In partnership with indigenous, environmentalist and peace and justice organizations around the world, GLOBAL RESPONSE develops "Actions" that describe specific, urgent threats to the environment. Each "Action" asks members to write personal letters to individuals in the corporations, governments or international organizations that have the power and responsibility to take corrective action. GR also issues "Young Environmentalists' Actions" and "Eco-Club Actions" designed to educate and motivate elementary and high school students to practice earth stewardship. To receive Global Response "Actions" and "Emergency Actions" by email: Send a blank message to: [email protected] Visit our website at: http://www.globalresponse.org
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Category: Educational Resources > Environmental Ethics > Religion and the Environment
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BodyEarthSelf contains vital information for self-improvement, better health, environmental awareness, and simplifying your life. The information is designed to provide hope, positive thinking, and encouragement for a better, more environmentally prosperous life.
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Information about simpler living living free of chemicals with natural substitutions and effective viable suggestions and ideas to help you maintain your body/mind/spirit and increase your environmental awareness.
It is my hope that through my writing and my special compassionate colorful words people will glean hope, positivity, love, faith, and higher awareness. Plato's theory was correct. Everyone has a different perspective and outlook on the world and life and the glass is either half full or half empty, depending on how you perceive it. The one true genuine way to succeed in life and the world and achieve happiness is through compassion, passion, love, kindness, generosity, and most of all truth.
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Dedicated to preserving endangered sites within the Walden Woods ecosystem (Concord-Lincoln, Mass.) and educating the public on the importance of land preservation.
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Henry David Thoreau (1817-1862), the author of WALDEN, "Civil Disobedience," and other famous writings, is justly regarded as the founder of the environmental movement in America. Thoreau lived in the Walden Woods during his famous sojourn at Walden Pond, and the Walden Woods was the living laboratory where Thoreau developed his seminal ideas on forest succession and the dispersion of seeds. The mission of the Walden Woods Project is to ensure that the integrity of this important ecosystem remains intact, even in the face of onslaughts from well-financed developers and officials who seem not to understand the cultural and ecological significance of this treasured landscape. In collaborating with the Thoreau Society on the Thoreau Institute, which is located in the midst of Walden Woods and less than half a mile from Walden Pond, the Walden Woods Project disseminates Thoreau's ideas to the public and supports research that clarifies and adds to Thoreau's many and varied legacies.
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Weather & Climate
Located above the surface of our planet is a complex mixture of gases and suspended liquid and solid particles known as the atmosphere. Operating within the atmosphere is a variety of processes we call weather. Some measurable variables associated with weather include air temperature, air pressure, humidity, wind, and precipitation. The atmosphere also contains organized phenomena that include things like tornadoes, thunderstorms, mid-latitude cyclones, hurricanes, and monsoons. Climate refers to the general pattern of weather for a region over specific period of time. Scientists have discovered that human activities can influence Earth’s climate and weather producing problems like global warming, ozone depletion, and acid precipitation.
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Newbie Member
4Jun2011,02:31 #1
Can I bond multiple internet servies together to get better speed?
Go4Expert Founder
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What type of services?
Mentor
4Jun2011,16:39 #3
Ask them.
Banned
19Apr2013,17:58 #4
No its not possible if you want to get a high speed on internet so you only take one plan just like a unlimited plan in this you will get a high speed. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T07:26:36.000Z | ts2qk6zca6tbba36qn5z74s6krlur7c5 | {
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} | cccc_CC-MAIN-2013-20 | About this Journal Submit a Manuscript Table of Contents
Case Reports in Oncological Medicine
Volume 2012 (2012), Article ID 539306, 4 pages
doi:10.1155/2012/539306
Case Report
Primary Small-Cell Carcinoma of the Palate with Cushing’s Syndrome: A Case Report
Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, Hubei, China
Received 31 July 2012; Accepted 16 September 2012
Academic Editors: K. Aogi, A. Goodman, E. Itakura, and J. I. Mayordomo
Copyright © 2012 Yingqiu Song et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Linked References
1. H. F. M. Van Der Heijden and Y. F. Heijdra, “Extrapulmonaiy small cell carcinoma,” Southern Medical Journal, vol. 98, no. 3, pp. 345–349, 2005. View at Publisher · View at Google Scholar · View at Scopus
2. A. M. E. Walenkamp, G. S. Sonke, and D. T. Sleijfer, “Clinical and therapeutic aspects of extrapulmonary small cell carcinoma,” Cancer Treatment Reviews, vol. 35, no. 3, pp. 228–236, 2009. View at Publisher · View at Google Scholar · View at Scopus
3. S. G. Kim and H. S. Jang, “Small cell carcinoma of the oral cavity: report of a case,” Journal of Oral and Maxillofacial Surgery, vol. 59, no. 6, pp. 680–684, 2001. View at Publisher · View at Google Scholar · View at Scopus
4. B. Peres-Ordonez, “Neuroendocrine tumours,” in World Health Organization Classification of Tumours: Pathology and Genetics of Head and Neck Tumours, L. Barnes, J. W. Eveson, P. Reichart, and D. Sidransky, Eds., pp. 26–27, IARC Press, Lyon, France, 2005.
5. K. O. Kim, H. Y. Lee, S. H. Chun et al., “Clinical overview of extrapulmonary small cell carcinoma,” Journal of Korean Medical Science, vol. 21, no. 5, pp. 833–837, 2006. View at Scopus
6. T. Goto, N. Bandoh, T. Nagato et al., “Primary small cell carcinoma of lacrimal sac: case report and literature review,” Journal of Laryngology and Otology, vol. 124, no. 11, pp. 1223–1226, 2010. View at Publisher · View at Google Scholar · View at Scopus
7. S. Lichtenstein, N. E. Albert, A. Muchnik, and M. Abraham, “Small cell carcinoma: an unusual location in a young healthy female,” Journal of Gastrointestinal and Liver Diseases, vol. 20, no. 4, pp. 427–430, 2011.
8. Y. Segawa, T. Nakashima, H. Shiratsuchi, R. Tanaka, K. Mitsugi, and S. Komune, “Small cell carcinoma of the tonsil treated with irinotecan and cisplatin: a case report and literature review,” Case Reports in Oncology, vol. 4, no. 3, pp. 587–591, 2011. View at Publisher · View at Google Scholar · View at Scopus
9. M. D. Weiss, H. O. DeFries, J. B. Taxy, and H. Braine, “Primary small cell carcinoma of the paranasal sinuses,” Archives of Otolaryngology, vol. 109, no. 5, pp. 341–343, 1983. View at Scopus
10. J. H. Kim, S. H. Lee, J. Park et al., “Extrapulmonary small-cell carcinoma: a single-institution experience,” Japanese Journal of Clinical Oncology, vol. 34, no. 5, pp. 250–254, 2004. View at Publisher · View at Google Scholar · View at Scopus
11. R. F. Baugh, G. T. Wolf, and K. D. McClatchey, “Small cell carcinoma of the head and neck,” Head and Neck Surgery, vol. 8, no. 5, pp. 343–354, 1986. View at Scopus
12. G. Lo Re, V. Canzonieri, A. Veronesi et al., “Extrapulmonary small cell carcinoma: a single-institution experience and review of the literature,” Annals of Oncology, vol. 5, no. 10, pp. 909–913, 1994. View at Scopus
13. S. Shahani, R. J. Nudelman, R. Nalini, H. S. Kim, and S. L. Samson, “Ectopic corticotropin-releasing hormone (CRH) syndrome from metastatic small cell carcinoma: a case report and review of the literature,” Diagnostic Pathology, vol. 5, article 56, 2010. View at Publisher · View at Google Scholar · View at Scopus
14. Y. Ma, C. Aitelli, R. W. Dobson, and K. Konduri, “Ectopic adrenocorticotropic hormone syndrome: a diagnostic challenge and review of the literature,” Proceedings (Baylor University. Medical Center), vol. 23, no. 4, pp. 426–428, 2010.
15. A. M. Isidori and A. Lenzi, “Ectopic ACTH syndrome,” Arquivos Brasileiros de Endocrinologia e Metabologia, vol. 51, no. 8, pp. 1217–1225, 2007. View at Scopus | v0 |
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} | cccc_CC-MAIN-2013-20 | About this Journal Submit a Manuscript Table of Contents
International Journal of Evolutionary Biology
Volume 2012 (2012), Article ID 970920, 8 pages
doi:10.1155/2012/970920
Research Article
Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome
1University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
2Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, India
3Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, Haldwani 263139, India
Received 20 March 2012; Revised 11 June 2012; Accepted 5 July 2012
Academic Editor: Frédéric Brunet
Copyright © 2012 P. C. Sharma et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Little data is available on microsatellite dynamics in the duplicated regions of the rice genome, even though efforts have been made in the past to align genome sequences of its two sub-species. Based on the coordinates of duplicated sequences in the indica genome as available in the public domain, we identified microsatellites in these regions. CCG and GAAAA repeats occurred most frequently. In all, 259 microsatellites could be identified in the duplicated sequences using the criteria of minimum 90% alignability spread over a minimum of 1 Kb sequence. More than 25% of the repeats in duplicated regions occurred in the genic sequences. Only 45 (17%) of these 259 microsatellites were found conserved in the duplicated paralogues. Among these repeats, 40% maintained both sequence and length conservation. The effect of mutability of nearby regions could also be clearly seen in microsatellite regions. The overall purpose of this study was to investigate, whether microsatellites follow an independent course of evolutionary dynamics subsequent to events like genome reshuffling that simply drives these elements to different locations in the genome. To the best of our knowledge, this is the first comprehensive analysis of microsatellite conservation in the duplicated regions of any genome.
1. Introduction
Microsatellites represent a class of tandem DNA repeats with 1 to 6 bp long repeat units. These sequences occur in almost all the organisms and frequently constitute the hypervariable regions of the genome. No specific functions have been assigned to most of the microsatellites till date. However, in some cases at least, microsatellite alleles provide protective or adaptive advantage to the host [1]. In many cases, occurrence of different alleles has been found associated with different phenotypes [2]. Microsatellites are not expected to be conserved for long evolutionary periods either, as argued by Buschiazzo and Gemmell [3]. Nevertheless, models of microsatellite mutational dynamics have been developed based on comparison of orthologous microsatellite loci in related taxa [47]. However, whether these models also describe microsatellites at paralogous loci created by segmental changes within a genome remains to be investigated.
Availability of whole-genome sequences for rice (Oryza sativa L.) allows analysis of noncoding DNA also within the segmentally duplicated regions in addition to the gene order, tandemly arranged genes (TAGs) and gene functions. A collective look emerging from different reports on mapping of duplicated regions in rice genome [810] reflects that these studies primarily focused on the analysis of genes in these regions. The strategy commonly used involved making blocks of genes, and mapping them elsewhere in the genome. In a way, the noncoding DNA, particularly, the repetitive DNA has been ignored due to nonemployment of methods suitable for this kind of mapping. Nevertheless, to understand the complete mechanism of speciation and genome evolution, the characterization of conserved noncoding DNA is equally important [11]. No information, to date, is available on the fate of microsatellites in newly duplicated locations. Signatures of ancient duplications, in terms of sequence similarity of genes, and their genomic order on chromosomes in rice, are widely available, as mapped by Yu et al. [10]. Using the same information as a reference, we have attempted to outline the dynamics of microsatellite DNA within the segmentally duplicated regions of the rice genome to enlighten the patterns of conservation and divergence of these sequences. The overall objective of this study was to investigate whether there is any participation of microsatellites in genome reshuffling or they are simply being carried over. We were also interested to know if after duplication the paralogous microsatellites (we call as “microsatellite twins”) follow independent dynamics as both the sites are now different or similar dynamics as the neighbouring environment is still essentially the same. The latter point is important to understand whether microsatellite hypermutability is random or directional.
2. Methods
2.1. Sequence Resources
Whole-genome sequence of Oryza sativa subspecies indica was downloaded from http://rise.genomics.org.cn/rice/index2.jsp (BGI release 2003-08-01) in FASTA format. Based on the coordinates of duplicated sequences as provided by Yu et al. [10], the sequences of duplicated regions were retrieved from the whole-genome sequence in a text editor and were used as plain text files. The first set of sequences described by Yu et al. [10] has been referred here as group I sequences, and their paralogous duplicated sequences have been designated as group II sequences. These sequences were further split into 2.0 Mb bins for further analysis.
2.2. Analysis of Duplicated Sequences
Repeatmasker (http://www.repeatmasker.org/) with WU-blast [12] search engine was used with default sensitivity and rice as “DNA source” for mining of microsatellite repeats, which were subsequently aligned using glocal algorithm [13] in Vista Genome Browser (http://pipeline.lbl.gov/cgi-bin/gateway2) [14] following the method described earlier by Roorkiwal et al. [7]. A simple sequence with repeat motif length of 1–6 bp spanning a minimal length of 20 bp was considered as a microsatellite. Genes were predicted using MolQuest ver. 1.6.2 (Softberry; http://www.molquest.com/). Following analysis of the aligned map, segmental duplications were identified by the criteria of similarity >90% and length ≥1 Kb [15] and analysed for microsatellites and coordinates of the predicted genes.
2.3. Statistical Analysis
The data generated by mining of duplicated sequences and associated microsatellites were subjected to statistical analysis using test and correlation test. The expected values were derived from the published reports [5, 7, 10].
3. Results and Discussion
Microsatellites constitute nearly 1% of the eukaryotic genomes, though in some organisms like Plasmodium they may be overrepresented [16]. Their biological significance to the host genomes has been a topic of debate in recent years. Moreover, little knowledge is available about their mutational dynamics [17, 18], primarily derived from the limited genomewide studies in model organisms [4, 5, 7]. Comprehensive surveys on microsatellite conservation across the species and within duplicated sequences of the same genome are, therefore, required to expand our understanding regarding their genomic significance. In the following sections, we present some points emerging from our study justifying our opinion that at least in part such a conservation and maintenance of microsatellites in segmentally duplicated sequences are visible in the rice genome.
3.1. Alignability of Duplicated Regions
Evidences exist for genome duplications in rice that occurred between 53 and 94 mya sometime prior to divergence of the cereal genomes [9, 10]. Further, a segmental duplication event between chromosomes 11 and 12 occurred around 5 mya is also well documented [19], in addition to numerous other individual gene duplications [1, 9]. In totality, the duplicated sequences in rice span 295 Mb, representing nearly two-third of the entire genome including 47% of the genic regions [10]. It is believed that duplication events are followed by several genomic changes including loss of gene functions, and in certain cases, loss of entire genes also [9].
Based on the data presented earlier by Yu et al. [10], we delimited total duplicated regions as 141 Mb of group I sequences and 154 Mb of group II sequences. However, the actual traceable duplicated segments meeting the criteria of >90% similarity and minimum of 1 Kb [15] length covered merely 3.8 Mb genome. The first and second groups of sequences spanned 1.89 and 1.90 Mb of the genome, respectively. Thus, the actual portion of the rice genome studied here came out to be merely 1% (~3.79 Mb). Maximum duplication events were observed on chromosome 2 (~0.34 Mb) and minimum on chromosome 7 spanning little lesser than 0.1 Mb (Table 1). Their distribution was obviously non random with . Further, no correlation was observed between the size of duplicated segments and the length of chromosomes. Average length of bins was found highest on chromosome 5, and minimum on chromosome 6.
Table 1: Occurrence of genes and microsatellite repeats in duplicated regions of the rice genome.
The size of the aligned pair and the alignment scores between two segments are generally in inverse relationship to their divergence time. However, in the present case, such a relationship has not been observed, as the most recent pair of duplicated sequences on chromosome 11 and 12 [19] was not the longest one (Table 1). Nevertheless, the mean similarity between the duplicated bins on chromosome 11 and 12 (Figure 1) was little higher at 94%, compared to mean similarity of 93.5% between duplicated bins of chromosome 2 and 4.
Figure 1: A representative figure of a duplicated segment mapped between chromosomes 11 and 12.
3.2. Microsatellite Abundance in Duplicated Regions
We earlier reported 45,782 microsatellites in 374.5 Mb of rice genome [7] using the same criteria and the tools used in the present study. Accordingly, 1% of the genome should have carried 458 microsatellites, had they been randomly distributed throughout the genome. However, only 259 microsatellites could be identified in this set of sequences, with 121 sequences identified in shorter set of 1.89 Mb, with an average frequency of one repeat locus per 16,453 bp, and 138 in group II of 1.9 Mb with average frequency of one repeat locus per 15,831 bp (Figure 2). When the frequency of specific microsatellite motifs in duplicated regions were plotted against the expected values, based on previous studies [5, 7], frequency of most of the microsatellites were found much lower , except for motifs like AAT, AGC, and CCG for which observed values corresponded to expected values. Clearly, there is certain level of purifying selection against the microsatellites in these duplicated regions of the rice genome.
Figure 2: Gene versus repeat density on the entire duplicated segments in the rice genome. Duplication ratio refers to the ratio of the segment reported duplicated by Yu et al. [10], and the length of the fragments that we found aligning with >90% similarity for a minimum length of 1 Kb.
CCG repeats (and direct and reverse complementary permutations thereof) were found most abundant in either set of sequences in consistency with the earlier reports [5, 7]. GAAAA repeats (and their permutations), known to be most abundant in rice genome among the penta-nucleotide repeats [5], were found the second most abundant and least mutable repeats (Table 2) among the duplicated sequences. Other repeats like A, AT, and so forth, otherwise abundant in rice genome, were not found preferentially distributed in duplicated regions (Figure 3). Relative abundance of each of the repeat motif in both of the sets of sequences was fairly comparable. Quite expectedly, majority of the microsatellites occurred in the intergenic sequences (Table 2), and least in the exonic sequences. Consistent with the previous findings [7], CCG repeats most frequently occurred in exonic sequences. As suggested earlier by some researchers [17, 18], intrinsic factors specific to the host genome and microsatellite themselves like repeat length, repeat sequence, neighboring genomic sequences, and so forth, are responsible for differential occurrence and conservation of microsatellites. Importantly, while the duplicated sequences have shown a higher frequency of genes, they have particularly shown a bias against the microsatellites (Figure 2).
Table 2: Traceability of microsatellites originating from group I sequences into group II sequences.
Figure 3: Abundance of microsatellite motifs in duplicated regions of the rice genome.
3.3. Microsatellite Conservation within the Duplicated Sequences
Out of the 259 microsatellites existing in the duplicated sequences, only 45 (17%) were found conserved in the paralogous sequences. Considering the mutability of microsatellites per locus per generation in rice, as described by Grover et al. [5], a microsatellite of 20 bp length may entirely be lost in around 2 million years provided all the mutations are unidirectional, targeting the shortening of the microsatellite. Thus, conservation of 17% of microsatellites in duplicated regions, with the average age of duplication around 56 mya, is especially significant as only 1% of the entire duplication blocks is identifiable today (discussed above). Interestingly, 42% of these repeats have their length conserved, which is significantly lesser than the global average in rice observed earlier [7], but clearly indicating that these alleles have been fixed in duplicated segments, most probably due to the vitality of their spatial occurrence [18]. Differences in the lengths of at least two paralogous microsatellites (with CCG motif) falling in exonic sequences on duplicated blocks on chromosome 11 and 12 indicate the relative advantage of repeatability and hypermutability of microsatellites in genes, as has been suggested earlier as well [1, 3, 2022].
It was also interesting to note that at some of the genomic positions a single microsatellite repeat corresponded to two microsatellite repeats with the same motif (Table 3). This is possible due to recurring splitting and expansion events at microsatellite loci [18]. Of all the paralogous microsatellites observed, 40% maintained both sequence and length characteristics. Majority of these microsatellites were located on duplicated segments of chromosomes 1 and 5. It is quite possible, that these loci might have been fixed. However, we do not overrule the possibility that one or both of the sequences have undergone a number of mutations purely in stochastic manner and eventually arriving to the same lengths simultaneously, now seen as conserved alleles. Out of these two possibilities, it is the first one that generates more interest, as microsatellites associated with important regions in the genome will display lower variability during genetic drift and selective sweeps [18, 23]. Consequently, lesser activity will be observed on a microsatellite locus that is lying next to a genomic region adapted to a given environment [24]. Therefore, we do not overrule the possibility that the microsatellites that show sequence as well as length conservation represent important “evolutionary chronometers” [25] and might have been tightly linked to genomic regions of significance [18]. Microsatellites located in mutationally constrained regions are expected to be maintained passively. Highly conserved microsatellites are often associated with other conserved genomic elements and show a stronger negative relationship with single nucleotide polymorphisms (SNPs) density [26]. Interestingly enough, in five instances, a particular microsatellite motif has given way to another motif, precisely at the same site (Table 3). Grover and Sharma [18] explained such events by calling them as “metamorphosis” at microsatellite sites. Apparently, in three of the five cases, the new microsatellites appeared originally by a single site substitution, which later expanded possibly by “polymerase slippage” to mature into a fully grown microsatellite. Evidently, both the abundance and conservation of microsatellites had a heterogeneous pattern across the rice chromosomes. However, the distribution of sequence motifs across the chromosomes and across the blocks and segments of duplications more or less remained the same. Conserved microsatellites within the duplicated regions of the genome are desired candidates to study the overall significance of microsatellite conservation in different genomes.
