The deplorable British policing practice of storing the DNA of suspects who've been exonerated or never even charged has been found to be illegal by a European court, and now the database must be destroyed. Remember the kid who was going home on the tube in 2005 and was mistaken for a subway bomber, taken into custody, apartment raided, all data on his computers copied, and his DNA stored forever -- even though the police admitted it was all a misunderstanding? Well at last his DNA should be removed from the database. The court said there was a particular risk that innocent people would be stigmatised because they were being treated in the same way as convicted criminals. The judges added that the fact DNA profiles could be used to identify family relationships between individuals, meant its indefinite retention also amounted to an interference with their right to respect for their private lives under the human rights convention. The case provoked an expression of disappointment from the home secretary, Jacqui Smith, and the promise that a working party, including senior police officials, will report back to Strasbourg by next March on how the government will comply with the judgement. "The government mounted a robust defence before the court and I strongly believe DNA and fingerprints play an invaluable role in fighting crime and bringing people to justice. The existing law will remain in place while we carefully consider the judgement." Christ that Jacqui Smith is a piece of work. Remember, come the next election: a vote for Labour is a vote for the party that thinks 1984 is a manual for statecraft. 17 judges, one ruling - and 857,000 records must be now wiped clear (Thanks, beep1o!)...br style="clear: both;"/ a href="http://www.pheedo.com/click.phdo?s=ffeba8702913fa3c2c7fa86eef8567c0p=1"img alt="" style="border: 0;" border="0" src="http://www.pheedo.com/img.phdo?s=ffeba8702913fa3c2c7fa86eef8567c0p=1"//a img src="http://www.pheedo.com/feeds/tracker.php?i=ffeba8702913fa3c2c7fa86eef8567c0" style="display: none;" border="0" height="1" width="1" alt=""/

Publication Date: 2008 Dec 2 PMID: 19050035br/Authors: Wabnik, K. - Hvidsten, T. R. - Kedzierska, A. - Van Leene, J. - De Jaeger, G. - Beemster, G. T. - Komorowski, J. - Kuiper, M. T.br/Journal: Bioinformaticsbr/br/MOTIVATION: Genome-scale 'omics' data constitutes a potentially rich source of information about biological systems and their function. There is a plethora of tools and methods available to mine omics data. However, the diversity and complexity of different omics data types is a stumbling block for multi-data integration, hence there is a dire need for additional methods to exploit potential synergy from integrated orthogonal data. Rough Sets provide an efficient means to use complex information in classification approaches. Here, we set out to explore the possibilities of Rough Sets to incorporate diverse information sources in a functional classification of unknown genes. RESULTS: We explored the use of Rough Sets for a novel data integration strategy where gene expression data, protein features, and GO annotations were combined to describe general and biologically relevant patterns represented by If-Then rules. The descriptive rules were used to predict the function of unknown genes in Arabidopsis thaliana and Schizosaccharomyces pombe. The If-Then rule models showed success rates of up to 0.89 (discriminative and predictive power for both modeled organisms) whereas models built solely of one data type (protein features or gene expression data) yielded success rates varying from 0.68 to 0.78. Our models were applied to generate classifications for many unknown genes, of which a sizeable number were confirmed either by PubMed literature reports or electronically interfered annotations. Finally, we studied cell cycle protein-protein interactions derived from both tandem affinity purification (TAP) experiments and in silico experiments in the BioGRID interactome database and found strong experimental evidence for the predictions generated by our models. The results show that our approach can be used to build very robust models that create synergy from integrating gene expression data and protein fea-tures. AVAILABILITY: The Rough Set-based method is implemented in the Rosetta toolkit kernel version 1.0.1 available at: http://rosetta.lcb.uu.se/ CONTACT: kuiper@nt.ntnu.no; krwab@psb.ugent.be SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19050035title=Entrez+PubmedCiteULike/a

