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	<title>EveryONE &#187; Open Access</title>
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		<title>Open Access to Development Data: The World Bank’s New Open Data Initiative</title>
		<link>http://blogs.plos.org/everyone/2010/04/27/open-access-to-development-data-the-world-bank%e2%80%99s-new-open-data-initiative/</link>
		<comments>http://blogs.plos.org/everyone/2010/04/27/open-access-to-development-data-the-world-bank%e2%80%99s-new-open-data-initiative/#comments</comments>
		<pubDate>Tue, 27 Apr 2010 10:21:26 +0000</pubDate>
		<dc:creator>Liz Allen</dc:creator>
				<category><![CDATA[General]]></category>
		<category><![CDATA[Open Access]]></category>
		<category><![CDATA[PLoS Medicine]]></category>

		<guid isPermaLink="false">http://everyone.plos.org/?p=3170</guid>
		<description><![CDATA[]]></description>
			<content:encoded><![CDATA[<p><strong>Guest blog by Meghan Reidy and Marco Schäferhoff, Evidence to  Policy Initiative (E2Pi), San Francisco, USA.  Also posted on the <em>PLoS Medicine</em> blog, <a href="http://speakingofmedicine.plos.org/2010/04/26/open-access-to-development-data-the-world-bank%E2%80%99s-new-open-data-initiative/">SpeakingofMedicine</a><br />
</strong></p>
<p>The World Bank announced this week a new <a href="http://web.worldbank.org/WBSITE/EXTERNAL/NEWS/0,,contentMDK:22546372%7EmenuPK:34463%7EpagePK:34370%7EpiPK:34424%7EtheSitePK:4607,00.html">open  data initiative</a>, which provides free and open access to the Bank’s  health and development data, including 2,000 social, economic,  financial, institutional, and environmental indicators. The World  Development Indicators, the Bank’s most popular statistical resource,  consist of over 900 indicators for 200 countries alone, including many  that go back to 1960. The Bank has also opened up access to the Global  Development Finance, Africa Development Indicators, Global Economic  Monitor, and indicators from the Doing Business Report.</p>
<p>This step is long overdue. Opening access to the Bank’s data is good  news for everyone who is interested in global health and development and  wants to get a quick overview of the latest trends or access the data  for policy-making, research, and advocacy purposes. Until this week,  only a fraction of this data was freely available, making it difficult  for interested individuals and organizations to use it. Individuals and  organizations in emerging markets and developing countries in particular  are often unable to pay subscription fees to access development data –  even when discounts are available for developing country residents.</p>
<p>Accessing high quality data should play a critical role in improving  accountability and in helping to overcome poverty. It will allow policy  makers, researchers, and civil society organizations to track the impact  of policies, develop new solutions, and measure the progress of  development more accurately. Development data should be transparent and  available to everyone around the globe.</p>
<p>The new initiative is truly <strong><em>open</em> </strong><em><strong>access</strong> </em>(not  just free access) because users are allowed to work with the data to  create new applications.  Indeed the Bank is encouraging such creative  reuse—it will soon launch an “Apps for Development” competition, to  prompt the health and development community to create applications and  “mash-ups” using World Bank data.</p>
<p>The World Bank’s open data initiative will be followed by the July 1  launch of the Bank’s new <a href="http://siteresources.worldbank.org/EXTINFODISCLOSURE/Resources/R2009-0259-2.pdf?&amp;resourceurlname=R2009-0259-2.pdf">Access  to Information Policy</a>, which provides access to an expanded range  of reports, documents, and information. This step is welcome, as it will  strengthen public ownership and oversight of Bank activities. If  implemented as outlined in the policy document, for the first time the  Bank will release information on projects under implementation—also a  long overdue measure. The Bank will publish important information  contained in a series of reports called “Implementation Status and  Results Reports,” including information about the status of project  implementation and overall ratings on project development objectives and  implementation progress. However, staff comments and detailed risk  ratings will be withheld. Reports from review missions, known as <em>aide </em><a href="http://www.dict.cc/englisch-deutsch/aide-m%C3%A9moire.html"><em>mémoire</em></a><em>s</em>,  which comment on the progress of projects and provide recommendations  on further actions, can be released if both the Bank and borrower agree.  Given that the <em>aide </em><a href="http://www.dict.cc/englisch-deutsch/aide-m%C3%A9moire.html"><em>mémoire</em></a><em>s</em> entail critical information, their open disclosure should be standard  practice. Others have <a href="http://www.bicusa.org/en/Document.102097.aspx">discussed</a> the gaps and limitations of the policy in more detail.</p>
<p>Nonetheless, despite these limitations, if fully implemented, the new  policy will bring the World Bank a long way in moving towards the  standard of transparency set by the <a href="http://www.theglobalfund.org/en/">Global Fund</a> to Fight  AIDS, Tuberculosis and Malaria. Since its inception, the Global Fund has  displayed a high level of transparency and publishes a range of  information on grant performance, financing, and Board decisions on its  website, though there remains <a href="http://www.cgdev.org/content/publications/detail/1424030">room  for improvement</a>. This information is provided by the Global Fund in  a systematic way, and it is relatively simple to access and read. It is  important that the World Bank follows the Global Fund’s example.</p>
<p>Finally, we note that both the World Bank and the Global Fund were  signatories to a recent <em>PLoS Medicine</em> <a href="http://www.plosmedicine.org/article/info:doi%2F10.1371%2Fjournal.pmed.1000223">essay</a> called “Meeting the Demand for Results and Accountability: A Call for  Action on Health Data from Eight Global Health Agencies.” In that essay,  the leaders of eight major global health agencies (the “H8”) made “a  public commitment on behalf of each of our organizations to work with  other stakeholders to develop a set of specific principles around data  sharing by our organizations within two years.” We hope they will live  up to this promise.</p>
<p>Acknowledgements: Thanks to Gavin Yamey, E2Pi, for helpful comments  on this blog.</p>