Table 3: Description of paralogous loci where microsatellite motif has been found altered either by splitting and integrating, or replaced with another motif.
3.4. Microsatellites versus Genes in Segmentally Duplicated Regions
Out of 259, only 68 (26.25%) microsatellites were found to be associated with genes. Out of these genic microsatellites, 17 (25%) were present in exonic regions and remaining 51 (75%) were located in the intronic regions. Interestingly, 18 of the repeats and their counterparts were located to different genomic entities. For example, while one locus was located in the intergenic region, its paralgoue occurred in the genic region. Such spatial distribution can occur due to homologous recombination [27] or some other minor genomic rearrangements due to retrotransposition, local genomic reorganization and reshuffling. Thus, such microsatellites can be considered as “genomic fossils,” which can help in retracing the evolutionary events in the genome.
Acknowledgments
The authors’ microsatellite research has been supported by Indian Council of Agricultural Research (ICAR), Department of Science and Technology (DST) and Defence Research and Development Organization (DRDO). M. Roorkiwal acknowledges research fellowship from University Grants Commission (UGC).
References
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“Do not let the exhortations of the Assyrian trouble you in the least, Chrysantas,” Cyrus answered; “for no speech of admonition can be so fine that it will all at once make those who hear it good men if they are not good already; it would surely not make archers good if they had not had previous practice in shooting; neither could it make lancers good, nor horsemen; it cannot even make men able to endure bodily labour, unless they have been trained to it before.”
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Robert Spring was a gardener who lived in the environs of Aberdeen, Scotland. What is known of him at this point is only what can be gathered from the christening records of his five children. His first two children were christened in the Kincardineshire parish of Banchory-Ternan (about 20 miles WSW of Aberdeen, along the Dee River), and his latter three children were christened in the Aberdeenshire parish of Udny (about 15 miles NNW of Aberdeen), suggesting that the family moved circa 1763. The christening records of the time typically only named the father, although the christening record of Mary names both a father and a mother. It is only a presumption that Mary's mother, Margaret Mearns, was the mother of all of the children, though it is also possible that the move from Banchory to Udny coincided with a second wife for Robert, and that the atypical nomination of a mother on the christening of Robert's first child in Udny was meant to indicate a different wife/mother than for his previous children.
Disambiguation
One might question whether the Robert Spring in Banchory was the same Robert Spring in Udny. However, the connection is supported by the configuration of children, who are themselves shown to be siblings. It can be shown that the Christian Spring who married Archibald Farquharson of Finzean had a brother Robert, a sister Isobel who married Robert Sherrat, and a sister Mary. Isobel and Mary both followed Christian to Finzean. In Christian's will, she identifies her brother Robert as well as the children of her sister Isobel. Only by viewing Robert Spring of Banchory and Robert Spring of Udny as one and the same can we find a family in the approximate right place and time with siblings Christian, Robert, Isobel, and Mary. Moreover, the regular and non-overlapping sequence of christening years in the two parishes would support them being the same Robert. | v0 |
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Mary Elizabeth "Betty" Taylor
b.20 APR 1824 Jefferson CO., KY
d.26 JUL 1909 Winchester, VA
m. 21 JUN 1810
1. Ann Margaret Mackall Taylor1811 - 1875
2. Sarah Knox Taylor1814 - 1835
3. Octavia Pannill Taylor1816 - 1820
4. Margaret Smith Taylor1819 - 1820
5. Mary Elizabeth "Betty" Taylor1824 - 1909
6. Richard Taylor1826 - 1879
Facts and Events
Name Mary Elizabeth "Betty" Taylor
Gender Female
Birth? 20 APR 1824 Jefferson CO., KY
Death? 26 JUL 1909 Winchester, VA
the text in this section is copied from an article in Wikipedia
Mary Elizabeth Taylor Bliss, born Mary Elizabeth Taylor (April 20, 1824 – July 25, 1909), was the youngest of the five daughters of President Zachary Taylor (1849-1850) and Margaret Mackall Smith Taylor.
In 1848, after her father was elected president, Mary Elizabeth married William Wallace Smith Bliss, an army officer who had served with her father. Taylor appointed William Bliss as Presidential Secretary. At the age of 22, Mary Elizabeth Bliss served as First Lady during her father's presidency, as her mother declined the social role.
Her father, mother and husband all died by 1853. Mary Elizabeth Bliss remarried five years later and had a long life.
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Watchers
NameGraettinger
TypeCity
Coordinates43.238°N 94.751°W
Located inPalo Alto, Iowa, United States
source: Getty Thesaurus of Geographic Names
source: Family History Library Catalog
the text in this section is copied from an article in Wikipedia
Graettinger is a city in Palo Alto County, Iowa, United States. The population was 844 at the 2010 census.
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Answers OnStartups is a question and answer site for entrepreneurs looking to start or run a new business. It's 100% free, no registration required.
Say I have a company called Business, and I've been operating under the domain name greatbusiness.com for 2 years. The "tm" symbol is on our logo and elsewhere on our website.
Then someone else comes along and registers greatbusiness.co and files for trademark "Great Business" at the USPTO and was approved. His company name is Great Business Inc.
What are my options at this point to get the trademark back? I want to file for a trademark.
share|improve this question
1 Answer
up vote 1 down vote accepted
Your options will cost money. What you can do depends on how much money you have to fight this and how important the mark is to you.
Your likelihood of success depends on the following factors among others:
• How similar your business is to his. If you sell software and he sells toothbrushes, then you might not have a case.
• How prominent your business is. If you have a lot of sales and sell to most states in the U.S. that helps your case. If you have a primarily local business and low sales, then that makes it a lot harder.
• How distinctive the word is. If it is a word in the dictionary, then you are less likely to succeed. If it is a made-up word, then you have a better chance.
Your options are (in increasing order of cost):
1. Negotiate with the other party. You could do this on your own, but having a lawyer will bring the other party to the table.
2. Oppose the trademark in the USPTO. You would have been better off doing this before the other party got the trademark, but you can still do it. You will need a lawyer to do this, and the initial stages are not so expensive. Are you willing to spend $10,000 on this?
3. File a lawsuit.
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Source link: http://archive.mises.org/16245/hoppe-best-interview-ever/
Hoppe: best interview ever?
March 28, 2011 by
Among many great points Hans Hoppe makes in this outstanding interview: “intellectual property rights and real property rights are incompatible, and the promotion of intellectual property must be seen as a most dangerous attack on the idea of ‘real’ property (in scarce goods).”
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Archive for general
Announcing Add-on SDK 1.13.2
The Jetpack team would like to announce the immediate availability of SDK 1.13.2, which addresses several issues, including a P1 Memshrink bug: Opening and closing browser windows seems to add FragmentOrElement objects to the CC graph when Addon SDK addons are installed which add an addonbar widget. (Bug 833783) Context-menu reuses the same worker when… Continue reading
Categories: builder, developers, general, jetpack, releases, sdk
Add-on SDK 2013 Roadmap
During December I worked with the rest of the SDK team as well as other stakeholders to develop a product road-map for the SDK for the next year. This road-map planning is critical as 2013 promises to be a very eventful year for both the Jetpack team and the SDK, and I think a very,… Continue reading
Categories: developers, general, jetpack, sdk | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T05:29:19.000Z | rnva5htrdszkkodtk3zipoh6e7kmynku | {
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} | cccc_CC-MAIN-2013-20 | Bullying: Risk Factors Becoming ‘Bullies’
Kasetchai Laeheem, Metta Kuning, Nittaya McNeil
Abstract
The primary purpose of this study was to analyze the internal consistency and construct validity of a classification of bullying outcomes, and to investigate the risk factors associated with bullying behaviour at Pattani primary schools, southern Thailand. A cross-sectional study was conducted with a sample of 1,440 students. Factor analysis, descriptive statistics, Pearson’s chi-squared test, and logistic regression were used for data analysis. The results showed that 20.9% of students in Pattani primary schools reported having bullied others. A four factors structure of bullying was clearly shown; serious, general physical, psychological-maligning parent and psychological-maligning student. Witnessing parental physical abuse was clearly the most strongly associated determinants, and much more strongly linked to bullying others than was the group who had never witnessed parental physical abuse (OR 7.60, 95% CI 5.60-10.31). The students who preferred action cartoons were more often bullies than were those who preferred comedy cartoons (OR 2.87, 95% CI 1.91-430).
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Iran's Supreme Leader Behind Enemy Lines with New Facebook Page
This post also available in:
Français · Iran : Le Guide Suprême "derrière les lignes ennemies" avec une nouvelle page Facebook
Español · Líder supremo iraní tras las líneas enemigas con nueva página de Facebook
So Facebook is Halal all of a sudden?
by Peyman Majidzadeh Excerpted from a longer post originally published on Arseh Sevom.
Amid all the discussions about launching a halal or national Internet in Iran, Ayatollah Khamenei, the Supreme Leader, took everybody by surprise with a new Facebook page launched on December 13, 2012. We are talking about the same Facebook, which for most Iranian citizens to access requires special software or a Virtual Private Network to bypass the country’s strict filtering! The news became official on December 15 when Mr. Khamenei’s Twitter account, believed to be run by his office, promoted the page by posting a link to it. According to The Guardian, Khamenei's official website has not yet confirmed the existence of the page, but the conservative news site Baztab reported that the account was run by his office.
In defense of Mr. Khamenei, Mehr News [fa] criticized Western news outlets for their reporting, stating:
“A simple search shows over a hundred accounts and similar pages attributed to Ayatollah Khamenei on Facebook.”
What Mehr fails to mention is that only one of these pages has been promoted through Khamenei’s Twitter account.
In addition to the recent Facebook account, Mr. Khamenei has a Twitter account and uses Instagram. On the flip side he has been very vocal about his opposition to social networks, reports Small Media [en].
Ayatollah Khamenei’s Facebook debut has generated heated debates in the Iranian online community. The ayatollah seems to have attracted over 20,000 “likes” so far. Unsurprisingly, the censorship apparatus seems to be on guard here too, as critical comments are being removed and many have been quickly blocked by the page’s admin. Masih Alinejad, an exiled journalist, posted on her Facebook page [fa]:
“The virtual guardianship of Khamenei on Facebook: If Mr. Khamenei or his office has officially joined Facebook, this implies that he has made up his mind to fight the ‘enemy’ behind the enemy’s line.”
She continues her post by publishing her own comments on the ayatollah’s page which were removed in the blink of an eye:
“If this is your official page, your majesty, you undoubtedly realized that there is no leader of a country nowadays who has never done an interview with a journalist throughout his leadership period. So please inbox me your telephone number so that I can bother you for an interview over the phone.”
Some have encouraged people to report this page as spam and ask Facebook to block the page. The have also created a new page called “No to Ayatollah Khamenei” and urged him to leave Facebook. They state that free access to information and the internet is everybody’s right, not one exclusive to the leader.
The blog Evolution-Adam [fa] posted a photoshopped screenshot of the page portraying Bashar Assad, Putin, Ayatollah Mesbah, [former] Judge Mortazavi, Seyed Hassan Nasrollah, Shariatmadari, and Kim Jong-un in the Facebook friends list of Khamenei.
Altered screenshot from the blog Evolution-Adam
In a blog entry titled “It is a crime for ordinary people, but it is permitted for him”, the author wrote [fa]:
“Ayatollah Khamenei has recently launched his own Facebook page while Facebook is blocked in Iran and the use of anti-filters is a crime!… What kind of a law is it when breaking it is easy for the authorities but ordinary people are jailed, lashed, or end up like Sattar Beheshti [a blogger who was killed] if they don't respect it.”
Former vice president Mohammad Ali Abtahi takes a different view. In his blog [fa] he writes:
“I believe this debut requires the attention of Internet policy makers and telecom organization officials. The most important thing here is to lift the filters on the page so that everybody can have access to it. Connecting to the highest-ranking official of the country for those inside by using circumvention is considered disrespectful to the people and to the Supreme Leader himself.”
On the page itself, many have commented only to have their comments swiftly removed by the page admin.
“When Bashar Assad falls, you will be next,” read a post which quickly disappeared. Another post with a similar fate read, “Which VPN do you use?”
Plenty of posts could also be seen urging the ayatollah to release political prisoners, grant freedom of expression and assembly, and allow free and fair elections. On the other hand, there are many comments praising Ayatollah Khamenei, which are not removed.
Despite the fact that the page has been widely publicized and commented on, so far there has been neither confirmation nor denial from Ayatollah Khamenei’s office of its authenticity. Confirmation from his office would highlight the double standards of the regime when it comes to social media. Meanwhile, Facebook is all about interaction and engagement, not just removing comments and blocking users. It is not clear how long the supreme leader will be able to maintain a similar no-comments approach.
Only time will tell.
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} | cccc_CC-MAIN-2013-20 | SIMULATION OF SORTING SEDIMENTATION IN THE CHANNEL OF HUANGHUA HARBOR BY USING 3D MULTI-SIZED SEDIMENT TRANSPORT MODEL OF EFDC
Qinghe Zhang, Feng Tan, Tao Han, Xiaoyuan Wang, Zhiqiang Hou, Hua Yang
Abstract
Huanghua Harbor, located in the south-west coast of Bohai Bay, China, has frequently encountered severe channel siltation with sorting sedimentation along the channel during storm events since its construction. For prediction of channel siltation, a 3D numerical model of multi-fraction sediment transport based on the coupling of modified EFDC model and SWAN model is developed to investigate the sediment transport. It is shown from simulated results that the sorted sedimentation in the channel was well simulated in storm events, and the high sediment concentration near sea bed for silty coast during storm process can also be basically reflected by the model.
Keywords
EFDC model; SWAN model; Sorting Sedimentation; multi-fraction sediment; sediment concentration
References
Booij, N.C., R.C. Ris, and L.H. Holthuijsen. 1999. A third-generation wave model for coastal regions: 1. Model description and validation, Journal of Geophysical Research, 104, 7649-7666.http://dx.doi.org/10.1029/98JC02622
Hamrick, J.M. 1992. A three-dimensional environmental fluid dynamics computer code: theoretical and computational aspects, Special Report, VIMS, Virginia, 317pp.
Han H.S., S.S. Li, and Q. Zhao. 2006. Experiment study of vertical distribution of suspended concentration for silt under breaking wave condition. Journal of Sediment Research, (6), 30-36. (in Chinese).
Mellor G.L., and T. Yamada. 1982. Development of a turbulence closure model for geophysical fluid problems, Reviews of Geophysics and Space Physics, 20, 851-875. http://dx.doi.org/10.1029/RG020i004p00851
van Rijn L.C., M. W. C. Nieuwjaar, T. van der Kaay, E. Nap and A. van Kampen. 1993. Transport of fine sands by currents and waves. Journal of Waterway, Port, Coastal and Ocean Engineering119(2),123-133. http://dx.doi.org/10.1061/(ASCE)0733-950X(1993)119:2(123)
van Rijn L.C. 2007. Unified View of Sediment Transport by Currents and Waves. II: Suspended Transport, Journal of Hydraulic Engineering, 133, 668-689. http://dx.doi.org/10.1061/(ASCE)0733-9429(2007)133:6(668)
Xu H.M., and Y.L. Feng. 1998. Study on sediment transport in Huanghua Port project, Journal of Sediment Research, (1), 20-29. (in Chinese).
Yan B. 2008. Study of Sediment Transport and Channel Siltation on Silty Coast, Ph.D. thesis, Tianjin University (in Chinese).
Yan X.X. 2005. The sediment composition and distribution in nearshore zones of Huanghua Port, Journal of Waterway and Harbor, 26, 144-148. (in Chinese).
Zhang Q.H., F.L. Hou, B. Xia, J.F. Zhang, and H. Yan. 2006. Two dimensional numerical simulation of siltation in outer channel of Huanghua Harbor, China Harbor Engineering, 5, 6-9. (in Chinese)
Zhang Q.H., C.X. Wang, and H. Yang. 2004. The characteristics and affects of seabed surface sediment of Huanghua port, China Harbour Engineering, 4, 14-17. (in Chinese)
Zhao Q. 2006. Fine sediment transport in storm event-the Huanghua experience, Proceedings of 30thInternational Conference on Coastal Engineering. ASCE, 2956-2968.
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Our lab is interested in the 'system' level properties of pattern formation in cells. We use tools from cell biology and biophysics, microscopy, molecular biology and numerical simulations.
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2) Variability in cell shape and its regulation in bacteria
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...his pale and haggard face, and gloomy bearing, had so far influenced the remark, that Edward was, for the moment, at a loss to answer him.
'Tut, tut,' said Mr Haredale, ''twas not very difficult to read a thought so natural. But you are mistaken nevertheless. I have had my share of sorrows--more than the common lot, perhaps, but I have borne them ill. I have broken where I should have bent; and have mused and brooded, when my spirit should have mixed with all God's great creation.
The men who learn endurance, are they who call the whole world, brother. I have turned FROM the world, and I pay the penalty.'
Edward would have interposed, but he went on without giving him time.
'It is too late to evade it now. I sometimes think, that if I had to live my life once more, I might amend this fault--not so much, I discover when I search my mind, for the love of what is right, as for my own sake. But even when I make these better resolutions, I instinctively recoil from the idea of suffering again what I have undergone; and in this...
Dickens, Charles
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Charles John Huffam Dickens FRSA (7 February 1812 - 9 June 1870), pen-name "Boz", was an English novelist. During his career Dickens achieved massive worldwide popularity, winning acclaim for his rich storytelling and memorable characters. Considered one of the English language's greatest writers, he was the foremost novelist of the Victorian era as well as a vigorous social campaigner.
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} | cccc_CC-MAIN-2013-20 | It's easy! Just pick the product you like and click-through to buy it from trusted partners of Quotations Book. We hope you like these personalized gifts as much as we do.
Make and then buy your OWN fantastic personalized gift from this quote
To the real artist in humanity, what are called bad manners are often the most picturesque and significant of all. Whitman, Walt
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212 - The Extra Degree
The one extra degree makes the difference. This simple analogy reflects the ultimate definition of excellence. Because it's the one extra degree of effort, in business and life, that can separate the good from the great. This powerful book by S.L. Parker and Mac Anderson gives great examples, great quotes and great stories to illustrate the 212° concept. A warning - once you read it, it will be hard to forget. Your company will have a target for everything you do ... 212°
Click here to buy this » | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:26:18.000Z | 6es6s4p7f2hhkxrzzg5abptgyez5ddkd | {
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Apologetics Press is a site that focuses on Christian apologetics. The site's editors compile topics related to Christianity, throw out the ones that don't agree with them, and makes the ones that do look trustworthy.
Apologetics Press seems to be written from a fundamentalist point of view, as they hold that there are no biblical contradictions. The site seems to enjoy archiving debates in which atheists have lost. They think this will make them more respectable because rhetoric is better than evidence. Who needs empirical evidence and consistent observation when you can just play on the audience's ignorance and persuade them that there is a magic man who'll take them to heaven if they believe in him?
Contents
[edit] Purpose
The logo of Apologetics press.
Apologetic Press's purpose is to make the scripture of their Oh So Holy and Truthful Divine Graceful All-Loving Merciful Christian God seem scientifically accurate. The site has stated what its authors believe, and then tries to bend logic and evidence to fit their faith.
[edit] Effect
Christian apologists will sometimes use Apologetics Press to damage what credibility they originally had.[more detail please] The site can be a useful tool to examine various apologist oxymorons, such as "Reason and Revelation." The site has a sleek design, having recently been revamped. Despite this, it still contains obvious bias and reversal of scientific method, the site is also a good place where one can practice one's knowledge of logical fallacies. The site's most popular ones are: the false dichotomy, non sequitur, argument from design, argument from authority and the typical straw man.
[edit] See also:
[edit] External links:
Apologetics Press
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2024-06-03T21:29:47.544Z | 2013-05-18T08:01:47.000Z | ghlxq7tychfxsdkkjzxxrlskvgdtp5j2 | {
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Take the Political IQ Test...
-and see if you're any better than the average idiot
This is a terrific test, albeit a couple months dated... very enlightening. But not in a good way... the pitiful results betray the fact that a solid majority of Americans have absolutely no idea what's going on in this country.
80% of the voting public doesn't have a clue
and got less than half right!
This goes some ways towards explaining how a shady post-turtle like Barack Obama found his way into the Oval Office- and how the public can continue to be so easily manipulated by the thoroughly-discredited MSM hacks that endeavor to prop him up.
And there are no trick questions here - just a very simple test to see if you are current on your information. It's only a dozen questions... but NO Googling during the test, kids~
I just took it and got two wrong, I'll admit... but that's still good-enough to put me in the 94%tile, what does that tell you about the American voter today...
Click here:
Pew Research Center | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:50:17.000Z | czadjtbarayyuahzsybmu5p7px57kpxh | {
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} | cccc_CC-MAIN-2013-20 | Kirby's Dream Land
From StrategyWiki, the video game walkthrough and strategy guide wiki
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This page is a stub. Help us expand it, and you get a cookie.