divimg alt="" src="http://hits.guardian.co.uk/b/ss/guardiangu-feeds/1/H.15.1/8513?ns=guardianpageName=Politics%3A+17+judges%2C+one+ruling+-+and+857%2C000+records+must+be+now+wiped+clearch=Politicsc3=The+Guardianc4=DNA+database+%28Politics%29%2CCivil+liberties%2CPrivacy%2CCriminal+justice+%28politics%29%2CCrime+-+UK+%28News%29%2CUK+news%2CPolitics%2CPolice+%28politics%29c5=Unclassified%2CPolicy+Society%2CNot+commercially+usefulc6=Alan+Travisc7=2008_12_05c8=1129220c9=articlec10=GUc11=Politicsc12=DNA+databasec13=c14=h2=GU%2FPolitics%2FDNA+database" width="1" height="1" //divpThe fingerprints and DNA samples of more than 857,000 innocent citizens who have been arrested or charged but never convicted of a criminal offence now face deletion from the national DNA database after a landmark ruling by the European court of human rights in Strasbourg./ppIn one of their most strongly worded judgments in recent years, the unanimous ruling from the 17 judges, including a British judge, Nicolas Bratza, condemned the "blanket and indiscriminate" nature of the powers given to the police in England, Wales and Northern Ireland to retain the DNA samples and fingerprints of suspects who have been released or cleared./ppThe judges were highly critical of the fact that the DNA samples could be retained without time limit and regardless of the seriousness of the offence, or the age of the suspect./ppThe court said there was a particular risk that innocent people would be stigmatised because they were being treated in the same way as convicted criminals. The judges added that the fact DNA profiles could be used to identify family relationships between individuals, meant its indefinite retention also amounted to an interference with their right to respect for their private lives under the human rights convention./ppThe case provoked an expression of disappointment from the home secretary, Jacqui Smith, and the promise that a working party, including senior police officials, will report back to Strasbourg by next March on how the government will comply with the judgement./pp"The government mounted a robust defence before the court and I strongly believe DNA and fingerprints play an invaluable role in fighting crime and bringing people to justice. The existing law will remain in place while we carefully consider the judgement."/ppIt is thought that the policy in Scotland, where DNA samples can only be held for a maximum of five years and only in serious violent and sexual cases, even if the suspect was not convicted, will be the first option to be looked at./ppThe Strasbourg court ruling came in a case brought by two Sheffield men who asked for their DNA records to be destroyed. The first man, Michael Marper, aged 45, was arrested in 2001 and charged with harassing his partner, but the case was dropped three months later after the couple were reconciled. He had no previous convictions. /ppIn the second case, a 19-year-old named only in court as S was arrested and charged with attempted robbery in January 2001 when he was 12, but was cleared five months later. /ppBoth asked the South Yorkshire police to remove and destroy their DNA samples and profiles and fingerprints. But police said they needed to retain them "to aid criminal investigation"./ppTheir lawyer, Peter Mahy, said last night: "This is a fantastic result after a seven-year hard fought battle against the UK government . We are obviously delighted that the European court of human rights found in our clients' favour. It will be very interesting to see how the government respond - they should start immediately to destroy the DNA records of innocent people on the DNA database. "/ppThe ruling will have a major impact in shaping the future development of the DNA database in Britain and its use across Europe. Set up in 1995, the British DNA database which now holds the samples of 4.3 million individuals in Britain, including children, is already proportionately the largest in the world. /ppThe Home Office acknowledged yesterday that its plans to extend the retention of DNA to low level, so-called non-recordable offences, including littering and minor traffic offences were now dead in the water. /ppTony Bunyan of Statewatch, the European civil liberties monitoring group, also said it put a question mark over EU plans to share fingerprint and DNA data across the 27 member states./ppThe Association of Chief Police Officers said the ruling would have profound impact on their use of DNA technology. They pointed out that over a four-year period from May 2001, 200,000 DNA samples taken from unconvicted suspects, had led to 8,500 individuals being linked with 14,000 offences including 114 murders and 116 rapes./ppBut Shami Chakrabarti, director of Liberty, said: "This is one of the most strongly worded judgements that Liberty has ever seen from the court of human rights. The court has used human rights principles and common sense to deliver the privacy protection of innocent people that the British government has shamefully failed to deliver."/ppThe Equality and Human Rights Commission said it welcomed the judgement and would work with the Home Office and the police to ensure the implications of the ruling were implemented./pdiv style="float: left; margin-right: 10px; margin-bottom: 10px;"ullia href="http://www.guardian.co.uk/politics/dna-database"DNA database/a/lilia href="http://www.guardian.co.uk/news/civilliberties"Civil liberties/a/lilia href="http://www.guardian.co.uk/uk/privacy"Privacy/a/lilia href="http://www.guardian.co.uk/politics/justice"Criminal justice/a/lilia href="http://www.guardian.co.uk/uk/ukcrime"Crime/a/lilia href="http://www.guardian.co.uk/politics/police"Police/a/li/ul/diva href="http://www.guardian.co.uk"guardian.co.uk/a copy; Guardian News Media Limited 2008 | Use of this content is subject to our a href="http://users.guardian.co.uk/help/article/0,,933909,00.html"Terms Conditions/a | a href="http://www.guardian.co.uk/webfeeds/1,,1309488,00.html"More Feeds/a pa href="http://feedads.googleadservices.com/~at/4UKhRguM-yB7MKwhwsSdrYovHoU/a"img src="http://feedads.googleadservices.com/~at/4UKhRguM-yB7MKwhwsSdrYovHoU/i" border="0" ismap="true"/img/a/p

