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 <title>Guest blog by Richard Smith: More evidence on why we need radical reform of science publishing</title>
 <link>http://feeds.feedburner.com/~r/plos/PublishingBlog/~3/413929286/409</link>
 <description>&lt;p&gt;&lt;em&gt;PLoS Medicine&lt;/em&gt; invited Richard Smith, former editor of the BMJ and&lt;br /&gt;
&lt;a href="http://www.plos.org/about/board.html" rel="nofollow"&gt; current board member of PLoS&lt;/a&gt;, to discuss an &lt;a href="http://medicine.plosjournals.org/perlserv/?request=get-document&amp;amp;doi=10.1371/journal.pmed.0050201" rel="nofollow"&gt;essay published this week by Neal Young, John Ioannidis and Omar Al-Ubaydli&lt;/a&gt; that argues that the current system of publication in biomedical research provides a distorted view of the reality of scientific data. &lt;/p&gt;
&lt;p&gt;&lt;strong&gt;More evidence on why we need radical reform of science publishing&lt;/strong&gt;, &lt;em&gt;Richard Smith&lt;/em&gt;&lt;/p&gt;
&lt;p&gt;Ask scientists whether they'd prefer an all expenses paid fortnight in the best hotel in San Tropez, a Ferrari, a Cezanne painting, or the publication of one of their original papers in &lt;em&gt;Nature&lt;/em&gt; - and most, I'd bet, would go for &lt;em&gt;Nature&lt;/em&gt;. Getting published in one of the few elite journals is a very big deal for researchers, but, argues a stimulating &lt;a href="http://medicine.plosjournals.org/perlserv/?request=get-document&amp;amp;doi=10.1371/journal.pmed.0050201" rel="nofollow"&gt;paper published in &lt;em&gt;PLoS Medicine&lt;/em&gt;&lt;/a&gt;, (1) the fact that it is so important is distorting science. And I think that the authors are right.&lt;/p&gt;
&lt;p&gt;Neal Young, John Ioannidis, and Omar Al-Ubaydli unusually for a scientific publication use economic concepts to make their case, and by doing so they illustrate the value of crossing disciplinary boundaries. Their argument is built around “the winner's curse.” Imagine many firms competing for a television franchise. Each will try to work out the value of the franchise, and inevitably there will be a range of bids. If the franchise is simply awarded to the highest bidder then there's a high chance that that bid is too high, meaning that the winner will lose money — hence “the winner's curse.” Those who run such bids often recognise the problem of the curse and discount the highest bid or go for a lower bid.&lt;/p&gt;
&lt;p&gt;This phenomenon operates in science publishing because the elite journals that accept only a fraction of papers submitted to them go for the “best” and are thus likely to be publishing papers that are suffering from the winner's curse — for example, in that they give dramatic results that are a considerable distance from the “true” results. They are exciting outliers — and so very attractive to the elite journals. The articles that the high impact journals publish are bound to be atypical and will present a distorted view of science, leading to false conclusions and "misallocation of resources." &lt;/p&gt;
&lt;p&gt;The authors have some empirical evidence to support their argument. A &lt;a href="http://jama.ama-assn.org/cgi/content/full/294/2/218" rel="nofollow"&gt;study&lt;/em&gt;&lt;/a&gt; of the 49 most highly cited papers on medical interventions published in high profile journals between 1990 and 2004 showed that a quarter of the randomised trials and five of six non-randomised studies had been contradicted or found to be exaggerated by 2005. (2) We know too that “positive” drug trials are much more likely to be published than “negative” trials, although we don't know how much this is the result of conscious manipulation by authors and sponsors and how much the result of “the winner's curse.” (3-5)&lt;/p&gt;
&lt;p&gt;Most scientists read a few high profile journals — and so are fed a systematically distorted view of the evidence. It's also these journals that are most widely reported in the media and fed to policy makers, so increasing the impact of the distortion.&lt;/p&gt;
&lt;p&gt;The hope of many is, of course, that the elite journals are selecting “the best” research — hence providing a way of coping with information overload. But we know from good evidence that peer review is a deeply flawed system and that it's very hard to know what will be important in the long term. So readers of &lt;em&gt;Nature&lt;/em&gt;, &lt;em&gt;Science&lt;/em&gt;, and the &lt;em&gt;New England Journal of Medicine&lt;/em&gt; are not reading “the best” but the “systematically distorted.”&lt;/p&gt;
&lt;p&gt;What might we do about this problem? Young and others suggest a range of options, including preferring publication of negative over positive results — a version of those choosing among bids discounting the highest. It's hard to see, however, how building such an explicit bias into the system would be helpful. Better might be for editors to pay no attention to whether the results are positive or negative but rather to concentrate simply on the importance of the question being asked and the rigour of the methods. We tried to do this when I was editor of the BMJ, but I'm not sure how successful we were. Inevitably you are excited by an unusual result, and the winner's curse can surely operate not only in relation to whether the results are positive or negative but also in relation to the “importance” of the question.&lt;/p&gt;
&lt;p&gt;For me this paper simply adds to the growing evidence and argument that we need radical reform of how we publish science. I foresee rapid publication of studies that include full datasets and the software used to manipulate them without prepublication peer review onto a large open access database that can be searched and mined. Instead of a few studies receiving disproportionate attention we will depend more on the systematic reviews that will be updated rapidly (and perhaps automatically) as new results appear.&lt;/p&gt;