Kirby's Dream Land
Developer(s) HAL Laboratory
Publisher(s) Nintendo
Distributor(s) 3DS Virtual Console
Release date(s)
Game Boy
Nintendo 3DS
Genre(s) Platform
System(s) Game Boy, Nintendo 3DS
Mode(s) Single player
Rating(s)
ESRB: Kids to Adults
Series Kirby
Neoseeker Related Pages
Kirby's Dream Land, known as Hoshi no Kābī (星のカービィ? lit. "Kirby of the Stars") in Japan, is a 1992 third party developed platform game developed by HAL Laboratory and published by Nintendo for the Game Boy handheld video game console. It was first released in Japan, and was later released in North America. It is both the first video game in the Kirby series and the debut of the Kirby character. Kirby's Dream Land was designed by Masahiro Sakurai, at HAL Laboratory who intended for Kirby's Dream Land to be a simple game that could be played by beginning gamers. As the inaugural Kirby title, Kirby's Dream Land created many conventions that would appear in later games in the series, including Kirby's basic moves. However, Kirby's trademark "copy" ability would not appear until Kirby's Adventure, released less than one year later. Kirby's Dream Land was re-released for the 3DS's Virtual Console service. It is also one of the games included in Kirby's Dream Collection, which was released to celebrate Kirby's 20th anniversary.
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} | cccc_CC-MAIN-2013-20 | Help Wikitravel grow by contributing to an article! Learn how.
Mount Isa
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Mount Isa [1] is a mining city in the north-west of the Australian state of Queensland, situated some 900 km west of Townsville and some 1900 km north-west of the capital Brisbane. Population 22,000. Geology is the key drawcard to Mount Isa, best represented in the World Heritage Riversleigh Fossil Field located near the city (250 km! - "near" for Queensland....).
Mount Isa Mines at dusk
[edit] Understand
Mount Isa is the birthplace of two Australian sporting greats: Greg Norman (golf) and Pat Rafter (tennis).
Mount Isa City municipality covers an area of over 43,310 square kilometres, making it geographically the second largest city in the world to Kalgoorlie-Boulder, Western Australia.
[edit] Get in
[edit] By train
Mount Isa is served by The Inlander passenger train [2] which travels overnight between Townsville (via Charters Towers) twice weekly (977 km). The air-conditioned train offers twinette, roomette, triple bunk and coach accommodation, and has a club car for movies and food.
[edit] Get around
[edit][add listing] See
The Mount Isa Rotary Rodeo [3] is the biggest and richest event Rodeo Event in the Southern Hemisphere. During Rodeo Week, Mount Isa's population swells almost three-fold with travelers coming from all over Australia and overseas to witness the thrills, the excitement, the raw power and courage that is rodeo. It's where city meets country, east meets west, man meets beast. With a packed program of rodeo events - saddle bronc riding, bareback bronc riding, bull riding, rope & tie, steer wrestling and team roping, wild horse racing, ladies barrel racing and ladies breakaway roping. Every year it all seems to get bigger better and more fun!
Outback at Isa - Hard Times Mines Mount Isa
• Riversleigh Fossils Centre, ph: +61 (0)7 4749 1555 or 1300 659 660, (email:mailto:[email protected] , fax: +61 (0)7 4743 6296,)[4] Conveniently displaying the results of excavation at the World Heritage site
[edit][add listing] Do
Hard Times Mine tour [5] Experience the history of Mount Isa's long and illustrious mining history in this purpose built mine. Guided by current and former miners from the Mount Isa mines, machinery demonstrations, old stories and hands on experience can all be experienced in a real underground environment. An amazing and unforgettable experience for locals and tourists alike.
[edit][add listing] Buy
[edit][add listing] Eat
Mount Isa, for a city of its size, is a considerable dining experience for the hearty traveller and local. Selections such as Indian, Italian, Chinese, German and French are all represented, either in the CBD or on the major roads. As well as this, all the major fast-food giants such as McDonalds, KFC, Eagle Boys, Red Rooster, Pizza Hut and Subway all have outlets in the Copper City.
• Abyssinia Cafe Restaurant [6], 103 Marian Sreet. ph: 07 4743 3328. The Abyssinia Cafe is a Licensed Restaurant serving traditional Ethiopean Cuisine as well as standard Australian meals and Indian food. For the last 20 years, Almaz Taye (Leila) Cashmore has owned and operated the cafe building up a broad reputation for excellent food. The Cafe has been featured on SBS for Ethipoean Cuisine
• The Isa Hotel] [7], 11 Miles Street. ph: 07 4749 8888. The Isa Hotel hosts the very popular Rodeo Bar & Grill. The ample menu focuses on the beef and barramundi found in the region while providing many alternative dishes to suit almost everybody. Bookings are recommended from Friday and Saturday nights.
[edit][add listing] Drink
Drinking aplenty in the Isa. The Irish Club [8], Buffs Club [9], The Overlander Hotel, The Isa and the Red Earth Hotel [10] and many others are make up the great selection of watering holes in the city. Many outlets have meals, happy hours and special promotions going all the time.
[edit][add listing] Sleep
Mount Isa offers a range of accommodation options to suit everyone's budget.
[edit] Budget
• Travellers Haven Backpacker Hostel [11], 75 Spence Street, ph: +61 (0)7 4743 0313. A relaxed, family-run hostel only 10 minutes walk from the city centre. The Haven offers free pick-up and drop-off from the bus and train station, cooking and laundry facilities, air conditioning, swimming pool, internet and off-street parking. Dorms from $25.
[edit] Mid-range
• Cityside Accommodation [12], 20 Fourth Avenue, Parkside. ph: (07) 4749 0007. Comfortable and quiet self-contained rooms to accommodate any traveler type. Located only minutes from cbd and within walking distance of Aquatic Centre. Clean outdoor shared areas - garden and BBQ. Friendly staff and strong sense of community among residents and guests.
• Townview Motel in Mount Isa [13], 103 Marian St. ph: +61 7 4743 3328. 4-star accommodation with 24 rooms that include Budget, Standard and 2 Bedroom Spa Suites. Most rooms include cooking facilities. There is also a 3 bedroom house for longer stays. The Abyssinia Cafe Restaurant is on site which serves traditional Ethiopean Cuisine as well as standard Australian meals and Indian food.
[edit] Get out
The roads into and out of Mount Isa are generally of good quality and passable for all vehicles. Care should be taken if travelling during the wet season as many of these roads can become flooded and impassable. Never try to cross covered causeways even if no signage or barricades are erected at the site. Purpose built signs are placed along the Barkly Highway to Townsville to indicate what roads are passable during flood times. Alternatively, asking locals of possible road conditions can give surprising accuracy.
• Flights can be booked with Airnorth, Qantas, Rex and Skytrans to various locations around the Queensland and Northern Territory (depending on carrier)
• Train services are run twice per week to Townsville and other towns along the Barkly Highway with the Inlander
• Bus services between Mount Isa and surrounding areas are run by Greyhound Australia [14]
General Distances
This is a usable article. It has information for getting in as well as some complete entries for restaurants and hotels. An adventurous person could use this article, but please plunge forward and help it grow!
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} | cccc_CC-MAIN-2013-20 | Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
1307.6 - Tasmanian State and Regional Indicators, Jun 2009
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 29/07/2009
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EDUCATION
SCHOOLS
In August 2008, there were 277 schools in Tasmania, of which 210 (75.8%) were government schools and 67 (24.2%) were non-government schools. There were 169 (61.0%) primary only schools, 46 (16.6%) secondary only schools, 56 (20.2%) combined primary/secondary schools and 6 (2.2%) special schools.
The number of schools in a particular year can be affected by structural change in the composition of schooling rather than necessarily a change in the number of sites delivering full-time school education. That stated, over the ten-year period 1998-2008, the numbers and proportions of primary only and secondary only schools have remained steady. In 1998, there were 176 primary only schools in Tasmania representing 64.0% of all schools (not including special schools) and 47 secondary only schools (17.1%).
SCHOOLS(a), Tasmania
SCHOOL STUDENTS
In August 2008, there were 81,591 full-time school students in Tasmania. From 1998 to 2008, the number of full-time students attending government schools fell by 7.5% (from 62,978 to 58,280), while the number attending non-government schools increased by 10.3% (from 21,138 to 23,311).
In August 2008, 54.9% of all full-time school students in Tasmania were attending primary schools (44,770); 45.1% were attending secondary schools (36,821).
In August 2008, apart from the Northern Territory (NT), Tasmania had the lowest proportion of full-time students attending non-government schools (28.6%). By contrast, the state or territory with the highest proportion was the Australian Capital Territory with 42.5%.
PROPORTION OF NON-GOVERNMENT FULL-TIME STUDENTS, Tasmania
There were 1,546 part-time school students in Tasmania in August 2008, a significant decrease (42.8%) on the numbers in 1998 (2,701). There were 5,017 indigenous full-time school students, a significant increase (22.1%) on the numbers in 1998 (4,108).
HIGHER EDUCATION STUDENTS
In 2007, there were 19,531 higher education students in Tasmania. Of these, 53.7% were female, 73.4% were undertaking a bachelor degree and 17.6% were undertaking postgraduate study. The most popular field of education study by Tasmanian higher education students in 2006 was 'society and culture' (22.3% of all students) followed by 'management and commerce' (18.8%).
PROPORTION OF HIGHER EDUCATION STUDENTS, Tasmania
AGE PARTICIPATION RATES
The school age participation rate indicates the proportion of the resident population who are at school. Occasionally, a participation rate can exceed 100%, mainly due to the enrolment of students in schools who are not residents of that state. The age participation rates for full-time Tasmanian school students in August 2008 were 99.8% for 14 year olds, 99.7% for 15 year olds, 86.3% for 16 year olds and 60.6% for 17 year olds.
Tasmania's participation rate for 17 year olds exceeded that of Western Australia (41.4%), the NT (5.2%) and Queensland (47.1%).
APPARENT RETENTION RATES
The apparent retention rate is the number of school students in a designated level/year of education expressed as a percentage of their respective cohort group. To calculate the apparent retention rate of full-time secondary school students in Tasmania, the total of full-time students in Year 12 in August 2008 is divided by the number of full-time students that were in Year 7 in 2003. The resultant figure is converted to a percentage. Care should be taken in interpreting apparent retention rates as the method of calculation does not take into account a range of factors. Please refer to paragraphs 20 and 22 of the explanatory notes in Schools, Australia, 2008 (ABS cat no. 4221.0).
In August 2008, the apparent retention rate of full-time Tasmanian students from Year 7/8 to Year 12 was 64.8%, compared to 62.1% in 1998. The apparent retention rate for females in 2008 was 71.1% and for males 58.9%.
In recent years, apparent retention rates for students in non-government schools have exceeded those for students in government schools. In August 2008, the apparent retention rate of full-time Tasmanian students from Year 10 to Year 12 was 71.8% for those in non-government schools, compared to 61.8% for those in government schools.
APPARENT RETENTION RATES, Year 10 to Year 12, Tasmania
STUDENTS ACHIEVING BENCHMARK
In March 1997, all state, territory and commonwealth education ministers agreed on the national goal: that every child leaving primary school should be numerate and able to read, write and spell at an appropriate level. The Ministerial Council for Education, Early Childhood Development and Youth Affairs (MCEECDYA) publishes national reports which include the results of testing conducted to identify the achievement of students in each of Years 3, 5, 7 and 9 as measured against national benchmarks for reading, writing and numeracy.
In general, the results for Tasmania for 2008 show that the large majority of Years 3, 5, 7 and 9 students are achieving at the benchmark level or better in reading, writing and numeracy. The highest percentage results for Tasmania were gained by Year 3 students for writing and numeracy where this cohort saw a respective 97.1% and 96.7% of students achieving at the benchmark level or better; the lowest percentage results were gained by Year 9 for writing (84.1%) and Year 5 for reading (89.7%).
Across all categories and years except one, Tasmanian female school students achieved better benchmark results than equivalent male school students. The one exception was for Year 9 numeracy where 92.6% of males achieved the benchmark or better compared to 92.0% for females.
PERCENTAGE OF STUDENTS ACHIEVING BENCHMARK IN READING, Tasmania, 2008
PERCENTAGE OF STUDENTS ACHIEVING BENCHMARK IN WRITING, Tasmania, 2008
PERCENTAGE OF STUDENTS ACHIEVING BENCHMARK IN NUMERACY, Tasmania, 2008
SCHOOL TEACHERS
There were 6,973 teaching staff in Tasmania in August 2008. Of these, 4,921 were female and 2,052 were male.
There were 5,816 full-time equivalent (FTE) teaching staff in Tasmania in August 2008. Of these, 4,122 were at government schools and 1,694 were at non-government schools; 2,976 were at secondary schools and 2,840 were at primary schools; and 3,952 were female and 1,864 were male.
PROPORTION OF FULL-TIME EQUIVALENT TEACHING STAFF, Tasmania
The proportion of Tasmanian FTE female teaching staff has continued to rise, albeit slowly, since 1998. Conversely, the proportion of male staff has fallen. In August 2008, 67.9% of all Tasmanian FTE teachers were female; this compared to 65.2% in 1998. In August 2008, 32.1% of all Tasmanian FTE teachers were male; this compared to 34.8% in 1998.
Tasmanian primary schools have significantly more female teachers than male teachers. In August 2008, 80.0% of all FTE teachers in primary schools were female compared to 56.5% in secondary schools. The comparable figures in 1998 were 78.8% and 52.2% respectively.
Overall, in August 2008, the average number of FTE Tasmanian primary school students per FTE teacher was 15.8. In government primary schools the average was 15.5; in non-government primary schools it was 16.5. The equivalent figures for secondary schools were 12.7 students, with an average of 13.0 in government secondary schools and 11.9 in non-government secondary schools.
SOURCES
Ministerial Council for Education, Early Childhood Development and Youth Affairs (MCEECDYA)
Schools, Australia (ABS cat no. 4221.0)
Further information can also be found on the Education and Training Statistics Theme Page of the ABS website.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us. | v0 |
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Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Catalogue Number
1267.0 - Australian Standard Classification of Languages (ASCL), 2011
Latest ISSUE Released at 11:30 AM (CANBERRA TIME) 16/08/2011
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CONTENTS
About the classification
Includes: Overview of the classification, Definition of language, Scope of the classification
Building the classification
Includes: Design constraints, Classification structure, Classification criteria and their application
About codes
Includes: Coding scheme, Codes for residual categories, Supplementary codes
Index for coding responses
Includes: Why we use it, How it was developed, Coding rules
Using the classification
Includes: Editing specifications, Coding, storage and presentation of data
About the review
Includes: Purpose of the review, How it was done
What's changed
Includes: Summary of changes, Comparing current and previous editions of the classification
© Commonwealth of Australia 2013
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} | cccc_CC-MAIN-2013-20 | Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Catalogue Number
1301.0 - Year Book Australia, 2012
Latest ISSUE Released at 11:30 AM (CANBERRA TIME) 24/05/2012
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INTRODUCTION
Housing satisfies the essential needs of people for shelter, security and privacy. Shelter is recognised throughout the world as a basic human right. The adequacy or otherwise of housing is an important component of individual wellbeing. Housing also has great significance in the national economy, through its relationships with investment levels, interest rates, building activity and employment.
In the 1920s, the Australian Government started providing financial assistance for home ownership to moderate and low income earners. Governments have continued to actively promote home ownership as part of an overall policy directed at achieving people's self-reliance in housing and a quality of housing adequate for their needs. Australia currently has one of the highest rates of home ownership in the world. Governments also provide assistance to low income households to rent suitable and affordable housing.
The predominance of separate, free-standing houses situated on 'quarter-acre blocks' has historically been a feature of Australian urban development. More recently, governments have moved to promote higher housing density in order to provide greater choice of housing types and to make better use of existing infrastructure.
This chapter provides information on the types of dwellings Australians live in, their tenure type and housing costs. It also looks at a range of factors associated with buying a home, including home loans, house prices and the characteristics of recent home-buyer households. It includes comparisons between states and territories and between households at different life cycle stages. Most of the statistics are from the 2009–10 Survey of Income and Housing, conducted by the Australian Bureau of Statistics (ABS).
Information on construction of residential dwellings can be found in chapter 21 CONSTRUCTION.
This chapter contains the special article Co-operative housing in Victoria.
Other related information can be found in chapters 9 INCOME AND WELFARE and 29 PRICES.
Previous Page | Next Page
Statistics contained in the Year Book are the most recent available at the time of preparation. In many cases, the ABS website and the websites of other organisations provide access to more recent data. Each Year Book table or graph and the bibliography at the end of each chapter provides hyperlinks to the most up to date data release where available.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T05:23:42.000Z | 2bskoshyawouboxro3lamx6x4e2p6ymc | {
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} | cccc_CC-MAIN-2013-20 | Methodology article
Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing
Olafur Fridjonsson1*, Kristinn Olafsson1, Scott Tompsett2, Snaedis Bjornsdottir1, Sonia Consuegra2, David Knox4, Carlos G de Leaniz3, Steinunn Magnusdottir1, Gudbjorg Olafsdottir1, Eric Verspoor4 and Sigridur Hjorleifsdottir1
Author Affiliations
1 Matís, Vínlandsleið 12, 113 Reykjavík, Iceland
2 Institute of Biological Sciences, University of Wales, Aberystwyth, UK
3 Department of Pure & Applied Ecology, Swansea University, Swansea SA2 8PP, UK
4 Freshwater Laboratory, Marine Scotland, Pitlochry, Scotland PH16 5LB, UK
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BMC Genomics 2011, 12:179 doi:10.1186/1471-2164-12-179
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2164/12/179
Received:21 October 2010
Accepted:7 April 2011
Published:7 April 2011
© 2011 Fridjonsson et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background
Approximately half of the mitochondrial genome inherent within 546 individual Atlantic salmon (Salmo salar) derived from across the species' North Atlantic range, was selectively amplified with a novel combination of standard PCR and pyro-sequencing in a single run using 454 Titanium FLX technology (Roche, 454 Life Sciences). A unique combination of barcoded primers and a partitioned sequencing plate was employed to designate each sequence read to its original sample. The sequence reads were aligned according to the S. salar mitochondrial reference sequence (NC_001960.1), with the objective of identifying single nucleotide polymorphisms (SNPs). They were validated if they met with the following three stringent criteria: (i) sequence reads were produced from both DNA strands; (ii) SNPs were confirmed in a minimum of 90% of replicate sequence reads; and (iii) SNPs occurred in more than one individual.
Results
Pyrosequencing generated a total of 179,826,884 bp of data, and 10,765 of the total 10,920 S. salar sequences (98.6%) were assigned back to their original samples. The approach taken resulted in a total of 216 SNPs and 2 indels, which were validated and mapped onto the S. salar mitochondrial genome, including 107 SNPs and one indel not previously reported. An average of 27.3 sequence reads with a standard deviation of 11.7 supported each SNP per individual.
Conclusion
The study generated a mitochondrial SNP panel from a large sample group across a broad geographical area, reducing the potential for ascertainment bias, which has hampered previous studies. The SNPs identified here validate those identified in previous studies, and also contribute additional potentially informative loci for the future study of phylogeography and evolution in the Atlantic salmon. The overall success experienced with this novel application of HT sequencing of targeted regions suggests that the same approach could be successfully applied for SNP mining in other species.
Background
Single nucleotide polymorphisms (SNPs), representing single base differences between individuals, are a common form of genome variation [1]. Once identified, SNPs have the potential to be used as genotyping markers for population assignment or in phylogeographic analysis, and are rapidly becoming the marker of choice within this field of study [2]. The emergence of high-throughput (HT) sequencing technologies provides an unparalleled opportunity for the cost-effective sequencing of targeted genomic regions for SNP identification. HT sequencing has been applied for SNP discovery in humans [3,4], animals [5], plants [6,7] and bacteria [8] - in species where reference genomes exist. In organisms lacking a sequenced reference genome, SNPs have also been mined from the random sequencing of either expressed sequence tags (ESTs) [9,10] or reduced representation libraries [11-13]. However, with an available reference sequence, specific genetic regions of interest can be amplified using PCR prior to HT sequencing. The sequence reads of about 400 bp obtained using the Titanium GS FLX chemistry (Roche, 454 Life Sciences) make the 454 sequencing platform particularly suitable for sequencing PCR generated amplicons. This approach involves the emulsion based amplification of individual PCR products and simultaneous, parallel pyrosequencing of DNA strands [14].
Mitochondrial DNA (mtDNA) has been widely used in studies of phylogenetics, molecular ecology and phylogeography in a range of organisms, including the Atlantic salmon based on RFLP or sequences from using Sanger technology [15-17]. As SNPs represent the main form of polymorphism observed in the mtDNA, recent research has been focused upon the identification of a geographically informative mitochondrial SNP panel suitable for high-throughput genotyping (e.g. mtSNP mini-sequencing) [18].