divimg alt="" src="http://hits.guardian.co.uk/b/ss/guardiangu-feeds/1/H.15.1/78946?ns=guardianpageName=Music%3A+Under+the+radar%2C+over+the+topch=Musicc3=The+Guardianc4=Electronic+music%2CAlexis+Petridis+on+pop%2CCulture+section%2CClubbing+%28Music%29%2CMusicc5=Pop+Music%2CNot+commercially+useful%2CElectronic+and+Dancec6=Alexis+Petridisc7=2008_12_05c8=1128673c9=articlec10=GUc11=Musicc12=Electronic+musicc13=c14=h2=GU%2FMusic%2FElectronic+music" width="1" height="1" //divpChristine looks about 15. She is wearing a pair of vertiginously heeled ankle boots that make her both tall and a little wobbly and which form the basis of a pretty remarkable ensemble. She is also wearing fluorescent tights, a clashing fluorescent tutu, a T-shirt that she appears to have accessorised by snapping a glowstick in two and splashing its luminous contents over herself, a pair of lens-less glasses that also glow in the dark, and an expression of profound suspicion. The suspicion is aimed in my direction. "You," she says, narrowing her eyes, "don't look like a raver. What are you doing here?"/ppThis is a question I started asking myself the moment I walked into Aberdeen's AECC Exhibition Centre, where the second Clubland Live arena tour of 2008 is in full swing. Ignored or derided as the apotheosis of cheesy, worthless pop by the mainstream media, Clubland is nevertheless Britain's "biggest-selling dance brand" - Clubland and its parent label, All Around the World, have spawned 21 No 1 albums, millions of record sales, sellout tours, and their own TV channel - and the place is accordingly thronged with kids: primary school children accompanied by parents wearing weary expressions, gangs of adolescent girls striding around arm in arm, boys playfighting and getting each other in headlocks, and older teenagers whose unsteady gait suggests Grampian police's rigorous attempts to stop underage drinking before the event have met with only partial success. /ppRegardless of age, everyone is going berserk. The uproar is continuous. Everyone screams at everything all the time - the performers onstage who do their 20 minutes and scuttle off; the DJs who fill in between them playing thumping hardcore remixes of Katy Perry's I Kissed a Girl, the Sugababes' About You Now and, most startling of all, Cascada's unlikely cover version of Patti Smith's Because the Night. At one point, an announcement about the venue's regulations regarding flash photography comes over the PA, and goes down like the Beatles at Shea Stadium. When the fans really like something, they express their approval by pelting the stage and each other with glowsticks. The really big acts appear to be performing under a kind of neon hailstorm./ppIf Clubland's audience isn't discombobulating enough to an outsider, there are Clubland's stars to contend with. If you're over 21, it seems highly unlikely that any of their names will ring much of a bell, unless you've been paying very close attention to the album charts or glued to Clubland TV: Kelly Llorenna, September, Eyeopener, Cascada, N-Force, Darren Styles. You won't have heard them on Radio 1 - the station will have little to do with them. Clubland's architects, Matt Cadman and Cris Nuttall of All Around the World, claim that at one juncture they were told by a station representative that they weren't interested because All Around the World released "music for kids who live on council estates". "That was one of our favourites," Cadman says. "In fairness, the people at Radio 1 have changed since then, so you can't really pin that one on them, but I think that statement still has an underlying truth to it. It's perceived Clubland doesn't reach the kind of people Radio 1 wants to attract." Clubland TV, meanwhile, was set up in response to the lack of interest other music channels showed in playing that kind of music./ppTellingly, Cadman says All Around the World began in the early 90s, releasing big northern rave anthems like Love Decade's Is This a Dream? and Control's Dance With Me (I'm Your Ecstasy) - "records that no one else understood, that were popular in the north-west, but no one knew about in London and that remains true to this day"./ppCertainly there's still a noticeable regional bias to Clubland's appeal (this tour goes no further south than Birmingham, although the cancellation of a date in Plymouth apparently had more to do with logistics than a lack of demand). And since the release of the first Clubland compilation album in 2002, Cadman and Nuttall