&lt;p&gt;References&lt;/p&gt;
&lt;p&gt;1. Young NS, Ioannidis JPA, Al-Ubaydli O (2008) Why Current Publication Practices May Distort Science. PLoS Med 5(10): e201 doi:10.1371/journal.pmed.0050201. &lt;a href="http://medicine.plosjournals.org/perlserv/?request=get-document&amp;amp;doi=10.1371/journal.pmed.0050201" rel="nofollow"&gt;Find this paper online&lt;/a&gt;.&lt;/p&gt;
&lt;p&gt;2. Ioannidis JPA (2005) Contradicted and initially stronger effects in highly cited clinical research. JAMA 2005: 294:218-28. &lt;a href="http://jama.ama-assn.org/cgi/content/full/294/2/218" rel="nofollow"&gt;Find this paper online&lt;/a&gt;.&lt;/p&gt;
&lt;p&gt;3. Lee K, Bacchetti P, Sim I (2008) Publication of Clinical Trials Supporting Successful New Drug Applications: A Literature Analysis PLoS Medicine Vol. 5, No. 9, e191 doi:10.1371/journal.pmed.0050191. &lt;a href="http://medicine.plosjournals.org/perlserv/?request=get-document&amp;amp;doi=10.1371/journal.pmed.0050191" rel="nofollow"&gt;Find this paper online&lt;/a&gt;.&lt;/p&gt;
&lt;p&gt;4. Turner EH, Matthews AM, Linardatos E, Tell RA, Rosenthal R (2008) Selective Publication of Antidepressant Trials and Its Influence on Apparent Efficacy Turner EH, Matthews AM, Linardatos E, Tell RA, Rosenthal R. NEJM 2008; 358: 252-60.  &lt;a href="http://content.nejm.org/cgi/content/full/358/3/252" rel="nofollow"&gt;Find this paper online&lt;/a&gt;.&lt;/p&gt;
&lt;p&gt;5. Melander H,  Ahlqvist-Rastad J, Meijer G, Beermann B (2003) Evidence b(i)ased medicine—selective reporting from studies sponsored by pharmaceutical industry: review of studies in new drug applications. BMJ  2003;326:1171-1173 (31 May), doi:10.1136/bmj.326.7400.1171 &lt;a href="http://www.bmj.com/cgi/content/full/326/7400/1171" rel="nofollow"&gt;Find this paper online&lt;/a&gt;.&lt;/p&gt;

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 <category domain="http://www.plos.org/cms/plosmedicine">PLoS Medicine</category>
 <category domain="http://www.plos.org/cms/pub">Publishing</category>
 <pubDate>Tue,  7 Oct 2008 08:57:12 -0700</pubDate>
 <dc:creator>Andrew Hyde</dc:creator>
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 <title>PLoS Pathogens is exhibiting at Prion 2008, Madrid, Spain</title>
 <link>http://feeds.feedburner.com/~r/plos/PublishingBlog/~3/400186889/401</link>
 <description>&lt;p&gt;&lt;a href="http://www.plospathogens.org" rel="nofollow"&gt;&lt;em&gt;PLoS Pathogens&lt;/em&gt;&lt;/a&gt; is getting ready for &lt;a href="http://www.prion2008.com" rel="nofollow"&gt;Prion 2008&lt;/a&gt; (Madrid, Spain, October 8-10), where you’ll find us at Booth 6 in the exhibition area of the Auditorium Hotel.   &lt;/p&gt;
&lt;p&gt;Here is just a sample of some Prion research articles published in &lt;em&gt;PLoS Pathogens&lt;/em&gt;:     &lt;/p&gt;
&lt;p&gt;&lt;a href="http://www.plospathogens.org/doi/ppat.1000156" rel="nofollow"&gt;BSE Case Associated with Prion Protein Gene Mutation&lt;/a&gt; by Richt JA, Hall SM.      &lt;/p&gt;
&lt;p&gt;&lt;a href="http://www.plospathogens.org/doi/ppat.1000113 " rel="nofollow"&gt;Prion protein amino acid determinants of differential susceptibility and molecular feature of prion strains in mice and voles&lt;/a&gt; by Agrimi U, Nonno R, Dell’Omo G, Di Bari MA, Conte M, Chiappini B, Esposito E, Di Guardo G, Windl O, Vaccari G, Lipp HP.   &lt;/p&gt;
&lt;p&gt;&lt;a href="http://www.plospathogens.org/doi/ppat.0030125" rel="nofollow"&gt;&lt;/a&gt;&lt;a href="http://www.plospathogens.org/doi/ppat.0030125" rel="nofollow"&gt;In vitro and in vivo neurotoxicity of prion protein oligomers&lt;/a&gt; by Simoneau S, Rezaei H, Salès N, Kaiser-Schulz G, Lefebvre-Roque M, Vidal C, Fournier JG, Comte J, Wopfner F, Grosclaude J, Schätzl H, Lasmézas CI.     &lt;/p&gt;
&lt;p&gt; &lt;a href="http://www.plospathogens.org/doi/ppat.0030093" rel="nofollow"&gt;Oral transmissibility of prion disease is enhanced by binding to soil particles&lt;/a&gt; by Johnson CJ, Pedersen JA, Chappell RJ, McKenzie D, Aiken JM.      &lt;/p&gt;
&lt;p&gt;&lt;a href="http://www.plospathogens.org/doi/ppat.0030066" rel="nofollow"&gt;Accumulation of pathological prion protein PrPSc in the skin of animals with experimental and natural scrapie&lt;/a&gt; by Thomzig A, Schulz-Schaeffer W, Wrede A, Wemheuer W, Brenig B, Kratzel C, Lemmer K, Beekes M.      &lt;/p&gt;
&lt;p&gt;In addition, &lt;em&gt;PLoS Pathogens&lt;/em&gt; also commissions Reviews and Opinion pieces of interest to the community.    &lt;/p&gt;
&lt;p&gt;Visit our booth and you can meet the team—&lt;em&gt;PLoS Pathogens&lt;/em&gt; team member &lt;a href="http://www.plos.org/about/people/community.html#mkohut" rel="nofollow"&gt;Mary Kohut&lt;/a&gt; and &lt;a href="http://www.plos.org/about/people/community.html#ebrown" rel="nofollow"&gt;Evie Browne&lt;/a&gt; will answer your questions about PLoS, Open Access, the NIH Public Access Policy, and publishing your work in &lt;em&gt;PLoS Pathogens&lt;/em&gt;. They will be joined on the booth (Thursday, 1-2.20pm) by editorial board member David Westaway, University of Alberta, Edmonton, Alberta, Canada who may also be there at other times as and when his schedule permits.   &lt;/p&gt;
&lt;p&gt;We&amp;#39;ve also got some cool giveaways  for those of you that come and visit the PLoS booth: &lt;/p&gt;
&lt;p&gt;T-Shirts—&lt;em&gt;PLoS Pathogens&lt;/em&gt; will be giving away t-shirts to delegates who sign up to receive free e-mail content alerts. This shirt with its unique design is only available to the wider public at this event, so be sure to stop by, sign up, and claim yours while stocks last.     &lt;/p&gt;
&lt;p&gt;Buttons/Badges—designed for our authors, Editorial Board members, readers, and supporters.   &lt;/p&gt;
&lt;p&gt;Fact Sheets—that showcase the Editorial Board and top papers.    &lt;/p&gt;
&lt;p&gt;Postcards—to remind yourself and your colleagues why you should publish in PLoS Pathogens.    &lt;/p&gt;