Traditional Sanger-based sequencing methods are relatively expensive and time-consuming, restricting the number of individuals and gene regions that can be sequenced, given the funding available for most studies. Consequently, often a relatively few individuals from restricted geographical areas have been sequenced in order to obtain SNP panels. The SNPs have been subsequently used to screen larger samples from a broader geographical range [1], which has led to low power in resolving lineages and their relationships. It has also raised potentially serious concerns associated with ascertainment bias, such as the situation whereby inferences are significantly conditioned by the gene region screened or the populations used to identify the polymorphisms. The latter could potentially lead to a biased interpretation of the extent to which individuals and populations are related.
HT sequencing technologies offer the potential to overcome these limitations by allowing the rapid and economic sequencing of large genome regions. However, most applications of HT technology to-date have been designed to sequence a large number of fragments from relatively few individuals. In this study, a novel approach was developed by combining the traditional PCR amplification of known gene regions with 454 Titanium FLX (Roche, 454 Life Sciences) sequencing. This approach allowed the sequencing of extensive regions of the mtDNA genome within a broad sample group both quickly and in accordance with a limited budget. The method was tested on the Atlantic salmon (Salmo salar) - a fish extensively surveyed using both nuclear [19] and mitochondrial DNA markers, including a mtDNA SNP variation [19-22], and for which 152 nuclear SNPs and 125 mtDNA SNPs [20,22,23] have already been reported. Here, 546 samples from 48 locations throughout the species' geographical range were screened for 7215 bp, encompassing approximately 43% of the mtDNA genome in order to minimize the degree of ascertainment bias relative to previous comparable studies.
Results
PCR Amplification
546 S. salar samples derived from across the species' North Atlantic range were included in this study (Figure 1). In addition, 12 brown trout and 18 Arctic charr samples were included in the sequencing setup as a part of another study. The samples were divided into 16 groups, each composed of 36 samples (see Additional file 1, Table S1). Ten regions of the S. salar mitochondrial genome covering the D-loop region and nine coding genes (ND1, ND2, COXI, COXII, ATP6, ND3, ND4, ND5, CYTB) were selected for the SNP detection (Table 1), taking into account those regions previously shown to have high levels of polymorphism by studies of EST libraries and genome sequencing [19,20,22]. Some of the target regions were divided into 2-3 amplicons of about 400 bp, which is the average sequence length obtained with the FLX Titanium chemistry (Table 1). Thus, each sample was subjected to a total of 20 PCR reactions. For each of the 16 sample groups, 720 PCR reactions were carried out separately (Figure 2). Single PCR products of the expected sizes were obtained from the majority of the 11,520 reactions performed. Only 127 PCR reactions (1.1%) with S. salar DNA yielded low quantities of amplified products, despite optimization. Geographic bias was not pronounced; although the amplification of approximately half of the samples from two rivers produced low yields. This could be attributed to limited or low quality DNA isolated from the corresponding samples (data not shown).
Figure 1. A map showing the sampling locations. See also Additional file 1, Table S1: Sampling sites, the number of samples and the division into groups.
Additional file 1. Table S1: Sampling locations. The file shows the sampling locations and the number of individuals per location as well as grouping of samples
Format: DOCX Size: 19KB Download file
Table 1. Target regions used in this study and the number of validated SNPs
Figure 2. The experimental setup. In order to sequence 20 mitochondrial amplicons from 576 samples of Atlantic salmon, brown trout and Arctic charr, in a single run, the isolated DNA was divided into 16 groups, each containing 36 samples. The mitochondrial fragments were amplified from each group in a matrix of PCR reactions, using barcoded primers (MIDs) (A). 20 matrices of PCR reactions, one for each mitochondrion fragment, were carried out (B). Up to 720 amplicons from each group were pooled together in near equimolar concentrations. The 16 pools created were used to generate single stranded fragment DNA templates for the FLX sequencing. 16 amplified sst libraries, consisting of DNA fragments on beads, were loaded onto a PicoTiterPlate equipped with a sixteen-lane gasket where each library was assigned one lane (C). Based on the combination of MIDs on both sites of the amplicons within each group (library), individual sequencing reads were assigned to the corresponding samples.
Pyrosequencing and Amplicon Analysis
The PCR products for each group were pooled for sequencing in near equimolar concentrations and the sequencing was carried out as described in Materials and Methods. The pyrosequencing yielded a total of 179,826,884 filter passed base pairs. An average of 11,546,081 bp (±1,612,536 SD) was obtained from each of the 16 regions on the picotiter plate, excluding one that yielded 6,635,668 bp. The majority of sequence reads were between 400-420 bp, corresponding to the size of the amplicons (see Additional file 2, Figure S1 and Table S2, on the distribution of read length). Each PCR product contained multiplex identifying sequences [MIDs], designed by Roche (454 Life Sciences), at both ends, which enabled the identification of the corresponding sample within a group (Figure 2). Hence, to correctly assign a PCR product to a sample, its entire sequence was required, including both MIDs. The GS Amplicon Variant Analyzer software from Roche, 454 Life Sciences was used to align and assign the sequence reads. The sequences obtained were assigned to 10,765 of the 10,920 S. salar products targeted by PCR (98.6%). The number of sequence reads (sequence coverage) supporting a SNP per individual was on average 27.3 with a standard deviation of 11.74. The yield of sequenced S. salar amplicons was generally high, with less than 1.5% of samples missing on average. The exception to this observation was amplicon 18 (Table 1), where no sequences were obtained for 62 of 546 S. salar samples (12%).
Additional file 2. Figure S1: Distribution of read length Table S2: Read length statistics of the FLX sequencing run. The file contains a graph showing the number of reads vs. read length and a table indicating the read length statistics of the FLX sequencing run.
Format: DOCX Size: 26KB Download file
SNP Analysis
The GS Amplicon Variant Analyzer software identified a total of 1714 variants following alignment of the raw sequence data. Applying the first stringency filter, requiring sequence reads from both DNA strands, reduced this number to 904. After rejecting variants resulting from potential sequencing errors, including under-reads of homopolymer regions, and single base insertions, the variants were confined to those confirmed in at least 90% of replicate sequence reads. Subsequently, 242 variants remained. Thereof, 24 variants were rejected since they occurred in only one individual. Consequently, the alignment analysis and filtering yielded a total of 218 variants, consisting of 216 SNPs and 2 indels. Maps of the S. salar mitochondrial genome, indicating the regions selected for the SNP analysis and the accepted SNPs for each region are shown in Figure 3 and 4, respectively. (See also Table 1, and Additional file 3, Table S3, for further details on 454 read statistics). The greatest number of SNPs was observed in the ND4 gene region (38), whilst the lowest number (10) was observed in the ND3 gene. When considered as a proportion of the length of each region, the D-loop had the highest density of SNPs (0.55 SNPs bp-1) whilst the COX2 region gene yielded the least (0.021 SNPs bp-1). Of the variants observed, 196 are transitions while 20 are transversions, and nearly half of the latter is located in the D-Loop region (Table 1). In three cases (D-Loop: bp973; ND1: bp3989 and CYT-B: bp16421) both a transition and transversion were observed at the same locus in different samples. Indels were only observed within the D-Loop region, with a two bp insertion (CT) at bp 963 and a two bp deletion at bp 967. When compared to previous studies of smaller [20] and more geographically constrained discovery panels [15,19,22-24], 109 of the SNPs and one of the indels had been reported, while 107 new SNPs and one indel were identified in this study (Figure 4). When this data is considered according to populations, 0.5% of SNPs were found in all geographic locations, whilst 13.1% existed in only one. Additionally, a further 56.3% were found in less than 10 populations, whilst 13.1% were found in more than 50% of populations.
Figure 3. A map of the Salmo salar mitochondrial genome. The regions selected for sequence analysis in this study are shown.
Figure 4. Maps of the accepted SNPs obtained in this study, shown for each region. New SNPs are shown red.
Additional file 3. Table S3: mtDNA SNPs validated in this study. The file shows the validated SNPs, their location according to S. salar mitochondrial DNA reference sequence (NC_001960.1); the number of individuals supporting the SNP; and the sequence coverage per individual.
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Discussion
Next generation sequencing technology, such as 454 sequencing, is rapidly expanding the possibility for SNP mining by genome sequencing within a reasonable budget. However, the technology to-date has generally been restricted to the sequencing of large regions of the genome using relatively few samples [12,13]. In this work, a large SNP ascertainment panel was obtained at a relatively low cost by amplifying multiple regions of a mitochondrial genome in numerous samples and their subsequent sequencing using the 454 technology. The resultant SNP panel provides the least likelihood of ascertainment bias [25], with a discovery panel of 546 samples from 48 locations across the North Atlantic range of S. salar, making this the most informative and geographically comprehensive SNP panel for the species to-date (Figure 1).
The cost of sequencing using the 454 platform was minimized by carefully designing the experiment to require only a single pyrosequencing run, whilst obtaining sufficient sequence reads in both directions to yield a robust result, essentially minimizing false positives and avoid missing true polymorphisms from each ~400 bp read. The most challenging aspect faced was the need to ensure that each individual amplicon of a given type could be traced to the original sample. This was achieved using a sequencing plate with a 16-region gasket, and a set of 5' MID primer sequences. To decrease the primer cost (and ultimately the overall cost), the necessary adaptor sequences for the 454 sequencing were ligated to the PCR products instead of including them in the primer sequences; this may have also reduced complications in the PCR reactions due to the shorter 5' non-complementary primer sequences. Thus, sequencing libraries were prepared for the 16 PCR pools using the GS FLX Titanium General Library Preparation protocol for shotgun sequencing, instead of using amplicon sequencing (Roche, 454 Life Sciences). Furthermore, a Taq-comparable polymerase was used for generating the PCR pools of 11,520 reactions, instead of using an expensive high fidelity polymerase. The lack of proof-reading activity during the PCR might have increased the error rate in the sequence data, although the numerous specimens used here as well as the sequence coverage obtained should adequately compensate for this. Furthermore, variations observed in a single individual were not accepted as SNPs in accordance with the set criteria. Even if legitimate SNPs were necessarily discarded in this manner, their low frequency suggests that any information that was lost was probably minimal. Given that there is no geographical or population association, it can be assumed that this would not compromise the informative essence of the overall SNP suite, at least from the perspective of the studies of biodiversity and phylogeography. Considering the high coverage obtained in this experiment, the application of a high fidelity polymerase could enable the reliable SNP detection for simultaneous processing of even greater sample numbers than in the current study. Thus, if the budget is not restricting, the processing capacity of the method can be further increased by applying a high fidelity polymerase to generate the amplicons, at the cost of sequence coverage.
The sequence yield in this experiment was approximately 179 million bp, which is within the range of 160-320 million bp expected for Titanium 454 sequencing, using a 16-region gasket (Roche, 454 Life Sciences). However, for an undetermined reason, the sequence yield ranged from 6,635,668 to 13,135,520 filter-passed base pairs between different regions of the sequencing plate. Also, the sequence yield for amplicon 18 was relatively low in comparison to that of the other amplicons. This could be due to a bias in the sample pooling. Nevertheless, the distribution of sequences was relatively similar over the sample range, resulting in an average coverage of 27.3 (±11.7) sequence reads per SNP per individual. The sequencing setup described here also included 30 brown trout and Arctic charr samples. The data sets obtained for these samples were not included in this analysis, and they will be the subject of future studies. Nevertheless, they are mentioned here since they were a part of the original experimental setup of 576 individuals divided into 16 groups, each with 36 individuals. The total number of base pairs that were to be sequenced in this study (including the brown trout and Arctic charr samples) was 4,115,840 bp (number of sequenced bases for 576 individuals). The total sequence data obtained consisted of 179.826.884 bp, so 39-fold coverage would therefore be expected. However, a substantial part of the sequence reads were not assigned to any sample and were consequently excluded from the analysis. The anticipated reason behind this is accounted to short sequence reads missing a MID from either end. Fusing MID sequences to only one end of an amplicon should reduce this problem and increase the number of analysed sequence reads. This practice, however, reduces the number of samples, which can be analysed simultaneously, although with the emergence of new MID sequences validated for 454 sequencing, more samples with only one MID could be assigned.
Although the existence of MIDs on both ends of a sequence read was requisite in order to assign it to the corresponding individual, some global and consensi alignments (made with the GS Amplicon Variant Analyzer) included partial sequences. This was the result of default stringency levels causing parts of some sequences with low quality bases to be discarded. The trimming was however performed following the alignment of the sequence reads. Hence, as the design of the MIDs allows for (corrects) two sequencing errors, these partial sequences could still be assigned to the corresponding individual prior to the trimming.
As expected for high-throughput sequencing methods, which produce high amounts of reads, numerous deviations from the reference sequence were observed in the raw data. The stringent criteria applied here for the SNP validation rejected the great majority of these variants. However, the filtering may also have eliminated legitimate SNPs. Such variants could be identified by a modest reduction in the stringency levels and verified by Sanger sequencing. Following the validation, about 3.0% of the bases screened exhibited sequence variance and the final number of variants, 218 (including two indels), is nearly double the number of mtDNA SNPs previously reported. The new SNPs are predominantly transitions although the number of transversions is relatively high in the non-coding D-loop region (Table 1). Similar transition/transversion ratios were observed in other studies on the genetic variability of the S. salar mitochondrion [19,20,22]. The 107 new SNPs and a new indel identified in this study are indicated in Figure 4 in red letters. Although the average number of sequence reads supporting the new SNPs per individual is similar to that of those reported, the number of individuals harbouring the new SNPs is generally lower (see Additional file 3, Table S3). This is due to the numerous samples and the great geographical range analyzed here, which consequently allowed the detection of new rare variants. The greater the number of amplicons and individuals screened, the more likely it is that an accurate picture of the extent and nature of SNP variation will be revealed, and that a suite of SNP markers for population genetic studies can be compiled. The challenge remains to determine the optimal balance between the number of amplicons (i.e. proportion of mtDNA genome screened), the number of populations (i.e. representativeness of species as a whole) and the number of individuals per population for studies of matrilineal variation in the target species, Atlantic salmon. This will only be achieved by a detailed analysis of the within and among population variation and a consideration of the robustness of its evolutionary and phylogeographic implications. It should, however, provide a basis for robust inferences concerning the general levels of genetic diversity in the species and broad scale, deep phylogenetic structuring. Given, though, that the geographical sampling is extensive rather than intensive, and that sample sizes per population are limited, the ability to resolve any finer scale, shallower evolutionary structuring on the regional level will be diminished. To achieve the latter, a more focused and intensive search, based on sequencing of the entire mtDNA genome from more individuals would be of greater use since a higher proportion of regionally or population restricted or low frequency polymorphisms could be detected.
The analysis of within and among population distribution of variation is currently underway and can be expected to yield considerable insights into the phylogeography and matrilineal evolution of the Atlantic salmon. Analysis of the linkage of variation and its spatial distribution should also assist in the identification of a subset of the overall SNP suite that can be genetically typed more cost-effectively using PCR-based SNP assays. The SNP subset could then be investigated within samples from a wider geographical range and in archival material, in order to establish a more accurate assessment of the mixed stock assignment and population evolutionary hypotheses extracted from the current data set. Additionally, the markers that were identified in the study will likely prove highly useful as genetic tags for use in the assessment of the extent of population processes such as female mediated gene flow, as well as for tracking individual family groups in experimental studies.
Conclusion
A novel approach that combines targeted PCR amplification and a single HT sequencing run proved successful in screening numerous targeted genomic regions in a large number of individuals. This technique presents a valuable tool for the identification of SNPs for population studies in other species, and also minimizes the risks of ascertainment bias associated with previous approaches that screened either confined regions of the genome or only several individuals from few populations.
Methods
Samples and DNA Extraction
Atlantic salmon samples (N = 546) were collected from 48 locations throughout the North Atlantic range of the species using electro-fishing. Additionally, 12 brown trout (Salmo trutta) and 18 Arctic charr (Salvelinus alpinus) samples were included in the sequencing run as a part of the experimental setup shown in Figure 2. Table S1 submitted as Additional file 1 lists the sampling sites, the number of samples, and their subdivision into 16 groups. DNA was isolated from fin-clip tissue samples using the DNeasy Blood & Tissue Kit (Qiagen) and standard protocols, and DNA concentrations were measured with a NanoDrop ND1000 spectrophotometer. The concentrations of stock DNA eluted were 9-484 ng/μl and diluted to 2-10 ng/μl for subsequent PCR reactions.
Primer Design
Ten regions of the S. salar mitochondrial genome (DLOOPB, ND1, ND2, COXI, COXII, ATP6, ND3, ND4, ND5, CYTB) were selected for SNP detection (Table 1). Seven of the ten selected gene regions were amplified in two or three fragments of approximately 400 bps, resulting in a total of 20 amplicons covering 7,215 bps excluding the primer binding sites (Table 1). Primers were designed according to the reference sequence (16.7 kb) of the S. salar mitochondrion (NC_001960.1) (see Additional File 4, Table S4). Barcodes or multiplex identifying sequences (MIDs) of 10 bp were added to the 5' end of each primer, providing a unique means of identification for every sample in a single sequence group. The MIDs used (Figure 2), were those designed by Roche, 454 Life Sciences for automated software identification of samples following sequencing and allow up to 2 sequencing errors in the MID region before a read is misidentified. To minimize the number of MID tagged primers required, samples were divided into 16 groups, each composed of 36 individuals (see Additional File 1, Table S1, for subdivision of samples). Six forward MID-primers (numbered 1-6) and six reverse MID-primers (numbered 7-12) were synthesized (Sigma Aldrich) for each of the 20 amplicons. As a consequence of using a combination of 6 forward and 6 reverse MID tagged primers, the same MIDs could be re-used by conducting the PCR and sequencing of each of the 16 groups separately (See primer matrix, Figure 2). Critically, this minimized the cost associated with the use of multiple MID tagged primers.
Additional file 4. Table S4: The primer set for the 20 amplicons used in this study. The file shows the designation and the sequence of the primers used, as well as the primer binding sites on the mitochondrial DNA according to the reference sequence (NC_001960.1).
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PCR Setup
In order to simultaneously amplify 20 traceable mitochondrial fragments from 576 samples in a single run, PCR reactions for each group of 36 samples were conducted separately, resulting in a total of 11,520 PCR reactions across all 16 groups. PCR was performed in 20 μl reactions containing 0.5 mM betaine (Sigma Aldrich), 50 μM dNTP mix, 1 × reaction buffer and 1 U Teg polymerase (Matís production, Taq comparable polymerase), 0.5 μM each primer (synthesized by Sigma Aldrich) and 2-3 μl DNA (2-10 ng/μl). Initial denaturation was at 94°C for 2 minutes followed by 31-33 cycles of 94°C for 60 seconds, 53°C for 45 seconds and 72°C for 90 seconds, and then a final extension of 5 minutes at 72°C. The relative amount of PCR products was estimated using gel electrophoresis and ethidium bromide staining. Subsequently, products from each group were pooled in near equimolar concentrations resulting in 16 pools of up to 720 amplicons.
Construction of single stranded DNA libraries
The DNA pools (3 μg) were electrophoresed on 1% agarose gels and a band of approximately 400 bp was purified from each pool using the QIAquick Gel Extraction Kit (Qiagen). These were subsequently examined using Bioanalyzer 2100 and a DNA 7500 LabChip (Agilent Technologies). Observed traces were correlative for all 16 sample groups, with an average fragment length of 425 bp. Both ends of the DNA fragments were repaired, phosphorylated and ligated to adaptor oligonucleotides A and B. The DNA fragments carrying the 5'-biotin of adaptor B were immobilized onto magnetic streptavidin coated beads. Single stranded template DNAs carrying adaptor A at the 5'-end and adaptor B at the 3'-end were then purified by alkaline denaturation. Reagents, enzymes and oligonucleotides for the single-stranded DNA (sst DNA) library construction were supplied with the GS FLX Titanium General Library Preparation Kit (Roche, 454 Life Sciences). The integrity and concentrations of the sst libraries were estimated using the Bioanalyzer and the RNA 6000 LabChip and Quant-iT Ribogreen DNA Assay Kit (Invitrogen), respectively.
454 pyrosequencing and assembly
Shotgun sequencing of the 16 sst DNA libraries was carried out using the GS FLX Titanium reagents as described by the manufacturer (Roche, 454 Life Sciences). Purified DNA fragments were hybridised onto DNA capture beads and the 16 sst DNA libraries were separately amplified by emulsion PCR. Beads containing amplified DNA were deposited onto a 75 × 75 mm Titanium PicoTiterPlate equipped with a sixteen-region gasket. Those corresponding to each of the 16 original DNA pools (20 amplicons from 36 individuals) were assigned one region and then the pyrosequencing was performed in a single run. The sequence data generated from each region, corresponding to each of the 16 groups, was assembled separately using the GS Amplicon Variant Analyzer software (Roche, 454 Life Sciences) with default stringency settings. Sequence reads were sorted according to the sequence and the combination of the MIDs, and the sequence reads from an individual for each amplicon were aligned with the S. salar reference sequence (NC_001960.1).