do seem to have constructed a genuine youth phenomenon out of the most unlikely ingredients: a selection of thunderingly uncool sub-genres of dance music that seem to have a peculiar appeal to teenagers too young to go clubbing - bouncy scouse house, happy hardcore, pop trance - and a stable of artists that you suspect wouldn't get past reception at any other record company. /ppThere is Ultrabeat, two Liverpudlian DJs called Chris and Mike. Chris and Mike are funny, friendly and charming and have a string of hits to their name, notably the 2003 smash Pretty Green Eyes, but, with the best will in the world, more closely resemble plumbers than pop stars, a fact rather underlined by their videos. These usually feature Chris and Mike looking a bit lost while women in suspenders lasciviously gyrate around them. "We've had things before where channels have gone, 'Oh, we don't want to play the Ultrabeat video, I don't like the guy in it.' But I'm slightly bored with the celebrity thing where everybody's got to look a certain way," Cadman says. "We're going, 'This is the guy who made this record,' and I think people relate to that, rather than some good-looking faccedil;ade." As if to prove his point, no sooner do I sit down with Matt and Chris than a lady asks for their autographs for her teenage daughter. "Nice to be nice, innit?" says Chris when she departs. "We're all normal people, everyone's the same, aren't they?"/ppThen there is Blackout Crew, Bolton's faintly terrifying tracksuit- and hair-gel- heavy progenitors of a genre called donk, whose last video, Put a Donk On It, has thus far racked up more than 3m hits on YouTube. There is Darren Styles, a former happy hardcore producer who finds himself, at 34, a slightly baffled teeny pin-up, purveying music that, on the basis of his Clubland live set, often sounds not unlike a Coldplay piano ballad sung in an Essex accent and inexplicably retooled with thumping 160bpm beats. "It's a bit daunting for me, to be honest," he says. "I enjoy it, but you spend 12 years standing behind the decks then you're put out in front of a huge crowd in a spotlight with a microphone, and it's completely out of my comfort zone." /ppAnd, most successful of all, there is Scooter, a novelty German rave act who emerged in the early 90s and managed to spin out their expected 15 minutes of fame into 14 years. Imagine if the people who made Sesame's Treet had gone on to release 13 albums and sell more than 14m records worldwide, and you get some idea of the sheer improbability of Scooter's career, although to really grasp how bizarre it is, you need to be conversant with their oeuvre, which is nuts. Scooter have variously released rave versions of Soft Cell's Sex Dwarf, Marian by the Sisters of Mercy, Hava Nagila, and the theme tune to Miss Marple. /ppThey've also recorded a medley of Shut Up and Dance's 1991 hardcore hit Raving I'm Raving with a bagpipe rendition of Scotland the Brave, and not one but two songs inspired by the work of forgotten mid-80s John Peel favourites Stump. Their current big thing is jumpstyle, a sort of synchronised hopping dance popular in the Netherlands, which Scooter have promoted with singles called Jumping All Over the World and Jump That Rock, a collaboration with Status Quo. If you feel like sniggering at this as precisely the kind of thing that causes British music fans to feel vastly superior to their clueless continental counterparts, it's worth noting that, with minimal radio play or media coverage - though there was a video clip shown on Zane Lowe's MTV show Gonzo, which the excitable Kiwi claimed was evidence that "music is finally dead" - Scooter's last album entered the British charts at No 1, knocking Madonna off the top spot. /ppBackstage in Aberdeen, their dressing room features plenty of rock star trappings, including a cooler full of vodka, a watchful manager there to ensure I don't overrun my allotted 15 minutes of face time, an immense PA system that apparently forms part of their pre-gig ritual - "for one hour, very loud music, a few drinks to get you in the mood" - and a certain bullishness about the derision their music attracts. They have, they tell me, recently been the subject of a series of paintings by a German artist called Albert Oehlen, who on his website claims to be "fascinated" by Scooter, "because they have no content, only form". Nevertheless, questions about Scooter's longevity are met with a shrug from frontman HP Baxxter, resplendent in skull rings and Black Sabbath T-shirt. "We never stop," he offers. "Nearly every year there is a new album. Maybe that's the reason why we've lasted so long." /ppThen again, bafflement at your own success is very much a Clubland trademark. Despite the success of the albums and the TV channel, Cadman and Nuttall managed to convince themselves the first Clubland tour would be a disaster: it sold out. Darren Styles says he thought his debut solo album would sell around 20,000 copies. It sold 22,000 in a week and entered the charts at No 4. "Coldplay were No 1, then Duffy, then Neil Diamond, then me. It was absolutely bizarre."