&lt;p&gt;We look forward to welcoming Prion 2008 delegates to our booth.&lt;/p&gt;

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 <category domain="http://www.plos.org/cms/pub">Publishing</category>
 <pubDate>Mon, 22 Sep 2008 14:55:20 -0700</pubDate>
 <dc:creator>Liz Allen</dc:creator>
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 <title>BSE Case Associated with Prion Protein Gene Mutation</title>
 <link>http://feeds.feedburner.com/~r/plos/PublishingBlog/~3/395426768/400</link>
 <description>&lt;p&gt;Last week, co-authors Jürgen Richt and S. Mark Hall published a &lt;a href="http://dx.plos.org/10.1371/journal.ppat.1000156" rel="nofollow"&gt;groundbreaking article&lt;/a&gt; in &lt;em&gt;&lt;a href="http://www.plospathogens.org/home.action" rel="nofollow"&gt;PLoS Pathogens&lt;/a&gt;&lt;/em&gt; related to mad cow disease. The authors were both affiliated with the US Department of Agriculture during the completion of their study. &lt;/p&gt;
&lt;p&gt;Through DNA sequence analysis, the authors identify a novel mutation in the bovine prion protein gene (&lt;em&gt;Prnp&lt;/em&gt;), called E211K, in a cow confirmed with atypical bovine spongiform encephalopathy (BSE). This is the first report of a confirmed case of BSE (mad cow disease) with a potential pathogenic mutation within the bovine &lt;em&gt;Prnp&lt;/em&gt; gene. This mutation is identical to the E200K pathogenic mutation in the human &lt;em&gt;Prnp&lt;/em&gt;, which has been described as the most common cause of genetic Creutzfeldt-Jakob disease.&lt;/p&gt;
&lt;p&gt;Richt notes that the mutation can show up at any time, and therefore cattle herders must be on watch. He further recommends that herders try to breed the mutation out of cattle, in order to guard against future BSE-related cases.&lt;/p&gt;
&lt;p&gt;About the paper Richt says, “Our BSE manuscript presents critical information on the origin of BSE and will help public and animal health authorities worldwide to design novel prophylactic strategies against this zoonotic pathogen. Your open-access journal is playing a critical role in the dissemination of this information.”&lt;/p&gt;
&lt;p&gt;The paper was covered in &lt;a href="http://uk.reuters.com/article/topNews/idUKN1250678120080912?sp=true" rel="nofollow"&gt;Reuters&lt;/a&gt; and on &lt;a href="http://scienceblogs.com/grrlscientist/2008/09/mad_cow_disease_genetic.php" rel="nofollow"&gt;ScienceBlogs&lt;/a&gt;, where the journal is properly attributed, as well as by &lt;a href="http://www.cbc.ca/health/story/2008/09/12/mad-cow-gene.html" rel="nofollow"&gt;CBC News&lt;/a&gt; and &lt;a href="http://english.kbs.co.kr/news/newsview_sub.php?menu=1&amp;amp;key=2008091308" rel="nofollow"&gt;KBS&lt;/a&gt; of South Korea, among others.  &amp;nbsp;&lt;/p&gt;

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 <category domain="http://www.plos.org/cms/news">In the News</category>
 <category domain="http://www.plos.org/cms/pub">Publishing</category>
 <pubDate>Wed, 17 Sep 2008 11:08:46 -0700</pubDate>
 <dc:creator>Shabnam Sigman</dc:creator>
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 <title>Computational Neuroscience, Developing Countries and more</title>
 <link>http://feeds.feedburner.com/~r/plos/PublishingBlog/~3/377990290/396</link>
 <description>&lt;p&gt;Today marks the publication of a special neuroscience &lt;a href="http://www.ploscompbiol.org/doi/pcbi.1000092" rel="nofollow"&gt;Review&lt;/a&gt; in &lt;em&gt;PLoS Computational Biology&lt;/em&gt; that we expect will become a key reference work. Gustavo Deco, Viktor K. Jirsa, Peter A. Robinson, Michael Breakspear, and Karl Friston present the results of several years of collaboration in response to a challenge posed at a &lt;a href="http://www.hirnforschung.net/bcw" rel="nofollow"&gt;Brain Connectivity Workshop&lt;/a&gt; to define and clarify the true meanings and usage of models in constant, but approximate use. Terms such as mean-field approximations, mass-action, neural-mass models, neural-field models, density-dynamics, etc. were in regular use but in undefined ways. This article tries to address how different models, used to simulate and predict observed brain dynamics, can be traced back to their common fundaments. In an  accompanying &lt;a href="http://www.ploscompbiol.org/doi/pcbi.1000081" rel="nofollow"&gt;Editorial&lt;/a&gt; also published today, Karl Friston, PLoS Computational Biology’s neuroscience editor, explains the origin and purpose of the article, which should standardise many concepts for some time.&lt;/p&gt;
&lt;p&gt;Another special notice for this month is the new Developing Computational Biology Collection, available for free at: &lt;a href="http://collections.plos.org/ploscompbiol/developing.php" rel="nofollow"&gt;http://collections.plos.org/ploscompbiol/developing.php&lt;/a&gt;. These articles, published over the last year, are a series of personal Perspectives from computational biologists in a variety of developing, and often under-represented, countries. Featuring viewpoints from Goran Neshich in &lt;a href="http://www.ploscompbiol.org/doi/pcbi.0030185" rel="nofollow"&gt;Brazil&lt;/a&gt;, Sebastian Bassi in &lt;a href="http://www.ploscompbiol.org/doi/pcbi.0030257" rel="nofollow"&gt;Argentina&lt;/a&gt;, Liping Wei in &lt;a href="http://www.ploscompbiol.org/doi/pcbi.1000020" rel="nofollow"&gt;China&lt;/a&gt;, and more, the series has brought a different voice to science around the world.&lt;/p&gt;
&lt;p&gt;And finally, &lt;em&gt;PLoS Computational Biology&lt;/em&gt; also sheds light on the difficulties for some of these same scientists to travel internationally, either to conferences or for more permanent work. In an &lt;a href="http://www.ploscompbiol.org/doi/pcbi.1000097" rel="nofollow"&gt;Editorial&lt;/a&gt; published in collaboration with the &lt;a href="http://www.iscb.org" rel="nofollow"&gt;International Society for Computational Biology&lt;/a&gt; following a survey conducted by the Society,  Barb Bryant considers the travel restrictions imposed on many scientists, especially with regard to US visas. If you have anything you would like to add to this topic, please use our commentary features to add your thoughts.&lt;/p&gt;