<p>Competing interest: E2Pi is funded by the Bill &amp; Melinda Gates  Foundation.  The Global Health Group is directed by Richard Feachem,  founding Executive Director of the Global Fund and former Director for  Health, Nutrition and Population at the World Bank.</p>
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		<title>PLoS ONE Publishes 10,000th Manuscript!</title>
		<link>http://blogs.plos.org/everyone/2010/04/02/plos-one-publishes-10000th-article/</link>
		<comments>http://blogs.plos.org/everyone/2010/04/02/plos-one-publishes-10000th-article/#comments</comments>
		<pubDate>Fri, 02 Apr 2010 21:57:54 +0000</pubDate>
		<dc:creator>Allison Van Gemert</dc:creator>
				<category><![CDATA[Interviews]]></category>
		<category><![CDATA[author spotlight]]></category>
		<category><![CDATA[Interview]]></category>
		<category><![CDATA[Open Access]]></category>

		<guid isPermaLink="false">http://everyone.plos.org/?p=3065</guid>
		<description><![CDATA[]]></description>
			<content:encoded><![CDATA[<p>PLoS ONE is pleased to announce the publication of our 10,000th article! Since its inception in December 2006, PLoS ONE has proven to be a great success, and this milestone shows that daily open-access publication is a viable model which enjoys wide support within the academic community. Thank you to our authors, community, and colleagues for helping us to reach this exciting goal.</p>
<p>I work in the <a href="http://www.plos.org/about/people/production.php" target="_blank">production group</a> at PLoS ONE, and as this milestone represents the output of our group, we thought it would be appropriate for me to interview the authors of the 10,000th article, <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010000" target="_blank"><strong>&#8220;Immunoproteomics Analysis of the Murine Antibody Response to Vaccination with an Improved <em>Francisella tularensis</em> Live Vaccine Strain (LVS)&#8221;</strong></a>, by Twine et. al.</p>
<p><a href="http://blogs.plos.org/everyone/files/2010/04/dr-suetwine.jpg"><img class="size-full wp-image-3115 alignleft" src="http://blogs.plos.org/everyone/files/2010/04/dr-suetwine.jpg" alt="" width="262" height="247" /></a></p>
<p>This is an article which focuses on the pathogen tularemia and the possible development of a human vaccine, and so we asked Dr. Sue Twine of the <a href="http://www.nrc-cnrc.gc.ca/eng/index.html" target="_blank">National Research Council Canada</a> to share her expertise, and experiences with PLoS, in order to help us celebrate. When asked how she felt about being published as our 10,000th article, Dr. Twine responded, <em>“I’m honoured – congratulations PLoS ONE!”<br />
</em><br />
<strong>AvG: Please tell us a bit about your scientific background – have you always tested vaccines and/or studied the tularemia disease?</strong></p>
<p><strong>ST:</strong> My interest in tularemia developed through a somewhat convoluted path. I’ve always been fascinated by proteins, so I spent my PhD studying protein-ligand interactions. I then moved from the UK to Canada to pursue postdoctoral studies, using biophysical approaches to study protein-protein interactions. I joined the National Research Council Canada in 2002 as part of the proteomics group – I wanted to study proteins on a much larger scale. It was through one of my mentors here, Dr Wayne Conlan, that I developed an interest in tularemia and vaccine development. His enthusiasm for this little known organism is infectious, and I quickly became fascinated by how little was known about the pathogen.</p>
<p><strong>AvG: Why do you think it is important to develop a tularemia vaccine?</strong></p>
<p><strong>ST:</strong> Bioterrorism is perceived to be a realistic threat with the potential to cause mass casualty events. Because of its extreme virulence, ease of aerosol dissemination, and capacity to cause severe disease in humans, F. tularensis is considered a potential biological weapon and is classified as a Category A select agent by the CDC. Among the bacterial diseases, anthrax, plague, and tularemia are considered the most serious biothreats. Anthrax vaccines already exist and are being stockpiled, and a new plague vaccine will soon go into production. LVS could serve as a stockpile vaccine for tularemia if it can meet the necessary regulatory requirements.</p>
<p><strong>AvG: What do you find most exciting about your findings?</strong></p>
<p><strong>ST: </strong>A major factor impeding the licensing of a tularemia vaccine is the absence of a well defined immune correlate of protection that can be used to predict whether or not a vaccine recipient has elicited a protective immune response. From a clinical perspective, an antibody response that correlates with protection is ideal for this purpose since blood samples are easy to obtain and analyze. In human experiments conducted by the US Army in the 1960s, everyone given LVS generated an antibody response against whole bacteria, but all were not protected from exposure to virulent Francisella tularensis. Thus, mere seroconversion cannot serve as a correlate of protection for this vaccine.  BALB/c mice are protected by vaccination with LVS, whereas C57BL/6 mice are not. Comparing the antibody repertoires generated in each mouse strain revealed several differences. Thus, our work indicates that examining the pattern of antibody responses to a diversity of Francisella antigens can reveal a correlate of protection that is not obvious by using reactivity to crude bulk antigen.</p>
<p><strong>AvG: What do you see as a next step with your results?<br />
</strong><br />
<strong>ST:</strong> The next step is to apply the immunoproteomics approach to sera from humans vaccinated with LVS, to determine whether a similar repertoire of antibodies are generated</p>
<p><strong>AvG: What made you decide to submit to PLoS ONE?<br />
</strong><br />
<strong>ST:</strong> Our manuscript describes work funded by a contract from NIAID as part of the efforts of the tularemia vaccine development team.  One of the main goals of the contract is to provide new useful and accessible tools to the larger tularemia research community.  Publishing in an open access journal like PLoS ONE means that our article potentially will reach a wider audience of researchers. This is therefore in line with this specific contract goal of the tularemia vaccine development team.</p>
<p><strong>AvG: Since this was your first PLoS ONE paper, how did you find the submission experience?</strong></p>