/ppPerhaps their surprise stems from the fact that everything about Clubland seems somehow wrong: it's as if it exists in a hermetically sealed bubble, apart from the rest of the music industry, where all the usual rules are turned on their heads. The artists are clearly huge stars despite the media blackout. (Styles actually thinks they might be successful because of the media blackout: "Maybe the fact that it's not so in your face, it's not all over TV and radio accounts for it's appeal - it seems a bit underground, it's not something that your mum and dad are listening to.") The TV channel is a huge success, despite disobeying the most basic principles of a music channel. "If the video's a bit average, music channels in general go, we love the track, but video's a bit cheap, so we're not going to show it," says Nuttall. "We would have a completely different view from that because if the track's brilliant and the video's a bit average, not big budget, who cares? Kids don't sit there watching TV going, 'Oh, they must have only spent a hundred grand on the video, I'm not watching it.' They like the tune, pure and simple."/ppAnd the All Around the World label sells vast quantities of CDs to precisely the audience that everyone assumes never buys CDs. "If you're a 15-year-old and you can work a computer, you can go and get a track you want in 30 seconds, it's really not that difficult," Cadman says. "So singles have become less valuable because people just steal them or Bluetooth them to each other in the playground. The value then becomes in the album. If the album genuinely is good, if there's not one tune and nine fillers, if there's three or four singles on it, the pound;8.99 in Asda or Tesco starts to seem like a bargain. For pound;8.99, I'm not going to download it all, I might as well pay for it. You've just got to encourage the value for money, and then records will sell physically. Clubland compilations have 60 tracks on them, take us months to compile, and sell for 10 quid. People trust us, because me and Chris genuinely love the music. It's not cool or perceived to be cool, but it's what we love. We'll sail with it and no doubt we'll go down with it when it stops selling."/ppBut there's no sign of that happening for the foreseeable future. The crowd in Aberdeen don't look like they'll be changing their allegiances any time soon. As Scooter take the stage, the hail of glowsticks grows denser than ever: HP Baxxter never flinches or falters, despite the surprising number of them that hit him squarely in the face. They play their medley of Raving I'm Raving and Scotland the Brave, but no one other than me seems bemused. They play Jumping All Over the World, and a crowd of boys at the back of the hall break into a delighted synchronised jumpstyle routine. Christine wobbles past again on her high heels: "You still here?" I ask her if she's having a good time. "Are you kidding?" she grins. I start to ask her what she likes about Clubland, but but she doesn't hear - the screaming again -and she wobbles away into the crowd./ppa href="http://www.clubland.fm/"Clubland.fm/a/pdiv style="float: left; margin-right: 10px; margin-bottom: 10px;"ullia href="http://www.guardian.co.uk/music/electronicmusic"Electronic music/a/lilia href="http://www.guardian.co.uk/music/alexispetridis"Alexis Petridis on pop/a/lilia href="http://www.guardian.co.uk/music/clubs"Clubbing/a/li/ul/diva href="http://www.guardian.co.uk"guardian.co.uk/a copy; Guardian News Media Limited 2008 | Use of this content is subject to our a href="http://users.guardian.co.uk/help/article/0,,933909,00.html"Terms Conditions/a | a href="http://www.guardian.co.uk/webfeeds/1,,1309488,00.html"More Feeds/a pa href="http://feedads.googleadservices.com/~at/M0rCGLsKbCYwSjNC2am_vyeOyZI/a"img src="http://feedads.googleadservices.com/~at/M0rCGLsKbCYwSjNC2am_vyeOyZI/i" border="0" ismap="true"/img/a/p