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 <comments>http://www.plos.org/cms/node/396#comment</comments>
 <category domain="http://www.plos.org/cms/pub">Publishing</category>
 <pubDate>Fri, 29 Aug 2008 03:57:01 -0700</pubDate>
 <dc:creator>Evie Browne</dc:creator>
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 <title>Max Planck Society covers publication fees for PLoS journals</title>
 <link>http://feeds.feedburner.com/~r/plos/PublishingBlog/~3/370999015/393</link>
 <description>&lt;p&gt;PLoS and the &lt;a href="http://www.mpg.de/english" / rel="nofollow"&gt;Max Planck Society (MPS)&lt;/a&gt; have recently established an agreement whereby &lt;a href="http://www.plos.org/journals/pubfees.html" rel="nofollow"&gt;open access publication fees&lt;/a&gt; in PLoS journals will be paid directly by the MPS for articles from researchers at &lt;a href="http://www.mpg.de/english/institutesProjectsFacilities/instituteChoice/index.html" rel="nofollow"&gt;Max Planck Institutes&lt;/a&gt;.&lt;/p&gt;
&lt;p&gt;The MPS is one of the world’s leading research organizations whose researchers have an international reputation for scientific excellence. We are delighted to be collaborating with the MPS in this way so that more MPS researchers will be encouraged to publish their work in PLoS journals, and to promote open access to research literature more broadly. For papers accepted in PLoS journals after July 1st, 2008, MPS will pay the publication fee directly to PLoS for all articles where the corresponding author is affiliated with a Max Planck Institute.&lt;/p&gt;
&lt;p&gt;In 2003 MPS was the co-initiator of the &lt;a href="http://oa.mpg.de/openaccess-berlin/berlindeclaration.html" rel="nofollow"&gt; Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities&lt;/a&gt; and ever since then, MPS has demonstrated consistent and strong leadership in the promotion of open access to research results. &lt;/p&gt;
&lt;p&gt;With the ever-expanding range of open access options available to authors, we encourage other research funders to set up funds to cover publication fees in open access journals or to include such expenses within their grants and research awards.&lt;/p&gt;

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&lt;div class="title"&gt;&lt;a href="http://coffeeandsci.wordpress.com/2008/08/22/max-planck-society-covers-publication-fees-for-plos-journals/"&gt;Max Planck Society covers publication fees for PLoS&amp;amp;nbsp;journal&lt;/a&gt;&lt;/div&gt;
&lt;div class="author"&gt;from Coffee and Sci(ence) on Fri, 2008-08-22 05:43&lt;/div&gt;
&lt;div class="content"&gt;&lt;p&gt;That&amp;#8217;s a quite clever move. I wonder how other research organizations will do in the near future.One can always dream to get a cherry at the top of his grant to decorate the publish milestone.&lt;/p&gt;
&lt;p&gt;Max Planck Society covers publication fees for PLoS...&lt;/p&gt;
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 <comments>http://www.plos.org/cms/node/393#comment</comments>
 <category domain="http://www.plos.org/cms/openaccess">Open Access</category>
 <category domain="http://www.plos.org/cms/pub">Publishing</category>
 <pubDate>Thu, 21 Aug 2008 07:44:04 -0700</pubDate>
 <dc:creator>Mark Patterson</dc:creator>
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<item>
 <title>A new face for PLoS.org on Facebook</title>
 <link>http://feeds.feedburner.com/~r/plos/PublishingBlog/~3/315633445/367</link>
 <description>&lt;p&gt;PLoS grew too big for its Facebook group (we have over 1500 members) so we&amp;#39;ve opened up a &lt;a href="http://www.facebook.com/pages/PLoSorg/47460995594?ref=ts" rel="nofollow"&gt;PLoS.org page&lt;/a&gt; instead. If you follow the link, you can get a flavor of the site without needing to join but to participate, you will need to sign up. Becoming a fan of the page is one good way to remain up-to-date with the latest developments at PLoS.     &lt;/p&gt;
&lt;p&gt;The &lt;a href="http://www.facebook.com/pages/PLoSorg/47460995594?ref=ts" rel="nofollow"&gt;PLoS.org page&lt;/a&gt; keeps the wider community and public informed of global progress in the OA movement, new journal launches, site enhancements, new PLoS blog posts, relevant insider jobs, discussions and is updated on a nearly daily basis. There are also opportunities for fans to add content such as photos and videos.  &lt;/p&gt;
&lt;p&gt;If you are new to Facebook and possibly a little wary of joining, let me reassure you that signing up is very quick and simple, there&amp;#39;s no need to generate an in-depth personal profile if you don&amp;#39;t want to (although some basic information is required). &lt;/p&gt;
&lt;p&gt;The page operates in as unobtrusive a manner as possible, for example, although Facebook offers the ability to email the whole group at once, that&amp;#39;s an option we rarely use, and if we do, it&amp;#39;s normally for an important announcement such as when we would like our fans to take some form of grass roots action on our behalf. &lt;/p&gt;
&lt;p&gt;Pre-existing members of the group should note that we&amp;#39;ve migrated you all to the new page (and closed the old group), so no action is required on your part, you are already fans. Naturally, if you don&amp;#39;t like what you see when you check us out for the first time you are free to leave (but we sincerely hope that you will not, rather that you&amp;#39;ll invite your friends to join!).&lt;/p&gt;
&lt;p&gt;We look forward to welcoming you to &lt;a href="http://www.facebook.com/pages/PLoSorg/47460995594?ref=ts" rel="nofollow"&gt;our page.&lt;/a&gt; &amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;/p&gt;

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 <category domain="http://www.plos.org/cms/pub">Publishing</category>