SNP analysis and mapping
Candidate SNPs were identified and checked against the global and consensus alignments of the corresponding sequence using the GS Amplicon Variant Analyzer software (Roche, 454 Life Sciences). Variants resulting from potential sequencing errors, including under-reads of homopolymer regions, and single base insertions (carry-forward events) were rejected [26]. Homopolymer under-reads and carry-forward events were observed in the misalignment of underlying consensi, by confirming support in both forward and reverse reads and, where necessary, the observation of underlying flowgrams. SNPs were accepted as valid only if they met the following criteria: (i) Sequence reads with variants were produced from both DNA strands. (ii) Those with >90% support from sequencing reads should have a total of more than 10 supporting reads in both read directions, or in cases of less than 10 supporting reads that the SNP in question should also be present in other samples with higher support. (iii) The final list of SNPs rejected those only found in one sample as these readings could be considered uninformative and possibly arose as a result of a PCR or sequencing error. To determine the sequence coverage for each SNP per individual, only sequence reads comprising the consensus sequence, truly supporting the SNP were taken into account, excluding those reads that did not show the variance (e.g. due to a sequencing error or truncation).
Availability
The SNPs identified and evaluated in this study have been deposited in the National Center of Biotechnology (NCBI) SNP database (dbSNP) under submitter handle MATIS. The accession numbers are: NCBI_ss 295476608 - 295476815.
Authors' contributions
The study was conceived and coordinated by SH and EV and set up by OF, ST and EV. DK, CGL and EV were responsible for the DNA collections. SM, SB, and GO organized and performed the PCR and the sequencing work. OF and SM prepared the sequence alignments and ST and KO did the SNP validations and variant analysis. OF, EV, SB, KO, ST, CGL and SC wrote the manuscript. All participants of this study read and approved the final draft.
Acknowledgements
This work is part of the EU SALSEA MERGE project (No. 212529, FP7-ENV-2007-1) and was sponsored by EU funding in association with internal fundings from Matis and Marine Scotland. Their support is gratefully acknowledged. We thank Vidar Wennevik for providing samples from Norwegian populations for the work. Most of the remaining samples used were drawn largely from archival material collected over the last two decades for other purposes, by numerous individuals. Their contribution to making the study possible is also acknowledged.
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Inequities in skilled attendance at birth in Namibia: A decomposition analysis
Eyob Zere1*, Doyin Oluwole1, Joses M Kirigia2, Chris N Mwikisa2 and Thomas Mbeeli3
Author Affiliations
1 Africa's Health in 2010, Academy for Educational Development, 1825 Connecticut Avenue, Washington, DC 20009, USA
2 World Health Organization, Regional Office for Africa, Brazzaville, Congo, Africa
3 Ministry of Health and Social Services, Windhoek, Namibia, Africa
For all author emails, please log on.
BMC Pregnancy and Childbirth 2011, 11:34 doi:10.1186/1471-2393-11-34
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2393/11/34
Received:13 December 2010
Accepted:14 May 2011
Published:14 May 2011
© 2011 Zere et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background
The fifth Millennium Development Goal (MDG5) aims at improving maternal health. Globally, the maternal mortality ratio (MMR) declined from 400 to 260 per 100000 live births between 1990 and 2008. During the same period, MMR in sub-Saharan Africa decreased from 870 to 640. The decreased in MMR has been attributed to increase in the proportion of deliveries attended by skilled health personnel. Global improvements maternal health and health service provision indicators mask inequalities both between and within countries. In Namibia, there are significant inequities in births attended by skilled providers that favour those that are economically better off. The objective of this study was to identify the drivers of wealth-related inequalities in child delivery by skilled health providers.
Methods
Namibia Demographic and Health Survey data of 2006-07 are analysed for the causes of inequities in skilled birth attendance using a decomposable health concentration index and the framework of the Commission on Social Determinants of Health.
Results
About 80.3% of the deliveries were attended by skilled health providers. Skilled birth attendance in the richest quintile is about 70% more than that of the poorest quintile. The rate of skilled attendance among educated women is almost twice that of women with no education. Furthermore, women in urban areas access the services of trained birth attendant 30% more than those in rural areas. Use of skilled birth attendants is over 90% in Erongo, Hardap, Karas and Khomas Regions, while the lowest (about 60-70%) is seen in Kavango, Kunene and Ohangwena. The concentration curve and concentration index show statistically significant wealth-related inequalities in delivery by skilled providers that are to the advantage of women from economically better off households (C = 0.0979; P < 0.001).
Delivery by skilled health provider by various maternal and household characteristics was 21 percentage points higher in urban than rural areas; 39 percentage points higher among those in richest wealth quintile than the poorest; 47 percentage points higher among mothers with higher level of education than those with no education; 5 percentage points higher among female headed households than those headed by men; 20 percentage points higher among people with health insurance cover than those without; and 31 percentage points higher in Karas region than Kavango region.
Conclusion
Inequalities in wealth and education of the mother are seen to be the main drivers of inequities in the percentage of births attended by skilled health personnel. This clearly implies that addressing inequalities in access to child delivery services should not be confined to the health system and that a concerted multi-sectoral action is needed in line with the principles of the Primary health Care.
Background
There is increasing evidence on the existence of pervasive inequalities in health and health care that are related to socio-economic position as may be measured by household income/expenditure/wealth, occupation, gender, area of residence etc. both between and within countries [1,2]. The existing evidence unequivocally reveals that morbidity and mortality are more prevalent at the lower end of the socio-economic ladder. In contrast, access to health services is concentrated among those at the upper end of the socio-economic spectrum.
The overwhelming evidence on socio-economic inequalities in health and health care has led to renewed interest globally and nationally to understand the causes of health sector inequalities and develop appropriate policy responses [3].
The differential in maternal health indicators is perhaps the largest differential in health status between rich and poor countries [4,5]. In Sub-Saharan Africa, the adjusted maternal mortality ratio in 2008 was 640 per 100,000 live births, as compared to 14 per 100,000 in the developed regions. Similarly, while the life time risk of maternal death is 1 in 31 in Sub-Saharan Africa, the corresponding figure in the developed regions of the world is 1 in 4,300 [6].
In the period 2000-2008, about 96% of child deliveries were attended by skilled health personnel in the European Region of the World Health Organization. However, despite global improvement in the proportion of women delivered by skilled health workers, the situation in Africa has not changed [7]. In the African Region only 47% of births were attended by skilled health personnel. The situation in Namibia is much better compared to this average - about 81% of births attended by skilled health personnel.
Data from low and middle-income countries also show significant within country gradients in health outcomes and utilization of health services. In the poorest 20% of the population, an infant is more than twice as likely to die before the age of 1 year and an under-five child is more than three times as likely to be stunted (short-for-age) compared to children from the 20% economically better-off households [8].
At the dawn of the current Millennium, World Leaders agreed to reduce maternal mortality by 75% in 2015 compared to its 1990 levels. One of the indicators for MDG 5 is the proportion of deliveries attended by trained health providers, which include doctors, nurses or midwives. Delivery by trained providers is necessary to reduce maternal mortality and is easy to monitor regularly and at reasonably short intervals compared to maternal mortality.
Global improvements mask inequalities both between and within countries. In Namibia, there are significant inequities in births attended by skilled providers that favour those that are economically better off [9]. Identifying the determinants of inequities in health and health care is essential to designing equitable interventions [10].
In line with the conceptual framework of the WHO Commission on Social Determinants of Health, access to delivery services by skilled health providers is shaped by political, social and economic forces. It then follows that addressing inequities requires a concerted multi-sectoral action, which is also in line with the Principles of Primary Health Care. The objective of this study was to identify the drivers of wealth-related inequalities in child delivery by skilled health providers using a decomposable health concentration index and the framework of the Commission on Social Determinants of Health (CSDH).
Brief country profile
Namibia is a country in the South Western part of Africa covering a land area of 824,000 square kilometers. According to the 2001 population and housing census, the population was about 1.8 million with an inter-censal growth rate of 2.6% per annum [11]. The country is divided into 13 Administrative Regions, which also correspond to the health regions.
Namibia is an upper middle income country [12] and one of those with the highest income inequality in the world [13]. Table 1 below depicts data on selected health and development indicators [13-16].
Table 1. Namibia: selected health and development indicators
As can be seen from Table 1, although the country is better off than many countries in sub-Saharan Africa in terms of resources for health and development, there is a significant amount of inequity and inefficiency. The potential loss in human development due to inequalities in each of the dimensions of the HDI (life expectancy at birth, gross national income per capita and schooling) amounts to about 44%. The HDI falls to a level which is less than that of countries classified as low human development (HDI = 0.393) [13]. Furthermore, the GNP per capita rank minus the HDI rank was -14 indicating inefficiency in translating resources into welfare, i.e. the country did not achieve the level of human development that could potentially have been achieved given its resources.
Antenatal care from a skilled provider (at least one visit) was about 95%. However, the proportion of pregnant women who received four or more antenatal care visits was only about 70%. The maternal mortality ratio of 449 per 100,000 live births in 2006/07 is a significant increase from the 1992 level, which was 225 per 100,000 live births. Apart from the direct and indirect causes of maternal mortality; limited access to emergency obstetric care and lack of transport and communication facilities also contribute to maternal mortality.
To reverse the increasing trend of maternal mortality and consequently accelerate the progress towards the achievement of the 5th Millennium Development Goal (MDG 5) of reducing the maternal mortality ratio by three-quarters between 1990 and 2015, the Government has embarked on a number of initiatives, including development and implementation of a Roadmap for Accelerating the Reduction of Maternal and Neonatal morbidity and mortality.
Methods
Measuring inequalities
In measuring equity in a health outcome or access to health interventions, the following are required:
- indicator of the health intervention of interest (delivery by skilled health providers)
- a variable (stratifier) capturing socio-economic status against which the distribution is to be assessed (wealth); and
- a measure of socio-economic inequality to quantify the degree of inequity in the indicator variable of interest.
A concentration index (C) is used to measure wealth-related inequalities in the observed use of delivery services by skilled health providers. The concentration index of a health care variable y (utilization of delivery services by trained health providers) can be defined using the concentration curve that links the cumulative proportion of individuals ranked by wealth to the corresponding cumulative proportion of y (use of delivery services by trained health providers). The concentration curve plots shares of the health care variable (y) against quantiles of the measure of socio-economic status (asset-based wealth index) [17].
The concentration index is defined as twice the area between the concentration curve and the line of equality and assumes values between -1 and +1. A negative value of the concentration index denotes inequity in skilled care at birth that is to the advantage of the lower wealth quintiles implying that women of lower socio-economic status are delivered by skilled health providers more than their counterparts who are wealthier. In this case the concentration curve lies above the line of equality. On the other hand, a positive concentration index implies inequality in the use of delivery services by skilled providers that favours women who are wealthier (the concentration curve lies below the line of equality). When the value of the concentration index is zero, there are no wealth related inequalities in the use of delivery services by skilled providers. The concentration curve overlaps with the 45-degree line.
From individual level data, the concentration index can be computed using the following formula [18]:
(1)
Where
hi is the health variable of interest (delivery by skilled health providers);
μ is the mean of hi;
Ri is the fractional rank of individual i in the distribution of socio-economic position; and
(; i = 1 for the poorest and i = n for the richest).
Decomposing the concentration index
Wagstaff et al. [19] demonstrated that the concentration index of a health variable is additively decomposable to the concentration indices of the determinants of that health variable. In other words, the concentration index of the health variable of interest can be expressed as the sum of the contributions of the various determinants of that variable, together with unexplained residual component.
In decomposing the concentration index of delivery by skilled providers, the following steps are pursued:
1. Regressing the health variable against its determinants:
(2)
Where: yi = 1 if the delivery was conducted by a skilled health provider;
xk: a set of exogenous determinants of delivery by trained health provider;
βk: coefficient of determinant xk; and
εi: random error term.
The dependent variable (delivery by skilled health personnel) is a binary variable with values of 1 (delivered by skilled provider) and 0 (otherwise). The linear probability model (LPM) in Equation 2 above has been used in order to satisfy the linearity assumption of the decomposition analysis, although the estimates are inefficient and the probability of delivery by skilled health providers may not fall within the conventional values of 0 ≤ p ≤ 1 and has heteroskedastic errors [20]. However, the estimated probabilities from the LPM model have been constrained within the conventional values and a comparison with a probit model has not shown significant variations between the coefficients of the LPM and the marginal (or average) effects of the probit regression derived using the dprobit Stata command [17]. Furthermore, to adjust for heteroskedasticity, the predicted values from the regression model have been saved and used as weights to run weighted least squares (WLS) using the "aweight" option in Stata [21]
2. Calculating concentration indices for the health variable and for its determinants (and generalized concentration index of the error term):
For any linearly additive regression model of the health variable of interest (yi) such as Equation 2 above, the concentration index for y, can be written as:
(3)
Where:
Cy: concentration index of skilled care at birth (i.e. concentration index of yi);
: mean value of determinant xk;
μ: mean of the outcome variable yi - that is the mean of deliveries by skilled health providers
ck: concentration index of determinant xk
GCε: residual component that captures wealth-related inequality in skilled care at birth that is not accounted for by systematic variation in determinants across wealth groups.
The term in parenthesis in Equation 3 above expresses the impact of each determinant on the probability of delivery by skilled health providers. In other words, it denotes the elasticity (ηk) of the outcome variable (delivery by skilled health providers) with respect to the determinant xk evaluated at the mean value of yi (delivery by skilled health providers). The concentration index of delivery by skilled health providers is thus a weighted sum of the inequality in each of its determinants, with the weights equal to the elasticities of the determinants:
(4)
The social determinants of health framework
Report of the WHO Commission on the Social Determinants of Health revitalized the need for sustained and concerted efforts to achieve health equity through action on the social determinants of health. The Commission's social determinants framework takes a holistic view of inequities in health and health care within and between countries. Inequities in health/healthcare are caused by the unequal distribution of power, income, goods and services nationally and internationally (Figure 1) [22].
Figure 1. Commission on Social Determinants of health conceptual framework.
The social determinants of health are the circumstances in which people are born, grow up, live, work and age, and the systems put in place to deal with illness. These circumstances are in turn influenced by a wider set of forces: economics, social policies and politics [22].
The social determinants framework suggests that interventions to address health inequities have to be geared towards:
1. The circumstances of daily living, which include: differential exposure to health risks in early life, the social and physical environments and work associated with social stratification; and health care responses.
2. Structural drivers including the nature and degree of social stratification; biases, norms and values within society; global and national economic and social policy; and processes of governance at all levels.
As observed in Figure 1, the health system is an important social determinant of health influenced by and influencing the other social determinants. However, the health system is not the only social determinant of health. The effect of the each of the factors in Figure 1 in the genesis and perpetuation of health/health care inequities may vary from one country to another. It is therefore important to try to identify the effect of the various social determinants of health on health outcomes and access to health care in order to design evidence-based interventions and policy instruments.
Data and Variables
Data from the Namibia Demographic and Health Survey 2006-07 was used for this study. The data is available on the MEASURE DHS website for registered users.
In the linear probability model of the determinants of delivery by skilled health providers and the decomposition analysis the following variables have been used:
1. Dependent variable: delivery by skilled health providers, which takes a value of 1 if the delivery has been attended by skilled health providers and a value of zero otherwise.
2. Independent variables:
• Region;
• Place of residence - urban/rural;
• Wealth as computed from the asset indices;
• Education of mother in years of schooling completed
• Head of household - a dummy where female household assumes a value of one; and
• Insurance coverage - a dummy with a value of one if the woman has insurance coverage.
In NDHS 2006-07, a representative two-stage probability sample of 10,000 households was selected. The first stage consisted of selection of 500 primary sampling units (PSUs) from a sampling frame of 3,750 PSUs with probability proportional to size; the size being the number of households in the 2001 Population Census. The second stage involved the systematic selection of 20 households in each PSU [14].
The demographic and health surveys do not contain data on household income or consumption expenditure. Instead wealth index is used as a proxy. The wealth index is based on household ownership of consumer goods (such as radio, television); dwelling characteristics; type of drinking water source; toilet facilities and other characteristics related to the household's socio-economic status. The asset indices are constructed using the method of principal component analysis (PCA) [14]. Studies have shown a close relationship between asset ownership and consumption expenditure in developing countries [23] and that household asset is a good indicator of the long-run economic status of households [24]
Data analysis
Data was analyzed using STATA 10 statistical software and MS Excel.
Results
Descriptive statistics
About 80.3% of the deliveries were attended by skilled health providers. A breakdown by various maternal and household characteristics is provided in Table 2.
Table 2. Delivery by skilled health provider by various maternal and household characteristics
Delivery by skilled health providers is observed to differ by the various characteristics provided in Table 2. Most pronounced differences are seen by the household wealth status and mother's level of education. Skilled birth attendance in the richest quintile is about 70% more than that of the poorest quintile. The rate of skilled attendance among educated women is almost twice that of women with no education. Furthermore, women in urban areas access the services of trained birth attendant 30% more than those in rural areas.
Use of skilled birth attendants is over 90% in Erongo, Hardap, Karas and Khomas Regions, while the lowest (about 60-70%) is seen in Kavango, Kunene and Ohangwena. Parturient women in Erongo, Hardap, Karas and Khomas utilize the services of skilled attendants by more than 40% compared to those in Kavango. In six out of the thirteen regions, use of skilled delivery is less than the national average of 81%.
The concentration curve (Figure 2) and concentration index show statistically significant wealth-related inequalities in delivery by skilled providers that are to the advantage of women from economically better off households (C = 0.0979; P = < 0.001). The concentration curve in Figure 2 lies below the main diagonal indicating that economically better off women are skilled birth attendants more than those who are economically worse off.
Figure 2. Concentration curve: delivery by skilled health providers.
Decomposition analysis
The decomposition analysis clarifies how each determinant of delivery by skilled providers contributes to the total wealth-related inequality in delivery by skilled health providers [25]. As can be observed from formula 4 (), the contribution of each determinant depends on: (i) its impact on delivery by skilled health providers (elasticity); and (ii) how unequally distributed over wealth the determinant is (its concentration index). The results of the decomposition analysis are depicted in Table 3.
Table 3. Results of the decomposition analysis
The concentration indices of Erongo, Hardap, Karas, Khomas have a high pro-wealthy concentration index (P < 0.001) implying that most of the relatively wealthy people inhabit this regions. In contrast, most of the relatively less wealthy people live in Ohangwena, Omusati and Oshikoto regions (P < 0.001). The concentration indices for urban residence, education of mother, and insurance coverage have a statistically significant positive value indicating that they are more prevalent among the relatively wealthier segment of the population. On the other hand, female household heads are seen more among those that are less wealthy.
It is also observed that the three regions (Kavango, Kunene and Ohangwena) with the lowest rates of skilled birth attendance are mainly inhabited by the poor, as demonstrated by the negative concentration indices.
As discussed above, the contribution of each of the determinants to the total concentration index of delivery by skilled health providers depends on the impact of the determinant and its concentration index. A determinant that has a high impact but with no wealth-related gradient will have less contribution to the overall concentration index as opposed to one that with a high impact and high wealth-related inequality.
Figure 3 presents a summary of the contribution of the determinants to the overall concentration index of the variable, delivery by skilled health providers.
Figure 3. Contribution of the determinants to the concentration index of delivery by skilled health providers.
It is clearly observed that most of the inequality in delivery by skilled health providers that is to the advantage of the wealthier segment of the population is explained by inequalities in income, education and urban residence. The variables: region, insurance coverage and female-headed household seem to have inequality reducing effect, although not substantial.
Discussion
To the best of our knowledge this is the first study of its kind in Namibia. An attempt is made to identify the drivers of wealth-related inequalities in child delivery by skilled health providers using a decomposable health concentration index and the framework of the Commission on Social Determinants of Health. Addressing inequities in health and health care requires action on the social determinants of health [1]. Design of appropriate evidence-based policy responses entails identification of those social determinants of health and health care that significantly influence inequities.
The findings of this study highlight the significant role that social determinants play in access to child delivery services by trained providers. Health systems are a social determinant of health that influence and are influenced by the other social determinants. Inequalities in wealth and education of the mother are seen to be the main drivers of inequities in the health system variable - delivery by trained health providers. This brings to the fore that addressing inequalities in access to child delivery services should not be confined to the health system and that a concerted multi-sectoral action is needed in line with the principles of the Primary Health Care [26].
In Namibia, inequality in wealth is found to be one of the major contributors of inequity in access to child delivery by trained providers. The country is one of those with the highest income inequality in the world. It is therefore imperative to address this unacceptably high level of income inequality, in order to improve inequities in access to delivery services by trained health providers. There has been a debate on the relationship between income inequality and health; findings and conclusions have been far from consistent [27]. However, income inequality is one of the markers of the unequal distribution of goods and services [22] including health-enhancing ones. Addressing inequities in delivery care by skilled attendants is essential for achieving MDG targets for maternal health [28]. Hence, addressing wealth inequalities contributes to improving equity in delivery by skilled attendants and consequently to achievement of the MDG related to improving maternal health. It is, however, important to note that redressing wealth inequalities alone can not be an effective intervention to inequities in access to maternity care in the absence of interventions that also tackle the other social determinants such as education [27].
