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Corruption in academia
From Issuepedia
Jump to: navigation, search
Contents
[edit] Overview
This article is a seed. You can help Issuepedia by watering it.
[edit] Links
[edit] News
[edit] The Larry Summers Incident
[edit] Editorial
[edit] Sites
• PsyCrit is an online academic journal dedicated to criticizing published scientific papers in the field of psychology
Personal tools
bookmarking
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source: josm/trunk/data/en_GB.lang @ 5204
Last change on this file since 5204 was 5204, checked in by simon04, 13 months ago
I18n update
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HTML preview not available, since no preview renderer could handle it. Try downloading the file instead.
Note: See TracBrowser for help on using the repository browser.
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HYDROGEOLOGICAL BREAKING CHARACTERISTICS OF WAVES ABOVE FRESH WATER SUBAQUEOUS SOURCES
Agatino D'Arrigo
Abstract
After a short review of the usefulness of maritime structures, particularly vertical wall breakwaters, long term observations of hydrogeological breaking on the bottom of Italy's Seas, as caused by the subaqueous source of fresh water, are discussed. The correlation between hydrogeological breaking and wave motion perturbation produced by compressed air or by oil is presented. These considerations are related to the observations of Admiral Alessandro Cialdi on the morphological breaking of waves above sand banks, thus producing calmness in the upper water.
Therefore, it appears possible to establish a very suggestive analogy between the atomic disintegration of the transformation of potential energy of the oscillatory tide wave into kinematic energy of its components (because of breaking), in accordance with the disintegration of the circular motion.
Keywords
breaking; subaqueous flow; maritime structures
Full Text: PDF
This work is licensed under a Creative Commons Attribution 3.0 License.
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[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [tdf-discuss] Missing recent nightly builds for Windows
Pieter E. Zanstra schrieb:
The last available is dated 8th of June. Are they in a different
place now, or is there a hickup in the production? Pieter
Hallo,
although those builds still are rather experimental, I usually do such tests with Builds from <http://dev-builds.libreoffice.org/daily/Win-x86@7-MinGW/master/>, what are really "dayily" available. Only for most UI Bugs those builds IMHO are unusable.
Best regards
Rainer Bielefeld
--
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[tdf-discuss] Missing recent nightly builds for Windows"Pieter E. Zanstra" <pieter@zanstra.eu>
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Art For The Weekend: SP Arte
If you are in São Paulo this week, make sure to take the time to visit SP Arte, which is going on at the Bienal building until Sunday and just so happens to be the biggest fair for art galleries in Brazil. I was there last night, and I am definitely going back over the weekend since some of the galleries have more accessible work on display on Saturday and Sunday.
And for those of you interested in getting a copy of Made In Brazil Magazine, Galeria Mezanino at SP Arte has a limited number of advanced copies of the first issue for sale.
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The power of the 1 and how open innovation changed global health
Image by opensource.com
(4 votes)
[The following is the speech text for the keynote I gave at the SwitchPoint Conference April 20, 2012]
It is sometimes said that computer scientists worry about only three numbers: 0, 1, and N, where N tends to get very large. Sometimes such oversimplifications can lead to astonishing insights, such as the one that I had 25 years ago in June of 1987.
Do you remember 1987? Greed was good, junk bonds were king, and zero was the biggest and most important number on Wall Street. Zero drove all the arbitrage equations, because both sides of the arbitrage are supposed to sum to zero. Arbitrage is a special case of the zero-sum game, a prominent theory promulgated by all respectable business schools of the day. Zero-sum logic made it a moral imperative to ensure that success was not just about winning, but about making sure that everybody else lost. You were not forced to like the terms of the game, but you were damn sure forced to accept them as they only way to play.
I didn't accept those terms for two reasons. First, I had been rejected by every respectable business school I applied to. Second, I realized that zero was not the only number in the playbook. N, especially when N becomes very large, is an even more interesting number.
Consider that every year the Earth receives 120 Petawatts of energy from the sun. That's 120 followed by fifteen zeros; it's also 8,000 times what we humans generate at our current industrial scale--120 x 1015 a really big N! It's so big, in fact, that thinking about life on Earth as a zero-sum game just makes no sense. This positive energy flux not only powers life itself, but it represents an enormous flow of available possibilities. As soon as I realized that we were living in a positive-sum world, at least when it comes to energy flux, I realized that the strategies for "winning" the zero-sum game and the positive-sum game were quite different. We win by having more winners, not by increasing the number of losers. What a different game that is! And what an opportunity to win!
It is here that I should give some credit to those who taught me mathematics, logic, and theory. Perhaps you have read Gödel Escher Bach by Douglas Hofstadter, which includes the very accessible story of how Kurt Gödel managed to prove that any system of logic powerful enough to prove a statement true or false is necessarily incomplete (meaning there are true things that cannot be proved) or inconsistent (meaning that there are true things that can nevertheless be proved false). If you have, you know that Gödel takes some amazing leaps in directions that make almost no sense until he brings them all together in a logical tour-de-force. Perhaps it was that very story that gave me the confidence to not worry at all about the individual propositions of the positive-sum game (which, by the way, are each absurd in the zero-sum context), but rather to let them all take shape as a community of ideas, and to be prepared for an astonishing result.
The answer I derived happened to agree perfectly with The GNU Manefesto, a polemic written by Richard Stallman, founder of the Free Software Foundation and creator of the GNU Project. Stallman railed against the injustice of software hoarding; I calculated that excluding valuable participants from an effort was self-defeating. Stallman talked about the moral imperative of sharing; I saw free redistribution as a frictionless way to build market share. Stallman talked about the vital importance of community; I realized that a diverse marketplace of people having problems and people solving problems would lead to more rapid and more relevant innovation. As I recently posted on Google+, I was so sure that this way of thinking could lead to a $1B company that I started Cygnus Support in 1989 just to prove it. Red Hat acquired Cygnus in 2000, and twelve years later grew through the $1B mark in convincing fashion. But being first to $1B does not mean we are the only winners. The founders of Facebook, Google, and Twitter have all said that they could never have started their companies without open source software. They are also winners who recognize the power of open innovation. And open innovation reaches far beyond software.
Harold Varmus shared the Nobel Prize in medicine in 1989 for "discovery of the cellular origin of retroviral oncogenes." Varmus went on to lead the NIH, dramatically increasing its funding from $11B per year to $16B per year during his appointment under President Clinton. I met Dr. Varmus in Kyoto at the Science, Technology and Society summit in 2006. He told me that of all the things he did after winning the Nobel Prize, the one he thought was most important, because of its long-term and wide-ranging impact, was to spearhead open Internet access for medical research. In 2007 Varmus summarized his inspiration in a speech, quoting Panizzi (the librarian of the British Museum from 1837-1866):
"I want a poor student to have the same means of indulging his learned curiosity, of following his rational pursuits, of consulting the same authorities, of fathoming the most intricate enquiry as the richest man in the kingdom, as far as books go, and I contend that the Government is bound to give him the most liberal and unlimited assistance in this respect."
As Varmus explained to me, the instant he saw the World Wide Web, he recognized that open access publications could be deposited in an online public repository immediately upon publication and also offer access to the widest array of users possible. Varmus saw what I, too, saw in my own experiences with open innovation: the advancement of information and communication technology coupled with the economies they provide led to a fundamental shift in both human productivity and, more importantly, the capacity of the community. It did not matter whether the information came from the analog world or was born digital: once the information was infinitely available at virtually zero cost, the rules of a whole new game were in play. For Varmus, this meant that digital libraries could "rise above the strangulating effects of [the] so-called 'Gutenberg liabilities' inherent in traditional scholarly publishing."
In 2010, the Public Library of Science, founded by Varmus, Patrick Brown, and Michael Eisen in 2000, received more than 20,000 scholarly submissions, publishing nearly 10,000 with an operating budget of approximately $13M, which is very close to the list price they offer of $1,500 to have a paper properly reviewed and published. That may sound like a lot of money compared to what newspapers charge for classified ads, but contrast this with Elsevier, which publishes 250,000 articles in 2,000 journals with revenues of $3.2B and a profit margin of more than 36%. Elsevier averages nearly 10x the cost, but remember: cost-per-article alone is not the only problem that Varmus was trying to address. An article from WIRED magazine explains:
[Patrick] Brown and a fellow of his, Michael Eisen, were using a technique for genetic analysis that benefits particularly from information-sharing across many labs. Eisen had written a program to enable such exchanges, but it was constantly banging up against copyright restrictions from journals that didn't want the data in their articles passed around. Brown and Eisen thought that was insane. For a decade, the physics community had run an electronic archive out of Los Alamos National Laboratory, where researchers could upload their papers even before having them formally accepted by journals. The physicists loved it. Why not create something similar for the bio-medical community?
The conversation clicked with Varmus. Soon, he, Brown, Eisen, and David Lipman, an NIH colleague, drafted a proposal for "E-Biomed," a public, one-stop repository of biomedical papers. Researchers could submit papers through a peer-review process similar to that used in the current journal system, or they could post work fresh out of the test tube.
E-Biomed evolved, and today in addition to the Public Library of Science, PubMed, PubMed Central, 38 other databases are all cross-linked, many in a multitude of dimensions, now provides virtually all biotech information known to the NIH through a single, easy-to-use open source interface called Entrez (ftp sources here). Several of these databases have more than 10M entries and many more have more than 1M entries. Just imagine all the connections between all these datasets, and how that informs what we know and what we wish we knew about how our own source code actually works. And imagine how powerful it is to have the freedom to write programs that can traverse all this data and develop new knowledge and connections. I have spoken with numerous heads of other nation's medical research facilities, and for all of them, the NIH's open access policies are the gold standard around the world. The openness is the innovation, and the numbers show it: at last count more than 1M researchers a day ran an annual aggregate of 1.8B searches against MEDLINE/PubMed and downloaded 4TB of data per day from the National Library of Medicine's servers.
But not everybody wants to play by these rules, and in true zero-sum fashion, they want to prevent us from playing by these rules, too. A decade ago, Varmus tried to make peace with the other side by offering to delay public access to results published in traditional journals for a period of six months--a bitter but pragmatic compromise in his view. Bitter because Benjamin Franklin could regularly correspond with his fellow scientists across the Atlantic every 6-8 weeks. You would think that with the Internet and 250 years of technology advances that scientific dissemination would speed up, not slow down. But alas that was not enough for those who place profits ahead of progress and monopoly—the very enemy of democracy—above community welfare. In January of this year, lobbyists for the traditional publishers helped draft the Research Works Act, which, among other things, stipulated:
No Federal agency may adopt, implement, maintain, continue, or otherwise engage in any policy, program, or other activity that:
(1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher of such work; or
(2) requires that any actual or prospective author, or the employer of such an actual or prospective author, assent to network dissemination of a private-sector research work.
Needless to say, such a bill would not only end the NIH's Public Access Policy, but it would forbid any effort on the part of any agency to ensure taxpayer access to work funded by the federal government. That bill has been killed once, largely by the same wave that sunk SOPA and PIPA, but you know as well as I do that bills in Congress are like zombies and we must remain vigilant. We're the ones spending $28B per year on medical research--we have a right to share in the data we paid to develop!
Let me close by taking a step back and competing the two games I have presented: the zero-sum and the positive-sum. Which game itself is the winner? The finite game, where every resource, every move, must be subtracted from one column before being added to another, or the infinite game, where multiple possibilities co-exist, either cooperatively or independently? The closed game, where you can be excluded from playing, either because you don't know the trade secrets necessary to play or because you don't have the necessary rights to practice patents or share in the fruits of what has already been paid for? Or is the open game better, where all the rules are published, and all who want to learn them can play?
This is where the number 1 comes in. Gandhi famously said "Whatever you do will be insignificant, but it is very important that you do it." Each of you is the 1. I am the 1. When one person can successfully add energy to the efforts of the community at large, that person augments and amplifies the power of the larger community. In the positive-sum world, everything we do adds up. I am just one person, but I've put 25 years into open source software, and I've seen other creative, open, collaborative communities emerge: Creative Commons, the Science Commons, the Conservation Commons, and more. One by one, day after day, year after year, we have created billions of lines of software source code, hundreds of millions of creative, copyrightable but also shareable artifacts, and we are just getting started. I can't wait to see what the next 25 years can bring!
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IGEM:MIT/2007
From OpenWetWare
(Difference between revisions)
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===Meeting Logistics===
===Meeting Logistics===
-
*'''[[Room Reservations]]'''
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*'''[[/Onduty|Gradvisor "On Duty" Shifts]]'''
*'''[[/Onduty|Gradvisor "On Duty" Shifts]]'''
Revision as of 09:54, 28 June 2007
• iGEM is the international genetically engineered machines competition.
• The objective of the competition is to design and build an engineered biological system using DNA.
• To see examples of the amazing possibilities of iGEM, check out last year's presentations
to the MIT 2007 iGEM team.
Resources
Interested in being a learning more about iGEM 2007? Explore below for an example of what's possible.
For more info on this year's iGEM please see www.igem2007.com and the official iGEM 2007 wiki
Many more valuable links and helpful tidbits are available at the iGEM Resources page
What will be this year's project for the 2007 MIT team? We're busy brainstorming ideas as you read this!
External links
For visitors
Internal links
Information
Want to join the team?
• Graduate students interested in advising the team should email grads [AT] igem.mit.edu
• Undergraduate students will have to wait until 2008!
Schedule
• April 8 - Application deadline (5pm on Sunday)
• April 7-9 - Undergrad interviews
• April 12 - UROP funding deadline
• April 30 - iGEM 2007 registration closes
• May 1 - Team 2-page proposals due
• May 15 - Preliminary team rosters due
• May 26 - Teach the teachers workshop
• May 30 - Team registration fee due
• June 4 - Team training begins
• June 11 - Team starts in the lab (summer term begins)
• July 1 - Team project descriptions due
• September 1 - Final team rosters due
• October 26 - Project and part documentation due
• October 26 - BioBrick Part DNA received by the Registry
• November 3-4 - iGEM competition Jamboree, MIT, USA
Brainstorming
Meeting Logistics
Last year's MIT iGEM contact info
• Email grads: grads06 [AT] igem.mit.edu
• Email team: smellers [AT] igem.mit.edu
People
The MIT iGEM team consists of six undergraduate students working fulltime during summer 2007 on engineering a biological system. In addition, we have a number of graduate student and faculty advisors.
New: iGEM chat room!
Students
Email us: team [AT] igem.mit.edu
Advisors
Email grads: grads [AT] igem.mit.edu Email all: igem [AT] igem.mit.edu
Personal tools
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User:Kelsey J.R.P. Byers
From OpenWetWare
Revision as of 03:35, 7 July 2010 by Kelsey J.R.P. Byers (Talk | contribs)
(diff) ←Older revision | Current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search
I am a new member of OpenWetWare!
Contents
Contact Info
Kelsey J.R.P. Byers (an artistic interpretation)
Kelsey J.R.P. Byers
University of Washington
Department of Biology
24 Kincaid Hall
Box 351800
Seattle, WA 98105 (USA)
Academic website
Email me through OpenWetWare
I work in the lab of Dr. H.D. "Toby" Bradshaw, Jr. at the University of Washington in Seattle, WA, studying the genetic basis of speciation in Mimulus (Lamiales), a developing model genus. I specifically work on speciation driven by pollinator-based prezygotic reproductive isolation; my pollinators of interest include hummingbirds, bumblebees, and hawkmoths (though I have a certain fondness for bats).
Education
• (expect 2014), PhD (in progress), University of Washington
• 2007, SB, Massachusetts Institute of Technology
• 2003, Biotechnology Academy (4 years), Minuteman Regional High School, Lexington, MA
Research interests
1. Speciation (various, particularly driven by prezygotic isolation)
2. Natural population variation
3. Remote sensing techniques and development
4. Pollination ecology
Publications
1. Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, and Bulyk ML. . pmid:19158363. PubMed HubMed [Paper1]
Work done in the lab of Dr. Martha Bulyk, Harvard Medical School
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ColorSync
Info
Search:
A system extension developed by Apple Computer for the Macintosh which is designed to facilitate color management for all attached devices and their respective color spaces. See Color Management System.
All text and images are licensed under a Creative Commons License
permitting sharing and adaptation with attribution. (See Copyrights for details.)
PrintWiki – the Free Encyclopedia of Print
About PrintWiki Policies Hosted by WhatTheyThink
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Digimon World: Dawn and Dusk/Explore Limit Valley
From StrategyWiki, the video game walkthrough and strategy guide wiki
Jump to: navigation, search
Exploring Limit Valley! This area is a great area to get closer to Champion.
When you enter, go up into the next area. ...Second thought, this area shouldn't be too hard to navigate through. Dead ends are common, but this area has no key or puzzle.
You can encounter (on your first visit) Koromon, Agumon, Biyomon, and Renamon on the bright side. The dark side has level 20-25 Digimon, so be cautious in battle. This side has Seasarmon, SandYanmamon, another version of Goburimon (witch is a technical type, so be wary in battle against it), and occasionally Renamon.
At the end (save!), you'll see mystic energy. Fight his level 28 Seasarmon (300 exp), and he'll make you fight 3 SandYanmamon! But before that happens, your friends pop up and take them on, while you fight the boss of this dungeon... Grimmon!!!
Grimmon is level... 40? And is suprisingly a Champion. He's unobtainable. Grimmon covers 3 zones, so if your Gaomon has Small Tornado, or if your Biyomon has Suprise Blow, you'll be able to attack him twice, but the zones each have different weaknesses, those of which CHANGE when he uses AT change.
Winning gets you 300 of 4 different exps, bringing you to a whopping 1200 exp total! Now Lunamon should be able to digivolve if you're playing Dusk.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
4512.0 - Corrective Services, Australia, Dec 2005
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 23/03/2006
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EXPLANATORY NOTES
INTRODUCTION
1 This publication presents statistical series on persons held in either adult corrective services custody or who are serving adult community-based orders in Australia. It contains data on the number of persons by their sex, Indigenous status, type of custody, legal status and sentence type; the number of sentenced persons received into corrective services custody each month; and the number of federal prisoners.
2 Statistics presented in this publication are compiled in three ways:
• Average daily prisoner population: Counts taken on each day of the month are summed and divided by the number of days in that month to determine the average daily prisoner population for that month. The average daily periodic detainee population is a count of persons on periodic detention on each day a centre is open, divided by the number of days a centre is open.
• Sentenced prisoner reception figures: Counts are provided each month on the number of receptions where a prisoner is received as a sentenced prisoner. This includes prisoners with a change of legal status from unsentenced to sentenced.
• First day of the month prisoner population: Counts of prisoner populations, taken on or near the first day of the month (see Explanatory Notes, paragraphs 4 and 5), and counts of persons serving community-based corrections orders.
3 Although national standards and classifications are used in the compilation of these statistics, some discrepancies remain between the states and territories. These are due to legislative and procedural differences between jurisdictions and the way that these differences are reflected in agencies' administrative data systems. As part of its quality assurance strategy, the ABS is working with corrective services agencies to minimise the effect of these differences.
REFERENCE PERIOD/DATE
4 The reference period for average daily prisoner population statistics and sentenced reception counts is the complete reference month. Prior to the December quarter 2004, average daily statistics for Australian Capital Territory prisoners held in New South Wales could not be supplied, and a single count taken on a specific day of the month was used instead. The reference date for all other figures is the first day of the reference month. However, not all states and territories report strictly according to this 'first day of the month' rule:
• The Western Australian and Victorian prison population and Australian Capital Territory prisoners in New South Wales prisons are counted as at midnight on the last day of the month. In these cases the figures provided are taken to represent the prison population at the beginning of the following month to align with practices in other states and territories.
• Prior to the September quarter 2004, the New South Wales prison population was counted on the last Sunday of the month. The New South Wales community-based corrections population is counted on the first day of the month.
5 Calculation of figures for the entire quarter and entire year varies depending on the counting unit and method of counting prisoners:
• Average daily figures: Figures are calculated by weighting the average according to the number of days in each month or year.
• First day of the month: Figures are simple averages. For quarterly figures, the sum of the monthly data is divided by three; for yearly figures, the figures for each month are added and the total divided by twelve.
• Sentenced receptions: Figures are totals of each month.
• These figures may be subject to rounding.
SCOPE
6 The scope of the statistics in this publication includes all persons remanded or sentenced to adult custodial corrective services agencies (including Work Outreach Camps and Community Custody Centres in Queensland), or who are serving adult community-based orders in each state and territory in Australia.
7 Counts of prisoners in the following custodial facilities are included in the collection:
• gazetted prisons in all jurisdictions
• periodic detention centres in New South Wales and the Australian Capital Territory
• Community Custody Centres and Work Outreach Camps in Queensland
• cells in court complexes administered by corrective services in New South Wales
• transitional centres in New South Wales
• lock-ups in Western Australia operated by the police but designated as a prison by the Chief Executive Officer of Corrective Services.
8 The prisons and community corrections collection excludes the following custodial facilities:
• police lockups, police prisons and cells in court complexes not administered and controlled by corrective services
• gazetted police prisons in the Northern Territory
• juvenile detention centres, including those under the authority of adult corrective services
• immigration detention centres
• military prisons.
9 This collection includes counts of persons remanded or sentenced to adult custody facilities, or directed to serve community based orders administered by adult corrective services agencies. In all states and territories except Victoria and Queensland, persons are considered adults if aged 18 years and over. In Victoria and Queensland persons are considered adults if aged 17 years and over. The vast majority of persons counted in the collection are adults. However, juveniles may be included in exceptional circumstances.
10 Federal prisoners include those persons charged and sentenced under a Commonwealth statute, and those persons who are charged and sentenced under the laws of another country but transferred to an Australian prison to serve their sentence under the International Transfer of Prisoners Act 1997 (Cwlth). To give practical effect to this legislation in Australia, the framework was introduced in January 2003. For the purposes of this publication, federal sentenced prisoners are those persons who are recognised by the Criminal Law Division of the Australian Government Attorney-General's Department as having been charged and sentenced under a Commonwealth statute, or transferred from another country to serve their sentence in Australia.
11 Community-based corrections includes those persons with breached or suspended orders, with the exception of Victoria and Tasmania.
DATA SOURCE
12 Statistics in this publication are derived from information provided to the ABS from administrative records held by corrective services agencies within each state and territory. Statistics on federal prisoners are derived from records kept by the Criminal Law Division of the Australian Government Attorney-General's Department.
13 Tasmanian first day of month data for reference periods prior to the September quarter 2003 are under enumerated. Prior to January 2004, sentenced reception figures for Tasmania do not include all prisoners changing from unsentenced custody to sentenced custody.
14 New South Wales have implemented regular quality assurance processes on their community-based corrections data. Prior to the September quarter 2003, pre-sentence reports were omitted from reported bail figures, and therefore data for earlier reference periods are under enumerated.
COUNTING RULES
15 Statistics for persons held in custody are presented by the state or territory in which they were held and therefore may not be the sentencing jurisdiction. The only exception to this are data for federal sentenced prisoners. These are presented by the state or territory in which they were sentenced, not where they were held in custody.
16 Sentenced prisoners who have other offences that are unsentenced are counted as sentenced. Prisoners may be unsentenced because they are awaiting the outcome of their trial, convicted but awaiting sentence, or awaiting deportation.
17 If an offender has two or more different types of community-based orders operating simultaneously, then each order will be counted. If two or more community-based orders are of the same type, these orders together will only be counted as one order.
INDIGENOUS IDENTIFICATION
18 In all states and territories persons are asked during entry into custody whether they are of Aboriginal or Torres Strait Islander origin. It is uncommon for corrective services agencies to collect Indigenous status information from sources other than the person's own identification.
19 Some persons in custody are recorded with an unknown Indigenous status on the information systems of corrective services agencies as their status has not been able to be obtained. Persons with Indigenous status unknown are excluded from tables 10-13. Counts of persons with an unknown Indigenous status are included in all other tables.
AUSTRALIAN CAPITAL TERRITORY PRISONERS
20 Persons sentenced to full-time custody by the Australian Capital Territory are usually held in New South Wales prisons. The Australian Capital Territory has two remand centres for unsentenced prisoners and a periodic detention centre. During 2000 the Australian Capital Territory commenced detaining prisoners sentenced for fine default only at their remand centres. Unsentenced Australian Capital Territory prisoners may also be detained in New South Wales prisons.
21 To provide greater understanding of the number of prisoners attributed to the Australian Capital Territory, while presenting an accurate picture of the New South Wales prisoner population, statistics relating to Australian Capital Territory prisoners in New South Wales prisons are presented as a subset of the New South Wales figures.
22 Imprisonment rate data for the Australian Capital Territory are included in the publication and are calculated on the basis of the total number of Australian Capital Territory prisoners (i.e. Australian Capital Territory prisoners held in New South Wales prisons, and Australian Capital Territory prisoners held in the Australian Capital Territory) divided by the estimated resident Australian Capital Territory adult population and multiplied by 100,000. For New South Wales, the imprisonment rate is based on the count of New South Wales prisoners, excluding Australian Capital Territory prisoners held in New South Wales prisons, divided by the estimated resident New South Wales adult population and multiplied by 100,000. Time series data have also been derived on this basis.
RATES
23 Imprisonment and community-based corrections rates enable comparisons of prisoner numbers to be made across states and territories. Prisoner and community-based corrections rates are expressed per 100,000 adult population.
24 In this publication the population figures used in the calculation of rates are for persons aged 18 years and over for all states and territories except Victoria and Queensland where the population is persons aged 17 years and over (see Explanatory Notes, paragraph 9).
25 Rates for the total adult prisoner population and persons in community-based corrections are calculated using the estimated resident population (ERP) for each of the states and territories (refer Australian Demographic Statistics (cat. no. 3101.0)). All estimates for the Australian Capital Territory exclude Jervis Bay Territory. All estimates for Australia exclude the external territories of Christmas Island and the Cocos (Keeling) Island. As the population changes over time the denominator used for the calculation of rates varies, depending on the reference period. The most current ERP data available at the time of publication are used to calculate rates as follows:
• for the March quarter, ERP is from the previous September quarter;
• for the June quarter, ERP is from the previous December quarter;
• for the September quarter, ERP is from the previous March quarter;
• for the December quarter, ERP is from the previous June quarter; and
• annual rates are an average of the rates of the contributing quarters.
Indigenous imprisonment rates
26 Rates for the Indigenous adult population in this publication are based on the low series projections for 30 June of the current calendar year (refer to Experimental Estimates and Projections, Aboriginal and Torres Strait Islander Australians, 30 June 1991 to 30 June 2009 (cat. no. 3238.0)). These projections are based on the 2001 Census of Population and Housing.
27 The low series are one of two series of these projections that have been published for the years 2002 to 2009.
• The low series assumes no ‘unexplained growth’ - that is, the Indigenous population recorded in the 2001 Census of Population and Housing is projected to change only as a result of births and deaths (natural increase) and, for the states and territories, as a result of interstate migration.
• The high series assumes that there will be ‘unexplained growth’ in the Indigenous population - that is, the Indigenous population is projected to change as a result of an unexplained component in addition to the effects of natural increase and interstate migration. The size of the unexplained component is based on the ‘unexplained growth’ observed between the 1996 and 2001 censuses.
28 The decision to use the low series as the denominator in the calculation of Indigenous imprisonment rates from 2002 followed consultation with the National Corrective Services Statistics Unit Advisory Group and other stakeholders.
Revisions to historical Indigenous rates
29 Historical rates for Indigenous prisoners have been revised using Indigenous population projections based on the 2001 Census of Population and Housing (low series) for 2002 to 2004.
SIGNIFICANT EVENTS
30 The administrative classification of the following NSW correctional facilities was altered at 1 July 2005: Cooma, Dilwynia, Paramatta and Berrima. These facilities changed classification from 'open' to 'secure' to reflect alterations in the profile of inmates held, and the operational requirements of those centres. As such, the proportion of persons in secure and open custody altered in the September quarter 2005 compared to previous quarters.
31 In December 2004 Victoria's Beechworth Prison closed while a new correctional facility (Beechworth Correctional Centre) opened in February 2005. The old Beechworth Prison was classified as medium security and the new Correctional Centre is classified as minimum security. Data previously published for secure custody were overcounted and open custody were undercounted. Data for the March and June quarters have been revised to reflect this change.
32 The Maryborough Correctional Centre, Queensland, was officially opened in April 2003. The Centre has the capacity to hold 500 prisoners.
33 Data extracted from the South Australian information system for the June quarter 2005 and September quarter 2005 may be subject to data processing time lags. Procedures to overcome this have been implemented for the December quarter 2005.
34 During 2003 in Western Australia there was an increase in the number of Indigenous persons sentenced to imprisonment by the courts, mostly in relation to 'Driving/Traffic', 'Against the Person' and 'Justice/Good Order' offences.
35 A range of amendments to Western Australian corrections legislation came into effect in 2003 and 2004. As a result, bail figures were included for the first time in the December quarter 2003 for Western Australia. Prior to the September quarter 2004, counts of restricted movement orders included conditional bail orders (that may have a restricted movement condition). All conditional bail orders are now counted as bail orders.
36 In the June quarter 2005, Western Australia implemented a strategy to reduce the number of fine defaulters being taken into custody by offering alternative means of payment. This has resulted in a decrease in the number of sentenced receptions into custody for the September quarter 2005.
37 In the Northern Territory, over the 12 months to 30 June 2003, there was an increase in the number of Indigenous persons sentenced to imprisonment for a range of assault and driving offences.
RELATED PUBLICATIONS
ABS Publications
38 Other ABS publications that may be of interest include:
Australian Demographic Statistics (cat. no. 3101.0) - issued quarterly
Australian Social Trends (cat. no. 4102.0) - issued annually
Australian Standard Offence Classification (cat. no.1234.0) - irregular
Crime and Safety, Australia (cat. no. 4509.0) - irregular
Criminal Courts, Australia (cat. no. 4513.0) - issued annually
Experimental Estimates and Projections, Aboriginal and Torres Strait Islander Australians, 30 June 1991 to 30 June 2009 (cat. no. 3280.0)
General Social Survey: Summary Results, Australia (cat. no. 4159.0) - irregular
Information Paper: Measuring Crime Victimisation, Australia: The Impact of Different Collection Methodologies (cat. no. 4522.0.55.001) - single issue
Information paper: National Information Development Plan for Crime and Justice Statistics 2005 (cat. no. 4520.0) - single issue
Measures of Australia's Progress (cat. no. 1370.0) - issued annually
Prisoners in Australia (cat. no. 4517.0) - issued annually
Recorded Crime - Victims, Australia (cat. no. 4510.0) - issued annually
Sexual Assault in Australia: A Statistical Overview (cat. no. 4523.0) - single issue
Year Book Australia (cat. no. 1301.0) - issued annually
39 Current publications and other products released by the ABS are listed in the Catalogue of Publications and Products (cat. no. 1101.0). The Catalogue is available from the ABS web site. The ABS also issues a daily Release Advice on the web site that details products to be released in the week ahead. The National Centre for Crime and Justice Statistics releases a biannual newsletter that is published on the ABS web site. The Centre can be contacted by email through <crime.justice@abs.gov.au>.
Non-ABS Publications
40 Non-ABS sources that may be of interest include:
Department of Justice, Northern Territory, Northern Territory Quarterly Crime and
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
1362.6 - Regional Statistics, Tasmania, 2006
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 21/02/2006
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Contents >> Forestry >> Further information about Tasmanian forestry
For further information about Tasmanian forestry see Statistics - Tasmania.
Previous PageNext Page
© Commonwealth of Australia 2013
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Software
GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins
Patrick Durand1,5*, Laurent Labarre1,2, Alain Meil1, Jean-Louis Divo11, Yves Vandenbrouck3,6, Alain Viari4 and Jérôme Wojcik1,7
Author Affiliations
1 Hybrigenics SA, 3–5 Impasse Reille, 75014 Paris, France
2 AGC, UMR CNRS 8030 – Genoscope, 2 rue Gaston Crémieux, 91000 Evry, France
3 Genome Express, 11 Chemin des Prés, 38944 Meylan, France
4 INRIA Rhône-Alpes, 655 Avenue de l'Europe, 38334 Saint-Ismier Cedex, France
5 IRISA-INRIA, Campus de Beaulieu, 35402 Rennes Cedex, France
6 DRDC/BIM, CEA-Grenoble, 17 Avenue des martyrs, 38054 Grenoble Cedex 9, France
7 Serono Genetics Institute, Route Nationale 7, 91030 Evry Cedex, France
For all author emails, please log on.
BMC Bioinformatics 2006, 7:21 doi:10.1186/1471-2105-7-21
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/7/21
Received:20 June 2005
Accepted:17 January 2006
Published:17 January 2006
© 2006 Durand 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
A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs.
Results
GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces.
Conclusion
GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at academy@genostar.com. A commercial licence form can be obtained for profit company at info@genostar.com. See also http://www.genostar.org webcite.
Background
The development of genomic and post-genomic technologies is producing a large amount of heterogeneous data for investigating the functions of the genes and their products. Biological data are spreaded across an increasing number of databases that differ widely in terms of quality, consistency, diversity and availability [1]. The biologists are now faced with the problem of analysing this information and turning it into new knowledge. Simple analysis is usually performed directly on a database through a query language (usually SQL for relational databases) or using a pre-defined set of queries. More sophisticated analyses require to integrate heterogeneous data coming from various sources and rely upon the use of specialized algorithms and data structures, since database models are not suitable for direct algorithmic use.
An efficient way to analyse the functions of the genes/proteins consists in exploring the relationships between various kinds of biological data [2]. As a very simple example, it is possible to assign a function to a protein from a given organism knowing that this protein is encoded by a gene which is ortholog to another gene encoding a well-known protein in another organism (Figure 1). In that case, a network of objects (genes, proteins and organisms) is actually explored using relationships (a gene 'belongs' to an organism, a gene 'encodes' a protein and a protein 'is similar' to another one).
Figure 1. Example of a graph representing biological data and how it can be used to infer new information. The graph vertices are represented by boxes and are associated to biological entities (Organism, Chromosome, Gene etc). The edges (arrows) represent the relationships between these entities (Chromosome BelongsTo Organism, Gene IstranslatedTo Protein). On this example, genes holA and HP1247 are known to be orthologs (COG1466) but the protein product of HP1247 is not annotated in the sequence databank (RefSeq). The graph suggests to annotate the product of HP1247 as the delta subunit of polymerase III.
More generally, such a network can be modelled as a graph. A graph is defined by two sets (V,E) where V is a set of vertices and E is a set of edges. A vertex represents an object in the network (see Figure 1). An edge connects two vertices and corresponds to a particular relationship in the network (see Figure 1). A graph is said to be directed (resp. undirected) if it is exclusively made of oriented (resp. not oriented) edges. Graphs benefit from efficient algorithms and are widely used in computer science. During the past few years, graph theory has been used in biology for data modelling purpose, especially for molecular interaction databases (e.g. IntAct, [3]) and metabolic pathway databases (see [4] for a review). Graph-based algorithms have also been used to answer various biological questions, such as in the field of protein-protein interactions networks (e.g. [5]) or biochemical networks (see [6] for a recent review). Most of the current solutions are dedicated to restricted set of data and/or particular analyses, and they cannot be easily modified to accommodate new data/methods. Another approach to target data graph analysis in a more general way consists in using a graph database. Significant systems like GOOD [7], Hy+ [8], Gql [9], Hyperlog [10] and the system from Butler et al. [11] provide visual interfaces and pattern-oriented query languages allowing the end-user to answer various biological questions through the use of diagram-based queries. This approach is more intuitive and more generic than the previous ones, it can be applied to various data types, and does not require the design of particular algorithms to answer particular questions. However, current graph database systems have a limited data modelling power since they rely on a flat (i.e. non hierarchical) data model. Graph querying approach could greatly benefits from object-oriented data modelling techniques since they provide a higher level of abstraction (especially through objects inheritance) that is especially well-suited to represent complex biological data. In this context, the Snow system (under development, see [12]) provides an environment dedicated to the representation and analysis of biological networks which is based on an entity-relationship data model.
This work is concerned with the development of GenoLink, a generic software application dedicated to the exploration of graphs, where vertices and edges are enriched with data modelled using an entity-relationship model. GenoLink can be seen either as a generic graph querying and browsing engine or as a dedicated application for biologists. From the first point of view, GenoLink provides a generic graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. It is important to note that the graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, since our primary goal concerns genomic and post-genomic applications, GenoLink is distributed with a default data model for this particular purpose.
System and methods
Overview
The overall architecture of GenoLink, represented on Figure 2 is composed of two main components : the core and the data storage system. The core provides the graph representation of the data on the top of which querying and display operations are performed. It interacts with the storage system through an API based on an entity-relationship model (like UML). This API basically allows data retrieval, creation or modification. The core relies on a simple and generic graph model made of two entities: vertices and edges. In order to link them to actual data, vertices and edges have two attributes: a data identifier (ID) and a data type. The ID is a unique identifier to a piece of data kept in the storage system (e.g. a gene), and the data type identifies the corresponding type for this data. The API is therefore composed of two parts (Figure 2): one to access the data (API-D), and one to access the data model (API-M).
Figure 2. GenoLink overall architecture. The GenoLink core provides the generic graph data structure on the top of which querying and display operations are performed. It is separated from the storage system and interacts with it through an API based on an entity-relationship model. Data can be imported in two ways into the system: 1) through the storage system or through external XML files. (See text for more details).
Accessing the data model has several important consequences to the functionalities of the core. First, the data model can specify that data types are organized into hierarchies (i.e. classes and subclasses in an object-oriented model). In that case, the core engine will retrieve this information (through the API-M) and can further use it in the querying process. For instance, if, during a query, the user requires that a vertex should be of type 'Gene' and if 'ProteinGene' is a subtype of 'Gene', then all data of type 'ProteinGene' should match this vertex as well. A second aspect relates to data consistency. By querying the model (through API-M) the core can easily ensure that a user query is consistent with the data model, for instance that types are connected through the proper relationships. Finally, a last aspect relates to the content of the data itself. A piece of data in the storage system is described by an identifier (the ID) and a set of attributes. For instance a gene may have attributes to describe its name, its description and its length. During a query, some constraints will be ascribed to these attributes (for instance "length > 1000"). Again, by querying the data model, the core is able to control the consistency between the user's constraints and the data model.
In this architecture, any kind of data storage system could, in theory, be used, as long as it can accommodate the API-M and API-D. In practice, we implement GenoLink by using an object-oriented DBMS (OO-DBMS), based on the AROM system [13]. The reason for using an OO-DBMS is that the mapping between the generic graph model and the object model is greatly simplified.
Data connection and data import
There are basically two mechanisms to transfer data sets from external sources into the GenoLink system: data connection and data import.