 <pubDate>Thu, 19 Jun 2008 12:00:09 -0700</pubDate>
 <dc:creator>Liz Allen</dc:creator>
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 <title>2007 Impact factors for PLoS Journals</title>
 <link>http://feeds.feedburner.com/~r/plos/PublishingBlog/~3/314599619/366</link>
 <description>&lt;p&gt;The latest impact factors (for 2007) have just been released from &lt;a href="http://scientific.thomsonreuters.com/products/jcr/" rel="nofollow"&gt;Thomson Reuters&lt;/a&gt;.  They are as follows:&lt;br /&gt;
PLoS Biology - 13.5&lt;br /&gt;
PLoS Medicine - 12.6&lt;br /&gt;
PLoS Computational Biology - 6.2&lt;br /&gt;
PLoS Genetics - 8.7&lt;br /&gt;
PLoS Pathogens - 9.3&lt;/p&gt;
&lt;p&gt;As &lt;a href="http://medicine.plosjournals.org/perlserv/?request=get-document&amp;amp;doi=10.1371/journal.pmed.0030291" rel="nofollow"&gt;we&lt;/a&gt;  and &lt;a href="http://www.jcb.org/cgi/content/full/179/6/1091" rel="nofollow"&gt;others&lt;/a&gt; have frequently pointed out, impact factors should be interpreted with caution and only as one of a number of measures which provide insight into a journal’s, or rather its articles’, impact.  Nevertheless, the 2007 figures for PLoS Biology and PLoS Medicine are consistent with the many other indicators (e.g. submission volume, web statistics, reader and community feedback) that these journals are firmly established as top-flight open-access general interest journals in the life and health sciences respectively. &lt;/p&gt;
&lt;p&gt;The increases in the impact factors for the discipline-based, community-run PLoS journals also tally with indicators that these journals are going from strength to strength.  For example, submissions to PLoS Computational Biology, PLoS Genetics and PLoS Pathogens have almost doubled over the past year - each journal now routinely receives 80-120 submissions per month of which around 20-25 are published.   The hard work and commitment of the Editors-in-Chief and the Editorial Boards (&lt;a href="http://www.ploscompbiol.org/static/edboard.action" rel="nofollow"&gt;here&lt;/a&gt;, &lt;a href="http://www.plosgenetics.org/static/edboard.action" rel="nofollow"&gt;here&lt;/a&gt; and &lt;a href="http://www.plosgenetics.org/static/edboard.action" rel="nofollow"&gt;here&lt;/a&gt;) are setting the highest possible standards for community-run open-access journals. &lt;/p&gt;
&lt;p&gt;Another measure of impact is media coverage, and all of our journals routinely attract substantial media attention, which reflects the importance and public interest of much of the work that is published.  Witness for example &lt;a href="http://www.plos.org/cms/node/335" rel="nofollow"&gt;coverage&lt;/a&gt; of the recent &lt;a href="http://medicine.plosjournals.org/perlserv/?request=get-document&amp;amp;doi=10.1371%2Fjournal.pmed.0050045" rel="nofollow"&gt;research article&lt;/a&gt; about anti-depressants in PLoS Medicine.  And our two newest journals, PLoS Neglected Tropical Diseases and PLoS ONE, are no strangers to the world’s media (see the recent &lt;a href="http://www.plos.org/cms/node/359" rel="nofollow"&gt;coverage&lt;/a&gt; of a &lt;a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002271" rel="nofollow"&gt;PLoS ONE paper about pterosaurs&lt;/a&gt;).  We provide regular digests of this media coverage both in traditional media and the blogosphere, via the &lt;a href="http://www.plos.org/cms/news" rel="nofollow"&gt;‘In the news’ channel&lt;/a&gt; of the PLoS blog.  &lt;/p&gt;
&lt;p&gt;Although Thomson is yet to index our two youngest journals, other indexing databases are. The subscription-only &lt;a href="http://info.scopus.com/" rel="nofollow"&gt;Scopus citation index&lt;/a&gt; (owned by Elsevier and, incidentally, including many more journals than Thomson’s offering) is already covering PLoS ONE (though so far, only as far back as June 2007).  But authors don’t need to rely on subscription-only indexes such as those owned by Thomson and Elsevier, and can instead use the freely-available &lt;a href="http://scholar.google.com/" rel="nofollow"&gt;Google Scholar&lt;/a&gt;.  Using Google Scholar, for example, one can find that the &lt;a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000219" rel="nofollow"&gt;article by Neal Fahlgren and coauthors&lt;/a&gt;, about the cataloguing of an important class of RNA in plants and one of the most highly cited PLoS ONE articles so far has been &lt;a href="http://scholar.google.com/scholar?hl=en&amp;amp;lr=&amp;amp;cites=1168630959823582830" rel="nofollow"&gt;cited 42 times&lt;/a&gt; -  strong evidence that good research, even if published in a new journal, will rapidly find its place in the scientific record when it’s made freely available to all.&lt;/p&gt;

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&lt;div class="title"&gt;&lt;a href="http://marlenescorner.blogspirit.com/archive/2008/07/03/le-marche-du-mardi-n-15.html"&gt;Le marché du mardi, n°15&lt;/a&gt;&lt;/div&gt;
&lt;div class="author"&gt;from Marlene's corner on Thu, 2008-07-03 07:55&lt;/div&gt;
&lt;div class="content"&gt;&lt;p&gt;TECHNO&lt;br /&gt;
- On connaissait les outils pour raccourcir les urls (type TinyURL), voici un outil pour raccourcir les textes : TinyPaste réduit un texte en une url (courte).&lt;br /&gt;
- Transformer son blog (ou n'importe quel fil rss) en un joli document pdf pour le...&lt;/p&gt;
&lt;/div&gt;
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&lt;div class="trackback" id="trackback-4298"&gt;
&lt;div class="title"&gt;&lt;a href="http://scienceblogs.com/gregladen/2008/07/is_plos_coming_of_age.php"&gt;Is PLoS Coming of Age?&lt;/a&gt;&lt;/div&gt;
&lt;div class="author"&gt;from Greg Laden's Blog on Wed, 2008-07-02 18:12&lt;/div&gt;
&lt;div class="content"&gt;&lt;p&gt;Heavyweight science journalist Sir Delcan Butler has published an update, of sorts, on the status of the Public Library of Science (PLoS), published today in the journal Nature.* In it, he presents a study carried out by Nature on the financial status ...&lt;/p&gt;