<p><strong>ST:</strong> From start to finish it was by far the most straightforward and rapid submission experience I have ever had. I was surprised how quickly the article went through the peer review process. I was able to address reviewers’ concerns quickly, and my article was sent to production within two weeks of submission!</p>
<p><strong>AvG: How did you find the production experience?</strong></p>
<p><strong>ST:</strong> The PLoS ONE production staff was great to work with. Again, I was surprised how efficiently the article went through the production process.</p>
<p><strong>AvG: Would you be interested in publishing with PLoS ONE again?</strong></p>
<p><strong>ST:</strong> Absolutely yes!</p>
<p>Congratulations to Dr Twine and her co-authors, Mireille D. Petit, Kelly M. Fulton, Robert V. House, and J. Wayne Conlan. We are proud to have reached this milestone, and we look forward to publishing more great research in future years!</p>
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		<title>Open Access Week has started</title>
		<link>http://blogs.plos.org/everyone/2009/10/19/open-access-week-has-started/</link>
		<comments>http://blogs.plos.org/everyone/2009/10/19/open-access-week-has-started/#comments</comments>
		<pubDate>Mon, 19 Oct 2009 18:29:34 +0000</pubDate>
		<dc:creator>Bora Zivkovic</dc:creator>
				<category><![CDATA[Open Access]]></category>
		<category><![CDATA[Developing World]]></category>
		<category><![CDATA[PLoS Medicine]]></category>

		<guid isPermaLink="false">http://everyone.plos.org/?p=2308</guid>
		<description><![CDATA[]]></description>
			<content:encoded><![CDATA[<p><img alt="OAWeek.jpg" src="http://scienceblogs.com/clock/OAWeek.jpg" width="468" height="60" class="mt-image-center" style="text-align:center;margin:0 auto 20px" /></p>
<p>This week &#8211; 19th-23rd October 2009 &#8211; is the Open Access week around the world &#8211; fitting nicely with the 5th birthday of <a href="http://www.plosmedicine.org/home.action" target="_blank" title="">PLoS Medicine</a>. And when I say &#8216;around the world&#8217; I really mean it. Just <a href="http://oad.simmons.edu/oadwiki/Events_celebrating_Open_Access_Week" target="_blank" title="">check out all the global events</a> happening this week.</p>
<p>The OA Week is co-organized by <a href="http://oad.simmons.edu/" target="_blank" title="">Open Access Directory</a>, <a href="http://www.plos.org/" target="_blank" title="">PLoS</a>, <a href="http://www.arl.org/sparc" target="_blank" title="">SPARC</a>, <a href="http://freeculture.org/" target="_blank" title="">Students for Free Culture</a>, <a href="http://www.eifl.net/cps/sections/home" target="_blank" title="">eIFL (Electronic Information for Libraries)</a> and <a href="http://www.openoasis.org/" target="_blank" title="">OASIS</a>.</p>
<p>Many countries are participating this year, including some with numerous events all around the country. See, for example, all the events in <a href="http://open-access.net/de_en/activities/international_open_access_week/participants_2009/" target="_blank" title="">Germany</a> (there are 67 events in that country alone!), <a href="http://www.openaccessweek.org/2009/10/05/netherland-oa-week-activities/" target="_blank" title="">Netherlands</a>, <a href="http://www.openaccessweek.org/2009/10/11/open-access-plos-and-article-level-metrics-webcast-in-china/" target="_blank" title="">China</a> and <a href="http://www.openaccessweek.org/2009/09/29/oa-week-events-in-japan/" target="_blank" title="">Japan</a>.</p>
<p>You can get all the information and follow the events on the <a href="http://www.openaccessweek.org" target="_blank" title="">Open Access Week blog</a>. There is also a nice <a href="http://www.arl.org/sparc/media/09-1019.shtml" target="_blank" title="">round-up</a> on the SPARC site.</p>
<p>As the week unfolds, we will blog more about it here. In the meantime, you can follow the news of the OA week on <a href="http://www.facebook.com/event.php?eid=61888632230" target="_blank" title="">Facebook</a> or by following PLoS on <a href="http://twitter.com/PLoS" target="_blank" title="">Twitter</a>.You may also want to sign up to participate in the <a href="http://oaspa.org/blog/2009/10/05/oaspa-open-access-week-webinar-live-qa-session-with-five-oa-publishers/" target="_blank" title="">OASPA webinar</a> (locationless &#8211; sign up to participate online).</p>
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		<title>Creative ways to semantically enrich an Open Access PLoS research article</title>
		<link>http://blogs.plos.org/everyone/2009/04/27/creative-ways-to-semanticallyenrich-an-open-access-plos-research-article/</link>
		<comments>http://blogs.plos.org/everyone/2009/04/27/creative-ways-to-semanticallyenrich-an-open-access-plos-research-article/#comments</comments>
		<pubDate>Mon, 27 Apr 2009 23:09:31 +0000</pubDate>
		<dc:creator>Liz Allen</dc:creator>
				<category><![CDATA[Creative re-use]]></category>
		<category><![CDATA[Open Access]]></category>
		<category><![CDATA[semantic]]></category>

		<guid isPermaLink="false">http://everyone.plos.org/?p=1161</guid>
		<description><![CDATA[]]></description>
			<content:encoded><![CDATA[<p>We&#8217;re always happy to learn about scientists who have added value in different ways to PLoS articles because it illustrates the power of open access.  We call this &#8220;creative re-use&#8221; and it can only really flourish when entire articles (not just abstracts) are freely accessible online with no permission required to use them in any way desired.</p>
<p>Imagine the delight of the <a href="http://www.plos.org/about/people/community.html"><em>PLoS Neglected Tropical Diseases</em></a> team when they learned that Dr David Shotton, and his team from <a href="http://www.zoo.ox.ac.uk/staff/academics/shotton_dm.htm">Oxford University</a> had invested the effort to enrich the content of one of their <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0000228">journal articles</a>, the results of which can be seen online <a href="http://imageweb.zoo.ox.ac.uk/pub/2008/plospaper/latest/#top">here</a>.</p>
<p>The enhanced version includes features like highlighted tagging which you can turn on or off (tagged terms include disease names, organisms, places, people, taxa), citations which include a pop-up containing the relevant quotation from the cited article, document and study summaries, tag clouds and citation analysis.</p>
<p>With a single click you can re-arrange the reference list by number of times each paper is cited, or add in the authors’ analysis of how the reference is used in the paper (<em>obtains background from, confirms, extends, shares authors with, uses method in</em>). The group has also provided interactive versions of some of the figures: compare the original, static <a href="http://www.plosntds.org/article/slideshow.action?uri=info:doi/10.1371/journal.pntd.0000228&amp;imageURI=info:doi/10.1371/journal.pntd.0000228.g003">Figure 3</a> to the <a href="http://imageweb.zoo.ox.ac.uk/pub/2008/datavisualisationwidgets/overlay/fig3/">moveable, overlaying, enhanced</a> version.</p>