The link between education of the mother and use of delivery services by trained health providers is well established [29]. Influences of maternal education can be observed in two ways: (i) education can improve the ability of individuals to produce health (without relying on health services) by influencing their life style; and (ii) increasing the use of health care services through improved knowledge, attitude and practice [30]. A study in Thailand using data from Multiple Indicator Cluster Survey (MICS) found that education of the mother is the major determinant of inequities in delivery by skilled health workers [31]. Our study indicates that inequality in maternal level of education is the major driver of inequities in delivery by trained health providers. Hence, bridging inequalities in the maternal levels of education is an important undertaking to narrow inequities in the use of delivery services by skilled health providers.
The other determinant of inequities in delivery by skilled providers is distribution according to residential location. It has been observed that there is a very high positive concentration index in urban residence implying that there is a high concentration of the economically better off segment of society in urban areas. It may be difficult in the current study to identify the mechanisms by which inequalities in urban residence influence inequities in delivery by skilled attendants. It may partly be explained by supply-side factors, where there is commonly a differential access to services favoring urban areas (urban-bias). There may also be a high concentration of the economically better off and the better educated in urban areas, which may contribute to the influence of inequalities of urban location to inequities in delivery by skilled attendants. It is thus important to carefully understand the mechanisms of influence and take appropriate equity-enhancing measures accordingly.
The social determinants of health such as education, income and place of residence are closely linked to access, experiences and benefits from health care, which is itself a social determinant of health [32]. The findings of this study are in line with this assertion of the WHO Commission on Social Determinants of Health. Therefore, addressing inequities in the use of delivery services by skilled health providers requires tackling these social determinants of health systems through a concerted multi-sectoral action. The four sets of Primary Health Care reforms that include: (i) the universal coverage reforms; (ii) service delivery reforms; (iii) public policy reforms; and (iv) leadership reforms [33] are very relevant here in bridging the observed inequities in the use of delivery services by skilled health providers and consequently contribute to the achievement of the MDG 5 targets.
Conclusions
Most of the inequality in births attended by skilled health personnel, which is skewed towards the wealthier segment of the population, is explained by inequalities in income, education and urban residence. The region, insurance coverage and female-headed household variables seem to have inequality reducing effect, although not substantial.
Therefore, the fact that inequalities in wealth and education of the mother are the main drivers of inequities in the percentage of births attended by skilled health personnel implies that policy interventions for addressing inequalities in access to child delivery services should be multi-sectoral in line with the principles of the Primary health Care.
List of abbreviations
C: Concentration index; CSDH: WHO Commission on Social Determinants of Health; DHS: Demographic and Health Survey; HDI: Human Development Index (HDI); LPM: Linear probability model; MDGs: Millennium Development Goals; MMR: Maternal mortality ratio; MICS: Multiple Indicator Cluster Survey; PHC: Primary health care
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
EZ conceived the research, performed the analysis and drafted the manuscript. DO, TM, CNM and JMK contributed to the drafting of and review of the manuscript. All authors read and approved the final manuscript.
Acknowledgements
The authors would like to thank all the teams that conducted the Namibia Demographic and Health Survey. The manuscript contains the analysis and views of the authors only and does not represent the decisions or stated policies of the institutions that they work for.
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J Epidemiol Community Health 2007, 61:1038-1041. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
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Pre-publication history
The pre-publication history for this paper can be accessed here:
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Poster presentation
Design of novel semisynethetic metalloenzyme from thermolysin
Mohd BA Rahman1*, Ahmad H Jaafar1, Mahiran Basri1, Raja NZRA Rahman2, Abu B Salleh2 and Habibah A Wahab3
Author Affiliations
1 Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
2 Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
3 Laborotary of Biocrystallography and Bioinformatic Structure, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
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BMC Systems Biology 2007, 1(Suppl 1):P68 doi:10.1186/1752-0509-1-S1-P68
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Published:8 May 2007
© 2007 Rahman et al; licensee BioMed Central Ltd.
Background
Initial applications of biocatalysis involved the used of naturally occurring enzyme. With new challenges in green chemical reaction, biocatalyst that shed the light is metalloenzyme, which function as enzyme and contain metal that are tightly attached and always isolated with the protein [1]. In recent years, enzyme engineering has proven to be an invaluable tool for elucidating biocatalytic mechanisms as well as producing enzymes for industrial purposes. Approaches developed for in vivo chemical modification and in silico computational methods promise to increase the scope and have already been used successfully to alter existing protein so that they have better stability and functionality [2]. This task might be good to address in designing a new biocatalyst with improved properties.
Methods
The AutoDock programme 3.05 was employed in order to identify the binding conformations of the ligands and the metal ions and to perform docking using Lamarckian Genetic Algorithm (LGA) [3]. The coordinate of thermolysin-substrate free structure coded as 1KEI was taken from Brookhaven Protein Data Bank (PDB).
Results
The predicted KEI-ligand complexes with the lowest final docked energy for PSE and PHN were -6.71 kcal/mol at pocket 45 and -6.60 kcal/mol at pocket 47, respectively. Non-covalent interactions of hydrogen bond and hydrophobic interaction between protein and ligands established the final conformation. Analysis on finding the most favorable metal ions to dock onto each complex found that Mg2+ was docked onto KEI-PSE45 complex with final docked energy of -1.09 kcal/mol and performed four interactions with the PSE ligand. Meanwhile, Ca2+ represented the best metal ions to dock to the KEI-PHN47 complex with final docked energy of -4.12 kcal/mol and performed three interactions with the nearby residues.
Conclusion
An important branch of novel protein design is through engineering and design of new metal-binding sites into native proteins. By employing in silico approach of molecular docking, screening of putative ligand for possible interactions may enhance the discovery of novel semisynthetic enzyme and lead to a new protein function. Finally, the framework which was introduced for the experiment may be a competent method for screening potential metal ions in this in vivo route.
References
1. Davies RR, Kuang H, Qi D, Mazhary A, Mayaan E, Distefeno MD: Artificial Metalloenzymes Based on Protein Cavities: Exploring the Effect of Altering the Metal Ligand Attachment Position by Site Directed Mutagenesis.
Bioorg Med Chem Lett 1999, 9:79-84. PubMed Abstract | Publisher Full Text
2. Abdul Rahman MB, Misran A, Abdul Wahab H, Abdul Rahman RNZ, Salleh AB, Basri M: Screening and Docking of Chemical Ligands onto Pocket Cavities of Protease for Designing a Biocatalyst.
Biocatal Biotransform 2005, 23:211-216. Publisher Full Text
3. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ: Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function.
J Comput Chem 1998, 19:1639-1662. Publisher Full Text | v0 |
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Proceedings
Comparison of linear mixed model analysis and genealogy-based haplotype clustering with a Bayesian approach for association mapping in a pedigreed population
Golam R Dashab1,2, Naveen K Kadri1*, Mohammad M Shariati1,2 and Goutam Sahana1*
Author Affiliations
1 Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, DK-8830 Tjele, Denmark
2 Department of Animal Science, Ferdowsi University of Mashhad, 91775 Mashhad, Iran
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BMC Proceedings 2012, 6(Suppl 2):S4 doi:10.1186/1753-6561-6-S2-S4
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Published:21 May 2012
© 2012 Dashab et al.; licensee BioMed Central Ltd.
Abstract
Background
Despite many success stories of genome wide association studies (GWAS), challenges exist in QTL detection especially in datasets with many levels of relatedness. In this study we compared four methods of GWA on a dataset simulated for the 15th QTL-MAS workshop. The four methods were 1) Mixed model analysis (MMA), 2) Random haplotype model (RHM), 3) Genealogy-based mixed model (GENMIX), and 4) Bayesian variable selection (BVS). The data consisted of phenotypes of 2000 animals from 20 sire families and were genotyped with 9990 SNPs on five chromosomes.
Results
Out of the eight simulated QTL, these four methods MMA, RHM, GENMIX and BVS identified 6, 6, 8 and 7 QTL respectively and 4 QTL were common across the methods. GENMIX had the highest power to detect QTL however it also produced 4 false positives. BVS was the second best method in terms of power, detecting all QTL except the one on chromosome 5 with epistatic interaction. Two spurious associations were obtained across methods. Though all the methods considered the full pedigree in the analyses, it was not sufficient to avoid all the spurious associations arising due to family structure.
Conclusions
Using several methods with divergent approaches for GWAS can be useful in gaining confidence on the QTL identified. In our comparison, GENMIX was found to be the best method in terms of power but it needs appropriate correction for multiple testing to avoid the false positives. This study shows that the issues of multiple testing and the relatedness among study samples need special attention in GWAS.
Background
Despite many successes, genome-wide association studies (GWAS) still present major challenges. This is particularly true for samples drawn from a population with multiple levels of relatedness, such as population structure and/or familial relatedness. The efficiency of a GWAS method to detect a quantitative trait locus (QTL) depends on several factors, for example, the genetic architecture, allele frequency and heritability of the QTL, and the linkage disequilibrium with the marker. The population structure and relatedness of the samples may result in spurious associations. We applied a range of GWAS methods to map quantitative trait loci (QTL) in the simulated dataset provided by the 15th QTL-MAS workshop [1] and compared their efficiency in QTL detection with respected to this particular dataset.
We compared four different methods of GWAS, 1) Mixed model analysis (MMA); 2) Random haplotype model (RHM); 3) Genealogy-based mixed model (GENMIX) and 4) Bayesian variable selection method (BVS). The mixed model approach [2] utilizes the full relationship matrix and is the method of choice when the samples are drawn from a complex pedigreed population. The haplotype-based association methods using mixed models are generally regarded as more powerful than methods based on single markers [3,4] since they fully exploit LD information from multiple markers. On the other hand, genealogy based clustering of haplotypes in GENMIX not only consider the local LD but also takes the history of the origin of these haplotypes [5]. Contrary to the above three methods which analyze single markers or a few markers at a time, Bayesian variable selection [6] simultaneously fits multiple marker effects and avoids the problem of multiple testing. Therefore, it is useful to compare such Bayesian methods with more standard frequentist approaches where a single or a few SNPs are fitted at a time. The above-mentioned methods were compared for power, precision of location estimate, and type I error rate.
Methods
The simulated population consisted of 20 sire families, each sire was mated to 10 dams and each full-sib family had 15 progeny. The phenotype was available for 10 progeny per full-sib family i.e. a total of 2000 individuals. There were five chromosomes each with 1998 SNPs at equal distance of 0.05 cM. The four GWAS method used for association mapping are described below.
Mixed model analysis (MMA)
The association between each SNP and the phenotype was assessed by a linear mixed model analysis [2], using DMU software [7]. The model was as follows:
Where y is the vector of 2,000 phenotypes, 1 is a vector of 1s of length 2,000, μ is the general mean, g is the additive effect of the SNP and X is a vector with genotypic indicators (0, 1, or 2) associating records to the marker effect, u is the random polygenic effect with the normal distribution , where A is the additive relationship matrix and is the polygenic variance. Z is an incidence matrix relating phenotypes to the corresponding random polygenic effect, and e is a vector of random environmental deviates with the normal distribution , where is the error variance and I is the identity matrix. Testing was done using a Wald test against a null hypothesis of H0:gi=0. The significance threshold was determined using a Bonferroni correction for the number of markers tested to obtain an experiment-wise P-value of 0.05.
Random haplotype model (RHM)
The SNP genotype data were phased using software FastPhase [8].The haplotypes were 4 SNP long and they were tested for association sliding windows from SNP to SNP. The model for testing the association of the haplotypes at position j and the phenotype can be clarified in scalar form as follows:
Where yi is the phenotype of animal i, μ is the population mean, ui is the random polygenic effect, and are the random effects of the maternal and paternal haplotypes carried by individual i, and ei is the random residual effect as defined for MMA. The other random effect q was assumed to be normally distributed with mean zero and variances (assuming equal variance for paternal and maternal haplotypes). The significance of the haplotype substitution effect was assessed with a likelihood ratio test comparing the RHM model with a null-model containing mean, polygenic effect and random error terms but no haplotype effects. Analysis was performed using the DMU software package [7]. Significant threshold was fixed at genome wide 5% level after Bonferroni correction and the mid-point of significant haplotypes were considered as the putative QTL positions.
Genealogy based mixed-model (GENMIX)
The efficiency of GENMIX for association mapping was described by Sahana et al. [5]. In contrast to regular genome-wide association studies where phenotypic differences are either associated with single markers or with groups of markers organized in to haplo-groups in a non-stratified fashion, here phenotypes were associated using a hierarchical approach. Both grouping of markers into haplo-groups and clustering of observed haplotypes was done based on local genealogies [9]. This method identifies the widest possible region surrounding a marker that allows construction of a genealogy forming a bifurcating tree without either recurrent mutation or recombination, in other words it satisfies the four-gamete condition of Hudson and Kaplan [10]. Each bifurcation in the binary tree corresponds to one bi-allelic marker. Splitting the tree at the top generates two clusters of haplotypes. Splitting the tree at any other node generates three clusters: one above the split point and two corresponding to the two branches below. For the analyses presented in this paper we split the tree at the top (one set of two clusters), the second level (two sets of three clusters) and at the third level (four sets of three clusters). Successively each clustering of haplotypes was included as a random effect in the model for analysis:
where yi is the phenotype of individual i, μ is the population mean, ui is as described above in the MMA; and are two haplotype effects of individual i, where h1i and h2i can take values 11, 12, 13, 22, 23, and 33 and , is the haplotype variance, and ei is a random residual as defined for MMA. The local genealogies were constructed using the software Blossoc (http://www.daimi.au.dk/~mailund/Blossoc/ webcite) and variance component analysis was carried out using the software DMU [7]. The significance of the SNP association was tested using likelihood ratio test and the significant threshold was fixed at genome-wide 5% level after Bonferroni correction for multiple testing for the total number of markers.
Bayesian variable selection (BVS)
The method is based on specifying a mixture distribution for SNP effects while all SNP are fitted simultaneously in the model [6]. It was assumed that most markers had very small effects on the trait (98% of SNP in this analysis) and only few markers (2%) had large effects. The allocation of each SNP to either of these two distributions is done using an indicator variable in Gibbs sampling. The averaged mixture indicator estimates a posterior probability for that SNP to come from the distribution with large effects, which is interpreted as the probability for presence of an associated marker or QTL. The analysis was performed using BAYZ software [11] and the variances of the two mixture components were estimated. The SNP with posterior probability of the mixture indicator higher than 0.10; that corresponds to a Bayes factor of 5.5 were reported as QTL. In cases where adjacent markers showed a decreasing or increasing posterior probability of association due to linkage disequilibrium, only the SNP with highest probability was reported as QTL.
Results
The results of our analysis from four methods are summarised in Table 1 and graphically represented in Figure 1. A QTL was considered as identified if the putative location was within 10 cM of the true simulated location of the QTL. Out of the 8 simulated QTL, these four methods, MMA, RHM, GENMIX and BVS identified 6, 6, 8 and 7 QTL, respectively. Four QTL regions, one on chromosome 1 and 5 and two on chromosome 3, were identified by all the four methods. The numbers of false positives for these methods were 2, 6, 4 and 2 respectively (Table 1).
Table 1. Positions (cM) of identified QTL with the four methods
Figure 1. Comparison of the positions of the simulated and detected QTL by four methods. The positions of the detected QTL are given chromosome-wise for the four methods. The correct identifications are given in red diamonds and the false positives are given in gray circles.
The effects of the QTL localised by MMA are given in table 2. The QTL with the biggest effect, explaining 10.2% of the variation in the phenotype was localised on chromosome 1 at 3.55 cM region. The 6 QTL detected by MMA together explained 18.4% of the phenotypic variance.
Table 2. QTL effects estimated by single marker analysis based on linear mixed model; fitting all the detected QTL simultaneously
Precision of the methods was assessed by the average of absolute differences between the positions of the simulated and the detected QTL, whenever it was identified. The QTL with the biggest effect on chromosome 1 was detected with high precision (on average ± 0.3 cM from the simulated QTL) and the epistatic QTL on chromosome 5 was detected with least precision (on an average 8 cM from the simulated QTL). In general the MMA identified the QTL with higher precision.
Discussion
In our study we used additive models without considering the genetic architecture of the simulated QTL; however the methods performed well in localising the true simulated QTL. Out of the four methods employed, GENMIX performed comparatively better in QTL detection. It detected all the 8 simulated QTL and 6 were mapped accurately within a 2 cM region of the QTL region. However, it also identified 4 false positives (FP). The number of tests carried out in GENMIX was approximately 7 times the number of markers and we used Bonferroni multiple testing correction for the number of total marker but not for the total number of tests (i.e. ~7 times the number of markers) which could have resulted in increased number of false positives. Besides the number of haplotypes in a lineage goes down as we moved down the tree [5] which can give numerical instability. Out of these four FPs in GENMIX, two (on chromosome 4 and 5) were identified by other methods at the same location (Figure 1). Divergent approaches of GWAS picking up the same FP could be due to insufficient correction for family structure. A likely explanation is that some SNPs in these two regions were positively correlated (in linkage disequilibrium) with the QTL because of linkage (within family). It is thus not straightforward to distinguish true associations from spurious, regardless of the correction for the pedigree structure. This underlines the importance of replication study before a follow-up study can be taken up for identifying causal mutation underlying a QTL.
BVS was the second best method in terms of power to identify QTL and it had less FP compared to GENMIX. It detected all the simulated QTL except the one on chromosome 5 with epistatic interactions. BVS fits all the SNPs simultaneously and given that the first epistatic QTL was fitted in the model, there was a little chance for the second one to be significant in the model. In other words, the first QTL explains most of the variation induced by both QTL because of their dependency. Especially, this can happen if the epistasis is of additive by additive nature, where most of the epistatic variance is converted to additive [12]. In order to confirm this, we ran the MMA for all SNP on chromosome 5 where the first epistatic QTL was already in the model. As a result, the second epistatic QTL was not detected (results not shown).
The MMA identified six QTL. The two linked QTL on chromosome 2 were both identified by MMA but only the first one (the most significant) was reported in the workshop as the second QTL was not significant when fitted along with first one in the model. On the other hand RHM detected both of them but the first QTL was mapped 10 cM downstream the true QTL.
The highest significant SNP for the multi-allelic QTL on chromosome 1 (largest QTL) in MMA was 0.7 cM away from the true position, while the other methods mapped it closer to its position. No individual SNP (bi-allelic) can be in perfect LD with this QTL (multi-allelic) which might have resulted in poor precision for this QTL in MMA.
The imprinted QTL on chromosome 4 was only detected by GENMIX and BVS. The power of detection of the QTL will decrease if the model does not reflect the true genetic architecture of the QTL. However, GENMIX and BVS methods were sensitive enough to identify the imprinted QTL, though both of them model its effect as additive.
Sahana et al. [13] observed very high false positives when haplotypes were considered as fixed effects in the model. Because the frequency of some haplotypes can be very low, this could result in low accuracy of estimates and result in false positive when haplotypes are fitted as fixed effect. We expected this problem can be taken care by fitting haplotypes as random where the effects of the low frequent haplotypes will be regressed towards zero. However, RHM still had very high false positive rate.
Conclusions
Using several methods in analysing GWA can be useful in gaining confidence on the QTL identified. Though, genealogy-based mixed model can be a powerful approach for GWAS, appropriate multiple testing correction is necessary to avoid false positives. Our study also shows that correction for pedigree relationship is not always enough to avoid spurious association arising due to family structure.
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
All the authors have contributed in planning the study, analyses of data and writing the article.
Acknowledgements
NKK and GS were supported by a grant No. 3405-10-0137, funded jointly by the Danish Ministry of Food, Agriculture and Fisheries, The Milk Levy Fund, Viking Genetics, and Nordic Cattle Genetic Evaluation. GRD acknowledges financial support by The Ministry of Science, Research and Technology of Iran.
This article has been published as part of BMC Proceedings Volume 6 Supplement 2, 2012: Proceedings of the 15th European workshop on QTL mapping and marker assisted selection (QTL-MAS). The full contents of the supplement are available online at http://www.biomedcentral.com/bmcproc/supplements/6/S2.
References
1. [https://colloque.inra.fr/qtlmas] webcite
2. Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB: A unified mixed-model method for association mapping that accounts for multiple levels of relatedness.
Nature genetics 2005, 38:203-208. PubMed Abstract | Publisher Full Text
3. Akey J, Jin L, Xiong M: Haplotypes vs single marker linkage disequilibrium tests: what do we gain?
European Journal of Human Genetics 2001, 9:291-300. PubMed Abstract | Publisher Full Text
4. Morris RW, Kaplan NL: On the advantage of haplotype analysis in the presence of multiple disease susceptibility alleles.
Genetic epidemiology 2002, 23:221-233. PubMed Abstract | Publisher Full Text
5. Sahana G, Mailund T, Lund M, Guldbrandtsen B: A New Powerful Method for Genome-wide Association Mapping Using Local Genealogies in a Mixed Model.
Local Genealogies in a Linear Mixed Model for Genome-Wide Association Mapping in Complex Pedigreed Populations. PLoS ONE 2011, 11(6):e27061.