&lt;/div&gt;
&lt;/div&gt;
&lt;div class="trackback" id="trackback-4295"&gt;
&lt;div class="title"&gt;&lt;a href="http://scienceblogs.com/clock/2008/06/impact_factors_2007.php"&gt;Impact Factors 2007&lt;/a&gt;&lt;/div&gt;
&lt;div class="author"&gt;from A Blog Around The Clock on Wed, 2008-06-18 11:24&lt;/div&gt;
&lt;div class="content"&gt;&lt;p&gt;If anyone is interested, Thompson has just released the new Impact Factors for scientific journals. Mark Patterson takes a look at IFs for PLoS journals and puts them in cool-headed perspective. One day, hopefully very soon, this will not be...&lt;/p&gt;
&lt;/div&gt;
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 <category domain="http://www.plos.org/cms/openaccess">Open Access</category>
 <category domain="http://www.plos.org/cms/plosbiology">PLoS Biology</category>
 <category domain="http://www.plos.org/cms/plosmedicine">PLoS Medicine</category>
 <category domain="http://www.plos.org/cms/ploscjs">PLoS Neglected Tropical Diseases</category>
 <category domain="http://www.plos.org/cms/plosone">PLoS ONE</category>
 <category domain="http://www.plos.org/cms/pub">Publishing</category>
 <pubDate>Wed, 18 Jun 2008 05:57:13 -0700</pubDate>
 <dc:creator>Mark Patterson</dc:creator>
 <guid isPermaLink="false">366 at http://www.plos.org/cms</guid>
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 <title>PLoS Computational Biology at ISMB 2008 – news, events and giveaways</title>
 <link>http://feeds.feedburner.com/~r/plos/PublishingBlog/~3/309018391/361</link>
 <description>&lt;p&gt;&lt;a href="http://www.ploscomputationalbiology.org" rel="nofollow"&gt;PLoS Computational Biology&lt;/a&gt;, the official journal of the International Society for Computational Biology, is getting ready for this year&amp;#39;s &lt;a href="http://www.iscb.org/ismb2008/index.php" rel="nofollow"&gt;ISMB meeting&lt;/a&gt; (Toronto, Canada, July 19-23), where you’ll find us at &lt;a href="http://www.iscb.org/ismb2008/exhibitfloorplan.php" rel="nofollow"&gt;Booth 1&lt;/a&gt; in the exhibition hall.   &lt;/p&gt;
&lt;p&gt;We’re delighted to be involved in two special events at this year’s meeting:        &lt;/p&gt;
&lt;p&gt;1. &lt;a href="http://www.iscb.org/ismb2008/tutorials.php#TutorialAM1" rel="nofollow"&gt;Professional Development Tutorial&lt;/a&gt; (Saturday July 19th 8.30am-12.30pm)—Run by Editor-In-Chief Philip E. Bourne, the Tutorial will follow the structure and content of the hugely popular &lt;a href="http://collections.plos.org/ploscompbiol/tensimplerules.php" rel="nofollow"&gt;Ten Simple Rules Collection&lt;/a&gt; and is aimed at graduate students and postdoctoral fellows. Topics covered are varied and include guidance for how to publish your work, make a good poster presentation, ensure successful collaboration, or apply for a grant.     &lt;/p&gt;
&lt;p&gt;2. &lt;a href="http://www.iscb.org/ismb2008/special_sessions.php#session5" rel="nofollow"&gt;Special Session on the Future of Scientific Publishing&lt;/a&gt; (Wednesday July 23rd 10.45am-12.40pm)—Organized by Scott Markel, ISCB Publications Committee Chair and Editorial Board member of PLoS Computational Biology, the Session includes talks by Robert Murphy on Mining the Combination of Images and Text in Literature Archives, Mark Gerstein on Mining Publications to Study the Structure of Science, and Gianni Cesareni on the FEBS Letters Initiative. To close, speakers from BioMed Central, Oxford University Press, and the Public Library of Science will address the question &amp;quot;How do you see scientific publishing changing in the next five years?&amp;quot;      &lt;/p&gt;
&lt;p&gt;What else do we have going on at this event?   &lt;/p&gt;
&lt;p&gt;ISCB Annual Awards —The ISCB awards two prizes at the conference in July:  the Accomplishment by a Senior Scientist Award and the Overton Prize.  This year, we are pleased that both recipients – &lt;a href="http://www.iscb.org/2008_awards.shtml" rel="nofollow"&gt;David Haussler and Aviv Regev&lt;/a&gt;, respectively – are members of the Editorial Board of PLoS Computational Biology.  Be sure to attend their Keynote presentations at the meeting.        &lt;/p&gt;
&lt;p&gt;Meet the Team—PLoS Computational Biology team members Evie Browne, Publications Manager, and Catherine Nancarrow, Managing Editor, will answer your questions at Booth 1 about PLoS, open access, the NIH Public Access Policy, and publishing your work in PLoS Computational Biology, the highest ranking journal in the Mathematical and Computational Biology category.  &lt;/p&gt;
&lt;p&gt;Don&amp;#39;t forget to visit the booth and collect some FREE PLoS goodies:        &lt;/p&gt;
&lt;p&gt;• T-Shirts - Once again, PLoS will be giving away our 2008 t-shirt to delegates who sign up to receive free email content alerts. This year’s shirt with its unique design is only available at this event, so be sure to stop by, sign up, and claim yours while stocks last.   &lt;/p&gt;
&lt;p&gt;• Buttons/Badges designed for our Authors, Editorial Board members, readers, and supporters     &lt;/p&gt;
&lt;p&gt;• Fact sheets that showcase the editorial board and top papers       &lt;/p&gt;
&lt;p&gt;• Postcards, to remind yourself and your colleagues why you should publish in PLoS Computational Biology.     &lt;/p&gt;
&lt;p&gt;We look forward to seeing you very soon.&lt;/p&gt;

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 <comments>http://www.plos.org/cms/node/361#comment</comments>
 <category domain="http://www.plos.org/cms/pub">Publishing</category>
 <pubDate>Tue, 10 Jun 2008 11:27:57 -0700</pubDate>
 <dc:creator>Liz Allen</dc:creator>
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 <title>Why Did the EPA Fire a Respected Toxicologist? A Longtime Defender of Scientific Integrity Speaks Out</title>
 <link>http://feeds.feedburner.com/~r/plos/PublishingBlog/~3/289034026/349</link>