Data connection is straightforward: when the core is started, it connects trough the API-D to the storage system and constructs a 'shallow graph' representation of this data. We use the term 'shallow graph' to point out that the graph model does only retain in memory the graph topology and the identifiers and data types attached to the vertices and edges, not the whole data set itself. Indeed, when a specific part of data is needed (e.g. the value of some attributes) the core will dynamically request it to the storage system through API-D.
The data connection mode is conceptually simple but has the drawback that all the data should be already available in the storage system. This does not allow a great flexibility for the user to add some specific data. To this purpose, GenoLink provides a data import mechanism. In this mode the data are described in one or more external XML-formatted flat files. Such a file contains the description of a data graph in terms of vertices and edges. Each XML vertex (or edge) should specify a data type and an ID. When loading the file, the core first checks that the provided data type is known (through API-M). Then it checks whether the ID already exists. If it does not, a new piece of data (object) will be created in the storage system (through API-D). The XML vertex (or edge) may also contain attributes. Again, the core checks that each provided attribute is correct for this type and will assign the provided value to it (unless the attribute was already valuated). This mechanism provides a flexible way of instantiating the data into the storage system since several pieces of information pertaining to the same object can be progressively put together by successively loading external files. For instance, genomic information can be first loaded to instantiate genes together with their relationships to an organism, and additional information, such as their homology relationships or their involvement in metabolic processes, can then be added. Of course this integration process relies on using the same identifier to designate the same object in the various files.
In the context of genomic and post-genomic applications, GenoLink is distributed with a set of parsers and XSL transformation sheets to facilitate the construction of these XML files, as described later.
Data Exploration
Exploring a data graph consists in finding vertices or paths between two vertices or, more generally, sub-graphs of particular interest. With currently available applications, this can be done with dedicated graph algorithms (e.g. [14]) or constraint programming systems (e.g. [15]; for a recent review on graph matching, see [16]). However, GenoLink proposes an exploration mechanism based on a graphical 'query/browse' system adapted to data graphs.
In GenoLink, exploring a data graph is done in two steps. First, the user formulates a query on the data graph. The results of such a query are sub-graphs representing portions of the whole data graph of particular interest. Then, the user graphically browses into the whole graph by using these sub-graphs as starting points.
The creation of a query can be achieved in two ways: either using a dedicated graphical user interface, or using a query language (GenoLink Query Language, or GQL). The former does not require any programming skills.
Formally, a GenoLink query is a graph pattern where vertices and edges are made of the data types defined by the data model (Figure 3). These vertices and edges may carry local constraints consisting of algebraic expressions involving the vertex or edge attributes. A query may also define a global constraint consisting in algebraic expressions involving attributes of different vertices or edges. An occurrence of a graph pattern in the data graph is a sub-graph of this data graph where the vertices and the edges fully satisfy the graph pattern constraints: topology, data type (or subtypes) of vertices and edges and constraints on attributes.
Figure 3. Example of a GenoLink query. (a) A simple query represented as a graph pattern. This simple query will retrieve hetero (Name1 != Name2) protein-protein interactions where at least one of the two proteins has an annotated known function (Name !: "hypothetical"). (b) The GQL script describing the same query. GQL reserved keywords are indicated in bold. In the declaration of variable p1, the expression located to the right of the 'where' clause is a local constraint (here: the name must not contain hypothetical). In the declaration of my_query, the expression located to the right of the 'where' clause is the global constraint (here: the two names must be different). (c) Result obtained by executing this query against the data graph shown in Figure 4b. When applied to the entire Helicobatcer pylori strain 26695 data set, this query yields 896 different answers.
In addition to query declaration, GenoLink is also able to compute union, difference or intersection between sub-graphs. A full description of querying and graph operation capabilities of GenoLink are provided with the documentation distributed with the software.
The matching algorithm
The search engine of GenoLink is responsible for searching for all matches of a graph pattern (hereafter called the query graph) against the whole data graph. This graph search problem is related to the sub-graph isomorphism problem, which is known to be NP-complete [17]. One of the most commonly used algorithms to solve that problem is the backtracking algorithm proposed by Ullmann [18]. The algorithm used by GenoLink is inspired from the Ullmann's one but present some slight differences that mostly come from the fact that, in the sub-graph isomorphism problem, one has to compare two graphs of the same kind whereas, in the graph pattern problem, the nature of the vertices and edges is not strictly the same between the graph pattern and the data graph. Nevertheless, due to the close similarities between the two problems we (abusively) state that a result sub-graph is 'isomorphic' to the pattern graph.
GenoLink relies on a depth-first search (DFS) approach which is guaranteed to find all the ways a query graph matches the data graph. Local and global constraints are used in the algorithm in order to prune the search space. More precisely, the algorithm uses a two-steps process. First, it uses the data types declared in the vertices and edges of the query graph to find out which one returns the smallest number of vertex/edge instances from the data graph. That particular vertex or edge will be used as a seed for the DFS exploration. The DFS proceeds through the data graph, using the query graph as a guide, and will progressively add vertices and edges into the nascent sub-graph. At each step, data types and local constraints are checked to prune the search. Finally, each time a sub-graph has been completed, the global constraint is applied.
At the end of the DFS, an additional filtering step may optionally be added in order to discard redundant result graphs (such redundancies may arise from symmetrical relationships). This step is similar to the use of a distinct clause in SQL queries.
Implementation
Default DBMS
As mentioned earlier, GenoLink comes with a default storage system implemented using the AROM (Associating Relations and Objects for Modelling, [13]) Java-based system. AROM is an entity-relationship knowledge modelling and management system freely available (see [19]). It provides data management services: formal description of the data model, creation and modification of instances and data persistence. It has a richer metamodel than GenoLink that makes it easy to connect to the API. On the other hand, it has the drawback of keeping all the instances in memory that limits its usage to the available RAM (see the Results section for order of magnitude of the RAM required). In the future we plan to extend GenoLink to other OO-DBMS, to XML storage systems or to Relational DBMS. The later case is the most difficult since the metamodels are quite different and will probably require a simplification and refactoring of the API.
Default data model
GenoLink comes with a default data model (implemented in AROM) targeted at representing microbial genomics and functional genomic data. The data model comprises 25 classes and 28 associations. A UML representation of the main classes and associations is depicted on Figure 4. There are basically three main categories of classes: one for representing nucleic biological entities (e.g. Gene); one for representing proteic biological entities (e.g. Polypeptide), the later being typically linked to the former by the 'isCodingFor' association. The last category relates to sets of entities like functional classifications. A typical example is a gene orthology classification (like COG) or the EC number classification for proteins. Additional specific associations allow representing the results of particular experiments. A typical example, depicted on Figure 4, is the 'HasPhysicalInteractionWith' association between peptidic entities which allows representing the results of protein-protein interaction experiments.
Figure 4. GenoLink default data model and example of a data graph. (a) Excerpt of the UML diagram describing the main classes and associations of the default data model provided with GenoLink. Classes are indicated by boxes (white arrows indicate inheritance) and association names are indicated in italics. For clarity, class and association attributes have not been indicated (an example is shown to the right part of the figure, with the Polypeptide class). The complete diagram is distributed with the GenoLink software documentation. (b) An example of data graph based on this data model. It represents a portion of the genome of the bacterium Helicobacter pylori strain 26695 (NCBI RefSeq entry no. NC000915); IRO, ILO, ICF, IIG, HPA, CD and HPIW stand for edges that are instances of associations: IsRepliconOf, IsLocatedOn, IsCodingFor, IsInGeneOrtholog, HasPolypeptideAnnotation, ContainsDomain and HasPhysicalInteractionWith. The entire data graph for this genome actually contains 3197 vertices (1 Organism, 1 Replicon, 1576 ProteinGenes, 43 RNAGenes, 1576 Polypeptides) and 4664 edges (1 IsRepliconOf, 1619 IsLocatedOn, 1576 IsCodingFor and 1468 HasPhysicalInteractionWith). The dashed box displays the attributes for the Polypeptide ureB. COG, EC and IPR data are from the COG database [21], the Enzyme Commission database [24], and the InterPro database [23], respectively. Protein-protein interactions are public data available from Hybrigenics [30] and distributed with GenoLink.
The default data model can be easily modified or, even, completely replaced by another one, in order to accommodate other experiments or different biological problems. This is done by editing the AROM model text file. Thanks to the API-M, the GenoLink core will dynamically adapt to the modified or new data model.
Default data import
Together with the default data model, GenoLink provides a set of default data parsers for popular data formats: the genomes from the RefSeq division of GenBank [20], the NCBI COG database of pre-computed clusters of orthologous genes and its functional classification [21], the Gene Ontology (GO) classification [22], the InterPro domains database [23], the Enzyme Commission (EC) classification [24], and protein-protein interactions formatted using HUPO PSI-MI [3].
The purpose of these parsers is to produce (or transform) files coming from the above mentioned data bases into GenoLink XML-formatted files. These files are then loaded on the fly by the XML import module as previously described. Of course these XML files fit to the default data model. If the user changes this model, then the parsers should be modify accordingly.
User interfaces
GenoLink comes with various viewers/editors, namely the KB Rider, the Annotator, the Query Builder, the Table Rider and the Graph Rider.
The KB Rider is responsible for displaying the data model. By using the API-M it allows to browse the classes and associations that have been defined in the model. In a similar way, the Annotator allows to browse and edit the data actually attached to vertices and edges.
The Query Builder allows to graphically create a query graph (i.e. without knowledge of the GQL language). A typical screenshot is displayed on Figure 5. As shown in Figure 5a, the user can compose the query graph by selecting vertices (and edges) in a window (right part of the figure). Clicking on a vertex (or edge) will call the constraint editor as shown on Figure 5b, allowing to add an algebraic constraint on the corresponding object.
Figure 5. The Query Builder: a graphical user interface to create a query. (a) Main window. This snapshot shows the interactive construction of query Q7 presented in Table 1 [see 1]. The left panel displays the graph pattern being constructed. The right panel displays either the hierarchy of classes or the hierarchy of associations of the data model. Here the user is adding an association therefore the hierarchy of associations is shown. The associations with non empty set of instances are marked "V". (b) Clicking on a vertex or edge will popup this constraint editor to add an algebraic constraint on the corresponding object. Here the name of the organism (represented by vertex v2) should match "coli".
Once a query has been composed, the query engine can be launched and the sub-graph results can be further explored by using the Table and the Graph Riders. The Table Rider provides a tabular view of all the results. To this purpose, each sub-graph is linearized and associated to a line in the table. The columns correspond to the attributes of vertices and edges (Figure 6). The Table Rider therefore provides an overall view of the results and allows to select interesting lines (i.e. sub-graphs). Once a line is selected, the Graph Rider provides a graphic view of the corresponding sub-graph (Figure 7) and allows to browse the whole data graph by exploring the neighbours of displayed vertices.
Figure 6. The Table Rider: a graphical interface to display the query results in a tabular form. The results of the execution of query in Figure 5 are displayed in a tabular form. Each row of the table corresponds to a result sub-graph. Each column's header contains two lines: the first one indicates the label of a vertex from the query graph (see Figure 5); the second line indicates the name of an attribute of this vertex (the user can select which attributes to display: in this example only the "Name" attributes have been selected).
Figure 7. The Graph Rider: a graphical interface to display the query results in a graph form. By selecting a line in the Table Rider (Figure 6), the user can display the actual sub-graph associated to it. This snapshot shows an example of result sub-graph corresponding to the Query Q7 (Table 1 [see 1] and Figure 5). The edge linking the two H. pylori Polypeptides corresponds to a physical interaction (HPIW). The red crosshair on the top-right of some vertices denotes that they are linked to some others that are not currently shown. These vertices may therefore be further expanded to gain more information about the full data graph. In this example, this operation has been performed on vertices holA and holB (from E. coli) in order to display the corresponding Polypeptides (DNA polymerase III) that were not part of the query (see Figure 5).
Core API and tasks
Besides the graphical user interface, all operations of the GenoLink Core, such as graph creation, data import, graph querying and display, can be executed and controlled programmatically through a Java Core API. User-provided Java code can be dynamically loaded and executed in the system (this functionality is provided by an extension of the AROM system called AROM Tasks). This allows the user having some programming skills to design her/his own tasks to perform some specialized work. The core API and several tasks examples are distributed with the software's documentation.
Implementation
GenoLink, like all modules of the Genostar platform, is written in Java. It uses standard Java libraries such as Xerces (XML parser, [25]) and Xalan (extensible style sheet transformations (XSLT) engine [26]) from the Apache Software Foundation, Castor (Java to XML binding, [27]) from "Exolab.org" and GNU RegExp (regular expression pattern matching engine, [28]) from "Castor.org". The AROM task interpreter is built upon Beanshell [29]. All graphical user interfaces are written with the Java Swing library.
Results and discussion
We now illustrate the querying capabilities of the system by investigating the functions of genes and proteins from bacteria Escherichia coli and Helicobacter pylori. To this purpose, we imported the following data: the complete genomes of the two bacteria (RefSeq entries NC000913 and NC000915) along with the annotations coming from COG [21], InterPro [23] and Enzyme Classification data [24]. The resulting data graph contains 21109 objects (proteins, genes, organisms, chromosomes, clusters of orthologous genes, etc.) linked together through 58064 relations. It takes about 5 minutes for GenoLink to read and to integrate the data into a single data graph occupying around 90 Mo in main memory (a data graph can be saved on disk for later reuse. In this example, it takes 30 seconds to reload the data graph from the saved binary file, which is 10 Mo in size).
Table 1 [see 1] displays several examples of queries addressing various biological questions in this context.
Additional File 1. GenoLink query graph examples. Each row corresponds to a different query (from simple to more sophisticated ones). The Query column gives an informal statement of the query, the Query-Graph column displays the corresponding graph pattern, that has to be constructed in the Query Builder (Figure 5). The Results column indicates the number of distinct results obtained (see text for information about the origin of data). The Time column indicates the execution time (in seconds). In the sake of clarity, the following code as been used to denote the type of edges: ILO for IsLocatedOn, IRO for IsRepliconOf, ICF for IsCodingFor, HPA for HasPolypeptideAnnotation, IIG for IsInGeneOrtholog, CD for ContainsDomain and HPIW for HasPhysicalInteractionWith. When applicable, constraints are displayed in italics under the concerned vertex or edge.
Format: PDF Size: 27KB Download file
This file can be viewed with: Adobe Acrobat Reader
Query Q1 is a very simple example showing how to retrieve all CDS from E. coli. The constraint on the Organism reads as 'the Name attributes matches "coli"' and is indicated in italics below the Organism vertex.
Query Q2 illustrates how to search for E. coli 'hypothetical' proteins that are annotated with the Enzyme Commission database. When this query is run against the complete data graph, 94 'hypothetical' proteins are found that are annotated with an EC number. Now, it is worth noting that the same query executed against a data graph containing only the E. coli RefSeq genome does not return any result. The difference illustrates the data integration process: the RefSeq E. coli genome has been dynamically augmented with new annotations (i.e. links between proteins and EC numbers) when we imported the EC database.
GenoLink can be used to refine a query, depending upon the results of a previous one. As an example, query Q3 retrieves all pairs of orthologous genes (according to the COG database) between H. pylori and E. coli. Query Q4 refines the previous one by restricting to genes coding for 'hypothetical' proteins.
Query Q5 illustrates how to retrieve all pairs of genes between H. pylori and E. coli encoding for proteins having a common InterPro domain.
Query Q6 shows how it is possible to handle negation. In this example we are interested in finding genes with no (COG) orthologs between the two species; by extension, we could suspect this genes are specific to each organism. To this purpose, GQL proposes a 'neighbours' operator. This operator explores the immediate neighbourhood of a vertex in a data graph and counts the number of vertices of a given type that are connected to it. In query Q6 that operator is used as follows: when the query engine examines vertex of type ProteinGene, it will count how many GeneOrtholog vertices are linked to that ProteinGene and will retain this vertex only if this number is 0 (therefore the ProteinGene has no orthologs).
Query Q7 gives an example of how some information can be inferred from one organism to the other. In this example we would like to infer unknown protein-protein interactions into E. coli from already known interactions in H. pylori and gene orthology relationships. To this purpose, we first load the complete protein-protein interactions map from H. pylori [30]. Then, we built up query Q7 under the assumption that if it exists an interaction between two proteins in H. pylori, and if these proteins are encoded by genes having (COG) orthologs in E. coli, then we may hypothesize that these E. coli proteins could interact as well. In this example, this yields 457 different answers, one of them is displayed in Figure 7. For this kind of query, the Table Rider (see section User interfaces) proved to be very useful since it provides a synthetic view allowing for a quick visual inspection of the 457 couples of possibly interacting proteins (Figure 6).
Conclusion
GenoLink is a new software platform adding to existing DBMS new functionalities dedicated to the querying and exploration of data graphs. GenoLink handles graphs where vertices and edges are enriched with data modelled using an entity-relationship model. The platform provides the biologists with a rich visual environment to graphically explore genomic and post-genomic data, without prior knowledge of any programming or database querying languages. GenoLink provides the bioinformaticians with more advanced features such as a generic data graph exploration tool able to accommodate user-provided data models, a query language well-adapted to query graphs and a programming API.
Availability and requirements
GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at academy@genostar.com. A commercial licence form can be obtained for profit company at info@genostar.com. The distributions have been successfully tested on computers running RedHat Linux, Windows 2000/XP or MacOS X. The GenoLink distribution also incorporates a complete user's guide including a beginner's tutorial.
Authors' contributions
PD and JW conceived the software architecture, designed the graph query language, the graph pattern matching algorithm and the whole set of graphical interfaces. PD managed the overall project, wrote most of the software code and documentation, and wrote the manuscript. LL and JLD participated in coding the graphical interfaces. AM and PD encoded the graph library used by GenoLink. AV and JW initiated the project in the Genostar consortium. All authors participated in the development of the data model used to investigate the functions of genes and proteins, in testing the software and in editing the manuscript.
Acknowledgements
The development of GenoLink is a research and development work from the Genostar Consortium http://www.genostar.org. Created by the end of 1999, and headed by François Rechenmann (INRIA Rhône-Alpes, Grenoble), the Consortium aims at developing Genostar, a bioinformatics platform for exploratory genomics. The Consortium brings together four partners: two biotech companies, Hybrigenics (Paris) and Genome Express (Grenoble), and two research institutes, the Pasteur Institute (Paris) and the INRIA Rhône-Alpes (Grenoble). This work has been supported by the French Agency for Innovation (ANVAR) and the French Ministry of Research through the program 'Genopole' of the 'Direction de la Recherche' and the program 'GenHomme' of the 'Direction de la Technologie'. We thank François Rechenmann and Jacques Nicolas for reading the manuscript and for helpful discussions.
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Research article
Pathogen-induced Caenorhabditis elegans developmental plasticity has a hormetic effect on the resistance to biotic and abiotic stresses
Magali Leroy, Thomas Mosser, Xavier Manière, Diana F Alvarez and Ivan Matic*
Author Affiliations
Laboratory of Evolutive, Medical and Molecular Genetics, Inserm U1001, Université Paris Descartes, Sorbonne Paris Cité, Faculté De Médecine Paris Descartes, 156 rue de Vaugirard, Paris, 75730 cedex 15, France
For all author emails, please log on.
BMC Evolutionary Biology 2012, 12:187 doi:10.1186/1471-2148-12-187
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2148/12/187
Received:8 May 2012
Accepted:17 September 2012
Published:21 September 2012
© 2012 Leroy 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
Phenotypic plasticity, i.e. the capacity to change the phenotype in response to changes in the environment without alteration of the genotype, is important for coping with unstable environments. In spite of the ample evidence that microorganisms are a major environmental component playing a significant role in eukaryotic organisms health and disease, there is not much information about the effect of microorganism-induced developmental phenotypic plasticity on adult animals’ stress resistance and longevity.
Results
We examined the consequences of development of Caenorhabditis elegans larvae fed with different bacterial strains on stress resistance and lifespan of adult nematodes. Bacterial strains used in this study were either pathogenic or innocuous to nematodes. Exposure to the pathogen during development did not affect larval survival. However, the development of nematodes on the pathogenic bacterial strains increased lifespan of adult nematodes exposed to the same or a different pathogen. A longer nematode lifespan, developed on pathogens and exposed to pathogens as adults, did not result from an enhanced capacity to kill bacteria, but is likely due to an increased tolerance to the damage inflicted by the pathogenic bacteria. We observed that adult nematodes developed on a pathogen induce higher level of expression of the hsp-16.2 gene and have higher resistance to heat shock than nematodes developed on an innocuous strain. Therefore, the increased resistance to pathogens could be, at least partially, due to the early induction of the heat shock response in nematodes developed on pathogens. The lifespan increase is controlled by the DBL-1 transforming growth factor beta-like, DAF-2/DAF-16 insulin-like, and p38 MAP kinase pathways. Therefore, the observed modulation of adult nematode lifespans by developmental exposure to a pathogen is likely a genetically controlled response.
Conclusions
Our study shows that development on pathogens has a hormetic effect on adult nematodes, as it results in increased resistance to different pathogens and to heat shock. Such developmental plasticity of C. elegans nematodes, which are self-fertilizing homozygous animals producing offspring with negligible genetic variation, could increase the probability of survival in changing environments.
Keywords:
Caenorhabditis elegans; Development; Lifespan; Stress resistance; Hormesis; Pathogens
Background
Multicellular organisms have evolve powerful controlling mechanisms to cope with diverse perturbations in order to assure phenotypically quasi-invariant developmental outcome [1]. However, development can be influenced by environmental stimuli, e.g., temperature, nutrients and oxygen availability, and the presence of predators or parasites. The exposure to stresses during development can be deleterious or beneficial to the adults. For example, changes during development influence adulthood disease propensity in humans [2]. The adult Caenorhabditis elegans that transiently passed through the stress-induced dauer larval stage exhibit an extended lifespan compared to animals with normal development [3]. Environmental conditions, i.e., temperature, and oxygen and carbon dioxide concentrations [4,5], were shown to direct the development of nematode Strongyloides ratti to distinct parasitic or free-living adults whose aging rates can differ by 30-fold [6]. Biotic factors can also induce dramatic developmental alterations. For example, in response to waterborne cues from predators, some Daphnia species grow protective helmets [7]. Microorganisms, which are a major environmental component, also have an important impact on development. The effect of microorganisms on development was established by comparing axenic animals against animals colonized with microbes. In fruit fly and zebrafish, axenic development can result in slower development, reduced fecundity, and/or early death [8,9]. Axenic C. elegans have a slower development, reduced fecundity, and increased lifespan [10]. In mammals, microorganisms can affect the maturation of the mucosal immune system [11], modulate the proliferation and the differentiation of intestinal epithelia [12], regulate angiogenesis [13], and play a key role in the extraction and the processing of nutrients [14].
Microorganisms are classified as commensals when they are innocuous and/or beneficial for the host, and pathogens when they are harmful to the host [15]. It should be noted that pathogens most frequently do not kill their hosts, but decrease host fitness and increase host susceptibility to environmental challenges. Adult hosts mount different responses to various types of microorganisms, which have a profound effect on the hosts themselves. While it is clear that presence or absence of microorganisms can have an important impact on development, how exposure to different types of microorganism, i.e. innocuous and pathogenic, during development affects adult animals health, stress resistance and longevity is unknown. Thus, in this study we examined the consequences of exposure of C. elegans nematodes during development to different bacterial strains. C. elegans was chosen because it is a well-studied animal model for aging, development, and host-pathogen interactions, and isogenic populations can be generated and maintained. The bacterium Escherichia coli was chosen because it is a well-studied model organism and a species with a wide virulence spectrum, ranging from innocuous to highly pathogenic in diverse hosts. It is also of particular importance that the standard laboratory food for C. elegans is one E. coli strain, OP50 [16,17]. Survival/longevity of nematodes fed with OP50 is considered as the baseline for all C. elegans studies. E. coli strains are among the first colonizers of the intestinal tract of newborn warm-blooded animals. E. coli strains are mainly harmless commensals, but some strains are able to cause intestinal and extra-intestinal diseases, which by their frequency and potential severity cause considerable morbidity and significant health-care costs [18]. We previously demonstrated that E. coli pathogenic strains can significantly reduce the lifespan of the adult C. elegans[19,20], and that E. coli pathogenicity factors are responsible for the observed lifespan reduction.
For this study, C. elegans nematodes were fed on different bacterial strains during development and then with the same or different bacteria as adults. We found that nematodes developed on a pathogen lived longer when exposed to pathogens as adults than nematodes that were developed on an innocuous strain. Some of the findings observed with the pathogenic E. coli were confirmed using a second pathogen, a Gram-positive Enterococcus faecalis. The observed increase in nematode lifespans is controlled by the DBL-1 transforming growth factor beta-like, DAF-2/DAF-16 insulin-like signaling, and partially by the PMK-1 p38 MAP kinase pathways. Developmental exposure to one pathogen increases resistance of adult nematodes to the same and other pathogens, as well as to heat shock. Hence, development on pathogens has a hormetic effect on adult nematodes. Hormesis is a response of organisms to low doses of a damaging environmental factor resulting in resistance to higher doses of the same, but also to other stressful environmental factors [21,22]. The possible consequences of the observed hormetic effect in natural environments are also discussed.
Results
For this study, we used the reference OP50 and pathogenic 536 E. coli strains, as well as Enterococcus faecalis OG1RF strain. The innocuity of the OP50 strain was attested by observation that the mean lifespan of the C. elegans fer-15 nematodes was the same on the live and UV-killed OP50 bacteria [20]. fer-15 is a derivative of the C. elegans N2 strain, which we used in the present study. Strain 536 is an uropathogenic E. coli isolated from a patient with acute pyelonephritis [23]. Pathogenicity of the 536 strain was previously demonstrated in the mice sepsis model and in C. elegans[19]. Adult fer-15 nematodes exposed to strain 536 have a 50% shorter mean lifespan compared to nematodes exposed to the OP50 strain [19]. Deletion of pathogenicity islands II and III significantly reduces the pathogenicity of strain 536 in C. elegans fer-15[19], while it does not reduce the bacterial growth rates nor resistance to biologically relevant stressors [24]. This shows that strain 536 reduces C. elegans lifespan because of its pathogenicity factors and not because it does not provide an adequate food source.
N2 nematodes were developed on one bacterial strain and late L4 stage nematodes were subsequently maintained on the same strain or transferred to a different one. For this reason, the designation of each experimental condition contains: (i) the name of the strain on which larvae were developed and (ii) the name of the strain to which adult nematodes were exposed. For example, OP50/536 indicates that nematodes were developed on OP50 and then transferred onto strain 536. All experiments were performed at 25°C.
Lifespan of nematode populations developed on different bacterial strains
First, we compared the developmental success, defined as the fraction of nematodes reaching adulthood from an initial number of eggs, for C. elegans fed either on the OP50 or on the pathogenic 536 strain. We observed no significant difference (unpaired t-test, p > 0.7549) in the fraction of nematodes that reached adulthood between these two experimental conditions (mean ± s.e.m.: 91.6% ± 1.7% developmental success on OP50, n = 263; 92.3% ± 1.6% on 536, n = 262). Therefore, it can be concluded that nematode development is robust and that larvae survival is not affected by the pathogen.
Second, we investigated the lifespan of adult nematodes on the innocuous OP50 strain after they were developed on OP50 or on the pathogenic 536 strain. For these experiments, we eliminated bacteria from the L4 nematodes by antibiotic treatment and then transferred them on OP50 strain. No difference (Gehan-Breslow-Wilcoxon Test (GBWT), p = 0.7334) in lifespan was observed between OP50/OP50 and 536/OP50 nematodes (Figure 1A). These results suggest that development on pathogens produce healthy adult nematodes that, when exposed to non-stressful conditions, have identical lifespan to that of nematodes exposed to the innocuous bacterial strain throughout life.
Figure 1 . Survival of C. elegans developed on different E. coli strains. (A) Survival of N2 nematodes to the innocuous E. coli OP50 strain following development on the pathogenic 536 strain (536/OP50 n = 93 and OP50/OP50 n = 90, independent replicates N = 3). There is no difference in nematodes survival despite the difference in developmental condition indicating that development on the pathogenic 536 strain has no deleterious effect on survival. (B) Survival of N2 nematodes to E. coli 536 strain following development on the pathogenic 536 strain (536/536 n = 80 and OP50/536 n = 80, N = 7). N2 nematodes had a significantly greater survival on strain 536 following development on 536 than on OP50 strains. (C) Survival of N2 nematodes to E. faecalis OG1RF strain following development on E. faecalis OG1RF (OG1RF/OG1RF n = 86, OP50/OG1RF n = 81, N = 3). As seen with E. coli 536, development on E. faecalis OG1RF prior to adults exposure to the same strain significantly increases nematodes survival compared to those developed on OP50 strain. (D) Survival of N2 nematodes to E. faecalis OG1RF strain following development on E. coli 536 (536/OG1RF n = 100 and OP50/OG1RF n = 104, N = 3). Development on E. coli 536 significantly increases survival to E. faecalis OG1RF strain in a similar manner as development on E. faecalis OG1RF, and is thus not due to adaptation to one bacterial strain during nematode development. Graphed: ns: not significant, *: p < 0.05, **: p < 0.01, ***: p < 0.001, ****: p < 0.0001.
Third, we investigated the lifespan of adult nematodes on the pathogenic 536 strain after they were developed on OP50 or on the 536 strain. As shown in Figure 1B, the exposure of nematodes to the pathogen during development increased median lifespan (TD50) by 50% (OP50/536 TD50 = 4 days and 536/536 TD50 = 6 days, GBWT, p < 0.0001). The increase of survival was also significant during the reproductive period (days 1 to 4) (OP50/536 survival at day 4 SD4 = 35.8% ± 5.5% to 536/536 SD4 = 67.9% ± 5.3%, chi-square test, p = 1.18×10-7). The beneficial effect of developmental exposure to pathogen on the adult nematodes’ lifespan was also observed with Gram-positive Enterococcus faecalis OG1RF strain, i.e., OG1RF/OG1RF nematodes had significantly increased (GBWT, p = 0.0007) median lifespan compared to OP50/OG1RF nematodes (Figure 1C).
Observed lifespan extension for nematodes developed and maintained through adulthood on pathogens could be explained by adaptation to a particular type of stress encountered during development, which renders adult nematodes more resistant to the same stress, i.e., exposure to the pathogenic 536 strain. In order to verify this possibility, we developed nematodes on E. coli 536 strain, eliminated the bacteria from the L4 nematodes by antibiotic treatment and transferred them on the E. faecalis OG1RF strain. Development on E. coli 536 strain significantly (GBWT, p < 0.0001) increased lifespan of adults exposed to the E. faecalis OG1RF strain (Figure 1D) to the same extent as development on OG1RF itself did (Figure 1C). These results show that the beneficial effect of developmental exposure to pathogens on nematode lifespan was not due to adaptation to one particular type of strain or stress, but also provides protection against other bacterial strains. Developmental exposure to Gram-positive and -negative bacterial strains has a cross protective effect, indicating that the recognition of membrane lipopolysaccharides, which are present at the surface of Gram-negative but not of the Gram-positive bacteria, is not involved in this phenomenon.
C. elegans signaling pathways involved in lifespan extension following development on pathogens
We examined the role of different immune signaling pathways in the nematode lifespan extension following development on pathogens. We first evaluated if two signaling pathways implicated in C. elegans development and in adult immunity are involved in the observed development-induced modulation of the adult lifespan: the DAF-2/DAF-16 insulin-like pathway [25] and the DBL-1 transforming growth factor ß-like (TGFß-like) pathway [26]. These two signaling pathways function from the first larval stages of nematode development, are involved in the signaling and regulation of the immune response to pathogens and in stress responses to environmental factors in adults [27]. When DAF-2/DAF-16 insulin-like or TGFß-like pathways were inactivated, there were no significant lifespan differences between adult populations exposed to the pathogen after development on OP50 or on 536 (Figure 2A-C, GBWT, daf-16 mutants p = 0.9368 and p = 0.4082 for alleles mu86 and mgDf50, respectively, dbl-1 mutant p = 0.1985). We also tested the implication of another innate immunity pathway, the p38 MAP kinase pathway via the pmk-1 mutant [28]. The difference in lifespan of the pmk-1 nematodes between OP50/536 and 536/536 conditions was reduced, but still significantly different (GBWT, p = 0.0106, Figure 2D). The mean lifespan of pmk-1 nematodes was 25% shorter compared to the two other innate immunity pathways mutants, which indicates that the lack of differential survival of daf-16 and dbl-1 mutants was not due to the saturation of our assay with maximal killing. Thus, it can be concluded that the observed reduction of the mortality of adult N2 nematodes (Figure 1B) is mainly modulated by the DAF-2/DAF-16 insulin-like pathway and TGFß-like pathway. Therefore, the observed modulation of adult nematodes lifespan by developmental exposure to pathogens is likely a genetically controlled nematode response.
Figure 2 . C. elegans signaling pathways involved in developmental modulation of longevity. Survival of C. elegans mutants to E. coli 536 pathogen following development on strains 536 (536/536) or OP50 (OP50/536) and life through OP50 control (OP50/OP50). (A &B) C. elegans daf-16 mutants allele mu86 (536/536 n = 80, OP50/536 n = 80, and OP50/OP50 n = 80, independent repeats N = 4) and mgDf50 (536/536 n = 65, OP50/536 n = 56, and OP50/OP50 n = 61, N = 3), (C) C. elegans dbl-1 mutant (536/536 n = 127, OP50/536 n = 124, and OP50/OP50 n = 88, N = 4), and (D) C. elegans pmk-1 mutant (536/536 n = 80, OP50/536 n = 78, and OP50/OP50 n = 77, N = 8). No differential survival of daf-16 and dbl-1 nematodes to E. coli 536 based on developmental conditions was observed, while a small but statistically significant difference in survival to E. coli 536 strain was observed for C. elegans pmk-1 mutant depending on developmental conditions. Graphed: ns: not significant, *: p < 0.05, **: p < 0.01, ***: p < 0.001, ****: p < 0.0001.
C. elegans resistance to heat shock following development on pathogens
Induction of the heat shock response in C. elegans limits the accumulation of damaged proteins, increases stress resistance, resistance to pathogens, and lifespan [29-31]. It was also reported that the capacity to induce the heat shock response early in life correlates positively with the nematode life expectancy [32]. For these reasons, we tested whether development on pathogens (i) increases the capacity of adult nematodes to resist heat shock, and (ii) if it results in the induction of the heat shock response.
First, we found that nematodes developed on pathogens resist significantly (unpaired t-test, p = 0.0009) better than nematodes developed on OP50 to a 10 h heat shock at 35°C (Figure 3A). Second, we measured the induction of the heat shock response in these two groups of nematodes. For this, we used a C. elegans strain carrying a fusion of a gene coding for the Green Fluorescent Protein (GFP) with the hsp-16.2 gene promoter. The expression of hsp-16.2 gene, which codes for a chaperon, is regulated by the Heat Shock Factor 1 (HSF-1) and DAF-16. We observed that development on the 536 strain, compared to development on OP50, induced a significant (unpaired t-test, p = 0.0138) upregulation of hsp-16.2 expression in L4 nematodes (Figure 3B). The observed difference was also highly significant (Tukey’s Multiple Comparison Test (TMCT), p < 0.001) in 2-day old nematodes (Figure 3C). The difference in hsp-16.2 induction cannot be explained by the amount of live bacteria in the intestinal tract, as there was no significant difference in the number of live bacteria in the intestine of 2-day old nematodes exposed to the 536 strain whether they were developed on OP50 or 536 (Figure 3D). Therefore, the induction of hsp-16.2 depends on developmental and adulthood conditions, and correlates with the resistance to heath shock and the lifespan extension of adult nematodes exposed to pathogens, relative to the nematodes developed on the OP50 strain.
Figure 3 . Heat-shock resistance and hsp-16.2 induction in C. elegans developed on different E. coli strains. (A) Survival proportion of nematodes developed on OP50 or 536 E. coli strains after a 10 h heat shock at 35°C. Following development on strain 536, 20% more nematodes survived the 10 h heat shock treatment compared to nematodes developed on strain OP50. (B) Level of fluorescence of the hsp-16.2::GFP reporter in young adult nematodes (day 0) developed on E. coli 536 pathogen (n=75) or OP50 strain (n=75). (C) Two day-old adult nematodes exposed to the 536 pathogenic strain had a higher level of induction of hsp-16.2 following development on strain 536 (536/536 n=150) than those developed on strain OP50 (OP50/536 n=88) and those maintained life through on strain OP50 (OP50/OP50 n=98). (D) Quantity of live bacterial cells in the intestinal tract of 2-day old nematodes exposed to E. coli 536 following development on strains 536 (536/536 n=5) or OP50 (OP50/536 n=5) and controls maintained life through on strain OP50 (OP50/OP50 n=5). The observed difference in the level of hsp-16.2 induction cannot be correlated with the amount of live bacteria colonizing the nematode intestinal tracts as there was no significant difference in the mean bacterial density in the intestine of 2-day old nematodes exposed to E. coli 536 independently of whether they were developed on strains OP50 or 536. Graphed: mean ± s.e.m., *: p<0.05, **: p<0.01, ***: p<0.001.
Discussion
We showed that the development of nematodes on bacterial pathogens increases the lifespan of adult nematodes exposed to the same or different pathogens, and increases resistance of nematodes to heat shock. It is important to note that such increased robustness of nematodes developed on pathogens is not due to the culling of weak individuals from the population, as the same fraction of nematode larvae reached adulthood following development on pathogenic and innocuous strains. In addition, there was no difference in the lifespan of adult nematodes on the innocuous OP50 strain after they developed on OP50 or on the pathogenic 536 strain, which indicates that development on a pathogen does not damage larvae.
Hosts can defend themselves from pathogens using a variety of strategies [33]. The avoidance strategy minimizes the risk of infection with pathogen and economizes the nematode’s resources, which otherwise would be used for the activation of its defenses [34]. The avoidance strategy requires that host first detects pathogens. In nature, C. elegans is predominantly found in decaying organic matter where it feeds on microorganisms, which can be good or harmful food [35]. C. elegans possesses a complex chemosensory neuronal system that allows discrimination between these two groups of microorganisms based on the detection of a number of volatile odorant and water-soluble compounds [36-38]. For example, nematodes are repulsed by a cyclic lipodepsipentapeptide produced by Serratia marcescens, a bacterium that is harmful to nematodes [39]. C. elegans also has the capacity to identify pathogens and harmful xenobiotics by monitoring its essential cellular activities, such as protein translation or oxidative respiration. Perturbations of these functions induce aversion behavior and defense mechanisms [37]. We did not study the molecular basis of the discrimination between different bacterial strains by nematodes. However, the fact that the observed hormetic effect is not bacterial species specific suggests that it is more likely induced by the nematode surveillance of its own essential cellular functions, rather than by recognition of the specific compounds produced by bacteria.