6. George EI, McCulloch RE: Variable selection via Gibbs sampling.
Journal of the American Statistical Association 1993, 88:881-889. Publisher Full Text
7. Madsen P, Jensen J: DMU-A user's guide, A package for analyzing multivariate mixed models. [http://www.dmu.agrsci.dk/dmuv6_guide.5.0.pdf] webcite
Version 6, DJF, Foulum, Denmark 2011. Release 5
8. Scheet P, Stephens M: A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase.
The American Journal of Human Genetics 2006, 78:629-644. Publisher Full Text
9. Mailund T, Besenbacher S, Schierup MH: Whole genome association mapping by incompatibilities and local perfect phylogenies.
BMC bioinformatics 2006, 7:454. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text
10. Hudson RR, Kaplan NL: Statistical properties of the number of recombination events in the history of a sample of DNA sequences.
Genetics 1985, 111:147. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
11. Janss L: BAYZ Manual version 2.02.
Janss Biostatistics, Leiden, Netherlands 2011.
12. Hill WG, Goddard ME, Visscher PM: Data and theory point to mainly additive genetic variance for complex traits.
PLoS Genetics 2008, 4:e1000008. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
13. Sahana G, Guldbrandtsen B, Janss L, Lund MS: Comparison of association mapping methods in a complex pedigreed population.
Genetic epidemiology 2010, 34:455-462. PubMed Abstract | Publisher Full Text | v0 |
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} | cccc_CC-MAIN-2013-20 | Antarctic Geoscience Project
Geoscience Australia's Antarctic Geoscience project advises the Australian Government on Antarctic Geoscience issues, as required, in support of the Australian Government’s Antarctic Science Strategic Plan (2011-21) and the Australian government’s commitments and obligations under the Antarctic Treaty System.
In this role Geoscience Australia’s Antarctic Geoscience program:
• Provides leadership for Antarctic geoscience research by directing research contributing to the Australian Governments’ Antarctic Strategic Plan
• carries out marine and onshore applied geoscience research in the Antarctic to service the Australian Government's objectives for Antarctic research in line with Geoscience Australia’s Strategic Plan and the Australian Government Science Strategic Plan for Antarctic Research
• provides geoscience advice for formulating appropriate environmental management of vulnerable and threatened onshore and marine ecosystems and non-living features within the Australian Antarctic Territory and adjacent marine jurisdictions
• publication of geoscience maps and related products of the Australian Antarctic Territory.
Topic contact: [email protected] Last updated: April 4, 2013 | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:00:01.000Z | o3eawdwuneqhuk75fh5oxjxfcymyraoi | {
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} | cccc_CC-MAIN-2013-20 | About this Journal Submit a Manuscript Table of Contents
ISRN Software Engineering
Volume 2012 (2012), Article ID 162305, 11 pages
doi:10.5402/2012/162305
Research Article
Lessons Learnt from Gauging Software Metrics of Cabin Software in a Commercial Airliner
1TCC4 System Integration—Communication, EADS Innovation Works, 81663 Munich, Germany
2Software Engineering Group, University of Mannheim, 68131 Mannheim, Germany
Received 14 June 2012; Accepted 4 September 2012
Academic Editors: C. Calero and R. J. Walker
Copyright © 2012 Stefan Burger and Oliver Hummel. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
In order to achieve high safety standards, avionic software needs to be developed with very high requirements regarding safety, reliability, and determinism as well as real-time constraints, which are often in conflict with the development of maintainable software systems. Nevertheless, the ability to change the software of an airplane is of increasing importance, since it consists of a multitude of partially hardware-specific subsystems which may need replacement during a plane’s lifespan of typically numerous decades. Thus, as a first step towards optimizing maintainability of avionic software we have benchmarked the cabin software of a commercial airliner with common software metrics. Such a benchmarking of avionic software contributes valuable insights into the current practice of developing critical software and the application of software metrics in this context. We conclude from the obtained results that it is important to pay more attention to long-term maintainability of aviation software. Additionally we have derived some initial recommendations for the development of future avionic software systems. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T07:26:44.000Z | b336jbg5nrjcsa5xdwwc6cio5ed7ybcj | {
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} | cccc_CC-MAIN-2013-20 | About this Journal Submit a Manuscript Table of Contents
Abstract and Applied Analysis
Volume 2012 (2012), Article ID 156541, 12 pages
doi:10.1155/2012/156541
Research Article
On the Regularized Solutions of Optimal Control Problem in a Hyperbolic System
Department of Mathematics, Faculty of Science, Atatürk University, 25240 Erzurum, Turkey
Received 7 March 2012; Accepted 12 June 2012
Academic Editor: Valery Covachev
Copyright © 2012 Yeşim Saraç and Murat Subaşı. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
We use the initial condition on the state variable of a hyperbolic problem as control function and formulate a control problem whose solution implies the minimization at the final time of the distance measured in a suitable norm between the solution of the problem and given targets. We prove the existence and the uniqueness of the optimal solution and establish the optimality condition. An iterative algorithm is constructed to compute the required optimal control as limit of a suitable subsequence of controls. An iterative procedure is implemented and used to numerically solve some test problems. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T05:34:46.000Z | gpujfevkr3leexvibjxwfihqt2rhymks | {
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} | cccc_CC-MAIN-2013-20 | Bibliography: Cover: A Dog Called Demolition
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Title: Cover: A Dog Called Demolition
Author: Robert Rankin
Year: unknown
Type: COVERART
ISFDB Record Number: 865207
User Rating: This title has fewer than 5 votes. VOTE
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Publications:
Copyright (c) 1995-2011 Al von Ruff.
ISFDB Engine - Version 4.00 (04/24/06) | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:21:59.000Z | cbb52ioy56jvugu5fqyyist4wq2hemp5 | {
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} | cccc_CC-MAIN-2013-20 | Remote Sens. 2010, 2(7), 1731-1750; doi:10.3390/rs2071731
Article
The Function of Remote Sensing in Support of Environmental Policy
1 International Livestock Research Institute (ILRI), Nairobi, Kenya 2 ITC, University of Twente, Enschede, The Netherlands 3 NIAES, Ecosystem Research Group, Tsukuba, Japan 4 Frogs International Environmental Management and Consultancy, The Hague, The Netherlands 5 Ministry of Environment, Ulan Bataar, Mongolia
* Author to whom correspondence should be addressed.
Received: 20 May 2010; in revised form: 13 June 2010 / Accepted: 17 June 2010 / Published: 12 July 2010
Download PDF Full-Text [666 KB, uploaded 12 July 2010 13:49 CEST]
Abstract: Limited awareness of environmental remote sensing’s potential ability to support environmental policy development constrains the technology’s utilization. This paper reviews the potential of earth observation from the perspective of environmental policy. A literature review of “remote sensing and policy” revealed that while the number of publications in this field increased almost twice as rapidly as that of remote sensing literature as a whole (15.3 versus 8.8% yr−1), there is apparently little academic interest in the societal contribution of environmental remote sensing. This is because none of the more than 300 peer reviewed papers described actual policy support. This paper describes and discusses the potential, actual support, and limitations of earth observation with respect to supporting the various stages of environmental policy development. Examples are given of the use of remote sensing in problem identification and policy formulation, policy implementation, and policy control and evaluation. While initially, remote sensing contributed primarily to the identification of environmental problems and policy implementation, more recently, interest expanded to applications in policy control and evaluation. The paper concludes that the potential of earth observation to control and evaluate, and thus assess the efficiency and effectiveness of policy, offers the possibility of strengthening governance.
Keywords: earth observation; remote sensing; environment; policy; governance
Article Statistics
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Cite This Article
MDPI and ACS Style
De Leeuw, J.; Georgiadou, Y.; Kerle, N.; De Gier, A.; Inoue, Y.; Ferwerda, J.; Smies, M.; Narantuya, D. The Function of Remote Sensing in Support of Environmental Policy. Remote Sens. 2010, 2, 1731-1750.
AMA Style
De Leeuw J, Georgiadou Y, Kerle N, De Gier A, Inoue Y, Ferwerda J, Smies M, Narantuya D. The Function of Remote Sensing in Support of Environmental Policy. Remote Sensing. 2010; 2(7):1731-1750.
Chicago/Turabian Style
De Leeuw, Jan; Georgiadou, Yola; Kerle, Norman; De Gier, Alfred; Inoue, Yoshio; Ferwerda, Jelle; Smies, Maarten; Narantuya, Davaa. 2010. "The Function of Remote Sensing in Support of Environmental Policy." Remote Sens. 2, no. 7: 1731-1750.
Remote Sens. EISSN 2072-4292 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:26:47.000Z | 6mzd4koiwozfkp3fmhijxegghypdd7io | {
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} | cccc_CC-MAIN-2013-20 | Anonymous target Azeri Special State Protection Service
PanARMENIAN.Net - Anonymous hackers have published more than 1.7 GB of data allegedly stolen from Azerbaijan’s Special State Protection Service (dmx.gov.az).
The information leaked not only belonged to the Special State Protection Service, but also to other related organizations, including ING Geneva, Sumato Energy, BNP Paribas, Taurus Petroleum and even security solutions provider Prolexic.
The data were published on par-anoia.net, a site belonging to the Anonymous Intelligence Agency.
The hackers say the files contain passport scans, reports, confidential shareholder documents, account statements, letters of credit, and details of oil drilling technologies, news.softpedia.com reported.
Partner news
Top stories
It’s not the first time Yahoo CEO Marissa Mayer has been interested in the New York-based hipster blogging service.
The number of new smartphones delivered with Android jumped to 162.1 million in the first three months in 2013.
“We believe Samsung generates more revenue and profit from the Android platform than Google does,” Neil Mawston said.
The service now also makes it easier for users to add new contacts sent to them by friends, and has support for Simplified Chinese.
Partner news
Employers and job seekers: how to find each other
Arpine Grigoryan։ each job seeker should understand why to apply for this “x” job in this “x” company but not for “y” job in “y” company. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T05:50:44.000Z | 2rmp46f73r7x56u3u3unwmmk5sxknynh | {
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} | cccc_CC-MAIN-2013-20 | IHelpYou Forum Super Moderators Resign
Mar 13, 2005 • 9:46 pm | (0) by | Filed Under SEO & SEM Forum News
I reported the other day about Danny Sullivan Called Out by Doug (IHelpYou). The thread with the information was pulled, but it was not pretty. I have learned that three "Super Moderators" from Doug's IHelpYou forums have resigned due to the incident. Of the three are Alan Perkins (respected SES speaker and white hat), Dan Thies (keyword research expert and SES speaker), and Kalena Jordan (Search Engine College founder). I am also told, other non-super moderators have stepped down.
This is a major shake up in SEM forum politics. :)
Previous story: Forums to Re-Organize Yahoo & Overture Sections
blog comments powered by Disqus | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T07:13:37.000Z | 6ywuujsrn3ikkbwpkwwclrwxr4ynjirz | {
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} | cccc_CC-MAIN-2013-20 | Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
8501.0 - Retail Trade, Australia, Jan 2010
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 02/03/2010
Page tools: Print Page Print All RSS Search this Product
JANUARY KEY FIGURES
Jan 10
Dec 09 to Jan 10
$m
% change
Turnover at current prices
Trend estimates
20 088.3
0.4
Seasonally adjusted estimates
20 144.9
1.2
Monthly Turnover, Current prices - Trend estimate
JANUARY KEY POINTS
CURRENT PRICES
• The trend estimate increased 0.4% in January 2010. This follows a 0.4% increase in December 2009 and a 0.4% increase in November 2009.
• The seasonally adjusted estimate increased 1.2% in January 2010. This follows a 0.9% decrease in December 2009 and a 1.5% increase in November 2009.
• In original terms, Australian turnover decreased 23.8% in January 2010. Australian turnover increased 2.0% in January 2010 compared with January 2009.
• In trend terms, all industry groups increased in January 2010. The largest increase was in Cafes, restaurants and takeaway food services (0.7%) followed by Department stores (0.4%), Clothing, footwear and personal accessory retailing (0.4%), Household good retailing (0.3%), Food retailing (0.3%) and Other Retailing (0.3%).
• The following states and territories increased in trend terms in January 2010: Western Australia (0.7%), New South Wales (0.6%), the Australian Capital Territory (0.5%), South Australia (0.3%), Victoria (0.3%) and the Northern Territory (0.2%). Tasmania (-0.2%) decreased while Queensland (0.0%) remained unchanged in January 2010.
NOTES
FORTHCOMING ISSUES
ISSUE Release Date
February 2010 31 March 2010
March 2010 6 May 2010
April 2010 1 June 2010
May 2010 1 July 2010
June 2010 3 August 2010
July 2010 31 August 2010
CHANGES IN THIS ISSUE
There are no changes in this issue.
REVISIONS
There are no revisions to the original estimates. Revisions to seasonally adjusted estimates are due to the concurrent methodology for deriving seasonal factors.
TIME SERIES DATA
Data available from the Downloads tab include longer time series of tables in this publication, the quarterly chain volume measures and the following additional current price monthly series:
• Retail turnover by state and 15 industry subgroups in trend, seasonally adjusted and original terms
• Retail turnover completely enumerated and sample sector, by six industry groups in original terms
• Retail turnover completely enumerated and sample sector, by state in original terms
• Retail turnover completely enumerated sector, total level in trend, seasonally adjusted and original terms.
INQUIRIES
For further information about these and related statistics, contact the National Information and Referral Service on 1300 135 070 or Paul Slater on Sydney (02) 9268 4568.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T05:48:37.000Z | erhckui62bune2ebfanv7pqyrc2uyteo | {
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} | cccc_CC-MAIN-2013-20 | Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
8166.0 - Summary of IT Use and Innovation in Australian Business, 2009-10 Quality Declaration
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 23/06/2011
Page tools: Print Page Print All RSS Search this Product
MEDIA RELEASE
23 June, 2011
Embargoed: 11.30 am (Canberra time)
80/2011
Australian businesses take $143 billion worth of internet orders
Just under $143 billion dollars worth of internet orders were received by Australian businesses in 2009-10, up 15% on the previous year, according to figures released today by the Australian Bureau of Statistics (ABS).
Wholesale trade and manufacturing industries continued their lead as the main businesses receiving online orders, both at over 40%. The retail industry came in at fifth place.
Nearly all (94%) of Australia's large businesses had a web presence at 30 June 2010, while micro businesses (employing up to four people) are still the least likely to, with only about one-third offering some form of web presence. Broadband dominated as the internet access method (97%), with little variation between industries.
Primary industry - agriculture, forestry and fishing - was least likely to place online orders, with just over one-quarter (26%) using the internet to make purchases.
Australian businesses continue to innovate
Undertaking some form of innovation - developing or introducing of new or significantly improved goods, services, processes or methods - was reported by 44% of Australian businesses in 2009-10.
Large businesses were more than twice as likely to undertake innovative activity than micro businesses (74% compared to 36%).
Wholesale trade was the most innovative, with almost 60% of businesses in the industry reporting some form of innovation. Innovation in the agriculture, forestry and fishing industry was reported by about one-third of those businesses.
Further information is available in Summary of IT Use and Innovation in Australian Business (cat. no. 8166.0).
Media note:
When reporting ABS data the Australian Bureau of Statistics (or ABS) must be attributed as the source.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T07:27:07.000Z | ut5ggwcnijkcqodbtbqw5fgma7te3o7d | {
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} | cccc_CC-MAIN-2013-20 | 4
votes
2answers
188 views
Shopping list of tools and services for new startup
I'm looking for good-value, top-class applications and tools to support a new software startup. What recommendations do you have in the following categories? Domain name / hosting / website / blog ...
2
votes
3answers
2k views
Recommend a good support ticket system that integrates with Salesforce [closed]
I have a question similar to the following http://answers.onstartups.com/questions/1876/low-cost-issue-tracker-maybe-with-crm I'm looking for a issue tracking system that integrates with Salesforce, ...
3
votes
10answers
1k views
Low-cost issue tracker, maybe with CRM? [closed]
I and my team members have a handful of outstanding issues we would like to track, ranging from technical to business-oriented. We are looking for a free/low-cost issue tracker, perhaps with CRM. ... | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:33:31.000Z | axslkipcth5upxhgyslvkwbrfe3h4xtd | {
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} | cccc_CC-MAIN-2013-20 | 116 reputation
bio website
location Corona, CA
age
visits member for 6 months
seen May 1 at 15:06
stats profile views 4
I am a student on a F1 Visa in the US and would like to learn about finance in the US to lead a better life.
Being a non US Citizen and on a student Visa, I am unauthorized to work off campus, and so I am restricted to work upto 20 hours a week on a hourly wage and have no fixed monthly income.
This user has no revisions | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T05:49:44.000Z | 2ycuq6dxqu5j3m2rvdaoqigq6n7rm4l3 | {
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} | cccc_CC-MAIN-2013-20 | Southern California Hot Spot Hits 812 Degrees, Baffles Experts
rating: 0+x
Summary
August 6, 2008: In Ventura Coutry, just north of Los Angeles, California, a mysterious "hot spot" appeared that caused the ground to reach a temperature of over 800 degrees Fahrenheit on August 1st, 2008. The exact cause is unknown, though some geologists suspect that natural gases might have caused a fire deep underground, which in turn caused the high surface temperature.
Source
Game and Story Use
• It might have been caused by some large entity of fire living below California which is slowly moving towards the surface.
• In a fantasy campaign with a stereotypical "Underdark", this might be a local temperature hazard that doesn't have anything to do with streams of lava.
Unless otherwise stated, the content of this page is licensed under Creative Commons Attribution-ShareAlike 3.0 License | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T05:29:21.000Z | syf6prn3tay5y7sevp3ogkt2lsisvjyo | {
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} | cccc_CC-MAIN-2013-20 | Regulating Petroleum Industry and Revenues: What Does Norway Get Out of the Petroleum Industry?
Noralv Veggeland
Abstract
The Norwegian Ministry of Petroleum and Energy (MPE) has from the beginning of the discovery of petroleum
heavily regulated the production, transport, sale and revenues of oil and gas. The financial Government Pension
Fund – Global was established, and later ethical guidelines have strictly regulated the Fund’s foreign investments.
The regulations are manifold and complex, which complicate both national and global implementations. This
study shows that strong political will has made the adherence to the regulations successful. There remains one
question, however: what do Norwegians themselves get out of the financial savings, besides a modest interest and
dividend yield? The export surplus is said to be so large that spending more than a small fraction at home would
cause inflation. The study elaborates the dilemma: public infrastructure represents the largest capital expenditure
in almost every country, yet little trace of its economic role appears today in Norwegian infrastructure accounts.
Full Text: PDF DOI: 10.5539/ijbm.v7n3p64
This work is licensed under a Creative Commons Attribution 3.0 License.
International Journal of Business and Management ISSN 1833-3850 (Print) ISSN 1833-8119 (Online)
Copyright © Canadian Center of Science and Education
To make sure that you can receive messages from us, please add the 'ccsenet.org' domain to your e-mail 'safe list'. If you do not receive e-mail in your 'inbox', check your 'bulk mail' or 'junk mail' folders.
| v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:19:37.000Z | ao3mqise7co3k73fijspij3tyxug7yvk | {
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} | cccc_CC-MAIN-2013-20 | BaSTA (1.2)
A package for estimating age-specific survival from incomplete capture-recapture/recovery data.
http://cran.r-project.org/web/packages/BaSTA
This package estimates survival and mortality with covariates from capture-recapture/recovery data in a Bayesian framework when many individuals are of unknown age. It includes tools for data checking, model diagnostics and outputs such as life-tables and plots.
Maintainer: Fernando Colchero
Author(s): Fernando Colchero, Owen Jones, Maren Rebke
License: GPL
Uses: msm, snowfall
Released about 1 year ago. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T08:01:30.000Z | rzi532lvr25vprdl537s43qr4t6wyzc6 | {
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0 users
Estimation of (Local) False Discovery Rates and Higher Criticism.
http://strimmerlab.org/software/fdrtool/
http://cran.r-project.org/web/packages/fdrtool
This package allows to estimate both tail area-based false discovery rates (Fdr) as well as local false discovery rates (fdr) for a variety of null models (p-values, z-scores, correlation coefficients, t-scores). The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), for the half-normal and correlation distributions, and for computing empirical higher criticism (HC) scores and the corresponding decision threshold.
Maintainer: Korbinian Strimmer
Author(s): Bernd Klaus and Korbinian Strimmer.
License: GPL (>= 3)
Uses: Does not use any package
Reverse depends: GeneCycle, GeneNet, sda, st
Reverse suggests: frontier, MALDIquant, mutoss, qgraph
Released 10 months ago.
6 previous versions
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Visit fdrtool on R Graphical Manual. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:57:07.000Z | dzyfzhkit24jngfu3me6f3fff53qhied | {
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Test Driven Development with the ASP.NET MVC framework - screencast
0
kicks
Test Driven Development with the ASP.NET MVC framework - screencast (Unpublished)
A while ago, KatrienDG asked me to do some screencasts on the ASP.NET MVC framework for the MSDN Chopsticks page. I've been working on 2 screencasts: an introductory talk to the ASP.NET MVC framework and a Test Driven Development story. Feel free to leave some comments! This video explains you how to develop ASP.NET MVC web applications using 2 different approaches: regular development and test-driven development.