<p>David Shotton’s group hopes that this largely manual effort will demonstrate what practical enhancements can be made to scientific papers through the application of existing technology. Once the methods employed by Dr Shotton and his colleagues become more routine, all open-access literature could be semantically enhanced and redistributed without restriction.</p>
<p>Whether the next steps towards semantic markup are implemented by authors, publishers or post-publication text miners remains to be seen, but we welcome your feedback on this idea. Should you be interested in how this was done, a <a href="http://www.ploscompbiol.org/doi/pcbi.1000361">Review article</a> published 4.17.2009 in <a href="http://www.ploscompbiol.org/"><em>PLoS Computational Biology</em></a> describes the process in more detail.</p>
<p>This post with thanks to Shabnam Sigman, Publication Manager, <em>PLoS Neglected Tropical Diseases </em>and Evie Browne, Publication Manager, <em>PLoS Computational Biology.</em></p>
<p style="text-align:center"><a href="http://www.plos.org/support/index.html"><img class="size-full wp-image-765 aligncenter" src="http://blogs.plos.org/everyone/files/2009/03/donateandjoin.jpg" alt="Donate and Join" width="244" height="42" /></a></p>
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		<title>Journalists like PLoS ONE and Open Access</title>
		<link>http://blogs.plos.org/everyone/2009/04/20/journalists-like-plos-one-and-open-access/</link>
		<comments>http://blogs.plos.org/everyone/2009/04/20/journalists-like-plos-one-and-open-access/#comments</comments>
		<pubDate>Mon, 20 Apr 2009 19:28:58 +0000</pubDate>
		<dc:creator>Liz Allen</dc:creator>
				<category><![CDATA[Open Access]]></category>
		<category><![CDATA[Media]]></category>

		<guid isPermaLink="false">http://everyone.plos.org/?p=1117</guid>
		<description><![CDATA[]]></description>
			<content:encoded><![CDATA[<p><a href="http://everyone.plos.org/2009/04/17/weekly-plos-one-news-and-blog-round-up-2/">Every</a> <a href="http://everyone.plos.org/2009/04/10/weekly-plos-one-news-and-blog-round-up/">Friday</a> on this blog, my colleague <a href="http://www.plos.org/about/people/one.html#rwalton">Bex Walton</a>, does an excellent round up of the week&#8217;s media coverage of stories that originated with a PLoS ONE research article. It&#8217;s a significant task for her to keep up with the number and breadth of coverage, plus she (along with <a href="http://www.plos.org/about/people/one.html#jlaloup">Jen Laloup</a>) is also a pivotal figure in terms of making sure that <a href="http://everyone.plos.org/media/">journalists receive timely and accurate Press Releases from PLoS ONE</a>.</p>
<p>For those of you who are avid media followers, you can receive immediate updates of which PLoS articles are making the news from the <a href="http://twitter.com/PLoS">PLoS Twitter stream</a> and <a href="http://www.facebook.com/home.php#/pages/PLoSorg/47460995594">PLoS Facebook page</a> or from Coturnix (Bora Zivkovic our Online Discussion Expert) via his <a href="http://scienceblogs.com/clock/">Blog Around the Clock</a>.</p>
<p>Over the weekend, we were pleased to read <a href="http://anneminard.com/2009/04/19/day-85-open-access-journals-are-our-tax-dollars-in-print/">this blog post</a> from Anne Minard &#8211; a freelance science journalist who has written stories for National Geographic News, the New York Times (among many other outlets)  and has recently launched a new blog, “100 Days of Science&#8221;.</p>
<p>In her post, it is clear that Anne is a convert to PLoS ONE and Open Access, here&#8217;s an excerpt from it:</p>
<p>&#8220;I  got my first glimpse of the open access universe as soon as I started to blog. First, I discovered the journal PLoS ONE, largely through the publicity efforts of a man who calls himself Coturnix, at A Blog Around the Clock. I’ve perused PLoS ONE regularly and found no less than 10 science gems in there for “100 Days of Science. ”</p>
<p>I loved the PLoS journals (there’s actually a whole suite of them here) at first sight: all that original science, free for the reading. AND WHY NOT, I’ve come to think. After all, my tax dollars fed the grants that allowed those studies to happen. People complain about America’s scientific literacy, and I would submit (I do submit!) that open-access journals are a giant leap in the right direction&#8221;.</p>
<p>At PLoS, we are always seeking converts to Open Access. That&#8217;s one reason why we help to run <a href="http://www.openaccessweek.org">Open Access Week</a> (19-23 October 2009) which seeks to broaden awareness and understanding of Open Access to research, including access policies from all types of research funders, within the international higher education community and to the general public. The now-annual event has been expanded from a single day to accommodate widespread global interest in the movement toward open, public access to scholarly research results. If you want to get involved in this international event <a href="http://www.formspring.com/forms/?549982-pmL85oKcVL">please sign up today</a>.</p>
<p style="text-align:center"><a href="http://www.plos.org/support/index.html"><img class="size-full wp-image-765 aligncenter" src="http://blogs.plos.org/everyone/files/2009/03/donateandjoin.jpg" alt="Donate and Join" width="244" height="42" /></a></p>
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		<title>Academic Editor Interview &#8211; Adam Ratner</title>
		<link>http://blogs.plos.org/everyone/2009/04/06/academic-editor-interview-adam-ratner/</link>
		<comments>http://blogs.plos.org/everyone/2009/04/06/academic-editor-interview-adam-ratner/#comments</comments>
		<pubDate>Mon, 06 Apr 2009 19:31:35 +0000</pubDate>
		<dc:creator>Allison Hawxhurst</dc:creator>
				<category><![CDATA[Interviews]]></category>
		<category><![CDATA[Open Access]]></category>

		<guid isPermaLink="false">http://everyone.plos.org/?p=832</guid>
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			<content:encoded><![CDATA[<p><a href="http://www.ratnerlab.org/" target="_blank">Adam Ratner, MD</a> is an Assistant Professor of Pediatrics and Microbiology at Columbia University. He is one of the first people to join the Editorial Board at <a href="http://www.plosone.org">PLoS ONE</a> and is now our Section Editor for Infectious Diseases. We talked over Skype about medicine, Open Access, PLoS and the world of scientific publishing.</p>