Nematodes also have a capacity to memorize, into adulthood, environmental cues encountered during early life [40]. Can avoidance behavior based on memory of past conditions contribute to the longer lifespan of nematodes developed on a pathogen and exposed to the same pathogen as adults, compared to nematodes developed on an innocuous strain and exposed to pathogens as adults? This is probably not the case in our study because independently of the developmental conditions, nematodes have the same amount of the 536 pathogenic bacteria in their intestine, which indicates that 536/536 nematodes do not live longer than OP50/536 nematodes because they avoid pathogens and eat less. The fact that the intestinal pathogen burden is independent of developmental conditions also suggests that, in our case, the longer lifespan of nematodes developed on, and then exposed to, pathogens as adults were not the result of enhanced capacity to kill bacteria, but likely due to the increased tolerance to the damages inflicted by pathogenic bacteria. Tolerance is defined as the ability to limit negative impact on hosts by increasing cellular repair and maintenance capacity, without affecting pathogen burden [33,41]. Increased investment in repair and maintenance function often comes with a cost for the host. In our study there is no evidence of such cost as, nematodes developed on pathogen and then transferred to non-stressful conditions, i.e., innocuous bacterial strain, have lifespans identical to the lifespan of nematodes exposed to the innocuous bacterial strain throughout life. However, it cannot be excluded that the cost of tolerance becomes evident under experimental conditions that are closer to those found in natural environments.
From a molecular perspective, increased tolerance to pathogens of the nematodes developed on pathogens could be, at least partially, due to the induction of the heat shock response. We observed that adult nematodes developed on pathogens induce higher levels of expression of the hsp-16.2 gene than nematodes developed on an innocuous strain. The hsp-16.2 gene expression was shown to be regulated by DAF-16 and HSF-1 transcription factors in the N2 nematodes [42-44]. It was previously observed that the expression level of hsp-16.2 in individual nematodes exposed to a mild heat shock was predictive both of thermotolerance and lifespan [32,45]. Overproduction of HSP-16.2 also suppresses beta-amyloid peptide toxicity [46]. There are many other examples of the correlation between increased stress resistance and longevity in nematodes [47]. For example, the DAF-2/DAF-16 insulin-like pathway mediates stress resistance, longevity and pathogen resistance in C. elegans[48]. This supports our hypothesis that the nematode’s response to developmental conditions observed in this study is genetically controlled by the DAF-2/DAF-16 insulin-like pathway. However, it was reported that daf-16 and dbl-1 mutants have an increased amount of live bacteria in their intestine compared to N2 nematodes when maintained on E. coli OP50 [49]. On the contrary, a pmk-1 mutant has similar amount of live bacteria in its intestine when compared to that of N2 nematodes. Thus, the absence of increased survival for daf-16 and dbl-1 mutants could also be due to an increased intestinal bacterial load following development on the pathogen, counterbalancing the beneficial effect of early pathogen exposure. Further investigation of these signaling pathways will be necessary to determine the direct or indirect involvement of these pathways in the control of nematode response to developmental exposure to bacterial pathogens.
Observed effect of developmental conditions on the adult lifespan and stress resistance could be described as hormetic. Hormetic response in C. elegans, i.e., increased stress resistance and/or increased lifespan, was shown to be induced with sub-lethal abiotic stresses, like oxidative and thermal stress [47,50]. However, all forms of stress, e.g. UV or ionizing radiation, do not produce hormetic effects in C. elegans[51]. Our study shows that some biotic factors, i.e., bacterial pathogens, can be added to the list of known hormetic stressors. One possible explanation for the hormetic effects of exposure to low levels of stress is that the level of response to stress is more than necessary to repair the damage caused, thus increasing the nematode defense capacity and allowing tolerance to future stresses. A particularity of our study, contrary to other above-mentioned studies of the hormetic effect of different stressors on C. elegans, is that we induced hormetic effect by exposing nematodes to bacterial pathogens during development as stressors. We hypothesize that hormetic effects of early exposure to bacteria are common in nature as they were observed in a variety of organisms. For example, priming of innate immunity by pathogens has been reported for invertebrates such as C. elegans[52,53] and insects [54]. In some cases, immune priming can even be trans-generational, as observed for the mealworm beetle Tenebrio molitor[55]. It was shown that the presence of bacteria during the first week of the Drosophila melanogaster adult life increases the flies lifespan [56]. The early life interactions between human host and bacteria, which largely occur through the colonization of the newborn intestine, are also increasingly recognized as being critical for the maturation of human immune system as well as for the metabolic homeostasis of the host [57]. Newborn babies whose intestinal colonization was modified by the mode of delivery (natural vs. Cesarean section) or by antibiotic treatments, show a delay in immune response maturation [58]. Early exposure of children, up to five years of age, to non-septic bacteria-rich environments, has a significant protective effect against the onset of allergies [59]. Epidemiologic studies also show an increased occurrence of autoimmune diseases in human populations in “clean” environments [60]. These observations constitute the basis of the “hygiene hypothesis,” according to which the lack of exposure to microbes due to high hygienic conditions commonly found in the Western world prevents correct maturation of the immune system and predisposes individuals to allergies and other immune diseases. These observations also correspond to the programming concept, which refers to stimuli that during critical periods of development may “program” the long-term structure or function of an organism [61]. Our data establish that, at least in the C. elegans model, intentional administration of particular bacterial strains during early life could indeed modulate disease susceptibility during adulthood.
Our study strongly suggests that variations induced during development are maintained in genetically identical adult nematodes, as it was previously reported for the nematodes that transiently passed through the stress-induced dauer larval stage [3]. In C. elegans, the molecular basis of such life-long memory of modifications of developmental transcription profiles is mediated by histone modifications [3]. Whether histone modifications are also responsible for the phenotypes we observed remains to be determined.
Although natural selection might favor improved sensing and response mechanisms, adaptation could also result in the emergence of more sophisticated response strategies. Developmental plasticity allows for the production of phenotypically diverse offspring in populations of genetically identical individuals, which increases the probability of survival in changing and challenging environments. The evolution of the ability to mount such predictive developmental modifications depends on a number of features, such as the cost of developmental plasticity, ability to correctly detect and interpret environmental cues that depends on the frequency by which various environmental conditions are encountered, and finally on the long term fitness advantage provided. Therefore, as described for E. coli plus Saccharomyces cerevisiae[62], and C. elegans[52], the observed phenomenon could extend beyond merely sensing and responding immediately to a given stimulus and could contribute to a predictive response strategy that uses the appearance of a stimulus as a cue that future conditions might be stressful.
Conclusions
Our study shows that development on pathogens has a hormetic effect on adult nematodes, as it results in increased resistance to different pathogens and to heat shock. Such developmental plasticity of C. elegans nematodes, which are self-fertilizing homozygous animals producing offspring with negligible genetic variation, could increase the probability of survival in changing environments.
Methods
Nematode and bacterial strains
C. elegans N2 (ancestral) strain used for all experiments unless otherwise indicated was kindly provided by J.J. Ewbank (Marseille, France). Strain TJ375 (gpIs1[hsp-16.2::GFP]) and mutant strains CF1038 (daf-16 (mu86) I), GR1307 (daf-16 (mgDf50) I), NU3 (dbl-1 (nk3) V), and KU25 (pmk-1(km25) IV) were obtained from the Caenorhabditis Genetics Center (Minneapolis, Minnesota, USA). N2 control was included in every experiment with nematode mutants.
E. coli strains used in this study were pathogenic strain 536 [23], and the uracil deficient strain OP50 [16]. Genotypic and phenotypic characterization of these strains was described previously [19]. Enterococcus faecalis strain OG1RF [63] (previously named Streptococcus faecalis OG1-RF1) was kindly provided by Dr. P. Courvalin (Paris, France).
Nematode maintenance and synchronization
Nematodes were maintained at 25°C on nematode growth medium (NGM) agar plates seeded with 0.1 mL LB grown stationary phase bacterial culture, and incubated 18 h at 37°C to densities of 7.3 × 109 ± 3 × 108, 1.4 × 1010 ± 5 × 109, and 1.5 × 1010 ± 2 × 109 CFU/plate for E. coli OP50, 536, and E. faecalis OG1RF, respectively. Age-synchronized populations of nematodes were initiated from eggs recovered following sodium hydroxide (0.5 M final) and sodium hypochlorite (0.96% final) treatment of gravid adults maintained at 25°C and fed E. coli OP50. All assays were carried out at 25°C with nematodes synchronized a second time at the end of development by selecting exclusively nematodes at the end of the 4th larval (L4) stage based on vulva morphology.
Survival assays
Survival assays were carried out at least in triplicate. For survival assays, all nematode strains were developed and maintained at 25°C, transferred onto new plates every day during the first 5 days to eliminate progeny, and every 2–3 days thereafter. Dead nematodes were scored every 24 h. A nematode was considered dead when it failed to move spontaneously or respond to a gentle touch with a platinum wire. Nematodes buried in the agar or on the sides of the plates were censured from the analyses. Lifespan was measured as the time from the end of L4 larval stage (beginning of adulthood) until death.
Elimination of bacteria from nematodes intestine
When experiments involved nematodes developed on E. coli 536 or E. faecalis OG1RF and then transfer to a different bacteria strain, L4 stage nematodes were washed and treated with antibiotics to remove the initial strain from their intestinal tract. Nematodes were washed in M9 minimal salts buffer to remove excess bacteria from their surface and then incubated in NGM for 1 h to allow them to expurgate intestinal bacteria. Nematodes were then treated for 1 h with 20 μg/ml Polymyxin B antibiotic in M9 minimal salts buffer. Finally, nematodes were washed in M9 minimal salts buffer and transferred on plates containing the appropriate bacterial strain. The effect of antibiotic treatment on nematode survival was taken into account by applying the treatment to all nematode populations involved in the assays. For survival experiments, treated nematodes were regularly checked for the absence of the initial bacterial strain. A few nematodes were sampled from the survival assay, crushed in a Dounce homogenizer and the extract plated on LB agar media for colony observation (see below quantification of live bacterial cells in nematode intestine for detail on this procedure). Colony morphology and color allowed for direct visual discrimination between the different bacterial strains used in this study.
Measurements of nematode heat shock resistance
L4 nematodes developed on OP50 or 536 were washed in Polymyxin B antibiotic (see above elimination of bacteria from nematodes intestine). Then, nematodes were transferred onto OP50 lawn in order to measure heat shock resistance using nematodes that have the same bacterial strain in their intestines. After allowing nematodes to recover for 12 h at 25°C, they were transferred for 10 h at 35°C. Dead nematodes were scored at the end of the 10 h incubation at 35°C. This assay was performed in triplicate with internal triplicate controls.
Measurements of nematode heat shock protein (HSP) expression
HSP expression measurement assays were carried out with C. elegans strain TJ375 carrying a fluorescent reporter under the control of the hsp-16.2 promoter (gpIs1hsp-16-2::GFP]). Nematodes were collected with cold (4°C) sterile water, fixed immediately by addition of an equal volume of cold 2% formaldehyde in 2 × Phosphate Buffered Saline (PBS), and incubated 10 min on ice. Fixed nematodes were collected by gravity sedimentation and washed in cold 1× PBS before being loaded into a 96-well plate kept at 4°C in the dark until analyzed. Two-day old adults were separated from their progeny on the first and second day by gravity sedimentation in 15 ml falcon tubes for 2 min in M9 minimal salts buffer, the larvae being removed with the supernatant. The absence of eggs and larvae was verified under a dissecting microscope. Gene reporter levels were quantified with the COPAS Biosort (Union Biometrica) as described in [64]. Briefly, worms were analyzed for size (TOF) and green (GFP) fluorescence. Raw data were filtered on the TOF (200–1000) to exclude dust, bubbles, and aggregated worms. Fluorescence data was acquired from two independent experiments, including internal replicates.
Quantification of live bacterial cells in nematode intestine
Two-day old nematodes were handled at 4°C to stop defecation. Nematodes were transferred to a new plate without bacteria, recovered in 1.5 ml 10-2 M MgSO4, and vortexed 30 seconds to remove excess bacteria from nematode cuticles. Then, individual nematodes were again transferred to a new plate without bacteria and rubbed across the plate to remove all bacteria from the cuticle. Nematodes were then individually crushed in a Dounce homogeneizer with the fitted mortar (B) in 10-2 M MgSO4. The amount of live bacteria was determined by plating of appropriate dilutions on LB agar. After overnight incubation at 37°C, grown colonies were counted.
Statistical analyses and figures
Statistical analyses and graphic displays were made using Prism 5.0d from GraphPad Software, Inc. Measurement assays were analyzed by unpaired t-test for comparison of two groups or, when more than two groups were involved, using 1-way analysis of variance (ANOVA) followed by Tukey’s Multiple Comparison Test (TMCT) also known as Tukey-Kramer test, comparing all pairs of group and allowing for unequal sample sizes. Survival assays were analyzed using the Gehan-Breslow-Wilcoxon Test (GBWT) comparing conditions by pairs and allowing for unequal hazard ratios. Data presented are mean ± s.e.m., unless otherwise indicated. For survival assays, a typical, representative experiment is presented, the absence of significant difference between replicates was verified using GBWT .
Competing interests
The authors declare that they have no competing interests.
Authors’ contributions
ML, TM, XM and IM designed experiments, analyzed and interpreted data, and drafted the manuscript. ML, TM, XM and DFA performed experiments. All authors read and approved the final manuscript.
Acknowledgements
We acknowledge Dr. J.J. Ewbank (Centre d’Immunologie de Marseille-Luminy, INSERM/CNRS/Université de la Méditerranée, Marseille, France) for access to the worm sorter apparatus and for providing nematode strain. We also acknowledge the C. elegans Gene Knockout Consortium (http://www.celeganskoconsortium.omrf.org) and the Caenorhabditis Genetics Center (http://www.cbs.umn.edu/CGC) for providing nematode mutant strains, and Dr. P. Courvalin (Unité des Agents Antibactériens, Institut Pasteur, Paris, France) for providing bacterial strain E. faecalis OG1RF.
This work was supported in part by a 2008 fellowship from the Nestlé Fondation to M.L., Servier PhD fellowship to X.M., AXA master fellowship to D.F.A. and ANR grant ANR-06-BLAN-0406/AGING to I.M.
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Research article
Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevance
Oliver C Jann1*, Dirk Werling2, Jung-Su Chang3, David Haig4 and Elizabeth J Glass1
Author Affiliations
1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin Biocentre, Midlothian, EH25 9PS, UK
2 Department of Pathology and Infectious Diseases, The Royal Veterinary College, Hawkshead Lane, Hatfield, Herts AL9 7TA, UK
3 Division of Virology, Moredun Research Institute, Pentland Science Park, Edinburgh, EH26 OPZ, UK
4 School of Veterinary Medicine and Science, Nottingham University, Sutton Bonington LE12 5RD, UK
For all author emails, please log on.
BMC Evolutionary Biology 2008, 8:288 doi:10.1186/1471-2148-8-288
Published: 20 October 2008
Abstract
Background
There is accumulating evidence that polymorphism in Toll-like receptor (TLR) genes might be associated with disease resistance or susceptibility traits in livestock. Polymorphic sites affecting TLR function should exhibit signatures of positive selection, identified as a high ratio of non-synonymous to synonymous nucleotide substitutions (ω). Phylogeny based models of codon substitution based on estimates of ω for each amino acid position can therefore offer a valuable tool to predict sites of functional relevance. We have used this approach to identify such polymorphic sites within the bovine TLR2 genes from ten Bos indicus and Bos taurus cattle breeds. By analysing TLR2 gene phylogeny in a set of mammalian species and a subset of ruminant species we have estimated the selective pressure on individual sites and domains and identified polymorphisms at sites of putative functional importance.
Results
The ω were highest in the mammalian TLR2 domains thought to be responsible for ligand binding and lowest in regions responsible for heterodimerisation with other TLR-related molecules. Several positively-selected sites were detected in or around ligand-binding domains. However a comparison of the ruminant subset of TLR2 sequences with the whole mammalian set of sequences revealed that there has been less selective pressure among ruminants than in mammals as a whole. This suggests that there have been functional changes during ruminant evolution. Twenty newly-discovered non-synonymous polymorphic sites were identified in cattle. Three of them were localised at positions shaped by positive selection in the ruminant dataset (Leu227Phe, His305Pro, His326Gln) and in domains involved in the recognition of ligands. His326Gln is of particular interest as it consists of an exchange of differentially-charged amino acids at a position which has previously been shown to be crucial for ligand binding in human TLR2.
Conclusion
Within bovine TLR2, polymorphisms at amino acid positions 227, 305 and 326 map to functionally important sites of TLR2 and should be considered as candidate SNPs for immune related traits in cattle. A final proof of their functional relevance requires further studies to determine their functional effect on the immune response after stimulation with relevant ligands and/or their association with immune related traits in animals.
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Case report
Two cases of "cannabis acute psychosis" following the administration of oral cannabis
Bernard Favrat1*, Annick Ménétrey2, Marc Augsburger2, Laura E Rothuizen3, Monique Appenzeller3, Thierry Buclin3, Marie Pin1, Patrice Mangin2 and Christian Giroud2
Author Affiliations
1 Unité de Médecine du Trafic, Institut Universitaire de Médecine Légale (IUML), 1005 Lausanne, Switzerland
2 Laboratoire de Toxicologie et Chimie Forensiques (LTCF), Institut Universitaire de Médecine Légale (IUML), Rue du Bugnon 21, 1005 Lausanne, Switzerland
3 Division de pharmacologie et toxicologie cliniques, CHUV, 1011 Lausanne, Switzerland
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BMC Psychiatry 2005, 5:17 doi:10.1186/1471-244X-5-17
Published: 1 April 2005
Abstract
Background
Cannabis is the most commonly used illegal drug and its therapeutic aspects have a growing interest. Short-term psychotic reactions have been described but not clearly with synthetic oral THC, especially in occasional users.
Case presentations
We report two cases of healthy subjects who were occasional but regular cannabis users without psychiatric history who developed transient psychotic symptoms (depersonalization, paranoid feelings and derealisation) following oral administration of cannabis. In contrast to most other case reports where circumstances and blood concentrations are unknown, the two cases reported here happened under experimental conditions with all subjects negative for cannabis, opiates, amphetamines, cocaine, benzodiazepines and alcohol, and therefore the ingested dose, the time-events of effects on behavior and performance as well as the cannabinoid blood levels were documented.
Conclusion
While the oral route of administration achieves only limited blood concentrations, significant psychotic reactions may occur.
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< 10 F#@king Years
The Frotzophone Considered >
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You are here: Home / The European environment – state and outlook 2010 / Country assessments / Finland / Land use - National Responses (Finland)
Land use - National Responses (Finland)
Land use - National Responses
Topic
Land
Published: Nov 26, 2010 Modified: Nov 23, 2010
Monitoring of the living environment and urban structure
Information on land use is collected in many ways and monitoring of the living environment and urban structure is one of these. At the moment, monitoring of the living environment covers
• Population
• Buildings
• Living and households
• Services
• Transport
• Workplaces and commuting
• Land use and urban structure.
In the future also natural environment and landscapes, recreational areas, community development and energy, environmental nuisances as well as social environment will be included in the monitoring.
The monitoring of the urban structure[1] aims to collect information on the state and trends of the urban structure. Monitoring addresses the physical and functional entity formed by dwellings, workplaces, services and green areas as well as the connections between them.
Land-use planning[2]
Land-use planning has a central role in the development of the living environment. As importantly, land-use planning also promotes sustainable development. In Finland, land-use planning has several levels.
The regional land use plan is created and approved by the Regional Council and confirmed by the Ministry of Environment. The local authorities create and approve the local master plans and the local detailed plans. All these three types of plans are drawn up in a participatory process. The provisions in the higher plans are binding for the lower plans.
The Government defines the national land-use guidelines[3]. The national land-use guidelines are a tool for Government to steer policy on land-use issues that are important for the whole country. The guidelines relate to the regional and urban structure, the quality of the living environment, communication networks, energy supply, natural and cultural heritage and use of natural resources. The national land-use guidelines were revised[4] in November 2008.
In the revision, the main emphasis was put on a more coherent urban structure, reduction of the volume of traffic, energy issues in land-use planning, adaptation to climate change, and housing production, transport and land use in the Helsinki region.
Legislation on land use and building[5]
The most important legislation controlling land use, spatial planning and construction in Finland is contained in the Land Use and Building Act[6], which came into force in 2000. The general objectives of the Act are, among others, to organise land use and construction to create the basis for high quality living environments, and to promote ecologically, economically, socially and culturally sustainable developments. The more specific objects are related to controls over land-use planning and construction.
More detailed regulations and controls on land use and construction are included in the Land Use and Building Decree[7]. The Land Use and Building Act is complemented by the National Building Code[8].
See also: Living environment and urban structure, Eco-efficiency and energy consumption in buildings, and International co-operation on spatial planning (Ministry of the Environment)
[1] Monitoring of the urban structure, Ministry of the Environment (in Finnish)
[2] Land use planning, Ministry of the Environment
[3] National land use guidelines, Ministry of the Environment
[5] Legislation on land use and building, Finnish Environmental Administration
[6] Land Use and Building Act (132/1999) - Unofficial translation of the original Act, PDF format in Finlex, the Data Bank of Finnish Legislation
[7] Land Use and Building Decree (895/1999) - Unofficial translation, PDF format in Finlex, the Data Bank of Finnish Legislation
[8] National Building Code of Finland, Finnish Environmental Administration
Disclaimer
The country assessments are the sole responsibility of the EEA member and cooperating countries supported by the EEA through guidance, translation and editing.
European Environment Agency (EEA)
Kongens Nytorv 6
1050 Copenhagen K
Denmark
Phone: +45 3336 7100
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Williamson County, IllinoisEdit This Page
From FamilySearch Wiki
United States Illinois Williamson County
Guide to Williamson County Illinois genealogy. Birth records, marriage records, death records, census records, family history, and military records.
Illinois
Online Records
Coordinates: 37.73°0′N 88.93°0′W / 37.73°N 88.93°W / 37.73; -88.93
Williamson County, Illinois
Map
Location in the state of Illinois
Location of Illinois in the U.S.
Facts
Founded: February 28, 1839
County Seat Marion
Courthouse
Address Williamson County Courthouse
200 West Jefferson Street
Marion, IL 62959
(618) 997-1301
Williamson County Website
Contents
Williamson County Organization
Williamson County's civil records start the following years:
Birth Marriage Death Census Land Probate
1877 1839 1877 1840 1818 1839
County records are most often kept at the County Courthouse or another local repository. For further information about where the records for Williamson County are kept, see the Williamson County Courthouse page.
Historical Facts
Williamson County, Illinois is named for Williamson County, Tennessee because of the many settlers who originated from that area.
1839--Williamson County was created 28 February 1839 from Franklin County.
County seat: Marion [1]
Boundary Changes
The present area of Williamson County, or parts of it, were at one time included in the following counties[2]:
1818–1839 Franklin
1816–1818 Jackson
1812–1818 Gallatin
1812–1816 Johnson
1795–1816 Randolph
1790–1801 Knox, Northwest Territory
See an interactive map of Williamson County boundary changes.
Record Loss
30 May 1875: - Courthouse burned and some records were lost or damaged.
For further information on researching in burned counties, see the following:
Places/Localities
To see a list of places in Williamson County, click on [Show], in the bar above. The preceding list of places includes incorporated cities and towns, unincorporated towns and communities, and place names that may have been used in family histories. Some have well-organized records and even have web sites. Some are simply social communities with no official records, but which may be referenced in small-town newspapers. The list is provided to help researchers identify localities within the county. Localities listed in red have no wiki page yet. As records or histories of these localities are identified, a page will be added for each of these place names.
Records and Resources
Biography
Cemeteries
The Illinois Cemeteries page provides general explanations of the following online Williamson County resources:
Bibliography Online Gravestone Transcriptions Cemetery Gazetteers
FHLC Find A Grave | national search | county list ePodunk
WorldCat USGenWeb Tombstone Transcription Project The American History and Genealogy Project
Illinois Cemeteries
USGenWeb Archives
I Dream of Genealogy
Many Confederate veterans were buried in Williamson County, for a list visit Genealogy Trails. A few politicians were also buried in the county, see Political Graveyard.
Census
Historical populations
Census Pop.
18404,457
18507,21661.9%
186012,20569.1%
187017,32942.0%
188019,32411.5%
189022,22615.0%
190027,79625.1%
191045,09862.2%
192061,09235.5%
193053,880−11.8%
194051,424−4.6%
195048,621−5.5%
196046,117−5.2%
197049,0216.3%
198056,53815.3%
199057,7332.1%
200061,2966.2%
201066,3578.3%
Illinois Counties 1900-1990[3]
1840, 1850, 1860, 1870, 1880, 1900, 1910, 1920, and 1930 federal population schedules of Williamson County are available online. For tips on accessing census records online, see Illinois Census.
See Williamson County, IL census assignments, including links to transcribed files. [The USGenWeb Census Project].
1840 Pensioners
• A Census of Pensioners for Revolutionary or Military Services: With their Names, Ages, and Places of Residence, as Returned by the Marshalls of the Several Judicial Districts, Under the Act for Taking the Sixth Census. Washington, D.C., 1841. FHL 973 X2pc 1840; FHL 2321; digital version at Google Books. [See Illinois, Williamson County on page 188.]
Church Records
A chapter on early Williamson County, Illinois church history appears in an 1887 local history, available for free online, beginning on page 515.
Histories of early churches in the county appear in:
See also:
Baptist
Catholic
FamilySearch has made parish records from four Belleville Diocese Catholic churches in Williamson County available online (free registration is required). The records include first communions, confirmations, marriages, and deaths:
Christian
• Abney, Ella Lorine Rogers et al. Membership and Friends, First Christian Church: Disciples of Christ. Marion, Ill.: First Christian Church (Disciples of Christ, Marion, Ill.), 1999. FHL Book 977.3993/M1 K2ae.
• Lake Creek Christian Church. Church Records, 1892-1897. MSS. Copy: FHL Film 966139 Item 9.
Church of Christ
Disciples of Christ
Methodist
Court Records
1840–Present Original Court records are available at the Williamson County, Illinois Courthouse. See Illinois Court Records for information about how to use county court records.
The following records are abstracted:
Ethnic Research
African American
United States African Americans Illinois African Americans
Genealogy
It is anticipated that this bibliography will eventually identify all known family histories published about residents of this county. Use this list to:
• Locate publications about direct ancestors
• Find the most updated accounts of an ancestor's family
• Identify publications, to quote Elizabeth Shown Mills, about an ancestor's "FAN Club" [Friends, Associates, and Neighbors]
Message Boards
General
As of March 2011, a query for persons born in Williamson (County), Illinois at World Connect, results in more than 30,000 entries.
Parks' collection is a great place to learn if genealogists have studied your Williamson County family in the past:
The following collections contain genealogies about many families in the county:
• Crain, Charles L. and Barbara Crain. Whose Family Line Is It ... Anyway: A Brief History of the Crain, Snider, Burkitt, Plumlee, Shingleton and Isom Families in Franklin, Williamson and Surrounding Counties in Southern Illinois. n.p.: C.L. Crain, 2001. FHL CD-ROM no. 772.
• Grisham, Violet Lee Carter. My Williamson County Pioneer Kinfolks and Descendants. Marion, Ill.: V.L.C. Grisham, 1995. FHL Book 929.273 G919gva.
• Lind, Helen Sutt, Charla Schroeder Murphy, et al. The Barham Connection: Barham Cemetery Inscriptions and Family Genealogy. 1997? FHL Book 977.3993/M1 V3L.
• Malone, Daisy Hearne Roberts. A Group of Family Trees of the Early Settlers of Corinth Township, Williamson County, Illinois and Allied Families. Pueblo, Colo.: Rocky Mountain Bank Note Co., 1939. FHL Book 977.3993/C1 D2m
Bibliography
• [Bohannan] Cotton, Yvonne Bohannan. The Bohannan Family: Ancestors and Descendants of John Ervin and Sarah Bohannan. Glen Rose, Texas: Y.B. Cotton, n.d. FHL Book 929.273 B634c.
• [Carter] Grisham, Violet Lee Carter. Charles T. Carter, Revolutionary Soldier Whose Children Came to Southern Illinois: Their Related Families, Cunningham, Owens, Croslin, Aikin, Gregory. Marion, Ill.: Violet Grisham, 1994. FHL Book 929.273 C245g
• [Childers]. Cast a Long Shadow: A Saga of Three Generations of a Southern Illinois Family, Reaching from Williamson County to Belgaum, India. Wilmore, Ky.: R. Seamands, 1994. FHL Book 929.273 C437sr; digital version at Family History Archives.
• [Cox] Cox, Avis E. and Marion R. Cox. From the Banks of the Dan, a Cox Family Genealogy. Winona, Minn.: A.E. and M.R. Cox, 1994. FHL Book 929.273 C839fc.
• [Culbreath] Green, John Stinson. Leroy Culbreath and Mary Fulk of Williamson County, Illinois and Stafford County, Kansas. Wichita, Kan.: J.S. Green, 199-?. FHL Fiche 6004641; digital version at Family History Archives.
• [DeBose], Donald F. Descendants of Isaiah Debose. Carterville, Ill.: D.F. Shrake, 2005. FHL CD-ROM no. 2442.
• [Duncan] "Descendants of James Frank Duncan," in Effie Maria McFarland Genealogical Collection. MSS. Microfilmed 2002. FHL VAULT Film 1574106 Item 1.
• [Goddard] Moore, Mary Jo. The Goddard, Spiller, Goodall Connection. Marion, Ill.: M.J. Moore, 1997. FHL Book 929.273 G541m.
• [Grove] Grisham, Violet Lee Carter. Pioneers to Williamson County, Illinois, George Zacharias and Isaac Groves and Their Descendants. Marion, Ill.: V.L.C. Grisham, 199-?. FHL Book 929.273 Z11c.
• [Groves] Grisham, Violet Lee Carter. Legends in the New World - The Beginnings. Marion, Ill.: V. Grisham, 1991. FHL Book 929.273 G887g.
• [Groves] Grisham, Violet Lee Carter and Edward Dean Grisham. Time Traveler. Marion, Ill.: V. Grisham, 1994. FHL Book 929.273 G919gv.
• [Howell] Howell, Frank R. Historical Sketch of the Howell Family and Biography of William Marion Howell, 1845-1927. Typescript, 1946. FHL Film 960427 Item 9.
• [Jeter] Jeter, Loren E. and Jeanette Feltl Jeter. Who Am I? A Jeter Family Saga. Cottonwood, Ariz.: L.E. Jeter, Sr., 1989. FHL Book 921.73 J511j.
• [Klope] Grisham, Violet Lee Carter. Legends in the New World - The Beginnings. Marion, Ill.: V. Grisham, 1991. FHL Book 929.273 G887g.
• [Potter] Moore, Mary Jo. The Potter Family Tragedy. Marion, Ill.: Williamson County Historical Society & Museum, 1996. FHL Book 929.273 P851m.
• [Pritchett] "John & Amelia (Mosley) Prichett, TN-Williamson Co., IL," in Doris Melissa Pritchett Horlacher, Pritchett in America, Waller, Pritchard, Prickett, Phelan, 1987. Orem, Utah: Horlacher & Sons, 1987. FHL Film 1421821 Item 9.
• [Pritchett] Stephens-Dewey, Wanda Dolores. Pritchett Family, 1827-1999: Including Ramsey, Franklin, Coffman, Pryor, Stephens. [Fort Wayne, Texas: W.D. Stephens-Dewey, 1999?]. FHL Book 929.273 P939sd.
• [Rich] Abney, Ella Lorine Rogers. William Rich and His Descendants of Southern Illinois. Marion, Ill.: E.L. Abney, 2000. FHL Book 929.273 R379a.
• [Spiller] Gottschalk, Kathrine Cox. The Spiller Family of Prince William County, Virginia; Robertson County, Tennessee; Williamson County, Illinois. Typescript. Microfilmed 1972. FHL Film 896608 Item 2
• [Spiller] Moore, Mary Jo. The Goddard, Spiller, Goodall Connection. Marion, Ill.: M.J. Moore, 1997. FHL Book 929.273 G541m
• [Stilley] Stilley, William Douglas. The William Davis Stilley and Nancy Swofford-Stilley Family History and Genealogy. Raytown, Mo.: W.D. Stilley, 1980. FHL Book 929.273 St54sti.
• [Tanner] Tanner, John W. Six James Tanners. Typescript, Williamson County Historical Society, Ill. Microfilmed 1974. FHL Film 966149 Item 2.
• [Walker] Keyser, Helen Walker Linsenmeyer. Illinois Pioneer, Matthew Moore Walker, and Descendants. Mountain, Home, Ark.: H.W.L. Keyser, 1993. FHL Book 929.273 W153k; digital version at Family History Archives.
• [Ward] Abney, Ella Lorine Rogers. The Ward Family. Marion, Ill.: E. Abney, 1985. FHL Book 929.273 W21a.
• [Zacharias] Grisham, Violet Lee Carter. Pioneers to Williamson County, Illinois, George Zacharias and Isaac Groves and Their Descendants. Marion, Ill.: V.L.C. Grisham, 199-?. FHL Book 929.273 Z11c.
History
Local Histories
The 1876 local history is also available at Ancestry ($).
• History of Gallatin, Saline, Hamilton, Franklin, and Williamson Counties, Illinois: From the Earliest Time to the Present, Together with Sundry and Interesting Biographical Sketches, Notes, Reminiscences, etc., etc. Chicago: The Goodspeed Publishing Co., 1887. Digital versions at Ancestry ($) (1967 reprint); Internet Archive.
• Centennial History of McKendree College. 1928. Digital version at The USGenWeb Project. Includes chapters on St. Clair's history under French rule, under British rule, under American rule, and information about early settlers.
Land and Property
See Illinois Land and Property for more information.
1836-present The original land and property records for Williamson County are held by the County Recorder. See the Williamson County Courthouse page for contact information. The following copies are available:
The following abstracts are available:
Online Resources
Maps
Military
Revolutionary War
Veterans of the Revolutionary War settled in Williamson County.
See also Census
War of 1812
Veterans of the War of 1812 settled in Williamson County.
• List of Pensioners on the Roll, January 1, 1883; Giving the Name of Each Pensioner, the Cause for Why Pensioned, the Post-Office Address, the Rate of Pension Per Month, and the Date of Original Allowance... Washington, D.C.: Government Printing Office, 1883. FHL Book 973 M2Lp v. 3; digital versions at Google Books and Internet Archive. [See Vol. 3, Illinois, Williamson County, pp. 640-642. Identifies War of 1812 and other veterans living in the county in 1883.]
Civil War
Civil War service men from Williamson County served in various regiments. Men often joined a company (within a regiment) that originated in their county. Listed below are companies or regiments that were formed from men of Williamson County.
- 9th Regiment, Illinois Infantry, Company G.
- 29th Regiment, Illinois Infantry, Company E.
- 31st Regiment, Illinois Infantry, Companies C and E.
- 56th Regiment, Illinois Infantry, Company E.
- 60th Regiment, Illinois Infantry, Company E.
- 81st Regiment, Illinois Infantry, Companies E, G and H.
- 107th Regiment, Illinois Infantry, Company G.
- 110th Regiment, Illinois Infantry, Company C.
- 120th Regiment, Illinois Infantry, Company G.
- 128th Regiment, Illinois Infantry, Companies A, B, C, D, E, F, G, H, and I.
World War I
• Baird, S. S. Williamson County, Illinois, in the World War: Containing a Brief Review of the World War, Complete History of Williamson County's Activities, Photographs and Service Records of Williamson County's Soldiers, Sailors and Marines, Industrial Review of Business and Professional Firms Who Have Made This History Possible. Marion: Williamson County War History Society, c1919. Digital versions at Ancestry ($); Internet Archive.
Naturalization
Newspapers and Obituaries
Information about the following newspapers is available through the Illinios Newspapers Project:
Probate Records
For more information about probate records see Illinois Probate Records.
1840–present The original probate records for Williamson County are held by the Circuit Court Clerk. See the Williamson County Courthouse page for contact information. The following copies are available:
The following abstracts are available:
• 1847–1872 Grisham, Violet Lee Carter. Williamson County, Il. Wills, Book A.(Marion, Illinois):V.L.C.Grisham, 1998. WorldcatFHL Book 977.3993 P2g
• 1898–1911 Murphy, Charla Schroeder. Probate Book C, Circuit Clerk's Office: Administrators Book A, County Clerk's Office, Williamson County, Illinois. S.l: C.S. Murphy, 2004.Worldcat FHL Book 977.3993 P2mc
Online Resources
• 1853–1919 Probate records are also available in Illinois, Probate Records, 1819-1970. Click on the browse through images link, select Williamson County, and select the record type you are interested in.
Repositories
County Courthouse
County records are most often kept at the County Courthouse or another local repository. For further information about where the records for Williamson County are kept, see the Williamson County Courthouse page.
Family History Centers
Illinois Regional Archives Depository (IRAD)
IRAD is a system of Illinois Regional Archives Depositories managed by the Illinois State Archives, housing the archival records of local Illinois counties, townships, municipalities and school districts. The seven Regional Depositories are housed on state university campuses scattered throughout Illinois. Southern Illinois University houses the records for Williamson County.
Public Libraries
Social Groups Online
Societies
Marion Carnegie Library
206 South Market Street
Marion, IL 62959
(618) 993-5935
Genealogical Society of Southern Illinois
John A. Logan College Library
700 Logan College Road
Carterville, Illinois 62918
Telephone: 618-985-2828, Ext. 8338
Hours: vary by season, see website
Williamson County, IL Historical Society Museum
Marion, IL 62959
Nannie Gray Parks' map of the early settlers of Williamson County is for sale at the book shop.
Genealogical Society of Southern Illinois
John A. Logan College Library
700 Logan College Road
Carterville, Illinois 62918
(618) 985-2828, Ext. 8338
Hours: vary by season, see website
The Society focuses on Alexander, Clay, Clinton, Edwards, Franklin, Gallatin, Hamilton, Hardin, Jackson, Jefferson, Johnson, Lawrence, Marion, Massac, Monroe, Perry, Pope, Pulaski, Randolph, Richland, Saline, St. Clair, Union, Wabash, Washington, Wayne, White, and Williamson counties. The Society's book and microfilm collection is housed at the John A. Logan College Library. The Society publishes a newsletter (click here for recent issues) and a quarterly journal The Saga of Southern Illinois (click here for a topical index that breaks down what has been published county-by-county).