Kicked By:
Drop Kicked By: | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:56:06.000Z | ok5rnsc57ngflfrgbm6v6b6nd2z33dyg | {
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} | cccc_CC-MAIN-2013-20 | Error!
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Upgrading Dot Net BlogEngine to VistaDB 4
0
kicks
Upgrading Dot Net BlogEngine to VistaDB 4 (Unpublished)
Our blog uses the excellent Dot Net Blog Engine as our blogging platform. You can use VistaDB as the backend store quite easily. Al Nyveldt’s blog has some great posts about setting up and configuring VistaDB with Blog Engine, but they are all for VistaDB 3.x. The Dot Net Blog Engine knows how to load provider factories, so it is quite easy to update the configuration to talk to VistaDB 4. I did these steps on our blog a while ago and everything has continued to run smoothly.
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2024-06-03T21:29:47.544Z | 2013-05-18T07:26:19.000Z | ewfnacswp6wvg26pnuy6vjhutswmrblf | {
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Nyctalus lasiopterus
Document Actions
GreaterNoctule
Scientific nameNyctalus lasiopterus Taxonomic rankSpecies
Author(Schreber, 1780) Valid nameyes
Taxonomic information Reference
Kingdom Animalia PESI webservices (simplified taxonony) (2012)
Phylum Chordata
Class Mammalia
Order Chiroptera
Family Vespertilionidae
Genus Nyctalus
External links
International Threat Status
Area Status International threat code Reference
World Lower Risk: Near Theatened LRn IUCN (2000)
World Lower Risk: Near Theatened LRn IUCN (2004)
European Union (25 Member States) Data Deficient DD IUCN (2009)
Europe Data Deficient DD IUCN (2009)
Synonyms
Scientific name Author
Nyctalus noctula maxima Fatio, 1869
Pterygistes maximus Trouessart, 1910
Vespertilio ferrugineus Brehm, 1827
Vespertilio lasiopterus Schreber, 1780
Vesperugo noctula maxima Fatio, 1869
Vespertilio noctula sicula Mina-Palumbo, 1868
Nyctalus siculus Ognev & Kuzyakin
EUNIS
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This site conforms to the following standards: | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T05:55:46.000Z | 2kgxnave5mpqri56yzyn67b53wou3ar7 | {
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} | cccc_CC-MAIN-2013-20 | Kingston, New YorkEdit This Page
From FamilySearch Wiki
United States New York Ulster County City and Town of Kingston
Contents
Resources
Cemeteries
• Roney, Lila James. "Inscriptions of the Ancient Gravestones int he Churchyard of the Old First Dutch Reformed Church at Kingston, N.Y.," The New York Genealogical and Biographical Record, Vol. 58, No. 4 (Oct. 1927):318-325. Digital version at New York Family History ($); FHL Book 974.7 B2n v. 58. Mostly eighteenth- and nineteenth-century burials.
Church Records
Early records for Kingston, Ulster County, New York A valuable source records for genealogists with ancestors from Kingston, Dutchess, and Albany counties New York is the Baptismal and marriage registers of the Old Dutch Church of Kingston, Ulster County, New York. It contains records from 1660 to 1809. (The book on Google Books is fully searchable.) Since this church was the only established congregation between New York City and Albany it contains information for many residents of the area, the only records that exist.
• 1739-1795 - Scott, Kenneth. "Kingston Dutch Church, Ulster County, New York: Burials, 1739-1795," National Genealogical Society Quarterly, Vol. 61 (1973):189-194, 270-277. FHL Book 973 B2ng v. 61 (1973).
• 1805-1831 - Mearns, Shirley A. "Kingston, New York, Old Dutch Church: Burials," The New York Genealogical and Biographical Record, 1805-1810: Vol. 113, No. 3 (Jul. 1982):165-168; 1810-1816: Vol. 113, No. 4 (Oct. 1982):199-202; 1816-1831: Vol. 114, No. 1 (Jan. 1983):42-46. Digital version at New York Family History ($); FHL Book 974.7 B2n v. 113-114.
• 1810-1877 - Roney, Lila James. Baptisms of the Old Dutch Church of Kingston, New York, 1810-1877. 1989. Digital version at Ancestry ($).
City/Town Records
To locate additional published and transcribed records for Kingston, New York check:
• Gordon L. Remington, New York Towns, Villages, and Cities: A Guide to Genealogical Sources (Boston: New England Historic Genealogical Society, 2002). American Ancestors online edition; At various libraries (WorldCat); FHL Book 974.7 D27r. Alphabetical list including date founded, if a town history exists, church and cemetery sources, and if a Civil War register (TCR) exists. The codes used under Church and Cemetery are defined in the link above the listing of towns, cities and villages.
Repositories
Archives, Libraries and Museums
Societies
City/Town Clerk
Kingston City ClerkLaura L. Joy,
Town Hall, 906 Sawkill Road,
Kingston, NY 12401
Phone: 845-336-8853
City/Town Historian
Kingston City Historian G. Ernest Smith,
Town Hall, 906 Sawkill Road,
Kingston, NY 12401
Phone: 845-382-1446
Family History Centers
Newspapers
• Kingston Daily Freeman. 1914-1950. Indexed and searchable at Ancestry ($).
Vital Records
• 1667-1672 - Scott, Kenneth. "Kingston Marriages," The New York Genealogical and Biographical Record, Vol. 106, No. 4 (Oct. 1975):193-194. Digital version at New York Family History ($); FHL Book 974.7 B2n v. 106. Supplement to Hoes' Registers of the Old Dutch Church at Kingston.
References
Places
Need additional research help? Contact our research help specialists.
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• This page was last modified on 2 November 2012, at 13:08.
• This page has been accessed 1,128 times. | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T07:20:00.000Z | pa6rjhs7rluwqoucbcyzqj7l6zda273a | {
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} | cccc_CC-MAIN-2013-20 | Maryland CemeteriesEdit This Page
From FamilySearch Wiki
Revision as of 02:00, 14 December 2011 by Ellenward (Talk | contribs)
United States > Maryland > Maryland Cemeteries
Contents
Websites
The following websites will help you find cemetery records, transcriptions, and headstone photographs currently available online:
Resources at the Maryland State Archives
• Tombstones and Cemetery Records. A bibliography for each county in Maryland is listed on this site. Other resources are also available.
• Funeral Home Records are closely related to a search for cemetery records. The Maryland State Archives website maintains a list of funeral homes and identifies where some of the records are located.
National Cemeteries in Maryland
African American Cemeteries in Maryland
Cemetery records at the Family History Library
Click here to see the full list of cemetery records available at the Family History Library for Maryland: Maryland cemetery records at the Family History Library. A few examples from this list include: Historic graves of Maryland and the District of Columbia : with the inscriptions appearing on the tombstones in most of the counties of the state and in Washington and Georgetown
Maryland Cemetery Message Boards and Online Mailing Lists
If you need help finding the cemetery where your ancestor was buried in Maryland, an online message board or mailing list might be helpful:
Maryland counties
See the individual county pages for a list of cemeteries within each county and links to available records:
Need additional research help? Contact our research help specialists.
Need wiki, indexing, or website help? Contact our product teams.
Did you find this article helpful?
You're invited to explain your rating on the discussion page (you must be signed in). | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:56:07.000Z | mxkukdob6hmymt3x76gplu7malh5jvw4 | {
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} | cccc_CC-MAIN-2013-20 | GlobalVoices in Learn more »
Anguilla
Country archive · 13 posts
Latest stories about Anguilla
3 November 2008
Caribbean: Region Scores Big in Stanford 20/20 Cricket
U.S. billionaire Allen Stanford is trying to remake the face of cricket. His latest "big idea" is a 20/20 contest in which the winning team walks away with US$20 million (that's US$1 million per man) and the loser gets...well, nothing. It all happened this past weekend and West Indian bloggers put in their two cents' worth...
27 January 2008
Brazil: Countdown to Carnival
There is a popular belief that in Brazil the year only starts after Carnival. Be this an exaggeration or not, there is not much else being talked about on the country's blogosphere: everyone is dusting off their costumes, getting into the mood and counting down the days for the biggest street party on Earth. Here's a round up of bloggers expectations in Rio de Janeiro, Bahia, Pernambuco, and the lesser known carnival in Minas Gerais.
30 May 2007
One Caribbean; Many Identities…
Calypsonian Lord Nelson once sang, “all ah we is one family”. Optimists in the Caribbean may well agree with these words, but the reality is that if you were to describe Caribbean states as a family, you would have to call it a complex unit - and one in which there is much sibling rivalry. Trinidadian blogger Karel Mc Intosh discusses the intricate subject of Caribbean unity with Jamaicans Geoffrey Philp and Francis Wade and Guyanese blogger Media Critic.
25 April 2007
Caribbean: Farewell to a cricketing legend
In the early ’90s, the West Indies' dominance of the international cricket scene entered its long decline. There were fewer victories to celebrate, fewer exceptional demonstrations of the brilliance to which West Indian fans had become so accustomed. And when there were bright spots, they often came courtesy of one man: Brian Charles Lara. Lara played his last ever international cricket match in Barbados on April 21, 2007, in front of thousands of fans and visitors. The Caribbean blogosphere pays tribute to the man some consider the greatest cricketer of all time.
18 June 2006
Haiti: Telecom Wars
Digicel billboard, Martinique. By blogger Greg at InternetRapide.com. Jamaica-based Caribbean telecom giant Digicel has a presence in over a dozen countries in the region. Digicel officially launched operations on the...
6 June 2006
Global Voices, Caribbean Accents: report on Caribbean blogging roundtable
THE CARIBBEAN STUDIES ASSOCIATION (CSA), one of the major assemblies of scholars of the history, culture, and society of the Caribbean region, held its annual conference in Port of Spain,...
22 May 2006
Montserrat volcano watch and West Indies cricket
A woman looks at the rear window of her car, broken by a flying rock from the nearby Soufriere Hills Volcano, Montserrat, on Saturday. Photo from the Trinidad Express website...
28 April 2006
West Indian literature online
One of the crucial elements in the rapid development of the literature of the Anglophone Caribbean in the 1940s and 50s was a weekly radio programme called Caribbean Voices, broadcast...
17 April 2006
Village cricket match, Caribbean-style
Easter Sunday cricket match — Howsen Village, Trinidad. From caribbeanfreephoto At this time of year, thoughts in the English-speaking Caribbean turn to the game of cricket. Travel around any of...
9 April 2006
Guilt-Free Food Blogs Review
#1: From Japan, I was just really very hungry Milking the soy bean, part 1: learn how to make soy milk with no special equipment. Milking the soy bean, part...
World regions
Countries
Languages | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:02:42.000Z | lxyrrk6cxwqssjuyxcxphsxesrrhxp5g | {
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An unofficial blog that watches Google's attempts to move your operating system online.
Send your tips to [email protected].
April 13, 2011
Google Calendar's Favicon Changes Every Day
When Google Calendar changed the favicon, many people wondered why it only shows 31. "Does it mean that starting today, every day will be the 31st ? Serously, favicon should be changed everyday to match the date," suggested a Google Calendar user.
Google listened to the feedback and the favicon will now change every day. "When you look at the Google Calendar icon at the top of your browser window, it will no longer always display 31 but will instead change to reflect the current day of the month. Today's date is now always a short glance away."
Google Calendar is the first Google service that has a dynamic favicon, but you can change Gmail's favicon to show the number of unread messages.
| v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T05:55:26.000Z | jjbigs3gog3wzzywm4rzb43qg6vvqsez | {
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} | cccc_CC-MAIN-2013-20 | Humble Indie Bundle 7 Is Out Now !
Posted on 20th December 2012 in Uncategorized
Humble Indie Bundle 7 has arrived and is guaranteed to keep you entertained all winter long! Pay what you want for The Binding of Isaac (and its DLC, Wrath of the Lamb!), Closure, Shank 2, Snapshot, and the documentary feature film Indie Game: The Movie! If you choose to pay more than the average, you’ll [...] | v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T06:31:20.000Z | aoyg7bzsx3olwmlmm53php6zb64bwrx6 | {
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"uncompressed_offset": 190737208,
"url": "opendotdotdot.blogspot.com/2007/11/openness-purity-of-essence.html",
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"warc_url": "http://opendotdotdot.blogspot.com/2007/11/openness-purity-of-essence.html"
} | cccc_CC-MAIN-2013-20 | 23 November 2007
Openness: Purity of Essence
I wrote a piece for Linux Journal recently warning that Microsoft was beginning to hijack the meaning of the phrase "open source". But the problem is much bigger than this: the other opens face similar pressures, as Peter Murray-Rust notes.
In some ways it's even more serious for fledgling movements like open access and open data: there, the real meaning has barely been established, and so defending it is harder than for open source, which has had a well-defined definition for some time. Given the importance of labels, this is a matter that needs to be addressed with some urgency before "open access" and "open data" become little more than bland marketing terms.
| v0 |
2024-06-03T21:29:47.544Z | 2013-05-18T08:03:59.000Z | yt67gvchx3goqytrpyqa22e4qnyw5d2a | {
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} | cccc_CC-MAIN-2013-20 | David Lowry
From OpenWetWare
Revision as of 22:00, 8 August 2012 by Lowry (Talk | contribs)
Jump to: navigation, search
The University of Texas at Austin: USDA Postdoctoral Fellow, 2010-2012
Duke University: PhD, 2004-2010
The University of California, Berkeley: BS, 1997-2001
Research Interests
Phenotypic diversity of Switchgrass, Panicum virgatum
Field experiment with Mimulus guttatus
The genetics of adaptation and speciation
Adaptation is the most fundamental way that the environment can mold the diverse phenotypes of organisms. Adaptations can also lead to the formation of reproductive isolating barriers, which are the building blocks of new species. I am very interested in understanding the genetic underpinnings of reproductive isolation at various stages in the speciation process.
Understanding adaptation is also crucial to predicting how organisms will respond to future global change and will help inform management decisions as well as guide future agricultural breeding.
Landscape evolutionary genomics
One of the core goals of my research program is to understand how the natural landscape molds the genomes of organisms through adaptation. To that end, I am using a combination of genetic mapping and genome sequencing approaches to identify genes involved with adaptation to the heterogeneity of the natural landscape. During my dissertation, I focused on how adaptive alleles in Mimulus guttatus are spread across the landscape and what phenotypic effects they have in different environments across western North America. Currently, I am developing Panicum grasses as a model system to understand adaptation along a longitudinal soil moisture cline across Southwestern United States and a latitudinal temperature cline across the Great Plains. Our lab recently received funding from the Department of Energy to develop Panicum hallii as a model system for local adaptation and bioenergy research.
The role of the genome structure in phenotypic evolution
Whether or not a gene will be involved in adaptation and phenotypic evolution is dependent on the position of that gene in the genome. Differential rates of recombination and selection across the genome can have a large impact on patterns of standing genetic variation, which is raw source of evolution. I am currently using multi-genome data sets in Arabidopsis thaliana to understand how genome structure impacts phenotypic evolution.
Field experiment with Panicum hallii
Using evolutionary biology to improve bioenergy crops
Civilization is built on a foundation of domesticated grasses. Without those grasses (corn, wheat, rice, oats, barley, sorghum) there would be no ballet and human beings would never of landed on the moon. Plant breeders have quietly worked in the shadows to increase the yield of crops and in turn maintain our modern world.
Now, there may actually be potential to domesticate a new set of grass species to use to help combat the growing energy problem. My research is focused understanding the factors involved in local adaptation in the bioenergy crop switchgrass (Panicum virgatum). Loci involved in local adaptation are likely to be of high value to crop breeders interested in improving drought, heat, cold, herbivore, and disease tolerance.
Publications
Cover photo for PLoS Biology
Lowry, D. B., C. T. Purmal, T. E. Juenger. A population genetic transect of Panicum hallii (Poaceae). In review
Wright, K. M., D. Lloyd, D. B. Lowry, M. R. Macnair, J. H. Willis. Indirect evolution of hybrid lethality due to linkage with selected locus in Mimulus guttatus. In review
Lowry D. B., R. Hopkins. (2012) “Speciation and Natural Selection.” Invited book chapter in The Princeton Guide to Evolution, edited by Jonathan Losos. Princeton, NJ: Princeton University Press. In press
Lowry D. B. (2012) Local adaptation in The model plant. New Phytologist. 194: 888-890.
Lowry D. B. (2012) Ecotypes and the controversy over stages in the formation of new species. Biological Journal of the Linnean Society. 106: 241-257.
Lowry, D. B., C. T. Purmal, E. Meyer, T. E. Juenger. (2012) Microsatellite markers for the native Texas perennial grass, Panicum hallii (Poaceae). American Journal of Botany Primer Notes & Protocols. 99: e114-e116
Lowry, D. B., C. S. Sheng, Z. Zhu, T. E. Juenger, B. Lahner, D. E. Salt, J. H. Willis. (2012) Mapping of ionomic traits in Mimulus guttatus reveals Mo and Cd QTLs that colocalize with MOT1 homologues. PLoS One 7: e30730.
Lowry D. B., C. S. Sheng,, J. R. Lasky, J.H. Willis. (2012) Five anthocyanin polymorphisms are associated with an R2R3-MYB cluster in Mimulus guttatus. American Journal of Botany 99:82-91
Lowry, D.B., J. H. Willis. (2010) A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biology 8: e1000500
Hall M. C., D. B. Lowry, J. H. Willis. (2010). Hall M. C., D. B. Lowry, J. H. Willis. (2010) Is local adaptation in Mimulus guttatus caused by trade-offs at individual loci? Molecular Ecology. 19: 2739-2753
Lowry, D. B. (2010) Landscape evolutionary genomics. Biology Letters. 6: 502-504
Wu, C. A., D. B. Lowry, L. I. Nutter, J. H. Willis. (2010) Natural variation for drought response in the Mimulus guttatus species complex. Oecologia 162: 23-33
Lowry, D. B., M. C. Hall, D. E. Salt, J. H. Willis. (2009). Genetic and physiological basis of adaptive salt tolerance divergence between coastal and inland Mimulus guttatus. New Phytologist 183: 776-788
Lowry, D. B., J. L. Modliszewski, K. M. Wright, C. A. Wu, J. H. Willis. (2008). The strength and genetic basis of reproductive isolating barriers in flowering plants. Philosophical Transactions of the Royal Society B 363: 3009-3021
Lowry, D. B., R. C. Rockwood, J. H. Willis. (2008). Ecological reproductive isolation of coast and inland races of Mimulus guttatus. Evolution 62: 2196-2214
Wu, C. A., D. B. Lowry, A. M. Cooley, K. M. Wright, Y. W. Lee, and J. H. Willis. (2008). Mimulus is an emerging model system for the integration of ecological and genomic studies. Heredity 100: 220-230.
Important Things
• Contact Info: You can contact me at [email protected].
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Contents
Idea Collection
Project One
• E.coli to decompose polluted water and sludge PPT
Project Two
• Taming Cancer by Inducing Immunity via E.coli PPT
Project Three
• Constructing E.coli cells to act like multicellular organisms PPT
Project Four
• Bio Control Element PPT
Project Five
• Discovery Research via in vivo Evolution PPT
(This is chosen to be our final project)
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We have not lost faith, but we have transferred it from God to the medical profession. Shaw, George Bernard
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George Bernard Shaw (July 26, 1856 November 2, 1950) was an Irish playwright and winner of the Nobel Prize for Literature in 1925.
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The first thing to do in life is to do with purpose what one purposes to do. Casals, Pablo
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Pau Carlos Salvador Casals i Defill (December 29, 1876 October 22, 1973), commonly known as Pablo Casals, was a virtuoso Catalan cello player (and later conductor). He made many recordings throughout his career, of solo, chamber, and orchestral music, also as conductor, but Casals is best remembered for the recording of Bach's Cello Suites he made from 1936 to 1939.
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Work is a part of life, not the point of it. Adams, Sean
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This is a personal quote I (sean adams) came up with. I am not a published author or celebrity
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2024-06-03T21:29:47.544Z | 2013-05-18T05:43:48.000Z | czgwz5fefhjiawvczhypwoq5pulsc77c | {
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In order to be a realist you must believe in miracles. Bailey, Henry Christopher
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212 - The Extra Degree
The one extra degree makes the difference. This simple analogy reflects the ultimate definition of excellence. Because it's the one extra degree of effort, in business and life, that can separate the good from the great. This powerful book by S.L. Parker and Mac Anderson gives great examples, great quotes and great stories to illustrate the 212° concept. A warning - once you read it, it will be hard to forget. Your company will have a target for everything you do ... 212°
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2024-06-03T21:29:47.544Z | 2013-05-18T06:37:02.000Z | kgm7agsy7tibgdp7myjwumsfvd2muwsx | {
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How can we live without our lives? How will we know its us without our past? Steinbeck, John
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212 - The Extra Degree
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