 <description>&lt;p&gt;Last week, &lt;a href="http://www.chicagotribune.com/features/lifestyle/green/chi-epa-official-resigns_webmay02,0,4655733.story " rel="nofollow"&gt;the Chicago Tribune reported&lt;/a&gt;, the US Environmental Protection Agency forced the director of its Midwest Office to quit after she refused to let Dow Chemical off the hook for stalling on the cleanup of dioxin-contaminated soil stretching 50 miles from its Midland, Mich., plant. Regional Administrator Mary Gade had ordered Dow to dredge a number of dioxin hotspots over the past year and balked at the company’s attempts to negotiate a more comprehensive cleanup as stalling.&amp;nbsp;&lt;/p&gt;
&lt;p&gt;Dioxin, a highly toxic, persistent organochlorine, causes cancer and disrupts the immune and reproductive systems, &lt;a href="http://www.epa.gov/ORD/researchaccomplishments/dioxin.html" rel="nofollow"&gt;according to the EPA’s own Web site&lt;/a&gt;. “Dow responded by appealing to officials in Washington,” the Tribune reported, based on “heavily redacted letters” the paper obtained under the Freedom of Information Act. Even though Gade’s work won &lt;a href="http://www.chicagotribune.com/features/lifestyle/green/chi-epa-official_sidebar_02may02,0,6556187.story" rel="nofollow"&gt;praise from the agency&lt;/a&gt;, she was asked to quit or be fired. She resigned. Dow has long resisted a government role in any cleanup, but does not deny its responsibility for dioxin contamination near its Michigan headquarters.   &amp;nbsp;&lt;/p&gt;
&lt;p&gt;In March, the US House Energy and Commerce Committee &lt;a href="http://www.msnbc.msn.com/id/23680591/" rel="nofollow"&gt;launched an investigation&lt;/a&gt;  into potential conflicts of interest in scientific panels that advise the Environmental Protection Agency on the human health effects of toxic chemicals. The committee identified eight scientists that served as consultants or members of EPA science advisory panels while getting research support from the chemical industry to study the chemicals under review. Two scientists were actually employed by companies that made or worked with manufacturers of the chemicals under review.  	&amp;nbsp;&lt;/p&gt;
&lt;p&gt;Such conflicts, &lt;a href="http://energycommerce.house.gov/Press_110/110nr227.shtml" rel="nofollow"&gt;Chairman John Dingell (D-Mich.) noted&lt;/a&gt;, stand in stark contrast to the agency’s dismissal last summer of highly respected public health scientist Deborah Rice, an expert in toxicology, from a panel examining the health impacts of the flame retardant deca. The EPA fired Rice after the chemical industry’s trade group, the American Chemistry Council, complained that she could not provide an objective scientific review because she had spoken out about the health hazards posed by deca. &lt;/p&gt;
&lt;p&gt;This trend is neither new nor unique, argues legendary lead researcher &lt;a href="http://www.heinzawards.net/recipients.asp?action=detail&amp;amp;recipientID=29 " rel="nofollow"&gt;Herbert Needleman&lt;/a&gt;, a pediatrician and child psychiatrist, in &lt;a href="http://biology.plosjournals.org/perlserv/?request=get-document&amp;amp;doi=10.1371/journal.pbio.0060129  " rel="nofollow"&gt;“The Case of Deborah Rice: Who is the Environmental Protection Agency Protecting?” &lt;/a&gt;published today in &lt;a href="http://biology.plosjournals.org/perlserv/?request=index-html&amp;amp;issn=1545-7885" rel="nofollow"&gt;PLoS Biology.&lt;/a&gt; With his groundbreaking research on the cognitive effects of lead on children, Needleman laid the foundation for one of the greatest environmental health successes of modern times – a five-fold reduction in the prevalence of lead poisoning in American children.  &amp;nbsp;&lt;/p&gt;
&lt;p&gt;The EPA summarily fired Rice, Needleman argues, even though it had honored her just a few years before with one of its most prestigious scientific awards for “exceptionally high-quality research into lead’s toxicity.” Why? Because the American Chemistry Council asked the agency to fire her.  “EPA, without examining or contesting the charge of bias, complied,” Needleman writes. “There is now no evidence that she ever participated in the EPA proceedings, or was even in the room.” Rice, who is “widely admired by her colleagues for her intelligence, integrity and moral compass,” Needleman writes, will “withstand this insult and continue to contribute to the public welfare.”  &amp;nbsp;&lt;/p&gt;
&lt;p&gt;But who will protect scientists and public safety from industry pressure and government collusion? In a March 13 letter to EPA Administrator Stephen Johnson, Rep. Dingell writes: “The ACC does not assert that Dr. Rice has any pecuniary interest in the human health assessment at issue, and therefore seems to argue that scientific expertise with regard to a particular chemical and its human health effects is a basis for disqualification from a peer review board. This does not seem sensible on its face.” Only time will tell whether Dingell’s investigation, or others like it, will ultimately lead to new laws to safeguard scientific integrity, and public health, from the undue influence of industry.&lt;/p&gt;

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 <pubDate>Mon, 12 May 2008 16:39:15 -0700</pubDate>
 <dc:creator>Liza Gross</dc:creator>
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 <title>The Amphibian Extinction Crisis: Will Humans Rise to the Challenge? Guest Blog by Kevin Zippel</title>