Taxation
Vital Records
Births
1877–present - The original Williamson County birth records 1877-present are housed at the County Clerk's office. The following copies are available:
The following abstracts are available:
Marriage
1839–present - The original Williamson County marriage records 1877-present are housed at the County Clerk's office.
Copies of marriage licenses and other marriage records are available through the Illinois Regional Archives Depository system at Southern Illinois University. How to use IRAD
• 1839–1870 Marriage Licenses, 1839- 1870 IRAD-SIU 6/0325/09
• 1839–1916 Marriage Record, 1839-1916 IRAD-SIU 6/0325/07
• 1865–1885 Marriage Record Index 1865-1885 IRAD-SIU 6/0325/06
Other copies of marriage records:
The following abstracts are available:
• 1830–1850 Illinois USGenWeb Archives
• 1839–1853, 1865 Winget, Judy Walley. Williamson County, Illinois marriages, 1839 to 1853 and 1865; Pope County, Illinois marriages, 1826 to 1845; Johnson County, Illinois marriages, 1857 to 1860. S.P.: Saline County Genealogical Society (Illinois), 1984. Worldcat FHL Book 977.399 V2w
• 1839–1902 Hoffard, Gay Roberson and Joyce Stephens Smith.Marriages on Record in Marion, Williamson County, Illinois Courthouse. Marion, Illinois: Williamson County Historical Society [Illinois], 1988. WorldcatFHL Book 977.3993 V2h Vol. 1-5
The Williamson County Marriage Project is a user-contributed listing of about 600 Williamson County marriages. Many listings include e-mail contact information for the individual who contributed the information.
Deaths
1877–present The original Williamson County death records 1877–present are housed at the County Clerk's office. The following copies are available:
The following abstracts are available:
Web Sites
References
1. The Handybook for Genealogists: United States of America,10th ed. (Draper, UT:Everton Publishers, 2002).
2. "Williamson County Fact Sheet." The Official Web site for Illinois Secretary of State Jesse White. N.p., n.d. Web. 29 Mar. 2011. http://www.cyberdriveillinois.com/departments/archives/irad/williamson.html
3. Template:Citation
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• This page was last modified on 12 April 2013, at 19:54.
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About this Journal Submit a Manuscript Table of Contents
Stroke Research and Treatment
Volume 2011 (2011), Article ID 534362, 9 pages
doi:10.4061/2011/534362
Clinical Study
Treatment Challenges in Pediatric Stroke Patients
1Department of Pediatric Neurology, School of Medicine, Ankara University, Turkey
2Department of Pediatric Neurology, Dışkapı Hematology-Oncology Hospital, Turkey
3Department of Pediatric Molecular Genetics, School of Medicine, Ankara University, Turkey
4Department of Pediatric Hematology, School of Medicine, Ankara University, Turkey
Received 15 September 2010; Accepted 18 November 2010
Academic Editor: Turgut Tatlisumak
Copyright © 2011 A. Yılmaz 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.
How to Cite this Article
A. Yılmaz, S. Teber, Ö. Bektaş, et al., “Treatment Challenges in Pediatric Stroke Patients,” Stroke Research and Treatment, vol. 2011, Article ID 534362, 9 pages, 2011. doi:10.4061/2011/534362
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The continuing low-level seismicity in the vicinity of the Idukki Reservoir, Kerala, is interesting from the perspective of hydrologically triggered earthquakes. While the frequency of triggered earthquakes in the vicinity of a reservoir usually reduces with time and the largest earthquake usually occurs within a few years on the initial filling, the triggered seismicity in the proximity of the Idukki Reservoir seems to be showing a second, delayed peak, as the 1977 (M 3.5)
The Central Ground Water Board (CGWB) on Monday signed a contract with the Council of Scientific Industrial Research–National Geophysical Research Institute (CSIR-NGRI) to implement a pilot project
The International Centre for Integrated Mountain Development (ICIMOD)-organised international conference on Himalayan glaciers concluded in the capital today.
The risk of there not being enough water in the stream — the ‘hydrology risk’ — is the “single largest risk” that a small hydro project faces, says a study of the rating and analysis agency, ICRA.
The report of the Empowered Committee, though subject to condtions, was in favour of constructing a new dam to replace the existing one at Mullaperiyar, Chief Minister Oommen Chandy has said.
The nominee of the State on the committee, K.T. Thomas, had done his best to protect the interests of Kerala. He had expressed the views of Kerala in his dissent note and had listed six reasons for keeping the water level in the reservoir at 136 feet. The only objection was that he had not made any dissent on the finding that the dam was safe, Mr. Chandy said.
LUCKNOW: Once considered as an agent of salvation and lifeline of Lucknow, Gomti today is neither sacred nor clean.
CHENNAI: The five-member Supreme Court empowered committee on the Mullaiperiyar issue has emphasised on Tamil Nadu’s rights over the existing dam and all its waters, under the 1886 lease deed and t
Chief minister J. Jayalalithaa said on Saturday that the state government’s stand on the Mullaperiyar dam has been vindicated by the Supreme Court appointed empowered committee’s report, which vouched for the safety of the dam.
The five-member SC committee, headed by former Chief Justice of India A. S. Anand, had said “the dam is hydrologically, structurally and seismically safe” and asked Kerala to reconsider its decision to decommission the existing dam and build a new one.
Ground water levels are being measured four times a year during January, April/ May, August and November. The regime monitoring started in the year 1969 by Central Ground Water Board. At present a network of 14966 observation wells located all over the country is being monitored.
Setting at rest the controversy over the safety of the 116-year-old Mullaperiyar dam, the Empowered Committee, headed by the former Chief Justice of India A.S. Anand, has said it is “structurally and hydrologically safe, and Tamil Nadu can raise the water level from 136 to 142 feet after carrying out certain repairs.”
In its report submitted to the Supreme Court on Wednesday, the committee is understood to have said: “The dam is seismically safe.” Last year's earth tremors in that region “did not have any impact on the Mullaperiyar dam and the Idukki reservoir and there was no danger to the safety of the two dams.”
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Bibliography: Cover: Science Fantasy, August 1965
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Title: Cover: Science Fantasy, August 1965
Author: Keith Roberts
Year: 1965
Type: COVERART
ISFDB Record Number: 1102909
User Rating: This title has fewer than 5 votes. VOTE
Current Tags: None Add Tags
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Copyright (c) 1995-2011 Al von Ruff.
ISFDB Engine - Version 4.00 (04/24/06)
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Sensors 2011, 11(3), 2715-2727; doi:10.3390/s110302715
Article
Wireless Remote Weather Monitoring System Based on MEMS Technologies
1 Department of Mechanical Engineering, Chinese Military Academy, Kaohsiung 830, Taiwan 2 Department of Mechanical and Automation Engineering, Da-Yeh University, Changhua 515, Taiwan 3 Department of Materials Engineering, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
* Author to whom correspondence should be addressed.
Received: 31 December 2010; in revised form: 12 February 2011 / Accepted: 14 February 2011 / Published: 1 March 2011
(This article belongs to the Special Issue 10 Years Sensors - A Decade of Publishing)
Download PDF Full-Text [382 KB, uploaded 1 March 2011 16:39 CET]
Abstract: This study proposes a wireless remote weather monitoring system based on Micro-Electro-Mechanical Systems (MEMS) and wireless sensor network (WSN) technologies comprising sensors for the measurement of temperature, humidity, pressure, wind speed and direction, integrated on a single chip. The sensing signals are transmitted between the Octopus II-A sensor nodes using WSN technology, following amplification and analog/digital conversion (ADC). Experimental results show that the resistance of the micro temperature sensor increases linearly with input temperature, with an average TCR (temperature coefficient of resistance) value of 8.2 × 10−4 (°C−1). The resistance of the pressure sensor also increases linearly with air pressure, with an average sensitivity value of 3.5 × 10−2 (Ω/kPa). The sensitivity to humidity increases with ambient temperature due to the effect of temperature on the dielectric constant, which was determined to be 16.9, 21.4, 27.0, and 38.2 (pF/%RH) at 27 °C, 30 °C, 40 °C, and 50 °C, respectively. The velocity of airflow is obtained by summing the variations in resistor response as airflow passed over the sensors providing sensitivity of 4.2 × 10−2, 9.2 × 10−2, 9.7 × 10−2 (Ω/ms−1) with power consumption by the heating resistor of 0.2, 0.3, and 0.5 W, respectively. The passage of air across the surface of the flow sensors prompts variations in temperature among each of the sensing resistors. Evaluating these variations in resistance caused by the temperature change enables the measurement of wind direction.
Keywords: MEMS; WSN; weather monitoring system
Article Statistics
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Cite This Article
MDPI and ACS Style
Ma, R.-H.; Wang, Y.-H.; Lee, C.-Y. Wireless Remote Weather Monitoring System Based on MEMS Technologies. Sensors 2011, 11, 2715-2727.
AMA Style
Ma R-H, Wang Y-H, Lee C-Y. Wireless Remote Weather Monitoring System Based on MEMS Technologies. Sensors. 2011; 11(3):2715-2727.
Chicago/Turabian Style
Ma, Rong-Hua; Wang, Yu-Hsiang; Lee, Chia-Yen. 2011. "Wireless Remote Weather Monitoring System Based on MEMS Technologies." Sensors 11, no. 3: 2715-2727.
Sensors EISSN 1424-8220 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
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Sensors 2013, 13(1), 221-240; doi:10.3390/s130100221
Article
The Aeroflex: A Bicycle for Mobile Air Quality Measurements
1 VITO — Flemish Institute for Technological Research, Boeretang 200, 2400 Mol, Belgium 2 Department of Information Technology (INTEC), Ghent University, Sint-Pietersnieuwstraat 41, 9000 Ghent, Belgium These authors contributed equally to this work.
* Author to whom correspondence should be addressed.
Received: 27 September 2012; in revised form: 6 December 2012 / Accepted: 17 December 2012 / Published: 24 December 2012
(This article belongs to the Special Issue Workshop Sensing A Changing World 2012)
Download PDF Full-Text [1388 KB, uploaded 24 December 2012 09:40 CET]
Abstract: Fixed air quality stations have limitations when used to assess people's real life exposure to air pollutants. Their spatial coverage is too limited to capture the spatial variability in, e.g., an urban or industrial environment. Complementary mobile air quality measurements can be used as an additional tool to fill this void. In this publication we present the Aeroflex, a bicycle for mobile air quality monitoring. The Aeroflex is equipped with compact air quality measurement devices to monitor ultrafine particle number counts, particulate mass and black carbon concentrations at a high resolution (up to 1 second). Each measurement is automatically linked to its geographical location and time of acquisition using GPS and Internet time. Furthermore, the Aeroflex is equipped with automated data transmission, data pre-processing and data visualization. The Aeroflex is designed with adaptability, reliability and user friendliness in mind. Over the past years, the Aeroflex has been successfully used for high resolution air quality mapping, exposure assessment and hot spot identification.
Keywords: measurement bike; mobile sensing; automated data infrastructure; spatio-temporal data; air quality; air pollution ; monitoring; mapping; exposure; PM10
Article Statistics
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MDPI and ACS Style
Elen, B.; Peters, J.; Poppel, M.V.; Bleux, N.; Theunis, J.; Reggente, M.; Standaert, A. The Aeroflex: A Bicycle for Mobile Air Quality Measurements. Sensors 2013, 13, 221-240.
AMA Style
Elen B, Peters J, Poppel MV, Bleux N, Theunis J, Reggente M, Standaert A. The Aeroflex: A Bicycle for Mobile Air Quality Measurements. Sensors. 2013; 13(1):221-240.
Chicago/Turabian Style
Elen, Bart; Peters, Jan; Poppel, Martine V.; Bleux, Nico; Theunis, Jan; Reggente, Matteo; Standaert, Arnout. 2013. "The Aeroflex: A Bicycle for Mobile Air Quality Measurements." Sensors 13, no. 1: 221-240.
Sensors EISSN 1424-8220 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
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kae
Contributions
kv-webme 1822 commits Feb 2011 to Present
CEO at KV SItes
Designed it, built most of it, even wrote a book on it.
webworks-webme 441 commits Nov 2008 to Oct 2011
developer
SaorFM 50 commits Aug 2010 to Sep 2010
Developer
design, documentation, code, testing
KFM - Kae's File Manager 248 commits Nov 2007 to Jun 2010
Copyright © 2013 Black Duck Software, Inc. and its contributors, Some Rights Reserved. Unless otherwise marked, this work is licensed under a Creative Commons Attribution 3.0 Unported License . Ohloh ® and the Ohloh logo are trademarks of Black Duck Software, Inc. in the United States and/or other jurisdictions. All other trademarks are the property of their respective holders.
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User:Hala Ouzon-Shubeita
From OpenWetWare
Revision as of 14:57, 18 January 2013 by Hala Ouzon-Shubeita (Talk | contribs)
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I am a new member of OpenWetWare!
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Hala Ouzon-Shubeita (an artistic interpretation)
I work in the Your Lab at XYZ University. I learned about OpenWetWare from my professor, and I've joined because class requirement.
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• Year, PhD, Institute
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• Year, BS, Institute
Research interests
1. Interest 1
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3. Interest 3
Publications
1. Goldbeter A and Koshland DE Jr. . pmid:6947258. PubMed HubMed [Paper1]
2. JACOB F and MONOD J. . pmid:13718526. PubMed HubMed [Paper2]
leave a comment about a paper here
3. Mark Ptashne. A genetic switch. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2004. isbn:0879697164. [Book1]
All Medline abstracts: PubMed HubMed
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Personal tools
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[10] The devil who deceived them was thrown into the lake of fire and sulfur, where the beast and the false prophet are also. They will be tormented day and night forever and ever.
This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 United States License.
An XML version of this text is available for download, with the additional restriction that you offer Perseus any modifications you make. Perseus provides credit for all accepted changes, storing new additions in a versioning system.
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Menu Bar
Home Calendar Topics Just Charlestown About Us
Thursday, June 14, 2012
Builders' Bill dies, again
No Wine at Markets, No Sharps in Trash, No Big Pets
By TIM FAULKNER/ecoRI.org News staff
PROVIDENCE — The House and Senate worked past midnight today to wrap up the 2012 session. Several environmental bills passed, and others stalled, such as a bill (pdf) to establish the East Bay Energy Consortium.
The House and Senate also passed an override of a veto by Gov. Lincoln Chafee on a bill (pdf) exempting property owners in Warwick from connecting to the municipal sewage system. The bill was opposed by the state Department of Environmental Management (DEM).
• Here are the environmental bills that passed:
Paint. The House and Senate approved legislation (pdf) for disposal of unused paint products at paint stores. The program would be funded through a fee on the sale of paint.
Children's jewelry, but not toys or clothes, would conform to national safety standards in a bill (pdf) passed by the House and Senate.
Paper and packaging. A nine-member commission has a year to study (pdf) methods for cutting paper and packaging waste in order to extend the life of the Central Landfill in Johnston.
Climate change. The House and Senate passed a bill (pdf) that places an advisory council under the Coastal Resources Management Council (CRMC) as part of the Climate Risk Reduction Act of 2010.
Medical sharps. Legislation (pdf) passed requiring hospitals and pharmacies to provide disposal of medical sharps, such as syringes and epi-pens and other sharp medical instruments.
Landfill. Three bills passed in response to last year's odor crisis at the Central Landfill. Paper, glass, wood, food waste, plaster, drywall and leaves are banned from the daily cover of the landfill in a bill (pdf) that aims to reduce items suspected of contributing to the problem.
Terms (pdf) of an existing but inactive citizens advisory board at the Rhode Island Resource Recovery Corporation were revised to address governance at the Central Landfill. The thirdbill (pdf) requires the installation of six air-monitoring stations that must be built near the landfill to gauge odors.
Court action on land trust property. The Senate and the House both passed guidelines(pdf) defining which entities can challenge conservation restrictions on land trust properties.
Pets. Those weighing less than 35 pounds will be allowed (pdf) at state campgrounds. Standards (pdf) for tethering dogs were also passed by the Senate and House.
Artificial reef. Old boats will be used for an artificial reef program (pdf) in Block Island Sound.
Tanning beds. Persons younger than 18 will need parental consent to use tanning salons.
Efficient power generation. Electric companies will be required to install combined heat and power (CHP) or cogeneration systems to recapture lost energy in a bill (pdf) that modifies existing efficiency standards.
Sewage and wetlands. Zoning rules relating to sewage systems and wetlands must be approved by the DEM in a bill (pdf) passed by the General Assembly.
Livestock standards. The Senate and the House passed a bill (pdf) creating an advisory board for setting standards for the welfare of farm animals. The committee would report to the DEM director. Docking or altering of cows' tails would be prohibited in a bill (pdf) passed by the House and Senate.
• These bills were left waiting at the altar:
Beer and wine at farmers markets. The House passed a bill (pdf) allowing local vineyards to sell wine at farmers markets, but the Senate did not reciprocate.
Drugs in the water. The Senate passed a bill (pdf) creating a commission to study the health risks of pharmaceutical waste in the water supply. The House, however, took no action.
Outdoor wood boilers. The House passed a bill (pdf) regulating outdoor wood boilers, but the Senate didn't pass the legislation out of committee.
Tree care and mulch. The House passed a bill (pdf) adding tree care and mulch to the state definition of agricultural operations in the state Right to Farm laws.
Dry Lands Act. The annual effort (pdf) by the construction industry to increase building near environmentally sensitive areas such as wetlands wasn't voted out of committee.
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Place:Mountville, Lancaster, Pennsylvania, United States
Watchers
NameMountville
TypeBorough
Coordinates40.04°N 76.432°W
Located inLancaster, Pennsylvania, United States
source: Getty Thesaurus of Geographic Names
the text in this section is copied from an article in Wikipedia
Mountville is a borough in Lancaster County, Pennsylvania, United States. The population was 2,444 at the 2000 census. The original Charles Chips potato chip factory was located here.
Research Tips
This page uses content from the English Wikipedia. The original content was at Mountville, Pennsylvania. The list of authors can be seen in the page history. As with WeRelate, the content of Wikipedia is available under the Creative Commons Attribution/Share-Alike License.
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Flocculation
Jump to: navigation, search
Separation processes
File:ChemSepProcDiagram.svg
Processes
Acid-base extractionChromatographyCrystallizationDissolved air flotationDistillationDryingElectrochromatographyFiltrationFlocculationFroth flotationLiquid-liquid extractionRecrystallizationSedimentationSublimation
Devices
API oil-water separatorCentrifugeMixer-settlerProtein skimmerSublimation apparatusStill
Multiphase systems
Aqueous two phase systemAzeotropeEutectic
This box: view talk edit
Flocculation is a process where a solute comes out of solution in the form of floc or "flakes." The term is also used to refer to the process by which fine particulates are caused to clump together into floc. The floc may then float to the top of the liquid, settle to the bottom of the liquid, or can be readily filtered from the liquid.
In chemistry: flocculation-gentle agitation that promotes collision between these small aggregates to form floc, it will large enough to settle.
In geology, flocculation is a condition in which clays, polymers or other small charged particles become attached and form a fragile structure, a floc. In dispersed clay slurries, flocculation occurs after mechanical agitation ceases and the dispersed clay platelets spontaneously form flocs because of attractions between negative face charges and positive edge charges.
In biology the process is used to refer to the asexual aggregation of microorganisms, most commonly brewing yeast at the end of a brew.
Flocculation & sedimentation is widely employed in the purification of drinking water as well as sewage treatment, stormwater treatment and treatment of other industrial wastewater streams.
Flocculants
Flocculants, or flocculating agents, are chemicals that promote flocculation by causing colloids and other suspended particles in liquids to aggregate, forming a floc. Flocculants are used in water treatment processes to improve the sedimentation or filterability of small particles. For example, a flocculant may be used in swimming pool or drinking water filtration to aid removal of microscopic particles which would otherwise cause the water to be cloudy and which would be difficult or impossible to remove by filtration alone.
Many flocculants are multivalent cations such as aluminium, iron, calcium or magnesium. These positively charged molecules interact with negatively charged particles and molecules to reduce the barriers to aggregation. In addition, many of these chemicals, under appropriate pH and other conditions, react with water to form insoluble hydroxides which, upon precipitating, link together to form long chains or meshes, physically trapping small particles into the larger floc.
Long-chain polymer flocculants, such as modified polyacrylamides, are manufactured and sold by the flocculant producing business.
Modified Polyacrylamides can be supplied in dry or liquid form for use in the flocculation process. The most common liquid polyacrylamide is supplied as an emulsion with 10-40% actives and the rest is a carrier fluid, surfactants and latex. Emulsion polymers require activation to invert the emulsion and allow the electrolyte groups to be exposed.
Other factors such as pH, temperature, and salinity can induce flocculation or influence flocculation rates.
The following chemicals are used as flocculants:
The following natural products are used as flocculants:
Coagulants
The terms flocculant and coagulant are sometimes used interchangeably, but it is more accurate to use the term coagulant for a chemical that contributes to molecular aggregation, rather than particulant aggregation.[citation needed] Usually dissolved substances are aggregated into microscopic particles by a coagulant and then these particles may be flocculated into a macroscopic floc with a flocculant. In general, coagulants will have higher net charge and a lower molecular weight than flocculants.
Cougulation: addition of reagent that cause aggregation of collodial particles.
Note: Flocculation is not the same as coagulation. Coagulation is the irreversible clumping of particles, ie. caking had occurred. [citation needed]
Deflocculation
A deflocculant is a chemical that is added to prevent a colloid from coming out of suspension.
See also
External links
References
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{
"content_type": "text/html",
"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:64893",
"uncompressed_offset": 816849778,
"url": "www.yam-mag.com/news/trailers/happy-feet-2-trailer/",
"warc_date": "2013-11-22T14:34:11.000Z",
"warc_filename": "<urn:uuid:b0cc4120-f660-4433-a222-c9bdaf682239>",
"warc_url": "http://www.yam-mag.com/news/trailers/happy-feet-2-trailer/"
}
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ARTICLE
Happy Feet 2 Trailer//
posted Thursday, October 6th, 2011
by | Comments (2)
Following the teaser trailer posted back in July, we got more information on Happy Feet 2, including a confirmation that Pink’s voice in the film will not only be for a singing role.
Elijah Wood is back to reprise his role as the voice of Mumble. Robin Williams will once again voice Ramon and Lovelace. The cast is rounded out with the voices of Sofia Vergara, Hank Azaria, and special appearances by Matt Damon and Brad Pitt as The Krill.
Happy Feet 2 opens on November 18th in the United States.
UPCOMING EVENTS//
EVENTS//
ADS//
POLLS//
Who is your reigning Queen or Princess of Pop? [choose up to 5]
Total Voters: 252
Loading ...
TWEETS//
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{
"content_type": "text/html",
"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:64905",
"uncompressed_offset": 18849392,
"url": "ask.wireshark.org/questions/8615/inbound-and-outbound-traffic",
"warc_date": "2013-11-22T14:35:11.000Z",
"warc_filename": "<urn:uuid:d93becc7-24db-4083-8270-8e3b2e06778f>",
"warc_url": "http://ask.wireshark.org/questions/8615/inbound-and-outbound-traffic"
}
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Hi, I'm writing a Lua program to process data that captured by tshark, and I'm in need for a filter to separate inbound traffic from outbound traffic in our network to process each group alone. Can some one help me in this, because I'm new in both: Lua and Wireshark. Thanks
asked 25 Jan '12, 22:39
Leena
51131721
accept rate: 0%
edited 26 Jan '12, 00:46
I'm assuming you're interested in IP traffic only.
You would create two taps (aka "Listeners") -- one filtered for incoming packets to your host and another for outgoing:
local HOST_IP = '1.2.3.4'
local tap_in = Listener.new(nil, 'ip.dst=='..HOST_IP)
local tap_out = Listener.new(nil, 'ip.src=='..HOST_IP)
-- handles packets going to $HOST_IP
function tap_in.packet(pinfo, buf)
print('#'..pinfo.number, '<IN>', tostring(buf))
end
-- handles packets going out from $HOST_IP
function tap_out.packet(pinfo, buf)
print('#'..pinfo.number, '<OUT>', tostring(buf))
end
Copy this file to a temporary directory (e.g., /tmp/test.lua), and run it from TShark as follows:
$ tshark -Xlua_script:/tmp/test.lua
You can also load this from Wireshark (as shown in a recent post).
link
answered 02 Feb '12, 18:53
helloworld
2.6k21739
accept rate: 27%
Your answer
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Asked: 25 Jan '12, 22:39
Seen: 1,401 times
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{
"content_type": "text/html",
"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:64959",
"uncompressed_offset": 89985016,
"url": "elinux.org/ELinuxWiki:History",
"warc_date": "2013-11-22T14:35:11.000Z",
"warc_filename": "<urn:uuid:d93becc7-24db-4083-8270-8e3b2e06778f>",
"warc_url": "http://elinux.org/ELinuxWiki:History"
}
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ELinuxWiki:History
From eLinux.org
Jump to: navigation, search
Here is some historical information about the eLinux wiki:
Tim Riker created the first elinux.org web site, which focused on hosting information about embedded Linux development on specific boards and products. Mostly, the site held information useful for people placing (or customizing) embedded Linux on existing hardware products.
The current form of the eLinux wiki was created in 2006, sponsored by the CE Linux Forum in collaboration with Tim Riker. Tim donated the domain name, and the software was changed from MoinMoin to MediaWiki.
It was initially hosted by Movial, then moved to a virtual server hosted by GoDaddy, in February of 2008.
Initial general technology content was converted from material from CELF's public developer wiki.
Contests
In November of 2008, CELF sponsored it's first "editor contest". See ELCE2008 Editor Contest
The second "editor contest" was held in 2009. See ELC2009_Editor_Contest
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{
"content_type": "text/html",
"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:64971",
"uncompressed_offset": 100273434,
"url": "familysearch.org/learn/wiki/en/Chisago_County,_Minnesota",
"warc_date": "2013-11-22T14:35:11.000Z",
"warc_filename": "<urn:uuid:d93becc7-24db-4083-8270-8e3b2e06778f>",
"warc_url": "http://familysearch.org/learn/wiki/en/Chisago_County,_Minnesota"
}
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Chisago County, MinnesotaEdit This Page
From FamilySearch Wiki
United States Minnesota Chisago County
Guide to Chisago County Minnesota genealogy. Birth records, marriage records, death records, census records, family history, and military records.
Minnesota
Online Records
Chisago County, Minnesota
Map
Location in the state of Minnesota
Location of Minnesota in the U.S.
Facts
Founded March 31, 1851
County Seat Center City
Courthouse
Address Chisago County Courthouse
313 North Main Street
Center City, MN 55012
Phone: 651-257-1300
Phone: 612-213-0438
Chisago County Website
Contents
County Courthouse
Clerk District Court has birth and death records from 1870,
marriage records from 1852, court records from 1880 and divorce records; Probate Judge has probate records.
Register of Deeds has land records.[1]
History
Parent County
1851--Chisago County was created 31 March 1851 from Washington and Ramsey Counties.
• County seat: Center City [2]
• For a brief history of how Chisago County was named, click here, then select Chisago County.
Boundary Changes
Record Loss
Places/Localities
Populated Places
Cities
Center City | Chisago City | Harris | Lindstrom | North Branch | Rush City | Shafer | Stacy | Taylors Falls | Wyoming
Townships
Amador Township | Chisago Lake Township | Fish Lake Township | Franconia Township | Lent Township | Nessel Township | Rushseba Township | Shafer Township | Sunrise Township | Wyoming Township
Unincorporated Communities
Almelund | Franconia | Palmdale | Rush Point | Stark | Sunrise
Neighboring Counties
Resources
Cemeteries
Church
Court
Land
Local Histories
Maps
Military
Civil War
Civil War service men from Chisago County served in various regiments. Men often joined a company (within a regiment) that originated in their county. Listed below are companies or regiments that were formed from men of Chisago County.
- 1st Regiment, Minnesota Cavalry (Mounted Rangers), Company M.
- 1st Regiment, Minnesota Infantry, Company C.
- 7th Regiment, Minnesota Infantry, Company C.
Newspapers
Probate
Taxation
Vital Records
Societies and Libraries
Family History Centers
Web Sites
References
1. Handybook for Genealogists: United States of America, 10th ed. (Draper, Utah: Everton Pub., 2002), Chisago County, Minnesota page 363, At various libraries (WorldCat); FHL Book 973 D27e 2002.
2. The Handybook for Genealogists: United States of America,10th ed. (Draper, UT:Everton Publishers, 2002).
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).
• This page was last modified on 12 April 2013, at 03:15.
• This page has been accessed 1,570 times.
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{
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"uncompressed_offset": 100291894,
"url": "familysearch.org/learn/wiki/en/Roach_Research_Resources_for_Missionaries",
"warc_date": "2013-11-22T14:35:11.000Z",
"warc_filename": "<urn:uuid:d93becc7-24db-4083-8270-8e3b2e06778f>",
"warc_url": "http://familysearch.org/learn/wiki/en/Roach_Research_Resources_for_Missionaries"
}
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Roach Research Resources for MissionariesEdit This Page
From FamilySearch Wiki
This list of resources is designed to help missionaries while they are helping others with their Family History, but during and after their missions. A special thanks to Merrill White for providing suggested materials and websites!
FamilySearch Wiki
Search for specific genealogical research guidance on a location: It is like a google.com for all of the old research outlines, and contains more updated information.
FamilySearch Research Guidance
Click on ‘research guidance.’ This is a more awkward method of searching, but allows the searcher to get suggestions of records to search.
Random Acts of Genealogical Kindness
Trade research or help someone, and they will help you with gathering a record! This is a great way to network with other researchers or just everyday individuals who are willing to help someone with records around the world!
Research Helps
This site contains several sites to help even the most basic researcher.
FamilySearch Wiki
Click on ‘Record Search,’ then register to search records that have been indexed AND those that are digitized, but not yet indexed! These databases are updated daily, so check back if you don’t find what you are looking for!
Family History Library
Click on ‘Services’ in the left-hand column for phone numbers and e-mail addresses for free help and consultation, and to download forms to order copies by mail!
Family History Library Catalog
The Catalog will contain links to all digitized books in the future! Also, new material is being added every day. If the records were not there last time you checked, check back on a regular basis to see what is new!
Family History Consultants and Priesthood Leaders
If you or someone else is called as a consultant, the first step should be registering as a consultant. Many consultants confuse this with registering for FamilySearch. This is different. Special training is available to consultants, but only if they are registered! See also this site.
Personal Ancestral File
Notice there is NO www. in front! This site is like taking a class right at the library, but at your own pace! It contains everything from basic data entry to advanced focus filter! It includes step-by-step instructions and hands-on demonstrations with audio!
BYU Family History Site
Once again, no www. Check ‘Resources,’ and ‘Current Projects’ regularly. Students and teachers collaborate together each year to make resources available free to the public!
US Census Tutorial
Once again, no www. The US Federal Census is the most valuable federal records available, because they allow the searcher to Learn how to use the Census to locate ancestors! Enter, and then click on ‘Tutorial’ at the top of the page.
Family History Lessons
No www. Click on ‘Online Lessons’ or ‘Printable Lessons’ to learn valuable steps. Whether you are learning, or teaching (click on ‘Teaching Outlines’), this is a valuable resource.
Family History Archives
Look up a digital family history that you may view at home! This collection grows every day, so check back if you don’t find anything!
Family Insight
Remember, if you need help with PAF Insight, this is not a church product. Use the link and click on the ‘Support’ tab at the top of the page. The producers of this software will provide needed support and help.
Product Support: 1-866-406-1830
This number is easy to remember because the church was organized on 4/06/1830. Just remember it is 866- not 800-. This toll-free number may be used for any FamilySearch Products, including the New FamilySearch and PAF.
RootsWeb
This is the oldest free genealogy website online, hosted by ancestry.com. Take time to search for free databases containing a variety of records depending on the area.
FamilySearch Support
Go to this website to fill out an online form to request help with research support, or send an e-mail directly to support@familysearch.org. (This last link is not a website, but an e-mail address. Open your e-mail account and send messages to this address with research questions).
Distribution Materials
• A Member’s Guide to Temple and Family History Work (34697)
• How Do I Start My Family History? (32916)
• Church Handbook of Instructions, Book 2 Section 9, “Temple and Family History Work” (35709)
• Mormon Immigration Index (50174000)
• A Guide to Research (30971)
• Training for Family History Leaders DVD (00410090)
• Welcome to the Family History Center (35753000)
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).
• This page was last modified on 27 February 2012, at 15:25.
• This page has been accessed 1,373 times.
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{
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"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:65012",
"uncompressed_offset": 127399725,
"url": "hitchwiki.org/en/Agrigento",
"warc_date": "2013-11-22T14:35:11.000Z",
"warc_filename": "<urn:uuid:d93becc7-24db-4083-8270-8e3b2e06778f>",
"warc_url": "http://hitchwiki.org/en/Agrigento"
}
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Agrigento
From Hitchwiki
Jump to: navigation, search
Agrigento
Information
Country: Flag of Italy Italy
State: Agrigento (Province)
Population: 59.100
Licence Plate: AG
Motorways:
More Info:
Agrigento is a city on Sicily
Hitching out
Northwest towards Catania
From the roundabout right by the bus station, walk out onto the huge bridge on the same side as traffic leaving the town. Follow it all the way until the bridge ends and take the first ramp that goes up to the right for the national road SS122. At the top, you can stand on the white line area and hitch.
Other useful info
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{
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}
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Image:Laporan Praktikum 3 pH, titrasi dan pengenceran.pdf
From OpenWetWare
(Difference between revisions)
Jump to: navigation, search
Laporan_Praktikum_3_pH,_titrasi_dan_pengenceran.pdf (file size: 84 KB, MIME type: application/pdf)
Revision as of 21:55, 31 October 2012
File history
Click on a date/time to view the file as it appeared at that time.
Date/TimeDimensionsUserComment
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Personal tools
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{
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"url": "quotationsbook.com/book/aleah_bree/",
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"warc_url": "http://quotationsbook.com/book/aleah_bree/"
}
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aleah_bree's bookmarks
"Don't part with your illusions. When they are gone you may still exist, but you have ceased to live."
Twain, Mark on deception
33 fans of this quote
"We should be careful to get out of an experience only the wisdom that is in it -- and stop there; lest we be like the cat that sits down on a hot stove-lid. She will never sit down on a hot stove-lid again -- and that is well; but also she will never sit down on a cold one anymore."
Twain, Mark on experience
13 fans of this quote
"Where a blood relation sobs, an intimate friend should choke up, a distant acquaintance should sigh, a stranger should merely fumble sympathetically with his handkerchief."
Twain, Mark on funerals
3 fans of this quote
aleah's quote collection
I'm female and made my book on 30th November 2012.
My book as a pdf
My feed
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{
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"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:65080",
"uncompressed_offset": 220224200,
"url": "quotationsbook.com/book/miredo/",
"warc_date": "2013-11-22T14:35:11.000Z",
"warc_filename": "<urn:uuid:d93becc7-24db-4083-8270-8e3b2e06778f>",
"warc_url": "http://quotationsbook.com/book/miredo/"
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miredo's bookmarks
"Neither irony or sarcasm is argument."
Butler, Samuel on argument
"Humor does not include sarcasm, invalid irony, sardonicism, innuendo, or any other form of cruelty. When these things are raised to a high point they can become wit, but unlike the French and the English, we have not been much good at wit since the days of Benjamin Franklin."
Thurber, James on wit
Mel's quote collection
I'm female and made my book on 5th March 2010.
My book as a pdf
My feed
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{
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"url": "quotationsbook.com/quote/gift/34333/",
"warc_date": "2013-11-22T14:35:11.000Z",
"warc_filename": "<urn:uuid:d93becc7-24db-4083-8270-8e3b2e06778f>",
"warc_url": "http://quotationsbook.com/quote/gift/34333/"
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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
Love prefers twilight to daylight. Holmes, Oliver Wendell
Make a fabulous personalised bracelet or other form of jewellery with this quote
Click the banner below to pick the kind of jewellery you'd like ...
Choose something popular ...
Make a custom wrapped canvas ...
Make custom holiday cards ...
Make custom t-shirts ...
Make custom holiday gifts for boys ...
Make custom holiday gifts for girls ...
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A selection of more great products and gifts!
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 »
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{
"content_type": "text/html",
"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:65083",
"uncompressed_offset": 220244259,
"url": "quotationsbook.com/quote/gift/7281/",
"warc_date": "2013-11-22T14:35:11.000Z",
"warc_filename": "<urn:uuid:d93becc7-24db-4083-8270-8e3b2e06778f>",
"warc_url": "http://quotationsbook.com/quote/gift/7281/"
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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
I've not got a first in philosophy without being able to muddy things pretty satisfactory. Banham, John
Make a fabulous personalised bracelet or other form of jewellery with this quote
Click the banner below to pick the kind of jewellery you'd like ...
Choose something popular ...
Make a custom wrapped canvas ...
Make custom holiday cards ...
Make custom t-shirts ...
Make custom holiday gifts for boys ...
Make custom holiday gifts for girls ...
Make custom holiday gifts for men ...
A selection of more great products and gifts!
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 »
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{
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"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:65084",
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"warc_url": "http://quotationsbook.com/quotes/author/2628/"
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Quotes by Frederick The Great, (Frederick II)
We don't have a biography. Please consult wikipedia.
"I must in the face of a storm, think, live and die as a king."
Frederick The Great, (Frederick II) on destiny
"In trying to defend everything he defended nothing."
Frederick The Great, (Frederick II) on focus
"An educated people can be easily governed."
Frederick The Great, (Frederick II) on government
"Every man must get to Heaven his own way."
Frederick The Great, (Frederick II) on individuality
5 fans of this quote
"They say that kings are made in the image of God. If that is what he looks like, I feel sorry for God."
Frederick The Great, (Frederick II) on kings
"Don't forget your great guns, which are the most respectable arguments of the rights of kings."
Frederick The Great, (Frederick II) on kings
"It seems to me that man is made to act rather than to know: the principles of things escape our most persevering researches."
Frederick The Great, (Frederick II) on knowledge
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Frederick The Great, (Frederick II) on opposition
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Frederick The Great, (Frederick II) on philosophers and philosophy
"The greatest and noblest pleasure which men can have in this world is to discover new truths; and the next is to shake off old prejudices."