Opera 10.0a1Opera is an alternative internet web browser that is very fast, small, easy to use, and complies with all of the web browser standards.
WHAT'S NEW

Version 10.0a1: Opera 10.0 includes the Presto 2.2 rendering engine. Detailed changes since Presto 2.1.1 are listed below:

Rendering

• Significant performance improvements
• Added Web font support, allowing the download of fonts specified in font descriptors in @font-face at-rules; TrueType (TTF), OpenType (OTF), and SVG fonts are supported (demos)
• Achieved 100/100 and pixel-perfect rendering on the Acid3 test
• Pretty-printing of unstyled XML (using unstyledxml.css in the Styles sub-directory of Opera's installation directory)
• Added support for CSS3 RGBA color values (demo)
• Added support for CSS3 HSLA color values (demo)
• Added support for the CSS3 color: transparent value
• Added support for the viewport meta tag key
• Improved HTML5 support, including end-tag and start-tag parsing, whitespace parsing, and DOCTYPE parsing
• CSS files must be served with the correct MIME type ("text/css") in Strict mode or they will be ignored

JavaScript/DOM

• New regular expression engine, which greatly improves performance on regular-expression-heavy pages such as the SunSpider JavaScript Benchmark
• Added support for the W3C Selectors API
• Renamed the objects returned by getClientRects() and getBoundingClientRect() to ClientRectList and ClientRect instead of TextRectangle and TextRectangleList, respectively
• XMLHttpRequests will now trigger start-loading/end-loading events
• Removed the proprietary window.setDocument method
• Added support for the SVGElement.currentFps and SVGElement.targetFps properties to read and control, respectively, SVG frames per second
• The load event for scripts is now sent after the script is executed rather than before
• The load event is now sent to frame/iframe/object elements before it is sent to the document
• A highlight will no longer be added when HTMLElement.focus() is called unless keyboard navigation is already activated

Other

• Removed UTF-32 encoding support
• User JS files will now be executed in alphabetical order rather than file system order
• HTML5 canvas elements can now export images to the JPEG format
• HTML5 canvas transforms are applied when building a path, not when painting it (this change is made to work like Mozilla)
• The first ID (instead of the last) is now used on pages with duplicate IDs when navigating to fragment IDs
• Added support for the altGlyph element in SVGs
• Added support for 32-bit alpha in BMP and RLE-encoded BMP images
• Implemented HTML5's algorithms for detecting charsets in HTML
• The http://www.w3.org/TR/REC-html40 namespace is no longer treated as an alias to http://www.w3.org/1999/xhtml

User Interface

• Auto-Update
• Inline Spelling Checker

Mail/News

• Rich Text Message Composition
• Bold styling, italic styling, and underline styling can be toggled using ⌘B, ⌘I, and ⌘U, respectively.
• Rich text message signatures are not yet supported.
• Delete After X Days (POP-only)

Other changes...

REQUIREMENTSMac OS X 10.3.9 or later.
DEVELOPEROpera Software
DOWNLOADS190842
DOWNLOAD NOW (13.4 MB)
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NEW YORK (AP) -- Sean Avery surged past camera crews and reporters Thursday, choosing to save his comments this time for NHL commissioner Gary Bettman during a three-hour disciplinary hearing. The Dallas Stars forward was suspended indefinitely on Tuesday just hours after he used a crude expression to describe former girlfriends now dating others while speaking to reporters....