<p>BZ: I&#8217;d like to start with a bit more detail on your scientific and medical background &#8211; what brought you into infectious diseases research?</p>
<p>AR: My interest and my clinical training are in pediatric infectious diseases. My research direction started during a postdoctoral stint at University of Pennsylvania where I could see the power of new methods: we could simultaneously genetically modify a pathogen &#8211; <em>Streptococcus pneumoniae</em>, the bacterium responsible for a number of childhood diseases, and its model host &#8211; the mouse. With this approach we could study both how the pathogen affects the host and how the host responds to the pathogen.</p>
<p>Most of my work is now focused on research, but for about eight weeks every year I treat pediatric patients. I find it good to combine the lab and the clinic as the two inform each other.</p>
<p>BZ: What was it that attracted you to PLoS ONE in the first place?</p>
<p>AR: I liked the idea of Open Access from the very beginning, especially when PLoS started its first journals &#8211; Biology and Medicine. When PLoS put out the call for manuscripts for its new journal &#8211; PLoS Pathogens &#8211; I persuaded my collaborators that we should support this journal and send our papers there. Actually, our paper, <a href="http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.0010001" target="_blank">The Role of Innate Immune Responses in the Outcome of Interspecies Competition for Colonization of Mucosal Surfaces</a>, was the very first article published in PLoS Pathogens &#8211; number 001.</p>
<p>The following year, when PLoS announced the founding of PLoS ONE, I was intrigued. I admit I was a little skeptical at first, but more I thought about it, more I realized that a journal like this &#8211; of broad scope, accepting papers that are scientifically sound without regard to potential impact, is exactly what the scientific community needed. Soon I became a believer, and joined the Academic Board among the very first people to do so, at the beginning of the journal.</p>
<p>BZ: How many hours a week would you say you devote to PLoS ONE and when do you fit that into your busy schedule?</p>
<p>AR: I try to devote 1-2 hours to PLoS ONE every day, as I understand the need for quick turnaround. So I try to move the manuscripts to Academic Editors and reviewers quickly.</p>
<p>BZ: How does the peer-review process on PLoS ONE work? What is the standard of peer-review on PLoS ONE?</p>
<p>AR: In some ways, the review system in PLoS ONE is very similar to other journals in the areas of infectious diseases or microbiology, yet in other ways it is very different. The process is identical to other journals in that manuscripts are sent out to reviewers who do their job seriously and apply the same scientific standards to the work. On the other hand, it makes a huge difference that no manuscript is rejected early because &#8220;it is not of interest to us&#8221; &#8211; there are none of those limitations.</p>
<p>Thus, the reviewing process is rigorous &#8211; reviewers are evaluating if the work is hypothesis driven, is the work of high quality, and are conclusions supported by the data, but not trying to meet any subjective criteria.</p>
<p>BZ: How quickly does this process move?</p>
<p>AR: Speed is an important aspect of PLoS ONE. I read each manuscript myself, which takes a day or two, and then decide which other Academic Editors or external reviewers to send it to. There, the review process may last an additional two to three weeks or so, at which point we can make a decision to reject, accept with modifications or accept as is.</p>
<p>BZ: What&#8217;s the general quality of submissions like?</p>
<p>AR: It is similar to other quality journals. Sure, some manuscripts are sub-par, and our system allows the Academic Editors to reject such papers quickly, without necessarily burdening the external reviewers with them. But most are very good. What is very good about PLoS ONE is that it is a natural home for studies that are interdisciplinary &#8211; thus not fitting neatly into other specialized journals&#8217; criteria of what they like to publish. And such interdisciplinary studies are now becoming very frequent. Also, this is a good place for negative or confirmatory results, which, though they may not be exciting, are very useful, especially in clinical areas of biomedical science. The fact that PLoS ONE does not care about the tyranny of Impact Factor allows it to publish a wealth of medically important studies.</p>
<p>BZ: What would you say is the &#8216;best&#8217; paper you have handled and why?</p>
<p>AR: It is hard to choose, but I would like to point out a series of papers about tuberculosis in The Gambia. A group there is looking at sensitivity and specificity of TB tests on the ground, in a place where tuberculosis is highly prevalent. Look at, for instance, <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000068" target="_blank">Surprisingly High Specificity of the PPD Skin Test for M. tuberculosis Infection from Recent Exposure in The Gambia</a> and <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000183" target="_blank">Using ELISPOT to Expose False Positive Skin Test Conversion in Tuberculosis Contacts</a>. Those are important studies in themselves, but they also showcase the importance of Open Access in the developing world &#8211; both medical personnel and researchers there need access to the literature on the diseases that are prevalent in those parts of the world.</p>
<p>BZ: What do you feel makes PLoS ONE relevant to scientists?</p>
<p>AR: The best thing about PLoS ONE is that it does not impose boundaries between disciplines. †Thus, cross-disciplinary work that does not fit neatly anywhere else (as much as there is a lot of lip-service about the importance of such work), fits perfectly in PLoS ONE.</p>
<p>BZ: And finally, what would you say is the thing about Open Access that most excites you?</p>
<p>AR: There is a social justice aspect to Open Access that I find particularly compelling. Especially, as we just mentioned, in the international sphere: making sure that all the existing medical knowledge is available to physicians everywhere on the planet.</p>
<p>BZ: Thank you very much for your time. It was great fun talking to you.</p>
<p>We also asked Dr.Ratner to choose his top five papers from those he has edited and provide brief explanations about why he picked them. Here are his choices and reasons. We welcome <a href="http://www.plosone.org/static/checklist.action">more submissions</a> from this community.</p>