Frederick The Great, (Frederick II) on pleasure
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Frederick The Great, (Frederick II) on talent
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Frederick The Great, (Frederick II) on writers and writing
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Best Slideshow about Open Access
Have you ever wondered what the problems of publishing science are, how to solve these and what exactly open access means? Martin Fenner will answer all of your questions:
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1709 Blog: for all the copyright community
Thursday, 2 February 2012
Seminar news
You're never too young
to learn about copyright
The 1709 Blog's Red Bus seminar on Tuesday 21 February now has over 80 people signed up, including a couple from overseas who are coming all the way from over the sea to hear Michael Edenborough QC explain the ruling in Temple Island Collections v New England Tea (you can read the judgment and enjoy the buses here). I can now reveal that we have another speaker: copyright commentator, author and enthusiast Brigitte Lindner will be comparing the analysis of Judge Birss QC with the sort of approach we might expect from a court with a civil law tradition, and the panel has been enriched by the presence of that affable Australian legend and writer of IP blockbusters Professor Sam Ricketson. Two further panelists remain to be confirmed.
If you'd like to join us in the pleasant setting of Olswang LLP's High Holborn office, under the chairmanship of indigenous 1709 Blog team member John Enser, there are still a few spaces left -- but not many. Email here, with subject line "Red Bus Seminar", to secure your place.
*******************************************
The 1709 Blog has another seminar coming up, this time on Tuesday 3 April 2012. We have a speaker, a subject and a time (William Patry, "How to Fix Copyright" and breakfast, 8.30am to 10am). What we don't yet have is a venue. If you wish to offer your premises, together with a breakfast buffet spread, for a bunch of copyright enthusiasts, in return for the eternal gratitude of the 1709 Blog team and even some half-decent publicity, please email me here and let me know.
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"Wikitravel has a speed and convenience the books' publishers can only envy." Time Europe
Category:Dili
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UN/LOCODE:TLDIL
lat/long: -8.55/125.5667
Media in category "Dili"
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Naples (New York)
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Naples is a city in the Finger Lakes.
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Naples is located at the south end of Canandaigua Lake, about 30 minutes south of Canandaigua.
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• Bob & Ruth's
Great diner food. Excellent milkshakes.
204 North Main St, Naples
585-374-5122
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
6321.0.55.001 - Industrial Disputes, Australia, Sep 2008 Quality Declaration
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 04/12/2008
Page tools: Print Page Print All RSS Search this Product
SEPTEMBER KEY FIGURES
Quarter
Year ended
June 2008
September 2008
September 2007
September 2008
Number of disputes
Commenced in period (no.)
52
48
141
169
Total (no.)
60
56
151
172
Employees involved
Newly involved ('000)
59.9
9.7
72.2
135.1
Total ('000)
69.0
60.5
72.9
135.2
Working days lost ('000)
86.5
36.2
79.6
189.8
Working days lost
SEPTEMBER KEY POINTS
QUARTERLY ESTIMATES
• For the September quarter 2008, there were 56 disputes, 4 less than in the June quarter 2008.
• The number of employees involved in industrial disputes in the September quarter 2008 was 60,500, a decrease from 69,000 in the June quarter 2008.
• There were 36,200 working days lost due to industrial disputation in the September quarter 2008, a decrease from 86,500 in the June quarter 2008.
• The Education and Health and community services industries accounted for 17,900 (49%) of the total number of working days lost in the September quarter 2008. The Coal mining industry had the highest number of working days lost per thousand employees (46.5) for the quarter.
• In the September quarter 2008, New South Wales accounted for 14,700 (41%) of working days lost. South Australia had the highest number of working days lost per thousand employees (6.3) for the quarter.
YEAR ENDED ESTIMATES
• During the year ended September 2008, there were 172 disputes, 21 more than in the year ended September 2007.
• During the year ended September 2008, there were 189,800 working days lost compared with 79,600 in the year ended September 2007.
NOTES
FORTHCOMING ISSUES
ISSUE (QUARTER) Release Date
December 2008 13 March 2009
March 2009 4 June 2009
FORTHCOMING CHANGES
From the March quarter 2009 issue of this publication, to be released in June 2009, industry statistics will be presented on the basis of a new edition (2006) of the Australian and New Zealand Standard Industrial Classification (ANZSIC).
The December quarter 2008 issue, to be released in March 2009, will be the last release of industry data on the basis of the 1993 edition of ANZSIC.
For further details see paragraphs 15 to 18 of the Explanatory Notes.
REVISIONS
There are no revisions to data in this issue.
INQUIRIES
For further information about these and related statistics, contact the National Information and Referral Service on 1300 135 070.
© 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.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Catalogue Number
1367.5 - Western Australian Statistical Indicators, 2010
Latest ISSUE Released at 11:30 AM (CANBERRA TIME) 20/01/2011 Final
Page tools: Print Page Print All RSS Search this Product
Contents >> Consumption >> Retail
RETAIL
NOVEMBER KEY FIGURES, Western Australia
Nov 2010
Oct 2010 to Nov 2010
Nov 2009 to Nov 2010
Turnover at current prices
$m
% change
% change
Trend estimates
2 217.6
0.3
2.2
Seasonally adjusted estimates
2 210.9
-0.2
1.5
Source: Retail Trade, Australia (cat. no. 8501.0).
• While the seasonally adjusted estimate decreased marginally (-0.2%) in November 2010, WA was one of four states to record positive growth in retail turnover in trend terms (0.3%).
• Despite flattening in early 2010, the WA trend estimate rose for four consecutive months to November 2010, to be 2.2% higher than for November 2009.
Monthly Retail Turnover, Current Prices
• Growth in monthly retail turnover in WA slowed following the global economic downturn. In the three years to November 2010, the average monthly increase in turnover was just 0.2%, compared with an average monthly increase of 0.6% during the previous three years.
Retail Turnover, Selected Industries: Seasonally Adjusted -
Change from Nov 2009 to Nov 2010
• The increase in retail turnover between November 2009 and November 2010 (1.5% in seasonally adjusted terms) was predominately driven by increased turnover in Cafes, restaurants and takeaway food services (up 11%).
• For the same period, decreases in turnover were recorded for Household goods retailing (down 3.6%) and Clothing, footwear and personal accessory (down 2.5%) .
This link takes you to time series spreadsheets from Retail Trade, Australia, Nov 2010 (cat. no.8501.0). Tables 3 and 4 contain monthly turnover data by state. Tables 11-13 contain retail turnover by state and industry.
Previous PageNext Page
© 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.
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Research article
Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus
Sandip Paul1, Anirban Dutta1, Sumit K Bag2,3, Sabyasachi Das2,4 and Chitra Dutta1,2*
Author Affiliations
1 Structural Biology & Bioinformatics Division, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 700 032, India
2 Bioinformatics Centre, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 700 032, India
3 Present address: Plant Molecular Biology & Genetic Engineering Division, National Botanical Research Institute, Rana Pratap Marg, Lucknow - 226001, India
4 Present address: Department of Pathology and Laboratory Medicine, Emory Vaccine Center, School of Medicine, Emory University, Atlanta, GA 30322, USA
For all author emails, please log on.
BMC Genomics 2010, 11:103 doi:10.1186/1471-2164-11-103
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2164/11/103
Received:5 October 2009
Accepted:10 February 2010
Published:10 February 2010
© 2010 Paul 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 marine cyanobacterium Prochlorococcus marinus, having multiple ecotypes of distinct genotypic/phenotypic traits and being the first documented example of genome shrinkage in free-living organisms, offers an ideal system for studying niche-driven molecular micro-diversity in closely related microbes. The present study, through an extensive comparative analysis of various genomic/proteomic features of 6 high light (HL) and 6 low light (LL) adapted strains, makes an attempt to identify molecular determinants associated with their vertical niche partitioning.
Results
Pronounced strand-specific asymmetry in synonymous codon usage is observed exclusively in LL strains. Distinct dinucleotide abundance profiles are exhibited by 2 LL strains with larger genomes and G+C-content ≈ 50% (group LLa), 4 LL strains having reduced genomes and G+C-content ≈ 35-37% (group LLb), and 6 HL strains. Taking into account the emergence of LLa, LLb and HL strains (based on 16S rRNA phylogeny), a gradual increase in average aromaticity, pI values and beta- & coil-forming propensities and a decrease in mean hydrophobicity, instability indices and helix-forming propensities of core proteins are observed. Greater variations in orthologous gene repertoire are found between LLa and LLb strains, while higher number of positively selected genes exist between LL and HL strains.
Conclusion
Strains of different Prochlorococcus groups are characterized by distinct compositional, physicochemical and structural traits that are not mere remnants of a continuous genetic drift, but are potential outcomes of a grand scheme of niche-oriented stepwise diversification, that might have driven them chronologically towards greater stability/fidelity and invoked upon them a special ability to inhabit diverse oceanic environments.
Background
Evolution of a microbe is often driven by its environment or life-style. Microorganisms adapted to some specialized environmental conditions have been reported to display conspicuous genome and/or proteome features [1-8]. Species of widely varying taxonomic origins, but thriving in same/similar environmental conditions such as high temperature or high salinity, may converge to similar genome and/or proteome composition. In contrast, closely related bacterial species inhabiting distinct ecological niches may display substantial genomic diversity [1-3,6,8-11]. Unveiling the plausible causes/consequences, at the genome and proteome levels, of such niche-dependent evolution of the microbial world poses a major challenge to the present-day life-scientists. The marine cyanobacterium Prochlorococcus marinus [12], having multiple ecotypes exhibiting distinct niche-specific phenotypic as well as genotypic characteristics, offers a useful system to address this issue.
Prochlorococcus are one of the most abundant life forms on this planet and more importantly, are major contributors to global photosynthesis [13-15]. A variety of Prochlorococcus strains, each specialized to dwell in different conditions of light, temperature and nutrient abundances [14,16-18] dominate the euphotic zones of the ocean - mostly between latitudes 40°S and 40°N, and sometimes beyond. To date, the complete genomes of 12 different strains of P. marinus have been sequenced (listed in Table 1) and wide variations have been observed in genetic architectures, genome sizes and genomic G+C-content of these strains [19]. On the basis of vertical niche partitioning, these 12 strains are classified into two major Prochlorococcus ecotypes: high light adapted (HL) ecotype being most abundant in surface waters and low light adapted (LL) ecotype dominating deeper waters [19,20]. 6 of the sequenced strains have been identified to belong to the LL group and the other 6 have been found to survive at HL conditions [19]. The phenomenon of oceanic niche differentiation for P. marinus has been previously investigated into - and several inferences regarding the effects of light adaptation, nutrient availability and predator influence on their genome evolution and diversification has been arrived at [21-24]. However, the full expanse of ecologically relevant differences in genomic, physicochemical and physiological characteristics among these strains are yet to be explored. In the present study, we have attempted to identify novel niche-specific molecular signatures in the genome and proteome compositions of 12 different Prochlorococcus strains, and also investigated the adaptive strategies of different Prochlorococcus strains for their survival in diverse oceanic environments.
Table 1. General features of 12 Prochlorococcus strains under study
It is worth mentioning in this context that Prochlorococcus is the first documented example of genome shrinkage along with A+T enrichment in a free-living organism [25]. Earlier examples of genome reduction had been restricted to endosymbionts or pathogens with a host-dependent lifestyle, which evolve under the constraint of frequent population bottlenecks with a subsequent increase in genetic drift [2,3,26-29]. Considering the abundance of P. marinus in the marine ecosystem, their reductive genome evolution might not be influenced by similar population bottlenecks and resulting genetic drifts, and thus seems to be a more complex phenomenon to explain. Although P. marinus genome evolution has been investigated previously [25,30] and the event of genome shrinkage have been ascribed to various factors related to their growth in oligotrophic waters [20,23,31], selection for metabolic economy [25,31,32], loss of low fitness genes [33], and smaller cell sizes [25], it is still unclear to what extent it has been driven by any random genetic drift and/or other specific selection force(s). Our analyses indicate that the ecotype-specific molecular signatures exhibited by P. marinus strains under study are not mere remnants of a continuous genetic drift, but a potential outcome of niche-oriented stepwise diversification of Prochlorococcus, orchestrated by an array of interplaying adaptive forces.
Results
In an attempt to understand the trends in molecular evolution in Prochlorococcus, we have analyzed various genome and proteome characteristics of 6 LL and 6 HL strains of P. marinus. The analyses of genome/proteome in P. marinus include the study of trends in codon, dinucleotide and amino acid usages, gene synteny of orthologous sequences, intergenic sequence composition, physicochemical properties of the encoded proteins and the extent of positive selection among different strains. These analyses were primarily directed towards the identification of niche-specific variations within different Prochlorococcus strains.
Strand-specific asymmetry in synonymous codon usage in low light adapted P. marinus genomes
In order to find out the trends in synonymous codon usage, we have carried out correspondence analysis (COA) on relative synonymous codon usage (RSCU) of 12 different strains of P. marinus. Figure 1 shows the positions of the individual genes on the planes defined by the first and second major axes generated by COA on RSCU values of coding sequences of respective Prochlorococcus genomes under study. Interestingly, in cases of all LL strains, the genes transcribed from the leading and the lagging strands of replication are segregated in two distinguishable clusters (with little overlap between them), either along Axis1 or Axis2 or both. Similar scatter plots with two distinct clusters of genes were observed earlier in cases of microbial genomes with pronounced strand-specific mutational bias [2,3,34,35]. When the positions of all synonymous codons are plotted on the plane defined by the first and second major axis of COA on RSCU for genes of all LL strains (plot not shown), a clear separation between G-/U- ending codons and A-/C- ending codons is observed, indicating the presence of asymmetric mutational bias at synonymous codon usage level in low light (LL) adapted genomes of P. marinus. In contrast, for each of the HL strains, a single cluster of genes (i.e., no segregation between the leading and lagging strand genes) is found on the Axis1-Axis2 plane of COA on their RSCU values (Figure 1), suggesting the absence of any pronounced strand-specific asymmetry in their synonymous codon usage. For all LL strains, GT3-content of genes exhibit significant correlations with Axis1 and/or Axis2 values (Table 2). 3 of the 6 LL strains, viz. LL1, LL3 and LL4 show highly significant correlations between Axis1 and GT3-content of genes, whereas LL2, LL5 and LL6 strains show significantly high correlations between Axis2 and GT3-content (Table 2). In LL strains the positions of the leading and lagging strand genes on the planes defined by Axis1 and Axis2 of COA (Figure 1), therefore, clearly indicate the overall GT3-richness of the leading strand genes. However, for the HL strains of Prochlorococcus, the percentage of variance explained by the first two principal axes are relatively low and the correlation values of these axes with GC3- or GT3-contents of genes are either insignificant or much lower than those observed for LL strains (Table 2). This suggests that no single axis and/or parameter can explain strand-specific variations in synonymous codon usage of HL strains.
Table 2. General features and correlations of GC3 and GT3 content with first two axes of COA on RSCU values of genes in 12 Prochlorococcus genomes
Figure 1. Position of genes on the planes defined by the first (horizontal Axis1) and second (vertical Axis2) major axes generated by COA on RSCU values of coding sequences for each of the 12 Prochlorococcus strains (a to l). Genes transcribed from the leading and lagging strands are represented by red and blue coloured dots respectively.
Chi-square tests on occurrences of different codons on two replicating strands of representative LL strains (LL1 and LL6) further reveal significant overrepresentation of 28 and 22 G-/U- ending codons on the leading strands of LL1 and LL6 respectively (p < 0.001); while 28 and 25 A-/C- ending codons are overrepresented in the genes encoded on the lagging strands of LL1 and LL6 respectively (p < 0.001) (Additional files 1 and 2). The codon 'CUG' is the only exception, which, in spite of being G-ending, is significantly overrepresented in the lagging strand genes of LL1.
Additional file 1. Relative Synonymous Codon Usage of leading and lagging strand genes of P. marinus str. MIT9313 (LL1).
Format: PDF Size: 99KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 2. Relative Synonymous Codon Usage of leading and lagging strand genes of P. marinus str. NATL2A (LL6).
Format: PDF Size: 99KB Download file
This file can be viewed with: Adobe Acrobat Reader
In microbial genomes characterized by pronounced strand asymmetry [2,3,34,35], replicational-transcriptional selection usually play a major role in shaping genome organization. The leading strands of replication of such organisms, in general, contain higher number of genes due to replicational selection, and are also enriched with highly expressed genes as an effect of transcriptional selection. However, in LL strains of P. marinus, the predicted protein coding sequences are found to be distributed almost equally in two strands. In fact, in three LL strains (LL1, LL2 and LL3), the number of predicted protein coding sequences are lower in the leading strands than in the lagging strands (approximately 48% in the leading strands and 52% in the lagging strands), indicating the absence of replicational selection. The lagging strands of the strains MIT9313 (LL1) and MIT9303 (LL2) are also found to be enriched in ribosomal proteins, which are typically highly expressed. Only two such genes are encoded by each of their leading strands, leaving 36 and 37 ribosomal proteins to be encoded by their lagging strands (LL1 and LL2 respectively). For other LL strains, the distribution of ribosomal genes is quite conventional (≈ 25 on leading strands and ≈ 12 on lagging strands). However, most of the other potentially highly expressed genes (e.g., RNA polymerases, transcription and translation processing factors, etc.), are present in higher numbers in the leading strands of all LL strains. Hence it is difficult to arrive at any definite conclusion regarding the effects of transcriptional selection on the LL strains of Prochlorococcus.
Larger extent of genomic rearrangements between small and large P. marinus genomes
In order to understand the nature and extent of genomic rearrangements during the events of niche specific diversification, we have analyzed the conservation of the relative order or synteny of orthologs across the chromosomes of different P. marinus strains. Figure 2 represents graphically, the gene synteny of 519 orthologs (see methods) in three low light (LL1, LL3 and LL6) and two high light adapted (HL3 and HL4) strains of P. marinus. The low light strains of Prochlorococcus have considerable variations in their genomic size and G+C-content (Table 1). The LL1 strain here represents the high G+C and large genome containing LL strains, while the LL3 & LL6 strains represent the other members of the LL group which have lower G+C-content and reduced genome size. HL3 and HL4 strains are representatives of the HL group, which also share smaller genome and lower G+C content. Interestingly, the extent of variation in order and orientation of orthologous genes between two strains of similar light optima but of distinct genome sizes and G+C-content (viz., between LL1 and LL3, Figure 2), is significantly greater than that between two strains with distinct light optima, but having similar genome size and G+C-content (e.g., between LL6 and HL3). It is worth mentioning at this point that this conclusion holds good for all 12 P. marinus strains under study, i.e., the results will be similar even if the representative strains selected here are replaced with any other strains form the groups they represent. The analysis, therefore, suggests that genome reduction in P. marinus has been accompanied by numerous seemingly random genome rearrangements such as translocations and inversions. Amongst the reduced genomes, the order and orientation of orthologous gene clusters remain more or less conserved except some local reorientation of genome fragments, the number and extent of reorientations being higher between the strains with distinct light adaptation (Figure 2).
Figure 2. Order of arrangement of 519 orthologs on chromosomes of 5 representative Prochlorococcus strains (LL1, LL3, LL6, HL3 and HL4). The red and blue lines join the locations of pair of orthologs on the linearly depicted chromosomes. Red lines indicate presence of the orthologous pairs on the same strand (either +/+ or -/-) of the two chromosomes they join, while the blue colour indicates the presence of the orthologs on different strands (+/- or -/+). Chromosomal scales are shown in megabase pairs (MB) and 0 MB represents the predicted origins of replication for the 5 strains.
Niche-specific dinucleotide abundance values of P. marinus genomes
It has been reported previously that dinucleotide abundance values are usually similar in related species and can be regarded as a genome signature [36]. To understand the patterns in dinucleotide signature, we have calculated dinucleotide abundance values for all P. marinus genomes and also for E. coli (a representative outgroup). The genomic G+C-bias of E. coli is similar to that of LL1 and LL2 Prochlorococcus strains. The results are shown diagrammatically in Figure 3. Some Prochlorococcus-specific trends are exhibited by all P. marinus organisms under study, irrespective of their G+C-bias or ecological adaptation. For instance, the dinucleotide CG is appreciably overrepresented in E. coli, but significantly underrepresented in all P. marinus, including the strains which have similar G+C-content to that of E. coli. Contrasting trends in E. coli and P. marinus strains are also observed for the dinucleotides AG/CT and GA/TC. The dinucleotide abundance values of AC/GT are also significantly underrepresented in all P. marinus strains, but not in E. coli.
Figure 3. Plot of dinucleotide abundance profiles of E. coli and 12 Prochlorococcus strains. Differently coloured lines join the abundance values of dinucleotide pairs for each of the organisms. Abundance values ≥ 1.23 or ≤ 0.78 are significantly over or underrepresented (as described by Karlin et al., Theoretical population biology, 61, 367-390, 2002).
However, significant intra-Prochlorococcus differences are also present in dinucleotide abundance profiles, on the basis of which all P. marinus strains under study may be divided into three distinct groups:
(a) Group LLa, comprised of the two LL strains P. marinus MIT 9313 (LL1) and MIT 9303 (LL2) - both having larger genomes (≈ 2.5 MB) and average G+C-content ≈ 50%: Genomes of these two strains are characterized by significantly high values of CA/TG and low values of TA (Additional file 3). The values for AT, AC/GT and CG are also relatively higher and that of CC/GG are lower, as compared to other P. marinus strains.
Additional file 3. Dinucleotide abundance values of twelve P. marinus genomes and E. coli.
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(b) Group LLb, consisting of other four LL strains (LL3, LL4, LL5 and LL6), characterized by relatively lower G+C-content (between 35% - 37%) and small genome size (< 2 MB): These four LL strains exhibit highly similar patterns, which are visibly distinct mainly at CA/TG and CC/GG from the almost overlapping profile of HL strains (Figure 3).
(c) Group HL, including all 6 HL strains having reduced genome and G+C-content ≈ 31%: The dinucleotide CC/GG is significantly overrepresented only in the HL Prochlorococcus strains.
Clustering by amino acid composition reveals a balance between genomic G+C-bias and Prochlorococcus-specific selection forces
In an attempt to investigate whether the strand-specific mutational bias has any impact on amino acid usage in gene products of LL strains of P. marinus in comparison to their HL counterparts, we performed correspondence analysis (COA) on relative amino acid usage (RAAU) of the encoded proteins of each organism. No clear segregation can be observed for proteins encoded by the leading and lagging strands in any of the P. marinus genomes under study (data not shown), implying that the strand-specific mutational bias has hardly any influence on the amino acid compositions of the gene products of LL strains of Prochlorococcus. In all the strains of P. marinus, the first three axes generated by COA on amino acid usage cumulatively explain about 39% of the total variability. Both mean hydrophobicity and aromaticity of the encoded proteins exhibit strong correlations with either of the first two principal axes and seem to be the major contributors to amino acid usage variation in P. marinus proteins (data not shown).
In order to check whether the amino acid usage patterns in LL and HL groups of Prochlorococcus follow any specific trends, we carried out a clustering analysis on relative abundances (with respect to E. coli) of different amino acid residues of each organism (Figure 4) in a dataset comprising of all P. marinus strains under study along with a cyanobacterial representative Cyanothece sp. (having G+C-content similar to those of E. coli and two LLa strains), and two non-cyanobacterial species - the bacteroidetes/chlorobi G. foresetii (average genomic G+C-content = 36.6%, similar to those of LLb strains) and the epsilon-proteobacteria C. jejuni (average genomic G+C-content = 30.3%, similar to those of HL strains). Branching patterns suggest an optimization between the G+C-bias and P. marinus group-specific selection for amino acid usage. As can be seen in Figure 4, a major branching between the organisms occurs according to the average genomic G+C-content. Organisms having average G+C-content around 50% - viz. E. coli, Cyanothece sp. and the two LLa strains - cluster together under the node 'a', while the organisms with lower G+C-content (30-37%) form a distinct cluster at the node 'b'. However, within the A+T-rich or relatively G+C-rich clusters, finer segregation occur according to taxonomy, i.e., between the cyanobacterial and non-cyanobacterial species. For instance, node 'a' acts as a bifurcation point between the gamma-proteobacteria E. coli and the three cyanobacterial species, followed by another bifurcation at node 'c' between the two LLa strains and non-Prochlorococcus species Cyanothece. Similarly, within the A+T-rich cluster, the HL strains of P. marinus with G+C-content ≈ 30-31% club together with their LLb counterparts (average G+C-content ≈ 35-37%) under the node 'f', distinctly separated from C. jejuni and G. foresetii. Node 'f' also acts as the point of divergence of LLb and HL strains, which cluster separately under the nodes 'g' and 'j' (containing 4 LLb strains and 6 HL strains respectively). These observations indicate that though the amino acid usage patterns in Prochlorococcus are primarily guided by their directional mutational bias, other selection pressures must also have exerted some significant influence. Three cyanobacterial species, namely Cyanothece sp., P. marinus str. MIT9313 (LL1) and P. marinus str. MIT9303 (LL2) - all have nearly the same G+C-content as E. coli, yet their amino acid usage abundance patterns are quite distinct from that of E. coli. Similarly, the LLb and HL strains of P. marinus display significant differences in amino acid usage patterns from that of non- P. marinus species (G. foresetii and C. jejuni, respectively) having similar G+C-content. A careful examination of Figure 4 delineates the Prochlorococcus-specific features in amino acid usage patterns. For instance, as compared to E. coli, Thr is underrepresented in all strains of P. marinus, including those having ≈ 50% G+C-content (and also in C. jejuni, but not in Cyanothece and G. forsetti). Ser is overrepresented in all A+T-rich P. marinus species, especially in comparison to C. jejuni and G. foresetii. Tyr is typically underrepresented in all Prochlorococcus strains, compared to the non-Prochlorococcus species of similar G+C-content. Frequency of Phe is also relatively lower in Prochlorococcus in comparison to any other species of similar G+C-bias. All these observations suggest that the amino acid usage in P. marinus is a result orchestrated by the forces of species-specific selection acting on mutational bias and genetic drift.
Figure 4. Single linkage (Euclidean distances) clustering based on standardized amino acid usages (with respect to E. coli) of 12 Prochlorococcus strains and 4 other microbes, accompanied by a heatmap representation of the standardized amino acid usage values. The overrepresentation or underrepresentation of amino acid residues in the organisms are shown in green and red colored blocks of varying colour intensities, respectively. [Abbreviations, EC → E. coli; CJ → C. jejuni; GF → G. foresetii and CTH → Cyanothece sp.]
Niche-specific variations in physicochemical and structural features of Prochlorococcus orthologs
In an attempt to have a better insight into the niche-specific physicochemical and structural properties of P. marinus proteins, if any, we performed a comparative analysis of the core proteins, i.e., proteins found to be present in all P. marinus strains under study. Different proteomic properties of 519 orthologous proteins between all 12 P. marinus strains are summarized in Table 3, which shows a gradual increase in average aromaticity and pI values and decrease in mean hydrophobicity and instability indices of orthologs, as one moves from the members of group LLa to group LLb to group HL. In other words, the core proteins of LL strains are, in general, more hydrophobic, more acidic, less aromatic and less stable than their HL orthologs. The comparison of structural properties reveals that among the three groups, members of the group LLa exhibit the highest propensity for helix formation and lowest propensity for beta-sheet and coil formation. LLb group orthologs are characterized by intermediate values for all three propensities, and group HL orthologs display trends opposite to that of group LLa - i.e. lowest propensity for helix formation and highest propensity for beta-sheet/coil formation (Table 3).
Table 3. Different amino acid indices and secondary structural traits of 519 orthologous proteins present in 12 Prochlorococcus strains
However, one may argue that these inter-group variations in physicochemical properties and structural propensities of P. marinus strains can only be a reflection of their varying genomic G+C-bias rather than being niche specific. In order to address this issue, we carried out a comparative analysis of various proteomic features of orthologous sequences from three representative P. marinus strains LL1, LL3 and HL3 (from groups LLa, LLb and HL respectively) with those of three other caynobacterial species, Synechococcus elongatus (55.5% G+C-content), Synechocystis sp.(47.4% G+C-content) and Nostoc sp.(41.3% G+C-content) as well as three non-cyanobacterial species namely E. coli, Bacillus cereus and Francisella tularensis. The non-cyanobacterial species were chosen as reference organisms, due to their close average genomic G+C-content to those of LLa, LLb and HL strains (50.8%, 35.5% and 32.3% for E. coli, B. cereus &F. tularensis, respectively), and the significant number of orthologs they share with these P. marinus strains. Values of different physicochemical parameters and structural propensities of the orthologs from these reference species and the representative P. marinus strains are summarized in the Table 4. It reveals that the values of any specific parameter, say of hydrophobicity index or instability index, is in most cases, not comparable between orthologs from P. marinus strains and outgroup organisms of similar G+C-bias. For instance, the values observed for B. cereus are quite different from those of LL3 - the genomic G+C-content of both being quite similar. The average pI value of B. cereus proteins is not only significantly less than that of their LL3 orthologs, it is even lesser than LL1 proteins. The average instability index of B. cereus proteins is also much less than that of the Prochlorococcus orthologs. The average helix forming propensity of B. cereus proteins is closer to that of LL1 proteins, while their beta sheet forming propensity is almost same to that of HL3 proteins. Similarly, the aromaticity and instability indices or helix forming propensities of E. coli proteins are significantly different from those of Prochlorococcus strain LL1, while most of the F. tularensis protein characteristics differ widely from those of the P. marinus HL3 strain with similar G+C-bias. Comparing between the cyanobacterial species, amino acid indices and secondary structural traits of Synechococcus (the closest taxonomic relative of Prochlorococcus) seem to be guided by its G+C-content (Table 4: Set IV). The hydrophobicity values and the helix-forming propensities of the other two cyanobacteria also gradually decrease with decrease in genomic G+C-content within the set. However, the other indices and structural traits of Synechocystis and Nostoc do not reflect any systematic co-variation with their G+C-bias. These observations suggest that the variations in proteomic features of Prochlorococcus might not be a mere outcome of their G+C-bias, there could be significant influence of other selection forces as well.
Table 4. Comparison between various amino acid indices and secondary structural traits of six sets of proteins of Prochlorococcus and non-Prochlorococcus orthologs
Higher positive selection between orthologs from strains with opposite light optima
In order to better understand the evolutionary trends in different P. marinus species having distinct genome composition and/or light adaptation, the rates of synonymous and non-synonymous substitutions (dS and dN) were calculated between 519 orthologous sequences of LL1, LL6 and HL3 strains (representatives of groups LLa, LLb and HL respectively), and the number of genes showing positive selection (dN > dS) between each possible pair of organisms were determined. Figure 5 depicts a Venn diagram for the number of positively selected genes among the strains under study. Out of 519 orthologs, maximum number of positively selected genes (90) is found between LL1 and HL3 - the strains that differ in genome size, G+C-composition and light adaptation. The strains LL6 and HL3 having nearly similar genome size and G+C-bias, but distinct light optima come next with 78 positively selected genes among them and the two strains LL1 and LL6 of the same light group, but distinct genome size and G+C-bias, exhibit the minimum number (68) of positively selected genes. Among these three sets, there are several genes, which are positively selected between any two out of the three possible pairs of P. marinus strains under study. There are 25 genes selected positively between HL3 and either of the LL strains i.e. between the strains of two opposite light optima, irrespective of their G+C-bias and genome size. 17 genes are positively selected between the strains of distinct G+C-bias and genome size - between the relatively G+C-rich and large genome strain LL1 and either of the A+T-rich and reduced genome strains LL6 or HL3. Only 7 genes display common positive selection between LL6 and LL1 (the strains with similar light adaptation but of different genome size and G+C-bias) and between LL6 and HL3 (the strains having relatively lower G+C-bias and genome size). Thus, our study indicates the presence of a considerable positive selection pressure in diversification of the Prochlorococcus core genome, which in turn, suggests an appreciable role of random genetic drift in vertical niche partitioning of the strains.
Figure 5. Venn diagram depicting the number of positively selected (dN/dS > 1) orthologs between pairs of different Prochlorococcus strains. The 519 core proteins of 3 representative organisms (LL1, LL6 & HL3) were considered for the analysis. dN/dS could be calculated for 414 × 3 pairs out of the 519 × 3 pairs considered.
Pronounced effects of directional mutational bias in the intergenic regions of HL P. marinus strains
In an attempt to examine whether the G+C-bias of intergenic regions of the different strains (with varying genomic G+C-content), follow trends similar to the respective coding regions, G+C-content of intergenic regions were calculated. The intergenic regions are, in general, more A+T rich than the overall genomic G+C-content of respective organisms (Additional file 4). Also, the A+T bias of intergenic regions are more pronounced in HL strains than their LL counterparts.
Additional file 4. Average G+C-contents (%) of the overall genome, coding sequences and intergenic sequences of 12 Prochlorococcus strains.
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Unconstrained intergenic regions are more prone to mutational change. Accumulation of unfavourable mutations may render a coding region nonfunctional, facilitating its removal from the genome in course of time. We have identified probable remnants of coding sequences within intergenic regions of two representative Prochlorococcus strains having reduced genomes (LL6 and HL3). The G+C-content of these remnants are, in most cases, higher than that of average intergenic DNA, but lower than the average G+C-content of the bona fide coding regions (Table 5 and Additional file 5). These particular non-coding sequences, therefore, may be remnants of coding sequences that are in the process of being eliminated from the genome.
Additional file 5. List of putative remnants of coding regions in LL6 and HL3.
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Table 5. Putative remnants of coding regions and their G+C-content (%)
Discussion
Exhibition of a wide range of genomic G+C-content (30.8% to 50.7%) and genome sizes (1.6 Mb to 2.7 Mb) by different strains of P. marinus, and also their adaptation to different ecological niches - a situation encountered rarely in the microbial world - demand detailed investigation. We have performed a large scale comprehensive study to critically analyze the direction and strength of mutational pressure and genomic/proteomic determinants associated with the adaptation of these strains to oceanic environments subject to different light intensities. From this study it appears that (a) low light adapted (LL) free living Prochlorococcus strains exclusively show strand asymmetry in synonymous codon usage, (b) general trends in amino acid usage in LLa, LLb and HL strains differ appreciably, (c) distinct dinucleotide abundance profiles are exhibited by LLa, LLb and HL strains, (d) higher number of genes have undergone positive selection between the strains with distinct light optima, i.e., between LL and HL strains and (e) there are definite trends in variations of different physicochemical and structural features in core proteomes of different groups of Prochlorococcus strains, which are not solely governed by their genomic G+C-bias. These observations, along with the findings on large-scale genome reduction associated with gradual increase in genomic A+T-content and extensive chromosomal rearrangements between different strains, strongly suggest a stepwise diversification of Prochlorococcus strains, in course of their adaptive evolution (Figure 6).
Figure 6. Trends in genome/proteome evolution of Prochlorococcus, suggesting a stepwise diversification of the ecotypes. The model is based on the 16S rRNA phylogeny of the 12 strains, inferred from a bootstrap consensus tree (500 replicates) generated using the Minimum Evolution method (CNI algorithm), with the software MEGA (version 4).
Among several genome/proteome signatures of P. marinus strains reported for the first time in this work, the most notable is the impact of pronounced replication-strand-specific asymmetry on synonymous codon usage, observed exclusively in the low light adapted strains of P. marinus (Figure 1). This is noteworthy for two reasons: (i) Presence of pronounced strand-specific mutational bias with detectable influence on codon usage was observed so far mostly for obligatory intracellular microorganisms having reduced genomes [2,3,5]. Interestingly, all 6 LL strains of P. marinus exhibiting strand-specific synonymous codon usage are free-living and two of them (LL1 and LL2) are characterized by relatively larger genome size. On the other hand, for the reduced genomes of 6 HL strains, no perceivable sign of strand asymmetry could be seen in their usage of synonymous codons. (ii) In most of the other microbial genomes with asymmetric mutational bias, the genes, especially the highly expressed ones, are present in the leading strands of replication in significantly higher numbers, the phenomenon referred to as replicational-transcriptional selection [2,3,34,35]. No such definite significant bias in gene distribution is observed in either of the strands of replication in the LL strains of P. marinus. Strand asymmetry in codon usage of Prochlorococcus, therefore, may not bear an explicit causality to the event of genome reduction or with replicational-transcriptional selection.
The homogenization of the strand asymmetric bias in the HL strains may be attributed, at least partially, to the absence of a specific type of DNA repair enzyme MutY. In previous studies of Rocap et al. [20] and Dufresne et al. [25] it have been shown that the enzyme MutY is absent in the strain P. marinus str. CCMP1986 (HL3), while it is present in P. marinus str. CCMP1375 (LL3) and P. marinus str. MIT9313 (LL1). MutY, an A/G-specific DNA glycosylase, acts with MutT (NTP pyrophosphohydrolase) and MutM (formamido-pyrimidine-DNA glycosylase) to avoid misincorporation of oxidized guanine (8-oxoG) in DNA and to repair the base mismatches A:8-oxoG [37]. Knocking out both mutM and mutY in E. coli results in a 1,000-fold increase of G:C to A:T transversions in comparison to the wild-type strain [38]. Our analysis reveals (through BLASTP search) that mutY is present only in the LL strains, but not in any of the 6 HL strains. The excess number of 'G's present in the leading strands of LL strains might have transversed to 'A's in the HL strains due to the absence of mutY in the later, and this in turn, caused a simultaneous increase of 'T's in the lagging strands, eventually leading to homogenization of the G+T and A+C frequencies in two strands of replication in the HL strains. Existing mutational drift towards A+T-enrichment in the HL strains might also have facilitated achieving the uniformity in those strains. Further insights may be accumulated in this regard with the availability of more completely sequenced Prochlorococcus genomes in future.
In the process of gradual genome reduction, mutations often accumulate in expendable genes, thereby transforming them, by degrees, to pseudogenes, to small fragments, to extinction [39]. In the reduced genomes of P. marinus, we have found some putative remnants of coding regions, the A+T-content of which are, in general, higher than that of coding regions, but lower than other non-coding regions. This is in agreement with the fact that the reduced genomes of P. marinus (especially those of HL strains) are subject to a strong mutational A+T-drift, and will therefore result in gradual A+T-enrichment of the genic remnants already released from amino-acid-coding constraints in recent past. The base composition of such remnants is expected to gradually approach the A+T-content of bona fide non-coding regions.
Comparison of orthologous gene synteny from five representative strains having different genome size and G+C-content clearly points at a high level of chromosomal rearrangement during genome shrinkage in Prochlorococcus. This finding is in agreement with earlier findings on association of chromosomal rearrangement events with higher rates of chromosomal evolution and/or the phenomenon of genome reduction, as in Arabidopsis thaliana [40] and different endoparasites/endosymbionts [41,42]. Intra-chromosomal recombination at duplicated sequences often results in deletion of intervening sequences, and rearrangement of flanking regions, thereby leading to genome shrinkage [39].