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div class="image"a href="http://pixhost.ws/avaxhome/big_show.php?/avaxhome/6a/fc/0009fc6a.jpeg" target="_blank"img src="http://pixhost.ws/avaxhome/6a/fc/0009fc6a_medium.jpeg" id="external_img_654442"//a/divbr/ div class="center"bWord Myths: Debunking Linguistic Urban Legends By David Wilton/bbr/ Publisher: Oxford University Press, USA 2004-12 | 240 Pages | ISBN: 0195172841 | PDF | 1 MB/divbr/ Do you "know" that posh comes from an acronym meaning "port out, starboard home"? That "the whole nine yards" comes from (pick one) the length of a WWII gunner's belt; the amount of fabric needed to make a kilt; a sarcastic football expression? That Chicago is called "The Windy City" because of the bloviating habits of its politicians, and not the breeze off the lake?..

Big Canvas Applications Make iPhone an Artistic Tool for Creative Expression (PRWeb Dec 4, 2008)

Read the full story at http://www.prweb.com/releases/2008/12/prweb1704584.htm

Publication Date: 2008 Dec 1 PMID: 19046434br/Authors: Blangiardo, M. - Richardson, S.br/Journal: BMC Bioinformaticsbr/br/ABSTRACT: BACKGROUND: In gene expression studies a key role is played by the so called ;;pre-processing'', a series of steps designed to extract the signal and account for the sources of variability due to the technology used rather than to biological differences between the RNA samples. At the moment there is no commonly agreed gold standard pre-processing method and each researcher has the responsibility to choose one method, incurring the risk of false positive and false negative features arising from the particular method chosen. RESULTS: We propose a Bayesian calibration model that makes use of the information provided by several pre-processing methods and we show that this model gives a better assessment of the ;true' unknown differential expression between two conditions. We demonstrate how to estimate the posterior distribution of the differential expression values of interest from the combined information. CONCLUSIONS: On simulated data and on the spike-in Latin Square dataset from Affymetrix the Bayesian calibration model proves to have more power than each pre-processing method. Its biological interest is demonstrated through an experimental example on publicly available data.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046434title=Entrez+PubmedCiteULike/a

Motivation: Bacterial small ribonucleic acids (sRNAs) that are not ribosomal and transfer or messenger RNAs were initially identified in the sixties, whereas their molecular functions are still under active investigation today. It is now widely accepted that most play central roles in gene expression regulation in response to environmental changes. Interestingly, some are also implicated in bacterial virulence. Functional studies revealed that a large subset of these sRNAs act by an antisense mechanism thanks to pairing interactions with dedicated mRNA targets, usually around their translation start sites, to modulate gene expression at the posttranscriptional level. Some sRNAs modulate protein activity or mimic the structure of other macromolecules. In the last few years, in silico methods have been developed to detect more bacterial sRNAs. Among these, computational analyses of the bacterial genomes by comparative genomics have predicted the existence of a plethora of sRNAs, some that were confirmed to be expressed in vivo. The prediction accuracy of these computational tools is highly variable and can be perfectible. Here we review the computational studies that have contributed to detecting the sRNA gene and mRNA targets in bacteria and the methods for their experimental testing. In addition, the remaining challenges are discussed.

Contact: bfelden@univ-rennes1.fr

Motivation: Tissue microarrays (TMAs) quantify tissue-specific protein expression of cancer biomarkers via high-density immuno-histochemical staining assays. Standard analysis approach estimates a sample mean expression in the tumor, ignoring the complex tissue-specific staining patterns observed on tissue arrays.

Methods: In this article, a cell mixture model (CMM) is proposed to reconstruct tumor expression patterns in TMA experiments. The concept is to assemble the whole-tumor expression pattern by aggregating over the subpopulation of tissue specimens sampled by needle biopsies. The expression pattern in each individual tissue element is assumed to be a zero-augmented Gamma distribution to assimilate the non-staining areas and the staining areas. A hierarchical Bayes model is imposed to borrow strength across tissue specimens and across tumors. A joint model is presented to link the CMM expression model with a survival model for censored failure time observations. The implementation involves imputation steps within each Markov chain Monte Carlo iteration and Monte Carlo integration technique.

Results: The model-based approach provides estimates for various tumor expression characteristics including the percentage of staining, mean intensity of staining and a composite meanstaining to associate with patient survival outcome.