<p><a href="http://www.plos.org/cms/node/442">Surprisingly High Specificity of the PPD Skin Test for M.tuberculosis Infection from Recent Exposure in The Gambia</a>. Hill PC, Brookes RH, Fox A, Jackson-Sillah D, Lugos MD, et al. This paper is a perfect example of the importance of open access to international health. Hill et al. studied a common tuberculosis test (the PPD skin test) on the ground in a high-prevalence area. These data are valuable for practitioners and researchers all over the world and can be most widely available through PLoS ONE.</p>
<p><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001582">RNA-Containing Cytoplasmic Inclusion Bodies in Ciliated Bronchial Epithelium Months to Years after Acute Kawasaki Disease</a>. Rowley AH, Baker SC, Shulman ST, Garcia FL, Fox LM, et al. This manuscript uses analysis of samples from patients who died of Kawasaki Disease (KD) in order to explore the hypothesis that an unidentified RNA virus may be the inciting agent of this KD. The etiology of KD has been a topic of great controversy for decades, and this paper adds valuable data. KD occurs worldwide, and the wide dissemination of information gained from autopsy studies of KD fatalities is important.</p>
<p><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002683">Evolution of Streptococcus pneumoniae and Its Close Commensal Relatives</a>. Kilian M, Poulsen K, Blomqvist T, Håvarstein LS, Bek-Thomsen M, et al. Streptococcus pneumoniae is a tremendously important cause of disease worldwide, accounting for approximately 1 million deaths in children under 5 annually. Kilian et al. performed a detailed evolutionary analysis of S. pneumoniae and closely related species, many of which are rarely pathogenic. This sets the stage for a more detailed understanding of S. pneumoniae pathogenesis and is important information for researchers all over the world.</p>
<p><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002636">Phase 1 Trial of Malaria Transmission Blocking Vaccine Candidates Pfs25 and Pvs25 Formulated with Montanide ISA 51</a>.Wu Y, Ellis RD, Shaffer D, Fontes E, Malkin EM, et al. This is a Phase I trial of candidate malaria vaccines in which there was an unexpectedly high rate of adverse reactions to the adjuvant used. I chose this article because this is the kind of study that might have difficulty finding a &#8220;home&#8221; without a forum such as PLoS ONE. There is a tremendous amount to be learned from early stage trials, even those in which the intervention tested is a &#8220;failure,&#8221; in this case as a result of reactogenicity. PLoS ONE publishes work such as this, allowing it to inform future studies.</p>
<p><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003056">Microbial Prevalence, Diversity and Abundance in Amniotic Fluid During Preterm Labor: A Molecular and Culture-Based Investigation</a>. DiGiulio DB, Romero R, Amogan HP, Kusanovic JP, Bik EM, et al. Preterm birth is a major cause of morbidity and mortality worldwide and is often of unclear etiology. DiGiuio et al. took a broad, culture-independent approach to understanding the population of microorganisms in the amniotic fluid of women with and without preterm birth. Their findings reveal surprising microbial diversity in this site and are an important foundation for future work in this area.</p>
<p>To add your work to the quality articles already published in PLoS ONE, simply <a href="http://www.plosone.org/static/checklist.action">submit your manuscript</a> to us today.</p>
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		<title>Academic Editor Interview &#8211; Tom Tregenza</title>
		<link>http://blogs.plos.org/everyone/2009/03/26/academic-editor-interview-tom-tregenza/</link>
		<comments>http://blogs.plos.org/everyone/2009/03/26/academic-editor-interview-tom-tregenza/#comments</comments>
		<pubDate>Thu, 26 Mar 2009 18:04:57 +0000</pubDate>
		<dc:creator>Allison Hawxhurst</dc:creator>
				<category><![CDATA[Interviews]]></category>
		<category><![CDATA[Open Access]]></category>

		<guid isPermaLink="false">http://everyone.plos.org/?p=835</guid>
		<description><![CDATA[]]></description>
			<content:encoded><![CDATA[<p><a href="http://www.selfishgene.org/Tom/" target="_blank">Tom Tregenza</a> is a Royal Society Research Fellow at the Centre for Ecology &amp; Conservation at the University of Exeter&#8217;s Cornwall campus. He recently became the Section Editor for Evolution at <a href="http://www.plosone.org">PLoS ONE</a> and in this capacity he has already handled 82 manuscripts. We talked over Skype last week about his science and about the world of scientific publishing.</p>
<p>BZ: I’d like to start with a bit more detail on your scientific background. How did you get into science, and in particular why evolutionary and behavioral biology?</p>
<p>TT: Like many others, I was excited about nature as a child. Living close to the coast here in the UK, where the tides are very large, every time the tide was low it exposed a rich and magical world of creatures living there. Later on, reading Richard Dawkins&#8217; &#8220;The Selfish Gene&#8221; was a trigger for me to study biology. The elegant concept of Natural Selection is an incredibly powerful explanation for the diversity and adaptations of living creatures.  Behavior, in particular, is such a complex emergent property that it is a constant source of wonder.  It illustrates the constraints on Natural Selection, where it is really the survival of the fitter, not the fittest, that drives evolution.</p>
<p>I focus my research mainly on sexual selection, where the emphasis is less on the survival of the fittest and more on other ways that genes can increase their representation in the next generation. For instance, my studies on sexual conflict reveal adaptations that favor one member of a mating pair, even if they are bad for his/her (usually his) mate. In a sense, a male is a parasite on the female and mate choice and courtship behaviors are a struggle between the interests of the two.</p>
<p>I started out my postdoctoral studies with Roger Butlin at the University of Leeds,  using grasshoppers as a model system. I was interested in their biogeography and what made populations diverge and form new species. Later, I switched to crickets as they are much easier to take care of in the laboratory. After a number of lab studies on crickets in the lab, I am now testing the ideas about sexual conflict and sexual selection in the field.  I would like to see if the laboratory results reflect what is really happening out in nature, as well as to develop a model system that can be equally easily studied both indoors and outdoors. We now have 100 cameras trained at the burrows and we are filming marked individuals continuously. We then analyze who mated with whom, genotype the individuals, then genotype their offspring in the next generation.</p>