Previous analyses with endosymbiotic or endoparasitic organisms like Bartonella, Tropheryma, Buchnera, Wigglesworthia etc. [2,3,28,29] revealed that the phenomenon of genome reduction is normally associated with population bottlenecks or other mechanisms such as selective sweeps. In case of the hyperthermophile Nanoarchaeum equitans, extreme genome reduction is a feature of its thermoparasitic adaptation [1]. Although our knowledge of bacterial populations in open oceans is not exhaustive, it may certainly be assumed that P. marinus ecotypes, the most abundant free-living marine cyanobacteria and an important contributor to global photosynthesis, are not subject to small population sizes [13-15,30]. More importantly, the HL strains with reduced genomes are apparently biologically superior than their LL counterparts [21]. It is possible that the bias towards reduced A+T rich genomes in HL strains is consistent with cellular economy at regions with limited nitrogen and phosphorous near the ocean surface. Scarcity of these elements that are essential in DNA synthesis favors the incorporation of an AT base-pair containing seven atoms of nitrogen, one less than a GC base-pair. It is worth mentioning at this point that the trends in amino acid usage in different P. marinus strains, as observed in this study are quite compatible with the earlier report by Lv et al. [43] on influence of resource availability on proteome composition of these species. For instance, increase in overall aromaticity from LLa to LLb and HL strains is in full agreement with the observations by Lv et al. [43] on increased carbon-content in the encoded proteins of different HL strains as compared to that of LL strains. The average instability indices of the HL proteins are significantly lower than those of their LL orthologs, suggesting that the HL proteins, in general, may be more stable. Proteins characterized by higher percentages of helix structures, experience increased overall packing that imparts more rigidity [44] and, hence, a decrease in regions with helix-forming propensities with a subsequent increase in coiled structures in HL proteins probably makes them more flexible. It is also tempting to presume that higher values of aromaticity and pI in HL proteins, as compared to LL orthologs, might facilitate cation-pi interactions in the former, imparting more stability. The central issue in the adaptation of HL proteins to their environmental niches may, therefore, be the conservation of their functional state, characterized by a well-balanced optimization of stability and flexibility.
Conclusion
The current study advocates for the presence of adaptive selection forces that might have played significant role in governing Prochlorococcus evolution and fitness at the genome and proteome levels. An optimization between these adaptive forces and directional mutational bias has set definite trends in molecular evolution of P. marinus. This characterizes different P. marinus ecotypes with distinct niche-specific compositional, physicochemical and structural traits, thereby driving them chronologically towards increasing stability and/or fidelity.
Methods
Sequence retrieval
All predicted protein coding sequences and the complete genome sequences of the 12 different strains of P. marinus were retrieved from the NCBI GenBank (listed in Table 1). For comparison, the predicted protein coding sequences of E. coli (NC_000913.2), Bacillus cereus (NC_003909.8), Francisella tularensis (NC_006570.1), Synechococcus elongatus (NC_006576.1), Synechocystis sp. (NC_000911.1), Nostoc sp. (NC_003272.1), Campylobacter jejuni (NC_003912.7), Cyanothece (NC_011884.1) and Gramella forsetii (NC_008571.1) were also retrieved from GenBank. Annotated ORFs, which encode proteins less than 100 amino acids long, were not considered for further analysis.
Determination of leading and lagging strand genes
In order to identify the replication origin (oriC) or termination (ter) sites we performed GC-skew (G-C/G+C) analysis using a sliding window of 10 Kb along the genome sequence. The sites were validated by checking the neighbouring gene organization (e.g. identified origins in Prochlorococcus genomes were flanked by DNA polymerase beta subunit III gene on the 3' side and the Threonine synthatase gene on the 5' side) and the presence of DnaA boxes in their vicinity [45]. Based on the predicted oriC and ter sites (Additional file 6), the leading strands and lagging strands of replication for each genomes were identified along with the genes encoded on the two strands.
Additional file 6. Predicted locations of origins and termini of replication of the 12 Prochlorococcus strains.
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Multivariate analyses on synonymous codon and amino acid usage and cluster analysis on amino acid usage
Correspondence analysis (COA) on relative synonymous codon usage (RSCU) and amino acid usage of genes/proteins were performed on individual genomes in order to identify any significant variation in the usage of codons or amino acids, if present, and help ascertain the underlying cause(s), using the program CODONW 1.4.2 [46].
To find out the variation in amino acid usage between LL and HL Prochlorococcus strains, a cluster analysis on standardized amino acid usage was carried out using STATISTICA (version 6.0, published by Statsoft Inc., USA) for all 12 Prochlorococcus organisms (Table 1) along with E. coli, Cyanothece, C. jejuni and G. forsetii having G+C-content nearly equal to the different LL and HL strains. The amino acid usage of E. coli was chosen as a well-defined reference for standardizing the amino acid composition for the analysis and to produce an accompanying heat map. With the help of a program developed in-house in Visual Basic, a 16 × 20 matrix (heatmap) was generated, where the rows and the columns correspond to data sources (i.e., organisms in the cluster) and standardized amino acid usage values, respectively. The overrepresentation or underrepresentation of standardized amino acid usage values of the organisms in the matrix are shown in green or red colored blocks (Figure 4) respectively, and their intensities varying in accordance with their deviation from the standard (yellow). The extreme left column represents the genomic G+C-content of the respective organisms.
Dinucleotide analysis of DNA sequences
For all Prochlorococcus genomes and E. coli, the dinucleotide abundance for each possible dinucleotide was calculated as the ratio between the observed and expected frequencies of the concerned dinucleotide in its genomic context [47]. Dinucleotide abundance values generally represent the genomic signature of any species [48] and here we were interested to see whether all Prochlorococcus genomes follow a similar trend or not.
Determination of orthologs
Stand alone BLAST package (ver. 2.2.18) was downloaded from the NCBI FTP site and using the package, all-to-all BLASTN and BLASTP searches were performed with the genes from all the 12 strains of P. marinus. Orthologs across these organisms were defined for this study as protein coding genes having a BLASTP sequence Identity ≥ 60%, not more than 20% difference in length and E-value ≤ 1e-20. The resultant list of 'orthologs' were checked for consistency with the data obtained from Genplot http://www.ncbi.nlm.nih.gov/sutils/geneplot.cgi webcite, which houses a pair-wise list of genes giving mutually best BLASTP hits when all genes from the genomes of any two organisms are 'blasted' against each other. We have identified 519 orthologs present in all 12 P. marinus genomes as their core proteome. The stringent measures employed for the similarity search ensure that these orthologs have been sufficiently conserved throughout the adaptive evolution of P. marinus, and any niche-specific features deciphered from this dataset would certainly not be a trivial outcome. For comparative analysis with suitable outgroup organisms, we retrieved orthologs of nine organisms including three representative P. marinus strains (LL1, LL3 and HL3), E. coli, B. cereus, F. tularensis, S. elongatus, Synechocystis sp. and Nostoc sp. from NCBI GenePlot by filtering the symmetrical best hits of protein homologs.
Estimation of synonymous and non-synonymous substitution patterns in orthologous sequences
Positive selection can be inferred from a higher proportion of non-synonymous over synonymous substitutions per site (dN/dS > 1). The dN and dS values were calculated for 519 orthologs of LL1, LL6 and HL3 using the software MEGA (version 4) [49]. The calculation was based on the modified Nei-Gojobori Jukes-Cantor method that considers deviations from an equal frequency of transitions and transversions [50,51].
Gene synteny visualization
Comparison of the gene repertoire or gene synteny between 5 representative Prochlorococcus strains (LL1, LL3, LL6, HL3 and HL4) were carried out using a Java program developed in-house. It can represent the arrangement of orthologous genes between two chromosomes by joining the locations of the orthologs by differently coloured lines. The red lines represent the genes present on the same strand (+/-) and blue lines represent orthologs coded on different strands of chromosomes being compared.
Calculation of codon/amino acid usage indices and estimation of secondary structure of proteins
Indices like relative synonymous codon usage (RSCU) [52], G+C and G+T-content at third codon positions (GC3 & GT3 respectively), aromaticity and average hydrophobicity (Gravy score) [53] of protein coding sequences were calculated to find out the factors influencing codon and amino acid usages. The isoelectric point (pI) and instability index [54] of each protein were calculated using the Expasy proteomics server [55]. Secondary structures of the identified orthologs were computed using the software PREDATOR [56] and the varying percentages of the structural components (viz. helices, sheets, and coils) in proteins from different strains were also noted.
Identification of intergenic regions
The sequences coding for mRNAs and structural RNAs were noted from the protein table and structural RNA table respectively (available from NCBI) for each of the organisms. Intergenic regions were identified by subtracting the regions of these gene sequences from the whole genome. The overall G+C-content of the intergenic regions were calculated after concatenating all the intergenic sequences together, for each of the 12 Prochlorococcus strains. For identification of probable pseudogenes/remnants of coding DNA in LL6 and HL3 (two representative strains of groups LLb and HL having reduced genomes), their intergenic regions were subjected to a similarity search (tBlastX) against a pool of Prochlorococcal genes (consisting of sequences from three representative strains LL1, LL6, HL3). 48 hits for LL6 and 93 hits for HL3 were identified, having sequence identities ≥ 30%, aligned lengths ≥ 15 amino acids, and E-values < 1e-3.
Abbreviations
COA: correspondence analysis; LL: low light; HL: high light; pI: isoelectric point; RSCU: relative synonymous codon usage; GT3: G+T-content at third codon positions; GC3: G+C-content at third codon positions.
Authors' contributions
SP and AD made substantial contributions to the design of the study, devised and carried out the overall strategy and drafted the manuscript. SKB developed relevant programs for data mining and analysis of genome sequences and also participated in sequence analysis. SD participated in the initial phase of the work, made thoughtful discussion during execution of the project and preparation of the manuscript. CD conceived and coordinated the study and revised the manuscript critically for important intellectual content. All authors read and approved the final manuscript.
Acknowledgements
We thank Sanjib Chatterjee and Avik Datta, IICB for giving technical support in calculating dinucleotide abundance and synonymous and non-synonymous divergence. This work was supported by the Department of Biotechnology, Government of India (Grant Number BT/BI/04/055-2001) and Council of Scientific and Industrial Research (Project no. CMM 0017). SP and AD are supported by Senior Research Fellowships from Council of Scientific and Industrial Research, India.
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Research article
Long term follow-up of drug resistant and drug susceptible tuberculosis contacts in a Low incidence setting
James Johnston1,2*, Andrew Admon3, Amir Ibrahim2, Kevin Elwood1, Patrick Tang4, Victoria Cook1,2 and Mark Fitzgerald2
Author affiliations
1 Division of Tuberculosis Control, British Columbia Centre for Disease Control, Vancouver, BC, Canada
2 Department of Medicine, University of British Columbia, Vancouver, BC, Canada
3 Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI, 48109, USA
4 Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
For all author emails, please log on.
Citation and License
BMC Infectious Diseases 2012, 12:266 doi:10.1186/1471-2334-12-266
Published: 22 October 2012
Abstract
Background
Studies examining the transmission of multidrug-resistant tuberculosis (MDR-TB) strains have yielded conflicting results.
Methods
We examined transmission of MDR-TB strains using contact tracing data from a low incidence setting. Contacts of MDR-TB cases diagnosed in British Columbia, Canada, from 1990-2008 were identified through a provincial tuberculosis (TB) registry. Tuberculin skin test (TST) results and TB disease incident rates were determined for contacts. For comparison, TB disease incident rates and TST results were measured in close contacts of isoniazid mono-resistant (HMR-TB) and drug susceptible TB (DS-TB) cases.
Results
Of 89 identified close contacts of MDR-TB patients, 5 patients (6%) developed TB disease and 42 (47%) were TST positive. The incidence rate of TB disease (3%, p = 0.31) and TST positivity (49%, p = 0.82) were similar in contacts of HMR-TB cases. Compared with MDR-TB contacts, DS-TB contacts had lower incidence rate of TB disease (2%, p = 0.04) and TST positivity (32%, p < 0.01). All MDR-TB contacts with culture positive TB diagnosed in follow-up were drug-susceptible; three of six HMR-TB contacts with culture positive TB were HMR-TB. Multivariate analysis demonstrated that contact with MDR-TB (adjusted OR 1.72; 95%CI 1.05-2.81) and HMR-TB (adjusted OR 1.99; 95%CI 1.48-2.67) was associated with TST positivity. In addition, adult age, male gender, BCG positivity, source case sputum smear positivity, foreign birth and fewer contacts per source case were significantly associated with TST positivity in the multivariate model.
Conclusion
Contacts of MDR-TB and HMR-TB patients in a low incidence setting show high rates of TST positivity and TB disease but low rates of drug resistance.
Keywords:
Tuberculosis; Multidrug-resistant; Contact investigation; Epidemiology; Latent tuberculosis
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Research article
De-identification of primary care electronic medical records free-text data in Ontario, Canada
Karen Tu1,2,3*, Julie Klein-Geltink1, Tezeta F Mitiku1, Chiriac Mihai1 and Joel Martin4
Author Affiliations
1 Institute for Clinical Evaluative Sciences (ICES) G106, 2075 Bayview Avenue, Toronto, Ontario, M4N 3M5, Canada
2 Department of Family and Community Medicine-University of Toronto, 263 McCaul Street, 5th Floor Toronto, Ontario, M5T 1W7, Canada
3 Toronto Western Hospital Family Health Team-University Health Network, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada
4 Institute for Information Technology, National Research Council, 1200 Montreal Road, Ottawa, Ontario, K1A 0R6, Canada
For all author emails, please log on.
BMC Medical Informatics and Decision Making 2010, 10:35 doi:10.1186/1472-6947-10-35
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1472-6947/10/35
Received:9 March 2010
Accepted:18 June 2010
Published:18 June 2010
© 2010 Tu 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
Electronic medical records (EMRs) represent a potentially rich source of health information for research but the free-text in EMRs often contains identifying information. While de-identification tools have been developed for free-text, none have been developed or tested for the full range of primary care EMR data
Methods
We used deid open source de-identification software and modified it for an Ontario context for use on primary care EMR data. We developed the modified program on a training set of 1000 free-text records from one group practice and then tested it on two validation sets from a random sample of 700 free-text EMR records from 17 different physicians from 7 different practices in 5 different cities and 500 free-text records from a group practice that was in a different city than the group practice that was used for the training set. We measured the sensitivity/recall, precision, specificity, accuracy and F-measure of the modified tool against manually tagged free-text records to remove patient and physician names, locations, addresses, medical record, health card and telephone numbers.
Results
We found that the modified training program performed with a sensitivity of 88.3%, specificity of 91.4%, precision of 91.3%, accuracy of 89.9% and F-measure of 0.90. The validations sets had sensitivities of 86.7% and 80.2%, specificities of 91.4% and 87.7%, precisions of 91.1% and 87.4%, accuracies of 89.0% and 83.8% and F-measures of 0.89 and 0.84 for the first and second validation sets respectively.
Conclusion
The deid program can be modified to reasonably accurately de-identify free-text primary care EMR records while preserving clinical content.
Background
The uptake of electronic medical records (EMRs) is increasing amongst family physicians in Canada and around the world[1,2]. EMRs contain comprehensive clinical information regarding the course of care including lab results, prescriptions, patient risk factors, family history and past medical history in addition to many physical measures such as height, weight, blood pressure and detailed information on clinical encounters not presently available from other data sources. However, EMRs were not designed for research but rather to help physicians improve their clinical practice. As such, secondary use of this data is impeded by the fact that much of the rich clinical data contained in EMRs is not entered in a format that lends itself easily to analysis[3]. Specifically, the lack of methods for de-identifying the narrative free-text portions of EMR data in order to preserve privacy has presented a major challenge for researchers interested in utilizing this data.
At the Institute for Clinical Evaluative Sciences (ICES) we have developed an Electronic Medical Record Administrative data Linked Database (EMRALD) using data from family physician EMRs. This EMR data is linked through unique scrambled health card numbers to the multiple health related administrative databases for the province of Ontario, housed at ICES. ICES is an independent, not-for-profit health services research organization with a unique designation as a 'prescribed entity' in Section 45(1) of the Personal Health Information Protection Act (PHIPA), Ontario's privacy legislation[4]. This means that ICES has policies and procedures in place to protect the privacy and confidentiality of patients[5] as required by the Act (s.45(3)), which have been reviewed and approved by the Information and Privacy Commissioner of Ontario. This status allows ICES to receive and use health information without consent for the purposes of analysis and compiling statistical information about our health care system. Even though ICES does not release any individual level information, a free-text de-identification tool is needed in order to further enhance privacy measures through all steps of in-house EMR data analysis.
Although a number of software programs have been developed to address the issue of de-identification of narrative free-text for different types of medical data, [6-17] none have been customized for the full range of primary care EMR notes. These notes contain free-text from a wide variety of sources including point form progress notes, consultation letters from different practitioners in a variety of specialties, diagnostic test results, pathology reports and hospital discharge summaries. These free-text records use a wide variety of formatting and syntax, making it more complex to devise a tool.
Approaches to free-text de-identification include machine-learning based systems[11,13] or lexicon and pattern-based systems[6-8,10,15-17]. The machine-learning systems use labeled examples to automatically search for a statistical pattern of indicator features. For example, a human annotator would label U.S. zip codes or Canadian postal codes as elements to remove from EMRs. Then, features from the text such as the capitalization pattern, the appearance of digits, the term itself, the part of speech and syntactic dependencies are used to find a statistical rule that distinguishes between the postal codes and other text. Success in de-identifying medical discharge summaries has been achieved using a support vector machine (SVM) as the machine-learning algorithm[11]. In this case, the SVM attempts to find a separating hyperplane between the positive (labeled) and negative examples where the examples are described using a specified set of text-based features.
On the other hand, the lexicon and pattern approach uses a manually (instead of automatically) built collection of word lists, regular expressions, and heuristics. This second approach has the disadvantage that experts must spend time to create and organize the word lists and patterns. However, this characteristic can also be an advantage because the expert can include knowledge of the field that goes beyond the available training examples or beyond a fixed set of local features.
It is possible to adapt either type of system, but the style of adaptation differs. Adaptation of a machine-learning based system emphasizes adding additional training examples and modifying the set of text-based features. This adaptation would require expertise to label the new examples and then would require a large number of iterations to evaluate the effect of different features. Given that we are regularly adding EMR records from clinics in different geographic locations that receive information from different institutions and specialty areas, the adaptation of a lexicon and pattern system[17] emphasizing extending word lists, adding new word lists and adding and removing regular expressions appeared to be more appropriate for our needs. For the most part, new words and patterns can be added independently of each other such that the effects of a change are predictable to the expert. This type of adaptation can require more time from the expert, but again presents the possibility of quickly introducing additional domain knowledge without having to constantly retrain the system each time a new clinic is introduced.
Most of the work done previously in this area has been designed to de-identify all personal health information (PHI) as outlined by the Heath Insurance Portability and Accountability Act (HIPAA) in the United States. While PHI such as names and locations are not necessary to preserve, PHI such as age, dates of hospitalizations, procedures and visits have clinical implications which are important to preserve in EMR data in order to fully utilize the data for research and evaluation purposes.
We set out to determine if deid, [17] an open source software program designed and tested on hospital nursing notes, could be modified to de-identify primary care EMR records in EMRALD with high precision and while preserving clinically important content.
Methods
Initial name removal
The EMRALD database has been developed using data from family physicians in Ontario using Practice Solutions® EMR, which is owned and operated by the Canadian Medical Association, and is the leading EMR software vendor in Ontario with approximately 50% of the market share of government funding supported EMRs[18]. All clinically relevant data fields from volunteering family physician's using Practice Solutions® EMR for at least two years are extracted through an automated 'plug-in' triggered by the physician or their designate. Structured names and address fields are not extracted and the data goes through an initial name removal as part of the extraction process. This name removal is based on the patient name and family physician name captured in structured fields. The program searches for the occurrence of the name in the free-text data and replaces it with a randomly generated fake gender-specific first and last name. This preliminary de-identification does not remove all names, as names of family members, nicknames and misspelled names, or names of physicians or other healthcare providers that are working outside the clinic are not removed. Next the extracted data is encrypted and transmitted securely and electronically to ICES. Immediately upon arrival at ICES, data covenanters partition off the health card numbers to be scrambled for linkage to administrative data. Other identifying information such as date of birth, gender and postal code are stripped and kept in files separated from the main bulk of the data.
Creating a reference standard
Free-text fields in the EMR include all fields in the cumulative patient profile (history of past health, active problems, family history and allergies), progress notes generated at each physician visit, referral letters, consultation letters and diagnostic tests. A random sample of 1000 free-text notes from all the different types of free-text fields from a group practice with over 10,000 patients was used as a training set for the modified deid. We pulled an additional two sets of free-text notes to serve as validation sets. One set was comprised of 700 notes from 17 physicians located in 7 different clinics distributed throughout Southern Ontario, while another had 500 notes from a group practice located in a geographic location that was different then the location of the practice used in the training set.
Free-text fields were manually 'tagged' for patient and physician names, hospitals and other healthcare facilities/clinics, street names, Ontario cities, businesses, health card numbers, postal codes, phone and medical record numbers, websites and email addresses, by one of the study staff. All of the tagged records were run through the program which generated a list of words that were removed, false positives and false negatives. The lists were reviewed in detail and any word that appeared to be incorrectly removed by the program was reviewed by using a simple word search function to identify where it appeared in the text. If a tagging error was made the tag was corrected. This process was repeated several times for each data set until we believed there were no more tagging errors. These corrected tagged records served as the reference standard for evaluating the performance of the modified program.
The original deid program and the modified deid program were run on the training records in an incremental fashion. First it was run on 500 free-text training records, tests of accuracy were performed, false positives and negatives were reviewed, further modifications were made to the program and then it was tested on the original 500 plus an additional 250 training records, a similar process was repeated and then the program was run on the full 1000 free-text training records.
Once the final modified deid program was optimized to achieve the best results possible on the training data, the program was run on the two validation sets to assess the validity and generalizability of the newly modified program.
Deid Program Modifications
Dates
In order to preserve clinical context and to allow for linkage to the administrative databases at ICES that records dates and reasons for hospitalization and billing dates of physician clinical encounters, we disabled the date removal functionality in the deid software to preserve dates recorded in the EMR. Since birth dates are captured and stored elsewhere in the database, we removed date of birth from the free-text fields by performing a separate search for date of birth based on the information captured in the structured date of birth field.
In addition, in order to avoid having the program erroneously recognize months of the year as someone's name, all months that were written in text format were changed to number format (ie. June 1, 2007 was changed to 06/01/2007).
Assessing the original deid program
The deid program works by scanning the medical text line by line and parsing the text into individual words. The program identifies PHI by using lists and regular expressions. PHI that involve numeric patterns, such as street addresses or telephone numbers, are identified by regular expressions based on numeric patterns as well as appearances of context words such as "road" for street address or "pager" for pager number. In the case of non-numeric patterns, like names and locations, dictionary look-ups and context are used to locate both known and potential PHI. Next, the program performs pattern matching using regular expressions that look for patterns with various context keywords to find more named entities. Simple heuristics are used to qualify or disqualify ambiguous terms as PHI. Finally, each PHI is replaced with a tag denoting its corresponding category. After changing the date functionality of the program we ran the rest of the original deid program on the first 500 notes from the training set of free-text records.
Locations, healthcard and medical record numbers
The pre-existing deid software uses lists based on American context, thus these lists were replaced with Ontario lists for street names,[19] municipalities,[20] healthcare facilities[21] and businesses[22]. Healthcare facilities were separated and grouped according to type in order to replace the facility with another similar type to preserve clinical context. Pharmacies and insurance companies and business names that were also commonly used phrases were removed from the businesses list. Radiology clinics, medical laboratories and physiotherapy clinics were removed from the businesses list and placed in the healthcare facilities list. Municipalities and businesses were split into 'ambiguous' and 'unambiguous' by cross referencing against all of the other lists. Those that also appeared on other lists were placed into 'ambiguous' lists while all others remained on the 'unambiguous' lists.
To the number string searches we added modifications to detect Canadian postal codes (letter number letter number letter number) and Ontario healthcard numbers (a string of 10 numbers that may or may not be separated into groups of 4, 3 and 3 digits plus or minus one, or two letter version codes). To remove medical record numbers we removed numbers that were between 5 and 9 digits. In addition, the ethnicity, international cities and local places lists that were part of the original deid program were also removed either for irrelevance or in order to preserve clinical context.
Names
The existing deid program name removal is based on both a dictionary look up for known patient and provider names and context checks. This dictionary look up is akin to our 'initial name removal' phase that is performed at the physician office before data is transferred to ICES. For the context checks it groups names into names that are either, 'ambiguous', 'unambiguous' or 'popular.' 'Ambiguous' names are only removed if they occur beside a first name or a last name, or if there is an immediate word preceding or following such as 'Dr.', 'Mr.', 'daughter', 'mother', 'husband', etc. For the 'ambiguous' names list we used the existing list and added a separated list of first names and last names from the Registered Persons Database (RPDB) which records the first and last names of all residents in the province of Ontario and includes over 700,000 unique last names. We also incorporated a list of nicknames[23] developed by a team of researchers at the University of Ottawa to the 'ambiguous' name list. 'Unambiguous' names are removed with every occurrence in the text. To this list we added additional names that were not included in the original list and were used as the replacement names for the preliminary name de-identification that occurred in the physician office prior to data transfer. The original deid 'popular' names list was not altered and names that were in the 'popular' names list and also on the other name lists were removed from the other lists. Names that were on both the 'unambiguous' and 'ambiguous' names list were removed from the 'ambiguous' names list. For physician names we used a separated list of first and last names from the 2006 Canadian Medical Directory[24].
After the lists were created, all except the 'unambiguous' names list were checked against a list of common English words that came with the original deid program and any names or words that were also commonly used English words were removed so as to prevent removal of words that were a part of phrases describing clinical information. The 'unambiguous' names was checked against a shorter list of the most common English words that also came with the original deid program, in order to detect the names that were also one of the most common English names and if the name was on the list it was similarly removed.
Protecting medical eponyms
Medical eponyms are diseases, syndromes, signs or symptoms that are named after someone, often the physician or person that first described or discovered it, or a patient that was afflicted with it. Some examples include Parkinson's disease, Homan's sign and Apgar score. All are common terms used in the medical realm but to an automated de-identification system, may appear to be a person and then erroneously removed. Although deid had a short list of around 25 medical eponyms to check names and words that were identified as potentially identifying we expanded this by including 600 more chosen from a list of over 6000 medical eponyms[25]. These 600 were the most commonly used, as determined by the family physician/investigator (KT).
Further modifications and the creation of a 'do not remove' list
After running the program initially, several recurrent program errors were identified. Thus we added coding to prevent the removal of single letters followed by punctuation. This was done to protect single letter short forms such as the acronym S O A P standing for subjective, objective, assessment and plan, a commonly used format for physicians to record clinical encounters. We also added coding in order to prevent removal of typical medical nomenclature, that could be mistaken for a postal code, such as maternal pregnancy history depicted as G2P1A1 denoting gravida of 2, parity of 1 and abortions 1, C6C7T1 denoting cervical spine 6, cervical spine 7 and thoracic spine 1, or S1S2S4 nomenclature denoting heart sounds. The program also removed words such as Operative-Smith considering it to be a hyphenated last name, thus we modified the program to prevent this error. Last, we modified the context street address part of the program requiring a number followed by a word for all Drive's to be removed as the program was erroneously removing phrases such as, 'fitness to drive.'
After these further modifications were made, there were still recurrent errors identified necessitating the creation of a 'do not remove' list. This list of words and phrases was used to over-ride decisions made by deid. It included the countries and states from the original deid program to preserve ethnicity and travel that may have clinical implications. As well, it included medications, common medical acronyms (ie.1 mm ST elevation as typically used in descriptions of electrocardiograms), parts of the body and words that are commonly used in a clinical context. The list of medications was taken from the Ontario Drug Benefit formulary. The list of body parts and systems was derived from the Canadian Classification of Health Interventions (CCI), and the list of common words and phrases was created after reviewing the list of words that were deemed false positive or negative and recognizing common words or phrases that were being removed such as assessment and emergency.
Performance measures used
We report sensitivity/recall as the percentage of positive labeled instances of PHI that were predicted as positive, specificity as the percentage of negative (unlabeled) instances that were predicted as negative, precision (or positive predictive value) as the percentage of positive predictions that were correct and accuracy as the percentage of predictions that were correct. F- measure, a combination of precision and recall with equal weighting, was measured using the formula: F-measure = 2(precision × recall)/(precision + recall).
This project received ethics approval from Sunnybrook Health Sciences Centre Research Ethics Board.
Results
The original deid program, prior to any modifications, performed with a similar precision but more than 10% lower recall on our data compared to the performance on US nursing notes reported by the originators showing 74.9% precision and 96.7% recall[17]. Modifying the program and replacing US locations and business lists with Ontario ones resulted in an improvement in recall while the addition of our name lists did not make further substantial improvements. Adding the medical eponyms list had no impact and adding the protection for common acronyms and nomenclature resulted in minimal improvements. However, adding the 'do not remove' lists greatly improved the specificity, precision, accuracy and F-measure while only slightly decreasing the recall. (see Table 1)
Table 1. Results of the original deid program and modified program on the training set and two validation sets
When the final modified program was run on the validation sets, the sensitivity and accuracy dropped but the specificity and precision was similar to that in the final training set thereby supporting the generalizability of the modified program while protecting clinical content. (see Table 1)
Discussion
We found that deid could be modified to fit and work on free-text primary care EMR data in Ontario, Canada. However major modifications to the program were necessary to bring the specificity, precision and accuracy up to an acceptable level in order to prevent loss of clinical information in the de-identification process.
While other de-identification programs report very high recall (> 95%) on defined types of medical free-text documents such as discharge summaries[11,13-15] or pathology reports,[8-10,16] our results are inclusive of all types of free-text records contained in primary care EMRs including point-form progress notes, diagnostic tests, operatives reports, consultation letters and discharge summaries. Furthermore, our data was real world data from multiple different geographic locations, with text from multiple types of physicians and allied health professionals. The aim of other programs have been for maximal recall whereas not overzealously replacing words or phrases that may have clinical relevance was of greater importance to us. Additionally, our data goes through a first pass name removal and then instances of PHI are replaced by pseudonyms that are generated by our modified program. To a reader, missed occurrences of PHI that are not replaced are difficult to detect as they are mixed in with the pseudonym PHI.
Adaptation of deid to Swedish[26] and French[27] has been generally unsuccessful. Both attempts were confined to hospital records and both had challenges of adaptation into a different language with different grammatical rules. It was not surprising to find that both groups found deid to cause over-deidentification similar to what we found in the English language until we created a 'do not remove' list consisting of common over de-identification terms that was a result of the context portion of the deid program.
Admittedly there are number of limitations to our modified deid program that affect the generalizability of this tool. First, the main de-identification process occurs at ICES to allow for in-house analysis of data. ICES given its 'prescribed entity' status and designated data covenanters that are permitted to handle identifiable personal level health information and therefore can partition the data and run the de-identification software, is a relatively unique situation not only in Canada but also the rest of the world. Thus application of this software in other jurisdictions may not be sufficient to meet general privacy standards. However, as the development of 'one patient one record' programs develop in other provinces and other countries the findings here are likely to contribute to this growing field. Second, this program was developed on Practice Solutions® EMR software with its unique data structure and layout leading to a tendency for physicians to insert data into their EMR in an optical character recognition (OCR) format which renders the text searchable and editable. Not all EMR data from other vendors is structured this way and often in other EMRs external paper documents are scanned in, captured and stored in a picture like format such as a tiff, pdf, or jpeg. Documents that are stored in this manner need to be further processed and converted to an OCR format before de-identification can occur and doing so can distort words or introduce typographical errors that can be missed by an automated system looking for matching words. Third, to train and test our program, we took a sample of records from all of our current data and although our validation set results were comparable to our training set results, it is possible that not all ways of entering data were captured in our random sample. New physicians that we add to the database may have their own unique style of entering data and this may lead to errors in our de-identification processing. Last, given the large additional lists we have added to the program, de-identification of documents is time consuming taking approximately 47 hours to process 5 years of data on 2900 patients.
Conclusion
Despite these limitations we now have a reasonably accurate tool for de-identifying primary care EMR data in EMRALD. Future research could focus on developing efficient tools to de-identify data at the extraction point and prior to transfer. Nonetheless this tool will be applied to all of our free-text EMR data currently existing in our database and future data that will be collected. This greatly facilitates the use of all of the valuable information contained in the free-text fields of the EMR which will allow for a more maximal use of EMR data not impeded by patient privacy and confidentiality issues.
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
All of the authors were involved in the conception and design of the study. JM led the initial conceptual approach to the de-identification of free-text EMR data. MC was primarily responsible for the program modifications, with additional conceptual contributions from JK, KT and TM. KT and JK prepared the first draft of the article, and KT was responsible for subsequent revisions. All of the authors critically reviewed the article and approved the final version.
Funding
Data acquisition was supported by a grant from the Canadian Institutes of Health Research (CIHR) to the Canadian Cardiovascular Outcomes Research Team (CCORT) grant FRN:CTP79847. The National Research Council of Canada provided the support for the initial conceptual design and students. Finally, the analysis was supported by a grant from the Ontario Ministry of Health and Long-Term Care Enhancing Quality in Primary Care.
This study was supported by the Institute for Clinical Evaluative Sciences (ICES), which is funded by an annual grant from the Ontario Ministry of Health and Long-Term Care (MOHLTC). The opinions, results and conclusions reported in this paper are those of the authors and are independent from the funding sources. No endorsement by ICES or the Ontario MOHLTC is intended or should be inferred.
Acknowledgements
We would like to thank Yang Liu and Hashmat Rohian of York University for their assistance in literature review and program identification.
References
1. Report of the WHO Global Observatory for eHealth: Building foundations for eHealth: progress of member states: report of the Global Observatory for eHealth. Geneva, WHO Press; 2006.
2. Canada Health Infoway [http://www.infoway-inforoute.ca/lang-en] webcite
3. Mitiku T, Tu K: Using data from electronic medical records: theory versus practice.
Healthcare Quarterly 2008, 11:19-21.
4. Personal Health Information Protection Act, 2004. S.O. 2004, c.3, Schedule A [http://www.e-laws.gov.on.ca/html/statutes/english/elaws_statutes_04p03_e.htm] webcite
5. Privacy Code: Protecting Personal Health Information at ICES [http://www.ices.on.ca/file/ICES%20Privacy%20Code%20Version%204.pdf] webcite
6. Taira RK, Bui AA, Kangarloo H: Identification of patient name references within medical documents using semantic selectional restrictions.
Proc AMIA Symp 2002, 757-761. PubMed Abstract | PubMed Central Full Text
7. Sweeney L: Replacing personally-identifying information in medical records, the Scrub system.
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8. Berman JJ: Concept-match medical data scrubbing. How pathology text can be used in research.
Arch Pathol Lab Med 2003, 127:680-686. PubMed Abstract | Publisher Full Text
9. Gupta D, Saul M, Gilbertson J: Evaluation of a deidentification (De-Id) software engine to share pathology reports and clinical documents for research.
Am J Clin Pathol 2004, 121:176-186. PubMed Abstract | Publisher Full Text
10. Beckwith BA, Mahaadevan R, Balis UJ, Kuo F: Development and evaluation of an open source software tool for deidentification of pathology reports.
BMC Med Inform Decis Mak 2006, 6:12. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text
11. Uzuner O, Sibanda T, Luo Y, Szolovits : A de-identifier for medical discharge summaries.
Artificial Intelligence in Medicine 2008, 42:13-35. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
12. Role of local contect in automatic deidentification of ungrammatical, fragmented text
Proceedings of the North American Chapter of Association for Computational Linguistics/Human Language Technology (NAACL-HLT 2006) New York, NY, June 5-7 2006, 65-73.
13. Szarvas G, Farkas R, Busa-Fekete R: State-of-the-art anonymization of medical records using an iterative machine learning framework.
J Am Med Inform Assoc 2007, 14:574-580. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
14. Uzuner O, Luo Y, Szolovits P: Evaluating the state-of-the-art in automatic de-identification.
J Am Med Inform Assoc 2007, 14:550-563. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
15. Wellner B, Huyck M, Mardis S, Aberdeen J, Morgan A, Peshkin L, et al.: Rapidly retargetable approaches to de-identification in medical records.
J Am Med Inform Assoc 2007, 14:564-573. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
16. Thomas SM, Mamlin B, Schadow G, McDonald C: A successful technique for removing names in pathology reports using an augmented search and replace method.
Proc AMIA Symp 2002, 777-781. PubMed Abstract | PubMed Central Full Text
17. Neamatullah I, Douglass MM, Lehman LH, Reisner A, Viallarroel M, Long WJ, et al.: Automated de-identification of free-text medical records.
BMC Medical Informatics and Decision Making 2008., 8: PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text
18. Ontario MD Funding Eligible CMS Offerings/EMR Advisor [https://www.emradvisor.ca/node/253] webcite
19. DMTI Spatial Inc: CanMap Route Logistics, Ontario Version (Street Names). Markham, ON, DMTI Spatial Inc; 2003.
20. Land Information Data [https:/ / www.applio.lrc.gov.on.ca/ lidslogin/ SecureLogin.asp?SessionID=196516501] webcite
21. 2008 Master Numbering System [http:/ / www.health.gov.on.ca/ english/ public/ pub/ ministry_reports/ master_numsys/ master_numsys08.html] webcite
22. DMTI Spatial Inc: Enhanced Points of Interest, Ontario Version (Business Names). Markham, ON, DMTI Spatial Inc; 2006.
23. Sokolova M, El Emam K, Chowdhury S, Emilio N, Rose S, Jonker E: Evaluation of rare event detection. Springer, 2010.
Advances in Artificial Intelligence 2010, 23:379-383.
(Canadian Al 2010)
Publisher Full Text
24. Scott's Directories: Canadian Medical Directory.
Don Mills, ON 52nd edition. 2006.
25. Who Named It? Eponyms A-Z [http://www.whonamedit.com/azeponyms.cfm/A.html] webcite
26. Velupillai S, Dalianis H, Hassel M, Nilsson GH: Developing a standard for de-identifying electronic patient records written in Swedish: Precision, recall and F-measure in a manual and computerized annotation trial.
International Journal of Medical Informatics 2009, 78:e19-e26. PubMed Abstract | Publisher Full Text
27. Grouin C, Rosier A, Dameron O, Zweigenbaum P: Testing tactics to localize de-identification.
Medical Informatics in a United and Healthy Europe. IOS Press 2009, 735-739.