Availability: R package to fit CMM model is available at http://www.mskcc.org/mskcc/html/85130.cfm

Contact: shenr@mskcc.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Motivation: Microarray designs have become increasingly probe-rich, enabling targeting of specific features, such as individual exons or single nucleotide polymorphisms. These arrays have the potential to achieve quantitative high-throughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts.

Results: To study cross-hybridization, we map Affymetrix exon array probes to a set of annotated mRNA transcripts, allowing a small number of mismatches or insertion/deletions between the two sequences. Based on a systematic study of the degree to which probes with a given match type to a transcript are affected by cross-hybridization, we developed a strategy to correct for cross-hybridization biases of gene-level expression estimates. Comparison with Solexa ultra high-throughput sequencing data demonstrates that correction for cross-hybridization leads to a significant improve-ment of gene expression estimates.

Availability: We provide mappings between human and mouse exon array probes and off-target transcripts and provide software extending the GeneBASE program for generating gene-level expression estimates including the cross-hybridization correction http://biogibbs.stanford.edu/~kkapur/GeneBase/.

Contact: whwong@stanford.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Motivation: Modern transcriptomics and proteomics enable us to survey the expression of RNAs and proteins at large scales. While these data are usually generated and analyzed separately, there is an increasing interest in comparing and co-analyzing transcriptome and proteome expression data. A major open question is whether transcriptome and proteome expression is linked and how it is coordinated.

Results: Here we have developed a probabilistic clustering model that permits analysis of the links between transcriptomic and proteomic profiles in a sensible and flexible manner. Our coupled mixture model defines a prior probability distribution over the component to which a protein profile should be assigned conditioned on which component the associated mRNA profile belongs to. We apply this approach to a large dataset of quantitative transcriptomic and proteomic expression data obtained from a human breast epithelial cell line (HMEC). The results reveal a complex relationship between transcriptome and proteome with most mRNA clusters linked to at least two protein clusters, and vice versa. A more detailed analysis incorporating information on gene function from the Gene Ontology database shows that a high correlation of mRNA and protein expression is limited to the components of some molecular machines, such as the ribosome, cell adhesion complexes and the TCP-1 chaperonin involved in protein folding.

Availability: Matlab code is available from the authors on request.

Contact: srogers@dcs.gla.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Summary: Rice (Oryza sativa L.) is an important model monocot and cereal crop. While the rice genome sequence has been published and annotated, relatively little is known about the transcriptional networks that regulate rice gene expression. For this reason, we have developed Osiris, a database containing promoter sequences, predicted transcription factor (TF) binding sites, gene ontology annotation and microarray expression data for 24 209 genes in the rice genome. These tools are seamlessly integrated in the Osiris web site, allowing the user to visualize TF binding sites in multiple promoters; analyze the statistical significance of enriched TF binding sites; query for genes containing similar promoter regulatory logic or gene function and visualize the microarray expression patterns of queried or selected gene sets.

Availability: http://www.bioinformatics2.wsu.edu/Osiris

Contact: jwyrick@wsu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Summary: CARPET (collection of automated routine programs for easy tiling) is a set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip and expression tiling data, both for standard and custom chip designs. CARPET allows rapid experimental data entry, simple quality control, normalization, easy identification and annotation of enriched ChIP-chip regions, detection of the absolute or relative transcriptional status of genes assessed by expression tiling experiments and, more importantly, it allows the integration of ChIP-chip and expression data. Results can be visualized instantly in a genomic context within the UCSC genome browser as graph-based custom tracks through Galaxy2. All generated and uploaded data can be stored within sessions and are easily shared with other users.

Availability: http://bio.ifom-ieo-campus.it/galaxy

Contacts: matteo.cesaroni@ifom-ieo-campus.it; lucilla.luzi@ifom-ieo-campus.it

Expression cloning and radiotracer uptakes in Xenopus laevis oocytes

Nature Protocols 3, 1975 (2008). doi:10.1038/nprot.2008.151

Author: Daniel Markovich

This protocol describes the method of expression cloning of heterologous proteins using Xenopus laevis oocytes and the functional characterization of membrane proteins using radiotracer assays. It can be used to isolate proteins for which sequence data is unavailable and to characterize the functions of