<p>Finally, I’m involved in an ongoing collaboration with Dr.Mark Norman and Dr.Julian Finn from the museum of Victoria, Melbourne, and the University of Tasmania, studying mimicry in cephalopods. My colleagues go out on the boat, dive, look at the behaviors in the field and make videos.  They then send me the video and their ideas and we try to put the work in an evolutionary framework to see what we can learn from cephalopods about nature in general . The observed behaviors are mind-boggling, for example, the mimic octopus can, very quickly, change its shape, posture, color and movements to mimic either a sea snake or a lionfish or some other creatures.  We are assuming that there must be something advantageous for the octopus to be able to mimic two or more different predators instead of just one. Perhaps this is frequency-dependent, making it more difficult for predators to learn that the mimic is not actually dangerous. Octopuses are known to be very smart, but this range of dynamic mimicry has not been seen before in any other animal.</p>
<p>BZ: Apart from behavior and evolution, you have also published a number of papers on the topic of science publishing. You have recently published an article in PLoS ONE on this topic &#8211; <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003202" target="_blank">Systematic Variation in Reviewer Practice According to Country and Gender in the Field of Ecology and Evolution</a>. What was your motivation to scientifically study the world of scientific publishing?</p>
<p>TT: It is glaringly obvious that that there are far fewer women at senior levels than at junior levels in science, which does not reflect their abilities. The reasons for this are multifarious, but the resulting gender bias is, first, not fair to the women, and second, not good for science as we are missing their talent. Recent studies suggest that there may be subtle sources of gender disparity in the peer-review system, with manuscripts written by women being judged more strictly than those written by men. Also, as peer-reviewers, men and women behave differently. Biases in peer-review and in academia as a whole are very difficult to study as there are many factors involved. It is not that male scientists are deliberately sexist, but that many aspects of the way science is organized subtly favor men over women.  But just because something is difficult to study does not mean we should not study it at all. It is important to make inroads into this study even if the early work is not perfect. Much of the work I’ve done has major limitations, which I do not dispute, however, I think to demand perfection at this early stage of such research is to miss the point of why we are doing it.</p>
<p>BZ: Is this related to what it was that attracted you to PLoS ONE in the first place?</p>
<p>TT: Yes. Peer-review in PLoS ONE gets away from value judgement and subjectivity to a great extent. Work is judged on merit &#8211; are the experiments properly done and do conclusions follow from the data. Grading on novelty is a lot of time wasted on debates between editors, reviewers and authors. PLoS ONE got rid of it &#8211; the reviewers only judge if the paper is fundamentally sound.</p>
<p>BZ: How many hours a week would you say you devote to PLoS ONE and when do you fit that into your busy schedule?</p>
<p>TT: I&#8217;d say I spend about 4 hours per week as a Section Editor at PLoS ONE. And I feel it is time well spent.</p>
<p>BZ: How does the peer-review process on PLoS ONE work?</p>
<p>TT: The peer-review process in PLoS ONE is very similar to many other journals, although I think it has some advantages, especially over the weekly journals, as it concentrates on the question of whether or not the manuscript is fundamentally correct instead of how novel the findings are, which is a subjective judgment. I am actually surprised that we do not see many papers in PLoS ONE that describe repeats or negative results &#8211; most of our papers describe novel and original research. Yet, novelty is not what the reviewers are looking at.  I would actually like to see more repetitions of famous studies being done and being published.</p>
<p>As a result of the PloS ONE review policy, authors can write more objectively.  They do not need to use the polemical marketing tone in order to &#8220;sell&#8221; their work to the reviewers and editors. In high impact journals, like Science and Nature, manuscripts tend to be &#8216;sexed-up&#8217; with large claims of novelty, leading to a high rate of <a href="http://en.wikipedia.org/wiki/False_positive#Type_I_error" target="_blank">Type I errors</a> in such journals. In contrast, peer-review at PLoS ONE is just as rigorous, but authors do not need to apply their salesmanship skills &#8211; the research is judged on its own merits.</p>
<p>BZ: What do you feel makes PLoS ONE relevant to scientists? When you suggest to your colleagues to publish in PLoS ONE, what do you tell them?</p>
<p>TT: I tell them that their papers will be widely read and easy to find.  The publication is rapid, as the review is not bogged down in discussions about novelty. I also believe that the age of the Impact Factor is shortly going to be behind us and that in the nearest future individual papers will be evaluated regardless of the journal in which they are published.</p>
<p>BZ: Thank you very much for your time. Your research is fascinating and this was a very enjoyable conversation.</p>
<p>We are also pleased to highlight Dr.Tregenza&#8217;s top picks of articles in Evolutionary Biology (selected from those which he has overseen as the Academic Editor). He has provided some insight into why each one was of interest to him. We welcome <a href="http://www.plosone.org/static/checklist.action">more submissions</a> from this community.</p>
<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002544"> Attitudes Toward Consumption and Conservation of Tigers in China</a> by Gratwicke B et al.  This paper reports on a very straightforward, but thorough and well designed survey, which provides chilling data on just how vast the market for Tiger product in China is.  It makes a very powerful case that allowing a lifting on the ban on the trafficking of tiger products would be a huge mistake.</p>