Pre-publication history
The pre-publication history for this paper can be accessed here:
http://www.biomedcentral.com/1472-6947/10/35/prepub
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Research Article
Superlinear Singular Problems on the Half Line
Irena Rachůnková* and Jan Tomeček
Author affiliations
Department of Mathematical Analysis and Applications of Mathematics, Faculty of Science, Palacký University, tř . 17. listopadu 12, 771 46 Olomouc, Czech Republic
For all author emails, please log on.
Citation and License
Boundary Value Problems 2010, 2010:429813 doi:10.1155/2010/429813
Published: 15 December 2010
Abstract
The paper studies the singular differential equation , which has a singularity at . Here the existence of strictly increasing solutions satisfying is proved under the assumption that has two zeros 0 and and a superlinear behaviour near . The problem generalizes some models arising in hydrodynamics or in the nonlinear field theory.
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<D <M <Y
Y> M> D>
: Register writer hates life, film at 11.
: I now have an account on Advogato, although I'm not sure what benefits I obtain from such. I don't feel comfortable certifying people as one thing or another, and I already have an online journal.
: I guess certification isn't so bad so long as you stick to certifying people you actually know.
: Scott explains the Lynx feature that allegedly lets people other than me be lazy.
Newshub doesn't work anymore anyway.
: I'm getting a ride with Josh up to Bakersfield. Woo!
[Main]
Unless otherwise noted, all content licensed by Leonard Richardson
under a Creative Commons License.
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Changes related to "User group meeting agenda & minutes 18 June 2008"
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Remnant Data
From Forensics Wiki
Revision as of 09:36, 16 March 2007 by Simsong (Talk | contribs)
Jump to: navigation, search
Remnant Data is data that is unintentionally left behind on computer media. In forensic usage, remnant data is typically left behind after attempts have been made to delete the data, after the data has been forgotten, or after the media on which the data resides has been decomissioned.
Remnant data appears at all levels of modern computer systems:
• Computer systems that are discarded.
• Partitions in hard drives that are deleted.
• Files on hard drives that are deleted but not overwritten.
• Snippets of text in Microsoft Word files.
• Heap variables that are freed with free()
• Automatic variables left on the stack of languages like C or garbage collected in languages like Java.
Originally the phrase "remnant data" was used to describe data left behind on magnetic recording media such as tapes and floppy disks. On these kinds of media it was suggested that previous generations of data could be recovered---a process that is easy to observe with analog cassette and reel-to-reel tapes.
Papers
Byers, Simon. Scalable Exploitation of, and Responses to Information Leakage Through Hidden Data in Published Documents, AT&T Research, April 2003
Chow, J., B. Pfaff, T. Garfinkel, K. Christopher, M. Rosenblum, Understanding Data Lifetime via Whole System Simulation, Proceedings of the 13th USENIX Security Symposium, 2004.
Garfinkel, S. and Shelat, A., "Remembrance of Data Passed: A Study of Disk Sanitization Practices," IEEE Security and Privacy, January/February 2003.
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Team A 6th Stage "Mokugekisha"
From generasia
Revision as of 23:24, 8 January 2011 by Lambchopsuey (Talk | contribs)
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Album Cover
Artist
AKB48
Album
Team A 6th Stage "Mokugekisha" (チームA 6th Stage 「目撃者」)
Released
2010.09.18
Catalog Number
AKB-D2059
Price
¥3000
Tracklist/Setlist
1. Miniskirt no Yousei (ミニスカートの要請) Zensa Girls
2. overture
3. Mokugekisha (目撃者)
4. Zenjin Mitou (前人未踏)
5. Ibitsu na Shinju (いびつな真珠)
6. Akogare no Pop Star (憧れのポップスター)
7. Ude wo Kunde (腕を組んで) Nakaya Sayaka, Maeda Atsuko, Kuramochi Asuka
8. Enjou Rosen (炎上路線) Takajo Aki, Sashihara Rino
9. Itoshisa no Accel (愛しさのアクセル) Takahashi Minami
10. Hoshi no Mukougawa (☆の向こう側) Iwasa Misaki, Kojima Haruna, Oota Aika, Nakata Chisato
11. Saboten no Gold Rush (サボテンのゴルドラッシュ) Ooya Shizuka, Katayama Haruka, Maeda Ami, Shinoda Mariko, Matsubara Natsumi, Nakagawa Haruka
12. Utsukushiki Mono (美しき者)
13. Ai wo Kure (アイヲクレ)
14. Matenrou no Kyori (摩天楼の距離)
15. Inochi no Imi (命の意味)
16. I'm crying
17. Zutto Zutto (ずっと ずっと)
18. Pioneer
Information
Team A 6th Stage "Mokugekisha" is the sixth stage show from AKB48's Team A. It started performances on July 27th, 2010. Like Team B's fifth stage and Team K's sixth stage, it has a Kenkyuusei act called 'Zensa Girls' before each performance. The album had limited distribution; therefore, it was not counted on the Oricon charts.
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About this Journal Submit a Manuscript Table of Contents
Evidence-Based Complementary and Alternative Medicine
Volume 1 (2004), Issue 1, Pages 35-40
doi:10.1093/ecam/neh016
Review
Functional Somatic Syndromes: Emerging Biomedical Models and Traditional Chinese Medicine
Center for Neurovisceral Sciences and Women's Health, Department of Medicine, Physiology and Psychiatry, David Geffen School of Medicine, UCLA, USA
Received 19 December 2003; Accepted 24 February 2004
Copyright © 2004 Steven Tan 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
The so-called functional somatic syndromes comprise a group of disorders that are primarily symptom-based, multisystemic in presentation and probably involve alterations in mind-brain-body interactions. The emerging neurobiological models of allostasis/allostatic load and of the emotional motor system show striking similarities with concepts used by Traditional Chinese Medicine (TCM) to understand the functional somatic disorders and their underlying pathogenesis. These models incorporate a macroscopic perspective, accounting for the toll of acute and chronic traumas, physical and emotional stressors and the complex interactions between the mind, brain and body. The convergence of these biomedical models with the ancient paradigm of TCM may provide a new insight into scientifically verifiable diagnostic and therapeutic approaches for these common disorders.
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About this Journal Submit a Manuscript Table of Contents
International Journal of Distributed Sensor Networks
Volume 2012 (2012), Article ID 247346, 11 pages
doi:10.1155/2012/247346
Research Article
Onto: Ontological Context-Aware Model Based on 5W1H
Department of Computer and Radio Communications Engineering, Korea University, Seoul 136-701, Republic of Korea
Received 11 October 2011; Accepted 24 December 2011
Academic Editor: Tai Hoon Kim
Copyright © 2012 Jeong-Dong Kim 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.
How to Cite this Article
Jeong-Dong Kim, Jiseong Son, and Doo-Kwon Baik, “ Onto: Ontological Context-Aware Model Based on 5W1H,” International Journal of Distributed Sensor Networks, vol. 2012, Article ID 247346, 11 pages, 2012. doi:10.1155/2012/247346
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About this Journal Submit a Manuscript Table of Contents
Journal of Probability and Statistics
Volume 2012 (2012), Article ID 617678, 26 pages
doi:10.1155/2012/617678
Research Article
Bayesian Approach to Zero-Inflated Bivariate Ordered Probit Regression Model, with an Application to Tobacco Use
1Department of Economics, Andrew Young School of Policy Studies, Georgia State University, P.O. Box 3992, Atlanta, GA 30302, USA
2Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
Received 13 July 2011; Revised 18 September 2011; Accepted 2 October 2011
Academic Editor: Wenbin Lu
Copyright © 2012 Shiferaw Gurmu and Getachew A. Dagne. 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
This paper presents a Bayesian analysis of bivariate ordered probit regression model with excess of zeros. Specifically, in the context of joint modeling of two ordered outcomes, we develop zero-inflated bivariate ordered probit model and carry out estimation using Markov Chain Monte Carlo techniques. Using household tobacco survey data with substantial proportion of zeros, we analyze the socioeconomic determinants of individual problem of smoking and chewing tobacco. In our illustration, we find strong evidence that accounting for excess zeros provides good fit to the data. The example shows that the use of a model that ignores zero-inflation masks differential effects of covariates on nonusers and users.
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Bibliography: Foreign Language Pubs
You are not logged in. If you create a free account and sign in, you will be able to customize what is displayed.
Title: Foreign Language Pubs
Author: Nora Roberts
Year: 1900
Type: NOVEL
ISFDB Record Number: 177037
User Rating: This title has fewer than 5 votes. VOTE
Current Tags: None Add Tags
Publications:
Copyright (c) 1995-2011 Al von Ruff.
ISFDB Engine - Version 4.00 (04/24/06)
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Inactive
× You must be logged in to change this data. If you don't have an account, Please join.
Settings : Code Locations
Analyzed 8 days ago based on code collected 8 days ago.
Showing page 1 of 1
Repository URL SCM Type Update Status Ignored Files
http://py4sea.googlecode.com/svn/trunk Subversion (via SvnSync) Ohloh update completed 8 days ago. All files included.
About Code Locations
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Default
Jahia
Community rating:
Notes:
What is a Stack?
It's a list of software used to accomplish something. LAMP is an example.
To add a project to your stack, click 'Show Recommendations for this Stack' at the top middle of this page and then click I use it on the projects you use.
More questions? Stack FAQ
Embed
Show the world what open source projects you use.
Default Stack
Copyright © 2013 Black Duck Software, Inc. and its contributors, Some Rights Reserved. Unless otherwise marked, this work is licensed under a Creative Commons Attribution 3.0 Unported License . Ohloh ® and the Ohloh logo are trademarks of Black Duck Software, Inc. in the United States and/or other jurisdictions. All other trademarks are the property of their respective holders.
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"url": "www.openwetware.org/index.php?redirect=no&title=BioMicroCenter%3A2100BioAnalyzer",
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BioMicroCenter:2100BioAnalyzer
From OpenWetWare
Jump to: navigation, search
The Agilent 2100 BioAnalyzer is a nanofluidics device that preforms size fractionation and quantification of small samples of DNA, RNA, or Protein. In addition, the BioAnalyzer is able to preform flow cytometry on small numbers of cells. Samples can be run on the BioAnalyzer either by individual scientists or by the BioMicro Center. Most samples submitted to the BMC for analysis on the BioAnalyzer can be processed within 24 hours.
More information about the BioAnalyzer, including examples of the data that we generate in the BioMicro Center can be found on the BioAnalyzer Information page.
Contents
BioMicro Center Services
Samples may be run on the BioAnalyzer either as a full service with sample preparation done by BioMicro Center technicians, or by individual scientists as supervised users following a one hour training session by Manlin or Justin.
Full Service
Samples can be dropped off in the BioMicro Center for analysis along with the SAMPLE SUBMISSION FORM. Completed analysis will be sent to your email address. Finished analysis includes the electropherogram (right) as well as automated quantification of peak volumes (mass/molarity). We also can send the data file to allow you to perform your own quantification (please indicate on the submission form).
Supervised Service
Samples can also be run by individual users on the BioAnalyzer after a user has received training by Manlin or Justin (Core Labs only please). This service is being run on a trial basis and will be discontinued if we find the machine is abused. We do request that you use the chips in the BioMicro Center to help us turn over our inventory (so the kits are always in date). Once you are trained in the use of the BioAnalyzer you are welcome to use the machine off business hours (please use the sign in sheet next to the BioAnalyzer). During regular business hours, you must check with someone in BMC to confirm that the machine is available.
IMPORTANT: BIOMICRO CENTER BUSINESS ALWAYS HAS PRIORITY ON THE BIOANALYZER
Sample Type Price (per chip)
-------------- ---------------
Training $50 (per session)
DNA $40
RNA $40
small RNA $55
Protein $40
High Sens. Ptn $70
Flow Cytometry $40
Rates are slightly higher then the cost of the individual chips to include the cost of the service contract, etc.
Available Analyses
DNA
• DNA 1000 Kit: 25bp - 1,000bp, 0.1-50ng/uL
• DNA 7500 Kit: 100bp - 7,500bp, 0.1-50ng/uL
• DNA 12000 Kit: 100bp - 12,000bp, 0.1-50ng/ul
• High Sensitivity DNA kit: 50bp - 7,000bp, 5-500pg/ul
RNA
• RNA Nano: 25-500 ng/ul total RNA
• RNA Pico: 0.05-5 ng/ul total RNA
• small RNA: 0.05-2 ng/ul miRNAs
PROTEIN
• Protein 80 5kD- 80kD 60ng/ul
• Protein 230 14kD-230kD 30ng/ul
• High Sensitivity 10kD-250kD 0.3ng/ul
FLOW CYTOMETRY
Software
Agilent is now providing software for the analysis of BioAnalyzer data to be used on your own PCs. Users have found it somewhat clunky, but it does give you more freedom. The software is available for download from BioMicro at http://bmc-apps.mit.edu/ or from Agilent at http://www.chem.agilent.com/en-US/products/instruments/lab-on-a-chip/2100bioanalyzer/pages/formpage730.aspx
Software Tips and Tricks
• Click the Peak Description button on the top toolbar to switch between peak height, concentration, size, molarity, and migration time.
• Toggle the X axis to change from time to base pairs.
• Using your own standard ladder with corresponding concentrations will generate calibrations and standard curves.
• Customize your own color-coded flags.
• Changing parameters on Globing Scaling will set the same scaling standards for each sample per run.
Personal tools
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Image:M1D3 SKH final.pdf
From OpenWetWare
(Difference between revisions)
Jump to: navigation, search
M1D3_SKH_final.pdf (file size: 1.26 MB, MIME type: application/pdf)
Current revision
File history
Click on a date/time to view the file as it appeared at that time.
Date/TimeDimensionsUserComment
current15:52, 15 February 2013 (1.26 MB)Shannon K. Alford (Talk | contribs)
The following file is a duplicate of this file:
There are no pages that link to this file.
Personal tools
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User:Daniel Goodman
From OpenWetWare
(Difference between revisions)
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(Contact Info)
(Contact Info)
Line 1: Line 1:
==Contact Info==
==Contact Info==
-
[image:http://www.dbgoodman.com/daniel.jpg thumb|right|Daniel Goodman]
+
[image:http://www.dbgoodman.com/daniel.jpg|thumb|right|Daniel Goodman]
*Daniel Goodman ([[http://www.dbgoodman.com|www.dbgoodman.com]]
*Daniel Goodman ([[http://www.dbgoodman.com|www.dbgoodman.com]]
Revision as of 07:25, 17 July 2008
Contents
Contact Info
[image:http://www.dbgoodman.com/daniel.jpg|thumb|right|Daniel Goodman]
• Daniel Goodman ([[1]]
• University of Cambridge
I just graduated from the University of California, San Diego, but this year I'm working as a Whitaker Bioengineering Fellow in the Department of Oncology at the University of Cambridge. I'm a member of the Cambridge 2008 iGEM team, which is most likely why you are reading this.
Education
• Year, PhD, Institute
• 2008-2009, Whitaker International Bioengineering Fellow, University of Cambridge
• 2008, BS in Bioengineering w/ spec. in Bioinformatics, University of California, San Diego
Research interests
1. Computational Systems Biology
2. Complex Systems
3. Biological Algorithms and Modeling
Publications
Check out my publications and CV at my website: www.dbgoodman.com.
Useful links
Personal tools
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Place:Chest Springs, Cambria, Pennsylvania, United States
Watchers
NameChest Springs
TypeBorough
Coordinates40.579°N 78.61°W
Located inCambria, Pennsylvania, United States
source: Getty Thesaurus of Geographic Names
the text in this section is copied from an article in Wikipedia
Chest Springs is a borough in Cambria County, Pennsylvania, United States. It is part of the Johnstown, Pennsylvania Metropolitan Statistical Area. The population was 110 at the 2000 census.
Research Tips
This page uses content from the English Wikipedia. The original content was at Chest Springs, Pennsylvania. The list of authors can be seen in the page history. As with WeRelate, the content of Wikipedia is available under the Creative Commons Attribution/Share-Alike License.
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Tell me more ×
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 the California LLC-12 form, Item 12 is "Type of Business". How specific should my answer be? I want to leave it as general as possible give myself the maximum flexibility.
In case I need to be specific, what should I write to describe a enterprise software company (i.e., there is a licensing component as well as a services component). I don't want to write something stupid and get classified as a body shop.
Can I just write "All lawful business"?
Link to LLC-12: http://www.sos.ca.gov/business/llc/forms/llc-12.pdf
share|improve this question
2 Answers
up vote 1 down vote accepted
You should give the tax authorities a general idea of what you category you are working in as they classify all businesses according to the North America Industry Classification System (NAICS). It's not the same thing as the corporation Articles which require you to state that you are able to be engaged in "all lawful business" in California. Rather, they want to have a general idea of your business for statistical purposes. "Technology" or "Internet software" should be fine, "All lawful business" is probably not a good idea here.
Note: This is not legal advice nor does this create an attorney-client relationship.
share|improve this answer
Consult a CA tax lawyer. The implications for your choice may have tax consequences, although based on what you've described, I personally do not know of any tax distinctions between the general business and your enterprise software business.
share|improve this answer
Your Answer
discard
By posting your answer, you agree to the privacy policy and terms of service.
Not the answer you're looking for? Browse other questions tagged or ask your own question.
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5
votes
5answers
425 views
how to deal with a slanderous website that is using a trademarked domain name
A friend of mine accidentally let the .com domain of their US business expire, and it was snatched up by an unknown person who has a personal grudge against them. The website is now full of slanderous ...
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| Edit | | History |
From DDO wiki
(Redirected from Aegis of Flame)
Jump to: navigation, search
Aegis of Flame
Shield Type Large Shield
Proficiency Shield Proficiency (General)
Minimum Level 16
Binding Bound to Character on AcquireBound to Character on Acquire: This item is Bound to Character on Acquire
Shield Bonus +10
Max Dex Bonus None
Damage Reduction 10
Armor Check Penalty None
Arcane Spell Failure 5%
Damage [2d6] + 5 Bludgeon, Good, Silver, Mithral, Magic
Critical Roll 20 / x2
Durability 165
Material MithralMithral: Mithral armor is one type lighter then normal. Arcane Spell Failure decreased by 10%. Maximum dexterity bonus increased by 2. Armor check penalty reduced by 3.
Hardness 24
Base Value 00065020006,502pp
Weight 7.50 lbs
Location Silver Flame Nugget, End reward
Enchantments
Upgradeable?
Not upgradeable
Description Clerics and Paladins often use their shields to bash their opponents, no doubt why this one is ordained with several sharp metal spikes.
Tips
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Error!
Success!
Graphics Mill from Aurigma Splits Up!
0
kicks
Graphics Mill from Aurigma Splits Up! (Unpublished)
Aurigma Inc. announces an anniversary version of Graphics Mill for .NET, the popular SDK for the developers of image processing solutions. Version 5.0 marks a new milestone in the product life cycle: Graphics Mill is now offered in two flavors, Standard and Pro. This allows the developers to choose the optimal tool for precisely addressing the goals in an economically efficient manner. Now the developers of basic imaging solutions do not need to pay for expert Pro version functionality, having the Standard package contain all necessary imaging features. Normally, Standard version proves sufficient for such solutions as image editing web applications, image viewers, photo galleries and catalogs, etc. More demanding customers, however, would rather choose to buy the Pro version that includes all the expert features needed to develop such serious products as preprint preparation solutions, document management systems, satellite photo processing applications, etc. Graphics Mill Pro has native support for x64 platforms that allows for addressing more than 2 gigabytes of RAM per process for imaging needs.
Kicked By:
Drop Kicked By:
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Kanawha Trail
From FamilySearch Wiki
(Difference between revisions)
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<span style="line-height: 1.5em;">William Fischer Jr., TRAILS/THE KANAWHA TRAIL</span>
<span style="line-height: 1.5em;">William Fischer Jr., TRAILS/THE KANAWHA TRAIL</span>
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[[Category:Emigration and Immigration]]
Revision as of 02:41, 5 February 2013
Herds of buffalo seeking easy access to salt licks and grazing lands wore trails through the hills and mountains of what would become colonial America when it was an Indian no-man's land. Later, Indians found the same trails suitable for their needs whether they were for peaceful purposes or war parties.
The Kanawha or Buffalo Trail followed the Kanawha River from the Ohio River to Cedar Grove, then overland to Ansted. From there it followed the Meadow River and the Midland Trail (now U.S. 60) to Virginia. An alternate of this trail ran through Teays Valley from the Ohio River to the Kanawha River, near St. Albans. Another variation crossed the New River above the mouth of the Bluestone, passed through present Beckley, and followed Paint Creek north to the Kanawha River.
Not only were these paths highways, they were often the 'highest' way. Indians found ridges and summits much easier to travel than the valleys because they were drier, wind-swept of snow, never clogged by flood debris, offered a better vantage point in time of need and were generally safer. Shawnee warriors, intent on raiding Virginia frontier settlements used this trail because of its ease of access to the settlements. This trail was used by the party of Shawnees who took Mary Ingles captive in 1755, during the raid on Drapers Meadows.
Fur traders also used this route for their pelt-laden pack trains. The settlers from the east coast were the next group to use these trails for many of the same reasons the Indians used them.
There were numerous Indian villages along the Kanawha Trail until the middle 1600s. Exotic artifacts such as engraved marine shell gorgets from the eastern Tennessee region, as well as European copper and brass ornaments, and glass trade beads have been found at Pratt and Marmet, Kanawha County, and Buffalo, Putnam County, indicating movement along this route.
The Kanawha Trail also followed a portion of the route called the Ohio Branch of the Great Indian Warpath by William E. Myer in Indian Trails of the Southeast(1928). The Ohio Branch extended from Creek territory in Georgia and Alabama, up through eastern Tennessee and southwestern Virginia to the New and Kanawha rivers. At the mouth of the Kanawha several trails met. The main trail continued in a northwesterly direction through Ohio to Lake Erie.
First the buffalo and other game animals, then the native Americans and finally the settlers used these trails to get from one place to the other because they followed the natural lay of the land as far as ease of travel went. Today many of these trails have both State and U.S. highways that use the same routes as these earlier travelers.
References:
Darla S Spencer, INDIAN TRAILS
William Fischer Jr., TRAILS/THE KANAWHA TRAIL
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Modify
#6678 closed defect (fixed)
[Patch] Automatic tag correction (when reversing a way) should not attempt to change "FIXME" tags.
Reported by: rickmastfan67 Owned by: team
Priority: minor Component: Core
Version: latest Keywords:
Cc:
Description
1. Download attachment.
2. Hit "r" to reverse the only way in the file (once the way is selected of course).
What should happen: The way should be reversed without having the "Automatic tag correction" screen show up suggesting a change of the "FIXME" tag because the first word in it is "Western".
What does happen: The "Automatic tag correction" shows up suggesting that the word "Western" be changed to "eastern" in the "FIXME" tag.
=====
The "FIXME" tag should never be suggested for an "Automatic tag correction" because of people intentionally putting the specific "side" (Western, Eastern, Northern, Southern) of the road that needs to be fixed (for whatever reason). When just revering a way, it doesn't effect whatever cardinal direction is mentioned because the way itself hasn't been changed, just the order of the nodes has been.
NOTE: This only happens when the first word in the "FIXME" tag is a cardinal direction. If any other word starts off the "FIXME" tag, this problem doesn't happen.
Attachments (2)
ticket6678.osm (6.1 KB) - added by rickmastfan67 22 months ago.
6678.patch (1.3 KB) - added by simon04 21 months ago.
Download all attachments as: .zip
Change History (5)
Changed 22 months ago by rickmastfan67
comment:1 Changed 22 months ago by rickmastfan67
Changed 21 months ago by simon04
comment:2 Changed 21 months ago by simon04
• Summary changed from Automatic tag correction (when reversing a way) should not attempt to change "FIXME" tags. to [Patch] Automatic tag correction (when reversing a way) should not attempt to change "FIXME" tags.
Last edited 21 months ago by simon04 (previous) (diff)
comment:3 Changed 21 months ago by stoecker
• Resolution set to fixed
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"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:65374",
"uncompressed_offset": 196717756,
"url": "openwetware.org/index.php?diff=577342&oldid=577341&title=Haynes%3AAssembly101",
"warc_date": "2013-11-22T14:39:41.000Z",
"warc_filename": "<urn:uuid:51a14dce-53f8-465e-80fe-28f40d1a411c>",
"warc_url": "http://openwetware.org/index.php?title=Haynes:Assembly101&diff=577342&oldid=577341"
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Haynes:Assembly101
From OpenWetWare
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Jump to: navigation, search
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| dH<sub>2</sub>O || ___ μL || ___ μL + insert volume
| dH<sub>2</sub>O || ___ μL || ___ μL + insert volume
|-
|-
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| || 10.0 μL total
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| || 10.0 μL total || same
|-
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| colspan="3" | Mix the reaction(s) thoroughly by flicking the tube.<br>Incubate at room temperature for 10 minutes.
| colspan="3" | Mix the reaction(s) thoroughly by flicking the tube.<br>Incubate at room temperature for 10 minutes.
Revision as of 22:37, 20 January 2012
Model Procedure for Assembling Parts: Classic Ligation for Beginners
or, Cloning Sensei's Guide For the Aspiring Cloning Ninja
by Karmella Haynes, 2012
When I was a postdoc in Pam Silver's lab at Harvard (2008 - 2011), my lab mates and I generated large numbers of BioBrick assemblies so rapidly, and perhaps stealthily, that one of our colleagues in the department referred to us as "cloning ninjas." This guide is based on the MIT Registry of Standard Biological Parts suggested approach, which I've modified to make ligation-based assembly as quick and painless as possible. Let's begin.
Day 1*: Pick and amplify the desired plasmid DNA by growing transformed DH5α Turbo bacteria.
Make streaks from glycerol stocks 6 hours
1. Warm an agar plate at 37°C for at least 20 min.
2. Label the plate with the bacterial strain name (e.g., DH5α), the antibiotic, the BioBrick part(s) name, your initials, and the date.
3. Locate the desired -80°C glycerol stock. Use a sterile wooden toothpick to scrape up a tiny bit of the frozen bacteria and streak the plate.
4. Incubate the plate at 37°C for 6 hours to grow the bacteria.<br
Grow liquid cultures
1. Label 15 ml sterile culture tube(s) appropriately. Fill each tube with 2 ml of LB growth medium + appropriate antibiotic (e.g., 100 μg/ml ampicillin).
2. Using a sterile pipette tip, touch the bacterial streak (or pick up a single colony) and put the tip into the LB medium (bacterial end down).
3. Grow the cultures overnight in a shaking 37°C incubator.
*This may take two days instead of one if you're starting with a slow-growing strain.
Day 2: Extract the plasmids. Digest (cut), purify, and ligate (paste) the BioBricks. Put the assembled plasmid into bacteria
Extract the plasmid DNA: Qiagen Miniprep Kit 1.5 hours
To extract the plasmid DNA from the bacteria, perform a mini prep (refer to the Qiagen miniprep protocol). 2 ml of culture usually gives a yield of about 200 ng/μl (elution vol. = 75 μl).
Digest (cut) the DNA with restriction enzymes 30 minutes
1. First, write out a brief assembly strategy:
New Construct Name: BioBrick Insert Name, size (bp), cut sites + BioBrick Vector Name, size+backbone (bp), cut sites
2. Set up your digest reaction(s) as shown below:
Plasmid DNA 15.0 μl*
Fermentas FastDigest enzyme 1 1.0 μl
Fermentas FastDigest enzyme 2 1.0 μl
10x FastDigest buffer + green loading dye 3.0 μl
dH2O 10.0 μl
30.0 μl total
*For low yield DNA, use up to 25 μL; decrease dH2O accordingly.
Mix the reaction(s) thoroughly by flicking the tube.
Incubate at 37°C for 10 minutes.
Separate the fragments via gel electrophoresis and purify the fragments 2 hours
1. Make a 0.8% gel: add 0.48 g agarose to ~60 ml 1x TAE buffer in a glass flask.
2. Mix by swirling and microwave for 40 seconds. Mix by swirling again (to eliminate air pockets and prevent boiling-over) and microwave for 40 seconds.
3. Set up a gel mold and comb. Make sure the teeth are the right size to hold 30 μL of sample.
4. Add 5 μl of 10 mg/ml ethidium bromide (etBr) to the agarose for a final concentration of ~0.8 μg/mL etBr. Mix by swirling (avoid making bubbles).
5. Pour the gel into the gel mold. Allow it to cool until it becomes opaque.
6. Fill a gel electrophoresis chamber with 1x TAE.
7. Remove the comb from the gel and carefully submerge the gel into the filled electrophoresis chamber.
8. Carefully pipette 15 μL pre-made 1 kb ladder mix into the first empty well and the DNA samples into the other empty wells.
9. Connect the electrical leads so that the positive end is at the bottom (DNA migrates to the positive end). Run the gel at 100 V.
10. Stop the gel when the yellow dye (Orange G) reaches the desired place on the gel (~1 hr.).
11. Remove the gel from the chamber and photograph under UV light.
12. Use a scalpel to cut the appropriate sized band(s) from the gel, place each gel slice in a 1.5 mL tube, and purify the DNA (refer to the Qiagen gel purification protocol; elute with 30 μL EB buffer).
13. Measure the concentration of the purified fragment samples with a Nanodrop Spectrophotometer.
14. Record the absorbance (A260), purity (A260/A280), and concentration (ng/μl) for each sample.
Ligate (paste) the DNA fragments together
1. Calculate how many ng of insert you need to get a 2:1 ratio of insert molecules to 50 ng vector molecules
X ng insert = (bp insert / bp vector) x 2 x 50 ng vector
2. Calculate how many μL of insert and vector you will need for each ligation:
X μL insert = desired ng insert ÷ insert concentration ng/μL (do the same for vector)
3. Set up your ligation reaction(s) in sterile 0.5 mL tubes as shown below:
Ligation Negative Control
Insert DNA (X ng) ___ μL none
Vector DNA (50 ng) ___ μL same
2x Roche Rapid Ligation buffer 5.0 μl same
NEB T4 ligase 1.0 μl same
dH2O ___ μL ___ μL + insert volume
10.0 μL total same
Mix the reaction(s) thoroughly by flicking the tube.
Incubate at room temperature for 10 minutes.
Transform bacteria with the ligated plasmids 30 minutes
1. Warm selection agar plates at 37°C.
2. Incubate DH5α Turbo competent cells on ice just until thawed. Use 30 μL per ligation.
3. Add 30 μL thawed cells to the ligation reaction. Immediately place on ice and incubate for 10 min. (Do not heat shock; No 30 min. recovery is required for Amp resistance)
4. Label the pre-warmed plates with the antibiotic name, strain name, ligation (e.g., "BB part A insert + BB part B vector"), your initials, and the date.
5. Pipette the total volume of cells + ligation onto the agar; speared using sterile glass beads.
6. Incubate overnight at 37°C to get colonies
Note: The negative control will show you the number of “background” colonies so that you can determine whether your transformation worked, or is just the result of vector self-ligation or selection failure.
Day 3: Confirm the assembly
Check the plates, grow cultures, and do minipreps 6 hours
1. Compare the plates to estimate the ratio of “ligation” colonies to “negative control” colonies.
2. If the ratio is 10:1 or greater, great job! Pick 2 colonies for separate liquid cultures (see Day 1, Grow liquid cultures). If the ratio is less than 10:1, pick more colonies or trouble shoot and repeat the ligation & transformation.
3. Miniprep the DNA from the liquid cultures (see Day 1, Extract the plasmid DNA: Qiagen Miniprep Kit)
4. Digest 2 uL of each DNA sample with EcoRI/ PstI and check via gel electrophoresis (1% agarose) to confirm the assembled construct size. You should see one fragment that is the backbone, and another fragment that equals the total size of the two BioBrick parts you assembled.
Timeline
• Level 1, Newbie: Undergraduates and unseasoned scientists can expect to spend a week on one assembly step. You will inevitably spill something, forget a step, plan an assembly incorrectly, or mess up some other inventive way.
• Level 2, Graduate Student: Typically have experience pipetting and handling samples well and can expect to spend 3 days per assembly. If you have no life and are super-ambitious, you can crank out an assembly cycle in two days (when Day 3 is done within the same day as Day 2), and complete three assemblies in one week.
• Level 3, Postdoc "Cloning Ninja": If you have no life, are super-impatient, and are trying to publish papers, you can crank out an assembly cycle in two days (when Day 3 is done within the same day as Day 2), and complete three assemblies in one week.
Personal tools
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{
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"warc_url": "http://quotationsbook.com/book/sawman/"
}
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sawman's bookmarks
"The humblest individual exerts some influence, either for good or evil, upon others."
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I'm male and made my book on 16th July 2012.
My book as a pdf
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{
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"warc_url": "http://quotationsbook.com/quote/18298/"
}
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The greatest joy of life is to love and be loved. Clyde, R.D.
This quote is about happiness · Search on Google Books to find all references and sources for this quotation.
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{
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Falsehood is invariably the child of fear in one form or another. Crowley, Aleister
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The wise man regulates his conduct by the theories both of religion and science. But he regards these theories not as statements of ultimate fact but as art-forms. Haldane, John B. S.
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{
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If we desire to avoid insult, we must be able to repel it; if we desire to secure peace, one of the most powerful instruments of our rising prosperity, it must be known, that we are at all times ready for War. Washington, George
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{
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Begin where you are; work where you are; the hour which you are now wasting, dreaming of some far off success may be crowded with grand possibilities. Marden, Orison Swett
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{
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"warc_url": "http://quotationsbook.com/quote/gift/11555/"
}
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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.
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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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{
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When one paints an ideal, one does not need to limit one's imagination. Key, Ellen
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{
"content_type": "text/html",
"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:65404",
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"warc_date": "2013-11-22T14:39:41.000Z",
"warc_filename": "<urn:uuid:51a14dce-53f8-465e-80fe-28f40d1a411c>",
"warc_url": "http://quotationsbook.com/quote/gift/37250/"
}
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Walking uplifts the spirit. Breathe out the poisons of tension, stress, and worry; breathe in the power of God. Send forth little silent prayers of goodwill toward those you meet. Walk with a sense of being a part of a vast universe. Consider the thousands of miles of earth beneath your feet; think of the limitless expanse of space above your head. Walk in awe, wonder, and humility. Walk at all times of day. In the early morning when the world is just waking up. Late at night under the stars. Along a busy city street at noontime. Peterson, Wilferd A.
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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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Treat your customers like lifetime partners. Leboeuf, Michael
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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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Celtkicks: Red’s Army Annual Party
KWAPT March 12, 2013 CeltKicks Comments Off
Scott and I saw some fantastic kicks walk through the door at last Sunday’s Red’s Army party. From classics like the Air Jordan “Bred” XI, to rare treats like Lauren’s Paul Pierce Nike Air Legacy, folks brought-out the heat! Check out this photo gallery that includes the best kicks from Sunday’s bash:
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Cutest Story of 2011: Parents Get Insulin-Pump Tattoos To Support Diabetic Child
I was just making preparations for the top 2011 posts I’m planning to write in the upcoming days when I bumped into this cute story about a diabetic kid who felt ashamed to wear the insulin pump so his parents got insulin pump tattoos.
Some parents get tattoos of their child’s name, but Philippe Aumond and Camille Boivin went one better.
In a show of solidarity, they each have an image of an insulin pump tattooed on their abdomens, declaring that they are “forever linked” to their son Jacob.
“It is a great thing for him, and we were thrilled just to see his smile when he saw those pumps. It made our day, that’s for sure,” said Boivin, 36, from the family’s home in La Sarre, Que.
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Research article
Association between adherence to calcium-channel blocker and statin medications and likelihood of cardiovascular events among US managed care enrollees
Richard H Chapman1*, Jason Yeaw1 and Craig S Roberts2
Author Affiliations
1 US Health Economics & Outcomes Research, IMS Health, Falls Church, VA, USA
2 Global Outcomes Research, Pfizer Inc, New York, NY, USA
For all author emails, please log on.
BMC Cardiovascular Disorders 2010, 10:29 doi:10.1186/1471-2261-10-29
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2261/10/29
Received:20 November 2009
Accepted:17 June 2010
Published:17 June 2010
© 2010 Chapman 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
Prior studies have found that patients taking single-pill amlodipine/atorvastatin (SPAA) have greater likelihood of adherence at 6 months than those taking 2-pill calcium-channel blocker and statin combinations (CCB/statin). This study examines whether this adherence benefit results in fewer cardiovascular (CV) events.
Methods
A retrospective cohort study was conducted using administrative claims data from the IMS LifeLink: US Health Plan Claims database, identifying adults already taking CCB or statin (but not both) who had an index event of either initiating treatment with SPAA or adding CCB to statin (or vice versa) between April 1, 2004 to August 31, 2005. Inclusion criteria included age 18+ years, continuously enrolled for minimum of 6 months prior and 18 months following treatment initiation, >1 diagnosis of hypertension, and no prescription claims for SPAA or added CCB or statin for 6 months prior. Exclusion criteria included >1 claim with missing or invalid days supplied, age 65+ years and not enrolled in Medicare Advantage, or history of prior CV events, cancer diagnosis, or chronic renal failure. The primary outcome measure was the rate of CV events (myocardial infarction, heart failure, angina, other ischemic heart disease, stroke, peripheral vascular disease, or revascularization procedure) from 6 to 18 months following index date, analyzed at three levels: 1) all adherent vs. non-adherent patients, 2) SPAA vs. dual-pill patients (regardless of adherence level), and 3) adherent SPAA, adherent dual-pill, and non-adherent SPAA patients vs. non-adherent dual-pill patients.
Results
Of 1,537 SPAA patients, 56.5% were adherent at 6 months, compared with 21.4% of the 17,910 CCB/statin patients (p < 0.001). Logistic regression found SPAA patients more likely to be adherent (OR = 4.7, p < 0.001) than CCB/statin patients. In Cox proportional hazards models, being adherent to either regimen was associated with significantly lower risk of CV event (HR = 0.77, p = 0.003). A similar effect was seen for SPAA vs. CCB/statin patients (HR = 0.68, p = 0.02). In a combined model, the risk of CV events was significantly lower for adherent CCB/statin patients (HR = 0.79, p = 0.01) and adherent SPAA patients (HR = 0.61, p = 0.03) compared to non-adherent CCB/statin patients.
Conclusions
Patients receiving SPAA rather than a 2-pill CCB/statin regimen are more likely to be adherent. In turn, adherence to CCB and statin medications is associated with lower risk of CV events in primary prevention patients.