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 <description>&lt;p&gt;In a new &lt;em&gt;PLoS Biology&lt;/em&gt; article, “&lt;a href="http://biology.plosjournals.org/perlserv/?request=get-document&amp;amp;doi=10.1371/journal.pbio.0060118" target="_blank" title="The Challenge of Conserving Amphibian Megadiversity in Madagascar" rel="nofollow"&gt;The Challenge of Conserving Amphibian Megadiversity in Madagascar&lt;/a&gt;,” Franco Andreone et al. argue that governments and conservation organizations should invest in proactive efforts to protect amphibians in Madagascar, which harbors some of the richest groups of amphibian fauna in the world, before the populations go into decline. We asked &lt;a href="http://www.amphibianark.org/index.htm" target="_blank" title="Kevin Zippel" rel="nofollow"&gt;Kevin Zippel&lt;/a&gt;, program director of the &lt;a href="http://biology.plosjournals.org/perlserv/?request=get-document&amp;amp;doi=10.1371%2Fjournal.pbio.0060024" target="_blank" title="Amphibian Ark" rel="nofollow"&gt;Amphibian Ark&lt;/a&gt;, created to keep “threatened amphibian species afloat” through captive management programs, to explain the value of the authors’ approach.&lt;/p&gt;
&lt;p&gt;&lt;strong&gt;The Amphibian Extinction Crisis: Will Humans Rise to the Challenge? Guest Blog by Kevin Zippel &lt;/strong&gt;      &lt;/p&gt;
&lt;p&gt;We are at a unique point in the history of the planet. This is not the first time one group of organisms has brought on a mass extinction event. One can look, for example, to the “oxygen holocaust” created by the first photosynthetic bacteria when the earth was half its current age. But this is the first time it is being done by organisms who, “by the power of a glorious evolutionary accident called intelligence,” quipped Gould, comprehend the impact of their actions. We can either continue utilizing the short-term survival instincts that served us well in the past but are now maladaptive—growing our population exponentially and consuming the planet’s precious resources unsustainably, jeopardizing biodiversity, entire ecosystems, and the earth’s very ability to support life—or we can use our intellect to reveal long-term survival instincts, looking beyond our immediate desires to consider our long-term needs, voluntarily limiting our growth and consumption and so becoming responsible stewards of all life on earth.      &lt;/p&gt;
&lt;p&gt;In terms of biodiversity loss, nowhere is this issue more poignant than with the Amphibia (Stuart et al. 2004). Of the ~6000 described species, 32% are threatened with extinction, likely in our lifetimes. Another 23% are so poorly known, and likely also threatened, that we can only call them Data Deficient. And with estimates of another 3000-6000 undescribed amphibian species so rare as to have avoided our detection to date, the anticipated losses in this single clade are staggering, on par with those faced by the Dinosauria 65 million years ago, an event the amphibians survived. Recent estimates suggest that the background extinction rate amphibians currently face is, on the conservative end, 200-2700 times higher than anything they have seen in their 360-million-year history (Roelants et al. 2007), and perhaps as much as 25-45 thousand times higher (McCallum 2007). This is the greatest extinction event in the history of amphibians and the greatest taxon-specific conservation challenge in the history of humanity.   &lt;/p&gt;
&lt;p&gt;And in terms of hotspots of amphibian diversity, the new study published in &lt;em&gt;PLoS Biology&lt;/em&gt; today by Andreone et al. rightly focus on the significance and uniqueness of the Malagasy amphibian fauna. Habitat destruction and global warming are already straining Malagasy amphibians. And with a susceptibility of at least some Malagasy amphibians to the chytrid fungus, &lt;em&gt;Bd&lt;/em&gt;, in captivity (pers. obs.), this precious jewel of biodiversity is an open Petri dish waiting for the first spore to land. Thus the call of Andreone et al. for conservation action that is “pro-active, rather than reactive, or simply post-mortem” could not be more timely or wise. We have watched &lt;em&gt;Bd&lt;/em&gt; impacting amphibians on every continent where they are found, and in almost every case, even when we knew where it was going and when, our response has been a salvage operation after the outbreak because we lacked the timely resources to do otherwise. This is unconscionable and unethical. As responsible stewards we must act now to safeguard biophilic havens like Madagascar, protecting key habitat areas and safeguarding in captivity those species that would otherwise succumb to threats that cannot be controlled in the wild. ACSAM is the recipe for how to proceed.      &lt;/p&gt;
&lt;p&gt;Although as individuals we lack the money to effect the requisite changes called for by Andreone et al., we have something more powerful than money—a vote. We must demand action from the governments of the world, to support addressing this conservation crisis and all environmental ills. And if they refuse, then we must use our vote to replace them with someone who will respond appropriately. There is no political issue more paramount that protecting the future of all life on earth. The current amphibian extinction crisis in the perfect test: if we cannot perform an act so simple as saving the frogs, then what hope do we have for ourselves? Like the frogs of Madagascar, we have only one home, we are endemic to planet earth. It is time for us to start using our superior intellect for the long-term benefit of the world, of ourselves. Onward!&lt;/p&gt;

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&lt;div class="title"&gt;&lt;a href="http://scienceblogs.com/clock/2008/05/new_and_exciting_in_plos_one_34.php"&gt;New and Exciting in PLoS ONE&lt;/a&gt;&lt;/div&gt;
&lt;div class="author"&gt;from A Blog Around The Clock on Wed, 2008-05-07 05:33&lt;/div&gt;
&lt;div class="content"&gt;&lt;p&gt;There are 56 new articles published in PLoS ONE this week and it was hard to make the picks as this seems to be a very, very good week with lots of cool papers. Here are some of the...&lt;/p&gt;
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 <pubDate>Tue,  6 May 2008 15:54:11 -0700</pubDate>
 <dc:creator>Micah Dubreuil</dc:creator>
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