<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000952">Do Individual Females Differ Intrinsically in Their Propensity to Engage in Extra-Pair Copulations?</a> by Forstmeier W. This paper addresses the woefully neglected question of whether certain female birds (in this example, Zebra Finches) are simply more willing to mate than other females.  Studies of sexual selection have typically asked whether females have preferences for particular males, and sometimes ask whether females differ in their preferences for particular males.  However, the much simpler question of whether some females are simply more ready to mate has rarely been examined.</p>
<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000422">A Preference for a Sexual Signal Keeps Females Safe</a> by Kim TW et al. This is a nice piece of classic behavioural ecology.  The question of why females choose to mate with certain males has many potential answers.  Among the most straightforward potential explanations, but one that has received less attention than it probably should have, is that the signals that females find attractive actually provide females directly with a benefit.  In this study, structures made by male fiddler crabs become more attractive to females when there is more perceived risk from predators, indicating that the structures provide females with shelter from predators.</p>
<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000118">Swordtail Fry Attend to Chemical and Visual Cues in Detecting Predators and Conspecifics</a> by Coleman SW and Rosenthal GG. This is a well designed study that examines the possibility that young fish can use both chemical and visual cues to detect predators and conspecfics.  The work shows that baby swordtails use both chemical and visual sources of information, and that together they have a larger effect than if one of the two is presented on its own.  This suggests that baby fish may on the one hand have the capacity to use multiple cues, and on the other hand may actually need both types of cue to respond maximally, with implications for understanding effects of disturbance on their environment.</p>
<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000522">Phylogeny of Diving Beetles Reveals a Coevolutionary Arms Race between the Sexes</a> by Bergsten J and Miller KB. I love this paper because it describes what at first glance seems a potentially rather dull subject – a phylogeny of diving beetles.  However, as it turns out males and females of these beetles are involved in an ongoing arms-race in which males have evolved suction cups on their feet for gripping females and females in turn have evolved patterns of pits and furrows that prevent these suckers from allowing males to grab hold of females.  Where males have big suctions cups, females have concomitantly larger patterns of depressions, and a closely related pair of species from Japan suggest that this battle of the sexes may have driven speciation in the group.</p>
<p>If you would like to experience PLoS ONE for yourself, <a href="http://www.plosone.org/static/checklist.action" target="_blank">submit your work</a> to us today.</p>
<p style="text-align: center;"><a href="http://www.plos.org/support/index.html"><img class="size-full wp-image-765 aligncenter" src="http://blogs.plos.org/everyone/files/2009/03/donateandjoin.jpg" alt="Donate and Join" width="244" height="42" /></a></p>
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		<title>OA on a roll &#8211; four institutions move forwards</title>
		<link>http://blogs.plos.org/everyone/2009/03/25/oa-on-a-roll-four-institutions-move-forwards/</link>
		<comments>http://blogs.plos.org/everyone/2009/03/25/oa-on-a-roll-four-institutions-move-forwards/#comments</comments>
		<pubDate>Wed, 25 Mar 2009 19:55:12 +0000</pubDate>
		<dc:creator>Liz Allen</dc:creator>
				<category><![CDATA[Open Access]]></category>

		<guid isPermaLink="false">http://everyone.plos.org/?p=814</guid>
		<description><![CDATA[]]></description>
			<content:encoded><![CDATA[<p>The Open Access world has seen a few red letter days over the past few weeks.</p>
<p>Yesterday, Lund University announced that they have established an OA publication fund and set up a relationship with PLoS. Below is an excerpt from their <a href="http://www.sciecom.org/ojs/index.php/sciecominfo/article/viewFile/1508/1243">Press Release</a>:</p>
<p><em>In accordance with its commitment to ensure public availability of its research output, the Lund University (LU) has reached an agreement with the Public Library of Science (PLoS) for the central funding of publication fees of LU scientists without burdening the budget of the individual researcher.</em></p>
<p><em>Like many Open Access journals, PLoS journals charge a fee for publication. For papers accepted in PLoS journals after March 1st 2009, LU will pay the publication fee directly to PLoS from central funds for all articles where the corresponding author is affiliated with a LU department.</em></p>
<p>&#8220;Lund University is committed to the movement towards open access to scientific information and PLoS is a top quality Open Access publisher&#8221;<em> says Lars Björnshauge, Director of Libraries, Lund University.</em></p>
<p>Last week, MIT unanimously adopted a university wide OA mandate which is best summed up by quoting MIT Faculty Chair Bish Sanyal, who said that the vote was “a signal to the world that we speak in a unified voice; that what we value is the free flow of ideas.” <a href="http://www.earlham.edu/~peters/fos/2009/03/mit-adopts-university-wide-oa-mandate.html">Peter Suber&#8217;s blog reported this story.<br />
</a></p>
<p>In addition, Harvard&#8217;s Kennedy School also embraced OA last week and adopted a Mandate, that&#8217;s in addition to the historic vote by the Faculty of Arts and Sciences&#8217;s (FAS) in February, 2008. In the words of Kennedy School Dean, David T. Ellwood &#8220;In the developing world especially, where access to expensive journals is rare, there is a pressing need for access to the latest policy advice and scholarship coming from HKS faculty&#8221;. You can read more in the <a href="http://www.libraryjournal.com/article/CA6644842.html?&amp;rid=reg_visitor_id&amp;source=title">Library Journal</a>.</p>
<p>Finally earlier this month, <a href="http://osulibrary.oregonstate.edu/library-faculty-grant-open-access-their-work">Oregon State University Library Faculty Adopted a  Strong OA Policy</a>, the first library faculty in the USA to do so.</p>
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