Background
CVD is the number one cause of death globally and will remain so, taking an estimated 20 million lives annually by 2015 [1]. Two of the most prevalent and modifiable risk factors for CVD -- hypertension and dyslipidemia -- commonly coexist. The risk of CVD is greater in people with both of these risk factors than it is in those with either condition alone [2,3]. Effective treatment of these two CVD risk factors is widely available and has been proven to reduce CV events. The benefits of antihypertensive medications and 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors (statins) for reducing CHD and stroke risk in patients at a high risk of CHD have been demonstrated in several well-known clinical trials [4,5]. Also, meta-analyses have shown the consistent effects from antihypertensive [6] and statin [7-9] medications in reducing CV events. Despite these effective treatments for hypertension and dyslipidemia, and the associated reduction in CV events, control of these conditions often remains suboptimal, partly due to poor patient adherence [10].
Recent analyses report that fixed dose combination (FDC) therapy for hypertension and dyslipidemia is associated with a greater likelihood of adherence than the historic approach of prescribing medication for each risk factor separately [10,11]. For example, patients taking single-pill amlodipine/atorvastatin (SPAA) have a greater likelihood of adherence at 6 months than those taking 2-pill calcium-channel blocker and statin combinations (CCB/statin) [10]. Other studies show that when two-pill CCB/statin regimens are initiated close together in time, adherence is greater than when therapy is initiated sequentially, [12-14] and that, in general, adherence is better with single-pill regimens vs. 2-pill regimens [15,16]. The reasons for better adherence with FDC therapy for hypertension and dyslipidemia may include reduced pill burden [17] and reduced patient-borne medication costs [18,19].
Efforts to improve patient adherence to CVD medication therapy are important, as retrospective analyses have shown that adherence to statins and to antihypertensive medications have been associated with reduced rates of CV events [20-23]. In a recent review of the literature, poor compliance with lipid-lowering treatment has been shown to be associated with poorer clinical outcomes and increased cardiovascular morbidity and mortality [20]. Bouchard et al. [21], using a nested case-control design, found that adherence to statins that exceeded 90% was associated with a significant reduction in nonfatal CAD events after one year of treatment. Another nested case-control analysis, by Perreault et al. [22], found that high adherence levels to antihypertensive therapy were associated with relative risk reduction in CAD events compared to low levels of adherence. Mazzaglia et al. [23] reported a similar finding among newly diagnosed hypertensive patients in a retrospective cohort analysis. To build upon the growing body of evidence supporting the impact of adherence on reduction in CV events, this study examines whether the adherence benefit previously demonstrated with SPAA results in fewer CV events than for patients on 2-pill regimens.
Methods
We conducted a retrospective cohort study using administrative claims that include medical and pharmacy data from the IMS LifeLink: US Health Plan Claims database for October 1, 2003 through August 31, 2006. The database is comprised of fully adjudicated medical & pharmaceutical claims for over 65 million unique patients from over 90 health plans across the US (with approximately 16 million covered lives per year). It includes both inpatient and outpatient diagnoses and procedures as well as prescription records, and is generally representative of the national, commercially-insured population in terms of age, gender, and type of health plan. The data is longitudinal, with average member enrollment duration of nearly two years. Only health plans that submit data for all members are included in the database, ensuring complete data capture & representative samples. The data are subjected to a series of quality checks to ensure standardized format & minimal error rates.
Study population
We identified adults taking CCB or statin (but not both) who then initiated treatment with SPAA or added CCB to statin (or vice versa) from April 1, 2004 to August 31, 2005. Inclusion criteria included age ≥18 years, at least one prescription for SPAA or CCB + statin (with first prescription for SPAA or the added CCB or statin in the study period considered the index date), continuously enrolled for minimum of 6 months prior to and 18 months following index date, >1 diagnosis of hypertension prior to or on the index date, and no claims for the index prescription(s) for 6 months prior to index date. Exclusion criteria included at least one prescription claim with missing or invalid days supplied, age 65 years or greater and not enrolled in Medicare Advantage, or history of prior CV events, cancer diagnosis, or chronic renal failure. Patients were considered secondary prevention patients if they had evidence during the pre-index period of any of the specified CV-related events or procedures, and were excluded from analysis. Otherwise, patients' treatment was considered to be for primary prevention.
This study included 3 time periods, as illustrated in Figure 1:
Figure 1. Illustration of the study time periods
1. Pre-index: 6-month period in which patients were taking either statin or CCB
2. Adherence measurement period: 6-month period following initiation of SPAA or dual therapy (index) where adherence is assessed
3. Follow-up period: ≥12 months in which CV events are tabulated
Adherence
The proportion of days covered (PDC) for each of the two drug cohorts was calculated for the 6-month adherence measurement period. Adherence was capped at 100%, and calculated as the total days supplied of index drug divided by the number of days in the follow-up period (a denominator of 180 days). Claims extending beyond day 179 were pro-rated to include only the portion of days' supply captured within the observation period. Additionally, if a patient refilled a prescription early, any days with overlapping prescriptions were counted only once. Advantages of using PDC as an adherence measure are that it simultaneously reflects both compliance and persistence, [24,25] and is a commonly used measure in adherence studies [12,26-30], allowing useful comparisons of adherence levels across studies.
For this analysis, patients were considered "adherent" if PDC by SPAA or CCB and statin was ≥80%, and non-adherent if PDC <80% for the 6-month period. Unadjusted adherence rates of patients in the two treatment groups are reported for the 6-month follow-up period. Multivariable logistic regression models with adherence status (</≥80% PDC) as the dependent variable were also run.
Study Outcomes
The primary outcome of interest was the rate of CV events, as well as its relationship to 6-month adherence levels. CV events were defined as hospitalization for myocardial infarction (MI), heart failure, angina, other ischemic heart disease, stroke, peripheral vascular disease, or CV revascularization procedure. CV event definition included events with either a primary discharge diagnosis of interest or a procedure of interest using only inpatient claims; outpatient claims were not considered. To allow sufficient time for events of interest to occur, this analysis was restricted to patients with at least 18 months of continuous enrollment following their medication-based index date.
Rates of CV events were analyzed at three levels:
1) all adherent patients vs. all non-adherent patients;
2) SPAA patients vs. dual-pill patients (regardless of adherence level);
3) adherent SPAA patients, adherent dual-pill patients, and non-adherent SPAA patients vs. non-adherent dual-pill patients.
All CV events were reviewed starting at 180 days post-index (to allow a 6-month period for the establishment of adherence) and ending with patient disenrollment or the end of the study period. Any CV events that may have occurred in the first 180 days post-index were ignored for the purpose of this analysis. CV events were defined as the presence of claims with an ICD-9 code for a relevant diagnosis or a CPT-4 code for a procedure of interest, which were: myocardial infarction (MI, ICD-9 410.xx, 412), other ischemic heart disease including unstable angina (411.xx, 414.xx, 427.xx, V45.81, V45.82), stroke/TIA (433.xx, 434.xx, 435.x, 436, 437.0, 437.1, 438), peripheral vascular disease (440, 440.1, 443.xx), angina with hospitalization (413.xx), coronary artery bypass graft (CABG, CPT-4 code 33503 - 33545), carotid endarterectomy (35301, 35390, 35901), coronary stenting (92980, 92981), percutaneous transluminal coronary angioplasty (PTCA)/thrombectomy/atherectomy (92973, 92982, 92984, 92995, 92996), or percutaneous transluminal pulmonary artery balloon angioplasty (92997, 92998). Only the first CV event in the observation period per patient was included in the analysis. The total number of events overall and in each of the treatment groups are reported. Additionally, the rate of CV events was calculated as the total number of events divided by the total amount of patient-time contributed to the analysis for each treatment group. Patient-time was allowed to vary, with a minimum value of 360 days per patient. The crude rates of events (total events divided by total person-days) are reported overall and for each cohort.
In addition to the crude rates described above, the adjusted CV event rates for all patients and by treatment group were determined using Cox proportional hazards models, with covariates to account for potentially confounding factors. The dependent variable was days to CV event. Independent variables included all relevant demographic and clinical characteristics.
Statistical analyses
Time to CV event was plotted using the Kaplan-Meier estimator. To adjust for differences in patient characteristics for each treatment group, the time to CV event was also modeled using a Cox proportional hazards model, with days from index date to CV event as the dependent variable. Independent variables included therapy type (SPAA vs. combination), adherence status, gender, age group, geographic region, health plan type, insurance type, related pre-index comorbidities, and number of pre-index antihypertensive classes being taken.
Results
Patient characteristics
As shown in Figure 2, after applying our inclusion and exclusion criteria, 19,447 patients were available for analysis; Table 1 details the demographic and clinical characteristics of these patients. The mean (SD) age was 53.5 (7.6) years for SPAA patients and 54.8 (8.5) years for the CCB+statin patients (p < 0.001). SPAA patients were more likely to be male than CCB+statin patients (58.6% vs. 52.1%, respectively; p < 0.001). SPAA patients were less likely to have diabetes but more likely to have a dyslipidemia diagnosis than were CCB+statin patients, and on average were taking fewer other medications pre-index (Table 1).
Table 1. Demographic and clinical characteristics of SPAA and CCB+statin primary prevention patients
Figure 2. Study cohort identification procedure, with reasons for inclusion/exclusion through the selection process
Adherence
Of the 1537 SPAA patients, 56.5% were adherent (PDC ≥80%) at 6 months, compared with 21.4% of the 17,910 CCB+statin patients (Table 2). Although adherence continued to decline over time in both groups, the percentage of patients adherent remained significantly higher in the SPAA group than in the CCB+statin group at 18 months (42.3% vs. 18.7%, respectively; p < 0.001). After adjusting for patients' clinical and demographic characteristics (as listed above), SPAA patients were significantly more likely to be adherent (OR = 4.7, p < 0.001, Table 3) than CCB/statin patients, as were patients with dyslipidemia (OR = 1.2).
Table 2. Adherence measures for SPAA and CCB+statin primary prevention patients
Table 3. Logistic regression model of medication adherence (PDC ≥80%) at 6 months following initiation of SPAA or CCB+statin
CV event rates
The crude (unadjusted) CV event rate for each patient stratification is shown in Table 4. Non-adherent patients and CCB/statin patients experienced higher CV event rates than adherent and SPAA patients, respectively (Table 4). A similar pattern was observed when time to CV event was examined in Kaplan-Meier analyses (Figure 3).
Table 4. CV events from 6 months following initiation of SPAA or CCB+statin in primary prevention patients
Figure 3. Kaplan-Meier analysis of days to CV event in SPAA and CCB/statin primary prevention patients with no history of cancer or chronic renal failure
In multivariable Cox proportional hazards models adjusting for the independent variables listed above in Methods, being adherent to either regimen (pooled) was associated with significantly lower risk of CV event (HR = 0.77, p = 0.003). In a separate model that did not adjust for adherence status, CV events were lower for SPAA than for CCB+statin patients (HR = 0.68, p = 0.02). A combined model compared 4 cohorts based on the combination of treatment and adherence status. Using non-adherent CCB + statin patients as the reference group, the risk of CV events was significantly lower among adherent CCB + statin patients (HR = 0.79, p = 0.01) and adherent SPAA patients (HR = 0.61, p = 0.03); the risk was similar for non-adherent SPAA patients (HR = 0.69, p = 0.14)..
Discussion
As with prior analyses, CCB or statin patients who start on SPAA are more likely to be adherent to antihypertensive and statin therapy in the first six months than are patients who add a CCB to statin or a statin to CCB as 2 separate pills [10,11]. As an extension of increased adherence due to single pill advantages, this study found that greater adherence to hypertension and dyslipidemia therapy appears to have translated into a lower risk of CV events over time compared to non-adherent patients.
Slightly over 56% of the 1537 SPAA patients had at least 80% PDC adherence in the six months following initiation of therapy, compared with 21% of the 17,910 patients prescribed both a CCB and a statin. These adherence rates are consistent with other studies of single and dual-pill treatment of naïve patients with antihypertensive or statin therapy. In a study by Jackson et al., [31] the effect of additional pills was evaluated as to its impact on patient adherence to medication, specifically measured via the medication possession ratio (MPR). Findings from this study suggest that an inverse relationship exists between additional medication tablets (pills) and patient MPR, as measured among patients receiving antihypertensive therapy in a managed care setting. MPR values were reduced from 75.4% among patients with a 2-tablet amlodipine regimen to 60.5% among patients with a 3-tablet amlodipine regimen. In another study with similar adherence findings to this study, Gerbino et al. [32] also showed a positive relationship between utilization of the fixed dose regimen and patient adherence, with MPR-based adherence measured at nearly 20% less among patients with ACE inhibitors plus CCB versus patients with a fixed dose amlodipine-benazepril.
This study demonstrates that patients' risk of cardiovascular events was significantly decreased among adherent patients compared with non-adherent patients. Unadjusted results found that the 12-month cardiovascular event incidence rate was only 1.88 per 100 person-years for adherent patients compared with 2.47 per 100 person-years in non-adherent patients. Adherence to either of the regimens included in the study was associated with a significantly lower risk of CV event (HR = 0.77, p = 0.003) after adjusting for potentially confounding baseline characteristics in multivariable Cox proportional hazards models.
This association between adherence and cardiovascular risks is in agreement with previous studies, including the 2007 study by Munger et al. [33] In this review, medication nonadherence was found to be responsible for several adverse health and economic outcomes, including an increased risk of death among patients with a prior myocardial infarction, an estimated annual cost of $396 to $792 million, and 33% to 66% of medication-related hospital admissions. Sever et al. [34,35] found that three years of atorvastatin therapy produced a 79% reduction in coronary heart disease related events, from 22.8 events per 1,000 patient years to 4.8 events per 1,000 patient years. That study also found benefits of amlodipine and atorvastatin in reducing nonfatal MI by 46% [hazard ratio 0.54, confidence interval (CI) 0.40-0.72, P < 0.0001], stroke by 37% [hazard ratio 0.63, CI 0.46-0.87, P = 0.004] and total cardiovascular events and procedures by 27% [hazard ratio 0.73, CI 0.63-0.86, P < 0.0001].
This study has several limitations worth noting. Since PDC calculations are based on the assumption that patients take all medications for which they have prescriptions filled, these measures may overestimate adherence. Additionally, these adherence calculations fail to account for the possibility that patients received medications from sources other than the pharmacies included in the database used in this study.
Because of the way adherence was calculated in this analysis (patients had to remain on both CCB and statin to be considered adherent), our adherence rates may appear low relative to what has been reported in the literature. However, given that the patients in this analysis were prescribed both drugs, we believe patients should be considered nonadherent for the purposes of this study if they discontinue either CCB or statin.
Adherence was measured in a time period separate and distinct from the period during which CV events were identified and recorded. Due to this fact, it is possible that CV events occurred in the 6-month adherence measurement period and were not accounted for in our analysis, or that patient adherence measured prior to CV event monitoring is not representative of refill behavior had adherence and events been measured concurrently. To the extent that patients' adherence to their index medications differed between the 6-month period immediately following initiation of therapy and the minimum 12-month subsequent period, the estimates for adherence may vary from the time-specific values.
Cardiovascular events were identified by healthcare claims containing specific ICD-9 diagnosis codes. Due to the potential for unreported, misreported or miscoded cardiovascular events, the estimates for CV event incidence may overestimate or underestimate the actual number of clinical events. Since this limitation is similar for both cohorts, we do not expect it to bias the analysis for or against a cohort.
Two final limitations exist relative to analysis using a retrospective cohort design and adjudicated healthcare claims. Findings in this study are representative only of the U.S. commercially insured population of patients, not the overall population of treated patients who may have other forms of healthcare coverage (Medicaid, Medicare, etc.) not captured through this study methodology. Additionally, factors associated with both patient adherence and the incidence of cardiovascular events are limited within this study to those elements available through health plan enrollment files and insurance claims. Unmeasured and unknown confounding factors related to both baseline characteristics and clinical outcomes may exist, and their effect on these results cannot be accurately quantified.
Conclusions
Patients receiving SPAA rather than a two-pill CCB + statin regimen are more likely to be adherent. In turn, adherence to CCB and statin medications was associated with lower risk of CV events in primary prevention patients.
Competing interests
This study was sponsored by Pfizer Inc, New York, NY. Dr. R.H. Chapman and Mr. Jason Yeaw of IMS Health were paid consultants to Pfizer Inc in connection with the development of the manuscript. Dr. C.S. Roberts is an employee of Pfizer Inc. Editorial support provided by Katharine Coyle at IMS Health was funded by Pfizer Inc.
Authors' contributions
RHC participated in the study design and analysis, and helped to draft the manuscript. JY participated in the design of the study, performed the statistical analysis, and helped to draft the manuscript. CSR conceived of the study, participated in its design, and helped to draft the manuscript. All authors read and approved the final manuscript.
Acknowledgements
Editorial support was provided by Katharine Coyle of IMS Health.
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8. Amarenco P, Labreuche J, Lavallée P, Touboul PJ: Statins in stroke prevention and carotid atherosclerosis: systematic review and up-to-date meta-analysis.
Stroke 2004, 35:2902-2909. PubMed Abstract | Publisher Full Text
9. Baigent C, Keech A, Kearney PM, Blackwell L, Buck G, Pollicino C, Kirby A, Sourjina T, Peto R, Collins R, Simes R, Cholesterol Treatment Trialists' (CTT) Collaborators: Efficacy and safety of cholesterol-lowering treatment: prospective meta-analysis of data from 90,056 participants in 14 randomised trials of statins.
Lancet 2005, 366:1267-1278.
(Erratum in: Lancet 2005;366(9494):1358; Lancet 2008;371(9630):2084)
PubMed Abstract | Publisher Full Text
10. Patel BV, Leslie RS, Thiebaud P, Nichol MB, Tang ST, Solomon H, Honda D, Foody JM: Adherence with single-pill amlodipine/atorvastatin vs a two-pill regimen.
Vasc Health Risk Manag 2008, 4:673-681. PubMed Abstract | PubMed Central Full Text
11. Chapman RH, Pelletier EM, Smith PJ, Roberts CS: Can adherence to antihypertensive therapy be used to promote adherence to statin therapy?
Patient Preference Adherence 2009, 3:265-275. Publisher Full Text
12. Chapman RH, Benner JS, Petrilla AA, Tierce JC, Collins SR, Battleman DS, Schwartz JS: Predictors of adherence with antihypertensive and lipid-lowering therapy.
Arch Intern Med 2005, 165:1147-1152. PubMed Abstract | Publisher Full Text
13. Chapman RH, Petrilla AA, Benner JS, Schwartz JS, Tang SS: Predictors of adherence to concomitant antihypertensive and lipid-lowering medications in older adults: a retrospective, cohort study.
Drugs Aging 2008, 25:885-892. PubMed Abstract | Publisher Full Text
14. Wolf-Maier K, Cooper RS, Kramer H, Banegas JR, Giampaoli S, Joffres MR, Poulter N, Primatesta P, Stegmayr B, Thamm M: Hypertension treatment and control in five European countries, Canada, and the United States.
Hypertension 2004, 43:10-17. PubMed Abstract | Publisher Full Text
15. Dezii CM: A retrospective study of persistence with single-pill combination therapy vs. concurrent two-pill therapy in patients with hypertension.
Manag Care 2000, 9(9 Suppl):2-6. PubMed Abstract
16. Julius S, Cohn JN, Neutel J, Weber M, Turlapaty P, Shen Y, Dong V, Batchelor A, Lagast H: Antihypertensive utility of perindopril in a large, general practice-based clinical trial.
J Clin Hypertens 2004, 6:10-17. Publisher Full Text
17. Benner JS, Pollack MF, Smith TW, Bullano MF, Willey VJ, Williams SA: Association between short-term effectiveness of statins and long-term adherence to lipid-lowering therapy.
Am J Health Syst Pharm 2005, 62:1468-1475. PubMed Abstract | Publisher Full Text
18. Goldman DP, Joyce GF, Zheng Y: Prescription drug cost sharing: associations with medication and medical utilization and spending and health.
JAMA 2007, 298:61-69. PubMed Abstract | Publisher Full Text
19. Taira N: Nifedipine: a novel vasodilator.
Drugs 2006, 66:1-3.
Erratum in: Drugs 2007;67(13):1849
PubMed Abstract | Publisher Full Text
20. Liberopoulos EN, Florentin M, Mikhailidis DP, Elisaf MS: Compliance with lipid-lowering therapy and its impact on cardiovascular morbidity and mortality.
Expert Opin Drug Saf 2008, 7:717-725. PubMed Abstract | Publisher Full Text
21. Bouchard MH, Dragomir A, Blais L, Bérard A, Pilon D, Perreault S: Impact of adherence to statins on coronary artery disease in primary prevention.
J Clin Pharmacol 2007, 63:698-708.
22. Perreault S, Dragomir A, Roy L, White M, Blais L, Lalonde L, Bérard A: Adherence level of antihypertensive agents in coronary artery disease.
Br J Clin Pharmacol 2010, 69:74-84. PubMed Abstract | Publisher Full Text
23. Mazzaglia G, Ambrosioni E, Alacqua M, Filippi A, Sessa E, Immordino V, Borghi C, Brignoli O, Caputi AP, Cricelli C, Mantovani LG: Adherence to antihypertensive medications and cardiovascular morbidity among newly diagnosed hypertensive patients.
Circulation 2009, 120:1598-605. PubMed Abstract | Publisher Full Text
24. Peterson AM, Nau DP, Cramer JA, Benner J, Gwadry-Sridhar F, Nichol M: A checklist for medication compliance and persistence studies using retrospective databases.
Value Health 2007, 10:3-12. PubMed Abstract | Publisher Full Text
25. Cramer JA, Roy A, Burrell A, Fairchild CJ, Fuldeore MJ, Ollendorf DA, Wong PK: Medication compliance and persistence: terminology and definitions.
Value Health 2008, 11:44-47. PubMed Abstract | Publisher Full Text
26. Ho PM, Rumsfeld JS, Masoudi FA, McClure DL, Plomondon ME, Steiner JF, Magid DJ: Effect of medication nonadherence on hospitalization and mortality among patients with diabetes mellitus.
Arch Intern Med 2006, 166:1836-1841. PubMed Abstract | Publisher Full Text
27. Ho PM, Magid DJ, Shetterly SM, Olson KL, Maddox TM, Peterson PN, Masoudi FA, Rumsfeld JS: Medication nonadherence is associated with a broad range of adverse outcomes in patients with coronary artery disease.
Am Heart J 2008, 155:772-779. PubMed Abstract | Publisher Full Text
28. Benner JS, Chapman RH, Petrilla AA, Tang SS, Rosenberg N, Schwartz JS: Association between prescription burden and medication adherence in patients initiating antihypertensive and lipid-lowering therapy.
Am J Health Syst Pharm 2009, 66:1471-1477. PubMed Abstract | Publisher Full Text
29. Donnelly LA, Doney AS, Morris AD, Palmer CN, Donnan PT: Long-term adherence to statin treatment in diabetes.
Diabet Med 2008, 25:850-855. PubMed Abstract | Publisher Full Text
30. LaFleur J, Thompson CJ, Joish VN, Charland SL, Oderda GM, Brixner DI: Adherence and persistence with single-dosage form extended-release niacin/lovastatin compared with statins alone or in combination with extended-release niacin.
Ann Pharmacother 2006, 40:1274-1279. PubMed Abstract | Publisher Full Text
31. Jackson KC, Sheng X, Nelson RE, Keskinaslan A, Brixner DI: Adherence with multiple-combination antihypertensive pharmacotherapies in a US managed care database.
Clin Ther 2008, 30:1558-1563. PubMed Abstract | Publisher Full Text
32. Gerbino PP, Shoheiber O: Adherence patterns among patients treated with fixed-dose combination versus separate antihypertensive agents.
Am J Health Syst Pharm 2007, 64:1279-1283. PubMed Abstract | Publisher Full Text
33. Munger MA, Van Tassell BW, LaFleur J: Medication nonadherence: an unrecognized cardiovascular risk factor.
MedGenMed 2007, 9:58. PubMed Abstract | PubMed Central Full Text
34. Sever PS, Poulter NR, Mastorantonakis S, Chang C, Dahlof B, Wedel H: Coronary heart disease benefits from blood pressure and lipid-lowering.
Int J Cardiol 2009, 135:218-222. PubMed Abstract | Publisher Full Text
35. Sever PS, Poulter NR, Dahlof B, Wedel H, ASCOT Investigators: Antihypertensive therapy and the benefits of atorvastatin in the Anglo-Scandinavian Cardiac Outcomes Trial: lipid-lowering arm extension.
J Hypertens 2009, 27:947-54. PubMed Abstract | Publisher Full Text
Pre-publication history
The pre-publication history for this paper can be accessed here:
http://www.biomedcentral.com/1471-2261/10/29/prepub
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Tuesday, November 01, 2005
Good news about texting
Texting teenagers are proving 'more literate than ever before'
Despite this [use of texting abbreviations], the two-year study found that today’s teenagers are using far more complex sentence structures, a wider vocabulary and a more accurate use of capital letters, punctuation and spelling.
What do you know, the quality of writing increases when kids have access to technology. This doesn't surprise me, as one of the best way to become a better writer is through practice. And when kids are hammering out gobs of text messages, that's what they are doing.
What's next, games raising kid's IQs? Oh wait, that's that's been done.
The bottom line: technology isn't good or bad (for kids or anyone), it's how we use it. So use it wisely.
LinkWithin
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Research
Asymptotic analysis for reaction-diffusion equations with absorption
Wanjuan Du* and Zhongping Li
Author affiliations
College of Mathematic and Information, China West Normal University, Nanchong, 637009, P.R. China
For all author emails, please log on.
Citation and License
Boundary Value Problems 2012, 2012:84 doi:10.1186/1687-2770-2012-84
Published: 2 August 2012
Abstract
In this paper, we study the blow-up and nonextinction phenomenon of reaction-diffusion equations with absorption under the null Dirichlet boundary condition. We at first discuss the existence and nonexistence of global solutions to the problem, and then give the blow-up rate estimates for the nonglobal solutions. In addition, the nonextinction of solutions is also concerned.
MSC: 35B33, 35K55, 35K60.
Keywords:
reaction-diffusion; absorption; blow-up; blow-up rate; non-extinction
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Aghaloo, DerryEdit This Page
From FamilySearch Wiki
Ireland County Derry Aghaloo Civil Parish
The following information is a starting point for records about the civil parish of Aghaloo. The information is based on locations and records before 1922.
Contents
Historical Overview
History
Add a brief statement about historical background, including a Web site link if available.
Localities
List the names of townlands in this civil parish List the names of the surrounding parishes List the names and give a description of a district, poor law union, etc.
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Records
Cemeteries
Add references to indexes to gravestones or monumental inscriptions.
Census
The purpose of a census was to gather information about people who lived in an area. While the government began census taking in 1821, only fragments exist before 1901. Censuses for 1901 and 1911 are available. Read more about the records in the Ireland Census article.
Add information here about census substitutes that you know about.
Church records
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Methodist
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Others
Name(s) of ecclesiastical parish, records, availability, archive, online indexes, notes.
Civil Registration
Government registration of births and deaths began in 1864. Registration of Protestant marriages began in 1845, with all marriages being registered by 1864. Go to the Ireland Civil Registration article to read more about these records.
Land records
The Registry of Deeds started in 1708. Land transactions were recorded, including immovable property passed on in a will and property given to a daughter at her marriage. Read more about these records in the Ireland Land and Property article.
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Read more about these records in the Ireland Schools article. Add records for this parish.
Tax records
The valuation of property for tax purposes was started in the 1840s by Richard Griffith. A tax paid to the church, call Tithe Applotments, began in the 1820s. Read about these records in the Ireland Taxation and Ireland Land and Property articles. Add records for this parish that you know about.
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• This page was last modified on 22 June 2010, at 20:58.
• This page has been accessed 207 times.
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User:National Institute sandbox AIEdit This Page
From FamilySearch Wiki
The original content for this article was contributed by The National Institute for Genealogical Studies in June 2012. It is an excerpt from their course Canadian: Religious Records by Brenda Dougall Merriman, CG, CGL. The Institute offers over 200 comprehensive genealogy courses for a fee ($).
Contents
Marriages and Burials
Marriage Records
The best kept of the three BMD records are the marriage records. This is because of their special double status, as both church records and as civil contracts. A couple were not only married in the sight of God and the congregation there present, but also in the eyes of the law had formed a union which would have effects on the inheritance of land and money. It was therefore important that the clergy keep accurate accounts of the marriages they performed.
In Québec, where church records and civil records were the same, the legal nature of the marriage record was bolstered by marriage contracts drawn up and supervised by notaries. The theological basis of marriage as viewed by the Roman Catholic Church, to which most of Québec society belonged, insured that the church records remained equally important despite the existence of the notarial records also. This can also be said of Acadian records, although the survival of early Acadian records has been more problematic. [1]
In the rest of Canada, the view of church marriage records was affected by the traditions and laws of England. There, marriages had to be performed by a priest according to the rites of the state church, with some few exceptions. The marriage in church had the same force as any other legal contract. When it became apparent that there was considerable traffic in clandestine marriages in the 18th century, Parliament had enacted a new way of recording marriages which made illegal records more difficult to procure.
As the various provinces which would later form Canada were organized, the governments imported ideas then prevalent in England about marriage along with other legal concepts. Since the right to perform marriages in the mother country was restricted to Church of England priests with a few exceptions, this idea naturally had a place in Canada also.
The Québec Act of 1774 had guaranteed French Canadians the right to praxes Roman Catholicism, and so marriages could be performed by Catholic priests without any legal difficulties. In fact, Roman Catholics in Québec had more rights than Roman Catholics in Britain at this time.
When the government of Ontario was established in the 1790s, the first idea was to establish a narrow range of who might marry, consisting of Church of England and Roman Catholic priests, but almost immediately exceptions were made, with Lutherans and then others being added to the list. The reason for this, here as elsewhere, was simply that there were not enough priests to cover the vast area of the new colonies. It was not reasonable for people to be expected either to wait for a priest to come by so they could be married, or to travel a long distance to find a priest at a time when travel was difficult and expensive.
The rule in Ontario was that if there was not an Anglican priest within a certain distance, someone else could be licensed to perform marriages. These were often Methodist clergy.
By the time the Methodists had begun their evangelical drives in the 1830s, there were many Methodist clergy in the countryside, and people could turn to them for marriage even if their own religion was something else. It was important that there should be a liberal minded clergyman in any area for couples to approach if they had difficulty being married by their own minister, for any reason. These reasons might be theological differences, difficulties over consent or approval of parents, ‘mixed’ marriages (where the bride and bridegroom were of different denominations) or some social situation.
In Waterloo County, Ontario, for example, the Lutheran pastor F. W. Bindemann came from a Reformed background and was quite unusually ecumenically minded for his time. From his arrival in the 1830s for thirty years he traveled widely in the area and was known to perform marriages for anyone who came to him. In fact, there is a story that his front parlour was once so crowded with couples that he saved time by saying, “You want each other? You’ve got each other. Two dollars, please.” This is undoubtedly apocryphal and unlikely, but illustrates his liberality. His (incomplete) marriage records contain names of every ethnic and religious background in the county. Clergy like him could probably be found everywhere in the country.
Aside from this, couples who were uncertain of their reception by their own clergy (as some would be in Presbyterian circles under various circumstances, for instance), everyone knew that they could turn to the Church of England priest and he would marry them. The English tradition that a couple who came to be married to a parish priest had to be married (after the calling of banns, and in public) carried over to Canada. The status of the Church of England as a state (or government) church, as it was in Newfoundland, for instance, and in Ontario until the 1820s, should be remembered.
The message from all this is that researchers should remain open-minded about where they might find marriage records for their relatives. People might wait for a clergyman to come round to baptize their children, and would be unlikely to travel distances to seek someone to christen them. They could easily bury a family member without benefit of clergy, and often had to do so. Marriage, however, was more portable. People might not wish to wait, or might be obliged not to wait, and so would seek out a clergyman wherever they could.
Far-flung Marriages
If you have looked for a wedding in local churches in your area, but have not found the one you want, you must begin to look farther afield. Consider the possibility of a circuit rider or missionary.
If your relatives lived on an obvious transportation route, especially water, then the solution is to examine the places where people could go most easily. Those along the coasts of the Atlantic provinces, for instance, could easily board a boat and go to a large nearby town to be married. Those along the St. Lawrence and through the Great Lakes system to the Lake of the Woods might do the same, or cross the border into the United States.
In fact, the traffic between Ontario and New York state for marital purposes was considerable. This often had nothing to do with lack of clergy in one place or the other, or even convenience, but was simply a wish to combine a small trip with the wedding itself, creating what we might call a honeymoon. In 1857 the Ogdensburgh (N.Y.) Republican had an editorial which told that the cost of marrying in Canada had gone up, resulting in a flood of couples crossing Lake Ontario to be married in cheaper New York.[2]
And that brings us to an important but little-known phenomenon which we might call the ‘railway marriage.’
Railway Marriages
From the time that the railway was established up to World War II, the railway marriage was a means for couples to be married easily, have a small trip or adventure into the bargain, and avoid the complications and expense of a wedding at home.
It was a simple matter. They would slip away (sometimes unannounced, sometimes with the knowledge of their friends) on the train, journey a short distance, seek out a church in the destination town, and be married. They might stay overnight, but perhaps not, and then return. Depending on the family’s circumstances, they might have a house party or other small celebration once they were back. In the country, there was always the possibility their neighbours would hold a charivari (‘chivaree’) anyway.[3]
These railway marriages happened all over North America, so anyone with a lost marriage from 1850 to 1945 would be advised to consider the possibility. To find the likely town of marriage, obtain a railway map (many old atlases include railway lines) from the period, and follow the line to a logical place. The town is probably not far away, certainly not more than a day’s journey. Hub towns, or towns at the end of a railway line are good candidates. Once you choose a town, see which churches were near the railway station. They are good possibilities.
However, almost any church is likely. Clergy at this time were very used to people coming to the parsonage seeking to be married, and if they had the necessary license (if required), it was a matter of a few minutes’ work only. Clergy in denominations which required the marriage to be in church (such as the Roman Catholics) might require more notice, but Methodists and Presbyterians in particular could be quite welcoming. In these cases you may find that the witnesses bear the same name as the clergyman, as his wife and grown children would act in this capacity.[4]
One hint about these marriages might appear in a newspaper notice. If a couple were married secretly, or at least without previous announcement, then it became news for the community to share. If they lived in the country or a small town, the local newspaper might contain a reference which you can use. Here is an example from the Orono News (Ontario) of 26 January 1911:
Mr. Randolph Woodward and Miss Maggie Lunn made a trip to Peterborough the other week, and after a quiet ceremony returned home man and wife. They are now residing in Oshawa.
In fact, the Woodwards were married in the manse of the church nearest the train station, very handy for everyone, themselves and researchers alike.
One bride of 1934 made it clear that the reason for her ‘railway marriage’ was money. She and her groom took a male cousin and sister (as witnesses), journeyed forty miles on the train, were married, saw a movie and stayed overnight with another cousin before returning home. “We had two dollars when we left and two dollars when we got home,” she said.
References
1. A summary of this issue can be found in Terrence Punch, Genealogist’s handbook for Atlantic Canada research (2d edition, 1997), p. 143.
2. Quoted in the introduction to The missing marriages of Hastings County (Victoria District), 1850-1861 (1999).
3. A charivari (pronounced ‘chivaree’) was a wedding celebration staged without notice, with a crowd descending at night (after bedtime) on the house of the newlywed couple. They would make a great deal of noise. The new husband was obliged to invite them in and give them drink, after which there would probably be a party.fckLRAlthough early charivaris were often directed at weddings with something unusual about them (such as an older bridegroom and young bride, or a bride of advanced years being married for the first time), they became more usual as a means of acknowledging the new status of the couple. They had a raucous reputation but many were no more than regular house parties. They continued in some rural areas past the mid-20th century.
4. Later in the 19th century, some Presbyterian clergy were less relaxed about whom they might marry than before 1850, when the various schisms and theological controversies in Scotland had made everyone prickly.
____________________________________________________________
Information in this Wiki page is excerpted from the online course Canadian: Religious Records offered by The National Institute for Genealogical Studies. To learn more about this course or other courses available from the Institute, see our website. We can be contacted at wiki@genealogicalstudies.com
We welcome updates and additions to this Wiki page.
• This page was last modified on 15 March 2013, at 02:13.
• This page has been accessed 84 times.
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Nmap
From Forensics Wiki
Jump to: navigation, search
nmap
Maintainer: Gordon Lyon
OS: Linux,Windows, OS X
Genre: Network forensics
License: GPL
Website: nmap.org
Nmap (Network Mapper) is a network security scanner.
Features
General features:
• Host discovery
• Port scanning (enumerating open/closed/filtered ports on one or more target hosts)
• Service detection (determining service types and version numbers)
• OS detection
Other features:
• IP protocol scan
• Uptime detection (using TCP timestamps)
• Traceroute
• DNS resolution
• Idle scan (using "zombies")
• FTP bounce scan (using proxy FTP connections)
• etc
Typical uses
• Identifying open ports on a compromised host
• Auditing the security of a network, by identifying unexpected computers
External Links
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Calculator application without GUI
GCK
Newbie Member
30Jun2012,10:04 #1
I am trying to write code for a calculator in a way it appears in GUI.What i mean here is ,i want to display a zero and then replace it with a value (typed) there after perform operations.I am using Visual Studio 2010 ,i want my output to appear as explained above in the Output window of visual studio.
Is there any KEYWORD in C++ (may be advanced C++) to replace a value or variable??
Lastly, is my question right??
Can this be done on the console window of visual studio ??
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Bibliography: Paint Box
You are not logged in. If you create a free account and sign in, you will be able to customize what is displayed.
Title: Paint Box
Author: Lisanne Norman
Year: 2001
Type: SHORTFICTION
Storylen: novelette
ISFDB Record Number: 489401
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Copyright (c) 1995-2011 Al von Ruff.
ISFDB Engine - Version 4.00 (04/24/06)
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v0
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2024-06-03T21:29:50.578Z
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2013-05-18T09:10:04.000Z
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sctcbc6qhtac2d6egvcnwdyal3mrpepj
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{
"content_type": "text/html",
"provenance": "cccc-CC-MAIN-2013-20-0000.json.gz:65519",
"uncompressed_offset": 571650189,
"url": "www.libreoffice.org/download/?lang=tt&type=rpm-x86_64&version=4.0.2",
"warc_date": "2013-11-22T14:39:41.000Z",
"warc_filename": "<urn:uuid:51a14dce-53f8-465e-80fe-28f40d1a411c>",
"warc_url": "http://www.libreoffice.org/download/?type=rpm-x86_64&lang=tt&version=4.0.2"
}
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cccc_CC-MAIN-2013-20
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The free office suite
Download LibreOffice
LibreOffice Linux - rpm (x86_64), version 4.0.2, Tatar. Not the version you wanted? Change System, Version or Language
You need to download and install these files in order:
• Source code
LibreOffice is an open source project and you can therefore download the source code to build your own installer.
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v0
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